mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Code style cleanup.
This commit is contained in:
Dave B
@@ -58,7 +58,7 @@ class MetadataGenerator( object ):
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repository_files_dir = self.repository.repo_files_directory( self.app )
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if metadata_dict is None:
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# Shed related tool panel configs are only relevant to Galaxy.
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self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) }
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self.metadata_dict = { 'shed_config_filename': self.shed_config_dict.get( 'config_filename', None ) }
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else:
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self.metadata_dict = metadata_dict
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else:
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@@ -13,7 +13,7 @@ from tool_shed.util import hg_util
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class HTTPRedirectWithDataHandler( urllib2.HTTPRedirectHandler ):
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def __init__( self, method ):
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'''
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Upon first inspection, it would seem that this shouldn't be necessary, but for some reason
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@@ -259,7 +259,7 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine
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valid_tools=None,
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workflows=None,
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valid_data_managers=None
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)
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)
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if repository_metadata:
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metadata = repository_metadata.metadata
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lock = threading.Lock()
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@@ -405,19 +405,19 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine
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continue
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# We have a dictionary that looks something like this:
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# {
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# 'missing_test_components': [],
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# 'failed_tests': [],
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# 'passed_tests':
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# [{'tool_id': 'effectiveT3',
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# 'test_id': 'test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)',
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# 'tool_version': '0.0.12'},
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# {'tool_id': 'effectiveT3',
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# 'test_id': 'test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)',
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# 'tool_version': '0.0.12'}],
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# 'test_environment':
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# {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic',
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# 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a',
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# 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'},
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# 'missing_test_components': [],
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# 'failed_tests': [],
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# 'passed_tests':
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# [{'tool_id': 'effectiveT3',
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# 'test_id': 'test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)',
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# 'tool_version': '0.0.12'},
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# {'tool_id': 'effectiveT3',
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# 'test_id': 'test_tool_000001 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/...)',
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# 'tool_version': '0.0.12'}],
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# 'test_environment':
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# {'python_version': '2.7.4', 'tool_shed_mercurial_version': '2.2.3', 'system': 'Linux 3.8.0-30-generic',
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# 'tool_shed_database_version': 21, 'architecture': 'x86_64', 'galaxy_revision': '11573:a62c54ddbe2a',
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# 'galaxy_database_version': 117, 'time_tested': '2013-12-03 09:11:48', 'tool_shed_revision': '11556:228156daa575'},
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# 'installation_errors': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []},
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# 'successful_installations': {'current_repository': [], 'repository_dependencies': [], 'tool_dependencies': []}
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# }
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@@ -554,10 +554,10 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine
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for missing_test_components_dict in missing_test_components_dicts:
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missing_test_component_id += 1
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try:
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missing_components = missing_test_components_dict.get( 'missing_components', '' )
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tool_guid = missing_test_components_dict.get( 'tool_guid', '' )
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tool_id = missing_test_components_dict.get( 'tool_id', '' )
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tool_version = missing_test_components_dict.get( 'tool_version', '' )
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missing_components = missing_test_components_dict.get( 'missing_components', '' )
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tool_guid = missing_test_components_dict.get( 'tool_guid', '' )
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tool_id = missing_test_components_dict.get( 'tool_id', '' )
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tool_version = missing_test_components_dict.get( 'tool_version', '' )
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except Exception, e:
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missing_components = str( e )
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tool_guid = 'unknown'
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@@ -572,9 +572,9 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine
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installation_error_dict = tool_test_results_dict.get( 'installation_errors', {} )
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if len( installation_error_dict ) > 0:
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# 'installation_errors':
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# {'current_repository': [],
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# 'repository_dependencies': [],
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# 'tool_dependencies':
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# {'current_repository': [],
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# 'repository_dependencies': [],
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# 'tool_dependencies':
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# [{'error_message': 'some traceback string' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}]
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# }
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current_repository_installation_error_dicts = installation_error_dict.get( 'current_repository', [] )
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@@ -679,9 +679,9 @@ class ToolShedUtilityContainerManager( utility_container_manager.UtilityContaine
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successful_installation_dict = tool_test_results_dict.get( 'successful_installations', {} )
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if len( successful_installation_dict ) > 0:
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# 'successful_installation':
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# {'current_repository': [],
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# 'repository_dependencies': [],
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# 'tool_dependencies':
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# {'current_repository': [],
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# 'repository_dependencies': [],
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# 'tool_dependencies':
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# [{'installation_directory': 'some path' 'type': 'package', 'name': 'MIRA', 'version': '4.0'}]
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# }
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# We won't display the current repository in this container. I fit is not displaying installation errors,
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@@ -469,7 +469,7 @@ class UtilityContainerManager( object ):
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container_object_tool_id += 1
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requirements = tool_dict.get( 'requirements', None )
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if requirements is not None:
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# 'requirements': [{'version': '1.56.0', 'type': 'package', 'name': 'picard'}],
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# 'requirements': [{'version': '1.56.0', 'type': 'package', 'name': 'picard'}],
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requirements_str = ''
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for requirement_dict in requirements:
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try:
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@@ -643,7 +643,7 @@ class UtilityContainerManager( object ):
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repository_id=repository_id )
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folder.workflows.append( workflow )
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for workflow_tup in workflows:
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workflow_dict=workflow_tup[ 1 ]
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workflow_dict = workflow_tup[ 1 ]
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steps = workflow_dict.get( 'steps', [] )
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if steps:
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steps = str( len( steps ) )
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@@ -779,12 +779,7 @@ class UtilityContainerManager( object ):
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installation_status = None
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can_create_dependency = not self.is_subfolder_of( sub_folder, repository_dependency )
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if can_create_dependency:
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toolshed, \
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repository_name, \
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repository_owner, \
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changeset_revision, \
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prior_installation_required, \
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only_if_compiling_contained_td = \
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toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
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common_util.parse_repository_dependency_tuple( repository_dependency )
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repository_dependency_id += 1
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repository_dependency = RepositoryDependency( id=repository_dependency_id,
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@@ -801,12 +796,7 @@ class UtilityContainerManager( object ):
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return repository_dependencies_folder, folder_id, repository_dependency_id
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def is_subfolder_of( self, folder, repository_dependency ):
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toolshed, \
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repository_name, \
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repository_owner, \
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changeset_revision, \
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prior_installation_required, \
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only_if_compiling_contained_td = \
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toolshed, repository_name, repository_owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
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common_util.parse_repository_dependency_tuple( repository_dependency )
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key = container_util.generate_repository_dependencies_key_for_repository( toolshed,
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repository_name,
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@@ -835,10 +825,10 @@ class UtilityContainerManager( object ):
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key_prior_installation_required = components_list[ 4 ]
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key_only_if_compiling_contained_td = components_list[ 5 ]
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if repository_name == key_name and \
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repository_owner == key_owner and \
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changeset_revision == key_changeset_revision and \
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prior_installation_required == key_prior_installation_required and \
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only_if_compiling_contained_td == key_only_if_compiling_contained_td:
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repository_owner == key_owner and \
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changeset_revision == key_changeset_revision and \
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prior_installation_required == key_prior_installation_required and \
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only_if_compiling_contained_td == key_only_if_compiling_contained_td:
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return True
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return False
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