1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/856800d4c915/ Changeset: 856800d4c915 User: Dave Bouvier Date: 2013-05-21 22:02:21 Summary: Add the ability to define a list of repositories or changeset revisions of repositories that should not be tested by the automated testing framework. Affected #: 1 file

diff -r fe0905ea52874c451303f5e60d5158387695aaef -r 856800d4c91546d51948176f4b78a7bd4b1a1b8b 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 @@ -129,6 +129,7 @@

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 tool_shed_api_key is None: print "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variable to be set and non-empty." @@ -243,6 +244,13 @@ extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) return extended_dict

+def get_repository_tuple_from_elem( elem ): + attributes = elem.attrib + name = attributes.get( 'name', None ) + owner = attributes.get( 'owner', None ) + changeset_revision = attributes.get( 'changeset_revision', None ) + return ( name, owner, changeset_revision ) + def get_repositories_to_install( tool_shed_url, latest_revision_only=True ): ''' Get a list of repository info dicts to install. This method expects a json list of dicts with the following structure: @@ -266,6 +274,7 @@ skip_tool_test='false' ) ) api_url = get_api_url( base=tool_shed_url, parts=[ 'repository_revisions' ], params=params ) base_repository_list = json_from_url( api_url ) + log.info( 'The api returned %d metadata revisions.', len( base_repository_list ) ) known_repository_ids = {} detailed_repository_list = [] for repository_to_install_dict in base_repository_list: @@ -336,6 +345,49 @@ raise return parsed_json

+def parse_exclude_list( xml_filename ): + ''' + This method should return a list with the following structure: + [ + { + 'reason': The default reason or the reason specified in this section, + 'repositories': + [ + ( name, owner, changeset revision if changeset revision else None ), + ( name, owner, changeset revision if changeset revision else None ) + ] + }, + { + 'reason': The default reason or the reason specified in this section, + 'repositories': + [ + ( name, owner, changeset revision if changeset revision else None ), + ( name, owner, changeset revision if changeset revision else None ) + ] + }, + ] + ''' + exclude_list = [] + xml_tree = parse_xml( xml_filename ) + tool_sheds = xml_tree.findall( 'repositories' ) + xml_element = None + for tool_shed in tool_sheds: + if galaxy_tool_shed_url != tool_shed.attrib[ 'tool_shed' ]: + continue + else: + xml_element = tool_shed + for reason_section in xml_element: + print reason_section + reason_text = reason_section.find( 'text' ).text + repositories = reason_section.findall( 'repository' ) + exclude_dict = dict( reason=reason_text, repositories=[] ) + for repository in repositories: + repository_tuple = get_repository_tuple_from_elem( repository ) + if repository_tuple not in exclude_dict[ 'repositories' ]: + exclude_dict[ 'repositories' ].append( repository_tuple ) + exclude_list.append( exclude_dict ) + return exclude_list + def register_test_result( url, metadata_id, test_results_dict, repository_info_dict, params ): ''' Update the repository metadata tool_test_results and appropriate flags using the API. @@ -566,6 +618,10 @@ repositories_passed = [] repositories_failed = [] repositories_failed_install = [] + exclude_list = [] + if os.path.exists( exclude_list_file ): + exclude_list = parse_exclude_list( exclude_list_file ) + log.info( exclude_list ) try: # Get a list of repositories to test from the tool shed specified in the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable. log.info( "Retrieving repositories to install from the URL:\n%s\n", str( galaxy_tool_shed_url ) ) @@ -623,8 +679,43 @@ # Get the name and owner out of the repository info dict. name = str( repository_info_dict[ 'name' ] ) owner = str( repository_info_dict[ 'owner' ] ) - log.info( "Installing and testing revision %s of repository id %s (%s/%s)...", - str( changeset_revision ), str( repository_id ), owner, name ) + # Populate the repository_status dict now. + repository_status = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) + if 'test_environment' not in repository_status: + repository_status[ 'test_environment' ] = {} + test_environment = get_test_environment( repository_status[ 'test_environment' ] ) + test_environment[ 'galaxy_database_version' ] = get_database_version( app ) + test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) + repository_status[ 'test_environment' ] = test_environment + repository_status[ 'passed_tests' ] = [] + repository_status[ 'failed_tests' ] = [] + repository_status[ 'skip_reason' ] = None + # Iterate through the list of repositories defined not to be installed. This should be a list of dicts in the following format: + # { + # 'reason': The default reason or the reason specified in this section, + # 'repositories': + # [ + # ( name, owner, changeset revision if changeset revision else None ), + # ( name, owner, changeset revision if changeset revision else None ) + # ] + # }, + # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified + # revision should be skipped. + # TODO: When a repository is selected to be skipped, use the API to update the tool shed with the defined skip reason. + skip_this_repository = False + skip_because = None + for exclude_by_reason in exclude_list: + reason = exclude_by_reason[ 'reason' ] + exclude_repositories = exclude_by_reason[ 'repositories' ] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + skip_this_repository = True + skip_because = reason + break + if skip_this_repository: + log.info( "Not testing revision %s of repository %s owned by %s.", changeset_revision, name, owner ) + continue + else: + log.info( "Installing and testing revision %s of repository %s owned by %s...", changeset_revision, name, owner ) # Explicitly clear tests from twill's test environment. remove_generated_tests( app ) # Use the repository information dict to generate an install method that will install the repository into the embedded @@ -638,15 +729,6 @@ # repository, with tool and repository dependencies also selected for installation. result, _ = run_tests( test_config ) success = result.wasSuccessful() - repository_status = get_tool_test_results_from_api( galaxy_tool_shed_url, metadata_revision_id ) - if 'test_environment' not in repository_status: - repository_status[ 'test_environment' ] = {} - test_environment = get_test_environment( repository_status[ 'test_environment' ] ) - test_environment[ 'galaxy_database_version' ] = get_database_version( app ) - test_environment[ 'galaxy_revision'] = get_repository_current_revision( os.getcwd() ) - repository_status[ 'test_environment' ] = test_environment - repository_status[ 'passed_tests' ] = [] - repository_status[ 'failed_tests' ] = [] repository_status[ 'installation_errors' ] = dict( current_repository=[], repository_dependencies=[], tool_dependencies=[] ) try: repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) @@ -750,16 +832,19 @@ # If the repository does not have a test-data directory, any functional tests in the tool configuration will # fail. Mark the repository as failed and skip installation. log.error( 'Test data is missing for this repository. Updating repository and skipping functional tests.' ) - # Record the lack of test data. - for tool in repository.metadata[ 'tools' ]: - tool_id = tool[ 'id' ] - tool_version = tool[ 'version' ] - tool_guid = tool[ 'guid' ] - # In keeping with the standard display layout, add the error message to the dict for each tool individually. - missing_components = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, - missing_components="Repository %s is missing a test-data directory." % name ) - if missing_components not in repository_status[ 'missing_test_components' ]: - repository_status[ 'missing_test_components' ].append( missing_components ) + # Record the lack of test data if the repository metadata defines tools. + if 'tools' in repository.metadata: + for tool in repository.metadata[ 'tools' ]: + tool_id = tool[ 'id' ] + tool_version = tool[ 'version' ] + tool_guid = tool[ 'guid' ] + # In keeping with the standard display layout, add the error message to the dict for each tool individually. + missing_components = dict( tool_id=tool_id, tool_version=tool_version, tool_guid=tool_guid, + missing_components="Repository %s is missing a test-data directory." % name ) + if missing_components not in repository_status[ 'missing_test_components' ]: + repository_status[ 'missing_test_components' ].append( missing_components ) + else: + continue # Record the status of this repository in the tool shed. set_do_not_test = not is_latest_downloadable_revision( galaxy_tool_shed_url, repository_info_dict ) params[ 'tools_functionally_correct' ] = False

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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