1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/0bd2cc07fdd8/ changeset: 0bd2cc07fdd8 user: greg date: 2012-08-13 20:54:07 summary: Fixes for setting metadata on tool shed repositories and specific add tool lineage information on the view tool metadata page in the tool shed as well as for tool shed repositories installed into a local Galaxy instance. affected #: 10 files

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -132,7 +132,11 @@ tool_panel_dict_for_tool_config = generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( self.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=self.app, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush()

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -324,7 +324,7 @@ # Eliminate the port, if any, since it will result in an invalid directory name. return tool_shed_url.split( ':' )[ 0 ] return tool_shed_url.rstrip( '/' ) -def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): +def clone_repository( repository_clone_url, repository_file_dir, ctx_rev ): """Clone the repository up to the specified changeset_revision. No subsequent revisions will be present in the cloned repository.""" commands.clone( get_configured_ui(), str( repository_clone_url ), @@ -548,24 +548,55 @@ if not can_generate_dependency_metadata: break return can_generate_dependency_metadata -def generate_metadata_for_changeset_revision( app, repository_files_dir, repository_clone_url ): +def generate_metadata_for_changeset_revision( app, repository_clone_url, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=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 - disk files, so the value of repository_files_dir will not always be repository.repo_path (it could be a temporary directory containing a clone). + disk files, so the value of repository_files_dir will not always be repository.repo_path (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. """ metadata_dict = {} invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None - datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir ) + original_tool_data_path = app.config.tool_data_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. + app.config.tool_data_path = repository_files_dir + else: + # Use a temporary working directory to copy all sample files. + work_dir = tempfile.mkdtemp() + # 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 + app.config.tool_data_path = work_dir + # Handle proprietary datatypes, if any. + datatypes_config = get_config_from_disk( 'datatypes_conf.xml', files_dir ) if datatypes_config: metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files = get_sample_files_from_disk( repository_files_dir ) + # Get the relative path to all sample files included in the repository for storage in the repository's metadata. + sample_files = get_sample_files_from_disk( repository_files_dir=files_dir, + relative_install_dir=relative_install_dir, + resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) if sample_files: metadata_dict[ 'sample_files' ] = sample_files - # Find all tool configs and exported workflows. - for root, dirs, files in os.walk( repository_files_dir ): + # 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_files: + copy_sample_file( app, sample_file, dest_path=work_dir ) + # If the list of sample files includes a tool_data_table_conf.xml.sample file, laad it's table elements into memory. + relative_path, filename = os.path.split( sample_file ) + if filename == 'tool_data_table_conf.xml.sample': + new_table_elems = app.tool_data_tables.add_new_entries_from_config_file( config_filename=sample_file, + tool_data_path=app.config.tool_data_path, + tool_data_table_config_path=app.config.tool_data_table_config_path, + persist=False ) + # Find all tool configs and exported workflows and add them to the repository's metadata. + 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' ) @@ -586,11 +617,19 @@ if is_tool: try: tool = app.toolbox.load_tool( full_path ) + except KeyError, e: + tool = None + invalid_tool_configs.append( name ) + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + invalid_file_tups.append( ( name, error_message ) ) except Exception, e: tool = None invalid_tool_configs.append( name ) + invalid_file_tups.append( ( name, str( e ) ) ) if tool is not None: - invalid_files_and_errors_tups = check_tool_input_params( app, repository_files_dir, name, tool, sample_files ) + invalid_files_and_errors_tups = check_tool_input_params( app, files_dir, name, tool, sample_files ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: @@ -598,7 +637,15 @@ invalid_tool_configs.append( name ) break if can_set_metadata: - metadata_dict = generate_tool_metadata( os.path.join( root, name ), tool, repository_clone_url, metadata_dict ) + if resetting_all_metadata_on_repository: + full_path_to_tool_config = os.path.join( root, name ) + stripped_path_to_tool_config = full_path_to_tool_config.replace( work_dir, '' ) + if stripped_path_to_tool_config.startswith( '/' ): + stripped_path_to_tool_config = stripped_path_to_tool_config[ 1: ] + relative_path_to_tool_config = os.path.join( relative_install_dir, stripped_path_to_tool_config ) + else: + relative_path_to_tool_config = os.path.join( root, name ) + metadata_dict = generate_tool_metadata( relative_path_to_tool_config, tool, repository_clone_url, metadata_dict ) else: invalid_file_tups.extend( invalid_files_and_errors_tups ) # Find all exported workflows @@ -612,11 +659,16 @@ metadata_dict = generate_workflow_metadata( relative_path, exported_workflow_dict, metadata_dict ) 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', repository_files_dir ) + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', files_dir ) if tool_dependencies_config: metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + if resetting_all_metadata_on_repository: + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( app ) + # Reset the value of the app's tool_data_path to it's original value. + app.config.tool_data_path = original_tool_data_path return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( 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.""" @@ -1028,13 +1080,24 @@ if tool: repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups -def get_sample_files_from_disk( relative_install_dir ): +def get_sample_files_from_disk( repository_files_dir, 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_files = [] - for root, dirs, files in os.walk( relative_install_dir ): + for root, dirs, files in os.walk( repository_files_dir ): if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): - sample_files.append( os.path.join( root, name ) ) + 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 ) + else: + relative_path_to_sample_file = os.path.join( root, name ) + sample_files.append( relative_path_to_sample_file ) return sample_files def get_shed_tool_conf_dict( app, shed_tool_conf ): """

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -497,6 +497,9 @@ trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' return get_repository_file_contents( file_path ) + def get_versions_of_tool( self, app, guid ): + tool_version = get_tool_version( app, guid ) + return tool_version.get_version_ids( app ) @web.expose @web.require_admin def initiate_repository_installation( self, trans, shed_repository_ids, encoded_kwd, reinstalling=False ): @@ -684,7 +687,11 @@ Generate the metadata for the installed tool shed repository, among other things. This method is called from Galaxy (never the tool shed) when an admin is installing a new repository or reinstalling an uninstalled repository. """ - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -779,7 +786,14 @@ message = "The repository information has been updated." elif params.get( 'set_metadata_button', False ): repository_clone_url = generate_clone_url( trans, repository ) - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) + # TODO: Fix this by setting up a temporary work_dir - there is currently no way for an admin to reset metadata on an + # installed tool shed repository because the manage_repository template checs the value of can_reset_metadata, whic is + # currently always False. + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository_clone_url=repository_clone_url, + relative_install_dir=None, + repository_files_dir=repository_files_dir, + resetting_all_metadata_on_repository=True ) if metadata_dict: repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -1479,7 +1493,11 @@ update_repository( repo, latest_ctx_rev ) # Update the repository metadata. tool_shed = clean_tool_shed_url( tool_shed_url ) - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository_clone_url=repository_clone_url, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision @@ -1515,17 +1533,21 @@ webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) metadata = {} + tool_lineage = [] tool = None if 'tools' in repository.metadata: for tool_metadata_dict in repository.metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: metadata = tool_metadata_dict tool = trans.app.toolbox.load_tool( os.path.abspath( metadata[ 'tool_config' ] ), guid=metadata[ 'guid' ] ) + if tool: + tool_lineage = self.get_versions_of_tool( trans.app, tool.id ) break return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako", repository=repository, tool=tool, metadata=metadata, + tool_lineage=tool_lineage, message=message, status=status ) def __generate_clone_url( self, trans, repository ):

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -105,34 +105,6 @@ trans.sa_session.flush() return item_rating

-def add_repository_metadata_tool_versions( trans, id, changeset_revisions ): - # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. - for index, changeset_revision in enumerate( changeset_revisions ): - tool_versions_dict = {} - repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tool_dicts = metadata.get( 'tools', [] ) - if index == 0: - # The first changset_revision is a special case because it will have no ancestor changeset_revisions in which to match tools. - # The parent tool id for tools in the first changeset_revision will be the "old_id" in the tool config. - for tool_dict in tool_dicts: - tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] - else: - for tool_dict in tool_dicts: - # We have at least 2 changeset revisions to compare tool guids and tool ids. - parent_id = get_parent_id( trans, - id, - tool_dict[ 'id' ], - tool_dict[ 'version' ], - tool_dict[ 'guid' ], - changeset_revisions[ 0:index ] ) - tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id - if tool_versions_dict: - repository_metadata.tool_versions = tool_versions_dict - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() def changeset_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -155,7 +127,6 @@ # We sometimes see multiple records with the same changeset revision value - no idea how this happens. We'll assume we can delete the older # records, so we'll order by update_time descending and delete records that have the same changeset_revision we come across later.. changeset_revisions_checked = [] - cleaned_changeset_revisions = [] for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ .filter( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ) ) \ .order_by( trans.model.RepositoryMetadata.table.c.changeset_revision, @@ -165,9 +136,6 @@ if can_delete: trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() - else: - cleaned_changeset_revisions.append( changeset_revision ) - return cleaned_changeset_revisions def compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict, current_changeset_revision, current_metadata_dict ): # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. This changeset_revision is an ancestor of # current_changeset_revision which is associated with current_metadata_dict. A new repository_metadata record will be created only @@ -599,7 +567,7 @@ is a valid (downloadable) changset revision. The tool config will be located in the repository manifest between the received valid changeset revision and the first changeset revision in the repository, searching backwards. """ - def load_from_tmp_config( ctx, ctx_file, work_dir ): + def load_from_tmp_config( toolbox, ctx, ctx_file, work_dir ): tool = None message = '' tmp_tool_config = get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) @@ -614,10 +582,12 @@ if tmp_code_file_name: tmp_code_files.append( tmp_code_file_name ) try: - tool = load_tool( trans, tmp_tool_config ) + tool = toolbox.load_tool( tmp_tool_config ) + except KeyError, e: + message = '<b>%s</b> - This file requires an entry for %s in the tool_data_table_conf.xml file. ' % ( tool_config_filename, str( e ) ) + message += 'Upload a file named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct this error. ' except Exception, e: - tool = None - message = "Error loading tool: %s. " % str( e ) + message = 'Error loading tool: %s. ' % str( e ) for tmp_code_file in tmp_code_files: try: os.unlink( tmp_code_file ) @@ -634,16 +604,15 @@ repo_files_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_files_dir ) ctx = get_changectx_for_changeset( repo, changeset_revision ) - tool = None message = '' work_dir = tempfile.mkdtemp() sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) if sample_files: trans.app.config.tool_data_path = work_dir - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) - if tool_data_table_config: - error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) found = False # Get the latest revision of the tool config from the repository manifest up to the value of changeset_revision. for changeset in reversed_upper_bounded_changelog( repo, changeset_revision ): @@ -655,16 +624,16 @@ found = True break if found: - tool, message = load_from_tmp_config( manifest_ctx, ctx_file, work_dir ) + tool, message = load_from_tmp_config( trans.app.toolbox, manifest_ctx, ctx_file, work_dir ) break - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) try: shutil.rmtree( work_dir ) except: pass if sample_files: trans.app.config.tool_data_path = original_tool_data_path + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return tool, message def load_tool_from_tmp_directory( trans, repo, repo_dir, ctx, filename, dir ): is_tool_config = False @@ -763,6 +732,41 @@ # The received metadata_dict includes no metadata for workflows, so a new repository_metadata table record is not needed. return False def reset_all_metadata_on_repository( trans, id, **kwd ): + def reset_all_tool_versions( trans, id, repo ): + changeset_revisions = [] + for changeset in repo.changelog: + changeset_revision = str( repo.changectx( changeset ) ) + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if metadata.get( 'tools', None ): + changeset_revisions.append( changeset_revision ) + # The list of changeset_revisions is now filtered to contain only those that are downloadable and contain tools. + # If a repository includes tools, build a dictionary of { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. + for index, changeset_revision in enumerate( changeset_revisions ): + tool_versions_dict = {} + repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) + metadata = repository_metadata.metadata + tool_dicts = metadata[ 'tools' ] + if index == 0: + # The first changset_revision is a special case because it will have no ancestor changeset_revisions in which to match tools. + # The parent tool id for tools in the first changeset_revision will be the "old_id" in the tool config. + for tool_dict in tool_dicts: + tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] + else: + for tool_dict in tool_dicts: + parent_id = get_parent_id( trans, + id, + tool_dict[ 'id' ], + tool_dict[ 'version' ], + tool_dict[ 'guid' ], + changeset_revisions[ 0:index ] ) + tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id + if tool_versions_dict: + repository_metadata.tool_versions = tool_versions_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -784,10 +788,14 @@ work_dir = tempfile.mkdtemp() current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) - print "Cloning repository revision: ", str( ctx.rev() ) + log.debug( "Cloning repository revision: %s", str( ctx.rev() ) ) clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) - print "Generating metadata for changset revision: ", str( ctx.rev() ) - current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, work_dir, repository_clone_url ) + log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) + current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository_clone_url=repository_clone_url, + relative_install_dir=repo_dir, + repository_files_dir=work_dir, + resetting_all_metadata_on_repository=True ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -842,27 +850,49 @@ except: pass # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. - cleaned_changeset_revisions = clean_repository_metadata( trans, id, changeset_revisions ) - # Set tool version information for all downloadable changeset revisions. - add_repository_metadata_tool_versions( trans, id, cleaned_changeset_revisions ) + clean_repository_metadata( trans, id, changeset_revisions ) + # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. + reset_all_tool_versions( trans, id, repo ) def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ + 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 + tool_versions_dict = {} + for tool_dict in metadata.get( 'tools', [] ): + # We have at least 2 changeset revisions to compare tool guids and tool ids. + parent_id = get_parent_id( trans, + id, + tool_dict[ 'id' ], + tool_dict[ 'version' ], + tool_dict[ 'guid' ], + changeset_revisions ) + tool_versions_dict[ tool_dict[ 'guid' ] ] = parent_id + if tool_versions_dict: + repository_metadata.tool_versions = tool_versions_dict + trans.sa_session.add( repository_metadata ) + trans.sa_session.flush() message = '' status = 'done' - repository_clone_url = generate_clone_url( trans, trans.security.encode_id( repository.id ) ) + encoded_id = trans.security.encode_id( repository.id ) + repository_clone_url = generate_clone_url( trans, encoded_id ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, + repository_clone_url=repository_clone_url, + relative_install_dir=repo_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False ) if metadata_dict: downloadable = is_downloadable( metadata_dict ) repository_metadata = None if new_tool_metadata_required( trans, repository, metadata_dict ) or new_workflow_metadata_required( trans, repository, metadata_dict ): # Create a new repository_metadata table row. repository_metadata = create_or_update_repository_metadata( trans, - trans.security.encode_id( repository.id ), + encoded_id, repository, repository.tip, metadata_dict ) @@ -882,21 +912,18 @@ else: # There are no tools in the repository, and we're setting metadata on the repository tip. repository_metadata = create_or_update_repository_metadata( trans, - trans.security.encode_id( repository.id ), + encoded_id, repository, repository.tip, metadata_dict ) if 'tools' in metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is critical, so we use the repo's changelog. - downloadable_changeset_revisions = [ rm.changeset_revision for rm in repository.downloadable_revisions ] changeset_revisions = [] for changeset in repo.changelog: changeset_revision = str( repo.changectx( changeset ) ) - if changeset_revision in downloadable_changeset_revisions: + if get_repository_metadata_by_changeset_revision( trans, encoded_id, changeset_revision ): changeset_revisions.append( changeset_revision ) - # Now append the latest changeset_revision we just updated above. - changeset_revisions.append( repository_metadata.changeset_revision ) - add_repository_metadata_tool_versions( trans, trans.security.encode_id( repository.id ), changeset_revisions ) + add_tool_versions( trans, encoded_id, repository_metadata, changeset_revisions ) elif len( repo ) == 1 and not invalid_file_tups: message = "Revision '%s' includes no tools, datatypes or exported workflows for which metadata can " % str( repository.tip ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance."

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/webapps/community/controllers/hg.py --- a/lib/galaxy/webapps/community/controllers/hg.py +++ b/lib/galaxy/webapps/community/controllers/hg.py @@ -6,7 +6,6 @@ from galaxy import eggs eggs.require('mercurial') import mercurial.__version__ -from mercurial import hg, ui, commands from mercurial.hgweb.hgwebdir_mod import hgwebdir from mercurial.hgweb.request import wsgiapplication

@@ -20,33 +19,24 @@ hg_version = mercurial.__version__.version cmd = kwd.get( 'cmd', None ) wsgi_app = wsgiapplication( make_web_app ) - # 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). Older versions require checking for 'listkeys'. - push_from_command_line = ( hg_version < '2.2.3' and cmd == 'listkeys' ) or ( hg_version >= '2.2.3' and cmd == 'pushkey' ) - if push_from_command_line: + 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. There is a weakness if the mercurial version < '2.2.3' because several commands include - # listkeys, so repository metadata will be set, but only for the files currently on disk, so doing so is not too expensive. - # If mercurial version < '2.2.3: - # capabilities -> batch -> branchmap -> unbundle -> listkeys - # If mercurial version >= '2.2.3': - # capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey + # 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 ) if path_info: owner, name = path_info.split( '/' ) repository = get_repository_by_name_and_owner( trans, name, owner ) if repository: - if hg_version < '2.2.3': - # We're forced to update the repository so the disk files include the changes in the push. This is handled in the - # pushkey hook in mercurial version 2.2.3 and newer. - repo = hg.repository( ui.ui(), repository.repo_path ) - update_repository( repo ) - # Set metadata using the repository files on disk. - error_message, status = set_repository_metadata( trans, repository ) - if status not in [ 'ok' ] and error_message: - log.debug( "Error resetting metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) ) - elif status in [ 'ok' ] and error_message: - log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( str( repository.name ), str( error_message ) ) ) + if hg_version >= '2.2.3': + # Set metadata using the repository files on disk. + error_message, status = set_repository_metadata( trans, repository ) + if status not in [ 'ok' ] and error_message: + log.debug( "Error resetting metadata on repository '%s': %s" % ( str( repository.name ), str( error_message ) ) ) + elif status in [ 'ok' ] and error_message: + log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( str( repository.name ), str( error_message ) ) ) return wsgi_app

def make_web_app():

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -10,7 +10,8 @@ from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * from galaxy.util.shed_util import create_repo_info_dict, get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, NOT_TOOL_CONFIGS -from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path, to_html_escaped, update_repository +from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, reversed_upper_bounded_changelog, strip_path +from galaxy.util.shed_util import to_html_escaped, update_repository from galaxy.tool_shed.encoding_util import * from common import *

@@ -1268,6 +1269,36 @@ update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) return tool_shed_encode( update_dict ) + def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): + """Return the tool lineage in descendant order for the received guid contained in the received repsitory_metadata.tool_versions.""" + encoded_id = trans.security.encode_id( repository.id ) + repo_dir = repository.repo_path + repo = hg.repository( get_configured_ui(), repo_dir ) + # Initialize the tool lineage + tool_guid_lineage = [ guid ] + # Get all ancestor guids of the received guid. + current_child_guid = guid + for changeset in reversed_upper_bounded_changelog( repo, repository_metadata.changeset_revision ): + ctx = repo.changectx( changeset ) + rm = get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) ) + if rm: + parent_guid = rm.tool_versions.get( current_child_guid, None ) + if parent_guid: + tool_guid_lineage.append( parent_guid ) + current_child_guid = parent_guid + # Get all descendant guids of the received guid. + current_parent_guid = guid + for changeset in reversed_lower_upper_bounded_changelog( repo, repository_metadata.changeset_revision, repository.tip ): + ctx = repo.changectx( changeset ) + rm = get_repository_metadata_by_changeset_revision( trans, encoded_id, str( ctx ) ) + if rm: + tool_versions = rm.tool_versions + for child_guid, parent_guid in tool_versions.items(): + if parent_guid == current_parent_guid: + tool_guid_lineage.insert( 0, child_guid ) + current_parent_guid = child_guid + break + return tool_guid_lineage @web.expose def help( self, trans, **kwd ): params = util.Params( kwd ) @@ -1348,23 +1379,12 @@ webapp = get_webapp( trans, **kwd ) repository_clone_url = generate_clone_url( trans, repository_id ) repository = get_repository( trans, repository_id ) - repo_dir = repository.repo_path - repo = hg.repository( get_configured_ui(), repo_dir ) - ctx = get_changectx_for_changeset( repo, changeset_revision ) - invalid_message = '' - metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) - for invalid_file_tup in invalid_file_tups: - invalid_tool_config, invalid_msg = invalid_file_tup - invalid_tool_config_name = strip_path( invalid_tool_config ) - if tool_config == invalid_tool_config_name: - invalid_message = invalid_msg - break tool, error_message = load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) try: - if invalid_message: - message = invalid_message + if error_message: + message = error_message return trans.fill_template( "/webapps/community/repository/tool_form.mako", repository=repository, changeset_revision=changeset_revision, @@ -2165,20 +2185,25 @@ status = params.get( 'status', 'done' ) webapp = get_webapp( trans, **kwd ) repository = get_repository( trans, repository_id ) - metadata = {} + tool_metadata_dict = {} + tool_lineage = [] tool = None + guid = None revision_label = get_revision_label( trans, repository, changeset_revision ) - repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ).metadata - if 'tools' in repository_metadata: - for tool_metadata_dict in repository_metadata[ 'tools' ]: + repository_metadata = get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) + metadata = repository_metadata.metadata + if 'tools' in metadata: + for tool_metadata_dict in metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: - metadata = tool_metadata_dict + guid = tool_metadata_dict[ 'guid' ] try: # We may be attempting to load a tool that no longer exists in the repository tip. - tool = load_tool( trans, os.path.abspath( metadata[ 'tool_config' ] ) ) + tool = load_tool( trans, os.path.abspath( tool_metadata_dict[ 'tool_config' ] ) ) except: tool = None break + if guid: + tool_lineage = self.get_versions_of_tool( trans, repository, repository_metadata, guid ) is_malicious = changeset_is_malicious( trans, repository_id, repository.tip ) changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, @@ -2188,7 +2213,8 @@ return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, - metadata=metadata, + tool_metadata_dict=tool_metadata_dict, + tool_lineage=tool_lineage, changeset_revision=changeset_revision, revision_label=revision_label, changeset_revision_select_field=changeset_revision_select_field,

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/webapps/community/framework/middleware/hg.py --- a/lib/galaxy/webapps/community/framework/middleware/hg.py +++ b/lib/galaxy/webapps/community/framework/middleware/hg.py @@ -57,9 +57,9 @@ connection.execute( "update repository set times_downloaded = %d where user_id = %d and name = '%s'" % ( times_downloaded, user_id, name.lower() ) ) connection.close() if cmd == 'unbundle': - # This is an hg push from the command line. When doing this, the following 7 commands, in order, - # will be retrieved from environ (see the docs at http://mercurial.selenic.com/wiki/WireProtocol): - # between -> capabilities -> heads -> branchmap -> unbundle -> unbundle -> listkeys + # This is an hg push from the command line. When doing this, the following commands, in order, + # will be retrieved from environ (see the docs at http://mercurial.selenic.com/wiki/WireProtocol): + # # If mercurial version >= '2.2.3': capabilities -> batch -> branchmap -> unbundle -> listkeys -> pushkey # # The mercurial API unbundle() ( i.e., hg push ) method ultimately requires authorization. # We'll force password entry every time a change set is pushed.

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -200,7 +200,7 @@ self.repository = repository self.category = category

-class Tag ( object ): +class Tag( object ): def __init__( self, id=None, type=None, parent_id=None, name=None ): self.id = id self.type = type @@ -209,7 +209,7 @@ def __str__ ( self ): return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name )

-class ItemTagAssociation ( object ): +class ItemTagAssociation( object ): def __init__( self, id=None, user=None, item_id=None, tag_id=None, user_tname=None, value=None ): self.id = id self.user = user

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a templates/admin/tool_shed_repository/view_tool_metadata.mako --- a/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -26,6 +26,11 @@ <div class="toolFormTitle">${metadata[ 'name' ]} tool metadata</div><div class="toolFormBody"><div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Miscellaneous</td></tr> + </table> + </div> + <div class="form-row"><label>Name:</label> ${metadata[ 'name' ]} <div style="clear: both"></div> @@ -65,33 +70,35 @@ <div style="clear: both"></div></div> %endif - %if tool: - <div class="form-row"> - <label>Command:</label> - <pre>${tool.command}</pre> - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Interpreter:</label> - ${tool.interpreter} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Is multi-byte:</label> - ${tool.is_multi_byte} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Forces a history refresh:</label> - ${tool.force_history_refresh} - <div style="clear: both"></div> - </div> - <div class="form-row"> - <label>Parallelism:</label> - ${tool.parallelism} - <div style="clear: both"></div> - </div> - %endif + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Version lineage of this tool (guids ordered most recent to oldest)</td></tr> + </table> + </div> + <div class="form-row"> + %if tool_lineage: + <table class="grid"> + %for guid in tool_lineage: + <tr> + <td> + %if guid == metadata[ 'guid' ]: + ${guid} <b>(this tool)</b> + %else: + ${guid} + %endif + </td> + </tr> + %endfor + </table> + %else: + No tool versions are defined for this tool so it is critical that you <b>Set tool versions</b> from the <b>Manage repository</b> page. + %endif + </div> + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Requirements (dependencies defined in the &lt;requirements&gt; tag set)</td></tr> + </table> + </div><% if 'requirements' in metadata: requirements = metadata[ 'requirements' ] @@ -122,7 +129,48 @@ </table><div style="clear: both"></div></div> + %else: + <div class="form-row"> + No requirements defined + </div> %endif + %if tool: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Additional information about this tool</td></tr> + </table> + </div> + <div class="form-row"> + <label>Command:</label> + <pre>${tool.command}</pre> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Interpreter:</label> + ${tool.interpreter} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Is multi-byte:</label> + ${tool.is_multi_byte} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Forces a history refresh:</label> + ${tool.force_history_refresh} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Parallelism:</label> + ${tool.parallelism} + <div style="clear: both"></div> + </div> + %endif + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Functional tests</td></tr> + </table> + </div><% if 'tests' in metadata: tests = metadata[ 'tests' ] @@ -166,6 +214,10 @@ %endfor </table></div> + %else: + <div class="form-row"> + No functional tests defined + </div> %endif </div></div>

diff -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b -r 0bd2cc07fdd896ca0bdbc6d23f7ac077218f007a templates/webapps/community/repository/view_tool_metadata.mako --- a/templates/webapps/community/repository/view_tool_metadata.mako +++ b/templates/webapps/community/repository/view_tool_metadata.mako @@ -85,31 +85,14 @@ <div class="toolForm"><div class="toolFormTitle">Repository revision</div><div class="toolFormBody"> - %if len( changeset_revision_select_field.options ) > 1: - <form name="change_revision" id="change_revision" action="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=metadata[ 'id' ], webapp=webapp )}" method="post" > - <div class="form-row"> - <% - if changeset_revision == repository.tip: - tip_str = 'repository tip' - else: - tip_str = '' - %> - ${changeset_revision_select_field.get_html()} <i>${tip_str}</i> - <div class="toolParamHelp" style="clear: both;"> - Select a revision to inspect and download versions of tools from this repository. - </div> - </div> - </form> - %else: - <div class="form-row"> - <label>Revision:</label> - %if can_view_change_log: - <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> - %else: - ${revision_label} - %endif - </div> - %endif + <div class="form-row"> + <label>Revision:</label> + %if can_view_change_log: + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> + %else: + ${revision_label} + %endif + </div></div></div><p/> @@ -127,47 +110,89 @@ <b>Repository name:</b><br/> ${repository.name} %endif -%if metadata: +%if tool_metadata_dict: <p/><div class="toolForm"> - <div class="toolFormTitle">${metadata[ 'name' ]} tool metadata</div> + <div class="toolFormTitle">${tool_metadata_dict[ 'name' ]} tool metadata</div><div class="toolFormBody"><div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Miscellaneous</td></tr> + </table> + </div> + <div class="form-row"><label>Name:</label> - <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=metadata[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${metadata[ 'name' ]}</a> + <a href="${h.url_for( controller='repository', action='display_tool', repository_id=trans.security.encode_id( repository.id ), tool_config=tool_metadata_dict[ 'tool_config' ], changeset_revision=changeset_revision, webapp=webapp )}">${tool_metadata_dict[ 'name' ]}</a><div style="clear: both"></div></div> - %if 'description' in metadata: + %if 'description' in tool_metadata_dict: <div class="form-row"><label>Description:</label> - ${metadata[ 'description' ]} + ${tool_metadata_dict[ 'description' ]} <div style="clear: both"></div></div> %endif - %if 'id' in metadata: + %if 'id' in tool_metadata_dict: <div class="form-row"><label>Id:</label> - ${metadata[ 'id' ]} + ${tool_metadata_dict[ 'id' ]} <div style="clear: both"></div></div> %endif - %if 'guid' in metadata: + %if 'guid' in tool_metadata_dict: <div class="form-row"><label>Guid:</label> - ${metadata[ 'guid' ]} + ${tool_metadata_dict[ 'guid' ]} <div style="clear: both"></div></div> %endif - %if 'version' in metadata: + %if 'version' in tool_metadata_dict: <div class="form-row"><label>Version:</label> - ${metadata[ 'version' ]} + ${tool_metadata_dict[ 'version' ]} <div style="clear: both"></div></div> %endif + %if 'version_string_cmd' in tool_metadata_dict: + <div class="form-row"> + <label>Version command string:</label> + ${tool_metadata_dict[ 'version_string_cmd' ]} + <div style="clear: both"></div> + </div> + %endif + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Version lineage of this tool (guids ordered most recent to oldest)</td></tr> + </table> + </div> + <div class="form-row"> + %if tool_lineage: + <table class="grid"> + %for guid in tool_lineage: + <tr> + <td> + %if guid == tool_metadata_dict[ 'guid' ]: + ${guid} <b>(this tool)</b> + %else: + ${guid} + %endif + </td> + </tr> + %endfor + </table> + %else: + No tool versions are defined for this tool so it is critical that you <b>Reset all repository metadata</b> from the + <b>Manage repository</b> page. + %endif + </div> + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Requirements (dependencies defined in the &lt;requirements&gt; tag set)</td></tr> + </table> + </div><% - if 'requirements' in metadata: - requirements = metadata[ 'requirements' ] + if 'requirements' in tool_metadata_dict: + requirements = tool_metadata_dict[ 'requirements' ] else: requirements = None %> @@ -195,16 +220,18 @@ </table><div style="clear: both"></div></div> - %endif - %if 'version_string_cmd' in metadata: + %else: <div class="form-row"> - <label>Version command string:</label> - ${metadata[ 'version_string_cmd' ]} - <div style="clear: both"></div> + No requirements defined </div> %endif %if tool: <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Additional information about this tool</td></tr> + </table> + </div> + <div class="form-row"><label>Command:</label><pre>${tool.command}</pre><div style="clear: both"></div> @@ -230,9 +257,14 @@ <div style="clear: both"></div></div> %endif + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Functional tests</td></tr> + </table> + </div><% - if 'tests' in metadata: - tests = metadata[ 'tests' ] + if 'tests' in tool_metadata_dict: + tests = tool_metadata_dict[ 'tests' ] else: tests = None %> @@ -273,6 +305,10 @@ %endfor </table></div> + %else: + <div class="form-row"> + No functional tests defined + </div> %endif </div></div>

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

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