galaxy-commits December 2013

galaxy-commits@lists.galaxyproject.org

1 participants
207 discussions

commit/galaxy-central: greg: Fix imports in the tool shed install and test framework.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0f70f0b46167/ Changeset: 0f70f0b46167 User: greg Date: 2013-12-22 01:07:38 Summary: Fix imports in the tool shed install and test framework. Affected #: 3 files diff -r 85098aa5c52a2cc66ac590357a52af73545c093e -r 0f70f0b461678cd8224861857055f3eaf7646b05 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 @@ -14,7 +14,6 @@ import ConfigParser import galaxy.webapps.tool_shed.config as tool_shed_config -import galaxy.webapps.tool_shed.model.mapping import tool_shed.util.shed_util_common as suc import logging import shutil diff -r 85098aa5c52a2cc66ac590357a52af73545c093e -r 0f70f0b461678cd8224861857055f3eaf7646b05 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 @@ -23,7 +23,6 @@ from mercurial import __version__ import galaxy.webapps.tool_shed.config as tool_shed_config -import galaxy.webapps.tool_shed.model.mapping 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 diff -r 85098aa5c52a2cc66ac590357a52af73545c093e -r 0f70f0b461678cd8224861857055f3eaf7646b05 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 @@ -30,6 +30,8 @@ from galaxy.util import listify from galaxy.util import unicodify from galaxy.util.json import from_json_string +import galaxy.webapps.tool_shed.model.mapping + from nose.plugins import Plugin from tool_shed.util import tool_dependency_util 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 displaying successful installations in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/85098aa5c52a/ Changeset: 85098aa5c52a User: greg Date: 2013-12-22 01:00:57 Summary: Fix for displaying successful installations in the tool shed's install and test framework. Affected #: 1 file diff -r 427b0b131c3c74c12b115d36406b19d7fab1874a -r 85098aa5c52a2cc66ac590357a52af73545c093e lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1402,11 +1402,11 @@ 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 ) + RepositorySuccessfulInstallation( 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'}] 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 attempt to install a repository if it was installed in a previous test within the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 22 Dec '13

22 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/427b0b131c3c/ Changeset: 427b0b131c3c User: greg Date: 2013-12-22 00:54:51 Summary: Don't attempt to install a repository if it was installed in a previous test within the tool shed's install and test framework. Affected #: 3 files diff -r 024ff5391a92b637cb71345ec078c0baf7f8b0a9 -r 427b0b131c3c74c12b115d36406b19d7fab1874a 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 @@ -24,8 +24,6 @@ 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 @@ -387,6 +385,16 @@ log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) return repository_dicts, error_message +def get_repository( name, owner, changeset_revision ): + """Return a repository record associated with the received name, owner, changeset_revision if one exists.""" + repository = None + try: + repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + except: + # The repository may not have been installed in a previous test. + pass + return repository + def get_repository_current_revision( repo_path ): """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. @@ -608,9 +616,9 @@ # 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: + # Get the repository record now that the tests that install it have completed. + repository = get_repository( name, owner, changeset_revision ) + if repository is None: 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 diff -r 024ff5391a92b637cb71345ec078c0baf7f8b0a9 -r 427b0b131c3c74c12b115d36406b19d7fab1874a 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 @@ -196,85 +196,93 @@ 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 ) - 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 - params = dict( test_install_error=True ) - # 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, + # See if the repository was installed in a previous test. + repository = get_repository( name, owner, changeset_revision ) + if repository is None: + # The repository was not previously installed, so install it now. + 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 + params = dict( test_install_error=True ) + # 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 ) + else: + # The repository was successfully installed. + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + params, install_and_test_statistics_dict, tool_test_results_dict = \ + install_and_test_base_util.register_installed_and_missing_dependencies( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_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 + # missing test components. + 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: + 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, + params=params, + can_update_tool_shed=can_update_tool_shed ) + else: + 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. + # and configure and run functional tests for this repository. This is equivalent to + # sh run_functional_tests.sh -installed + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + # Find the path to the test-data directory within the installed repository. + 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 temporary + # 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: + 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 ) + tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) + # Record the status of this repository in the tool shed. + params[ 'tools_functionally_correct' ] = 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 ) else: - # The repository was successfully installed. - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + log.debug( 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) ) - params, install_and_test_statistics_dict, tool_test_results_dict = \ - install_and_test_base_util.register_installed_and_missing_dependencies( app, - repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_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 - # missing test components. - 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: - 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, - params=params, - can_update_tool_shed=can_update_tool_shed ) - else: - 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. - # and configure and run functional tests for this repository. This is equivalent to - # sh run_functional_tests.sh -installed - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - # Find the path to the test-data directory within the installed repository. - 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 temporary - # 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: - 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 ) - tool_test_results_dict[ 'failed_tests' ].append( exception_message ) - install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) - # Record the status of this repository in the tool shed. - params[ 'tools_functionally_correct' ] = 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( 'it was previously installed and currently has status %s' % str( repository.status ) ) return install_and_test_statistics_dict, error_message def main(): diff -r 024ff5391a92b637cb71345ec078c0baf7f8b0a9 -r 427b0b131c3c74c12b115d36406b19d7fab1874a 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 @@ -134,39 +134,47 @@ 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 ) - 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 - params = dict( test_install_error=True ) - # 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 ) + # See if the repository was installed in a previous test. + repository = get_repository( name, owner, changeset_revision ) + if repository is None: + # The repository was not previously installed, so install it now. + 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 + params = dict( test_install_error=True ) + # 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 ) + else: + # The repository was successfully installed. + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + params, install_and_test_statistics_dict, tool_test_results_dict = \ + install_and_test_base_util.register_installed_and_missing_dependencies( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_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 ) else: - # The repository was successfully installed. - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + log.debug( 'Skipped attempt to install revision %s of repository %s owned by %s because ' % \ ( changeset_revision, name, owner ) ) - params, install_and_test_statistics_dict, tool_test_results_dict = \ - install_and_test_base_util.register_installed_and_missing_dependencies( app, - repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_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 ) + log.debug( 'it was previously installed and currently has status %s' % str( repository.status ) ) return install_and_test_statistics_dict, error_message def main(): 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: Improved logging for handling repositories excluded from the tool shed's install and test runs.
by commits-noreply＠bitbucket.org 21 Dec '13

21 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/024ff5391a92/ Changeset: 024ff5391a92 User: greg Date: 2013-12-21 18:59:00 Summary: Improved logging for handling repositories excluded from the tool shed's install and test runs. Affected #: 1 file diff -r 8c7c4af96ecc11f44ca71b997774b621ad5295eb -r 024ff5391a92b637cb71345ec078c0baf7f8b0a9 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 @@ -627,11 +627,12 @@ # [( name, owner, changeset_revision if changeset_revision else None ), # ( name, owner, changeset_revision if changeset_revision else None )] if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + log.debug( 'Revision %s of repository %s owned by %s is excluded from testing because:\n%s' % \ + ( str( changeset_revision ), str( name ), str( owner ), str( reason ) ) ) return True, reason # Skip this repository if it has a repository dependency that is in the exclude list. repository_dependency_dicts, error_message = \ - get_repository_dependencies_for_changeset_revision( galaxy_tool_shed_url, - encoded_repository_metadata_id ) + get_repository_dependencies_for_changeset_revision( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ ( changeset_revision, name, owner ) ) @@ -643,13 +644,17 @@ rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ ( rd_name, rd_owner, None ) in exclude_repositories: + log_msg = 'Revision %s of repository %s owned by %s is excluded from testing because ' % \ + ( str( changeset_revision ), str( name ), str( owner ), str( reason ) ) + log_msg += 'it requires revision %s of repository %s owned by %s (which is excluded from testing).' % \ + ( rd_changeset_revision, rd_name, rd_owner ) + log.debug( log_msg ) reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ ( rd_changeset_revision, rd_name, rd_owner ) return True, reason break return False, None - def is_latest_downloadable_revision( url, repository_dict ): name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) @@ -686,10 +691,10 @@ # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), # ( name, owner, changeset_revision if changeset_revision else None )]}] exclude_list = [] - exclude_verbose = [] + exclude_tups = [] 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' % \ + log.debug( 'The exclude file %s 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' ) @@ -701,23 +706,30 @@ else: xml_element = tool_shed for reason_section in xml_element: - reason_text = reason_section.find( 'text' ).text + reason_text = reason_section.find( 'text' ) + if reason_text: + reason = str( reason_text.text ) + else: + reason = 'No reason provided.' repositories = reason_section.findall( 'repository' ) - exclude_dict = dict( reason=reason_text, repositories=[] ) + exclude_dict = dict( reason=reason, 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_tups.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 ) ) ) - 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 ) ) ) + if exclude_tups: + log.debug( 'The exclude file %s defines the following %d repositories to be excluded from testing:' % \ + ( str( xml_filename ), exclude_count ) ) + for name, owner, changeset_revision in exclude_tups: + if changeset_revision: + log.debug( 'Revision %s of repository %s owned by %s.' % ( str( changeset_revision ), str( name ), str( owner ) ) ) + else: + log.debug( 'All revisions of repository %s owned by %s.' % ( str( name ), str( owner ) ) ) + else: + log.debug( 'The exclude file %s defines no repositories to be excluded from testing.' % str( xml_filename ) ) return exclude_list def register_installed_and_missing_dependencies( app, repository, repository_identifier_dict, install_and_test_statistics_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: Refactor and fix prep scripts for the tool shed's install and test frameowrk.
by commits-noreply＠bitbucket.org 21 Dec '13

21 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8c7c4af96ecc/ Changeset: 8c7c4af96ecc User: greg Date: 2013-12-21 14:07:11 Summary: Refactor and fix prep scripts for the tool shed's install and test frameowrk. Affected #: 3 files diff -r b83064c6c323217a6072e869afafec19ce965b0f -r 8c7c4af96ecc11f44ca71b997774b621ad5295eb 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 @@ -23,6 +23,7 @@ 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 install_and_test_tool_shed_repositories.base.util import RepositoryMetadataApplication from galaxy.model.orm import and_ from galaxy.model.orm import not_ from galaxy.model.orm import select @@ -36,32 +37,6 @@ log = logging.getLogger( 'check_repositories_for_functional_tests' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) - -class RepositoryMetadataApplication( object ): - """Application that enables updating repository_metadata table records in the Tool Shed.""" - - def __init__( self, config ): - self.config = config - if self.config.database_connection is False: - self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str( config.database ) - log.debug( 'Using database connection: %s' % str( self.config.database_connection ) ) - # Setup the database engine and ORM - self.model = galaxy.webapps.tool_shed.model.mapping.init( self.config.file_path, - self.config.database_connection, - engine_options={}, - create_tables=False ) - self.hgweb_config_manager = self.model.hgweb_config_manager - self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir - log.debug( 'Using hgweb.config file: %s' % str( self.hgweb_config_manager.hgweb_config ) ) - - @property - def sa_session( self ): - """Returns a SQLAlchemy session.""" - return self.model.context.current - - def shutdown( self ): - pass - def check_and_update_repository_metadata( app, info_only=False, verbosity=1 ): """ This method will iterate through all records in the repository_metadata table, checking each one for tool metadata, diff -r b83064c6c323217a6072e869afafec19ce965b0f -r 8c7c4af96ecc11f44ca71b997774b621ad5295eb 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 @@ -27,6 +27,7 @@ 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 install_and_test_tool_shed_repositories.base.util import RepositoryMetadataApplication from galaxy.model.orm import and_ from galaxy.model.orm import not_ from galaxy.model.orm import select @@ -40,30 +41,6 @@ assert sys.version_info[ :2 ] >= ( 2, 6 ) -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 - # Setup the database engine and ORM - self.model = galaxy.webapps.tool_shed.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False ) - self.hgweb_config_manager = self.model.hgweb_config_manager - self.hgweb_config_manager.hgweb_config_dir = config.hgweb_config_dir - print "# Using configured hgweb.config file: ", self.hgweb_config_manager.hgweb_config - - @property - def sa_session( self ): - """ - Returns a SQLAlchemy session -- currently just gets the current - session from the threadlocal session context, but this is provided - to allow migration toward a more SQLAlchemy 0.4 style of use. - """ - return self.model.context.current - - def shutdown( self ): - pass - def main(): '''Script that validates all repositories of type tool_dependency_definition.''' parser = OptionParser() @@ -93,8 +70,7 @@ 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 ) - + app = RepositoryMetadataApplication( config ) if options.info_only: print "# Displaying info only ( --info_only )" if options.verbosity: diff -r b83064c6c323217a6072e869afafec19ce965b0f -r 8c7c4af96ecc11f44ca71b997774b621ad5295eb 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 @@ -181,6 +181,32 @@ return passed_tests return [] + +class RepositoryMetadataApplication( object ): + """Application that enables updating repository_metadata table records in the Tool Shed.""" + + def __init__( self, config ): + self.config = config + if self.config.database_connection is False: + self.config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str( config.database ) + log.debug( 'Using database connection: %s' % str( self.config.database_connection ) ) + # Setup the database engine and ORM + self.model = galaxy.webapps.tool_shed.model.mapping.init( self.config.file_path, + self.config.database_connection, + engine_options={}, + create_tables=False ) + self.hgweb_config_manager = self.model.hgweb_config_manager + self.hgweb_config_manager.hgweb_config_dir = self.config.hgweb_config_dir + log.debug( 'Using hgweb.config file: %s' % str( self.hgweb_config_manager.hgweb_config ) ) + + @property + def sa_session( self ): + """Returns a SQLAlchemy session.""" + return self.model.context.current + + def shutdown( self ): + pass + def display_repositories_by_owner( repository_dicts ): # Group summary display by repository owner. repository_dicts_by_owner = {} 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 testing tool dependency definitions with the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 21 Dec '13

21 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b83064c6c323/ Changeset: b83064c6c323 User: greg Date: 2013-12-21 13:49:59 Summary: Fix for testing tool dependency definitions with the tool shed's install and test framework. Affected #: 2 files diff -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 -r b83064c6c323217a6072e869afafec19ce965b0f 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 @@ -197,7 +197,6 @@ ( changeset_revision, name, owner ) ) else: tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) - # 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: diff -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 -r b83064c6c323217a6072e869afafec19ce965b0f 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 @@ -120,7 +120,7 @@ owner, changeset_revision, encoded_repository_metadata_id ) - if this_repository_is_in_the_exclude_list or requires_excluded: + if is_excluded: # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) @@ -142,8 +142,7 @@ 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 - params = dict( test_install_error=True, - do_not_test=False ) + params = dict( test_install_error=True ) # 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, @@ -153,6 +152,8 @@ can_update_tool_shed ) else: # The repository was successfully installed. + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) params, install_and_test_statistics_dict, tool_test_results_dict = \ install_and_test_base_util.register_installed_and_missing_dependencies( app, repository, 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: martenson: docs
by commits-noreply＠bitbucket.org 21 Dec '13

21 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/38b88dceb82e/ Changeset: 38b88dceb82e User: martenson Date: 2013-12-21 00:53:41 Summary: docs Affected #: 2 files diff -r 11c30107da4eba80c0e76613d1da223f2af8ffe8 -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -64,7 +64,6 @@ @web.expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): - # oh, sphinx - you bastard """ show( trans, id, deleted='False' ) * GET /api/histories/{id}: diff -r 11c30107da4eba80c0e76613d1da223f2af8ffe8 -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 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 @@ -30,15 +30,14 @@ """ show( self, trans, id, **kwd ) * GET /api/libraries/datasets/{encoded_dataset_id}: - Displays information about the dataset identified by the encoded id. + Displays information about the dataset identified by the encoded ID. - + :param id: the encoded id of the dataset to query :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()` + :returns: detailed dataset information from base controller + .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset` """ # Get dataset. try: @@ -66,18 +65,16 @@ """ download( self, trans, format, **kwd ) * GET /api/libraries/datasets/download/{format} + Downloads requested datasets (identified by encoded IDs) in requested format. - .. code-block:: - example: - GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828 + example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828`` + .. note:: supported format values are: 'zip', 'tgz', 'tbz', 'uncompressed' + + :param format: string representing requested archive format :type format: string - :param format: string representing requested archive format - - .. note:: supported formats are: zip, tgz, tbz, uncompressed - + :param lddas[]: an array of encoded ids :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 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: inithello: Fix for removing generated test definitions from the global scope after a repository has been tested.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11c30107da4e/ Changeset: 11c30107da4e User: inithello Date: 2013-12-20 18:55:49 Summary: Fix for removing generated test definitions from the global scope after a repository has been tested. Affected #: 1 file diff -r 68c080722bc7f6accf73325bdf049eb84125da27 -r 11c30107da4eba80c0e76613d1da223f2af8ffe8 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 @@ -254,8 +254,6 @@ 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 ) ) ) - # Remove twills' old generated test before building the new tests for the current tools. - remove_tests( app ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -570,6 +568,14 @@ """ tests_to_delete = [] tools_to_delete_by_id = [] + + # Push all the toolbox tests to module level + G = globals() + + # Eliminate all previous tests from G. + for key, val in G.items(): + if key.startswith( 'TestForTool_' ): + del G[ key ] global test_toolbox # Find all tests previously generated by twill. for key in test_toolbox.__dict__: @@ -590,17 +596,6 @@ if tool_id in app.toolbox.tools_by_id: log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) del app.toolbox.tools_by_id[ tool_id ] - # Push all the toolbox tests to module level - for key in test_install_repositories.__dict__: - if key.startswith( 'TestInstallRepository_' ): - log.debug( 'Repository installation process test %s discovered.' % str( key ) ) - # We can't delete this test just yet, we're still iterating over __dict__. - tests_to_delete.append( key ) - # Delete the discovered twill-generated tests. - for key in tests_to_delete: - if key in test_install_repositories.__dict__: - log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) - del test_install_repositories.__dict__[ key ] def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): @@ -674,6 +669,8 @@ 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 ) ) + # Remove twills' old generated test before building the new tests for the current tools. + remove_tests( app ) return install_and_test_statistics_dict if __name__ == "__main__": 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: 2 new changesets
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c62316e9a5b/ Changeset: 2c62316e9a5b User: inithello Date: 2013-12-20 18:22:01 Summary: Order repository revisions by ID, descending. Affected #: 1 file diff -r c125d7050c3b5a34305c377cd31b3a77be753d99 -r 2c62316e9a5bd985b264e7bf7d10eadc1b74cde8 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -155,7 +155,7 @@ try: query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ .filter( and_( *clause_list ) ) \ - .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ + .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id.desc() ) \ .all() for repository_metadata in query: repository_metadata_dict = repository_metadata.to_dict( view='collection', https://bitbucket.org/galaxy/galaxy-central/commits/68c080722bc7/ Changeset: 68c080722bc7 User: inithello Date: 2013-12-20 18:22:24 Summary: Fix for error message when resetting metadata on an installed repository. Affected #: 1 file diff -r 2c62316e9a5bd985b264e7bf7d10eadc1b74cde8 -r 68c080722bc7f6accf73325bdf049eb84125da27 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -247,12 +247,16 @@ bold_start = '' bold_end = '' message = '' + if trans.webapp.name == 'galaxy': + tip_rev = str( repository.changeset_revision ) + else: + tip_rev = str( repository.tip( trans.app ) ) if not displaying_invalid_tool: if metadata_dict: - message += "Metadata may have been defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) + message += "Metadata may have been defined for some items in revision '%s'. " % tip_rev message += "Correct the following problems if necessary and reset metadata.%s" % new_line else: - message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip( trans.app ) ) + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % tip_rev message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line for itc_tup in invalid_file_tups: tool_file, exception_msg = itc_tup 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: carlfeberhard: UI: remove BaseView from base-mvc; replace with View in assoc. files
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c125d7050c3b/ Changeset: c125d7050c3b User: carlfeberhard Date: 2013-12-20 18:18:50 Summary: UI: remove BaseView from base-mvc; replace with View in assoc. files Affected #: 6 files diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/mvc/annotations.js --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -1,6 +1,6 @@ /** A view on any model that has a 'annotation' attribute */ -var AnnotationEditor = BaseView.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ +var AnnotationEditor = Backbone.View.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ tagName : 'div', className : 'annotation-display', diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -1,23 +1,3 @@ -/** - * Base view that handles visibility based on model's hidden attribute. - */ -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(); - } - } -}); - - //============================================================================== /** @class Mixin to add logging capabilities to an object. * Designed to allow switching an objects log output off/on at one central diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/mvc/visualizations/scatterplotControlForm.js @@ -63,7 +63,7 @@ * * initialize attributes REQUIRES a dataset and an apiDatasetsURL */ -var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ +var ScatterplotControlForm = Backbone.View.extend( LoggableMixin ).extend({ //logger : console, className : 'scatterplot-control-form', diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/packed/mvc/annotations.js --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1,1 +1,1 @@ -var AnnotationEditor=BaseView.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(a){a=a||{};this.tooltipConfig=a.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(b){a.$annotation().text(b);a.model.save({annotation:b},{silent:true}).fail(function(){a.$annotation().text(a.model.previous("annotation"))})}});return this},_template:function(){var a=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',a,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}}); \ No newline at end of file +var AnnotationEditor=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(a){a=a||{};this.tooltipConfig=a.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(b){a.$annotation().text(b);a.model.save({annotation:b},{silent:true}).fail(function(){a.$annotation().text(a.model.previous("annotation"))})}});return this},_template:function(){var a=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',a,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}}); \ No newline at end of file diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 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 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.$elementShown,arguments)}}; \ No newline at end of file +var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$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 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/packed/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js @@ -1,1 +1,1 @@ -var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find("[title]").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file +var ScatterplotControlForm=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find("[title]").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ 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

Jump to page:

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

galaxy-commits December 2013