commit/galaxy-central: greg: Add classes for managing tool shed repository metadata.
1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4d2e744f8efc/ Changeset: 4d2e744f8efc User: greg Date: 2014-07-17 19:20:49 Summary: Add classes for managing tool shed repository metadata. Affected #: 20 files diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -11,6 +11,7 @@ from galaxy.web.base.controller import BaseAPIController from tool_shed.galaxy_install.install_manager import InstallRepositoryManager +from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager from tool_shed.util import common_util from tool_shed.util import encoding_util @@ -417,7 +418,8 @@ for repository in query: repository_id = trans.security.encode_id( repository.id ) try: - invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_installed_repository( trans.app, repository_id ) + irmm = InstalledRepositoryMetadataManager( trans.app ) + invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a 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 @@ -16,7 +16,6 @@ from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import metadata_util from tool_shed.util import readme_util from tool_shed.util import repository_maintenance_util from tool_shed.util import shed_util_common as suc @@ -27,8 +26,9 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.grids import admin_toolshed_grids +from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager -import tool_shed.galaxy_install.grids.admin_toolshed_grids as admin_toolshed_grids from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager log = logging.getLogger( __name__ ) @@ -1704,7 +1704,8 @@ @web.require_admin def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - message, status = metadata_util.reset_metadata_on_selected_repositories( trans.app, trans.user, **kwd ) + irmm = InstalledRepositoryMetadataManager( trans.app ) + message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -1723,17 +1724,17 @@ tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata + irmm = InstalledRepositoryMetadataManager( trans.app ) metadata_dict, invalid_file_tups = \ - metadata_util.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, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) + irmm.generate_metadata_for_changeset_revision( 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, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) repository.metadata = metadata_dict if metadata_dict != original_metadata_dict: suc.update_in_shed_tool_config( trans.app, repository ) @@ -1926,17 +1927,17 @@ if repository.includes_data_managers: data_manager_util.remove_from_data_manager( trans.app, repository ) # Update the repository metadata. + irmm = InstalledRepositoryMetadataManager( trans.app ) metadata_dict, invalid_file_tups = \ - metadata_util.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_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) + irmm.generate_metadata_for_changeset_revision( 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_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) if 'tools' in metadata_dict: tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -4,19 +4,21 @@ import tarfile import tempfile from time import strftime -from galaxy import eggs + from galaxy import util from galaxy import web from galaxy.model.orm import and_ from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import HTTPBadRequest from galaxy.web.framework.helpers import time_ago + from tool_shed.capsule import capsule_manager -import tool_shed.repository_types.util as rt_util +from tool_shed.metadata import repository_metadata_manager +from tool_shed.repository_types import util as rt_util + from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -428,8 +430,9 @@ log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) try: + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = \ - metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans.app, trans.user, repository_id ) + rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, @@ -508,10 +511,10 @@ results = dict( start_time=start_time, repository_status=[] ) try: + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = \ - metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans.app, - trans.user, - trans.security.encode_id( repository.id ) ) + rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, + trans.security.encode_id( repository.id ) ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -1,13 +1,18 @@ import logging + +from galaxy import util +from galaxy.util import inflector +from galaxy import web + from galaxy.web.base.controller import BaseUIController from galaxy.web.base.controllers.admin import Admin -from galaxy import util -from galaxy import web -from galaxy.util import inflector -import tool_shed.util.shed_util_common as suc -import tool_shed.util.metadata_util as metadata_util + +import tool_shed.grids.admin_grids as admin_grids +from tool_shed.metadata import repository_metadata_manager + +from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util -import tool_shed.grids.admin_grids as admin_grids +from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) @@ -344,7 +349,8 @@ @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - message, status = metadata_util.reset_metadata_on_selected_repositories( trans.app, trans.user, **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -3,7 +3,7 @@ from galaxy.web.base.controller import BaseUIController from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository -from tool_shed.util.metadata_util import set_repository_metadata +from tool_shed.metadata import repository_metadata_manager from galaxy import eggs eggs.require('mercurial') @@ -28,9 +28,11 @@ return hgwebapp wsgi_app = wsgiapplication( make_web_app ) if hg_version >= '2.2.3' and cmd == 'pushkey': - # When doing an "hg push" from the command line, the following commands, in order, will be retrieved from environ, depending - # upon the mercurial version being used. In mercurial version 2.2.3, section 15.2. Command changes includes a new feature: - # pushkey: add hooks for pushkey/listkeys (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29). + # When doing an "hg push" from the command line, the following commands, in order, will be + # retrieved from environ, depending upon the mercurial version being used. In mercurial + # version 2.2.3, section 15.2. Command changes includes a new feature: + # pushkey: add hooks for pushkey/listkeys + # (see http://mercurial.selenic.com/wiki/WhatsNew#Mercurial_2.2.3_.282012-07-01.29). # We require version 2.2.3 since the pushkey hook was added in that version. # If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey path_info = kwd.get( 'path_info', None ) @@ -39,13 +41,15 @@ repository = get_repository_by_name_and_owner( trans.app, name, owner ) if repository: if hg_version >= '2.2.3': - # Update the repository on disk to the tip revision, because the web upload form uses the on-disk working - # directory. If the repository is not updated on disk, pushing from the command line and then uploading - # via the web interface will result in a new head being created. + # Update the repository on disk to the tip revision, because the web upload + # form uses the on-disk working directory. If the repository is not updated + # on disk, pushing from the command line and then uploading via the web + # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) # Set metadata using the repository files on disk. - error_message, status = set_repository_metadata( trans.app, trans.request.host, trans.user, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + error_message, status = rmm.set_repository_metadata( trans.request.host, trans.user, repository ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -19,6 +19,7 @@ from tool_shed.dependencies.repository import relation_builder from tool_shed.galaxy_install import dependency_display +from tool_shed.metadata import repository_metadata_manager from tool_shed.util import basic_util from tool_shed.util import common_util @@ -2610,14 +2611,20 @@ repository_dependencies_dict = metadata[ 'repository_dependencies' ] rd_tups = repository_dependencies_dict.get( 'repository_dependencies', [] ) for rd_tup in rd_tups: - rdtool_shed, rd_name, rd_owner, rd_changeset_revision, rd_prior_installation_required, rd_only_if_compiling_contained_td = \ + rdtool_shed, \ + 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 ) if not util.asbool( rd_only_if_compiling_contained_td ): invalid = True break if invalid: - message = metadata_util.generate_message_for_invalid_repository_dependencies( metadata, - error_from_tuple=False ) + dd = dependency_display.DependencyDisplayer( trans.app ) + message = dd.generate_message_for_invalid_repository_dependencies( metadata, + error_from_tuple=False ) status = 'error' else: repository_metadata_id = None @@ -2735,11 +2742,15 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = \ - metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans.app, trans.user, id, **kwd ) + rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, id, **kwd ) if invalid_file_tups: repository = suc.get_repository_in_tool_shed( trans.app, id ) - message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, repository, metadata_dict ) + message = tool_util.generate_message_for_invalid_tools( trans.app, + invalid_file_tups, + repository, + metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2753,7 +2764,8 @@ @web.expose def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ): if 'reset_metadata_on_selected_repositories_button' in kwd: - message, status = metadata_util.reset_metadata_on_selected_repositories( trans.app, trans.user, **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -2817,11 +2829,11 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( trans.app, - trans.request.host, - trans.user, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, + trans.user, + repository, + **kwd ) if error_message: message = error_message else: diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -12,12 +12,12 @@ from tool_shed.dependencies import attribute_handlers from tool_shed.galaxy_install import dependency_display +from tool_shed.metadata import repository_metadata_manager import tool_shed.repository_types.util as rt_util from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import hg_util -from tool_shed.util import metadata_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util from tool_shed.util import xml_util @@ -262,12 +262,13 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( trans.app, - trans.request.host, - trans.user, - repository, - content_alert_str=content_alert_str, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + status, error_message = \ + rmm.set_repository_metadata_due_to_new_tip( trans.request.host, + trans.user, + repository, + content_alert_str=content_alert_str, + **kwd ) if error_message: message = error_message kwd[ 'message' ] = message @@ -303,8 +304,8 @@ status = 'error' # Handle messaging for invalid repository dependencies. invalid_repository_dependencies_message = \ - metadata_util.generate_message_for_invalid_repository_dependencies( metadata_dict, - error_from_tuple=True ) + dd.generate_message_for_invalid_repository_dependencies( metadata_dict, + error_from_tuple=True ) if invalid_repository_dependencies_message: message += invalid_repository_dependencies_message status = 'error' diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -7,23 +7,26 @@ import urllib from time import gmtime from time import strftime -import tool_shed.repository_types.util as rt_util + from galaxy import web from galaxy.util import asbool from galaxy.util import CHUNK_SIZE from galaxy.util.odict import odict + from tool_shed.dependencies.repository.relation_builder import RelationBuilder from tool_shed.dependencies import attribute_handlers +from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyInstallManager +from tool_shed.metadata import repository_metadata_manager +import tool_shed.repository_types.util as rt_util + from tool_shed.util import basic_util from tool_shed.util import commit_util from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import metadata_util from tool_shed.util import repository_maintenance_util from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util -from tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager import RepositoryDependencyInstallManager log = logging.getLogger( __name__ ) @@ -33,6 +36,7 @@ def __init__( self ): self.exported_repository_elems = [] + class ExportRepositoryManager( object ): def __init__( self, app, user, tool_shed_url, repository, changeset_revision, export_repository_dependencies, using_api ): @@ -723,11 +727,11 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - status, error_message = metadata_util.set_repository_metadata_due_to_new_tip( self.app, - self.host, - self.user, - repository, - content_alert_str=content_alert_str ) + rmm = repository_metadata_manager.RepositoryMetadataManager( self.app ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, + self.user, + repository, + content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/tool_shed/galaxy_install/dependency_display.py --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -48,6 +48,57 @@ tool_dependencies[ dependency_key ] = requirements_dict return tool_dependencies + 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 generate_message_for_invalid_tool_dependencies( self, metadata_dict ): """ Tool dependency definitions can only be invalid if they include a definition for a complex diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -22,17 +22,17 @@ from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import metadata_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager +from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager -from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager log = logging.getLogger( __name__ ) @@ -499,17 +499,17 @@ """ install_model = self.app.install_model shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) + irmm = InstalledRepositoryMetadataManager( self.app ) metadata_dict, invalid_file_tups = \ - metadata_util.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=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) + irmm.generate_metadata_for_changeset_revision( 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, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -0,0 +1,92 @@ +import logging +import os + +from galaxy import util +from galaxy.util import inflector + +from tool_shed.metadata import metadata_generator + +from tool_shed.util import common_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import tool_util + +log = logging.getLogger( __name__ ) + + +class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): + + def __init__( self, app ): + super( InstalledRepositoryMetadataManager, self ).__init__( app ) + self.app = app + + def reset_all_metadata_on_installed_repository( self, id ): + """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" + invalid_file_tups = [] + metadata_dict = {} + repository = suc.get_installed_tool_shed_repository( self.app, id ) + repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) + if relative_install_dir: + original_metadata_dict = repository.metadata + metadata_dict, invalid_file_tups = \ + self.generate_metadata_for_changeset_revision( repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( self.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + repository.metadata = metadata_dict + if metadata_dict != original_metadata_dict: + suc.update_in_shed_tool_config( self.app, repository ) + self.app.install_model.context.add( repository ) + self.app.install_model.context.flush() + log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + else: + log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + else: + log.debug( 'Error locating installation directory for repository %s.' % repository.name ) + return invalid_file_tups, metadata_dict + + def reset_metadata_on_selected_repositories( self, user, **kwd ): + """ + Inspect the repository changelog to reset metadata for all appropriate changeset revisions. + This method is called from both Galaxy and the Tool Shed. + """ + repository_ids = util.listify( kwd.get( 'repository_ids', None ) ) + message = '' + status = 'done' + if repository_ids: + successful_count = 0 + unsuccessful_count = 0 + for repository_id in repository_ids: + try: + repository = suc.get_installed_tool_shed_repository( self.app, repository_id ) + owner = str( repository.owner ) + invalid_file_tups, metadata_dict = \ + self.reset_all_metadata_on_installed_repository( repository_id ) + if invalid_file_tups: + message = tool_util.generate_message_for_invalid_tools( self.app, + invalid_file_tups, + repository, + None, + as_html=False ) + log.debug( message ) + unsuccessful_count += 1 + else: + log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + successful_count += 1 + except: + log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) + unsuccessful_count += 1 + message = "Successfully reset metadata on %d %s. " % \ + ( successful_count, inflector.cond_plural( successful_count, "repository" ) ) + if unsuccessful_count: + message += "Error setting metadata on %d %s - see the paster log for details. " % \ + ( unsuccessful_count, inflector.cond_plural( unsuccessful_count, "repository" ) ) + else: + message = 'Select at least one repository to on which to reset all metadata.' + status = 'error' + return message, status diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -8,15 +8,18 @@ import tempfile import threading import logging + from galaxy import util from galaxy.tools import ToolSection + from tool_shed.galaxy_install import install_manager -import tool_shed.util.shed_util_common as suc +from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager + from tool_shed.util import basic_util from tool_shed.util import common_util from tool_shed.util import datatype_util from tool_shed.util import hg_util -from tool_shed.util import metadata_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util from tool_shed.util import xml_util @@ -381,17 +384,17 @@ log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() + irmm = InstalledRepositoryMetadataManager( self.app ) metadata_dict, invalid_file_tups = \ - metadata_util.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, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) + irmm.generate_metadata_for_changeset_revision( 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, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) tool_shed_repository.metadata = metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() diff -r 5af80141674f5ac3166b6782385c408258606d0a -r 4d2e744f8efc73dc265c3d3bf33c4c2886888b7a lib/tool_shed/metadata/metadata_generator.py --- /dev/null +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -0,0 +1,1038 @@ +import json +import logging +import os +import tempfile + +from galaxy import util +from galaxy.datatypes import checkers +from galaxy.model.orm import and_ +from galaxy.tools.data_manager.manager import DataManager +from galaxy.web import url_for + +from tool_shed.repository_types import util as rt_util + +from tool_shed.util import basic_util +from tool_shed.util import common_util +from tool_shed.util import hg_util +from tool_shed.util import readme_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import tool_dependency_util +from tool_shed.util import tool_util +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class MetadataGenerator( object ): + + def __init__( self, app ): + self.app = app + self.sa_session = app.model.context.current + self.NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, + rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] + + def generate_data_manager_metadata( self, repository, repo_dir, data_manager_config_filename, metadata_dict, + shed_config_dict=None ): + """ + Update the received metadata_dict with information from the parsed data_manager_config_filename. + """ + if data_manager_config_filename is None: + return metadata_dict + repo_path = repository.repo_path( self.app ) + try: + # Galaxy Side. + repo_files_directory = repository.repo_files_directory( self.app ) + repo_dir = repo_files_directory + repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) + except AttributeError: + # Tool Shed side. + repo_files_directory = repo_path + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository ) + relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) + rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, + os.path.split( data_manager_config_filename )[1] ) + data_managers = {} + invalid_data_managers = [] + data_manager_metadata = { 'config_filename': rel_data_manager_config_filename, + 'data_managers': data_managers, + 'invalid_data_managers': invalid_data_managers, + 'error_messages': [] } + metadata_dict[ 'data_manager' ] = data_manager_metadata + tree, error_message = xml_util.parse_xml( data_manager_config_filename ) + if tree is None: + # We are not able to load any data managers. + data_manager_metadata[ 'error_messages' ].append( error_message ) + return metadata_dict + tool_path = None + if shed_config_dict: + tool_path = shed_config_dict.get( 'tool_path', None ) + tools = {} + for tool in metadata_dict.get( 'tools', [] ): + tool_conf_name = tool[ 'tool_config' ] + if tool_path: + tool_conf_name = os.path.join( tool_path, tool_conf_name ) + tools[ tool_conf_name ] = tool + root = tree.getroot() + data_manager_tool_path = root.get( 'tool_path', None ) + if data_manager_tool_path: + relative_data_manager_dir = os.path.join( relative_data_manager_dir, data_manager_tool_path ) + for i, data_manager_elem in enumerate( root.findall( 'data_manager' ) ): + tool_file = data_manager_elem.get( 'tool_file', None ) + data_manager_id = data_manager_elem.get( 'id', None ) + if data_manager_id is None: + log.error( 'Data Manager entry is missing id attribute in "%s".' % ( data_manager_config_filename ) ) + invalid_data_managers.append( { 'index': i, + 'error_message': 'Data Manager entry is missing id attribute' } ) + continue + # FIXME: default behavior is to fall back to tool.name. + data_manager_name = data_manager_elem.get( 'name', data_manager_id ) + version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) + guid = self.generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) + data_tables = [] + if tool_file is None: + log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) + invalid_data_managers.append( { 'index': i, + 'error_message': 'Data Manager entry is missing tool_file attribute' } ) + continue + else: + bad_data_table = False + for data_table_elem in data_manager_elem.findall( 'data_table' ): + data_table_name = data_table_elem.get( 'name', None ) + if data_table_name is None: + log.error( 'Data Manager data_table entry is missing name attribute in "%s".' % ( data_manager_config_filename ) ) + invalid_data_managers.append( { 'index': i, + 'error_message': 'Data Manager entry is missing name attribute' } ) + bad_data_table = True + break + else: + data_tables.append( data_table_name ) + if bad_data_table: + continue + data_manager_metadata_tool_file = os.path.normpath( os.path.join( relative_data_manager_dir, tool_file ) ) + tool_metadata_tool_file = os.path.join( repo_files_directory, data_manager_metadata_tool_file ) + tool = tools.get( tool_metadata_tool_file, None ) + if tool is None: + log.error( "Unable to determine tools metadata for '%s'." % ( data_manager_metadata_tool_file ) ) + invalid_data_managers.append( { 'index': i, + 'error_message': 'Unable to determine tools metadata' } ) + continue + data_managers[ data_manager_id ] = { 'id': data_manager_id, + 'name': data_manager_name, + 'guid': guid, + 'version': version, + 'tool_config_file': data_manager_metadata_tool_file, + 'data_tables': data_tables, + 'tool_guid': tool[ 'guid' ] } + log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) + return metadata_dict + + def generate_datatypes_metadata( self, repository, repository_clone_url, repository_files_dir, datatypes_config, + metadata_dict ): + """Update the received metadata_dict with information from the parsed datatypes_config.""" + tree, error_message = xml_util.parse_xml( datatypes_config ) + if tree is None: + return metadata_dict + root = tree.getroot() + repository_datatype_code_files = [] + datatype_files = root.find( 'datatype_files' ) + if datatype_files is not None: + for elem in datatype_files.findall( 'datatype_file' ): + name = elem.get( 'name', None ) + repository_datatype_code_files.append( name ) + metadata_dict[ 'datatype_files' ] = repository_datatype_code_files + datatypes = [] + registration = root.find( 'registration' ) + if registration is not None: + for elem in registration.findall( 'datatype' ): + converters = [] + display_app_containers = [] + datatypes_dict = {} + # Handle defined datatype attributes. + display_in_upload = elem.get( 'display_in_upload', None ) + if display_in_upload: + datatypes_dict[ 'display_in_upload' ] = display_in_upload + dtype = elem.get( 'type', None ) + if dtype: + datatypes_dict[ 'dtype' ] = dtype + extension = elem.get( 'extension', None ) + if extension: + datatypes_dict[ 'extension' ] = extension + max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) + if max_optional_metadata_filesize: + datatypes_dict[ 'max_optional_metadata_filesize' ] = max_optional_metadata_filesize + mimetype = elem.get( 'mimetype', None ) + if mimetype: + datatypes_dict[ 'mimetype' ] = mimetype + subclass = elem.get( 'subclass', None ) + if subclass: + datatypes_dict[ 'subclass' ] = subclass + # Handle defined datatype converters and display applications. + for sub_elem in elem: + if sub_elem.tag == 'converter': + # <converter file="bed_to_gff_converter.xml" target_datatype="gff"/> + tool_config = sub_elem.attrib[ 'file' ] + target_datatype = sub_elem.attrib[ 'target_datatype' ] + # Parse the tool_config to get the guid. + tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) + full_path = os.path.abspath( tool_config_path ) + tool, valid, error_message = \ + tool_util.load_tool_from_config( self.app, self.app.security.encode_id( repository.id ), full_path ) + if tool is None: + guid = None + else: + guid = suc.generate_tool_guid( repository_clone_url, tool ) + converter_dict = dict( tool_config=tool_config, + guid=guid, + target_datatype=target_datatype ) + converters.append( converter_dict ) + elif sub_elem.tag == 'display': + # <display file="ucsc/bigwig.xml" /> + # Should we store more than this? + display_file = sub_elem.attrib[ 'file' ] + display_app_dict = dict( display_file=display_file ) + display_app_containers.append( display_app_dict ) + if converters: + datatypes_dict[ 'converters' ] = converters + if display_app_containers: + datatypes_dict[ 'display_app_containers' ] = display_app_containers + if datatypes_dict: + datatypes.append( datatypes_dict ) + if datatypes: + metadata_dict[ 'datatypes' ] = datatypes + return metadata_dict + + def generate_environment_dependency_metadata( self, elem, valid_tool_dependencies_dict ): + """ + The value of env_var_name must match the value of the "set_environment" type + in the tool config's <requirements> tag set, or the tool dependency will be + considered an orphan. + """ + # The value of the received elem looks something like this: + # <set_environment version="1.0"> + # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> + # </set_environment> + for env_elem in elem: + # <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> + env_name = env_elem.get( 'name', None ) + if env_name: + requirements_dict = dict( name=env_name, type='set_environment' ) + if 'set_environment' in valid_tool_dependencies_dict: + valid_tool_dependencies_dict[ 'set_environment' ].append( requirements_dict ) + else: + valid_tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] + return valid_tool_dependencies_dict + + def generate_guid_for_object( self, repository_clone_url, guid_type, obj_id, version ): + tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) + + def generate_metadata_for_changeset_revision( self, 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 its 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 disk files, so the value of repository_files_dir will not + always be repository.repo_path( self.app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of relative_install_dir + must contain repository.repo_path( self.app ). + + The value of persist will be True when the installed repository contains a valid + tool_data_table_conf.xml.sample file, in which case the entries should ultimately be + persisted to the file referred to by self.app.config.shed_tool_data_table_config. + """ + if shed_config_dict is None: + shed_config_dict = {} + if updating_installed_repository: + # Keep the original tool shed repository metadata if setting metadata on a repository + # installed into a local Galaxy instance for which we have pulled updates. + original_repository_metadata = repository.metadata + else: + original_repository_metadata = None + readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) + if self.app.name == 'galaxy': + # Shed related tool panel configs are only relevant to Galaxy. + metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + else: + metadata_dict = {} + readme_files = [] + invalid_file_tups = [] + invalid_tool_configs = [] + tool_dependencies_config = None + original_tool_data_path = self.app.config.tool_data_path + original_tool_data_table_config_path = self.app.config.tool_data_table_config_path + if resetting_all_metadata_on_repository: + if not relative_install_dir: + raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + # Keep track of the location where the repository is temporarily cloned so that we can + # strip the path when setting metadata. The value of repository_files_dir is the full + # path to the temporary directory to which the repository was cloned. + work_dir = repository_files_dir + files_dir = repository_files_dir + # Since we're working from a temporary directory, we can safely copy sample files included + # in the repository to the repository root. + self.app.config.tool_data_path = repository_files_dir + self.app.config.tool_data_table_config_path = repository_files_dir + else: + # Use a temporary working directory to copy all sample files. + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-gmfcr" ) + # All other files are on disk in the repository's repo_path, which is the value of + # relative_install_dir. + files_dir = relative_install_dir + if shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + self.app.config.tool_data_path = work_dir #FIXME: Thread safe? + self.app.config.tool_data_table_config_path = work_dir + # Handle proprietary datatypes, if any. + datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) + if datatypes_config: + metadata_dict = self.generate_datatypes_metadata( repository, + repository_clone_url, + files_dir, + datatypes_config, + metadata_dict ) + # Get the relative path to all sample files included in the repository for storage in + # the repository's metadata. + sample_file_metadata_paths, sample_file_copy_paths = \ + self.get_sample_files_from_disk( repository_files_dir=files_dir, + tool_path=shed_config_dict.get( 'tool_path' ), + relative_install_dir=relative_install_dir, + resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) + if sample_file_metadata_paths: + metadata_dict[ 'sample_files' ] = sample_file_metadata_paths + # Copy all sample files included in the repository to a single directory location so we + # can load tools that depend on them. + for sample_file in sample_file_copy_paths: + tool_util.copy_sample_file( self.app, sample_file, dest_path=work_dir ) + # If the list of sample files includes a tool_data_table_conf.xml.sample file, load + # its table elements into memory. + relative_path, filename = os.path.split( sample_file ) + if filename == 'tool_data_table_conf.xml.sample': + new_table_elems, error_message = \ + self.app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, + tool_data_path=self.app.config.tool_data_path, + shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, + persist=False ) + if error_message: + invalid_file_tups.append( ( filename, error_message ) ) + for root, dirs, files in os.walk( files_dir ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) + for name in files: + # See if we have a repository dependencies defined. + if name == rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME: + path_to_repository_dependencies_config = os.path.join( root, name ) + metadata_dict, error_message = \ + self.generate_repository_dependency_metadata( path_to_repository_dependencies_config, + metadata_dict, + updating_installed_repository=updating_installed_repository ) + if error_message: + invalid_file_tups.append( ( name, error_message ) ) + # See if we have one or more READ_ME files. + elif name.lower() in readme_file_names: + relative_path_to_readme = self.get_relative_path_to_repository_file( root, + name, + relative_install_dir, + work_dir, + shed_config_dict, + resetting_all_metadata_on_repository ) + readme_files.append( relative_path_to_readme ) + # See if we have a tool config. + elif name not in self.NOT_TOOL_CONFIGS and name.endswith( '.xml' ): + full_path = str( os.path.abspath( os.path.join( root, name ) ) ) + if os.path.getsize( full_path ) > 0: + if not ( checkers.check_binary( full_path ) or + checkers.check_image( full_path ) or + checkers.check_gzip( full_path )[ 0 ] or + checkers.check_bz2( full_path )[ 0 ] or + checkers.check_zip( full_path ) ): + # Make sure we're looking at a tool config and not a display application + # config or something else. + element_tree, error_message = xml_util.parse_xml( full_path ) + if element_tree is None: + is_tool = False + else: + element_tree_root = element_tree.getroot() + is_tool = element_tree_root.tag == 'tool' + if is_tool: + tool, valid, error_message = \ + tool_util.load_tool_from_config( self.app, + self.app.security.encode_id( repository.id ), + full_path ) + if tool is None: + if not valid: + invalid_tool_configs.append( name ) + invalid_file_tups.append( ( name, error_message ) ) + else: + invalid_files_and_errors_tups = \ + tool_util.check_tool_input_params( self.app, + files_dir, + name, + tool, + sample_file_copy_paths ) + can_set_metadata = True + for tup in invalid_files_and_errors_tups: + if name in tup: + can_set_metadata = False + invalid_tool_configs.append( name ) + break + if can_set_metadata: + relative_path_to_tool_config = \ + self.get_relative_path_to_repository_file( root, + name, + relative_install_dir, + work_dir, + shed_config_dict, + resetting_all_metadata_on_repository ) + metadata_dict = self.generate_tool_metadata( relative_path_to_tool_config, + tool, + repository_clone_url, + metadata_dict ) + else: + for tup in invalid_files_and_errors_tups: + invalid_file_tups.append( tup ) + # Find all exported workflows. + elif name.endswith( '.ga' ): + relative_path = os.path.join( root, name ) + if os.path.getsize( os.path.abspath( relative_path ) ) > 0: + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + if workflow_text: + valid_exported_galaxy_workflow = True + try: + exported_workflow_dict = json.loads( workflow_text ) + except Exception, e: + log.exception( "Skipping file %s since it does not seem to be a valid exported Galaxy workflow: %s" \ + % str( relative_path ), str( e ) ) + valid_exported_galaxy_workflow = False + if valid_exported_galaxy_workflow and \ + 'a_galaxy_workflow' in exported_workflow_dict and \ + exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + metadata_dict = self.generate_workflow_metadata( relative_path, + exported_workflow_dict, + metadata_dict ) + # Handle any data manager entries + data_manager_config = hg_util.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ) + metadata_dict = self.generate_data_manager_metadata( repository, + files_dir, + data_manager_config, + metadata_dict, + shed_config_dict=shed_config_dict ) + + if readme_files: + metadata_dict[ 'readme_files' ] = readme_files + # This step must be done after metadata for tools has been defined. + tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir ) + if tool_dependencies_config: + metadata_dict, error_message = \ + self.generate_tool_dependency_metadata( repository, + changeset_revision, + repository_clone_url, + tool_dependencies_config, + metadata_dict, + original_repository_metadata=original_repository_metadata ) + if error_message: + invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, 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. + self.app.config.tool_data_path = original_tool_data_path + self.app.config.tool_data_table_config_path = original_tool_data_table_config_path + basic_util.remove_dir( work_dir ) + return metadata_dict, invalid_file_tups + + def generate_package_dependency_metadata( self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): + """ + Generate the metadata for a tool dependencies package defined for a repository. The + value of package_name must match the value of the "package" type in the tool config's + <requirements> tag set. + """ + # TODO: make this function a class. + repository_dependency_is_valid = True + 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: + 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. If the returned value of repository_dependency_is_valid + # is True, the tool dependency definition will be set as invalid. This is currently the only case + # where a tool dependency definition is considered invalid. + repository_dependency_tup, repository_dependency_is_valid, error_message = \ + self.handle_repository_elem( repository_elem=sub_elem, + only_if_compiling_contained_td=False, + updating_installed_repository=False ) + elif sub_elem.tag == 'install': + package_install_version = sub_elem.get( 'version', '1.0' ) + if package_install_version == '1.0': + # Complex repository dependencies can be defined within the last <actions> tag set contained in an + # <actions_group> tag set. Comments, <repository> tag sets and <readme> tag sets will be skipped + # in tool_dependency_util.parse_package_elem(). + actions_elem_tuples = tool_dependency_util.parse_package_elem( sub_elem, + platform_info_dict=None, + include_after_install_actions=False ) + if actions_elem_tuples: + # We now have a list of a single tuple that looks something like: + # [(True, <Element 'actions' at 0x104017850>)] + actions_elem_tuple = actions_elem_tuples[ 0 ] + in_actions_group, actions_elem = actions_elem_tuple + if in_actions_group: + # Since we're inside an <actions_group> tag set, inspect the actions_elem to see if a complex + # repository dependency is defined. By definition, complex repository dependency definitions + # contained within the last <actions> tag set within an <actions_group> tag set will have the + # value of "only_if_compiling_contained_td" set to True in + for action_elem in actions_elem: + if action_elem.tag == 'package': + # <package name="libgtextutils" version="0.6"> + # <repository name="package_libgtextutils_0_6" owner="test" prior_installation_required="True" /> + # </package> + ae_package_name = action_elem.get( 'name', None ) + ae_package_version = action_elem.get( 'version', None ) + if ae_package_name and ae_package_version: + for sub_action_elem in action_elem: + if sub_action_elem.tag == 'repository': + # We have a complex repository dependency. + repository_dependency_tup, repository_dependency_is_valid, error_message = \ + self.handle_repository_elem( repository_elem=sub_action_elem, + only_if_compiling_contained_td=True, + updating_installed_repository=False ) + elif action_elem.tag == 'action': + # <action type="set_environment_for_install"> + # <repository changeset_revision="b107b91b3574" name="package_readline_6_2" owner="devteam" prior_installation_required="True" toolshed="http://localhost:9009"> + # <package name="readline" version="6.2" /> + # </repository> + # </action> + for sub_action_elem in action_elem: + if sub_action_elem.tag == 'repository': + # We have a complex repository dependency. + repository_dependency_tup, repository_dependency_is_valid, error_message = \ + self.handle_repository_elem( repository_elem=sub_action_elem, + only_if_compiling_contained_td=True, + updating_installed_repository=False ) + if requirements_dict: + dependency_key = '%s/%s' % ( package_name, package_version ) + if repository_dependency_is_valid: + valid_tool_dependencies_dict[ dependency_key ] = requirements_dict + else: + # Append the error message to the requirements_dict. + requirements_dict[ 'error' ] = error_message + invalid_tool_dependencies_dict[ dependency_key ] = requirements_dict + return valid_tool_dependencies_dict, \ + invalid_tool_dependencies_dict, \ + repository_dependency_tup, \ + repository_dependency_is_valid, \ + error_message + + def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict, + updating_installed_repository=False ): + """ + Generate a repository dependencies dictionary based on valid information defined in the received + repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. + """ + error_message = '' + # Make sure we're looking at a valid repository_dependencies.xml file. + tree, error_message = xml_util.parse_xml( repository_dependencies_config ) + if tree is None: + xml_is_valid = False + else: + root = tree.getroot() + xml_is_valid = root.tag == 'repositories' + if xml_is_valid: + invalid_repository_dependencies_dict = dict( description=root.get( 'description' ) ) + invalid_repository_dependency_tups = [] + valid_repository_dependencies_dict = dict( description=root.get( 'description' ) ) + valid_repository_dependency_tups = [] + for repository_elem in root.findall( 'repository' ): + repository_dependency_tup, repository_dependency_is_valid, err_msg = \ + self.handle_repository_elem( repository_elem, + only_if_compiling_contained_td=False, + updating_installed_repository=updating_installed_repository ) + if repository_dependency_is_valid: + valid_repository_dependency_tups.append( repository_dependency_tup ) + else: + # Append the error_message to the repository dependencies tuple. + toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + repository_dependency_tup + repository_dependency_tup = ( toolshed, + name, + owner, + changeset_revision, + prior_installation_required, + only_if_compiling_contained_td, + err_msg ) + invalid_repository_dependency_tups.append( repository_dependency_tup ) + error_message += err_msg + if invalid_repository_dependency_tups: + invalid_repository_dependencies_dict[ 'repository_dependencies' ] = invalid_repository_dependency_tups + metadata_dict[ 'invalid_repository_dependencies' ] = invalid_repository_dependencies_dict + if valid_repository_dependency_tups: + valid_repository_dependencies_dict[ 'repository_dependencies' ] = valid_repository_dependency_tups + metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict + return metadata_dict, error_message + + def generate_tool_metadata( self, tool_config, tool, repository_clone_url, metadata_dict ): + """Update the received metadata_dict with changes that have been applied to the received tool.""" + # Generate the guid. + guid = suc.generate_tool_guid( repository_clone_url, tool ) + # Handle tool.requirements. + tool_requirements = [] + for tool_requirement in tool.requirements: + name = str( tool_requirement.name ) + type = str( tool_requirement.type ) + version = str( tool_requirement.version ) if tool_requirement.version else None + requirement_dict = dict( name=name, + type=type, + version=version ) + tool_requirements.append( requirement_dict ) + # Handle tool.tests. + tool_tests = [] + if tool.tests: + for ttb in tool.tests: + required_files = [] + for required_file in ttb.required_files: + value, extra = required_file + required_files.append( ( value ) ) + inputs = [] + for param_name, values in ttb.inputs.iteritems(): + # Handle improperly defined or strange test parameters and values. + if param_name is not None: + if values is None: + # An example is the 3rd test in http://testtoolshed.g2.bx.psu.edu/view/devteam/samtools_rmdup + # which is defined as: + # <test> + # <param name="input1" value="1.bam" ftype="bam" /> + # <param name="bam_paired_end_type_selector" value="PE" /> + # <param name="force_se" /> + # <output name="output1" file="1.bam" ftype="bam" sort="True" /> + # </test> + inputs.append( ( param_name, values ) ) + else: + if len( values ) == 1: + inputs.append( ( param_name, values[ 0 ] ) ) + else: + inputs.append( ( param_name, values ) ) + outputs = [] + for output in ttb.outputs: + name, file_name, extra = output + outputs.append( ( name, basic_util.strip_path( file_name ) if file_name else None ) ) + if file_name not in required_files and file_name is not None: + required_files.append( file_name ) + test_dict = dict( name=str( ttb.name ), + required_files=required_files, + inputs=inputs, + outputs=outputs ) + tool_tests.append( test_dict ) + # Determine if the tool should be loaded into the tool panel. Examples of valid tools that + # should not be displayed in the tool panel are datatypes converters and DataManager tools + # (which are of type 'manage_data'). + datatypes = metadata_dict.get( 'datatypes', None ) + add_to_tool_panel_attribute = self.set_add_to_tool_panel_attribute_for_tool( tool=tool, + guid=guid, + datatypes=datatypes ) + tool_dict = dict( id=tool.id, + guid=guid, + name=tool.name, + version=tool.version, + description=tool.description, + version_string_cmd = tool.version_string_cmd, + tool_config=tool_config, + tool_type=tool.tool_type, + requirements=tool_requirements, + tests=tool_tests, + add_to_tool_panel=add_to_tool_panel_attribute ) + if 'tools' in metadata_dict: + metadata_dict[ 'tools' ].append( tool_dict ) + else: + metadata_dict[ 'tools' ] = [ tool_dict ] + return metadata_dict + + def generate_tool_dependency_metadata( self, 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 and the list of tool + # dictionaries in the metadata. + original_valid_tool_dependencies_dict = original_repository_metadata.get( 'tool_dependencies', None ) + original_invalid_tool_dependencies_dict = original_repository_metadata.get( 'invalid_tool_dependencies', None ) + else: + original_valid_tool_dependencies_dict = None + original_invalid_tool_dependencies_dict = None + tree, error_message = xml_util.parse_xml( tool_dependencies_config ) + if tree is None: + return metadata_dict, error_message + root = tree.getroot() + tool_dependency_is_valid = True + valid_tool_dependencies_dict = {} + invalid_tool_dependencies_dict = {} + valid_repository_dependency_tups = [] + invalid_repository_dependency_tups = [] + tools_metadata = metadata_dict.get( 'tools', None ) + description = root.get( 'description' ) + for elem in root: + if elem.tag == 'package': + valid_tool_dependencies_dict, \ + invalid_tool_dependencies_dict, \ + repository_dependency_tup, \ + repository_dependency_is_valid, \ + message = self.generate_package_dependency_metadata( elem, + valid_tool_dependencies_dict, + invalid_tool_dependencies_dict ) + if repository_dependency_is_valid: + if repository_dependency_tup and repository_dependency_tup not in valid_repository_dependency_tups: + # We have a valid complex repository dependency. + valid_repository_dependency_tups.append( repository_dependency_tup ) + else: + if repository_dependency_tup and repository_dependency_tup not in invalid_repository_dependency_tups: + # We have an invalid complex repository dependency, so mark the tool dependency as invalid. + tool_dependency_is_valid = False + # Append the error message to the invalid repository dependency tuple. + toolshed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td \ + = repository_dependency_tup + repository_dependency_tup = \ + ( toolshed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td, \ + message ) + invalid_repository_dependency_tups.append( repository_dependency_tup ) + error_message = '%s %s' % ( error_message, message ) + elif elem.tag == 'set_environment': + valid_tool_dependencies_dict = \ + self.generate_environment_dependency_metadata( elem, valid_tool_dependencies_dict ) + if valid_tool_dependencies_dict: + if original_valid_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. + irm = self.app.installed_repository_manager + updated_tool_dependency_names, deleted_tool_dependency_names = \ + irm.handle_existing_tool_dependencies_that_changed_in_update( repository, + original_valid_tool_dependencies_dict, + valid_tool_dependencies_dict ) + metadata_dict[ 'tool_dependencies' ] = valid_tool_dependencies_dict + if invalid_tool_dependencies_dict: + metadata_dict[ 'invalid_tool_dependencies' ] = invalid_tool_dependencies_dict + if valid_repository_dependency_tups: + metadata_dict = \ + self.update_repository_dependencies_metadata( metadata=metadata_dict, + repository_dependency_tups=valid_repository_dependency_tups, + is_valid=True, + description=description ) + if invalid_repository_dependency_tups: + metadata_dict = \ + self.update_repository_dependencies_metadata( metadata=metadata_dict, + repository_dependency_tups=invalid_repository_dependency_tups, + is_valid=False, + description=description ) + return metadata_dict, error_message + + def generate_workflow_metadata( self, relative_path, exported_workflow_dict, metadata_dict ): + """ + Update the received metadata_dict with changes that have been applied to the + received exported_workflow_dict. + """ + if 'workflows' in metadata_dict: + metadata_dict[ 'workflows' ].append( ( relative_path, exported_workflow_dict ) ) + else: + metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] + return metadata_dict + + def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict, + resetting_all_metadata_on_repository ): + if resetting_all_metadata_on_repository: + full_path_to_file = os.path.join( root, name ) + stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) + if stripped_path_to_file.startswith( '/' ): + stripped_path_to_file = stripped_path_to_file[ 1: ] + relative_path_to_file = os.path.join( relative_install_dir, stripped_path_to_file ) + else: + relative_path_to_file = os.path.join( root, name ) + if relative_install_dir and \ + shed_config_dict.get( 'tool_path' ) and \ + relative_path_to_file.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): + relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] + return relative_path_to_file + + def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None, + resetting_all_metadata_on_repository=False ): + if resetting_all_metadata_on_repository: + # Keep track of the location where the repository is temporarily cloned so that we can strip + # it when setting metadata. + work_dir = repository_files_dir + sample_file_metadata_paths = [] + sample_file_copy_paths = [] + for root, dirs, files in os.walk( repository_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + if resetting_all_metadata_on_repository: + full_path_to_sample_file = os.path.join( root, name ) + stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) + if stripped_path_to_sample_file.startswith( '/' ): + stripped_path_to_sample_file = stripped_path_to_sample_file[ 1: ] + relative_path_to_sample_file = os.path.join( relative_install_dir, stripped_path_to_sample_file ) + if os.path.exists( relative_path_to_sample_file ): + sample_file_copy_paths.append( relative_path_to_sample_file ) + else: + sample_file_copy_paths.append( full_path_to_sample_file ) + else: + relative_path_to_sample_file = os.path.join( root, name ) + sample_file_copy_paths.append( relative_path_to_sample_file ) + if tool_path and relative_install_dir: + if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ): + 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 handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): + """ + Process the received repository_elem which is a <repository> tag either from a + repository_dependencies.xml file or a tool_dependencies.xml file. If the former, + we're generating repository dependencies metadata for a repository in the Tool Shed. + If the latter, we're generating package dependency metadata within Galaxy or the + Tool Shed. + """ + is_valid = True + error_message = '' + toolshed = repository_elem.get( 'toolshed', None ) + name = repository_elem.get( 'name', None ) + owner = repository_elem.get( 'owner', None ) + changeset_revision = repository_elem.get( 'changeset_revision', None ) + prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) + if self.app.name == 'galaxy': + if updating_installed_repository: + pass + else: + # We're installing a repository into Galaxy, so make sure its contained repository + # dependency definition is valid. + if toolshed is None or name is None or owner is None or changeset_revision is None: + # Raise an exception here instead of returning an error_message to keep the + # installation from proceeding. Reaching here implies a bug in the Tool Shed + # framework. + error_message = 'Installation halted because the following repository dependency definition is invalid:\n' + error_message += xml_util.xml_to_string( repository_elem, use_indent=True ) + raise Exception( error_message ) + if not toolshed: + # Default to the current tool shed. + toolshed = str( url_for( '/', qualified=True ) ).rstrip( '/' ) + repository_dependency_tup = [ toolshed, + name, + owner, + changeset_revision, + prior_installation_required, + str( only_if_compiling_contained_td ) ] + user = None + repository = None + toolshed = common_util.remove_protocol_from_tool_shed_url( toolshed ) + if self.app.name == 'galaxy': + # We're in Galaxy. We reach here when we're generating the metadata for a tool + # dependencies package defined for a repository or when we're generating metadata + # for an installed repository. See if we can locate the installed repository via + # the changeset_revision defined in the repository_elem (it may be outdated). If + # we're successful in locating an installed repository with the attributes defined + # in the repository_elem, we know it is valid. + repository = suc.get_repository_for_dependency_relationship( self.app, + toolshed, + name, + owner, + changeset_revision ) + if repository: + return repository_dependency_tup, is_valid, error_message + else: + # Send a request to the tool shed to retrieve appropriate additional changeset + # revisions with which the repository + # may have been installed. + text = suc.get_updated_changeset_revisions_from_tool_shed( self.app, + toolshed, + name, + owner, + changeset_revision ) + if text: + updated_changeset_revisions = util.listify( text ) + for updated_changeset_revision in updated_changeset_revisions: + repository = suc.get_repository_for_dependency_relationship( self.app, + toolshed, + name, + owner, + updated_changeset_revision ) + if repository: + return repository_dependency_tup, is_valid, error_message + if updating_installed_repository: + # The repository dependency was included in an update to the installed + # repository, so it will not yet be installed. Return the tuple for later + # installation. + return repository_dependency_tup, is_valid, error_message + if updating_installed_repository: + # The repository dependency was included in an update to the installed repository, + # so it will not yet be installed. Return the tuple for later installation. + return repository_dependency_tup, is_valid, error_message + # Don't generate an error message for missing repository dependencies that are required + # only if compiling the dependent repository's tool dependency. + if not only_if_compiling_contained_td: + # We'll currently default to setting the repository dependency definition as invalid + # if an installed repository cannot be found. This may not be ideal because the tool + # shed may have simply been inaccessible when metadata was being generated for the + # installed tool shed repository. + error_message = "Ignoring invalid repository dependency definition for tool shed %s, name %s, owner %s, " % \ + ( toolshed, name, owner ) + error_message += "changeset revision %s." % changeset_revision + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message + else: + # We're in the tool shed. + if suc.tool_shed_is_this_tool_shed( toolshed ): + try: + user = self.sa_session.query( self.app.model.User ) \ + .filter( self.app.model.User.table.c.username == owner ) \ + .one() + except Exception, e: + error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, " % \ + ( toolshed, name, owner ) + error_message += "changeset revision %s because the owner is invalid. " % changeset_revision + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message + try: + repository = self.sa_session.query( self.app.model.Repository ) \ + .filter( and_( self.app.model.Repository.table.c.name == name, + self.app.model.Repository.table.c.user_id == user.id ) ) \ + .one() + except: + error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, " % \ + ( toolshed, name, owner ) + error_message += "changeset revision %s because the name is invalid. " % changeset_revision + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message + repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) + + # The received changeset_revision may be None since defining it in the dependency definition is optional. + # If this is the case, the default will be to set its value to the repository dependency tip revision. + # This probably occurs only when handling circular dependency definitions. + tip_ctx = repo.changectx( repo.changelog.tip() ) + # Make sure the repo.changlog includes at least 1 revision. + if changeset_revision is None and tip_ctx.rev() >= 0: + changeset_revision = str( tip_ctx ) + repository_dependency_tup = [ toolshed, + name, + owner, + changeset_revision, + prior_installation_required, + str( only_if_compiling_contained_td ) ] + return repository_dependency_tup, is_valid, error_message + else: + # Find the specified changeset revision in the repository's changelog to see if it's valid. + found = False + for changeset in repo.changelog: + changeset_hash = str( repo.changectx( changeset ) ) + if changeset_hash == changeset_revision: + found = True + break + if not found: + error_message = "Ignoring repository dependency definition for tool shed %s, name %s, owner %s, " % \ + ( toolshed, name, owner ) + error_message += "changeset revision %s because the changeset revision is invalid. " % changeset_revision + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message + else: + # Repository dependencies are currently supported within a single tool shed. + error_message = "Repository dependencies are currently supported only within the same tool shed. Ignoring " + error_message += "repository dependency definition for tool shed %s, name %s, owner %s, changeset revision %s. " % \ + ( toolshed, name, owner, changeset_revision ) + log.debug( error_message ) + is_valid = False + return repository_dependency_tup, is_valid, error_message + return repository_dependency_tup, is_valid, error_message + + def set_add_to_tool_panel_attribute_for_tool( self, tool, guid, datatypes ): + """ + Determine if a tool should be loaded into the Galaxy tool panel. Examples of valid tools that + should not be displayed in the tool panel are datatypes converters and DataManager tools. + """ + if hasattr( tool, 'tool_type' ): + if tool.tool_type in [ 'manage_data' ]: + # We have a DataManager tool. + return False + if datatypes: + for datatype_dict in datatypes: + converters = datatype_dict.get( 'converters', None ) + # [{"converters": + # [{"target_datatype": "gff", + # "tool_config": "bed_to_gff_converter.xml", + # "guid": "localhost:9009/repos/test/bed_to_gff_converter/CONVERTER_bed_to_gff_0/2.0.0"}], + # "display_in_upload": "true", + # "dtype": "galaxy.datatypes.interval:Bed", + # "extension": "bed"}] + if converters: + for converter_dict in converters: + converter_guid = converter_dict.get( 'guid', None ) + if converter_guid: + if converter_guid == guid: + # We have a datatypes converter. + return False + return True + + def update_repository_dependencies_metadata( self, metadata, repository_dependency_tups, is_valid, description ): + if is_valid: + repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) + else: + repository_dependencies_dict = metadata.get( 'invalid_repository_dependencies', None ) + for repository_dependency_tup in repository_dependency_tups: + if is_valid: + tool_shed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td \ + = repository_dependency_tup + else: + tool_shed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td, \ + error_message \ + = repository_dependency_tup + if repository_dependencies_dict: + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + 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[ 'repository_dependencies' ] = repository_dependencies + else: + repository_dependencies_dict = dict( description=description, + repository_dependencies=repository_dependency_tups ) + if repository_dependencies_dict: + if is_valid: + metadata[ 'repository_dependencies' ] = repository_dependencies_dict + else: + metadata[ 'invalid_repository_dependencies' ] = repository_dependencies_dict + return metadata This diff is so big that we needed to truncate the remainder. 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