1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/e19bf2b11763/ changeset: e19bf2b11763 user: greg date: 2012-12-10 22:27:29 summary: Handle circular repository dependencies to "n" levels of depth. affected #: 3 files

diff -r c460f284077f0b400901e4cd791d94a311425751 -r e19bf2b117638221414239698f840730a2cd0569 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1,8 +1,6 @@ import os, tempfile, shutil, logging, urllib2 from galaxy import util -from galaxy.datatypes.checkers import * -from galaxy.util.json import * -from galaxy.util.shed_util_common import * +from shed_util_common import * from galaxy.tools.search import ToolBoxSearch from galaxy.tool_shed.tool_dependencies.install_util import create_or_update_tool_dependency, install_package, set_environment from galaxy.tool_shed.encoding_util import *

diff -r c460f284077f0b400901e4cd791d94a311425751 -r e19bf2b117638221414239698f840730a2cd0569 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -194,28 +194,18 @@ option_value = trans.security.encode_id( repository.id ) repositories_select_field.add_option( option_label, option_value ) return repositories_select_field -def can_add_entry_to_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): - """ - Handle circular repository dependencies that could result in an infinite loop by determining if it is safe to add an entry to the - repository dependencies container. - """ - # First check for an exact match - if this is true, the changeset revision was not updated. - repository_dependency_as_key = container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], - repository_dependency[ 1 ], - repository_dependency[ 2 ], - repository_dependency[ 3] ) - current_repository_key_as_repository_dependency = current_repository_key.split( container_util.STRSEP ) - if repository_dependency_as_key in all_repository_dependencies: - val = all_repository_dependencies[ repository_dependency_as_key ] - if current_repository_key_as_repository_dependency in val: - return False - # Now handle the case where an update to the changeset revision was done, so everything will match except the changeset_revision. - repository_dependency_as_partial_key = container_util.STRSEP.join( [ repository_dependency[ 0 ], repository_dependency[ 1 ], repository_dependency[ 2 ] ] ) - for key in all_repository_dependencies: - if key.startswith( repository_dependency_as_partial_key ): - val = all_repository_dependencies[ key ] - if current_repository_key_as_repository_dependency in val: - return False +def can_add_to_key_rd_dicts( key_rd_dict, key_rd_dicts ): + """Handle the case where an update to the changeset revision was done.""" + k = key_rd_dict.keys()[ 0 ] + rd = key_rd_dict[ k ] + partial_rd = rd[ 0:3 ] + for kr_dict in key_rd_dicts: + key = kr_dict.keys()[ 0 ] + if key == k: + val = kr_dict[ key ] + for repository_dependency in val: + if repository_dependency[ 0:3 ] == partial_rd: + return False return True def can_generate_tool_dependency_metadata( root, metadata_dict ): """ @@ -555,13 +545,15 @@ metadata = repository_metadata.metadata if metadata: # Get a dictionary of all repositories upon which the contents of the received repository depends. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, - all_repository_dependencies=None ) + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, + all_repository_dependencies=None, + handled_key_rd_dicts=None, + circular_repository_dependencies=None ) # Cast unicode to string. repo_info_dict[ str( repository.name ) ] = ( str( repository.description ), str( repository_clone_url ), @@ -1037,6 +1029,11 @@ if ctx_file_name == stripped_filename: return manifest_ctx, ctx_file return None, None +def get_key_for_repository_changeset_revision( toolshed_base_url, repository, repository_metadata ): + return container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, + repository_name=repository.name, + repository_owner=repository.user.username, + changeset_revision=repository_metadata.changeset_revision ) def get_file_context_from_ctx( ctx, filename ): # We have to be careful in determining if we found the correct file because multiple files with the same name may be in different directories # within ctx if the files were moved within the change set. For example, in the following ctx.files() list, the former may have been moved to @@ -1197,123 +1194,68 @@ .filter( and_( trans.model.Repository.table.c.name == name, trans.model.Repository.table.c.user_id == user.id ) ) \ .first() -def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, repository_dependencies=None, - all_repository_dependencies=None, handled=None ): +def get_repository_dependencies_for_changeset_revision( trans, repo, repository, repository_metadata, toolshed_base_url, + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, + handled_key_rd_dicts=None, circular_repository_dependencies=None ): """ Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend. The dictionary keys are name-spaced values consisting of toolshed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of repository_dependency tuples consisting of ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). This method ensures that all required repositories to the nth degree are returned. """ - if handled is None: - handled = [] + if handled_key_rd_dicts is None: + handled_key_rd_dicts = [] if all_repository_dependencies is None: all_repository_dependencies = {} - if repository_dependencies is None: - repository_dependencies = [] + if key_rd_dicts_to_be_processed is None: + key_rd_dicts_to_be_processed = [] + if circular_repository_dependencies is None: + circular_repository_dependencies = [] + # Assume the current repository does not have repository dependencies defined for it. + current_repository_key = None metadata = repository_metadata.metadata if metadata and 'repository_dependencies' in metadata: + current_repository_key = get_key_for_repository_changeset_revision( toolshed_base_url, repository, repository_metadata ) repository_dependencies_dict = metadata[ 'repository_dependencies' ] - # The repository_dependencies entry in the metadata is a dictionary that may have a value for a 'description' key. We want to - # store the value of this key only once, the first time through this recursive method. - current_repository_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=toolshed_base_url, - repository_name=repository.name, - repository_owner=repository.user.username, - changeset_revision=repository_metadata.changeset_revision ) if not all_repository_dependencies: - # Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value. - all_repository_dependencies[ 'root_key' ] = current_repository_key - all_repository_dependencies[ current_repository_key ] = [] - if 'description' not in all_repository_dependencies: - description = repository_dependencies_dict.get( 'description', None ) - all_repository_dependencies[ 'description' ] = description - # The next key of interest in repository_dependencies_dict is 'repository_dependencies', which is a list of tuples. - repository_dependencies_tups = repository_dependencies_dict[ 'repository_dependencies' ] - if repository_dependencies_tups and current_repository_key: - # Remove all repository dependencies that point to a revision within its own repository. - repository_dependencies_tups = remove_ropository_dependency_reference_to_self( repository_dependencies_tups, current_repository_key ) - for repository_dependency in repository_dependencies_tups: - if repository_dependency not in handled and repository_dependency not in repository_dependencies: - # The following if statement handles repositories dependencies that are circular in nature. - if current_repository_key: - if current_repository_key in all_repository_dependencies: - # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. - all_repository_dependencies_val = all_repository_dependencies[ current_repository_key ] - if repository_dependency not in all_repository_dependencies_val: - all_repository_dependencies_val.append( repository_dependency ) - all_repository_dependencies[ current_repository_key ] = all_repository_dependencies_val - elif can_add_entry_to_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): - # We don't have a circular dependency that could result in an infinite loop. - all_repository_dependencies[ current_repository_key ] = [ repository_dependency ] - repository_dependencies.append( repository_dependency ) - else: - # The current repository does not have repository dependencies defined for it. - current_repository_key = None - # The following if statement handles repositories dependencies that are circular in nature. - if current_repository_key and current_repository_key in all_repository_dependencies: - repository_dependencies_tups = [ rd for rd in all_repository_dependencies[ current_repository_key ] ] - if repository_dependencies_tups: - repository_dependency = repository_dependencies_tups.pop( 0 ) - if repository_dependency not in handled: - handled.append( repository_dependency ) - if repository_dependency in repository_dependencies: - repository_dependencies.remove( repository_dependency ) - toolshed, name, owner, changeset_revision = repository_dependency - if tool_shed_is_this_tool_shed( toolshed ): - required_repository = get_repository_by_name_and_owner( trans, name, owner ) - required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, - trans.security.encode_id( required_repository.id ), - changeset_revision ) - if required_repository_metadata: - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) - else: - # The repository changeset_revision is no longer installable, so see if there's been an update. - required_repo_dir = required_repository.repo_path( trans.app ) - required_repo = hg.repository( get_configured_ui(), required_repo_dir ) - required_changeset_revision = get_next_downloadable_changeset_revision( required_repository, required_repo, changeset_revision ) - required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, - trans.security.encode_id( required_repository.id ), - required_changeset_revision ) - if required_repository_metadata: - # The changeset_revision defined in a repository_dependencies.xml file is outdated, so we need to fix appropriate - # entries in our all_repository_dependencies dictionary. - updated_repository_dependency = [ toolshed, name, owner, required_changeset_revision ] - for k, v in all_repository_dependencies.items(): - if k in [ 'root_key', 'description' ]: - continue - for i, current_repository_dependency in enumerate( v ): - cts, cn, co, ccr = current_repository_dependency - if toolshed == cts and name == cn and owner == co and changeset_revision == ccr: - if updated_repository_dependency in v: - # We've already stored the updated repository_dependency, so remove the outdated one. - v = v.remove( repository_dependency ) - all_repository_dependencies[ k ] = v - else: - # Store the updated repository_dependency. - v[ i ] = updated_repository_dependency - all_repository_dependencies[ k ] = v - if required_repository_metadata: - # The required_repository_metadata changeset_revision is installable. - required_metadata = required_repository_metadata.metadata - if required_metadata: - for repository_dependency in repository_dependencies_tups: - if repository_dependency not in repository_dependencies: - repository_dependencies.append( repository_dependency ) - return get_repository_dependencies_for_changeset_revision( trans=trans, - repo=required_repo, - repository=required_repository, - repository_metadata=required_repository_metadata, - toolshed_base_url=toolshed, - repository_dependencies=repository_dependencies, - all_repository_dependencies=all_repository_dependencies, - handled=handled ) - 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. Ignoring repository dependency definition " - error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision ) - log.debug( error_message ) + all_repository_dependencies = initialize_all_repository_dependencies( current_repository_key, + repository_dependencies_dict, + all_repository_dependencies ) + # Handle the repository dependencies defined in the current repository, if any, and populate the various repository dependency objects for + # this round of processing. + current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies = \ + populate_repository_dependency_objects_for_processing( trans, + current_repository_key, + repository_dependencies_dict, + key_rd_dicts_to_be_processed, + handled_key_rd_dicts, + circular_repository_dependencies, + all_repository_dependencies ) + if current_repository_key: + if current_repository_key_rd_dicts: + # There should be only a single current_repository_key_rd_dict in this list. + current_repository_key_rd_dict = current_repository_key_rd_dicts[ 0 ] + # Handle circular repository dependencies. + if not in_circular_repository_dependencies( current_repository_key_rd_dict, circular_repository_dependencies ): + if current_repository_key in all_repository_dependencies: + handle_current_repository_dependency( trans, + current_repository_key, + key_rd_dicts_to_be_processed, + all_repository_dependencies, + handled_key_rd_dicts, + circular_repository_dependencies ) + elif key_rd_dicts_to_be_processed: + handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + elif key_rd_dicts_to_be_processed: + handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) + elif key_rd_dicts_to_be_processed: + handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ) return all_repository_dependencies +def get_repository_dependency_as_key( repository_dependency ): + return container_util.generate_repository_dependencies_key_for_repository( repository_dependency[ 0 ], + repository_dependency[ 1 ], + repository_dependency[ 2 ], + repository_dependency[ 3] ) def get_repository_file_contents( file_path ): if checkers.is_gzip( file_path ): safe_str = to_safe_string( '\ngzip compressed file\n' ) @@ -1415,11 +1357,77 @@ relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths +def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ): + updated_key_rd_dicts = [] + for key_rd_dict in key_rd_dicts: + key = key_rd_dict.keys()[ 0 ] + repository_dependency = key_rd_dict[ key ] + toolshed, name, owner, changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( toolshed ): + repository = get_repository_by_name_and_owner( trans, name, owner ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + # The repository changeset_revision is installable, so no updates are available. + new_key_rd_dict = {} + new_key_rd_dict[ key ] = repository_dependency + updated_key_rd_dicts.append( key_rd_dict ) + else: + # The repository changeset_revision is no longer installable, so see if there's been an update. + repo_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + changeset_revision = get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + new_key_rd_dict = {} + new_key_rd_dict[ key ] = [ toolshed, name, owner, repository_metadata.changeset_revision ] + # We have the updated changset revision. + updated_key_rd_dicts.append( new_key_rd_dict ) + return updated_key_rd_dicts def get_user_by_username( trans, username ): """Get a user from the database by username""" return trans.sa_session.query( trans.model.User ) \ .filter( trans.model.User.table.c.username == username ) \ .one() +def handle_circular_repository_dependency( repository_key, repository_dependency, circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies ): + all_repository_dependencies_root_key = all_repository_dependencies[ 'root_key' ] + repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) + repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) + update_circular_repository_dependencies( repository_key, + repository_dependency, + all_repository_dependencies[ repository_dependency_as_key ], + circular_repository_dependencies ) + if all_repository_dependencies_root_key != repository_dependency_as_key: + all_repository_dependencies[ repository_key ] = [ repository_dependency ] + return circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies +def handle_current_repository_dependency( trans, current_repository_key, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, + circular_repository_dependencies ): + current_repository_key_rd_dicts = [] + for rd in all_repository_dependencies[ current_repository_key ]: + rd_copy = [ str( item ) for item in rd ] + new_key_rd_dict = {} + new_key_rd_dict[ current_repository_key ] = rd_copy + current_repository_key_rd_dicts.append( new_key_rd_dict ) + if current_repository_key_rd_dicts: + toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ + handle_key_rd_dicts_for_repository( trans, + current_repository_key, + current_repository_key_rd_dicts, + key_rd_dicts_to_be_processed, + handled_key_rd_dicts, + circular_repository_dependencies ) + return get_repository_dependencies_for_changeset_revision( trans=trans, + repo=required_repo, + repository=required_repository, + repository_metadata=required_repository_metadata, + toolshed_base_url=toolshed, + key_rd_dicts_to_be_processed=key_rd_dicts_to_be_processed, + all_repository_dependencies=all_repository_dependencies, + handled_key_rd_dicts=handled_key_rd_dicts, + circular_repository_dependencies=circular_repository_dependencies ) def handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_dependency_dict, new_dependency_dict ): """ This method is called when a Galaxy admin is getting updates for an installed tool shed repository in order to cover the case where an @@ -1438,6 +1446,56 @@ else: deleted_tool_dependency_names.append( original_dependency_val_dict[ 'name' ] ) return updated_tool_dependency_names, deleted_tool_dependency_names +def handle_key_rd_dicts_for_repository( trans, current_repository_key, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, circular_repository_dependencies ): + key_rd_dict = repository_key_rd_dicts.pop( 0 ) + repository_dependency = key_rd_dict[ current_repository_key ] + toolshed, name, owner, changeset_revision = repository_dependency + if tool_shed_is_this_tool_shed( toolshed ): + required_repository = get_repository_by_name_and_owner( trans, name, owner ) + required_repository_metadata = get_repository_metadata_by_repository_id_changset_revision( trans, + trans.security.encode_id( required_repository.id ), + changeset_revision ) + if required_repository_metadata: + required_repo_dir = required_repository.repo_path( trans.app ) + required_repo = hg.repository( get_configured_ui(), required_repo_dir ) + # 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 in_key_rd_dicts( current_repository_key_rd_dict, key_rd_dicts_to_be_processed ): + key_rd_dicts_to_be_processed.append( current_repository_key_rd_dict ) + # Mark the current repository_dependency as handled_key_rd_dicts. + if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ): + handled_key_rd_dicts.append( key_rd_dict ) + # Remove the current repository from the list of repository_dependencies to be processed. + if in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + key_rd_dicts_to_be_processed = remove_from_key_rd_dicts( key_rd_dict, 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. Ignoring repository dependency definition " + error_message += "for tool shed %s, name %s, owner %s, changeset revision %s" % ( toolshed, name, owner, changeset_revision ) + log.debug( error_message ) + return toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts +def handle_next_repository_dependency( trans, key_rd_dicts_to_be_processed, all_repository_dependencies, handled_key_rd_dicts, circular_repository_dependencies ): + next_repository_key_rd_dict = key_rd_dicts_to_be_processed.pop( 0 ) + next_repository_key_rd_dicts = [ next_repository_key_rd_dict ] + next_repository_key = next_repository_key_rd_dict.keys()[ 0 ] + toolshed, required_repo, required_repository, required_repository_metadata, repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts = \ + handle_key_rd_dicts_for_repository( trans, + next_repository_key, + next_repository_key_rd_dicts, + key_rd_dicts_to_be_processed, + handled_key_rd_dicts, + circular_repository_dependencies ) + return get_repository_dependencies_for_changeset_revision( trans=trans, + repo=required_repo, + repository=required_repository, + repository_metadata=required_repository_metadata, + toolshed_base_url=toolshed, + key_rd_dicts_to_be_processed=key_rd_dicts_to_be_processed, + all_repository_dependencies=all_repository_dependencies, + handled_key_rd_dicts=handled_key_rd_dicts, + circular_repository_dependencies=circular_repository_dependencies ) def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ): # Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories. message = '' @@ -1489,8 +1547,59 @@ message = str( e ) error = True return error, message +def in_all_repository_dependencies( repository_key, repository_dependency, all_repository_dependencies ): + """Return True if { repository_key :repository_dependency } is in all_repository_dependencies.""" + for key, val in all_repository_dependencies.items(): + if key != repository_key: + continue + if repository_dependency in val: + return True + return False +def in_circular_repository_dependencies( repository_key_rd_dict, circular_repository_dependencies ): + """ + Return True if any combination of a circular dependency tuple is the key : value pair defined in the received repository_key_rd_dict. This + means that each circular dependency tuple is converted into the key : value pair for vomparision. + """ + for tup in circular_repository_dependencies: + rd_0, rd_1 = tup + rd_0_as_key = get_repository_dependency_as_key( rd_0 ) + rd_1_as_key = get_repository_dependency_as_key( rd_1 ) + if rd_0_as_key in repository_key_rd_dict and repository_key_rd_dict[ rd_0_as_key ] == rd_1: + return True + if rd_1_as_key in repository_key_rd_dict and repository_key_rd_dict[ rd_1_as_key ] == rd_0: + return True + return False +def in_key_rd_dicts( key_rd_dict, key_rd_dicts ): + k = key_rd_dict.keys()[ 0 ] + v = key_rd_dict[ k ] + for key_rd_dict in key_rd_dicts: + for key, val in key_rd_dict.items(): + if key == k and val == v: + return True + return False +def is_circular_repository_dependency( repository_key, repository_dependency, all_repository_dependencies ): + """ + Return True if the received repository_dependency is a key in all_repository_dependencies whose list of repository dependencies + includes the received repository_key. + """ + repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) + repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) + for key, val in all_repository_dependencies.items(): + if key != repository_dependency_as_key: + continue + if repository_key_as_repository_dependency in val: + return True + return False def is_downloadable( metadata_dict ): return 'datatypes' in metadata_dict or 'repository_dependencies' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict +def initialize_all_repository_dependencies( current_repository_key, repository_dependencies_dict, all_repository_dependencies ): + # Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value. + all_repository_dependencies[ 'root_key' ] = current_repository_key + all_repository_dependencies[ current_repository_key ] = [] + # Store the value of the 'description' key only once, the first time through this recursive method. + description = repository_dependencies_dict.get( 'description', None ) + all_repository_dependencies[ 'description' ] = description + return all_repository_dependencies def load_tool_from_config( app, full_path ): try: tool = app.toolbox.load_tool( full_path ) @@ -1553,24 +1662,78 @@ "key": full_path } folder_contents.append( node ) return folder_contents +def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, + handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): + current_repository_key_rd_dicts = [] + for rd in repository_dependencies_dict[ 'repository_dependencies' ]: + new_key_rd_dict = {} + new_key_rd_dict[ current_repository_key ] = rd + current_repository_key_rd_dicts.append( new_key_rd_dict ) + if current_repository_key_rd_dicts and current_repository_key: + # Remove all repository dependencies that point to a revision within its own repository. + current_repository_key_rd_dicts = remove_ropository_dependency_reference_to_self( current_repository_key_rd_dicts ) + current_repository_key_rd_dicts = get_updated_changeset_revisions_for_repository_dependencies( trans, current_repository_key_rd_dicts ) + for key_rd_dict in current_repository_key_rd_dicts: + is_circular = False + if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + repository_dependency = key_rd_dict[ current_repository_key ] + if current_repository_key in all_repository_dependencies: + # Add all repository dependencies for the current repository into it's entry in all_repository_dependencies. + all_repository_dependencies_val = all_repository_dependencies[ current_repository_key ] + if repository_dependency not in all_repository_dependencies_val: + all_repository_dependencies_val.append( repository_dependency ) + all_repository_dependencies[ current_repository_key ] = all_repository_dependencies_val + elif not in_all_repository_dependencies( current_repository_key, repository_dependency, all_repository_dependencies ): + # Handle circular repository dependencies. + if is_circular_repository_dependency( current_repository_key, repository_dependency, all_repository_dependencies ): + is_circular = True + circular_repository_dependencies, handled_key_rd_dicts, all_repository_dependencies = \ + handle_circular_repository_dependency( current_repository_key, + repository_dependency, + circular_repository_dependencies, + handled_key_rd_dicts, + all_repository_dependencies ) + else: + all_repository_dependencies[ current_repository_key ] = [ repository_dependency ] + if not is_circular and can_add_to_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + new_key_rd_dict = {} + new_key_rd_dict[ current_repository_key ] = repository_dependency + key_rd_dicts_to_be_processed.append( new_key_rd_dict ) + return current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies def remove_dir( dir ): if os.path.exists( dir ): try: shutil.rmtree( dir ) except: pass -def remove_ropository_dependency_reference_to_self( repository_dependencies, repository_key ): +def remove_from_key_rd_dicts( key_rd_dict, key_rd_dicts ): + k = key_rd_dict.keys()[ 0 ] + v = key_rd_dict[ k ] + clean_key_rd_dicts = [] + for krd_dict in key_rd_dicts: + key = krd_dict.keys()[ 0 ] + val = krd_dict[ key ] + if key == k and val == v: + continue + clean_key_rd_dicts.append( krd_dict ) + return clean_key_rd_dicts +def remove_ropository_dependency_reference_to_self( key_rd_dicts ): """Remove all repository dependencies that point to a revision within its own repository.""" - clean_repository_dependencies = [] - repository_tup = repository_key.split( container_util.STRSEP ) + clean_key_rd_dicts = [] + key = key_rd_dicts[ 0 ].keys()[ 0 ] + repository_tup = key.split( container_util.STRSEP ) rd_toolshed, rd_name, rd_owner, rd_changeset_revision = repository_tup - for repository_dependency in repository_dependencies: + for key_rd_dict in key_rd_dicts: + k = key_rd_dict.keys()[ 0 ] + repository_dependency = key_rd_dict[ k ] toolshed, name, owner, changeset_revision = repository_dependency if rd_toolshed == toolshed and rd_name == name and rd_owner == owner: log.debug( "Removing repository dependency for repository %s owned by %s since it refers to a revision within itself." % ( name, owner ) ) else: - clean_repository_dependencies.append( repository_dependency ) - return clean_repository_dependencies + 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 remove_tool_dependency_installation_directory( dependency_install_dir ): if os.path.exists( dependency_install_dir ): try: @@ -1841,6 +2004,19 @@ else: translated_string = '' return translated_string +def update_circular_repository_dependencies( repository_key, repository_dependency, repository_dependencies, circular_repository_dependencies ): + repository_dependency_as_key = get_repository_dependency_as_key( repository_dependency ) + repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) + if repository_key_as_repository_dependency in repository_dependencies: + found = False + for tup in circular_repository_dependencies: + if repository_dependency in tup and repository_key_as_repository_dependency in tup: + # The circular dependency has already been included. + found = True + if not found: + new_circular_tup = [ repository_dependency, repository_key_as_repository_dependency ] + circular_repository_dependencies.append( new_circular_tup ) + return circular_repository_dependencies def update_existing_tool_dependency( app, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set pulled by a Galaxy administrator when getting updates @@ -1889,8 +2065,7 @@ sa_session.flush() new_tool_dependency = tool_dependency else: - # We have no new tool dependency definition based on a matching dependency name, so remove the existing tool dependency record - # from the database. + # We have no new tool dependency definition based on a matching dependency name, so remove the existing tool dependency record from the database. log.debug( "Deleting tool dependency with name '%s', type '%s' and version '%s' from the database since it is no longer defined." % \ ( str( tool_dependency.name ), str( tool_dependency.type ), str( tool_dependency.version ) ) ) sa_session.delete( tool_dependency )

diff -r c460f284077f0b400901e4cd791d94a311425751 -r e19bf2b117638221414239698f840730a2cd0569 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1782,14 +1782,14 @@ is_malicious = repository_metadata.malicious if repository_metadata: # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, - handled=None ) + handled_key_rd_dicts=None ) if is_malicious: if trans.app.security_agent.can_push( trans.app, trans.user, repository ): message += malicious_error_can_push @@ -1895,14 +1895,14 @@ repository_metadata_id = trans.security.encode_id( repository_metadata.id ), metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, - handled=None ) + handled_key_rd_dicts=None ) else: repository_metadata_id = None metadata = None @@ -2417,14 +2417,14 @@ repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. - repository_dependencies = get_repository_dependencies_for_changeset_revision( trans, - repo, - repository, - repository_metadata, - str( url_for( '/', qualified=True ) ).rstrip( '/' ), - repository_dependencies=None, + repository_dependencies = get_repository_dependencies_for_changeset_revision( trans=trans, + repo=repo, + repository=repository, + repository_metadata=repository_metadata, + toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, - handled=None ) + handled_key_rd_dicts=None ) else: repository_metadata_id = None metadata = None

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

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