1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/4c6b4cc9e060/ Changeset: 4c6b4cc9e060 User: greg Date: 2014-01-07 19:15:46 Summary: Restrict population of repository dependency installation containers during the tool shed's install and test run if they were last populated 12 hours previously or less. Affected #: 1 file

diff -r 5fbd5656e3dde2ba871f39f01a0841cea656a669 -r 4c6b4cc9e060f98ec0c060bbbf8f5ac9cd54c75f test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -24,6 +24,9 @@ import tool_shed.util.shed_util_common as suc import urllib

+from datetime import datetime +from datetime import timedelta + from common import update

from galaxy.util import asbool @@ -312,7 +315,7 @@ dependency tree will be inspected. """ log.debug( 'Checking revision %s of repository %s owned by %s for missing repository dependencies.' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) missing_repository_dependencies = repository.missing_repository_dependencies for missing_required_repository in missing_repository_dependencies: log.debug( 'Revision %s of required repository %s owned by %s has status %s.' % \ @@ -331,7 +334,7 @@ dependency tree will be inspected. """ log.debug( 'Checking revision %s of repository %s owned by %s for missing tool dependencies.' % \ - ( str( repository.changeset_revision ), str( repository.name ), str( repository.changeset_revision ) ) ) + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) missing_tool_dependencies = repository.missing_tool_dependencies for missing_tool_dependency in missing_tool_dependencies: log.debug( 'Tool dependency %s version %s has status %s.' % \ @@ -517,6 +520,26 @@ static_style_dir = os.path.join( static_dir, 'june_2007_style', 'blue' ), static_robots_txt = os.path.join( static_dir, 'robots.txt' ) )

+def get_time_last_tested( tool_shed_url, encoded_repository_metadata_id ): + """ + Return the datetime value stored in the Tool Shed's repository_metadata.time_last_tested column + via the Tool Shed API. + """ + error_message = '' + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id ] + api_url = get_api_url( base=tool_shed_url, parts=parts ) + repository_metadata_dict, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + if isinstance( repository_metadata_dict, dict ): + # The tool_test_results used to be stored as a single dictionary rather than a list, but we currently + # return a list. + time_last_tested = repository_metadata_dict.get( 'time_last_tested', None ) + return time_last_tested, error_message + else: + error_message = 'The url %s returned the invalid repository_metadata_dict %s' % ( str( api_url ), str( repository_metadata_dict ) ) + return None, error_message + def get_tool_test_results_dict( tool_test_results_dicts ): if tool_test_results_dicts: # Inspect the tool_test_results_dict for the last test run to make sure it contains only a test_environment @@ -862,7 +885,7 @@ name = str( repository_dependencies_dict[ 'name' ] ) owner = str( repository_dependencies_dict[ 'owner' ] ) changeset_revision = str( repository_dependencies_dict[ 'changeset_revision' ] ) - log.debug( 'Checking installation containers for revision %s of required repository %s owned by %s' % \ + log.debug( 'Checking installation containers for revision %s of repository dependency %s owned by %s' % \ ( changeset_revision, name, owner ) ) required_repository_metadata_id = repository_dependencies_dict[ 'id' ] # Get the current list of tool_test_results dictionaries associated with the repository_metadata @@ -870,78 +893,92 @@ tool_test_results_dicts, error_message = get_tool_test_results_dicts( galaxy_tool_shed_url, required_repository_metadata_id ) if error_message: - log.debug( 'Cannot check install container for version %s of repository %s owned by %s ' % \ + log.debug( 'Cannot check install container for version %s of repository dependency %s owned by %s ' % \ ( changeset_revision, name, owner ) ) log.debug( 'due to the following error getting tool_test_results:\n%s' % str( error_message ) ) else: - # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated + # Check the required repository's time_last_tested value to see if its tool_test_results column + # has been updated within the past 12 hours. + twelve_hours_ago = datetime.utcnow() - timedelta( hours=12 ) + time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, repository_metadata_id ) + if time_last_tested is not None and time_last_tested < twelve_hours_ago: + log.debug( 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'populated within the past 12 hours (likely in this test run), so skipping this check.' ) + continue + if time_last_tested is None: + log.debug( 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + elif time_last_tested < twelve_hours_ago: + log.debug( 'Version %s of repository dependency %s owned by %s was last tested less than 12 hours ago.' % \ + ( changeset_revision, name, owner ) ) + else: + log.debug( 'Version %s of repository dependency %s owned by %s was last tested more than 12 hours ago.' % \ + ( changeset_revision, name, owner ) ) + # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: - populated = False tool_test_results_dict = {} else: tool_test_results_dict = tool_test_results_dicts[ 0 ] if len( tool_test_results_dict ) <= 1: - populated = False tool_test_results_dict = tool_test_results_dicts.pop( 0 ) elif len( tool_test_results_dict ) == 2 and \ 'test_environment' in tool_test_results_dict and \ 'missing_test_components' in tool_test_results_dict: - populated = False tool_test_results_dict = tool_test_results_dicts.pop( 0 ) else: - populated = True - if not populated: - # Make sure all expected entries are available in the tool_test_results_dict. - tool_test_results_dict = initialize_tool_tests_results_dict( app, tool_test_results_dict ) - # Get the installed repository record from the Galaxy database. - cleaned_tool_shed_url = clean_tool_shed_url( galaxy_tool_shed_url ) - required_repository = \ - suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, - cleaned_tool_shed_url, - name, - owner, - changeset_revision ) - if required_repository is not None: - repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - if required_repository.is_installed: - # The required_repository was successfully installed, so populate the installation - # containers (success and error) for the repository's immediate dependencies. - params, install_and_test_statistics_dict, tool_test_results_dict = \ - populate_dependency_install_containers( app, - required_repository, - repository_identifier_dict, - install_and_test_statistics_dict, - tool_test_results_dict ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('\n=============================================================\n' ) - else: - # The required repository's installation failed. - tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) - params = dict( test_install_error=True, - do_not_test=False ) - response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, - tool_test_results_dicts, - tool_test_results_dict, - repository_dependencies_dict, - params, - can_update_tool_shed ) - log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ - ( changeset_revision, name, owner, str( response_dict ) ) ) - log.debug('\n=============================================================\n' ) + tool_test_results_dict = {} + # Make sure all expected entries are available in the tool_test_results_dict. + tool_test_results_dict = initialize_tool_tests_results_dict( app, tool_test_results_dict ) + # Get the installed repository record from the Galaxy database. + cleaned_tool_shed_url = clean_tool_shed_url( galaxy_tool_shed_url ) + required_repository = \ + suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, + cleaned_tool_shed_url, + name, + owner, + changeset_revision ) + if required_repository is not None: + repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) + if required_repository.is_installed: + # The required_repository was successfully installed, so populate the installation + # containers (success and error) for the repository's immediate dependencies. + params, install_and_test_statistics_dict, tool_test_results_dict = \ + populate_dependency_install_containers( app, + required_repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) else: - log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ - ( changeset_revision, name, owner ) ) - log.debug( 'so tool_test_results cannot be saved.' ) - log.debug( 'The attributes used to retrieve the record are:' ) - log.debug( '\ntool_shed: %s name: %s owner: %s changeset_revision: %s' % \ - ( cleaned_tool_shed_url, name, owner, changeset_revision ) ) + # The required repository's installation failed. + tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = str( required_repository.error_message ) + params = dict( test_install_error=True, + do_not_test=False ) + response_dict = save_test_results_for_changeset_revision( galaxy_tool_shed_url, + tool_test_results_dicts, + tool_test_results_dict, + repository_dependencies_dict, + params, + can_update_tool_shed ) + log.debug( 'Result of inserting tool_test_results for revision %s of repository %s owned by %s:\n%s' % \ + ( changeset_revision, name, owner, str( response_dict ) ) ) + log.debug('\n=============================================================\n' ) + else: + log.debug( 'Cannot retrieve revision %s of required repository %s owned by %s from the database ' % \ + ( changeset_revision, name, owner ) ) + log.debug( 'so tool_test_results cannot be saved.' ) + log.debug( 'The attributes used to retrieve the record are:\n' ) + log.debug( 'tool_shed: %s name: %s owner: %s changeset_revision: %s' % \ + ( cleaned_tool_shed_url, name, owner, changeset_revision ) )

def run_tests( test_config ): loader = nose.loader.TestLoader( config=test_config )

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

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