1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/0b9bd1fdc765/ Changeset: 0b9bd1fdc765 User: Dave Bouvier Date: 2013-05-21 18:15:17 Summary: Add an option to install and test every installable changeset revision of every repository returned by the tool shed API call. Default behavior changed to only install and test the most recent installable changeset revision of each repository. Affected #: 1 file

diff -r 82f83d00dfd419c035c76b100ec0e88a10bb900c -r 0b9bd1fdc765d18d0831aa2ecbf419e16bbfd15b 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 @@ -225,13 +225,25 @@ url += '&%s' % params return url

+def get_latest_downloadable_changeset_revision( url, name, owner ): + api_url_parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] + params = urllib.urlencode( dict( name=name, owner=owner ) ) + api_url = get_api_url( url, api_url_parts, params ) + changeset_revisions = json_from_url( api_url ) + if changeset_revisions: + return changeset_revisions[ -1 ] + else: + return '000000000000' + def get_repository_info_from_api( url, repository_info_dict ): parts = [ 'api', 'repositories', repository_info_dict[ 'repository_id' ] ] api_url = get_api_url( base=url, parts=parts ) extended_dict = json_from_url( api_url ) + latest_changeset_revision = get_latest_downloadable_changeset_revision( url, extended_dict[ 'name' ], extended_dict[ 'owner' ] ) + extended_dict[ 'latest_revision' ] = str( latest_changeset_revision ) return extended_dict

-def get_repositories_to_install( location, source='file', format='json' ): +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: [ @@ -246,24 +258,49 @@ ] NOTE: If the tool shed URL specified in any dict is not present in the tool_sheds_conf.xml, the installation will fail. ''' - if source == 'file': - listing = file( location, 'r' ).read() - elif source == 'url': - assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.' - params = urllib.urlencode( dict( do_not_test='false', - downloadable='true', - malicious='false', - includes_tools='true', - skip_tool_test='false' ) ) - api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params ) - if format == 'json': - return json_from_url( api_url ) + assert tool_shed_api_key is not None, 'Cannot proceed without tool shed API key.' + params = urllib.urlencode( dict( do_not_test='false', + downloadable='true', + malicious='false', + includes_tools='true', + 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 ) + known_repository_ids = {} + detailed_repository_list = [] + for repository_to_install_dict in base_repository_list: + # 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_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict ) + if repository_info_dict[ 'latest_revision' ] == '000000000000': + continue + owner = repository_info_dict[ 'owner' ] + name = repository_info_dict[ 'name' ] + changeset_revision = repository_to_install_dict[ 'changeset_revision' ] + repository_id = repository_to_install_dict[ 'repository_id' ] + # We are testing deprecated repositories, because it is possible that a deprecated repository contains valid + # and functionally correct tools that someone has previously installed. Deleted repositories have never been installed, + # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. + if repository_info_dict[ 'deleted' ]: + log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted...", + changeset_revision, + repository_id, + name, + owner ) + continue + # Now merge the dict returned from /api/repository_revisions with the detailed dict we just retrieved. + if latest_revision_only: + if changeset_revision == repository_info_dict[ 'latest_revision' ]: + detailed_repository_list.append( dict( repository_info_dict.items() + repository_to_install_dict.items() ) ) + else: + detailed_repository_list.append( dict( repository_info_dict.items() + repository_to_install_dict.items() ) ) + repositories_tested = len( detailed_repository_list ) + if latest_revision_only: + skipped_previous = ' and metadata revisions that are not the most recent' else: - raise AssertionError( 'Do not know how to handle source type %s.' % source ) - if format == 'json': - return from_json_string( listing ) - else: - raise AssertonError( 'Unknown format %s.' % format ) + skipped_previous = '' + log.info( 'After removing deleted repositories%s from the list, %d remain to be tested.', skipped_previous, repositories_tested ) + return detailed_repository_list

def get_tool_info_from_test_id( test_id ): ''' @@ -286,13 +323,7 @@ return tool_test_results

def is_latest_downloadable_revision( url, repository_info_dict ): - api_url_parts = [ 'api', 'repositories', 'get_ordered_installable_revisions' ] - params = urllib.urlencode( dict( name=repository_info_dict[ 'name' ], owner=repository_info_dict[ 'owner' ] ) ) - api_url = get_api_url( url, api_url_parts, params ) - changeset_revisions = json_from_url( api_url ) - # The get_ordered_installable_revisions returns a list of changeset hashes, with the last hash in the list - # being the most recent installable revision. - latest_revision = changeset_revisions.pop() + latest_revision = get_latest_downloadable_changeset_revision( url, name=repository_info_dict[ 'name' ], owner=repository_info_dict[ 'owner' ] ) return str( repository_info_dict[ 'changeset_revision' ] ) == str( latest_revision )

def json_from_url( url ): @@ -532,41 +563,25 @@ shed_tool_data_table_config=None, persist=False ) # Initialize some variables for the summary that will be printed to stdout. - repositories_tested = 0 repositories_passed = [] repositories_failed = [] repositories_failed_install = [] try: - detailed_repository_list = [] # 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 ) ) - repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) + if '-check_all_revisions' not in sys.argv: + repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, latest_revision_only=True ) + else: + repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, latest_revision_only=False ) log.info( "Retrieved %d repositories from the API.", len( repositories_to_install ) ) - for repository_to_install_dict in repositories_to_install: - # 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_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict ) - # We are testing deprecated repositories, because it is possible that a deprecated repository contains valid - # and functionally correct tools that someone has previously installed. Deleted repositories have never been installed, - # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. - if repository_info_dict[ 'deleted' ]: - log.info( "Skipping revision %s of repository id %s (%s/%s) since the repository is deleted...", - repository_to_install_dict[ 'changeset_revision' ], - repository_to_install_dict[ 'repository_id' ], - repository_info_dict[ 'owner' ], - repository_info_dict[ 'name' ] ) - continue - # Now merge the dict returned from /api/repository_revisions with the detailed dict we just retrieved. - detailed_repository_list.append( dict( repository_info_dict.items() + repository_to_install_dict.items() ) ) - repositories_tested = len( detailed_repository_list ) - log.info( 'After removing deleted repositories from the list, %d remain to be tested.', repositories_tested ) if '-list_repositories' in sys.argv: log.info( "The API returned the following repositories, not counting deleted:" ) - for repository_info_dict in detailed_repository_list: + for repository_info_dict in repositories_to_install: log.info( "%s owned by %s changeset revision %s", repository_info_dict.get( 'name', None ), repository_info_dict.get( 'owner', None ), repository_info_dict.get( 'changeset_revision', None ) ) + repositories_tested = len( repositories_to_install ) # This loop will iterate through the list of repositories generated by the above code, having already filtered out any # that were marked as deleted. For each repository, it will generate a test method that will use Twill to install that # repository into the embedded Galaxy application that was started up, selecting to install repository and tool @@ -575,7 +590,7 @@ # it will record the result of the tests, and if any failed, the traceback and captured output of the tool that was run. # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with # the next repository's functional tests. - for repository_info_dict in detailed_repository_list: + for repository_info_dict in repositories_to_install: """ Each repository_info_dict looks something like: { @@ -600,8 +615,8 @@ """ repository_status = dict() params = dict() - repository_id = repository_info_dict.get( 'repository_id', None ) - changeset_revision = repository_info_dict.get( 'changeset_revision', None ) + repository_id = str( repository_info_dict.get( 'repository_id', None ) ) + changeset_revision = str( repository_info_dict.get( 'changeset_revision', None ) ) metadata_revision_id = repository_info_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_info_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url

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

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