diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py index abe0973b7f9..be5ada91bb0 100644 --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -58,7 +58,7 @@ class MetadataGenerator( object ): repository_files_dir = self.repository.repo_files_directory( self.app ) if metadata_dict is None: # Shed related tool panel configs are only relevant to Galaxy. - self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + self.metadata_dict = { 'shed_config_filename': self.shed_config_dict.get( 'config_filename', None ) } else: self.metadata_dict = metadata_dict else: diff --git a/lib/tool_shed/scripts/api/common.py b/lib/tool_shed/scripts/api/common.py index 7e3bb377efe..244b3278d57 100644 --- a/lib/tool_shed/scripts/api/common.py +++ b/lib/tool_shed/scripts/api/common.py @@ -13,7 +13,7 @@ from tool_shed.util import hg_util class HTTPRedirectWithDataHandler( urllib2.HTTPRedirectHandler ): - + def __init__( self, method ): ''' Upon first inspection, it would seem that this shouldn't be necessary, but for some reason diff --git a/lib/tool_shed/utility_containers/__init__.py b/lib/tool_shed/utility_containers/__init__.py index 22e871534a5..36280474c63 100644 --- a/lib/tool_shed/utility_containers/__init__.py +++ b/lib/tool_shed/utility_containers/__init__.py @@ -259,7 +259,7 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine valid_tools=None, workflows=None, valid_data_managers=None - ) + ) if repository_metadata: metadata = repository_metadata.metadata lock = threading.Lock() @@ -405,19 +405,19 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine continue # We have a dictionary that looks something like this: # { - # 'missing_test_components': [], - # 'failed_tests': [], - # 'passed_tests': - # [{'tool_id': 'effectiveT3', - # 'test_id': 'test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)', - # 'tool_version': '0.0.12'}, - # {'tool_id': 'effectiveT3', - # 'test_id': 'test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)', - # 'tool_version': '0.0.12'}], - # 'test_environment': - # {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic', - # 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a', - # 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'}, + # 'missing_test_components': [], + # 'failed_tests': [], + # 'passed_tests': + # [{'tool_id': 'effectiveT3', + # 'test_id': 'test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)', + # 'tool_version': '0.0.12'}, + # {'tool_id': 'effectiveT3', + # 'test_id': 'test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)', + # 'tool_version': '0.0.12'}], + # 'test_environment': + # {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic', + # 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a', + # 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'}, # 'installation_errors': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []}, # 'successful_installations': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []} # } @@ -554,10 +554,10 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine for missing_test_components_dict in missing_test_components_dicts: missing_test_component_id += 1 try: - 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', '' ) + 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', '' ) except Exception, e: missing_components = str( e ) tool_guid = 'unknown' @@ -572,9 +572,9 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine installation_error_dict = tool_test_results_dict.get( 'installation_errors', {} ) if len( installation_error_dict ) > 0: # 'installation_errors': - # {'current_repository': [], - # 'repository_dependencies': [], - # 'tool_dependencies': + # {'current_repository': [], + # 'repository_dependencies': [], + # 'tool_dependencies': # [{'error_message': 'some traceback string' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] # } current_repository_installation_error_dicts = installation_error_dict.get( 'current_repository', [] ) @@ -679,9 +679,9 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine successful_installation_dict = tool_test_results_dict.get( 'successful_installations', {} ) if len( successful_installation_dict ) > 0: # 'successful_installation': - # {'current_repository': [], - # 'repository_dependencies': [], - # 'tool_dependencies': + # {'current_repository': [], + # 'repository_dependencies': [], + # 'tool_dependencies': # [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}] # } # We won't display the current repository in this container. I fit is not displaying installation errors, diff --git a/lib/tool_shed/utility_containers/utility_container_manager.py b/lib/tool_shed/utility_containers/utility_container_manager.py index 972b860c87e..b79bfd190f4 100644 --- a/lib/tool_shed/utility_containers/utility_container_manager.py +++ b/lib/tool_shed/utility_containers/utility_container_manager.py @@ -469,7 +469,7 @@ class UtilityContainerManager( object ): container_object_tool_id += 1 requirements = tool_dict.get( 'requirements', None ) if requirements is not None: - # 'requirements': [{'version': '1.56.0', 'type': 'package', 'name': 'picard'}], + # 'requirements': [{'version': '1.56.0', 'type': 'package', 'name': 'picard'}], requirements_str = '' for requirement_dict in requirements: try: @@ -643,7 +643,7 @@ class UtilityContainerManager( object ): repository_id=repository_id ) folder.workflows.append( workflow ) for workflow_tup in workflows: - workflow_dict=workflow_tup[ 1 ] + workflow_dict = workflow_tup[ 1 ] steps = workflow_dict.get( 'steps', [] ) if steps: steps = str( len( steps ) ) @@ -779,12 +779,7 @@ class UtilityContainerManager( object ): installation_status = None can_create_dependency = not self.is_subfolder_of( sub_folder, repository_dependency ) if can_create_dependency: - toolshed, \ - repository_name, \ - repository_owner, \ - changeset_revision, \ - prior_installation_required, \ - only_if_compiling_contained_td = \ + toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ common_util.parse_repository_dependency_tuple( repository_dependency ) repository_dependency_id += 1 repository_dependency = RepositoryDependency( id=repository_dependency_id, @@ -801,12 +796,7 @@ class UtilityContainerManager( object ): return repository_dependencies_folder, folder_id, repository_dependency_id def is_subfolder_of( self, folder, repository_dependency ): - toolshed, \ - repository_name, \ - repository_owner, \ - changeset_revision, \ - prior_installation_required, \ - only_if_compiling_contained_td = \ + toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ common_util.parse_repository_dependency_tuple( repository_dependency ) key = container_util.generate_repository_dependencies_key_for_repository( toolshed, repository_name, @@ -835,10 +825,10 @@ class UtilityContainerManager( object ): key_prior_installation_required = components_list[ 4 ] key_only_if_compiling_contained_td = components_list[ 5 ] if repository_name == key_name and \ - repository_owner == key_owner and \ - changeset_revision == key_changeset_revision and \ - prior_installation_required == key_prior_installation_required and \ - only_if_compiling_contained_td == key_only_if_compiling_contained_td: + repository_owner == key_owner and \ + changeset_revision == key_changeset_revision and \ + prior_installation_required == key_prior_installation_required and \ + only_if_compiling_contained_td == key_only_if_compiling_contained_td: return True return False