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commit/galaxy-central: greg: A bit of code cleanup.
by commits-noreply＠bitbucket.org 27 Nov '13

27 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32205f911e74/ Changeset: 32205f911e74 User: greg Date: 2013-11-27 21:53:29 Summary: A bit of code cleanup. Affected #: 1 file diff -r 8b613225f1def637af4774b860578a77a7fb0fe4 -r 32205f911e7442fb6eed7155f8306df7aafb731e lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1066,9 +1066,6 @@ else: containing_folder = tool_test_results_root_folder test_results_dict_id += 1 - #folder_id += 1 - #test_results_folder = Folder( id=folder_id, key='test_results', label='Automated test environment', parent=containing_folder ) - #containing_folder.folders.append( test_results_folder ) folder_id += 1 folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) containing_folder.folders.append( folder ) @@ -1204,7 +1201,6 @@ subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) installation_error_base_folder.folders.append( subfolder ) containing_folder.installation_errors.append( installation_error_base_folder ) - #containing_folder.folders.append( containing_folder ) if multiple_tool_test_results_dicts: tool_test_results_root_folder.folders.append( containing_folder ) else: 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: Dave Bouvier: Fix imports.
by commits-noreply＠bitbucket.org 27 Nov '13

27 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8b613225f1de/ Changeset: 8b613225f1de User: Dave Bouvier Date: 2013-11-27 21:37:02 Summary: Fix imports. Affected #: 1 file diff -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 -r 8b613225f1def637af4774b860578a77a7fb0fe4 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 @@ -15,6 +15,7 @@ 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 import tempfile @@ -31,8 +32,6 @@ from mercurial import __version__ from optparse import OptionParser from time import strftime -from tool_shed.util.shed_util_common import clone_repository -from tool_shed.util.shed_util_common import get_configured_ui log = logging.getLogger( 'check_repositories_for_functional_tests' ) assert sys.version_info[ :2 ] >= ( 2, 6 ) @@ -129,9 +128,9 @@ testable_revision = False # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) - repo = hg.repository( get_configured_ui(), repo_dir ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-cafr" ) - cloned_ok, error_message = clone_repository( repo_dir, work_dir, changeset_revision ) + cloned_ok, error_message = suc.clone_repository( repo_dir, work_dir, changeset_revision ) if cloned_ok: # Iterate through all the directories in the cloned changeset revision and determine whether there's a # directory named test-data. If this directory is not present update the metadata record for the changeset 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: Fixes for the tool shed's install and test framework and enhancements to allow a configurable number of test runs to be stored and displayed.
by commits-noreply＠bitbucket.org 27 Nov '13

27 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11028b31d3f0/ Changeset: 11028b31d3f0 User: greg Date: 2013-11-27 21:28:03 Summary: Fixes for the tool shed's install and test framework and enhancements to allow a configurable number of test runs to be stored and displayed. Affected #: 10 files diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -453,5 +453,7 @@ value_mapper = { 'id' : trans.security.encode_id, 'repository_id' : trans.security.encode_id } if repository_metadata.time_last_tested is not None: - value_mapper[ 'time_last_tested' ] = time_ago + # For some reason the Dictifiable.to_dict() method in ~/galaxy/model/item_attrs.py requires + # a function rather than a mapped value, so just pass the time_ago function here. + value_mapper[ 'time_last_tested' ] = time_ago return value_mapper diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 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 @@ -166,12 +166,11 @@ repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) flush_needed = False for key, new_value in payload.items(): - if hasattr( repository_metadata, key ): + if key == 'time_last_tested': + repository_metadata.time_last_tested = datetime.datetime.utcnow() + flush_needed = True + elif hasattr( repository_metadata, key ): setattr( repository_metadata, key, new_value ) - if key in [ 'tools_functionally_correct', 'time_last_tested' ]: - # Automatically update repository_metadata.time_last_tested. - repository_metadata.time_last_tested = datetime.datetime.utcnow() - flush_needed = True flush_needed = True if flush_needed: trans.sa_session.add( repository_metadata ) @@ -192,5 +191,7 @@ value_mapper = { 'id' : trans.security.encode_id, 'repository_id' : trans.security.encode_id } if repository_metadata.time_last_tested is not None: + # For some reason the Dictifiable.to_dict() method in ~/galaxy/model/item_attrs.py requires + # a function rather than a mapped value, so just pass the time_ago function here. value_mapper[ 'time_last_tested' ] = time_ago return value_mapper diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -53,6 +53,8 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None ) + # Install and test framework for testing tools contained in repositories. + self.num_tool_test_results_saved = kwargs.get( 'num_tool_test_results_saved', 5 ) # Location for dependencies if 'tool_dependency_dir' in kwargs: self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.root ) diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 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 @@ -1515,51 +1515,59 @@ tool_shed_url = web.url_for( '/', qualified=True ) functional_test_results = [] - for metadata_row in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( metadata_filter ) \ .join( trans.model.Repository ) \ .filter( and_( trans.model.Repository.table.c.deleted == False, trans.model.Repository.table.c.private == False, trans.model.Repository.table.c.deprecated == False, trans.model.Repository.table.c.user_id == user.id ) ): - if not metadata_row.tool_test_results: - continue - if metadata_row.changeset_revision != metadata_row.repository.tip( trans.app ): - continue - current_repository_errors = [] - tool_dependency_errors = [] - repository_dependency_errors = [] - description_lines = [] - # Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822 - # section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT - time_tested = metadata_row.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' ) - repository = metadata_row.repository - # Generate a citable URL for this repository with owner and changeset revision. - repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, metadata_row.changeset_revision ) - passed_tests = len( metadata_row.tool_test_results.get( 'passed_tests', [] ) ) - failed_tests = len( metadata_row.tool_test_results.get( 'failed_tests', [] ) ) - missing_test_components = len( metadata_row.tool_test_results.get( 'missing_test_components', [] ) ) - installation_errors = metadata_row.tool_test_results.get( 'installation_errors', [] ) - if installation_errors: - tool_dependency_errors = installation_errors.get( 'tool_dependencies', [] ) - repository_dependency_errors = installation_errors.get( 'repository_dependencies', [] ) - current_repository_errors = installation_errors.get( 'current_repository', [] ) - description_lines.append( '%d tests passed, %d tests failed, %d tests missing test components.' % \ - ( passed_tests, failed_tests, missing_test_components ) ) - if current_repository_errors: - description_lines.append( '\nThis repository did not install correctly. ' ) - if tool_dependency_errors or repository_dependency_errors: - description_lines.append( '\n%d tool dependencies and %d repository dependencies failed to install. ' % \ - ( len( tool_dependency_errors ), len( repository_dependency_errors ) ) ) - title = 'Revision %s of %s' % ( metadata_row.changeset_revision, repository.name ) - # The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated - # if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable - # that behavior. - functional_test_results.append( dict( title=title, - guid=repository_citable_url, - link=repository_citable_url, - description='\n'.join( description_lines ), - pubdate=time_tested ) ) + repository = repository_metadata.repository + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + latest_downloadable_changeset_revsion = suc.get_latest_downloadable_changeset_revision( trans, repository, repo ) + if repository_metadata.changeset_revision == latest_downloadable_changeset_revsion: + # We'll display only the test run for the latest installable revision in the rss feed. + tool_test_results = repository_metadata.tool_test_results + if tool_test_results is not None: + # The tool_test_results column used to contain a single dictionary, but was recently enhanced to contain + # a list of dictionaries, one for each install and test run. We'll display only the latest run in the rss + # feed for nwo. + if isinstance( tool_test_results, list ): + tool_test_results = tool_test_results[ 0 ] + current_repository_errors = [] + tool_dependency_errors = [] + repository_dependency_errors = [] + description_lines = [] + # Per the RSS 2.0 specification, all dates in RSS feeds must be formatted as specified in RFC 822 + # section 5.1, e.g. Sat, 07 Sep 2002 00:00:01 UT + time_tested = repository_metadata.time_last_tested.strftime( '%a, %d %b %Y %H:%M:%S UT' ) + # Generate a citable URL for this repository with owner and changeset revision. + repository_citable_url = suc.url_join( tool_shed_url, 'view', user.username, repository.name, repository_metadata.changeset_revision ) + passed_tests = len( tool_test_results.get( 'passed_tests', [] ) ) + failed_tests = len( tool_test_results.get( 'failed_tests', [] ) ) + missing_test_components = len( tool_test_results.get( 'missing_test_components', [] ) ) + installation_errors = tool_test_results.get( 'installation_errors', [] ) + if installation_errors: + tool_dependency_errors = installation_errors.get( 'tool_dependencies', [] ) + repository_dependency_errors = installation_errors.get( 'repository_dependencies', [] ) + current_repository_errors = installation_errors.get( 'current_repository', [] ) + description_lines.append( '%d tests passed, %d tests failed, %d tests missing test components.' % \ + ( passed_tests, failed_tests, missing_test_components ) ) + if current_repository_errors: + description_lines.append( '\nThis repository did not install correctly. ' ) + if tool_dependency_errors or repository_dependency_errors: + description_lines.append( '\n%d tool dependencies and %d repository dependencies failed to install. ' % \ + ( len( tool_dependency_errors ), len( repository_dependency_errors ) ) ) + title = 'Revision %s of %s' % ( repository_metadata.changeset_revision, repository.name ) + # The guid attribute in an RSS feed's list of items allows a feed reader to choose not to show an item as updated + # if the guid is unchanged. For functional test results, the citable URL is sufficiently unique to enable + # that behavior. + functional_test_results.append( dict( title=title, + guid=repository_citable_url, + link=repository_citable_url, + description='\n'.join( description_lines ), + pubdate=time_tested ) ) trans.response.set_content_type( 'application/rss+xml' ) return trans.fill_template( '/rss.mako', title='Tool functional test results', diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -229,11 +229,14 @@ class RepositoryMetadata( object, Dictifiable ): - dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'has_repository_dependencies', 'includes_datatypes', - 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows', 'time_last_tested' ) - dict_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'tools_functionally_correct', 'do_not_test', - 'test_install_error', 'time_last_tested', 'tool_test_results', 'has_repository_dependencies', 'includes_datatypes', - 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', 'includes_workflows' ) + dict_collection_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components', + 'tools_functionally_correct', 'do_not_test', 'test_install_error', 'has_repository_dependencies', + 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', 'includes_tools_for_display_in_tool_panel', + 'includes_workflows', 'time_last_tested' ) + dict_element_visible_keys = ( 'id', 'repository_id', 'changeset_revision', 'malicious', 'downloadable', 'missing_test_components', + 'tools_functionally_correct', 'do_not_test', 'test_install_error', 'time_last_tested', 'tool_test_results', + 'has_repository_dependencies', 'includes_datatypes', 'includes_tools', 'includes_tool_dependencies', + 'includes_tools_for_display_in_tool_panel', 'includes_workflows' ) def __init__( self, id=None, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False, missing_test_components=None, tools_functionally_correct=False, do_not_test=False, test_install_error=False, time_last_tested=None, @@ -242,8 +245,8 @@ self.id = id self.repository_id = repository_id self.changeset_revision = changeset_revision - self.metadata = metadata or dict() - self.tool_versions = tool_versions or dict() + self.metadata = metadata + self.tool_versions = tool_versions self.malicious = malicious self.downloadable = downloadable self.missing_test_components = missing_test_components @@ -251,7 +254,7 @@ self.do_not_test = do_not_test self.test_install_error = test_install_error self.time_last_tested = time_last_tested - self.tool_test_results = tool_test_results or dict() + self.tool_test_results = tool_test_results self.has_repository_dependencies = has_repository_dependencies # We don't consider the special case has_repository_dependencies_only_if_compiling_contained_td here. self.includes_datatypes = includes_datatypes diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 lib/tool_shed/scripts/api/common.py --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -158,7 +158,7 @@ print e.read( 1024 ) sys.exit( 1 ) else: - return 'Error. '+ str( e.read( 1024 ) ) + return 'Error. ' + str( e.read( 1024 ) ) if not return_formatted: return r print 'Response' diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 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 @@ -25,6 +25,7 @@ from galaxy.model.orm import and_ from galaxy.model.orm import not_ from galaxy.model.orm import select +from galaxy.util import listify from mercurial import hg from mercurial import ui from mercurial import __version__ @@ -41,16 +42,17 @@ """Application that enables updating repository_metadata table records in the Tool Shed.""" def __init__( self, config ): - if config.database_connection is False: - config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % str( config.database ) - log.debug( 'Using database connection: %s' % str( config.database_connection ) ) + 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( config.file_path, - config.database_connection, + 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 = config.hgweb_config_dir + 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 @@ -72,19 +74,7 @@ "id": "tool_wrapper", "name": "Map with Tool Wrapper", "requirements": [], - "tests": [ - { - "inputs": [ [ "parameter", "value" ], [ "other_parameter", "other_value" ], ], - "name": "Test-1", - "outputs": [ - [ - "output_field_name", - "output_file_name.bed" - ] - ], - "required_files": [ '1.bed', '2.bed', '3.bed' ] - } - ], + "tests": [], "tool_config": "database/community_files/000/repo_1/tool_wrapper.xml", "tool_type": "default", "version": "1.2.3", @@ -120,11 +110,6 @@ missing_test_components = [] repository = repository_metadata.repository records_checked += 1 - # 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 - else: - tool_test_results_dict = {} # Check the next repository revision. changeset_revision = str( repository_metadata.changeset_revision ) name = repository.name @@ -141,7 +126,7 @@ tool_dicts = metadata.get( 'tools', None ) if tool_dicts is not None: has_test_data = False - testable_revision_found = False + testable_revision = False # Clone the repository up to the changeset revision we're checking. repo_dir = repository.repo_path( app ) repo = hg.repository( get_configured_ui(), repo_dir ) @@ -236,7 +221,7 @@ if test_errors not in missing_test_components: missing_test_components.append( test_errors ) if tool_has_tests and has_test_files: - testable_revision_found = True + testable_revision = True # Remove the cloned repository path. This has to be done after the check for required test files, for obvious reasons. if os.path.exists( work_dir ): shutil.rmtree( work_dir ) @@ -253,6 +238,27 @@ if 'missing_components' in invalid_test: print '# %s' % invalid_test[ 'missing_components' ] if not info_only: + # Get or create the list of tool_test_results dictionaries. + 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, but we need to 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 ) + 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 = {} test_environment_dict = tool_test_results_dict.get( 'test_environment', {} ) test_environment_dict[ 'tool_shed_database_version' ] = get_database_version( app ) test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version @@ -270,12 +276,24 @@ # changeset revision will be created, either of which will be automatically checked and flagged as appropriate. # In the install and test script, this behavior is slightly different, since we do want to always run functional # tests on the most recent downloadable changeset revision. - if should_set_do_not_test_flag( app, repository_metadata.repository, changeset_revision ) and not testable_revision_found: + if should_set_do_not_test_flag( app, repository, changeset_revision, testable_revision ): + print "# Setting do_not_test to True on revision %s of repository %s because it is missing test components" % \ + ( changeset_revision, name ) + print "# and it is not the latest downloadable revision." repository_metadata.do_not_test = True repository_metadata.tools_functionally_correct = False repository_metadata.missing_test_components = True tool_test_results_dict[ 'missing_test_components' ] = missing_test_components - repository_metadata.tool_test_results = tool_test_results_dict + # Store only the configured number of test runs. + num_tool_test_results_saved = int( app.config.num_tool_test_results_saved ) + if len( tool_test_results_dicts ) >= num_tool_test_results_saved: + test_results_index = num_tool_test_results_saved - 1 + new_tool_test_results_dicts = tool_test_results_dicts[ :test_results_index ] + else: + new_tool_test_results_dicts = [ d for d in tool_test_results_dicts ] + # Insert the new element into the first position in the list. + new_tool_test_results_dicts.insert( 0, tool_test_results_dict ) + repository_metadata.tool_test_results = new_tool_test_results_dicts app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time() @@ -313,19 +331,6 @@ changelog_tuples.append( ( ctx.rev(), str( ctx ) ) ) return changelog_tuples -def is_most_recent_downloadable_revision( app, repository, changeset_revision, downloadable_revisions ): - # Get a list of ( numeric revision, changeset hash ) tuples from the changelog. - changelog = get_repo_changelog_tuples( repository.repo_path( app ) ) - latest_downloadable_revision = None - for ctx_rev, changeset_hash in changelog: - if changeset_hash in downloadable_revisions: - # The last changeset hash in the changelog that is present in the list of downloadable revisions will always be the most - # recent downloadable revision, since the changelog tuples are ordered from earliest to most recent. - latest_downloadable_revision = changeset_hash - if latest_downloadable_revision == changeset_revision: - return True - return False - def main(): '''Script that checks repositories to see if the tools contained within them have functional tests defined.''' parser = OptionParser() @@ -345,7 +350,7 @@ config_parser.read( ini_file ) config_dict = {} for key, value in config_parser.items( "app:main" ): - config_dict[key] = value + config_dict[ key ] = value config = tool_shed_config.Configuration( **config_dict ) config_section = options.section now = strftime( "%Y-%m-%d %H:%M:%S" ) @@ -361,34 +366,27 @@ print "# Displaying extra information ( --verbosity = %d )" % options.verbosity check_and_update_repository_metadata( app, info_only=options.info_only, verbosity=options.verbosity ) -def should_set_do_not_test_flag( app, repository, changeset_revision ): - ''' - Returns True if: - a) There are multiple downloadable revisions, and the provided changeset revision is not the most recent downloadable revision. In this case, - the revision will never be updated with correct data, and re-testing it would be redundant. - b) There are one or more downloadable revisions, and the provided changeset revision is the most recent downloadable revision. In this case, if - the repository is updated with test data or functional tests, the downloadable changeset revision that was tested will either be replaced - with the new changeset revision, or a new downloadable changeset revision will be created, either of which will be automatically checked and - flagged as appropriate. In the install and test script, this behavior is slightly different, since we do want to always run functional tests - on the most recent downloadable changeset revision. - ''' - repository_revisions = app.sa_session.query( app.model.RepositoryMetadata ) \ - .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, - app.model.RepositoryMetadata.table.c.repository_id == repository.id ) ) \ - .all() - downloadable_revisions = [ repository_metadata.changeset_revision for repository_metadata in repository_revisions ] - is_latest_revision = is_most_recent_downloadable_revision( app, repository, changeset_revision, downloadable_revisions ) - if len( downloadable_revisions ) == 1: - return True - elif len( downloadable_revisions ) > 1 and is_latest_revision: - return True - elif len( downloadable_revisions ) > 1 and not is_latest_revision: - return True - else: - return False +def should_set_do_not_test_flag( app, repository, changeset_revision, testable_revision ): + """ + The received testable_revision is True if the tool has defined tests and test files are in the repository + This method returns True if the received repository has multiple downloadable revisions and the received + changeset_revision is not the most recent downloadable revision and the received testable_revision is False. + In this case, the received changeset_revision will never be updated with correct data, and re-testing it + would be redundant. + """ + if not testable_revision: + repo_dir = repository.repo_path( app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) + if len( changeset_revisions ) > 1: + latest_downloadable_revision = changeset_revisions[ -1 ] + if changeset_revision != latest_downloadable_revision: + return True + return False if __name__ == "__main__": - # The repository_metadata.tool_test_results json value should have the following structure: + # The repository_metadata.tool_test_results json value should have the following list structure: + # [ # { # "test_environment": # { @@ -467,6 +465,7 @@ # }, # ] # } + # ] # # Optionally, "traceback" may be included in a test_errors dict, if it is relevant. No script should overwrite anything other # than the list relevant to what it is testing. diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 lib/tool_shed/util/container_util.py --- a/lib/tool_shed/util/container_util.py +++ b/lib/tool_shed/util/container_util.py @@ -1,7 +1,7 @@ import logging import os import threading -from galaxy.util import asbool +import galaxy.util from galaxy.web.framework.helpers import time_ago from tool_shed.util import common_util from tool_shed.util import readme_util @@ -72,8 +72,8 @@ repository_name=name, repository_owner=owner, changeset_revision=changeset_revision, - prior_installation_required=asbool( prior_installation_required ), - only_if_compiling_contained_td=asbool( only_if_compiling_contained_td ) ) + prior_installation_required=galaxy.util.asbool( prior_installation_required ), + only_if_compiling_contained_td=galaxy.util.asbool( only_if_compiling_contained_td ) ) class DataManager( object ): @@ -497,8 +497,8 @@ repository_name=name, repository_owner=owner, changeset_revision=changeset_revision, - prior_installation_required=asbool( prior_installation_required ), - only_if_compiling_contained_td=asbool( only_if_compiling_contained_td ), + prior_installation_required=galaxy.util.asbool( prior_installation_required ), + only_if_compiling_contained_td=galaxy.util.asbool( only_if_compiling_contained_td ), error=error ) folder.invalid_repository_dependencies.append( ird ) invalid_repository_dependencies_folder.folders.append( folder ) @@ -831,16 +831,12 @@ label='Valid tools' ) containers_dict[ 'valid_tools' ] = valid_tools_root_folder # Tool test results container. - tool_test_results = repository_metadata.tool_test_results + tool_test_results = galaxy.util.listify( repository_metadata.tool_test_results ) # Only create and populate this folder if there are actual tool test results to display. if can_display_tool_test_results( tool_test_results, exclude=exclude ): - time_tested = repository_metadata.time_last_tested - if time_tested is not None: - time_tested = time_ago( time_tested ) folder_id, tool_test_results_root_folder = build_tool_test_results_folder( trans, folder_id, tool_test_results, - time_tested, label='Tool test results' ) containers_dict[ 'tool_test_results' ] = tool_test_results_root_folder # Workflows container. @@ -1052,153 +1048,165 @@ tool_dependencies_root_folder = None return folder_id, tool_dependencies_root_folder -def build_tool_test_results_folder( trans, folder_id, tool_test_results_dict, time_tested, label='Tool test results' ): +def build_tool_test_results_folder( trans, folder_id, tool_test_results_dicts, label='Tool test results' ): """Return a folder hierarchy containing tool dependencies.""" # This container is displayed only in the tool shed. - if tool_test_results_dict: + if tool_test_results_dicts: + multiple_tool_test_results_dicts = len( tool_test_results_dicts ) > 1 + test_results_dict_id = 0 folder_id += 1 tool_test_results_root_folder = Folder( id=folder_id, key='root', label='root', parent=None ) - test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) - if test_environment_dict is not None: - folder_id += 1 - test_results_folder = Folder( id=folder_id, key='test_results', label=label, parent=tool_test_results_root_folder ) - tool_test_results_root_folder.folders.append( test_results_folder ) - folder_id += 1 - folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=test_results_folder ) - test_results_folder.folders.append( folder ) - architecture = test_environment_dict.get( 'architecture', '' ) - galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) - galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) - python_version = test_environment_dict.get( 'python_version', '' ) - system = test_environment_dict.get( 'system', '' ) - time_tested = time_tested - tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) - tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) - tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) - test_environment = TestEnvironment( id=1, - architecture=architecture, - galaxy_database_version=galaxy_database_version, - galaxy_revision=galaxy_revision, - python_version=python_version, - system=system, - time_tested=time_tested, - tool_shed_database_version=tool_shed_database_version, - tool_shed_mercurial_version=tool_shed_mercurial_version, - tool_shed_revision=tool_shed_revision ) - folder.test_environments.append( test_environment ) - not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) - if not_tested_dict: - folder_id += 1 - folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=test_results_folder ) - test_results_folder.folders.append( folder ) - not_tested_id = 0 - not_tested = NotTested( id=not_tested_id, - reason=not_tested_dict.get( 'reason', '' ) ) - folder.not_tested.append( not_tested ) - passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) - if passed_tests_dicts: - folder_id += 1 - folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=test_results_folder ) - test_results_folder.folders.append( folder ) - passed_test_id = 0 - for passed_tests_dict in passed_tests_dicts: - passed_test_id += 1 - passed_test = PassedTest( id=passed_test_id, - test_id=passed_tests_dict.get( 'test_id' '' ), - tool_id=passed_tests_dict.get( 'tool_id', '' ), - tool_version=passed_tests_dict.get( 'tool_version', '' ) ) - folder.passed_tests.append( passed_test ) - failed_tests_dicts = tool_test_results_dict.get( 'failed_tests', [] ) - if failed_tests_dicts: - folder_id += 1 - folder = Folder( id=folder_id, key='failed_tests', label='Tests that failed', parent=test_results_folder ) - test_results_folder.folders.append( folder ) - failed_test_id = 0 - for failed_tests_dict in failed_tests_dicts: - failed_test_id += 1 - failed_test = FailedTest( id=failed_test_id, - stderr=failed_tests_dict.get( 'stderr', '' ), - test_id=failed_tests_dict.get( 'test_id', '' ), - tool_id=failed_tests_dict.get( 'tool_id', '' ), - tool_version=failed_tests_dict.get( 'tool_version', '' ), - traceback=failed_tests_dict.get( 'traceback', '' ) ) - folder.failed_tests.append( failed_test ) - missing_test_components_dicts = tool_test_results_dict.get( 'missing_test_components', [] ) - if missing_test_components_dicts: - folder_id += 1 - folder = Folder( id=folder_id, key='missing_test_components', label='Tools missing tests or test data', parent=test_results_folder ) - test_results_folder.folders.append( folder ) - missing_test_component_id = 0 - for missing_test_components_dict in missing_test_components_dicts: - missing_test_component_id += 1 - missing_test_component = MissingTestComponent( id=missing_test_component_id, - missing_components=missing_test_components_dict.get( 'missing_components', '' ), - tool_guid=missing_test_components_dict.get( 'tool_guid', '' ), - tool_id=missing_test_components_dict.get( 'tool_id', '' ), - tool_version=missing_test_components_dict.get( 'tool_version', '' ) ) - folder.missing_test_components.append( missing_test_component ) - installation_error_dicts = tool_test_results_dict.get( 'installation_errors', {} ) - if installation_error_dicts: - current_repository_errors = installation_error_dicts.get( 'current_repository', [] ) - repository_dependency_errors = installation_error_dicts.get( 'repository_dependencies', [] ) - tool_dependency_errors = installation_error_dicts.get( 'tool_dependencies', [] ) - if current_repository_errors or repository_dependency_errors or tool_dependency_errors: + for index, tool_test_results_dict in enumerate( tool_test_results_dicts ): + test_environment_dict = tool_test_results_dict.get( 'test_environment', None ) + if test_environment_dict is not None: + time_tested = test_environment_dict.get( 'time_tested', 'unknown_%d' % index ) + if multiple_tool_test_results_dicts: + folder_id += 1 + containing_folder = Folder( id=folder_id, key='test_results', label=time_tested, parent=tool_test_results_root_folder ) + else: + containing_folder = tool_test_results_root_folder + test_results_dict_id += 1 + #folder_id += 1 + #test_results_folder = Folder( id=folder_id, key='test_results', label='Automated test environment', parent=containing_folder ) + #containing_folder.folders.append( test_results_folder ) folder_id += 1 - installation_error_base_folder = Folder( id=folder_id, - key='installation_errors', - label='Installation errors', - parent=test_results_folder ) - if current_repository_errors: + folder = Folder( id=folder_id, key='test_environment', label='Automated test environment', parent=containing_folder ) + containing_folder.folders.append( folder ) + architecture = test_environment_dict.get( 'architecture', '' ) + galaxy_database_version = test_environment_dict.get( 'galaxy_database_version', '' ) + galaxy_revision = test_environment_dict.get( 'galaxy_revision', '' ) + python_version = test_environment_dict.get( 'python_version', '' ) + system = test_environment_dict.get( 'system', '' ) + tool_shed_database_version = test_environment_dict.get( 'tool_shed_database_version', '' ) + tool_shed_mercurial_version = test_environment_dict.get( 'tool_shed_mercurial_version', '' ) + tool_shed_revision = test_environment_dict.get( 'tool_shed_revision', '' ) + test_environment = TestEnvironment( id=1, + architecture=architecture, + galaxy_database_version=galaxy_database_version, + galaxy_revision=galaxy_revision, + python_version=python_version, + system=system, + time_tested=time_tested, + tool_shed_database_version=tool_shed_database_version, + tool_shed_mercurial_version=tool_shed_mercurial_version, + tool_shed_revision=tool_shed_revision ) + folder.test_environments.append( test_environment ) + not_tested_dict = tool_test_results_dict.get( 'not_tested', {} ) + if not_tested_dict: + folder_id += 1 + folder = Folder( id=folder_id, key='not_tested', label='Not tested', parent=containing_folder ) + containing_folder.folders.append( folder ) + not_tested_id = 0 + not_tested = NotTested( id=not_tested_id, + reason=not_tested_dict.get( 'reason', '' ) ) + folder.not_tested.append( not_tested ) + passed_tests_dicts = tool_test_results_dict.get( 'passed_tests', [] ) + if passed_tests_dicts: + folder_id += 1 + folder = Folder( id=folder_id, key='passed_tests', label='Tests that passed successfully', parent=containing_folder ) + containing_folder.folders.append( folder ) + passed_test_id = 0 + for passed_tests_dict in passed_tests_dicts: + passed_test_id += 1 + passed_test = PassedTest( id=passed_test_id, + test_id=passed_tests_dict.get( 'test_id' '' ), + tool_id=passed_tests_dict.get( 'tool_id', '' ), + tool_version=passed_tests_dict.get( 'tool_version', '' ) ) + folder.passed_tests.append( passed_test ) + failed_tests_dicts = tool_test_results_dict.get( 'failed_tests', [] ) + if failed_tests_dicts: + folder_id += 1 + folder = Folder( id=folder_id, key='failed_tests', label='Tests that failed', parent=containing_folder ) + containing_folder.folders.append( folder ) + failed_test_id = 0 + for failed_tests_dict in failed_tests_dicts: + failed_test_id += 1 + failed_test = FailedTest( id=failed_test_id, + stderr=failed_tests_dict.get( 'stderr', '' ), + test_id=failed_tests_dict.get( 'test_id', '' ), + tool_id=failed_tests_dict.get( 'tool_id', '' ), + tool_version=failed_tests_dict.get( 'tool_version', '' ), + traceback=failed_tests_dict.get( 'traceback', '' ) ) + folder.failed_tests.append( failed_test ) + missing_test_components_dicts = tool_test_results_dict.get( 'missing_test_components', [] ) + if missing_test_components_dicts: + folder_id += 1 + folder = Folder( id=folder_id, key='missing_test_components', label='Tools missing tests or test data', parent=containing_folder ) + containing_folder.folders.append( folder ) + missing_test_component_id = 0 + for missing_test_components_dict in missing_test_components_dicts: + missing_test_component_id += 1 + missing_test_component = MissingTestComponent( id=missing_test_component_id, + missing_components=missing_test_components_dict.get( 'missing_components', '' ), + tool_guid=missing_test_components_dict.get( 'tool_guid', '' ), + tool_id=missing_test_components_dict.get( 'tool_id', '' ), + tool_version=missing_test_components_dict.get( 'tool_version', '' ) ) + folder.missing_test_components.append( missing_test_component ) + installation_error_dicts = tool_test_results_dict.get( 'installation_errors', {} ) + if installation_error_dicts: + current_repository_errors = installation_error_dicts.get( 'current_repository', [] ) + repository_dependency_errors = installation_error_dicts.get( 'repository_dependencies', [] ) + tool_dependency_errors = installation_error_dicts.get( 'tool_dependencies', [] ) + if current_repository_errors or repository_dependency_errors or tool_dependency_errors: folder_id += 1 - subfolder = Folder( id=folder_id, - key='current_repository_errors', - label='This repository', - parent=installation_error_base_folder ) - repository_error_id = 0 - for repository_error_dict in current_repository_errors: - repository_error_id += 1 - repository_installation_error = RepositoryInstallationError( id=repository_error_id, - tool_shed=repository_error_dict.get( 'tool_shed', '' ), - name=repository_error_dict.get( 'name', '' ), - owner=repository_error_dict.get( 'owner', '' ), - changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), - error_message=repository_error_dict.get( 'error_message', '' ) ) - subfolder.current_repository_installation_errors.append( repository_installation_error ) - installation_error_base_folder.folders.append( subfolder ) - if repository_dependency_errors: - folder_id += 1 - subfolder = Folder( id=folder_id, - key='repository_dependency_errors', - label='Repository dependencies', - parent=installation_error_base_folder ) - repository_error_id = 0 - for repository_error_dict in repository_dependency_errors: - repository_error_id += 1 - repository_installation_error = RepositoryInstallationError( id=repository_error_id, - tool_shed=repository_error_dict.get( 'tool_shed', '' ), - name=repository_error_dict.get( 'name', '' ), - owner=repository_error_dict.get( 'owner', '' ), - changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), - error_message=repository_error_dict.get( 'error_message', '' ) ) - subfolder.repository_installation_errors.append( repository_installation_error ) - installation_error_base_folder.folders.append( subfolder ) - if tool_dependency_errors: - folder_id += 1 - subfolder = Folder( id=folder_id, - key='tool_dependency_errors', - label='Tool dependencies', - parent=installation_error_base_folder ) - tool_dependency_error_id = 0 - for tool_dependency_error_dict in tool_dependency_errors: - tool_dependency_error_id += 1 - tool_dependency_installation_error = ToolDependencyInstallationError( id=tool_dependency_error_id, - type=tool_dependency_error_dict.get( 'type', '' ), - name=tool_dependency_error_dict.get( 'name', '' ), - version=tool_dependency_error_dict.get( 'version', '' ), - error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) - subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) - installation_error_base_folder.folders.append( subfolder ) - test_results_folder.installation_errors.append( installation_error_base_folder ) + installation_error_base_folder = Folder( id=folder_id, + key='installation_errors', + label='Installation errors', + parent=containing_folder ) + if current_repository_errors: + folder_id += 1 + subfolder = Folder( id=folder_id, + key='current_repository_errors', + label='This repository', + parent=installation_error_base_folder ) + repository_error_id = 0 + for repository_error_dict in current_repository_errors: + repository_error_id += 1 + repository_installation_error = RepositoryInstallationError( id=repository_error_id, + tool_shed=repository_error_dict.get( 'tool_shed', '' ), + name=repository_error_dict.get( 'name', '' ), + owner=repository_error_dict.get( 'owner', '' ), + changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), + error_message=repository_error_dict.get( 'error_message', '' ) ) + subfolder.current_repository_installation_errors.append( repository_installation_error ) + installation_error_base_folder.folders.append( subfolder ) + if repository_dependency_errors: + folder_id += 1 + subfolder = Folder( id=folder_id, + key='repository_dependency_errors', + label='Repository dependencies', + parent=installation_error_base_folder ) + repository_error_id = 0 + for repository_error_dict in repository_dependency_errors: + repository_error_id += 1 + repository_installation_error = RepositoryInstallationError( id=repository_error_id, + tool_shed=repository_error_dict.get( 'tool_shed', '' ), + name=repository_error_dict.get( 'name', '' ), + owner=repository_error_dict.get( 'owner', '' ), + changeset_revision=repository_error_dict.get( 'changeset_revision', '' ), + error_message=repository_error_dict.get( 'error_message', '' ) ) + subfolder.repository_installation_errors.append( repository_installation_error ) + installation_error_base_folder.folders.append( subfolder ) + if tool_dependency_errors: + folder_id += 1 + subfolder = Folder( id=folder_id, + key='tool_dependency_errors', + label='Tool dependencies', + parent=installation_error_base_folder ) + tool_dependency_error_id = 0 + for tool_dependency_error_dict in tool_dependency_errors: + tool_dependency_error_id += 1 + tool_dependency_installation_error = ToolDependencyInstallationError( id=tool_dependency_error_id, + type=tool_dependency_error_dict.get( 'type', '' ), + name=tool_dependency_error_dict.get( 'name', '' ), + version=tool_dependency_error_dict.get( 'version', '' ), + error_message=tool_dependency_error_dict.get( 'error_message', '' ) ) + subfolder.tool_dependency_installation_errors.append( tool_dependency_installation_error ) + installation_error_base_folder.folders.append( subfolder ) + containing_folder.installation_errors.append( installation_error_base_folder ) + #containing_folder.folders.append( containing_folder ) + if multiple_tool_test_results_dicts: + tool_test_results_root_folder.folders.append( containing_folder ) else: tool_test_results_root_folder = None return folder_id, tool_test_results_root_folder @@ -1247,13 +1255,13 @@ workflows_root_folder = None return folder_id, workflows_root_folder -def can_display_tool_test_results( tool_test_results_dict, exclude=None ): +def can_display_tool_test_results( tool_test_results_dicts, exclude=None ): # Only create and populate the tool_test_results container if there are actual tool test results to display. if exclude is None: exclude = [] if 'tool_test_results' in exclude: return False - if tool_test_results_dict: + for tool_test_results_dict in tool_test_results_dicts: # We check for more than a single entry in the tool_test_results dictionary because it may have # only the "test_environment" entry, but we want at least 1 of "passed_tests", "failed_tests", # "installation_errors", "missing_test_components" "skipped_tests", "not_tested" or any other @@ -1288,7 +1296,7 @@ if key_is_current_repositorys_key( repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, key ): label = 'Repository dependencies' else: - if asbool( prior_installation_required ): + if galaxy.util.asbool( prior_installation_required ): prior_installation_required_str = " <i>(prior install required)</i>" else: prior_installation_required_str = "" @@ -1432,8 +1440,8 @@ repository_name=repository_name, repository_owner=repository_owner, changeset_revision=changeset_revision, - prior_installation_required=asbool( prior_installation_required ), - only_if_compiling_contained_td=asbool( only_if_compiling_contained_td ), + prior_installation_required=galaxy.util.asbool( prior_installation_required ), + only_if_compiling_contained_td=galaxy.util.asbool( only_if_compiling_contained_td ), installation_status=installation_status, tool_shed_repository_id=tool_shed_repository_id ) # Insert the repository_dependency into the folder. diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -58,7 +58,6 @@ from mercurial import __version__ from nose.plugins import Plugin from paste import httpserver -from time import strftime from tool_shed.util import tool_dependency_util from tool_shed.util.xml_util import parse_xml @@ -80,6 +79,12 @@ default_galaxy_test_host = '127.0.0.1' default_galaxy_master_api_key = None +# 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 @@ -157,7 +162,7 @@ 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 @@ -325,16 +330,16 @@ missing_tool_dependencies.extend( get_missing_tool_dependencies( repository_dependency ) ) return missing_tool_dependencies -def get_repository_info_from_api( url, repository_dict ): +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 - latest_changeset_revision, error_message = get_latest_downloadable_changeset_revision( url, - extended_dict[ 'name' ], - extended_dict[ 'owner' ] ) + 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 ) @@ -361,8 +366,9 @@ repository_dicts = [] params = urllib.urlencode( dict( do_not_test='false', downloadable='true', + includes_tools='true', malicious='false', - includes_tools='true', + missing_test_components='false', skip_tool_test='false' ) ) api_url = get_api_url( base=tool_shed_url, parts=[ 'repository_revisions' ], params=params ) baseline_repository_dicts, error_message = json_from_url( api_url ) @@ -372,7 +378,7 @@ 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_info_from_api( galaxy_tool_shed_url, baseline_repository_dict ) + repository_dict, error_message = get_repository_dict( galaxy_tool_shed_url, baseline_repository_dict ) if error_message: log.debug( 'Error getting additional details about repository %s from the API: %s' % ( str( name ), error_message ) ) else: @@ -447,16 +453,18 @@ tool_id = parts[ -2 ] return tool_id, tool_version -def get_tool_test_results_dict( tool_shed_url, encoded_repository_metadata_id ): +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 = '' api_path = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] api_url = get_api_url( base=tool_shed_url, parts=api_path ) repository_metadata, error_message = json_from_url( api_url ) if error_message: return None, error_message - tool_test_results = repository_metadata.get( 'tool_test_results', {} ) - if tool_test_results is None: - return None, error_message + tool_test_results = repository_metadata.get( 'tool_test_results', [] ) return tool_test_results, error_message def get_webapp_global_conf(): @@ -466,7 +474,8 @@ global_conf.update( get_static_settings() ) return global_conf -def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dict, results_dict ): +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 @@ -494,7 +503,8 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=True ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + # TODO: do something usefule 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'. @@ -608,6 +618,13 @@ name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) changeset_revision = str( repository_dict[ 'changeset_revision' ] ) + # Populate the tool_test_results_dict. + tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, encoded_repository_metadata_id ) + # The preparation script ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered + # information in the 'test_environment' and possibly the 'missing_test_components' entries of the first + # tool_test_results_dict in the list of tool_test_results_dicts. We need to be careful to not lose this + # information. + tool_test_results_dict = tool_test_results_dicts.pop( 0 ) # See if this repository should be skipped for any reason. skip_this_repository = False skip_reason = None @@ -622,21 +639,20 @@ tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( tools_functionally_correct=False, do_not_test=False ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + # TODO: do something usefule with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( "Not testing revision %s of repository %s owned by %s." % ( changeset_revision, name, owner ) ) else: - # Populate the tool_test_results_dict. - tool_test_results_dict, error_message = get_tool_test_results_dict( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: log.debug( error_message ) else: - # The preparation script ~/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. We need to be careful to not lose this information. For all other repositories, - # no changes will have been made to this dictionary by the preparation script, and tool_test_results_dict will be None. - # 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', None ) test_environment_dict = get_test_environment( test_environment_dict ) + # 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" ) + test_environment_dict[ 'time_tested' ] = now test_environment_dict[ 'galaxy_database_version' ] = get_database_version( app ) test_environment_dict[ 'galaxy_revision' ] = get_repository_current_revision( os.getcwd() ) tool_test_results_dict[ 'test_environment' ] = test_environment_dict @@ -662,8 +678,8 @@ params = dict( tools_functionally_correct=False, test_install_error=True, do_not_test=False ) - - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + # TODO: do something usefule with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) try: if deactivate: # We are deactivating this repository and all of its repository dependencies. @@ -697,6 +713,7 @@ repository, missing_tool_dependencies, repository_dict, + tool_test_results_dicts, tool_test_results_dict, results_dict ) else: @@ -705,7 +722,12 @@ 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_dict, results_dict ) + results_dict = test_repository_tools( app, + repository, + repository_dict, + tool_test_results_dicts, + tool_test_results_dict, + results_dict ) except Exception, e: exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) log.exception( exception_message ) @@ -714,7 +736,12 @@ params = dict( tools_functionally_correct=False, do_not_test=False, test_install_error=False ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + # TODO: do something usefule with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dict, + params ) results_dict[ 'repositories_failed' ].append( dict( name=name, owner=owner, changeset_revision=changeset_revision ) ) total_repositories_tested += 1 results_dict[ 'total_repositories_tested' ] = total_repositories_tested @@ -937,7 +964,7 @@ tool_data_path=additional_tool_data_path, shed_tool_data_table_config=None, persist=False ) - now = strftime( "%Y-%m-%d %H:%M:%S" ) + now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" print "# %s - running repository installation and testing script." % now print "####################################################################################" @@ -949,12 +976,12 @@ repositories_passed = results_dict[ 'repositories_passed' ] repositories_failed = results_dict[ 'repositories_failed' ] repositories_failed_install = results_dict[ 'repositories_failed_install' ] - now = strftime( "%Y-%m-%d %H:%M:%S" ) + 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 '-info_only' in sys.argv: - print "# -info_only set, not updating the tool shed." + if not can_update_tool_shed: + print "# This run will not update the Tool Shed database." if total_repositories_tested > 0: if repositories_passed: print '# ----------------------------------------------------------------------------------' @@ -1048,26 +1075,26 @@ log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list -def register_test_result( url, test_results_dict, repository_dict, params ): +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 '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: - return {} - else: + 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. - time_tested = datetime.utcnow() - test_results_dict[ 'time_last_tested' ] = time_ago( time_tested ) - params[ 'tool_test_results' ] = test_results_dict + 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 remove_generated_tests( app ): @@ -1138,7 +1165,7 @@ for repository in repositories_by_owner[ owner ]: print "# %s owned by %s, changeset revision %s" % ( repository[ 'name' ], repository[ 'owner' ], repository[ 'changeset_revision' ] ) -def test_repository_tools( app, repository, repository_dict, tool_test_results_dict, results_dict ): +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 ) owner = str( repository.owner ) @@ -1175,7 +1202,8 @@ params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + # TODO: do something usefule with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed and passed functional tests.' % ( str( changeset_revision ), str( name ) ) ) else: tool_test_results_dict[ 'failed_tests' ].append( extract_log_data( result, from_tool_test=True ) ) @@ -1184,7 +1212,8 @@ params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) - register_test_result( galaxy_tool_shed_url, tool_test_results_dict, repository_dict, params ) + # TODO: do something usefule with response_dict + response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params ) log.debug( 'Revision %s of repository %s installed successfully but did not pass functional tests.' % \ ( str( changeset_revision ), str( name ) ) ) # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the diff -r ad38b77e96fafc96060f9ee8031094f4a15df278 -r 11028b31d3f024ef920c3168d3f752bc13ba3ad8 tool_shed_wsgi.ini.sample --- a/tool_shed_wsgi.ini.sample +++ b/tool_shed_wsgi.ini.sample @@ -74,6 +74,9 @@ # path to sendmail sendmail_path = /usr/sbin/sendmail +# Number of saved tool test results produced by the install and test framework for each repository. +#num_tool_test_results_saved = 5 + # For use by email messages sent from the tool shed #smtp_server = smtp.your_tool_shed_server #email_from = your_tool_shed_email@server 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: Pack scripts
by commits-noreply＠bitbucket.org 27 Nov '13

27 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad38b77e96fa/ Changeset: ad38b77e96fa User: guerler Date: 2013-11-27 20:06:06 Summary: Pack scripts Affected #: 1 file diff -r 9be62566dbb6f0a0bfc20f6a8027832399838861 -r ad38b77e96fafc96060f9ee8031094f4a15df278 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({title:"Shared Data",content:"library/index"});g.addMenu({title:"Data Libraries",content:"library/index",divider:true});g.addMenu({title:"Published Histories",content:"history/list_published"});g.addMenu({title:"Published Workflows",content:"workflow/list_published"});g.addMenu({title:"Published Visualizations",content:"visualization/list_published"});g.addMenu({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({title:"Lab"});h.addMenu({title:"Sequencing Requests",content:"requests/index"});h.addMenu({title:"Find Samples",content:"requests/find_samples_index"});h.addMenu({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({title:"Visualization",content:"visualization/list"});k.addMenu({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.addMenu({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({title:"Cloud",content:"cloudlaunch/index"});e.addMenu({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({title:"Help"});if(this.options.biostar_url){j.addMenu({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.addMenu({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.addMenu({title:"Support",content:this.options.support_url,target:"_blank"});j.addMenu({title:"Search",content:this.options.search_url,target:"_blank"});j.addMenu({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.addMenu({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.addMenu({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.addMenu({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.addMenu({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedout-only"});if(this.options.allow_user_creation){i.addMenu({title:"Login",content:"user/login",target:"galaxy_main"})}if(this.options.allow_user_creation){i.addMenu({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedin-only"});i.addMenu({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.addMenu({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.addMenu({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.addMenu({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.addMenu({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.addMenu({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.addMenu({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.addMenu({title:"Saved Pages",content:"page/list",target:"_top"});i.addMenu({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.addMenu({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({title:"Shared Data",content:"library/index"});g.addMenu({title:"Data Libraries",content:"library/index",divider:true});g.addMenu({title:"Published Histories",content:"history/list_published"});g.addMenu({title:"Published Workflows",content:"workflow/list_published"});g.addMenu({title:"Published Visualizations",content:"visualization/list_published"});g.addMenu({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({title:"Lab"});h.addMenu({title:"Sequencing Requests",content:"requests/index"});h.addMenu({title:"Find Samples",content:"requests/find_samples_index"});h.addMenu({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({title:"Visualization",content:"visualization/list"});k.addMenu({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.addMenu({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({title:"Cloud",content:"cloudlaunch/index"});e.addMenu({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({title:"Help"});if(this.options.biostar_url){j.addMenu({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.addMenu({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.addMenu({title:"Support",content:this.options.support_url,target:"_blank"});j.addMenu({title:"Search",content:this.options.search_url,target:"_blank"});j.addMenu({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.addMenu({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.addMenu({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.addMenu({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.addMenu({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedout-only"});i.addMenu({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.addMenu({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedin-only"});i.addMenu({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.addMenu({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.addMenu({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.addMenu({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.addMenu({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.addMenu({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.addMenu({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.addMenu({title:"Saved Pages",content:"page/list",target:"_top"});i.addMenu({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.addMenu({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}}});return{GalaxyMenu:a}}); \ 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: guerler: Masthead: Fix login
by commits-noreply＠bitbucket.org 27 Nov '13

27 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9be62566dbb6/ Changeset: 9be62566dbb6 User: guerler Date: 2013-11-27 19:44:25 Summary: Masthead: Fix login Affected #: 1 file diff -r 97940f59772dd8567c68cb8f895d00d99487fdb9 -r 9be62566dbb6f0a0bfc20f6a8027832399838861 static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -223,14 +223,11 @@ }); // login - if (this.options.allow_user_creation) - { - tab_user.addMenu({ - title : "Login", - content : "user/login", - target : "galaxy_main" - }); - } + tab_user.addMenu({ + title : "Login", + content : "user/login", + target : "galaxy_main" + }); // register if (this.options.allow_user_creation) 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: jmchilton: Mimic Galaxy functional test handling of GALAXY_TEST_DB_TEMPLATE for tool shed functional tests.
by commits-noreply＠bitbucket.org 27 Nov '13

27 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/97940f59772d/ Changeset: 97940f59772d User: jmchilton Date: 2013-11-27 15:37:30 Summary: Mimic Galaxy functional test handling of GALAXY_TEST_DB_TEMPLATE for tool shed functional tests. See 83a95ea606d9fcd15f7554b71804625e203eb1ed for full details (essentially GALAXY_TEST_DB_TEMPLATE can be sqlite file path or URL - will be copied over so original left in pristine state and auto upgraded as needed. Affected #: 1 file diff -r 0712180dc77d6df0f19870046562cc34317eb3cc -r 97940f59772dd8567c68cb8f895d00d99487fdb9 test/tool_shed/functional_tests.py --- a/test/tool_shed/functional_tests.py +++ b/test/tool_shed/functional_tests.py @@ -32,6 +32,7 @@ import twill, unittest, time import sys, threading, random import httplib, socket +import urllib from paste import httpserver # This is for the tool shed application. import galaxy.webapps.tool_shed.app @@ -186,10 +187,20 @@ toolshed_database_connection = os.environ[ 'TOOL_SHED_TEST_DBURI' ] else: toolshed_database_connection = 'sqlite:///' + os.path.join( shed_db_path, 'community_test.sqlite' ) + galaxy_database_auto_migrate = False if 'GALAXY_TEST_DBURI' in os.environ: galaxy_database_connection = os.environ[ 'GALAXY_TEST_DBURI' ] else: - galaxy_database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'universe_test.sqlite' ) + db_path = os.path.join( galaxy_db_path, 'universe.sqlite' ) + if 'GALAXY_TEST_DB_TEMPLATE' in os.environ: + # Middle ground between recreating a completely new + # database and pointing at existing database with + # GALAXY_TEST_DBURI. The former requires a lot of setup + # time, the latter results in test failures in certain + # cases (namely tool shed tests expecting clean database). + __copy_database_template(os.environ['GALAXY_TEST_DB_TEMPLATE'], db_path) + galaxy_database_auto_migrate = True + galaxy_database_connection = 'sqlite:///%s' % db_path tool_shed_global_conf = get_webapp_global_conf() tool_shed_global_conf[ '__file__' ] = 'tool_shed_wsgi.ini.sample' kwargs = dict( admin_users = 'test(a)bx.psu.edu', @@ -311,6 +322,7 @@ admin_users = 'test(a)bx.psu.edu', allow_library_path_paste = True, database_connection = galaxy_database_connection, + database_auto_migrate = galaxy_database_auto_migrate, datatype_converters_config_file = "datatype_converters_conf.xml.sample", enable_tool_shed_check = True, file_path = galaxy_file_path, @@ -449,6 +461,22 @@ else: return 1 + +def __copy_database_template( source, db_path ): + """ + Copy a 'clean' sqlite template database (from file or URL) to specified + database path. + """ + os.makedirs( os.path.dirname( db_path ) ) + if os.path.exists( source ): + shutil.copy( source, db_path ) + assert os.path.exists( db_path ) + elif source.startswith("http"): + urllib.urlretrieve( source, db_path ) + else: + raise Exception( "Failed to copy database template from source %s" % source ) + + if __name__ == "__main__": try: sys.exit( 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: carlfeberhard: UI: temporary workaround for popupmenus v. XSS security
by commits-noreply＠bitbucket.org 26 Nov '13

26 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0712180dc77d/ Changeset: 0712180dc77d User: carlfeberhard Date: 2013-11-27 00:08:42 Summary: UI: temporary workaround for popupmenus v. XSS security Affected #: 2 files diff -r 451af16e671a1be729d0cae6e7ecb1c838af48bd -r 0712180dc77d6df0f19870046562cc34317eb3cc static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -297,18 +297,26 @@ function closePopup( event ){ $( document ).off( 'click.close_popup' ); if( window.parent !== window ){ - $( window.parent.document ).off( "click.close_popup" ); + try { + $( window.parent.document ).off( "click.close_popup" ); + } catch( err ){} } else { - $( 'iframe#galaxy_main' ).contents().off( "click.close_popup" ); + try { + $( 'iframe#galaxy_main' ).contents().off( "click.close_popup" ); + } catch( err ){} } menu.remove(); } $( 'html' ).one( "click.close_popup", closePopup ); if( window.parent !== window ){ - $( window.parent.document ).find( 'html' ).one( "click.close_popup", closePopup ); + try { + $( window.parent.document ).find( 'html' ).one( "click.close_popup", closePopup ); + } catch( err ){} } else { - $( 'iframe#galaxy_main' ).contents().one( "click.close_popup", closePopup ); + try { + $( 'iframe#galaxy_main' ).contents().one( "click.close_popup", closePopup ); + } catch( err ){} } }, diff -r 451af16e671a1be729d0cae6e7ecb1c838af48bd -r 0712180dc77d6df0f19870046562cc34317eb3cc static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var b=this;function a(c){$(document).off("click.close_popup");if(window.parent!==window){$(window.parent.document).off("click.close_popup")}else{$("iframe#galaxy_main").contents().off("click.close_popup")}b.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){$(window.parent.document).find("html").one("click.close_popup",a)}else{$("iframe#galaxy_main").contents().one("click.close_popup",a)}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((a.target)?(' target="'+a.target+'"'):("")),' href="',((a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};var searchInput=function(k){var a=27,h=13,i=$("<div/>"),b={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onsearch:function(l){},minSearchLen:0,escWillClear:true,oninit:function(){}};if(jQuery.type(k)==="object"){k=jQuery.extend(true,b,k)}function d(l){var m=$(this).parent().children("input");m.val("");m.trigger("clear:searchInput");k.onclear()}function j(m,l){$(this).trigger("search:searchInput",l);k.onsearch(l)}function c(){return['<input type="text" name="',k.name,'" placeholder="',k.placeholder,'" ','class="search-query ',k.classes,'" ',"/>"].join("")}function g(){return $(c()).css({width:"100%","padding-right":"24px"}).focus(function(l){$(this).select()}).keyup(function(m){if(m.which===a&&k.escWillClear){d.call(this,m)}else{var l=$(this).val();if((m.which===h)||(k.minSearchLen&&l.length>=k.minSearchLen)){j.call(this,m,l)}else{if(!l.length){d.call(this,m)}}}}).val(k.initialVal)}function f(){return'<span class="search-clear fa fa-times-circle"></span>'}function e(){return $(f()).css({position:"absolute",right:"15px","font-size":"1.4em","line-height":"23px",color:"grey"}).click(function(l){d.call(this,l)})}return i.append([g(),e()])};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b||$("<div/>");this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return 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fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((a.target)?(' target="'+a.target+'"'):("")),' href="',((a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};var searchInput=function(k){var a=27,h=13,i=$("<div/>"),b={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onsearch:function(l){},minSearchLen:0,escWillClear:true,oninit:function(){}};if(jQuery.type(k)==="object"){k=jQuery.extend(true,b,k)}function d(l){var m=$(this).parent().children("input");m.val("");m.trigger("clear:searchInput");k.onclear()}function j(m,l){$(this).trigger("search:searchInput",l);k.onsearch(l)}function c(){return['<input type="text" name="',k.name,'" placeholder="',k.placeholder,'" ','class="search-query ',k.classes,'" ',"/>"].join("")}function g(){return $(c()).css({width:"100%","padding-right":"24px"}).focus(function(l){$(this).select()}).keyup(function(m){if(m.which===a&&k.escWillClear){d.call(this,m)}else{var l=$(this).val();if((m.which===h)||(k.minSearchLen&&l.length>=k.minSearchLen)){j.call(this,m,l)}else{if(!l.length){d.call(this,m)}}}}).val(k.initialVal)}function f(){return'<span class="search-clear fa fa-times-circle"></span>'}function e(){return $(f()).css({position:"absolute",right:"15px","font-size":"1.4em","line-height":"23px",color:"grey"}).click(function(l){d.call(this,l)})}return i.append([g(),e()])};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ 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: jgoecks: Add backbone dependency to trackster module; this is needed for Trackster router to function. Pack script.
by commits-noreply＠bitbucket.org 26 Nov '13

26 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/451af16e671a/ Changeset: 451af16e671a User: jgoecks Date: 2013-11-26 21:46:10 Summary: Add backbone dependency to trackster module; this is needed for Trackster router to function. Pack script. Affected #: 2 files diff -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be -r 451af16e671a1be729d0cae6e7ecb1c838af48bd static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["viz/visualization","viz/trackster_ui"],function(a,b){var c=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(d){browser_router=new a.TrackBrowserRouter(d);Backbone.history.start()},view_existing:function(){var d=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:d.title,vis_id:d.vis_id,dbkey:d.dbkey},d.viewport,d.tracks,d.bookmarks,true);this.init_editor()},view_new:function(){var d=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(e){Galaxy.modal.show({title:"New Visualization",body:d.template_view_new(e),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){d.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(d){var f='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var e=0;e<d.length;e++){f+='<option value="'+d[e][1]+'">'+d[e][0]+"</option>"}f+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return f},create_browser:function(e,d){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e,dbkey:d},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(d){view.add_drawable(b.object_from_template(d,view,view))}})}$("#add-bookmark-button").click(function(){var e=view.chrom+":"+view.low+"-"+view.high,d="Bookmark description";return ui.add_bookmark(e,d,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:c}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f=0;f<e.length;f++){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be -r 451af16e671a1be729d0cae6e7ecb1c838af48bd static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -29,8 +29,8 @@ }); // trackster viewer -define( ["viz/visualization", "viz/trackster_ui"], - function(visualization, trackster_ui) +define( ["libs/backbone/backbone", "viz/visualization", "viz/trackster_ui"], + function(backbone, visualization, trackster_ui) { var TracksterView = Backbone.View.extend( Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Replace Backbone-relational usage with manually model chaining and remove backbone-relational scripts. Fix default colors bug in Trackster. Pack scripts.
by commits-noreply＠bitbucket.org 26 Nov '13

26 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f4832c4ace99/ Changeset: f4832c4ace99 User: jgoecks Date: 2013-11-26 20:50:41 Summary: Replace Backbone-relational usage with manually model chaining and remove backbone-relational scripts. Fix default colors bug in Trackster. Pack scripts. Affected #: 33 files diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.masthead", "libs/backbone/backbone-relational"], function(mod_masthead) { +define(["galaxy.masthead"], function(mod_masthead) { // frame manager var GalaxyFrame = Backbone.View.extend( diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/galaxy.masthead.js --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -3,7 +3,7 @@ */ // dependencies -define(["utils/galaxy.utils", "libs/backbone/backbone-relational"], function(mod_utils) { +define(["utils/galaxy.utils"], function(mod_utils) { // masthead var GalaxyMasthead = Backbone.View.extend( diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/galaxy.menu.js --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.masthead", "libs/backbone/backbone-relational"], function(mod_masthead) { +define(["galaxy.masthead"], function(mod_masthead) { // frame manager var GalaxyMenu = Backbone.Model.extend( diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -3,7 +3,7 @@ */ // dependencies -define(["libs/backbone/backbone-relational"], function() { +define([], function() { // frame manager var GalaxyModal = Backbone.View.extend( diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_masthead, mod_utils) { +define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "utils/galaxy.uploadbox"], function(mod_modal, mod_masthead, mod_utils) { // galaxy upload var GalaxyUpload = Backbone.View.extend( diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/libs/backbone/backbone-relational.js --- a/static/scripts/libs/backbone/backbone-relational.js +++ /dev/null @@ -1,1919 +0,0 @@ -/* vim: set tabstop=4 softtabstop=4 shiftwidth=4 noexpandtab: */ -/** - * Backbone-relational.js 0.8.5 - * (c) 2011-2013 Paul Uithol and contributors (https://github.com/PaulUithol/Backbone-relational/graphs/contributors) - * - * Backbone-relational may be freely distributed under the MIT license; see the accompanying LICENSE.txt. - * For details and documentation: https://github.com/PaulUithol/Backbone-relational. - * Depends on Backbone (and thus on Underscore as well): https://github.com/documentcloud/backbone. - */ -( function( undefined ) { - "use strict"; - - /** - * CommonJS shim - **/ - var _, Backbone, exports; - if ( typeof window === 'undefined' ) { - _ = require( 'underscore' ); - Backbone = require( 'backbone' ); - exports = Backbone; - typeof module === 'undefined' || ( module.exports = exports ); - } - else { - _ = window._; - Backbone = window.Backbone; - exports = window; - } - - Backbone.Relational = { - showWarnings: true - }; - - /** - * Semaphore mixin; can be used as both binary and counting. - **/ - Backbone.Semaphore = { - _permitsAvailable: null, - _permitsUsed: 0, - - acquire: function() { - if ( this._permitsAvailable && this._permitsUsed >= this._permitsAvailable ) { - throw new Error( 'Max permits acquired' ); - } - else { - this._permitsUsed++; - } - }, - - release: function() { - if ( this._permitsUsed === 0 ) { - throw new Error( 'All permits released' ); - } - else { - this._permitsUsed--; - } - }, - - isLocked: function() { - return this._permitsUsed > 0; - }, - - setAvailablePermits: function( amount ) { - if ( this._permitsUsed > amount ) { - throw new Error( 'Available permits cannot be less than used permits' ); - } - this._permitsAvailable = amount; - } - }; - - /** - * A BlockingQueue that accumulates items while blocked (via 'block'), - * and processes them when unblocked (via 'unblock'). - * Process can also be called manually (via 'process'). - */ - Backbone.BlockingQueue = function() { - this._queue = []; - }; - _.extend( Backbone.BlockingQueue.prototype, Backbone.Semaphore, { - _queue: null, - - add: function( func ) { - if ( this.isBlocked() ) { - this._queue.push( func ); - } - else { - func(); - } - }, - - // Some of the queued events may trigger other blocking events. By - // copying the queue here it allows queued events to process closer to - // the natural order. - // - // queue events [ 'A', 'B', 'C' ] - // A handler of 'B' triggers 'D' and 'E' - // By copying `this._queue` this executes: - // [ 'A', 'B', 'D', 'E', 'C' ] - // The same order the would have executed if they didn't have to be - // delayed and queued. - process: function() { - var queue = this._queue; - this._queue = []; - while ( queue && queue.length ) { - queue.shift()(); - } - }, - - block: function() { - this.acquire(); - }, - - unblock: function() { - this.release(); - if ( !this.isBlocked() ) { - this.process(); - } - }, - - isBlocked: function() { - return this.isLocked(); - } - }); - /** - * Global event queue. Accumulates external events ('add:<key>', 'remove:<key>' and 'change:<key>') - * until the top-level object is fully initialized (see 'Backbone.RelationalModel'). - */ - Backbone.Relational.eventQueue = new Backbone.BlockingQueue(); - - /** - * Backbone.Store keeps track of all created (and destruction of) Backbone.RelationalModel. - * Handles lookup for relations. - */ - Backbone.Store = function() { - this._collections = []; - this._reverseRelations = []; - this._orphanRelations = []; - this._subModels = []; - this._modelScopes = [ exports ]; - }; - _.extend( Backbone.Store.prototype, Backbone.Events, { - /** - * Create a new `Relation`. - * @param {Backbone.RelationalModel} [model] - * @param {Object} relation - * @param {Object} [options] - */ - initializeRelation: function( model, relation, options ) { - var type = !_.isString( relation.type ) ? relation.type : Backbone[ relation.type ] || this.getObjectByName( relation.type ); - if ( type && type.prototype instanceof Backbone.Relation ) { - new type( model, relation, options ); // Also pushes the new Relation into `model._relations` - } - else { - Backbone.Relational.showWarnings && typeof console !== 'undefined' && console.warn( 'Relation=%o; missing or invalid relation type!', relation ); - } - }, - - /** - * Add a scope for `getObjectByName` to look for model types by name. - * @param {Object} scope - */ - addModelScope: function( scope ) { - this._modelScopes.push( scope ); - }, - - /** - * Remove a scope. - * @param {Object} scope - */ - removeModelScope: function( scope ) { - this._modelScopes = _.without( this._modelScopes, scope ); - }, - - /** - * Add a set of subModelTypes to the store, that can be used to resolve the '_superModel' - * for a model later in 'setupSuperModel'. - * - * @param {Backbone.RelationalModel} subModelTypes - * @param {Backbone.RelationalModel} superModelType - */ - addSubModels: function( subModelTypes, superModelType ) { - this._subModels.push({ - 'superModelType': superModelType, - 'subModels': subModelTypes - }); - }, - - /** - * Check if the given modelType is registered as another model's subModel. If so, add it to the super model's - * '_subModels', and set the modelType's '_superModel', '_subModelTypeName', and '_subModelTypeAttribute'. - * - * @param {Backbone.RelationalModel} modelType - */ - setupSuperModel: function( modelType ) { - _.find( this._subModels, function( subModelDef ) { - return _.find( subModelDef.subModels || [], function( subModelTypeName, typeValue ) { - var subModelType = this.getObjectByName( subModelTypeName ); - - if ( modelType === subModelType ) { - // Set 'modelType' as a child of the found superModel - subModelDef.superModelType._subModels[ typeValue ] = modelType; - - // Set '_superModel', '_subModelTypeValue', and '_subModelTypeAttribute' on 'modelType'. - modelType._superModel = subModelDef.superModelType; - modelType._subModelTypeValue = typeValue; - modelType._subModelTypeAttribute = subModelDef.superModelType.prototype.subModelTypeAttribute; - return true; - } - }, this ); - }, this ); - }, - - /** - * Add a reverse relation. Is added to the 'relations' property on model's prototype, and to - * existing instances of 'model' in the store as well. - * @param {Object} relation - * @param {Backbone.RelationalModel} relation.model - * @param {String} relation.type - * @param {String} relation.key - * @param {String|Object} relation.relatedModel - */ - addReverseRelation: function( relation ) { - var exists = _.any( this._reverseRelations, function( rel ) { - return _.all( relation || [], function( val, key ) { - return val === rel[ key ]; - }); - }); - - if ( !exists && relation.model && relation.type ) { - this._reverseRelations.push( relation ); - this._addRelation( relation.model, relation ); - this.retroFitRelation( relation ); - } - }, - - /** - * Deposit a `relation` for which the `relatedModel` can't be resolved at the moment. - * - * @param {Object} relation - */ - addOrphanRelation: function( relation ) { - var exists = _.any( this._orphanRelations, function( rel ) { - return _.all( relation || [], function( val, key ) { - return val === rel[ key ]; - }); - }); - - if ( !exists && relation.model && relation.type ) { - this._orphanRelations.push( relation ); - } - }, - - /** - * Try to initialize any `_orphanRelation`s - */ - processOrphanRelations: function() { - // Make sure to operate on a copy since we're removing while iterating - _.each( this._orphanRelations.slice( 0 ), function( rel ) { - var relatedModel = Backbone.Relational.store.getObjectByName( rel.relatedModel ); - if ( relatedModel ) { - this.initializeRelation( null, rel ); - this._orphanRelations = _.without( this._orphanRelations, rel ); - } - }, this ); - }, - - /** - * - * @param {Backbone.RelationalModel.constructor} type - * @param {Object} relation - * @private - */ - _addRelation: function( type, relation ) { - if ( !type.prototype.relations ) { - type.prototype.relations = []; - } - type.prototype.relations.push( relation ); - - _.each( type._subModels || [], function( subModel ) { - this._addRelation( subModel, relation ); - }, this ); - }, - - /** - * Add a 'relation' to all existing instances of 'relation.model' in the store - * @param {Object} relation - */ - retroFitRelation: function( relation ) { - var coll = this.getCollection( relation.model, false ); - coll && coll.each( function( model ) { - if ( !( model instanceof relation.model ) ) { - return; - } - - new relation.type( model, relation ); - }, this ); - }, - - /** - * Find the Store's collection for a certain type of model. - * @param {Backbone.RelationalModel} type - * @param {Boolean} [create=true] Should a collection be created if none is found? - * @return {Backbone.Collection} A collection if found (or applicable for 'model'), or null - */ - getCollection: function( type, create ) { - if ( type instanceof Backbone.RelationalModel ) { - type = type.constructor; - } - - var rootModel = type; - while ( rootModel._superModel ) { - rootModel = rootModel._superModel; - } - - var coll = _.find( this._collections, function(item) { - return item.model === rootModel; - }); - - if ( !coll && create !== false ) { - coll = this._createCollection( rootModel ); - } - - return coll; - }, - - /** - * Find a model type on one of the modelScopes by name. Names are split on dots. - * @param {String} name - * @return {Object} - */ - getObjectByName: function( name ) { - var parts = name.split( '.' ), - type = null; - - _.find( this._modelScopes, function( scope ) { - type = _.reduce( parts || [], function( memo, val ) { - return memo ? memo[ val ] : undefined; - }, scope ); - - if ( type && type !== scope ) { - return true; - } - }, this ); - - return type; - }, - - _createCollection: function( type ) { - var coll; - - // If 'type' is an instance, take its constructor - if ( type instanceof Backbone.RelationalModel ) { - type = type.constructor; - } - - // Type should inherit from Backbone.RelationalModel. - if ( type.prototype instanceof Backbone.RelationalModel ) { - coll = new Backbone.Collection(); - coll.model = type; - - this._collections.push( coll ); - } - - return coll; - }, - - /** - * Find the attribute that is to be used as the `id` on a given object - * @param type - * @param {String|Number|Object|Backbone.RelationalModel} item - * @return {String|Number} - */ - resolveIdForItem: function( type, item ) { - var id = _.isString( item ) || _.isNumber( item ) ? item : null; - - if ( id === null ) { - if ( item instanceof Backbone.RelationalModel ) { - id = item.id; - } - else if ( _.isObject( item ) ) { - id = item[ type.prototype.idAttribute ]; - } - } - - // Make all falsy values `null` (except for 0, which could be an id.. see '/issues/179') - if ( !id && id !== 0 ) { - id = null; - } - - return id; - }, - - /** - * Find a specific model of a certain `type` in the store - * @param type - * @param {String|Number|Object|Backbone.RelationalModel} item - */ - find: function( type, item ) { - var id = this.resolveIdForItem( type, item ); - var coll = this.getCollection( type ); - - // Because the found object could be of any of the type's superModel - // types, only return it if it's actually of the type asked for. - if ( coll ) { - var obj = coll.get( id ); - - if ( obj instanceof type ) { - return obj; - } - } - - return null; - }, - - /** - * Add a 'model' to its appropriate collection. Retain the original contents of 'model.collection'. - * @param {Backbone.RelationalModel} model - */ - register: function( model ) { - var coll = this.getCollection( model ); - - if ( coll ) { - var modelColl = model.collection; - coll.add( model ); - this.listenTo( model, 'destroy', this.unregister, this ); - this.listenTo( model, 'relational:unregister', this.unregister, this ); - model.collection = modelColl; - } - }, - - /** - * Check if the given model may use the given `id` - * @param model - * @param [id] - */ - checkId: function( model, id ) { - var coll = this.getCollection( model ), - duplicate = coll && coll.get( id ); - - if ( duplicate && model !== duplicate ) { - if ( Backbone.Relational.showWarnings && typeof console !== 'undefined' ) { - console.warn( 'Duplicate id! Old RelationalModel=%o, new RelationalModel=%o', duplicate, model ); - } - - throw new Error( "Cannot instantiate more than one Backbone.RelationalModel with the same id per type!" ); - } - }, - - /** - * Explicitly update a model's id in its store collection - * @param {Backbone.RelationalModel} model - */ - update: function( model ) { - var coll = this.getCollection( model ); - // This triggers updating the lookup indices kept in a collection - coll._onModelEvent( 'change:' + model.idAttribute, model, coll ); - - // Trigger an event on model so related models (having the model's new id in their keyContents) can add it. - model.trigger( 'relational:change:id', model, coll ); - }, - - /** - * Remove a 'model' from the store. - * @param {Backbone.RelationalModel} model - */ - unregister: function( model, collection, options ) { - this.stopListening( model ); - var coll = this.getCollection( model ); - coll && coll.remove( model, options ); - }, - - /** - * Reset the `store` to it's original state. The `reverseRelations` are kept though, since attempting to - * re-initialize these on models would lead to a large amount of warnings. - */ - reset: function() { - this.stopListening(); - this._collections = []; - this._subModels = []; - this._modelScopes = [ exports ]; - } - }); - Backbone.Relational.store = new Backbone.Store(); - - /** - * The main Relation class, from which 'HasOne' and 'HasMany' inherit. Internally, 'relational:<key>' events - * are used to regulate addition and removal of models from relations. - * - * @param {Backbone.RelationalModel} [instance] Model that this relation is created for. If no model is supplied, - * Relation just tries to instantiate it's `reverseRelation` if specified, and bails out after that. - * @param {Object} options - * @param {string} options.key - * @param {Backbone.RelationalModel.constructor} options.relatedModel - * @param {Boolean|String} [options.includeInJSON=true] Serialize the given attribute for related model(s)' in toJSON, or just their ids. - * @param {Boolean} [options.createModels=true] Create objects from the contents of keys if the object is not found in Backbone.store. - * @param {Object} [options.reverseRelation] Specify a bi-directional relation. If provided, Relation will reciprocate - * the relation to the 'relatedModel'. Required and optional properties match 'options', except that it also needs - * {Backbone.Relation|String} type ('HasOne' or 'HasMany'). - * @param {Object} opts - */ - Backbone.Relation = function( instance, options, opts ) { - this.instance = instance; - // Make sure 'options' is sane, and fill with defaults from subclasses and this object's prototype - options = _.isObject( options ) ? options : {}; - this.reverseRelation = _.defaults( options.reverseRelation || {}, this.options.reverseRelation ); - this.options = _.defaults( options, this.options, Backbone.Relation.prototype.options ); - - this.reverseRelation.type = !_.isString( this.reverseRelation.type ) ? this.reverseRelation.type : - Backbone[ this.reverseRelation.type ] || Backbone.Relational.store.getObjectByName( this.reverseRelation.type ); - - this.key = this.options.key; - this.keySource = this.options.keySource || this.key; - this.keyDestination = this.options.keyDestination || this.keySource || this.key; - - this.model = this.options.model || this.instance.constructor; - this.relatedModel = this.options.relatedModel; - if ( _.isString( this.relatedModel ) ) { - this.relatedModel = Backbone.Relational.store.getObjectByName( this.relatedModel ); - } - - if ( !this.checkPreconditions() ) { - return; - } - - // Add the reverse relation on 'relatedModel' to the store's reverseRelations - if ( !this.options.isAutoRelation && this.reverseRelation.type && this.reverseRelation.key ) { - Backbone.Relational.store.addReverseRelation( _.defaults( { - isAutoRelation: true, - model: this.relatedModel, - relatedModel: this.model, - reverseRelation: this.options // current relation is the 'reverseRelation' for its own reverseRelation - }, - this.reverseRelation // Take further properties from this.reverseRelation (type, key, etc.) - ) ); - } - - if ( instance ) { - var contentKey = this.keySource; - if ( contentKey !== this.key && typeof this.instance.get( this.key ) === 'object' ) { - contentKey = this.key; - } - - this.setKeyContents( this.instance.get( contentKey ) ); - this.relatedCollection = Backbone.Relational.store.getCollection( this.relatedModel ); - - // Explicitly clear 'keySource', to prevent a leaky abstraction if 'keySource' differs from 'key'. - if ( this.keySource !== this.key ) { - delete this.instance.attributes[ this.keySource ]; - } - - // Add this Relation to instance._relations - this.instance._relations[ this.key ] = this; - - this.initialize( opts ); - - if ( this.options.autoFetch ) { - this.instance.fetchRelated( this.key, _.isObject( this.options.autoFetch ) ? this.options.autoFetch : {} ); - } - - // When 'relatedModel' are created or destroyed, check if it affects this relation. - this.listenTo( this.instance, 'destroy', this.destroy ) - .listenTo( this.relatedCollection, 'relational:add relational:change:id', this.tryAddRelated ) - .listenTo( this.relatedCollection, 'relational:remove', this.removeRelated ) - } - }; - // Fix inheritance :\ - Backbone.Relation.extend = Backbone.Model.extend; - // Set up all inheritable **Backbone.Relation** properties and methods. - _.extend( Backbone.Relation.prototype, Backbone.Events, Backbone.Semaphore, { - options: { - createModels: true, - includeInJSON: true, - isAutoRelation: false, - autoFetch: false, - parse: false - }, - - instance: null, - key: null, - keyContents: null, - relatedModel: null, - relatedCollection: null, - reverseRelation: null, - related: null, - - /** - * Check several pre-conditions. - * @return {Boolean} True if pre-conditions are satisfied, false if they're not. - */ - checkPreconditions: function() { - var i = this.instance, - k = this.key, - m = this.model, - rm = this.relatedModel, - warn = Backbone.Relational.showWarnings && typeof console !== 'undefined'; - - if ( !m || !k || !rm ) { - warn && console.warn( 'Relation=%o: missing model, key or relatedModel (%o, %o, %o).', this, m, k, rm ); - return false; - } - // Check if the type in 'model' inherits from Backbone.RelationalModel - if ( !( m.prototype instanceof Backbone.RelationalModel ) ) { - warn && console.warn( 'Relation=%o: model does not inherit from Backbone.RelationalModel (%o).', this, i ); - return false; - } - // Check if the type in 'relatedModel' inherits from Backbone.RelationalModel - if ( !( rm.prototype instanceof Backbone.RelationalModel ) ) { - warn && console.warn( 'Relation=%o: relatedModel does not inherit from Backbone.RelationalModel (%o).', this, rm ); - return false; - } - // Check if this is not a HasMany, and the reverse relation is HasMany as well - if ( this instanceof Backbone.HasMany && this.reverseRelation.type === Backbone.HasMany ) { - warn && console.warn( 'Relation=%o: relation is a HasMany, and the reverseRelation is HasMany as well.', this ); - return false; - } - // Check if we're not attempting to create a relationship on a `key` that's already used. - if ( i && _.keys( i._relations ).length ) { - var existing = _.find( i._relations, function( rel ) { - return rel.key === k; - }, this ); - - if ( existing ) { - warn && console.warn( 'Cannot create relation=%o on %o for model=%o: already taken by relation=%o.', - this, k, i, existing ); - return false; - } - } - - return true; - }, - - /** - * Set the related model(s) for this relation - * @param {Backbone.Model|Backbone.Collection} related - */ - setRelated: function( related ) { - this.related = related; - - this.instance.acquire(); - this.instance.attributes[ this.key ] = related; - this.instance.release(); - }, - - /** - * Determine if a relation (on a different RelationalModel) is the reverse - * relation of the current one. - * @param {Backbone.Relation} relation - * @return {Boolean} - */ - _isReverseRelation: function( relation ) { - return relation.instance instanceof this.relatedModel && this.reverseRelation.key === relation.key && - this.key === relation.reverseRelation.key; - }, - - /** - * Get the reverse relations (pointing back to 'this.key' on 'this.instance') for the currently related model(s). - * @param {Backbone.RelationalModel} [model] Get the reverse relations for a specific model. - * If not specified, 'this.related' is used. - * @return {Backbone.Relation[]} - */ - getReverseRelations: function( model ) { - var reverseRelations = []; - // Iterate over 'model', 'this.related.models' (if this.related is a Backbone.Collection), or wrap 'this.related' in an array. - var models = !_.isUndefined( model ) ? [ model ] : this.related && ( this.related.models || [ this.related ] ); - _.each( models || [], function( related ) { - _.each( related.getRelations() || [], function( relation ) { - if ( this._isReverseRelation( relation ) ) { - reverseRelations.push( relation ); - } - }, this ); - }, this ); - - return reverseRelations; - }, - - /** - * When `this.instance` is destroyed, cleanup our relations. - * Get reverse relation, call removeRelated on each. - */ - destroy: function() { - this.stopListening(); - - if ( this instanceof Backbone.HasOne ) { - this.setRelated( null ); - } - else if ( this instanceof Backbone.HasMany ) { - this.setRelated( this._prepareCollection() ); - } - - _.each( this.getReverseRelations(), function( relation ) { - relation.removeRelated( this.instance ); - }, this ); - } - }); - - Backbone.HasOne = Backbone.Relation.extend({ - options: { - reverseRelation: { type: 'HasMany' } - }, - - initialize: function( opts ) { - this.listenTo( this.instance, 'relational:change:' + this.key, this.onChange ); - - var related = this.findRelated( opts ); - this.setRelated( related ); - - // Notify new 'related' object of the new relation. - _.each( this.getReverseRelations(), function( relation ) { - relation.addRelated( this.instance, opts ); - }, this ); - }, - - /** - * Find related Models. - * @param {Object} [options] - * @return {Backbone.Model} - */ - findRelated: function( options ) { - var related = null; - - options = _.defaults( { parse: this.options.parse }, options ); - - if ( this.keyContents instanceof this.relatedModel ) { - related = this.keyContents; - } - else if ( this.keyContents || this.keyContents === 0 ) { // since 0 can be a valid `id` as well - var opts = _.defaults( { create: this.options.createModels }, options ); - related = this.relatedModel.findOrCreate( this.keyContents, opts ); - } - - // Nullify `keyId` if we have a related model; in case it was already part of the relation - if ( this.related ) { - this.keyId = null; - } - - return related; - }, - - /** - * Normalize and reduce `keyContents` to an `id`, for easier comparison - * @param {String|Number|Backbone.Model} keyContents - */ - setKeyContents: function( keyContents ) { - this.keyContents = keyContents; - this.keyId = Backbone.Relational.store.resolveIdForItem( this.relatedModel, this.keyContents ); - }, - - /** - * Event handler for `change:<key>`. - * If the key is changed, notify old & new reverse relations and initialize the new relation. - */ - onChange: function( model, attr, options ) { - // Don't accept recursive calls to onChange (like onChange->findRelated->findOrCreate->initializeRelations->addRelated->onChange) - if ( this.isLocked() ) { - return; - } - this.acquire(); - options = options ? _.clone( options ) : {}; - - // 'options.__related' is set by 'addRelated'/'removeRelated'. If it is set, the change - // is the result of a call from a relation. If it's not, the change is the result of - // a 'set' call on this.instance. - var changed = _.isUndefined( options.__related ), - oldRelated = changed ? this.related : options.__related; - - if ( changed ) { - this.setKeyContents( attr ); - var related = this.findRelated( options ); - this.setRelated( related ); - } - - // Notify old 'related' object of the terminated relation - if ( oldRelated && this.related !== oldRelated ) { - _.each( this.getReverseRelations( oldRelated ), function( relation ) { - relation.removeRelated( this.instance, null, options ); - }, this ); - } - - // Notify new 'related' object of the new relation. Note we do re-apply even if this.related is oldRelated; - // that can be necessary for bi-directional relations if 'this.instance' was created after 'this.related'. - // In that case, 'this.instance' will already know 'this.related', but the reverse might not exist yet. - _.each( this.getReverseRelations(), function( relation ) { - relation.addRelated( this.instance, options ); - }, this ); - - // Fire the 'change:<key>' event if 'related' was updated - if ( !options.silent && this.related !== oldRelated ) { - var dit = this; - this.changed = true; - Backbone.Relational.eventQueue.add( function() { - dit.instance.trigger( 'change:' + dit.key, dit.instance, dit.related, options, true ); - dit.changed = false; - }); - } - this.release(); - }, - - /** - * If a new 'this.relatedModel' appears in the 'store', try to match it to the last set 'keyContents' - */ - tryAddRelated: function( model, coll, options ) { - if ( ( this.keyId || this.keyId === 0 ) && model.id === this.keyId ) { // since 0 can be a valid `id` as well - this.addRelated( model, options ); - this.keyId = null; - } - }, - - addRelated: function( model, options ) { - // Allow 'model' to set up its relations before proceeding. - // (which can result in a call to 'addRelated' from a relation of 'model') - var dit = this; - model.queue( function() { - if ( model !== dit.related ) { - var oldRelated = dit.related || null; - dit.setRelated( model ); - dit.onChange( dit.instance, model, _.defaults( { __related: oldRelated }, options ) ); - } - }); - }, - - removeRelated: function( model, coll, options ) { - if ( !this.related ) { - return; - } - - if ( model === this.related ) { - var oldRelated = this.related || null; - this.setRelated( null ); - this.onChange( this.instance, model, _.defaults( { __related: oldRelated }, options ) ); - } - } - }); - - Backbone.HasMany = Backbone.Relation.extend({ - collectionType: null, - - options: { - reverseRelation: { type: 'HasOne' }, - collectionType: Backbone.Collection, - collectionKey: true, - collectionOptions: {} - }, - - initialize: function( opts ) { - this.listenTo( this.instance, 'relational:change:' + this.key, this.onChange ); - - // Handle a custom 'collectionType' - this.collectionType = this.options.collectionType; - if ( _.isString( this.collectionType ) ) { - this.collectionType = Backbone.Relational.store.getObjectByName( this.collectionType ); - } - if ( this.collectionType !== Backbone.Collection && !( this.collectionType.prototype instanceof Backbone.Collection ) ) { - throw new Error( '`collectionType` must inherit from Backbone.Collection' ); - } - - var related = this.findRelated( opts ); - this.setRelated( related ); - }, - - /** - * Bind events and setup collectionKeys for a collection that is to be used as the backing store for a HasMany. - * If no 'collection' is supplied, a new collection will be created of the specified 'collectionType' option. - * @param {Backbone.Collection} [collection] - * @return {Backbone.Collection} - */ - _prepareCollection: function( collection ) { - if ( this.related ) { - this.stopListening( this.related ); - } - - if ( !collection || !( collection instanceof Backbone.Collection ) ) { - var options = _.isFunction( this.options.collectionOptions ) ? - this.options.collectionOptions( this.instance ) : this.options.collectionOptions; - - collection = new this.collectionType( null, options ); - } - - collection.model = this.relatedModel; - - if ( this.options.collectionKey ) { - var key = this.options.collectionKey === true ? this.options.reverseRelation.key : this.options.collectionKey; - - if ( collection[ key ] && collection[ key ] !== this.instance ) { - if ( Backbone.Relational.showWarnings && typeof console !== 'undefined' ) { - console.warn( 'Relation=%o; collectionKey=%s already exists on collection=%o', this, key, this.options.collectionKey ); - } - } - else if ( key ) { - collection[ key ] = this.instance; - } - } - - this.listenTo( collection, 'relational:add', this.handleAddition ) - .listenTo( collection, 'relational:remove', this.handleRemoval ) - .listenTo( collection, 'relational:reset', this.handleReset ); - - return collection; - }, - - /** - * Find related Models. - * @param {Object} [options] - * @return {Backbone.Collection} - */ - findRelated: function( options ) { - var related = null; - - options = _.defaults( { parse: this.options.parse }, options ); - - // Replace 'this.related' by 'this.keyContents' if it is a Backbone.Collection - if ( this.keyContents instanceof Backbone.Collection ) { - this._prepareCollection( this.keyContents ); - related = this.keyContents; - } - // Otherwise, 'this.keyContents' should be an array of related object ids. - // Re-use the current 'this.related' if it is a Backbone.Collection; otherwise, create a new collection. - else { - var toAdd = []; - - _.each( this.keyContents, function( attributes ) { - if ( attributes instanceof this.relatedModel ) { - var model = attributes; - } - else { - // If `merge` is true, update models here, instead of during update. - model = this.relatedModel.findOrCreate( attributes, - _.extend( { merge: true }, options, { create: this.options.createModels } ) - ); - } - - model && toAdd.push( model ); - }, this ); - - if ( this.related instanceof Backbone.Collection ) { - related = this.related; - } - else { - related = this._prepareCollection(); - } - - // By now, both `merge` and `parse` will already have been executed for models if they were specified. - // Disable them to prevent additional calls. - related.set( toAdd, _.defaults( { merge: false, parse: false }, options ) ); - } - - // Remove entries from `keyIds` that were already part of the relation (and are thus 'unchanged') - this.keyIds = _.difference( this.keyIds, _.pluck( related.models, 'id' ) ); - - return related; - }, - - /** - * Normalize and reduce `keyContents` to a list of `ids`, for easier comparison - * @param {String|Number|String[]|Number[]|Backbone.Collection} keyContents - */ - setKeyContents: function( keyContents ) { - this.keyContents = keyContents instanceof Backbone.Collection ? keyContents : null; - this.keyIds = []; - - if ( !this.keyContents && ( keyContents || keyContents === 0 ) ) { // since 0 can be a valid `id` as well - // Handle cases the an API/user supplies just an Object/id instead of an Array - this.keyContents = _.isArray( keyContents ) ? keyContents : [ keyContents ]; - - _.each( this.keyContents, function( item ) { - var itemId = Backbone.Relational.store.resolveIdForItem( this.relatedModel, item ); - if ( itemId || itemId === 0 ) { - this.keyIds.push( itemId ); - } - }, this ); - } - }, - - /** - * Event handler for `change:<key>`. - * If the contents of the key are changed, notify old & new reverse relations and initialize the new relation. - */ - onChange: function( model, attr, options ) { - options = options ? _.clone( options ) : {}; - this.setKeyContents( attr ); - this.changed = false; - - var related = this.findRelated( options ); - this.setRelated( related ); - - if ( !options.silent ) { - var dit = this; - Backbone.Relational.eventQueue.add( function() { - // The `changed` flag can be set in `handleAddition` or `handleRemoval` - if ( dit.changed ) { - dit.instance.trigger( 'change:' + dit.key, dit.instance, dit.related, options, true ); - dit.changed = false; - } - }); - } - }, - - /** - * When a model is added to a 'HasMany', trigger 'add' on 'this.instance' and notify reverse relations. - * (should be 'HasOne', must set 'this.instance' as their related). - */ - handleAddition: function( model, coll, options ) { - //console.debug('handleAddition called; args=%o', arguments); - options = options ? _.clone( options ) : {}; - this.changed = true; - - _.each( this.getReverseRelations( model ), function( relation ) { - relation.addRelated( this.instance, options ); - }, this ); - - // Only trigger 'add' once the newly added model is initialized (so, has its relations set up) - var dit = this; - !options.silent && Backbone.Relational.eventQueue.add( function() { - dit.instance.trigger( 'add:' + dit.key, model, dit.related, options ); - }); - }, - - /** - * When a model is removed from a 'HasMany', trigger 'remove' on 'this.instance' and notify reverse relations. - * (should be 'HasOne', which should be nullified) - */ - handleRemoval: function( model, coll, options ) { - //console.debug('handleRemoval called; args=%o', arguments); - options = options ? _.clone( options ) : {}; - this.changed = true; - - _.each( this.getReverseRelations( model ), function( relation ) { - relation.removeRelated( this.instance, null, options ); - }, this ); - - var dit = this; - !options.silent && Backbone.Relational.eventQueue.add( function() { - dit.instance.trigger( 'remove:' + dit.key, model, dit.related, options ); - }); - }, - - handleReset: function( coll, options ) { - var dit = this; - options = options ? _.clone( options ) : {}; - !options.silent && Backbone.Relational.eventQueue.add( function() { - dit.instance.trigger( 'reset:' + dit.key, dit.related, options ); - }); - }, - - tryAddRelated: function( model, coll, options ) { - var item = _.contains( this.keyIds, model.id ); - - if ( item ) { - this.addRelated( model, options ); - this.keyIds = _.without( this.keyIds, model.id ); - } - }, - - addRelated: function( model, options ) { - // Allow 'model' to set up its relations before proceeding. - // (which can result in a call to 'addRelated' from a relation of 'model') - var dit = this; - model.queue( function() { - if ( dit.related && !dit.related.get( model ) ) { - dit.related.add( model, _.defaults( { parse: false }, options ) ); - } - }); - }, - - removeRelated: function( model, coll, options ) { - if ( this.related.get( model ) ) { - this.related.remove( model, options ); - } - } - }); - - /** - * A type of Backbone.Model that also maintains relations to other models and collections. - * New events when compared to the original: - * - 'add:<key>' (model, related collection, options) - * - 'remove:<key>' (model, related collection, options) - * - 'change:<key>' (model, related model or collection, options) - */ - Backbone.RelationalModel = Backbone.Model.extend({ - relations: null, // Relation descriptions on the prototype - _relations: null, // Relation instances - _isInitialized: false, - _deferProcessing: false, - _queue: null, - _attributeChangeFired: false, // Keeps track of `change` event firing under some conditions (like nested `set`s) - - subModelTypeAttribute: 'type', - subModelTypes: null, - - constructor: function( attributes, options ) { - // Nasty hack, for cases like 'model.get( <HasMany key> ).add( item )'. - // Defer 'processQueue', so that when 'Relation.createModels' is used we trigger 'HasMany' - // collection events only after the model is really fully set up. - // Example: event for "p.on( 'add:jobs' )" -> "p.get('jobs').add( { company: c.id, person: p.id } )". - if ( options && options.collection ) { - var dit = this, - collection = this.collection = options.collection; - - // Prevent `collection` from cascading down to nested models; they shouldn't go into this `if` clause. - delete options.collection; - - this._deferProcessing = true; - - var processQueue = function( model ) { - if ( model === dit ) { - dit._deferProcessing = false; - dit.processQueue(); - collection.off( 'relational:add', processQueue ); - } - }; - collection.on( 'relational:add', processQueue ); - - // So we do process the queue eventually, regardless of whether this model actually gets added to 'options.collection'. - _.defer( function() { - processQueue( dit ); - }); - } - - Backbone.Relational.store.processOrphanRelations(); - - this._queue = new Backbone.BlockingQueue(); - this._queue.block(); - Backbone.Relational.eventQueue.block(); - - try { - Backbone.Model.apply( this, arguments ); - } - finally { - // Try to run the global queue holding external events - Backbone.Relational.eventQueue.unblock(); - } - }, - - /** - * Override 'trigger' to queue 'change' and 'change:*' events - */ - trigger: function( eventName ) { - if ( eventName.length > 5 && eventName.indexOf( 'change' ) === 0 ) { - var dit = this, - args = arguments; - - Backbone.Relational.eventQueue.add( function() { - if ( !dit._isInitialized ) { - return; - } - - // Determine if the `change` event is still valid, now that all relations are populated - var changed = true; - if ( eventName === 'change' ) { - // `hasChanged` may have gotten reset by nested calls to `set`. - changed = dit.hasChanged() || dit._attributeChangeFired; - dit._attributeChangeFired = false; - } - else { - var attr = eventName.slice( 7 ), - rel = dit.getRelation( attr ); - - if ( rel ) { - // If `attr` is a relation, `change:attr` get triggered from `Relation.onChange`. - // These take precedence over `change:attr` events triggered by `Model.set`. - // The relation sets a fourth attribute to `true`. If this attribute is present, - // continue triggering this event; otherwise, it's from `Model.set` and should be stopped. - changed = ( args[ 4 ] === true ); - - // If this event was triggered by a relation, set the right value in `this.changed` - // (a Collection or Model instead of raw data). - if ( changed ) { - dit.changed[ attr ] = args[ 2 ]; - } - // Otherwise, this event is from `Model.set`. If the relation doesn't report a change, - // remove attr from `dit.changed` so `hasChanged` doesn't take it into account. - else if ( !rel.changed ) { - delete dit.changed[ attr ]; - } - } - else if ( changed ) { - dit._attributeChangeFired = true; - } - } - - changed && Backbone.Model.prototype.trigger.apply( dit, args ); - }); - } - else { - Backbone.Model.prototype.trigger.apply( this, arguments ); - } - - return this; - }, - - /** - * Initialize Relations present in this.relations; determine the type (HasOne/HasMany), then creates a new instance. - * Invoked in the first call so 'set' (which is made from the Backbone.Model constructor). - */ - initializeRelations: function( options ) { - this.acquire(); // Setting up relations often also involve calls to 'set', and we only want to enter this function once - this._relations = {}; - - _.each( _.result(this, 'relations') || [], function( rel ) { - Backbone.Relational.store.initializeRelation( this, rel, options ); - }, this ); - - this._isInitialized = true; - this.release(); - this.processQueue(); - }, - - /** - * When new values are set, notify this model's relations (also if options.silent is set). - * (Relation.setRelated locks this model before calling 'set' on it to prevent loops) - */ - updateRelations: function( options ) { - if ( this._isInitialized && !this.isLocked() ) { - _.each( this._relations, function( rel ) { - // Update from data in `rel.keySource` if data got set in there, or `rel.key` otherwise - var val = this.attributes[ rel.keySource ] || this.attributes[ rel.key ]; - if ( rel.related !== val ) { - this.trigger( 'relational:change:' + rel.key, this, val, options || {} ); - } - - // Explicitly clear 'keySource', to prevent a leaky abstraction if 'keySource' differs from 'key'. - if ( rel.keySource !== rel.key ) { - delete rel.instance.attributes[ rel.keySource ]; - } - }, this ); - } - }, - - /** - * Either add to the queue (if we're not initialized yet), or execute right away. - */ - queue: function( func ) { - this._queue.add( func ); - }, - - /** - * Process _queue - */ - processQueue: function() { - if ( this._isInitialized && !this._deferProcessing && this._queue.isBlocked() ) { - this._queue.unblock(); - } - }, - - /** - * Get a specific relation. - * @param key {string} The relation key to look for. - * @return {Backbone.Relation} An instance of 'Backbone.Relation', if a relation was found for 'key', or null. - */ - getRelation: function( key ) { - return this._relations[ key ]; - }, - - /** - * Get all of the created relations. - * @return {Backbone.Relation[]} - */ - getRelations: function() { - return _.values( this._relations ); - }, - - /** - * Retrieve related objects. - * @param key {string} The relation key to fetch models for. - * @param [options] {Object} Options for 'Backbone.Model.fetch' and 'Backbone.sync'. - * @param [refresh=false] {boolean} Fetch existing models from the server as well (in order to update them). - * @return {jQuery.when[]} An array of request objects - */ - fetchRelated: function( key, options, refresh ) { - // Set default `options` for fetch - options = _.extend( { update: true, remove: false }, options ); - - var setUrl, - requests = [], - rel = this.getRelation( key ), - idsToFetch = rel && ( ( rel.keyIds && rel.keyIds.slice( 0 ) ) || ( ( rel.keyId || rel.keyId === 0 ) ? [ rel.keyId ] : [] ) ); - - // On `refresh`, add the ids for current models in the relation to `idsToFetch` - if ( refresh ) { - var models = rel.related instanceof Backbone.Collection ? rel.related.models : [ rel.related ]; - _.each( models, function( model ) { - if ( model.id || model.id === 0 ) { - idsToFetch.push( model.id ); - } - }); - } - - if ( idsToFetch && idsToFetch.length ) { - // Find (or create) a model for each one that is to be fetched - var created = [], - models = _.map( idsToFetch, function( id ) { - var model = Backbone.Relational.store.find( rel.relatedModel, id ); - - if ( !model ) { - var attrs = {}; - attrs[ rel.relatedModel.prototype.idAttribute ] = id; - model = rel.relatedModel.findOrCreate( attrs, options ); - created.push( model ); - } - - return model; - }, this ); - - // Try if the 'collection' can provide a url to fetch a set of models in one request. - if ( rel.related instanceof Backbone.Collection && _.isFunction( rel.related.url ) ) { - setUrl = rel.related.url( models ); - } - - // An assumption is that when 'Backbone.Collection.url' is a function, it can handle building of set urls. - // To make sure it can, test if the url we got by supplying a list of models to fetch is different from - // the one supplied for the default fetch action (without args to 'url'). - if ( setUrl && setUrl !== rel.related.url() ) { - var opts = _.defaults( - { - error: function() { - var args = arguments; - _.each( created, function( model ) { - model.trigger( 'destroy', model, model.collection, options ); - options.error && options.error.apply( model, args ); - }); - }, - url: setUrl - }, - options - ); - - requests = [ rel.related.fetch( opts ) ]; - } - else { - requests = _.map( models, function( model ) { - var opts = _.defaults( - { - error: function() { - if ( _.contains( created, model ) ) { - model.trigger( 'destroy', model, model.collection, options ); - options.error && options.error.apply( model, arguments ); - } - } - }, - options - ); - return model.fetch( opts ); - }, this ); - } - } - - return requests; - }, - - get: function( attr ) { - var originalResult = Backbone.Model.prototype.get.call( this, attr ); - - // Use `originalResult` get if dotNotation not enabled or not required because no dot is in `attr` - if ( !this.dotNotation || attr.indexOf( '.' ) === -1 ) { - return originalResult; - } - - // Go through all splits and return the final result - var splits = attr.split( '.' ); - var result = _.reduce(splits, function( model, split ) { - if ( _.isNull(model) || _.isUndefined( model ) ) { - // Return undefined if the path cannot be expanded - return undefined; - } - if ( !( model instanceof Backbone.Model ) ) { - throw new Error( 'Attribute must be an instanceof Backbone.Model. Is: ' + model + ', currentSplit: ' + split ); - } - - return Backbone.Model.prototype.get.call( model, split ); - }, this ); - - if ( originalResult !== undefined && result !== undefined ) { - throw new Error( "Ambiguous result for '" + attr + "'. direct result: " + originalResult + ", dotNotation: " + result ); - } - - return originalResult || result; - }, - - set: function( key, value, options ) { - Backbone.Relational.eventQueue.block(); - - // Duplicate backbone's behavior to allow separate key/value parameters, instead of a single 'attributes' object - var attributes; - if ( _.isObject( key ) || key == null ) { - attributes = key; - options = value; - } - else { - attributes = {}; - attributes[ key ] = value; - } - - try { - var id = this.id, - newId = attributes && this.idAttribute in attributes && attributes[ this.idAttribute ]; - - // Check if we're not setting a duplicate id before actually calling `set`. - Backbone.Relational.store.checkId( this, newId ); - - var result = Backbone.Model.prototype.set.apply( this, arguments ); - - // Ideal place to set up relations, if this is the first time we're here for this model - if ( !this._isInitialized && !this.isLocked() ) { - this.constructor.initializeModelHierarchy(); - Backbone.Relational.store.register( this ); - this.initializeRelations( options ); - } - // The store should know about an `id` update asap - else if ( newId && newId !== id ) { - Backbone.Relational.store.update( this ); - } - - if ( attributes ) { - this.updateRelations( options ); - } - } - finally { - // Try to run the global queue holding external events - Backbone.Relational.eventQueue.unblock(); - } - - return result; - }, - - clone: function() { - var attributes = _.clone( this.attributes ); - if ( !_.isUndefined( attributes[ this.idAttribute ] ) ) { - attributes[ this.idAttribute ] = null; - } - - _.each( this.getRelations(), function( rel ) { - delete attributes[ rel.key ]; - }); - - return new this.constructor( attributes ); - }, - - /** - * Convert relations to JSON, omits them when required - */ - toJSON: function( options ) { - // If this Model has already been fully serialized in this branch once, return to avoid loops - if ( this.isLocked() ) { - return this.id; - } - - this.acquire(); - var json = Backbone.Model.prototype.toJSON.call( this, options ); - - if ( this.constructor._superModel && !( this.constructor._subModelTypeAttribute in json ) ) { - json[ this.constructor._subModelTypeAttribute ] = this.constructor._subModelTypeValue; - } - - _.each( this._relations, function( rel ) { - var related = json[ rel.key ], - includeInJSON = rel.options.includeInJSON, - value = null; - - if ( includeInJSON === true ) { - if ( related && _.isFunction( related.toJSON ) ) { - value = related.toJSON( options ); - } - } - else if ( _.isString( includeInJSON ) ) { - if ( related instanceof Backbone.Collection ) { - value = related.pluck( includeInJSON ); - } - else if ( related instanceof Backbone.Model ) { - value = related.get( includeInJSON ); - } - - // Add ids for 'unfound' models if includeInJSON is equal to (only) the relatedModel's `idAttribute` - if ( includeInJSON === rel.relatedModel.prototype.idAttribute ) { - if ( rel instanceof Backbone.HasMany ) { - value = value.concat( rel.keyIds ); - } - else if ( rel instanceof Backbone.HasOne ) { - value = value || rel.keyId; - } - } - } - else if ( _.isArray( includeInJSON ) ) { - if ( related instanceof Backbone.Collection ) { - value = []; - related.each( function( model ) { - var curJson = {}; - _.each( includeInJSON, function( key ) { - curJson[ key ] = model.get( key ); - }); - value.push( curJson ); - }); - } - else if ( related instanceof Backbone.Model ) { - value = {}; - _.each( includeInJSON, function( key ) { - value[ key ] = related.get( key ); - }); - } - } - else { - delete json[ rel.key ]; - } - - if ( includeInJSON ) { - json[ rel.keyDestination ] = value; - } - - if ( rel.keyDestination !== rel.key ) { - delete json[ rel.key ]; - } - }); - - this.release(); - return json; - } - }, - { - /** - * - * @param superModel - * @returns {Backbone.RelationalModel.constructor} - */ - setup: function( superModel ) { - // We don't want to share a relations array with a parent, as this will cause problems with - // reverse relations. - this.prototype.relations = ( this.prototype.relations || [] ).slice( 0 ); - - this._subModels = {}; - this._superModel = null; - - // If this model has 'subModelTypes' itself, remember them in the store - if ( this.prototype.hasOwnProperty( 'subModelTypes' ) ) { - Backbone.Relational.store.addSubModels( this.prototype.subModelTypes, this ); - } - // The 'subModelTypes' property should not be inherited, so reset it. - else { - this.prototype.subModelTypes = null; - } - - // Initialize all reverseRelations that belong to this new model. - _.each( this.prototype.relations || [], function( rel ) { - if ( !rel.model ) { - rel.model = this; - } - - if ( rel.reverseRelation && rel.model === this ) { - var preInitialize = true; - if ( _.isString( rel.relatedModel ) ) { - /** - * The related model might not be defined for two reasons - * 1. it is related to itself - * 2. it never gets defined, e.g. a typo - * 3. the model hasn't been defined yet, but will be later - * In neither of these cases do we need to pre-initialize reverse relations. - * However, for 3. (which is, to us, indistinguishable from 2.), we do need to attempt - * setting up this relation again later, in case the related model is defined later. - */ - var relatedModel = Backbone.Relational.store.getObjectByName( rel.relatedModel ); - preInitialize = relatedModel && ( relatedModel.prototype instanceof Backbone.RelationalModel ); - } - - if ( preInitialize ) { - Backbone.Relational.store.initializeRelation( null, rel ); - } - else if ( _.isString( rel.relatedModel ) ) { - Backbone.Relational.store.addOrphanRelation( rel ); - } - } - }, this ); - - return this; - }, - - /** - * Create a 'Backbone.Model' instance based on 'attributes'. - * @param {Object} attributes - * @param {Object} [options] - * @return {Backbone.Model} - */ - build: function( attributes, options ) { - // 'build' is a possible entrypoint; it's possible no model hierarchy has been determined yet. - this.initializeModelHierarchy(); - - // Determine what type of (sub)model should be built if applicable. - var model = this._findSubModelType(this, attributes) || this; - - return new model( attributes, options ); - }, - - /** - * Determines what type of (sub)model should be built if applicable. - * Looks up the proper subModelType in 'this._subModels', recursing into - * types until a match is found. Returns the applicable 'Backbone.Model' - * or null if no match is found. - * @param {Backbone.Model} type - * @param {Object} attributes - * @return {Backbone.Model} - */ - _findSubModelType: function (type, attributes) { - if ( type._subModels && type.prototype.subModelTypeAttribute in attributes ) { - var subModelTypeAttribute = attributes[type.prototype.subModelTypeAttribute]; - var subModelType = type._subModels[subModelTypeAttribute]; - if ( subModelType ) { - return subModelType; - } else { - // Recurse into subModelTypes to find a match - for ( subModelTypeAttribute in type._subModels ) { - subModelType = this._findSubModelType(type._subModels[subModelTypeAttribute], attributes); - if ( subModelType ) { - return subModelType; - } - } - } - } - return null; - }, - - /** - * - */ - initializeModelHierarchy: function() { - // Inherit any relations that have been defined in the parent model. - this.inheritRelations(); - - // If we came here through 'build' for a model that has 'subModelTypes' then try to initialize the ones that - // haven't been resolved yet. - if ( this.prototype.subModelTypes ) { - var resolvedSubModels = _.keys(this._subModels); - var unresolvedSubModels = _.omit(this.prototype.subModelTypes, resolvedSubModels); - _.each( unresolvedSubModels, function( subModelTypeName ) { - var subModelType = Backbone.Relational.store.getObjectByName( subModelTypeName ); - subModelType && subModelType.initializeModelHierarchy(); - }); - } - }, - - inheritRelations: function() { - // Bail out if we've been here before. - if (!_.isUndefined( this._superModel ) && !_.isNull( this._superModel )) { - return; - } - // Try to initialize the _superModel. - Backbone.Relational.store.setupSuperModel( this ); - - // If a superModel has been found, copy relations from the _superModel if they haven't been inherited automatically - // (due to a redefinition of 'relations'). - if ( this._superModel ) { - // The _superModel needs a chance to initialize its own inherited relations before we attempt to inherit relations - // from the _superModel. You don't want to call 'initializeModelHierarchy' because that could cause sub-models of - // this class to inherit their relations before this class has had chance to inherit it's relations. - this._superModel.inheritRelations(); - if ( this._superModel.prototype.relations ) { - // Find relations that exist on the '_superModel', but not yet on this model. - var inheritedRelations = _.select( this._superModel.prototype.relations || [], function( superRel ) { - return !_.any( this.prototype.relations || [], function( rel ) { - return superRel.relatedModel === rel.relatedModel && superRel.key === rel.key; - }, this ); - }, this ); - - this.prototype.relations = inheritedRelations.concat( this.prototype.relations ); - } - } - // Otherwise, make sure we don't get here again for this type by making '_superModel' false so we fail the - // isUndefined/isNull check next time. - else { - this._superModel = false; - } - }, - - /** - * Find an instance of `this` type in 'Backbone.Relational.store'. - * - If `attributes` is a string or a number, `findOrCreate` will just query the `store` and return a model if found. - * - If `attributes` is an object and is found in the store, the model will be updated with `attributes` unless `options.update` is `false`. - * Otherwise, a new model is created with `attributes` (unless `options.create` is explicitly set to `false`). - * @param {Object|String|Number} attributes Either a model's id, or the attributes used to create or update a model. - * @param {Object} [options] - * @param {Boolean} [options.create=true] - * @param {Boolean} [options.merge=true] - * @param {Boolean} [options.parse=false] - * @return {Backbone.RelationalModel} - */ - findOrCreate: function( attributes, options ) { - options || ( options = {} ); - var parsedAttributes = ( _.isObject( attributes ) && options.parse && this.prototype.parse ) ? - this.prototype.parse( _.clone( attributes ) ) : attributes; - - // Try to find an instance of 'this' model type in the store - var model = Backbone.Relational.store.find( this, parsedAttributes ); - - // If we found an instance, update it with the data in 'item' (unless 'options.merge' is false). - // If not, create an instance (unless 'options.create' is false). - if ( _.isObject( attributes ) ) { - if ( model && options.merge !== false ) { - // Make sure `options.collection` and `options.url` doesn't cascade to nested models - delete options.collection; - delete options.url; - - model.set( parsedAttributes, options ); - } - else if ( !model && options.create !== false ) { - model = this.build( attributes, options ); - } - } - - return model; - }, - - /** - * Find an instance of `this` type in 'Backbone.Relational.store'. - * - If `attributes` is a string or a number, `find` will just query the `store` and return a model if found. - * - If `attributes` is an object and is found in the store, the model will be updated with `attributes` unless `options.update` is `false`. - * @param {Object|String|Number} attributes Either a model's id, or the attributes used to create or update a model. - * @param {Object} [options] - * @param {Boolean} [options.merge=true] - * @param {Boolean} [options.parse=false] - * @return {Backbone.RelationalModel} - */ - find: function( attributes, options ) { - options || ( options = {} ); - options.create = false; - return this.findOrCreate( attributes, options ); - } - }); - _.extend( Backbone.RelationalModel.prototype, Backbone.Semaphore ); - - /** - * Override Backbone.Collection._prepareModel, so objects will be built using the correct type - * if the collection.model has subModels. - * Attempts to find a model for `attrs` in Backbone.store through `findOrCreate` - * (which sets the new properties on it if found), or instantiates a new model. - */ - Backbone.Collection.prototype.__prepareModel = Backbone.Collection.prototype._prepareModel; - Backbone.Collection.prototype._prepareModel = function ( attrs, options ) { - var model; - - if ( attrs instanceof Backbone.Model ) { - if ( !attrs.collection ) { - attrs.collection = this; - } - model = attrs; - } - else { - options || ( options = {} ); - options.collection = this; - - if ( typeof this.model.findOrCreate !== 'undefined' ) { - model = this.model.findOrCreate( attrs, options ); - } - else { - model = new this.model( attrs, options ); - } - - if ( model && model.isNew() && !model._validate( attrs, options ) ) { - this.trigger( 'invalid', this, attrs, options ); - model = false; - } - } - - return model; - }; - - - /** - * Override Backbone.Collection.set, so we'll create objects from attributes where required, - * and update the existing models. Also, trigger 'relational:add'. - */ - var set = Backbone.Collection.prototype.__set = Backbone.Collection.prototype.set; - Backbone.Collection.prototype.set = function( models, options ) { - // Short-circuit if this Collection doesn't hold RelationalModels - if ( !( this.model.prototype instanceof Backbone.RelationalModel ) ) { - return set.apply( this, arguments ); - } - - if ( options && options.parse ) { - models = this.parse( models, options ); - } - - if ( !_.isArray( models ) ) { - models = models ? [ models ] : []; - } - - var newModels = [], - toAdd = []; - - //console.debug( 'calling add on coll=%o; model=%o, options=%o', this, models, options ); - _.each( models, function( model ) { - if ( !( model instanceof Backbone.Model ) ) { - model = Backbone.Collection.prototype._prepareModel.call( this, model, options ); - } - - if ( model ) { - toAdd.push( model ); - - if ( !( this.get( model ) || this.get( model.cid ) ) ) { - newModels.push( model ); - } - // If we arrive in `add` while performing a `set` (after a create, so the model gains an `id`), - // we may get here before `_onModelEvent` has had the chance to update `_byId`. - else if ( model.id != null ) { - this._byId[ model.id ] = model; - } - } - }, this ); - - // Add 'models' in a single batch, so the original add will only be called once (and thus 'sort', etc). - // If `parse` was specified, the collection and contained models have been parsed now. - set.call( this, toAdd, _.defaults( { parse: false }, options ) ); - - _.each( newModels, function( model ) { - // Fire a `relational:add` event for any model in `newModels` that has actually been added to the collection. - if ( this.get( model ) || this.get( model.cid ) ) { - this.trigger( 'relational:add', model, this, options ); - } - }, this ); - - return this; - }; - - /** - * Override 'Backbone.Collection.remove' to trigger 'relational:remove'. - */ - var remove = Backbone.Collection.prototype.__remove = Backbone.Collection.prototype.remove; - Backbone.Collection.prototype.remove = function( models, options ) { - // Short-circuit if this Collection doesn't hold RelationalModels - if ( !( this.model.prototype instanceof Backbone.RelationalModel ) ) { - return remove.apply( this, arguments ); - } - - models = _.isArray( models ) ? models.slice( 0 ) : [ models ]; - options || ( options = {} ); - - var toRemove = []; - - //console.debug('calling remove on coll=%o; models=%o, options=%o', this, models, options ); - _.each( models, function( model ) { - model = this.get( model ) || ( model && this.get( model.cid ) ); - model && toRemove.push( model ); - }, this ); - - if ( toRemove.length ) { - remove.call( this, toRemove, options ); - - _.each( toRemove, function( model ) { - this.trigger('relational:remove', model, this, options); - }, this ); - } - - return this; - }; - - /** - * Override 'Backbone.Collection.reset' to trigger 'relational:reset'. - */ - var reset = Backbone.Collection.prototype.__reset = Backbone.Collection.prototype.reset; - Backbone.Collection.prototype.reset = function( models, options ) { - options = _.extend( { merge: true }, options ); - reset.call( this, models, options ); - - if ( this.model.prototype instanceof Backbone.RelationalModel ) { - this.trigger( 'relational:reset', this, options ); - } - - return this; - }; - - /** - * Override 'Backbone.Collection.sort' to trigger 'relational:reset'. - */ - var sort = Backbone.Collection.prototype.__sort = Backbone.Collection.prototype.sort; - Backbone.Collection.prototype.sort = function( options ) { - sort.call( this, options ); - - if ( this.model.prototype instanceof Backbone.RelationalModel ) { - this.trigger( 'relational:reset', this, options ); - } - - return this; - }; - - /** - * Override 'Backbone.Collection.trigger' so 'add', 'remove' and 'reset' events are queued until relations - * are ready. - */ - var trigger = Backbone.Collection.prototype.__trigger = Backbone.Collection.prototype.trigger; - Backbone.Collection.prototype.trigger = function( eventName ) { - // Short-circuit if this Collection doesn't hold RelationalModels - if ( !( this.model.prototype instanceof Backbone.RelationalModel ) ) { - return trigger.apply( this, arguments ); - } - - if ( eventName === 'add' || eventName === 'remove' || eventName === 'reset' || eventName === 'sort' ) { - var dit = this, - args = arguments; - - if ( _.isObject( args[ 3 ] ) ) { - args = _.toArray( args ); - // the fourth argument is the option object. - // we need to clone it, as it could be modified while we wait on the eventQueue to be unblocked - args[ 3 ] = _.clone( args[ 3 ] ); - } - - Backbone.Relational.eventQueue.add( function() { - trigger.apply( dit, args ); - }); - } - else { - trigger.apply( this, arguments ); - } - - return this; - }; - - // Override .extend() to automatically call .setup() - Backbone.RelationalModel.extend = function( protoProps, classProps ) { - var child = Backbone.Model.extend.apply( this, arguments ); - - child.setup( this ); - - return child; - }; -})(); diff -r a58f6ca10843c91727807e7150b549ecd9b13ec5 -r f4832c4ace99f24bc42dcf275b55c0b2671fb6be static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -2,7 +2,7 @@ * Simple base model for any visible element. Includes useful attributes and ability * to set and track visibility. */ -var BaseModel = Backbone.RelationalModel.extend({ +var BaseModel = Backbone.Model.extend({ defaults: { name: null, hidden: false 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.

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commit/galaxy-central: guerler: Upload: Backup id of current history
by commits-noreply＠bitbucket.org 26 Nov '13

26 Nov '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a58f6ca10843/ Changeset: a58f6ca10843 User: guerler Date: 2013-11-26 18:52:51 Summary: Upload: Backup id of current history Affected #: 1 file diff -r 9f31145b33ceb83e539bcdd571b48ff440b4c1eb -r a58f6ca10843c91727807e7150b549ecd9b13ec5 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -17,6 +17,9 @@ // upload mod uploadbox: null, + // current history + current_history: null, + // extension types select_extension :[['Auto-detect', 'auto']], @@ -227,7 +230,6 @@ sy.addClass(this.state.running); // get configuration - var current_history = Galaxy.currHistoryPanel.model.get('id'); var file_type = it.find('#extension').val(); var genome = it.find('#genome').val(); var url_paste = it.find('#text-content').val(); @@ -251,7 +253,7 @@ // setup data data = {}; - data['history_id'] = current_history; + data['history_id'] = this.current_history; data['tool_id'] = 'upload1'; data['inputs'] = JSON.stringify(tool_input); @@ -375,6 +377,9 @@ } }); + // backup current history + this.current_history = Galaxy.currHistoryPanel.model.get('id'); + // update running this.counter.running = this.counter.announce; this.update_screen(); 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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