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commit/galaxy-central: greg: Add a tool shed container to display successful repository and tool dependency installations and improve statistics and reporting in the tool shed's install and test runs.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0e80a712c37/ Changeset: a0e80a712c37 User: greg Date: 2013-12-19 18:49:50 Summary: Add a tool shed container to display successful repository and tool dependency installations and improve statistics and reporting in the tool shed's install and test runs. Affected #: 8 files diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -265,8 +265,7 @@ """Return the repository's tool dependencies that are currently installed, but possibly in an error state.""" installed_dependencies = [] for tool_dependency in self.tool_dependencies: - if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, - ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED ]: installed_dependencies.append( tool_dependency ) return installed_dependencies @@ -442,6 +441,16 @@ return dependencies_being_installed @property + def tool_dependencies_installed_or_in_error( self ): + """Return the repository's tool dependencies that are currently installed, but possibly in an error state.""" + installed_dependencies = [] + for tool_dependency in self.tool_dependencies: + if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, + ToolDependency.installation_status.ERROR ]: + installed_dependencies.append( tool_dependency ) + return installed_dependencies + + @property def tool_dependencies_missing_or_being_installed( self ): dependencies_missing_or_being_installed = [] for tool_dependency in self.tool_dependencies: diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2733,7 +2733,7 @@ def build_dependency_shell_commands( self ): """Return a list of commands to be run to populate the current environment to include this tools requirements.""" if self.tool_shed_repository: - installed_tool_dependencies = self.tool_shed_repository.installed_tool_dependencies + installed_tool_dependencies = self.tool_shed_repository.tool_dependencies_installed_or_in_error else: installed_tool_dependencies = None return self.app.toolbox.dependency_manager.dependency_shell_commands( self.requirements, diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -255,7 +255,7 @@ tool_shed_repository.uninstalled = True # Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any # repository dependencies. - tool_dependencies_to_uninstall = tool_shed_repository.installed_tool_dependencies + tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed ) for tool_dependency in tool_dependencies_to_uninstall: uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency ) diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -21,26 +21,29 @@ self.key = key self.label = label self.parent = parent + self.current_repository_installation_errors = [] + self.current_repository_successful_installations = [] self.description = None self.datatypes = [] + self.failed_tests = [] self.folders = [] + self.invalid_data_managers = [] self.invalid_repository_dependencies = [] self.invalid_tool_dependencies = [] self.invalid_tools = [] - self.current_repository_installation_errors = [] - self.repository_installation_errors = [] - self.tool_dependency_installation_errors = [] - self.valid_tools = [] - self.valid_data_managers = [] - self.invalid_data_managers = [] - self.tool_dependencies = [] - self.failed_tests = [] self.missing_test_components = [] self.not_tested = [] self.passed_tests = [] + self.readme_files = [] + self.repository_dependencies = [] + self.repository_installation_errors = [] + self.repository_successful_installations = [] self.test_environments = [] - self.repository_dependencies = [] - self.readme_files = [] + self.tool_dependencies = [] + self.tool_dependency_installation_errors = [] + self.tool_dependency_successful_installations = [] + self.valid_tools = [] + self.valid_data_managers = [] self.workflows = [] def contains_folder( self, folder ): @@ -230,6 +233,17 @@ self.error_message = error_message +class RepositorySuccessfulInstallation( object ): + """Repository installation object""" + + def __init__( self, id=None, tool_shed=None, name=None, owner=None, changeset_revision=None ): + self.id = id + self.tool_shed = tool_shed + self.name = name + self.owner = owner + self.changeset_revision = changeset_revision + + class TestEnvironment( object ): """Tool test environment object""" @@ -294,6 +308,16 @@ self.error_message = error_message +class ToolDependencySuccessfulInstallation( object ): + """Tool dependency installation object""" + + def __init__( self, id=None, type=None, name=None, version=None, installation_directory=None ): + self.id = id + self.type = type + self.name = name + self.version = version + self.installation_directory = installation_directory + class Workflow( object ): """Workflow object.""" @@ -1097,7 +1121,8 @@ # {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic', # 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a', # 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'}, - # 'installation_errors': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []} + # 'installation_errors': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []}, + # 'successful_installations': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []} # } test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) if test_environment_dict is None: @@ -1335,6 +1360,82 @@ version=td_version, error_message=td_error_message ) tool_dependencies_folder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) + successful_installation_dict = tool_test_results_dict.get( 'successful_installations', {} ) + if len( successful_installation_dict ) > 0: + # 'successful_installation': + # {'current_repository': [], + # 'repository_dependencies': [], + # 'tool_dependencies': + # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] + # } + current_repository_successful_installation_dicts = successful_installation_dict.get( 'current_repository', [] ) + repository_dependency_successful_installation_dicts = successful_installation_dict.get( 'repository_dependencies', [] ) + tool_dependency_successful_installation_dicts = successful_installation_dict.get( 'tool_dependencies', [] ) + if len( current_repository_successful_installation_dicts ) > 0 or \ + len( repository_dependency_successful_installation_dicts ) > 0 or \ + len( tool_dependency_successful_installation_dicts ) > 0: + repository_installation_success_id = 0 + folder_id += 1 + successful_installation_base_folder = Folder( id=folder_id, + key='successful_installations', + label='Successful installations', + parent=containing_folder ) + containing_folder.folders.append( successful_installation_base_folder ) + # Displaying the successful installation of the current repository is not really necessary, so we'll skip it. + if len( repository_dependency_successful_installation_dicts ) > 0: + folder_id += 1 + repository_dependencies_folder = Folder( id=folder_id, + key='repository_dependency_successful_installations', + label='Repository dependencies', + parent=successful_installation_base_folder ) + successful_installation_base_folder.folders.append( repository_dependencies_folder ) + for repository_dependency_successful_installation_dict in repository_dependency_successful_installation_dicts: + repository_installation_success_id += 1 + try: + rd_tool_shed = str( repository_dependency_successful_installation_dict.get( 'tool_shed', '' ) ) + rd_name = str( repository_dependency_successful_installation_dict.get( 'name', '' ) ) + rd_owner = str( repository_dependency_successful_installation_dict.get( 'owner', '' ) ) + rd_changeset_revision = str( repository_dependency_successful_installation_dict.get( 'changeset_revision', '' ) ) + except Exception, e: + rd_tool_shed = 'unknown' + rd_name = 'unknown' + rd_owner = 'unknown' + rd_changeset_revision = 'unknown' + repository_installation_success = \ + RepositoryInstallationSuccess( id=repository_installation_success_id, + tool_shed=rd_tool_shed, + name=rd_name, + owner=rd_owner, + changeset_revision=rd_changeset_revision ) + repository_dependencies_folder.repository_successful_installations.append( repository_installation_success ) + if len( tool_dependency_successful_installation_dicts ) > 0: + # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] + folder_id += 1 + tool_dependencies_folder = Folder( id=folder_id, + key='tool_dependency_successful_installations', + label='Tool dependencies', + parent=successful_installation_base_folder ) + successful_installation_base_folder.folders.append( tool_dependencies_folder ) + tool_dependency_error_id = 0 + for tool_dependency_successful_installation_dict in tool_dependency_successful_installation_dicts: + tool_dependency_error_id += 1 + try: + td_type = str( tool_dependency_successful_installation_dict.get( 'type', '' ) ) + td_name = str( tool_dependency_successful_installation_dict.get( 'name', '' ) ) + td_version = str( tool_dependency_successful_installation_dict.get( 'version', '' ) ) + td_installation_directory = tool_dependency_successful_installation_dict.get( 'installation_directory', '' ) + except Exception, e: + td_type = 'unknown' + td_name = 'unknown' + td_version = 'unknown' + td_installation_directory = str( e ) + tool_dependency_successful_installation = \ + ToolDependencySuccessfulInstallation( id=tool_dependency_error_id, + type=td_type, + name=td_name, + version=td_version, + installation_directory=td_installation_directory ) + tool_dependencies_folder.tool_dependency_successful_installations.append( tool_dependency_successful_installation ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -396,17 +396,27 @@ %for tool_dependency_installation_error in folder.tool_dependency_installation_errors: ${render_tool_dependency_installation_error( tool_dependency_installation_error, pad, my_row, row_counter )} %endfor - %endif + %endif + %if folder.tool_dependency_successful_installations: + %for tool_dependency_successful_installation in folder.tool_dependency_successful_installations: + ${render_tool_dependency_successful_installation( tool_dependency_successful_installation, pad, my_row, row_counter )} + %endfor + %endif %if folder.repository_installation_errors: %for repository_installation_error in folder.repository_installation_errors: ${render_repository_installation_error( repository_installation_error, pad, my_row, row_counter, is_current_repository=False )} %endfor - %endif + %endif %if folder.current_repository_installation_errors: %for repository_installation_error in folder.current_repository_installation_errors: ${render_repository_installation_error( repository_installation_error, pad, my_row, row_counter, is_current_repository=True )} %endfor - %endif + %endif + %if folder.repository_successful_installations: + %for repository_successful_installation in folder.repository_successful_installations: + ${render_repository_successful_installation( repository_successful_installation, pad, my_row, row_counter )} + %endfor + %endif </%def><%def name="render_datatype( datatype, pad, parent, row_counter, row_is_header=False )"> @@ -714,6 +724,36 @@ %></%def> +<%def name="render_tool_dependency_successful_installation( successful_installation, pad, parent, row_counter, row_is_header=False )"> + <% + encoded_id = trans.security.encode_id( successful_installation.id ) + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-rtdsi-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table id="test_environment"> + <tr bgcolor="#FFFFCC"> + <th>Type</th><th>Name</th><th>Version</th> + </tr> + <tr> + <td>${successful_installation.name | h}</td> + <td>${successful_installation.type | h}</td> + <td>${successful_installation.version | h}</td> + </tr> + <tr><th>Installation directory</th></tr> + <tr><td colspan="3">${successful_installation.installation_directory | h}</td></tr> + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_repository_installation_error( installation_error, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"><% from galaxy.util import unicodify @@ -748,6 +788,37 @@ %></%def> +<%def name="render_repository_successful_installation( successful_installation, pad, parent, row_counter, row_is_header=False, is_current_repository=False )"> + <% + encoded_id = trans.security.encode_id( successful_installation.id ) + %> + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + %endif + id="libraryItem-rrsi-${encoded_id}"> + <td style="padding-left: ${pad+20}px;"> + <table id="test_environment"> + %if not is_current_repository: + <tr bgcolor="#FFFFCC"> + <th>Tool shed</th><th>Name</th><th>Owner</th><th>Changeset revision</th> + </tr> + <tr> + <td>${successful_installation.tool_shed | h}</td> + <td>${successful_installation.name | h}</td> + <td>${successful_installation.owner | h}</td> + <td>${successful_installation.changeset_revision | h}</td> + </tr> + %endif + </table> + </td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> +</%def> + <%def name="render_not_tested( not_tested, pad, parent, row_counter, row_is_header=False )"><% encoded_id = trans.security.encode_id( not_tested.id ) diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -119,7 +119,6 @@ # a definition for that tool shed. galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', None ) tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) -exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'install_test_exclude.xml' ) if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: galaxy_encode_secret = 'changethisinproductiontoo' @@ -182,6 +181,46 @@ return passed_tests return [] +def display_repositories_by_owner( repository_dicts ): + # Group summary display by repository owner. + repository_dicts_by_owner = {} + for repository_dict in repository_dicts: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + if owner in repository_dicts_by_owner: + repository_dicts_by_owner[ owner ].append( repository_dict ) + else: + repository_dicts_by_owner[ owner ] = [ repository_dict ] + # Display grouped summary. + for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): + print "# " + for repository_dict in grouped_repository_dicts: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) + +def display_tool_dependencies_by_name( tool_dependency_dicts ): + # Group summary display by repository owner. + tool_dependency_dicts_by_name = {} + for tool_dependency_dict in tool_dependency_dicts: + name = str( tool_dependency_dict[ 'name' ] ) + type = str( tool_dependency_dict[ 'type' ] ) + version = str( tool_dependency_dict[ 'version' ] ) + if name in tool_dependency_dicts_by_name: + tool_dependency_dicts_by_name[ name ].append( tool_dependency_dict ) + else: + tool_dependency_dicts_by_name[ name ] = [ tool_dependency_dict ] + # Display grouped summary. + for name, grouped_tool_dependency_dicts in tool_dependency_dicts_by_name.items(): + print "# " + for tool_dependency_dict in grouped_tool_dependency_dicts: + type = str( tool_dependency_dict[ 'type' ] ) + name = str( tool_dependency_dict[ 'name' ] ) + version = str( tool_dependency_dict[ 'version' ] ) + print "# %s %s version %s" % ( type, name, version ) + def get_api_url( base, parts=[], params=None ): if 'api' in parts and parts.index( 'api' ) != 0: parts.pop( parts.index( 'api' ) ) @@ -474,18 +513,14 @@ def initialize_install_and_test_statistics_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = {} + install_and_test_statistics_dict[ 'total_repositories_processed' ] = 0 + install_and_test_statistics_dict[ 'successful_repository_installations' ] = [] + install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ] = [] + install_and_test_statistics_dict[ 'repositories_with_installation_error' ] = [] + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] = [] if test_framework == REPOSITORIES_WITH_TOOLS: - install_and_test_statistics_dict[ 'total_repositories_processed' ] = 0 install_and_test_statistics_dict[ 'all_tests_passed' ] = [] install_and_test_statistics_dict[ 'at_least_one_test_failed' ] = [] - install_and_test_statistics_dict[ 'successful_installations' ] = [] - install_and_test_statistics_dict[ 'repositories_with_installation_error' ] = [] - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] = [] - elif test_framework == TOOL_DEPENDENCY_DEFINITIONS: - install_and_test_statistics_dict[ 'total_repositories_processed' ] = 0 - install_and_test_statistics_dict[ 'successful_installations' ] = [] - install_and_test_statistics_dict[ 'repositories_with_installation_error' ] = [] - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] = [] return install_and_test_statistics_dict def initialize_tool_tests_results_dict( app, tool_test_results_dict ): @@ -516,6 +551,9 @@ tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) + tool_test_results_dict[ 'successful_installations' ] = dict( current_repository=[], + repository_dependencies=[], + tool_dependencies=[] ) return tool_test_results_dict def install_repository( app, repository_dict ): @@ -563,7 +601,17 @@ def parse_exclude_list( xml_filename ): """Return a list of repositories to exclude from testing.""" - # This method should return a list with the following structure: + # This method expects an xml document that looks something like this: + # <?xml version="1.0"?> + # <blacklist> + # <repositories tool_shed="http://testtoolshed.g2.bx.psu.edu"> + # <reason> + # <text>Some reason</text> + # <repository name="some_name" owner="some_owner" /> + # </reason> + # </repositories> + # </blacklist> + # A list is returned with the following structure: # [{ 'reason': The default reason or the reason specified in this section, # 'repositories': [( name, owner, changeset revision if changeset revision else None ), # ( name, owner, changeset revision if changeset revision else None )]}] @@ -640,26 +688,6 @@ result = test_runner.run( tests ) return result, test_config.plugins._plugins -def show_summary_output( repository_dicts ): - # Group summary display by repository owner. - repository_dicts_by_owner = {} - for repository_dict in repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - if owner in repository_dicts_by_owner: - repository_dicts_by_owner[ owner ].append( repository_dict ) - else: - repository_dicts_by_owner[ owner ] = [ repository_dict ] - # Display grouped summary. - for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): - print "# " - for repository_dict in grouped_repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) - def uninstall_repository_and_repository_dependencies( app, repository_dict ): """Uninstall a repository and all of its repository dependencies.""" # This method assumes that the repositor defined by the received repository_dict is not a repository @@ -740,7 +768,7 @@ tool_dependency_install_path = tool_dependency.installation_directory( app ) uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) if error_message: - log.debug( 'There was an error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) + log.debug( 'Error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) log.debug( error_message ) else: log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -66,6 +66,9 @@ default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir +# This file is copied to the Galaxy root directory by buildbot. +# It is managed by cfengine and is not locally available. +exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'repositories_with_tools_exclude.xml' ) # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: @@ -144,7 +147,7 @@ if error_message: return None, error_message # Handle repositories not to be tested. - if os.path.exists( install_and_test_base_util.exclude_list_file ): + if os.path.exists( exclude_list_file ): # Entries in the exclude_list look something like this. # { 'reason': The default reason or the reason specified in this section, # 'repositories': @@ -157,8 +160,8 @@ # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ - str( install_and_test_base_util.exclude_list_file ) ) - exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) + str( exclude_list_file ) ) + exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: exclude_list = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was @@ -299,7 +302,7 @@ test_toolbox.toolbox = app.toolbox else: # This repository and all of its dependencies were successfully installed. - install_and_test_statistics_dict[ 'successful_installations' ].append( repository_identifier_dict ) + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed remove_install_tests() log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) @@ -560,33 +563,33 @@ total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] all_tests_passed = install_and_test_statistics_dict[ 'all_tests_passed' ] at_least_one_test_failed = install_and_test_statistics_dict[ 'at_least_one_test_failed' ] - successful_installations = install_and_test_statistics_dict[ 'successful_installations' ] + successful_repository_installations = install_and_test_statistics_dict[ 'successful_repository_installations' ] repositories_with_installation_error = install_and_test_statistics_dict[ 'repositories_with_installation_error' ] tool_dependencies_with_installation_error = install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" print "# %s - installation script for repositories containing tools completed." % now print "# Repository revisions processed: %s" % str( total_repositories_processed ) - if successful_installations: + if successful_repository_installations: print "# ----------------------------------------------------------------------------------" - print "# The following %d revisions with all dependencies were successfully installed:" % len( successful_installations ) - install_and_test_base_util.show_summary_output( successful_installations ) + print "# The following %d revisions were successfully installed:" % len( successful_repository_installations ) + install_and_test_base_util.display_repositories_by_owner( successful_repository_installations ) if all_tests_passed: print '# ----------------------------------------------------------------------------------' - print "# %d repositories successfully passed all functional tests:" % len( all_tests_passed ) - install_and_test_base_util.show_summary_output( all_tests_passed ) + print "# The following %d revisions successfully passed all functional tests:" % len( all_tests_passed ) + install_and_test_base_util.display_repositories_by_owner( all_tests_passed ) if at_least_one_test_failed: print '# ----------------------------------------------------------------------------------' - print "# %d repositories failed at least 1 functional test:" % len( at_least_one_test_failed ) - install_and_test_base_util.show_summary_output( at_least_one_test_failed ) + print "# The following %d revisions failed at least 1 functional test:" % len( at_least_one_test_failed ) + install_and_test_base_util.display_repositories_by_owner( at_least_one_test_failed ) if repositories_with_installation_error: print '# ----------------------------------------------------------------------------------' - print "# %d repositories have installation errors:" % len( repositories_with_installation_error ) - install_and_test_base_util.show_summary_output( repositories_with_installation_error ) + print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error ) + install_and_test_base_util.display_repositories_by_owner( repositories_with_installation_error ) if tool_dependencies_with_installation_error: print "# ----------------------------------------------------------------------------------" print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) - install_and_test_base_util.show_summary_output( tool_dependencies_with_installation_error ) + install_and_test_base_util.display_tool_dependencies_by_name( tool_dependencies_with_installation_error ) print "####################################################################################" log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. diff -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b -r a0e80a712c37754d2d33260919469a7dccb2f1b1 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -64,6 +64,9 @@ default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir +# This file is copied to the Galaxy root directory by buildbot. +# It is managed by cfengine and is not locally available. +exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'tool_dependency_definition_exclude.xml' ) # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: @@ -83,7 +86,7 @@ if error_message: return None, error_message # Handle repositories not to be tested. - if os.path.exists( install_and_test_base_util.exclude_list_file ): + if os.path.exists( exclude_list_file ): # Entries in the exclude_list look something like this. # { 'reason': The default reason or the reason specified in this section, # 'repositories': @@ -96,8 +99,8 @@ # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ - str( install_and_test_base_util.exclude_list_file ) ) - exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) + str( exclude_list_file ) ) + exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: exclude_list = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was @@ -176,7 +179,8 @@ # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + repository = \ + test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) except Exception, e: error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ ( changeset_revision, name, owner, str( e ) ) @@ -199,9 +203,34 @@ log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) else: + # The repository was successfully installed. log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ]\ + .append( repository_identifier_dict ) + params = dict( test_install_error=False, + do_not_test=False ) + if repository.missing_repository_dependencies: + params[ 'test_install_error' ] = True + # Keep statistics for this repository's repository dependencies that resulted in installation errors. + for missing_repository_dependency in repository.missing_repository_dependencies: + tool_shed = str( missing_repository_dependency.tool_shed ) + name = str( missing_repository_dependency.name ) + owner = str( missing_repository_dependency.owner ) + changset_revision = str( missing_repository_dependency.changeset_revision ) + error_message = unicodify( missing_repository_dependency.error_message ) + missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changset_revision=changset_revision, + error_message=error_message ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ]\ + .append( missing_repository_dependency_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ]\ + .append( missing_repository_dependency_info_dict ) if repository.missing_tool_dependencies: + params[ 'test_install_error' ] = True # Keep statistics for this repository's tool dependencies that resulted in installation errors. for missing_tool_dependency in repository.missing_tool_dependencies: name = str( missing_tool_dependency.name ) @@ -212,22 +241,47 @@ name=name, version=version, error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) - else: - # This repository and all of its dependencies were successfully installed. - install_and_test_statistics_dict[ 'successful_installations' ].append( repository_identifier_dict ) - tool_test_results_dict[ 'passed_tests' ].append( repository_identifier_dict ) - params = dict( test_install_error=False, - do_not_test=False ) - # TODO: do something useful with response_dict - response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params, - can_update_tool_shed ) - - install_and_test_statistics_dict[ 'total_repositories_processed' ] = total_repositories_processed + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ]\ + .append( missing_tool_dependency_info_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ]\ + .append( missing_tool_dependency_info_dict ) + if repository.installed_repository_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in successful installations. + for repository_dependency in repository.installed_repository_dependencies: + tool_shed = str( repository_dependency.tool_shed ) + name = str( repository_dependency.name ) + owner = str( repository_dependency.owner ) + changeset_revision = str( repository_dependency.changeset_revision ) + repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changeset_revision=changeset_revision ) + install_and_test_statistics_dict[ 'successful_repository_installations' ]\ + .append( repository_dependency_info_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'repository_dependencies' ]\ + .append( repository_dependency_info_dict ) + if repository.installed_tool_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in successful installations. + for tool_dependency in repository.installed_tool_dependencies: + name = str( tool_dependency.name ) + type = str( tool_dependency.type ) + version = str( tool_dependency.version ) + installation_directory = tool_dependency.installation_directory( app ) + tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + installation_directory=installation_directory ) + install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ]\ + .append( tool_dependency_info_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ]\ + .append( tool_dependency_info_dict ) + # TODO: do something useful with response_dict + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) return install_and_test_statistics_dict, error_message def main(): @@ -446,25 +500,30 @@ log.debug( error_message ) else: total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] - successful_installations = install_and_test_statistics_dict[ 'successful_installations' ] + successful_repository_installations = install_and_test_statistics_dict[ 'successful_repository_installations' ] + successful_tool_dependency_installations = install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ] repositories_with_installation_error = install_and_test_statistics_dict[ 'repositories_with_installation_error' ] tool_dependencies_with_installation_error = install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" print "# %s - installation script for repositories of type tool_dependency_definition completed." % now print "# Repository revisions processed: %s" % str( total_repositories_processed ) - if successful_installations: + if successful_repository_installations: print "# ----------------------------------------------------------------------------------" - print "# The following %d revisions with all dependencies were successfully installed:" % len( successful_installations ) - install_and_test_base_util.show_summary_output( successful_installations ) + print "# The following %d revisions were successfully installed:" % len( successful_repository_installations ) + install_and_test_base_util.display_repositories_by_owner( successful_repository_installations ) if repositories_with_installation_error: print "# ----------------------------------------------------------------------------------" print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error ) - install_and_test_base_util.show_summary_output( repositories_with_installation_error ) + install_and_test_base_util.successful_repository_installations( repositories_with_installation_error ) + if successful_tool_dependency_installations: + print "# ----------------------------------------------------------------------------------" + print "# The following %d tool dependencies were successfully installed:" % len( successful_tool_dependency_installations ) + install_and_test_base_util.display_tool_dependencies_by_name( successful_tool_dependency_installations ) if tool_dependencies_with_installation_error: print "# ----------------------------------------------------------------------------------" print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) - install_and_test_base_util.show_summary_output( tool_dependencies_with_installation_error ) + install_and_test_base_util.display_tool_dependencies_by_name( tool_dependencies_with_installation_error ) print "####################################################################################" log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. @@ -506,6 +565,36 @@ # "architecture": "x86_64", # "system": "Darwin 12.2.0" # }, + # "successful_installation": + # { + # 'tool_dependencies': + # [ + # { + # 'type': 'Type of tool dependency, e.g. package, set_environment, etc.', + # 'name': 'Name of the tool dependency.', + # 'version': 'Version if this is a package, otherwise blank.', + # 'installation_directory': 'The installation directory path.' + # }, + # ], + # 'repository_dependencies': + # [ + # { + # 'tool_shed': 'The tool shed that this repository was installed from.', + # 'name': 'The name of the repository that failed to install.', + # 'owner': 'Owner of the failed repository.', + # 'changeset_revision': 'Changeset revision of the failed repository.' + # }, + # ], + # 'current_repository': + # [ + # { + # 'tool_shed': 'The tool shed that this repository was installed from.', + # 'name': 'The name of the repository that failed to install.', + # 'owner': 'Owner of the failed repository.', + # 'changeset_revision': 'Changeset revision of the failed repository.' + # }, + # ], + # } # "installation_errors": # { # 'tool_dependencies': @@ -537,12 +626,6 @@ # 'error_message': 'The error message that was returned when the repository failed to install.', # }, # ], - # { - # "name": "The name of the repository.", - # "owner": "The owner of the repository.", - # "changeset_revision": "The changeset revision of the repository.", - # "error_message": "The message stored in tool_dependency.error_message." - # }, # } # } sys.exit( main() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 38 new changesets
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

38 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/57d618633209/ Changeset: 57d618633209 Branch: data_library User: martenson Date: 2013-10-08 22:41:08 Summary: start data_library branch Affected #: 3 files diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 57d618633209a35342f25a13a220fedce71f7a3f .hgignore --- a/.hgignore +++ b/.hgignore @@ -115,3 +115,6 @@ *.rej *~ + +syntax: regexp +^static/AAA_scratch$ \ No newline at end of file diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 57d618633209a35342f25a13a220fedce71f7a3f lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,12 +11,17 @@ log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents + Displays a collection (list) of a folder's contents (files and folders). + The /api/library_contents/{encoded_library_id}/contents lists everything in a library recursively, which is not what we want here. We could add a parameter to use the recursive @@ -25,7 +30,11 @@ rval = [] current_user_roles = trans.get_current_user_roles() + def traverse( folder ): + """ + Load contents of the folder (folders and datasets). + """ admin = trans.user_is_admin() rval = [] for subfolder in folder.active_folders: @@ -50,6 +59,8 @@ try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) +# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_library" + str(folder.parent_library.id)) +# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_id" + str(folder.parent_id)) parent_library = folder.parent_library except: folder = None @@ -62,15 +73,43 @@ if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + # TODO MARTEN Can it be that predecessors of current folder have different access rights? aka user shouldn't see them? + + # Search the path upwards and load the whole route of names and ids for breadcrumb purposes. + path_to_library = [] + + def build_path ( folder ): +# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id BEFORE " + str(folder.parent_id)) +# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id BEFORE " + str(folder.parent_library.id)) + if ( folder.parent_id != folder.parent_library.id ) and ( folder.parent_id is not None ): + log.debug("XXXXXXXXXXXXXXXXXXXXXXX LOADING UPPER FOLDER WITH ID: " + str(folder.parent_id)) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.id " + str(upper_folder.id)) + log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.name " + str(upper_folder.name)) + path_to_library.append( ( upper_folder.id, upper_folder.name ) ) + path_to_library.extend( build_path( upper_folder ) ) + else: + pass + return path_to_library + + full_path = build_path( folder ) for content in traverse( folder ): + return_item = {} encoded_id = trans.security.encode_id( content.id ) if content.api_type == 'folder': + encoded_parent_library_id = trans.security.encode_id( content.parent_library.id ) encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, + if content.parent_id is not None: # For folder return its parent's id for browsing back. + encoded_parent_id = 'F' + trans.security.encode_id( content.parent_id ) + return_item.update ( dict ( parent_id = encoded_parent_id ) ) + return_item.update( dict( id = encoded_id, type = content.api_type, name = content.name, + library_id = encoded_parent_library_id, + full_path = full_path, url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) + rval.append( return_item ) return rval @web.expose_api diff -r b61927f340f30a636204ec560522acf9b76fd262 -r 57d618633209a35342f25a13a220fedce71f7a3f lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,7 +49,7 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) item['id'] = trans.security.encode_id( item['id'] ) rval.append( item ) @@ -131,6 +131,9 @@ rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/db8fd059cf4c/ Changeset: db8fd059cf4c Branch: data_library User: martenson Date: 2013-10-17 18:56:34 Summary: working reverse traversing towards root library for every folder = good for path building Affected #: 1 file diff -r 57d618633209a35342f25a13a220fedce71f7a3f -r db8fd059cf4cae9a6b7dc8bdbe7be5d071325d09 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -27,11 +27,11 @@ we want here. We could add a parameter to use the recursive style, but this is meant to act similar to an "ls" directory listing. """ - rval = [] + folder_contents = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): + def load_folder_contents( folder ): """ Load contents of the folder (folders and datasets). """ @@ -76,41 +76,55 @@ # TODO MARTEN Can it be that predecessors of current folder have different access rights? aka user shouldn't see them? # Search the path upwards and load the whole route of names and ids for breadcrumb purposes. - path_to_library = [] + path_to_root = [] def build_path ( folder ): -# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id BEFORE " + str(folder.parent_id)) -# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id BEFORE " + str(folder.parent_library.id)) - if ( folder.parent_id != folder.parent_library.id ) and ( folder.parent_id is not None ): - log.debug("XXXXXXXXXXXXXXXXXXXXXXX LOADING UPPER FOLDER WITH ID: " + str(folder.parent_id)) + path_to_root = [] + # We are almost in root + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id: " + str( folder.parent_id ) ) + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id: " + str( folder.parent_library.id ) ) + if folder.parent_id is None: + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING: " + str( folder.name ) ) + path_to_root.append( ( folder.id, folder.name ) ) +# upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_library.id ) +# path_to_root.append( ( upper_folder.id, upper_folder.name ) ) + else: + # We add the current folder and traverse up one folder. + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) + path_to_root.append( ( folder.id, folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) - log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.id " + str(upper_folder.id)) - log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.name " + str(upper_folder.name)) - path_to_library.append( ( upper_folder.id, upper_folder.name ) ) - path_to_library.extend( build_path( upper_folder ) ) - else: - pass - return path_to_library + path_to_root.extend( build_path( upper_folder ) ) +# path_to_root = path_to_root.reverse() +# return path_to_root[::-1] + return path_to_root - full_path = build_path( folder ) + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] - for content in traverse( folder ): + # Go through every item in the folder and include its meta-data. + for content_item in load_folder_contents( folder ): return_item = {} - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_parent_library_id = trans.security.encode_id( content.parent_library.id ) + encoded_id = trans.security.encode_id( content_item.id ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) encoded_id = 'F' + encoded_id - if content.parent_id is not None: # For folder return its parent's id for browsing back. - encoded_parent_id = 'F' + trans.security.encode_id( content.parent_id ) + if content_item.parent_id is not None: # Return folder's parent id for browsing back. + encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) return_item.update ( dict ( parent_id = encoded_parent_id ) ) + + # For every item return also the default meta-data return_item.update( dict( id = encoded_id, - type = content.api_type, - name = content.name, + type = content_item.api_type, + name = content_item.name, library_id = encoded_parent_library_id, full_path = full_path, url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - rval.append( return_item ) - return rval + folder_contents.append( return_item ) + if len( folder_contents ) == 0: + folder_contents.append( dict( full_path = full_path ) ) + return folder_contents @web.expose_api def show( self, trans, id, library_id, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/1eda20e058eb/ Changeset: 1eda20e058eb Branch: data_library User: martenson Date: 2013-10-21 18:31:38 Summary: initial frontend commit Affected #: 3 files diff -r db8fd059cf4cae9a6b7dc8bdbe7be5d071325d09 -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -27,7 +27,7 @@ we want here. We could add a parameter to use the recursive style, but this is meant to act similar to an "ls" directory listing. """ - folder_contents = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() @@ -100,7 +100,8 @@ # Return the reversed path so it starts with the library node. full_path = build_path( folder )[::-1] - + folder_container.append( dict( full_path = full_path ) ) + folder_contents = [] # Go through every item in the folder and include its meta-data. for content_item in load_folder_contents( folder ): return_item = {} @@ -118,13 +119,11 @@ return_item.update( dict( id = encoded_id, type = content_item.api_type, name = content_item.name, - library_id = encoded_parent_library_id, - full_path = full_path, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) + library_id = encoded_parent_library_id + ) ) folder_contents.append( return_item ) - if len( folder_contents ) == 0: - folder_contents.append( dict( full_path = full_path ) ) - return folder_contents + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff -r db8fd059cf4cae9a6b7dc8bdbe7be5d071325d09 -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb static/AAA_scratch/data_library/index.html --- /dev/null +++ b/static/AAA_scratch/data_library/index.html @@ -0,0 +1,265 @@ +<!doctype html> +<html lang="en"> +<head> + <meta charset="utf-8"> + <title>Data Library</title> + <link rel="stylesheet" href="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/2.1.1/css/bootstrap…"> +</head> +<body> + + + <div class="container"> + <h1><a onclick="router.navigate('', {trigger: true})">Data Library</a></h1> + <hr /> + <div class="page"></div> + </div> + + + <script type="text/template" id="library-list-template"> + <table class="table striped"> + <thead> + <th>name</th> + <th>description</th> + <th>synopsis</th> + <th>model type</th> + <th>id</th> + + </thead> + <tbody> + <% _.each(libraries, function(library) { %> + <tr> + <td><a href="#/folders/<%- library.id %>"><%- library.get('name') %></a></td> + <td><%= htmlEncode(library.get('description')) %></td> + <td><%= htmlEncode(library.get('synopsis')) %></td> + <td><%= htmlEncode(library.get('model_class')) %></td> + <td><a href="#/folders/<%- library.id %>"><%= htmlEncode(library.get('id')) %></a></td> + </tr> + <% }); %> + </tbody> + </table> + </script> + + + + <script type="text/template" id="folder-content-template"> + <table class="table striped"> + <thead> + <th>name</th> + <th>type</th> + <th>parent id</th> + <th>id</th> + <th>library id</th> + </thead> + <tbody> + <% _.each(items, function(content_item) { %> + <tr> + <% if (content_item.get('type') === 'folder') { %> + <td><a href="#/folders/<%- content_item.id %>?library_id=<%- content_item.get('library_id') %>"><%- content_item.get('name') %></a></td> + <% } else { %> + <td><%- content_item.get('name') %></td> + <% } %> + <td><%= htmlEncode(content_item.get('type')) %></td> + <td><%= htmlEncode(content_item.get('parent_id')) %></td> + <td><a href="#/folders/<%- content_item.id %>"><%= htmlEncode(content_item.get('id')) %></a></td> + <td><a href="#/folders/<%- content_item.get('library_id') %>"><%= htmlEncode(content_item.get('library_id')) %></a></td> + </tr> + <% }); %> + </tbody> + </table> + + <hr/> + <div> + <% if ( typeof libraries !== undefined ) { %> + <% _.each(libraries.models, function(library) { %> + <%- library.get('name') %><br/> + <% }); %> + <% } else { %> + libraries are undefined + <% } %> + </div> + </script> + + + <script src="jquery-1.10.2.js" type="text/javascript"></script> + <script src="underscore.js" type="text/javascript"></script> + <script src="backbone.js" type="text/javascript"></script> + <script src="backbone.queryparams.js" type="text/javascript"></script> + + + <script> + + // ENCODE HTML + function htmlEncode(value){ + return $('<div/>').text(value).html(); + } + + // NESTED COLLECTIONS + function nestCollection(model, attributeName, nestedCollection) { + //setup nested references + for (var i = 0; i < nestedCollection.length; i++) { + model.attributes[attributeName][i] = nestedCollection.at(i).attributes; + } + + //create empty arrays if none + nestedCollection.bind('add', function (initiative) { + if (!model.get(attributeName)) { + model.attributes[attributeName] = []; + } + model.get(attributeName).push(initiative.attributes); + }); + + nestedCollection.bind('remove', function (initiative) { + var updateObj = {}; + updateObj[attributeName] = _.without(model.get(attributeName), initiative.attributes); + model.set(updateObj); + }); + return nestedCollection; + } + + var api_key = 'e48b2b2589b242a50538f8f9fa8e5ee9'; + + // MODIFICATIONS DONE JUST BEFORE THE REQUEST ITSELF + $.ajaxPrefilter( function( options, originalOptions, jqXHR ) { + options.url = 'http://martenson.bx.psu.edu:8080' + options.url + '?key=' + api_key; + }); + + // SERIALIZE JSON + $.fn.serializeObject = function() { + var o = {}; + var a = this.serializeArray(); + $.each(a, function() { + if (o[this.name] !== undefined) { + if (!o[this.name].push) { + o[this.name] = [o[this.name]]; + } + o[this.name].push(this.value || ''); + } else { + o[this.name] = this.value || ''; + } + }); + return o; + }; + + // LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries', + }); + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries', + model: Library + }); + + // ITEM + var Item = Backbone.Model.extend({ + }) + + // FOLDER + var Folder = Backbone.Collection.extend({ + model: Item + }) + + // Container including metadata + var FolderContainer = Backbone.Model.extend({ + defaults: { + folder: new Folder(), + full_path: "unknown", + urlRoot: "/api/folders/", + id: "unknown" + }, + parse: function(obj) { + full_path = obj[0].full_path; + // update the inner collection + this.get("folder").reset(obj[1].folder_contents); + + // this mightn't be necessary + // delete obj.folder; + + return obj; + } + }) + + var LibraryListView = Backbone.View.extend({ + el: '.page', + render: function () { + var that = this; + if (typeof libraries === "undefined") { + libraries = new Libraries(); + } + libraries.fetch({ + success: function (libraries) { + var template = _.template($('#library-list-template').html(), {libraries: libraries.models}); + that.$el.html(template); + } + }) + } + }); + + + var FolderContentView = Backbone.View.extend({ + el: '.page', + render: function (options, params) { + var that = this; + + var folderContainer = new FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + // var folder = new Folder({id: options.id}); + + folderContainer.fetch({ + success: function (container) { + folderContainer.attributes.folder = container.attributes.folder; + var template = _.template($('#folder-content-template').html(), {items: folderContainer.attributes.folder.models, id: options.id}); + that.$el.html(template); + } + }) + + // folder.fetch({ + // success: function (folder) { + // folderContainer.folder = folder; + // var template = _.template($('#folder-content-template').html(), {items: folderContainer.folder.models, id: options.id}); + // that.$el.html(template); + // } + // }) + + // var folder = new Folder({id: options.id}); + // folder.url = folder.urlRoot + options.id + '/contents'; + // folder.fetch({ + // success: function (folder) { + // // console.log(JSON.stringify(folder)) + // //create the template + // var template = _.template($('#folder-content-template').html(), {items: folder.models, id: options.id}); + // that.$el.html(template); + // } + // }) + + }, + }); + + + var libraryListView = new LibraryListView(); + var folderContentView = new FolderContentView(); + + var Router = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content" + } + }); + + var router = new Router; + + router.on('route:libraries', function() { + // render libraries list + libraryListView.render(); + }) + + router.on('route:folder_content', function(id, params) { + // render folder's content + folderContentView.render({id: id, params: params}); + }) + + Backbone.history.start(); + </script> + + +</body> +</html> diff -r db8fd059cf4cae9a6b7dc8bdbe7be5d071325d09 -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb static/AAA_scratch/data_library/index_working.html --- /dev/null +++ b/static/AAA_scratch/data_library/index_working.html @@ -0,0 +1,261 @@ +<!doctype html> +<html lang="en"> +<head> + <meta charset="utf-8"> + <title>Data Library</title> + <link rel="stylesheet" href="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/2.1.1/css/bootstrap…"> +</head> +<body> + + + <div class="container"> + <h1>Data Library</h1> + <hr /> + <div class="page"></div> + </div> + + + <script type="text/template" id="library-list-template"> + <a href="#/new" class="btn btn-primary">New Library</a> + <hr /> + <table class="table striped"> + <thead> + <th>name</th> + <th>description</th> + <th>synopsis</th> + <th></th> + <th></th> + </thead> + <tbody> + <% _.each(libraries, function(library) { %> + <tr> + <td><a href="#/folders/<%- library.id %>"><%- library.get('name') %></a></td> + <td><%= htmlEncode(library.get('description')) %></td> + <td><%= htmlEncode(library.get('synopsis')) %></td> + <td><a href="#/edit/<%= library.id %>" class="btn">Edit</td> + <td><button data-library-id="<%- library.id %>" class="btn btn-danger delete">Delete</button></td> + </tr> + <% }); %> + </tbody> + </table> + </script> + + + <script type="text/template" id="library-edit-template"> + <form class="library-edit-form"> + <legend>Create Library</legend> + <label>Name of the Library</label> + <input type="text" name="name" /> + <label>Description</label> + <input type="text" name="description" /> + <label>Synopsis</label> + <input type="text" name="synopsis" /> + <hr /> + <button type="submit" class="btn">Create Library</button> + </form> + </script> + + + + <script type="text/template" id="folders-list-template"> + <table class="table striped"> + <thead> + <th>name</th> + <th>type</th> + </thead> + <tbody> + <% _.each(folders, function(folder) { %> + <tr> + <% if (folder.get('type') === 'folder') { %> + <td><a href="#/folders/<%- folder.id %>"><%- folder.get('name') %></a></td> + <% } else { %> + <td><%- folder.get('name') %></td> + <% } %> + <td><%= htmlEncode(folder.get('type')) %></td> + </tr> + <% }); %> + </tbody> + </table> + </script> + + + <script src="jquery-1.10.2.js" type="text/javascript"></script> + <script src="underscore.js" type="text/javascript"></script> + <script src="backbone.js" type="text/javascript"></script> + + + <script> + + // ENCODE HTML + function htmlEncode(value){ + return $('<div/>').text(value).html(); + } + + var api_key = 'e48b2b2589b242a50538f8f9fa8e5ee9'; + + // MODIFICATIONS DONE JUST BEFORE THE REQUEST ITSELF + $.ajaxPrefilter( function( options, originalOptions, jqXHR ) { + options.url = 'http://martenson.bx.psu.edu:8080' + options.url + '?key=' + api_key; + }); + + // SERIALIZE JSON + $.fn.serializeObject = function() { + var o = {}; + var a = this.serializeArray(); + $.each(a, function() { + if (o[this.name] !== undefined) { + if (!o[this.name].push) { + o[this.name] = [o[this.name]]; + } + o[this.name].push(this.value || ''); + } else { + o[this.name] = this.value || ''; + } + }); + return o; + }; + +// LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries' + }); + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries' + }); +// FOLDER + var Folder = Backbone.Model.extend({ + urlRoot: '/api/folders/' + }) + var Folders = Backbone.Collection.extend({ + model: Folder, + urlRoot: '/api/folders/' + + }) + + var LibraryEditView = Backbone.View.extend({ + el: '.page', + events: { + 'submit .library-edit-form': 'saveLibrary' + }, + saveLibrary: function (ev) { + var libraryDetails = $(ev.currentTarget).serializeObject(); + var library = new Library(); + library.save(libraryDetails, { + success: function (library) { + router.navigate('', {trigger: true}) + } + }); + console.log(libraryDetails); + return false; + }, + render: function (options) { + var that = this; + if (options.id) { + this.library = new Library({id: options.id}); + this.library.fetch({ + success: function(library){ + var template = _.template($('#library-edit-template').html(), {library: library}); + that.$el.html(template); + } + }); + } else { + var template = _.template($('#library-edit-template').html(), {user: null}); + this.$el.html(template); + } + } + }); + + + var LibraryListView = Backbone.View.extend({ + el: '.page', + events: { + 'click .delete' : 'deleteLibrary' + }, + render: function () { + var that = this; + var libraries = new Libraries(); + libraries.fetch({ + success: function (libraries) { + var template = _.template($('#library-list-template').html(), {libraries: libraries.models}); + that.$el.html(template); + } + }) + }, + deleteLibrary : function (ev) { + // DELETE /libraries/{id} + var id_to_delete = $(ev.target).attr('data-library-id'); + var libraryToDelete = new Library({id: id_to_delete}) + libraryToDelete.destroy({ + success: function () { + libraryListView.render(); + } + }) + return false + }, + createLibrary : function (ev) { + // PUT /libraries + + } + }); + + + var FoldersListView = Backbone.View.extend({ + el: '.page', + render: function (options) { + var that = this; + var folders = new Folders({id: options.id}); + folders.url = folders.urlRoot + options.id + '/contents'; + folders.fetch({ + success: function (folders) { + var template = _.template($('#folders-list-template').html(), {folders: folders.models, id: options.id}); + that.$el.html(template); + } + }) + }, + }); + + + var libraryListView = new LibraryListView(); + var libraryEditView = new LibraryEditView(); + var foldersListView = new FoldersListView(); + + + var Router = Backbone.Router.extend({ + routes: { + "" : "home", + "new" : "edit_library", + "edit/:id" : "edit_library", + "delete/:id" : "delete_library", + "folders/:id" : "folders" + } + }); + + var router = new Router; + + router.on('route:home', function() { + // render libraries list + libraryListView.render(); + }) + router.on('route:edit_library', function(id) { + // render library edit form + libraryEditView.render({id: id}); + }) + router.on('route:delete_library', function() { + // render delete library form + libraryDeleteView.render(); + }) + // router.on('route:folders', function(parent_id, top_level) { + // // render folders list + // foldersListView.render({id: parent_id, top_level: true}); + // }) + router.on('route:folders', function(id) { + // render folders list + foldersListView.render({id: id}); + }) + + Backbone.history.start(); + </script> + + +</body> +</html> https://bitbucket.org/galaxy/galaxy-central/commits/dc735a38cf76/ Changeset: dc735a38cf76 Branch: data_library User: martenson Date: 2013-10-24 20:22:26 Summary: refactoring, modals start Affected #: 4 files diff -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1835,7 +1835,7 @@ return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description diff -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -15,42 +15,37 @@ Class controls retrieval, creation and updating of folder contents. """ + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items + @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents - Displays a collection (list) of a folder's contents (files and folders). - - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. """ folder_container = [] current_user_roles = trans.get_current_user_roles() - - def load_folder_contents( folder ): - """ - Load contents of the folder (folders and datasets). - """ - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - try: decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) except TypeError: @@ -59,69 +54,68 @@ try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) -# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_library" + str(folder.parent_library.id)) -# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_id" + str(folder.parent_id)) parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) - # TODO MARTEN Can it be that predecessors of current folder have different access rights? aka user shouldn't see them? - # Search the path upwards and load the whole route of names and ids for breadcrumb purposes. + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + path_to_root = [] - def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ path_to_root = [] # We are almost in root - log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id: " + str( folder.parent_id ) ) - log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id: " + str( folder.parent_library.id ) ) if folder.parent_id is None: log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING: " + str( folder.name ) ) - path_to_root.append( ( folder.id, folder.name ) ) + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) # upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_library.id ) # path_to_root.append( ( upper_folder.id, upper_folder.name ) ) else: # We add the current folder and traverse up one folder. log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) - path_to_root.append( ( folder.id, folder.name ) ) + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) path_to_root.extend( build_path( upper_folder ) ) -# path_to_root = path_to_root.reverse() -# return path_to_root[::-1] return path_to_root # Return the reversed path so it starts with the library node. full_path = build_path( folder )[::-1] folder_container.append( dict( full_path = full_path ) ) + folder_contents = [] # Go through every item in the folder and include its meta-data. - for content_item in load_folder_contents( folder ): + for content_item in self.load_folder_contents( trans, folder ): return_item = {} encoded_id = trans.security.encode_id( content_item.id ) # For folder return also hierarchy values if content_item.api_type == 'folder': - encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) +# encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) encoded_id = 'F' + encoded_id - if content_item.parent_id is not None: # Return folder's parent id for browsing back. - encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) - return_item.update ( dict ( parent_id = encoded_parent_id ) ) +# if content_item.parent_id is not None: # Return folder's parent id for browsing back. +# encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) + last_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count, last_updated = last_updated ) ) # For every item return also the default meta-data return_item.update( dict( id = encoded_id, type = content_item.api_type, - name = content_item.name, - library_id = encoded_parent_library_id + name = content_item.name + ) ) folder_contents.append( return_item ) + # Put the data in the container folder_container.append( dict( folder_contents = folder_contents ) ) return folder_container diff -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -51,7 +51,7 @@ for library in query: item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) rval.append( item ) return rval diff -r 1eda20e058ebb08a4f4b71ed6988f6f106b62fdb -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 static/AAA_scratch/data_library/index.html --- a/static/AAA_scratch/data_library/index.html +++ b/static/AAA_scratch/data_library/index.html @@ -1,10 +1,13 @@ -<!doctype html> +<!DOCTYPE html><html lang="en"><head><meta charset="utf-8"><title>Data Library</title> - <link rel="stylesheet" href="http://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/2.1.1/css/bootstrap…"> + <meta name="viewport" content="width=device-width, initial-scale=1.0"> +  + <link href="css/bootstrap.min.css" rel="stylesheet" media="screen"></head> + <body> @@ -16,7 +19,7 @@ <script type="text/template" id="library-list-template"> - <table class="table striped"> + <table class="table table-striped"><thead><th>name</th><th>description</th> @@ -42,45 +45,47 @@ <script type="text/template" id="folder-content-template"> - <table class="table striped"> + + <% _.each(path, function(path_item) { %> + <% if (path_item[0] != id) { %> + <a href='#/folders/<%- path_item[0] %>'><%- path_item[1] %></a> | + <% } else { %> + <%- path_item[1] %> + <% } %> + <% }); %> + + <table class="table table-hover table-condensed"><thead> + <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th><th>name</th><th>type</th> - <th>parent id</th> - <th>id</th> - <th>library id</th></thead><tbody><% _.each(items, function(content_item) { %> - <tr> + <tr class="folder_row" id="<%- content_item.id %>"> + <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td><% if (content_item.get('type') === 'folder') { %> - <td><a href="#/folders/<%- content_item.id %>?library_id=<%- content_item.get('library_id') %>"><%- content_item.get('name') %></a></td> + <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get('name') %></a> + <% if (content_item.get('item_count') === 0) { %> + <span class="muted">(empty folder)</span> + <% } %> + </td><% } else { %><td><%- content_item.get('name') %></td><% } %><td><%= htmlEncode(content_item.get('type')) %></td> - <td><%= htmlEncode(content_item.get('parent_id')) %></td> - <td><a href="#/folders/<%- content_item.id %>"><%= htmlEncode(content_item.get('id')) %></a></td> - <td><a href="#/folders/<%- content_item.get('library_id') %>"><%= htmlEncode(content_item.get('library_id')) %></a></td></tr><% }); %></tbody></table> - <hr/> - <div> - <% if ( typeof libraries !== undefined ) { %> - <% _.each(libraries.models, function(library) { %> - <%- library.get('name') %><br/> - <% }); %> - <% } else { %> - libraries are undefined - <% } %> - </div> + </script> + <script src="require.js"></script><script src="jquery-1.10.2.js" type="text/javascript"></script> + <script src="js/bootstrap.min.js"></script><script src="underscore.js" type="text/javascript"></script><script src="backbone.js" type="text/javascript"></script><script src="backbone.queryparams.js" type="text/javascript"></script> @@ -88,34 +93,27 @@ <script> + // configure require + // require.config({ + // baseUrl: "/", + // shim: { + // "libs/underscore": { exports: "_" }, + // "libs/backbone/backbone": { exports: "Backbone" }, + // "libs/backbone/backbone-relational": ["libs/backbone/backbone"] + // } + // }); + + // require(['galaxy.modal'], function(modal) + // { + // Galaxy.modal = new modal.GalaxyModal(); + // }); + + // ENCODE HTML function htmlEncode(value){ return $('<div/>').text(value).html(); } - // NESTED COLLECTIONS - function nestCollection(model, attributeName, nestedCollection) { - //setup nested references - for (var i = 0; i < nestedCollection.length; i++) { - model.attributes[attributeName][i] = nestedCollection.at(i).attributes; - } - - //create empty arrays if none - nestedCollection.bind('add', function (initiative) { - if (!model.get(attributeName)) { - model.attributes[attributeName] = []; - } - model.get(attributeName).push(initiative.attributes); - }); - - nestedCollection.bind('remove', function (initiative) { - var updateObj = {}; - updateObj[attributeName] = _.without(model.get(attributeName), initiative.attributes); - model.set(updateObj); - }); - return nestedCollection; - } - var api_key = 'e48b2b2589b242a50538f8f9fa8e5ee9'; // MODIFICATIONS DONE JUST BEFORE THE REQUEST ITSELF @@ -167,13 +165,10 @@ id: "unknown" }, parse: function(obj) { - full_path = obj[0].full_path; + this.full_path = obj[0].full_path; + // this.folder.reset(obj[1].folder_contents); // update the inner collection this.get("folder").reset(obj[1].folder_contents); - - // this mightn't be necessary - // delete obj.folder; - return obj; } }) @@ -197,41 +192,39 @@ var FolderContentView = Backbone.View.extend({ el: '.page', + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClicked' + }, render: function (options, params) { var that = this; var folderContainer = new FolderContainer({id: options.id}); folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; - // var folder = new Folder({id: options.id}); folderContainer.fetch({ success: function (container) { - folderContainer.attributes.folder = container.attributes.folder; - var template = _.template($('#folder-content-template').html(), {items: folderContainer.attributes.folder.models, id: options.id}); + // folderContainer.attributes.folder = container.attributes.folder; + var template = _.template($('#folder-content-template').html(), {path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id}); that.$el.html(template); } }) - - // folder.fetch({ - // success: function (folder) { - // folderContainer.folder = folder; - // var template = _.template($('#folder-content-template').html(), {items: folderContainer.folder.models, id: options.id}); - // that.$el.html(template); - // } - // }) - - // var folder = new Folder({id: options.id}); - // folder.url = folder.urlRoot + options.id + '/contents'; - // folder.fetch({ - // success: function (folder) { - // // console.log(JSON.stringify(folder)) - // //create the template - // var template = _.template($('#folder-content-template').html(), {items: folder.models, id: options.id}); - // that.$el.html(template); - // } - // }) - }, + selectAll : function (ev) { + var selected = ev.target.checked; + // Iterate each checkbox + $(':checkbox').each(function () { this.checked = selected; }); + }, + selectClicked : function (ev) { + var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') + if (checkbox[0] != undefined) { + if (checkbox[0].checked){ + checkbox[0].checked = ''; + } else { + checkbox[0].checked = 'selected'; + } + } + } }); @@ -258,8 +251,7 @@ }) Backbone.history.start(); + </script> - - </body></html> https://bitbucket.org/galaxy/galaxy-central/commits/518ded2c3f30/ Changeset: 518ded2c3f30 Branch: data_library User: martenson Date: 2013-11-06 23:15:41 Summary: work in progress on data libraries, integrated within galaxy framework with require, modularized Affected #: 7 files diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -76,6 +76,22 @@ library_list_grid = LibraryListGrid() + + @web.expose + def list( self, trans, **kwd ): + params = util.Params( kwd ) + + # define app configuration for generic mako template + app = { + 'jscript' : "galaxy.library" + } + + # fill template + return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + + +# return trans.fill_template( "/library/list.mako") + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 static/AAA_scratch/data_library/index.html --- a/static/AAA_scratch/data_library/index.html +++ b/static/AAA_scratch/data_library/index.html @@ -83,7 +83,7 @@ </script> - <script src="require.js"></script> + <script src="jquery-1.10.2.js" type="text/javascript"></script><script src="js/bootstrap.min.js"></script><script src="underscore.js" type="text/javascript"></script> @@ -93,22 +93,6 @@ <script> - // configure require - // require.config({ - // baseUrl: "/", - // shim: { - // "libs/underscore": { exports: "_" }, - // "libs/backbone/backbone": { exports: "Backbone" }, - // "libs/backbone/backbone-relational": ["libs/backbone/backbone"] - // } - // }); - - // require(['galaxy.modal'], function(modal) - // { - // Galaxy.modal = new modal.GalaxyModal(); - // }); - - // ENCODE HTML function htmlEncode(value){ return $('<div/>').text(value).html(); @@ -245,9 +229,9 @@ libraryListView.render(); }) - router.on('route:folder_content', function(id, params) { + router.on('route:folder_content', function(id) { // render folder's content - folderContentView.render({id: id, params: params}); + folderContentView.render({id: id}); }) Backbone.history.start(); diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 static/scripts/galaxy.library.js --- /dev/null +++ b/static/scripts/galaxy.library.js @@ -0,0 +1,333 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +// global variables +var view = null; +var library_router = null; + +// dependencies +define(["galaxy.modal", "galaxy.master", "galaxy.library.router"], function(mod_modal, mod_master, router) { + +// MMMMMMMMMMMMMMM +// === Models ==== +// MMMMMMMMMMMMMMM + + // LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries', + }); + + // LIBRARIES + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries', + model: Library + }); + + // ITEM + var Item = Backbone.Model.extend({ + }) + + // FOLDER + var Folder = Backbone.Collection.extend({ + model: Item + }) + + // Container for folder contents (folders, items and metadata). + var FolderContainer = Backbone.Model.extend({ + defaults: { + folder: new Folder(), + full_path: "unknown", + urlRoot: "/api/folders/", + id: "unknown" + }, + parse: function(obj) { + this.full_path = obj[0].full_path; + // this.folder.reset(obj[1].folder_contents); + // update the inner collection + this.get("folder").reset(obj[1].folder_contents); + return obj; + } + }) + +// MMMMMMMMMMMMMM +// === Views ==== +// MMMMMMMMMMMMMM + +// galaxy folder +var FolderContentView = Backbone.View.extend({ + el : '#center', + // initialize + initialize : function(){ + // view = this; + //set up the library router + // this.set_up_router(); + + //render + // this.render(); + }, + // set up router + set_up_router : function(){ + if (library_router === null){ + library_router = new router.LibraryRouter(); + Backbone.history.start(); + } + }, + template_folder : function (){ + tmpl_array = []; + + tmpl_array.push('<% _.each(path, function(path_item) { %>'); + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> |'); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<%- path_item[1] %>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + tmpl_array.push('<table class="table table-hover table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>type</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row" id="<%- content_item.id %>">'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); + tmpl_array.push(' <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td><%- content_item.get("name") %></td>'); + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <td><%= _.escape(content_item.get("type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' '); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + return tmpl_array.join(''); + }, + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClicked' + }, + render: function (options) { + var that = this; + + var folderContainer = new FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + + folderContainer.fetch({ + success: function (container) { + // folderContainer.attributes.folder = container.attributes.folder; + var template = _.template(that.template_folder(), {path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id}); + that.$el.html(template); + } + }) + }, + selectAll : function (ev) { + var selected = ev.target.checked; + // Iterate each checkbox + $(':checkbox').each(function () { this.checked = selected; }); + }, + selectClicked : function (ev) { + var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') + if (checkbox[0] != undefined) { + if (checkbox[0].checked){ + checkbox[0].checked = ''; + } else { + checkbox[0].checked = 'selected'; + } + } + } +}); + + +// galaxy library +var GalaxyLibraryview = Backbone.View.extend({ + el: '#center', + + events: { + 'click #create_new_library_btn' : 'show_library_modal' + }, + + + // initialize + initialize : function(){ + // view = this; + //set up the libray router + // this.set_up_router(); + + //render + // this.render(); + }, + + // set up router + set_up_router : function(){ + if (library_router === null){ + library_router = new router.LibraryRouter(); + Backbone.history.start(); + } + }, + + // template + template_library_list : function (){ + tmpl_array = []; + + tmpl_array.push(''); + tmpl_array.push('<h1>Welcome to the data libraries</h1>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary">New Library</a>'); + tmpl_array.push('<table class="table table-striped">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>description</th>'); + tmpl_array.push(' <th>synopsis</th> '); + tmpl_array.push(' <th>model type</th> '); + tmpl_array.push(' <th>id</th> '); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(libraries, function(library) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%- library.get("name") %></a></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%= _.escape(library.get("id")) %></a></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(''); + tmpl_array.push(''); + tmpl_array.push(''); + tmpl_array.push(''); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + return tmpl_array.join(''); + }, + + // render + render: function () { + var that = this; + // if (typeof libraries === "undefined") { + libraries = new Libraries(); + // } + libraries.fetch({ + success: function (libraries) { + var template = _.template(that.template_library_list(), {libraries: libraries.models}); + that.$el.html(template); + } + }) + }, + + // own modal + modal : null, + + // show/hide create library modal + show_library_modal : function (e) + { + // prevent default + e.preventDefault(); + + // create modal + if (!this.modal){ + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal( + { + title : 'Create New Library', + body : this.template_new_library(), + buttons : { + 'Create' : function() {self.create_new_library_event()}, + 'Close' : function() {self.modal.hide()} + } + }); + } + + // show modal + this.modal.show(); + }, + create_new_library_event: function(){ + var libraryDetails = this.serialize_new_library(); + var library = new Library(); + library.save(libraryDetails, { + success: function (library) { + + library_router.navigate('', {trigger: true}) + } + }); + // console.log(libraryDetails); + return false; + }, + serialize_new_library : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val(), + synopsis: $("input[name='Synopsis']").val() + }; + }, + // load html template + template_new_library: function() + { + tmpl_array = []; + tmpl_array.push('<div id="new_library_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + // tmpl_array.push('<label>Synopsis</label>'); + tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); + tmpl_array.push(''); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + return tmpl_array.join(''); + + + // return '<div id="'+ id +'"></div>'; + } +}); + +// galaxy library wrapper View +var GalaxyLibrary = Backbone.View.extend({ + folderContentView : null, + galaxyLibraryview : null, + initialize : function(){ + + folderContentView = new FolderContentView(); + galaxyLibraryview = new GalaxyLibraryview(); + + library_router = new router.LibraryRouter(); + + library_router.on('route:libraries', function() { + // render libraries list + galaxyLibraryview.render(); + }) + + library_router.on('route:folder_content', function(id) { + // render folder's contents + folderContentView.render({id: id}); + + }) + + // library_router.on('route:show_library_modal', function() { + // // render folder's contents + // galaxyLibraryview.show_library_modal(); + + // }) + + Backbone.history.start(); + + return this + } +}); + +// return +return { + GalaxyApp: GalaxyLibrary +}; + +}); diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 static/scripts/galaxy.library.router.js --- /dev/null +++ b/static/scripts/galaxy.library.router.js @@ -0,0 +1,21 @@ +define( [], function() { + +/** + * -- Routers -- + */ + +/** + * Router for library browser. + */ +var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content" + } +}); + +return { + LibraryRouter: LibraryRouter, +}; + +}) \ No newline at end of file diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,7 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'new_library', 'trackster' ]; var _ = grunt.util._; var fmt = _.sprintf; diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -102,12 +102,13 @@ }); ## load galaxy js-modules - require(['galaxy.master', 'galaxy.frame', 'galaxy.modal', 'galaxy.upload'], function(master, frame, modal, upload) + require(['galaxy.master', 'galaxy.frame', 'galaxy.modal', 'galaxy.upload', 'galaxy.library'], function(master, frame, modal, upload, library) { Galaxy.master = new master.GalaxyMaster(); Galaxy.frame_manager = new frame.GalaxyFrameManager(); Galaxy.modal = new modal.GalaxyModal(); - ##Galaxy.upload = new upload.GalaxyUpload(); + Galaxy.upload = new upload.GalaxyUpload(); + ##Galaxy.library = new library.GalaxyLibrary(); }); </script></%def> diff -r dc735a38cf76f93772027b34e489db1ef9d2d0a5 -r 518ded2c3f30cca803a29f76da2e80505b166647 templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -126,6 +126,7 @@ ## 'Shared Items' or Libraries tab. <% menu_options = [ + [ _('New Libraries'), h.url_for( controller='/library', action='list') ], [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], None, [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], https://bitbucket.org/galaxy/galaxy-central/commits/3ea8be4161ab/ Changeset: 3ea8be4161ab Branch: data_library User: martenson Date: 2013-11-12 22:48:56 Summary: transfer into modal window, requirejs, notifications, import to history, galaxy.modal changes, API for library datasets, start of API versioning Affected #: 6 files diff -r 518ded2c3f30cca803a29f76da2e80505b166647 -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2000,6 +2000,7 @@ genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, + peek = ( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ), template_data = template_data ) if ldda.dataset.uuid is None: rval['uuid'] = None diff -r 518ded2c3f30cca803a29f76da2e80505b166647 -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -0,0 +1,38 @@ +""" +API operations on the contents of a dataset from library. +""" +from galaxy import web +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems + +import logging +log = logging.getLogger( __name__ ) + +class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): + + @web.expose_api + def index( self, trans, **kwd ): + """ + GET /api/libraries/datasets + """ + trans.response.status = 501 + return 'not implemented' + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/libraries/datasets/{encoded_dataset_id} + Displays information about and/or content of a dataset identified by the lda ID. + """ + # Get dataset. + try: + dataset = self.get_library_dataset( trans, id = id ) + except Exception, e: + return str( e ) + try: + # Default: return dataset as dict. + rval = dataset.to_dict() + except Exception, e: + rval = "Error in dataset API at listing contents: " + str( e ) + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 + return rval \ No newline at end of file diff -r 518ded2c3f30cca803a29f76da2e80505b166647 -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,18 +46,19 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', - controller='admin_toolshed', - action='display_image_in_repository', - repository_id=None, - image_file=None ) + + # Add the controllers folder webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) + # Add the api folder + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) + # Add the api folder VERSION 2 + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api.v2', app ) + # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) # Force /activate to go to the controller webapp.add_route( '/activate', controller='user', action='activate' ) - # These two routes handle our simple needs at the moment + webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) @@ -66,8 +67,8 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', - controller='dataset', action='display_application', dataset_id=None, user_id=None, - app_name = None, link_name = None, app_action = None, action_param = None ) + controller='dataset', action='display_application', dataset_id=None, user_id=None, + app_name = None, link_name = None, app_action = None, action_param = None ) webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) @@ -75,22 +76,6 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # Add the web API - webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'content', 'contents', controller='history_contents', @@ -102,10 +87,6 @@ controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'user', 'users', controller='group_users', @@ -127,11 +108,6 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -147,31 +123,58 @@ path_prefix='/api/histories/:history_id/contents/:history_content_id' ) webapp.mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.mapper.resource( 'request', 'requests', path_prefix='/api' ) webapp.mapper.resource( 'form', 'forms', path_prefix='/api' ) webapp.mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) webapp.mapper.resource( 'role', 'roles', path_prefix='/api' ) webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) webapp.mapper.resource( 'genome', 'genomes', path_prefix='/api' ) webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) + + # ======================= + # ===== LIBRARY API ===== + # ======================= + + webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) + + webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) + webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) + + webapp.mapper.resource( 'content', 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource - webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", - controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) + webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) # visualizations registry generic template renderer - webapp.add_route( '/visualization/show/:visualization_name', - controller='visualization', action='render', visualization_name=None ) + webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) # "POST /api/workflows/import" => ``workflows.import_workflow()``. # Defines a named route "import_workflow". @@ -179,6 +182,15 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', @@ -191,6 +203,7 @@ path_prefix='/api', new={ 'install_repository_revision' : 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger diff -r 518ded2c3f30cca803a29f76da2e80505b166647 -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -80,18 +80,13 @@ @web.expose def list( self, trans, **kwd ): params = util.Params( kwd ) - # define app configuration for generic mako template app = { 'jscript' : "galaxy.library" } - # fill template return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) - - -# return trans.fill_template( "/library/list.mako") - + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r 518ded2c3f30cca803a29f76da2e80505b166647 -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -7,7 +7,7 @@ var library_router = null; // dependencies -define(["galaxy.modal", "galaxy.master", "galaxy.library.router"], function(mod_modal, mod_master, router) { +define(["galaxy.modal", "galaxy.master"], function(mod_modal, mod_master) { // MMMMMMMMMMMMMMM // === Models ==== @@ -15,40 +15,65 @@ // LIBRARY var Library = Backbone.Model.extend({ - urlRoot: '/api/libraries', - }); + urlRoot: '/api/libraries' + }); // LIBRARIES var Libraries = Backbone.Collection.extend({ url: '/api/libraries', model: Library - }); + }); // ITEM var Item = Backbone.Model.extend({ + urlRoot : '/api/libraries/datasets' }) // FOLDER var Folder = Backbone.Collection.extend({ model: Item - }) + }) - // Container for folder contents (folders, items and metadata). + // CONTAINER for folder contents (folders, items and metadata). var FolderContainer = Backbone.Model.extend({ - defaults: { - folder: new Folder(), - full_path: "unknown", - urlRoot: "/api/folders/", - id: "unknown" - }, - parse: function(obj) { - this.full_path = obj[0].full_path; - // this.folder.reset(obj[1].folder_contents); + defaults : { + folder : new Folder(), + full_path : "unknown", + urlRoot : "/api/folders/", + id : "unknown" + }, + parse : function(obj) { + this.full_path = obj[0].full_path; // update the inner collection this.get("folder").reset(obj[1].folder_contents); return obj; + } + }) + + // HISTORY ITEM + var HistoryItem = Backbone.Model.extend({ + urlRoot : '/api/histories/' + }); + + // HISTORY + var GalaxyHistory = Backbone.Model.extend({ + url : '/api/histories/' + }); + + // HISTORIES + var GalaxyHistories = Backbone.Collection.extend({ + url : '/api/histories', + model : GalaxyHistory + }); + + //ROUTER + var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content" } - }) + }); + // MMMMMMMMMMMMMM // === Views ==== @@ -56,67 +81,155 @@ // galaxy folder var FolderContentView = Backbone.View.extend({ - el : '#center', + //main element + el : '#center', // initialize initialize : function(){ - // view = this; - //set up the library router - // this.set_up_router(); + this.folders = []; + }, + // set up + templateFolder : function (){ + var tmpl_array = []; - //render - // this.render(); - }, - // set up router - set_up_router : function(){ - if (library_router === null){ - library_router = new router.LibraryRouter(); - Backbone.history.start(); - } + tmpl_array.push('<a href="#">Libraries</a> | '); + tmpl_array.push('<% _.each(path, function(path_item) { %>'); //breadcrumb + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> |'); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<%- path_item[1] %>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + tmpl_array.push('<table class="table table-hover table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>type</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row" id="<%- content_item.id %>">'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); //folder + tmpl_array.push(' <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); //empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td><a class="library-dataset" href="#"><%- content_item.get("name") %></a></td>'); //dataset + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <td><%= _.escape(content_item.get("type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' '); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + return tmpl_array.join(''); }, - template_folder : function (){ - tmpl_array = []; + templateDatasetModal : function(){ + var tmpl_array = []; - tmpl_array.push('<% _.each(path, function(path_item) { %>'); - tmpl_array.push('<% if (path_item[0] != id) { %>'); - tmpl_array.push('<a href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> |'); - tmpl_array.push('<% } else { %>'); - tmpl_array.push('<%- path_item[1] %>'); - tmpl_array.push('<% } %>'); - tmpl_array.push('<% }); %>'); - tmpl_array.push('<table class="table table-hover table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th>name</th>'); - tmpl_array.push(' <th>type</th>'); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody>'); - tmpl_array.push(' <% _.each(items, function(content_item) { %>'); - tmpl_array.push(' <tr class="folder_row" id="<%- content_item.id %>">'); - tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); - tmpl_array.push(' <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); - tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); - tmpl_array.push(' <span class="muted">(empty folder)</span>'); - tmpl_array.push(' <% } %>'); - tmpl_array.push(' </td>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <td><%- content_item.get("name") %></td>'); - tmpl_array.push(' <% } %> '); - tmpl_array.push(' <td><%= _.escape(content_item.get("type")) %></td>'); - tmpl_array.push(' </tr>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push(' '); - tmpl_array.push(' '); - tmpl_array.push(' '); - tmpl_array.push(' </tbody>'); - tmpl_array.push('</table>'); + tmpl_array.push('<div id="dataset_info_modal">'); + tmpl_array.push(' <table class="table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + // tmpl_array.push(' </table>'); + // tmpl_array.push(' <hr/>'); + // tmpl_array.push(' <table class="table table-striped">'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' '); + tmpl_array.push(' </table>'); + // tmpl_array.push(' <hr/>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); - return tmpl_array.join(''); - }, - events: { - 'click #select-all-checkboxes' : 'selectAll', - 'click .folder_row' : 'selectClicked' - }, + return tmpl_array.join(''); + }, + templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_footer" style="width:60%;">'); + tmpl_array.push('<select name="history_import" style="width:60%; margin-left: 2em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</span>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + // to string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClicked', + 'click .library-dataset' : 'showDatasetDetails' + }, + //self modal + modal : null, + //loaded folders + folders : null, + //render the view render: function (options) { var that = this; @@ -125,80 +238,131 @@ folderContainer.fetch({ success: function (container) { - // folderContainer.attributes.folder = container.attributes.folder; - var template = _.template(that.template_folder(), {path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id}); - that.$el.html(template); + // folderContainer.attributes.folder = container.attributes.folder; + var template = _.template(that.templateFolder(), {path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id}); + that.$el.html(template); } - }) - }, - selectAll : function (ev) { - var selected = ev.target.checked; - // Iterate each checkbox - $(':checkbox').each(function () { this.checked = selected; }); - }, - selectClicked : function (ev) { - var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') - if (checkbox[0] != undefined) { - if (checkbox[0].checked){ - checkbox[0].checked = ''; - } else { - checkbox[0].checked = 'selected'; - } + }) + }, + //show modal with dataset info + showDatasetDetails : function(e){ + // prevent default + e.preventDefault(); + + //TODO check whether we already have the data + + //load the ID of the row + var id = $(e.target).parent().parent().attr('id'); + + //create new item + var item = new Item(); + var histories = new GalaxyHistories(); + item.id = id; + var self = this; + //fetch the dataset info + item.fetch({ + success: function (item) { + //fetch user histories for import + histories.fetch({ + success: function (histories){self.modalFetchSuccess(item, histories)} + }); + } + }); + }, + + modalFetchSuccess : function(item, histories){ + var histories_modal = this.templateHistorySelectInModal(); + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal({ + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() {self.importIntoHistory()}, + // 'Notify' : function() {self.modal.showNotification("TEST")}, + 'Close' : function() {self.modal.hide()} + } + }); + $(".peek").html(item.get("peek")); + // this.modal.hideButton('Import'); + // $(this.modal.elMain).find('.modal-footer').prepend("<div>BUBUBUBU" + "</div>"); + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + + // show the prepared modal + this.modal.show(); + }, + + importIntoHistory : function(){ + var history_id = 'a0c15f4d91084599'; + var library_dataset_id = '03501d7626bd192f'; + + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + console.log(historyItem); + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + self.modal.showNotification('Dataset imported', 3000, '#e1f4e0', '#32a427'); + } + }); + }, + + selectAll : function (ev) { + var selected = ev.target.checked; + // Iterate each checkbox + $(':checkbox').each(function () { this.checked = selected; }); + }, + selectClicked : function (ev) { + var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') + if (checkbox[0] != undefined) { + if (checkbox[0].checked){ + checkbox[0].checked = ''; + } else { + checkbox[0].checked = 'selected'; + } + } } - } -}); + }); // galaxy library var GalaxyLibraryview = Backbone.View.extend({ el: '#center', - events: { + events: { 'click #create_new_library_btn' : 'show_library_modal' - }, + }, - // initialize initialize : function(){ - // view = this; - //set up the libray router - // this.set_up_router(); - - //render - // this.render(); }, - // set up router - set_up_router : function(){ - if (library_router === null){ - library_router = new router.LibraryRouter(); - Backbone.history.start(); - } - }, - // template template_library_list : function (){ tmpl_array = []; tmpl_array.push(''); tmpl_array.push('<h1>Welcome to the data libraries</h1>'); - tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary">New Library</a>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); tmpl_array.push('<table class="table table-striped">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th>name</th>'); tmpl_array.push(' <th>description</th>'); tmpl_array.push(' <th>synopsis</th> '); tmpl_array.push(' <th>model type</th> '); - tmpl_array.push(' <th>id</th> '); + // tmpl_array.push(' <th>id</th> '); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); tmpl_array.push(' <% _.each(libraries, function(library) { %>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%- library.get("name") %></a></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); - tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%= _.escape(library.get("id")) %></a></td>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%- library.get("name") %></a></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + // tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%= _.escape(library.get("id")) %></a></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% }); %>'); tmpl_array.push(''); @@ -219,18 +383,17 @@ // } libraries.fetch({ success: function (libraries) { - var template = _.template(that.template_library_list(), {libraries: libraries.models}); + var template = _.template(that.template_library_list(), { libraries : libraries.models }); that.$el.html(template); - } - }) + } + }) }, // own modal modal : null, // show/hide create library modal - show_library_modal : function (e) - { + show_library_modal : function (e){ // prevent default e.preventDefault(); @@ -255,15 +418,21 @@ create_new_library_event: function(){ var libraryDetails = this.serialize_new_library(); var library = new Library(); + var self = this; library.save(libraryDetails, { success: function (library) { - - library_router.navigate('', {trigger: true}) - } - }); - // console.log(libraryDetails); + self.modal.hide(); + self.clear_library_modal(); + self.render(); + } + }); return false; }, + clear_library_modal : function(){ + $("input[name='Name']").val(''); + $("input[name='Description']").val(''); + $("input[name='Synopsis']").val(''); + }, serialize_new_library : function(){ return { name: $("input[name='Name']").val(), @@ -279,7 +448,6 @@ tmpl_array.push('<form>'); tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); - // tmpl_array.push('<label>Synopsis</label>'); tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); tmpl_array.push(''); tmpl_array.push('</form>'); @@ -300,18 +468,18 @@ folderContentView = new FolderContentView(); galaxyLibraryview = new GalaxyLibraryview(); - library_router = new router.LibraryRouter(); - + library_router = new LibraryRouter(); + library_router.on('route:libraries', function() { // render libraries list galaxyLibraryview.render(); - }) - + }) + library_router.on('route:folder_content', function(id) { // render folder's contents folderContentView.render({id: id}); - - }) + + }) // library_router.on('route:show_library_modal', function() { // // render folder's contents @@ -319,10 +487,10 @@ // }) - Backbone.history.start(); +Backbone.history.start(); - return this - } +return this +} }); // return diff -r 518ded2c3f30cca803a29f76da2e80505b166647 -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -82,6 +82,7 @@ this.$footer = (this.$el).find('.modal-footer'); this.$buttons = (this.$el).find('.buttons'); this.$backdrop = (this.$el).find('.modal-backdrop'); + this.$notification = (this.$el).find('.notification-modal'); // append body this.$body.html(options.body); @@ -122,6 +123,35 @@ this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, + // hide buttons + hideButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).hide(); + }, + // show buttons + showButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).show(); + }, + + // show notification + showNotification : function(message, duration, bgColor, txtColor) { + // defaults + var duration = typeof duration !== 'undefined' ? duration : 1500; + var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; + var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + + var HTMLmessage = "<div class='notification-message' style='text-align:center; line-height:16px; '> " + message + " </div>"; + this.$notification.html("<div id='notification-bar' style='display:none; float: right; height: 16px; width:100%; background-color: " + bgColor + "; z-index: 100; color: " + txtColor + ";border-bottom: 1px solid " + txtColor + ";'>" + HTMLmessage + "</div>"); + + var self = this; + /*animate the bar*/ + $('#notification-bar').slideDown(function() { + setTimeout(function() { + $('#notification-bar').slideUp(function() {self.$notification.html('');}); + }, duration); + }); + + }, + // returns scroll top for body element scrollTop: function() { @@ -137,10 +167,11 @@ return '<div class="modal">' + '<div class="modal-backdrop fade in" style="z-index: -1;"></div>' + '<div class="modal-dialog">' + - '<div class="modal-content">' + + '<div class="modal-content"">' + '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + + '<span class="notification-modal"></span>' + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + https://bitbucket.org/galaxy/galaxy-central/commits/2bb7df095a5a/ Changeset: 2bb7df095a5a Branch: data_library User: martenson Date: 2013-12-03 22:43:06 Summary: slight refactoring and bugfix of db_next_hid generator Affected #: 1 file diff -r 3ea8be4161ab0a9ed2e1c17160c9d3d52d41b555 -r 2bb7df095a5a23e3dce2e02fb963a30ff3b7d377 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1988,8 +1988,18 @@ table = self.table trans = conn.begin() try: - next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() - table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + +# log.debug("XXXXXXXXXXXXXXX NEW GENERATOOOOOR") +# next_hid = table.update() \ +# .returning( table.c.hid_counter ) \ +# .where( table.c.id == self.id ) \ +# .values( hid_counter = hid_counter + 1 ) +# log.debug('XXXXXXXXXXXXXXXXXXXXXXXXXXX NEXT HID: ' + str(next_hid)) + + + current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + next_hid = current_hid + 1 + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) trans.commit() return next_hid except: https://bitbucket.org/galaxy/galaxy-central/commits/4e53d7b759d1/ Changeset: 4e53d7b759d1 Branch: data_library User: martenson Date: 2013-12-03 22:43:25 Summary: added dropdown menu plugin to bootstrap Affected #: 1 file diff -r 2bb7df095a5a23e3dce2e02fb963a30ff3b7d377 -r 4e53d7b759d1999758a30611e5d897e3e1d20782 static/scripts/libs/bootstrap.js --- a/static/scripts/libs/bootstrap.js +++ b/static/scripts/libs/bootstrap.js @@ -575,3 +575,158 @@ } }(window.jQuery); + +/* ======================================================================== + * Bootstrap: dropdown.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#dropdowns + * ======================================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== */ + + ++function ($) { "use strict"; + + // DROPDOWN CLASS DEFINITION + // ========================= + + var backdrop = '.dropdown-backdrop' + var toggle = '[data-toggle=dropdown]' + var Dropdown = function (element) { + var $el = $(element).on('click.bs.dropdown', this.toggle) + } + + Dropdown.prototype.toggle = function (e) { + var $this = $(this) + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) { + if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) { + // if mobile we we use a backdrop because click events don't delegate + $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus) + } + + $parent.trigger(e = $.Event('show.bs.dropdown')) + + if (e.isDefaultPrevented()) return + + $parent + .toggleClass('open') + .trigger('shown.bs.dropdown') + + $this.focus() + } + + return false + } + + Dropdown.prototype.keydown = function (e) { + if (!/(38|40|27)/.test(e.keyCode)) return + + var $this = $(this) + + e.preventDefault() + e.stopPropagation() + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + if (!isActive || (isActive && e.keyCode == 27)) { + if (e.which == 27) $parent.find(toggle).focus() + return $this.click() + } + + var $items = $('[role=menu] li:not(.divider):visible a', $parent) + + if (!$items.length) return + + var index = $items.index($items.filter(':focus')) + + if (e.keyCode == 38 && index > 0) index-- // up + if (e.keyCode == 40 && index < $items.length - 1) index++ // down + if (!~index) index=0 + + $items.eq(index).focus() + } + + function clearMenus() { + $(backdrop).remove() + $(toggle).each(function (e) { + var $parent = getParent($(this)) + if (!$parent.hasClass('open')) return + $parent.trigger(e = $.Event('hide.bs.dropdown')) + if (e.isDefaultPrevented()) return + $parent.removeClass('open').trigger('hidden.bs.dropdown') + }) + } + + function getParent($this) { + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && /#/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + var $parent = selector && $(selector) + + return $parent && $parent.length ? $parent : $this.parent() + } + + + // DROPDOWN PLUGIN DEFINITION + // ========================== + + var old = $.fn.dropdown + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('dropdown') + + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + // DROPDOWN NO CONFLICT + // ==================== + + $.fn.dropdown.noConflict = function () { + $.fn.dropdown = old + return this + } + + + // APPLY TO STANDARD DROPDOWN ELEMENTS + // =================================== + + $(document) + .on('click.bs.dropdown.data-api', clearMenus) + .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.bs.dropdown.data-api' , toggle, Dropdown.prototype.toggle) + .on('keydown.bs.dropdown.data-api', toggle + ', [role=menu]' , Dropdown.prototype.keydown) + +}(window.jQuery); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/44399512777b/ Changeset: 44399512777b Branch: data_library User: martenson Date: 2013-12-03 22:44:22 Summary: library work, galaxy modal changes, api v2 preparation, API tweaks, API for dataset downloading implementation Affected #: 9 files diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1768,7 +1768,7 @@ class Library( object, Dictifiable ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" self.description = description diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a dataset. +API operations on the contents of a history dataset. """ from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -42,19 +42,34 @@ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided as a separate object in response providing data for breadcrumb path building. """ folder_container = [] current_user_roles = trans.get_current_user_roles() + +# log.debug( 'XXXXXXXXXXXXXXXXXXXXX GOT id: ' + folder_id ) +# log.debug( 'XXXXXXXXXXXXXXXXXXXXX decode id: ' + folder_id[1:] ) +# log.debug( 'XXXXXXXXXXXXXXXXXXXXX call decode: ' + str(trans.security.decode_id( folder_id[1:] )) ) - try: - decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) +# try: +# decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) +# except TypeError: +# trans.response.status = 400 +# return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) +# log.debug( 'XXXXXXXXXXXXXXXXXXXXX decoded id: ' + decoded_folder_id ) + + if ( folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - parent_library = folder.parent_library +# log.debug( 'XXXXXXXXXXXXXXXXXXXXX FOLDER id: ' + str(folder.id) ) +# log.debug( 'XXXXXXXXXXXXXXXXXXXXX FOLDER name: ' + str(folder.name) ) +# parent_library = folder.parent_library except: folder = None log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) @@ -77,13 +92,17 @@ path_to_root = [] # We are almost in root if folder.parent_id is None: - log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING: " + str( folder.name ) ) + +# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING ID: " + str( folder.id ) ) +# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING NAME: " + str( folder.name ) ) path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) # upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_library.id ) # path_to_root.append( ( upper_folder.id, upper_folder.name ) ) else: # We add the current folder and traverse up one folder. - log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) +# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id " + str( folder.parent_id ) ) +# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING ID: " + str( folder.id ) ) +# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) path_to_root.extend( build_path( upper_folder ) ) diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -1,27 +1,69 @@ """ -API operations on the contents of a dataset from library. +API operations on the dataset from library. """ -from galaxy import web +import glob +import logging +import operator +import os +import os.path +import string +import sys +import tarfile +import tempfile +import urllib +import urllib2 +import zipfile +from galaxy.security import Action +from galaxy import util, web +from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems import logging log = logging.getLogger( __name__ ) +# Test for available compression types +# tmpd = tempfile.mkdtemp() +# comptypes = [] +# for comptype in ( 'gz', 'bz2' ): +# tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype ) +# try: +# archive = tarfile.open( tmpf, 'w:' + comptype ) +# archive.close() +# comptypes.append( comptype ) +# except tarfile.CompressionError: +# log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +ziptype = '32' +# tmpf = os.path.join( tmpd, 'compression_test.zip' ) +# try: +# archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) +# archive.close() +# comptypes.append( 'zip' ) +# ziptype = '64' +# except RuntimeError: +# log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +# except (TypeError, zipfile.LargeZipFile): +# # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped +# log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) +# comptypes.append( 'zip' ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +# os.rmdir( tmpd ) + + + class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): @web.expose_api - def index( self, trans, **kwd ): - """ - GET /api/libraries/datasets - """ - trans.response.status = 501 - return 'not implemented' - - @web.expose_api def show( self, trans, id, **kwd ): """ GET /api/libraries/datasets/{encoded_dataset_id} - Displays information about and/or content of a dataset identified by the lda ID. + Displays information about the dataset identified by the lda ID. """ # Get dataset. try: @@ -35,4 +77,165 @@ rval = "Error in dataset API at listing contents: " + str( e ) log.error( rval + ": %s" % str(e), exc_info=True ) trans.response.status = 500 - return rval \ No newline at end of file + + rval['id'] = trans.security.encode_id(rval['id']); + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + + return rval + + @web.expose + def download( self, trans, format, **kwd ): + """ + POST /api/libraries/datasets/download/{format} + POST data: ldda_ids = [] + Downloads dataset(s) in the requested format. + """ + lddas = [] +# is_admin = trans.user_is_admin() +# current_user_roles = trans.get_current_user_roles() + + datasets_to_download = kwd['ldda_ids%5B%5D'] + + if ( datasets_to_download != None ): + datasets_to_download = util.listify( datasets_to_download ) + for dataset_id in datasets_to_download: + try: + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + assert not ldda.dataset.purged + lddas.append( ldda ) + except: + ldda = None + message += "Invalid library dataset id (%s) specified. " % str( dataset_id ) + + if format in [ 'zip','tgz','tbz' ]: + error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if format == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) + tmpf = os.path.join( tmpd, 'library_download.' + format ) + if ziptype == '64' and trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + elif ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + elif trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif format == 'tgz': + if trans.app.config.upstream_gzip: + archive = StreamBall( 'w|' ) + outext = 'tar' + else: + archive = StreamBall( 'w|gz' ) + outext = 'tgz' + elif format == 'tbz': + archive = StreamBall( 'w|bz2' ) + outext = 'tbz2' + except ( OSError, zipfile.BadZipfile ): + error = True + log.exception( "Unable to create archive for download" ) + message = "Unable to create archive for download, please report this error" + status = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' + if not error: + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: + continue + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: + # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + else: # simple case + try: + archive.add( ldda.dataset.file_name, path ) + except IOError: + error = True + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + if not error: + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + elif format == 'uncompressed': + if len(lddas) != 1: + return 'Wrong request' + else: + single_dataset = lddas[0] + trans.response.set_content_type( single_dataset.get_mime() ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname + try: + return open( single_dataset.file_name ) + except: + return 'This dataset contains no content' + else: + return 'Wrong format'; \ No newline at end of file diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -52,6 +52,7 @@ item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) item['id'] = 'F' + trans.security.encode_id( item['id'] ) + item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] ) rval.append( item ) return rval diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -146,6 +146,7 @@ # ======================= webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) + webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', action='download', conditions=dict(method=["POST"]) ) webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -5,6 +5,9 @@ // global variables var view = null; var library_router = null; +var responses = []; +var KEYCODE_ENTER = 13; +var KEYCODE_ESC = 27; // dependencies define(["galaxy.modal", "galaxy.master"], function(mod_modal, mod_master) { @@ -70,52 +73,99 @@ var LibraryRouter = Backbone.Router.extend({ routes: { "" : "libraries", - "folders/:id" : "folder_content" + "folders/:id" : "folder_content", + "folders/:folder_id/download/:format" : "download" } }); // MMMMMMMMMMMMMM -// === Views ==== +// === VIEWS ==== // MMMMMMMMMMMMMM // galaxy folder var FolderContentView = Backbone.View.extend({ - //main element + // main element definition el : '#center', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // last selected history in modal for UX + lastSelectedHistory: '', + // self modal + modal : null, + // loaded folders + folders : null, + // initialize initialize : function(){ this.folders = []; + this.queue = jQuery.Deferred(); + this.queue.resolve(); }, + +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + // set up templateFolder : function (){ var tmpl_array = []; - tmpl_array.push('<a href="#">Libraries</a> | '); + // CONTAINER + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to Martin.</h3>'); + + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button id="toolbtn_create_folder" class="btn btn-primary" type="button">new folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" style="display: none; margin-left: 0.5em;" type="button">Import into History</button>'); + + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); + tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' Download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + // tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/uncompressed">uncompressed</a></li>'); + // tmpl_array.push(' <li class="divider"></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('</div>'); + + // BREADCRUMBS + tmpl_array.push('<a href="#">Libraries</a><b>|</b> '); tmpl_array.push('<% _.each(path, function(path_item) { %>'); //breadcrumb - tmpl_array.push('<% if (path_item[0] != id) { %>'); - tmpl_array.push('<a href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a> |'); - tmpl_array.push('<% } else { %>'); - tmpl_array.push('<%- path_item[1] %>'); - tmpl_array.push('<% } %>'); - tmpl_array.push('<% }); %>'); - tmpl_array.push('<table class="table table-hover table-condensed">'); - tmpl_array.push(' <thead>'); - tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th>name</th>'); - tmpl_array.push(' <th>type</th>'); - tmpl_array.push(' </thead>'); - tmpl_array.push(' <tbody>'); - tmpl_array.push(' <% _.each(items, function(content_item) { %>'); - tmpl_array.push(' <tr class="folder_row" id="<%- content_item.id %>">'); - tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<%- path_item[1] %>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + + // FODLER CONTENT + tmpl_array.push('<table id="folder_table" class="table table-hover table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>type</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row" id="<%- content_item.id %>">'); tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); //folder - tmpl_array.push(' <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); + tmpl_array.push(' <td style="text-align: center; "></td>'); + tmpl_array.push(' <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); //empty folder tmpl_array.push(' <span class="muted">(empty folder)</span>'); tmpl_array.push(' <% } %>'); tmpl_array.push(' </td>'); tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); tmpl_array.push(' <td><a class="library-dataset" href="#"><%- content_item.get("name") %></a></td>'); //dataset tmpl_array.push(' <% } %> '); tmpl_array.push(' <td><%= _.escape(content_item.get("type")) %></td>'); @@ -123,10 +173,10 @@ tmpl_array.push(' <% }); %>'); tmpl_array.push(' '); tmpl_array.push(' '); - tmpl_array.push(' '); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); + tmpl_array.push('</div>'); return tmpl_array.join(''); }, templateDatasetModal : function(){ @@ -135,7 +185,7 @@ tmpl_array.push('<div id="dataset_info_modal">'); tmpl_array.push(' <table class="table table-striped table-condensed">'); tmpl_array.push(' <tr>'); - tmpl_array.push(' <th scope="row">Name</th>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <tr>'); @@ -157,9 +207,6 @@ tmpl_array.push(' <th scope="row">Uploaded by</th>'); tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); tmpl_array.push(' </tr>'); - // tmpl_array.push(' </table>'); - // tmpl_array.push(' <hr/>'); - // tmpl_array.push(' <table class="table table-striped">'); tmpl_array.push(' <tr scope="row">'); tmpl_array.push(' <th scope="row">Data Lines</th>'); tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); @@ -183,31 +230,45 @@ tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); tmpl_array.push(' </tr>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' '); tmpl_array.push(' </table>'); - // tmpl_array.push(' <hr/>'); tmpl_array.push(' <pre class="peek">'); tmpl_array.push(' </pre>'); tmpl_array.push('</div>'); return tmpl_array.join(''); }, + templateHistorySelectInModal : function(){ var tmpl_array = []; - tmpl_array.push('<span id="history_modal_footer" style="width:60%;">'); - tmpl_array.push('<select name="history_import" style="width:60%; margin-left: 2em; "> '); + tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box - tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); - tmpl_array.push(' <% }); %>'); - tmpl_array.push('</span>'); - tmpl_array.push('</div>'); - tmpl_array.push(''); + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); - return tmpl_array.join(''); - }, - // to string + return tmpl_array.join(''); + }, + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + // convert size to nice string size_to_string : function (size) { // identify unit @@ -220,17 +281,26 @@ // return formatted string return (Math.round(size) / 10) + unit; }, - events: { + +// MMMMMMMMMMMMMMM +// === EVENTS ==== +// MMMMMMMMMMMMMMM + + // event binding + events: { 'click #select-all-checkboxes' : 'selectAll', 'click .folder_row' : 'selectClicked', + 'click #toolbtn_bulk_import' : 'modalBulkImport', + 'click #toolbtn_dl' : 'bulkDownload', 'click .library-dataset' : 'showDatasetDetails' }, - //self modal - modal : null, - //loaded folders - folders : null, - //render the view + + //render the folder view render: function (options) { + //hack to show scrollbars + $("#center").css('overflow','auto'); + + view = this; var that = this; var folderContainer = new FolderContainer({id: options.id}); @@ -241,15 +311,16 @@ // folderContainer.attributes.folder = container.attributes.folder; var template = _.template(that.templateFolder(), {path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id}); that.$el.html(template); - } - }) - }, - //show modal with dataset info + } + }) + }, + + //show modal with current dataset info showDatasetDetails : function(e){ // prevent default e.preventDefault(); - //TODO check whether we already have the data +//TODO check whether we already have the data //load the ID of the row var id = $(e.target).parent().parent().attr('id'); @@ -259,53 +330,90 @@ var histories = new GalaxyHistories(); item.id = id; var self = this; + //fetch the dataset info item.fetch({ success: function (item) { - //fetch user histories for import +// TODO can render here already + //fetch user histories for import purposes histories.fetch({ - success: function (histories){self.modalFetchSuccess(item, histories)} + success: function (histories){self.renderModalAfterFetch(item, histories)} }); } }); }, - modalFetchSuccess : function(item, histories){ - var histories_modal = this.templateHistorySelectInModal(); + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ var size = this.size_to_string(item.get('file_size')); var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + this.modal = null; // make modal var self = this; this.modal = new mod_modal.GalaxyModal({ title : 'Dataset Details', body : template, buttons : { - 'Import' : function() {self.importIntoHistory()}, - // 'Notify' : function() {self.modal.showNotification("TEST")}, - 'Close' : function() {self.modal.hide()} + 'Import' : function() { self.importCurrentIntoHistory() }, + 'Download' : function() { self.downloadCurrent() }, + 'Close' : function() { self.modal.hide(); $('.modal').html(''); self.modal = null; } // TODO refill nicely modal with data } }); $(".peek").html(item.get("peek")); - // this.modal.hideButton('Import'); - // $(this.modal.elMain).find('.modal-footer').prepend("<div>BUBUBUBU" + "</div>"); var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); - $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } // show the prepared modal this.modal.show(); }, - importIntoHistory : function(){ - var history_id = 'a0c15f4d91084599'; - var library_dataset_id = '03501d7626bd192f'; + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + // we assume the view is existent + folderContentView.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); var historyItem = new HistoryItem(); var self = this; historyItem.url = historyItem.urlRoot + history_id + '/contents'; - console.log(historyItem); + + // save the dataset into selected history historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ self.modal.showNotification('Dataset imported', 3000, '#e1f4e0', '#32a427'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, '#f4e0e1', '#a42732'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); } }); }, @@ -314,9 +422,11 @@ var selected = ev.target.checked; // Iterate each checkbox $(':checkbox').each(function () { this.checked = selected; }); + this.showTools(); }, - selectClicked : function (ev) { - var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') + + selectClicked : function (ev) { + var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') if (checkbox[0] != undefined) { if (checkbox[0].checked){ checkbox[0].checked = ''; @@ -324,11 +434,161 @@ checkbox[0].checked = 'selected'; } } - } + this.showTools(); + }, + + // show toolbar in case something is selected + showTools : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length > 0){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } else { + $('#toolbtn_bulk_import').hide(); + $('#toolbtn_dl').hide(); + } + + }, + + // show bulk import modal + modalBulkImport : function(){ + var self = this; + // fetch histories + var histories = new GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); + self.modal = new mod_modal.GalaxyModal({ + title : 'Import into History', + body : history_modal_tmpl, + buttons : { + 'Import' : function() {self.importAllIntoHistory()}, + 'Close' : function() {self.modal.hide()} + } + }); + // show the prepared modal + self.modal.show(); + } + }); + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + }; + + // call the recursive function to call ajax one after each other + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + self.modal.showNotification('All datasets imported', 3000, '#e1f4e0', '#32a427'); + // enable button again + self.modal.enableButton('Import'); + return + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + responses.push(a1); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + // progress bar + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + }; + } + }); - -// galaxy library +// galaxy library view var GalaxyLibraryview = Backbone.View.extend({ el: '#center', @@ -343,9 +603,10 @@ // template template_library_list : function (){ tmpl_array = []; + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); tmpl_array.push(''); - tmpl_array.push('<h1>Welcome to the data libraries</h1>'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to Martin.</h3>'); tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); tmpl_array.push('<table class="table table-striped">'); tmpl_array.push(' <thead>'); @@ -353,30 +614,27 @@ tmpl_array.push(' <th>description</th>'); tmpl_array.push(' <th>synopsis</th> '); tmpl_array.push(' <th>model type</th> '); - // tmpl_array.push(' <th>id</th> '); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); tmpl_array.push(' <% _.each(libraries, function(library) { %>'); - tmpl_array.push(' <tr>'); - tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%- library.get("name") %></a></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); - tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); - // tmpl_array.push(' <td><a href="#/folders/<%- library.id %>"><%= _.escape(library.get("id")) %></a></td>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><a href="#/folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <% }); %>'); - tmpl_array.push(''); - tmpl_array.push(''); - tmpl_array.push(''); - tmpl_array.push(''); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); - + + tmpl_array.push('</div>'); return tmpl_array.join(''); }, // render render: function () { + //hack to show scrollbars + $("#center").css('overflow','auto'); var that = this; // if (typeof libraries === "undefined") { libraries = new Libraries(); @@ -394,12 +652,11 @@ // show/hide create library modal show_library_modal : function (e){ - // prevent default + // prevent default, may be unnecessary e.preventDefault(); // create modal if (!this.modal){ - // make modal var self = this; this.modal = new mod_modal.GalaxyModal( { @@ -412,9 +669,11 @@ }); } - // show modal + // show prepared modal this.modal.show(); }, + + // create the new library from modal create_new_library_event: function(){ var libraryDetails = this.serialize_new_library(); var library = new Library(); @@ -428,11 +687,15 @@ }); return false; }, + + // clear the library modal once saved clear_library_modal : function(){ $("input[name='Name']").val(''); $("input[name='Description']").val(''); $("input[name='Synopsis']").val(''); }, + + // serialize data from the form serialize_new_library : function(){ return { name: $("input[name='Name']").val(), @@ -440,10 +703,12 @@ synopsis: $("input[name='Synopsis']").val() }; }, - // load html template + + // template for new library modal template_new_library: function() { tmpl_array = []; + tmpl_array.push('<div id="new_library_modal">'); tmpl_array.push('<form>'); tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); @@ -452,10 +717,8 @@ tmpl_array.push(''); tmpl_array.push('</form>'); tmpl_array.push('</div>'); + return tmpl_array.join(''); - - - // return '<div id="'+ id +'"></div>'; } }); @@ -473,19 +736,28 @@ library_router.on('route:libraries', function() { // render libraries list galaxyLibraryview.render(); - }) + }); library_router.on('route:folder_content', function(id) { // render folder's contents folderContentView.render({id: id}); + }); - }) + library_router.on('route:download', function(folder_id, format) { + // send download stream + if (typeof folderContentView === 'undefined'){ + alert('you cant touch this!'); + // } else if (folderContentView.modal !== null){ + // folderContentView.download(folder_id, format); + } else if ($('#center').find(':checked').length === 0) { // coming from outside of the library app + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + // TODO show message of redirection + } else { + folderContentView.download(folder_id, format); + library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } - // library_router.on('route:show_library_modal', function() { - // // render folder's contents - // galaxyLibraryview.show_library_modal(); - - // }) + }); Backbone.history.start(); diff -r 4e53d7b759d1999758a30611e5d897e3e1d20782 -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -20,9 +20,28 @@ // initialize initialize : function(options) { + self = this; // create if (options) this.create(options); + // bind the ESC key to hide() function + $(document).on('keyup', function(event){ + if (event.keyCode == 27) { self.hide(); } + }) + // bind the click anywhere to hide() function... + $('html').on('click', function(event){ + self.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').on('click', function(event){ + event.stopPropagation(); + }) + }, + + // destroy + destroy : function(){ + this.hide(); + $('.modal').html(''); }, // adds and displays a new frame/window https://bitbucket.org/galaxy/galaxy-central/commits/f466834f693f/ Changeset: f466834f693f Branch: data_library User: martenson Date: 2013-12-10 19:01:19 Summary: improved styles for libraries, added features to modal window, API tweaks Affected #: 5 files diff -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 -r f466834f693ff7ae0f60cf121d97f67a5338ea95 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1988,15 +1988,6 @@ table = self.table trans = conn.begin() try: - -# log.debug("XXXXXXXXXXXXXXX NEW GENERATOOOOOR") -# next_hid = table.update() \ -# .returning( table.c.hid_counter ) \ -# .where( table.c.id == self.id ) \ -# .values( hid_counter = hid_counter + 1 ) -# log.debug('XXXXXXXXXXXXXXXXXXXXXXXXXXX NEXT HID: ' + str(next_hid)) - - current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() next_hid = current_hid + 1 table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) diff -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 -r f466834f693ff7ae0f60cf121d97f67a5338ea95 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -46,17 +46,6 @@ """ folder_container = [] current_user_roles = trans.get_current_user_roles() - -# log.debug( 'XXXXXXXXXXXXXXXXXXXXX GOT id: ' + folder_id ) -# log.debug( 'XXXXXXXXXXXXXXXXXXXXX decode id: ' + folder_id[1:] ) -# log.debug( 'XXXXXXXXXXXXXXXXXXXXX call decode: ' + str(trans.security.decode_id( folder_id[1:] )) ) - -# try: -# decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) -# except TypeError: -# trans.response.status = 400 -# return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) -# log.debug( 'XXXXXXXXXXXXXXXXXXXXX decoded id: ' + decoded_folder_id ) if ( folder_id.startswith( 'F' ) ): try: @@ -67,9 +56,6 @@ try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) -# log.debug( 'XXXXXXXXXXXXXXXXXXXXX FOLDER id: ' + str(folder.id) ) -# log.debug( 'XXXXXXXXXXXXXXXXXXXXX FOLDER name: ' + str(folder.name) ) -# parent_library = folder.parent_library except: folder = None log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) @@ -92,17 +78,9 @@ path_to_root = [] # We are almost in root if folder.parent_id is None: - -# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING ID: " + str( folder.id ) ) -# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING NAME: " + str( folder.name ) ) path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) -# upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_library.id ) -# path_to_root.append( ( upper_folder.id, upper_folder.name ) ) else: # We add the current folder and traverse up one folder. -# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id " + str( folder.parent_id ) ) -# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING ID: " + str( folder.id ) ) -# log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) path_to_root.extend( build_path( upper_folder ) ) @@ -113,25 +91,40 @@ folder_container.append( dict( full_path = full_path ) ) folder_contents = [] + time_updated = '' + time_created = '' # Go through every item in the folder and include its meta-data. for content_item in self.load_folder_contents( trans, folder ): +# rval = content_item.to_dict() return_item = {} encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) +# log.debug('XXXXXXXXXXXXXXXXXXX api type: ' + str(content_item.api_type)) +# log.debug('XXXXXXXX ALL: ' + str(content_item.__dict__)) # For folder return also hierarchy values if content_item.api_type == 'folder': -# encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) encoded_id = 'F' + encoded_id -# if content_item.parent_id is not None: # Return folder's parent id for browsing back. -# encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) - last_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) - return_item.update ( dict ( item_count = content_item.item_count, last_updated = last_updated ) ) - +# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count ) ) + + if content_item.api_type == 'file': +# log.debug('XXXXX content item class: ' + str(content_item.__class__)) + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + # For every item return also the default meta-data return_item.update( dict( id = encoded_id, type = content_item.api_type, - name = content_item.name - + name = content_item.name, + time_updated = time_updated, + time_created = time_created ) ) folder_contents.append( return_item ) # Put the data in the container diff -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 -r f466834f693ff7ae0f60cf121d97f67a5338ea95 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -6,8 +6,16 @@ var view = null; var library_router = null; var responses = []; -var KEYCODE_ENTER = 13; -var KEYCODE_ESC = 27; + + +// load required libraries +require([ + // load js libraries + 'utils/galaxy.css', + ], function(css){ + // load css + css.load_file("static/style/library.css"); +}); // dependencies define(["galaxy.modal", "galaxy.master"], function(mod_modal, mod_master) { @@ -115,20 +123,18 @@ // CONTAINER tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); - tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to Martin.</h3>'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); - tmpl_array.push(' <button id="toolbtn_create_folder" class="btn btn-primary" type="button">new folder</button>'); - tmpl_array.push(' <button id="toolbtn_bulk_import" style="display: none; margin-left: 0.5em;" type="button">Import into History</button>'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-icon-plus"></span><span class="fa fa-icon-folder-close"></span> folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-icon-external-link"></span> to history</button>'); tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); - tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-default dropdown-toggle" data-toggle="dropdown">'); - tmpl_array.push(' Download <span class="caret"></span>'); + tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-icon-download"></span> download <span class="caret"></span>'); tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); - // tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/uncompressed">uncompressed</a></li>'); - // tmpl_array.push(' <li class="divider"></li>'); tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); @@ -138,41 +144,64 @@ tmpl_array.push('</div>'); // BREADCRUMBS - tmpl_array.push('<a href="#">Libraries</a><b>|</b> '); - tmpl_array.push('<% _.each(path, function(path_item) { %>'); //breadcrumb + tmpl_array.push('<div class="library_breadcrumb">'); + tmpl_array.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> '); + tmpl_array.push('<% _.each(path, function(path_item) { %>'); tmpl_array.push('<% if (path_item[0] != id) { %>'); - tmpl_array.push('<a href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); + tmpl_array.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); tmpl_array.push('<% } else { %>'); - tmpl_array.push('<%- path_item[1] %>'); + tmpl_array.push('<span title="You are in this folder"><%- path_item[1] %></span>'); tmpl_array.push('<% } %>'); tmpl_array.push('<% }); %>'); + tmpl_array.push('</div>'); - // FODLER CONTENT - tmpl_array.push('<table id="folder_table" class="table table-hover table-condensed">'); + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th class="button_heading">view</th>'); tmpl_array.push(' <th>name</th>'); - tmpl_array.push(' <th>type</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date</th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-arrow-up"></span> .. go up</td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); tmpl_array.push(' <% _.each(items, function(content_item) { %>'); - tmpl_array.push(' <tr class="folder_row" id="<%- content_item.id %>">'); - tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); //folder - tmpl_array.push(' <td style="text-align: center; "></td>'); - tmpl_array.push(' <td><a href="#/folders/<%- content_item.id %>"><%- content_item.get("name") %></a>'); - tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); //empty folder + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- content_item.get("name") %>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder tmpl_array.push(' <span class="muted">(empty folder)</span>'); tmpl_array.push(' <% } %>'); tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size tmpl_array.push(' <% } else { %>'); tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); - tmpl_array.push(' <td><a class="library-dataset" href="#"><%- content_item.get("name") %></a></td>'); //dataset + tmpl_array.push(' <td>'); + tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-eye-open"></span> details'); + tmpl_array.push(' </button>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size tmpl_array.push(' <% } %> '); - tmpl_array.push(' <td><%= _.escape(content_item.get("type")) %></td>'); + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated tmpl_array.push(' </tr>'); tmpl_array.push(' <% }); %>'); tmpl_array.push(' '); - tmpl_array.push(' '); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); @@ -292,7 +321,9 @@ 'click .folder_row' : 'selectClicked', 'click #toolbtn_bulk_import' : 'modalBulkImport', 'click #toolbtn_dl' : 'bulkDownload', - 'click .library-dataset' : 'showDatasetDetails' + 'click .library-dataset' : 'showDatasetDetails', + 'click #toolbtn_create_folder' : 'createFolderModal', + 'click .btn_open_folder' : 'navigateToFolder' }, //render the folder view @@ -308,22 +339,52 @@ folderContainer.fetch({ success: function (container) { - // folderContainer.attributes.folder = container.attributes.folder; - var template = _.template(that.templateFolder(), {path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id}); + + // prepare nice size strings + for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { + var model = folderContainer.attributes.folder.models[i] + if (model.get('type') === 'file'){ + model.set('readable_size', that.size_to_string(model.get('file_size'))) + } + }; + + // find the upper id + var path = folderContainer.full_path; + var upper_folder_id; + if (path.length === 1){ // library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } + + var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); + // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); that.$el.html(template); } }) }, + // handles the click on 'open' and 'upper' folder icons + navigateToFolder : function(event){ + var folder_id = $(event.target).attr('data-id'); + if (typeof folder_id === 'undefined') { + return false; + } else if (folder_id === '0'){ + library_router.navigate('#', {trigger: true, replace: true}); + } else { + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } + }, + //show modal with current dataset info - showDatasetDetails : function(e){ + showDatasetDetails : function(event){ // prevent default - e.preventDefault(); + event.preventDefault(); //TODO check whether we already have the data //load the ID of the row - var id = $(e.target).parent().parent().attr('id'); + var id = $(event.target).parent().parent().attr('id'); //create new item var item = new Item(); @@ -356,7 +417,7 @@ buttons : { 'Import' : function() { self.importCurrentIntoHistory() }, 'Download' : function() { self.downloadCurrent() }, - 'Close' : function() { self.modal.hide(); $('.modal').html(''); self.modal = null; } // TODO refill nicely modal with data + 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data } }); $(".peek").html(item.get("peek")); @@ -405,12 +466,12 @@ // save the dataset into selected history historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ - self.modal.showNotification('Dataset imported', 3000, '#e1f4e0', '#32a427'); + self.modal.showNotification('Dataset imported', 3000, 'success'); //enable the buttons self.modal.enableButton('Import'); self.modal.enableButton('Download'); }, error : function(){ - self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, '#f4e0e1', '#a42732'); + self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); //enable the buttons self.modal.enableButton('Import'); self.modal.enableButton('Download'); @@ -418,20 +479,32 @@ }); }, - selectAll : function (ev) { - var selected = ev.target.checked; + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; // Iterate each checkbox $(':checkbox').each(function () { this.checked = selected; }); this.showTools(); }, - selectClicked : function (ev) { - var checkbox = $("#" + ev.target.parentElement.id).find(':checkbox') + // click checkbox on folder click + selectClicked : function (event) { + var checkbox = $("#" + event.target.parentElement.id).find(':checkbox') if (checkbox[0] != undefined) { if (checkbox[0].checked){ checkbox[0].checked = ''; + // $(event.target.parentElement).css('background-color', '').css('color', ''); + $(event.target.parentElement).removeClass('dark'); + $(event.target.parentElement).find('a').removeClass('dark'); + $(event.target.parentElement).addClass('light'); + $(event.target.parentElement).find('a').addClass('light'); } else { checkbox[0].checked = 'selected'; + $(event.target.parentElement).removeClass('light'); + $(event.target.parentElement).find('a').removeClass('light'); + $(event.target.parentElement).addClass('dark'); + $(event.target.parentElement).find('a').addClass('dark'); + // $(event.target.parentElement).css('background-color', '#8389a1').css('color', 'white'); } } this.showTools(); @@ -464,7 +537,7 @@ body : history_modal_tmpl, buttons : { 'Import' : function() {self.importAllIntoHistory()}, - 'Close' : function() {self.modal.hide()} + 'Close' : function() {self.modal.hide(); $('.modal').remove(); self.modal = null;} } }); // show the prepared modal @@ -514,7 +587,7 @@ var self = this; var popped_item = history_item_set.pop(); if (typeof popped_item === "undefined") { - self.modal.showNotification('All datasets imported', 3000, '#e1f4e0', '#32a427'); + self.modal.showNotification('All datasets imported', 3000, 'success'); // enable button again self.modal.enableButton('Import'); return @@ -584,6 +657,11 @@ $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') .appendTo('body').submit().remove(); }; + }, + + // shows modal for creating folder + createFolderModal: function(){ + alert('creating folder'); } }); @@ -606,11 +684,12 @@ tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); tmpl_array.push(''); - tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to Martin.</h3>'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); - tmpl_array.push('<table class="table table-striped">'); + tmpl_array.push('<table class="table table-condensed">'); tmpl_array.push(' <thead>'); - tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th>name</th>'); tmpl_array.push(' <th>description</th>'); tmpl_array.push(' <th>synopsis</th> '); tmpl_array.push(' <th>model type</th> '); @@ -618,7 +697,9 @@ tmpl_array.push(' <tbody>'); tmpl_array.push(' <% _.each(libraries, function(library) { %>'); tmpl_array.push(' <tr>'); - tmpl_array.push(' <td><a href="#/folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); + tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- library.get("name") %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); @@ -651,12 +732,11 @@ modal : null, // show/hide create library modal - show_library_modal : function (e){ - // prevent default, may be unnecessary - e.preventDefault(); + show_library_modal : function (event){ + event.preventDefault(); + event.stopPropagation(); // create modal - if (!this.modal){ var self = this; this.modal = new mod_modal.GalaxyModal( { @@ -667,7 +747,6 @@ 'Close' : function() {self.modal.hide()} } }); - } // show prepared modal this.modal.show(); @@ -676,6 +755,7 @@ // create the new library from modal create_new_library_event: function(){ var libraryDetails = this.serialize_new_library(); + var valid = this.validate_new_library(libraryDetails); var library = new Library(); var self = this; library.save(libraryDetails, { @@ -683,7 +763,10 @@ self.modal.hide(); self.clear_library_modal(); self.render(); - } + }, + error: function(){ + self.modal.showNotification('An error occured', 5000, 'error'); + } }); return false; }, @@ -704,6 +787,11 @@ }; }, + validate_new_library: function(library){ + + }, + + // template for new library modal template_new_library: function() { @@ -714,7 +802,6 @@ tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); - tmpl_array.push(''); tmpl_array.push('</form>'); tmpl_array.push('</div>'); diff -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 -r f466834f693ff7ae0f60cf121d97f67a5338ea95 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -1,6 +1,5 @@ -/* - galaxy modal -*/ +// galaxy modal + // dependencies define(["libs/backbone/backbone-relational"], function() { @@ -24,24 +23,48 @@ // create if (options) this.create(options); - // bind the ESC key to hide() function - $(document).on('keyup', function(event){ - if (event.keyCode == 27) { self.hide(); } - }) - // bind the click anywhere to hide() function... - $('html').on('click', function(event){ - self.hide(); - }) - // ...but don't hide if the click is on modal content - $('.modal-content').on('click', function(event){ - event.stopPropagation(); - }) + + this.bindClick(event, self); }, + // bind the click-to-hide function + bindClick: function(event, that) { + // bind the ESC key to hide() function + $(document).on('keyup', function(event){ + if (event.keyCode == 27) { self.hide(); } + }) + // bind the click anywhere to hide() function... + $('html').on('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').on('click', function(event){ + event.stopPropagation(); + }) + }, + + // unbind the click-to-hide function + unbindClick: function(event, that){ + // bind the ESC key to hide() function + $(document).off('keyup', function(event){ + if (event.keyCode == 27) { that.hide(); } + }) + // unbind the click anywhere to hide() function... + $('html').off('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').off('click', function(event){ + event.stopPropagation(); + }) + }, + + // destroy destroy : function(){ this.hide(); - $('.modal').html(''); + this.unbindClick(); + $('.modal').remove(); }, // adds and displays a new frame/window @@ -152,16 +175,28 @@ }, // show notification - showNotification : function(message, duration, bgColor, txtColor) { + showNotification : function(message, duration, type) { // defaults var duration = typeof duration !== 'undefined' ? duration : 1500; - var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; - var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + // var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; + // var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + var bgColor; + var txtColor; + + if (type === 'error'){ + bgColor = '#f4e0e1'; + txtColor = '#a42732'; + // } else if (type === 'success'){ + } else { // success is default + bgColor = '#e1f4e0'; + txtColor = '#32a427'; + } var HTMLmessage = "<div class='notification-message' style='text-align:center; line-height:16px; '> " + message + " </div>"; this.$notification.html("<div id='notification-bar' style='display:none; float: right; height: 16px; width:100%; background-color: " + bgColor + "; z-index: 100; color: " + txtColor + ";border-bottom: 1px solid " + txtColor + ";'>" + HTMLmessage + "</div>"); var self = this; + /*animate the bar*/ $('#notification-bar').slideDown(function() { setTimeout(function() { diff -r 44399512777bdefb39ea3c99cc04b3f7947c5d33 -r f466834f693ff7ae0f60cf121d97f67a5338ea95 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,6 +29,50 @@ background-color: @table-bg-accent; } + +tr.light td +{ + background-color: white; + color: black; +} +tr.light:hover td +{ + background-color: #f5f5f5; + color: #8389a1; +} +tr.dark td +{ + background-color: #8389a1; + color: white; +} +tr.dark:hover td +{ + background-color: #bbbfd0; + color: white; +} +a.dark:hover +{ + color: yellow; + // text-decoration: none; +} +a.dark +{ + color: white; + // text-decoration: none; +} +th.button_heading +{ + width: 7em; +} +div.library_breadcrumb{ + padding-top: 0.8em; + padding-bottom: 0.8em; +} +div.library_breadcrumb a:hover{ + color:green; +} + + img.expanderIcon { padding-right: 4px; } https://bitbucket.org/galaxy/galaxy-central/commits/e2b8d3481d66/ Changeset: e2b8d3481d66 User: martenson Date: 2013-12-11 00:02:36 Summary: Merge data libraries branch to default Affected #: 19 files diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 .hgignore --- a/.hgignore +++ b/.hgignore @@ -116,3 +116,6 @@ *.rej *~ + +syntax: regexp +^static/AAA_scratch$ \ No newline at end of file diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1827,7 +1827,7 @@ class Library( object, Dictifiable ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" self.description = description @@ -1894,7 +1894,7 @@ return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description @@ -2060,6 +2060,7 @@ genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, + peek = ( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ), template_data = template_data ) if ldda.dataset.uuid is None: rval['uuid'] = None diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1878,8 +1878,9 @@ table = self.table trans = conn.begin() try: - next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() - table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + next_hid = current_hid + 1 + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) trans.commit() return next_hid except: diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a dataset. +API operations on the contents of a history dataset. """ from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,67 +11,125 @@ log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ + + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided as a separate object in response providing data for breadcrumb path building. """ - rval = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - - try: - decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + if ( folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + path_to_root = [] + def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + folder_container.append( dict( full_path = full_path ) ) + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every item in the folder and include its meta-data. + for content_item in self.load_folder_contents( trans, folder ): +# rval = content_item.to_dict() + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) +# log.debug('XXXXXXXXXXXXXXXXXXX api type: ' + str(content_item.api_type)) +# log.debug('XXXXXXXX ALL: ' + str(content_item.__dict__)) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id +# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count ) ) - for content in traverse( folder ): - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.name, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - return rval + if content_item.api_type == 'file': +# log.debug('XXXXX content item class: ' + str(content_item.__class__)) + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + # Put the data in the container + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -0,0 +1,241 @@ +""" +API operations on the dataset from library. +""" +import glob +import logging +import operator +import os +import os.path +import string +import sys +import tarfile +import tempfile +import urllib +import urllib2 +import zipfile +from galaxy.security import Action +from galaxy import util, web +from galaxy.util.streamball import StreamBall +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems + +import logging +log = logging.getLogger( __name__ ) + +# Test for available compression types +# tmpd = tempfile.mkdtemp() +# comptypes = [] +# for comptype in ( 'gz', 'bz2' ): +# tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype ) +# try: +# archive = tarfile.open( tmpf, 'w:' + comptype ) +# archive.close() +# comptypes.append( comptype ) +# except tarfile.CompressionError: +# log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +ziptype = '32' +# tmpf = os.path.join( tmpd, 'compression_test.zip' ) +# try: +# archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) +# archive.close() +# comptypes.append( 'zip' ) +# ziptype = '64' +# except RuntimeError: +# log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +# except (TypeError, zipfile.LargeZipFile): +# # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped +# log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) +# comptypes.append( 'zip' ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +# os.rmdir( tmpd ) + + + +class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/libraries/datasets/{encoded_dataset_id} + Displays information about the dataset identified by the lda ID. + """ + # Get dataset. + try: + dataset = self.get_library_dataset( trans, id = id ) + except Exception, e: + return str( e ) + try: + # Default: return dataset as dict. + rval = dataset.to_dict() + except Exception, e: + rval = "Error in dataset API at listing contents: " + str( e ) + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 + + rval['id'] = trans.security.encode_id(rval['id']); + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + + return rval + + @web.expose + def download( self, trans, format, **kwd ): + """ + POST /api/libraries/datasets/download/{format} + POST data: ldda_ids = [] + Downloads dataset(s) in the requested format. + """ + lddas = [] +# is_admin = trans.user_is_admin() +# current_user_roles = trans.get_current_user_roles() + + datasets_to_download = kwd['ldda_ids%5B%5D'] + + if ( datasets_to_download != None ): + datasets_to_download = util.listify( datasets_to_download ) + for dataset_id in datasets_to_download: + try: + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + assert not ldda.dataset.purged + lddas.append( ldda ) + except: + ldda = None + message += "Invalid library dataset id (%s) specified. " % str( dataset_id ) + + if format in [ 'zip','tgz','tbz' ]: + error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if format == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) + tmpf = os.path.join( tmpd, 'library_download.' + format ) + if ziptype == '64' and trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + elif ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + elif trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif format == 'tgz': + if trans.app.config.upstream_gzip: + archive = StreamBall( 'w|' ) + outext = 'tar' + else: + archive = StreamBall( 'w|gz' ) + outext = 'tgz' + elif format == 'tbz': + archive = StreamBall( 'w|bz2' ) + outext = 'tbz2' + except ( OSError, zipfile.BadZipfile ): + error = True + log.exception( "Unable to create archive for download" ) + message = "Unable to create archive for download, please report this error" + status = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' + if not error: + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: + continue + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: + # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + else: # simple case + try: + archive.add( ldda.dataset.file_name, path ) + except IOError: + error = True + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + if not error: + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + elif format == 'uncompressed': + if len(lddas) != 1: + return 'Wrong request' + else: + single_dataset = lddas[0] + trans.response.set_content_type( single_dataset.get_mime() ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname + try: + return open( single_dataset.file_name ) + except: + return 'This dataset contains no content' + else: + return 'Wrong format'; \ No newline at end of file diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,9 +49,10 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) + item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] ) rval.append( item ) return rval @@ -131,6 +132,9 @@ rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,6 +46,7 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) + # Add the controllers folder # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', controller='admin_toolshed', @@ -53,11 +54,17 @@ repository_id=None, image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) + # Add the api folder + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) + # Add the api folder VERSION 2 + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api.v2', app ) + # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) # Force /activate to go to the controller webapp.add_route( '/activate', controller='user', action='activate' ) # These two routes handle our simple needs at the moment + webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) @@ -66,8 +73,6 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', - controller='dataset', action='display_application', dataset_id=None, user_id=None, - app_name = None, link_name = None, app_action = None, action_param = None ) webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) @@ -171,9 +176,44 @@ #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) + webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) + + # ======================= + # ===== LIBRARY API ===== + # ======================= + + webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) + webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', action='download', conditions=dict(method=["POST"]) ) + + webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) + webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) + + webapp.mapper.resource( 'content', 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) + webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) webapp.mapper.connect( "create_api_key", "/api/users/:user_id/api_key", controller="users", action="api_key", user_id=None, conditions=dict( method=["POST"] ) ) @@ -181,6 +221,7 @@ # visualizations registry generic template renderer webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) + webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) # "POST /api/workflows/import" => ``workflows.import_workflow()``. # Defines a named route "import_workflow". @@ -188,6 +229,15 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -76,6 +76,17 @@ library_list_grid = LibraryListGrid() + + @web.expose + def list( self, trans, **kwd ): + params = util.Params( kwd ) + # define app configuration for generic mako template + app = { + 'jscript' : "galaxy.library" + } + # fill template + return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/scripts/galaxy.library.js --- /dev/null +++ b/static/scripts/galaxy.library.js @@ -0,0 +1,860 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +// global variables +var view = null; +var library_router = null; +var responses = []; + + +// load required libraries +// require([ +// // load js libraries +// 'utils/galaxy.css', +// ], function(css){ +// // load css +// css.load_file("static/style/library.css"); +// }); + +// dependencies +define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils"], function(mod_modal, mod_masthead, mod_utils) { + +// MMMMMMMMMMMMMMM +// === Models ==== +// MMMMMMMMMMMMMMM + + // LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries' + }); + + // LIBRARIES + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries', + model: Library + }); + + // ITEM + var Item = Backbone.Model.extend({ + urlRoot : '/api/libraries/datasets' + }) + + // FOLDER + var Folder = Backbone.Collection.extend({ + model: Item + }) + + // CONTAINER for folder contents (folders, items and metadata). + var FolderContainer = Backbone.Model.extend({ + defaults : { + folder : new Folder(), + full_path : "unknown", + urlRoot : "/api/folders/", + id : "unknown" + }, + parse : function(obj) { + this.full_path = obj[0].full_path; + // update the inner collection + this.get("folder").reset(obj[1].folder_contents); + return obj; + } + }) + + // HISTORY ITEM + var HistoryItem = Backbone.Model.extend({ + urlRoot : '/api/histories/' + }); + + // HISTORY + var GalaxyHistory = Backbone.Model.extend({ + url : '/api/histories/' + }); + + // HISTORIES + var GalaxyHistories = Backbone.Collection.extend({ + url : '/api/histories', + model : GalaxyHistory + }); + + //ROUTER + var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content", + "folders/:folder_id/download/:format" : "download" + } + }); + + +// MMMMMMMMMMMMMM +// === VIEWS ==== +// MMMMMMMMMMMMMM + +// galaxy folder +var FolderContentView = Backbone.View.extend({ + // main element definition + el : '#center', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // last selected history in modal for UX + lastSelectedHistory: '', + // self modal + modal : null, + // loaded folders + folders : null, + + // initialize + initialize : function(){ + this.folders = []; + this.queue = jQuery.Deferred(); + this.queue.resolve(); + }, + +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + // set up + templateFolder : function (){ + var tmpl_array = []; + + // CONTAINER + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-icon-plus"></span><span class="fa fa-icon-folder-close"></span> folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-icon-external-link"></span> to history</button>'); + + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); + tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-icon-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('</div>'); + + // BREADCRUMBS + tmpl_array.push('<div class="library_breadcrumb">'); + tmpl_array.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> '); + tmpl_array.push('<% _.each(path, function(path_item) { %>'); + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<span title="You are in this folder"><%- path_item[1] %></span>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + tmpl_array.push('</div>'); + + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th class="button_heading">view</th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-arrow-up"></span> .. go up</td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- content_item.get("name") %>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-eye-open"></span> details'); + tmpl_array.push(' </button>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + templateDatasetModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<div id="dataset_info_modal">'); + tmpl_array.push(' <table class="table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' </table>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + + templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + // convert size to nice string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + +// MMMMMMMMMMMMMMM +// === EVENTS ==== +// MMMMMMMMMMMMMMM + + // event binding + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClicked', + 'click #toolbtn_bulk_import' : 'modalBulkImport', + 'click #toolbtn_dl' : 'bulkDownload', + 'click .library-dataset' : 'showDatasetDetails', + 'click #toolbtn_create_folder' : 'createFolderModal', + 'click .btn_open_folder' : 'navigateToFolder' + }, + + //render the folder view + render: function (options) { + //hack to show scrollbars + $("#center").css('overflow','auto'); + + view = this; + var that = this; + + var folderContainer = new FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + + folderContainer.fetch({ + success: function (container) { + + // prepare nice size strings + for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { + var model = folderContainer.attributes.folder.models[i] + if (model.get('type') === 'file'){ + model.set('readable_size', that.size_to_string(model.get('file_size'))) + } + }; + + // find the upper id + var path = folderContainer.full_path; + var upper_folder_id; + if (path.length === 1){ // library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } + + var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); + // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); + that.$el.html(template); + } + }) + }, + + // handles the click on 'open' and 'upper' folder icons + navigateToFolder : function(event){ + var folder_id = $(event.target).attr('data-id'); + if (typeof folder_id === 'undefined') { + return false; + } else if (folder_id === '0'){ + library_router.navigate('#', {trigger: true, replace: true}); + } else { + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } + }, + + //show modal with current dataset info + showDatasetDetails : function(event){ + // prevent default + event.preventDefault(); + +//TODO check whether we already have the data + + //load the ID of the row + var id = $(event.target).parent().parent().attr('id'); + + //create new item + var item = new Item(); + var histories = new GalaxyHistories(); + item.id = id; + var self = this; + + //fetch the dataset info + item.fetch({ + success: function (item) { +// TODO can render here already + //fetch user histories for import purposes + histories.fetch({ + success: function (histories){self.renderModalAfterFetch(item, histories)} + }); + } + }); + }, + + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + this.modal = null; + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal({ + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() { self.importCurrentIntoHistory() }, + 'Download' : function() { self.downloadCurrent() }, + 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data + } + }); + $(".peek").html(item.get("peek")); + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + + // show the prepared modal + this.modal.show(); + }, + + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + // we assume the view is existent + folderContentView.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + self.modal.showNotification('Dataset imported', 3000, 'success'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; + // Iterate each checkbox + $(':checkbox').each(function () { this.checked = selected; }); + this.showTools(); + }, + + // click checkbox on folder click + selectClicked : function (event) { + var checkbox = $("#" + event.target.parentElement.id).find(':checkbox') + if (checkbox[0] != undefined) { + if (checkbox[0].checked){ + checkbox[0].checked = ''; + // $(event.target.parentElement).css('background-color', '').css('color', ''); + $(event.target.parentElement).removeClass('dark'); + $(event.target.parentElement).find('a').removeClass('dark'); + $(event.target.parentElement).addClass('light'); + $(event.target.parentElement).find('a').addClass('light'); + } else { + checkbox[0].checked = 'selected'; + $(event.target.parentElement).removeClass('light'); + $(event.target.parentElement).find('a').removeClass('light'); + $(event.target.parentElement).addClass('dark'); + $(event.target.parentElement).find('a').addClass('dark'); + // $(event.target.parentElement).css('background-color', '#8389a1').css('color', 'white'); + } + } + this.showTools(); + }, + + // show toolbar in case something is selected + showTools : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length > 0){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } else { + $('#toolbtn_bulk_import').hide(); + $('#toolbtn_dl').hide(); + } + + }, + + // show bulk import modal + modalBulkImport : function(){ + var self = this; + // fetch histories + var histories = new GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); + self.modal = new mod_modal.GalaxyModal({ + title : 'Import into History', + body : history_modal_tmpl, + buttons : { + 'Import' : function() {self.importAllIntoHistory()}, + 'Close' : function() {self.modal.hide(); $('.modal').remove(); self.modal = null;} + } + }); + // show the prepared modal + self.modal.show(); + } + }); + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + }; + + // call the recursive function to call ajax one after each other + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + self.modal.showNotification('All datasets imported', 3000, 'success'); + // enable button again + self.modal.enableButton('Import'); + return + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + responses.push(a1); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + // progress bar + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + }; + }, + + // shows modal for creating folder + createFolderModal: function(){ + alert('creating folder'); + } + + }); + +// galaxy library view +var GalaxyLibraryview = Backbone.View.extend({ + el: '#center', + + events: { + 'click #create_new_library_btn' : 'show_library_modal' + }, + + // initialize + initialize : function(){ + }, + + // template + template_library_list : function (){ + tmpl_array = []; + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); + + tmpl_array.push(''); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); + tmpl_array.push('<table class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>description</th>'); + tmpl_array.push(' <th>synopsis</th> '); + tmpl_array.push(' <th>model type</th> '); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(libraries, function(library) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- library.get("name") %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + + // render + render: function () { + //hack to show scrollbars + $("#center").css('overflow','auto'); + var that = this; + // if (typeof libraries === "undefined") { + libraries = new Libraries(); + // } + libraries.fetch({ + success: function (libraries) { + var template = _.template(that.template_library_list(), { libraries : libraries.models }); + that.$el.html(template); + } + }) + }, + + // own modal + modal : null, + + // show/hide create library modal + show_library_modal : function (event){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + this.modal = new mod_modal.GalaxyModal( + { + title : 'Create New Library', + body : this.template_new_library(), + buttons : { + 'Create' : function() {self.create_new_library_event()}, + 'Close' : function() {self.modal.hide()} + } + }); + + // show prepared modal + this.modal.show(); + }, + + // create the new library from modal + create_new_library_event: function(){ + var libraryDetails = this.serialize_new_library(); + var valid = this.validate_new_library(libraryDetails); + var library = new Library(); + var self = this; + library.save(libraryDetails, { + success: function (library) { + self.modal.hide(); + self.clear_library_modal(); + self.render(); + }, + error: function(){ + self.modal.showNotification('An error occured', 5000, 'error'); + } + }); + return false; + }, + + // clear the library modal once saved + clear_library_modal : function(){ + $("input[name='Name']").val(''); + $("input[name='Description']").val(''); + $("input[name='Synopsis']").val(''); + }, + + // serialize data from the form + serialize_new_library : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val(), + synopsis: $("input[name='Synopsis']").val() + }; + }, + + validate_new_library: function(library){ + + }, + + + // template for new library modal + template_new_library: function() + { + tmpl_array = []; + + tmpl_array.push('<div id="new_library_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + } +}); + +// galaxy library wrapper View +var GalaxyLibrary = Backbone.View.extend({ + folderContentView : null, + galaxyLibraryview : null, + initialize : function(){ + + folderContentView = new FolderContentView(); + galaxyLibraryview = new GalaxyLibraryview(); + + library_router = new LibraryRouter(); + + library_router.on('route:libraries', function() { + // render libraries list + galaxyLibraryview.render(); + }); + + library_router.on('route:folder_content', function(id) { + // render folder's contents + folderContentView.render({id: id}); + }); + + library_router.on('route:download', function(folder_id, format) { + // send download stream + if (typeof folderContentView === 'undefined'){ + alert('you cant touch this!'); + // } else if (folderContentView.modal !== null){ + // folderContentView.download(folder_id, format); + } else if ($('#center').find(':checked').length === 0) { // coming from outside of the library app + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + // TODO show message of redirection + } else { + folderContentView.download(folder_id, format); + library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + + }); + +Backbone.history.start(); + +return this +} +}); + +// return +return { + GalaxyApp: GalaxyLibrary +}; + +}); diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/scripts/galaxy.library.router.js --- /dev/null +++ b/static/scripts/galaxy.library.router.js @@ -0,0 +1,21 @@ +define( [], function() { + +/** + * -- Routers -- + */ + +/** + * Router for library browser. + */ +var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content" + } +}); + +return { + LibraryRouter: LibraryRouter, +}; + +}) \ No newline at end of file diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -58,6 +58,12 @@ tab_shared.add({ title : "Data Libraries", content : "library/index", + content : "library/index" + }); + + tab_shared.add({ + title : "New Libraries", + content : "library/list", divider : true }); diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -1,6 +1,3 @@ -/* - galaxy modal -*/ // dependencies define([], function() { @@ -25,8 +22,51 @@ // initialize initialize : function(options) { + self = this; if (options) this.create(options); + + this.bindClick(event, self); + }, + + // bind the click-to-hide function + bindClick: function(event, that) { + // bind the ESC key to hide() function + $(document).on('keyup', function(event){ + if (event.keyCode == 27) { self.hide(); } + }) + // bind the click anywhere to hide() function... + $('html').on('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').on('click', function(event){ + event.stopPropagation(); + }) + }, + + // unbind the click-to-hide function + unbindClick: function(event, that){ + // bind the ESC key to hide() function + $(document).off('keyup', function(event){ + if (event.keyCode == 27) { that.hide(); } + }) + // unbind the click anywhere to hide() function... + $('html').off('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').off('click', function(event){ + event.stopPropagation(); + }) + }, + + + // destroy + destroy : function(){ + this.hide(); + this.unbindClick(); + $('.modal').remove(); }, // adds and displays a new frame/window @@ -87,6 +127,7 @@ this.$footer = (this.$el).find('.modal-footer'); this.$buttons = (this.$el).find('.buttons'); this.$backdrop = (this.$el).find('.modal-backdrop'); + this.$notification = (this.$el).find('.notification-modal'); // append body this.$body.html(this.options.body); @@ -120,6 +161,47 @@ this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, + // hide buttons + hideButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).hide(); + }, + // show buttons + showButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).show(); + }, + + // show notification + showNotification : function(message, duration, type) { + // defaults + var duration = typeof duration !== 'undefined' ? duration : 1500; + // var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; + // var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + var bgColor; + var txtColor; + + if (type === 'error'){ + bgColor = '#f4e0e1'; + txtColor = '#a42732'; + // } else if (type === 'success'){ + } else { // success is default + bgColor = '#e1f4e0'; + txtColor = '#32a427'; + } + + var HTMLmessage = "<div class='notification-message' style='text-align:center; line-height:16px; '> " + message + " </div>"; + this.$notification.html("<div id='notification-bar' style='display:none; float: right; height: 16px; width:100%; background-color: " + bgColor + "; z-index: 100; color: " + txtColor + ";border-bottom: 1px solid " + txtColor + ";'>" + HTMLmessage + "</div>"); + + var self = this; + + /*animate the bar*/ + $('#notification-bar').slideDown(function() { + setTimeout(function() { + $('#notification-bar').slideUp(function() {self.$notification.html('');}); + }, duration); + }); + + }, + // returns scroll top for body element scrollTop: function() { @@ -135,10 +217,10 @@ return '<div class="modal">' + '<div class="modal-backdrop fade in" style="z-index: -1;"></div>' + '<div class="modal-dialog">' + - '<div class="modal-content">' + '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + + '<span class="notification-modal"></span>' + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/scripts/libs/bootstrap.js --- a/static/scripts/libs/bootstrap.js +++ b/static/scripts/libs/bootstrap.js @@ -575,3 +575,158 @@ } }(window.jQuery); + +/* ======================================================================== + * Bootstrap: dropdown.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#dropdowns + * ======================================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== */ + + ++function ($) { "use strict"; + + // DROPDOWN CLASS DEFINITION + // ========================= + + var backdrop = '.dropdown-backdrop' + var toggle = '[data-toggle=dropdown]' + var Dropdown = function (element) { + var $el = $(element).on('click.bs.dropdown', this.toggle) + } + + Dropdown.prototype.toggle = function (e) { + var $this = $(this) + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) { + if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) { + // if mobile we we use a backdrop because click events don't delegate + $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus) + } + + $parent.trigger(e = $.Event('show.bs.dropdown')) + + if (e.isDefaultPrevented()) return + + $parent + .toggleClass('open') + .trigger('shown.bs.dropdown') + + $this.focus() + } + + return false + } + + Dropdown.prototype.keydown = function (e) { + if (!/(38|40|27)/.test(e.keyCode)) return + + var $this = $(this) + + e.preventDefault() + e.stopPropagation() + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + if (!isActive || (isActive && e.keyCode == 27)) { + if (e.which == 27) $parent.find(toggle).focus() + return $this.click() + } + + var $items = $('[role=menu] li:not(.divider):visible a', $parent) + + if (!$items.length) return + + var index = $items.index($items.filter(':focus')) + + if (e.keyCode == 38 && index > 0) index-- // up + if (e.keyCode == 40 && index < $items.length - 1) index++ // down + if (!~index) index=0 + + $items.eq(index).focus() + } + + function clearMenus() { + $(backdrop).remove() + $(toggle).each(function (e) { + var $parent = getParent($(this)) + if (!$parent.hasClass('open')) return + $parent.trigger(e = $.Event('hide.bs.dropdown')) + if (e.isDefaultPrevented()) return + $parent.removeClass('open').trigger('hidden.bs.dropdown') + }) + } + + function getParent($this) { + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && /#/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + var $parent = selector && $(selector) + + return $parent && $parent.length ? $parent : $this.parent() + } + + + // DROPDOWN PLUGIN DEFINITION + // ========================== + + var old = $.fn.dropdown + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('dropdown') + + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + // DROPDOWN NO CONFLICT + // ==================== + + $.fn.dropdown.noConflict = function () { + $.fn.dropdown = old + return this + } + + + // APPLY TO STANDARD DROPDOWN ELEMENTS + // =================================== + + $(document) + .on('click.bs.dropdown.data-api', clearMenus) + .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.bs.dropdown.data-api' , toggle, Dropdown.prototype.toggle) + .on('keydown.bs.dropdown.data-api', toggle + ', [role=menu]' , Dropdown.prototype.keydown) + +}(window.jQuery); \ No newline at end of file diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,7 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'new_library', 'trackster' ]; var _ = grunt.util._; var fmt = _.sprintf; diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,6 +29,50 @@ background-color: @table-bg-accent; } + +tr.light td +{ + background-color: white; + color: black; +} +tr.light:hover td +{ + background-color: #f5f5f5; + color: #8389a1; +} +tr.dark td +{ + background-color: #8389a1; + color: white; +} +tr.dark:hover td +{ + background-color: #bbbfd0; + color: white; +} +a.dark:hover +{ + color: yellow; + // text-decoration: none; +} +a.dark +{ + color: white; + // text-decoration: none; +} +th.button_heading +{ + width: 7em; +} +div.library_breadcrumb{ + padding-top: 0.8em; + padding-bottom: 0.8em; +} +div.library_breadcrumb a:hover{ + color:green; +} + + img.expanderIcon { padding-right: 4px; } diff -r d5217f01960360a9d7298fa679b839c806cab893 -r e2b8d3481d668203bfad7efe306925c72c644839 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -357,4 +357,4 @@ ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout ${self.late_javascripts()} -</html> +</html> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/fb3161b21a4b/ Changeset: fb3161b21a4b User: martenson Date: 2013-12-11 00:12:14 Summary: aiding the merge of data_library branch Affected #: 5 files diff -r e2b8d3481d668203bfad7efe306925c72c644839 -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 .hgignore --- a/.hgignore +++ b/.hgignore @@ -114,8 +114,4 @@ *.orig .DS_Store *.rej -*~ - - -syntax: regexp -^static/AAA_scratch$ \ No newline at end of file +*~ \ No newline at end of file diff -r e2b8d3481d668203bfad7efe306925c72c644839 -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -100,8 +100,6 @@ encoded_id = trans.security.encode_id( content_item.id ) time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) -# log.debug('XXXXXXXXXXXXXXXXXXX api type: ' + str(content_item.api_type)) -# log.debug('XXXXXXXX ALL: ' + str(content_item.__dict__)) # For folder return also hierarchy values if content_item.api_type == 'folder': @@ -110,7 +108,6 @@ return_item.update ( dict ( item_count = content_item.item_count ) ) if content_item.api_type == 'file': -# log.debug('XXXXX content item class: ' + str(content_item.__class__)) library_dataset_dict = content_item.to_dict() library_dataset_dict['data_type'] library_dataset_dict['file_size'] diff -r e2b8d3481d668203bfad7efe306925c72c644839 -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 static/scripts/galaxy.library.router.js --- a/static/scripts/galaxy.library.router.js +++ /dev/null @@ -1,21 +0,0 @@ -define( [], function() { - -/** - * -- Routers -- - */ - -/** - * Router for library browser. - */ -var LibraryRouter = Backbone.Router.extend({ - routes: { - "" : "libraries", - "folders/:id" : "folder_content" - } -}); - -return { - LibraryRouter: LibraryRouter, -}; - -}) \ No newline at end of file diff -r e2b8d3481d668203bfad7efe306925c72c644839 -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -57,7 +57,6 @@ tab_shared.add({ title : "Data Libraries", - content : "library/index", content : "library/index" }); diff -r e2b8d3481d668203bfad7efe306925c72c644839 -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,7 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'new_library', 'trackster' ]; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; var _ = grunt.util._; var fmt = _.sprintf; https://bitbucket.org/galaxy/galaxy-central/commits/96f52c9fd562/ Changeset: 96f52c9fd562 User: martenson Date: 2013-12-11 00:21:06 Summary: Merged galaxy/galaxy-central into default Affected #: 3 files diff -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 -r 96f52c9fd562fe160fc8ac71aa6cddd902d23e0f config/plugins/visualizations/scatterplot/templates/scatterplot.mako --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -15,7 +15,6 @@ <script type="text/javascript" src="/static/scripts/libs/jquery/jquery.migrate.js"></script><script type="text/javascript" src="/static/scripts/libs/underscore.js"></script><script type="text/javascript" src="/static/scripts/libs/backbone/backbone.js"></script> -<script type="text/javascript" src="/static/scripts/libs/backbone/backbone-relational.js"></script><script type="text/javascript" src="/static/scripts/libs/handlebars.runtime.js"></script><script type="text/javascript" src="/static/scripts/libs/d3.js"></script><script type="text/javascript" src="/static/scripts/libs/bootstrap.js"></script> diff -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 -r 96f52c9fd562fe160fc8ac71aa6cddd902d23e0f lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -474,6 +474,9 @@ """Returns history data in the form of a dictionary. """ history_dict = history.to_dict( view='element', value_mapper={ 'id':trans.security.encode_id }) + history_dict[ 'user_id' ] = None + if history.user_id: + history_dict[ 'user_id' ] = trans.security.encode_id( history.user_id ) history_dict[ 'nice_size' ] = history.get_disk_size( nice_size=True ) history_dict[ 'annotation' ] = history.get_item_annotation_str( trans.sa_session, trans.user, history ) diff -r fb3161b21a4bfc1c5bd2f6bea8dc63c9c5bb4b38 -r 96f52c9fd562fe160fc8ac71aa6cddd902d23e0f lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -93,7 +93,7 @@ env_file_builder.append_line( action="source", value=required_tool_dependency_env_file_path ) return_code = env_file_builder.return_code if return_code: - error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name, str( return_code ) ) ) + error_message = 'Error defining env.sh file for package %s, return_code: %s' % ( str( package_name ), str( return_code ) ) tool_dependency = tool_dependency_util.handle_tool_dependency_installation_error( app, tool_dependency, error_message, https://bitbucket.org/galaxy/galaxy-central/commits/42e74befc796/ Changeset: 42e74befc796 User: martenson Date: 2013-12-11 00:29:50 Summary: aid after merge data_library branch Affected #: 1 file diff -r 96f52c9fd562fe160fc8ac71aa6cddd902d23e0f -r 42e74befc7962afb93baba6197273565755e086c lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -73,6 +73,8 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', + controller='dataset', action='display_application', dataset_id=None, user_id=None, + app_name = None, link_name = None, app_action = None, action_param = None ) webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) https://bitbucket.org/galaxy/galaxy-central/commits/8fcfddb3e1b5/ Changeset: 8fcfddb3e1b5 User: martenson Date: 2013-12-11 16:41:39 Summary: aiding problematic merging of data_library branch, removing duplicates, removing API v2 relicts Affected #: 3 files diff -r 42e74befc7962afb93baba6197273565755e086c -r 8fcfddb3e1b57ad627ebab3619920552a6e967ff .hgignore --- a/.hgignore +++ b/.hgignore @@ -114,4 +114,5 @@ *.orig .DS_Store *.rej -*~ \ No newline at end of file +*~ + diff -r 42e74befc7962afb93baba6197273565755e086c -r 8fcfddb3e1b57ad627ebab3619920552a6e967ff lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,7 +46,6 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Add the controllers folder # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', controller='admin_toolshed', @@ -54,17 +53,11 @@ repository_id=None, image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) - # Add the api folder - webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # Add the api folder VERSION 2 - webapp.add_api_controllers( 'galaxy.webapps.galaxy.api.v2', app ) - # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) # Force /activate to go to the controller webapp.add_route( '/activate', controller='user', action='activate' ) # These two routes handle our simple needs at the moment - webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) @@ -73,8 +66,8 @@ webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', - controller='dataset', action='display_application', dataset_id=None, user_id=None, - app_name = None, link_name = None, app_action = None, action_param = None ) + controller='dataset', action='display_application', dataset_id=None, user_id=None, + app_name = None, link_name = None, app_action = None, action_param = None ) webapp.add_route( '/u/:username/d/:slug/:filename', controller='dataset', action='display_by_username_and_slug', filename=None ) webapp.add_route( '/u/:username/p/:slug', controller='page', action='display_by_username_and_slug' ) webapp.add_route( '/u/:username/h/:slug', controller='history', action='display_by_username_and_slug' ) @@ -82,22 +75,12 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # Add the web API + # ================ + # ===== API ===== + # ================ + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'content', 'contents', controller='history_contents', @@ -109,10 +92,6 @@ controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'user', 'users', controller='group_users', @@ -134,11 +113,6 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -148,7 +122,6 @@ _add_item_annotation_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - _add_item_provenance_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -178,13 +151,12 @@ #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) - webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) - # ======================= # ===== LIBRARY API ===== # ======================= + + # The /folders section is experimental at this point: + log.debug( "app.config.api_folders: %s" % app.config.api_folders ) webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', action='download', conditions=dict(method=["POST"]) ) @@ -232,6 +204,9 @@ # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + # ==================== + # ===== TOOLSHED ===== + # ==================== # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', @@ -239,7 +214,7 @@ action='display_image_in_repository', repository_id=None, image_file=None ) - + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', @@ -253,6 +228,7 @@ path_prefix='/api', new={ 'install_repository_revision' : 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger @@ -273,11 +249,6 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking - try: - galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() - except: - pass # Return return webapp https://bitbucket.org/galaxy/galaxy-central/commits/4506583cb1bc/ Changeset: 4506583cb1bc User: martenson Date: 2013-12-11 16:51:21 Summary: aiding merg problems with data_library branch Affected #: 1 file diff -r 8fcfddb3e1b57ad627ebab3619920552a6e967ff -r 4506583cb1bc66db01d98c1619b6829fcda31e00 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,12 +46,6 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', - controller='admin_toolshed', - action='display_image_in_repository', - repository_id=None, - image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) @@ -187,7 +181,6 @@ # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) - webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) webapp.mapper.connect( "create_api_key", "/api/users/:user_id/api_key", controller="users", action="api_key", user_id=None, conditions=dict( method=["POST"] ) ) @@ -195,7 +188,6 @@ # visualizations registry generic template renderer webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) - webapp.add_route( '/visualization/show/:visualization_name', controller='visualization', action='render', visualization_name=None ) # "POST /api/workflows/import" => ``workflows.import_workflow()``. # Defines a named route "import_workflow". https://bitbucket.org/galaxy/galaxy-central/commits/2fb8dfdb5b19/ Changeset: 2fb8dfdb5b19 User: martenson Date: 2013-12-11 16:53:42 Summary: aiding merg problems with data_library branch Affected #: 1 file diff -r 4506583cb1bc66db01d98c1619b6829fcda31e00 -r 2fb8dfdb5b19378a5bc61ee713aa4da3f9767a91 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -241,6 +241,11 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass + # Close any pooled database connections before forking + try: + galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() + except: + pass # Return return webapp https://bitbucket.org/galaxy/galaxy-central/commits/78c39d32ac09/ Changeset: 78c39d32ac09 User: martenson Date: 2013-12-11 17:01:45 Summary: aiding merg problems with data_library branch Affected #: 1 file diff -r 2fb8dfdb5b19378a5bc61ee713aa4da3f9767a91 -r 78c39d32ac09a796966cc192636f4f8b1ba1bc07 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -357,4 +357,4 @@ ## Scripts can be loaded later since they progressively add features to ## the panels, but do not change layout ${self.late_javascripts()} -</html> \ No newline at end of file +</html> https://bitbucket.org/galaxy/galaxy-central/commits/8528640574a5/ Changeset: 8528640574a5 User: martenson Date: 2013-12-11 17:08:59 Summary: aiding merg problems with data_library branch Affected #: 1 file diff -r 78c39d32ac09a796966cc192636f4f8b1ba1bc07 -r 8528640574a5b981ffb0940477abb0bd65ea2885 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -217,11 +217,12 @@ return '<div class="modal">' + '<div class="modal-backdrop fade in" style="z-index: -1;"></div>' + '<div class="modal-dialog">' + + '<div class="modal-content">' + '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + '<span class="notification-modal"></span>' + - '</div>' + + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + '<div class="buttons" style="float: right;"></div>' + https://bitbucket.org/galaxy/galaxy-central/commits/181b293ea659/ Changeset: 181b293ea659 User: martenson Date: 2013-12-11 17:19:42 Summary: Merge with second head of ‘default’ branch Affected #: 17 files diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1827,7 +1827,7 @@ class Library( object, Dictifiable ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" self.description = description @@ -1894,7 +1894,7 @@ return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description @@ -2060,6 +2060,7 @@ genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, + peek = ( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ), template_data = template_data ) if ldda.dataset.uuid is None: rval['uuid'] = None diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1878,8 +1878,9 @@ table = self.table trans = conn.begin() try: - next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() - table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + next_hid = current_hid + 1 + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) trans.commit() return next_hid except: diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a dataset. +API operations on the contents of a history dataset. """ from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,67 +11,122 @@ log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ + + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided as a separate object in response providing data for breadcrumb path building. """ - rval = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - - try: - decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + if ( folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + path_to_root = [] + def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + folder_container.append( dict( full_path = full_path ) ) + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every item in the folder and include its meta-data. + for content_item in self.load_folder_contents( trans, folder ): +# rval = content_item.to_dict() + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id +# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count ) ) - for content in traverse( folder ): - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.name, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - return rval + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + # Put the data in the container + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -0,0 +1,241 @@ +""" +API operations on the dataset from library. +""" +import glob +import logging +import operator +import os +import os.path +import string +import sys +import tarfile +import tempfile +import urllib +import urllib2 +import zipfile +from galaxy.security import Action +from galaxy import util, web +from galaxy.util.streamball import StreamBall +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems + +import logging +log = logging.getLogger( __name__ ) + +# Test for available compression types +# tmpd = tempfile.mkdtemp() +# comptypes = [] +# for comptype in ( 'gz', 'bz2' ): +# tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype ) +# try: +# archive = tarfile.open( tmpf, 'w:' + comptype ) +# archive.close() +# comptypes.append( comptype ) +# except tarfile.CompressionError: +# log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +ziptype = '32' +# tmpf = os.path.join( tmpd, 'compression_test.zip' ) +# try: +# archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) +# archive.close() +# comptypes.append( 'zip' ) +# ziptype = '64' +# except RuntimeError: +# log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +# except (TypeError, zipfile.LargeZipFile): +# # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped +# log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) +# comptypes.append( 'zip' ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +# os.rmdir( tmpd ) + + + +class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/libraries/datasets/{encoded_dataset_id} + Displays information about the dataset identified by the lda ID. + """ + # Get dataset. + try: + dataset = self.get_library_dataset( trans, id = id ) + except Exception, e: + return str( e ) + try: + # Default: return dataset as dict. + rval = dataset.to_dict() + except Exception, e: + rval = "Error in dataset API at listing contents: " + str( e ) + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 + + rval['id'] = trans.security.encode_id(rval['id']); + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + + return rval + + @web.expose + def download( self, trans, format, **kwd ): + """ + POST /api/libraries/datasets/download/{format} + POST data: ldda_ids = [] + Downloads dataset(s) in the requested format. + """ + lddas = [] +# is_admin = trans.user_is_admin() +# current_user_roles = trans.get_current_user_roles() + + datasets_to_download = kwd['ldda_ids%5B%5D'] + + if ( datasets_to_download != None ): + datasets_to_download = util.listify( datasets_to_download ) + for dataset_id in datasets_to_download: + try: + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + assert not ldda.dataset.purged + lddas.append( ldda ) + except: + ldda = None + message += "Invalid library dataset id (%s) specified. " % str( dataset_id ) + + if format in [ 'zip','tgz','tbz' ]: + error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if format == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) + tmpf = os.path.join( tmpd, 'library_download.' + format ) + if ziptype == '64' and trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + elif ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + elif trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif format == 'tgz': + if trans.app.config.upstream_gzip: + archive = StreamBall( 'w|' ) + outext = 'tar' + else: + archive = StreamBall( 'w|gz' ) + outext = 'tgz' + elif format == 'tbz': + archive = StreamBall( 'w|bz2' ) + outext = 'tbz2' + except ( OSError, zipfile.BadZipfile ): + error = True + log.exception( "Unable to create archive for download" ) + message = "Unable to create archive for download, please report this error" + status = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' + if not error: + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: + continue + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: + # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + else: # simple case + try: + archive.add( ldda.dataset.file_name, path ) + except IOError: + error = True + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + if not error: + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + elif format == 'uncompressed': + if len(lddas) != 1: + return 'Wrong request' + else: + single_dataset = lddas[0] + trans.response.set_content_type( single_dataset.get_mime() ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname + try: + return open( single_dataset.file_name ) + except: + return 'This dataset contains no content' + else: + return 'Wrong format'; \ No newline at end of file diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,9 +49,10 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) + item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] ) rval.append( item ) return rval @@ -131,6 +132,9 @@ rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,12 +46,6 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', - controller='admin_toolshed', - action='display_image_in_repository', - repository_id=None, - image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) @@ -75,22 +69,12 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # Add the web API + # ================ + # ===== API ===== + # ================ + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'content', 'contents', controller='history_contents', @@ -102,10 +86,6 @@ controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'user', 'users', controller='group_users', @@ -127,11 +107,6 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -141,7 +116,6 @@ _add_item_annotation_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - _add_item_provenance_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -171,6 +145,39 @@ #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) + # ======================= + # ===== LIBRARY API ===== + # ======================= + + # The /folders section is experimental at this point: + log.debug( "app.config.api_folders: %s" % app.config.api_folders ) + + webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) + webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', action='download', conditions=dict(method=["POST"]) ) + + webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) + webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) + + webapp.mapper.resource( 'content', 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) @@ -188,6 +195,18 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + # ==================== + # ===== TOOLSHED ===== + # ==================== + + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', @@ -201,6 +220,7 @@ path_prefix='/api', new={ 'install_repository_revision' : 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger @@ -221,7 +241,7 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking + # Close any pooled database connections before forking try: galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() except: diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -76,6 +76,17 @@ library_list_grid = LibraryListGrid() + + @web.expose + def list( self, trans, **kwd ): + params = util.Params( kwd ) + # define app configuration for generic mako template + app = { + 'jscript' : "galaxy.library" + } + # fill template + return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 static/scripts/galaxy.library.js --- /dev/null +++ b/static/scripts/galaxy.library.js @@ -0,0 +1,860 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +// global variables +var view = null; +var library_router = null; +var responses = []; + + +// load required libraries +// require([ +// // load js libraries +// 'utils/galaxy.css', +// ], function(css){ +// // load css +// css.load_file("static/style/library.css"); +// }); + +// dependencies +define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils"], function(mod_modal, mod_masthead, mod_utils) { + +// MMMMMMMMMMMMMMM +// === Models ==== +// MMMMMMMMMMMMMMM + + // LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries' + }); + + // LIBRARIES + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries', + model: Library + }); + + // ITEM + var Item = Backbone.Model.extend({ + urlRoot : '/api/libraries/datasets' + }) + + // FOLDER + var Folder = Backbone.Collection.extend({ + model: Item + }) + + // CONTAINER for folder contents (folders, items and metadata). + var FolderContainer = Backbone.Model.extend({ + defaults : { + folder : new Folder(), + full_path : "unknown", + urlRoot : "/api/folders/", + id : "unknown" + }, + parse : function(obj) { + this.full_path = obj[0].full_path; + // update the inner collection + this.get("folder").reset(obj[1].folder_contents); + return obj; + } + }) + + // HISTORY ITEM + var HistoryItem = Backbone.Model.extend({ + urlRoot : '/api/histories/' + }); + + // HISTORY + var GalaxyHistory = Backbone.Model.extend({ + url : '/api/histories/' + }); + + // HISTORIES + var GalaxyHistories = Backbone.Collection.extend({ + url : '/api/histories', + model : GalaxyHistory + }); + + //ROUTER + var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content", + "folders/:folder_id/download/:format" : "download" + } + }); + + +// MMMMMMMMMMMMMM +// === VIEWS ==== +// MMMMMMMMMMMMMM + +// galaxy folder +var FolderContentView = Backbone.View.extend({ + // main element definition + el : '#center', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // last selected history in modal for UX + lastSelectedHistory: '', + // self modal + modal : null, + // loaded folders + folders : null, + + // initialize + initialize : function(){ + this.folders = []; + this.queue = jQuery.Deferred(); + this.queue.resolve(); + }, + +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + // set up + templateFolder : function (){ + var tmpl_array = []; + + // CONTAINER + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-icon-plus"></span><span class="fa fa-icon-folder-close"></span> folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-icon-external-link"></span> to history</button>'); + + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); + tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-icon-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('</div>'); + + // BREADCRUMBS + tmpl_array.push('<div class="library_breadcrumb">'); + tmpl_array.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> '); + tmpl_array.push('<% _.each(path, function(path_item) { %>'); + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<span title="You are in this folder"><%- path_item[1] %></span>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + tmpl_array.push('</div>'); + + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th class="button_heading">view</th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-arrow-up"></span> .. go up</td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- content_item.get("name") %>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-eye-open"></span> details'); + tmpl_array.push(' </button>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + templateDatasetModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<div id="dataset_info_modal">'); + tmpl_array.push(' <table class="table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' </table>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + + templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + // convert size to nice string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + +// MMMMMMMMMMMMMMM +// === EVENTS ==== +// MMMMMMMMMMMMMMM + + // event binding + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClicked', + 'click #toolbtn_bulk_import' : 'modalBulkImport', + 'click #toolbtn_dl' : 'bulkDownload', + 'click .library-dataset' : 'showDatasetDetails', + 'click #toolbtn_create_folder' : 'createFolderModal', + 'click .btn_open_folder' : 'navigateToFolder' + }, + + //render the folder view + render: function (options) { + //hack to show scrollbars + $("#center").css('overflow','auto'); + + view = this; + var that = this; + + var folderContainer = new FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + + folderContainer.fetch({ + success: function (container) { + + // prepare nice size strings + for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { + var model = folderContainer.attributes.folder.models[i] + if (model.get('type') === 'file'){ + model.set('readable_size', that.size_to_string(model.get('file_size'))) + } + }; + + // find the upper id + var path = folderContainer.full_path; + var upper_folder_id; + if (path.length === 1){ // library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } + + var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); + // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); + that.$el.html(template); + } + }) + }, + + // handles the click on 'open' and 'upper' folder icons + navigateToFolder : function(event){ + var folder_id = $(event.target).attr('data-id'); + if (typeof folder_id === 'undefined') { + return false; + } else if (folder_id === '0'){ + library_router.navigate('#', {trigger: true, replace: true}); + } else { + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } + }, + + //show modal with current dataset info + showDatasetDetails : function(event){ + // prevent default + event.preventDefault(); + +//TODO check whether we already have the data + + //load the ID of the row + var id = $(event.target).parent().parent().attr('id'); + + //create new item + var item = new Item(); + var histories = new GalaxyHistories(); + item.id = id; + var self = this; + + //fetch the dataset info + item.fetch({ + success: function (item) { +// TODO can render here already + //fetch user histories for import purposes + histories.fetch({ + success: function (histories){self.renderModalAfterFetch(item, histories)} + }); + } + }); + }, + + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + this.modal = null; + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal({ + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() { self.importCurrentIntoHistory() }, + 'Download' : function() { self.downloadCurrent() }, + 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data + } + }); + $(".peek").html(item.get("peek")); + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + + // show the prepared modal + this.modal.show(); + }, + + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + // we assume the view is existent + folderContentView.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + self.modal.showNotification('Dataset imported', 3000, 'success'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; + // Iterate each checkbox + $(':checkbox').each(function () { this.checked = selected; }); + this.showTools(); + }, + + // click checkbox on folder click + selectClicked : function (event) { + var checkbox = $("#" + event.target.parentElement.id).find(':checkbox') + if (checkbox[0] != undefined) { + if (checkbox[0].checked){ + checkbox[0].checked = ''; + // $(event.target.parentElement).css('background-color', '').css('color', ''); + $(event.target.parentElement).removeClass('dark'); + $(event.target.parentElement).find('a').removeClass('dark'); + $(event.target.parentElement).addClass('light'); + $(event.target.parentElement).find('a').addClass('light'); + } else { + checkbox[0].checked = 'selected'; + $(event.target.parentElement).removeClass('light'); + $(event.target.parentElement).find('a').removeClass('light'); + $(event.target.parentElement).addClass('dark'); + $(event.target.parentElement).find('a').addClass('dark'); + // $(event.target.parentElement).css('background-color', '#8389a1').css('color', 'white'); + } + } + this.showTools(); + }, + + // show toolbar in case something is selected + showTools : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length > 0){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } else { + $('#toolbtn_bulk_import').hide(); + $('#toolbtn_dl').hide(); + } + + }, + + // show bulk import modal + modalBulkImport : function(){ + var self = this; + // fetch histories + var histories = new GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); + self.modal = new mod_modal.GalaxyModal({ + title : 'Import into History', + body : history_modal_tmpl, + buttons : { + 'Import' : function() {self.importAllIntoHistory()}, + 'Close' : function() {self.modal.hide(); $('.modal').remove(); self.modal = null;} + } + }); + // show the prepared modal + self.modal.show(); + } + }); + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + }; + + // call the recursive function to call ajax one after each other + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + self.modal.showNotification('All datasets imported', 3000, 'success'); + // enable button again + self.modal.enableButton('Import'); + return + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + responses.push(a1); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + // progress bar + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + }; + }, + + // shows modal for creating folder + createFolderModal: function(){ + alert('creating folder'); + } + + }); + +// galaxy library view +var GalaxyLibraryview = Backbone.View.extend({ + el: '#center', + + events: { + 'click #create_new_library_btn' : 'show_library_modal' + }, + + // initialize + initialize : function(){ + }, + + // template + template_library_list : function (){ + tmpl_array = []; + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); + + tmpl_array.push(''); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); + tmpl_array.push('<table class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>description</th>'); + tmpl_array.push(' <th>synopsis</th> '); + tmpl_array.push(' <th>model type</th> '); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(libraries, function(library) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- library.get("name") %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + + // render + render: function () { + //hack to show scrollbars + $("#center").css('overflow','auto'); + var that = this; + // if (typeof libraries === "undefined") { + libraries = new Libraries(); + // } + libraries.fetch({ + success: function (libraries) { + var template = _.template(that.template_library_list(), { libraries : libraries.models }); + that.$el.html(template); + } + }) + }, + + // own modal + modal : null, + + // show/hide create library modal + show_library_modal : function (event){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + this.modal = new mod_modal.GalaxyModal( + { + title : 'Create New Library', + body : this.template_new_library(), + buttons : { + 'Create' : function() {self.create_new_library_event()}, + 'Close' : function() {self.modal.hide()} + } + }); + + // show prepared modal + this.modal.show(); + }, + + // create the new library from modal + create_new_library_event: function(){ + var libraryDetails = this.serialize_new_library(); + var valid = this.validate_new_library(libraryDetails); + var library = new Library(); + var self = this; + library.save(libraryDetails, { + success: function (library) { + self.modal.hide(); + self.clear_library_modal(); + self.render(); + }, + error: function(){ + self.modal.showNotification('An error occured', 5000, 'error'); + } + }); + return false; + }, + + // clear the library modal once saved + clear_library_modal : function(){ + $("input[name='Name']").val(''); + $("input[name='Description']").val(''); + $("input[name='Synopsis']").val(''); + }, + + // serialize data from the form + serialize_new_library : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val(), + synopsis: $("input[name='Synopsis']").val() + }; + }, + + validate_new_library: function(library){ + + }, + + + // template for new library modal + template_new_library: function() + { + tmpl_array = []; + + tmpl_array.push('<div id="new_library_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + } +}); + +// galaxy library wrapper View +var GalaxyLibrary = Backbone.View.extend({ + folderContentView : null, + galaxyLibraryview : null, + initialize : function(){ + + folderContentView = new FolderContentView(); + galaxyLibraryview = new GalaxyLibraryview(); + + library_router = new LibraryRouter(); + + library_router.on('route:libraries', function() { + // render libraries list + galaxyLibraryview.render(); + }); + + library_router.on('route:folder_content', function(id) { + // render folder's contents + folderContentView.render({id: id}); + }); + + library_router.on('route:download', function(folder_id, format) { + // send download stream + if (typeof folderContentView === 'undefined'){ + alert('you cant touch this!'); + // } else if (folderContentView.modal !== null){ + // folderContentView.download(folder_id, format); + } else if ($('#center').find(':checked').length === 0) { // coming from outside of the library app + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + // TODO show message of redirection + } else { + folderContentView.download(folder_id, format); + library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + + }); + +Backbone.history.start(); + +return this +} +}); + +// return +return { + GalaxyApp: GalaxyLibrary +}; + +}); diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -57,7 +57,12 @@ tab_shared.add({ title : "Data Libraries", - content : "library/index", + content : "library/index" + }); + + tab_shared.add({ + title : "New Libraries", + content : "library/list", divider : true }); diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -1,6 +1,3 @@ -/* - galaxy modal -*/ // dependencies define([], function() { @@ -25,8 +22,51 @@ // initialize initialize : function(options) { + self = this; if (options) this.create(options); + + this.bindClick(event, self); + }, + + // bind the click-to-hide function + bindClick: function(event, that) { + // bind the ESC key to hide() function + $(document).on('keyup', function(event){ + if (event.keyCode == 27) { self.hide(); } + }) + // bind the click anywhere to hide() function... + $('html').on('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').on('click', function(event){ + event.stopPropagation(); + }) + }, + + // unbind the click-to-hide function + unbindClick: function(event, that){ + // bind the ESC key to hide() function + $(document).off('keyup', function(event){ + if (event.keyCode == 27) { that.hide(); } + }) + // unbind the click anywhere to hide() function... + $('html').off('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').off('click', function(event){ + event.stopPropagation(); + }) + }, + + + // destroy + destroy : function(){ + this.hide(); + this.unbindClick(); + $('.modal').remove(); }, // adds and displays a new frame/window @@ -87,6 +127,7 @@ this.$footer = (this.$el).find('.modal-footer'); this.$buttons = (this.$el).find('.buttons'); this.$backdrop = (this.$el).find('.modal-backdrop'); + this.$notification = (this.$el).find('.notification-modal'); // append body this.$body.html(this.options.body); @@ -120,6 +161,47 @@ this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, + // hide buttons + hideButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).hide(); + }, + // show buttons + showButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).show(); + }, + + // show notification + showNotification : function(message, duration, type) { + // defaults + var duration = typeof duration !== 'undefined' ? duration : 1500; + // var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; + // var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + var bgColor; + var txtColor; + + if (type === 'error'){ + bgColor = '#f4e0e1'; + txtColor = '#a42732'; + // } else if (type === 'success'){ + } else { // success is default + bgColor = '#e1f4e0'; + txtColor = '#32a427'; + } + + var HTMLmessage = "<div class='notification-message' style='text-align:center; line-height:16px; '> " + message + " </div>"; + this.$notification.html("<div id='notification-bar' style='display:none; float: right; height: 16px; width:100%; background-color: " + bgColor + "; z-index: 100; color: " + txtColor + ";border-bottom: 1px solid " + txtColor + ";'>" + HTMLmessage + "</div>"); + + var self = this; + + /*animate the bar*/ + $('#notification-bar').slideDown(function() { + setTimeout(function() { + $('#notification-bar').slideUp(function() {self.$notification.html('');}); + }, duration); + }); + + }, + // returns scroll top for body element scrollTop: function() { @@ -139,7 +221,8 @@ '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + - '</div>' + + '<span class="notification-modal"></span>' + + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + '<div class="buttons" style="float: right;"></div>' + diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 static/scripts/libs/bootstrap.js --- a/static/scripts/libs/bootstrap.js +++ b/static/scripts/libs/bootstrap.js @@ -575,3 +575,158 @@ } }(window.jQuery); + +/* ======================================================================== + * Bootstrap: dropdown.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#dropdowns + * ======================================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== */ + + ++function ($) { "use strict"; + + // DROPDOWN CLASS DEFINITION + // ========================= + + var backdrop = '.dropdown-backdrop' + var toggle = '[data-toggle=dropdown]' + var Dropdown = function (element) { + var $el = $(element).on('click.bs.dropdown', this.toggle) + } + + Dropdown.prototype.toggle = function (e) { + var $this = $(this) + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) { + if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) { + // if mobile we we use a backdrop because click events don't delegate + $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus) + } + + $parent.trigger(e = $.Event('show.bs.dropdown')) + + if (e.isDefaultPrevented()) return + + $parent + .toggleClass('open') + .trigger('shown.bs.dropdown') + + $this.focus() + } + + return false + } + + Dropdown.prototype.keydown = function (e) { + if (!/(38|40|27)/.test(e.keyCode)) return + + var $this = $(this) + + e.preventDefault() + e.stopPropagation() + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + if (!isActive || (isActive && e.keyCode == 27)) { + if (e.which == 27) $parent.find(toggle).focus() + return $this.click() + } + + var $items = $('[role=menu] li:not(.divider):visible a', $parent) + + if (!$items.length) return + + var index = $items.index($items.filter(':focus')) + + if (e.keyCode == 38 && index > 0) index-- // up + if (e.keyCode == 40 && index < $items.length - 1) index++ // down + if (!~index) index=0 + + $items.eq(index).focus() + } + + function clearMenus() { + $(backdrop).remove() + $(toggle).each(function (e) { + var $parent = getParent($(this)) + if (!$parent.hasClass('open')) return + $parent.trigger(e = $.Event('hide.bs.dropdown')) + if (e.isDefaultPrevented()) return + $parent.removeClass('open').trigger('hidden.bs.dropdown') + }) + } + + function getParent($this) { + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && /#/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + var $parent = selector && $(selector) + + return $parent && $parent.length ? $parent : $this.parent() + } + + + // DROPDOWN PLUGIN DEFINITION + // ========================== + + var old = $.fn.dropdown + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('dropdown') + + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + // DROPDOWN NO CONFLICT + // ==================== + + $.fn.dropdown.noConflict = function () { + $.fn.dropdown = old + return this + } + + + // APPLY TO STANDARD DROPDOWN ELEMENTS + // =================================== + + $(document) + .on('click.bs.dropdown.data-api', clearMenus) + .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.bs.dropdown.data-api' , toggle, Dropdown.prototype.toggle) + .on('keydown.bs.dropdown.data-api', toggle + ', [role=menu]' , Dropdown.prototype.keydown) + +}(window.jQuery); \ No newline at end of file diff -r df88d6121d48b0b193d34445ce49916adf17a2d2 -r 181b293ea65936b7edb338bcbeac3bdea8e53063 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,6 +29,50 @@ background-color: @table-bg-accent; } + +tr.light td +{ + background-color: white; + color: black; +} +tr.light:hover td +{ + background-color: #f5f5f5; + color: #8389a1; +} +tr.dark td +{ + background-color: #8389a1; + color: white; +} +tr.dark:hover td +{ + background-color: #bbbfd0; + color: white; +} +a.dark:hover +{ + color: yellow; + // text-decoration: none; +} +a.dark +{ + color: white; + // text-decoration: none; +} +th.button_heading +{ + width: 7em; +} +div.library_breadcrumb{ + padding-top: 0.8em; + padding-bottom: 0.8em; +} +div.library_breadcrumb a:hover{ + color:green; +} + + img.expanderIcon { padding-right: 4px; } https://bitbucket.org/galaxy/galaxy-central/commits/17c16125da1a/ Changeset: 17c16125da1a User: martenson Date: 2013-12-11 17:22:38 Summary: Merged galaxy/galaxy-central into default Affected #: 4 files diff -r 181b293ea65936b7edb338bcbeac3bdea8e53063 -r 17c16125da1a00a53a020ff0fd84e5676dbabaf1 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1050,8 +1050,11 @@ Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), Column( "key", TrimmedString( 32 ), index=True, unique=True ) ) + # With the tables defined we can define the mappers and setup the # relationships between the model objects. +def simple_mapping( model, **kwds ): + mapper( model, model.table, properties=kwds ) mapper( model.Sample, model.Sample.table, @@ -1200,64 +1203,62 @@ mapper( model.ValidationError, model.ValidationError.table ) -mapper( model.HistoryDatasetAssociation, model.HistoryDatasetAssociation.table, - properties=dict( - dataset=relation( - model.Dataset, - primaryjoin=( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), - # .history defined in History mapper - copied_from_history_dataset_association=relation( - model.HistoryDatasetAssociation, - primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == model.HistoryDatasetAssociation.table.c.id ), - remote_side=[model.HistoryDatasetAssociation.table.c.id], - uselist=False ), - copied_to_history_dataset_associations=relation( - model.HistoryDatasetAssociation, - primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == model.HistoryDatasetAssociation.table.c.id ) ), - copied_from_library_dataset_dataset_association=relation( - model.LibraryDatasetDatasetAssociation, - primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == model.LibraryDatasetDatasetAssociation.table.c.id ), - uselist=False ), - copied_to_library_dataset_dataset_associations=relation( - model.LibraryDatasetDatasetAssociation, - primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == model.LibraryDatasetDatasetAssociation.table.c.id ) ), - implicitly_converted_datasets=relation( - model.ImplicitlyConvertedDatasetAssociation, - primaryjoin=( model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == model.HistoryDatasetAssociation.table.c.id ) ), - implicitly_converted_parent_datasets=relation( - model.ImplicitlyConvertedDatasetAssociation, - primaryjoin=( model.ImplicitlyConvertedDatasetAssociation.table.c.hda_id == model.HistoryDatasetAssociation.table.c.id ) ), - children=relation( - model.HistoryDatasetAssociation, - primaryjoin=( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ), - backref=backref( "parent", primaryjoin=( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ), remote_side=[model.HistoryDatasetAssociation.table.c.id], uselist=False ) ), - visible_children=relation( - model.HistoryDatasetAssociation, - primaryjoin=( ( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ) & ( model.HistoryDatasetAssociation.table.c.visible == True ) ) ), - tags=relation( model.HistoryDatasetAssociationTagAssociation, order_by=model.HistoryDatasetAssociationTagAssociation.table.c.id, backref='history_tag_associations' ), - annotations=relation( model.HistoryDatasetAssociationAnnotationAssociation, order_by=model.HistoryDatasetAssociationAnnotationAssociation.table.c.id, backref="hdas" ), - ratings=relation( model.HistoryDatasetAssociationRatingAssociation, order_by=model.HistoryDatasetAssociationRatingAssociation.table.c.id, backref="hdas" ) ) - ) +simple_mapping( model.HistoryDatasetAssociation, + dataset=relation( + model.Dataset, + primaryjoin=( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ), lazy=False ), + # .history defined in History mapper + copied_from_history_dataset_association=relation( + model.HistoryDatasetAssociation, + primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == model.HistoryDatasetAssociation.table.c.id ), + remote_side=[model.HistoryDatasetAssociation.table.c.id], + uselist=False ), + copied_to_history_dataset_associations=relation( + model.HistoryDatasetAssociation, + primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_history_dataset_association_id == model.HistoryDatasetAssociation.table.c.id ) ), + copied_from_library_dataset_dataset_association=relation( + model.LibraryDatasetDatasetAssociation, + primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == model.LibraryDatasetDatasetAssociation.table.c.id ), + uselist=False ), + copied_to_library_dataset_dataset_associations=relation( + model.LibraryDatasetDatasetAssociation, + primaryjoin=( model.HistoryDatasetAssociation.table.c.copied_from_library_dataset_dataset_association_id == model.LibraryDatasetDatasetAssociation.table.c.id ) ), + implicitly_converted_datasets=relation( + model.ImplicitlyConvertedDatasetAssociation, + primaryjoin=( model.ImplicitlyConvertedDatasetAssociation.table.c.hda_parent_id == model.HistoryDatasetAssociation.table.c.id ) ), + implicitly_converted_parent_datasets=relation( + model.ImplicitlyConvertedDatasetAssociation, + primaryjoin=( model.ImplicitlyConvertedDatasetAssociation.table.c.hda_id == model.HistoryDatasetAssociation.table.c.id ) ), + children=relation( + model.HistoryDatasetAssociation, + primaryjoin=( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ), + backref=backref( "parent", primaryjoin=( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ), remote_side=[model.HistoryDatasetAssociation.table.c.id], uselist=False ) ), + visible_children=relation( + model.HistoryDatasetAssociation, + primaryjoin=( ( model.HistoryDatasetAssociation.table.c.parent_id == model.HistoryDatasetAssociation.table.c.id ) & ( model.HistoryDatasetAssociation.table.c.visible == True ) ) ), + tags=relation( model.HistoryDatasetAssociationTagAssociation, order_by=model.HistoryDatasetAssociationTagAssociation.table.c.id, backref='history_tag_associations' ), + annotations=relation( model.HistoryDatasetAssociationAnnotationAssociation, order_by=model.HistoryDatasetAssociationAnnotationAssociation.table.c.id, backref="hdas" ), + ratings=relation( model.HistoryDatasetAssociationRatingAssociation, order_by=model.HistoryDatasetAssociationRatingAssociation.table.c.id, backref="hdas" ) +) -mapper( model.Dataset, model.Dataset.table, - properties=dict( - history_associations=relation( - model.HistoryDatasetAssociation, - primaryjoin=( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ) ), - active_history_associations=relation( - model.HistoryDatasetAssociation, - primaryjoin=( ( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ) & ( model.HistoryDatasetAssociation.table.c.deleted == False ) & ( model.HistoryDatasetAssociation.table.c.purged == False ) ) ), - purged_history_associations=relation( - model.HistoryDatasetAssociation, - primaryjoin=( ( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ) & ( model.HistoryDatasetAssociation.table.c.purged == True ) ) ), - library_associations=relation( - model.LibraryDatasetDatasetAssociation, - primaryjoin=( model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id ) ), - active_library_associations=relation( - model.LibraryDatasetDatasetAssociation, - primaryjoin=( ( model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( model.LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ), - tags=relation(model.DatasetTagAssociation, order_by=model.DatasetTagAssociation.table.c.id, backref='datasets') - ) ) +simple_mapping( model.Dataset, + history_associations=relation( + model.HistoryDatasetAssociation, + primaryjoin=( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ) ), + active_history_associations=relation( + model.HistoryDatasetAssociation, + primaryjoin=( ( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ) & ( model.HistoryDatasetAssociation.table.c.deleted == False ) & ( model.HistoryDatasetAssociation.table.c.purged == False ) ) ), + purged_history_associations=relation( + model.HistoryDatasetAssociation, + primaryjoin=( ( model.Dataset.table.c.id == model.HistoryDatasetAssociation.table.c.dataset_id ) & ( model.HistoryDatasetAssociation.table.c.purged == True ) ) ), + library_associations=relation( + model.LibraryDatasetDatasetAssociation, + primaryjoin=( model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id ) ), + active_library_associations=relation( + model.LibraryDatasetDatasetAssociation, + primaryjoin=( ( model.Dataset.table.c.id == model.LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( model.LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ), + tags=relation(model.DatasetTagAssociation, order_by=model.DatasetTagAssociation.table.c.id, backref='datasets') +) mapper( model.HistoryDatasetAssociationDisplayAtAuthorization, model.HistoryDatasetAssociationDisplayAtAuthorization.table, properties=dict( history_dataset_association = relation( model.HistoryDatasetAssociation ), @@ -1751,90 +1752,63 @@ ) ) # Tag tables. +simple_mapping( model.Tag, + children=relation(model.Tag, backref=backref( 'parent', remote_side=[model.Tag.table.c.id] ) ) +) -mapper( model.Tag, model.Tag.table, - properties=dict( children=relation(model.Tag, backref=backref( 'parent', remote_side=[model.Tag.table.c.id] ) ) - ) ) -mapper( model.HistoryTagAssociation, model.HistoryTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_histories"), user=relation( model.User ) ) - ) +def tag_mapping( tag_association_class, backref_name ): + simple_mapping( tag_association_class, tag=relation( model.Tag, backref=backref_name), user=relation( model.User ) ) -mapper( model.DatasetTagAssociation, model.DatasetTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_datasets"), user=relation( model.User ) ) - ) +tag_mapping( model.HistoryTagAssociation, "tagged_histories" ) -mapper( model.HistoryDatasetAssociationTagAssociation, model.HistoryDatasetAssociationTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_history_dataset_associations"), user=relation( model.User ) ) - ) +tag_mapping( model.DatasetTagAssociation, "tagged_datasets" ) -mapper( model.PageTagAssociation, model.PageTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_pages"), user=relation( model.User ) ) - ) +tag_mapping( model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations" ) -mapper( model.StoredWorkflowTagAssociation, model.StoredWorkflowTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_workflows"), user=relation( model.User ) ) - ) +tag_mapping( model.PageTagAssociation, "tagged_pages" ) -mapper( model.WorkflowStepTagAssociation, model.WorkflowStepTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_workflow_steps"), user=relation( model.User ) ) - ) +tag_mapping( model.StoredWorkflowTagAssociation, "tagged_workflows" ) -mapper( model.VisualizationTagAssociation, model.VisualizationTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_visualizations"), user=relation( model.User ) ) - ) +tag_mapping( model.WorkflowStepTagAssociation, "tagged_workflow_steps" ) -mapper( model.ToolTagAssociation, model.ToolTagAssociation.table, - properties=dict( tag=relation(model.Tag, backref="tagged_tools"), user=relation( model.User ) ) - ) +tag_mapping( model.VisualizationTagAssociation, "tagged_visualizations" ) + +tag_mapping( model.ToolTagAssociation, "tagged_tools" ) + # Annotation tables. +def annotation_mapping( annotation_class, **kwds ): + kwds = dict( [ (key, relation( value ) ) for key, value in kwds.iteritems() ] ) + simple_mapping( annotation_class, **dict(user=relation( model.User ), **kwds ) ) -mapper( model.HistoryAnnotationAssociation, model.HistoryAnnotationAssociation.table, - properties=dict( history=relation( model.History ), user=relation( model.User ) ) - ) +annotation_mapping( model.HistoryAnnotationAssociation, history=model.History ) -mapper( model.HistoryDatasetAssociationAnnotationAssociation, model.HistoryDatasetAssociationAnnotationAssociation.table, - properties=dict( hda=relation( model.HistoryDatasetAssociation ), user=relation( model.User ) ) - ) +annotation_mapping( model.HistoryDatasetAssociationAnnotationAssociation, hda=model.HistoryDatasetAssociation ) -mapper( model.StoredWorkflowAnnotationAssociation, model.StoredWorkflowAnnotationAssociation.table, - properties=dict( stored_workflow=relation( model.StoredWorkflow ), user=relation( model.User ) ) - ) +annotation_mapping( model.StoredWorkflowAnnotationAssociation, stored_workflow=model.StoredWorkflow ) -mapper( model.WorkflowStepAnnotationAssociation, model.WorkflowStepAnnotationAssociation.table, - properties=dict( workflow_step=relation( model.WorkflowStep ), user=relation( model.User ) ) - ) +annotation_mapping( model.WorkflowStepAnnotationAssociation, workflow_step=model.WorkflowStep ) -mapper( model.PageAnnotationAssociation, model.PageAnnotationAssociation.table, - properties=dict( page=relation( model.Page ), user=relation( model.User ) ) - ) +annotation_mapping( model.PageAnnotationAssociation, page=model.Page ) -mapper( model.VisualizationAnnotationAssociation, model.VisualizationAnnotationAssociation.table, - properties=dict( visualization=relation( model.Visualization ), user=relation( model.User ) ) - ) +annotation_mapping( model.VisualizationAnnotationAssociation, visualization=model.Visualization ) + # Rating tables. +def rating_mapping( rating_class, **kwds ): + kwds = dict( [ (key, relation( value ) ) for key, value in kwds.iteritems() ] ) + simple_mapping( rating_class, **dict(user=relation( model.User ), **kwds ) ) -mapper( model.HistoryRatingAssociation, model.HistoryRatingAssociation.table, - properties=dict( history=relation( model.History ), user=relation( model.User ) ) - ) +rating_mapping( model.HistoryRatingAssociation, history=model.History ) -mapper( model.HistoryDatasetAssociationRatingAssociation, model.HistoryDatasetAssociationRatingAssociation.table, - properties=dict( hda=relation( model.HistoryDatasetAssociation ), user=relation( model.User ) ) - ) +rating_mapping( model.HistoryDatasetAssociationRatingAssociation, hda=model.HistoryDatasetAssociation ) -mapper( model.StoredWorkflowRatingAssociation, model.StoredWorkflowRatingAssociation.table, - properties=dict( stored_workflow=relation( model.StoredWorkflow ), user=relation( model.User ) ) - ) +rating_mapping( model.StoredWorkflowRatingAssociation, stored_workflow=model.StoredWorkflow ) -mapper( model.PageRatingAssociation, model.PageRatingAssociation.table, - properties=dict( page=relation( model.Page ), user=relation( model.User ) ) - ) +rating_mapping( model.PageRatingAssociation, page=model.Page ) -mapper( model.VisualizationRatingAssociation, model.VisualizationRatingAssociation.table, - properties=dict( visualization=relation( model.Visualization ), user=relation( model.User ) ) - ) +rating_mapping( model.VisualizationRatingAssociation, visualizaiton=model.Visualization ) #Data Manager tables mapper( model.DataManagerHistoryAssociation, model.DataManagerHistoryAssociation.table, diff -r 181b293ea65936b7edb338bcbeac3bdea8e53063 -r 17c16125da1a00a53a020ff0fd84e5676dbabaf1 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -3003,10 +3003,10 @@ # Add link details. if link_details: # Add details for creating a hyperlink to the tool. - if not self.tool_type.startswith( 'data_source' ): - link = url_for( '/tool_runner', tool_id=self.id ) + if not isinstance( self, DataSourceTool ): + link = url_for( controller='tool_runner', tool_id=self.id ) else: - link = url_for( self.action, **self.get_static_param_values( trans ) ) + link = url_for( controller='tool_runner', action='data_source_redirect', tool_id=self.id ) # Basic information tool_dict.update( { 'link': link, diff -r 181b293ea65936b7edb338bcbeac3bdea8e53063 -r 17c16125da1a00a53a020ff0fd84e5676dbabaf1 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -6,6 +6,7 @@ import galaxy.util from galaxy import web from galaxy.tools import DefaultToolState +from galaxy.tools import DataSourceTool from galaxy.tools.actions import upload_common from galaxy.tools.parameters import params_to_incoming from galaxy.tools.parameters import visit_input_values @@ -233,6 +234,35 @@ **vars ) @web.expose + def data_source_redirect( self, trans, tool_id=None ): + """ + Redirects a user accessing a Data Source tool to its target action link. + This method will subvert mix-mode content blocking in several browsers when + accessing non-https data_source tools from an https galaxy server. + + Tested as working on Safari 7.0 and FireFox 26 + Subverting did not work on Chrome 31 + """ + if tool_id is None: + return trans.response.send_redirect( url_for( controller="root", action="welcome" ) ) + tool_version_select_field, tools, tool = self.__get_tool_components( tool_id, + tool_version=None, + get_loaded_tools_by_lineage=False, + set_selected=False ) + # No tool matching the tool id, display an error (shouldn't happen) + if not tool: + log.error( "data_source_redirect called with tool id '%s' but no such tool exists", tool_id ) + trans.log_event( "Tool id '%s' does not exist" % tool_id ) + trans.response.status = 404 + return "Tool '%s' does not exist, kwd=%s " % ( tool_id, kwd ) + + if isinstance( tool, DataSourceTool ): + link = url_for( tool.action, **tool.get_static_param_values( trans ) ) + else: + link = url_for( controller='tool_runner', tool_id=tool.id ) + return trans.response.send_redirect( link ) + + @web.expose def redirect( self, trans, redirect_url=None, **kwd ): if not redirect_url: return trans.show_error_message( "Required URL for redirection missing" ) diff -r 181b293ea65936b7edb338bcbeac3bdea8e53063 -r 17c16125da1a00a53a020ff0fd84e5676dbabaf1 test/unit/test_galaxy_mapping.py --- a/test/unit/test_galaxy_mapping.py +++ b/test/unit/test_galaxy_mapping.py @@ -3,10 +3,139 @@ class MappingTests( unittest.TestCase ): + + def test_annotations( self ): + model = self.model + + u = model.User( email="annotator(a)example.com", password="password" ) + self.persist( u ) + + def persist_and_check_annotation( annotation_class, **kwds ): + annotated_association = annotation_class() + annotated_association.annotation = "Test Annotation" + annotated_association.user = u + for key, value in kwds.iteritems(): + setattr(annotated_association, key, value) + self.persist( annotated_association ) + self.expunge() + stored_annotation = self.query( annotation_class ).all()[0] + assert stored_annotation.annotation == "Test Annotation" + assert stored_annotation.user.email == "annotator(a)example.com" + + sw = model.StoredWorkflow() + sw.user = u + self.persist( sw ) + persist_and_check_annotation( model.StoredWorkflowAnnotationAssociation, stored_workflow=sw ) + + workflow = model.Workflow() + workflow.stored_workflow = sw + self.persist( workflow ) + + ws = model.WorkflowStep() + ws.workflow = workflow + self.persist( ws ) + persist_and_check_annotation( model.WorkflowStepAnnotationAssociation, workflow_step=ws ) + + h = model.History( name="History for Annotation", user=u) + self.persist( h ) + persist_and_check_annotation( model.HistoryAnnotationAssociation, history=h ) + + d1 = model.HistoryDatasetAssociation( extension="txt", history=h, create_dataset=True, sa_session=model.session ) + self.persist( d1 ) + persist_and_check_annotation( model.HistoryDatasetAssociationAnnotationAssociation, hda=d1 ) + + page = model.Page() + page.user = u + self.persist( page ) + persist_and_check_annotation( model.PageAnnotationAssociation, page=page ) + + visualization = model.Visualization() + visualization.user = u + self.persist( visualization ) + persist_and_check_annotation( model.VisualizationAnnotationAssociation, visualization=visualization ) + + def test_ratings( self ): + model = self.model + + u = model.User( email="rater(a)example.com", password="password" ) + self.persist( u ) + + def persist_and_check_rating( rating_class, **kwds ): + rating_association = rating_class() + rating_association.rating = 5 + rating_association.user = u + for key, value in kwds.iteritems(): + setattr(rating_association, key, value) + self.persist( rating_association ) + self.expunge() + stored_annotation = self.query( rating_class ).all()[0] + assert stored_annotation.rating == 5 + assert stored_annotation.user.email == "rater(a)example.com" + + sw = model.StoredWorkflow() + sw.user = u + self.persist( sw ) + persist_and_check_rating( model.StoredWorkflowRatingAssociation, stored_workflow=sw ) + + h = model.History( name="History for Rating", user=u) + self.persist( h ) + persist_and_check_rating( model.HistoryRatingAssociation, history=h ) + + d1 = model.HistoryDatasetAssociation( extension="txt", history=h, create_dataset=True, sa_session=model.session ) + self.persist( d1 ) + persist_and_check_rating( model.HistoryDatasetAssociationRatingAssociation, hda=d1 ) + + page = model.Page() + page.user = u + self.persist( page ) + persist_and_check_rating( model.PageRatingAssociation, page=page ) + + visualization = model.Visualization() + visualization.user = u + self.persist( visualization ) + persist_and_check_rating( model.VisualizationRatingAssociation, visualization=visualization ) + + def test_tags( self ): + model = self.model + + my_tag = model.Tag(name="Test Tag") + u = model.User( email="tagger(a)example.com", password="password" ) + self.persist( my_tag, u ) + + def tag_and_test( taggable_object, tag_association_class, backref_name ): + assert len( getattr(self.query( model.Tag ).filter( model.Tag.name == "Test Tag" ).all()[0], backref_name) ) == 0 + + tag_association = tag_association_class() + tag_association.tag = my_tag + taggable_object.tags = [ tag_association ] + self.persist( tag_association, taggable_object ) + + assert len( getattr(self.query( model.Tag ).filter( model.Tag.name == "Test Tag" ).all()[0], backref_name) ) == 1 + + sw = model.StoredWorkflow() + sw.user = u + #self.persist( sw ) + tag_and_test( sw, model.StoredWorkflowTagAssociation, "tagged_workflows" ) + + h = model.History( name="History for Tagging", user=u) + tag_and_test( h, model.HistoryTagAssociation, "tagged_histories" ) + + d1 = model.HistoryDatasetAssociation( extension="txt", history=h, create_dataset=True, sa_session=model.session ) + tag_and_test( d1, model.HistoryDatasetAssociationTagAssociation, "tagged_history_dataset_associations" ) + + page = model.Page() + page.user = u + tag_and_test( page, model.PageTagAssociation, "tagged_pages" ) + + visualization = model.Visualization() + visualization.user = u + tag_and_test( visualization, model.VisualizationTagAssociation, "tagged_visualizations" ) + def test_basic( self ): - # Start the database and connect the mapping - model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True ) - assert model.engine is not None + model = self.model + + original_user_count = len( model.session.query( model.User ).all() ) + # Make some changes and commit them u = model.User( email="james(a)foo.bar.baz", password="password" ) # gs = model.GalaxySession() @@ -14,40 +143,64 @@ #h1.queries.append( model.Query( "h1->q1" ) ) #h1.queries.append( model.Query( "h1->q2" ) ) h2 = model.History( name=( "H" * 1024 ) ) - model.session.add_all( ( u, h1, h2 ) ) + self.persist( u, h1, h2 ) #q1 = model.Query( "h2->q1" ) metadata = dict( chromCol=1, startCol=2, endCol=3 ) d1 = model.HistoryDatasetAssociation( extension="interval", metadata=metadata, history=h2, create_dataset=True, sa_session=model.session ) #h2.queries.append( q1 ) #h2.queries.append( model.Query( "h2->q2" ) ) - model.session.add( ( d1 ) ) - model.session.flush() - model.session.expunge_all() + self.persist( d1 ) + # Check users = model.session.query( model.User ).all() - assert len( users ) == 1 - assert users[0].email == "james(a)foo.bar.baz" - assert users[0].password == "password" - assert len( users[0].histories ) == 1 - assert users[0].histories[0].name == "History 1" + assert len( users ) == original_user_count + 1 + user = [user for user in users if user.email == "james(a)foo.bar.baz"][0] + assert user.email == "james(a)foo.bar.baz" + assert user.password == "password" + assert len( user.histories ) == 1 + assert user.histories[0].name == "History 1" hists = model.session.query( model.History ).all() - assert hists[0].name == "History 1" - assert hists[1].name == ( "H" * 255 ) - assert hists[0].user == users[0] - assert hists[1].user is None - assert hists[1].datasets[0].metadata.chromCol == 1 + hist0 = [history for history in hists if history.name == "History 1"][0] + hist1 = [history for history in hists if history.name == "H" * 255][0] + assert hist0.name == "History 1" + assert hist1.name == ( "H" * 255 ) + assert hist0.user == user + assert hist1.user is None + assert hist1.datasets[0].metadata.chromCol == 1 # The filename test has moved to objecstore - #id = hists[1].datasets[0].id - #assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id ) + #id = hist1.datasets[0].id + #assert hist1.datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id ) # Do an update and check - hists[1].name = "History 2b" - model.session.flush() - model.session.expunge_all() + hist1.name = "History 2b" + self.expunge() hists = model.session.query( model.History ).all() - assert hists[0].name == "History 1" - assert hists[1].name == "History 2b" + hist0 = [history for history in hists if history.name == "History 1"][0] + hist1 = [history for history in hists if history.name == "History 2b"][0] + assert hist0.name == "History 1" + assert hist1.name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. + @classmethod + def setUpClass(cls): + # Start the database and connect the mapping + cls.model = mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True ) + assert cls.model.engine is not None + + @classmethod + def query( cls, type ): + return cls.model.session.query( type ) + + @classmethod + def persist(cls, *args): + for arg in args: + cls.model.session.add( arg ) + cls.expunge() + + @classmethod + def expunge(cls): + cls.model.session.flush() + cls.model.session.expunge_all() + def get_suite(): suite = unittest.TestSuite() https://bitbucket.org/galaxy/galaxy-central/commits/ff102054eec1/ Changeset: ff102054eec1 User: martenson Date: 2013-12-11 19:03:02 Summary: merge into default Affected #: 17 files diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1827,7 +1827,7 @@ class Library( object, Dictifiable ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" self.description = description @@ -1894,7 +1894,7 @@ return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description @@ -2060,6 +2060,7 @@ genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, + peek = ( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ), template_data = template_data ) if ldda.dataset.uuid is None: rval['uuid'] = None diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1852,8 +1852,9 @@ table = self.table trans = conn.begin() try: - next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() - table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + next_hid = current_hid + 1 + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) trans.commit() return next_hid except: diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a dataset. +API operations on the contents of a history dataset. """ from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,67 +11,122 @@ log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ + + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided as a separate object in response providing data for breadcrumb path building. """ - rval = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - - try: - decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + if ( folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + path_to_root = [] + def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + folder_container.append( dict( full_path = full_path ) ) + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every item in the folder and include its meta-data. + for content_item in self.load_folder_contents( trans, folder ): +# rval = content_item.to_dict() + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id +# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count ) ) - for content in traverse( folder ): - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.name, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - return rval + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + # Put the data in the container + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -0,0 +1,241 @@ +""" +API operations on the dataset from library. +""" +import glob +import logging +import operator +import os +import os.path +import string +import sys +import tarfile +import tempfile +import urllib +import urllib2 +import zipfile +from galaxy.security import Action +from galaxy import util, web +from galaxy.util.streamball import StreamBall +from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems + +import logging +log = logging.getLogger( __name__ ) + +# Test for available compression types +# tmpd = tempfile.mkdtemp() +# comptypes = [] +# for comptype in ( 'gz', 'bz2' ): +# tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype ) +# try: +# archive = tarfile.open( tmpf, 'w:' + comptype ) +# archive.close() +# comptypes.append( comptype ) +# except tarfile.CompressionError: +# log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +ziptype = '32' +# tmpf = os.path.join( tmpd, 'compression_test.zip' ) +# try: +# archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) +# archive.close() +# comptypes.append( 'zip' ) +# ziptype = '64' +# except RuntimeError: +# log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) +# except (TypeError, zipfile.LargeZipFile): +# # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped +# log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) +# comptypes.append( 'zip' ) +# try: +# os.unlink( tmpf ) +# except OSError: +# pass +# os.rmdir( tmpd ) + + + +class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + GET /api/libraries/datasets/{encoded_dataset_id} + Displays information about the dataset identified by the lda ID. + """ + # Get dataset. + try: + dataset = self.get_library_dataset( trans, id = id ) + except Exception, e: + return str( e ) + try: + # Default: return dataset as dict. + rval = dataset.to_dict() + except Exception, e: + rval = "Error in dataset API at listing contents: " + str( e ) + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 + + rval['id'] = trans.security.encode_id(rval['id']); + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + + return rval + + @web.expose + def download( self, trans, format, **kwd ): + """ + POST /api/libraries/datasets/download/{format} + POST data: ldda_ids = [] + Downloads dataset(s) in the requested format. + """ + lddas = [] +# is_admin = trans.user_is_admin() +# current_user_roles = trans.get_current_user_roles() + + datasets_to_download = kwd['ldda_ids%5B%5D'] + + if ( datasets_to_download != None ): + datasets_to_download = util.listify( datasets_to_download ) + for dataset_id in datasets_to_download: + try: + ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + assert not ldda.dataset.purged + lddas.append( ldda ) + except: + ldda = None + message += "Invalid library dataset id (%s) specified. " % str( dataset_id ) + + if format in [ 'zip','tgz','tbz' ]: + error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if format == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) + tmpf = os.path.join( tmpd, 'library_download.' + format ) + if ziptype == '64' and trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + elif ziptype == '64': + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + elif trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif format == 'tgz': + if trans.app.config.upstream_gzip: + archive = StreamBall( 'w|' ) + outext = 'tar' + else: + archive = StreamBall( 'w|gz' ) + outext = 'tgz' + elif format == 'tbz': + archive = StreamBall( 'w|bz2' ) + outext = 'tbz2' + except ( OSError, zipfile.BadZipfile ): + error = True + log.exception( "Unable to create archive for download" ) + message = "Unable to create archive for download, please report this error" + status = 'error' + except: + error = True + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + status = 'error' + if not error: + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: + continue + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: + # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set + except IOError: + error = True + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + archive.add( fpath,fname ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + message = "Unable to create archive for download, please report this error" + status = 'error' + continue + else: # simple case + try: + archive.add( ldda.dataset.file_name, path ) + except IOError: + error = True + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + message = "Unable to create archive for download, please report this error" + status = 'error' + if not error: + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + return archive.stream + elif format == 'uncompressed': + if len(lddas) != 1: + return 'Wrong request' + else: + single_dataset = lddas[0] + trans.response.set_content_type( single_dataset.get_mime() ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname + try: + return open( single_dataset.file_name ) + except: + return 'This dataset contains no content' + else: + return 'Wrong format'; \ No newline at end of file diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,9 +49,10 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) + item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] ) rval.append( item ) return rval @@ -131,6 +132,9 @@ rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,12 +46,6 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', - controller='admin_toolshed', - action='display_image_in_repository', - repository_id=None, - image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) @@ -75,22 +69,12 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # Add the web API + # ================ + # ===== API ===== + # ================ + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'content', 'contents', controller='history_contents', @@ -102,10 +86,6 @@ controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'user', 'users', controller='group_users', @@ -127,11 +107,6 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -141,7 +116,6 @@ _add_item_annotation_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - _add_item_provenance_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -171,6 +145,39 @@ #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) + # ======================= + # ===== LIBRARY API ===== + # ======================= + + # The /folders section is experimental at this point: + log.debug( "app.config.api_folders: %s" % app.config.api_folders ) + + webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) + webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', action='download', conditions=dict(method=["POST"]) ) + + webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) + webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) + + webapp.mapper.resource( 'content', 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", controller="histories", action="set_as_current", conditions=dict( method=["POST"] ) ) @@ -188,6 +195,18 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + # ==================== + # ===== TOOLSHED ===== + # ==================== + + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', @@ -201,6 +220,7 @@ path_prefix='/api', new={ 'install_repository_revision' : 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger @@ -221,7 +241,7 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking + # Close any pooled database connections before forking try: galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() except: diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -76,6 +76,17 @@ library_list_grid = LibraryListGrid() + + @web.expose + def list( self, trans, **kwd ): + params = util.Params( kwd ) + # define app configuration for generic mako template + app = { + 'jscript' : "galaxy.library" + } + # fill template + return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 static/scripts/galaxy.library.js --- /dev/null +++ b/static/scripts/galaxy.library.js @@ -0,0 +1,860 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +// global variables +var view = null; +var library_router = null; +var responses = []; + + +// load required libraries +// require([ +// // load js libraries +// 'utils/galaxy.css', +// ], function(css){ +// // load css +// css.load_file("static/style/library.css"); +// }); + +// dependencies +define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils"], function(mod_modal, mod_masthead, mod_utils) { + +// MMMMMMMMMMMMMMM +// === Models ==== +// MMMMMMMMMMMMMMM + + // LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries' + }); + + // LIBRARIES + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries', + model: Library + }); + + // ITEM + var Item = Backbone.Model.extend({ + urlRoot : '/api/libraries/datasets' + }) + + // FOLDER + var Folder = Backbone.Collection.extend({ + model: Item + }) + + // CONTAINER for folder contents (folders, items and metadata). + var FolderContainer = Backbone.Model.extend({ + defaults : { + folder : new Folder(), + full_path : "unknown", + urlRoot : "/api/folders/", + id : "unknown" + }, + parse : function(obj) { + this.full_path = obj[0].full_path; + // update the inner collection + this.get("folder").reset(obj[1].folder_contents); + return obj; + } + }) + + // HISTORY ITEM + var HistoryItem = Backbone.Model.extend({ + urlRoot : '/api/histories/' + }); + + // HISTORY + var GalaxyHistory = Backbone.Model.extend({ + url : '/api/histories/' + }); + + // HISTORIES + var GalaxyHistories = Backbone.Collection.extend({ + url : '/api/histories', + model : GalaxyHistory + }); + + //ROUTER + var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content", + "folders/:folder_id/download/:format" : "download" + } + }); + + +// MMMMMMMMMMMMMM +// === VIEWS ==== +// MMMMMMMMMMMMMM + +// galaxy folder +var FolderContentView = Backbone.View.extend({ + // main element definition + el : '#center', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // last selected history in modal for UX + lastSelectedHistory: '', + // self modal + modal : null, + // loaded folders + folders : null, + + // initialize + initialize : function(){ + this.folders = []; + this.queue = jQuery.Deferred(); + this.queue.resolve(); + }, + +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + // set up + templateFolder : function (){ + var tmpl_array = []; + + // CONTAINER + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-icon-plus"></span><span class="fa fa-icon-folder-close"></span> folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-icon-external-link"></span> to history</button>'); + + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); + tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-icon-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('</div>'); + + // BREADCRUMBS + tmpl_array.push('<div class="library_breadcrumb">'); + tmpl_array.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> '); + tmpl_array.push('<% _.each(path, function(path_item) { %>'); + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<span title="You are in this folder"><%- path_item[1] %></span>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + tmpl_array.push('</div>'); + + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th class="button_heading">view</th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-arrow-up"></span> .. go up</td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- content_item.get("name") %>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-eye-open"></span> details'); + tmpl_array.push(' </button>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + templateDatasetModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<div id="dataset_info_modal">'); + tmpl_array.push(' <table class="table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' </table>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + + templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + // convert size to nice string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + +// MMMMMMMMMMMMMMM +// === EVENTS ==== +// MMMMMMMMMMMMMMM + + // event binding + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClicked', + 'click #toolbtn_bulk_import' : 'modalBulkImport', + 'click #toolbtn_dl' : 'bulkDownload', + 'click .library-dataset' : 'showDatasetDetails', + 'click #toolbtn_create_folder' : 'createFolderModal', + 'click .btn_open_folder' : 'navigateToFolder' + }, + + //render the folder view + render: function (options) { + //hack to show scrollbars + $("#center").css('overflow','auto'); + + view = this; + var that = this; + + var folderContainer = new FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + + folderContainer.fetch({ + success: function (container) { + + // prepare nice size strings + for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { + var model = folderContainer.attributes.folder.models[i] + if (model.get('type') === 'file'){ + model.set('readable_size', that.size_to_string(model.get('file_size'))) + } + }; + + // find the upper id + var path = folderContainer.full_path; + var upper_folder_id; + if (path.length === 1){ // library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } + + var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); + // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); + that.$el.html(template); + } + }) + }, + + // handles the click on 'open' and 'upper' folder icons + navigateToFolder : function(event){ + var folder_id = $(event.target).attr('data-id'); + if (typeof folder_id === 'undefined') { + return false; + } else if (folder_id === '0'){ + library_router.navigate('#', {trigger: true, replace: true}); + } else { + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } + }, + + //show modal with current dataset info + showDatasetDetails : function(event){ + // prevent default + event.preventDefault(); + +//TODO check whether we already have the data + + //load the ID of the row + var id = $(event.target).parent().parent().attr('id'); + + //create new item + var item = new Item(); + var histories = new GalaxyHistories(); + item.id = id; + var self = this; + + //fetch the dataset info + item.fetch({ + success: function (item) { +// TODO can render here already + //fetch user histories for import purposes + histories.fetch({ + success: function (histories){self.renderModalAfterFetch(item, histories)} + }); + } + }); + }, + + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + this.modal = null; + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal({ + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() { self.importCurrentIntoHistory() }, + 'Download' : function() { self.downloadCurrent() }, + 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data + } + }); + $(".peek").html(item.get("peek")); + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + + // show the prepared modal + this.modal.show(); + }, + + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + // we assume the view is existent + folderContentView.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + self.modal.showNotification('Dataset imported', 3000, 'success'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; + // Iterate each checkbox + $(':checkbox').each(function () { this.checked = selected; }); + this.showTools(); + }, + + // click checkbox on folder click + selectClicked : function (event) { + var checkbox = $("#" + event.target.parentElement.id).find(':checkbox') + if (checkbox[0] != undefined) { + if (checkbox[0].checked){ + checkbox[0].checked = ''; + // $(event.target.parentElement).css('background-color', '').css('color', ''); + $(event.target.parentElement).removeClass('dark'); + $(event.target.parentElement).find('a').removeClass('dark'); + $(event.target.parentElement).addClass('light'); + $(event.target.parentElement).find('a').addClass('light'); + } else { + checkbox[0].checked = 'selected'; + $(event.target.parentElement).removeClass('light'); + $(event.target.parentElement).find('a').removeClass('light'); + $(event.target.parentElement).addClass('dark'); + $(event.target.parentElement).find('a').addClass('dark'); + // $(event.target.parentElement).css('background-color', '#8389a1').css('color', 'white'); + } + } + this.showTools(); + }, + + // show toolbar in case something is selected + showTools : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length > 0){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } else { + $('#toolbtn_bulk_import').hide(); + $('#toolbtn_dl').hide(); + } + + }, + + // show bulk import modal + modalBulkImport : function(){ + var self = this; + // fetch histories + var histories = new GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); + self.modal = new mod_modal.GalaxyModal({ + title : 'Import into History', + body : history_modal_tmpl, + buttons : { + 'Import' : function() {self.importAllIntoHistory()}, + 'Close' : function() {self.modal.hide(); $('.modal').remove(); self.modal = null;} + } + }); + // show the prepared modal + self.modal.show(); + } + }); + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + }; + + // call the recursive function to call ajax one after each other + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + self.modal.showNotification('All datasets imported', 3000, 'success'); + // enable button again + self.modal.enableButton('Import'); + return + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + responses.push(a1); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + // progress bar + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + }; + }, + + // shows modal for creating folder + createFolderModal: function(){ + alert('creating folder'); + } + + }); + +// galaxy library view +var GalaxyLibraryview = Backbone.View.extend({ + el: '#center', + + events: { + 'click #create_new_library_btn' : 'show_library_modal' + }, + + // initialize + initialize : function(){ + }, + + // template + template_library_list : function (){ + tmpl_array = []; + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); + + tmpl_array.push(''); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); + tmpl_array.push('<table class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>description</th>'); + tmpl_array.push(' <th>synopsis</th> '); + tmpl_array.push(' <th>model type</th> '); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(libraries, function(library) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- library.get("name") %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + + // render + render: function () { + //hack to show scrollbars + $("#center").css('overflow','auto'); + var that = this; + // if (typeof libraries === "undefined") { + libraries = new Libraries(); + // } + libraries.fetch({ + success: function (libraries) { + var template = _.template(that.template_library_list(), { libraries : libraries.models }); + that.$el.html(template); + } + }) + }, + + // own modal + modal : null, + + // show/hide create library modal + show_library_modal : function (event){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + this.modal = new mod_modal.GalaxyModal( + { + title : 'Create New Library', + body : this.template_new_library(), + buttons : { + 'Create' : function() {self.create_new_library_event()}, + 'Close' : function() {self.modal.hide()} + } + }); + + // show prepared modal + this.modal.show(); + }, + + // create the new library from modal + create_new_library_event: function(){ + var libraryDetails = this.serialize_new_library(); + var valid = this.validate_new_library(libraryDetails); + var library = new Library(); + var self = this; + library.save(libraryDetails, { + success: function (library) { + self.modal.hide(); + self.clear_library_modal(); + self.render(); + }, + error: function(){ + self.modal.showNotification('An error occured', 5000, 'error'); + } + }); + return false; + }, + + // clear the library modal once saved + clear_library_modal : function(){ + $("input[name='Name']").val(''); + $("input[name='Description']").val(''); + $("input[name='Synopsis']").val(''); + }, + + // serialize data from the form + serialize_new_library : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val(), + synopsis: $("input[name='Synopsis']").val() + }; + }, + + validate_new_library: function(library){ + + }, + + + // template for new library modal + template_new_library: function() + { + tmpl_array = []; + + tmpl_array.push('<div id="new_library_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + } +}); + +// galaxy library wrapper View +var GalaxyLibrary = Backbone.View.extend({ + folderContentView : null, + galaxyLibraryview : null, + initialize : function(){ + + folderContentView = new FolderContentView(); + galaxyLibraryview = new GalaxyLibraryview(); + + library_router = new LibraryRouter(); + + library_router.on('route:libraries', function() { + // render libraries list + galaxyLibraryview.render(); + }); + + library_router.on('route:folder_content', function(id) { + // render folder's contents + folderContentView.render({id: id}); + }); + + library_router.on('route:download', function(folder_id, format) { + // send download stream + if (typeof folderContentView === 'undefined'){ + alert('you cant touch this!'); + // } else if (folderContentView.modal !== null){ + // folderContentView.download(folder_id, format); + } else if ($('#center').find(':checked').length === 0) { // coming from outside of the library app + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + // TODO show message of redirection + } else { + folderContentView.download(folder_id, format); + library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + + }); + +Backbone.history.start(); + +return this +} +}); + +// return +return { + GalaxyApp: GalaxyLibrary +}; + +}); diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -57,7 +57,12 @@ tab_shared.add({ title : "Data Libraries", - content : "library/index", + content : "library/index" + }); + + tab_shared.add({ + title : "New Libraries", + content : "library/list", divider : true }); diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -1,6 +1,3 @@ -/* - galaxy modal -*/ // dependencies define([], function() { @@ -25,8 +22,51 @@ // initialize initialize : function(options) { + self = this; if (options) this.create(options); + + this.bindClick(event, self); + }, + + // bind the click-to-hide function + bindClick: function(event, that) { + // bind the ESC key to hide() function + $(document).on('keyup', function(event){ + if (event.keyCode == 27) { self.hide(); } + }) + // bind the click anywhere to hide() function... + $('html').on('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').on('click', function(event){ + event.stopPropagation(); + }) + }, + + // unbind the click-to-hide function + unbindClick: function(event, that){ + // bind the ESC key to hide() function + $(document).off('keyup', function(event){ + if (event.keyCode == 27) { that.hide(); } + }) + // unbind the click anywhere to hide() function... + $('html').off('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').off('click', function(event){ + event.stopPropagation(); + }) + }, + + + // destroy + destroy : function(){ + this.hide(); + this.unbindClick(); + $('.modal').remove(); }, // adds and displays a new frame/window @@ -87,6 +127,7 @@ this.$footer = (this.$el).find('.modal-footer'); this.$buttons = (this.$el).find('.buttons'); this.$backdrop = (this.$el).find('.modal-backdrop'); + this.$notification = (this.$el).find('.notification-modal'); // append body this.$body.html(this.options.body); @@ -120,6 +161,47 @@ this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, + // hide buttons + hideButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).hide(); + }, + // show buttons + showButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).show(); + }, + + // show notification + showNotification : function(message, duration, type) { + // defaults + var duration = typeof duration !== 'undefined' ? duration : 1500; + // var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; + // var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + var bgColor; + var txtColor; + + if (type === 'error'){ + bgColor = '#f4e0e1'; + txtColor = '#a42732'; + // } else if (type === 'success'){ + } else { // success is default + bgColor = '#e1f4e0'; + txtColor = '#32a427'; + } + + var HTMLmessage = "<div class='notification-message' style='text-align:center; line-height:16px; '> " + message + " </div>"; + this.$notification.html("<div id='notification-bar' style='display:none; float: right; height: 16px; width:100%; background-color: " + bgColor + "; z-index: 100; color: " + txtColor + ";border-bottom: 1px solid " + txtColor + ";'>" + HTMLmessage + "</div>"); + + var self = this; + + /*animate the bar*/ + $('#notification-bar').slideDown(function() { + setTimeout(function() { + $('#notification-bar').slideUp(function() {self.$notification.html('');}); + }, duration); + }); + + }, + // returns scroll top for body element scrollTop: function() { @@ -139,7 +221,8 @@ '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + - '</div>' + + '<span class="notification-modal"></span>' + + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + '<div class="buttons" style="float: right;"></div>' + diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 static/scripts/libs/bootstrap.js --- a/static/scripts/libs/bootstrap.js +++ b/static/scripts/libs/bootstrap.js @@ -575,3 +575,158 @@ } }(window.jQuery); + +/* ======================================================================== + * Bootstrap: dropdown.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#dropdowns + * ======================================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== */ + + ++function ($) { "use strict"; + + // DROPDOWN CLASS DEFINITION + // ========================= + + var backdrop = '.dropdown-backdrop' + var toggle = '[data-toggle=dropdown]' + var Dropdown = function (element) { + var $el = $(element).on('click.bs.dropdown', this.toggle) + } + + Dropdown.prototype.toggle = function (e) { + var $this = $(this) + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) { + if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) { + // if mobile we we use a backdrop because click events don't delegate + $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus) + } + + $parent.trigger(e = $.Event('show.bs.dropdown')) + + if (e.isDefaultPrevented()) return + + $parent + .toggleClass('open') + .trigger('shown.bs.dropdown') + + $this.focus() + } + + return false + } + + Dropdown.prototype.keydown = function (e) { + if (!/(38|40|27)/.test(e.keyCode)) return + + var $this = $(this) + + e.preventDefault() + e.stopPropagation() + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + if (!isActive || (isActive && e.keyCode == 27)) { + if (e.which == 27) $parent.find(toggle).focus() + return $this.click() + } + + var $items = $('[role=menu] li:not(.divider):visible a', $parent) + + if (!$items.length) return + + var index = $items.index($items.filter(':focus')) + + if (e.keyCode == 38 && index > 0) index-- // up + if (e.keyCode == 40 && index < $items.length - 1) index++ // down + if (!~index) index=0 + + $items.eq(index).focus() + } + + function clearMenus() { + $(backdrop).remove() + $(toggle).each(function (e) { + var $parent = getParent($(this)) + if (!$parent.hasClass('open')) return + $parent.trigger(e = $.Event('hide.bs.dropdown')) + if (e.isDefaultPrevented()) return + $parent.removeClass('open').trigger('hidden.bs.dropdown') + }) + } + + function getParent($this) { + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && /#/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + var $parent = selector && $(selector) + + return $parent && $parent.length ? $parent : $this.parent() + } + + + // DROPDOWN PLUGIN DEFINITION + // ========================== + + var old = $.fn.dropdown + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('dropdown') + + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + // DROPDOWN NO CONFLICT + // ==================== + + $.fn.dropdown.noConflict = function () { + $.fn.dropdown = old + return this + } + + + // APPLY TO STANDARD DROPDOWN ELEMENTS + // =================================== + + $(document) + .on('click.bs.dropdown.data-api', clearMenus) + .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.bs.dropdown.data-api' , toggle, Dropdown.prototype.toggle) + .on('keydown.bs.dropdown.data-api', toggle + ', [role=menu]' , Dropdown.prototype.keydown) + +}(window.jQuery); \ No newline at end of file diff -r 206055969b7cedcbfcac36c19428b9547cd5cb5d -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 static/style/src/less/library.less --- a/static/style/src/less/library.less +++ b/static/style/src/less/library.less @@ -29,6 +29,50 @@ background-color: @table-bg-accent; } + +tr.light td +{ + background-color: white; + color: black; +} +tr.light:hover td +{ + background-color: #f5f5f5; + color: #8389a1; +} +tr.dark td +{ + background-color: #8389a1; + color: white; +} +tr.dark:hover td +{ + background-color: #bbbfd0; + color: white; +} +a.dark:hover +{ + color: yellow; + // text-decoration: none; +} +a.dark +{ + color: white; + // text-decoration: none; +} +th.button_heading +{ + width: 7em; +} +div.library_breadcrumb{ + padding-top: 0.8em; + padding-bottom: 0.8em; +} +div.library_breadcrumb a:hover{ + color:green; +} + + img.expanderIcon { padding-right: 4px; } https://bitbucket.org/galaxy/galaxy-central/commits/caba1617084b/ Changeset: caba1617084b User: martenson Date: 2013-12-11 20:24:58 Summary: cleaning zip logic, jmchilton pull rq #208 Affected #: 1 file diff -r ff102054eec10f7bd1ad9f9663e1884dc7c75223 -r caba1617084b4a0d38f1ebce970dda675755cd1d lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -21,42 +21,6 @@ import logging log = logging.getLogger( __name__ ) -# Test for available compression types -# tmpd = tempfile.mkdtemp() -# comptypes = [] -# for comptype in ( 'gz', 'bz2' ): -# tmpf = os.path.join( tmpd, 'compression_test.tar.' + comptype ) -# try: -# archive = tarfile.open( tmpf, 'w:' + comptype ) -# archive.close() -# comptypes.append( comptype ) -# except tarfile.CompressionError: -# log.exception( "Compression error when testing %s compression. This option will be disabled for library downloads." % comptype ) -# try: -# os.unlink( tmpf ) -# except OSError: -# pass -ziptype = '32' -# tmpf = os.path.join( tmpd, 'compression_test.zip' ) -# try: -# archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) -# archive.close() -# comptypes.append( 'zip' ) -# ziptype = '64' -# except RuntimeError: -# log.exception( "Compression error when testing zip compression. This option will be disabled for library downloads." ) -# except (TypeError, zipfile.LargeZipFile): -# # ZIP64 is only in Python2.5+. Remove TypeError when 2.4 support is dropped -# log.warning( 'Max zip file size is 2GB, ZIP64 not supported' ) -# comptypes.append( 'zip' ) -# try: -# os.unlink( tmpf ) -# except OSError: -# pass -# os.rmdir( tmpd ) - - - class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): @web.expose_api @@ -77,13 +41,13 @@ rval = "Error in dataset API at listing contents: " + str( e ) log.error( rval + ": %s" % str(e), exc_info=True ) trans.response.status = 500 - + rval['id'] = trans.security.encode_id(rval['id']); rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) - + return rval - + @web.expose def download( self, trans, format, **kwd ): """ @@ -94,9 +58,9 @@ lddas = [] # is_admin = trans.user_is_admin() # current_user_roles = trans.get_current_user_roles() - + datasets_to_download = kwd['ldda_ids%5B%5D'] - + if ( datasets_to_download != None ): datasets_to_download = util.listify( datasets_to_download ) for dataset_id in datasets_to_download: @@ -107,7 +71,7 @@ except: ldda = None message += "Invalid library dataset id (%s) specified. " % str( dataset_id ) - + if format in [ 'zip','tgz','tbz' ]: error = False killme = string.punctuation + string.whitespace @@ -119,14 +83,10 @@ tmpd = tempfile.mkdtemp() util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) tmpf = os.path.join( tmpd, 'library_download.' + format ) - if ziptype == '64' and trans.app.config.upstream_gzip: + if trans.app.config.upstream_gzip: archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) - elif ziptype == '64': + else: archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) - elif trans.app.config.upstream_gzip: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED ) - else: - archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED ) archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) elif format == 'tgz': if trans.app.config.upstream_gzip: @@ -238,4 +198,4 @@ except: return 'This dataset contains no content' else: - return 'Wrong format'; \ No newline at end of file + return 'Wrong format'; https://bitbucket.org/galaxy/galaxy-central/commits/c653272fdbb3/ Changeset: c653272fdbb3 User: martenson Date: 2013-12-11 21:31:20 Summary: trimming whitespace, import library.less into base.less Affected #: 2 files diff -r caba1617084b4a0d38f1ebce970dda675755cd1d -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -7,16 +7,6 @@ var library_router = null; var responses = []; - -// load required libraries -// require([ -// // load js libraries -// 'utils/galaxy.css', -// ], function(css){ -// // load css -// css.load_file("static/style/library.css"); -// }); - // dependencies define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils"], function(mod_modal, mod_masthead, mod_utils) { @@ -42,7 +32,7 @@ // FOLDER var Folder = Backbone.Collection.extend({ - model: Item + model: Item }) // CONTAINER for folder contents (folders, items and metadata). @@ -78,7 +68,7 @@ }); //ROUTER - var LibraryRouter = Backbone.Router.extend({ + var LibraryRouter = Backbone.Router.extend({ routes: { "" : "libraries", "folders/:id" : "folder_content", @@ -98,26 +88,26 @@ // progress percentage progress: 0, // progress rate per one item - progressStep: 1, + progressStep: 1, // last selected history in modal for UX lastSelectedHistory: '', // self modal modal : null, // loaded folders folders : null, - + // initialize initialize : function(){ this.folders = []; this.queue = jQuery.Deferred(); this.queue.resolve(); - }, + }, // MMMMMMMMMMMMMMMMMM // === TEMPLATES ==== // MMMMMMMMMMMMMMMMMM - // set up + // set up templateFolder : function (){ var tmpl_array = []; @@ -127,12 +117,12 @@ // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); - tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-icon-plus"></span><span class="fa fa-icon-folder-close"></span> folder</button>'); - tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-icon-external-link"></span> to history</button>'); - + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); - tmpl_array.push(' <span class="fa fa-icon-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); tmpl_array.push(' </button>'); tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); @@ -166,20 +156,20 @@ tmpl_array.push(' <th>date</th>'); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-icon-arrow-up"></span> .. go up</td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' <td></td>'); - tmpl_array.push(' </tr>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-arrow-up"></span> .. go up</td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); tmpl_array.push(' <% _.each(items, function(content_item) { %>'); tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder tmpl_array.push(' <td></td>'); tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>'); tmpl_array.push(' <td><%- content_item.get("name") %>'); tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder tmpl_array.push(' <span class="muted">(empty folder)</span>'); @@ -191,7 +181,7 @@ tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); tmpl_array.push(' <td>'); tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-icon-eye-open"></span> details'); + tmpl_array.push(' <span class="fa fa-eye"></span> details'); tmpl_array.push(' </button>'); tmpl_array.push(' </td>'); tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset @@ -241,11 +231,11 @@ tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <th scope="row">Comment Lines</th>'); - tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); - tmpl_array.push(' <% } else { %>'); - tmpl_array.push(' <td scope="row">unknown</td>'); - tmpl_array.push(' <% } %>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); tmpl_array.push(' </tr>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <th scope="row">Number of Columns</th>'); @@ -280,7 +270,7 @@ tmpl_array.push('</span>'); return tmpl_array.join(''); - }, + }, templateBulkImportInModal : function(){ var tmpl_array = []; @@ -295,7 +285,7 @@ tmpl_array.push('</span>'); return tmpl_array.join(''); - }, + }, // convert size to nice string size_to_string : function (size) @@ -380,12 +370,12 @@ showDatasetDetails : function(event){ // prevent default event.preventDefault(); - + //TODO check whether we already have the data //load the ID of the row var id = $(event.target).parent().parent().attr('id'); - + //create new item var item = new Item(); var histories = new GalaxyHistories(); @@ -474,12 +464,12 @@ self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); //enable the buttons self.modal.enableButton('Import'); - self.modal.enableButton('Download'); + self.modal.enableButton('Download'); } }); }, - // select all datasets + // select all datasets selectAll : function (event) { var selected = event.target.checked; // Iterate each checkbox @@ -562,7 +552,7 @@ }); var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); - + // init the progress bar var progressStep = 100 / dataset_ids.length; this.initProgress(progressStep); @@ -610,7 +600,7 @@ $('.completion_span').text(txt_representation); }, - // progress bar + // progress bar templateProgressBar : function (){ var tmpl_array = []; @@ -644,14 +634,14 @@ // create hidden form and submit through POST to initialize download processDownload: function(url, data, method){ //url and data options required - if( url && data ){ + if( url && data ){ //data can be string of parameters or array/object data = typeof data == 'string' ? data : $.param(data); //split params into form inputs var inputs = ''; - $.each(data.split('&'), function(){ + $.each(data.split('&'), function(){ var pair = this.split('='); - inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; }); //send request $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') @@ -676,7 +666,7 @@ // initialize initialize : function(){ - }, + }, // template template_library_list : function (){ @@ -685,7 +675,7 @@ tmpl_array.push(''); tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); - tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary icon-file ">New Library</a>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); tmpl_array.push('<table class="table table-condensed">'); tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); @@ -698,7 +688,7 @@ tmpl_array.push(' <% _.each(libraries, function(library) { %>'); tmpl_array.push(' <tr>'); tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); - tmpl_array.push(' <span class="fa fa-icon-folder-open"></span> browse</td>'); + tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>'); tmpl_array.push(' <td><%- library.get("name") %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); @@ -707,7 +697,7 @@ tmpl_array.push(' <% }); %>'); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); - + tmpl_array.push('</div>'); return tmpl_array.join(''); }, @@ -735,7 +725,7 @@ show_library_modal : function (event){ event.preventDefault(); event.stopPropagation(); - + // create modal var self = this; this.modal = new mod_modal.GalaxyModal( @@ -747,7 +737,7 @@ 'Close' : function() {self.modal.hide()} } }); - + // show prepared modal this.modal.show(); }, @@ -828,7 +818,7 @@ library_router.on('route:folder_content', function(id) { // render folder's contents folderContentView.render({id: id}); - }); + }); library_router.on('route:download', function(folder_id, format) { // send download stream @@ -844,9 +834,9 @@ library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); } - }); + }); -Backbone.history.start(); +Backbone.history.start(); return this } diff -r caba1617084b4a0d38f1ebce970dda675755cd1d -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -23,6 +23,7 @@ // galaxy sub-components @import "frame.less"; @import "upload.less"; +@import "library.less"; // Mixins https://bitbucket.org/galaxy/galaxy-central/commits/267dcfd58a60/ Changeset: 267dcfd58a60 User: martenson Date: 2013-12-12 20:21:09 Summary: added library notifications, toaster, can be used outside of libraries as require.js module Affected #: 7 files diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -8,7 +8,7 @@ var responses = []; // dependencies -define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils"], function(mod_modal, mod_masthead, mod_utils) { +define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "libs/toastr"], function(mod_modal, mod_masthead, mod_utils, mod_toastr) { // MMMMMMMMMMMMMMM // === Models ==== @@ -706,18 +706,35 @@ render: function () { //hack to show scrollbars $("#center").css('overflow','auto'); + var that = this; - // if (typeof libraries === "undefined") { - libraries = new Libraries(); - // } + libraries = new Libraries(); + libraries.fetch({ success: function (libraries) { var template = _.template(that.template_library_list(), { libraries : libraries.models }); that.$el.html(template); - } + }, + error: function(model, response){ + if (response.statusCode().status === 403){ + //show notification + // var toast = mod_toastr; + mod_toastr.error('Please log in first. Redirecting to login page in 3s.'); + setTimeout(that.redirectToLogin, 3000); + } else { + library_router.navigate('#', {trigger: true, replace: true}); + } + } }) }, + redirectToSplash: function(){ + window.location = '../'; + }, + redirectToLogin: function(){ + window.location = '/user/login'; + }, + // own modal modal : null, diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -172,10 +172,7 @@ // show notification showNotification : function(message, duration, type) { - // defaults - var duration = typeof duration !== 'undefined' ? duration : 1500; - // var bgColor = typeof bgColor !== 'undefined' ? bgColor : "#F4E0E1"; - // var txtColor = typeof txtColor !== 'undefined' ? txtColor : "#A42732"; + var duration = typeof duration !== 'undefined' ? duration : 3000; var bgColor; var txtColor; diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/scripts/libs/toastr.js --- /dev/null +++ b/static/scripts/libs/toastr.js @@ -0,0 +1,307 @@ +/* + * Toastr + * Version 2.0.1 + * Copyright 2012 John Papa and Hans Fjällemark. + * All Rights Reserved. + * Use, reproduction, distribution, and modification of this code is subject to the terms and + * conditions of the MIT license, available at http://www.opensource.org/licenses/mit-license.php + * + * Author: John Papa and Hans Fjällemark + * Project: https://github.com/CodeSeven/toastr + */ +; (function (define) { + define([], function () { + var $ = jQuery; + return (function () { + var version = '2.0.1'; + var $container; + var listener; + var toastId = 0; + var toastType = { + error: 'error', + info: 'info', + success: 'success', + warning: 'warning' + }; + + var toastr = { + clear: clear, + error: error, + getContainer: getContainer, + info: info, + options: {}, + subscribe: subscribe, + success: success, + version: version, + warning: warning + }; + + return toastr; + + //#region Accessible Methods + function error(message, title, optionsOverride) { + return notify({ + type: toastType.error, + iconClass: getOptions().iconClasses.error, + message: message, + optionsOverride: optionsOverride, + title: title + }); + } + + function info(message, title, optionsOverride) { + return notify({ + type: toastType.info, + iconClass: getOptions().iconClasses.info, + message: message, + optionsOverride: optionsOverride, + title: title + }); + } + + function subscribe(callback) { + listener = callback; + } + + function success(message, title, optionsOverride) { + return notify({ + type: toastType.success, + iconClass: getOptions().iconClasses.success, + message: message, + optionsOverride: optionsOverride, + title: title + }); + } + + function warning(message, title, optionsOverride) { + return notify({ + type: toastType.warning, + iconClass: getOptions().iconClasses.warning, + message: message, + optionsOverride: optionsOverride, + title: title + }); + } + + function clear($toastElement) { + var options = getOptions(); + if (!$container) { getContainer(options); } + if ($toastElement && $(':focus', $toastElement).length === 0) { + $toastElement[options.hideMethod]({ + duration: options.hideDuration, + easing: options.hideEasing, + complete: function () { removeToast($toastElement); } + }); + return; + } + if ($container.children().length) { + $container[options.hideMethod]({ + duration: options.hideDuration, + easing: options.hideEasing, + complete: function () { $container.remove(); } + }); + } + } + //#endregion + + //#region Internal Methods + + function getDefaults() { + return { + tapToDismiss: true, + toastClass: 'toast', + containerId: 'toast-container', + debug: false, + + showMethod: 'fadeIn', //fadeIn, slideDown, and show are built into jQuery + showDuration: 300, + showEasing: 'swing', //swing and linear are built into jQuery + onShown: undefined, + hideMethod: 'fadeOut', + hideDuration: 1000, + hideEasing: 'swing', + onHidden: undefined, + + extendedTimeOut: 1000, + iconClasses: { + error: 'toast-error', + info: 'toast-info', + success: 'toast-success', + warning: 'toast-warning' + }, + iconClass: 'toast-info', + positionClass: 'toast-top-right', + timeOut: 5000, // Set timeOut and extendedTimeout to 0 to make it sticky + titleClass: 'toast-title', + messageClass: 'toast-message', + target: 'body', + closeHtml: '<button>×</button>', + newestOnTop: true + }; + } + + function publish(args) { + if (!listener) { + return; + } + listener(args); + } + + function notify(map) { + var + options = getOptions(), + iconClass = map.iconClass || options.iconClass; + + if (typeof (map.optionsOverride) !== 'undefined') { + options = $.extend(options, map.optionsOverride); + iconClass = map.optionsOverride.iconClass || iconClass; + } + + toastId++; + + $container = getContainer(options); + var + intervalId = null, + $toastElement = $('<div/>'), + $titleElement = $('<div/>'), + $messageElement = $('<div/>'), + $closeElement = $(options.closeHtml), + response = { + toastId: toastId, + state: 'visible', + startTime: new Date(), + options: options, + map: map + }; + + if (map.iconClass) { + $toastElement.addClass(options.toastClass).addClass(iconClass); + } + + if (map.title) { + $titleElement.append(map.title).addClass(options.titleClass); + $toastElement.append($titleElement); + } + + if (map.message) { + $messageElement.append(map.message).addClass(options.messageClass); + $toastElement.append($messageElement); + } + + if (options.closeButton) { + $closeElement.addClass('toast-close-button'); + $toastElement.prepend($closeElement); + } + + $toastElement.hide(); + if (options.newestOnTop) { + $container.prepend($toastElement); + } else { + $container.append($toastElement); + } + + + $toastElement[options.showMethod]( + { duration: options.showDuration, easing: options.showEasing, complete: options.onShown } + ); + if (options.timeOut > 0) { + intervalId = setTimeout(hideToast, options.timeOut); + } + + $toastElement.hover(stickAround, delayedhideToast); + if (!options.onclick && options.tapToDismiss) { + $toastElement.click(hideToast); + } + if (options.closeButton && $closeElement) { + $closeElement.click(function (event) { + event.stopPropagation(); + hideToast(true); + }); + } + + if (options.onclick) { + $toastElement.click(function () { + options.onclick(); + hideToast(); + }); + } + + publish(response); + + if (options.debug && console) { + console.log(response); + } + + return $toastElement; + + function hideToast(override) { + if ($(':focus', $toastElement).length && !override) { + return; + } + return $toastElement[options.hideMethod]({ + duration: options.hideDuration, + easing: options.hideEasing, + complete: function () { + removeToast($toastElement); + if (options.onHidden) { + options.onHidden(); + } + response.state = 'hidden'; + response.endTime = new Date(), + publish(response); + } + }); + } + + function delayedhideToast() { + if (options.timeOut > 0 || options.extendedTimeOut > 0) { + intervalId = setTimeout(hideToast, options.extendedTimeOut); + } + } + + function stickAround() { + clearTimeout(intervalId); + $toastElement.stop(true, true)[options.showMethod]( + { duration: options.showDuration, easing: options.showEasing } + ); + } + } + function getContainer(options) { + if (!options) { options = getOptions(); } + $container = $('#' + options.containerId); + if ($container.length) { + return $container; + } + $container = $('<div/>') + .attr('id', options.containerId) + .addClass(options.positionClass); + $container.appendTo($(options.target)); + return $container; + } + + function getOptions() { + return $.extend({}, getDefaults(), toastr.options); + } + + function removeToast($toastElement) { + if (!$container) { $container = getContainer(); } + if ($toastElement.is(':visible')) { + return; + } + $toastElement.remove(); + $toastElement = null; + if ($container.children().length === 0) { + $container.remove(); + } + } + //#endregion + + })(); + }); +}(typeof define === 'function' && define.amd ? define : function (deps, factory) { + if (typeof module !== 'undefined' && module.exports) { //Node + module.exports = factory(require(deps[0])); + } else { + window['toastr'] = factory(window['jQuery']); + } +})); diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -352,4 +352,4 @@ 'compatible' : compatible }; } -})(jQuery); \ No newline at end of file +})(jQuery); diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,7 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster', 'toastr' ]; var _ = grunt.util._; var fmt = _.sprintf; diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -24,6 +24,7 @@ @import "frame.less"; @import "upload.less"; @import "library.less"; +@import "toastr.less"; // Mixins diff -r c653272fdbb3e2fcc8e5dd83b2c71df8bd9b5c2a -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b static/style/src/less/toastr.less --- /dev/null +++ b/static/style/src/less/toastr.less @@ -0,0 +1,232 @@ +// Mix-ins +.borderRadius(@radius) { + -moz-border-radius: @radius; + -webkit-border-radius: @radius; + border-radius: @radius; +} + +.boxShadow(@boxShadow) { + -moz-box-shadow: @boxShadow; + -webkit-box-shadow: @boxShadow; + box-shadow: @boxShadow; +} + +.opacity(@opacity) { + @opacityPercent: @opacity * 100; + opacity: @opacity; + -ms-filter: ~"progid:DXImageTransform.Microsoft.Alpha(Opacity=@{opacityPercent})"; + filter: ~"alpha(opacity=@{opacityPercent})"; +} + +.wordWrap(@wordWrap: break-word) { + -ms-word-wrap: @wordWrap; + word-wrap: @wordWrap; +} + +// Variables +@black: #000000; +@grey: #999999; +@light-grey: #CCCCCC; +@white: #FFFFFF; +@near-black: #030303; +@green: #51A351; +@red: #BD362F; +@blue: #2F96B4; +@orange: #F89406; + +// Styles +.toast-title { + font-weight: bold; +} + +.toast-message { + .wordWrap(); + + a, + label { + color: @white; + } + + a:hover { + color: @light-grey; + text-decoration: none; + } +} + +.toast-close-button { + position: relative; + right: -0.3em; + top: -0.3em; + float: right; + font-size: 20px; + font-weight: bold; + color: @white; + -webkit-text-shadow: 0 1px 0 rgba(255,255,255,1); + text-shadow: 0 1px 0 rgba(255,255,255,1); + .opacity(0.8); + + &:hover, + &:focus { + color: @black; + text-decoration: none; + cursor: pointer; + .opacity(0.4); + } +} + +/*Additional properties for button version + iOS requires the button element instead of an anchor tag. + If you want the anchor version, it requires `href="#"`.*/ +button.toast-close-button { + padding: 0; + cursor: pointer; + background: transparent; + border: 0; + -webkit-appearance: none; +} + +//#endregion + +.toast-top-full-width { + top: 0; + right: 0; + width: 100%; +} + +.toast-bottom-full-width { + bottom: 0; + right: 0; + width: 100%; +} + +.toast-top-left { + top: 12px; + left: 12px; +} + +.toast-top-right { + top: 12px; + right: 12px; +} + +.toast-bottom-right { + right: 12px; + bottom: 12px; +} + +.toast-bottom-left { + bottom: 12px; + left: 12px; +} + +#toast-container { + position: fixed; + z-index: 999999; + + * { + -moz-box-sizing: border-box; + -webkit-box-sizing: border-box; + box-sizing: border-box; + } + + > div { + margin: 4em 0 6px; + padding: 15px 15px 15px 50px; + width: 300px; + .borderRadius(3px 3px 3px 3px); + background-position: 15px center; + background-repeat: no-repeat; + .boxShadow(0 0 12px @grey); + color: @white; + .opacity(0.8); + } + + > :hover { + .boxShadow(0 0 12px @black); + .opacity(1); + cursor: pointer; + } + + > .toast-info { + background-image: url("data:image/png;base64,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") !important; + } + + > .toast-error { + background-image: url("data:image/png;base64,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") !important; + } + + > .toast-success { + background-image: url("data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABgAAAAYCAYAAADgdz34AAAAAXNSR0IArs4c6QAAAARnQU1BAACxjwv8YQUAAAAJcEhZcwAADsMAAA7DAcdvqGQAAADsSURBVEhLY2AYBfQMgf///3P8+/evAIgvA/FsIF+BavYDDWMBGroaSMMBiE8VC7AZDrIFaMFnii3AZTjUgsUUWUDA8OdAH6iQbQEhw4HyGsPEcKBXBIC4ARhex4G4BsjmweU1soIFaGg/WtoFZRIZdEvIMhxkCCjXIVsATV6gFGACs4Rsw0EGgIIH3QJYJgHSARQZDrWAB+jawzgs+Q2UO49D7jnRSRGoEFRILcdmEMWGI0cm0JJ2QpYA1RDvcmzJEWhABhD/pqrL0S0CWuABKgnRki9lLseS7g2AlqwHWQSKH4oKLrILpRGhEQCw2LiRUIa4lwAAAABJRU5ErkJggg==") !important; + } + + > .toast-warning { + background-image: url("data:image/png;base64,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") !important; + } + + /*overrides*/ + &.toast-top-full-width > div, + &.toast-bottom-full-width > div { + width: 96%; + margin: auto; + } +} + +.toast { + background-color: @near-black; +} + +.toast-success { + background-color: @green; +} + +.toast-error { + background-color: @red; +} + +.toast-info { + background-color: @blue; +} + +.toast-warning { + background-color: @orange; +} + +/*Responsive Design*/ + +@media all and (max-width: 240px) { + #toast-container { + + > div { + padding: 8px 8px 8px 50px; + width: 11em; + } + + & .toast-close-button { + right: -0.2em; + top: -0.2em; + } + } +} + +@media all and (min-width: 241px) and (max-width: 480px) { + #toast-container { + > div { + padding: 8px 8px 8px 50px; + width: 18em; + } + + & .toast-close-button { + right: -0.2em; + top: -0.2em; + } + } +} + +@media all and (min-width: 481px) and (max-width: 768px) { + #toast-container { + > div { + padding: 15px 15px 15px 50px; + width: 25em; + } + } +} https://bitbucket.org/galaxy/galaxy-central/commits/9e7cd2749bde/ Changeset: 9e7cd2749bde User: martenson Date: 2013-12-13 20:33:06 Summary: rewrite of galaxy.library to use global notifications; removed previous notification engine from galaxy.modal.js; Affected #: 3 files diff -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b -r 9e7cd2749bdeb36bab9a7c883d95a877f9eaa2ca lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -144,38 +144,6 @@ parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) - - # ======================= - # ===== LIBRARY API ===== - # ======================= - - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - - webapp.mapper.connect( 'show_lda_item', '/api/libraries/datasets/:id', controller='lda_datasets', action='show', conditions=dict(method=["GET"]) ) - webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', action='download', conditions=dict(method=["POST"]) ) - - webapp.mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource @@ -195,6 +163,52 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + # ======================= + # ===== LIBRARY API ===== + # ======================= + + webapp.mapper.connect( 'show_lda_item', + '/api/libraries/datasets/:id', + controller='lda_datasets', + action='show', + conditions=dict( method=[ "GET" ] ) ) + + webapp.mapper.connect( 'download_lda_items', + '/api/libraries/datasets/download/:format', + controller='lda_datasets', + action='download', + conditions=dict( method=[ "POST", "GET" ] ) ) + + webapp.mapper.resource_with_deleted( 'library', + 'libraries', + path_prefix='/api' ) + webapp.mapper.resource( 'folder', + 'folders', + path_prefix='/api' ) + + webapp.mapper.resource( 'content', + 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) # ==================== # ===== TOOLSHED ===== diff -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b -r 9e7cd2749bdeb36bab9a7c883d95a877f9eaa2ca static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -8,7 +8,11 @@ var responses = []; // dependencies -define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "libs/toastr"], function(mod_modal, mod_masthead, mod_utils, mod_toastr) { +define([ + "galaxy.modal", + "galaxy.masthead", + "utils/galaxy.utils", + "libs/toastr"], function(mod_modal, mod_masthead, mod_utils, mod_toastr) { // MMMMMMMMMMMMMMM // === Models ==== @@ -308,7 +312,7 @@ // event binding events: { 'click #select-all-checkboxes' : 'selectAll', - 'click .folder_row' : 'selectClicked', + 'click .folder_row' : 'selectClickedRow', 'click #toolbtn_bulk_import' : 'modalBulkImport', 'click #toolbtn_dl' : 'bulkDownload', 'click .library-dataset' : 'showDatasetDetails', @@ -350,6 +354,7 @@ var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); that.$el.html(template); + } }) }, @@ -456,12 +461,14 @@ // save the dataset into selected history historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ - self.modal.showNotification('Dataset imported', 3000, 'success'); + mod_toastr.success('Dataset imported'); + // self.modal.showNotification('Dataset imported', 3000, 'success'); //enable the buttons self.modal.enableButton('Import'); self.modal.enableButton('Download'); }, error : function(){ - self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); + mod_toastr.error('An error occured! Dataset not imported. Please try again.') + // self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); //enable the buttons self.modal.enableButton('Import'); self.modal.enableButton('Download'); @@ -471,37 +478,69 @@ // select all datasets selectAll : function (event) { - var selected = event.target.checked; - // Iterate each checkbox - $(':checkbox').each(function () { this.checked = selected; }); - this.showTools(); - }, + var selected = event.target.checked; + that = this; + // Iterate each checkbox + $(':checkbox').each(function () { + this.checked = selected; + $row = $(this.parentElement.parentElement); + // Change color of selected/unselected + (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); + }); + // Show the tools in menu + this.checkTools(); + }, - // click checkbox on folder click - selectClicked : function (event) { - var checkbox = $("#" + event.target.parentElement.id).find(':checkbox') - if (checkbox[0] != undefined) { - if (checkbox[0].checked){ - checkbox[0].checked = ''; - // $(event.target.parentElement).css('background-color', '').css('color', ''); - $(event.target.parentElement).removeClass('dark'); - $(event.target.parentElement).find('a').removeClass('dark'); - $(event.target.parentElement).addClass('light'); - $(event.target.parentElement).find('a').addClass('light'); + // Check checkbox on row itself or row checkbox click + selectClickedRow : function (event) { + var checkbox = ''; + var $row; + var source; + if (event.target.localName === 'input'){ + checkbox = event.target; + $row = $(event.target.parentElement.parentElement); + source = 'input'; + } else if (event.target.localName === 'td') { + checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; + $row = $(event.target.parentElement); + source = 'td'; + } + if (checkbox === '') {event.stopPropagation(); return;} // button in row was clicked + + if (checkbox.checked){ + if (source==='td'){ + checkbox.checked = ''; + this.makeWhiteRow($row); + } else if (source==='input') { + this.makeDarkRow($row); + } } else { - checkbox[0].checked = 'selected'; - $(event.target.parentElement).removeClass('light'); - $(event.target.parentElement).find('a').removeClass('light'); - $(event.target.parentElement).addClass('dark'); - $(event.target.parentElement).find('a').addClass('dark'); - // $(event.target.parentElement).css('background-color', '#8389a1').css('color', 'white'); + if (source==='td'){ + checkbox.checked = 'selected'; + this.makeDarkRow($row); + } else if (source==='input') { + this.makeWhiteRow($row); + } } - } - this.showTools(); + this.checkTools(); + }, + + makeDarkRow: function($row){ + $row.removeClass('light'); + $row.find('a').removeClass('light'); + $row.addClass('dark'); + $row.find('a').addClass('dark'); + }, + + makeWhiteRow: function($row){ + $row.removeClass('dark'); + $row.find('a').removeClass('dark'); + $row.addClass('light'); + $row.find('a').addClass('light'); }, // show toolbar in case something is selected - showTools : function(){ + checkTools : function(){ var checkedValues = $('#folder_table').find(':checked'); if(checkedValues.length > 0){ $('#toolbtn_bulk_import').show(); @@ -577,7 +616,9 @@ var self = this; var popped_item = history_item_set.pop(); if (typeof popped_item === "undefined") { - self.modal.showNotification('All datasets imported', 3000, 'success'); + mod_toastr.success('All datasets imported'); + this.modal.hide(); + // self.modal.showNotification('All datasets imported', 3000, 'success'); // enable button again self.modal.enableButton('Import'); return @@ -646,12 +687,13 @@ //send request $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') .appendTo('body').submit().remove(); + mod_toastr.info('Your download will begin soon'); }; }, // shows modal for creating folder createFolderModal: function(){ - alert('creating folder'); + mod_toastr.info('This will create folder...in the future'); } }); @@ -704,7 +746,7 @@ // render render: function () { - //hack to show scrollbars + //hack to show scrollbars due to #center element inheritance $("#center").css('overflow','auto'); var that = this; @@ -717,18 +759,16 @@ }, error: function(model, response){ if (response.statusCode().status === 403){ - //show notification - // var toast = mod_toastr; mod_toastr.error('Please log in first. Redirecting to login page in 3s.'); setTimeout(that.redirectToLogin, 3000); } else { - library_router.navigate('#', {trigger: true, replace: true}); + mod_toastr.error('An error occured. Please try again.'); } } }) }, - redirectToSplash: function(){ + redirectToHome: function(){ window.location = '../'; }, redirectToLogin: function(){ @@ -762,19 +802,23 @@ // create the new library from modal create_new_library_event: function(){ var libraryDetails = this.serialize_new_library(); - var valid = this.validate_new_library(libraryDetails); - var library = new Library(); - var self = this; - library.save(libraryDetails, { - success: function (library) { - self.modal.hide(); - self.clear_library_modal(); - self.render(); - }, - error: function(){ - self.modal.showNotification('An error occured', 5000, 'error'); - } - }); + if (this.validate_new_library(libraryDetails)){ + var library = new Library(); + var self = this; + library.save(libraryDetails, { + success: function (library) { + self.modal.hide(); + self.clear_library_modal(); + self.render(); + mod_toastr.success('Library created'); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + } else { + mod_toastr.error('Library\'s name is missing'); + } return false; }, @@ -794,14 +838,13 @@ }; }, - validate_new_library: function(library){ - + // validate new library info + validate_new_library: function(libraryDetails){ + return libraryDetails.name !== ''; }, - // template for new library modal - template_new_library: function() - { + template_new_library: function(){ tmpl_array = []; tmpl_array.push('<div id="new_library_modal">'); @@ -824,34 +867,29 @@ folderContentView = new FolderContentView(); galaxyLibraryview = new GalaxyLibraryview(); - library_router = new LibraryRouter(); library_router.on('route:libraries', function() { // render libraries list galaxyLibraryview.render(); - }); + }); library_router.on('route:folder_content', function(id) { // render folder's contents folderContentView.render({id: id}); - }); + }); library_router.on('route:download', function(folder_id, format) { - // send download stream - if (typeof folderContentView === 'undefined'){ - alert('you cant touch this!'); - // } else if (folderContentView.modal !== null){ - // folderContentView.download(folder_id, format); - } else if ($('#center').find(':checked').length === 0) { // coming from outside of the library app + if ($('#center').find(':checked').length === 0) { + // this happens rarely when there is a server/data error and client gets an actual response instead of an attachment + // we don't know what was selected so we can't download again, we redirect to the folder provided library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); - // TODO show message of redirection } else { + // send download stream folderContentView.download(folder_id, format); library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); } - - }); + }); Backbone.history.start(); diff -r 267dcfd58a60d2de706d7c00c6fb6ec426eaaf5b -r 9e7cd2749bdeb36bab9a7c883d95a877f9eaa2ca static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -26,16 +26,17 @@ if (options) this.create(options); - this.bindClick(event, self); + // Bind the hiding events + this.bindEvents(event, self); }, // bind the click-to-hide function - bindClick: function(event, that) { + bindEvents: function(event, that) { // bind the ESC key to hide() function $(document).on('keyup', function(event){ if (event.keyCode == 27) { self.hide(); } }) - // bind the click anywhere to hide() function... + // bind the 'click anywhere' to hide() function... $('html').on('click', function(event){ that.hide(); }) @@ -46,26 +47,24 @@ }, // unbind the click-to-hide function - unbindClick: function(event, that){ + unbindEvents: function(event, that){ // bind the ESC key to hide() function $(document).off('keyup', function(event){ if (event.keyCode == 27) { that.hide(); } }) - // unbind the click anywhere to hide() function... + // unbind the 'click anywhere' to hide() function... $('html').off('click', function(event){ that.hide(); }) - // ...but don't hide if the click is on modal content $('.modal-content').off('click', function(event){ event.stopPropagation(); }) }, - // destroy destroy : function(){ this.hide(); - this.unbindClick(); + this.unbindEvents(); $('.modal').remove(); }, @@ -103,6 +102,7 @@ // set flag this.visible = false; + this.unbindEvents(); }, // create @@ -127,7 +127,6 @@ this.$footer = (this.$el).find('.modal-footer'); this.$buttons = (this.$el).find('.buttons'); this.$backdrop = (this.$el).find('.modal-backdrop'); - this.$notification = (this.$el).find('.notification-modal'); // append body this.$body.html(this.options.body); @@ -170,35 +169,6 @@ this.$buttons.find('#' + String(name).toLowerCase()).show(); }, - // show notification - showNotification : function(message, duration, type) { - var duration = typeof duration !== 'undefined' ? duration : 3000; - var bgColor; - var txtColor; - - if (type === 'error'){ - bgColor = '#f4e0e1'; - txtColor = '#a42732'; - // } else if (type === 'success'){ - } else { // success is default - bgColor = '#e1f4e0'; - txtColor = '#32a427'; - } - - var HTMLmessage = "<div class='notification-message' style='text-align:center; line-height:16px; '> " + message + " </div>"; - this.$notification.html("<div id='notification-bar' style='display:none; float: right; height: 16px; width:100%; background-color: " + bgColor + "; z-index: 100; color: " + txtColor + ";border-bottom: 1px solid " + txtColor + ";'>" + HTMLmessage + "</div>"); - - var self = this; - - /*animate the bar*/ - $('#notification-bar').slideDown(function() { - setTimeout(function() { - $('#notification-bar').slideUp(function() {self.$notification.html('');}); - }, duration); - }); - - }, - // returns scroll top for body element scrollTop: function() { @@ -218,7 +188,6 @@ '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + - '<span class="notification-modal"></span>' + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + https://bitbucket.org/galaxy/galaxy-central/commits/0522f7504094/ Changeset: 0522f7504094 User: martenson Date: 2013-12-13 21:05:26 Summary: switch download to GET, removed toaster from grunt file Affected #: 2 files diff -r 9e7cd2749bdeb36bab9a7c883d95a877f9eaa2ca -r 0522f7504094bd5be2be97846e695a0c790bf929 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -462,13 +462,11 @@ // save the dataset into selected history historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ mod_toastr.success('Dataset imported'); - // self.modal.showNotification('Dataset imported', 3000, 'success'); //enable the buttons self.modal.enableButton('Import'); self.modal.enableButton('Download'); }, error : function(){ mod_toastr.error('An error occured! Dataset not imported. Please try again.') - // self.modal.showNotification('An error occured! Dataset not imported. Please try again later.', 5000, 'error'); //enable the buttons self.modal.enableButton('Import'); self.modal.enableButton('Download'); @@ -618,7 +616,6 @@ if (typeof popped_item === "undefined") { mod_toastr.success('All datasets imported'); this.modal.hide(); - // self.modal.showNotification('All datasets imported', 3000, 'success'); // enable button again self.modal.enableButton('Import'); return @@ -669,7 +666,7 @@ var url = '/api/libraries/datasets/download/' + format; var data = {'ldda_ids' : dataset_ids}; - this.processDownload(url, data); + this.processDownload(url, data, 'get'); }, // create hidden form and submit through POST to initialize download diff -r 9e7cd2749bdeb36bab9a7c883d95a877f9eaa2ca -r 0522f7504094bd5be2be97846e695a0c790bf929 static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,7 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster', 'toastr' ]; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster']; var _ = grunt.util._; var fmt = _.sprintf; https://bitbucket.org/galaxy/galaxy-central/commits/5463295a3981/ Changeset: 5463295a3981 User: martenson Date: 2013-12-16 00:26:37 Summary: Merged galaxy/galaxy-central into default Affected #: 139 files diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -1,16 +1,10 @@ from __future__ import absolute_import -import sys, os, atexit +import sys +import os -from galaxy import config, jobs, util, tools, web -import galaxy.tools.search -import galaxy.tools.data -import tool_shed.galaxy_install -import tool_shed.tool_shed_registry -from galaxy.web import security +from galaxy import config, jobs import galaxy.model -import galaxy.datatypes.registry import galaxy.security -from galaxy.objectstore import build_object_store_from_config import galaxy.quota from galaxy.tags.tag_handler import GalaxyTagHandler from galaxy.visualization.genomes import Genomes @@ -27,7 +21,8 @@ import logging log = logging.getLogger( __name__ ) -class UniverseApplication( object ): + +class UniverseApplication( object, config.ConfiguresGalaxyMixin ): """Encapsulates the state of a Universe application""" def __init__( self, **kwargs ): print >> sys.stderr, "python path is: " + ", ".join( sys.path ) @@ -38,92 +33,38 @@ self.config.check() config.configure_logging( self.config ) self.configure_fluent_log() - # Determine the database url - if self.config.database_connection: - db_url = self.config.database_connection - else: - db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database - install_db_url = self.config.install_database_connection - # TODO: Consider more aggressive check here that this is not the same - # database file under the hood. - combined_install_database = not( install_db_url and install_db_url != db_url ) - # Set up the tool sheds registry - if os.path.isfile( self.config.tool_sheds_config ): - self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) - else: - self.tool_shed_registry = None - # Initialize database / check for appropriate schema version. # If this - # is a new installation, we'll restrict the tool migration messaging. - from galaxy.model.migrate.check import create_or_verify_database - create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) - if not combined_install_database: - from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database - tsi_create_or_verify_database( install_db_url, self.config.install_database_engine_options, app=self ) - # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. - from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options ) - # Object store manager - self.object_store = build_object_store_from_config(self.config, fsmon=True) + self._configure_tool_shed_registry() + + self._configure_object_store( fsmon=True ) + # Setup the database engine and ORM - from galaxy.model import mapping - self.model = mapping.init( self.config.file_path, - db_url, - self.config.database_engine_options, - map_install_models=combined_install_database, - database_query_profiling_proxy = self.config.database_query_profiling_proxy, - object_store = self.object_store, - trace_logger=self.trace_logger, - use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) ) + config_file = kwargs.get( 'global_conf', {} ).get( '__file__', None ) + self._configure_models( check_migrate_databases=True, check_migrate_tools=True, config_file=config_file ) - if combined_install_database: - log.info("Install database targetting Galaxy's database configuration.") - self.install_model = self.model - else: - from galaxy.model.tool_shed_install import mapping as install_mapping - install_db_url = self.config.install_database_connection - log.info("Install database using its own connection %s" % install_db_url) - install_db_engine_options = self.config.install_database_engine_options - self.install_model = install_mapping.init( install_db_url, - install_db_engine_options ) # Manage installed tool shed repositories. - self.installed_repository_manager = tool_shed.galaxy_install.InstalledRepositoryManager( self ) - # Create an empty datatypes registry. - self.datatypes_registry = galaxy.datatypes.registry.Registry() - # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We - # load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some - # generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used. - # However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype - # in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict - # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. - self.installed_repository_manager.load_proprietary_datatypes() - # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. - self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) + from tool_shed.galaxy_install import installed_repository_manager + self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self ) + + self._configure_datatypes_registry( self.installed_repository_manager ) galaxy.model.set_datatypes_registry( self.datatypes_registry ) + # Security helper - self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + self._configure_security() # Tag handler self.tag_handler = GalaxyTagHandler() # Genomes self.genomes = Genomes( self ) # Data providers registry. self.data_provider_registry = DataProviderRegistry() - # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. - self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( tool_data_path=self.config.tool_data_path, - config_filename=self.config.tool_data_table_config_path ) - # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. - self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, - tool_data_path=self.tool_data_tables.tool_data_path, - from_shed_config=False ) + + self._configure_tool_data_tables( from_shed_config=False ) + # Initialize the job management configuration self.job_config = jobs.JobConfiguration(self) - # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. - tool_configs = self.config.tool_configs - if self.config.migrated_tools_config not in tool_configs: - tool_configs.append( self.config.migrated_tools_config ) - self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) - # Search support for tools - self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + + self._configure_toolbox() + # Load Data Manager self.data_managers = DataManagers( self ) # If enabled, poll respective tool sheds to see if updates are available for any installed tool shed repositories. diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -473,6 +473,7 @@ rval[ key ] = value return rval + def configure_logging( config ): """ Allow some basic logging configuration to be read from ini file. @@ -513,3 +514,110 @@ sentry_handler.setLevel( logging.WARN ) root.addHandler( sentry_handler ) + +class ConfiguresGalaxyMixin: + """ Shared code for configuring Galaxy-like app objects. + """ + + def _configure_toolbox( self ): + # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. + tool_configs = self.config.tool_configs + if self.config.migrated_tools_config not in tool_configs: + tool_configs.append( self.config.migrated_tools_config ) + from galaxy import tools + self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) + # Search support for tools + import galaxy.tools.search + self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) + + def _configure_tool_data_tables( self, from_shed_config ): + from galaxy.tools.data import ToolDataTableManager + + # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. + self.tool_data_tables = ToolDataTableManager( tool_data_path=self.config.tool_data_path, + config_filename=self.config.tool_data_table_config_path ) + # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. + self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, + tool_data_path=self.tool_data_tables.tool_data_path, + from_shed_config=from_shed_config ) + + def _configure_datatypes_registry( self, installed_repository_manager=None ): + from galaxy.datatypes import registry + # Create an empty datatypes registry. + self.datatypes_registry = registry.Registry() + if installed_repository_manager: + # Load proprietary datatypes defined in datatypes_conf.xml files in all installed tool shed repositories. We + # load proprietary datatypes before datatypes in the distribution because Galaxy's default sniffers include some + # generic sniffers (eg text,xml) which catch anything, so it's impossible for proprietary sniffers to be used. + # However, if there is a conflict (2 datatypes with the same extension) between a proprietary datatype and a datatype + # in the Galaxy distribution, the datatype in the Galaxy distribution will take precedence. If there is a conflict + # between 2 proprietary datatypes, the datatype from the repository that was installed earliest will take precedence. + installed_repository_manager.load_proprietary_datatypes() + # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. + self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) + + def _configure_object_store( self, **kwds ): + from galaxy.objectstore import build_object_store_from_config + self.object_store = build_object_store_from_config( self.config, **kwds ) + + def _configure_security( self ): + from galaxy.web import security + self.security = security.SecurityHelper( id_secret=self.config.id_secret ) + + def _configure_tool_shed_registry( self ): + import tool_shed.tool_shed_registry + + # Set up the tool sheds registry + if os.path.isfile( self.config.tool_sheds_config ): + self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) + else: + self.tool_shed_registry = None + + def _configure_models( self, check_migrate_databases=False, check_migrate_tools=False, config_file=None ): + """ + Preconditions: object_store must be set on self. + """ + if self.config.database_connection: + db_url = self.config.database_connection + else: + db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database + install_db_url = self.config.install_database_connection + # TODO: Consider more aggressive check here that this is not the same + # database file under the hood. + combined_install_database = not( install_db_url and install_db_url != db_url ) + install_db_url = install_db_url or db_url + + if check_migrate_databases: + # Initialize database / check for appropriate schema version. # If this + # is a new installation, we'll restrict the tool migration messaging. + from galaxy.model.migrate.check import create_or_verify_database + create_or_verify_database( db_url, config_file, self.config.database_engine_options, app=self ) + if not combined_install_database: + from galaxy.model.tool_shed_install.migrate.check import create_or_verify_database as tsi_create_or_verify_database + tsi_create_or_verify_database( install_db_url, self.config.install_database_engine_options, app=self ) + + if check_migrate_tools: + # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. + from tool_shed.galaxy_install.migrate.check import verify_tools + verify_tools( self, install_db_url, config_file, self.config.database_engine_options ) + + from galaxy.model import mapping + self.model = mapping.init( self.config.file_path, + db_url, + self.config.database_engine_options, + map_install_models=combined_install_database, + database_query_profiling_proxy=self.config.database_query_profiling_proxy, + object_store=self.object_store, + trace_logger=getattr(self, "trace_logger", None), + use_pbkdf2=self.config.get_bool( 'use_pbkdf2', True ) ) + + if combined_install_database: + log.info("Install database targetting Galaxy's database configuration.") + self.install_model = self.model + else: + from galaxy.model.tool_shed_install import mapping as install_mapping + install_db_url = self.config.install_database_connection + log.info("Install database using its own connection %s" % install_db_url) + install_db_engine_options = self.config.install_database_engine_options + self.install_model = install_mapping.init( install_db_url, + install_db_engine_options ) diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -598,6 +598,9 @@ tool_xml_text = """ <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata"><type class="SetMetadataTool" module="galaxy.tools"/> + <requirements> + <requirement type="package">samtools</requirement> + </requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/><command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs> diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -688,10 +688,7 @@ if self.command_line and self.command_line.startswith( 'python' ): self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root # Shell fragment to inject dependencies - if self.app.config.use_tool_dependencies: - self.dependency_shell_commands = self.tool.build_dependency_shell_commands() - else: - self.dependency_shell_commands = None + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished job.command_line = self.command_line @@ -1435,10 +1432,7 @@ if self.command_line and self.command_line.startswith( 'python' ): self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root # Shell fragment to inject dependencies - if self.app.config.use_tool_dependencies: - self.dependency_shell_commands = self.tool.build_dependency_shell_commands() - else: - self.dependency_shell_commands = None + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished task.command_line = self.command_line diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/jobs/actions/post.py --- a/lib/galaxy/jobs/actions/post.py +++ b/lib/galaxy/jobs/actions/post.py @@ -12,7 +12,7 @@ form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + pja.output_name + "</span><div class='toolFormTitle'> %s <br/> on " + pja.output_name + "\ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) @@ -20,7 +20,7 @@ form = """ if (pja.action_type == "%s"){ p_str = "<div class='pjaForm toolForm'><span class='action_tag' style='display:none'>"+ pja.action_type + "</span><div class='toolFormTitle'> %s \ - <div style='float: right;' class='buttons'><img src='/static/images/delete_icon.png'></div></div><div class='toolFormBody'>"; + <div style='float: right;' class='buttons'><img src='/static/images/history-buttons/delete_icon.png'></div></div><div class='toolFormBody'>"; %s p_str += "</div><div class='toolParamHelp'>%s</div></div>"; }""" % (action_type, title, content, help) diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -198,7 +198,7 @@ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) return output_pairs - def _handle_metadata_externally(self, job_wrapper): + def _handle_metadata_externally( self, job_wrapper, resolve_requirements=False ): """ Set metadata externally. Used by the local and lwr job runners where this shouldn't be attached to command-line to execute. @@ -212,6 +212,12 @@ tmp_dir=job_wrapper.working_directory, #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior kwds={ 'overwrite' : False } ) + if resolve_requirements: + dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() + if dependency_shell_commands: + if isinstance( dependency_shell_commands, list ): + dependency_shell_commands = "&&".join( dependency_shell_commands ) + external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -110,7 +110,7 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job! try: job_wrapper.finish( stdout, stderr, exit_code ) diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -204,7 +204,7 @@ log.exception("failure running job %d" % job_wrapper.job_id) return if not LwrJobRunner.__remote_metadata( client ): - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job try: job_wrapper.finish( stdout, stderr ) diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -1,11 +1,11 @@ +import logging import os - from galaxy.model.item_attrs import Dictifiable - from galaxy.util.bunch import Bunch from galaxy.util import asbool +from tool_shed.util import common_util -from tool_shed.util import common_util +log = logging.getLogger( __name__ ) class ToolShedRepository( object ): @@ -61,9 +61,53 @@ def can_reset_metadata( self ): return self.status == self.installation_status.INSTALLED - @property - def can_uninstall( self ): - return self.status != self.installation_status.UNINSTALLED + def can_uninstall( self, app ): + # An installed repository cannot be uninstalled if other installed repositories or installed repository + # contents (i.e., tool dependencies) require it. + if self.status == self.installation_status.UNINSTALLED: + return False + this_repository_tup = ( str( self.tool_shed ), + str( self.name ), + str( self.owner ), + str( self.installed_changeset_revision ) ) + irm = app.installed_repository_manager + # See if this repository's current dependencies are restricted to a single circular relationship. This + # means that this repository has a single repository dependency which itself depends upon this repository. + # The repository dependency may have other repository dependencies, but that is not relevant here. + single_repository_dependency_tup = None + installed_repository_dependency_tups = \ + irm.installed_repository_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + # If this repository defines a circular relationship to another repository, then the list of tuples + # defining installed repository dependencies will include itself. + if len( installed_repository_dependency_tups ) == 2: + if this_repository_tup in installed_repository_dependency_tups: + # We have a single circular dependency definition, so get the other repository. + for installed_repository_dependency_tup in installed_repository_dependency_tups: + if installed_repository_dependency_tup != this_repository_tup: + single_repository_dependency_tup = installed_repository_dependency_tup + break + if single_repository_dependency_tup is not None: + installed_repository_dependency_tups = \ + irm.installed_repository_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + if this_repository_tup in installed_repository_dependency_tups: + # This repository is a dependency of the single repository upon which it depends, so we have + # a single circular relationship and this repository can be uninstalled. + return True + # Find other installed repositories that require this repository. + installed_dependent_repositories = \ + irm.installed_dependent_repositories_of_installed_repositories.get( this_repository_tup, [] ) + if installed_dependent_repositories: + # This repository cannot be uninstalled because other installed repositories require it. + return False + # Find installed tool dependencies that require this repository's installed tool dependencies. + installed_tool_dependencies = irm.installed_tool_dependencies_of_installed_repositories.get( this_repository_tup, [] ) + for td_tup in installed_tool_dependencies: + installed_dependent_td_tups = irm.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.get( td_tup, [] ) + if installed_dependent_td_tups: + # This repository cannot be uninstalled because it contains installed tool dependencies that + # are required at run time by other installed tool dependencies. + return False + return True @property def can_deactivate( self ): @@ -218,7 +262,7 @@ @property def installed_tool_dependencies( self ): - """Return the repository's tool dependencies that are currently installed.""" + """Return the repository's tool dependencies that are currently installed, but possibly in an error state.""" installed_dependencies = [] for tool_dependency in self.tool_dependencies: if tool_dependency.status in [ ToolDependency.installation_status.INSTALLED, @@ -313,9 +357,9 @@ required_repositories_missing_or_being_installed = [] for required_repository in self.repository_dependencies: if required_repository.status in [ self.installation_status.ERROR, - self.installation_status.INSTALLING, - self.installation_status.NEVER_INSTALLED, - self.installation_status.UNINSTALLED ]: + self.installation_status.INSTALLING, + self.installation_status.NEVER_INSTALLED, + self.installation_status.UNINSTALLED ]: required_repositories_missing_or_being_installed.append( required_repository ) return required_repositories_missing_or_being_installed @@ -507,7 +551,9 @@ @property def can_uninstall( self ): - return self.status in [ self.installation_status.ERROR, self.installation_status.INSTALLED ] + # A tool dependency can be uninstalled only if it is currently in an error state. Only the containing + # repository can be uninstalled if a tool dependency is properly installed. + return self.status in [ self.installation_status.ERROR ] @property def can_update( self ): @@ -516,6 +562,13 @@ self.installation_status.ERROR, self.installation_status.UNINSTALLED ] + def get_env_shell_file_path( self, app ): + installation_directory = self.installation_directory( app ) + file_path = os.path.join( installation_directory, 'env.sh' ) + if os.path.exists( file_path ): + return file_path + return None + @property def in_error_state( self ): return self.status == self.installation_status.ERROR @@ -536,6 +589,10 @@ self.tool_shed_repository.name, self.tool_shed_repository.installed_changeset_revision ) + @property + def is_installed( self ): + return self.status == self.installation_status.INSTALLED + class ToolVersion( object, Dictifiable ): dict_element_visible_keys = ( 'id', 'tool_shed_repository' ) @@ -549,23 +606,23 @@ def get_previous_version( self, app ): context = app.install_model.context tva = context.query( app.install_model.ToolVersionAssociation ) \ - .filter( app.install_model.ToolVersionAssociation.table.c.tool_id == self.id ) \ - .first() + .filter( app.install_model.ToolVersionAssociation.table.c.tool_id == self.id ) \ + .first() if tva: return context.query( app.install_model.ToolVersion ) \ - .filter( app.install_model.ToolVersion.table.c.id == tva.parent_id ) \ - .first() + .filter( app.install_model.ToolVersion.table.c.id == tva.parent_id ) \ + .first() return None def get_next_version( self, app ): context = app.install_model.context tva = context.query( app.install_model.ToolVersionAssociation ) \ - .filter( app.install_model.ToolVersionAssociation.table.c.parent_id == self.id ) \ - .first() + .filter( app.install_model.ToolVersionAssociation.table.c.parent_id == self.id ) \ + .first() if tva: return context.query( app.install_model.ToolVersion ) \ - .filter( app.install_model.ToolVersion.table.c.id == tva.tool_id ) \ - .first() + .filter( app.install_model.ToolVersion.table.c.id == tva.tool_id ) \ + .first() return None def get_versions( self, app ): diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/model/tool_shed_install/mapping.py --- a/lib/galaxy/model/tool_shed_install/mapping.py +++ b/lib/galaxy/model/tool_shed_install/mapping.py @@ -7,10 +7,8 @@ from galaxy.model.base import ModelMapping from galaxy.model.orm.engine_factory import build_engine - metadata = MetaData() - install_model.ToolShedRepository.table = Table( "tool_shed_repository", metadata, Column( "id", Integer, primary_key=True ), Column( "create_time", DateTime, default=now ), @@ -72,7 +70,6 @@ Column( "repository_path", TEXT ), Column( "version", Integer ) ) - mapper( install_model.ToolShedRepository, install_model.ToolShedRepository.table, properties=dict( tool_versions=relation( install_model.ToolVersion, primaryjoin=( install_model.ToolShedRepository.table.c.id == install_model.ToolVersion.table.c.tool_shed_repository_id ), @@ -112,17 +109,13 @@ """Connect mappings to the database""" # Load the appropriate db module engine = build_engine( url, engine_options ) - # Connect the metadata to the database. metadata.bind = engine - - result = ModelMapping([install_model], engine=engine) - + result = ModelMapping( [ install_model ], engine=engine ) # Create tables if needed if create_tables: metadata.create_all() # metadata.engine.commit() - result.create_tables = create_tables #load local galaxy security policy return result diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -40,7 +40,7 @@ from galaxy.tools.actions import DefaultToolAction from galaxy.tools.actions.data_source import DataSourceToolAction from galaxy.tools.actions.data_manager import DataManagerToolAction -from galaxy.tools.deps import DependencyManager, INDETERMINATE_DEPENDENCY +from galaxy.tools.deps import build_dependency_manager from galaxy.tools.deps.requirements import parse_requirements_from_xml from galaxy.tools.parameters import check_param, params_from_strings, params_to_strings from galaxy.tools.parameters.basic import (BaseURLToolParameter, @@ -700,14 +700,7 @@ return stored.latest_workflow def init_dependency_manager( self ): - if self.app.config.use_tool_dependencies: - dependency_manager_kwds = { - 'default_base_path': self.app.config.tool_dependency_dir, - 'conf_file': self.app.config.dependency_resolvers_config_file, - } - self.dependency_manager = DependencyManager( **dependency_manager_kwds ) - else: - self.dependency_manager = None + self.dependency_manager = build_dependency_manager( self.app.config ) @property def sa_session( self ): @@ -1082,6 +1075,22 @@ :returns: galaxy.jobs.JobDestination -- The destination definition and runner parameters. """ return self.app.job_config.get_destination(self.__get_job_tool_configuration(job_params=job_params).destination) + + def get_panel_section( self ): + for key, item in self.app.toolbox.integrated_tool_panel.items(): + if item: + if key.startswith( 'tool_' ): + if item.id == self.id: + return '', '' + if key.startswith( 'section_' ): + section_id = item.id or '' + section_name = item.name or '' + for section_key, section_item in item.elems.items(): + if section_key.startswith( 'tool_' ): + if section_item: + if section_item.id == self.id: + return section_id, section_name + return None, None def parse( self, root, guid=None ): """ @@ -3017,6 +3026,8 @@ if io_details: tool_dict[ 'inputs' ] = [ input.to_dict( trans ) for input in self.inputs.values() ] tool_dict[ 'outputs' ] = [ output.to_dict() for output in self.outputs.values() ] + + tool_dict[ 'panel_section_id' ], tool_dict[ 'panel_section_name' ] = self.get_panel_section() return tool_dict diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/tools/deps/__init__.py --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -15,6 +15,31 @@ from galaxy.util.submodules import submodules +def build_dependency_manager( config ): + if config.use_tool_dependencies: + dependency_manager_kwds = { + 'default_base_path': config.tool_dependency_dir, + 'conf_file': config.dependency_resolvers_config_file, + } + dependency_manager = DependencyManager( **dependency_manager_kwds ) + else: + dependency_manager = NullDependencyManager() + + return dependency_manager + + +class NullDependencyManager( object ): + + def uses_tool_shed_dependencies(self): + return False + + def dependency_shell_commands( self, requirements, **kwds ): + return [] + + def find_dep( self, name, version=None, type='package', **kwds ): + return INDETERMINATE_DEPENDENCY + + class DependencyManager( object ): """ A DependencyManager attempts to resolve named and versioned dependencies by @@ -76,6 +101,7 @@ return [ ToolShedPackageDependencyResolver(self), GalaxyPackageDependencyResolver(self), + GalaxyPackageDependencyResolver(self, versionless=True), ] def __parse_resolver_conf_xml(self, root): diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -265,6 +265,9 @@ if remove_from_disk_checked: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED tool_shed_repository.error_message = None + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.add( tool_shed_repository ) @@ -1564,7 +1567,7 @@ tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository if kwd.get( 'uninstall_tool_dependencies_button', False ): errors = False - # Filter tool dependencies to only those that are installed. + # Filter tool dependencies to only those that are installed but in an error state. tool_dependencies_for_uninstallation = [] for tool_dependency in tool_dependencies: if tool_dependency.can_uninstall: diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/webapps/galaxy/controllers/forms.py --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/lib/galaxy/webapps/galaxy/controllers/forms.py @@ -65,6 +65,9 @@ global_actions = [ grids.GridAction( "Create new form", dict( controller='forms', action='create_form_definition' ) ) ] + + def build_initial_query( self, trans, **kwargs ): + return trans.sa_session.query( self.model_class ).join (model.FormDefinition, self.model_class.latest_form_id == model.FormDefinition.id) class Forms( BaseUIController ): # Empty TextField diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -838,8 +838,8 @@ # Set imported history to be user's current history. trans.set_history( new_history ) return trans.show_ok_message( - message="""History "%s" has been imported. <br>You can <a href="%s">start using this history</a> or %s.""" - % ( new_history.name, web.url_for( '/' ), referer_message ), use_panels=True ) + message="""History "%s" has been imported. <br>You can <a href="%s" onclick="parent.window.location='%s';">start using this history</a> or %s.""" + % ( new_history.name, web.url_for( '/' ), web.url_for( '/' ), referer_message ), use_panels=True ) elif not user_history or not user_history.datasets or confirm: new_history = import_history.copy() new_history.name = "imported: " + new_history.name diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -932,7 +932,7 @@ repository_type = kwd.get( 'repository_type', rt_util.UNRESTRICTED ) if kwd.get( 'create_repository_button', False ): error = False - message = repository_maintenance_util.validate_repository_name( name, trans.user ) + message = repository_maintenance_util.validate_repository_name( trans.app, name, trans.user ) if message: error = True if not description: @@ -2085,7 +2085,7 @@ repository.long_description = long_description flush_needed = True if repository.times_downloaded == 0 and repo_name != repository.name: - message = repository_maintenance_util.validate_repository_name( repo_name, user ) + message = repository_maintenance_util.validate_repository_name( trans.app, repo_name, user ) if message: error = True else: diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/galaxy_install/__init__.py --- a/lib/tool_shed/galaxy_install/__init__.py +++ b/lib/tool_shed/galaxy_install/__init__.py @@ -1,54 +0,0 @@ -""" -Classes encapsulating the management of repositories installed from Galaxy tool sheds. -""" -import os, logging -import tool_shed.util.shed_util_common -import tool_shed.util.datatype_util -from galaxy.model.orm import and_ -from tool_shed.util import xml_util - -log = logging.getLogger( __name__ ) - -class InstalledRepositoryManager( object ): - def __init__( self, app ): - self.app = app - self.install_model = self.app.install_model - self.context = self.install_model.context - self.tool_configs = self.app.config.tool_configs - if self.app.config.migrated_tools_config not in self.tool_configs: - self.tool_configs.append( self.app.config.migrated_tools_config ) - self.installed_repository_dicts = [] - def get_repository_install_dir( self, tool_shed_repository ): - for tool_config in self.tool_configs: - tree, error_message = xml_util.parse_xml( tool_config ) - if tree is None: - return None - root = tree.getroot() - tool_path = root.get( 'tool_path', None ) - if tool_path: - ts = tool_shed.util.shed_util_common.clean_tool_shed_url( tool_shed_repository.tool_shed ) - relative_path = os.path.join( tool_path, - ts, - 'repos', - tool_shed_repository.owner, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision ) - if os.path.exists( relative_path ): - return relative_path - return None - def load_proprietary_datatypes( self ): - for tool_shed_repository in self.context.query( self.install_model.ToolShedRepository ) \ - .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, - self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ - .order_by( self.install_model.ToolShedRepository.table.c.id ): - relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) - if relative_install_dir: - installed_repository_dict = tool_shed.util.datatype_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) - if installed_repository_dict: - self.installed_repository_dicts.append( installed_repository_dict ) - def load_proprietary_converters_and_display_applications( self, deactivate=False ): - for installed_repository_dict in self.installed_repository_dicts: - if installed_repository_dict[ 'converter_path' ]: - tool_shed.util.datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) - if installed_repository_dict[ 'display_path' ]: - tool_shed.util.datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -31,6 +31,13 @@ latest_revision_tip_str = '' return '<img src="%s/june_2007_style/blue/ok_small.png" %s/>' % ( url_for( '/static' ), latest_revision_tip_str ) +def generate_repository_can_be_uninstalled_img_str( include_mouse_over=False ): + if include_mouse_over: + can_be_uninstalled_tip_str = 'class="icon-button" title="This repository can be uninstalled"' + else: + can_be_uninstalled_tip_str = '' + return '<img src="%s/images/fugue/toggle-bw.png" %s/>' % ( url_for( '/static' ), can_be_uninstalled_tip_str ) + def generate_revision_updates_img_str( include_mouse_over=False ): if include_mouse_over: revision_updates_tip_str = 'class="icon-button" title="Updates are available in the Tool Shed for this revision"' @@ -73,6 +80,8 @@ tool_shed_status_str += generate_includes_workflows_img_str( include_mouse_over=True ) else: tool_shed_status_str = generate_unknown_img_str( include_mouse_over=True ) + if tool_shed_repository.can_uninstall( trans.app ): + tool_shed_status_str += generate_repository_can_be_uninstalled_img_str( include_mouse_over=True ) return tool_shed_status_str @@ -210,6 +219,7 @@ legend_str += '%s  This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str() legend_str += '%s  This repository contains exported workflows<br/>' % generate_includes_workflows_img_str() legend_str += '%s  Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str() + legend_str += '%s  This repository can be uninstalled<br/>' % generate_repository_can_be_uninstalled_img_str() return legend_str diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/galaxy_install/installed_repository_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -0,0 +1,368 @@ +""" +Class encapsulating the management of repositories installed from Galaxy tool sheds. +""" +import logging +import os +import tool_shed.util.shed_util_common as suc +from tool_shed.util import datatype_util +from tool_shed.util import repository_dependency_util +from tool_shed.util import tool_dependency_util +from tool_shed.util import xml_util +from galaxy.model.orm import and_ + +log = logging.getLogger( __name__ ) + + +class InstalledRepositoryManager( object ): + + def __init__( self, app ): + """ + Among other things, keep in in-memory sets of tuples defining installed repositories and tool dependencies along with + the relationships between each of them. This will allow for quick discovery of those repositories or components that + can be uninstalled. The feature allowing a Galaxy administrator to uninstall a repository should not be available to + repositories or tool dependency packages that are required by other repositories or their contents (packages). The + uninstall feature should be available only at the repository hierarchy level where every dependency will be uninstalled. + The exception for this is if an item (repository or tool dependency package) is not in an INSTALLED state - in these + cases, the specific item can be uninstalled in order to attempt re-installation. + """ + self.app = app + self.install_model = self.app.install_model + self.context = self.install_model.context + self.tool_configs = self.app.config.tool_configs + if self.app.config.migrated_tools_config not in self.tool_configs: + self.tool_configs.append( self.app.config.migrated_tools_config ) + self.installed_repository_dicts = [] + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status can be anything) required by + # the key. The value defines the entire repository dependency tree. + self.repository_dependencies_of_installed_repositories = {} + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') required by + # the key. The value defines the entire repository dependency tree. + self.installed_repository_dependencies_of_installed_repositories = {} + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining tool_shed_repository objects (whose status is 'Installed') that require + # the key. + self.installed_dependent_repositories_of_installed_repositories = {} + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status can be anything). + # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the + # tool dependencies. + self.tool_dependencies_of_installed_repositories = {} + # Keep an in-memory dictionary whose keys are tuples defining tool_shed_repository objects (whose status is 'Installed') + # and whose values are a list of tuples defining its immediate tool_dependency objects (whose status is 'Installed'). + # The value defines only the immediate tool dependencies of the repository and does not include any dependencies of the + # tool dependencies. + self.installed_tool_dependencies_of_installed_repositories = {} + # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and + # whose values are a list of tuples defining tool_dependency objects (whose status can be anything) required by the + # installed tool dependency at runtime. The value defines the entire tool dependency tree. + self.runtime_tool_dependencies_of_installed_tool_dependencies = {} + # Keep an in-memory dictionary whose keys are tuples defining tool_dependency objects (whose status is 'Installed') and + # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key + # at runtime. The value defines the entire tool dependency tree. + self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} + # Load defined dependency relationships for installed tool shed repositories and their contents. + self.load_dependency_relationships() + + def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): + """ + Add an entry to self.installed_repository_dependencies_of_installed_repositories. A side-effect of this method + is the population of self.installed_dependent_repositories_of_installed_repositories. Since this method discovers + all repositories required by the received repository, it can use the list to add entries to the reverse dictionary. + """ + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_shed, name, owner, installed_changeset_revision = repository_tup + # Get the list of repository dependencies for this repository. + status = self.install_model.ToolShedRepository.installation_status.INSTALLED + repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=status ) + # Add an entry to self.installed_repository_dependencies_of_installed_repositories. + if repository_tup not in self.installed_repository_dependencies_of_installed_repositories: + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "to installed_repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + self.installed_repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups + # Use the repository_dependency_tups to add entries to the reverse dictionary + # self.installed_dependent_repositories_of_installed_repositories. + for required_repository_tup in repository_dependency_tups: + debug_msg = "Appending revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "to all dependent repositories in installed_dependent_repositories_of_installed_repositories." + log.debug( debug_msg ) + if required_repository_tup in self.installed_dependent_repositories_of_installed_repositories: + self.installed_dependent_repositories_of_installed_repositories[ required_repository_tup ].append( repository_tup ) + else: + self.installed_dependent_repositories_of_installed_repositories[ required_repository_tup ] = [ repository_tup ] + + def add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): + """Add an entry to self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup not in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Adding an entry for version %s of %s %s " % ( version, type, name ) + debug_msg += "to installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." + log.debug( debug_msg ) + status = self.install_model.ToolDependency.installation_status.INSTALLED + installed_runtime_dependent_tool_dependency_tups = \ + tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=status ) + self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] = \ + installed_runtime_dependent_tool_dependency_tups + + def add_entry_to_installed_tool_dependencies_of_installed_repositories( self, repository ): + """Add an entry to self.installed_tool_dependencies_of_installed_repositories.""" + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.installed_tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "to installed_tool_dependencies_of_installed_repositories." + log.debug( debug_msg ) + installed_tool_dependency_tups = [] + for tool_dependency in repository.tool_dependencies: + if tool_dependency.status == self.app.install_model.ToolDependency.installation_status.INSTALLED: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + installed_tool_dependency_tups.append( tool_dependency_tup ) + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] = installed_tool_dependency_tups + + def add_entry_to_repository_dependencies_of_installed_repositories( self, repository ): + """Add an entry to self.repository_dependencies_of_installed_repositories.""" + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.repository_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "to repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=None ) + self.repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups + + def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): + """Add an entry to self.runtime_tool_dependencies_of_installed_tool_dependencies.""" + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup not in self.runtime_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Adding an entry for version %s of %s %s " % ( version, type, name ) + debug_msg += "to runtime_tool_dependencies_of_installed_tool_dependencies." + log.debug( debug_msg ) + runtime_dependent_tool_dependency_tups = \ + tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=None ) + self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] = \ + runtime_dependent_tool_dependency_tups + + def add_entry_to_tool_dependencies_of_installed_repositories( self, repository ): + """Add an entry to self.tool_dependencies_of_installed_repositories.""" + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup not in self.tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "to tool_dependencies_of_installed_repositories." + log.debug( debug_msg ) + tool_dependency_tups = [] + for tool_dependency in repository.tool_dependencies: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + tool_dependency_tups.append( tool_dependency_tup ) + self.tool_dependencies_of_installed_repositories[ repository_tup ] = tool_dependency_tups + + def get_containing_repository_for_tool_dependency( self, tool_dependency_tup ): + tool_shed_repository_id, name, version, type = tool_dependency_tup + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ).get( tool_shed_repository_id ) + + def get_repository_install_dir( self, tool_shed_repository ): + for tool_config in self.tool_configs: + tree, error_message = xml_util.parse_xml( tool_config ) + if tree is None: + return None + root = tree.getroot() + tool_path = root.get( 'tool_path', None ) + if tool_path: + ts = suc.clean_tool_shed_url( tool_shed_repository.tool_shed ) + relative_path = os.path.join( tool_path, + ts, + 'repos', + str( tool_shed_repository.owner ), + str( tool_shed_repository.name ), + str( tool_shed_repository.installed_changeset_revision ) ) + if os.path.exists( relative_path ): + return relative_path + return None + + def handle_repository_install( self, repository ): + """Load the dependency relationships for a repository that was just installed or reinstalled.""" + # Populate self.repository_dependencies_of_installed_repositories. + self.add_entry_to_repository_dependencies_of_installed_repositories( repository ) + # Populate self.installed_repository_dependencies_of_installed_repositories. + self.add_entry_to_installed_repository_dependencies_of_installed_repositories( repository ) + # Populate self.tool_dependencies_of_installed_repositories. + self.add_entry_to_tool_dependencies_of_installed_repositories( repository ) + # Populate self.installed_tool_dependencies_of_installed_repositories. + self.add_entry_to_installed_tool_dependencies_of_installed_repositories( repository ) + for tool_dependency in repository.tool_dependencies: + # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies. + self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. + self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + + def handle_repository_uninstall( self, repository ): + """Remove the dependency relationships for a repository that was just uninstalled.""" + for tool_dependency in repository.tool_dependencies: + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + # Remove this tool_dependency from all values in + # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies + altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} + for td_tup, installed_runtime_dependent_tool_dependency_tups in \ + self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.items(): + if tool_dependency_tup in installed_runtime_dependent_tool_dependency_tups: + # Remove the tool_dependency from the list. + installed_runtime_dependent_tool_dependency_tups.remove( tool_dependency_tup ) + # Add the possibly altered list to the altered dictionary. + altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ td_tup ] = \ + installed_runtime_dependent_tool_dependency_tups + self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = \ + altered_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies + # Remove the entry for this tool_dependency from self.runtime_tool_dependencies_of_installed_tool_dependencies. + self.remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + # Remove the entry for this tool_dependency from + # self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. + self.remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + # Remove this repository's entry from self.installed_tool_dependencies_of_installed_repositories. + self.remove_entry_from_installed_tool_dependencies_of_installed_repositories( repository ) + # Remove this repository's entry from self.tool_dependencies_of_installed_repositories + self.remove_entry_from_tool_dependencies_of_installed_repositories( repository ) + # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories. + self.remove_entry_from_installed_repository_dependencies_of_installed_repositories( repository ) + # Remove this repository's entry from self.repository_dependencies_of_installed_repositories. + self.remove_entry_from_repository_dependencies_of_installed_repositories( repository ) + + def handle_tool_dependency_install( self, repository, tool_dependency ): + """Load the dependency relationships for a tool dependency that was just installed independently of its containing repository.""" + # The received repository must have a status of 'Installed'. The value of tool_dependency.status will either be + # 'Installed' or 'Error', but we only need to change the in-memory dictionaries if it is 'Installed'. + if tool_dependency.is_installed: + # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. + self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + # Populate self.installed_tool_dependencies_of_installed_repositories. + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if repository_tup in self.installed_tool_dependencies_of_installed_repositories: + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ].append( tool_dependency_tup ) + else: + self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] = [ tool_dependency_tup ] + + def load_dependency_relationships( self ): + """Load relationships for all installed repositories and tool dependencies into in-memnory dictionaries.""" + # Get the list of installed tool shed repositories. + for repository in self.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.status == + self.app.install_model.ToolShedRepository.installation_status.INSTALLED ): + # Populate self.repository_dependencies_of_installed_repositories. + self.add_entry_to_repository_dependencies_of_installed_repositories( repository ) + # Populate self.installed_repository_dependencies_of_installed_repositories. + self.add_entry_to_installed_repository_dependencies_of_installed_repositories( repository ) + # Populate self.tool_dependencies_of_installed_repositories. + self.add_entry_to_tool_dependencies_of_installed_repositories( repository ) + # Populate self.installed_tool_dependencies_of_installed_repositories. + self.add_entry_to_installed_tool_dependencies_of_installed_repositories( repository ) + # Get the list of installed tool dependencies. + for tool_dependency in self.context.query( self.app.install_model.ToolDependency ) \ + .filter( self.app.install_model.ToolDependency.table.c.status == + self.app.install_model.ToolDependency.installation_status.INSTALLED ): + # Populate self.runtime_tool_dependencies_of_installed_tool_dependencies. + self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + # Populate self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies. + self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) + + def load_proprietary_datatypes( self ): + for tool_shed_repository in self.context.query( self.install_model.ToolShedRepository ) \ + .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, + self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ + .order_by( self.install_model.ToolShedRepository.table.c.id ): + relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) + if relative_install_dir: + installed_repository_dict = datatype_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + if installed_repository_dict: + self.installed_repository_dicts.append( installed_repository_dict ) + + def load_proprietary_converters_and_display_applications( self, deactivate=False ): + for installed_repository_dict in self.installed_repository_dicts: + if installed_repository_dict[ 'converter_path' ]: + datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + if installed_repository_dict[ 'display_path' ]: + datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + + def remove_entry_from_installed_repository_dependencies_of_installed_repositories( self, repository ): + """ + Remove an entry from self.installed_repository_dependencies_of_installed_repositories. A side-effect of this method + is removal of appropriate value items from self.installed_dependent_repositories_of_installed_repositories. + """ + # Remove tuples defining this repository from value lists in self.installed_dependent_repositories_of_installed_repositories. + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + tool_shed, name, owner, installed_changeset_revision = repository_tup + altered_installed_dependent_repositories_of_installed_repositories = {} + for r_tup, v_tups in self.installed_dependent_repositories_of_installed_repositories.items(): + if repository_tup in v_tups: + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % \ + ( installed_changeset_revision, name, owner ) + r_tool_shed, r_name, r_owner, r_installed_changeset_revision = r_tup + debug_msg += "from the dependent list for revision %s of repository %s owned by %s " % \ + ( r_installed_changeset_revision, r_name, r_owner ) + debug_msg += "in installed_repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + v_tups.remove( repository_tup ) + altered_installed_dependent_repositories_of_installed_repositories[ r_tup ] = v_tups + self.installed_dependent_repositories_of_installed_repositories = \ + altered_installed_dependent_repositories_of_installed_repositories + # Remove this repository's entry from self.installed_repository_dependencies_of_installed_repositories. + if repository_tup in self.installed_repository_dependencies_of_installed_repositories: + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from installed_repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.installed_repository_dependencies_of_installed_repositories[ repository_tup ] + + def remove_entry_from_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): + """Remove an entry from self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies.""" + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup in self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Removing entry for version %s of %s %s " % ( version, type, name ) + debug_msg += "from installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies." + log.debug( debug_msg ) + del self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] + + def remove_entry_from_installed_tool_dependencies_of_installed_repositories( self, repository ): + """Remove an entry from self.installed_tool_dependencies_of_installed_repositories.""" + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.installed_tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from installed_tool_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.installed_tool_dependencies_of_installed_repositories[ repository_tup ] + + def remove_entry_from_repository_dependencies_of_installed_repositories( self, repository ): + """Remove an entry from self.repository_dependencies_of_installed_repositories.""" + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.repository_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) + debug_msg += "from repository_dependencies_of_installed_repositories." + log.debug( debug_msg ) + del self.repository_dependencies_of_installed_repositories[ repository_tup ] + + def remove_entry_from_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): + """Remove an entry from self.runtime_tool_dependencies_of_installed_tool_dependencies.""" + tool_dependency_tup = tool_dependency_util.get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ) + if tool_dependency_tup in self.runtime_tool_dependencies_of_installed_tool_dependencies: + tool_shed_repository_id, name, version, type = tool_dependency_tup + debug_msg = "Removing entry for version %s of %s %s from runtime_tool_dependencies_of_installed_tool_dependencies." % \ + ( version, type, name ) + log.debug( debug_msg ) + del self.runtime_tool_dependencies_of_installed_tool_dependencies[ tool_dependency_tup ] + + def remove_entry_from_tool_dependencies_of_installed_repositories( self, repository ): + """Remove an entry from self.tool_dependencies_of_installed_repositories.""" + repository_tup = repository_dependency_util.get_repository_tuple_for_installed_repository_manager( repository ) + if repository_tup in self.tool_dependencies_of_installed_repositories: + tool_shed, name, owner, installed_changeset_revision = repository_tup + debug_msg = "Removing entry for revision %s of repository %s owned by %s from tool_dependencies_of_installed_repositories." % \ + ( installed_changeset_revision, name, owner ) + log.debug( debug_msg ) + del self.tool_dependencies_of_installed_repositories[ repository_tup ] diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/galaxy_install/migrate/common.py --- a/lib/tool_shed/galaxy_install/migrate/common.py +++ b/lib/tool_shed/galaxy_install/migrate/common.py @@ -2,18 +2,10 @@ import os import sys import galaxy.config -import galaxy.datatypes.registry -from galaxy import tools -from galaxy.tools.data import ToolDataTableManager -from galaxy.web import security -import galaxy.model.mapping -import galaxy.tools.search -from galaxy.objectstore import build_object_store_from_config -import tool_shed.tool_shed_registry from tool_shed.galaxy_install import install_manager -class MigrateToolsApplication( object ): +class MigrateToolsApplication( object, galaxy.config.ConfiguresGalaxyMixin ): """Encapsulates the state of a basic Galaxy Universe application in order to initiate the Install Manager""" def __init__( self, tools_migration_config ): @@ -33,41 +25,23 @@ for key, value in config_parser.items( "app:main" ): galaxy_config_dict[ key ] = value self.config = galaxy.config.Configuration( **galaxy_config_dict ) - if not self.config.database_connection: - self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config.database + self.config.update_integrated_tool_panel = True - self.object_store = build_object_store_from_config( self.config ) - # Security helper - self.security = security.SecurityHelper( id_secret=self.config.id_secret ) - # Setup the database engine and ORM - self.model = galaxy.model.mapping.init( self.config.file_path, - self.config.database_connection, - engine_options={}, - create_tables=False, - object_store=self.object_store ) - # Create an empty datatypes registry. - self.datatypes_registry = galaxy.datatypes.registry.Registry() - # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. - self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) - # Initialize tool data tables using the config defined by self.config.tool_data_table_config_path. - self.tool_data_tables = ToolDataTableManager( tool_data_path=self.config.tool_data_path, - config_filename=self.config.tool_data_table_config_path ) - # Load additional entries defined by self.config.shed_tool_data_table_config into tool data tables. - self.tool_data_tables.load_from_config_file( config_filename=self.config.shed_tool_data_table_config, - tool_data_path=self.tool_data_tables.tool_data_path, - from_shed_config=True ) - # Initialize the tools, making sure the list of tool configs includes the reserved migrated_tools_conf.xml file. - tool_configs = self.config.tool_configs - if self.config.migrated_tools_config not in tool_configs: - tool_configs.append( self.config.migrated_tools_config ) - self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) - # Search support for tools - self.toolbox_search = galaxy.tools.search.ToolBoxSearch( self.toolbox ) - # Set up the tool sheds registry. - if os.path.isfile( self.config.tool_sheds_config ): - self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) - else: - self.tool_shed_registry = None + + self._configure_object_store() + + self._configure_security() + + self._configure_models() + + self._configure_datatypes_registry( ) + + self._configure_tool_data_tables( from_shed_config=True ) + + self._configure_toolbox() + + self._configure_tool_shed_registry() + # Get the latest tool migration script number to send to the Install manager. latest_migration_script_number = int( tools_migration_config.split( '_' )[ 0 ] ) # The value of migrated_tools_config is migrated_tools_conf.xml, and is reserved for containing only those tools that have been diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -504,8 +504,8 @@ query = trans.install_model.context.query( trans.install_model.ToolShedRepository ).filter( or_( *clause_list ) ) return encoded_kwd, query, tool_shed_repositories, encoded_repository_ids -def install_tool_shed_repository( trans, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path, install_tool_dependencies, - reinstalling=False ): +def install_tool_shed_repository( trans, tool_shed_repository, repo_info_dict, tool_panel_section_key, shed_tool_conf, tool_path, + install_tool_dependencies, reinstalling=False ): if tool_panel_section_key: try: tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] @@ -579,7 +579,11 @@ tool_dependencies_config=tool_dependencies_config, tool_dependencies=tool_shed_repository.tool_dependencies ) suc.remove_dir( work_dir ) - suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.INSTALLED ) + suc.update_tool_shed_repository_status( trans.app, + tool_shed_repository, + trans.install_model.ToolShedRepository.installation_status.INSTALLED ) + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. set_repository_attributes( trans, diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/galaxy_install/update_manager.py --- a/lib/tool_shed/galaxy_install/update_manager.py +++ b/lib/tool_shed/galaxy_install/update_manager.py @@ -30,7 +30,7 @@ # repository. This information includes items like newer installable repository revisions, current revision updates, whether # the repository revision is the latest installable revision, and whether the repository has been deprecated in the tool shed. for repository in self.context.query( self.app.install_model.ToolShedRepository ) \ - .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ): + .filter( self.app.install_model.ToolShedRepository.table.c.deleted == False ): tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, repository ) if tool_shed_status_dict: if tool_shed_status_dict != repository.tool_shed_status: diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- a/lib/tool_shed/scripts/check_repositories_for_functional_tests.py +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -253,6 +253,11 @@ # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts # since it will be re-inserted later. tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + elif len( tool_test_results_dict ) == 2 and \ + 'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict: + # We can re-use tool_test_results_dict if its only entries are "test_environment" and "missing_test_components". + # In this case, some tools are missing tests components while others are not. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. tool_test_results_dict = {} diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -41,6 +41,7 @@ class RepositoriesApplication( object ): """Encapsulates the state of a Universe application""" + def __init__( self, config ): if config.database_connection is False: config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database @@ -133,11 +134,12 @@ # Do not check metadata records that have an entry in the skip_tool_tests table, since they won't be tested anyway. skip_metadata_ids = select( [ app.model.SkipToolTest.table.c.repository_metadata_id ] ) # Get the list of metadata records to check, restricting it to records that have not been flagged do_not_test. - for repository_metadata in app.sa_session.query( app.model.RepositoryMetadata ) \ - .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, - app.model.RepositoryMetadata.table.c.do_not_test == False, - app.model.RepositoryMetadata.table.c.repository_id.in_( tool_dependency_defintion_repository_ids ), - not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): + for repository_metadata in \ + app.sa_session.query( app.model.RepositoryMetadata ) \ + .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, + app.model.RepositoryMetadata.table.c.do_not_test == False, + app.model.RepositoryMetadata.table.c.repository_id.in_( tool_dependency_defintion_repository_ids ), + not_( app.model.RepositoryMetadata.table.c.id.in_( skip_metadata_ids ) ) ) ): records_checked += 1 # Check the next repository revision. changeset_revision = str( repository_metadata.changeset_revision ) @@ -161,9 +163,31 @@ invalid_metadata += 1 if not info_only: # Create the tool_test_results_dict dictionary, using the dictionary from the previous test run if available. - if repository_metadata.tool_test_results: - tool_test_results_dict = repository_metadata.tool_test_results + if repository_metadata.tool_test_results is not None: + # We'll listify the column value in case it uses the old approach of storing the results of only a single test run. + tool_test_results_dicts = listify( repository_metadata.tool_test_results ) else: + tool_test_results_dicts = [] + if tool_test_results_dicts: + # Inspect the tool_test_results_dict for the last test run in case it contains only a test_environment + # entry. This will occur with multiple runs of this script without running the associated + # install_and_test_tool_sed_repositories.sh script which will further populate the tool_test_results_dict. + tool_test_results_dict = tool_test_results_dicts[ 0 ] + if len( tool_test_results_dict ) <= 1: + # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only + # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts + # since it will be re-inserted later. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + elif len( tool_test_results_dict ) == 2 and \ + 'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict: + # We can re-use tool_test_results_dict if its only entries are "test_environment" and "missing_test_components". + # In this case, some tools are missing tests components while others are not. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + else: + # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. + tool_test_results_dict = {} + else: + # Create a new dictionary for the most recent test run. tool_test_results_dict = {} # Initialize the tool_test_results_dict dictionary with the information about the current test environment. test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -71,8 +71,8 @@ def get_dependencies_for_repository( trans, tool_shed_url, repo_info_dict, includes_tool_dependencies ): """ - Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated with the repository defined - by the received repo_info_dict. + Return dictionaries containing the sets of installed and missing tool dependencies and repository dependencies associated + with the repository defined by the received repo_info_dict. """ repository = None installed_rd = {} @@ -102,7 +102,8 @@ # Discover all repository dependencies and retrieve information for installing them. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + has_repository_dependencies_only_if_compiling_contained_td = \ + all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) @@ -138,7 +139,8 @@ # We have a single repository with (possibly) no defined repository dependencies. all_repo_info_dict = get_required_repo_info_dicts( trans, tool_shed_url, util.listify( repo_info_dict ) ) has_repository_dependencies = all_repo_info_dict.get( 'has_repository_dependencies', False ) - has_repository_dependencies_only_if_compiling_contained_td = all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) + has_repository_dependencies_only_if_compiling_contained_td = \ + all_repo_info_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) includes_tools_for_display_in_tool_panel = all_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = all_repo_info_dict.get( 'includes_tool_dependencies', False ) includes_tools = all_repo_info_dict.get( 'includes_tools', False ) @@ -202,8 +204,8 @@ # Get the description from the metadata in case it has a value. repository_dependencies = metadata.get( 'repository_dependencies', {} ) description = repository_dependencies.get( 'description', None ) - # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the missing_repository_dependencies - # dictionaries for proper display parsing. + # We need to add a root_key entry to one or both of installed_repository_dependencies dictionary and the + # missing_repository_dependencies dictionaries for proper display parsing. root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, repository.name, repository.owner, @@ -460,7 +462,7 @@ if tool_dependency.can_install: # The database record is currently in a state that allows us to install the package on the file system. try: - dependencies_ignored = app.toolbox.dependency_manager and not app.toolbox.dependency_manager.uses_tool_shed_dependencies() + dependencies_ignored = not app.toolbox.dependency_manager.uses_tool_shed_dependencies() if dependencies_ignored: log.debug( "Skipping package %s because tool shed dependency resolver not enabled." % str( package_name ) ) # Tool dependency resolves have been configured and they do not include the tool shed. Do not install package. @@ -489,6 +491,8 @@ if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, app.install_model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) elif elem.tag == 'set_environment': # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -5,7 +5,6 @@ from galaxy.web.framework.helpers import time_ago from tool_shed.util import common_util from tool_shed.util import readme_util -from tool_shed.util.tool_dependency_util import tool_dependency_is_orphan import tool_shed.util.shed_util_common as suc log = logging.getLogger( __name__ ) @@ -269,7 +268,7 @@ """Tool dependency object""" def __init__( self, id=None, name=None, version=None, type=None, readme=None, installation_status=None, repository_id=None, - tool_dependency_id=None, is_orphan=None ): + tool_dependency_id=None ): self.id = id self.name = name self.version = version @@ -278,15 +277,6 @@ self.installation_status = installation_status self.repository_id = repository_id self.tool_dependency_id = tool_dependency_id - # The designation of a ToolDependency into the "orphan" category has evolved over time, and is significantly restricted since the - # introduction of the TOOL_DEPENDENCY_DEFINITION repository type. This designation is still critical, however, in that it handles - # the case where a repository contains both tools and a tool_dependencies.xml file, but the definition in the tool_dependencies.xml - # file is in no way related to anything defined by any of the contained tool's requirements tag sets. This is important in that it - # is often a result of a typo (e.g., dependency name or version) that differs between the tool dependency definition within the - # tool_dependencies.xml file and what is defined in the tool config's <requirements> tag sets. In these cases, the user should be - # presented with a warning message, and this warning message is is in fact displayed if the following is_orphan attribute is True. - # This is tricky because in some cases it may be intentional, and tool dependencies that are categorized as "orphan" are in fact valid. - self.is_orphan = is_orphan @property def listify( self ): @@ -318,42 +308,6 @@ self.repository_metadata_id = repository_metadata_id self.repository_id = repository_id -def add_orphan_settings_to_tool_dependencies( tool_dependencies, tools ): - """Inspect all received tool dependencies and label those that are orphans within the repository.""" - #orphan_env_dependencies = orphan_tool_dependencies.get( 'set_environment', None ) - new_tool_dependencies = {} - for td_key, requirements_dict in tool_dependencies.items(): - if td_key in [ 'set_environment' ]: - # "set_environment": [{"name": "R_SCRIPT_PATH", "type": "set_environment"}] - new_set_environment_dict_list = [] - for env_requirements_dict in requirements_dict: - try: - name = env_requirements_dict[ 'name' ] - type = env_requirements_dict[ 'type' ] - if tool_dependency_is_orphan( type, name, None, tools ): - env_requirements_dict[ 'is_orphan' ] = True - except Exception, e: - name = str( e ) - type = 'unknown' - is_orphan = 'unknown' - new_set_environment_dict_list.append( env_requirements_dict ) - new_tool_dependencies[ td_key ] = new_set_environment_dict_list - else: - # {"R/2.15.1": {"name": "R", "readme": "some string", "type": "package", "version": "2.15.1"} - try: - name = requirements_dict[ 'name' ] - type = requirements_dict[ 'type' ] - version = requirements_dict[ 'version'] - if tool_dependency_is_orphan( type, name, version, tools ): - requirements_dict[ 'is_orphan' ] = True - except Exception, e: - name = str( e ) - type = 'unknown' - version = 'unknown' - is_orphan = 'unknown' - new_tool_dependencies[ td_key ] = requirements_dict - return new_tool_dependencies - def build_data_managers_folder( trans, folder_id, data_managers, label=None ): """Return a folder hierarchy containing Data Managers.""" if data_managers: @@ -849,8 +803,6 @@ if 'tools' not in exclude: tools = metadata.get( 'tools', [] ) tools.extend( metadata.get( 'invalid_tools', [] ) ) - if tools: - tool_dependencies = add_orphan_settings_to_tool_dependencies( tool_dependencies, tools ) folder_id, tool_dependencies_root_folder = build_tool_dependencies_folder( trans, folder_id, tool_dependencies, @@ -1055,13 +1007,6 @@ tool_dependency_id += 1 if dependency_key in [ 'set_environment' ]: for set_environment_dict in requirements_dict: - if trans.webapp.name == 'tool_shed': - is_orphan = set_environment_dict.get( 'is_orphan', False ) - else: - # This is probably not necessary to display in Galaxy. - is_orphan = False - if is_orphan: - folder.description = not_used_by_local_tools_description try: name = set_environment_dict.get( 'name', None ) type = set_environment_dict[ 'type' ] @@ -1086,16 +1031,9 @@ readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id, - is_orphan=is_orphan ) + tool_dependency_id=td_id ) folder.tool_dependencies.append( tool_dependency ) else: - if trans.webapp.name == 'tool_shed': - is_orphan = requirements_dict.get( 'is_orphan', False ) - else: - is_orphan = False - if is_orphan: - folder.description = not_used_by_local_tools_description try: name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] @@ -1122,8 +1060,7 @@ readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id, - is_orphan=is_orphan ) + tool_dependency_id=td_id ) folder.tool_dependencies.append( tool_dependency ) else: tool_dependencies_root_folder = None diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -940,7 +940,12 @@ for required_file in ttb.required_files: value, extra = required_file required_files.append( ( value ) ) - inputs = [ input for input in ttb.inputs ] + inputs = [] + for input_field, values in ttb.inputs.iteritems(): + if len( values ) == 1: + inputs.append( ( input_field, values[0] ) ) + else: + inputs.append( ( input_field, values ) ) outputs = [] for output in ttb.outputs: name, file_name, extra = output diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -355,14 +355,53 @@ handled_key_rd_dicts, circular_repository_dependencies ) elif key_rd_dicts_to_be_processed: - handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + handle_next_repository_dependency( trans, + key_rd_dicts_to_be_processed, + all_repository_dependencies, + handled_key_rd_dicts, + circular_repository_dependencies ) elif key_rd_dicts_to_be_processed: - handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + handle_next_repository_dependency( trans, + key_rd_dicts_to_be_processed, + all_repository_dependencies, + handled_key_rd_dicts, + circular_repository_dependencies ) elif key_rd_dicts_to_be_processed: - handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + handle_next_repository_dependency( trans, + key_rd_dicts_to_be_processed, + all_repository_dependencies, + handled_key_rd_dicts, + circular_repository_dependencies ) all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies +def get_repository_dependency_tups_for_repository( app, repository, dependency_tups=None, status=None ): + """ + Return a list of of tuples defining tool_shed_repository objects (whose status can be anything) required by the + received repository. The returned list defines the entire repository dependency tree. + """ + if dependency_tups is None: + dependency_tups = [] + repository_tup = get_repository_tuple_for_installed_repository_manager( repository ) + for rrda in repository.required_repositories: + repository_dependency = rrda.repository_dependency + required_repository = repository_dependency.repository + if status is None or required_repository.status == status: + required_repository_tup = get_repository_tuple_for_installed_repository_manager( required_repository ) + if required_repository_tup == repository_tup: + # We have a circular repository dependency relationship, skip this entry. + continue + if required_repository_tup not in dependency_tups: + dependency_tups.append( required_repository_tup ) + return get_repository_dependency_tups_for_repository( app, required_repository, dependency_tups=dependency_tups ) + return dependency_tups + +def get_repository_tuple_for_installed_repository_manager( repository ): + return ( str( repository.tool_shed ), + str( repository.name ), + str( repository.owner ), + str( repository.installed_changeset_revision ) ) + def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): updated_key_rd_dicts = [] for key_rd_dict in key_rd_dicts: @@ -373,9 +412,10 @@ if suc.tool_shed_is_this_tool_shed( rd_toolshed ): repository = suc.get_repository_by_name_and_owner( trans.app, rd_name, rd_owner ) if repository: - repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, - trans.security.encode_id( repository.id ), - rd_changeset_revision ) + repository_metadata = \ + metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + trans.security.encode_id( repository.id ), + rd_changeset_revision ) if repository_metadata: # The repository changeset_revision is installable, so no updates are available. new_key_rd_dict = {} diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ b/lib/tool_shed/util/repository_maintenance_util.py @@ -137,7 +137,7 @@ results_message += 'This Tool Shed does not have the category <b>%s</b> so it will not be associated with this repository.' % \ str( category_name ) else: - category_ids.append( trans.security.encode_id( category.id ) ) + category_ids.append( trans.security.encode_id( category.id ) ) # Create the repository record in the database. repository, create_message = create_repository( trans, name, @@ -157,15 +157,18 @@ import_results_tups.append( ( ( str( name ), str( username ) ), results_message ) ) return import_results_tups -def validate_repository_name( name, user ): +def validate_repository_name( app, name, user ): # Repository names must be unique for each user, must be at least four characters # in length and must contain only lower-case letters, numbers, and the '_' character. if name in [ 'None', None, '' ]: return 'Enter the required repository name.' if name in [ 'repos' ]: return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name - for repository in user.active_repositories: - if repository.name == name: + check_existing = suc.get_repository_by_name_and_owner( app, name, user.username ) + if check_existing is not None: + if check_existing.deleted: + return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name + else: return "You already have a repository named <b>%s</b>, so choose a different name." % name if len( name ) < 4: return "Repository names must be at least 4 characters in length." diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -4,6 +4,7 @@ from galaxy import eggs from galaxy import util from galaxy.model.orm import and_ +from galaxy.model.orm import or_ import tool_shed.util.shed_util_common as suc import tool_shed.repository_types.util as rt_util from tool_shed.util import xml_util @@ -13,9 +14,10 @@ def add_installation_directories_to_tool_dependencies( trans, tool_dependencies ): """ - Determine the path to the installation directory for each of the received tool dependencies. This path will be displayed within the tool dependencies - container on the select_tool_panel_section or reselect_tool_panel_section pages when installing or reinstalling repositories that contain tools with the - defined tool dependencies. The list of tool dependencies may be associated with more than a single repository. + Determine the path to the installation directory for each of the received tool dependencies. This path will be + displayed within the tool dependencies container on the select_tool_panel_section or reselect_tool_panel_section + pages when installing or reinstalling repositories that contain tools with the defined tool dependencies. The + list of tool dependencies may be associated with more than a single repository. """ for dependency_key, requirements_dict in tool_dependencies.items(): if dependency_key in [ 'set_environment' ]: @@ -64,7 +66,10 @@ return tool_dependency def create_tool_dependency_objects( app, tool_shed_repository, relative_install_dir, set_status=True ): - """Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository.""" + """ + Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when + installing a new tool_shed_repository. + """ tool_dependency_objects = [] shed_config_dict = tool_shed_repository.get_shed_config_dict( app ) if shed_config_dict.get( 'tool_path' ): @@ -82,12 +87,13 @@ name = elem.get( 'name', None ) version = elem.get( 'version', None ) if name and version: + status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED tool_dependency = create_or_update_tool_dependency( app, tool_shed_repository, name=name, version=version, type=tool_dependency_type, - status=app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, + status=status, set_status=set_status ) tool_dependency_objects.append( tool_dependency ) elif tool_dependency_type == 'set_environment': @@ -96,12 +102,13 @@ name = env_elem.get( 'name', None ) action = env_elem.get( 'action', None ) if name and action: + status = app.install_model.ToolDependency.installation_status.NEVER_INSTALLED tool_dependency = create_or_update_tool_dependency( app, tool_shed_repository, name=name, version=None, type=tool_dependency_type, - status=app.install_model.ToolDependency.installation_status.NEVER_INSTALLED, + status=status, set_status=set_status ) tool_dependency_objects.append( tool_dependency ) return tool_dependency_objects @@ -185,12 +192,14 @@ def generate_message_for_repository_type_change( trans, repository ): message = '' if repository.can_change_type_to( trans.app, rt_util.TOOL_DEPENDENCY_DEFINITION ): - tool_dependency_definition_type_class = trans.app.repository_types_registry.get_class_by_label( rt_util.TOOL_DEPENDENCY_DEFINITION ) - message += "This repository currently contains a single file named <b>%s</b>. If additional files will " % suc.TOOL_DEPENDENCY_DEFINITION_FILENAME - message += "not be added to this repository, then it's type should be set to <b>%s</b>.<br/>" % tool_dependency_definition_type_class.label + tool_dependency_definition_type_class = \ + trans.app.repository_types_registry.get_class_by_label( rt_util.TOOL_DEPENDENCY_DEFINITION ) + message += "This repository currently contains a single file named <b>%s</b>. If additional files will " % \ + suc.TOOL_DEPENDENCY_DEFINITION_FILENAME + message += "not be added to this repository, then it's type should be set to <b>%s</b>.<br/>" % \ + tool_dependency_definition_type_class.label return message - - + def get_download_url_for_platform( url_templates, platform_info_dict ): ''' Compare the dict returned by get_platform_info() with the values specified in the url_template element. Return @@ -289,6 +298,31 @@ env_sh_file_path = os.path.join( env_sh_file_dir, 'env.sh' ) return env_sh_file_path +def get_runtime_dependent_tool_dependency_tuples( app, tool_dependency, status=None ): + """ + Return the list of tool dependency objects that require the received tool dependency at run time. The returned + list will be filtered by the received status if it is not None. This method is called only from Galaxy. + """ + runtime_dependent_tool_dependency_tups = [] + required_env_shell_file_path = tool_dependency.get_env_shell_file_path( app ) + if required_env_shell_file_path: + required_env_shell_file_path = os.path.abspath( required_env_shell_file_path ) + if required_env_shell_file_path is not None: + for td in app.install_model.context.query( app.install_model.ToolDependency ): + if status is None or td.status == status: + env_shell_file_path = td.get_env_shell_file_path( app ) + if env_shell_file_path is not None: + try: + contents = open( env_shell_file_path, 'r' ).read() + except Exception, e: + contents = None + log.debug( 'Error reading file %s, so cannot determine if package %s requires package %s at run time: %s' % \ + ( str( env_shell_file_path ), str( td.name ), str( tool_dependency.name ), str( e ) ) ) + if contents is not None and contents.find( required_env_shell_file_path ) >= 0: + td_tuple = get_tool_dependency_tuple_for_installed_repository_manager( td ) + runtime_dependent_tool_dependency_tups.append( td_tuple ) + return runtime_dependent_tool_dependency_tups + def get_tool_dependency( trans, id ): """Get a tool_dependency from the database via id""" return trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) ) @@ -353,6 +387,13 @@ repository_name, repository_changeset_revision ) ) +def get_tool_dependency_tuple_for_installed_repository_manager( tool_dependency ): + if tool_dependency.type is None: + type = None + else: + type = str( tool_dependency.type ) + return ( tool_dependency.tool_shed_repository_id, str( tool_dependency.name ), str( tool_dependency.version ), type ) + def handle_tool_dependency_installation_error( app, tool_dependency, error_message, remove_installation_path=False ): # Since there was an installation error, remove the installation directory because the install_package method uses # this: "if os.path.exists( install_dir ):". Setting remove_installation_path to True should rarely occur. It is @@ -479,6 +520,7 @@ return installed_tool_dependencies, missing_tool_dependencies def remove_tool_dependency( app, tool_dependency ): + """The received tool_dependency must be in an error state.""" context = app.install_model.context dependency_install_dir = tool_dependency.installation_directory( app ) removed, error_message = remove_tool_dependency_installation_directory( dependency_install_dir ) @@ -487,6 +529,9 @@ tool_dependency.error_message = None context.add( tool_dependency ) context.flush() + # Since the received tool_dependency is in an error state, nothing will need to be changed in any + # of the in-memory dictionaries in the installed_repository_manager because changing the state from + # error to uninstalled requires no in-memory changes.. return removed, error_message def remove_tool_dependency_installation_directory( dependency_install_dir ): diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a static/scripts/galaxy.workflow_editor.canvas.js --- a/static/scripts/galaxy.workflow_editor.canvas.js +++ b/static/scripts/galaxy.workflow_editor.canvas.js @@ -360,7 +360,7 @@ workflow.has_changes = true; canvas_manager.draw_overview(); }))) - .tooltip({delay:500, title: "Flag this as a workflow output. All non-flagged outputs will be hidden." }); + .tooltip({delay:500, title: "Mark dataset as a workflow output. All unmarked datasets will be hidden." }); callout.css({ top: '50%', margin:'-8px 0px 0px 0px', diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -173,6 +173,7 @@ //============================================================================== var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */{ +//TODO: since this is a mixin, consider moving toggle, hidden into HUAVOptions /** */ hiddenUntilActivated : function( $activator, options ){ @@ -184,7 +185,9 @@ showSpeed : 'fast' }; _.extend( this.HUAVOptions, options || {}); + /** has this been shown already (and onshowFirstTime called)? */ this.HUAVOptions.hasBeenShown = this.HUAVOptions.$elementShown.is( ':visible' ); + this.hidden = this.isHidden(); if( $activator ){ var mixin = this; @@ -194,21 +197,36 @@ } }, + isHidden : function(){ + return ( this.HUAVOptions.$elementShown.is( ':hidden' ) ); + }, + /** */ toggle : function(){ // can be called manually as well with normal toggle arguments - if( this.HUAVOptions.$elementShown.is( ':hidden' ) ){ + //TODO: better as a callback (when the show/hide is actually done) + // show + if( this.hidden ){ // fire the optional fns on the first/each showing - good for render() if( !this.HUAVOptions.hasBeenShown ){ if( _.isFunction( this.HUAVOptions.onshowFirstTime ) ){ this.HUAVOptions.hasBeenShown = true; this.HUAVOptions.onshowFirstTime.call( this ); } - } else { - if( _.isFunction( this.HUAVOptions.onshow ) ){ - this.HUAVOptions.onshow.call( this ); - } } + if( _.isFunction( this.HUAVOptions.onshow ) ){ + this.HUAVOptions.onshow.call( this ); + this.trigger( 'hiddenUntilActivated:shown', this ); + } + this.hidden = false; + + // hide + } else { + if( _.isFunction( this.HUAVOptions.onhide ) ){ + this.HUAVOptions.onhide.call( this ); + this.trigger( 'hiddenUntilActivated:hidden', this ); + } + this.hidden = true; } return this.HUAVOptions.showFn.apply( this.HUAVOptions.$elementShown, arguments ); } diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 5463295a3981c8487effbbbaa127fe028737491a static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -46,11 +46,11 @@ /** is the view currently in selection mode? */ this.selectable = attributes.selectable || false; /** is the view currently selected? */ - this.selected = attributes.selected || false; - /** is the body of this hda view expanded/not. */ - this.expanded = attributes.expanded || false; - /** is the body of this hda view expanded/not. */ - this.draggable = attributes.draggable || false; + this.selected = attributes.selected || false; + /** is the body of this hda view expanded/not? */ + this.expanded = attributes.expanded || false; + /** is the body of this hda view expanded/not? */ + this.draggable = attributes.draggable || false; this._setUpListeners(); }, @@ -423,7 +423,7 @@ toggleBodyVisibility : function( event, expand ){ // bail (with propagation) if keydown and not space or enter var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( ( event.type === 'keydown' ) + if( event && ( event.type === 'keydown' ) && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ return true; } This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/70aca9eee9d4/ Changeset: 70aca9eee9d4 User: martenson Date: 2013-12-16 00:22:01 Summary: activation link tweak: show proper message when trying to activate already active account Affected #: 1 file diff -r 0522f7504094bd5be2be97846e695a0c790bf929 -r 70aca9eee9d442a88e49dc99e08ff3b6bbea73d0 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -826,19 +826,22 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() + # If the user is active already don't try to activate + if user.active == True: + return trans.show_ok_message( "Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) if user.activation_token == activation_token: user.activation_token = None user.active = True trans.sa_session.add(user) trans.sa_session.flush() - return trans.show_ok_message( "Your account has been successfully activated!<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/d5be36722eb3/ Changeset: d5be36722eb3 Branch: data_library User: martenson Date: 2013-12-16 17:14:59 Summary: Closed branch data_library Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/2b83e7980707/ Changeset: 2b83e7980707 User: martenson Date: 2013-12-16 17:42:28 Summary: closing data_library branch Affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/commits/0b2f53ad1a20/ Changeset: 0b2f53ad1a20 User: martenson Date: 2013-12-16 18:01:35 Summary: Merge own default 2nd head Affected #: 1 file diff -r 2b83e798070736ea7279d5e4e33194f66f8ef7df -r 0b2f53ad1a2025dbfd7c15a76f329fc5e8a859ef lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -826,19 +826,22 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() + # If the user is active already don't try to activate + if user.active == True: + return trans.show_ok_message( "Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) if user.activation_token == activation_token: user.activation_token = None user.active = True trans.sa_session.add(user) trans.sa_session.flush() - return trans.show_ok_message( "Your account has been successfully activated!<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): https://bitbucket.org/galaxy/galaxy-central/commits/16d53da082b8/ Changeset: 16d53da082b8 User: martenson Date: 2013-12-17 19:22:55 Summary: added security checks when downloading lddas in archives Affected #: 1 file diff -r 0b2f53ad1a2025dbfd7c15a76f329fc5e8a859ef -r 16d53da082b89db1318a2a688aa8a18470b02f59 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -13,15 +13,17 @@ import urllib import urllib2 import zipfile +from paste.httpexceptions import HTTPBadRequest +from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException from galaxy.security import Action from galaxy import util, web from galaxy.util.streamball import StreamBall -from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixinItems +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin import logging log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesLibraryMixinItems ): +class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): @web.expose_api def show( self, trans, id, **kwd ): @@ -31,7 +33,7 @@ """ # Get dataset. try: - dataset = self.get_library_dataset( trans, id = id ) + dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: return str( e ) try: @@ -65,12 +67,22 @@ datasets_to_download = util.listify( datasets_to_download ) for dataset_id in datasets_to_download: try: - ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - assert not ldda.dataset.purged + ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) lddas.append( ldda ) - except: - ldda = None - message += "Invalid library dataset id (%s) specified. " % str( dataset_id ) + except ItemAccessibilityException: + trans.response.status = 403 + return 'Insufficient rights to access library dataset with id: (%s)' % str( dataset_id ) + except MessageException: + trans.response.status = 400 + return 'Wrong library dataset id: (%s)' % str( dataset_id ) + except ItemDeletionException: + trans.response.status = 400 + return 'The item with library dataset id: (%s) is deleted' % str( dataset_id ) + except HTTPBadRequest, e: + return 'http bad request' + str( e.err_msg ) + except Exception, e: + trans.response.status = 500 + return 'error of unknown kind' + str( e ) if format in [ 'zip','tgz','tbz' ]: error = False https://bitbucket.org/galaxy/galaxy-central/commits/2b4877fc1024/ Changeset: 2b4877fc1024 User: martenson Date: 2013-12-17 19:35:08 Summary: exception catching rewritten, it is now behaving better, not good but better than before Affected #: 1 file diff -r 16d53da082b89db1318a2a688aa8a18470b02f59 -r 2b4877fc1024180fadb5128187d447c0b84c7cd9 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -1,5 +1,5 @@ """ -API operations on the dataset from library. +API operations on the datasets from library. """ import glob import logging @@ -35,6 +35,7 @@ try: dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: + trans.response.status = 500 return str( e ) try: # Default: return dataset as dict. @@ -43,24 +44,22 @@ rval = "Error in dataset API at listing contents: " + str( e ) log.error( rval + ": %s" % str(e), exc_info=True ) trans.response.status = 500 + return "Error in dataset API at listing contents: " + str( e ) rval['id'] = trans.security.encode_id(rval['id']); rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) - + trans.response.status = 200 return rval @web.expose def download( self, trans, format, **kwd ): """ - POST /api/libraries/datasets/download/{format} - POST data: ldda_ids = [] - Downloads dataset(s) in the requested format. + GET /api/libraries/datasets/download/{format} + GET multiple params: ldda_ids = [] + Downloads dataset(s) in the requested format or plain. """ lddas = [] -# is_admin = trans.user_is_admin() -# current_user_roles = trans.get_current_user_roles() - datasets_to_download = kwd['ldda_ids%5B%5D'] if ( datasets_to_download != None ): @@ -111,15 +110,13 @@ archive = StreamBall( 'w|bz2' ) outext = 'tbz2' except ( OSError, zipfile.BadZipfile ): - error = True log.exception( "Unable to create archive for download" ) - message = "Unable to create archive for download, please report this error" - status = 'error' + trans.response.status = 500 + return "Unable to create archive for download, please report this error" except: - error = True log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) - message = "Unable to create archive for download, please report - %s" % sys.exc_info()[0] - status = 'error' + trans.response.status = 500 + return "Unable to create archive for download, please report - %s" % sys.exc_info()[0] if not error: composite_extensions = trans.app.datatypes_registry.get_composite_extensions() seen = [] @@ -150,11 +147,9 @@ try: archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set except IOError: - error = True log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) - message = "Unable to create archive for download, please report this error" - status = 'error' - continue + trans.response.status = 500 + return "Unable to create archive for download, please report this error" flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths for fpath in flist: efp,fname = os.path.split(fpath) @@ -163,19 +158,16 @@ try: archive.add( fpath,fname ) except IOError: - error = True log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) - message = "Unable to create archive for download, please report this error" - status = 'error' - continue + trans.response.status = 500 + return "Unable to create archive for download, please report this error" else: # simple case try: archive.add( ldda.dataset.file_name, path ) except IOError: - error = True log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) - message = "Unable to create archive for download, please report this error" - status = 'error' + trans.response.status = 500 + return "Unable to create archive for download, please report this error" if not error: lname = 'selected_dataset' fname = lname.replace( ' ', '_' ) + '_files' @@ -186,15 +178,18 @@ archive = util.streamball.ZipBall(tmpf, tmpd) archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 return archive.stream else: trans.response.set_content_type( "application/x-tar" ) trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) archive.wsgi_status = trans.response.wsgi_status() archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 return archive.stream elif format == 'uncompressed': if len(lddas) != 1: + trans.response.status = 400 return 'Wrong request' else: single_dataset = lddas[0] @@ -206,8 +201,11 @@ fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname try: + trans.response.status = 200 return open( single_dataset.file_name ) except: + trans.response.status = 500 return 'This dataset contains no content' else: - return 'Wrong format'; + trans.response.status = 400 + return 'Wrong format parameter specified'; https://bitbucket.org/galaxy/galaxy-central/commits/6f89cbaeb29c/ Changeset: 6f89cbaeb29c User: martenson Date: 2013-12-17 21:58:40 Summary: fix for errors thrown when requested underlying file of dataset does not exist; even better exception handling for ldda-archive downloading Affected #: 2 files diff -r 2b4877fc1024180fadb5128187d447c0b84c7cd9 -r 6f89cbaeb29c33ae8d662d84965bf3bdee7f179d lib/galaxy/util/streamball.py --- a/lib/galaxy/util/streamball.py +++ b/lib/galaxy/util/streamball.py @@ -3,6 +3,7 @@ """ import os import logging, tarfile +from galaxy.exceptions import ObjectNotFound log = logging.getLogger( __name__ ) @@ -14,8 +15,12 @@ self.mode = mode self.wsgi_status = None self.wsgi_headeritems = None - def add( self, file, relpath ): - self.members[file] = relpath + def add( self, file, relpath, check_file=False): + if check_file and len(file)>0: + if not os.path.isfile(file): + raise ObjectNotFound + else: + self.members[file] = relpath def stream( self, environ, start_response ): response_write = start_response( self.wsgi_status, self.wsgi_headeritems ) class tarfileobj: diff -r 2b4877fc1024180fadb5128187d447c0b84c7cd9 -r 6f89cbaeb29c33ae8d662d84965bf3bdee7f179d lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -14,7 +14,7 @@ import urllib2 import zipfile from paste.httpexceptions import HTTPBadRequest -from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException +from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound from galaxy.security import Action from galaxy import util, web from galaxy.util.streamball import StreamBall @@ -84,7 +84,7 @@ return 'error of unknown kind' + str( e ) if format in [ 'zip','tgz','tbz' ]: - error = False + # error = False killme = string.punctuation + string.whitespace trantab = string.maketrans(killme,'_'*len(killme)) try: @@ -117,12 +117,12 @@ log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) trans.response.status = 500 return "Unable to create archive for download, please report - %s" % sys.exc_info()[0] - if not error: + if True: composite_extensions = trans.app.datatypes_registry.get_composite_extensions() seen = [] for ldda in lddas: - if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: - continue + # if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: + # continue ext = ldda.extension is_composite = ext in composite_extensions path = "" @@ -135,6 +135,7 @@ path = os.path.join( parent_folder.name, path ) parent_folder = parent_folder.parent path += ldda.name + while path in seen: path += '_' seen.append( path ) @@ -145,30 +146,61 @@ if zpathext == '': zpath = '%s.html' % zpath # fake the real nature of the html file try: - archive.add(ldda.dataset.file_name,zpath) # add the primary of a composite set + if format=='zip': + archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set + else: + archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set except IOError: log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) trans.response.status = 500 return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths for fpath in flist: efp,fname = os.path.split(fpath) if fname > '': fname = fname.translate(trantab) try: - archive.add( fpath,fname ) + if format=='zip': + archive.add( fpath,fname ) + else: + archive.add( fpath,fname, check_file=True ) except IOError: log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) trans.response.status = 500 return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % fpath ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" else: # simple case try: - archive.add( ldda.dataset.file_name, path ) + if format=='zip': + archive.add( ldda.dataset.file_name, path ) + else: + archive.add( ldda.dataset.file_name, path, check_file=True ) except IOError: log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) trans.response.status = 500 return "Unable to create archive for download, please report this error" - if not error: + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + + if True: lname = 'selected_dataset' fname = lname.replace( ' ', '_' ) + '_files' if format == 'zip': https://bitbucket.org/galaxy/galaxy-central/commits/8090554de504/ Changeset: 8090554de504 User: martenson Date: 2013-12-18 17:41:24 Summary: minor cosmetic changes Affected #: 2 files diff -r 6f89cbaeb29c33ae8d662d84965bf3bdee7f179d -r 8090554de504ffa05e744fdca051b9350aeae93f static/scripts/utils/galaxy.uploadbox.js --- a/static/scripts/utils/galaxy.uploadbox.js +++ b/static/scripts/utils/galaxy.uploadbox.js @@ -353,3 +353,4 @@ }; } })(jQuery); + diff -r 6f89cbaeb29c33ae8d662d84965bf3bdee7f179d -r 8090554de504ffa05e744fdca051b9350aeae93f static/style/Gruntfile.js --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -6,7 +6,7 @@ var theme = grunt.option( 'theme', 'blue' ); var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster']; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; var _ = grunt.util._; var fmt = _.sprintf; https://bitbucket.org/galaxy/galaxy-central/commits/00fb5740d971/ Changeset: 00fb5740d971 User: martenson Date: 2013-12-19 18:44:34 Summary: refactor + docs Affected #: 2 files diff -r 8090554de504ffa05e744fdca051b9350aeae93f -r 00fb5740d971318d4384e69fc2fcc6b2318b2d44 doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -297,6 +297,14 @@ :undoc-members: :show-inheritance: +:mod:`lda_datasets` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.lda_datasets + :members: + :undoc-members: + :show-inheritance: + :mod:`libraries` Module ----------------------- diff -r 8090554de504ffa05e744fdca051b9350aeae93f -r 00fb5740d971318d4384e69fc2fcc6b2318b2d44 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -28,8 +28,17 @@ @web.expose_api def show( self, trans, id, **kwd ): """ - GET /api/libraries/datasets/{encoded_dataset_id} - Displays information about the dataset identified by the lda ID. + show( self, trans, id, **kwd ) + * GET /api/libraries/datasets/{encoded_dataset_id}: + Displays information about the dataset identified by the encoded id. + + + :type id: an encoded id string + :param id: the encoded id of the dataset to query + + :rtype: dictionary + :returns: detailed dataset information from + :func:`galaxy.web.base.controller.UsesVisualizationMixin.get_library_dataset.to_dict()` """ # Get dataset. try: @@ -55,9 +64,25 @@ @web.expose def download( self, trans, format, **kwd ): """ - GET /api/libraries/datasets/download/{format} - GET multiple params: ldda_ids = [] - Downloads dataset(s) in the requested format or plain. + download( self, trans, format, **kwd ) + * GET /api/libraries/datasets/download/{format} + + .. code-block:: + example: + GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828 + + :type format: string + :param format: string representing requested archive format + + .. note:: supported formats are: zip, tgz, tbz, uncompressed + + :type lddas[]: an array + :param lddas[]: an array of encoded ids + + :rtype: file + :returns: either archive with the requested datasets packed inside or a single uncompressed dataset + + :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound """ lddas = [] datasets_to_download = kwd['ldda_ids%5B%5D'] @@ -117,108 +142,101 @@ log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) trans.response.status = 500 return "Unable to create archive for download, please report - %s" % sys.exc_info()[0] - if True: - composite_extensions = trans.app.datatypes_registry.get_composite_extensions() - seen = [] - for ldda in lddas: - # if ldda.dataset.state in [ 'new', 'upload', 'queued', 'running', 'empty', 'discarded' ]: - # continue - ext = ldda.extension - is_composite = ext in composite_extensions - path = "" - parent_folder = ldda.library_dataset.folder - while parent_folder is not None: - # Exclude the now-hidden "root folder" - if parent_folder.parent is None: - path = os.path.join( parent_folder.library_root[0].name, path ) - break - path = os.path.join( parent_folder.name, path ) - parent_folder = parent_folder.parent - path += ldda.name - - while path in seen: - path += '_' - seen.append( path ) - zpath = os.path.split(path)[-1] # comes as base_name/fname - outfname,zpathext = os.path.splitext(zpath) - if is_composite: - # need to add all the components from the extra_files_path to the zip - if zpathext == '': - zpath = '%s.html' % zpath # fake the real nature of the html file + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + if format=='zip': + archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set + else: + archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set + except IOError: + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) try: if format=='zip': - archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set - else: - archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set + archive.add( fpath,fname ) + else: + archive.add( fpath,fname, check_file=True ) except IOError: - log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) trans.response.status = 500 return "Unable to create archive for download, please report this error" except ObjectNotFound: - log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + log.exception( "Requested dataset %s does not exist on the host." % fpath ) trans.response.status = 500 - return "Requested dataset does not exist on the host." - except: - trans.response.status = 500 - return "Unknown error, please report this error" - flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths - for fpath in flist: - efp,fname = os.path.split(fpath) - if fname > '': - fname = fname.translate(trantab) - try: - if format=='zip': - archive.add( fpath,fname ) - else: - archive.add( fpath,fname, check_file=True ) - except IOError: - log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) - trans.response.status = 500 - return "Unable to create archive for download, please report this error" - except ObjectNotFound: - log.exception( "Requested dataset %s does not exist on the host." % fpath ) - trans.response.status = 500 - return "Requested dataset does not exist on the host." - except: - trans.response.status = 500 - return "Unknown error, please report this error" - else: # simple case - try: - if format=='zip': - archive.add( ldda.dataset.file_name, path ) - else: - archive.add( ldda.dataset.file_name, path, check_file=True ) - except IOError: - log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) - trans.response.status = 500 - return "Unable to create archive for download, please report this error" - except ObjectNotFound: - log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) - trans.response.status = 500 - return "Requested dataset does not exist on the host." + return "Requested dataset does not exist on the host." except: trans.response.status = 500 return "Unknown error, please report this error" - - if True: - lname = 'selected_dataset' - fname = lname.replace( ' ', '_' ) + '_files' - if format == 'zip': - archive.close() - trans.response.set_content_type( "application/octet-stream" ) - trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) - archive = util.streamball.ZipBall(tmpf, tmpd) - archive.wsgi_status = trans.response.wsgi_status() - archive.wsgi_headeritems = trans.response.wsgi_headeritems() - trans.response.status = 200 - return archive.stream - else: - trans.response.set_content_type( "application/x-tar" ) - trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) - archive.wsgi_status = trans.response.wsgi_status() - archive.wsgi_headeritems = trans.response.wsgi_headeritems() - trans.response.status = 200 - return archive.stream + else: # simple case + try: + if format=='zip': + archive.add( ldda.dataset.file_name, path ) + else: + archive.add( ldda.dataset.file_name, path, check_file=True ) + except IOError: + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 + return archive.stream elif format == 'uncompressed': if len(lddas) != 1: trans.response.status = 400 https://bitbucket.org/galaxy/galaxy-central/commits/c1963ee06cb0/ Changeset: c1963ee06cb0 User: martenson Date: 2013-12-19 18:48:22 Summary: Merged in martenson/galaxy-central-marten (pull request #273) Initial Data Libraries Affected #: 24 files diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b doc/source/lib/galaxy.webapps.galaxy.api.rst --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -302,6 +302,14 @@ :undoc-members: :show-inheritance: +:mod:`lda_datasets` Module +-------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.lda_datasets + :members: + :undoc-members: + :show-inheritance: + :mod:`libraries` Module ----------------------- diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1827,7 +1827,7 @@ class Library( object, Dictifiable ): permitted_actions = get_permitted_actions( filter='LIBRARY' ) dict_collection_visible_keys = ( 'id', 'name' ) - dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis' ) + dict_element_visible_keys = ( 'id', 'deleted', 'name', 'description', 'synopsis', 'root_folder_id' ) def __init__( self, name=None, description=None, synopsis=None, root_folder=None ): self.name = name or "Unnamed library" self.description = description @@ -1894,7 +1894,7 @@ return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description @@ -2060,6 +2060,7 @@ genome_build = ldda.dbkey, misc_info = ldda.info, misc_blurb = ldda.blurb, + peek = ( lambda ldda: ldda.display_peek() if ldda.peek and ldda.peek != 'no peek' else None )( ldda ), template_data = template_data ) if ldda.dataset.uuid is None: rval['uuid'] = None diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -1852,8 +1852,9 @@ table = self.table trans = conn.begin() try: - next_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() - table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid + 1 ) ) + current_hid = select( [table.c.hid_counter], table.c.id == self.id, for_update=True ).scalar() + next_hid = current_hid + 1 + table.update( table.c.id == self.id ).execute( hid_counter = ( next_hid ) ) trans.commit() return next_hid except: diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/util/streamball.py --- a/lib/galaxy/util/streamball.py +++ b/lib/galaxy/util/streamball.py @@ -3,6 +3,7 @@ """ import os import logging, tarfile +from galaxy.exceptions import ObjectNotFound log = logging.getLogger( __name__ ) @@ -14,8 +15,12 @@ self.mode = mode self.wsgi_status = None self.wsgi_headeritems = None - def add( self, file, relpath ): - self.members[file] = relpath + def add( self, file, relpath, check_file=False): + if check_file and len(file)>0: + if not os.path.isfile(file): + raise ObjectNotFound + else: + self.members[file] = relpath def stream( self, environ, start_response ): response_write = start_response( self.wsgi_status, self.wsgi_headeritems ) class tarfileobj: diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a dataset. +API operations on the contents of a history dataset. """ from galaxy import web from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,67 +11,122 @@ log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ + + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. + Full path is provided as a separate object in response providing data for breadcrumb path building. """ - rval = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - - try: - decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) - except TypeError: - trans.response.status = 400 - return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) + if ( folder_id.startswith( 'F' ) ): + try: + decoded_folder_id = trans.security.decode_id( folder_id[1:] ) + except TypeError: + trans.response.status = 400 + return "Malformed folder id ( %s ) specified, unable to decode." % str( folder_id ) try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) - parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + path_to_root = [] + def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ + path_to_root = [] + # We are almost in root + if folder.parent_id is None: + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + else: + # We add the current folder and traverse up one folder. + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) + return path_to_root + + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] + folder_container.append( dict( full_path = full_path ) ) + + folder_contents = [] + time_updated = '' + time_created = '' + # Go through every item in the folder and include its meta-data. + for content_item in self.load_folder_contents( trans, folder ): +# rval = content_item.to_dict() + return_item = {} + encoded_id = trans.security.encode_id( content_item.id ) + time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + time_created = content_item.create_time.strftime( "%Y-%m-%d %I:%M %p" ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_id = 'F' + encoded_id +# time_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count ) ) - for content in traverse( folder ): - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, - type = content.api_type, - name = content.name, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - return rval + if content_item.api_type == 'file': + library_dataset_dict = content_item.to_dict() + library_dataset_dict['data_type'] + library_dataset_dict['file_size'] + library_dataset_dict['date_uploaded'] + return_item.update ( dict ( data_type = library_dataset_dict['data_type'], + file_size = library_dataset_dict['file_size'], + date_uploaded = library_dataset_dict['date_uploaded'] ) ) + + # For every item return also the default meta-data + return_item.update( dict( id = encoded_id, + type = content_item.api_type, + name = content_item.name, + time_updated = time_updated, + time_created = time_created + ) ) + folder_contents.append( return_item ) + # Put the data in the container + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/api/lda_datasets.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -0,0 +1,261 @@ +""" +API operations on the datasets from library. +""" +import glob +import logging +import operator +import os +import os.path +import string +import sys +import tarfile +import tempfile +import urllib +import urllib2 +import zipfile +from paste.httpexceptions import HTTPBadRequest +from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound +from galaxy.security import Action +from galaxy import util, web +from galaxy.util.streamball import StreamBall +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin + +import logging +log = logging.getLogger( __name__ ) + +class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): + + @web.expose_api + def show( self, trans, id, **kwd ): + """ + show( self, trans, id, **kwd ) + * GET /api/libraries/datasets/{encoded_dataset_id}: + Displays information about the dataset identified by the encoded id. + + + :type id: an encoded id string + :param id: the encoded id of the dataset to query + + :rtype: dictionary + :returns: detailed dataset information from + :func:`galaxy.web.base.controller.UsesVisualizationMixin.get_library_dataset.to_dict()` + """ + # Get dataset. + try: + dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) + except Exception, e: + trans.response.status = 500 + return str( e ) + try: + # Default: return dataset as dict. + rval = dataset.to_dict() + except Exception, e: + rval = "Error in dataset API at listing contents: " + str( e ) + log.error( rval + ": %s" % str(e), exc_info=True ) + trans.response.status = 500 + return "Error in dataset API at listing contents: " + str( e ) + + rval['id'] = trans.security.encode_id(rval['id']); + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['folder_id'] = 'f' + trans.security.encode_id(rval['folder_id']) + trans.response.status = 200 + return rval + + @web.expose + def download( self, trans, format, **kwd ): + """ + download( self, trans, format, **kwd ) + * GET /api/libraries/datasets/download/{format} + + .. code-block:: + example: + GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828 + + :type format: string + :param format: string representing requested archive format + + .. note:: supported formats are: zip, tgz, tbz, uncompressed + + :type lddas[]: an array + :param lddas[]: an array of encoded ids + + :rtype: file + :returns: either archive with the requested datasets packed inside or a single uncompressed dataset + + :raises: MessageException, ItemDeletionException, ItemAccessibilityException, HTTPBadRequest, OSError, IOError, ObjectNotFound + """ + lddas = [] + datasets_to_download = kwd['ldda_ids%5B%5D'] + + if ( datasets_to_download != None ): + datasets_to_download = util.listify( datasets_to_download ) + for dataset_id in datasets_to_download: + try: + ldda = self.get_hda_or_ldda( trans, hda_ldda='ldda', dataset_id=dataset_id ) + lddas.append( ldda ) + except ItemAccessibilityException: + trans.response.status = 403 + return 'Insufficient rights to access library dataset with id: (%s)' % str( dataset_id ) + except MessageException: + trans.response.status = 400 + return 'Wrong library dataset id: (%s)' % str( dataset_id ) + except ItemDeletionException: + trans.response.status = 400 + return 'The item with library dataset id: (%s) is deleted' % str( dataset_id ) + except HTTPBadRequest, e: + return 'http bad request' + str( e.err_msg ) + except Exception, e: + trans.response.status = 500 + return 'error of unknown kind' + str( e ) + + if format in [ 'zip','tgz','tbz' ]: + # error = False + killme = string.punctuation + string.whitespace + trantab = string.maketrans(killme,'_'*len(killme)) + try: + outext = 'zip' + if format == 'zip': + # Can't use mkstemp - the file must not exist first + tmpd = tempfile.mkdtemp() + util.umask_fix_perms( tmpd, trans.app.config.umask, 0777, self.app.config.gid ) + tmpf = os.path.join( tmpd, 'library_download.' + format ) + if trans.app.config.upstream_gzip: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_STORED, True ) + else: + archive = zipfile.ZipFile( tmpf, 'w', zipfile.ZIP_DEFLATED, True ) + archive.add = lambda x, y: archive.write( x, y.encode('CP437') ) + elif format == 'tgz': + if trans.app.config.upstream_gzip: + archive = StreamBall( 'w|' ) + outext = 'tar' + else: + archive = StreamBall( 'w|gz' ) + outext = 'tgz' + elif format == 'tbz': + archive = StreamBall( 'w|bz2' ) + outext = 'tbz2' + except ( OSError, zipfile.BadZipfile ): + log.exception( "Unable to create archive for download" ) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except: + log.exception( "Unexpected error %s in create archive for download" % sys.exc_info()[0] ) + trans.response.status = 500 + return "Unable to create archive for download, please report - %s" % sys.exc_info()[0] + composite_extensions = trans.app.datatypes_registry.get_composite_extensions() + seen = [] + for ldda in lddas: + ext = ldda.extension + is_composite = ext in composite_extensions + path = "" + parent_folder = ldda.library_dataset.folder + while parent_folder is not None: + # Exclude the now-hidden "root folder" + if parent_folder.parent is None: + path = os.path.join( parent_folder.library_root[0].name, path ) + break + path = os.path.join( parent_folder.name, path ) + parent_folder = parent_folder.parent + path += ldda.name + while path in seen: + path += '_' + seen.append( path ) + zpath = os.path.split(path)[-1] # comes as base_name/fname + outfname,zpathext = os.path.splitext(zpath) + if is_composite: # need to add all the components from the extra_files_path to the zip + if zpathext == '': + zpath = '%s.html' % zpath # fake the real nature of the html file + try: + if format=='zip': + archive.add( ldda.dataset.file_name, zpath ) # add the primary of a composite set + else: + archive.add( ldda.dataset.file_name, zpath, check_file=True ) # add the primary of a composite set + except IOError: + log.exception( "Unable to add composite parent %s to temporary library download archive" % ldda.dataset.file_name) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + flist = glob.glob(os.path.join(ldda.dataset.extra_files_path,'*.*')) # glob returns full paths + for fpath in flist: + efp,fname = os.path.split(fpath) + if fname > '': + fname = fname.translate(trantab) + try: + if format=='zip': + archive.add( fpath,fname ) + else: + archive.add( fpath,fname, check_file=True ) + except IOError: + log.exception( "Unable to add %s to temporary library download archive %s" % (fname,outfname)) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % fpath ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + else: # simple case + try: + if format=='zip': + archive.add( ldda.dataset.file_name, path ) + else: + archive.add( ldda.dataset.file_name, path, check_file=True ) + except IOError: + log.exception( "Unable to write %s to temporary library download archive" % ldda.dataset.file_name) + trans.response.status = 500 + return "Unable to create archive for download, please report this error" + except ObjectNotFound: + log.exception( "Requested dataset %s does not exist on the host." % ldda.dataset.file_name ) + trans.response.status = 500 + return "Requested dataset does not exist on the host." + except: + trans.response.status = 500 + return "Unknown error, please report this error" + lname = 'selected_dataset' + fname = lname.replace( ' ', '_' ) + '_files' + if format == 'zip': + archive.close() + trans.response.set_content_type( "application/octet-stream" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive = util.streamball.ZipBall(tmpf, tmpd) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 + return archive.stream + else: + trans.response.set_content_type( "application/x-tar" ) + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s.%s"' % (fname,outext) + archive.wsgi_status = trans.response.wsgi_status() + archive.wsgi_headeritems = trans.response.wsgi_headeritems() + trans.response.status = 200 + return archive.stream + elif format == 'uncompressed': + if len(lddas) != 1: + trans.response.status = 400 + return 'Wrong request' + else: + single_dataset = lddas[0] + trans.response.set_content_type( single_dataset.get_mime() ) + fStat = os.stat( ldda.file_name ) + trans.response.headers[ 'Content-Length' ] = int( fStat.st_size ) + valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' + fname = ldda.name + fname = ''.join( c in valid_chars and c or '_' for c in fname )[ 0:150 ] + trans.response.headers[ "Content-Disposition" ] = 'attachment; filename="%s"' % fname + try: + trans.response.status = 200 + return open( single_dataset.file_name ) + except: + trans.response.status = 500 + return 'This dataset contains no content' + else: + trans.response.status = 400 + return 'Wrong format parameter specified'; diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,9 +49,10 @@ trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) + item['root_folder_id'] = 'F' + trans.security.encode_id( item['root_folder_id'] ) rval.append( item ) return rval @@ -131,6 +132,9 @@ rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -46,12 +46,6 @@ atexit.register( app.shutdown ) # Create the universe WSGI application webapp = GalaxyWebApplication( app, session_cookie='galaxysession', name='galaxy' ) - # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. - webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', - controller='admin_toolshed', - action='display_image_in_repository', - repository_id=None, - image_file=None ) webapp.add_ui_controllers( 'galaxy.webapps.galaxy.controllers', app ) # Force /history to go to /root/history -- needed since the tests assume this webapp.add_route( '/history', controller='root', action='history' ) @@ -75,22 +69,12 @@ webapp.add_route( '/u/:username/v/:slug', controller='visualization', action='display_by_username_and_slug' ) webapp.add_route( '/search', controller='search', action='index' ) - # Add the web API + # ================ + # ===== API ===== + # ================ + webapp.add_api_controllers( 'galaxy.webapps.galaxy.api', app ) - # The /folders section is experimental at this point: - log.debug( "app.config.api_folders: %s" % app.config.api_folders ) - webapp.mapper.resource( 'folder', 'folders', path_prefix='/api' ) - webapp.mapper.resource( 'content', 'contents', - controller='folder_contents', - name_prefix='folder_', - path_prefix='/api/folders/:folder_id', - parent_resources=dict( member_name='folder', collection_name='folders' ) ) - webapp.mapper.resource( 'content', - 'contents', - controller='library_contents', - name_prefix='library_', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.mapper.resource( 'content', 'contents', controller='history_contents', @@ -102,10 +86,6 @@ controller="datasets", action="display", conditions=dict(method=["GET"])) - webapp.mapper.resource( 'permission', - 'permissions', - path_prefix='/api/libraries/:library_id', - parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.mapper.resource( 'user', 'users', controller='group_users', @@ -127,11 +107,6 @@ _add_item_tags_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - - _add_item_extended_metadata_controller( webapp, - name_prefix="library_dataset_", - path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) - _add_item_annotation_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -141,7 +116,6 @@ _add_item_annotation_controller( webapp, name_prefix="workflow_", path_prefix='/api/workflows/:workflow_id' ) - _add_item_provenance_controller( webapp, name_prefix="history_content_", path_prefix='/api/histories/:history_id/contents/:history_content_id' ) @@ -170,6 +144,7 @@ parent_resources=dict( member_name='datatype', collection_name='datatypes' ) ) #webapp.mapper.connect( 'run_workflow', '/api/workflow/{workflow_id}/library/{library_id}', controller='workflows', action='run', workflow_id=None, library_id=None, conditions=dict(method=["GET"]) ) webapp.mapper.resource( 'search', 'search', path_prefix='/api' ) + # add as a non-ATOM API call to support the notion of a 'current/working' history unique to the history resource webapp.mapper.connect( "set_as_current", "/api/histories/{id}/set_as_current", @@ -188,6 +163,64 @@ webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) # Preserve the following download route for now for dependent applications -- deprecate at some point webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + + # ======================= + # ===== LIBRARY API ===== + # ======================= + + webapp.mapper.connect( 'show_lda_item', + '/api/libraries/datasets/:id', + controller='lda_datasets', + action='show', + conditions=dict( method=[ "GET" ] ) ) + + webapp.mapper.connect( 'download_lda_items', + '/api/libraries/datasets/download/:format', + controller='lda_datasets', + action='download', + conditions=dict( method=[ "POST", "GET" ] ) ) + + webapp.mapper.resource_with_deleted( 'library', + 'libraries', + path_prefix='/api' ) + webapp.mapper.resource( 'folder', + 'folders', + path_prefix='/api' ) + + webapp.mapper.resource( 'content', + 'contents', + controller='folder_contents', + name_prefix='folder_', + path_prefix='/api/folders/:folder_id', + parent_resources=dict( member_name='folder', collection_name='folders' ) ) + + webapp.mapper.resource( 'content', + 'contents', + controller='library_contents', + name_prefix='library_', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + + webapp.mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) + + _add_item_extended_metadata_controller( webapp, + name_prefix="library_dataset_", + path_prefix='/api/libraries/:library_id/contents/:library_content_id' ) + + # ==================== + # ===== TOOLSHED ===== + # ==================== + + # Handle displaying tool help images and README file images contained in repositories installed from the tool shed. + webapp.add_route( '/admin_toolshed/static/images/:repository_id/:image_file', + controller='admin_toolshed', + action='display_image_in_repository', + repository_id=None, + image_file=None ) + # Galaxy API for tool shed features. webapp.mapper.resource( 'tool_shed_repository', 'tool_shed_repositories', @@ -201,6 +234,7 @@ path_prefix='/api', new={ 'install_repository_revision' : 'POST' }, parent_resources=dict( member_name='tool_shed_repository', collection_name='tool_shed_repositories' ) ) + # Connect logger from app if app.trace_logger: webapp.trace_logger = app.trace_logger @@ -221,7 +255,7 @@ galaxy.model.mapping.metadata.engine.connection_provider._pool.dispose() except: pass - # Close any pooled database connections before forking + # Close any pooled database connections before forking try: galaxy.model.tool_shed_install.mapping.metadata.engine.connection_provider._pool.dispose() except: diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/controllers/library.py --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -76,6 +76,17 @@ library_list_grid = LibraryListGrid() + + @web.expose + def list( self, trans, **kwd ): + params = util.Params( kwd ) + # define app configuration for generic mako template + app = { + 'jscript' : "galaxy.library" + } + # fill template + return trans.fill_template('galaxy.panels.mako', config = {'app' : app}) + @web.expose def index( self, trans, **kwd ): params = util.Params( kwd ) diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -826,19 +826,22 @@ if email is None or activation_token is None: # We don't have the email or activation_token, show error. - return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) + return trans.show_error_message( "You are using wrong activation link. Try to log-in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller="root", action="index" ) else: # Find the user user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email==email ).first() + # If the user is active already don't try to activate + if user.active == True: + return trans.show_ok_message( "Your account is already active. Nothing has changed. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) if user.activation_token == activation_token: user.activation_token = None user.active = True trans.sa_session.add(user) trans.sa_session.flush() - return trans.show_ok_message( "Your account has been successfully activated!<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_ok_message( "Your account has been successfully activated! <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) else: # Tokens don't match. Activation is denied. - return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email.<br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) + return trans.show_error_message( "You are using wrong activation link. Try to log in and we will send you a new activation email. <br><a href='%s'>Go to login page.</a>" ) % web.url_for( controller='root', action='index' ) return def __get_user_type_form_definition( self, trans, user=None, **kwd ): diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b static/scripts/galaxy.library.js --- /dev/null +++ b/static/scripts/galaxy.library.js @@ -0,0 +1,902 @@ +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM +// === GALAXY LIBRARY MODULE ==== +// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMM + +// global variables +var view = null; +var library_router = null; +var responses = []; + +// dependencies +define([ + "galaxy.modal", + "galaxy.masthead", + "utils/galaxy.utils", + "libs/toastr"], function(mod_modal, mod_masthead, mod_utils, mod_toastr) { + +// MMMMMMMMMMMMMMM +// === Models ==== +// MMMMMMMMMMMMMMM + + // LIBRARY + var Library = Backbone.Model.extend({ + urlRoot: '/api/libraries' + }); + + // LIBRARIES + var Libraries = Backbone.Collection.extend({ + url: '/api/libraries', + model: Library + }); + + // ITEM + var Item = Backbone.Model.extend({ + urlRoot : '/api/libraries/datasets' + }) + + // FOLDER + var Folder = Backbone.Collection.extend({ + model: Item + }) + + // CONTAINER for folder contents (folders, items and metadata). + var FolderContainer = Backbone.Model.extend({ + defaults : { + folder : new Folder(), + full_path : "unknown", + urlRoot : "/api/folders/", + id : "unknown" + }, + parse : function(obj) { + this.full_path = obj[0].full_path; + // update the inner collection + this.get("folder").reset(obj[1].folder_contents); + return obj; + } + }) + + // HISTORY ITEM + var HistoryItem = Backbone.Model.extend({ + urlRoot : '/api/histories/' + }); + + // HISTORY + var GalaxyHistory = Backbone.Model.extend({ + url : '/api/histories/' + }); + + // HISTORIES + var GalaxyHistories = Backbone.Collection.extend({ + url : '/api/histories', + model : GalaxyHistory + }); + + //ROUTER + var LibraryRouter = Backbone.Router.extend({ + routes: { + "" : "libraries", + "folders/:id" : "folder_content", + "folders/:folder_id/download/:format" : "download" + } + }); + + +// MMMMMMMMMMMMMM +// === VIEWS ==== +// MMMMMMMMMMMMMM + +// galaxy folder +var FolderContentView = Backbone.View.extend({ + // main element definition + el : '#center', + // progress percentage + progress: 0, + // progress rate per one item + progressStep: 1, + // last selected history in modal for UX + lastSelectedHistory: '', + // self modal + modal : null, + // loaded folders + folders : null, + + // initialize + initialize : function(){ + this.folders = []; + this.queue = jQuery.Deferred(); + this.queue.resolve(); + }, + +// MMMMMMMMMMMMMMMMMM +// === TEMPLATES ==== +// MMMMMMMMMMMMMMMMMM + + // set up + templateFolder : function (){ + var tmpl_array = []; + + // CONTAINER + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + + // TOOLBAR + tmpl_array.push('<div id="library_folder_toolbar" >'); + tmpl_array.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>'); + tmpl_array.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>'); + + tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">'); + tmpl_array.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">'); + tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>'); + tmpl_array.push(' </button>'); + tmpl_array.push(' <ul class="dropdown-menu" role="menu">'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>'); + tmpl_array.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>'); + tmpl_array.push(' </ul>'); + tmpl_array.push(' </div>'); + + tmpl_array.push('</div>'); + + // BREADCRUMBS + tmpl_array.push('<div class="library_breadcrumb">'); + tmpl_array.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> '); + tmpl_array.push('<% _.each(path, function(path_item) { %>'); + tmpl_array.push('<% if (path_item[0] != id) { %>'); + tmpl_array.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> '); + tmpl_array.push('<% } else { %>'); + tmpl_array.push('<span title="You are in this folder"><%- path_item[1] %></span>'); + tmpl_array.push('<% } %>'); + tmpl_array.push('<% }); %>'); + tmpl_array.push('</div>'); + + // FOLDER CONTENT + tmpl_array.push('<table id="folder_table" class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); + tmpl_array.push(' <th class="button_heading">view</th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>data type</th>'); + tmpl_array.push(' <th>size</th>'); + tmpl_array.push(' <th>date</th>'); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-arrow-up"></span> .. go up</td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% _.each(items, function(content_item) { %>'); + tmpl_array.push(' <tr class="folder_row light" id="<%- content_item.id %>">'); + tmpl_array.push(' <% if (content_item.get("type") === "folder") { %>'); // folder + tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- content_item.get("name") %>'); + tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>'); // empty folder + tmpl_array.push(' <span class="muted">(empty folder)</span>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td>folder</td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>'); // size + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>'); + tmpl_array.push(' <td>'); + tmpl_array.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-eye"></span> details'); + tmpl_array.push(' </button>'); + tmpl_array.push(' </td>'); + tmpl_array.push(' <td><%- content_item.get("name") %></td>'); // dataset + tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type + tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size + tmpl_array.push(' <% } %> '); + tmpl_array.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>'); // time updated + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' '); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + templateDatasetModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<div id="dataset_info_modal">'); + tmpl_array.push(' <table class="table table-striped table-condensed">'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("name")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Data type</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("data_type")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Genome build</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("genome_build")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Size</th>'); + tmpl_array.push(' <td><%= _.escape(size) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Date uploaded</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Uploaded by</th>'); + tmpl_array.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr scope="row">'); + tmpl_array.push(' <th scope="row">Data Lines</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <th scope="row">Comment Lines</th>'); + tmpl_array.push(' <% if (item.get("metadata_comment_lines") === "") { %>'); //folder + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>'); + tmpl_array.push(' <% } else { %>'); + tmpl_array.push(' <td scope="row">unknown</td>'); + tmpl_array.push(' <% } %>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Number of Columns</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Column Types</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <th scope="row">Miscellaneous information</th>'); + tmpl_array.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' </table>'); + tmpl_array.push(' <pre class="peek">'); + tmpl_array.push(' </pre>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + }, + + templateHistorySelectInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + templateBulkImportInModal : function(){ + var tmpl_array = []; + + tmpl_array.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">'); + tmpl_array.push('Select history: '); + tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> '); + tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box + tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</select>'); + tmpl_array.push('</span>'); + + return tmpl_array.join(''); + }, + + // convert size to nice string + size_to_string : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = "TB"; } else + if (size >= 100000000) { size = size / 100000000; unit = "GB"; } else + if (size >= 100000) { size = size / 100000; unit = "MB"; } else + if (size >= 100) { size = size / 100; unit = "KB"; } else + { size = size * 10; unit = "b"; } + // return formatted string + return (Math.round(size) / 10) + unit; + }, + +// MMMMMMMMMMMMMMM +// === EVENTS ==== +// MMMMMMMMMMMMMMM + + // event binding + events: { + 'click #select-all-checkboxes' : 'selectAll', + 'click .folder_row' : 'selectClickedRow', + 'click #toolbtn_bulk_import' : 'modalBulkImport', + 'click #toolbtn_dl' : 'bulkDownload', + 'click .library-dataset' : 'showDatasetDetails', + 'click #toolbtn_create_folder' : 'createFolderModal', + 'click .btn_open_folder' : 'navigateToFolder' + }, + + //render the folder view + render: function (options) { + //hack to show scrollbars + $("#center").css('overflow','auto'); + + view = this; + var that = this; + + var folderContainer = new FolderContainer({id: options.id}); + folderContainer.url = folderContainer.attributes.urlRoot + options.id + '/contents'; + + folderContainer.fetch({ + success: function (container) { + + // prepare nice size strings + for (var i = 0; i < folderContainer.attributes.folder.models.length; i++) { + var model = folderContainer.attributes.folder.models[i] + if (model.get('type') === 'file'){ + model.set('readable_size', that.size_to_string(model.get('file_size'))) + } + }; + + // find the upper id + var path = folderContainer.full_path; + var upper_folder_id; + if (path.length === 1){ // library is above us + upper_folder_id = 0; + } else { + upper_folder_id = path[path.length-2][0]; + } + + var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id, upper_folder_id: upper_folder_id }); + // var template = _.template(that.templateFolder(), { path: folderContainer.full_path, items: folderContainer.attributes.folder.models, id: options.id }); + that.$el.html(template); + + } + }) + }, + + // handles the click on 'open' and 'upper' folder icons + navigateToFolder : function(event){ + var folder_id = $(event.target).attr('data-id'); + if (typeof folder_id === 'undefined') { + return false; + } else if (folder_id === '0'){ + library_router.navigate('#', {trigger: true, replace: true}); + } else { + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } + }, + + //show modal with current dataset info + showDatasetDetails : function(event){ + // prevent default + event.preventDefault(); + +//TODO check whether we already have the data + + //load the ID of the row + var id = $(event.target).parent().parent().attr('id'); + + //create new item + var item = new Item(); + var histories = new GalaxyHistories(); + item.id = id; + var self = this; + + //fetch the dataset info + item.fetch({ + success: function (item) { +// TODO can render here already + //fetch user histories for import purposes + histories.fetch({ + success: function (histories){self.renderModalAfterFetch(item, histories)} + }); + } + }); + }, + + // show the current dataset in a modal + renderModalAfterFetch : function(item, histories){ + var size = this.size_to_string(item.get('file_size')); + var template = _.template(this.templateDatasetModal(), { item : item, size : size }); + this.modal = null; + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal({ + title : 'Dataset Details', + body : template, + buttons : { + 'Import' : function() { self.importCurrentIntoHistory() }, + 'Download' : function() { self.downloadCurrent() }, + 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data + } + }); + $(".peek").html(item.get("peek")); + var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); + $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); + + // preset last selected history if we know it + if (self.lastSelectedHistory.length > 0) { + $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); + } + + // show the prepared modal + this.modal.show(); + }, + + // download dataset shown currently in modal + downloadCurrent : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var library_dataset_id = []; + library_dataset_id.push($('#id_row').attr('data-id')); + var url = '/api/libraries/datasets/download/uncompressed'; + var data = {'ldda_ids' : library_dataset_id}; + + // we assume the view is existent + folderContentView.processDownload(url, data); + this.modal.enableButton('Import'); + this.modal.enableButton('Download'); + }, + + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); + + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use + + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + mod_toastr.success('Dataset imported'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + mod_toastr.error('An error occured! Dataset not imported. Please try again.') + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + // select all datasets + selectAll : function (event) { + var selected = event.target.checked; + that = this; + // Iterate each checkbox + $(':checkbox').each(function () { + this.checked = selected; + $row = $(this.parentElement.parentElement); + // Change color of selected/unselected + (selected) ? that.makeDarkRow($row) : that.makeWhiteRow($row); + }); + // Show the tools in menu + this.checkTools(); + }, + + // Check checkbox on row itself or row checkbox click + selectClickedRow : function (event) { + var checkbox = ''; + var $row; + var source; + if (event.target.localName === 'input'){ + checkbox = event.target; + $row = $(event.target.parentElement.parentElement); + source = 'input'; + } else if (event.target.localName === 'td') { + checkbox = $("#" + event.target.parentElement.id).find(':checkbox')[0]; + $row = $(event.target.parentElement); + source = 'td'; + } + if (checkbox === '') {event.stopPropagation(); return;} // button in row was clicked + + if (checkbox.checked){ + if (source==='td'){ + checkbox.checked = ''; + this.makeWhiteRow($row); + } else if (source==='input') { + this.makeDarkRow($row); + } + } else { + if (source==='td'){ + checkbox.checked = 'selected'; + this.makeDarkRow($row); + } else if (source==='input') { + this.makeWhiteRow($row); + } + } + this.checkTools(); + }, + + makeDarkRow: function($row){ + $row.removeClass('light'); + $row.find('a').removeClass('light'); + $row.addClass('dark'); + $row.find('a').addClass('dark'); + }, + + makeWhiteRow: function($row){ + $row.removeClass('dark'); + $row.find('a').removeClass('dark'); + $row.addClass('light'); + $row.find('a').addClass('light'); + }, + + // show toolbar in case something is selected + checkTools : function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length > 0){ + $('#toolbtn_bulk_import').show(); + $('#toolbtn_dl').show(); + } else { + $('#toolbtn_bulk_import').hide(); + $('#toolbtn_dl').hide(); + } + + }, + + // show bulk import modal + modalBulkImport : function(){ + var self = this; + // fetch histories + var histories = new GalaxyHistories(); + histories.fetch({ + success: function (histories){ + // make modal + var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); + self.modal = new mod_modal.GalaxyModal({ + title : 'Import into History', + body : history_modal_tmpl, + buttons : { + 'Import' : function() {self.importAllIntoHistory()}, + 'Close' : function() {self.modal.hide(); $('.modal').remove(); self.modal = null;} + } + }); + // show the prepared modal + self.modal.show(); + } + }); + }, + + // import all selected datasets into history + importAllIntoHistory : function (){ + //disable the button + this.modal.disableButton('Import'); + + var history_id = $("select[name=dataset_import_bulk] option:selected").val(); + var history_name = $("select[name=dataset_import_bulk] option:selected").text(); + + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + var progress_bar_tmpl = _.template(this.templateProgressBar(), { history_name : history_name }); + $(this.modal.elMain).find('.modal-body').html(progress_bar_tmpl); + + // init the progress bar + var progressStep = 100 / dataset_ids.length; + this.initProgress(progressStep); + + // prepare the dataset objects to be imported + var datasets_to_import = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + library_dataset_id = dataset_ids[i]; + var historyItem = new HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; + historyItem.content = library_dataset_id; + historyItem.source = 'library'; + datasets_to_import.push(historyItem); + }; + + // call the recursive function to call ajax one after each other + this.chainCall(datasets_to_import); + }, + + chainCall: function(history_item_set){ + var self = this; + var popped_item = history_item_set.pop(); + if (typeof popped_item === "undefined") { + mod_toastr.success('All datasets imported'); + this.modal.hide(); + // enable button again + self.modal.enableButton('Import'); + return + } + var promise = $.when(popped_item.save({content: popped_item.content, source: popped_item.source})).done(function(a1){ + self.updateProgress(); + responses.push(a1); + self.chainCall(history_item_set); + }); + }, + + initProgress: function(progressStep){ + this.progress = 0; + this.progressStep = progressStep; + }, + updateProgress: function(){ + this.progress += this.progressStep; + $('.progress-bar').width(Math.round(this.progress) + '%'); + txt_representation = Math.round(this.progress) + '% Complete'; + $('.completion_span').text(txt_representation); + }, + + // progress bar + templateProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('Importing selected datasets to history <b><%= _.escape(history_name) %></b>'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return tmpl_array.join(''); + }, + + // download selected datasets + download : function(folder_id, format){ + var dataset_ids = []; + $('#folder_table').find(':checked').each(function(){ + if (this.parentElement.parentElement.id != '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + + var url = '/api/libraries/datasets/download/' + format; + var data = {'ldda_ids' : dataset_ids}; + this.processDownload(url, data, 'get'); + }, + + // create hidden form and submit through POST to initialize download + processDownload: function(url, data, method){ + //url and data options required + if( url && data ){ + //data can be string of parameters or array/object + data = typeof data == 'string' ? data : $.param(data); + //split params into form inputs + var inputs = ''; + $.each(data.split('&'), function(){ + var pair = this.split('='); + inputs+='<input type="hidden" name="'+ pair[0] +'" value="'+ pair[1] +'" />'; + }); + //send request + $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') + .appendTo('body').submit().remove(); + mod_toastr.info('Your download will begin soon'); + }; + }, + + // shows modal for creating folder + createFolderModal: function(){ + mod_toastr.info('This will create folder...in the future'); + } + + }); + +// galaxy library view +var GalaxyLibraryview = Backbone.View.extend({ + el: '#center', + + events: { + 'click #create_new_library_btn' : 'show_library_modal' + }, + + // initialize + initialize : function(){ + }, + + // template + template_library_list : function (){ + tmpl_array = []; + tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); + + tmpl_array.push(''); + tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); + tmpl_array.push('<table class="table table-condensed">'); + tmpl_array.push(' <thead>'); + tmpl_array.push(' <th class="button_heading"></th>'); + tmpl_array.push(' <th>name</th>'); + tmpl_array.push(' <th>description</th>'); + tmpl_array.push(' <th>synopsis</th> '); + tmpl_array.push(' <th>model type</th> '); + tmpl_array.push(' </thead>'); + tmpl_array.push(' <tbody>'); + tmpl_array.push(' <% _.each(libraries, function(library) { %>'); + tmpl_array.push(' <tr>'); + tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">'); + tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>'); + tmpl_array.push(' <td><%- library.get("name") %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>'); + tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>'); + tmpl_array.push(' </tr>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push(' </tbody>'); + tmpl_array.push('</table>'); + + tmpl_array.push('</div>'); + return tmpl_array.join(''); + }, + + // render + render: function () { + //hack to show scrollbars due to #center element inheritance + $("#center").css('overflow','auto'); + + var that = this; + libraries = new Libraries(); + + libraries.fetch({ + success: function (libraries) { + var template = _.template(that.template_library_list(), { libraries : libraries.models }); + that.$el.html(template); + }, + error: function(model, response){ + if (response.statusCode().status === 403){ + mod_toastr.error('Please log in first. Redirecting to login page in 3s.'); + setTimeout(that.redirectToLogin, 3000); + } else { + mod_toastr.error('An error occured. Please try again.'); + } + } + }) + }, + + redirectToHome: function(){ + window.location = '../'; + }, + redirectToLogin: function(){ + window.location = '/user/login'; + }, + + // own modal + modal : null, + + // show/hide create library modal + show_library_modal : function (event){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + this.modal = new mod_modal.GalaxyModal( + { + title : 'Create New Library', + body : this.template_new_library(), + buttons : { + 'Create' : function() {self.create_new_library_event()}, + 'Close' : function() {self.modal.hide()} + } + }); + + // show prepared modal + this.modal.show(); + }, + + // create the new library from modal + create_new_library_event: function(){ + var libraryDetails = this.serialize_new_library(); + if (this.validate_new_library(libraryDetails)){ + var library = new Library(); + var self = this; + library.save(libraryDetails, { + success: function (library) { + self.modal.hide(); + self.clear_library_modal(); + self.render(); + mod_toastr.success('Library created'); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + } else { + mod_toastr.error('Library\'s name is missing'); + } + return false; + }, + + // clear the library modal once saved + clear_library_modal : function(){ + $("input[name='Name']").val(''); + $("input[name='Description']").val(''); + $("input[name='Synopsis']").val(''); + }, + + // serialize data from the form + serialize_new_library : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val(), + synopsis: $("input[name='Synopsis']").val() + }; + }, + + // validate new library info + validate_new_library: function(libraryDetails){ + return libraryDetails.name !== ''; + }, + + // template for new library modal + template_new_library: function(){ + tmpl_array = []; + + tmpl_array.push('<div id="new_library_modal">'); + tmpl_array.push('<form>'); + tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">'); + tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">'); + tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">'); + tmpl_array.push('</form>'); + tmpl_array.push('</div>'); + + return tmpl_array.join(''); + } +}); + +// galaxy library wrapper View +var GalaxyLibrary = Backbone.View.extend({ + folderContentView : null, + galaxyLibraryview : null, + initialize : function(){ + + folderContentView = new FolderContentView(); + galaxyLibraryview = new GalaxyLibraryview(); + library_router = new LibraryRouter(); + + library_router.on('route:libraries', function() { + // render libraries list + galaxyLibraryview.render(); + }); + + library_router.on('route:folder_content', function(id) { + // render folder's contents + folderContentView.render({id: id}); + }); + + library_router.on('route:download', function(folder_id, format) { + if ($('#center').find(':checked').length === 0) { + // this happens rarely when there is a server/data error and client gets an actual response instead of an attachment + // we don't know what was selected so we can't download again, we redirect to the folder provided + library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + } else { + // send download stream + folderContentView.download(folder_id, format); + library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); + } + }); + +Backbone.history.start(); + +return this +} +}); + +// return +return { + GalaxyApp: GalaxyLibrary +}; + +}); diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -57,7 +57,12 @@ tab_shared.add({ title : "Data Libraries", - content : "library/index", + content : "library/index" + }); + + tab_shared.add({ + title : "New Libraries", + content : "library/list", divider : true }); diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -1,6 +1,3 @@ -/* - galaxy modal -*/ // dependencies define([], function() { @@ -25,8 +22,50 @@ // initialize initialize : function(options) { + self = this; if (options) this.create(options); + + // Bind the hiding events + this.bindEvents(event, self); + }, + + // bind the click-to-hide function + bindEvents: function(event, that) { + // bind the ESC key to hide() function + $(document).on('keyup', function(event){ + if (event.keyCode == 27) { self.hide(); } + }) + // bind the 'click anywhere' to hide() function... + $('html').on('click', function(event){ + that.hide(); + }) + // ...but don't hide if the click is on modal content + $('.modal-content').on('click', function(event){ + event.stopPropagation(); + }) + }, + + // unbind the click-to-hide function + unbindEvents: function(event, that){ + // bind the ESC key to hide() function + $(document).off('keyup', function(event){ + if (event.keyCode == 27) { that.hide(); } + }) + // unbind the 'click anywhere' to hide() function... + $('html').off('click', function(event){ + that.hide(); + }) + $('.modal-content').off('click', function(event){ + event.stopPropagation(); + }) + }, + + // destroy + destroy : function(){ + this.hide(); + this.unbindEvents(); + $('.modal').remove(); }, // adds and displays a new frame/window @@ -63,6 +102,7 @@ // set flag this.visible = false; + this.unbindEvents(); }, // create @@ -120,6 +160,15 @@ this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); }, + // hide buttons + hideButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).hide(); + }, + // show buttons + showButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).show(); + }, + // returns scroll top for body element scrollTop: function() { @@ -139,7 +188,7 @@ '<div class="modal-header">' + '<button type="button" class="close" style="display: none;">×</button>' + '<h4 class="title">' + title + '</h4>' + - '</div>' + + '</div>' + '<div class="modal-body"></div>' + '<div class="modal-footer">' + '<div class="buttons" style="float: right;"></div>' + diff -r e304da0a99681c7fb8538c6861844f17c375097e -r c1963ee06cb0fc066c111b23d99a3ea49d66f90b static/scripts/libs/bootstrap.js --- a/static/scripts/libs/bootstrap.js +++ b/static/scripts/libs/bootstrap.js @@ -575,3 +575,158 @@ } }(window.jQuery); + +/* ======================================================================== + * Bootstrap: dropdown.js v3.0.0 + * http://twbs.github.com/bootstrap/javascript.html#dropdowns + * ======================================================================== + * Copyright 2012 Twitter, Inc. + * + * Licensed under the Apache License, Version 2.0 (the "License"); + * you may not use this file except in compliance with the License. + * You may obtain a copy of the License at + * + * http://www.apache.org/licenses/LICENSE-2.0 + * + * Unless required by applicable law or agreed to in writing, software + * distributed under the License is distributed on an "AS IS" BASIS, + * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + * See the License for the specific language governing permissions and + * limitations under the License. + * ======================================================================== */ + + ++function ($) { "use strict"; + + // DROPDOWN CLASS DEFINITION + // ========================= + + var backdrop = '.dropdown-backdrop' + var toggle = '[data-toggle=dropdown]' + var Dropdown = function (element) { + var $el = $(element).on('click.bs.dropdown', this.toggle) + } + + Dropdown.prototype.toggle = function (e) { + var $this = $(this) + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + clearMenus() + + if (!isActive) { + if ('ontouchstart' in document.documentElement && !$parent.closest('.navbar-nav').length) { + // if mobile we we use a backdrop because click events don't delegate + $('<div class="dropdown-backdrop"/>').insertAfter($(this)).on('click', clearMenus) + } + + $parent.trigger(e = $.Event('show.bs.dropdown')) + + if (e.isDefaultPrevented()) return + + $parent + .toggleClass('open') + .trigger('shown.bs.dropdown') + + $this.focus() + } + + return false + } + + Dropdown.prototype.keydown = function (e) { + if (!/(38|40|27)/.test(e.keyCode)) return + + var $this = $(this) + + e.preventDefault() + e.stopPropagation() + + if ($this.is('.disabled, :disabled')) return + + var $parent = getParent($this) + var isActive = $parent.hasClass('open') + + if (!isActive || (isActive && e.keyCode == 27)) { + if (e.which == 27) $parent.find(toggle).focus() + return $this.click() + } + + var $items = $('[role=menu] li:not(.divider):visible a', $parent) + + if (!$items.length) return + + var index = $items.index($items.filter(':focus')) + + if (e.keyCode == 38 && index > 0) index-- // up + if (e.keyCode == 40 && index < $items.length - 1) index++ // down + if (!~index) index=0 + + $items.eq(index).focus() + } + + function clearMenus() { + $(backdrop).remove() + $(toggle).each(function (e) { + var $parent = getParent($(this)) + if (!$parent.hasClass('open')) return + $parent.trigger(e = $.Event('hide.bs.dropdown')) + if (e.isDefaultPrevented()) return + $parent.removeClass('open').trigger('hidden.bs.dropdown') + }) + } + + function getParent($this) { + var selector = $this.attr('data-target') + + if (!selector) { + selector = $this.attr('href') + selector = selector && /#/.test(selector) && selector.replace(/.*(?=#[^\s]*$)/, '') //strip for ie7 + } + + var $parent = selector && $(selector) + + return $parent && $parent.length ? $parent : $this.parent() + } + + + // DROPDOWN PLUGIN DEFINITION + // ========================== + + var old = $.fn.dropdown + + $.fn.dropdown = function (option) { + return this.each(function () { + var $this = $(this) + var data = $this.data('dropdown') + + if (!data) $this.data('dropdown', (data = new Dropdown(this))) + if (typeof option == 'string') data[option].call($this) + }) + } + + $.fn.dropdown.Constructor = Dropdown + + + // DROPDOWN NO CONFLICT + // ==================== + + $.fn.dropdown.noConflict = function () { + $.fn.dropdown = old + return this + } + + + // APPLY TO STANDARD DROPDOWN ELEMENTS + // =================================== + + $(document) + .on('click.bs.dropdown.data-api', clearMenus) + .on('click.bs.dropdown.data-api', '.dropdown form', function (e) { e.stopPropagation() }) + .on('click.bs.dropdown.data-api' , toggle, Dropdown.prototype.toggle) + .on('keydown.bs.dropdown.data-api', toggle + ', [role=menu]' , Dropdown.prototype.keydown) + +}(window.jQuery); \ No newline at end of file This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Attempt to fix problems with toolshed
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e304da0a9968/ Changeset: e304da0a9968 User: guerler Date: 2013-12-19 18:29:41 Summary: Grids: Attempt to fix problems with toolshed Affected #: 2 files diff -r c91f3185e8ca68a006b755a9fdcbed3174b27fd9 -r e304da0a99681c7fb8538c6861844f17c375097e static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -322,7 +322,6 @@ var button = $('#grid-' + i + '-popup'); button.off(); var popup = new PopupMenu(button); - // load details var item = options['items'][i]; for (var j in options['operations']) @@ -655,9 +654,6 @@ // Initialize new grid config self.init_grid($.parseJSON(response_text)); - // Trigger custom event to indicate grid body has changed. - $('#grid-table-body').trigger('update'); - // Hide loading overlay. $('.loading-elt-overlay').hide(); }, diff -r c91f3185e8ca68a006b755a9fdcbed3174b27fd9 -r e304da0a99681c7fb8538c6861844f17c375097e static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var r=$(this).find("input.grid-row-select-checkbox");var q=$(this).find("span.grid-selected-count");var s=function(){q.text($(r).filter(":checked").length)};$(r).each(function(){$(this).change(s)});s()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var p=this.grid.attributes;var o=this;$(".page-link > a").each(function(){$(this).click(function(){o.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(q){o.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(q){o.execute({href:$(this).attr("href")});return false})});for(var h in p.items){var k=$("#grid-"+h+"-popup");k.off();var d=new PopupMenu(k);var n=p.items[h];for(var g in p.operations){var e=p.operations[g];var l=e.label;var c=n.operation_config[l];var f=n.encode_id;if(c.allowed&&e.allow_popup){var m={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};m.func=function(s){s.preventDefault();var r=$(s.target).html();var q=this.findItemByHtml(r);o.execute(q)};d.addItem(m)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$("#grid-table-body").trigger("update");$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(s){var l="";var t=0;var g=s.items.length;if(g==0){l+='<tr><td colspan="100"><em>No Items</em></td></tr>';t=1}for(i in s.items){var q=s.items[i];var c=q.encode_id;var h="grid-"+i+"-popup";l+="<tr ";if(s.current_item_id==q.id){l+='class="current"'}l+=">";if(s.show_item_checkboxes){l+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in s.columns){var f=s.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var r=q.column_config[f.label];var k=r.link;var m=r.value;var p=r.inbound;if(jQuery.type(m)==="string"){m=m.replace(/\/\//g,"/")}var d="";var o="";if(f.attach_popup){d="grid-"+i+"-popup";o="menubutton";if(k!=""){o+=" split"}o+=" popup"}l+="<td "+e+">";if(k){if(s.operations.length!=0){l+='<div id="'+d+'" class="'+o+'" style="float: left;">'}var n="";if(p){n="use-inbound"}else{n="use-outbound"}l+='<a class="label '+n+'" href="'+k+'" onclick="return false;">'+m+"</a>";if(s.operations.length!=0){l+="</div>"}}else{l+='<div id="'+d+'" class="'+o+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+m+"</label></div>"}l+="</td>"}}l+="</tr>";t++}return l},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var r=$(this).find("input.grid-row-select-checkbox");var q=$(this).find("span.grid-selected-count");var s=function(){q.text($(r).filter(":checked").length)};$(r).each(function(){$(this).change(s)});s()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var p=this.grid.attributes;var o=this;$(".page-link > a").each(function(){$(this).click(function(){o.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(q){o.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(q){o.execute({href:$(this).attr("href")});return false})});for(var h in p.items){var k=$("#grid-"+h+"-popup");k.off();var d=new PopupMenu(k);var n=p.items[h];for(var g in p.operations){var e=p.operations[g];var l=e.label;var c=n.operation_config[l];var f=n.encode_id;if(c.allowed&&e.allow_popup){var m={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};m.func=function(s){s.preventDefault();var r=$(s.target).html();var q=this.findItemByHtml(r);o.execute(q)};d.addItem(m)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(s){var l="";var t=0;var g=s.items.length;if(g==0){l+='<tr><td colspan="100"><em>No Items</em></td></tr>';t=1}for(i in s.items){var q=s.items[i];var c=q.encode_id;var h="grid-"+i+"-popup";l+="<tr ";if(s.current_item_id==q.id){l+='class="current"'}l+=">";if(s.show_item_checkboxes){l+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in s.columns){var f=s.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var r=q.column_config[f.label];var k=r.link;var m=r.value;var p=r.inbound;if(jQuery.type(m)==="string"){m=m.replace(/\/\//g,"/")}var d="";var o="";if(f.attach_popup){d="grid-"+i+"-popup";o="menubutton";if(k!=""){o+=" split"}o+=" popup"}l+="<td "+e+">";if(k){if(s.operations.length!=0){l+='<div id="'+d+'" class="'+o+'" style="float: left;">'}var n="";if(p){n="use-inbound"}else{n="use-outbound"}l+='<a class="label '+n+'" href="'+k+'" onclick="return false;">'+m+"</a>";if(s.operations.length!=0){l+="</div>"}}else{l+='<div id="'+d+'" class="'+o+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+m+"</label></div>"}l+="</td>"}}l+="</tr>";t++}return l},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History panel: bring error state HDA button order into line with other states
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c91f3185e8ca/ Changeset: c91f3185e8ca User: carlfeberhard Date: 2013-12-19 17:47:11 Summary: History panel: bring error state HDA button order into line with other states Affected #: 2 files diff -r 4fc04317cef36f002e071d391523450a7a956232 -r c91f3185e8ca68a006b755a9fdcbed3174b27fd9 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -354,7 +354,7 @@ html = '<div>' + this.model.get( 'misc_blurb' ) + '</div>' + html; } return this._render_stateBodyHelper( html, - this.defaultPrimaryActionButtonRenderers.concat([ this._render_downloadButton ]) + [ this._render_downloadButton ].concat( this.defaultPrimaryActionButtonRenderers ) ); }, diff -r 4fc04317cef36f002e071d391523450a7a956232 -r c91f3185e8ca68a006b755a9fdcbed3174b27fd9 static/scripts/packed/mvc/dataset/hda-base.js --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.linkTarget=c.linkTarget||"_blank";this.selectable=c.selectable||false;this.selected=c.selected||false;this.expanded=c.expanded||false;this.draggable=c.draggable||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());if(this.selectable){this.showSelector(0)}f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}if(this.draggable){this.draggableOn()}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={target:this.linkTarget,classes:"dataset-display"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){if(Galaxy.frame&&Galaxy.frame.active){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",content:c.urls.display})}}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>',"</a>"].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['<div popupmenu="'+f+'">','<a href="'+d.download+'">',_l("Download Dataset"),"</a>","<a>"+_l("Additional Files")+"</a>",_.map(e,function(g){return['<a class="action-button" href="',d.meta_download+g.file_type,'">',_l("Download")," ",g.file_type,"</a>"].join("")}).join("\n"),"</div>",'<div class="icon-btn-group">','<a href="'+d.download+'" title="'+_l("Download")+'" class="icon-btn">','<span class="fa fa-floppy-o"></span>','</a><a class="icon-btn popup" id="'+f+'">','<span class="fa fa-caret-down"></span>',"</a>","</div>"].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle"})},_render_body:function(){var d=$('<div>Error: unknown dataset state "'+this.model.get("state")+'".</div>'),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}this._setUpBehaviors(d);if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("<div>"+_l("This is a new dataset and not all of its data are available yet")+"</div>")},_render_body_noPermission:function(){return this._render_stateBodyHelper("<div>"+_l("You do not have permission to view this dataset")+"</div>")},_render_body_discarded:function(){return this._render_stateBodyHelper("<div>"+_l("The job creating this dataset was cancelled before completion")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("<div>"+_l("This job is waiting to run")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("<div>"+_l("This dataset is currently uploading")+"</div>")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("<div>"+_l("Metadata is being auto-detected")+"</div>")},_render_body_running:function(){return this._render_stateBodyHelper("<div>"+_l("This job is currently running")+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("<div>"+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"</div>",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['<span class="help-text">',_l("An error occurred with this dataset"),":</span>",'<div class="job-error-text">',$.trim(this.model.get("misc_info")),"</div>"].join("");if(!this.model.get("purged")){c="<div>"+this.model.get("misc_blurb")+"</div>"+c}return this._render_stateBodyHelper(c,[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers))},_render_body_empty:function(){return this._render_stateBodyHelper("<div>"+_l("No data")+": <i>"+this.model.get("misc_blurb")+"</i></div>",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('<div class="warningmessagesmall"></div>').append($("<strong/>").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility","keydown .dataset-title-bar":"toggleBodyVisibility","click .dataset-selector":"toggleSelect",},toggleBodyVisibility:function(f,d){var c=32,e=13;if(f&&(f.type==="keydown")&&!(f.keyCode===c||f.keyCode===e)){return true}var g=this.$el.find(".dataset-body");d=(d===undefined)?(!g.is(":visible")):(d);if(d){this.expandBody()}else{this.collapseBody()}return false},expandBody:function(){var c=this;function d(){c.$el.children(".dataset-body").replaceWith(c._render_body());c.$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},showSelector:function(e){if(this.$el.find(".dataset-selector").css("display")!=="none"){return}e=(e!==undefined)?(e):(this.fxSpeed);if(this.selected){this.select(null,true)}var d=this,c=32;if(e){this.$el.queue("fx",function(f){$(this).find(".dataset-primary-actions").fadeOut(e,f)});this.$el.queue("fx",function(f){$(this).find(".dataset-selector").show().animate({width:c},e,f);$(this).find(".dataset-title-bar").animate({"margin-left":c},e,f);d.selectable=true;d.trigger("selectable",true,d)})}else{this.$el.find(".dataset-primary-actions").hide();this.$el.find(".dataset-selector").show().css({width:c});this.$el.find(".dataset-title-bar").show().css({"margin-left":c});d.selectable=true;d.trigger("selectable",true,d)}},hideSelector:function(c){c=(c!==undefined)?(c):(this.fxSpeed);this.selectable=false;this.trigger("selectable",false,this);if(c){this.$el.queue("fx",function(d){$(this).find(".dataset-title-bar").show().css({"margin-left":"0"});$(this).find(".dataset-selector").animate({width:"0px"},c,function(){$(this).hide();d()})});this.$el.queue("fx",function(d){$(this).find(".dataset-primary-actions").fadeIn(c,d)})}else{$(this).find(".dataset-selector").css({width:"0px"}).hide();$(this).find(".dataset-primary-actions").show()}},toggleSelector:function(c){if(!this.$el.find(".dataset-selector").is(":visible")){this.showSelector(c)}else{this.hideSelector(c)}},select:function(c){this.$el.find(".dataset-selector span").removeClass("fa-square-o").addClass("fa-check-square-o");if(!this.selected){this.trigger("selected",this);this.selected=true}return false},deselect:function(c){this.$el.find(".dataset-selector span").removeClass("fa-check-square-o").addClass("fa-square-o");if(this.selected){this.trigger("de-selected",this);this.selected=false}return false},toggleSelect:function(c){if(this.selected){this.deselect(c)}else{this.select(c)}},draggableOn:function(){this.draggable=true;this.dragStartHandler=_.bind(this._dragStartHandler,this);this.dragEndHandler=_.bind(this._dragEndHandler,this);var c=this.$el.find(".dataset-title-bar").attr("draggable",true).get(0);c.addEventListener("dragstart",this.dragStartHandler,false);c.addEventListener("dragend",this.dragEndHandler,false)},draggableOff:function(){this.draggable=false;var c=this.$el.find(".dataset-title-bar").attr("draggable",false).get(0);c.removeEventListener("dragstart",this.dragStartHandler,false);c.removeEventListener("dragend",this.dragEndHandler,false)},toggleDraggable:function(){if(this.draggable){this.draggableOff()}else{this.draggableOn()}},_dragStartHandler:function(c){this.trigger("dragstart",this);c.dataTransfer.effectAllowed="move";c.dataTransfer.setData("text",JSON.stringify(this.model.toJSON()));return false},_dragEndHandler:function(c){this.trigger("dragend",this);return false},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: do not update title when empty string or unchanged
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4fc04317cef3/ Changeset: 4fc04317cef3 User: carlfeberhard Date: 2013-12-19 16:39:55 Summary: History panel: do not update title when empty string or unchanged Affected #: 2 files diff -r 67fe4b091f0ad66d68d06a36b8fb645aa445d032 -r 4fc04317cef36f002e071d391523450a7a956232 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -698,11 +698,16 @@ .attr( 'title', _l( 'Click to rename history' ) ).tooltip({ placement: 'bottom' }) .make_text_editable({ on_finish: function( newName ){ - $where.find( '.history-name' ).text( newName ); - panel.model.save({ name: newName }) - .fail( function(){ - $where.find( '.history-name' ).text( panel.model.previous( 'name' ) ); - }); + var previousName = panel.model.get( 'name' ); + if( newName && newName !== previousName ){ + panel.$el.find( '.history-name' ).text( newName ); + panel.model.save({ name: newName }) + .fail( function(){ + panel.$el.find( '.history-name' ).text( panel.model.previous( 'name' ) ); + }); + } else { + panel.$el.find( '.history-name' ).text( previousName ); + } } }); this._setUpDatasetActionsPopup( $where ); diff -r 67fe4b091f0ad66d68d06a36b8fb645aa445d032 -r 4fc04317cef36f002e071d391523450a7a956232 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){j.find(".history-name").text(l);k.model.save({name:l}).fail(function(){j.find(".history-name").text(k.model.previous("name"))})}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(k){var l=this;function n(o){l.searchFor=o;l.filters=[function(p){return p.matchesAll(l.searchFor)}];l.trigger("search:searching",o,l);l.renderHdas()}function j(o){if(l.model.hdas.haveDetails()){n(o);return}l.$el.find(".history-search-controls").searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){n(o)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}return k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m})},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls");if(!k.children().size()){k=this.renderSearchControls(k).hide()}k.show(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").hide(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){var m=k.model.get("name");if(l&&l!==m){k.$el.find(".history-name").text(l);k.model.save({name:l}).fail(function(){k.$el.find(".history-name").text(k.model.previous("name"))})}else{k.$el.find(".history-name").text(m)}}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(k){var l=this;function n(o){l.searchFor=o;l.filters=[function(p){return p.matchesAll(l.searchFor)}];l.trigger("search:searching",o,l);l.renderHdas()}function j(o){if(l.model.hdas.haveDetails()){n(o);return}l.$el.find(".history-search-controls").searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){n(o)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}return k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m})},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls");if(!k.children().size()){k=this.renderSearchControls(k).hide()}k.show(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").hide(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for determining a guid in the install_manager.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a9a0ac9c1afa/ Changeset: a9a0ac9c1afa Branch: stable User: greg Date: 2013-12-19 01:03:05 Summary: Fix for determining a guid in the install_manager. Affected #: 1 file diff -r 26da838b778c68a5577d4cca9836f6ef70b8ed1b -r a9a0ac9c1afae8dd0d662c9c800d0228c883c107 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -244,21 +244,20 @@ def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): if self.shed_config_dict.get( 'tool_path' ): - relative_install_dir = os.path.join( self.shed_config_dict['tool_path'], relative_install_dir ) - found = False + relative_install_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], relative_install_dir ) + tool_config_filename = suc.strip_path( tool_config ) for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: dirs.remove( '.hg' ) for name in files: - if name == tool_config: - found = True - break - if found: - break - full_path = str( os.path.abspath( os.path.join( root, name ) ) ) - tool = self.toolbox.load_tool( full_path ) - return suc.generate_tool_guid( repository_clone_url, tool ) + filename = suc.strip_path( name ) + if filename == tool_config_filename: + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) + tool = self.toolbox.load_tool( full_path ) + return suc.generate_tool_guid( repository_clone_url, tool ) + # Not quite sure what should happen here, throw an exception or what? + return None def get_prior_install_required_dict( self, tool_shed_repositories, repository_dependencies_dict ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Don't uninstall repositories when testing tool dependency definitions in the tool shed's install and test process.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/67fe4b091f0a/ Changeset: 67fe4b091f0a User: greg Date: 2013-12-19 14:47:20 Summary: Don't uninstall repositories when testing tool dependency definitions in the tool shed's install and test process. Affected #: 1 file diff -r 5bfa1d47b3999a695a04294adb13da0b5b3ec041 -r 67fe4b091f0ad66d68d06a36b8fb645aa445d032 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -201,28 +201,18 @@ else: log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) - # Keep statistics for this repository's tool dependencies that resulted in installation errors. - for missing_tool_dependency in repository.missing_tool_dependencies: - name = str( missing_tool_dependency.name ) - type = str( missing_tool_dependency.type ) - version = str( missing_tool_dependency.version ) - error_message = unicodify( missing_tool_dependency.error_message ) - missing_tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) - # Attempt to uninstall this repository and all of its dependencies if its repository dependencies or - # tool dependencies resulted in an installation error. - missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) - if missing_tool_dependencies or repository.missing_repository_dependencies: - install_and_test_base_util.handle_missing_dependencies( app=app, - repository=repository, - missing_tool_dependencies=missing_tool_dependencies, - repository_dict=repository_dict, - tool_test_results_dicts=tool_test_results_dicts, - tool_test_results_dict=tool_test_results_dict, - can_update_tool_shed=can_update_tool_shed ) + if repository.missing_tool_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in installation errors. + for missing_tool_dependency in repository.missing_tool_dependencies: + name = str( missing_tool_dependency.name ) + type = str( missing_tool_dependency.type ) + version = str( missing_tool_dependency.version ) + error_message = unicodify( missing_tool_dependency.error_message ) + missing_tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + error_message=error_message ) + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) else: # This repository and all of its dependencies were successfully installed. install_and_test_statistics_dict[ 'successful_installations' ].append( repository_identifier_dict ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for handling missing dependencies in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5bfa1d47b399/ Changeset: 5bfa1d47b399 User: greg Date: 2013-12-19 02:32:15 Summary: Fix for handling missing dependencies in the tool shed's install and test framework. Affected #: 2 files diff -r 4077a5a1f801a772acd01d19c9695329a42c5958 -r 5bfa1d47b3999a695a04294adb13da0b5b3ec041 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -286,16 +286,15 @@ if 'missing_test_components' not in tool_test_results_dict: tool_test_results_dict[ 'missing_test_components' ] = [] missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) - if missing_tool_dependencies or repository.missing_repository_dependencies: + if missing_tool_dependencies or repository.missing_repository_dependencies: install_and_test_statistics_dict = \ - install_and_test_base_util.handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - install_and_test_statistics_dict, - can_update_tool_shed ) + install_and_test_base_util.handle_missing_dependencies( app=app, + repository=repository, + missing_tool_dependencies=missing_tool_dependencies, + repository_dict=repository_dict, + tool_test_results_dicts=tool_test_results_dicts, + tool_test_results_dict=tool_test_results_dict, + can_update_tool_shed=can_update_tool_shed ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: diff -r 4077a5a1f801a772acd01d19c9695329a42c5958 -r 5bfa1d47b3999a695a04294adb13da0b5b3ec041 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -216,14 +216,13 @@ # tool dependencies resulted in an installation error. missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - install_and_test_base_util.handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - install_and_test_statistics_dict, - can_update_tool_shed ) + install_and_test_base_util.handle_missing_dependencies( app=app, + repository=repository, + missing_tool_dependencies=missing_tool_dependencies, + repository_dict=repository_dict, + tool_test_results_dicts=tool_test_results_dicts, + tool_test_results_dict=tool_test_results_dict, + can_update_tool_shed=can_update_tool_shed ) else: # This repository and all of its dependencies were successfully installed. install_and_test_statistics_dict[ 'successful_installations' ].append( repository_identifier_dict ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix imports in the tool shed's functional test framework.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4077a5a1f801/ Changeset: 4077a5a1f801 User: greg Date: 2013-12-19 01:09:11 Summary: Fix imports in the tool shed's functional test framework. Affected #: 3 files diff -r a53f2f700699c9d88b1896814b3eb2ec8cc028b8 -r 4077a5a1f801a772acd01d19c9695329a42c5958 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -595,7 +595,6 @@ exclude_list.append( exclude_dict ) log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ ( str( xml_filename ), str( exclude_count ) ) ) - #if '-list_repositories' in sys.argv: for name, owner, changeset_revision in exclude_verbose: if changeset_revision: log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) diff -r a53f2f700699c9d88b1896814b3eb2ec8cc028b8 -r 4077a5a1f801a772acd01d19c9695329a42c5958 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -45,6 +45,7 @@ from galaxy.app import UniverseApplication from galaxy.util.json import from_json_string from galaxy.util.json import to_json_string +from galaxy.util import unicodify from galaxy.web import buildapp from functional_tests import generate_config_file from nose.plugins import Plugin diff -r a53f2f700699c9d88b1896814b3eb2ec8cc028b8 -r 4077a5a1f801a772acd01d19c9695329a42c5958 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -45,6 +45,7 @@ from galaxy.app import UniverseApplication from galaxy.util.json import from_json_string from galaxy.util.json import to_json_string +from galaxy.util import unicodify from galaxy.web import buildapp from functional_tests import generate_config_file from nose.plugins import Plugin Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fix for determining a guid in the install_manager.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a53f2f700699/ Changeset: a53f2f700699 User: greg Date: 2013-12-19 01:03:05 Summary: Fix for determining a guid in the install_manager. Affected #: 1 file diff -r 9fa754a203b7312d58211b5e1e7140bf36aec76a -r a53f2f700699c9d88b1896814b3eb2ec8cc028b8 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -244,21 +244,20 @@ def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): if self.shed_config_dict.get( 'tool_path' ): - relative_install_dir = os.path.join( self.shed_config_dict['tool_path'], relative_install_dir ) - found = False + relative_install_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], relative_install_dir ) + tool_config_filename = suc.strip_path( tool_config ) for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: dirs.remove( '.hg' ) for name in files: - if name == tool_config: - found = True - break - if found: - break - full_path = str( os.path.abspath( os.path.join( root, name ) ) ) - tool = self.toolbox.load_tool( full_path ) - return suc.generate_tool_guid( repository_clone_url, tool ) + filename = suc.strip_path( name ) + if filename == tool_config_filename: + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) + tool = self.toolbox.load_tool( full_path ) + return suc.generate_tool_guid( repository_clone_url, tool ) + # Not quite sure what should happen here, throw an exception or what? + return None def get_prior_install_required_dict( self, tool_shed_repositories, repository_dependencies_dict ): """ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Pack scripts, remove grid_body from mako
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fa754a203b7/ Changeset: 9fa754a203b7 User: guerler Date: 2013-12-18 23:28:16 Summary: Grids: Pack scripts, remove grid_body from mako Affected #: 6 files diff -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a -r 9fa754a203b7312d58211b5e1e7140bf36aec76a static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var 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c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(s){var l="";var t=0;var g=s.items.length;if(g==0){l+='<tr><td colspan="100"><em>No Items</em></td></tr>';t=1}for(i in s.items){var q=s.items[i];var c=q.encode_id;var h="grid-"+i+"-popup";l+="<tr ";if(s.current_item_id==q.id){l+='class="current"'}l+=">";if(s.show_item_checkboxes){l+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in s.columns){var f=s.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var r=q.column_config[f.label];var k=r.link;var m=r.value;var p=r.inbound;if(jQuery.type(m)==="string"){m=m.replace(/\/\//g,"/")}var d="";var o="";if(f.attach_popup){d="grid-"+i+"-popup";o="menubutton";if(k!=""){o+=" split"}o+=" popup"}l+="<td "+e+">";if(k){if(s.operations.length!=0){l+='<div id="'+d+'" class="'+o+'" style="float: left;">'}var n="";if(p){n="use-inbound"}else{n="use-outbound"}l+='<a class="label '+n+'" href="'+k+'" onclick="return false;">'+m+"</a>";if(s.operations.length!=0){l+="</div>"}}else{l+='<div id="'+d+'" class="'+o+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+m+"</label></div>"}l+="</td>"}}l+="</tr>";t++}return l},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file diff -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a -r 9fa754a203b7312d58211b5e1e7140bf36aec76a static/scripts/packed/galaxy.workflow_editor.canvas.js --- a/static/scripts/packed/galaxy.workflow_editor.canvas.js +++ b/static/scripts/packed/galaxy.workflow_editor.canvas.js @@ -1,1 +1,1 @@ -function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Flag this as a workflow output. All non-flagged outputs will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa fa-times").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file +function Terminal(a){this.element=a;this.connectors=[]}$.extend(Terminal.prototype,{connect:function(a){this.connectors.push(a);if(this.node){this.node.changed()}},disconnect:function(a){this.connectors.splice($.inArray(a,this.connectors),1);if(this.node){this.node.changed()}},redraw:function(){$.each(this.connectors,function(a,b){b.redraw()})},destroy:function(){$.each(this.connectors.slice(),function(a,b){b.destroy()})}});function OutputTerminal(a,b){Terminal.call(this,a);this.datatypes=b}OutputTerminal.prototype=new Terminal();function InputTerminal(b,c,a){Terminal.call(this,b);this.datatypes=c;this.multiple=a}InputTerminal.prototype=new Terminal();$.extend(InputTerminal.prototype,{can_accept:function(a){if(this.connectors.length<1||this.multiple){for(var c in this.datatypes){var f=new Array();f=f.concat(a.datatypes);if(a.node.post_job_actions){for(var d in a.node.post_job_actions){var g=a.node.post_job_actions[d];if(g.action_type=="ChangeDatatypeAction"&&(g.output_name==""||g.output_name==a.name)&&g.action_arguments){f.push(g.action_arguments.newtype)}}}for(var b in f){if(f[b]=="input"||issubtype(f[b],this.datatypes[c])){return true}}}}return false}});function Connector(b,a){this.canvas=null;this.dragging=false;this.inner_color="#FFFFFF";this.outer_color="#D8B365";if(b&&a){this.connect(b,a)}}$.extend(Connector.prototype,{connect:function(b,a){this.handle1=b;if(this.handle1){this.handle1.connect(this)}this.handle2=a;if(this.handle2){this.handle2.connect(this)}},destroy:function(){if(this.handle1){this.handle1.disconnect(this)}if(this.handle2){this.handle2.disconnect(this)}$(this.canvas).remove()},redraw:function(){var d=$("#canvas-container");if(!this.canvas){this.canvas=document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(this.canvas)}d.append($(this.canvas));if(this.dragging){this.canvas.style.zIndex="300"}}var n=function(c){return $(c).offset().left-d.offset().left};var i=function(c){return $(c).offset().top-d.offset().top};if(!this.handle1||!this.handle2){return}var h=n(this.handle1.element)+5;var g=i(this.handle1.element)+5;var p=n(this.handle2.element)+5;var m=i(this.handle2.element)+5;var f=100;var k=Math.min(h,p);var a=Math.max(h,p);var j=Math.min(g,m);var t=Math.max(g,m);var b=Math.min(Math.max(Math.abs(t-j)/2,100),300);var o=k-f;var s=j-f;var q=a-k+2*f;var l=t-j+2*f;this.canvas.style.left=o+"px";this.canvas.style.top=s+"px";this.canvas.setAttribute("width",q);this.canvas.setAttribute("height",l);h-=o;g-=s;p-=o;m-=s;var r=this.canvas.getContext("2d");r.lineCap="round";r.strokeStyle=this.outer_color;r.lineWidth=7;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke();r.strokeStyle=this.inner_color;r.lineWidth=5;r.beginPath();r.moveTo(h,g);r.bezierCurveTo(h+b,g,p-b,m,p,m);r.stroke()}});function Node(a){this.element=a;this.input_terminals={};this.output_terminals={};this.tool_errors={}}$.extend(Node.prototype,{enable_input_terminal:function(f,b,c,a){var d=this;$(f).each(function(){var g=this.terminal=new InputTerminal(this,c,a);g.node=d;g.name=b;$(this).bind("dropinit",function(h,i){return $(i.drag).hasClass("output-terminal")&&g.can_accept(i.drag.terminal)}).bind("dropstart",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#BBFFBB"}}).bind("dropend",function(h,i){if(i.proxy.terminal){i.proxy.terminal.connectors[0].inner_color="#FFFFFF"}}).bind("drop",function(h,i){(new Connector(i.drag.terminal,g)).redraw()}).bind("hover",function(){if(g.connectors.length>0){var h=$("<div class='callout'></div>").css({display:"none"}).appendTo("body").append($("<div class='button'></div>").append($("<div/>").addClass("fa-icon-button fa fa-times").click(function(){$.each(g.connectors,function(j,i){if(i){i.destroy()}});h.remove()}))).bind("mouseleave",function(){$(this).remove()});h.css({top:$(this).offset().top-2,left:$(this).offset().left-h.width(),"padding-right":$(this).width()}).show()}});d.input_terminals[b]=g})},enable_output_terminal:function(d,a,b){var c=this;$(d).each(function(){var g=this;var f=this.terminal=new OutputTerminal(this,b);f.node=c;f.name=a;$(this).bind("dragstart",function(j,k){$(k.available).addClass("input-terminal-active");workflow.check_changes_in_active_form();var i=$('<div class="drag-terminal" style="position: absolute;"></div>').appendTo("#canvas-container").get(0);i.terminal=new OutputTerminal(i);var l=new Connector();l.dragging=true;l.connect(this.terminal,i.terminal);return i}).bind("drag",function(i,j){var h=function(){var l=$(j.proxy).offsetParent().offset(),k=j.offsetX-l.left,m=j.offsetY-l.top;$(j.proxy).css({left:k,top:m});j.proxy.terminal.redraw();canvas_manager.update_viewport_overlay()};h();$("#canvas-container").get(0).scroll_panel.test(i,h)}).bind("dragend",function(h,i){i.proxy.terminal.connectors[0].destroy();$(i.proxy).remove();$(i.available).removeClass("input-terminal-active");$("#canvas-container").get(0).scroll_panel.stop()});c.output_terminals[a]=f})},redraw:function(){$.each(this.input_terminals,function(a,b){b.redraw()});$.each(this.output_terminals,function(a,b){b.redraw()})},destroy:function(){$.each(this.input_terminals,function(a,b){b.destroy()});$.each(this.output_terminals,function(a,b){b.destroy()});workflow.remove_node(this);$(this.element).remove()},make_active:function(){$(this.element).addClass("toolForm-active")},make_inactive:function(){var a=this.element.get(0);(function(b){b.removeChild(a);b.appendChild(a)})(a.parentNode);$(a).removeClass("toolForm-active")},init_field_data:function(h){var g=this.element;if(h.type){this.type=h.type}this.name=h.name;this.form_html=h.form_html;this.tool_state=h.tool_state;this.tool_errors=h.tool_errors;this.tooltip=h.tooltip?h.tooltip:"";this.annotation=h.annotation;this.post_job_actions=h.post_job_actions?h.post_job_actions:{};this.workflow_outputs=h.workflow_outputs?h.workflow_outputs:[];if(this.tool_errors){g.addClass("tool-node-error")}else{g.removeClass("tool-node-error")}var d=this;var c=Math.max(150,g.width());var a=g.find(".toolFormBody");a.find("div").remove();var i=$("<div class='inputs'></div>").appendTo(a);$.each(h.data_inputs,function(k,f){var j=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(j,f.name,f.extensions,f.multiple);var b=$("<div class='form-row dataRow input-data-row' name='"+f.name+"'>"+f.label+"</div>");b.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(b);c=Math.max(c,b.outerWidth());b.css({position:"",left:"",top:"",display:""});b.remove();i.append(b.prepend(j))});if((h.data_inputs.length>0)&&(h.data_outputs.length>0)){a.append($("<div class='rule'></div>"))}$.each(h.data_outputs,function(k,b){var j=$("<div class='terminal output-terminal'></div>");d.enable_output_terminal(j,b.name,b.extensions);var f=b.name;if(b.extensions.indexOf("input")<0){f=f+" ("+b.extensions.join(", ")+")"}var m=$("<div class='form-row dataRow'>"+f+"</div>");if(d.type=="tool"){var l=$("<div class='callout "+f+"'></div>").css({display:"none"}).append($("<div class='buttons'></div>").append($("<img/>").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png").click(function(){if($.inArray(b.name,d.workflow_outputs)!=-1){d.workflow_outputs.splice($.inArray(b.name,d.workflow_outputs),1);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{d.workflow_outputs.push(b.name);l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}workflow.has_changes=true;canvas_manager.draw_overview()}))).tooltip({delay:500,title:"Mark dataset as a workflow output. All unmarked datasets will be hidden."});l.css({top:"50%",margin:"-8px 0px 0px 0px",right:8});l.show();m.append(l);if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}m.hover(function(){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-yellow.png")},function(){if($.inArray(b.name,d.workflow_outputs)===-1){l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small-outline.png")}else{l.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png")}})}m.css({position:"absolute",left:-1000,top:-1000,display:"none"});$("body").append(m);c=Math.max(c,m.outerWidth()+17);m.css({position:"",left:"",top:"",display:""});m.detach();a.append(m.append(j))});g.css("width",Math.min(250,Math.max(g.width(),c)));workflow.node_changed(this)},update_field_data:function(f){var c=$(this.element),d=this;this.tool_state=f.tool_state;this.form_html=f.form_html;this.tool_errors=f.tool_errors;this.annotation=f.annotation;var g=$.parseJSON(f.post_job_actions);this.post_job_actions=g?g:{};if(this.tool_errors){c.addClass("tool-node-error")}else{c.removeClass("tool-node-error")}var h=c.find("div.inputs");var b=$("<div class='inputs'></div>");var a=h.find("div.input-data-row");$.each(f.data_inputs,function(l,j){var k=$("<div class='terminal input-terminal'></div>");d.enable_input_terminal(k,j.name,j.extensions,j.multiple);h.find("div[name='"+j.name+"']").each(function(){$(this).find(".input-terminal").each(function(){var i=this.terminal.connectors[0];if(i){k[0].terminal.connectors[0]=i;i.handle2=k[0].terminal}});$(this).remove()});b.append($("<div class='form-row dataRow input-data-row' name='"+j.name+"'>"+j.label+"</div>").prepend(k))});h.replaceWith(b);h.find("div.input-data-row > .terminal").each(function(){this.terminal.destroy()});this.changed();this.redraw()},error:function(d){var a=$(this.element).find(".toolFormBody");a.find("div").remove();var c="<div style='color: red; text-style: italic;'>"+d+"</div>";this.form_html=c;a.html(c);workflow.node_changed(this)},changed:function(){workflow.node_changed(this)}});function Workflow(a){this.canvas_container=a;this.id_counter=0;this.nodes={};this.name=null;this.has_changes=false;this.active_form_has_changes=false}$.extend(Workflow.prototype,{add_node:function(a){a.id=this.id_counter;a.element.attr("id","wf-node-step-"+a.id);this.id_counter++;this.nodes[a.id]=a;this.has_changes=true;a.workflow=this},remove_node:function(a){if(this.active_node==a){this.clear_active_node()}delete this.nodes[a.id];this.has_changes=true},remove_all:function(){wf=this;$.each(this.nodes,function(b,a){a.destroy();wf.remove_node(a)})},rectify_workflow_outputs:function(){var b=false;var a=false;$.each(this.nodes,function(c,d){if(d.workflow_outputs&&d.workflow_outputs.length>0){b=true}$.each(d.post_job_actions,function(g,f){if(f.action_type==="HideDatasetAction"){a=true}})});if(b!==false||a!==false){$.each(this.nodes,function(c,g){if(g.type==="tool"){var f=false;if(g.post_job_actions==null){g.post_job_actions={};f=true}var d=[];$.each(g.post_job_actions,function(i,h){if(h.action_type=="HideDatasetAction"){d.push(i)}});if(d.length>0){$.each(d,function(h,j){f=true;delete g.post_job_actions[j]})}if(b){$.each(g.output_terminals,function(i,j){var h=true;$.each(g.workflow_outputs,function(l,m){if(j.name===m){h=false}});if(h===true){f=true;var k={action_type:"HideDatasetAction",output_name:j.name,action_arguments:{}};g.post_job_actions["HideDatasetAction"+j.name]=null;g.post_job_actions["HideDatasetAction"+j.name]=k}})}if(workflow.active_node==g&&f===true){workflow.reload_active_node()}}})}},to_simple:function(){var a={};$.each(this.nodes,function(c,f){var g={};$.each(f.input_terminals,function(i,j){g[j.name]=null;var h=[];$.each(j.connectors,function(k,l){h[k]={id:l.handle1.node.id,output_name:l.handle1.name};g[j.name]=h})});var b={};if(f.post_job_actions){$.each(f.post_job_actions,function(j,h){var k={action_type:h.action_type,output_name:h.output_name,action_arguments:h.action_arguments};b[h.action_type+h.output_name]=null;b[h.action_type+h.output_name]=k})}if(!f.workflow_outputs){f.workflow_outputs=[]}var d={id:f.id,type:f.type,tool_id:f.tool_id,tool_state:f.tool_state,tool_errors:f.tool_errors,input_connections:g,position:$(f.element).position(),annotation:f.annotation,post_job_actions:f.post_job_actions,workflow_outputs:f.workflow_outputs};a[f.id]=d});return{steps:a}},from_simple:function(b){wf=this;var c=0;wf.name=b.name;var a=false;$.each(b.steps,function(g,f){var d=prebuild_node("tool",f.name,f.tool_id);d.init_field_data(f);if(f.position){d.element.css({top:f.position.top,left:f.position.left})}d.id=f.id;wf.nodes[d.id]=d;c=Math.max(c,parseInt(g));if(!a&&d.type==="tool"){if(d.workflow_outputs.length>0){a=true}else{$.each(d.post_job_actions,function(i,h){if(h.action_type==="HideDatasetAction"){a=true}})}}});wf.id_counter=c+1;$.each(b.steps,function(g,f){var d=wf.nodes[g];$.each(f.input_connections,function(i,h){if(h){if($.isArray(h)){$.each(h,function(m,k){var n=wf.nodes[k.id];var o=new Connector();o.connect(n.output_terminals[k.output_name],d.input_terminals[i]);o.redraw()})}else{var j=wf.nodes[h.id];var l=new Connector();l.connect(j.output_terminals[h.output_name],d.input_terminals[i]);l.redraw()}}});if(a&&d.type==="tool"){$.each(d.output_terminals,function(h,i){if(d.post_job_actions["HideDatasetAction"+i.name]===undefined){d.workflow_outputs.push(i.name);callout=$(d.element).find(".callout."+i.name);callout.find("img").attr("src",galaxy_config.root+"static/images/fugue/asterisk-small.png");workflow.has_changes=true}})}})},check_changes_in_active_form:function(){if(this.active_form_has_changes){this.has_changes=true;$("#right-content").find("form").submit();this.active_form_has_changes=false}},reload_active_node:function(){if(this.active_node){var a=this.active_node;this.clear_active_node();this.activate_node(a)}},clear_active_node:function(){if(this.active_node){this.active_node.make_inactive();this.active_node=null}parent.show_form_for_tool("<div>No node selected</div>")},activate_node:function(a){if(this.active_node!=a){this.check_changes_in_active_form();this.clear_active_node();parent.show_form_for_tool(a.form_html+a.tooltip,a);a.make_active();this.active_node=a}},node_changed:function(a){this.has_changes=true;if(this.active_node==a){this.check_changes_in_active_form();parent.show_form_for_tool(a.form_html+a.tooltip,a)}},layout:function(){this.check_changes_in_active_form();this.has_changes=true;var i={};var b={};$.each(this.nodes,function(l,k){if(i[l]===undefined){i[l]=0}if(b[l]===undefined){b[l]=[]}});$.each(this.nodes,function(l,k){$.each(k.input_terminals,function(m,n){$.each(n.connectors,function(p,q){var o=q.handle1.node;i[k.id]+=1;b[o.id].push(k.id)})})});node_ids_by_level=[];while(true){level_parents=[];for(var a in i){if(i[a]==0){level_parents.push(a)}}if(level_parents.length==0){break}node_ids_by_level.push(level_parents);for(var f in level_parents){var j=level_parents[f];delete i[j];for(var g in b[j]){i[b[j][g]]-=1}}}if(i.length){return}var d=this.nodes;var h=80;v_pad=30;var c=h;$.each(node_ids_by_level,function(k,l){l.sort(function(p,o){return $(d[p].element).position().top-$(d[o].element).position().top});var m=0;var n=v_pad;$.each(l,function(o,r){var q=d[r];var p=$(q.element);$(p).css({top:n,left:c});m=Math.max(m,$(p).width());n+=$(p).height()+v_pad});c+=m+h});$.each(d,function(k,l){l.redraw()})},bounds_for_all_nodes:function(){var d=Infinity,b=-Infinity,c=Infinity,a=-Infinity,f;$.each(this.nodes,function(h,g){e=$(g.element);f=e.position();d=Math.min(d,f.left);b=Math.max(b,f.left+e.width());c=Math.min(c,f.top);a=Math.max(a,f.top+e.width())});return{xmin:d,xmax:b,ymin:c,ymax:a}},fit_canvas_to_nodes:function(){var a=this.bounds_for_all_nodes();var f=this.canvas_container.position();var i=this.canvas_container.parent();var d=fix_delta(a.xmin,100);var h=fix_delta(a.ymin,100);d=Math.max(d,f.left);h=Math.max(h,f.top);var c=f.left-d;var g=f.top-h;var b=round_up(a.xmax+100,100)+d;var j=round_up(a.ymax+100,100)+h;b=Math.max(b,-c+i.width());j=Math.max(j,-g+i.height());this.canvas_container.css({left:c,top:g,width:b,height:j});this.canvas_container.children().each(function(){var k=$(this).position();$(this).css("left",k.left+d);$(this).css("top",k.top+h)})}});function fix_delta(a,b){if(a<b||a>3*b){new_pos=(Math.ceil(((a%b))/b)+1)*b;return(-(a-new_pos))}return 0}function round_up(a,b){return Math.ceil(a/b)*b}function prebuild_node(l,j,r){var i=$("<div class='toolForm toolFormInCanvas'></div>");var g=new Node(i);g.type=l;if(l=="tool"){g.tool_id=r}var n=$("<div class='toolFormTitle unselectable'>"+j+"</div>");i.append(n);i.css("left",$(window).scrollLeft()+20);i.css("top",$(window).scrollTop()+20);var m=$("<div class='toolFormBody'></div>");var h="<div><img height='16' align='middle' src='"+galaxy_config.root+"static/images/loading_small_white_bg.gif'/> loading tool info...</div>";m.append(h);g.form_html=h;i.append(m);var k=$("<div class='buttons' style='float: right;'></div>");k.append($("<div>").addClass("fa-icon-button fa fa-times").click(function(b){g.destroy()}));i.appendTo("#canvas-container");var d=$("#canvas-container").position();var c=$("#canvas-container").parent();var a=i.width();var q=i.height();i.css({left:(-d.left)+(c.width()/2)-(a/2),top:(-d.top)+(c.height()/2)-(q/2)});k.prependTo(n);a+=(k.width()+10);i.css("width",a);$(i).bind("dragstart",function(){workflow.activate_node(g)}).bind("dragend",function(){workflow.node_changed(this);workflow.fit_canvas_to_nodes();canvas_manager.draw_overview()}).bind("dragclickonly",function(){workflow.activate_node(g)}).bind("drag",function(o,p){var f=$(this).offsetParent().offset(),b=p.offsetX-f.left,s=p.offsetY-f.top;$(this).css({left:b,top:s});$(this).find(".terminal").each(function(){this.terminal.redraw()})});return g}var ext_to_type=null;var type_to_type=null;function issubtype(b,a){b=ext_to_type[b];a=ext_to_type[a];return(type_to_type[b])&&(a in type_to_type[b])}function populate_datatype_info(a){ext_to_type=a.ext_to_class_name;type_to_type=a.class_to_classes}function ScrollPanel(a){this.panel=a}$.extend(ScrollPanel.prototype,{test:function(v,d){clearTimeout(this.timeout);var k=v.pageX,j=v.pageY,l=$(this.panel),c=l.position(),b=l.width(),i=l.height(),w=l.parent(),s=w.width(),a=w.height(),r=w.offset(),p=r.left,m=r.top,A=p+w.width(),u=m+w.height(),B=-(b-(s/2)),z=-(i-(a/2)),g=(s/2),f=(a/2),h=false,q=5,o=23;if(k-q<p){if(c.left<g){var n=Math.min(o,g-c.left);l.css("left",c.left+n);h=true}}else{if(k+q>A){if(c.left>B){var n=Math.min(o,c.left-B);l.css("left",c.left-n);h=true}}else{if(j-q<m){if(c.top<f){var n=Math.min(o,f-c.top);l.css("top",c.top+n);h=true}}else{if(j+q>u){if(c.top>z){var n=Math.min(o,c.top-B);l.css("top",(c.top-n)+"px");h=true}}}}}if(h){d();var l=this;this.timeout=setTimeout(function(){l.test(v,d)},50)}},stop:function(b,a){clearTimeout(this.timeout)}});function CanvasManager(b,a){this.cv=b;this.cc=this.cv.find("#canvas-container");this.oc=a.find("#overview-canvas");this.ov=a.find("#overview-viewport");this.init_drag()}$.extend(CanvasManager.prototype,{init_drag:function(){var b=this;var a=function(f,g){f=Math.min(f,b.cv.width()/2);f=Math.max(f,-b.cc.width()+b.cv.width()/2);g=Math.min(g,b.cv.height()/2);g=Math.max(g,-b.cc.height()+b.cv.height()/2);b.cc.css({left:f,top:g});b.update_viewport_overlay()};this.cc.each(function(){this.scroll_panel=new ScrollPanel(this)});var d,c;this.cv.bind("dragstart",function(){var g=$(this).offset();var f=b.cc.position();c=f.top-g.top;d=f.left-g.left}).bind("drag",function(f,g){a(g.offsetX+d,g.offsetY+c)}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});this.ov.bind("drag",function(k,l){var h=b.cc.width(),n=b.cc.height(),m=b.oc.width(),j=b.oc.height(),f=$(this).offsetParent().offset(),i=l.offsetX-f.left,g=l.offsetY-f.top;a(-(i/m*h),-(g/j*n))}).bind("dragend",function(){workflow.fit_canvas_to_nodes();b.draw_overview()});$("#overview-border").bind("drag",function(g,i){var j=$(this).offsetParent();var h=j.offset();var f=Math.max(j.width()-(i.offsetX-h.left),j.height()-(i.offsetY-h.top));$(this).css({width:f,height:f});b.draw_overview()});$("#overview-border div").bind("drag",function(){})},update_viewport_overlay:function(){var b=this.cc,f=this.cv,a=this.oc,c=this.ov,d=b.width(),j=b.height(),i=a.width(),g=a.height(),h=b.position();c.css({left:-(h.left/d*i),top:-(h.top/j*g),width:(f.width()/d*i)-2,height:(f.height()/j*g)-2})},draw_overview:function(){var j=$("#overview-canvas"),m=j.parent().parent().width(),i=j.get(0).getContext("2d"),d=$("#canvas-container").width(),l=$("#canvas-container").height();var g,a,k,f;var h=this.cv.width();var b=this.cv.height();if(d<h&&l<b){k=d/h*m;f=(m-k)/2;g=l/b*m;a=(m-g)/2}else{if(d<l){a=0;g=m;k=Math.ceil(g*d/l);f=(m-k)/2}else{k=m;f=0;g=Math.ceil(k*l/d);a=(m-g)/2}}j.parent().css({left:f,top:a,width:k,height:g});j.attr("width",k);j.attr("height",g);$.each(workflow.nodes,function(t,q){i.fillStyle="#D2C099";i.strokeStyle="#D8B365";i.lineWidth=1;var s=$(q.element),n=s.position(),c=n.left/d*k,r=n.top/l*g,o=s.width()/d*k,p=s.height()/l*g;if(q.tool_errors){i.fillStyle="#FFCCCC";i.strokeStyle="#AA6666"}else{if(q.workflow_outputs!=undefined&&q.workflow_outputs.length>0){i.fillStyle="#E8A92D";i.strokeStyle="#E8A92D"}}i.fillRect(c,r,o,p);i.strokeRect(c,r,o,p)});this.update_viewport_overlay()}}); \ No newline at end of file diff -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a -r 9fa754a203b7312d58211b5e1e7140bf36aec76a static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseModel=Backbone.Model.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.isHidden()){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this)}this.hidden=true}this.trigger("hiddenUntilActivated:"+((this.isHidden())?("shown"):("hidden")),this);return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file +var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file diff -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a -r 9fa754a203b7312d58211b5e1e7140bf36aec76a static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){j.find(".history-name").text(l);k.model.save({name:l}).fail(function(){j.find(".history-name").text(k.model.previous("name"))})}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(){var j=arguments;_.each(this.hdaViews,function(k){if(k.tagsEditor){k.tagsEditor.toggle.apply(k.tagsEditor,j)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(k){var l=this;function n(o){l.searchFor=o;l.filters=[function(p){return p.matchesAll(l.searchFor)}];l.trigger("search:searching",o,l);l.renderHdas()}function j(o){if(l.model.hdas.haveDetails()){n(o);return}l.$el.find(".history-search-controls").searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){n(o)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}return k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m})},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls");if(!k.children().size()){k=this.renderSearchControls(k).hide()}k.show(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").hide(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(c,f,a,i){var g=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});g.storageKey=function h(){return("history-panel")};var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(j){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([j],[true])))},removeExpandedHda:function(j){this.save("expandedHdas",_.omit(this.get("expandedHdas"),j))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function b(j){if(!j){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+j)}return("history:"+j)};var e=Backbone.View.extend(LoggableMixin).extend({defaultHDAViewClass:i.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(j){j=j||{};if(j.logger){this.logger=j.logger}this.log(this+".initialize:",j);this.HDAViewClass=j.HDAViewClass||this.defaultHDAViewClass;this.linkTarget=j.linkTarget||"_blank";this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.preferences=new g(_.extend({id:g.storageKey()},_.pick(j,_.keys(g.prototype.defaults))));this.filters=[];this.selecting=j.selecting||false;this.annotationEditorShown=j.annotationEditorShown||false;this._setUpListeners();if(this.model){this._setUpWebStorage(j.initiallyExpanded,j.show_deleted,j.show_hidden);this._setUpModelEventHandlers()}if(j.onready){j.onready.call(this)}},_setUpListeners:function(){this.on("error",function(k,n,j,m,l){this.errorHandler(k,n,j,m,l)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(j){this.log(this+"",arguments)},this)}},errorHandler:function(l,o,k,n,m){var j=this._parseErrorMessage(l,o,k,n,m);if(o&&o.status===0&&o.readyState===0){}else{if(o&&o.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",j.message,j.details)})}else{this.displayMessage("error",j.message,j.details)}}}},_parseErrorMessage:function(m,q,l,p,o){var k=Galaxy.currUser,j={message:this._bePolite(p),details:{user:(k instanceof User)?(k.toJSON()):(k+""),source:(m instanceof Backbone.Model)?(m.toJSON()):(m+""),xhr:q,options:(q)?(_.omit(l,"xhr")):(l)}};_.extend(j.details,o||{});if(q&&_.isFunction(q.getAllResponseHeaders)){var n=q.getAllResponseHeaders();n=_.compact(n.split("\n"));n=_.map(n,function(r){return r.split(": ")});j.details.xhr.responseHeaders=_.object(n)}return j},_bePolite:function(j){j=j||_l("An error occurred while getting updates from the server");return j+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(k){var j=this;return this.loadHistoryWithHDADetails("current",k).then(function(m,l){j.trigger("current-history",j)})},switchToHistory:function(m,l){var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories/"+m+"/set_as_current")};return this.loadHistoryWithHDADetails(m,l,k).then(function(o,n){j.trigger("switched-history",j)})},createNewHistory:function(l){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var j=this,k=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,l,k).then(function(n,m){j.trigger("new-history",j)})},loadHistoryWithHDADetails:function(m,l,k,o){var j=this,n=function(p){return j.getExpandedHdaIds(p.id)};return this.loadHistory(m,l,k,o,n)},loadHistory:function(m,l,k,p,n){this.trigger("loading-history",this);l=l||{};var j=this;var o=c.History.getHistoryData(m,{historyFn:k,hdaFn:p,hdaDetailIds:l.initiallyExpanded||n});return this._loadHistoryFromXHR(o,l).fail(function(s,q,r){j.trigger("error",j,s,l,_l("An error was encountered while "+q),{historyId:m,history:r||{}})}).always(function(){j.trigger("loading-done",j)})},_loadHistoryFromXHR:function(l,k){var j=this;l.then(function(m,n){j.setModel(m,n,k)});l.fail(function(n,m){j.render()});return l},setModel:function(l,j,k){k=k||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){l.user=Galaxy.currUser.toJSON()}this.model=new c.History(l,j,k);this._setUpWebStorage(k.initiallyExpanded,k.show_deleted,k.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(k,j,l){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(k)){this.storage.set("exandedHdas",k)}if(_.isBoolean(j)){this.storage.set("show_deleted",j)}if(_.isBoolean(l)){this.storage.set("show_hidden",l)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var j in sessionStorage){if(j.indexOf("history:")===0){sessionStorage.removeItem(j)}}},getStoredOptions:function(k){if(!k||k==="current"){return(this.storage)?(this.storage.get()):({})}var j=sessionStorage.getItem(d.historyStorageKey(k));return(j===null)?({}):(JSON.parse(j))},getExpandedHdaIds:function(j){var k=this.getStoredOptions(j).expandedHdas;return((_.isEmpty(k))?([]):(_.keys(k)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(k,m,j,l){this.errorHandler(k,m,j,l)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(j){this.model.fetch()},this);this.model.hdas.on("state:ready",function(k,l,j){if((!k.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[k.id])}},this)},render:function(l,m){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k;if(this.model){k=this.renderModel()}else{k=this.renderWithoutModel()}$(j).queue("fx",[function(n){if(l&&j.$el.is(":visible")){j.$el.fadeOut(l,n)}else{n()}},function(n){j.$el.empty();if(k){j.$el.append(k.children());j.renderBasedOnPrefs()}n()},function(n){if(l&&!j.$el.is(":visible")){j.$el.fadeIn(l,n)}else{n()}},function(n){if(m){m.call(this)}j.trigger("rendered",this);n()}]);return this},renderWithoutModel:function(){var j=$("<div/>"),k=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return j.append(k)},renderModel:function(){var j=$("<div/>");if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){j.append(e.templates.anonHistoryPanel(this.model.toJSON()))}else{j.append(e.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(j);this._renderAnnotation(j)}}j.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(j);this.renderHdas(j);return j},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},_renderTags:function(j){var k=this;this.tagsEditor=new TagsEditor({model:this.model,el:j.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("tagsEditorShown",true);k.toggleHDATagEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("tagsEditorShown",false);k.toggleHDATagEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("tagsEditorShown")){this.tagsEditor.toggle(true)}},_renderAnnotation:function(j){var k=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:j.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){k.preferences.set("annotationEditorShown",true);k.toggleHDAAnnotationEditors(true,k.fxSpeed)},onhide:function(){k.preferences.set("annotationEditorShown",false);k.toggleHDAAnnotationEditors(false,k.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(j.find(".history-secondary-actions"))});if(this.preferences.get("annotationEditorShown")){this.annotationEditor.toggle(true)}},_renderSearchButton:function(j){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_renderSelectButton:function(j){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(j){j=j||this.$el;j.find("[title]").tooltip({placement:"bottom"});if((!this.model)||(!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var k=this;j.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(l){j.find(".history-name").text(l);k.model.save({name:l}).fail(function(){j.find(".history-name").text(k.model.previous("name"))})}});this._setUpDatasetActionsPopup(j)},_setUpDatasetActionsPopup:function(j){var k=this;(new PopupMenu(j.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.hide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Unhide datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.unhide;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Delete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype["delete"];k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Undelete datasets"),func:function(){var l=f.HistoryDatasetAssociation.prototype.undelete;k.getSelectedHdaCollection().ajaxQueue(l)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var l=f.HistoryDatasetAssociation.prototype.purge;k.getSelectedHdaCollection().ajaxQueue(l)}}}]))},refreshHdas:function(k,j){if(this.model){return this.model.refresh(k,j)}return $.when()},addHdaView:function(m){this.log("add."+this,m);var k=this;if(!m.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function l(o){var n=k.$el.find(k.emptyMsgSelector);if(n.is(":visible")){n.fadeOut(k.fxSpeed,o)}else{o()}},function j(o){k.scrollToTop();var n=k.$el.find(k.datasetsSelector);k.createHdaView(m).$el.hide().prependTo(n).slideDown(k.fxSpeed)}])},createHdaView:function(l){var k=l.get("id"),j=this.storage.get("expandedHdas")[k],m=new this.HDAViewClass({model:l,linkTarget:this.linkTarget,expanded:j,tagsEditorShown:this.preferences.get("tagsEditorShown"),annotationEditorShown:this.preferences.get("annotationEditorShown"),selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(m);this.hdaViews[k]=m;return m.render()},_setUpHdaListeners:function(k){var j=this;k.on("body-expanded",function(l){j.storage.addExpandedHda(l)});k.on("body-collapsed",function(l){j.storage.removeExpandedHda(l)});k.on("error",function(m,o,l,n){j.errorHandler(m,o,l,n)})},handleHdaDeletionChange:function(j){if(j.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[j.id])}},handleHdaVisibleChange:function(j){if(j.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[j.id])}},removeHdaView:function(k){if(!k){return}var j=this;k.$el.fadeOut(j.fxSpeed,function(){k.off();k.remove();delete j.hdaViews[k.model.id];if(_.isEmpty(j.hdaViews)){j.$el.find(j.emptyMsgSelector).fadeIn(j.fxSpeed,function(){j.trigger("empty-history",j)})}})},renderHdas:function(l){l=l||this.$el;this.hdaViews={};var k=this,j=l.find(this.datasetsSelector),m=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);j.empty();if(m.length){m.each(function(n){j.prepend(k.createHdaView(n).$el)});l.find(this.emptyMsgSelector).hide()}else{l.find(this.emptyMsgSelector).show()}return this.hdaViews},toggleHDATagEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.tagsEditor){l.tagsEditor.toggle.apply(l.tagsEditor,k)}})},toggleHDAAnnotationEditors:function(j){var k=arguments;_.each(this.hdaViews,function(l){if(l.annotationEditor){l.annotationEditor.toggle.apply(l.annotationEditor,k)}})},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls","click .history-select-btn":function(j){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(j){j.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},renderSearchControls:function(k){var l=this;function n(o){l.searchFor=o;l.filters=[function(p){return p.matchesAll(l.searchFor)}];l.trigger("search:searching",o,l);l.renderHdas()}function j(o){if(l.model.hdas.haveDetails()){n(o);return}l.$el.find(".history-search-controls").searchInput("toggle-loading");l.model.hdas.fetchAllDetails({silent:true}).always(function(){l.$el.find(".history-search-controls").searchInput("toggle-loading")}).done(function(){n(o)})}function m(){l.searchFor="";l.filters=[];l.trigger("search:clear",l);l.renderHdas()}return k.searchInput({initialVal:l.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:j,onsearch:n,onclear:m})},showSearchControls:function(l){l=(l===undefined)?(this.fxSpeed):(l);var j=this,k=this.$el.find(".history-search-controls");if(!k.children().size()){k=this.renderSearchControls(k).hide()}k.show(l,function(){$(this).find("input").focus();j.preferences.set("searching",true)})},hideSearchControls:function(){speed=(speed===undefined)?(this.fxSpeed):(speed);var j=this;this.$el.find(".history-search-controls").hide(speed,function(){j.preferences.set("searching",false)})},toggleSearchControls:function(j){speed=(jQuery.type(j)==="number")?(j):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showSelectors:function(j){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(j);_.each(this.hdaViews,function(k){k.showSelector(j)})},hideSelectors:function(j){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(j);_.each(this.hdaViews,function(k){k.hideSelector(j)})},toggleSelectors:function(j){if(!this.selecting){this.showSelectors(j)}else{this.hideSelectors(j)}},selectAllDatasets:function(k){var j=this.$el.find(".history-select-all-datasets-btn");currMode=j.data("mode");if(currMode==="select"){_.each(this.hdaViews,function(l){l.select(k)});j.data("mode","deselect");j.text(_l("De-select all"))}else{if(currMode==="deselect"){_.each(this.hdaViews,function(l){l.deselect(k)});j.data("mode","select");j.text(_l("Select all"))}}},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(j){return j.selected})},getSelectedHdaCollection:function(){return new f.HDACollection(_.map(this.getSelectedHdaViews(),function(j){return j.model}),{historyId:this.model.id})},showLoadingIndicator:function(k,j,l){j=(j!==undefined)?(j):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,l)}else{this.$el.fadeOut(j);this.indicator.show(k,j,l)}},hideLoadingIndicator:function(j,k){j=(j!==undefined)?(j):(this.fxSpeed);if(this.indicator){this.indicator.hide(j,k)}},displayMessage:function(o,p,n){var l=this;this.scrollToTop();var m=this.$el.find(this.msgsSelector),j=$("<div/>").addClass(o+"message").html(p);if(!_.isEmpty(n)){var k=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(l.messageToModalOptions(o,p,n));return false});j.append(" ",k)}return m.html(j)},messageToModalOptions:function(n,p,m){var j=this,o=$("<div/>"),l={title:"Details"};function k(q){q=_.omit(q,_.functions(q));return["<table>",_.map(q,function(s,r){s=(_.isObject(s))?(k(s)):(s);return'<tr><td style="vertical-align: top; color: grey">'+r+'</td><td style="padding-left: 8px">'+s+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(m)){l.body=o.append(k(m))}else{l.body=o.html(m)}l.buttons={Ok:function(){Galaxy.modal.hide();j.clearMessages()}};return l},clearMessages:function(){var j=this.$el.find(this.msgsSelector);j.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(j){this.$el.parent().scrollTop(j)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(k,l){if(!l){this.$el.parent().parent().scrollTop(k);return this}var j=window,m=this.$el.parent().parent(),o=$(j).innerHeight(),n=(o/2)-(l/2);$(m).scrollTop(k-n);return this},scrollToId:function(k){if((!k)||(!this.hdaViews[k])){return this}var j=this.hdaViews[k].$el;this.scrollIntoView(j.offset().top,j.outerHeight());return this},scrollToHid:function(j){var k=this.model.hdas.getByHid(j);if(!k){return this}return this.scrollToId(k.id)},connectToQuotaMeter:function(j){if(!j){return this}this.listenTo(j,"quota:over",this.showQuotaMessage);this.listenTo(j,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(j&&j.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var j=this.$el.find(".quota-message");if(j.is(":hidden")){j.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var j=this.$el.find(".quota-message");if(!j.is(":hidden")){j.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(j){if(!j){return this}this.on("new-storage",function(l,k){if(j&&l){j.findItemByHtml(_l("Include Deleted Datasets")).checked=l.get("show_deleted");j.findItemByHtml(_l("Include Hidden Datasets")).checked=l.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});e.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:e}}); \ No newline at end of file diff -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a -r 9fa754a203b7312d58211b5e1e7140bf36aec76a static/scripts/packed/mvc/user/user-model.js --- a/static/scripts/packed/mvc/user/user-model.js +++ b/static/scripts/packed/mvc/user/user-model.js @@ -1,1 +1,1 @@ -var User=Backbone.Model.extend(LoggableMixin).extend({urlRoot:galaxy_config.root+"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return BaseModel.prototype.fetch.call(this,b)},clearSessionStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:galaxy_config.root+"api/users"}); \ No newline at end of file +var User=Backbone.Model.extend(LoggableMixin).extend({urlRoot:galaxy_config.root+"api/users",defaults:{id:null,username:"("+_l("anonymous user")+")",email:"",total_disk_usage:0,nice_total_disk_usage:"",quota_percent:null},initialize:function(a){this.log("User.initialize:",a);this.on("loaded",function(b,c){this.log(this+" has loaded:",b,c)});this.on("change",function(b,c){this.log(this+" has changed:",b,c.changes)})},isAnonymous:function(){return(!this.get("email"))},loadFromApi:function(d,b){d=d||User.CURRENT_ID_STR;b=b||{};var a=this,c=b.success;b.success=function(f,e){a.trigger("loaded",f,e);if(c){c(f,e)}};if(d===User.CURRENT_ID_STR){b.url=this.urlRoot+"/"+User.CURRENT_ID_STR}return Backbone.Model.prototype.fetch.call(this,b)},clearSessionStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},toString:function(){var a=[this.get("username")];if(this.get("id")){a.unshift(this.get("id"));a.push(this.get("email"))}return"User("+a.join(":")+")"}});User.CURRENT_ID_STR="current";User.getCurrentUserFromApi=function(b){var a=new User();a.loadFromApi(User.CURRENT_ID_STR,b);return a};var UserCollection=Backbone.Collection.extend(LoggableMixin).extend({model:User,urlRoot:galaxy_config.root+"api/users"}); \ No newline at end of file diff -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a -r 9fa754a203b7312d58211b5e1e7140bf36aec76a templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -207,18 +207,11 @@ ## <%def name="center_panel()"> - ${self.grid_body()} + ${self.load()} </%def> ## Render the grid's basic elements. Each of these elements can be subclassed. <%def name="body()"> - ${self.grid_body()} -</%def> - -## Because body() is special and always exists even if not explicitly defined, -## it's not possible to override body() in the topmost template in the chain. -## Because of this, override grid_body() instead. -<%def name="grid_body()"> ${self.load()} </%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Push code into js, async refresh based on json
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3e2c3464298/ Changeset: a3e2c3464298 User: guerler Date: 2013-12-18 23:16:43 Summary: Grids: Push code into js, async refresh based on json Affected #: 3 files diff -r 350c72df26815c0483a268fd1a097f0af8360930 -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -130,7 +130,13 @@ }); return url_data; + }, + + // Return URL for obtaining a new grid + get_url: function (args) { + return this.get('url_base') + "?" + $.param(this.get_url_data()) + '&' + $.param(args); } + }); // grid view @@ -140,9 +146,10 @@ grid: null, // Initialize - initialize: function(grid) + initialize: function(grid_config) { - this.init_grid(grid); + // initialize controls + this.init_grid(grid_config); this.init_grid_controls(); // Initialize text filters to select text on click and use normal font when user is typing. @@ -153,9 +160,30 @@ }, // Initialize - init_grid: function(grid) + init_grid: function(grid_config) { - this.grid = grid; + // link grid model + this.grid = new Grid(grid_config); + + // get options + var options = this.grid.attributes; + + // strip protocol and domain + var url = this.grid.get('url_base'); + url = url.replace(/^.*\/\/[^\/]+/, ''); + this.grid.set('url_base', url); + + // update div contents + $('#grid-table-body').html(this.template_body(options)); + $('#grid-table-footer').html(this.template_footer(options)); + + // update message + if (options.message) { + $('#grid-message').html(this.template_message(options)); + setTimeout( function() { $('#grid-message').html(''); }, 5000); + } + + // configure elements this.init_grid_elements(); }, @@ -537,7 +565,7 @@ // check for operation details if (operation && id) { // show confirmation box - if (confirmation_text && confirmation_text != '' && confirmation_text != 'None') + if (confirmation_text && confirmation_text != '' && confirmation_text != 'None' && confirmation_text != 'null') if(!confirm(confirmation_text)) return false; @@ -622,30 +650,16 @@ type: method, url: self.grid.get('url_base'), data: self.grid.get_url_data(), - error: function(response) { alert( "Grid refresh failed" );}, + error: function(response) { alert( 'Grid refresh failed' );}, success: function(response_text) { - // HACK: use a simple string to separate the elements in the - // response: (1) table body; (2) number of pages in table; and (3) message. - var parsed_response_text = response_text.split("*****"); - - // Update grid body and footer. - $('#grid-table-body').html(parsed_response_text[0]); - // FIXME: this does not work at all; what's needed is a function - // that updates page links when number of pages changes. - $('#grid-table-footer').html(parsed_response_text[1]); - + // Initialize new grid config + self.init_grid($.parseJSON(response_text)); + // Trigger custom event to indicate grid body has changed. $('#grid-table-body').trigger('update'); // Hide loading overlay. $('.loading-elt-overlay').hide(); - - // Show message if there is one. - var message = $.trim( parsed_response_text[2] ); - if (message !== "") { - $('#grid-message').html( message ).show(); - setTimeout( function() { $('#grid-message').hide(); }, 5000); - } }, complete: function() { // Clear grid of transient request attributes. @@ -688,6 +702,253 @@ if (cur_page !== null && cur_page !== undefined && cur_page !== 'all') { this.grid.set('cur_page', 1); } + }, + + // template + template_body: function(options) { + // initialize + var tmpl = ''; + var num_rows_rendered = 0; + var items_length = options.items.length; + + // empty grid? + if (items_length == 0) { + // No results. + tmpl += '<tr><td colspan="100"><em>No Items</em></td></tr>'; + num_rows_rendered = 1; + } + + // create rows + for (i in options.items) { + + // encode ids + var item = options.items[i]; + var encoded_id = item.encode_id; + var popupmenu_id = 'grid-' + i + '-popup'; + + // Tag current + tmpl += '<tr '; + if (options.current_item_id == item.id) { + tmpl += 'class="current"'; + } + tmpl += '>'; + + // Item selection column + if (options.show_item_checkboxes) { + tmpl += '<td style="width: 1.5em;">' + + '<input type="checkbox" name="id" value="' + encoded_id + '" id="' + encoded_id + '" class="grid-row-select-checkbox" />' + + '</td>'; + } + + // Data columns + for (j in options.columns) { + var column = options.columns[j]; + if (column.visible) { + // Nowrap + var nowrap = ''; + if (column.nowrap) { + nowrap = 'style="white-space:nowrap;"'; + } + + // get column settings + var column_settings = item.column_config[column.label]; + + // load attributes + var link = column_settings.link; + var value = column_settings.value; + var inbound = column_settings.inbound; + + // unescape value + if (jQuery.type( value ) === 'string') { + value = value.replace(/\/\//g, '/'); + } + + // Attach popup menu? + var id = ""; + var cls = ""; + if (column.attach_popup) { + id = 'grid-' + i + '-popup'; + cls = "menubutton" + if (link != '') { + cls += " split"; + } + cls += " popup"; + } + + // Check for row wrapping + tmpl += '<td ' + nowrap + '>'; + + // Link + if (link) { + if (options.operations.length != 0) { + tmpl += '<div id="' + id + '" class="' + cls + '" style="float: left;">'; + } + + var label_class = ""; + if (inbound) { + label_class = "use-inbound" + } else { + label_class = "use-outbound" + } + tmpl += '<a class="label ' + label_class + '" href="' + link + '" onclick="return false;">' + value + '</a>'; + if (options.operations.length != 0) { + tmpl += '</div>'; + } + } else { + tmpl += '<div id="' + id + '" class="' + cls + '"><label id="' + column.label_id_prefix + encoded_id + '" for="' + encoded_id + '">' + value + '</label></div>'; + } + tmpl += '</td>'; + } + } + tmpl += '</tr>'; + num_rows_rendered++; + } + return tmpl; + }, + + // template + template_footer: function(options) { + + // create template string + var tmpl = ''; + + // paging + if (options.use_paging && options.num_pages > 1) { + // get configuration + var num_page_links = options.num_page_links; + var cur_page_num = options.cur_page_num; + var num_pages = options.num_pages; + + // First pass on min page. + var page_link_range = num_page_links / 2; + var min_page = cur_page_num - page_link_range + var min_offset = 0; + if (min_page == 0) { + // Min page is too low. + min_page = 1; + min_offset = page_link_range - ( cur_page_num - min_page ); + } + + // Set max page. + var max_range = page_link_range + min_offset; + var max_page = cur_page_num + max_range; + if (max_page <= num_pages) { + // Max page is fine. + max_offset = 0; + } else { + // Max page is too high. + max_page = num_pages; + // +1 to account for the +1 in the loop below. + max_offset = max_range - ( max_page + 1 - cur_page_num ); + } + + // Second and final pass on min page to add any unused + // offset from max to min. + if (max_offset != 0) { + min_page -= max_offset + if (min_page < 1) { + min_page = 1 + } + } + + // template header + tmpl += '<tr id="page-links-row">'; + if (options.show_item_checkboxes) { + tmpl += '<td></td>'; + } + tmpl += '<td colspan="100">' + + '<span id="page-link-container">' + + 'Page:'; + + if (min_page > 1) { + tmpl += '<span class="page-link" id="page-link-1"><a href="' + this.grid.get_url({page : page_index}) + '" page_num="1" onclick="return false;">1</a></span> ...'; + } + + // create page urls + for (var page_index = min_page; page_index < max_page + 1; page_index++) { + + if (page_index == options.cur_page_num) { + tmpl += '<span class="page-link inactive-link" id="page-link-' + page_index + '">' + page_index + '</span>'; + } else { + tmpl += '<span class="page-link" id="page-link-' + page_index + '"><a href="' + this.grid.get_url({page : page_index}) + '" onclick="return false;" page_num="' + page_index + '">' + page_index + '</a></span>'; + } + } + + // show last page + if (max_page < num_pages) { + tmpl += '...' + + '<span class="page-link" id="page-link-' + num_pages + '"><a href="' + this.grid.get_url({page : num_pages}) + '" onclick="return false;" page_num="' + num_pages + '">' + num_pages + '</a></span>'; + } + tmpl += '</span>'; + + // Show all link + tmpl += '<span class="page-link" id="show-all-link-span"> | <a href="' + this.grid.get_url({page : 'all'}) + '" onclick="return false;" page_num="all">Show All</a></span>' + + '</td>' + + '</tr>'; + } + + // Grid operations for multiple items. + if (options.show_item_checkboxes) { + // start template + tmpl += '<tr>' + + '<input type="hidden" id="operation" name="operation" value="">' + + '<td></td>' + + '<td colspan="100">' + + 'For <span class="grid-selected-count"></span> selected ' + options.get_class_plural + ': '; + + // configure buttons for operations + for (i in options.operations) { + var operation = options.operations[i]; + if (operation.allow_multiple) { + tmpl += '<input type="button" value="' + operation.label + '" class="action-button" onclick="gridView.submit_operation(this, \'' + operation.confirm + '\')"> '; + } + } + + // finalize template + tmpl += '</td>' + + '</tr>'; + } + + // count global operations + var found_global = false; + for (i in options.operations) { + if (options.operations[i].global_operation) { + found_global = true; + break; + } + } + + // add global operations + if (found_global) { + tmpl += '<tr>' + + '<td colspan="100">'; + for (i in options.operations) { + var operation = options.operations[i]; + if (operation.global_operation) { + tmpl += '<a class="action-button" href="' + operation.global_operation + '">' + operation.label + '</a>'; + } + } + tmpl += '</td>' + + '</tr>'; + } + + // add legend + if (options.legend) { + tmpl += '<tr>' + + '<td colspan="100">' + options.legend + '</td>' + + '</tr>'; + } + + // return + return tmpl; + }, + + // template + template_message: function(options) { + return '<p>' + + '<div class="' + options.status + 'message transient-message">' + options.message + '</div>' + + '<div style="clear: both"></div>' + + '</p>'; } }); diff -r 350c72df26815c0483a268fd1a097f0af8360930 -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -1,6 +1,7 @@ <%! from galaxy.web.framework.helpers.grids import TextColumn, StateColumn, GridColumnFilter from galaxy.web.framework.helpers import iff + import urllib import galaxy.util def inherit(context): @@ -24,7 +25,7 @@ self.grid_javascripts() if embedded: self.render_grid_header( grid, False ) - self.render_grid_table( grid, show_item_checkboxes=show_item_checkboxes ) + self.render_grid_table( grid ) else: self.make_grid( grid ) endif @@ -50,6 +51,7 @@ 'show_item_checkboxes' : context.get('show_item_checkboxes', False), 'cur_page_num' : cur_page_num, 'num_pages' : num_pages, + 'num_page_links' : num_page_links, 'history_tag_autocomplete_url' : url( controller='tag', action='tag_autocomplete_data', item_class='History' ), 'history_name_autocomplete_url' : url( controller='history', action='name_autocomplete_data' ), 'status' : status, @@ -58,7 +60,6 @@ 'operations' : [], 'items' : [], 'columns' : [], - 'multiple_item_ops_exist' : None, 'get_class_plural' : get_class_plural( grid.model_class ).lower(), 'use_paging' : grid.use_paging, 'legend' : grid.legend, @@ -68,7 +69,7 @@ 'default_filter_dict' : default_filter_dict, 'advanced_search' : advanced_search } - + ## add current item if exists if current_item: self.grid_config['current_item_id'] = current_item.id @@ -119,7 +120,7 @@ 'global_operation' : False }) if operation.allow_multiple: - self.grid_config['multiple_item_ops_exist'] = True + self.grid_config['show_item_checkboxes'] = True if operation.global_operation: self.grid_config['global_operation'] = url( ** (operation.global_operation()) ) @@ -176,8 +177,6 @@ # Handle non-ascii chars. if isinstance(value, str): value = unicode(value, 'utf-8') - - # escape string value = value.replace('/', '//') endif @@ -242,7 +241,16 @@ } gridView.add_filter_condition("tags", tag); }; + + ## load grid viewer + $(function() { + require(['galaxy.grids'], function(mod_grids) { + gridView = new mod_grids.GridView(${h.to_json_string(self.grid_config)}); + }); + }); </script> + + ${handle_refresh_frames()} </%def><%def name="stylesheets()"> @@ -268,20 +276,13 @@ <td></td></tr><tr> - <td width="100%" id="grid-message" valign="top"> - %if message: - <p> - <div class="${self.grid_config['status']}message transient-message">${self.grid_config['message']}</div> - <div style="clear: both"></div> - </p> - %endif - </td> + <td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table> - ${self.render_grid_table( grid, show_item_checkboxes )} + ${self.render_grid_table( grid )} </%def><%def name="grid_title()"> @@ -328,16 +329,11 @@ </%def> ## Render grid. -<%def name="render_grid_table( grid, show_item_checkboxes=False)"> +<%def name="render_grid_table( grid )"><% # get configuration show_item_checkboxes = self.grid_config['show_item_checkboxes'] - multiple_item_ops_exist = self.grid_config['multiple_item_ops_exist'] sort_key = self.grid_config['sort_key'] - - # Show checkboxes if flag is set or if multiple item ops exist. - if show_item_checkboxes or multiple_item_ops_exist: - show_item_checkboxes = True %><form method="post" onsubmit="return false;"><table id="grid-table" class="grid"> @@ -364,238 +360,14 @@ </th> %endif %endfor - <th></th></tr></thead> - <tbody id="grid-table-body"> - ${render_grid_table_body_contents( grid, show_item_checkboxes )} - </tbody> - <tfoot id="grid-table-footer"> - ${render_grid_table_footer_contents( grid, show_item_checkboxes )} - </tfoot> + <tbody id="grid-table-body"></tbody> + <tfoot id="grid-table-footer"></tfoot></table></form></%def> -## Render grid table body contents. -<%def name="render_grid_table_body_contents(grid, show_item_checkboxes=False)"> - <% num_rows_rendered = 0 %> - %if len(self.grid_config['items']) == 0: - ## No results. - <tr><td colspan="100"><em>No Items</em></td></tr> - <% num_rows_rendered = 1 %> - %endif - %for i, item in enumerate( self.grid_config['items'] ): - <% encoded_id = item['encode_id'] %> - <% popupmenu_id = "grid-" + str(i) + "-popup" %> - <tr \ - %if self.grid_config['current_item_id'] == item['id']: - class="current" \ - %endif - > - ## Item selection column - %if show_item_checkboxes: - <td style="width: 1.5em;"> - <input type="checkbox" name="id" value="${encoded_id}" id="${encoded_id}" class="grid-row-select-checkbox" /> - </td> - %endif - ## Data columns - %for column in self.grid_config['columns']: - %if column['visible']: - <% - ## Nowrap - nowrap = "" - if column['nowrap']: - nowrap = 'style="white-space:nowrap;"' - - # get column settings - column_settings = item['column_config'][column['label']] - - # load attributes - link = column_settings['link'] - value = column_settings['value'] - inbound = column_settings['inbound'] - - # unescape value - if isinstance(value, unicode): - value = value.replace('//', '/') - - # Attach popup menu? - id = "" - cls = "" - if column['attach_popup']: - id = 'grid-%d-popup' % i - cls = "menubutton" - if link: - cls += " split" - endif - cls += " popup" - endif - %> - <td ${nowrap}> - %if link: - %if len(self.grid_config['operations']) != 0: - <div id="${id}" class="${cls}" style="float: left;"> - %endif - - <% - label_class = "" - if inbound: - label_class = "use-inbound" - else: - label_class = "use-outbound" - endif - %> - <a class="label ${label_class}" href="${link}" onclick="return false;">${value}</a> - %if len(self.grid_config['operations']) != 0: - </div> - %endif - %else: - <div id="${id}" class="${cls}"><label id="${column['label_id_prefix']}${encoded_id}" for="${encoded_id}">${value}</label></div> - %endif - </td> - %endif - %endfor - </tr> - <% num_rows_rendered += 1 %> - %endfor - - ## update configuration - <script type="text/javascript"> - $(function() { - require(['galaxy.grids'], function(mod_grids) { - ## get configuration - var grid_config = ${ h.to_json_string( self.grid_config ) }; - - // Create grid. - var grid = new mod_grids.Grid(grid_config); - - // strip protocol and domain - var url = grid.get('url_base'); - url = url.replace(/^.*\/\/[^\/]+/, ''); - grid.set('url_base', url); - - // Create view. - if (!gridView) - gridView = new mod_grids.GridView(grid); - else - gridView.init_grid(grid); - }); - }); - </script> - - ${handle_refresh_frames()} -</%def> - -## Render grid table footer contents. -<%def name="render_grid_table_footer_contents(grid, show_item_checkboxes=False)"> - <% - items_plural = self.grid_config['get_class_plural'] - num_pages = self.grid_config['num_pages'] - cur_page_num = self.grid_config['cur_page_num'] - %> - %if self.grid_config['use_paging'] and num_pages > 1: - <tr id="page-links-row"> - %if show_item_checkboxes: - <td></td> - %endif - <td colspan="100"> - <span id='page-link-container'> - ## Page links. Show 10 pages around current page. - <% - # - # Set minimum & maximum page. - # - page_link_range = num_page_links/2 - - # First pass on min page. - min_page = cur_page_num - page_link_range - if min_page >= 1: - # Min page is fine. - min_offset = 0 - else: - # Min page is too low. - min_page = 1 - min_offset = page_link_range - ( cur_page_num - min_page ) - - # Set max page. - max_range = page_link_range + min_offset - max_page = cur_page_num + max_range - if max_page <= num_pages: - # Max page is fine. - max_offset = 0 - else: - # Max page is too high. - max_page = num_pages - # +1 to account for the +1 in the loop below. - max_offset = max_range - ( max_page + 1 - cur_page_num ) - - # Second and final pass on min page to add any unused - # offset from max to min. - if max_offset != 0: - min_page -= max_offset - if min_page < 1: - min_page = 1 - %> - Page: - % if min_page > 1: - <span class='page-link' id="page-link-1"><a href="${url( page=1 )}" page_num="1" onclick="return false;">1</a></span> ... - % endif - %for page_index in range(min_page, max_page + 1): - %if page_index == cur_page_num: - <span class='page-link inactive-link' id="page-link-${page_index}">${page_index}</span> - %else: - <% args = { 'page' : page_index } %> - <span class='page-link' id="page-link-${page_index}"><a href="${url( args )}" onclick="return false;" page_num='${page_index}'>${page_index}</a></span> - %endif - %endfor - %if max_page < num_pages: - ... - <span class='page-link' id="page-link-${num_pages}"><a href="${url( page=num_pages )}" onclick="return false;" page_num="${num_pages}">${num_pages}</a></span> - %endif - </span> - - ## Show all link - <span class='page-link' id='show-all-link-span'> | <a href="${url( page='all' )}" onclick="return false;" page_num="all">Show All</a></span> - </td> - </tr> - %endif - ## Grid operations for multiple items. - %if show_item_checkboxes: - <tr> - ## place holder for multiple operation commands - <input type="hidden" id="operation" name="operation" value=""> - <td></td> - <td colspan="100"> - For <span class="grid-selected-count"></span> selected ${items_plural}: - %for operation in self.grid_config['operations']: - %if operation['allow_multiple']: - <input type="button" value="${operation['label']}" class="action-button" onclick="gridView.submit_operation(this, '${operation['confirm']}')"> - %endif - %endfor - </td> - </tr> - %endif - %if len([o for o in self.grid_config['operations'] if o['global_operation']]) > 0: - <tr> - <td colspan="100"> - %for operation in self.grid_config['operations']: - %if operation['global_operation']: - <a class="action-button" href="${operation['global_operation']}">${operation['label']}</a> - %endif - %endfor - </td> - </tr> - %endif - %if self.grid_config['legend']: - <tr> - <td colspan="100"> - ${self.grid_config['legend']} - </td> - </tr> - %endif -</%def> - ## Print grid search/filtering UI. <%def name="render_grid_filters( grid, render_advanced_search=True )"><% diff -r 350c72df26815c0483a268fd1a097f0af8360930 -r a3e2c3464298ebea3fd2ab93a43aac479ba9665a templates/grid_base_async.mako --- a/templates/grid_base_async.mako +++ b/templates/grid_base_async.mako @@ -1,18 +1,4 @@ -<%namespace file="./grid_base.mako" import="*" /> -<%namespace file="/display_common.mako" import="render_message" /> +<%namespace name="grid_base" file="./grid_base.mako" import="*" /> ${init()} - -<% - # Set flag to indicate whether grid has operations that operate on multiple items. - multiple_item_ops_exist = False - for operation in grid.operations: - if operation.allow_multiple: - multiple_item_ops_exist = True -%> - -${render_grid_table_body_contents( grid, show_item_checkboxes=( show_item_checkboxes or multiple_item_ops_exist ) )} -***** -${render_grid_table_footer_contents( grid, show_item_checkboxes=( show_item_checkboxes or multiple_item_ops_exist ) )} -***** -${render_message( message, status )} \ No newline at end of file +${h.to_json_string( grid_base.grid_config )} \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: simleo: tools/fastq/fastq_paired_end_joiner: added support for recent Illumina headers
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e232573b7c62/ Changeset: e232573b7c62 User: simleo Date: 2013-06-06 17:33:46 Summary: tools/fastq/fastq_paired_end_joiner: added support for recent Illumina headers Affected #: 2 files diff -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 -r e232573b7c629a94ab60e6b615ecedf156913308 tools/fastq/fastq_paired_end_joiner.py --- a/tools/fastq/fastq_paired_end_joiner.py +++ b/tools/fastq/fastq_paired_end_joiner.py @@ -1,38 +1,162 @@ -#Dan Blankenberg -import sys, os, shutil -from galaxy_utils.sequence.fastq import fastqReader, fastqNamedReader, fastqWriter, fastqJoiner +""" +Extended version of Dan Blankenberg's fastq joiner (adds support for +recent Illumina headers). +""" + +import sys, re +import galaxy_utils.sequence.fastq as fq + + +class IDManager(object): + + def __init__(self, sep="\t"): + """ + Recent Illumina FASTQ header format:: + + @<COORDS><FLAGS> + COORDS = <Instrument>:<Run #>:<Flowcell ID>:<Lane>:<Tile>:<X>:<Y> + FLAGS = <Read>:<Is Filtered>:<Control Number>:<Index Sequence> + + where the whitespace character between <COORDS> and <FLAGS> can be + either a space or a tab. + """ + self.sep = sep + + def parse_id(self, identifier): + try: + coords, flags = identifier.strip()[1:].split(self.sep, 1) + except ValueError: + raise RuntimeError("bad identifier: %r" % (identifier,)) + return coords.split(":"), flags.split(":") + + def join_id(self, parsed_id): + coords, flags = parsed_id + return "@%s%s%s" % (":".join(coords), self.sep, ":".join(flags)) + + def get_read_number(self, parsed_id): + return int(parsed_id[1][0]) + + def set_read_number(self, parsed_id, n): + parsed_id[1][0] = "%d" % n + + def get_paired_identifier(self, read): + t = self.parse_id(read.identifier) + n = self.get_read_number(t) + if n == 1: + pn = 2 + elif n == 2: + pn = 1 + else: + raise RuntimeError("Unknown read number '%d'" % n) + self.set_read_number(t, pn) + return self.join_id(t) + + +class FastqJoiner(fq.fastqJoiner): + + def __init__(self, format, force_quality_encoding=None, sep="\t"): + super(FastqJoiner, self).__init__(format, force_quality_encoding) + self.id_manager = IDManager(sep) + + def join(self, read1, read2): + force_quality_encoding = self.force_quality_encoding + if not force_quality_encoding: + if read1.is_ascii_encoded(): + force_quality_encoding = 'ascii' + else: + force_quality_encoding = 'decimal' + read1 = read1.convert_read_to_format( + self.format, force_quality_encoding=force_quality_encoding + ) + read2 = read2.convert_read_to_format( + self.format, force_quality_encoding=force_quality_encoding + ) + #-- + t1, t2 = [ + self.id_manager.parse_id(r.identifier) for r in (read1, read2) + ] + if self.id_manager.get_read_number(t1) == 2: + if not self.id_manager.get_read_number(t2) == 1: + raise RuntimeError("input files are not from mated pairs") + read1, read2 = read2, read1 + t1, t2 = t2, t1 + #-- + rval = fq.FASTQ_FORMATS[self.format]() + rval.identifier = read1.identifier + rval.description = "+" + if len(read1.description) > 1: + rval.description += rval.identifier[1:] + if rval.sequence_space == 'color': + # convert to nuc space, join, then convert back + rval.sequence = rval.convert_base_to_color_space( + read1.convert_color_to_base_space(read1.sequence) + + read2.convert_color_to_base_space(read2.sequence) + ) + else: + rval.sequence = read1.sequence + read2.sequence + if force_quality_encoding == 'ascii': + rval.quality = read1.quality + read2.quality + else: + rval.quality = "%s %s" % ( + read1.quality.strip(), read2.quality.strip() + ) + return rval + + def get_paired_identifier(self, read): + return self.id_manager.get_paired_identifier(read) + + +def sniff_sep(fastq_fn): + header = "" + with open(fastq_fn) as f: + while header == "": + try: + header = f.next().strip() + except StopIteration: + raise RuntimeError("%r: empty file" % (fastq_fn,)) + return re.search(r"\s", header).group() + def main(): - #Read command line arguments input1_filename = sys.argv[1] input1_type = sys.argv[2] or 'sanger' input2_filename = sys.argv[3] input2_type = sys.argv[4] or 'sanger' output_filename = sys.argv[5] - + fastq_style = sys.argv[6] or 'old' + #-- if input1_type != input2_type: - print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type ) - - input2 = fastqNamedReader( open( input2_filename, 'rb' ), input2_type ) - joiner = fastqJoiner( input1_type ) - out = fastqWriter( open( output_filename, 'wb' ), format = input1_type ) - + print "WARNING: trying to join files of different types: %s and %s" % ( + input1_type, input2_type + ) + if fastq_style == 'new': + sep = sniff_sep(input1_filename) + joiner = FastqJoiner(input1_type, sep=sep) + else: + joiner = fq.fastqJoiner(input1_type) + #-- + input2 = fq.fastqNamedReader(open(input2_filename, 'rb'), input2_type) + out = fq.fastqWriter(open(output_filename, 'wb'), format=input1_type) i = None skip_count = 0 - for i, fastq_read in enumerate( fastqReader( open( input1_filename, 'rb' ), format = input1_type ) ): - identifier = joiner.get_paired_identifier( fastq_read ) - fastq_paired = input2.get( identifier ) + for i, fastq_read in enumerate(fq.fastqReader( + open(input1_filename, 'rb' ), format=input1_type + )): + identifier = joiner.get_paired_identifier(fastq_read) + fastq_paired = input2.get(identifier) if fastq_paired is None: skip_count += 1 else: - out.write( joiner.join( fastq_read, fastq_paired ) ) + out.write(joiner.join(fastq_read, fastq_paired)) out.close() - if i is None: - print "Your file contains no valid FASTQ reads." + print "Your file contains no valid FASTQ reads" else: print input2.has_data() - print 'Joined %s of %s read pairs (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 ) + print 'Joined %s of %s read pairs (%.2f%%)' % ( + i - skip_count + 1, i + 1, (i - skip_count + 1) / (i + 1) * 100.0 + ) + if __name__ == "__main__": main() diff -r af91c734dbb76b8c0e3166c7471370f9ba8260b5 -r e232573b7c629a94ab60e6b615ecedf156913308 tools/fastq/fastq_paired_end_joiner.xml --- a/tools/fastq/fastq_paired_end_joiner.xml +++ b/tools/fastq/fastq_paired_end_joiner.xml @@ -1,9 +1,13 @@ -<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="1.0.0"> +<tool id="fastq_paired_end_joiner" name="FASTQ joiner" version="2.0.0"><description>on paired end reads</description> - <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file'</command> + <command interpreter="python">fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style'</command><inputs><param name="input1_file" type="data" format="fastqsanger,fastqcssanger" label="Left-hand Reads" /><param name="input2_file" type="data" format="fastqsanger,fastqcssanger" label="Right-hand Reads" /> + <param name="style" type="select" label="FASTQ Header Style"> + <option value="old" selected="true">old</option> + <option value="new">new</option> + </param></inputs><outputs><data name="output_file" format="input" /> @@ -18,14 +22,19 @@ <help> **What it does** -This tool joins paired end FASTQ reads from two separate files into a single read in one file. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is excluded from the output. - -Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user. +This tool joins paired end FASTQ reads from two separate files into a +single read in one file. The join is performed using sequence +identifiers, allowing the two files to contain differing ordering. If +a sequence identifier does not appear in both files, it is excluded +from the output. ----- **Input formats** +Both old and new (from recent Illumina software) style FASTQ headers +are supported. The following example uses the "old" style. + Left-hand Read:: @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 @@ -53,10 +62,26 @@ ------ -**Citation** +**The "new" style** -If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ +Recent Illumina FASTQ headers are structured as follows:: + @COORDS FLAGS + COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y + FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE +where the whitespace character between COORDS and FLAGS can be either +a space or a tab. + +------ + +**Credits** + +This is an extended version (adds support for "new" style FASTQ headers) +of D. Blankenberg's fastq joiner: + +`Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + +New style header support added by Simone Leo <simone.leo(a)crs4.it> </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Corrections to statistics for the tool shed's install and test runs and successful installation results for repositories of type tool_dependency_definition now reported to the tool shed.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a950019c26a9/ Changeset: a950019c26a9 User: greg Date: 2013-12-18 22:20:36 Summary: Corrections to statistics for the tool shed's install and test runs and successful installation results for repositories of type tool_dependency_definition now reported to the tool shed. Affected #: 5 files diff -r f1cb7f07af2c923d3f3be77a0ae0ccb25c6453a7 -r a950019c26a9189f145d4da87c589f64babaa8e2 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -70,12 +70,16 @@ done case $which in - dependencies) + # Use "-w tool_dependency_definitions" when you want to test repositories of type tool_dependency_definition. + tool_dependency_definitions) test_tool_dependency_definitions ;; - tools) + # Use "-w repositories_with_tools" parameter when you want to test repositories that contain tools. + repositories_with_tools) test_repositories_with_tools ;; + # No received parameters or any received parameter not in [ tool_dependency_definitions, repositories_with_tools ] + # will execute both scripts. *) test_tool_dependency_definitions test_repositories_with_tools diff -r f1cb7f07af2c923d3f3be77a0ae0ccb25c6453a7 -r a950019c26a9189f145d4da87c589f64babaa8e2 lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -89,8 +89,9 @@ now = strftime( "%Y-%m-%d %H:%M:%S" ) print "#############################################################################" - print "# %s - Validating repositories of type %s on %s..." % ( now, TOOL_DEPENDENCY_DEFINITION, config_parser.get( config_section, 'host' ) ) - print "# This tool shed is configured to listen on %s:%s" % ( config_parser.get( config_section, 'host' ), config_parser.get( config_section, 'port' ) ) + print "# %s - Validating repositories of type %s" % ( now, TOOL_DEPENDENCY_DEFINITION ) + print "# This tool shed is configured to listen on %s:%s" % ( config_parser.get( config_section, 'host' ), + config_parser.get( config_section, 'port' ) ) app = RepositoriesApplication( config ) diff -r f1cb7f07af2c923d3f3be77a0ae0ccb25c6453a7 -r a950019c26a9189f145d4da87c589f64babaa8e2 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -225,7 +225,8 @@ return suc.INITIAL_CHANGELOG_HASH, error_message def get_missing_tool_dependencies( repository ): - log.debug( 'Checking %s repository %s for missing tool dependencies.' % ( repository.status, repository.name ) ) + log.debug( 'Checking revision %s of repository %s owned by %s for missing tool dependencies.' % \ + ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) missing_tool_dependencies = repository.missing_tool_dependencies for tool_dependency in repository.tool_dependencies: log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) @@ -423,12 +424,13 @@ return global_conf def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dicts, - tool_test_results_dict, results_dict, can_update_tool_shed ): + tool_test_results_dict, can_update_tool_shed ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed # for the test to be considered reliable. - log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) + log.debug( 'The following dependencies of revision %s of repository %s owned by %s are missing.' % \ + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) # In keeping with the standard display layout, add the error message to the dict for each tool individually. for dependency in repository.missing_tool_dependencies: name = str( dependency.name ) @@ -436,24 +438,25 @@ version = str( dependency.version ) error_message = unicodify( dependency.error_message ) log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) - test_result = dict( type=dependency.type, - name=dependency.name, - version=dependency.version, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) + missing_tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + error_message=error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( missing_tool_dependency_info_dict ) for dependency in repository.missing_repository_dependencies: + tool_shed = str( dependency.tool_shed ) name = str( dependency.name ) owner = str( dependency.owner ) changeset_revision = str( dependency.changeset_revision ) error_message = unicodify( dependency.error_message ) log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ ( name, changeset_revision, owner, error_message ) ) - test_result = dict( tool_shed=dependency.tool_shed, - name=dependency.name, - owner=dependency.owner, - changeset_revision=dependency.changeset_revision, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changeset_revision=changeset_revision, + error_message=error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) # Record the status of this repository in the tool shed. params = dict( tools_functionally_correct=False, do_not_test=False, @@ -465,26 +468,25 @@ repository_dict, params, can_update_tool_shed ) - # Since this repository is missing components we do not want to test it, uninstall it. + # Uninstall this repository since it is missing dependencies. uninstall_repository_and_repository_dependencies( app, repository_dict ) - results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), - owner=str( repository.owner ), - changeset_revision=str( repository.changeset_revision ) ) ) - return results_dict -def initialize_results_dict( test_framework ): +def initialize_install_and_test_statistics_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. - results_dict = {} + install_and_test_statistics_dict = {} if test_framework == REPOSITORIES_WITH_TOOLS: - results_dict[ 'total_repositories_tested' ] = 0 - results_dict[ 'all_tests_passed' ] = [] - results_dict[ 'at_least_one_test_failed' ] = [] - results_dict[ 'repositories_failed_install' ] = [] + install_and_test_statistics_dict[ 'total_repositories_processed' ] = 0 + install_and_test_statistics_dict[ 'all_tests_passed' ] = [] + install_and_test_statistics_dict[ 'at_least_one_test_failed' ] = [] + install_and_test_statistics_dict[ 'successful_installations' ] = [] + install_and_test_statistics_dict[ 'repositories_with_installation_error' ] = [] + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] = [] elif test_framework == TOOL_DEPENDENCY_DEFINITIONS: - results_dict[ 'total_repositories_installed' ] = 0 - results_dict[ 'repositories_with_installation_error' ] = 0 - results_dict[ 'tool_dependencies_with_installation_error' ] = 0 - return results_dict + install_and_test_statistics_dict[ 'total_repositories_processed' ] = 0 + install_and_test_statistics_dict[ 'successful_installations' ] = [] + install_and_test_statistics_dict[ 'repositories_with_installation_error' ] = [] + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] = [] + return install_and_test_statistics_dict def initialize_tool_tests_results_dict( app, tool_test_results_dict ): test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) diff -r f1cb7f07af2c923d3f3be77a0ae0ccb25c6453a7 -r a950019c26a9189f145d4da87c589f64babaa8e2 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -134,10 +134,10 @@ return tool_id, tool_version def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = install_and_test_base_util.initialize_results_dict( test_framework ) + install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_tested = results_dict[ 'total_repositories_tested' ] + total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] repositories_to_install, error_message = \ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: @@ -213,8 +213,7 @@ break if this_repository_is_in_the_exclude_list: tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) - params = dict( tools_functionally_correct=False, - do_not_test=False ) + params = dict( do_not_test=False ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, @@ -223,30 +222,29 @@ params, can_update_tool_shed ) log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ - ( changeset_revision, name, owner ) ) + ( changeset_revision, name, owner ) ) else: tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) # Explicitly clear tests from twill's test environment. remove_generated_tests( app ) # Proceed with installing repositories and testing contained tools. repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) + install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: + # The repository installation failed. + log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) + log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) try: repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) except Exception, e: - error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ + ( changeset_revision, name, owner, str( e ) ) log.exception( error_message ) - test_result = dict( tool_shed=install_and_test_base_util.galaxy_tool_shed_url, - name=name, - owner=owner, - changeset_revision=changeset_revision, - error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params = dict( tools_functionally_correct=False, - test_install_error=True, + params = dict( test_install_error=True, do_not_test=False ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, @@ -263,18 +261,23 @@ ( changeset_revision, name, owner, str( e ) ) ) # Clean out any generated tests. This is necessary for Twill. remove_generated_tests( app ) - results_dict[ 'repositories_failed_install' ].append( repository_identifier_dict ) - log.debug( 'Repository %s failed to install correctly.' % str( name ) ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) else: - # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed - remove_install_tests() - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository - # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, - # and the tools_functionally_correct flag to False, as well as updating tool_test_results. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + # Keep statistics for this repository's tool dependencies that resulted in installation errors. + for missing_tool_dependency in repository.missing_tool_dependencies: + name = str( missing_tool_dependency.name ) + type = str( missing_tool_dependency.type ) + version = str( missing_tool_dependency.version ) + error_message = unicodify( missing_tool_dependency.error_message ) + missing_tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + error_message=error_message ) + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are @@ -283,28 +286,40 @@ tool_test_results_dict[ 'missing_test_components' ] = [] missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = install_and_test_base_util.handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict, - can_update_tool_shed ) + install_and_test_statistics_dict = \ + install_and_test_base_util.handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + install_and_test_statistics_dict, + can_update_tool_shed ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: + # This repository and all of its dependencies were successfully installed. + install_and_test_statistics_dict[ 'successful_installations' ].append( repository_identifier_dict ) + # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed + remove_install_tests() + log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository + # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, + # and the tools_functionally_correct flag to False, as well as updating tool_test_results. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, + from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional # test framework can find it. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) try: - results_dict = test_repository_tools( app, - repository, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) + install_and_test_statistics_dict = test_repository_tools( app, + repository, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + install_and_test_statistics_dict ) except Exception, e: exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) log.exception( exception_message ) @@ -321,10 +336,8 @@ repository_dict, params, can_update_tool_shed ) - results_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) - total_repositories_tested += 1 - results_dict[ 'total_repositories_tested' ] = total_repositories_tested - return results_dict, error_message + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) + return install_and_test_statistics_dict, error_message def main(): if install_and_test_base_util.tool_shed_api_key is None: @@ -535,35 +548,45 @@ persist=False ) now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" - print "# %s - running repository installation and testing script." % now + print "# %s - installation script for repositories containing tools started." % now + if not can_update_tool_shed: + print "# This run will not update the Tool Shed database." print "####################################################################################" - results_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) + install_and_test_statistics_dict, error_message = \ + install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) if error_message: log.debug( error_message ) else: - total_repositories_tested = results_dict[ 'total_repositories_tested' ] - all_tests_passed = results_dict[ 'all_tests_passed' ] - at_least_one_test_failed = results_dict[ 'at_least_one_test_failed' ] - repositories_failed_install = results_dict[ 'repositories_failed_install' ] + total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] + all_tests_passed = install_and_test_statistics_dict[ 'all_tests_passed' ] + at_least_one_test_failed = install_and_test_statistics_dict[ 'at_least_one_test_failed' ] + successful_installations = install_and_test_statistics_dict[ 'successful_installations' ] + repositories_with_installation_error = install_and_test_statistics_dict[ 'repositories_with_installation_error' ] + tool_dependencies_with_installation_error = install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" - print "# %s - repository installation and testing script completed." % now - print "# Repository revisions tested: %s" % str( total_repositories_tested ) - if not can_update_tool_shed: - print "# This run will not update the Tool Shed database." - if total_repositories_tested > 0: - if all_tests_passed: - print '# ----------------------------------------------------------------------------------' - print "# %d repositories successfully passed all functional tests:" % len( all_tests_passed ) - install_and_test_base_util.show_summary_output( all_tests_passed ) - if at_least_one_test_failed: - print '# ----------------------------------------------------------------------------------' - print "# %d repositories failed at least 1 functional test:" % len( at_least_one_test_failed ) - install_and_test_base_util.show_summary_output( at_least_one_test_failed ) - if repositories_failed_install: - print '# ----------------------------------------------------------------------------------' - print "# %d repositories have installation errors:" % len( repositories_failed_install ) - install_and_test_base_util.show_summary_output( repositories_failed_install ) + print "# %s - installation script for repositories containing tools completed." % now + print "# Repository revisions processed: %s" % str( total_repositories_processed ) + if successful_installations: + print "# ----------------------------------------------------------------------------------" + print "# The following %d revisions with all dependencies were successfully installed:" % len( successful_installations ) + install_and_test_base_util.show_summary_output( successful_installations ) + if all_tests_passed: + print '# ----------------------------------------------------------------------------------' + print "# %d repositories successfully passed all functional tests:" % len( all_tests_passed ) + install_and_test_base_util.show_summary_output( all_tests_passed ) + if at_least_one_test_failed: + print '# ----------------------------------------------------------------------------------' + print "# %d repositories failed at least 1 functional test:" % len( at_least_one_test_failed ) + install_and_test_base_util.show_summary_output( at_least_one_test_failed ) + if repositories_with_installation_error: + print '# ----------------------------------------------------------------------------------' + print "# %d repositories have installation errors:" % len( repositories_with_installation_error ) + install_and_test_base_util.show_summary_output( repositories_with_installation_error ) + if tool_dependencies_with_installation_error: + print "# ----------------------------------------------------------------------------------" + print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) + install_and_test_base_util.show_summary_output( tool_dependencies_with_installation_error ) print "####################################################################################" log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. @@ -632,7 +655,8 @@ # Now delete the tests found in the previous loop. del test_install_repositories.__dict__[ key ] -def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, results_dict ): +def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, + install_and_test_statistics_dict ): """Test tools contained in the received repository.""" name = str( repository.name ) owner = str( repository.owner ) @@ -685,7 +709,7 @@ failed_test_dicts = get_failed_test_dicts( result, from_tool_test=True ) tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts failed_repository_dict = repository_identifier_dict - results_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) set_do_not_test = not is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, @@ -708,7 +732,7 @@ remove_generated_tests( app ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox - return results_dict + return install_and_test_statistics_dict if __name__ == "__main__": # The tool_test_results_dict should always have the following structure: diff -r f1cb7f07af2c923d3f3be77a0ae0ccb25c6453a7 -r a950019c26a9189f145d4da87c589f64babaa8e2 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -73,10 +73,10 @@ test_framework = install_and_test_base_util.TOOL_DEPENDENCY_DEFINITIONS def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = install_and_test_base_util.initialize_results_dict( test_framework ) + install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_installed = results_dict[ 'total_repositories_installed' ] + total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] repositories_to_install, error_message = \ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: @@ -161,27 +161,26 @@ params, can_update_tool_shed ) log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ - ( changeset_revision, name, owner ) ) + ( changeset_revision, name, owner ) ) else: tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) + install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: + # The repository installation failed. + log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) + log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) try: repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) except Exception, e: - error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ + ( changeset_revision, name, owner, str( e ) ) log.exception( error_message ) - test_result = dict( tool_shed=install_and_test_base_util.galaxy_tool_shed_url, - name=name, - owner=owner, - changeset_revision=changeset_revision, - error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - params = dict( tools_functionally_correct=False, - test_install_error=True, + params = dict( test_install_error=True, do_not_test=False ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, @@ -196,22 +195,50 @@ except Exception, e: log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \ ( changeset_revision, name, owner, str( e ) ) ) - results_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) - log.debug( 'Repository %s failed to install correctly.' % str( name ) ) + log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) else: - log.debug( 'Installation of %s succeeded.' % str( repository.name ) ) + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + # Keep statistics for this repository's tool dependencies that resulted in installation errors. + for missing_tool_dependency in repository.missing_tool_dependencies: + name = str( missing_tool_dependency.name ) + type = str( missing_tool_dependency.type ) + version = str( missing_tool_dependency.version ) + error_message = unicodify( missing_tool_dependency.error_message ) + missing_tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + error_message=error_message ) + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) + # Attempt to uninstall this repository and all of its dependencies if its repository dependencies or + # tool dependencies resulted in an installation error. missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = install_and_test_base_util.handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict, - can_update_tool_shed ) - results_dict[ 'total_repositories_installed' ] = total_repositories_installed - return results_dict, error_message + install_and_test_base_util.handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + install_and_test_statistics_dict, + can_update_tool_shed ) + else: + # This repository and all of its dependencies were successfully installed. + install_and_test_statistics_dict[ 'successful_installations' ].append( repository_identifier_dict ) + tool_test_results_dict[ 'passed_tests' ].append( repository_identifier_dict ) + params = dict( test_install_error=False, + do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + + install_and_test_statistics_dict[ 'total_repositories_processed' ] = total_repositories_processed + return install_and_test_statistics_dict, error_message def main(): if install_and_test_base_util.tool_shed_api_key is None: @@ -419,28 +446,34 @@ persist=False ) now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" - print "# %s - running repository installation and testing script." % now + print "# %s - installation script for repositories of type tool_dependency_definition started." % now + if not can_update_tool_shed: + print "# This run will not update the Tool Shed database." print "####################################################################################" - results_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) + install_and_test_statistics_dict, error_message = \ + install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) if error_message: log.debug( error_message ) else: - total_repositories_installed = results_dict[ 'total_repositories_installed' ] - repositories_with_installation_error = results_dict[ 'repositories_with_installation_error' ] - tool_dependencies_with_installation_error = results_dict[ 'tool_dependencies_with_installation_error' ] + total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] + successful_installations = install_and_test_statistics_dict[ 'successful_installations' ] + repositories_with_installation_error = install_and_test_statistics_dict[ 'repositories_with_installation_error' ] + tool_dependencies_with_installation_error = install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" - print "# %s - repository installation and testing script completed." % now - print "# Repository revisions tested: %s" % str( total_repositories_installed ) - if not can_update_tool_shed: - print "# This run will not update the Tool Shed database." + print "# %s - installation script for repositories of type tool_dependency_definition completed." % now + print "# Repository revisions processed: %s" % str( total_repositories_processed ) + if successful_installations: + print "# ----------------------------------------------------------------------------------" + print "# The following %d revisions with all dependencies were successfully installed:" % len( successful_installations ) + install_and_test_base_util.show_summary_output( successful_installations ) if repositories_with_installation_error: - print '# ----------------------------------------------------------------------------------' - print "# %d repositories have installation errors:" % len( repositories_with_installation_error ) + print "# ----------------------------------------------------------------------------------" + print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error ) install_and_test_base_util.show_summary_output( repositories_with_installation_error ) if tool_dependencies_with_installation_error: - print '# ----------------------------------------------------------------------------------' - print "# %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) + print "# ----------------------------------------------------------------------------------" + print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) install_and_test_base_util.show_summary_output( tool_dependencies_with_installation_error ) print "####################################################################################" log.debug( "Shutting down..." ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f1cb7f07af2c/ Changeset: f1cb7f07af2c User: jmchilton Date: 2013-12-18 21:59:11 Summary: Use get_history() in tools API controller. Affected #: 1 file diff -r 0b2676366a82d61b5e46f4cae6a235e643548f78 -r f1cb7f07af2c923d3f3be77a0ae0ccb25c6453a7 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,7 +1,7 @@ import urllib from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin +from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, UsesHistoryMixin from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string from galaxy.visualization.data_providers.genome import * @@ -10,7 +10,7 @@ log = logging.getLogger( __name__ ) -class ToolsController( BaseAPIController, UsesVisualizationMixin ): +class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin ): """ RESTful controller for interactions with tools. """ @@ -86,8 +86,7 @@ # dataset upload. history_id = payload.get("history_id", None) if history_id: - target_history = trans.sa_session.query(trans.app.model.History).get( - trans.security.decode_id(history_id)) + target_history = self.get_history( trans, history_id ) else: target_history = None https://bitbucket.org/galaxy/galaxy-central/commits/26da838b778c/ Changeset: 26da838b778c Branch: stable User: jmchilton Date: 2013-12-18 21:59:11 Summary: Use get_history() in tools API controller. Affected #: 1 file diff -r e059c6607f34b603e92e85cf0113b7b9b9635571 -r 26da838b778c68a5577d4cca9836f6ef70b8ed1b lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,7 +1,7 @@ import urllib from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin +from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, UsesHistoryMixin from galaxy.visualization.genomes import GenomeRegion from galaxy.util.json import to_json_string, from_json_string from galaxy.visualization.data_providers.genome import * @@ -9,7 +9,7 @@ import logging log = logging.getLogger( __name__ ) -class ToolsController( BaseAPIController, UsesVisualizationMixin ): +class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin ): """ RESTful controller for interactions with tools. """ @@ -85,8 +85,7 @@ # dataset upload. history_id = payload.get("history_id", None) if history_id: - target_history = trans.sa_session.query(trans.app.model.History).get( - trans.security.decode_id(history_id)) + target_history = self.get_history( trans, history_id ) else: target_history = None Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0bb5714cb801/ Changeset: 0bb5714cb801 User: lepsiobec Date: 2013-12-18 19:59:20 Summary: aiding security flaw with downloading datasets in archives Affected #: 1 file diff -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 -r 0bb5714cb8012515824fd3e435b683afd554cdd2 lib/galaxy/webapps/galaxy/controllers/library_common.py --- a/lib/galaxy/webapps/galaxy/controllers/library_common.py +++ b/lib/galaxy/webapps/galaxy/controllers/library_common.py @@ -18,7 +18,7 @@ from galaxy.util import inflector from galaxy.util.json import to_json_string, from_json_string from galaxy.util.streamball import StreamBall -from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin +from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, build_select_field from galaxy.model.orm import and_, eagerload_all @@ -65,7 +65,7 @@ except: pass -class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin ): +class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMetadataMixin, UsesLibraryMixinItems ): @web.json def library_item_updates( self, trans, ids=None, states=None ): # Avoid caching @@ -1750,7 +1750,8 @@ ldda_ids = util.listify( ldda_ids ) for ldda_id in ldda_ids: try: - ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + # Load the ldda requested and check whether the user has access to them + ldda = self.get_library_dataset_dataset_association( trans, ldda_id ) assert not ldda.dataset.purged lddas.append( ldda ) except: https://bitbucket.org/galaxy/galaxy-central/commits/0b2676366a82/ Changeset: 0b2676366a82 User: lepsiobec Date: 2013-12-18 20:08:19 Summary: Merge Affected #: 1 file diff -r 0bb5714cb8012515824fd3e435b683afd554cdd2 -r 0b2676366a82d61b5e46f4cae6a235e643548f78 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -13,6 +13,10 @@ # If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to # a tool sheds configuration file that does specify that url or repository installation will fail. +# This script accepts the command line option -w to select which set of tests to run. The default behavior is to test +# first tool_dependency_definition repositories and then repositories with tools. Provide the value 'dependencies' +# to test only tool_dependency_definition repositories or 'tools' to test only repositories with tools. + if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." exit 1 @@ -39,14 +43,41 @@ fi fi -# Test installation of repositories of type tool_dependency_definition. -python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ - test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py +test_tool_dependency_definitions () { + # Test installation of repositories of type tool_dependency_definition. + python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} -# Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. -#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ -# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ -# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ -# test/functional/test_toolbox.py +test_repositories_with_tools () { + # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. + python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} + +which='both' + +while getopts "w:" arg; do + case $arg in + w) + which=$OPTARG + ;; + esac +done + +case $which in + dependencies) + test_tool_dependency_definitions + ;; + tools) + test_repositories_with_tools + ;; + *) + test_tool_dependency_definitions + test_repositories_with_tools + ;; +esac Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Add command line option to select which set of tests to run.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9c17939bb282/ Changeset: 9c17939bb282 User: inithello Date: 2013-12-18 19:53:18 Summary: Add command line option to select which set of tests to run. Affected #: 1 file diff -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 -r 9c17939bb28242a1532daf2c24c2920786b3502f install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -13,6 +13,10 @@ # If the tool shed url is not specified in tool_sheds_conf.xml, GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must be set to # a tool sheds configuration file that does specify that url or repository installation will fail. +# This script accepts the command line option -w to select which set of tests to run. The default behavior is to test +# first tool_dependency_definition repositories and then repositories with tools. Provide the value 'dependencies' +# to test only tool_dependency_definition repositories or 'tools' to test only repositories with tools. + if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." exit 1 @@ -39,14 +43,41 @@ fi fi -# Test installation of repositories of type tool_dependency_definition. -python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ - test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py +test_tool_dependency_definitions () { + # Test installation of repositories of type tool_dependency_definition. + python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} -# Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. -#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ -# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ -# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ -# test/functional/test_toolbox.py +test_repositories_with_tools () { + # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. + python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py +} + +which='both' + +while getopts "w:" arg; do + case $arg in + w) + which=$OPTARG + ;; + esac +done + +case $which in + dependencies) + test_tool_dependency_definitions + ;; + tools) + test_repositories_with_tools + ;; + *) + test_tool_dependency_definitions + test_repositories_with_tools + ;; +esac Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Another bugfix to the tool dependency cleaning script.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cbd1387437ce/ Changeset: cbd1387437ce User: inithello Date: 2013-12-18 19:14:24 Summary: Another bugfix to the tool dependency cleaning script. Affected #: 1 file diff -r d1b1558308dc1cbb8076d20a7b7d130ca4051e1d -r cbd1387437ceba5be9b47dcbf9eb951086e410a1 lib/tool_shed/scripts/clean_up_tool_dependency_directory.py --- a/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py +++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py @@ -11,10 +11,11 @@ else: for content in os.listdir( args.tool_dependency_dir ): print 'Deleting directory %s from %s.' % ( content, args.tool_dependency_dir ) - if os.path.isdir( content ): - shutil.rmtree( os.path.join( args.tool_dependency_dir, content ) ) + full_path = os.path.join( args.tool_dependency_dir, content ) + if os.path.isdir( full_path ): + shutil.rmtree( full_path ) else: - os.remove( content ) + os.remove( full_path ) if __name__ == '__main__': description = 'Clean out the configured tool dependency path, creating it if it does not exist.' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix error when attempting to remove a file.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1b1558308dc/ Changeset: d1b1558308dc User: inithello Date: 2013-12-18 19:11:37 Summary: Fix error when attempting to remove a file. Affected #: 1 file diff -r c4c6e8ea9837d4aa4fbbf08a681fd0c72b34f5b6 -r d1b1558308dc1cbb8076d20a7b7d130ca4051e1d lib/tool_shed/scripts/clean_up_tool_dependency_directory.py --- a/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py +++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py @@ -9,9 +9,12 @@ os.mkdir( args.tool_dependency_dir ) return 0 else: - for subdirectory in os.listdir( args.tool_dependency_dir ): - print 'Deleting directory %s from %s.' % ( subdirectory, args.tool_dependency_dir ) - shutil.rmtree( os.path.join( args.tool_dependency_dir, subdirectory ) ) + for content in os.listdir( args.tool_dependency_dir ): + print 'Deleting directory %s from %s.' % ( content, args.tool_dependency_dir ) + if os.path.isdir( content ): + shutil.rmtree( os.path.join( args.tool_dependency_dir, content ) ) + else: + os.remove( content ) if __name__ == '__main__': description = 'Clean out the configured tool dependency path, creating it if it does not exist.' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Clean up maintenance scripts for the EC2 environment.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4c6e8ea9837/ Changeset: c4c6e8ea9837 User: inithello Date: 2013-12-18 18:07:49 Summary: Clean up maintenance scripts for the EC2 environment. Affected #: 2 files diff -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 -r c4c6e8ea9837d4aa4fbbf08a681fd0c72b34f5b6 lib/tool_shed/scripts/clean_up_tool_dependency_directory.py --- a/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py +++ b/lib/tool_shed/scripts/clean_up_tool_dependency_directory.py @@ -4,55 +4,23 @@ import shutil def main( args ): - if not os.path.exists( args.basepath ): - print 'Tool dependency path %s does not exist.' % str( args.basepath ) - return 1 - if args.delete: - print 'Deleting contents of tool dependency path %s.' % args.basepath - for node in os.listdir( args.basepath ): - path = os.path.join( args.basepath, node ) - if os.path.isdir( path ): - try: - shutil.rmtree( path ) - print 'Deleted directory %s and all its contents.' % path - except Exception, e: - print 'Error deleting directory %s: %s' % ( path, str( e ) ) - pass - elif os.path.isfile( path ): - try: - os.remove( path ) - print 'Deleted file %s.' % path - except Exception, e: - print 'Error deleting file %s: %s' % ( path, str( e ) ) - pass - elif os.path.islink( path ): - print 'Deleting symlink %s with target %s.' % ( path, os.path.realpath( path ) ) - try: - os.remove( path ) - except Exception, e: - print 'Error deleting symlink %s: %s' % ( path, str( e ) ) - pass + if not os.path.exists( args.tool_dependency_dir ): + print 'Tool dependency base path %s does not exist, creating.' % str( args.tool_dependency_dir ) + os.mkdir( args.tool_dependency_dir ) + return 0 else: - print 'Tool dependency path %s contains the following files and directories:' % args.basepath - for element in os.listdir( args.basepath ): - print element - return 0 + for subdirectory in os.listdir( args.tool_dependency_dir ): + print 'Deleting directory %s from %s.' % ( subdirectory, args.tool_dependency_dir ) + shutil.rmtree( os.path.join( args.tool_dependency_dir, subdirectory ) ) if __name__ == '__main__': - description = 'Clean out or list the contents of the provided tool dependency path. Remove if ' - description += 'the --delete command line argument is provided.' + description = 'Clean out the configured tool dependency path, creating it if it does not exist.' parser = argparse.ArgumentParser( description=description ) - parser.add_argument( '--delete', - dest='delete', - required=False, - action='store_true', - default=False, - help='Whether to delete all folders and files or list them on exit.' ) - parser.add_argument( '--basepath', - dest='basepath', + parser.add_argument( '--tool_dependency_dir', + dest='tool_dependency_dir', required=True, action='store', metavar='name', - help='The base path where tool dependencies are installed.' ) + help='The base path where tool dependencies will be installed.' ) args = parser.parse_args() sys.exit( main( args ) ) diff -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 -r c4c6e8ea9837d4aa4fbbf08a681fd0c72b34f5b6 lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py --- /dev/null +++ b/lib/tool_shed/scripts/show_tool_dependency_installation_dir_contents.py @@ -0,0 +1,75 @@ +import argparse +import os +import sys + +new_path = [ os.path.join( os.getcwd(), "lib" ) ] +new_path.extend( sys.path[ 1: ] ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "SQLAlchemy >= 0.4" ) + +import galaxy.model +import galaxy.model.tool_shed_install.mapping as install_mapper +import galaxy.config as galaxy_config + + +class CleanUpDependencyApplication( object ): + """Application that enables querying the database using the tool_shed_install model.""" + + def __init__( self, config ): + self.config = config + # Setup the database engine and ORM + self.model = install_mapper.init( self.config.database_connection, engine_options={}, create_tables=False ) + + @property + def sa_session( self ): + """Returns a SQLAlchemy session.""" + return self.model.context.current + + def shutdown( self ): + pass + +def main( args, app ): + if not os.path.exists( args.basepath ): + print 'Tool dependency base path %s does not exist.' % str( args.basepath ) + return + print 'Checking tool dependency path %s' % args.basepath + tool_dependency_dirs = get_tool_dependency_dirs( app ) + for tool_dependency_dir in tool_dependency_dirs: + path = os.path.join( args.basepath, tool_dependency_dir ) + if os.path.exists( path ): + path_contents = os.listdir( path ) + if len( path_contents ) > 0: + print 'Found non-empty tool dependency installation directory %s.' % path + print 'Directory has the following contents: \n %s' % '\n '.join( path_contents ) + +def get_tool_dependency_dirs( app ): + dependency_paths = [] + for tool_dependency in app.sa_session.query( galaxy.model.tool_shed_install.ToolDependency ).all(): + dependency_paths.append( tool_dependency.installation_directory( app ) ) + return dependency_paths + +if __name__ == '__main__': + description = 'Clean out or list the contents any tool dependency directory under the provided' + description += 'tool dependency path. Remove any non-empty directories found if the ' + description += '--delete command line argument is provided.' + parser = argparse.ArgumentParser( description=description ) + parser.add_argument( '--basepath', + dest='basepath', + required=True, + action='store', + metavar='name', + help='The base path where tool dependencies are installed.' ) + parser.add_argument( '--dburi', + dest='dburi', + required=True, + action='store', + metavar='dburi', + help='The database URI to connect to.' ) + args = parser.parse_args() + database_connection = args.dburi + config_dict = dict( database_connection=database_connection, tool_dependency_dir=args.basepath ) + config = galaxy_config.Configuration( **config_dict ) + app = CleanUpDependencyApplication( config ) + sys.exit( main( args, app ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Enhance the tool shed's install and test framework to handle repositories of type tool_dependency_definition.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/356e0b061fb4/ Changeset: 356e0b061fb4 User: greg Date: 2013-12-18 18:29:01 Summary: Enhance the tool shed's install and test framework to handle repositories of type tool_dependency_definition. Affected #: 4 files diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 install_and_test_tool_shed_repositories.sh --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -40,10 +40,13 @@ fi # Test installation of repositories of type tool_dependency_definition. -# ...coming soon! +python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ + test/install_and_test_tool_shed_repositories/tool_dependency_definitions/run_functional_tests.html \ + test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ + test/functional/test_toolbox.py # Test installation of repositories that contain valid tools with defined functional tests and a test-data directory containing test files. -python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ - test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ - test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ - test/functional/test_toolbox.py +#python test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py $* -v --with-nosehtml --html-report-file \ +# test/install_and_test_tool_shed_repositories/repositories_with_tools/run_functional_tests.html \ +# test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ +# test/functional/test_toolbox.py diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -20,6 +20,7 @@ import nose import platform import time +import tool_shed.repository_types.util as rt_util import tool_shed.util.shed_util_common as suc import urllib @@ -142,6 +143,9 @@ else: testing_single_repository_dict[ 'changeset_revision' ] = None +# Test frameworks that use this utility module. +REPOSITORIES_WITH_TOOLS = 'repositories_with_tools' +TOOL_DEPENDENCY_DEFINITIONS = 'tool_dependency_definitions' class ReportResults( Plugin ): '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' @@ -230,7 +234,7 @@ missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) return missing_tool_dependencies -def get_repositories_to_install( tool_shed_url ): +def get_repositories_to_install( tool_shed_url, test_framework ): """ Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: [{ "changeset_revision": <revision>, @@ -247,12 +251,18 @@ parts = [ 'repository_revisions' ] # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility # is guaranteed and we currently do not guarantee reproducibility. - params = dict( do_not_test='false', - downloadable='true', - includes_tools='true', - malicious='false', - missing_test_components='false', - skip_tool_test='false' ) + if test_framework == REPOSITORIES_WITH_TOOLS: + params = dict( do_not_test='false', + downloadable='true', + includes_tools='true', + malicious='false', + missing_test_components='false', + skip_tool_test='false' ) + elif test_framework == TOOL_DEPENDENCY_DEFINITIONS: + params = dict( do_not_test='false', + downloadable='true', + malicious='false', + skip_tool_test='false' ) api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) baseline_repository_dicts, error_message = json_from_url( api_url ) if error_message: @@ -272,6 +282,9 @@ # Don't test empty repositories. changeset_revision = baseline_repository_dict[ 'changeset_revision' ] if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # If testing repositories of type tool_dependency_definition, filter accordingly. + if test_framework == TOOL_DEPENDENCY_DEFINITIONS and repository_dict[ 'type' ] != rt_util.TOOL_DEPENDENCY_DEFINITION: + continue # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and # append it to the list of repository_dicts to install and test. if latest_revision_only: @@ -299,7 +312,7 @@ # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL # environment variable. log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) - log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + log.debug( "...retrieved %d repository revisions for installation and possible testing." % len( repository_dicts ) ) log.debug( "Repository revisions for testing:" ) for repository_dict in repository_dicts: name = str( repository_dict.get( 'name', None ) ) @@ -309,15 +322,13 @@ return repository_dicts, error_message def get_repository_current_revision( repo_path ): - ''' - This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial - changes the API, this method will have to be updated or replaced. - ''' + """This method uses the python mercurial API to get the current working directory's mercurial changeset hash.""" # Initialize a mercurial repo object from the provided path. repo = hg.repository( ui.ui(), repo_path ) # Get the working directory's change context. ctx = repo[ None ] - # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the working directory was updated). + # Extract the changeset hash of the first parent of that change context (the most recent changeset to which the + # working directory was updated). changectx = ctx.parents()[ 0 ] # Also get the numeric revision, so we can return the customary id:hash changeset identifiers. ctx_rev = changectx.rev() @@ -461,13 +472,18 @@ changeset_revision=str( repository.changeset_revision ) ) ) return results_dict -def initialize_results_dict(): +def initialize_results_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. results_dict = {} - results_dict[ 'total_repositories_tested' ] = 0 - results_dict[ 'all_tests_passed' ] = [] - results_dict[ 'at_least_one_test_failed' ] = [] - results_dict[ 'repositories_failed_install' ] = [] + if test_framework == REPOSITORIES_WITH_TOOLS: + results_dict[ 'total_repositories_tested' ] = 0 + results_dict[ 'all_tests_passed' ] = [] + results_dict[ 'at_least_one_test_failed' ] = [] + results_dict[ 'repositories_failed_install' ] = [] + elif test_framework == TOOL_DEPENDENCY_DEFINITIONS: + results_dict[ 'total_repositories_installed' ] = 0 + results_dict[ 'repositories_with_installation_error' ] = 0 + results_dict[ 'tool_dependencies_with_installation_error' ] = 0 return results_dict def initialize_tool_tests_results_dict( app, tool_test_results_dict ): diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -52,7 +52,7 @@ from functional import database_contexts -log = logging.getLogger( 'install_and_test_repositories' ) +log = logging.getLogger( 'install_and_test_repositories_with_tools' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' ) @@ -72,6 +72,8 @@ else: can_update_tool_shed = True +test_framework = install_and_test_base_util.REPOSITORIES_WITH_TOOLS + def get_failed_test_dicts( test_result, from_tool_test=True ): """Extract any useful data from the test_result.failures and test_result.errors attributes.""" failed_test_dicts = [] @@ -132,12 +134,12 @@ return tool_id, tool_version def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = install_and_test_base_util.initialize_results_dict() + results_dict = install_and_test_base_util.initialize_results_dict( test_framework ) error_message = '' # Initialize a dictionary for the summary that will be printed to stdout. total_repositories_tested = results_dict[ 'total_repositories_tested' ] repositories_to_install, error_message = \ - install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url ) + install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: return None, error_message # Handle repositories not to be tested. @@ -153,7 +155,8 @@ # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. - log.debug( 'Loading the list of repositories excluded from testing from the file %s...', install_and_test_base_util.exclude_list_file ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ + str( install_and_test_base_util.exclude_list_file ) ) exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) else: exclude_list = [] diff -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec -r 356e0b061fb4c0500db7faf11de8bf5edb2f9c41 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- /dev/null +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -0,0 +1,525 @@ +#!/usr/bin/env python +""" +This script cannot be run directly, because it needs to have test/functional/test_toolbox.py in sys.argv in +order to run functional tests on repository tools after installation. The install_and_test_tool_shed_repositories.sh +will execute this script with the appropriate parameters. +""" +import os +import sys +# Assume we are run from the galaxy root directory, add lib to the python path +cwd = os.getcwd() +sys.path.append( cwd ) +new_path = [ os.path.join( cwd, "scripts" ), + os.path.join( cwd, "lib" ), + os.path.join( cwd, 'test' ), + os.path.join( cwd, 'scripts', 'api' ) ] +new_path.extend( sys.path ) +sys.path = new_path + +from galaxy import eggs +eggs.require( "nose" ) +eggs.require( "Paste" ) +eggs.require( 'mercurial' ) +# This should not be required, but it is under certain conditions thanks to this bug: +# http://code.google.com/p/python-nose/issues/detail?id=284 +eggs.require( "pysqlite" ) + +import httplib +import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util +import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories +import logging +import nose +import random +import re +import shutil +import socket +import string +import tempfile +import time +import threading + +import install_and_test_tool_shed_repositories.base.util as install_and_test_base_util + +from base.tool_shed_util import parse_tool_panel_config + +from galaxy.app import UniverseApplication +from galaxy.util.json import from_json_string +from galaxy.util.json import to_json_string +from galaxy.web import buildapp +from functional_tests import generate_config_file +from nose.plugins import Plugin +from paste import httpserver + +from functional import database_contexts + +log = logging.getLogger( 'install_and_test_tool_dependency_definitions' ) + +assert sys.version_info[ :2 ] >= ( 2, 6 ) +test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'tool_dependency_definitions' ) + +# Here's the directory where everything happens. Temporary directories are created within this directory to contain +# the database, new repositories, etc. +galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) +default_galaxy_locales = 'en' +default_galaxy_test_file_dir = "test-data" +os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir + +# This script can be run in such a way that no Tool Shed database records should be changed. +if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: + can_update_tool_shed = False +else: + can_update_tool_shed = True + +test_framework = install_and_test_base_util.TOOL_DEPENDENCY_DEFINITIONS + +def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + results_dict = install_and_test_base_util.initialize_results_dict( test_framework ) + error_message = '' + # Initialize a dictionary for the summary that will be printed to stdout. + total_repositories_installed = results_dict[ 'total_repositories_installed' ] + repositories_to_install, error_message = \ + install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) + if error_message: + return None, error_message + # Handle repositories not to be tested. + if os.path.exists( install_and_test_base_util.exclude_list_file ): + # Entries in the exclude_list look something like this. + # { 'reason': The default reason or the reason specified in this section, + # 'repositories': + # [( name, owner, changeset revision if changeset revision else None ), + # ( name, owner, changeset revision if changeset revision else None )] } + # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified + # revision should be skipped. + # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that + # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are + # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted + # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ + str( install_and_test_base_util.exclude_list_file ) ) + exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) + else: + exclude_list = [] + # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was + # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each + # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. + # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have + # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. + for repository_dict in repositories_to_install: + # Each repository_dict looks something like: + # { "changeset_revision": "13fa22a258b5", + # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", + # "deleted": false, + # "deprecated": false, + # "description": "Convert column case.", + # "downloadable": true, + # "id": "529fd61ab1c6cc36", + # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", + # "malicious": false, + # "name": "change_case", + # "owner": "test", + # "private": false, + # "repository_id": "529fd61ab1c6cc36", + # "times_downloaded": 0, + # "tool_shed_url": "http://toolshed.local:10001", + # "url": "/api/repository_revisions/529fd61ab1c6cc36", + # "user_id": "529fd61ab1c6cc36" } + encoded_repository_metadata_id = repository_dict.get( 'id', None ) + # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. + repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url + # Get the name and owner out of the repository info dict. + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) + repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + # Retrieve the stored list of tool_test_results_dicts. + tool_test_results_dicts, error_message = \ + install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) + if error_message: + log.debug( error_message ) + else: + tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) + # See if this repository should be skipped for any reason. + this_repository_is_in_the_exclude_list = False + skip_reason = None + for exclude_dict in exclude_list: + reason = exclude_dict[ 'reason' ] + exclude_repositories = exclude_dict[ 'repositories' ] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + this_repository_is_in_the_exclude_list = True + skip_reason = reason + break + if this_repository_is_in_the_exclude_list: + tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + params = dict( do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ + ( changeset_revision, name, owner ) ) + else: + tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) + repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) + if error_message: + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message + # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. + log.debug( 'Attempting to uninstall repository %s owned by %s.' % ( name, owner ) ) + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except Exception, e: + error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) + log.exception( error_message ) + test_result = dict( tool_shed=install_and_test_base_util.galaxy_tool_shed_url, + name=name, + owner=owner, + changeset_revision=changeset_revision, + error_message=error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + params = dict( tools_functionally_correct=False, + test_install_error=True, + do_not_test=False ) + # TODO: do something useful with response_dict + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + try: + # We are uninstalling this repository and all of its repository dependencies. + install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) + except Exception, e: + log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \ + ( changeset_revision, name, owner, str( e ) ) ) + results_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) + log.debug( 'Repository %s failed to install correctly.' % str( name ) ) + else: + log.debug( 'Installation of %s succeeded.' % str( repository.name ) ) + missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) + if missing_tool_dependencies or repository.missing_repository_dependencies: + results_dict = install_and_test_base_util.handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict, + can_update_tool_shed ) + results_dict[ 'total_repositories_installed' ] = total_repositories_installed + return results_dict, error_message + +def main(): + if install_and_test_base_util.tool_shed_api_key is None: + # If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. + log.debug( 'Cannot proceed without a valid tool shed API key set in the enviroment variable GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY.' ) + return 1 + if install_and_test_base_util.galaxy_tool_shed_url is None: + log.debug( 'Cannot proceed without a valid Tool Shed base URL set in the environment variable GALAXY_INSTALL_TEST_TOOL_SHED_URL.' ) + return 1 + # ---- Configuration ------------------------------------------------------ + galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', install_and_test_base_util.default_galaxy_test_host ) + # Set the GALAXY_INSTALL_TEST_HOST variable so that Twill will have the Galaxy url to which to + # install repositories. + os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host + # Set the GALAXY_TEST_HOST environment variable so that the toolbox tests will have the Galaxy url + # on which to to run tool functional tests. + os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host + galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( install_and_test_base_util.default_galaxy_test_port_max ) ) + os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) + if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: + os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales + galaxy_test_file_dir = os.environ.get( 'GALAXY_INSTALL_TEST_FILE_DIR', default_galaxy_test_file_dir ) + if not os.path.isabs( galaxy_test_file_dir ): + galaxy_test_file_dir = os.path.abspath( galaxy_test_file_dir ) + use_distributed_object_store = os.environ.get( 'GALAXY_INSTALL_TEST_USE_DISTRIBUTED_OBJECT_STORE', False ) + if not os.path.isdir( galaxy_test_tmp_dir ): + os.mkdir( galaxy_test_tmp_dir ) + # Set up the configuration files for the Galaxy instance. + shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) + galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', + install_and_test_base_util.tool_data_table_conf ) + galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) + galaxy_job_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_JOB_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_job_conf.xml' ) ) + galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) + galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) + galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', + os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) + galaxy_shed_tools_dict = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DICT_FILE', + os.path.join( galaxy_test_tmp_dir, 'shed_tool_dict' ) ) + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file so that + # test.base.twilltestcase.setUp will find and parse it properly. + os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict + if 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' in os.environ: + tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ) + else: + tool_data_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DATA_PATH' ] = tool_data_path + # Configure the database connection and path. + if 'GALAXY_INSTALL_TEST_DBPATH' in os.environ: + galaxy_db_path = os.environ[ 'GALAXY_INSTALL_TEST_DBPATH' ] + else: + tempdir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_db_path = os.path.join( tempdir, 'database' ) + # Configure the paths Galaxy needs to install and test tools. + galaxy_file_path = os.path.join( galaxy_db_path, 'files' ) + new_repos_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_tempfiles = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + galaxy_shed_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir, prefix='shed_tools' ) + galaxy_migrated_tool_path = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + # Set up the tool dependency path for the Galaxy instance. + tool_dependency_dir = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR', None ) + if tool_dependency_dir is None: + tool_dependency_dir = tempfile.mkdtemp( dir=galaxy_test_tmp_dir ) + os.environ[ 'GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir + os.environ[ 'GALAXY_TOOL_DEPENDENCY_DIR' ] = tool_dependency_dir + if 'GALAXY_INSTALL_TEST_DBURI' in os.environ: + database_connection = os.environ[ 'GALAXY_INSTALL_TEST_DBURI' ] + else: + database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'install_and_test_repositories.sqlite' ) + kwargs = {} + for dir in [ galaxy_test_tmp_dir ]: + try: + os.makedirs( dir ) + except OSError: + pass + print "Database connection: ", database_connection + # Generate the shed_tool_data_table_conf.xml file. + file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) + os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file + # ---- Start up a Galaxy instance ------------------------------------------------------ + # Generate the tool_conf.xml file. + file( galaxy_tool_conf_file, 'w' ).write( install_and_test_base_util.tool_conf_xml ) + # Generate the job_conf.xml file. + file( galaxy_job_conf_file, 'w' ).write( install_and_test_base_util.job_conf_xml ) + # Generate the tool_sheds_conf.xml file, but only if a the user has not specified an existing one in the environment. + if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: + file( galaxy_tool_sheds_conf_file, 'w' ).write( install_and_test_base_util.tool_sheds_conf_xml ) + # Generate the shed_tool_conf.xml file. + tool_conf_template_parser = string.Template( install_and_test_base_util.shed_tool_conf_xml_template ) + shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) + file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) + os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file + # Generate the migrated_tool_conf.xml file. + migrated_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path ) + file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml ) + # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for + # the external metadata script to find the right datasets. + kwargs = dict( admin_users = 'test(a)bx.psu.edu', + master_api_key = install_and_test_base_util.default_galaxy_master_api_key, + allow_user_creation = True, + allow_user_deletion = True, + allow_library_path_paste = True, + database_connection = database_connection, + datatype_converters_config_file = "datatype_converters_conf.xml.sample", + file_path = galaxy_file_path, + id_secret = install_and_test_base_util.galaxy_encode_secret, + job_config_file = galaxy_job_conf_file, + job_queue_workers = 5, + log_destination = "stdout", + migrated_tools_config = galaxy_migrated_tool_conf_file, + new_file_path = galaxy_tempfiles, + running_functional_tests = True, + shed_tool_data_table_config = shed_tool_data_table_conf_file, + shed_tool_path = galaxy_shed_tool_path, + template_path = "templates", + tool_config_file = ','.join( [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] ), + tool_data_path = tool_data_path, + tool_data_table_config_path = galaxy_tool_data_table_conf_file, + tool_dependency_dir = tool_dependency_dir, + tool_path = tool_path, + tool_parse_help = False, + tool_sheds_config_file = galaxy_tool_sheds_conf_file, + update_integrated_tool_panel = False, + use_heartbeat = False ) + galaxy_config_file = os.environ.get( 'GALAXY_INSTALL_TEST_INI_FILE', None ) + # If the user has passed in a path for the .ini file, do not overwrite it. + if not galaxy_config_file: + galaxy_config_file = os.path.join( galaxy_test_tmp_dir, 'install_test_tool_shed_repositories_wsgi.ini' ) + config_items = [] + for label in kwargs: + config_tuple = label, kwargs[ label ] + config_items.append( config_tuple ) + # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. + generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] + # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. + kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() + kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file + # ---- Build Galaxy Application -------------------------------------------------- + if not database_connection.startswith( 'sqlite://' ): + kwargs[ 'database_engine_option_max_overflow' ] = '20' + kwargs[ 'database_engine_option_pool_size' ] = '10' + kwargs[ 'config_file' ] = galaxy_config_file + app = UniverseApplication( **kwargs ) + database_contexts.galaxy_context = app.model.context + database_contexts.install_context = app.install_model.context + + log.debug( "Embedded Galaxy application started..." ) + # ---- Run galaxy webserver ------------------------------------------------------ + server = None + global_conf = install_and_test_base_util.get_webapp_global_conf() + global_conf[ 'database_file' ] = database_connection + webapp = buildapp.app_factory( global_conf, + use_translogger=False, + static_enabled=install_and_test_base_util.STATIC_ENABLED, + app=app ) + # Serve the app on a specified or random port. + if galaxy_test_port is not None: + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + else: + random.seed() + for i in range( 0, 9 ): + try: + galaxy_test_port = str( random.randint( install_and_test_base_util.default_galaxy_test_port_min, + install_and_test_base_util.default_galaxy_test_port_max ) ) + log.debug( "Attempting to serve app on randomly chosen port: %s", galaxy_test_port ) + server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) + break + except socket.error, e: + if e[0] == 98: + continue + raise + else: + raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % \ + ( install_and_test_base_util.default_galaxy_test_port_min, install_and_test_base_util.default_galaxy_test_port_max ) ) + os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_port + # Start the server. + t = threading.Thread( target=server.serve_forever ) + t.start() + # Test if the server is up. + for i in range( 10 ): + # Directly test the app, not the proxy. + conn = httplib.HTTPConnection( galaxy_test_host, galaxy_test_port ) + conn.request( "GET", "/" ) + if conn.getresponse().status == 200: + break + time.sleep( 0.1 ) + else: + raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) + log.debug( "Embedded galaxy web server started..." ) + log.debug( "The embedded Galaxy application is running on %s:%s" % ( str( galaxy_test_host ), str( galaxy_test_port ) ) ) + log.debug( "Repositories will be installed from the tool shed at %s" % str( install_and_test_base_util.galaxy_tool_shed_url ) ) + # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. + if install_and_test_base_util.additional_tool_data_tables: + app.tool_data_tables.add_new_entries_from_config_file( config_filename=install_and_test_base_util.additional_tool_data_tables, + tool_data_path=install_and_test_base_util.additional_tool_data_path, + shed_tool_data_table_config=None, + persist=False ) + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - running repository installation and testing script." % now + print "####################################################################################" + results_dict, error_message = install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ) + if error_message: + log.debug( error_message ) + else: + total_repositories_installed = results_dict[ 'total_repositories_installed' ] + repositories_with_installation_error = results_dict[ 'repositories_with_installation_error' ] + tool_dependencies_with_installation_error = results_dict[ 'tool_dependencies_with_installation_error' ] + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - repository installation and testing script completed." % now + print "# Repository revisions tested: %s" % str( total_repositories_installed ) + if not can_update_tool_shed: + print "# This run will not update the Tool Shed database." + if repositories_with_installation_error: + print '# ----------------------------------------------------------------------------------' + print "# %d repositories have installation errors:" % len( repositories_with_installation_error ) + install_and_test_base_util.show_summary_output( repositories_with_installation_error ) + if tool_dependencies_with_installation_error: + print '# ----------------------------------------------------------------------------------' + print "# %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) + install_and_test_base_util.show_summary_output( tool_dependencies_with_installation_error ) + print "####################################################################################" + log.debug( "Shutting down..." ) + # Gracefully shut down the embedded web server and UniverseApplication. + if server: + log.debug( "Shutting down embedded galaxy web server..." ) + server.server_close() + server = None + log.debug( "Embedded galaxy server stopped..." ) + if app: + log.debug( "Shutting down galaxy application..." ) + app.shutdown() + app = None + log.debug( "Embedded galaxy application stopped..." ) + # Clean up test files unless otherwise specified. + if 'GALAXY_INSTALL_TEST_NO_CLEANUP' not in os.environ: + for dir in [ galaxy_test_tmp_dir ]: + if os.path.exists( dir ): + try: + shutil.rmtree( dir ) + log.debug( "Cleaned up temporary files in %s", str( dir ) ) + except: + pass + else: + log.debug( 'GALAXY_INSTALL_TEST_NO_CLEANUP set, not cleaning up.' ) + # Return a "successful" response to buildbot. + return 0 + +if __name__ == "__main__": + # The tool_test_results_dict should always have the following structure: + # { + # "test_environment": + # { + # "galaxy_revision": "9001:abcd1234", + # "galaxy_database_version": "114", + # "tool_shed_revision": "9001:abcd1234", + # "tool_shed_mercurial_version": "2.3.1", + # "tool_shed_database_version": "17", + # "python_version": "2.7.2", + # "architecture": "x86_64", + # "system": "Darwin 12.2.0" + # }, + # "installation_errors": + # { + # 'tool_dependencies': + # [ + # { + # 'type': 'Type of tool dependency, e.g. package, set_environment, etc.', + # 'name': 'Name of the tool dependency.', + # 'version': 'Version if this is a package, otherwise blank.', + # 'error_message': 'The error message returned when installation was attempted.', + # }, + # ], + # 'repository_dependencies': + # [ + # { + # 'tool_shed': 'The tool shed that this repository was installed from.', + # 'name': 'The name of the repository that failed to install.', + # 'owner': 'Owner of the failed repository.', + # 'changeset_revision': 'Changeset revision of the failed repository.', + # 'error_message': 'The error message that was returned when the repository failed to install.', + # }, + # ], + # 'current_repository': + # [ + # { + # 'tool_shed': 'The tool shed that this repository was installed from.', + # 'name': 'The name of the repository that failed to install.', + # 'owner': 'Owner of the failed repository.', + # 'changeset_revision': 'Changeset revision of the failed repository.', + # 'error_message': 'The error message that was returned when the repository failed to install.', + # }, + # ], + # { + # "name": "The name of the repository.", + # "owner": "The owner of the repository.", + # "changeset_revision": "The changeset revision of the repository.", + # "error_message": "The message stored in tool_dependency.error_message." + # }, + # } + # } + sys.exit( main() ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refactor the tool shed's install and test framework in preparation for enhancements to test repositories of type tool_dependency_definition.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6f8a07b0c3/ Changeset: 0a6f8a07b0c3 User: greg Date: 2013-12-18 17:16:09 Summary: Refactor the tool shed's install and test framework in preparation for enhancements to test repositories of type tool_dependency_definition. Affected #: 2 files diff -r ce186eb5fefcb7ff332c73bd0869b9e222293d0b -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -1,25 +1,195 @@ -import logging import os import sys cwd = os.getcwd() -if cwd not in sys.path: - sys.path.append( cwd ) - -new_path = [ os.path.join( cwd, "lib" ) ] -if new_path not in sys.path: - new_path.extend( sys.path ) - sys.path = new_path +sys.path.append( cwd ) +new_path = [ os.path.join( cwd, "scripts" ), + os.path.join( cwd, "lib" ), + os.path.join( cwd, 'test' ), + os.path.join( cwd, 'scripts', 'api' ) ] +new_path.extend( sys.path ) +sys.path = new_path from galaxy import eggs +eggs.require( 'mercurial' ) +eggs.require( "nose" ) -eggs.require( 'mercurial' ) +import logging +import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util +import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories +import nose +import platform +import time +import tool_shed.util.shed_util_common as suc +import urllib + +from base.tool_shed_util import log_reason_repository_cannot_be_uninstalled + +from common import update + +from galaxy.util import asbool +from galaxy.util import listify +from galaxy.util import unicodify +from galaxy.util.json import from_json_string +from nose.plugins import Plugin +from tool_shed.util import tool_dependency_util + +from tool_shed.util.xml_util import parse_xml from mercurial import hg from mercurial import ui log = logging.getLogger(__name__) +# Set up a job_conf.xml that explicitly limits jobs to 10 minutes. +job_conf_xml = '''<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> + <limits> + <limit type="walltime">00:10:00</limit> + </limits> +</job_conf> +''' + +# Create a blank shed_tool_conf.xml to define the installed repositories. +shed_tool_conf_xml_template = '''<?xml version="1.0"?> +<toolbox tool_path="${shed_tool_path}"> +</toolbox> +''' + +# Since we will be running functional tests we'll need the upload tool, but the rest can be omitted. +tool_conf_xml = '''<?xml version="1.0"?> +<toolbox> + <section name="Get Data" id="getext"> + <tool file="data_source/upload.xml"/> + </section> +</toolbox> +''' + +# Set up an empty shed_tool_data_table_conf.xml. +tool_data_table_conf_xml_template = '''<?xml version="1.0"?> +<tables> +</tables> +''' + +# Optionally set the environment variable GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF to the location of a +# tool shed's configuration file that includes the tool shed from which repositories will be installed. +tool_sheds_conf_xml = '''<?xml version="1.0"?> +<tool_sheds> + <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> + <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> +</tool_sheds> +''' + +# Should this serve static resources (scripts, images, styles, etc.)? +STATIC_ENABLED = True + +# If we have a tool_data_table_conf.test.xml, set it up to be loaded when the UniverseApplication is started. +# This allows one to specify a set of tool data that is used exclusively for testing, and not loaded into any +# Galaxy instance. By default, this will be in the test-data-repo/location directory generated by buildbot_setup.sh. +if os.path.exists( 'tool_data_table_conf.test.xml' ): + additional_tool_data_tables = 'tool_data_table_conf.test.xml' + additional_tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_EXTRA_TOOL_DATA_PATH', + os.path.join( 'test-data-repo', 'location' ) ) +else: + additional_tool_data_tables = None + additional_tool_data_path = None + +# Set up default tool data tables. +if os.path.exists( 'tool_data_table_conf.xml' ): + tool_data_table_conf = 'tool_data_table_conf.xml' +elif os.path.exists( 'tool_data_table_conf.xml.sample' ): + tool_data_table_conf = 'tool_data_table_conf.xml.sample' +else: + tool_data_table_conf = None + +# The GALAXY_INSTALL_TEST_TOOL_SHED_URL and GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variables must be +# set for this script to work correctly. If the value of GALAXY_INSTALL_TEST_TOOL_SHED_URL does not refer to one +# of the defaults, the GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must refer to a tool shed configuration file that contains +# a definition for that tool shed. +galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', None ) +tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) +exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'install_test_exclude.xml' ) + +if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: + galaxy_encode_secret = 'changethisinproductiontoo' + os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] = galaxy_encode_secret +else: + galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] + +default_galaxy_test_port_min = 10000 +default_galaxy_test_port_max = 10999 +default_galaxy_test_host = '127.0.0.1' +# The following should be an actual value (not None). If developers manually specify their +# tests to use the API it will not work unless a master API key is specified. +default_galaxy_master_api_key = 123456 + +testing_single_repository_dict = {} +if 'repository_name' in os.environ and 'repository_owner' in os.environ: + testing_single_repository_dict[ 'name' ] = str( os.environ[ 'repository_name' ] ) + testing_single_repository_dict[ 'owner' ] = str( os.environ[ 'repository_owner' ] ) + if 'repository_revision' in os.environ: + testing_single_repository_dict[ 'changeset_revision' ] = str( os.environ[ 'repository_revision' ] ) + else: + testing_single_repository_dict[ 'changeset_revision' ] = None + + +class ReportResults( Plugin ): + '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' + name = "reportresults" + passed = {} + + def options( self, parser, env=os.environ ): + super( ReportResults, self ).options( parser, env=env ) + + def configure(self, options, conf): + super( ReportResults, self ).configure( options, conf ) + if not self.enabled: + return + + def addSuccess( self, test ): + '''Only record test IDs that correspond to tool functional tests.''' + if 'TestForTool' in test.id(): + test_id = test.id() + # Rearrange the test ID to match the format that is produced in test_results.failures + test_id_parts = test_id.split( '.' ) + fixed_test_id = '%s (%s)' % ( test_id_parts[ -1 ], '.'.join( test_id_parts[ :-1 ] ) ) + test_parts = fixed_test_id.split( '/' ) + owner = test_parts[ -4 ] + name = test_parts[ -3 ] + test_identifier = '%s/%s' % ( owner, name ) + if test_identifier not in self.passed: + self.passed[ test_identifier ] = [] + self.passed[ test_identifier ].append( fixed_test_id ) + + def getTestStatus( self, test_identifier ): + if test_identifier in self.passed: + passed_tests = self.passed[ test_identifier ] + del self.passed[ test_identifier ] + return passed_tests + return [] + +def get_api_url( base, parts=[], params=None ): + if 'api' in parts and parts.index( 'api' ) != 0: + parts.pop( parts.index( 'api' ) ) + parts.insert( 0, 'api' ) + elif 'api' not in parts: + parts.insert( 0, 'api' ) + url = suc.url_join( base, *parts ) + if params is not None: + query_string = urllib.urlencode( params ) + url += '?%s' % query_string + return url + def get_database_version( app ): ''' This method returns the value of the version column from the migrate_version table, using the provided app's SQLAlchemy session to determine @@ -37,6 +207,107 @@ break return version +def get_latest_downloadable_changeset_revision( url, name, owner ): + error_message = '' + parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] + params = dict( name=name, owner=owner ) + api_url = get_api_url( base=url, parts=parts, params=params ) + changeset_revisions, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + if changeset_revisions: + return changeset_revisions[ -1 ], error_message + else: + return suc.INITIAL_CHANGELOG_HASH, error_message + +def get_missing_tool_dependencies( repository ): + log.debug( 'Checking %s repository %s for missing tool dependencies.' % ( repository.status, repository.name ) ) + missing_tool_dependencies = repository.missing_tool_dependencies + for tool_dependency in repository.tool_dependencies: + log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) + for repository_dependency in repository.repository_dependencies: + if repository_dependency.includes_tool_dependencies: + missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) + return missing_tool_dependencies + +def get_repositories_to_install( tool_shed_url ): + """ + Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: + [{ "changeset_revision": <revision>, + "encoded_repository_id": <encoded repository id from the tool shed>, + "name": <name>, + "owner": <owner>, + "tool_shed_url": <url> }] + """ + error_message = '' + latest_revision_only = '-check_all_revisions' not in sys.argv + if latest_revision_only: + log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) + repository_dicts = [] + parts = [ 'repository_revisions' ] + # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility + # is guaranteed and we currently do not guarantee reproducibility. + params = dict( do_not_test='false', + downloadable='true', + includes_tools='true', + malicious='false', + missing_test_components='false', + skip_tool_test='false' ) + api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) + baseline_repository_dicts, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + for baseline_repository_dict in baseline_repository_dicts: + # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the + # module that will generate the install methods. + repository_dict, error_message = \ + get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) + if error_message: + log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) + else: + # Don't test deprecated repositories since testing them is necessary only if reproducibility is guaranteed + # and we are not currently guaranteeing reproducibility. + deprecated = asbool( repository_dict.get( 'deprecated', False ) ) + if not deprecated: + # Don't test empty repositories. + changeset_revision = baseline_repository_dict[ 'changeset_revision' ] + if changeset_revision != suc.INITIAL_CHANGELOG_HASH: + # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and + # append it to the list of repository_dicts to install and test. + if latest_revision_only: + latest_revision = repository_dict[ 'latest_revision' ] + if changeset_revision == latest_revision: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + else: + repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) + if testing_single_repository_dict: + tsr_name = testing_single_repository_dict[ 'name' ] + tsr_owner = testing_single_repository_dict[ 'owner' ] + tsr_changeset_revision = testing_single_repository_dict[ 'changeset_revision' ] + log.debug( 'Testing single repository with name %s and owner %s.' % ( str( tsr_name ), str( tsr_owner ) ) ) + for repository_to_install in repository_dicts: + rti_name = repository_to_install[ 'name' ] + rti_owner = repository_to_install[ 'owner' ] + rti_changeset_revision = repository_to_install[ 'changeset_revision' ] + if rti_name == tsr_name and rti_owner == tsr_owner: + if tsr_changeset_revision is None: + return [ repository_to_install ], error_message + else: + if tsr_changeset_revision == rti_changeset_revision: + return repository_dicts, error_message + return repository_dicts, error_message + # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL + # environment variable. + log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) + log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) + log.debug( "Repository revisions for testing:" ) + for repository_dict in repository_dicts: + name = str( repository_dict.get( 'name', None ) ) + owner = str( repository_dict.get( 'owner', None ) ) + changeset_revision = str( repository_dict.get( 'changeset_revision', None ) ) + log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) + return repository_dicts, error_message + def get_repository_current_revision( repo_path ): ''' This method uses the python mercurial API to get the current working directory's mercurial changeset hash. Note that if the author of mercurial @@ -52,3 +323,415 @@ ctx_rev = changectx.rev() hg_id = '%d:%s' % ( ctx_rev, str( changectx ) ) return hg_id + +def get_repository_dict( url, repository_dict ): + error_message = '' + parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] + api_url = get_api_url( base=url, parts=parts ) + extended_dict, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + name = str( extended_dict[ 'name' ] ) + owner = str( extended_dict[ 'owner' ] ) + latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) + if error_message: + return None, error_message + extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) + return extended_dict, error_message + +def get_repository_tuple_from_elem( elem ): + attributes = elem.attrib + name = attributes.get( 'name', None ) + owner = attributes.get( 'owner', None ) + changeset_revision = attributes.get( 'changeset_revision', None ) + return ( name, owner, changeset_revision ) + +def get_static_settings(): + """ + Return a dictionary of the settings necessary for a Galaxy application to be wrapped in the static + middleware. This mainly consists of the file system locations of url-mapped static resources. + """ + cwd = os.getcwd() + static_dir = os.path.join( cwd, 'static' ) + #TODO: these should be copied from universe_wsgi.ini + #TODO: static_enabled needed here? + return dict( static_enabled = True, + static_cache_time = 360, + static_dir = static_dir, + static_images_dir = os.path.join( static_dir, 'images', '' ), + static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), + static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), + static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), + static_robots_txt = os.path.join( static_dir, 'robots.txt' ) ) + +def get_tool_test_results_dict( tool_test_results_dicts ): + if tool_test_results_dicts: + # Inspect the tool_test_results_dict for the last test run to make sure it contains only a test_environment + # entry. If it contains more entries, then the script ~/tool_shed/api/check_repositories_for_functional_tests.py + # was not executed in preparation for this script's execution, so we'll just create an empty dictionary. + tool_test_results_dict = tool_test_results_dicts[ 0 ] + if len( tool_test_results_dict ) <= 1: + # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only + # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts + # since it will be re-inserted later. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + elif len( tool_test_results_dict ) == 2 and \ + 'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict: + # We can re-use tool_test_results_dict if its only entries are "test_environment" and "missing_test_components". + # In this case, some tools are missing tests components while others are not. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) + else: + # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. + tool_test_results_dict = {} + else: + # Create a new dictionary for this test test run, + tool_test_results_dict = {} + return tool_test_results_dict + +def get_tool_test_results_dicts( tool_shed_url, encoded_repository_metadata_id ): + """ + Return the list of dictionaries contained in the Tool Shed's repository_metadata.tool_test_results + column via the Tool Shed API. + """ + error_message = '' + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] + api_url = get_api_url( base=tool_shed_url, parts=parts ) + repository_metadata, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently + # return a list. + tool_test_results = listify( repository_metadata.get( 'tool_test_results', [] ) ) + return tool_test_results, error_message + +def get_webapp_global_conf(): + """Return the global_conf dictionary sent as the first argument to app_factory.""" + global_conf = {} + if STATIC_ENABLED: + global_conf.update( get_static_settings() ) + return global_conf + +def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dicts, + tool_test_results_dict, results_dict, can_update_tool_shed ): + """Handle missing repository or tool dependencies for an installed repository.""" + # If a tool dependency fails to install correctly, this should be considered an installation error, + # and functional tests should be skipped, since the tool dependency needs to be correctly installed + # for the test to be considered reliable. + log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) + # In keeping with the standard display layout, add the error message to the dict for each tool individually. + for dependency in repository.missing_tool_dependencies: + name = str( dependency.name ) + type = str( dependency.type ) + version = str( dependency.version ) + error_message = unicodify( dependency.error_message ) + log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) + test_result = dict( type=dependency.type, + name=dependency.name, + version=dependency.version, + error_message=dependency.error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) + for dependency in repository.missing_repository_dependencies: + name = str( dependency.name ) + owner = str( dependency.owner ) + changeset_revision = str( dependency.changeset_revision ) + error_message = unicodify( dependency.error_message ) + log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ + ( name, changeset_revision, owner, error_message ) ) + test_result = dict( tool_shed=dependency.tool_shed, + name=dependency.name, + owner=dependency.owner, + changeset_revision=dependency.changeset_revision, + error_message=dependency.error_message ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) + # Record the status of this repository in the tool shed. + params = dict( tools_functionally_correct=False, + do_not_test=False, + test_install_error=True ) + # TODO: do something useful with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) + # Since this repository is missing components we do not want to test it, uninstall it. + uninstall_repository_and_repository_dependencies( app, repository_dict ) + results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), + owner=str( repository.owner ), + changeset_revision=str( repository.changeset_revision ) ) ) + return results_dict + +def initialize_results_dict(): + # Initialize a dictionary for the summary that will be printed to stdout. + results_dict = {} + results_dict[ 'total_repositories_tested' ] = 0 + results_dict[ 'all_tests_passed' ] = [] + results_dict[ 'at_least_one_test_failed' ] = [] + results_dict[ 'repositories_failed_install' ] = [] + return results_dict + +def initialize_tool_tests_results_dict( app, tool_test_results_dict ): + test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) + if len( test_environment_dict ) == 0: + # Set information about the tool shed to nothing since we cannot currently determine it from here. + # We could eventually add an API method... + test_environment_dict = dict( tool_shed_database_version='', + tool_shed_mercurial_version='', + tool_shed_revision='' ) + # Add the current time as the approximate time that this test run occurs. A similar value will also be + # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed + # may be configured to store multiple test run results, so each must be associated with a time stamp. + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) + # Add information about the current platform. + test_environment_dict[ 'time_tested' ] = now + test_environment_dict[ 'python_version' ] = platform.python_version() + test_environment_dict[ 'architecture' ] = platform.machine() + operating_system, hostname, operating_system_version, uname, arch, processor = platform.uname() + test_environment_dict[ 'system' ] = '%s %s' % ( operating_system, operating_system_version ) + # Add information about the current Galaxy environment. + test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) + # Initialize and populate the tool_test_results_dict. + tool_test_results_dict[ 'test_environment' ] = test_environment_dict + tool_test_results_dict[ 'passed_tests' ] = [] + tool_test_results_dict[ 'failed_tests' ] = [] + tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], + repository_dependencies=[], + tool_dependencies=[] ) + return tool_test_results_dict + +def install_repository( app, repository_dict ): + """Install a repository defined by the received repository_dict from the tool shed into Galaxy.""" + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + error_message = '' + repository = None + log.debug( "Installing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) + # Use the repository information dictionary to generate an install method that will install the repository into the + # embedded Galaxy application, with tool dependencies and repository dependencies, if any. + test_install_repositories.generate_install_method( repository_dict ) + # Configure nose to run the install method as a test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to + # install the specified repository with tool and repository dependencies also selected for installation. + result, _ = run_tests( test_config ) + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except Exception, e: + error_message = 'Error getting revision %s of repository %s owned by %s: %s' % ( changeset_revision, name, owner, str( e ) ) + log.exception( error_message ) + return repository, error_message + +def is_latest_downloadable_revision( url, repository_dict ): + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + latest_revision = get_latest_downloadable_changeset_revision( url, name=name, owner=owner ) + return changeset_revision == str( latest_revision ) + +def json_from_url( url ): + error_message = '' + url_handle = urllib.urlopen( url ) + url_contents = url_handle.read() + try: + parsed_json = from_json_string( url_contents ) + except Exception, e: + error_message = str( url_contents ) + log.exception( 'Error parsing JSON data in json_from_url(): %s.' % str( e ) ) + return None, error_message + return parsed_json, error_message + +def parse_exclude_list( xml_filename ): + """Return a list of repositories to exclude from testing.""" + # This method should return a list with the following structure: + # [{ 'reason': The default reason or the reason specified in this section, + # 'repositories': [( name, owner, changeset revision if changeset revision else None ), + # ( name, owner, changeset revision if changeset revision else None )]}] + exclude_list = [] + exclude_verbose = [] + xml_tree, error_message = parse_xml( xml_filename ) + if error_message: + log.debug( 'The xml document %s defining the exclude list is invalid, so no repositories will be excluded from testing: %s' % \ + ( str( xml_filename ), str( error_message ) ) ) + return exclude_list + tool_sheds = xml_tree.findall( 'repositories' ) + xml_element = [] + exclude_count = 0 + for tool_shed in tool_sheds: + if galaxy_tool_shed_url != tool_shed.attrib[ 'tool_shed' ]: + continue + else: + xml_element = tool_shed + for reason_section in xml_element: + reason_text = reason_section.find( 'text' ).text + repositories = reason_section.findall( 'repository' ) + exclude_dict = dict( reason=reason_text, repositories=[] ) + for repository in repositories: + repository_tuple = get_repository_tuple_from_elem( repository ) + if repository_tuple not in exclude_dict[ 'repositories' ]: + exclude_verbose.append( repository_tuple ) + exclude_count += 1 + exclude_dict[ 'repositories' ].append( repository_tuple ) + exclude_list.append( exclude_dict ) + log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ + ( str( xml_filename ), str( exclude_count ) ) ) + #if '-list_repositories' in sys.argv: + for name, owner, changeset_revision in exclude_verbose: + if changeset_revision: + log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) + else: + log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) + return exclude_list + +def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ): + """ + Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method + updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags + to the appropriate values and updates the time_last_tested field to the value of the received time_tested. + """ + if can_update_tool_shed: + metadata_revision_id = repository_dict.get( 'id', None ) + if metadata_revision_id is not None: + tool_test_results_dicts.insert( 0, tool_test_results_dict ) + params[ 'tool_test_results' ] = tool_test_results_dicts + # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. + params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' + url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + try: + return update( tool_shed_api_key, url, params, return_formatted=False ) + except Exception, e: + log.exception( 'Error attempting to register test results: %s' % str( e ) ) + return {} + else: + return {} + +def run_tests( test_config ): + loader = nose.loader.TestLoader( config=test_config ) + test_config.plugins.addPlugin( ReportResults() ) + plug_loader = test_config.plugins.prepareTestLoader( loader ) + if plug_loader is not None: + loader = plug_loader + tests = loader.loadTestsFromNames( test_config.testNames ) + test_runner = nose.core.TextTestRunner( stream=test_config.stream, + verbosity=test_config.verbosity, + config=test_config ) + plug_runner = test_config.plugins.prepareTestRunner( test_runner ) + if plug_runner is not None: + test_runner = plug_runner + result = test_runner.run( tests ) + return result, test_config.plugins._plugins + +def show_summary_output( repository_dicts ): + # Group summary display by repository owner. + repository_dicts_by_owner = {} + for repository_dict in repository_dicts: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + if owner in repository_dicts_by_owner: + repository_dicts_by_owner[ owner ].append( repository_dict ) + else: + repository_dicts_by_owner[ owner ] = [ repository_dict ] + # Display grouped summary. + for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): + print "# " + for repository_dict in grouped_repository_dicts: + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) + +def uninstall_repository_and_repository_dependencies( app, repository_dict ): + """Uninstall a repository and all of its repository dependencies.""" + # This method assumes that the repositor defined by the received repository_dict is not a repository + # dependency of another repository. + sa_session = app.install_model.context + # The dict contains the only repository the app should have installed at this point. + name = str( repository_dict[ 'name' ] ) + owner = str( repository_dict[ 'owner' ] ) + changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + # Since this install and test framework uninstalls repositories immediately after installing and testing + # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be + # the same. + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + if repository.can_uninstall( app ): + # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order + # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see + # if it can be uninstalled. + uninstall_repository_dict = dict( name=name, + owner=owner, + changeset_revision=changeset_revision ) + log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) + try: + test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed + # repository and all of its repository dependencies, deleting each of them from disk. + result, _ = run_tests( test_config ) + repository_uninstall_successful = result.wasSuccessful() + except Exception, e: + repository_uninstall_successful = False + log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ + ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) + if repository_uninstall_successful: + # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. + # We have to do this through Twill in order to maintain app.toolbox and shed_tool_conf.xml in a state that + # is valid for future tests. Since some of the repository's repository dependencies may require other of + # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. + processed_repository_dependency_ids = [] + while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): + for repository_dependency in repository.repository_dependencies: + if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): + processed_repository_dependency_ids.append( repository_dependency.id ) + rd_name = str( repository_dependency.name ) + rd_owner = str( repository_dependency.owner ) + rd_changeset_revision = str( repository_dependency.changeset_revision ) + uninstall_repository_dict = dict( name=rd_name, + owner=rd_owner, + changeset_revision=rd_changeset_revision ) + log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) ) + # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's + # web interface. + try: + test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. + result, _ = run_tests( test_config ) + if not result.wasSuccessful(): + # We won't set ok here because we'll continue to uninstall whatever we can. + log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) ) + except Exception, e: + log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ + ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) + else: + log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) + else: + log_reason_repository_cannot_be_uninstalled( app, repository ) + +def uninstall_tool_dependency( app, tool_dependency ): + """Attempt to uninstall a tool dependency.""" + sa_session = app.install_model.context + # Clean out any generated tests. This is necessary for Twill. + tool_dependency_install_path = tool_dependency.installation_directory( app ) + uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) + if error_message: + log.debug( 'There was an error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) + log.debug( error_message ) + else: + log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) + if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: + tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED + sa_session.add( tool_dependency ) + sa_session.flush() + if os.path.exists( tool_dependency_install_path ): + log.debug( 'Uninstallation of tool dependency succeeded, but the installation path still exists on the filesystem. It is now being explicitly deleted.') + suc.remove_dir( tool_dependency_install_path ) + diff -r ce186eb5fefcb7ff332c73bd0869b9e222293d0b -r 0a6f8a07b0c3ca8d58302cb3714ed01d132e52ec test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -24,13 +24,11 @@ # http://code.google.com/p/python-nose/issues/detail?id=284 eggs.require( "pysqlite" ) -test_toolbox = None import httplib import install_and_test_tool_shed_repositories.base.test_db_util as test_db_util import install_and_test_tool_shed_repositories.functional.test_install_repositories as test_install_repositories import logging import nose -import platform import random import re import shutil @@ -39,37 +37,27 @@ import tempfile import time import threading -import tool_shed.util.shed_util_common as suc -import urllib -from base.tool_shed_util import log_reason_repository_cannot_be_uninstalled +import install_and_test_tool_shed_repositories.base.util as install_and_test_base_util + from base.tool_shed_util import parse_tool_panel_config -from install_and_test_tool_shed_repositories.base.util import get_database_version -from install_and_test_tool_shed_repositories.base.util import get_repository_current_revision -from common import update -from datetime import datetime + from galaxy.app import UniverseApplication -from galaxy.util import asbool -from galaxy.util import listify -from galaxy.util import unicodify from galaxy.util.json import from_json_string from galaxy.util.json import to_json_string from galaxy.web import buildapp -from galaxy.web.framework.helpers import time_ago from functional_tests import generate_config_file -from mercurial import __version__ from nose.plugins import Plugin from paste import httpserver -from tool_shed.util import tool_dependency_util -from tool_shed.util.xml_util import parse_xml from functional import database_contexts log = logging.getLogger( 'install_and_test_repositories' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) -test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories' ) -default_test_file_dir = os.path.join( test_home_directory, 'test_data' ) +test_home_directory = os.path.join( cwd, 'test', 'install_and_test_tool_shed_repositories', 'repositories_with_tools' ) + +test_toolbox = None # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. @@ -78,184 +66,12 @@ default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -default_galaxy_test_port_min = 10000 -default_galaxy_test_port_max = 10999 -default_galaxy_test_host = '127.0.0.1' -# The following should be an actual value (not None). If developers manually specify their -# tests to use the API it will not work unless a master API key is specified. -default_galaxy_master_api_key = 123456 - # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: can_update_tool_shed = False else: can_update_tool_shed = True -# Should this serve static resources (scripts, images, styles, etc.)? -STATIC_ENABLED = True - -# Set up a job_conf.xml that explicitly limits jobs to 10 minutes. -job_conf_xml = '''<?xml version="1.0"?> - -<job_conf> - <plugins> - <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> - </plugins> - <handlers> - <handler id="main"/> - </handlers> - <destinations> - <destination id="local" runner="local"/> - </destinations> - <limits> - <limit type="walltime">00:10:00</limit> - </limits> -</job_conf> -''' - -# Create a blank shed_tool_conf.xml to define the installed repositories. -shed_tool_conf_xml_template = '''<?xml version="1.0"?> -<toolbox tool_path="${shed_tool_path}"> -</toolbox> -''' - -# Since we will be running functional tests we'll need the upload tool, but the rest can be omitted. -tool_conf_xml = '''<?xml version="1.0"?> -<toolbox> - <section name="Get Data" id="getext"> - <tool file="data_source/upload.xml"/> - </section> -</toolbox> -''' - -# Set up an empty shed_tool_data_table_conf.xml. -tool_data_table_conf_xml_template = '''<?xml version="1.0"?> -<tables> -</tables> -''' - -# Optionally set the environment variable GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF to the location of a -# tool shed's configuration file that includes the tool shed from which repositories will be installed. -tool_sheds_conf_xml = '''<?xml version="1.0"?> -<tool_sheds> - <tool_shed name="Galaxy main tool shed" url="http://toolshed.g2.bx.psu.edu/"/> - <tool_shed name="Galaxy test tool shed" url="http://testtoolshed.g2.bx.psu.edu/"/> -</tool_sheds> -''' - -# If we have a tool_data_table_conf.test.xml, set it up to be loaded when the UniverseApplication is started. -# This allows one to specify a set of tool data that is used exclusively for testing, and not loaded into any -# Galaxy instance. By default, this will be in the test-data-repo/location directory generated by buildbot_setup.sh. -if os.path.exists( 'tool_data_table_conf.test.xml' ): - additional_tool_data_tables = 'tool_data_table_conf.test.xml' - additional_tool_data_path = os.environ.get( 'GALAXY_INSTALL_TEST_EXTRA_TOOL_DATA_PATH', - os.path.join( 'test-data-repo', 'location' ) ) -else: - additional_tool_data_tables = None - additional_tool_data_path = None - -# Set up default tool data tables. -if os.path.exists( 'tool_data_table_conf.xml' ): - tool_data_table_conf = 'tool_data_table_conf.xml' -elif os.path.exists( 'tool_data_table_conf.xml.sample' ): - tool_data_table_conf = 'tool_data_table_conf.xml.sample' -else: - tool_data_table_conf = None - -# The GALAXY_INSTALL_TEST_TOOL_SHED_URL and GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variables must be -# set for this script to work correctly. If the value of GALAXY_INSTALL_TEST_TOOL_SHED_URL does not refer to one -# of the defaults, the GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF must refer to a tool shed configuration file that contains -# a definition for that tool shed. -galaxy_tool_shed_url = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_URL', None ) -tool_shed_api_key = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY', None ) -exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'install_test_exclude.xml' ) - -if 'GALAXY_INSTALL_TEST_SECRET' not in os.environ: - galaxy_encode_secret = 'changethisinproductiontoo' - os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] = galaxy_encode_secret -else: - galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] - -testing_single_repository_dict = {} -if 'repository_name' in os.environ and 'repository_owner' in os.environ: - testing_single_repository_dict[ 'name' ] = str( os.environ[ 'repository_name' ] ) - testing_single_repository_dict[ 'owner' ] = str( os.environ[ 'repository_owner' ] ) - if 'repository_revision' in os.environ: - testing_single_repository_dict[ 'changeset_revision' ] = str( os.environ[ 'repository_revision' ] ) - else: - testing_single_repository_dict[ 'changeset_revision' ] = None - - -class ReportResults( Plugin ): - '''Simple Nose plugin to record the IDs of all tests run, regardless of success.''' - name = "reportresults" - passed = {} - - def options( self, parser, env=os.environ ): - super( ReportResults, self ).options( parser, env=env ) - - def configure(self, options, conf): - super( ReportResults, self ).configure( options, conf ) - if not self.enabled: - return - - def addSuccess( self, test ): - '''Only record test IDs that correspond to tool functional tests.''' - if 'TestForTool' in test.id(): - test_id = test.id() - # Rearrange the test ID to match the format that is produced in test_results.failures - test_id_parts = test_id.split( '.' ) - fixed_test_id = '%s (%s)' % ( test_id_parts[ -1 ], '.'.join( test_id_parts[ :-1 ] ) ) - test_parts = fixed_test_id.split( '/' ) - owner = test_parts[ -4 ] - name = test_parts[ -3 ] - test_identifier = '%s/%s' % ( owner, name ) - if test_identifier not in self.passed: - self.passed[ test_identifier ] = [] - self.passed[ test_identifier ].append( fixed_test_id ) - - def getTestStatus( self, test_identifier ): - if test_identifier in self.passed: - passed_tests = self.passed[ test_identifier ] - del self.passed[ test_identifier ] - return passed_tests - return [] - -def deactivate_repository( app, repository_dict ): - sa_session = app.install_model.context - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - # The dict contains the only repository the app should have installed at this point. - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - repository_dict_for_deactivation = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Changeset revision %s of repository %s owned by %s selected for deactivation.' % ( changeset_revision, name, owner ) ) - test_install_repositories.generate_deactivate_method( repository_dict_for_deactivation ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the deactivate method which uses the Galaxy web interface to deactivate the repository. - result, _ = run_tests( test_config ) - success = result.wasSuccessful() - if not success: - log.debug( 'Deactivation of revision %s repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - -def get_api_url( base, parts=[], params=None ): - if 'api' in parts and parts.index( 'api' ) != 0: - parts.pop( parts.index( 'api' ) ) - parts.insert( 0, 'api' ) - elif 'api' not in parts: - parts.insert( 0, 'api' ) - url = suc.url_join( base, *parts ) - if params is not None: - query_string = urllib.urlencode( params ) - url += '?%s' % query_string - return url - def get_failed_test_dicts( test_result, from_tool_test=True ): """Extract any useful data from the test_result.failures and test_result.errors attributes.""" failed_test_dicts = [] @@ -304,146 +120,6 @@ failed_test_dicts.append( test_status_dict ) return failed_test_dicts -def get_latest_downloadable_changeset_revision( url, name, owner ): - error_message = '' - parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = dict( name=name, owner=owner ) - api_url = get_api_url( base=url, parts=parts, params=params ) - changeset_revisions, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - if changeset_revisions: - return changeset_revisions[ -1 ], error_message - else: - return suc.INITIAL_CHANGELOG_HASH, error_message - -def get_missing_tool_dependencies( repository ): - log.debug( 'Checking %s repository %s for missing tool dependencies.' % ( repository.status, repository.name ) ) - missing_tool_dependencies = repository.missing_tool_dependencies - for tool_dependency in repository.tool_dependencies: - log.debug( 'Tool dependency %s version %s has status %s.' % ( tool_dependency.name, tool_dependency.version, tool_dependency.status ) ) - for repository_dependency in repository.repository_dependencies: - if repository_dependency.includes_tool_dependencies: - missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) - return missing_tool_dependencies - -def get_repository_dict( url, repository_dict ): - error_message = '' - parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] - api_url = get_api_url( base=url, parts=parts ) - extended_dict, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - name = str( extended_dict[ 'name' ] ) - owner = str( extended_dict[ 'owner' ] ) - latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, name, owner ) - if error_message: - return None, error_message - extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) - return extended_dict, error_message - -def get_repository_tuple_from_elem( elem ): - attributes = elem.attrib - name = attributes.get( 'name', None ) - owner = attributes.get( 'owner', None ) - changeset_revision = attributes.get( 'changeset_revision', None ) - return ( name, owner, changeset_revision ) - -def get_repositories_to_install( tool_shed_url ): - """ - Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: - [{ "changeset_revision": <revision>, - "encoded_repository_id": <encoded repository id from the tool shed>, - "name": <name>, - "owner": <owner>, - "tool_shed_url": <url> }] - """ - error_message = '' - latest_revision_only = '-check_all_revisions' not in sys.argv - if latest_revision_only: - log.debug( 'Testing is restricted to the latest downloadable revision in this test run.' ) - repository_dicts = [] - parts = [ 'repository_revisions' ] - # We'll filter out deprecated repositories from testing since testing them is necessary only if reproducibility - # is guaranteed and we currently do not guarantee reproducibility. - params = dict( do_not_test='false', - downloadable='true', - includes_tools='true', - malicious='false', - missing_test_components='false', - skip_tool_test='false' ) - api_url = get_api_url( base=tool_shed_url, parts=parts, params=params ) - baseline_repository_dicts, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - for baseline_repository_dict in baseline_repository_dicts: - # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the - # module that will generate the install methods. - repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) - if error_message: - log.debug( 'Error getting additional details from the API: %s' % str( error_message ) ) - else: - # Don't test deprecated repositories since testing them is necessary only if reproducibility is guaranteed - # and we are not currently guaranteeing reproducibility. - deprecated = asbool( repository_dict.get( 'deprecated', False ) ) - if not deprecated: - # Don't test empty repositories. - changeset_revision = baseline_repository_dict[ 'changeset_revision' ] - if changeset_revision != suc.INITIAL_CHANGELOG_HASH: - # Merge the dictionary returned from /api/repository_revisions with the detailed repository_dict and - # append it to the list of repository_dicts to install and test. - if latest_revision_only: - latest_revision = repository_dict[ 'latest_revision' ] - if changeset_revision == latest_revision: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - else: - repository_dicts.append( dict( repository_dict.items() + baseline_repository_dict.items() ) ) - if testing_single_repository_dict: - tsr_name = testing_single_repository_dict[ 'name' ] - tsr_owner = testing_single_repository_dict[ 'owner' ] - tsr_changeset_revision = testing_single_repository_dict[ 'changeset_revision' ] - log.debug( 'Testing single repository with name %s and owner %s.' % ( str( tsr_name ), str( tsr_owner ) ) ) - for repository_to_install in repository_dicts: - rti_name = repository_to_install[ 'name' ] - rti_owner = repository_to_install[ 'owner' ] - rti_changeset_revision = repository_to_install[ 'changeset_revision' ] - if rti_name == tsr_name and rti_owner == tsr_owner: - if tsr_changeset_revision is None: - return [ repository_to_install ], error_message - else: - if tsr_changeset_revision == rti_changeset_revision: - return repository_dicts, error_message - return repository_dicts, error_message - # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL - # environment variable. - log.debug( "The Tool Shed's API url...\n%s" % str( api_url ) ) - log.debug( "...retrieved %d repository revisions for testing." % len( repository_dicts ) ) - log.debug( "Repository revisions for testing:" ) - for repository_dict in repository_dicts: - name = str( repository_dict.get( 'name', None ) ) - owner = str( repository_dict.get( 'owner', None ) ) - changeset_revision = str( repository_dict.get( 'changeset_revision', None ) ) - log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) - return repository_dicts, error_message - -def get_static_settings(): - """ - Return a dictionary of the settings necessary for a Galaxy application to be wrapped in the static - middleware. This mainly consists of the file system locations of url-mapped static resources. - """ - cwd = os.getcwd() - static_dir = os.path.join( cwd, 'static' ) - #TODO: these should be copied from universe_wsgi.ini - #TODO: static_enabled needed here? - return dict( static_enabled = True, - static_cache_time = 360, - static_dir = static_dir, - static_images_dir = os.path.join( static_dir, 'images', '' ), - static_favicon_dir = os.path.join( static_dir, 'favicon.ico' ), - static_scripts_dir = os.path.join( static_dir, 'scripts', '' ), - static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), - static_robots_txt = os.path.join( static_dir, 'robots.txt' ) ) - def get_tool_info_from_test_id( test_id ): """ Test IDs come in the form test_tool_number @@ -455,137 +131,17 @@ tool_id = parts[ -2 ] return tool_id, tool_version -def get_tool_test_results_dicts( tool_shed_url, encoded_repository_metadata_id ): - """ - Return the list of dictionaries contained in the Tool Shed's repository_metadata.tool_test_results - column via the Tool Shed API. - """ +def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + results_dict = install_and_test_base_util.initialize_results_dict() error_message = '' - parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] - api_url = get_api_url( base=tool_shed_url, parts=parts ) - repository_metadata, error_message = json_from_url( api_url ) - if error_message: - return None, error_message - # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently - # return a list. - tool_test_results = listify( repository_metadata.get( 'tool_test_results', [] ) ) - return tool_test_results, error_message - -def get_webapp_global_conf(): - """Return the global_conf dictionary sent as the first argument to app_factory.""" - global_conf = {} - if STATIC_ENABLED: - global_conf.update( get_static_settings() ) - return global_conf - -def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, - tool_test_results_dicts, tool_test_results_dict, results_dict ): - """Handle missing repository or tool dependencies for an installed repository.""" - # If a tool dependency fails to install correctly, this should be considered an installation error, - # and functional tests should be skipped, since the tool dependency needs to be correctly installed - # for the test to be considered reliable. - log.debug( 'The following dependencies of this repository are missing, so skipping functional tests.' ) - # In keeping with the standard display layout, add the error message to the dict for each tool individually. - for dependency in repository.missing_tool_dependencies: - name = str( dependency.name ) - type = str( dependency.type ) - version = str( dependency.version ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing tool dependency %s of type %s version %s: %s' % ( name, type, version, error_message ) ) - test_result = dict( type=dependency.type, - name=dependency.name, - version=dependency.version, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( test_result ) - for dependency in repository.missing_repository_dependencies: - name = str( dependency.name ) - owner = str( dependency.owner ) - changeset_revision = str( dependency.changeset_revision ) - error_message = unicodify( dependency.error_message ) - log.debug( 'Missing repository dependency %s changeset revision %s owned by %s: %s' % \ - ( name, changeset_revision, owner, error_message ) ) - test_result = dict( tool_shed=dependency.tool_shed, - name=dependency.name, - owner=dependency.owner, - changeset_revision=dependency.changeset_revision, - error_message=dependency.error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( test_result ) - # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=True ) - # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) - # Since this repository is missing components, we do not want to test it, so deactivate it or uninstall it. - # The deactivate flag is set to True if the environment variable GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES - # is set to 'true'. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) - if deactivate: - for missing_tool_dependency in missing_tool_dependencies: - uninstall_tool_dependency( app, missing_tool_dependency ) - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) - results_dict[ 'repositories_failed_install' ].append( dict( name=str( repository.name ), - owner=str( repository.owner ), - changeset_revision=str( repository.changeset_revision ) ) ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox - return results_dict - -def initialize_results_dict(): - # Initialize a dictionary for the summary that will be printed to stdout. - results_dict = {} - results_dict[ 'total_repositories_tested' ] = 0 - results_dict[ 'all_tests_passed' ] = [] - results_dict[ 'at_least_one_test_failed' ] = [] - results_dict[ 'repositories_failed_install' ] = [] - return results_dict - -def install_repository( app, repository_dict ): - """Install a repository defined by the received repository_dict from the tool shed into Galaxy.""" - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - error_message = '' - repository = None - log.debug( "Installing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) - # Explicitly clear tests from twill's test environment. - remove_generated_tests( app ) - # Use the repository information dictionary to generate an install method that will install the repository into the - # embedded Galaxy application, with tool dependencies and repository dependencies, if any. - test_install_repositories.generate_install_method( repository_dict ) - # Configure nose to run the install method as a test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to - # install the specified repository with tool and repository dependencies also selected for installation. - result, _ = run_tests( test_config ) - try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Error getting revision %s of repository %s owned by %s: %s' % ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) - return repository, error_message - -def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): - results_dict = initialize_results_dict() - error_message = '' - # Allow the option to keep or delete tool dependencies when a repository has been tested. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) # Initialize a dictionary for the summary that will be printed to stdout. total_repositories_tested = results_dict[ 'total_repositories_tested' ] - repositories_to_install, error_message = get_repositories_to_install( galaxy_tool_shed_url ) + repositories_to_install, error_message = \ + install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url ) if error_message: return None, error_message # Handle repositories not to be tested. - if os.path.exists( exclude_list_file ): + if os.path.exists( install_and_test_base_util.exclude_list_file ): # Entries in the exclude_list look something like this. # { 'reason': The default reason or the reason specified in this section, # 'repositories': @@ -597,8 +153,8 @@ # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. - log.debug( 'Loading the list of repositories excluded from testing from the file %s...', exclude_list_file ) - exclude_list = parse_exclude_list( exclude_list_file ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...', install_and_test_base_util.exclude_list_file ) + exclude_list = install_and_test_base_util.parse_exclude_list( install_and_test_base_util.exclude_list_file ) else: exclude_list = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was @@ -627,7 +183,7 @@ # "user_id": "529fd61ab1c6cc36" } encoded_repository_metadata_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. - repository_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url # Get the name and owner out of the repository info dict. name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) @@ -635,31 +191,13 @@ log.debug( "Processing revision %s of repository %s owned by %s..." % ( changeset_revision, name, owner ) ) repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) # Retrieve the stored list of tool_test_results_dicts. - tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) + tool_test_results_dicts, error_message = \ + install_and_test_base_util.get_tool_test_results_dicts( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) if error_message: log.debug( error_message ) else: - if tool_test_results_dicts: - # Inspect the tool_test_results_dict for the last test run to make sure it contains only a test_environment - # entry. If it contains more entries, then the script ~/tool_shed/api/check_repositories_for_functional_tests.py - # was not executed in preparation for this script's execution, so we'll just create an empty dictionary. - tool_test_results_dict = tool_test_results_dicts[ 0 ] - if len( tool_test_results_dict ) <= 1: - # We can re-use the mostly empty tool_test_results_dict for this run because it is either empty or it contains only - # a test_environment entry. If we use it we need to temporarily eliminate it from the list of tool_test_results_dicts - # since it will be re-inserted later. - tool_test_results_dict = tool_test_results_dicts.pop( 0 ) - elif len( tool_test_results_dict ) == 2 and \ - 'test_environment' in tool_test_results_dict and 'missing_test_components' in tool_test_results_dict: - # We can re-use tool_test_results_dict if its only entries are "test_environment" and "missing_test_components". - # In this case, some tools are missing tests components while others are not. - tool_test_results_dict = tool_test_results_dicts.pop( 0 ) - else: - # The latest tool_test_results_dict has been populated with the results of a test run, so it cannot be used. - tool_test_results_dict = {} - else: - # Create a new dictionary for this test test run, - tool_test_results_dict = {} + tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) # See if this repository should be skipped for any reason. this_repository_is_in_the_exclude_list = False skip_reason = None @@ -675,37 +213,20 @@ params = dict( tools_functionally_correct=False, do_not_test=False ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( "Not testing revision %s of repository %s owned by %s because it is in the exclude list for this test run." % \ ( changeset_revision, name, owner ) ) else: - test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) - if len( test_environment_dict ) == 0: - # Set information about the tool shed to nothing since we cannot currently determine it from here. - # We could eventually add an API method... - test_environment_dict = dict( tool_shed_database_version='', - tool_shed_mercurial_version='', - tool_shed_revision='' ) - # Add the current time as the approximate time that this test run occurs. A similar value will also be - # set to the repository_metadata.time_last_tested column, but we also store it here because the Tool Shed - # may be configured to store multiple test run results, so each must be associated with a time stamp. - now = time.strftime( "%Y-%m-%d %H:%M:%S" ) - # Add information about the current platform. - test_environment_dict[ 'time_tested' ] = now - test_environment_dict[ 'python_version' ] = platform.python_version() - test_environment_dict[ 'architecture' ] = platform.machine() - operating_system, hostname, operating_system_version, uname, arch, processor = platform.uname() - test_environment_dict[ 'system' ] = '%s %s' % ( operating_system, operating_system_version ) - # Add information about the current Galaxy environment. - test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) - # Initialize and populate the tool_test_results_dict. - tool_test_results_dict[ 'test_environment' ] = test_environment_dict - tool_test_results_dict[ 'passed_tests' ] = [] - tool_test_results_dict[ 'failed_tests' ] = [] - tool_test_results_dict[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) + tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) + # Explicitly clear tests from twill's test environment. + remove_generated_tests( app ) # Proceed with installing repositories and testing contained tools. - repository, error_message = install_repository( app, repository_dict ) + repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) if error_message: tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. @@ -715,7 +236,7 @@ except Exception, e: error_message = 'Unable to find installed repository %s owned by %s: %s.' % ( name, owner, str( e ) ) log.exception( error_message ) - test_result = dict( tool_shed=galaxy_tool_shed_url, + test_result = dict( tool_shed=install_and_test_base_util.galaxy_tool_shed_url, name=name, owner=owner, changeset_revision=changeset_revision, @@ -725,20 +246,20 @@ test_install_error=True, do_not_test=False ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) try: - if deactivate: - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) - except: - log.exception( 'Encountered error attempting to deactivate or uninstall %s.', str( repository_dict[ 'name' ] ) ) + # We are uninstalling this repository and all of its repository dependencies. + install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) + except Exception, e: + log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \ + ( changeset_revision, name, owner, str( e ) ) ) + # Clean out any generated tests. This is necessary for Twill. + remove_generated_tests( app ) results_dict[ 'repositories_failed_install' ].append( repository_identifier_dict ) log.debug( 'Repository %s failed to install correctly.' % str( name ) ) else: @@ -757,15 +278,18 @@ # missing test components. if 'missing_test_components' not in tool_test_results_dict: tool_test_results_dict[ 'missing_test_components' ] = [] - missing_tool_dependencies = get_missing_tool_dependencies( repository ) + missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - results_dict = handle_missing_dependencies( app, - repository, - missing_tool_dependencies, - repository_dict, - tool_test_results_dicts, - tool_test_results_dict, - results_dict ) + results_dict = install_and_test_base_util.handle_missing_dependencies( app, + repository, + missing_tool_dependencies, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict, + can_update_tool_shed ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox else: # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional # test framework can find it. @@ -787,49 +311,35 @@ do_not_test=False, test_install_error=False ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = \ + install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) results_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested return results_dict, error_message -def is_latest_downloadable_revision( url, repository_dict ): - latest_revision = get_latest_downloadable_changeset_revision( url, name=repository_dict[ 'name' ], owner=repository_dict[ 'owner' ] ) - return str( repository_dict[ 'changeset_revision' ] ) == str( latest_revision ) - -def json_from_url( url ): - error_message = '' - url_handle = urllib.urlopen( url ) - url_contents = url_handle.read() - try: - parsed_json = from_json_string( url_contents ) - except Exception, e: - error_message = str( url_contents ) - log.exception( 'Error parsing JSON data in json_from_url(): %s.' % str( e ) ) - return None, error_message - return parsed_json, error_message - def main(): - if tool_shed_api_key is None: + if install_and_test_base_util.tool_shed_api_key is None: # If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. log.debug( 'Cannot proceed without a valid tool shed API key set in the enviroment variable GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY.' ) return 1 - if galaxy_tool_shed_url is None: + if install_and_test_base_util.galaxy_tool_shed_url is None: log.debug( 'Cannot proceed without a valid Tool Shed base URL set in the environment variable GALAXY_INSTALL_TEST_TOOL_SHED_URL.' ) return 1 # ---- Configuration ------------------------------------------------------ - galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) + galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', install_and_test_base_util.default_galaxy_test_host ) # Set the GALAXY_INSTALL_TEST_HOST variable so that Twill will have the Galaxy url to which to # install repositories. os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host # Set the GALAXY_TEST_HOST environment variable so that the toolbox tests will have the Galaxy url # on which to to run tool functional tests. os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host - galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) ) + galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( install_and_test_base_util.default_galaxy_test_port_max ) ) os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: @@ -844,7 +354,7 @@ shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', - tool_data_table_conf ) + install_and_test_base_util.tool_data_table_conf ) galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) galaxy_job_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_JOB_CONF', @@ -896,18 +406,18 @@ pass print "Database connection: ", database_connection # Generate the shed_tool_data_table_conf.xml file. - file( shed_tool_data_table_conf_file, 'w' ).write( tool_data_table_conf_xml_template ) + file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file # ---- Start up a Galaxy instance ------------------------------------------------------ # Generate the tool_conf.xml file. - file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml ) + file( galaxy_tool_conf_file, 'w' ).write( install_and_test_base_util.tool_conf_xml ) # Generate the job_conf.xml file. - file( galaxy_job_conf_file, 'w' ).write( job_conf_xml ) + file( galaxy_job_conf_file, 'w' ).write( install_and_test_base_util.job_conf_xml ) # Generate the tool_sheds_conf.xml file, but only if a the user has not specified an existing one in the environment. if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: - file( galaxy_tool_sheds_conf_file, 'w' ).write( tool_sheds_conf_xml ) + file( galaxy_tool_sheds_conf_file, 'w' ).write( install_and_test_base_util.tool_sheds_conf_xml ) # Generate the shed_tool_conf.xml file. - tool_conf_template_parser = string.Template( shed_tool_conf_xml_template ) + tool_conf_template_parser = string.Template( install_and_test_base_util.shed_tool_conf_xml_template ) shed_tool_conf_xml = tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path ) file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file @@ -917,14 +427,14 @@ # Write the embedded web application's specific configuration to a temporary file. This is necessary in order for # the external metadata script to find the right datasets. kwargs = dict( admin_users = 'test(a)bx.psu.edu', - master_api_key = default_galaxy_master_api_key, + master_api_key = install_and_test_base_util.default_galaxy_master_api_key, allow_user_creation = True, allow_user_deletion = True, allow_library_path_paste = True, database_connection = database_connection, datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, - id_secret = galaxy_encode_secret, + id_secret = install_and_test_base_util.galaxy_encode_secret, job_config_file = galaxy_job_conf_file, job_queue_workers = 5, log_destination = "stdout", @@ -955,7 +465,7 @@ generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. - kwargs[ 'global_conf' ] = get_webapp_global_conf() + kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() kwargs[ 'global_conf' ][ '__file__' ] = galaxy_config_file # ---- Build Galaxy Application -------------------------------------------------- if not database_connection.startswith( 'sqlite://' ): @@ -972,11 +482,11 @@ log.debug( "Embedded Galaxy application started..." ) # ---- Run galaxy webserver ------------------------------------------------------ server = None - global_conf = get_webapp_global_conf() + global_conf = install_and_test_base_util.get_webapp_global_conf() global_conf[ 'database_file' ] = database_connection webapp = buildapp.app_factory( global_conf, use_translogger=False, - static_enabled=STATIC_ENABLED, + static_enabled=install_and_test_base_util.STATIC_ENABLED, app=app ) # Serve the app on a specified or random port. if galaxy_test_port is not None: @@ -985,7 +495,8 @@ random.seed() for i in range( 0, 9 ): try: - galaxy_test_port = str( random.randint( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) + galaxy_test_port = str( random.randint( install_and_test_base_util.default_galaxy_test_port_min, + install_and_test_base_util.default_galaxy_test_port_max ) ) log.debug( "Attempting to serve app on randomly chosen port: %s", galaxy_test_port ) server = httpserver.serve( webapp, host=galaxy_test_host, port=galaxy_test_port, start_loop=False ) break @@ -995,7 +506,7 @@ raise else: raise Exception( "Unable to open a port between %s and %s to start Galaxy server" % \ - ( default_galaxy_test_port_min, default_galaxy_test_port_max ) ) + ( install_and_test_base_util.default_galaxy_test_port_min, install_and_test_base_util.default_galaxy_test_port_max ) ) os.environ[ 'GALAXY_INSTALL_TEST_PORT' ] = galaxy_test_port # Start the server. t = threading.Thread( target=server.serve_forever ) @@ -1012,12 +523,11 @@ raise Exception( "Test HTTP server did not return '200 OK' after 10 tries" ) log.debug( "Embedded galaxy web server started..." ) log.debug( "The embedded Galaxy application is running on %s:%s" % ( str( galaxy_test_host ), str( galaxy_test_port ) ) ) - log.debug( "Repositories will be installed from the tool shed at %s" % str( galaxy_tool_shed_url ) ) - success = False + log.debug( "Repositories will be installed from the tool shed at %s" % str( install_and_test_base_util.galaxy_tool_shed_url ) ) # If a tool_data_table_conf.test.xml file was found, add the entries from it into the app's tool data tables. - if additional_tool_data_tables: - app.tool_data_tables.add_new_entries_from_config_file( config_filename=additional_tool_data_tables, - tool_data_path=additional_tool_data_path, + if install_and_test_base_util.additional_tool_data_tables: + app.tool_data_tables.add_new_entries_from_config_file( config_filename=install_and_test_base_util.additional_tool_data_tables, + tool_data_path=install_and_test_base_util.additional_tool_data_path, shed_tool_data_table_config=None, persist=False ) now = time.strftime( "%Y-%m-%d %H:%M:%S" ) @@ -1042,21 +552,15 @@ if all_tests_passed: print '# ----------------------------------------------------------------------------------' print "# %d repositories successfully passed all functional tests:" % len( all_tests_passed ) - show_summary_output( all_tests_passed ) + install_and_test_base_util.show_summary_output( all_tests_passed ) if at_least_one_test_failed: print '# ----------------------------------------------------------------------------------' print "# %d repositories failed at least 1 functional test:" % len( at_least_one_test_failed ) - show_summary_output( at_least_one_test_failed ) + install_and_test_base_util.show_summary_output( at_least_one_test_failed ) if repositories_failed_install: - # Set success to False so that the return code will not be 0. - success = False print '# ----------------------------------------------------------------------------------' print "# %d repositories have installation errors:" % len( repositories_failed_install ) - show_summary_output( repositories_failed_install ) - else: - success = True - else: - success = True + install_and_test_base_util.show_summary_output( repositories_failed_install ) print "####################################################################################" log.debug( "Shutting down..." ) # Gracefully shut down the embedded web server and UniverseApplication. @@ -1081,78 +585,8 @@ pass else: log.debug( 'GALAXY_INSTALL_TEST_NO_CLEANUP set, not cleaning up.' ) - # Normally the value of 'success' would determine whether this test suite is marked as passed or failed - # in the automated buildbot framework. However, due to the procedure used here we only want to report - # failure if a repository fails to install correctly, so we have overriden the value of 'success' here - # based on what actions the script has executed. - if success: - return 0 - else: - return 1 - -def parse_exclude_list( xml_filename ): - """Return a list of repositories to exclude from testing.""" - # This method should return a list with the following structure: - # [{ 'reason': The default reason or the reason specified in this section, - # 'repositories': [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )]}] - exclude_list = [] - exclude_verbose = [] - xml_tree, error_message = parse_xml( xml_filename ) - if error_message: - log.debug( 'The xml document %s defining the exclude list is invalid, so no repositories will be excluded from testing: %s' % \ - ( str( xml_filename ), str( error_message ) ) ) - return exclude_list - tool_sheds = xml_tree.findall( 'repositories' ) - xml_element = [] - exclude_count = 0 - for tool_shed in tool_sheds: - if galaxy_tool_shed_url != tool_shed.attrib[ 'tool_shed' ]: - continue - else: - xml_element = tool_shed - for reason_section in xml_element: - reason_text = reason_section.find( 'text' ).text - repositories = reason_section.findall( 'repository' ) - exclude_dict = dict( reason=reason_text, repositories=[] ) - for repository in repositories: - repository_tuple = get_repository_tuple_from_elem( repository ) - if repository_tuple not in exclude_dict[ 'repositories' ]: - exclude_verbose.append( repository_tuple ) - exclude_count += 1 - exclude_dict[ 'repositories' ].append( repository_tuple ) - exclude_list.append( exclude_dict ) - log.debug( 'The xml document %s containing the exclude list defines the following %s repositories to be excluded from testing...' % \ - ( str( xml_filename ), str( exclude_count ) ) ) - #if '-list_repositories' in sys.argv: - for name, owner, changeset_revision in exclude_verbose: - if changeset_revision: - log.debug( 'Repository %s owned by %s, changeset revision %s.' % ( str( name ), str( owner ), str( changeset_revision ) ) ) - else: - log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) - return exclude_list - -def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ): - """ - Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method - updates tool_test_results with the relevant data, sets the do_not_test and tools_functionally correct flags - to the appropriate values and updates the time_last_tested field to the value of the received time_tested. - """ - if can_update_tool_shed: - metadata_revision_id = repository_dict.get( 'id', None ) - if metadata_revision_id is not None: - tool_test_results_dicts.insert( 0, tool_test_results_dict ) - params[ 'tool_test_results' ] = tool_test_results_dicts - # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. - params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' - url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) - try: - return update( tool_shed_api_key, url, params, return_formatted=False ) - except Exception, e: - log.exception( 'Error attempting to register test results: %s' % str( e ) ) - return {} - else: - return {} + # Return a "successful" response to buildbot. + return 0 def remove_generated_tests( app ): """ @@ -1195,42 +629,6 @@ # Now delete the tests found in the previous loop. del test_install_repositories.__dict__[ key ] -def run_tests( test_config ): - loader = nose.loader.TestLoader( config=test_config ) - test_config.plugins.addPlugin( ReportResults() ) - plug_loader = test_config.plugins.prepareTestLoader( loader ) - if plug_loader is not None: - loader = plug_loader - tests = loader.loadTestsFromNames( test_config.testNames ) - test_runner = nose.core.TextTestRunner( stream=test_config.stream, - verbosity=test_config.verbosity, - config=test_config ) - plug_runner = test_config.plugins.prepareTestRunner( test_runner ) - if plug_runner is not None: - test_runner = plug_runner - result = test_runner.run( tests ) - return result, test_config.plugins._plugins - -def show_summary_output( repository_dicts ): - # Group summary display by repository owner. - repository_dicts_by_owner = {} - for repository_dict in repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - if owner in repository_dicts_by_owner: - repository_dicts_by_owner[ owner ].append( repository_dict ) - else: - repository_dicts_by_owner[ owner ] = [ repository_dict ] - # Display grouped summary. - for owner, grouped_repository_dicts in repository_dicts_by_owner.items(): - print "# " - for repository_dict in grouped_repository_dicts: - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - print "# Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) - def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, results_dict ): """Test tools contained in the received repository.""" name = str( repository.name ) @@ -1241,12 +639,12 @@ test_toolbox.toolbox = app.toolbox # Generate the test methods for this installed repository. We need to pass in True here, or it will look # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. - test_toolbox.build_tests( testing_shed_tools=True, master_api_key=default_galaxy_master_api_key ) + test_toolbox.build_tests( testing_shed_tools=True, master_api_key=install_and_test_base_util.default_galaxy_master_api_key ) # Set up nose to run the generated functional tests. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) # Run the configured tests. - result, test_plugins = run_tests( test_config ) + result, test_plugins = install_and_test_base_util.run_tests( test_config ) if result.wasSuccessful(): # This repository's tools passed all functional tests. Use the ReportResults nose plugin to get a list # of tests that passed. @@ -1271,11 +669,12 @@ # controller with the status of the test. This also sets the do_not_test and tools_functionally # correct flags and updates the time_last_tested field to today's date. # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed and passed functional tests.' % \ ( changeset_revision, name, owner ) ) else: @@ -1284,127 +683,30 @@ tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts failed_repository_dict = repository_identifier_dict results_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) - set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_dict ) + set_do_not_test = not is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) # TODO: do something useful with response_dict - response_dict = register_test_result( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dict, - params ) + response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params, + can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ ( changeset_revision, name, owner ) ) # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the # repository using Twill. - deactivate = asbool( os.environ.get( 'GALAXY_INSTALL_TEST_KEEP_TOOL_DEPENDENCIES', False ) ) - if deactivate: - log.debug( 'Deactivating changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) - # We are deactivating this repository and all of its repository dependencies. - deactivate_repository( app, repository_dict ) - else: - log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) - # We are uninstalling this repository and all of its repository dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) + log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) + # We are uninstalling this repository and all of its repository dependencies. + install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) + # Clean out any generated tests. This is necessary for Twill. + remove_generated_tests( app ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox return results_dict -def uninstall_repository_and_repository_dependencies( app, repository_dict ): - """Uninstall a repository and all of its repository dependencies.""" - # This method assumes that the repositor defined by the received repository_dict is not a repository - # dependency of another repository. - sa_session = app.install_model.context - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - # The dict contains the only repository the app should have installed at this point. - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - # Since this install and test framework uninstalls repositories immediately after installing and testing - # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be - # the same. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - if repository.can_uninstall( app ): - # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order - # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see - # if it can be uninstalled. - uninstall_repository_dict = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and all of its repository dependencies, deleting each of them from disk. - result, _ = run_tests( test_config ) - repository_uninstall_successful = result.wasSuccessful() - except Exception, e: - repository_uninstall_successful = False - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - if repository_uninstall_successful: - # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. - # We have to do this through Twill in order to maintain app.toolbox and shed_tool_conf.xml in a state that - # is valid for future tests. Since some of the repository's repository dependencies may require other of - # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. - processed_repository_dependency_ids = [] - while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): - for repository_dependency in repository.repository_dependencies: - if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): - processed_repository_dependency_ids.append( repository_dependency.id ) - rd_name = str( repository_dependency.name ) - rd_owner = str( repository_dependency.owner ) - rd_changeset_revision = str( repository_dependency.changeset_revision ) - uninstall_repository_dict = dict( name=rd_name, - owner=rd_owner, - changeset_revision=rd_changeset_revision ) - log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's - # web interface. - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. - result, _ = run_tests( test_config ) - if not result.wasSuccessful(): - # We won't set ok here because we'll continue to uninstall whatever we can. - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - except Exception, e: - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - else: - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - else: - log_reason_repository_cannot_be_uninstalled( app, repository ) - -def uninstall_tool_dependency( app, tool_dependency ): - """Attempt to uninstall a tool dependency.""" - sa_session = app.install_model.context - # Clean out any generated tests. This is necessary for Twill. - tool_dependency_install_path = tool_dependency.installation_directory( app ) - uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) - if error_message: - log.debug( 'There was an error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) - log.debug( error_message ) - else: - log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) - if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: - tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() - if os.path.exists( tool_dependency_install_path ): - log.debug( 'Uninstallation of tool dependency succeeded, but the installation path still exists on the filesystem. It is now being explicitly deleted.') - suc.remove_dir( tool_dependency_install_path ) - if __name__ == "__main__": # The tool_test_results_dict should always have the following structure: # { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: In upload tool sort FTP files by default.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ce186eb5fefc/ Changeset: ce186eb5fefc User: jmchilton Date: 2013-12-18 15:19:58 Summary: In upload tool sort FTP files by default. Not doing enough... but it is a step forward. http://dev.list.galaxyproject.org/sort-list-of-ftp-uploaded-files-tp4662859… Affected #: 1 file diff -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 -r ce186eb5fefcb7ff332c73bd0869b9e222293d0b lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py +++ b/lib/galaxy/web/form_builder.py @@ -3,6 +3,8 @@ """ import logging, sys, os, time + +from operator import itemgetter from cgi import escape from galaxy.util import restore_text, relpath, nice_size, unicodify from galaxy.web import url_for @@ -212,6 +214,7 @@ ctime=time.strftime( "%m/%d/%Y %I:%M:%S %p", time.localtime( statinfo.st_ctime ) ) ) ) if not uploads: rval += '<tr><td colspan="4"><em>Your FTP upload directory contains no files.</em></td></tr>' + uploads = sorted(uploads, key=itemgetter("path")) for upload in uploads: rval += FTPFileField.trow % ( prefix, self.name, upload['path'], upload['path'], upload['size'], upload['ctime'] ) rval += FTPFileField.tfoot Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Backout of 714f5b1 for now.
by commits-noreply＠bitbucket.org 18 Dec '13

18 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c5c4deabb731/ Changeset: c5c4deabb731 User: jmchilton Date: 2013-12-18 08:23:27 Summary: Backout of 714f5b1 for now. jgoecks_: jmchilto1: 714f5b1 seems to have broken HDA ordering in history panel Affected #: 3 files diff -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -19,7 +19,6 @@ import socket import time from string import Template -from itertools import ifilter import galaxy.datatypes import galaxy.datatypes.registry @@ -44,11 +43,6 @@ # Default Value Required for unit tests datatypes_registry.load_datatypes() -# When constructing filters with in for a fixed set of ids, maximum -# number of items to place in the IN statement. Different databases -# are going to have different limits so it is likely best to not let -# this be unlimited - filter in Python if over this limit. -MAX_IN_FILTER_LENGTH = 100 class NoConverterException(Exception): def __init__(self, value): @@ -899,32 +893,6 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval - def contents_iter( self, **kwds ): - """ - Fetch filtered list of contents of history. - """ - python_filter = None - db_session = object_session( self ) - assert db_session != None - query = db_session.query( HistoryDatasetAssociation ).filter( HistoryDatasetAssociation.table.c.history_id == self.id ) - deleted = galaxy.util.string_as_bool_or_none( kwds.get( 'deleted', None ) ) - if deleted is not None: - query = query.filter( HistoryDatasetAssociation.deleted == bool( kwds['deleted'] ) ) - visible = galaxy.util.string_as_bool_or_none( kwds.get( 'visible', None ) ) - if visible is not None: - query = query.filter( HistoryDatasetAssociation.visible == bool( kwds['visible'] ) ) - if 'ids' in kwds: - ids = kwds['ids'] - max_in_filter_length = kwds.get('max_in_filter_length', MAX_IN_FILTER_LENGTH) - if len(ids) < max_in_filter_length: - query = query.filter( HistoryDatasetAssociation.id.in_(ids) ) - else: - python_filter = lambda hda: hda.id in ids - if python_filter: - return ifilter(python_filter, query) - else: - return query - def copy_tags_from(self,target_user,source_history): for src_shta in source_history.tags: new_shta = src_shta.copy() diff -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -51,28 +51,47 @@ else: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=True ) - contents_kwds = {} + # if ids, return _FULL_ data (as show) for each id passed if ids: - ids = map( lambda id: trans.security.decode_id( id ), ids.split( ',' ) ) - contents_kwds[ 'ids' ] = ids - # If explicit ids given, always used detailed result. - details = 'all' + ids = ids.split( ',' ) + for index, hda in enumerate( history.datasets ): + encoded_hda_id = trans.security.encode_id( hda.id ) + if encoded_hda_id in ids: + #TODO: share code with show + rval.append( self._detailed_hda_dict( trans, hda ) ) + + # if no ids passed, return a _SUMMARY_ of _all_ datasets in the history else: - contents_kwds[ 'deleted' ] = kwd.get( 'deleted', None ) - contents_kwds[ 'visible' ] = kwd.get( 'visible', None ) # details param allows a mixed set of summary and detailed hdas #TODO: this is getting convoluted due to backwards compat details = kwd.get( 'details', None ) or [] if details and details != 'all': details = util.listify( details ) - for hda in history.contents_iter( **contents_kwds ): - encoded_hda_id = trans.security.encode_id( hda.id ) - detailed = details == 'all' or ( encoded_hda_id in details ) - if detailed: - rval.append( self._detailed_hda_dict( trans, hda ) ) - else: - rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + # by default return all datasets - even if deleted or hidden (defaulting the next switches to None) + # if specified return those datasets that match the setting + # backwards compat + return_deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) + return_visible = util.string_as_bool_or_none( kwd.get( 'visible', None ) ) + + for hda in history.datasets: + # if either return_ setting has been requested (!= None), skip hdas that don't match the request + if return_deleted is not None: + if( ( return_deleted and not hda.deleted ) + or ( not return_deleted and hda.deleted ) ): + continue + if return_visible is not None: + if( ( return_visible and not hda.visible ) + or ( not return_visible and hda.visible ) ): + continue + + encoded_hda_id = trans.security.encode_id( hda.id ) + if( ( encoded_hda_id in details ) + or ( details == 'all' ) ): + rval.append( self._detailed_hda_dict( trans, hda ) ) + else: + rval.append( self._summary_hda_dict( trans, history_id, hda ) ) + except Exception, e: # for errors that are not specific to one hda (history lookup or summary list) rval = "Error in history API at listing contents: " + str( e ) diff -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 -r c5c4deabb7316f2ef45ff8fb2718d167d91d09c0 test/unit/test_galaxy_mapping.py --- a/test/unit/test_galaxy_mapping.py +++ b/test/unit/test_galaxy_mapping.py @@ -180,39 +180,6 @@ assert hist1.name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. - def test_history_contents( self ): - model = self.model - u = model.User( email="contents(a)foo.bar.baz", password="password" ) - # gs = model.GalaxySession() - h1 = model.History( name="HistoryContentsHistory1", user=u) - - self.persist( u, h1, expunge=True ) - - d1 = self.new_hda( h1, name="1" ) - d2 = self.new_hda( h1, name="2", visible=False ) - d3 = self.new_hda( h1, name="3", deleted=True ) - d4 = self.new_hda( h1, name="4", visible=False, deleted=True ) - - def contents_iter_names(**kwds): - history = model.context.query( model.History ).filter( - model.History.name == "HistoryContentsHistory1" - ).first() - return set( map( lambda hda: hda.name, history.contents_iter( **kwds ) ) ) - - assert contents_iter_names() == set( [ "1", "2", "3", "4" ] ) - assert contents_iter_names( deleted=False ) == set( [ "1", "2" ] ) - assert contents_iter_names( visible=True ) == set( [ "1", "3" ] ) - assert contents_iter_names( visible=False ) == set( [ "2", "4" ] ) - assert contents_iter_names( deleted=True, visible=False ) == set( [ "4" ] ) - - assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ] ) == set( [ "1", "2", "3", "4" ] ) - assert contents_iter_names( ids=[ d1.id, d2.id, d3.id, d4.id ], max_in_filter_length=1 ) == set( [ "1", "2", "3", "4" ] ) - - assert contents_iter_names( ids=[ d1.id, d3.id ] ) == set( [ "1", "3" ] ) - - def new_hda( self, history, **kwds ): - return self.persist( self.model.HistoryDatasetAssociation( history=history, create_dataset=True, sa_session=self.model.session, **kwds ), flush=True ) - @classmethod def setUpClass(cls): # Start the database and connect the mapping @@ -224,16 +191,10 @@ return cls.model.session.query( type ) @classmethod - def persist(cls, *args, **kwargs): - session = cls.model.session - flush = kwargs.get('flush', True) + def persist(cls, *args): for arg in args: - session.add( arg ) - if flush: - session.flush() - if kwargs.get('expunge', not flush): - cls.expunge() - return arg # Return last or only arg. + cls.model.session.add( arg ) + cls.expunge() @classmethod def expunge(cls): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fixes for test scripts 1010, 1080, 1400, and 1460.
by commits-noreply＠bitbucket.org 17 Dec '13

17 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41c6ee05c8ac/ Changeset: 41c6ee05c8ac User: inithello Date: 2013-12-17 21:54:55 Summary: Fixes for test scripts 1010, 1080, 1400, and 1460. Affected #: 5 files diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1338,7 +1338,7 @@ def verify_installed_repository_data_table_entries( self, required_data_table_entries ): # The value of the received required_data_table_entries will be something like: [ 'sam_fa_indexes' ] - data_tables = xml_util.parse_xml( self.shed_tool_data_table_conf ) + data_tables, error_message = xml_util.parse_xml( self.shed_tool_data_table_conf ) found = False # With the tool shed, the "path" attribute that is hard-coded into the tool_data_tble_conf.xml # file is ignored. This is because the tool shed requires the directory location to which this diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -285,6 +285,7 @@ 'Uninstalled' ] self.display_installed_repository_manage_page( installed_convert_repository, strings_displayed=strings_displayed ) + self.test_db_util.install_session.refresh( installed_column_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, 'column_maker' ) def test_0065_reinstall_column_repository( self ): @@ -330,6 +331,7 @@ 'Deactivated' ] self.display_installed_repository_manage_page( installed_column_repository, strings_displayed=strings_displayed ) + self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_chars' ) def test_0075_uninstall_column_repository( self ): @@ -387,8 +389,8 @@ common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=False ) self.uninstall_repository( installed_convert_repository, remove_from_disk=False ) - self.test_db_util.ga_refresh( installed_column_repository ) - self.test_db_util.ga_refresh( installed_convert_repository ) + self.test_db_util.install_session.refresh( installed_column_repository ) + self.test_db_util.install_session.refresh( installed_convert_repository ) self.check_galaxy_repository_tool_panel_section( installed_column_repository, '' ) self.check_galaxy_repository_tool_panel_section( installed_convert_repository, 'convert_chars' ) diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1160_circular_prior_installation_required.py --- a/test/tool_shed/functional/test_1160_circular_prior_installation_required.py +++ b/test/tool_shed/functional/test_1160_circular_prior_installation_required.py @@ -247,7 +247,7 @@ convert_repository = self.test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) # Filtering was selected for reinstallation, so convert chars and column maker should have been installed first. for repo in [ convert_repository, column_repository, filter_repository ]: - self.test_db_util.ga_session.refresh( repo ) + self.test_db_util.install_session.refresh( repo ) assert filter_repository.update_time > convert_repository.update_time, 'Prior installed convert_chars_0160 shows a later update time than filtering_0160' assert filter_repository.update_time > column_repository.update_time, 'Prior installed column_maker_0160 shows a later update time than filtering_0160' diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional/test_1400_review_migration_stages.py --- a/test/tool_shed/functional/test_1400_review_migration_stages.py +++ b/test/tool_shed/functional/test_1400_review_migration_stages.py @@ -34,8 +34,8 @@ migrated_tool_dependencies = [ 'emboss', '5.0.0', 'freebayes', '0.9.4_9696d0ce8a962f7bb61c4791be5ce44312b81cf8', 'samtools', '0.1.18', 'blast+', '2.2.26+', 'bwa', '0.5.9', 'picard', '1.56.0', 'lastz', '1.02.00', 'bowtie', '0.12.7', 'FreeBayes requires g++', 'ncurses', 'zlib', - 'zlib and libpthread', 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', - 'samtools', '0.1.16', 'cufflinks', '2.1.1', 'R', '2.11.0' ] + 'blast.ncbi.nlm.nih.gov', 'fastx_toolkit', '0.0.13', 'samtools', '0.1.16', 'cufflinks', + '2.1.1', 'R', '2.11.0' ] migration_scripts = [ '0002_tools.sh', '0003_tools.sh', '0004_tools.sh', '0005_tools.sh', '0006_tools.sh', '0007_tools.sh', '0008_tools.sh' ] stages.extend( migration_scripts + migrated_tool_dependencies + migrated_repository_names ) diff -r 43b23f5503997727debf8232239434974491e55e -r 41c6ee05c8acf2e98c69687bc894f1c596c930b0 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -391,7 +391,7 @@ use_heartbeat = False ) # ---- Build Galaxy Application -------------------------------------------------- - if not galaxy_database_connection.startswith( 'sqlite://' ): + if not galaxy_database_connection.startswith( 'sqlite://' ) and not install_galaxy_database_connection.startswith( 'sqlite://' ): kwargs[ 'database_engine_option_pool_size' ] = '10' kwargs[ 'database_engine_option_max_overflow' ] = '20' galaxyapp = GalaxyUniverseApplication( **kwargs ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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