Python common_util.parse_repository_dependency_tuple函数代码示例

 def remove_repository_dependency_reference_to_self( self, key_rd_dicts ):
     """Remove all repository dependencies that point to a revision within its own repository."""
     clean_key_rd_dicts = []
     key = next(iter(key_rd_dicts[ 0 ]))
     repository_tup = key.split( container_util.STRSEP )
     rd_toolshed, rd_name, rd_owner, rd_changeset_revision, \
         rd_prior_installation_required, \
         rd_only_if_compiling_contained_td = \
         common_util.parse_repository_dependency_tuple( repository_tup )
     cleaned_rd_toolshed = common_util.remove_protocol_from_tool_shed_url( rd_toolshed )
     for key_rd_dict in key_rd_dicts:
         k = next(iter(key_rd_dict))
         repository_dependency = key_rd_dict[ k ]
         toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
             common_util.parse_repository_dependency_tuple( repository_dependency )
         cleaned_toolshed = common_util.remove_protocol_from_tool_shed_url( toolshed )
         if cleaned_rd_toolshed == cleaned_toolshed and rd_name == name and rd_owner == owner:
             debug_msg = "Removing repository dependency for repository %s owned by %s " % ( name, owner )
             debug_msg += 'since it refers to a revision within itself.'
             log.debug( debug_msg )
         else:
             new_key_rd_dict = {}
             new_key_rd_dict[ key ] = repository_dependency
             clean_key_rd_dicts.append( new_key_rd_dict )
     return clean_key_rd_dicts

 def requires_prior_installation_of( self ):
     """
     Return a list of repository dependency tuples like (tool_shed, name, owner, changeset_revision, prior_installation_required) for this
     repository's repository dependencies where prior_installation_required is True.  By definition, repository dependencies are required to
     be installed in order for this repository to function correctly.  However, those repository dependencies that are defined for this
     repository with prior_installation_required set to True place them in a special category in that the required repositories must be
     installed before this repository is installed.  Among other things, this enables these "special" repository dependencies to include
     information that enables the successful installation of this repository.  This method is not used during the initial installation of
     this repository, but only after it has been installed (metadata must be set for this repository in order for this method to be useful).
     """
     required_rd_tups_that_must_be_installed = []
     if self.has_repository_dependencies:
         rd_tups = self.metadata[ 'repository_dependencies' ][ 'repository_dependencies' ]
         for rd_tup in rd_tups:
             if len( rd_tup ) == 5:
                 tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
                     common_util.parse_repository_dependency_tuple( rd_tup, contains_error=False )
                 if asbool( prior_installation_required ):
                     required_rd_tups_that_must_be_installed.append( ( tool_shed, name, owner, changeset_revision, 'True', 'False' ) )
             elif len( rd_tup ) == 6:
                 tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
                     common_util.parse_repository_dependency_tuple( rd_tup, contains_error=False )
                 # The repository dependency will only be required to be previously installed if it does not fall into the category of
                 # a repository that must be installed only so that its contained tool dependency can be used for compiling the tool
                 # dependency of the dependent repository.
                 if not asbool( only_if_compiling_contained_td ):
                     if asbool( prior_installation_required ):
                         required_rd_tups_that_must_be_installed.append( ( tool_shed, name, owner, changeset_revision, 'True', 'False' ) )
     return required_rd_tups_that_must_be_installed

 def get_prior_installation_required_and_only_if_compiling_contained_td( self ):
     """
     This method is called from the tool shed and never Galaxy.  If self.all_repository_dependencies
     contains a repository dependency tuple that is associated with self.repository, return the
     value of the tuple's prior_installation_required component.
     """
     cleaned_toolshed_base_url = common_util.remove_protocol_from_tool_shed_url( self.tool_shed_url )
     if self.all_repository_dependencies:
         for rd_key, rd_tups in self.all_repository_dependencies.items():
             if rd_key in [ 'root_key', 'description' ]:
                 continue
             for rd_tup in rd_tups:
                 rd_toolshed, \
                 rd_name, \
                 rd_owner, \
                 rd_changeset_revision, \
                 rd_prior_installation_required, \
                 rd_only_if_compiling_contained_td = \
                     common_util.parse_repository_dependency_tuple( rd_tup )
                 cleaned_rd_toolshed = common_util.remove_protocol_from_tool_shed_url( rd_toolshed )
                 if cleaned_rd_toolshed == cleaned_toolshed_base_url and \
                     rd_name == self.repository.name and \
                     rd_owner == self.repository.user.username and \
                     rd_changeset_revision == self.repository_metadata.changeset_revision:
                     return rd_prior_installation_required, rd_only_if_compiling_contained_td
     elif self.repository_metadata:
         # Get the list of changeset revisions from the tool shed to which self.repository may be updated.
         metadata = self.repository_metadata.metadata
         current_changeset_revision = str( self.repository_metadata.changeset_revision )
         # Get the changeset revision to which the current value of required_repository_changeset_revision
         # should be updated if it's not current.
         text = suc.get_updated_changeset_revisions( self.app,
                                                     name=str( self.repository.name ),
                                                     owner=str( self.repository.user.username ),
                                                     changeset_revision=current_changeset_revision )
         if text:
             valid_changeset_revisions = listify( text )
             if current_changeset_revision not in valid_changeset_revisions:
                 valid_changeset_revisions.append( current_changeset_revision )
         else:
             valid_changeset_revisions = [ current_changeset_revision ]
         repository_dependencies_dict = metadata[ 'repository_dependencies' ]
         rd_tups = repository_dependencies_dict.get( 'repository_dependencies', [] )
         for rd_tup in rd_tups:
             rd_toolshed, \
             rd_name, \
             rd_owner, \
             rd_changeset_revision, \
             rd_prior_installation_required, \
             rd_only_if_compiling_contained_td = \
                 common_util.parse_repository_dependency_tuple( rd_tup )
             cleaned_rd_toolshed = common_util.remove_protocol_from_tool_shed_url( rd_toolshed )
             if cleaned_rd_toolshed == cleaned_toolshed_base_url and \
                 rd_name == self.repository.name and \
                 rd_owner == self.repository.user.username and \
                 rd_changeset_revision in valid_changeset_revisions:
                 return rd_prior_installation_required, rd_only_if_compiling_contained_td
     # Default both prior_installation_required and only_if_compiling_contained_td to False.
     return 'False', 'False'

 def generate_message_for_invalid_repository_dependencies( self, metadata_dict, error_from_tuple=False ):
     """
     Get or generate and return an error message associated with an invalid repository dependency.
     """
     message = ''
     if metadata_dict:
         if error_from_tuple:
             # Return the error messages associated with a set of one or more invalid repository
             # dependency tuples.
             invalid_repository_dependencies_dict = metadata_dict.get( 'invalid_repository_dependencies', None )
             if invalid_repository_dependencies_dict is not None:
                 invalid_repository_dependencies = \
                     invalid_repository_dependencies_dict.get( 'invalid_repository_dependencies', [] )
                 for repository_dependency_tup in invalid_repository_dependencies:
                     toolshed, \
                     name, \
                     owner, \
                     changeset_revision, \
                     prior_installation_required, \
                     only_if_compiling_contained_td, error = \
                         common_util.parse_repository_dependency_tuple( repository_dependency_tup, contains_error=True )
                     if error:
                         message += '%s  ' % str( error )
         else:
             # The complete dependency hierarchy could not be determined for a repository being installed into
             # Galaxy.  This is likely due to invalid repository dependency definitions, so we'll get them from
             # the metadata and parse them for display in an error message.  This will hopefully communicate the
             # problem to the user in such a way that a resolution can be determined.
             message += 'The complete dependency hierarchy could not be determined for this repository, so no required '
             message += 'repositories will not be installed.  This is likely due to invalid repository dependency definitions.  '
             repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None )
             if repository_dependencies_dict is not None:
                 rd_tups = repository_dependencies_dict.get( 'repository_dependencies', None )
                 if rd_tups is not None:
                     message += 'Here are the attributes of the dependencies defined for this repository to help determine the '
                     message += 'cause of this problem.<br/>'
                     message += '<table cellpadding="2" cellspacing="2">'
                     message += '<tr><th>Tool shed</th><th>Repository name</th><th>Owner</th><th>Changeset revision</th>'
                     message += '<th>Prior install required</th></tr>'
                     for rd_tup in rd_tups:
                         tool_shed, name, owner, changeset_revision, pir, oicct = \
                             common_util.parse_repository_dependency_tuple( rd_tup )
                         if util.asbool( pir ):
                             pir_str = 'True'
                         else:
                             pir_str = ''
                         message += '<tr><td>%s</td><td>%s</td><td>%s</td><td>%s</td><td>%s</td></tr>' % \
                             ( tool_shed, name, owner, changeset_revision, pir_str )
                     message += '</table>'
     return message

 def handle_key_rd_dicts_for_repository( self, current_repository_key, repository_key_rd_dicts ):
     key_rd_dict = repository_key_rd_dicts.pop( 0 )
     repository_dependency = key_rd_dict[ current_repository_key ]
     toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
         common_util.parse_repository_dependency_tuple( repository_dependency )
     if suc.tool_shed_is_this_tool_shed( toolshed ):
         required_repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( self.app, name, owner )
         self.repository = required_repository
         repository_id = self.app.security.encode_id( required_repository.id )
         required_repository_metadata = \
             metadata_util.get_repository_metadata_by_repository_id_changeset_revision( self.app,
                                                                                        repository_id,
                                                                                        changeset_revision )
         self.repository_metadata = required_repository_metadata
         if required_repository_metadata:
             # The required_repository_metadata changeset_revision is installable.
             required_metadata = required_repository_metadata.metadata
             if required_metadata:
                 for current_repository_key_rd_dict in repository_key_rd_dicts:
                     if not self.in_key_rd_dicts( current_repository_key_rd_dict, self.key_rd_dicts_to_be_processed ):
                         # Add the current repository_dependency into self.key_rd_dicts_to_be_processed.
                         self.key_rd_dicts_to_be_processed.append( current_repository_key_rd_dict )
         if not self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ):
             # Add the current repository_dependency into self.handled_key_rd_dicts.
             self.handled_key_rd_dicts.append( key_rd_dict )
         if self.in_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed ):
             # Remove the current repository from self.key_rd_dicts_to_be_processed.
             self.key_rd_dicts_to_be_processed = self.remove_from_key_rd_dicts( key_rd_dict, self.key_rd_dicts_to_be_processed )
     else:
         # The repository is in a different tool shed, so build an url and send a request.
         error_message = "Repository dependencies are currently supported only within the same Tool Shed.  "
         error_message += "Ignoring repository dependency definition for tool shed "
         error_message += "%s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision )
         log.debug( error_message )

def get_repository_dependency_tups_from_repository_metadata( app, repository_metadata, deprecated_only=False ):
    """
    Return a list of of tuples defining repository objects required by the received repository.  The returned
    list defines the entire repository dependency tree.  This method is called only from the Tool Shed.
    """
    dependency_tups = []
    if repository_metadata is not None:
        metadata = repository_metadata.metadata
        if metadata:
            repository_dependencies_dict = metadata.get( 'repository_dependencies', None )
            if repository_dependencies_dict is not None:
                repository_dependency_tups = repository_dependencies_dict.get( 'repository_dependencies', None )
                if repository_dependency_tups is not None:
                    # The value of repository_dependency_tups is a list of repository dependency tuples like this:
                    # ['http://localhost:9009', 'package_samtools_0_1_18', 'devteam', 'ef37fc635cb9', 'False', 'False']
                    for repository_dependency_tup in repository_dependency_tups:
                        toolshed, name, owner, changeset_revision, pir, oicct = \
                            common_util.parse_repository_dependency_tuple( repository_dependency_tup )
                        repository = tool_shed.util.repository_util.get_repository_by_name_and_owner( app, name, owner )
                        if repository:
                            if deprecated_only:
                                if repository.deprecated:
                                    dependency_tups.append( repository_dependency_tup )
                            else:
                                dependency_tups.append( repository_dependency_tup )
                        else:
                            log.debug( "Cannot locate repository %s owned by %s for inclusion in repository dependency tups." %
                                ( name, owner ) )
    return dependency_tups

def render_render_deprecated_repository_dependencies_message(context,deprecated_repository_dependency_tups):
    context.caller_stack._push_frame()
    try:
        __M_writer = context.writer()
        # SOURCE LINE 54
        __M_writer(u'\n    <div class="warningmessage">\n        ')
        # SOURCE LINE 56

        from tool_shed.util.common_util import parse_repository_dependency_tuple
        msg = '<ul>'
        for deprecated_repository_dependency_tup in deprecated_repository_dependency_tups:
            toolshed, name, owner, changeset_revision, pir, oicct = \
                parse_repository_dependency_tuple( deprecated_repository_dependency_tup )
            msg += '<li>Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b></li>' % \
                    ( changeset_revision, name, owner )
        msg += '</ul>'
                
        
        # SOURCE LINE 65
        __M_writer(u'\n        This repository depends upon the following deprecated repositories<br/>\n        ')
        # SOURCE LINE 67
        __M_writer(unicode(msg))
        __M_writer(u'\n    </div>\n')
        return ''
    finally:
        context.caller_stack._pop_frame()

 def create_or_update_tool_shed_repository_records( self, name, changeset_revision, repository_dependencies_dict ):
     """
     Make sure the repository defined by name and changeset_revision and all of its repository dependencies have
     associated tool_shed_repository table rows in the Galaxy database.
     """
     created_tool_shed_repositories = []
     description = repository_dependencies_dict.get( 'description', None )
     tool_shed_repository = self.create_or_update_tool_shed_repository_record( name,
                                                                               self.repository_owner,
                                                                               changeset_revision,
                                                                               description=description )
     if tool_shed_repository:
         created_tool_shed_repositories.append( tool_shed_repository )
     for rd_key, rd_tups in repository_dependencies_dict.items():
         if rd_key in [ 'root_key', 'description' ]:
             continue
         for rd_tup in rd_tups:
             parsed_rd_tup = common_util.parse_repository_dependency_tuple( rd_tup )
             rd_tool_shed, rd_name, rd_owner, rd_changeset_revision = parsed_rd_tup[ 0:4 ]
             # TODO: Make sure the repository description is applied to the new repository record during installation.
             tool_shed_repository = self.create_or_update_tool_shed_repository_record( rd_name,
                                                                                       rd_owner,
                                                                                       rd_changeset_revision,
                                                                                       description=None )
             if tool_shed_repository:
                 created_tool_shed_repositories.append( tool_shed_repository )
     return created_tool_shed_repositories

 def get_repository_dependency_as_key( self, repository_dependency ):
     tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
         common_util.parse_repository_dependency_tuple( repository_dependency )
     return container_util.generate_repository_dependencies_key_for_repository( tool_shed,
                                                                                name,
                                                                                owner,
                                                                                changeset_revision,
                                                                                prior_installation_required,
                                                                                only_if_compiling_contained_td )

 def has_repository_dependencies( self ):
     if self.metadata:
         repository_dependencies_dict = self.metadata.get( 'repository_dependencies', {} )
         repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] )
         # [["http://localhost:9009", "package_libgtextutils_0_6", "test", "e2003cbf18cd", "True", "True"]]
         for rd_tup in repository_dependencies:
             tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
                 common_util.parse_repository_dependency_tuple( rd_tup )
             if not asbool( only_if_compiling_contained_td ):
                 return True
     return False

 def is_subfolder_of( self, folder, repository_dependency ):
     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,
                                                                               repository_owner,
                                                                               changeset_revision,
                                                                               prior_installation_required,
                                                                               only_if_compiling_contained_td )
     for sub_folder in folder.folders:
         if key == sub_folder.key:
             return True
     return False

 def filter_only_if_compiling_contained_td( self, key_rd_dict ):
     """
     Return a copy of the received key_rd_dict with repository dependencies that are needed
     only_if_compiling_contained_td filtered out of the list of repository dependencies for
     each rd_key.
     """
     filtered_key_rd_dict = {}
     for rd_key, required_rd_tup in key_rd_dict.items():
         tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
             common_util.parse_repository_dependency_tuple( required_rd_tup )
         if not asbool( only_if_compiling_contained_td ):
             filtered_key_rd_dict[ rd_key ] = required_rd_tup
     return filtered_key_rd_dict

def can_eliminate_repository_dependency(metadata_dict, tool_shed_url, name, owner):
    """
    Determine if the relationship between a repository_dependency record
    associated with a tool_shed_repository record on the Galaxy side
    can be eliminated.
    """
    rd_dict = metadata_dict.get('repository_dependencies', {})
    rd_tups = rd_dict.get('repository_dependencies', [])
    for rd_tup in rd_tups:
        tsu, n, o, none1, none2, none3 = common_util.parse_repository_dependency_tuple(rd_tup)
        if tsu == tool_shed_url and n == name and o == owner:
            # The repository dependency is current, so keep it.
            return False
    return True

 def build_invalid_repository_dependencies_root_folder( self, folder_id, invalid_repository_dependencies_dict ):
     """Return a folder hierarchy containing invalid repository dependencies."""
     label = 'Invalid repository dependencies'
     if invalid_repository_dependencies_dict:
         invalid_repository_dependency_id = 0
         folder_id += 1
         invalid_repository_dependencies_root_folder = \
             utility_container_manager.Folder( id=folder_id,
                                               key='root',
                                               label='root',
                                               parent=None )
         folder_id += 1
         invalid_repository_dependencies_folder = \
             utility_container_manager.Folder( id=folder_id,
                                               key='invalid_repository_dependencies',
                                               label=label,
                                               parent=invalid_repository_dependencies_root_folder )
         invalid_repository_dependencies_root_folder.folders.append( invalid_repository_dependencies_folder )
         invalid_repository_dependencies = invalid_repository_dependencies_dict[ 'repository_dependencies' ]
         for invalid_repository_dependency in invalid_repository_dependencies:
             folder_id += 1
             invalid_repository_dependency_id += 1
             toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \
                 common_util.parse_repository_dependency_tuple( invalid_repository_dependency, contains_error=True )
             key = container_util.generate_repository_dependencies_key_for_repository( toolshed,
                                                                                       name,
                                                                                       owner,
                                                                                       changeset_revision,
                                                                                       prior_installation_required,
                                                                                       only_if_compiling_contained_td )
             label = "Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>" % ( name, changeset_revision, owner )
             folder = utility_container_manager.Folder( id=folder_id,
                                                        key=key,
                                                        label=label,
                                                        parent=invalid_repository_dependencies_folder )
             ird = InvalidRepositoryDependency( id=invalid_repository_dependency_id,
                                                toolshed=toolshed,
                                                repository_name=name,
                                                repository_owner=owner,
                                                changeset_revision=changeset_revision,
                                                prior_installation_required=util.asbool( prior_installation_required ),
                                                only_if_compiling_contained_td=util.asbool( only_if_compiling_contained_td ),
                                                error=error )
             folder.invalid_repository_dependencies.append( ird )
             invalid_repository_dependencies_folder.folders.append( folder )
     else:
         invalid_repository_dependencies_root_folder = None
     return folder_id, invalid_repository_dependencies_root_folder

 def get_prior_install_required_dict( self, tool_shed_repositories, repository_dependencies_dict ):
     """
     Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received
     list of tsr_ids and whose associated repository must be installed prior to the repository associated with the tsr_id key.
     """
     # Initialize the dictionary.
     prior_install_required_dict = {}
     tsr_ids = [ tool_shed_repository.id for tool_shed_repository in tool_shed_repositories ]
     for tsr_id in tsr_ids:
         prior_install_required_dict[ tsr_id ] = []
     # Inspect the repository dependencies about to be installed and populate the dictionary.
     for rd_key, rd_tups in repository_dependencies_dict.items():
         if rd_key in [ 'root_key', 'description' ]:
             continue
         for rd_tup in rd_tups:
             prior_install_ids = []
             tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \
                 common_util.parse_repository_dependency_tuple( rd_tup )
             if util.asbool( prior_installation_required ):
                 for tsr in tool_shed_repositories:
                     if tsr.name == name and tsr.owner == owner and tsr.changeset_revision == changeset_revision:
                         prior_install_ids.append( tsr.id )
                     prior_install_required_dict[ tsr.id ] = prior_install_ids
     return prior_install_required_dict