[galaxy-commits] commit/galaxy-central: greg: Handle complex repository dependency definitions in the tool shed.

1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/3cc16ea80b08/ changeset: 3cc16ea80b08 user: greg date: 2013-01-25 17:48:04 summary: Handle complex repository dependency definitions in the tool shed. affected #: 6 files

diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -181,6 +181,7 @@ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = self.shed_config_dict, relative_install_dir=relative_install_dir,

diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -1323,9 +1323,8 @@ installed_repository_dependencies, missing_repository_dependencies = get_installed_and_missing_repository_dependencies( trans, repository ) # Handle the current repository's tool dependencies. repository_tool_dependencies = metadata.get( 'tool_dependencies', None ) - repository_installed_tool_dependencies, repository_missing_tool_dependencies = get_installed_and_missing_tool_dependencies( trans, - repository, - repository_tool_dependencies ) + repository_installed_tool_dependencies, repository_missing_tool_dependencies = \ + get_installed_and_missing_tool_dependencies( trans, repository, repository_tool_dependencies ) if reinstalling: installed_tool_dependencies, missing_tool_dependencies = \ populate_tool_dependencies_dicts( trans=trans,

diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -103,26 +103,52 @@ defined tool dependencies. The list of tool dependencies may be associated with more than a single repository. """ for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key not in [ 'set_environment' ]: - repository_name = requirements_dict.get( 'repository_name', 'unknown' ) - repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) - changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) - dependency_name = requirements_dict[ 'name' ] - version = requirements_dict[ 'version' ] - type = requirements_dict[ 'type' ] - if trans.app.config.tool_dependency_dir: - root_dir = trans.app.config.tool_dependency_dir + if dependency_key in [ 'set_environment' ]: + continue + repository_name = requirements_dict.get( 'repository_name', 'unknown' ) + repository_owner = requirements_dict.get( 'repository_owner', 'unknown' ) + changeset_revision = requirements_dict.get( 'changeset_revision', 'unknown' ) + dependency_name = requirements_dict[ 'name' ] + version = requirements_dict[ 'version' ] + type = requirements_dict[ 'type' ] + if trans.app.config.tool_dependency_dir: + root_dir = trans.app.config.tool_dependency_dir + else: + root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' + install_dir = os.path.join( root_dir, + dependency_name, + version, + repository_owner, + repository_name, + changeset_revision ) + requirements_dict[ 'install_dir' ] = install_dir + tool_dependencies[ dependency_key ] = requirements_dict + return tool_dependencies +def add_tool_shed_orphan_settings_to_tool_dependencies( tool_dependencies, tools ): + """Inspect all received tool dependencies and label those that are orphans within the repository in the tool shed.""" + new_tool_dependencies = {} + if tool_dependencies: + for td_key, requirements_dict in tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + type = 'set_environment' + name = set_environment_dict.get( 'name', None ) + version = None + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + set_environment_dict[ 'is_orphan_in_tool_shed' ] = is_orphan_in_tool_shed + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ td_key ] = new_set_environment_dict_list + new_tool_dependencies[ td_key ] = new_set_environment_dict_list else: - root_dir = '<set your tool_dependency_dir in your Galaxy configuration file>' - install_dir = os.path.join( root_dir, - dependency_name, - version, - repository_owner, - repository_name, - changeset_revision ) - requirements_dict[ 'install_dir' ] = install_dir - tool_dependencies[ dependency_key ] = requirements_dict - return tool_dependencies + type = requirements_dict.get( 'type', 'package' ) + name = requirements_dict.get( 'name', None ) + version = requirements_dict.get( 'version', None ) + if type and name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + requirements_dict[ 'is_orphan_in_tool_shed' ] = is_orphan_in_tool_shed + new_tool_dependencies[ td_key ] = requirements_dict + return new_tool_dependencies def add_tool_versions( trans, id, repository_metadata, changeset_revisions ): # Build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in repository_metadata. metadata = repository_metadata.metadata @@ -316,6 +342,9 @@ if metadata: if 'tool_dependencies' in metadata: tool_dependencies = metadata[ 'tool_dependencies' ] + if trans.webapp.name == 'community': + tools = metadata.get( 'tools', None ) + tool_dependencies = add_tool_shed_orphan_settings_to_tool_dependencies( tool_dependencies, tools ) folder_id, tool_dependencies_root_folder = container_util.build_tool_dependencies_folder( trans, folder_id, tool_dependencies, @@ -441,55 +470,6 @@ if repository_dependency[ 0:3 ] == partial_rd: return False return True -def can_generate_tool_dependency_metadata( root, metadata_dict ): - """ - Make sure the combination of name, version and type (the type will be the value of elem.tag) of each root element tag in the tool_dependencies.xml - file is defined in the <requirement> tag for at least one tool in the repository. - """ - can_generate_dependency_metadata = False - for elem in root: - tool_dependency_type = elem.tag - tool_dependency_version = elem.get( 'version', None ) - if tool_dependency_type == 'package': - can_generate_dependency_metadata = False - tool_dependency_name = elem.get( 'name', None ) - if tool_dependency_name and tool_dependency_version: - for tool_dict in metadata_dict.get( 'tools', [] ): - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - req_name = requirement_dict.get( 'name', None ) - req_version = requirement_dict.get( 'version', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==tool_dependency_name and req_version==tool_dependency_version and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - if not can_generate_dependency_metadata: - break - elif tool_dependency_type == 'set_environment': - # Here elem is something like: <set_environment version="1.0"> - for env_var_elem in elem: - can_generate_dependency_metadata = False - # <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> - env_var_name = env_var_elem.get( 'name', None ) - if env_var_name: - for tool_dict in metadata_dict.get( 'tools', [] ): - requirements = tool_dict.get( 'requirements', [] ) - for requirement_dict in requirements: - # {"name": "R_SCRIPT_PATH", "type": "set_environment", "version": null} - req_name = requirement_dict.get( 'name', None ) - req_type = requirement_dict.get( 'type', None ) - if req_name==env_var_name and req_type==tool_dependency_type: - can_generate_dependency_metadata = True - break - if requirements and not can_generate_dependency_metadata: - # We've discovered at least 1 combination of name, version and type that is not defined in the <requirement> - # tag for any tool in the repository. - break - return can_generate_dependency_metadata def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ): """ Determine if repository's tool config file on disk can be used. This method is restricted to tool config files since, with the @@ -573,7 +553,7 @@ sample_found = True break if not sample_found: - correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file_name ) correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) return invalid_files_and_errors_tups @@ -1007,8 +987,8 @@ for env_elem in elem: env_name = env_elem.get( 'name', None ) if env_name: - requirements_dict [ 'name' ] = env_name - requirements_dict [ 'type' ] = 'set_environment' + requirements_dict[ 'name' ] = env_name + requirements_dict[ 'type' ] = 'set_environment' if requirements_dict: if 'set_environment' in tool_dependencies_dict: tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) @@ -1051,8 +1031,9 @@ correction_msg = exception_msg.replace( '<br/>', new_line ).replace( '<b>', bold_start ).replace( '</b>', bold_end ) message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) return message -def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False ): +def generate_metadata_for_changeset_revision( app, repository, changeset_revision, repository_clone_url, shed_config_dict=None, relative_install_dir=None, + repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access that changeset revision's @@ -1202,37 +1183,48 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files - if 'tools' in metadata_dict: - # This step must be done after metadata for tools has been defined. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( app, - repository, - tool_dependencies_config, - metadata_dict, - original_repository_metadata=original_repository_metadata ) + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) + if tool_dependencies_config: + metadata_dict, error_message = generate_tool_dependency_metadata( app, + repository, + changeset_revision, + repository_clone_url, + tool_dependencies_config, + metadata_dict, + original_repository_metadata=original_repository_metadata ) + if error_message: + invalid_file_tups.append( ( 'tool_dependencies.xml', error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. app.config.tool_data_path = original_tool_data_path app.config.tool_data_table_config_path = original_tool_data_table_config_path return metadata_dict, invalid_file_tups -def generate_package_dependency_metadata( elem, tool_dependencies_dict ): +def generate_package_dependency_metadata( app, elem, tool_dependencies_dict ): """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set.""" + repository_dependency_tup = [] requirements_dict = {} + error_message = '' package_name = elem.get( 'name', None ) package_version = elem.get( 'version', None ) if package_name and package_version: - dependency_key = '%s/%s' % ( package_name, package_version ) - requirements_dict [ 'name' ] = package_name - requirements_dict [ 'version' ] = package_version - requirements_dict [ 'type' ] = 'package' + requirements_dict[ 'name' ] = package_name + requirements_dict[ 'version' ] = package_version + requirements_dict[ 'type' ] = 'package' for sub_elem in elem: if sub_elem.tag == 'readme': requirements_dict[ 'readme' ] = sub_elem.text + elif sub_elem.tag == 'repository': + # We have a complex repository dependency. + current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app=app, + repository_elem=sub_elem, + repository_dependencies_tups=None ) + repository_dependency_tup = current_rd_tups[ 0 ] if requirements_dict: + dependency_key = '%s/%s' % ( package_name, package_version ) tool_dependencies_dict[ dependency_key ] = requirements_dict - return tool_dependencies_dict + return tool_dependencies_dict, repository_dependency_tup, error_message def generate_repository_dependency_metadata_for_installed_repository( app, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method @@ -1281,63 +1273,27 @@ log.debug( error_message ) is_valid = False if is_valid: - sa_session = app.model.context.current for repository_elem in root.findall( 'repository' ): - toolshed = repository_elem.attrib[ 'toolshed' ] - name = repository_elem.attrib[ 'name' ] - owner = repository_elem.attrib[ 'owner'] - changeset_revision = repository_elem.attrib[ 'changeset_revision' ] - user = None - repository = None - if tool_shed_is_this_tool_shed( toolshed ): - try: - user = sa_session.query( app.model.User ) \ - .filter( app.model.User.table.c.username == owner ) \ - .one() - except Exception, e: - error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return metadata_dict, error_message - if user: - try: - repository = sa_session.query( app.model.Repository ) \ - .filter( and_( app.model.Repository.table.c.name == name, - app.model.Repository.table.c.user_id == user.id ) ) \ - .first() - except: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return metadata_dict, error_message - if repository: - repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) - if repository_dependencies_tup not in repository_dependencies_tups: - repository_dependencies_tups.append( repository_dependencies_tup ) - else: - error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) - log.debug( error_message ) - return metadata_dict, error_message - else: - error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) - log.debug( error_message ) - return metadata_dict, error_message - else: - # Repository dependencies are currentlhy supported within a single tool shed. - error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) - error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ) + if error_message: log.debug( error_message ) return metadata_dict, error_message + for crdt in current_rd_tups: + repository_dependencies_tups.append( crdt ) if repository_dependencies_tups: repository_dependencies_dict = dict( description=root.get( 'description' ), repository_dependencies=repository_dependencies_tups ) metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict return metadata_dict, error_message -def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): +def generate_tool_dependency_metadata( app, repository, changeset_revision, repository_clone_url, tool_dependencies_config, metadata_dict, + original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ + error_message = '' if original_repository_metadata: - # Keep a copy of the original tool dependencies dictionary in the metadata. + # Keep a copy of the original tool dependencies dictionary and the list of tool dictionaries in the metadata. original_tool_dependencies_dict = original_repository_metadata.get( 'tool_dependencies', None ) else: original_tool_dependencies_dict = None @@ -1349,24 +1305,49 @@ root = tree.getroot() ElementInclude.include( root ) tool_dependencies_dict = {} - if can_generate_tool_dependency_metadata( root, metadata_dict ): - for elem in root: - if elem.tag == 'package': - tool_dependencies_dict = generate_package_dependency_metadata( elem, tool_dependencies_dict ) - elif elem.tag == 'set_environment': - tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) - # Handle tool dependency installation via other means here (future). - if tool_dependencies_dict: - metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - else: - log.debug( "Name, version and type from the <requirement> tag does not match the information in the tool_dependencies.xml file. Tool dependencies will be ignored." ) + repository_dependency_tups = [] + for elem in root: + if elem.tag == 'package': + tool_dependencies_dict, repository_dependency_tup, message = generate_package_dependency_metadata( app, elem, tool_dependencies_dict ) + if repository_dependency_tup and repository_dependency_tup not in repository_dependency_tups: + repository_dependency_tups.append( repository_dependency_tup ) + if message: + log.debug( message ) + error_message = '%s %s' % ( error_message, message ) + elif elem.tag == 'set_environment': + tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) if tool_dependencies_dict: if original_tool_dependencies_dict: # We're generating metadata on an update pulled to a tool shed repository installed into a Galaxy instance, so handle changes to # tool dependencies appropriately. handle_existing_tool_dependencies_that_changed_in_update( app, repository, original_tool_dependencies_dict, tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - return metadata_dict + if repository_dependency_tups: + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + if app.name == 'community': + repository_owner = repository.user.username + else: + repository_owner = repository.owner + rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=tool_shed, + repository_name=repository.name, + repository_owner=repository_owner, + changeset_revision=changeset_revision ) + repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', None ) + if repository_dependencies_dict: + if rd_key in repository_dependencies_dict: + repository_dependencies = repository_dependencies_dict[ rd_key ] + for repository_dependency_tup in repository_dependency_tups: + if repository_dependency_tup not in repository_dependencies: + repository_dependencies.append( repository_dependency_tup ) + repository_dependencies_dict[ rd_key ] = repository_dependencies + else: + repository_dependencies_dict[ rd_key ] = repository_dependency_tups + else: + repository_dependencies_dict = dict( root_key=rd_key, + description=root.get( 'description' ), + repository_dependencies=repository_dependency_tups ) + metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict + return metadata_dict, error_message def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): if tool_section is not None: tool_elem = SubElement( tool_section, 'tool' ) @@ -2481,6 +2462,79 @@ message = str( e ) error = True return error, message +def has_orphan_tool_dependencies_in_tool_shed( metadata ): + """Inspect tool dependencies included in the received metadata and determine if any of them are orphans within the repository in the tool shed.""" + if metadata: + tools = metadata.get( 'tools', None ) + tool_dependencies = metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + for td_key, requirements_dict in tool_dependencies.items(): + if td_key in [ 'set_environment' ]: + for set_environment_dict in requirements_dict: + type = 'set_environment' + name = set_environment_dict.get( 'name', None ) + version = None + if name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + if is_orphan_in_tool_shed: + return True + else: + type = requirements_dict.get( 'type', None ) + name = requirements_dict.get( 'name', None ) + version = requirements_dict.get( 'version', None ) + if type and name: + is_orphan_in_tool_shed = tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ) + if is_orphan_in_tool_shed: + return True + return False +def handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ): + if repository_dependencies_tups is None: + new_rd_tups = [] + else: + new_rd_tups = [ rdt for rdt in repository_dependencies_tups ] + error_message = '' + sa_session = app.model.context.current + toolshed = repository_elem.attrib[ 'toolshed' ] + name = repository_elem.attrib[ 'name' ] + owner = repository_elem.attrib[ 'owner' ] + changeset_revision = repository_elem.attrib[ 'changeset_revision' ] + user = None + repository = None + if tool_shed_is_this_tool_shed( toolshed ): + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == owner ) \ + .one() + except Exception, e: + error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name ) + log.debug( error_message ) + return new_rd_tups, error_message + if user: + try: + repository = sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + except: + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) + log.debug( error_message ) + return new_rd_tups, error_message + if repository: + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in new_rd_tups: + new_rd_tups.append( repository_dependencies_tup ) + else: + error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner ) + log.debug( error_message ) + else: + error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name ) + log.debug( error_message ) + else: + # Repository dependencies are currentlhy supported within a single tool shed. + error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name ) + error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored." + log.debug( error_message ) + return new_rd_tups, error_message def has_previous_repository_reviews( trans, repository, changeset_revision ): """Determine if a repository has a changeset revision review prior to the received changeset revision.""" repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) @@ -2932,6 +2986,7 @@ original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, @@ -3012,6 +3067,7 @@ log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) current_metadata_dict, invalid_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=current_changeset_revision, repository_clone_url=repository_clone_url, relative_install_dir=repo_dir, repository_files_dir=work_dir, @@ -3148,6 +3204,7 @@ repo = hg.repository( get_configured_ui(), repo_dir ) metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.tip( trans.app ), repository_clone_url=repository_clone_url, relative_install_dir=repo_dir, repository_files_dir=None, @@ -3197,7 +3254,7 @@ reset_tool_data_tables( trans.app ) return message, status def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): - # Set metadata on the repository tip. + """Set metadata on the repository tip in the tool shed - this method is not called from Galaxy.""" error_message, status = set_repository_metadata( trans, repository, content_alert_str=content_alert_str, **kwd ) if error_message: # If there is an error, display it. @@ -3214,6 +3271,32 @@ except: file_name = fpath return file_name +def tool_dependency_is_orphan_in_tool_shed( type, name, version, tools ): + """ + Determine if the combination of the received type, name and version is defined in the <requirement> tag for at least one tool in the received list of tools. + If not, the tool dependency defined by the combination is considered an orphan in it's repository in the tool shed. + """ + if tools: + if type == 'package': + if name and version: + for tool_dict in tools: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_version = requirement_dict.get( 'version', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name == name and req_version == version and req_type == type: + return False + elif type == 'set_environment': + if name: + for tool_dict in tools: + requirements = tool_dict.get( 'requirements', [] ) + for requirement_dict in requirements: + req_name = requirement_dict.get( 'name', None ) + req_type = requirement_dict.get( 'type', None ) + if req_name == name and req_type == type: + return False + return True def to_safe_string( text, to_html=True ): """Translates the characters in text to an html string""" if text:

diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/webapps/community/controllers/upload.py --- a/lib/galaxy/webapps/community/controllers/upload.py +++ b/lib/galaxy/webapps/community/controllers/upload.py @@ -175,11 +175,10 @@ metadata_dict = repository.metadata_revisions[0].metadata else: metadata_dict = {} - if 'tool_dependencies' not in metadata_dict: + if suc.has_orphan_tool_dependencies_in_tool_shed( metadata_dict ): message += 'Name, version and type from a tool requirement tag does not match the information in the "tool_dependencies.xml file", ' - message += 'so the tool dependency definitions will be ignored.' + message += 'so one or more of the defined tool dependencies are considered orphans within this repository.' status = 'warning' - log.debug( 'Error in tool dependencies for repository with id %s and name %s: %s' % ( str( repository.id ), str( repository.name ), message ) ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. suc.reset_tool_data_tables( trans.app ) trans.response.send_redirect( web.url_for( controller='repository',

diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -102,7 +102,7 @@ class ToolDependency( object ): """Tool dependency object""" def __init__( self, id=None, name=None, version=None, type=None, install_dir=None, readme=None, installation_status=None, repository_id=None, - tool_dependency_id=None ): + tool_dependency_id=None, is_orphan=None ): self.id = id self.name = name self.version = version @@ -112,6 +112,7 @@ self.installation_status = installation_status self.repository_id = repository_id self.tool_dependency_id = tool_dependency_id + self.is_orphan = is_orphan @property def listify( self ): return [ self.name, self.version, self.type ] @@ -322,17 +323,35 @@ version='Version', type='Type', install_dir='Install directory', - installation_status='Installation status' ) + readme=None, + installation_status='Installation status', + repository_id=None, + tool_dependency_id=None, + is_orphan=None ) else: tool_dependency = ToolDependency( id=tool_dependency_id, name='Name', version='Version', - type='Type' ) + type='Type', + install_dir=None, + readme=None, + installation_status=None, + repository_id=None, + tool_dependency_id=None, + is_orphan=None ) folder.tool_dependencies.append( tool_dependency ) + is_orphan_description = "these dependencies may not be required by tools in this repository" for dependency_key, requirements_dict in tool_dependencies.items(): tool_dependency_id += 1 - if dependency_key == 'set_environment': + if dependency_key in [ 'set_environment' ]: for set_environment_dict in requirements_dict: + if trans.webapp.name == 'community': + is_orphan = set_environment_dict.get( 'is_orphan_in_tool_shed', False ) + else: + # TODO: handle this is Galaxy + is_orphan = False + if is_orphan: + folder.description = is_orphan_description name = set_environment_dict.get( 'name', None ) type = set_environment_dict[ 'type' ] repository_id = set_environment_dict.get( 'repository_id', None ) @@ -343,12 +362,23 @@ installation_status = None tool_dependency = ToolDependency( id=tool_dependency_id, name=name, + version=None, type=type, + install_dir=None, + readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id ) + tool_dependency_id=td_id, + is_orphan=is_orphan ) folder.tool_dependencies.append( tool_dependency ) else: + if trans.webapp.name == 'community': + is_orphan = requirements_dict.get( 'is_orphan_in_tool_shed', False ) + else: + # TODO: handle this is Galaxy + is_orphan = False + if is_orphan: + folder.description = is_orphan_description name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] type = requirements_dict[ 'type' ] @@ -364,9 +394,11 @@ version=version, type=type, install_dir=install_dir, + readme=None, installation_status=installation_status, repository_id=repository_id, - tool_dependency_id=td_id ) + tool_dependency_id=td_id, + is_orphan=is_orphan ) folder.tool_dependencies.append( tool_dependency ) else: tool_dependencies_root_folder = None

diff -r b99d93d0f1378bb3d7065ba9700f6363324ce5ec -r 3cc16ea80b08e9faa2f721051d89167959aceb2a lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -661,6 +661,7 @@ shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict=shed_config_dict, relative_install_dir=relative_install_dir, @@ -1692,6 +1693,7 @@ original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, @@ -1887,6 +1889,7 @@ # Update the repository metadata. metadata_dict, invalid_file_tups = suc.generate_metadata_for_changeset_revision( app=trans.app, repository=repository, + changeset_revision=latest_changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir,

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

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