1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/10c58feed93f/ Changeset: 10c58feed93f User: greg Date: 2014-07-16 15:16:35 Summary: Rename the ~/tool_shed/dependencies/dependency_manager.py module to be attribute_handlers.py Affected #: 4 files diff -r 6a548e4e607f57942bc874ab10eb738522d5e9d9 -r 10c58feed93f26d8247be96baa111b3408970784 lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -8,7 +8,7 @@ from galaxy import util from galaxy import web from galaxy.datatypes import checkers -from tool_shed.dependencies import dependency_manager +from tool_shed.dependencies import attribute_handlers import tool_shed.repository_types.util as rt_util from tool_shed.util import basic_util from tool_shed.util import commit_util @@ -95,8 +95,8 @@ uploaded_file_filename = os.path.split( file_data.filename )[ -1 ] isempty = os.path.getsize( os.path.abspath( uploaded_file_name ) ) == 0 if uploaded_file or uploaded_directory: - rdah = dependency_manager.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) - tdah = dependency_manager.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) + rdah = attribute_handlers.RepositoryDependencyAttributeHandler( trans.app, unpopulate=False ) + tdah = attribute_handlers.ToolDependencyAttributeHandler( trans.app, unpopulate=False ) ok = True isgzip = False isbz2 = False diff -r 6a548e4e607f57942bc874ab10eb738522d5e9d9 -r 10c58feed93f26d8247be96baa111b3408970784 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -13,8 +13,7 @@ from galaxy.util import CHUNK_SIZE from galaxy.util.odict import odict from tool_shed.dependencies.repository.relation_builder import RelationBuilder -from tool_shed.dependencies.dependency_manager import RepositoryDependencyAttributeHandler -from tool_shed.dependencies.dependency_manager import ToolDependencyAttributeHandler +from tool_shed.dependencies import attribute_handlers from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import common_util @@ -130,8 +129,8 @@ return sub_elements def generate_repository_archive( self, repository, changeset_revision, work_dir ): - rdah = RepositoryDependencyAttributeHandler( self.app, unpopulate=True ) - tdah = ToolDependencyAttributeHandler( self.app, unpopulate=True ) + rdah = attribute_handlers.RepositoryDependencyAttributeHandler( self.app, unpopulate=True ) + tdah = attribute_handlers.ToolDependencyAttributeHandler( self.app, unpopulate=True ) file_type_str = basic_util.get_file_type_str( changeset_revision, self.file_type ) file_name = '%s-%s' % ( repository.name, file_type_str ) return_code, error_message = hg_util.archive_repository_revision( self.app, @@ -646,8 +645,8 @@ def import_repository_archive( self, repository, repository_archive_dict ): """Import a repository archive contained within a repository capsule.""" - rdah = RepositoryDependencyAttributeHandler( self.app, unpopulate=False ) - tdah = ToolDependencyAttributeHandler( self.app, unpopulate=False ) + rdah = attribute_handlers.RepositoryDependencyAttributeHandler( self.app, unpopulate=False ) + tdah = attribute_handlers.ToolDependencyAttributeHandler( self.app, unpopulate=False ) archive_file_name = repository_archive_dict.get( 'archive_file_name', None ) capsule_file_name = repository_archive_dict[ 'capsule_file_name' ] encoded_file_path = repository_archive_dict[ 'encoded_file_path' ] diff -r 6a548e4e607f57942bc874ab10eb738522d5e9d9 -r 10c58feed93f26d8247be96baa111b3408970784 lib/tool_shed/dependencies/attribute_handlers.py --- /dev/null +++ b/lib/tool_shed/dependencies/attribute_handlers.py @@ -0,0 +1,203 @@ +import copy +import logging + +from galaxy.util import asbool +from galaxy.util.odict import odict +from galaxy.web import url_for + +from tool_shed.dependencies.tool import tag_attribute_handler +from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME +from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util +log = logging.getLogger( __name__ ) + + +class RepositoryDependencyAttributeHandler( object ): + + def __init__( self, app, unpopulate ): + self.app = app + self.file_name = REPOSITORY_DEPENDENCY_DEFINITION_FILENAME + self.unpopulate = unpopulate + + def check_tag_attributes( self, elem ): + # <repository name="molecule_datatypes" owner="test" /> + error_message = '' + name = elem.get( 'name' ) + if not name: + error_message += 'The tag is missing the required name attribute. ' + owner = elem.get( 'owner' ) + if not owner: + error_message += 'The tag is missing the required owner attribute. ' + log.debug( error_message ) + return error_message + + def handle_complex_dependency_elem( self, parent_elem, elem_index, elem ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes of a + <repository> tag that defines a complex repository dependency. + """ + # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> + altered, new_elem, error_message = self.handle_elem( elem ) + if error_message: + error_message += ' The %s file contains an invalid <repository> tag.' % TOOL_DEPENDENCY_DEFINITION_FILENAME + return altered, new_elem, error_message + + def handle_elem( self, elem ): + """Populate or unpopulate the changeset_revision and toolshed attributes of repository tags.""" + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> + # <package name="xorg_macros" version="1.17.1" /> + # </repository> + error_message = '' + name = elem.get( 'name' ) + owner = elem.get( 'owner' ) + # The name and owner attributes are always required, so if either are missing, return the error message. + if not name or not owner: + error_message = self.check_tag_attributes( elem ) + return False, elem, error_message + altered = False + toolshed = elem.get( 'toolshed' ) + changeset_revision = elem.get( 'changeset_revision' ) + # Over a short period of time a bug existed which caused the prior_installation_required attribute + # to be set to False and included in the <repository> tag when a repository was exported along with + # its dependencies. The following will eliminate this problematic attribute upon import. + prior_installation_required = elem.get( 'prior_installation_required' ) + if prior_installation_required is not None and not asbool( prior_installation_required ): + del elem.attrib[ 'prior_installation_required' ] + sub_elems = [ child_elem for child_elem in list( elem ) ] + if len( sub_elems ) > 0: + # At this point, a <repository> tag will point only to a package. + # <package name="xorg_macros" version="1.17.1" /> + # Coerce the list to an odict(). + sub_elements = odict() + packages = [] + for sub_elem in sub_elems: + sub_elem_type = sub_elem.tag + sub_elem_name = sub_elem.get( 'name' ) + sub_elem_version = sub_elem.get( 'version' ) + if sub_elem_type and sub_elem_name and sub_elem_version: + packages.append( ( sub_elem_name, sub_elem_version ) ) + sub_elements[ 'packages' ] = packages + else: + # Set to None. + sub_elements = None + if self.unpopulate: + # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes + # from the <repository> tag. + if toolshed or changeset_revision: + attributes = odict() + attributes[ 'name' ] = name + attributes[ 'owner' ] = owner + prior_installation_required = elem.get( 'prior_installation_required' ) + if asbool( prior_installation_required ): + attributes[ 'prior_installation_required' ] = 'True' + new_elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) + altered = True + return altered, new_elem, error_message + # From here on we're populating the toolshed and changeset_revision attributes if necessary. + if not toolshed: + # Default the setting to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + elem.attrib[ 'toolshed' ] = toolshed + altered = True + if not changeset_revision: + # Populate the changeset_revision attribute with the latest installable metadata revision for + # the defined repository. We use the latest installable revision instead of the latest metadata + # revision to ensure that the contents of the revision are valid. + repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + if repository: + repo = hg_util.get_repo_for_repository( self.app, + repository=repository, + repo_path=None, + create=False ) + lastest_installable_changeset_revision = \ + suc.get_latest_downloadable_changeset_revision( self.app, repository, repo ) + if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: + elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision + altered = True + else: + error_message = 'Invalid latest installable changeset_revision %s ' % \ + str( lastest_installable_changeset_revision ) + error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) + else: + error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) + return altered, elem, error_message + + def handle_sub_elem( self, parent_elem, elem_index, elem ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes for each of + the following tag sets. + <action type="set_environment_for_install"> + <action type="setup_r_environment"> + <action type="setup_ruby_environment"> + """ + sub_elem_altered = False + error_message = '' + for sub_index, sub_elem in enumerate( elem ): + # Make sure to skip comments and tags that are not <repository>. + if sub_elem.tag == 'repository': + altered, new_sub_elem, message = self.handle_elem( sub_elem ) + if message: + error_message += 'The %s file contains an invalid <repository> tag. %s' % \ + ( TOOL_DEPENDENCY_DEFINITION_FILENAME, message ) + if altered: + if not sub_elem_altered: + sub_elem_altered = True + elem[ sub_index ] = new_sub_elem + if sub_elem_altered: + parent_elem[ elem_index ] = elem + return sub_elem_altered, parent_elem, error_message + + def handle_tag_attributes( self, config ): + """ + Populate or unpopulate the toolshed and changeset_revision attributes of a + <repository> tag. Populating will occur when a dependency definition file + is being uploaded to the repository, while unpopulating will occur when the + repository is being exported. + """ + # Make sure we're looking at a valid repository_dependencies.xml file. + tree, error_message = xml_util.parse_xml( config ) + if tree is None: + return False, None, error_message + root = tree.getroot() + root_altered = False + new_root = copy.deepcopy( root ) + for index, elem in enumerate( root ): + if elem.tag == 'repository': + # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> + altered, new_elem, error_message = self.handle_elem( elem ) + if error_message: + error_message = 'The %s file contains an invalid <repository> tag. %s' % ( self.file_name, error_message ) + return False, None, error_message + if altered: + if not root_altered: + root_altered = True + new_root[ index ] = new_elem + return root_altered, new_root, error_message + + +class ToolDependencyAttributeHandler( object ): + + def __init__( self, app, unpopulate ): + self.app = app + self.file_name = TOOL_DEPENDENCY_DEFINITION_FILENAME + self.unpopulate = unpopulate + + def handle_tag_attributes( self, tool_dependencies_config ): + """ + Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> + tag defined within a tool_dependencies.xml file. + """ + rdah = RepositoryDependencyAttributeHandler( self.app, self.unpopulate ) + tah = tag_attribute_handler.TagAttributeHandler( self.app, rdah, self.unpopulate ) + altered = False + error_message = '' + # Make sure we're looking at a valid tool_dependencies.xml file. + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + return False, None, error_message + root = tree.getroot() + altered, new_root, error_message = tah.process_config( root ) + return altered, new_root, error_message diff -r 6a548e4e607f57942bc874ab10eb738522d5e9d9 -r 10c58feed93f26d8247be96baa111b3408970784 lib/tool_shed/dependencies/dependency_manager.py --- a/lib/tool_shed/dependencies/dependency_manager.py +++ /dev/null @@ -1,203 +0,0 @@ -import copy -import logging - -from galaxy.util import asbool -from galaxy.util.odict import odict -from galaxy.web import url_for - -from tool_shed.dependencies.tool import tag_attribute_handler -from tool_shed.repository_types.util import REPOSITORY_DEPENDENCY_DEFINITION_FILENAME -from tool_shed.repository_types.util import TOOL_DEPENDENCY_DEFINITION_FILENAME -from tool_shed.util import hg_util -from tool_shed.util import shed_util_common as suc -from tool_shed.util import xml_util -log = logging.getLogger( __name__ ) - - -class RepositoryDependencyAttributeHandler( object ): - - def __init__( self, app, unpopulate ): - self.app = app - self.file_name = REPOSITORY_DEPENDENCY_DEFINITION_FILENAME - self.unpopulate = unpopulate - - def check_tag_attributes( self, elem ): - # <repository name="molecule_datatypes" owner="test" /> - error_message = '' - name = elem.get( 'name' ) - if not name: - error_message += 'The tag is missing the required name attribute. ' - owner = elem.get( 'owner' ) - if not owner: - error_message += 'The tag is missing the required owner attribute. ' - log.debug( error_message ) - return error_message - - def handle_complex_dependency_elem( self, parent_elem, elem_index, elem ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes of a - <repository> tag that defines a complex repository dependency. - """ - # <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" /> - altered, new_elem, error_message = self.handle_elem( elem ) - if error_message: - error_message += ' The %s file contains an invalid <repository> tag.' % TOOL_DEPENDENCY_DEFINITION_FILENAME - return altered, new_elem, error_message - - def handle_elem( self, elem ): - """Populate or unpopulate the changeset_revision and toolshed attributes of repository tags.""" - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - # <repository changeset_revision="xxx" name="package_xorg_macros_1_17_1" owner="test" toolshed="yyy"> - # <package name="xorg_macros" version="1.17.1" /> - # </repository> - error_message = '' - name = elem.get( 'name' ) - owner = elem.get( 'owner' ) - # The name and owner attributes are always required, so if either are missing, return the error message. - if not name or not owner: - error_message = self.check_tag_attributes( elem ) - return False, elem, error_message - altered = False - toolshed = elem.get( 'toolshed' ) - changeset_revision = elem.get( 'changeset_revision' ) - # Over a short period of time a bug existed which caused the prior_installation_required attribute - # to be set to False and included in the <repository> tag when a repository was exported along with - # its dependencies. The following will eliminate this problematic attribute upon import. - prior_installation_required = elem.get( 'prior_installation_required' ) - if prior_installation_required is not None and not asbool( prior_installation_required ): - del elem.attrib[ 'prior_installation_required' ] - sub_elems = [ child_elem for child_elem in list( elem ) ] - if len( sub_elems ) > 0: - # At this point, a <repository> tag will point only to a package. - # <package name="xorg_macros" version="1.17.1" /> - # Coerce the list to an odict(). - sub_elements = odict() - packages = [] - for sub_elem in sub_elems: - sub_elem_type = sub_elem.tag - sub_elem_name = sub_elem.get( 'name' ) - sub_elem_version = sub_elem.get( 'version' ) - if sub_elem_type and sub_elem_name and sub_elem_version: - packages.append( ( sub_elem_name, sub_elem_version ) ) - sub_elements[ 'packages' ] = packages - else: - # Set to None. - sub_elements = None - if self.unpopulate: - # We're exporting the repository, so eliminate all toolshed and changeset_revision attributes - # from the <repository> tag. - if toolshed or changeset_revision: - attributes = odict() - attributes[ 'name' ] = name - attributes[ 'owner' ] = owner - prior_installation_required = elem.get( 'prior_installation_required' ) - if asbool( prior_installation_required ): - attributes[ 'prior_installation_required' ] = 'True' - new_elem = xml_util.create_element( 'repository', attributes=attributes, sub_elements=sub_elements ) - altered = True - return altered, new_elem, error_message - # From here on we're populating the toolshed and changeset_revision attributes if necessary. - if not toolshed: - # Default the setting to the current tool shed. - toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) - elem.attrib[ 'toolshed' ] = toolshed - altered = True - if not changeset_revision: - # Populate the changeset_revision attribute with the latest installable metadata revision for - # the defined repository. We use the latest installable revision instead of the latest metadata - # revision to ensure that the contents of the revision are valid. - repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) - if repository: - repo = hg_util.get_repo_for_repository( self.app, - repository=repository, - repo_path=None, - create=False ) - lastest_installable_changeset_revision = \ - suc.get_latest_downloadable_changeset_revision( self.app, repository, repo ) - if lastest_installable_changeset_revision != hg_util.INITIAL_CHANGELOG_HASH: - elem.attrib[ 'changeset_revision' ] = lastest_installable_changeset_revision - altered = True - else: - error_message = 'Invalid latest installable changeset_revision %s ' % \ - str( lastest_installable_changeset_revision ) - error_message += 'retrieved for repository %s owned by %s. ' % ( str( name ), str( owner ) ) - else: - error_message = 'Unable to locate repository with name %s and owner %s. ' % ( str( name ), str( owner ) ) - return altered, elem, error_message - - def handle_sub_elem( self, parent_elem, elem_index, elem ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes for each of - the following tag sets. - <action type="set_environment_for_install"> - <action type="setup_r_environment"> - <action type="setup_ruby_environment"> - """ - sub_elem_altered = False - error_message = '' - for sub_index, sub_elem in enumerate( elem ): - # Make sure to skip comments and tags that are not <repository>. - if sub_elem.tag == 'repository': - altered, new_sub_elem, message = self.handle_elem( sub_elem ) - if message: - error_message += 'The %s file contains an invalid <repository> tag. %s' % \ - ( TOOL_DEPENDENCY_DEFINITION_FILENAME, message ) - if altered: - if not sub_elem_altered: - sub_elem_altered = True - elem[ sub_index ] = new_sub_elem - if sub_elem_altered: - parent_elem[ elem_index ] = elem - return sub_elem_altered, parent_elem, error_message - - def handle_tag_attributes( self, config ): - """ - Populate or unpopulate the toolshed and changeset_revision attributes of a - <repository> tag. Populating will occur when a dependency definition file - is being uploaded to the repository, while unpopulating will occur when the - repository is being exported. - """ - # Make sure we're looking at a valid repository_dependencies.xml file. - tree, error_message = xml_util.parse_xml( config ) - if tree is None: - return False, None, error_message - root = tree.getroot() - root_altered = False - new_root = copy.deepcopy( root ) - for index, elem in enumerate( root ): - if elem.tag == 'repository': - # <repository name="molecule_datatypes" owner="test" changeset_revision="1a070566e9c6" /> - altered, new_elem, error_message = self.handle_elem( elem ) - if error_message: - error_message = 'The %s file contains an invalid <repository> tag. %s' % ( self.file_name, error_message ) - return False, None, error_message - if altered: - if not root_altered: - root_altered = True - new_root[ index ] = new_elem - return root_altered, new_root, error_message - - -class ToolDependencyAttributeHandler( object ): - - def __init__( self, app, unpopulate ): - self.app = app - self.file_name = TOOL_DEPENDENCY_DEFINITION_FILENAME - self.unpopulate = unpopulate - - def handle_tag_attributes( self, tool_dependencies_config ): - """ - Populate or unpopulate the tooshed and changeset_revision attributes of each <repository> - tag defined within a tool_dependencies.xml file. - """ - rdah = RepositoryDependencyAttributeHandler( self.app, self.unpopulate ) - tah = tag_attribute_handler.TagAttributeHandler( self.app, rdah, self.unpopulate ) - altered = False - error_message = '' - # Make sure we're looking at a valid tool_dependencies.xml file. - tree, error_message = xml_util.parse_xml( tool_dependencies_config ) - if tree is None: - return False, None, error_message - root = tree.getroot() - altered, new_root, error_message = tah.process_config( root ) - return altered, new_root, error_message Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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