galaxy-commits August 2012

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commit/galaxy-central: greg: 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.
by Bitbucket 13 Aug '12

13 Aug '12

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: + ${guid} + %endif + </td> + </tr> + %endfor + </table> + %else: + No tool versions are defined for this tool so it is critical that you <b>Set tool versions</b> from the <b>Manage repository</b> page. + %endif + </div> + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Requirements (dependencies defined in the <requirements> tag set)</td></tr> + </table> + </div><% if 'requirements' in metadata: requirements = metadata[ 'requirements' ] @@ -122,7 +129,48 @@ </table><div style="clear: both"></div></div> + %else: + <div class="form-row"> + No requirements defined + </div> %endif + %if tool: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Additional information about this tool</td></tr> + </table> + </div> + <div class="form-row"> + <label>Command:</label> + <pre>${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 <requirements> 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/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 4 new changesets
by Bitbucket 13 Aug '12

13 Aug '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d960803cbacc/ changeset: d960803cbacc user: jmchilton date: 2012-08-09 22:15:23 summary: JJ's initial work on extending the API to allow operations on groups. affected #: 5 files diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -544,7 +544,10 @@ else: return False -class Group( object ): +class Group( object, APIItem ): + api_collection_visible_keys = ( 'id', 'name' ) + api_element_visible_keys = ( 'id', 'name' ) + def __init__( self, name = None ): self.name = name self.deleted = False diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/api/group_roles.py --- /dev/null +++ b/lib/galaxy/web/api/group_roles.py @@ -0,0 +1,124 @@ +""" +API operations on Group objects. +""" +import logging +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy import web + +log = logging.getLogger( __name__ ) + +class GroupRolesAPIController( BaseAPIController ): + + @web.expose_api + @web.require_admin + def index( self, trans, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/roles + Displays a collection (list) of groups. + """ + decoded_group_id = trans.security.decode_id( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + rval = [] + try: + for gra in group.roles: + role = gra.role + encoded_id = trans.security.encode_id( role.id ) + rval.append( dict( id = encoded_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=encoded_id, ) ) ) + except Exception, e: + rval = "Error in group API at listing roles" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 + return rval + + @web.expose_api + @web.require_admin + def show( self, trans, id, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/roles/{encoded_role_id} + Displays information about a group role. + """ + role_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_role_id = trans.security.decode_id( role_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) + for gra in group.roles: + if gra.role == role: + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This + if not item: + item = "role %s not in group %s" % (role.name,group.name) + except Exception, e: + item = "Error in group_role API group %s role %s" % (group.name, role.name) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def update( self, trans, id, group_id, **kwd ): + """ + PUT /api/groups/{encoded_group_id}/roles/{encoded_role_id} + Adds a role to a group + """ + role_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_role_id = trans.security.decode_id( role_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) + for gra in group.roles: + if gra.role == role: + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) + if not item: + gra = trans.app.model.GroupRoleAssociation( group, role ) + # Add GroupRoleAssociation + trans.sa_session.add( gra ) + trans.sa_session.flush() + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) + except Exception, e: + item = "Error in group_role API Adding role %s to group %s" % (role.name,group.name) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def delete( self, trans, id, group_id, **kwd ): + """ + DELETE /api/groups/{encoded_group_id}/roles/{encoded_role_id} + Removes a role from a group + """ + role_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_role_id = trans.security.decode_id( role_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) + for gra in group.roles: + if gra.role == role: + trans.sa_session.delete( gra ) + trans.sa_session.flush() + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) + if not item: + item = "role %s not in group %s" % (role.name,group.name) + except Exception, e: + item = "Error in group_role API Removing role %s from group %s" % (role.name,group.name) + log.error(item + ": %s" % str(e)) + return item diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/api/group_users.py --- /dev/null +++ b/lib/galaxy/web/api/group_users.py @@ -0,0 +1,124 @@ +""" +API operations on Group objects. +""" +import logging +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy import web + +log = logging.getLogger( __name__ ) + +class GroupUsersAPIController( BaseAPIController ): + + @web.expose_api + @web.require_admin + def index( self, trans, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/users + Displays a collection (list) of groups. + """ + decoded_group_id = trans.security.decode_id( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + rval = [] + try: + for uga in group.users: + user = uga.user + encoded_id = trans.security.encode_id( user.id ) + rval.append( dict( id = encoded_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=encoded_id, ) ) ) + except Exception, e: + rval = "Error in group API at listing users" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 + return rval + + @web.expose_api + @web.require_admin + def show( self, trans, id, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/users/{encoded_user_id} + Displays information about a group user. + """ + user_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_user_id = trans.security.decode_id( user_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) + for uga in group.users: + if uga.user == user: + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This + if not item: + item = "user %s not in group %s" % (user.email,group.name) + except Exception, e: + item = "Error in group_user API group %s user %s" % (group.name, user.email) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def update( self, trans, id, group_id, **kwd ): + """ + PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + Adds a user to a group + """ + user_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_user_id = trans.security.decode_id( user_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) + for uga in group.users: + if uga.user == user: + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) + if not item: + uga = trans.app.model.UserGroupAssociation( user, group ) + # Add UserGroupAssociations + trans.sa_session.add( uga ) + trans.sa_session.flush() + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) + except Exception, e: + item = "Error in group_user API Adding user %s to group %s" % (user.email,group.name) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def delete( self, trans, id, group_id, **kwd ): + """ + DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + Removes a user from a group + """ + user_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_user_id = trans.security.decode_id( user_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) + for uga in group.users: + if uga.user == user: + trans.sa_session.delete( uga ) + trans.sa_session.flush() + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) + if not item: + item = "user %s not in group %s" % (user.email,group.name) + except Exception, e: + item = "Error in group_user API Removing user %s from group %s" % (user.email,group.name) + log.error(item + ": %s" % str(e)) + return item diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/api/groups.py --- /dev/null +++ b/lib/galaxy/web/api/groups.py @@ -0,0 +1,128 @@ +""" +API operations on Group objects. +""" +import logging +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy import web + + +log = logging.getLogger( __name__ ) + + +class GroupAPIController( BaseAPIController ): + + @web.expose_api + @web.require_admin + def index( self, trans, **kwd ): + """ + GET /api/groups + Displays a collection (list) of groups. + """ + rval = [] + for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted == False ): + if trans.user_is_admin(): + item = group.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) + encoded_id = trans.security.encode_id( group.id ) + item['url'] = url_for( 'group', id=encoded_id ) + rval.append( item ) + return rval + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + POST /api/groups + Creates a new group. + """ + log.info("groups payload%s\n" % (payload)) + if not trans.user_is_admin(): + trans.response.status = 403 + return "You are not authorized to create a new group." + name = payload.get( 'name', None ) + if not name: + trans.response.status = 400 + return "Enter a valid name" + if trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first(): + trans.response.status = 400 + return "A group with that name already exists" + + group = trans.app.model.Group( name=name ) + trans.sa_session.add( group ) + user_ids = payload.get( 'user_ids', [] ) + for i in user_ids: + log.info("user_id: %s\n" % (i )) + log.info("%s %s\n" % (i, trans.security.decode_id( i ) )) + users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ] + role_ids = payload.get( 'role_ids', [] ) + roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ] + trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users ) + """ + # Create the UserGroupAssociations + for user in users: + trans.app.security_agent.associate_user_group( user, group ) + # Create the GroupRoleAssociations + for role in roles: + trans.app.security_agent.associate_group_role( group, role ) + """ + trans.sa_session.flush() + encoded_id = trans.security.encode_id( group.id ) + item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) + item['url'] = url_for( 'group', id=encoded_id ) + return [ item ] + + @web.expose_api + @web.require_admin + def show( self, trans, id, **kwd ): + """ + GET /api/groups/{encoded_group_id} + Displays information about a group. + """ + group_id = id + try: + decoded_group_id = trans.security.decode_id( group_id ) + except TypeError: + trans.response.status = 400 + return "Malformed group id ( %s ) specified, unable to decode." % str( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) + item['url'] = url_for( 'group', id=group_id ) + item['users_url'] = url_for( 'group_users', group_id=group_id ) + item['roles_url'] = url_for( 'group_roles', group_id=group_id ) + return item + + @web.expose_api + @web.require_admin + def update( self, trans, id, payload, **kwd ): + """ + PUT /api/groups/{encoded_group_id} + Modifies a group. + """ + group_id = id + try: + decoded_group_id = trans.security.decode_id( group_id ) + except TypeError: + trans.response.status = 400 + return "Malformed group id ( %s ) specified, unable to decode." % str( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + name = payload.get( 'name', None ) + if name: + group.name = name + trans.sa_session.add(group) + user_ids = payload.get( 'user_ids', [] ) + users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ] + role_ids = payload.get( 'role_ids', [] ) + roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ] + trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users,delete_existing_assocs=False ) + trans.sa_session.flush() + diff -r 1cb2fdf2c7cf22d74ec46e6877609f7056372d7c -r d960803cbacc5cdeea67ffa9a26010adba1120d6 lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -122,6 +122,18 @@ 'permissions', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'user', + 'users', + controller='group_users', + name_prefix='group_', + path_prefix='/api/groups/:group_id', + parent_resources=dict( member_name='group', collection_name='groups' ) ) + webapp.api_mapper.resource( 'role', + 'roles', + controller='group_roles', + name_prefix='group_', + path_prefix='/api/groups/:group_id', + parent_resources=dict( member_name='group', collection_name='groups' ) ) webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -129,6 +141,7 @@ webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' ) webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) + webapp.api_mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) https://bitbucket.org/galaxy/galaxy-central/changeset/761c58466d97/ changeset: 761c58466d97 user: jmchilton date: 2012-08-09 22:18:00 summary: Merge. affected #: 19 files diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 buildbot_setup.sh --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -68,8 +68,13 @@ datatypes_conf.xml.sample universe_wsgi.ini.sample tool_data_table_conf.xml.sample +migrated_tools_conf.xml.sample +tool-data/shared/ensembl/builds.txt.sample +tool-data/shared/igv/igv_build_sites.txt.sample +tool-data/shared/ncbi/builds.txt.sample +tool-data/shared/rviewer/rviewer_build_sites.txt.sample tool-data/shared/ucsc/builds.txt.sample -migrated_tools_conf.xml.sample +tool-data/shared/ucsc/publicbuilds.txt.sample " DIRS=" diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 contrib/multiproccess.sh --- a/contrib/multiproccess.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash - -# copy this script to the top level galaxy directory and modify the following -# for your environment - -web_server_names=(web{0..2}) # server names: web0 web1 web2 -runner_server_names=(runner0) # server name: runner0 - -web_config='universe_wsgi.webapp.ini' -runner_config='universe_wsgi.runner.ini' - -# actually do the requested action - -if [ -z "$1" ]; then - echo "usage: multiprocess.sh <--daemon|--stop-daemon>" - exit 1 -fi - -for server_name in ${web_server_names[@]}; do - echo "[$server_name]" - python ./scripts/paster.py serve $web_config --server-name=$server_name --pid-file=$server_name.pid --log-file=$server_name.log $@ -done -for server_name in ${runner_server_names[@]}; do - echo "[$server_name]" - python ./scripts/paster.py serve $runner_config --server-name=$server_name --pid-file=$server_name.pid --log-file=$server_name.log $@ -done diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -2,7 +2,7 @@ Manage automatic installation of tools configured in the xxx.xml files in ~/scripts/migrate_tools (e.g., 0002_tools.xml). All of the tools were at some point included in the Galaxy distribution, but are now hosted in the main Galaxy tool shed. """ -import urllib2 +import urllib2, tempfile from galaxy.tools import ToolSection from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * @@ -132,7 +132,7 @@ 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 = generate_metadata_using_disk_files( self.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( self.app, relative_install_dir, repository_clone_url ) tool_shed_repository.metadata = metadata_dict self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() @@ -142,7 +142,7 @@ else: tool_dependencies = None if 'tools' in metadata_dict: - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() repository_tools_tups = get_repository_tools_tups( self.app, metadata_dict ) if repository_tools_tups: sample_files = metadata_dict.get( 'sample_files', [] ) @@ -195,7 +195,7 @@ tool_shed_repository.includes_datatypes = True self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() datatypes_config = get_config_from_repository( self.app, 'datatypes_conf.xml', tool_shed_repository, diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -4,6 +4,7 @@ import pkg_resources pkg_resources.require( "simplejson" ) +pkg_resources.require( "Mako" ) import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback import simplejson @@ -2344,7 +2345,7 @@ command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip() except Exception, e: # Modify exception message to be more clear - #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ) ) + #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ), ) raise if self.interpreter: # TODO: path munging for cluster/dataset server relocatability @@ -2441,7 +2442,7 @@ if code: return code( *args, **kwargs ) except Exception, e: - e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ) ) + e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ), ) raise def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -3,6 +3,7 @@ from datetime import date, datetime, timedelta from time import strftime, gmtime from galaxy import util +from galaxy.tools import parameters from galaxy.datatypes.checkers import * from galaxy.util.json import * from galaxy.tools.search import ToolBoxSearch @@ -247,6 +248,52 @@ except: pass return converter_path, display_path +def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): + """ + Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make + sure the files exist. + """ + invalid_files_and_errors_tups = [] + correction_msg = '' + for input_param in tool.input_params: + if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: + # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. + options = input_param.dynamic_options or input_param.options + if options: + if options.tool_data_table or options.missing_tool_data_table_name: + # Make sure the repository contains a tool_data_table_conf.xml.sample file. + sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) + if sample_tool_data_table_conf: + error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf ) + if error: + invalid_files_and_errors_tups.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) + else: + options.missing_tool_data_table_name = None + else: + correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " + correction_msg += "to the repository that includes the required entry to correct this error.<br/>" + invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + if options.index_file or options.missing_index_file: + # Make sure the repository contains the required xxx.loc.sample file. + index_file = options.index_file or options.missing_index_file + index_file_name = strip_path( index_file ) + sample_found = False + for sample_file in sample_files: + sample_file_name = strip_path( sample_file ) + if sample_file_name == '%s.sample' % index_file_name: + options.index_file = index_file_name + options.missing_index_file = None + if options.tool_data_table: + options.tool_data_table.missing_index_file = None + sample_found = True + break + if not sample_found: + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) + invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( app ) + return invalid_files_and_errors_tups def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): # Persist the current in-memory list of config_elems to a file named by the value of config_filename. fd, filename = tempfile.mkstemp() @@ -383,7 +430,7 @@ def create_tool_dependency_objects( app, tool_shed_repository, current_changeset_revision, set_status=True ): # Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository. tool_dependency_objects = [] - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_repository( app, 'tool_dependencies.xml', @@ -501,6 +548,76 @@ 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 ): + """ + 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). + """ + metadata_dict = {} + invalid_file_tups = [] + invalid_tool_configs = [] + tool_dependencies_config = None + datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir ) + if datatypes_config: + metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) + sample_files = get_sample_files_from_disk( repository_files_dir ) + 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 ): + if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: + if '.hg' in dirs: + dirs.remove( '.hg' ) + for name in files: + # Find all tool configs. + if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): + full_path = os.path.abspath( os.path.join( root, name ) ) + if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] + or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): + try: + # Make sure we're looking at a tool config and not a display application config or something else. + element_tree = util.parse_xml( full_path ) + element_tree_root = element_tree.getroot() + is_tool = element_tree_root.tag == 'tool' + except Exception, e: + print "Error parsing %s", full_path, ", exception: ", str( e ) + is_tool = False + if is_tool: + try: + tool = app.toolbox.load_tool( full_path ) + except Exception, e: + tool = None + invalid_tool_configs.append( name ) + if tool is not None: + invalid_files_and_errors_tups = check_tool_input_params( app, repository_files_dir, name, tool, sample_files ) + 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: + metadata_dict = generate_tool_metadata( os.path.join( root, name ), tool, repository_clone_url, metadata_dict ) + else: + invalid_file_tups.extend( invalid_files_and_errors_tups ) + # Find all exported workflows + elif name.endswith( '.ga' ): + relative_path = os.path.join( root, name ) + fp = open( relative_path, 'rb' ) + workflow_text = fp.read() + fp.close() + exported_workflow_dict = from_json_string( workflow_text ) + if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': + 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 ) + 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 + 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.""" requirements_dict = {} @@ -517,58 +634,6 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict -def generate_metadata_using_disk_files( toolbox, relative_install_dir, repository_clone_url ): - """Generate metadata using only the repository files on disk - files are not retrieved from the repository manifest.""" - metadata_dict = {} - tool_dependencies_config = None - datatypes_config = get_config_from_disk( 'datatypes_conf.xml', relative_install_dir ) - if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files = get_sample_files_from_disk( relative_install_dir ) - if sample_files: - metadata_dict[ 'sample_files' ] = sample_files - # Find all tool configs and exported workflows. - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - if '.hg' in dirs: - dirs.remove( '.hg' ) - for name in files: - # Find all tool configs. - if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) - element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' - except Exception, e: - log.debug( "Error parsing %s, exception: %s" % ( full_path, str( e ) ) ) - is_tool = False - if is_tool: - try: - tool = toolbox.load_tool( full_path ) - except Exception, e: - tool = None - if tool is not None: - tool_config = os.path.join( root, name ) - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) - # Find all exported workflows - elif name.endswith( '.ga' ): - relative_path = os.path.join( root, name ) - fp = open( relative_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - 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', relative_install_dir ) - if tool_dependencies_config: - metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) - return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for @@ -1266,7 +1331,7 @@ def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ): # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. metadata = repository.metadata - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() repository_dict = None datatypes_config = get_config_from_repository( app, 'datatypes_conf.xml', @@ -1293,17 +1358,6 @@ def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): # Load or deactivate proprietary datatype display applications app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) -def make_tmp_directory(): - tmp_dir = os.getenv( 'TMPDIR', '' ) - if tmp_dir: - tmp_dir = tmp_dir.strip() - else: - home_dir = os.getenv( 'HOME' ) - tmp_dir = os.path.join( home_dir, 'tmp' ) - work_dir = os.path.join( tmp_dir, 'work_tmp' ) - if not os.path.exists( work_dir ): - os.makedirs( work_dir ) - return work_dir def open_repository_files_folder( trans, folder_path ): try: files_list = get_repository_files( trans, folder_path ) diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -1,4 +1,4 @@ -import urllib2 +import urllib2, tempfile from galaxy.web.controllers.admin import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * @@ -522,7 +522,7 @@ # Get the tool_shed_repository from one of the tool_dependencies. message = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_repository( trans.app, 'tool_dependencies.xml', @@ -654,7 +654,7 @@ message += "from the installed repository's <b>Repository Actions</b> menu. " status = 'error' if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() # Install tool dependencies. update_tool_shed_repository_status( trans.app, tool_shed_repository, @@ -684,7 +684,7 @@ 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 = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) tool_shed_repository.metadata = metadata_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() @@ -695,7 +695,7 @@ repository_tools_tups = get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() repository_tools_tups = handle_missing_data_table_entry( trans.app, tool_shed_repository, tool_shed_repository.changeset_revision, @@ -726,7 +726,7 @@ tool_shed_repository.includes_datatypes = True trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() - work_dir = make_tmp_directory() + work_dir = tempfile.mkdtemp() datatypes_config = get_config_from_repository( trans.app, 'datatypes_conf.xml', tool_shed_repository, @@ -779,7 +779,7 @@ message = "The repository information has been updated." elif params.get( 'set_metadata_button', False ): repository_clone_url = generate_clone_url( trans, repository ) - metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) if metadata_dict: repository.metadata = metadata_dict trans.sa_session.add( repository ) @@ -1479,7 +1479,7 @@ update_repository( repo, latest_ctx_rev ) # Update the repository metadata. tool_shed = clean_tool_shed_url( tool_shed_url ) - metadata_dict = generate_metadata_using_disk_files( trans.app.toolbox, relative_install_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, relative_install_dir, repository_clone_url ) repository.metadata = metadata_dict # Update the repository changeset_revision in the database. repository.changeset_revision = latest_changeset_revision diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/web/controllers/data_admin.py --- a/lib/galaxy/web/controllers/data_admin.py +++ b/lib/galaxy/web/controllers/data_admin.py @@ -30,25 +30,28 @@ @web.expose @web.require_admin def manage_data( self, trans, **kwd ): - genomes = dict() if trans.app.config.get_bool( 'enable_beta_job_managers', False ) == False: - return trans.fill_template( '/admin/data_admin/betajob.mako' ) - for line in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data: - defstate = dict( state='Generate', style=self.jobstyles[ 'new' ] ) - indexers = dict( bowtie_indexes=defstate, bowtie2_indexes=defstate, bwa_indexes=defstate, perm_base_indexes=defstate, srma_indexes=defstate, sam_fa_indexes=defstate ) - dbkey = line[0] - name = line[2] - indexers[ 'name' ] = name - indexers[ 'fapath' ] = line[3] - genomes[ dbkey ] = indexers - for table in [ 'bowtie_indexes', 'bowtie2_indexes', 'bwa_indexes', 'srma_indexes' ]: - for line in trans.app.tool_data_tables.data_tables[ table ].data: - dbkey = line[0] - genomes[ dbkey ][ table ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) - for line in trans.app.tool_data_tables.data_tables[ 'sam_fa_indexes' ].data: - genomes[ line[1] ][ 'sam_fa_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) - for line in trans.app.tool_data_tables.data_tables[ 'perm_base_indexes' ].data: - genomes[ line[1].split(':')[0] ][ 'perm_base_indexes' ] = dict( state='Generated', style=self.jobstyles[ 'done' ] ) + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.' ) + if 'all_fasta' not in trans.app.tool_data_tables.data_tables: + return trans.fill_template( '/admin/data_admin/generic_error.mako', message='The local data manager requires that an all_fasta entry exists in your tool_data_table_conf.xml.' ) + indextable = {} + dbkeys = [] + labels = { 'bowtie_indexes': 'Bowtie', 'bowtie2_indexes': 'Bowtie 2', 'bwa_indexes': 'BWA', 'srma_indexes': 'Picard', 'sam_fa_indexes': 'SAM', 'perm_base_indexes': 'PerM' } + tablenames = { 'Bowtie': 'bowtie_indexes', 'Bowtie 2': 'bowtie2_indexes', 'BWA': 'bwa_indexes', 'Picard': 'srma_indexes', 'SAM': 'sam_fa_indexes', 'PerM': 'perm_base_indexes' } + indexfuncs = dict( bowtie_indexes='bowtie', bowtie2_indexes='bowtie2', bwa_indexes='bwa', srma_indexes='picard', sam_fa_indexes='sam', perm_base_indexes='perm' ) + for genome in trans.app.tool_data_tables.data_tables[ 'all_fasta' ].data: + dbkey = genome[0] + dbkeys.append( dbkey ) + indextable[ dbkey ] = dict( indexes=dict(), name=genome[2], path=genome[3] ) + for genome in indextable: + for label in labels: + indextable[ genome ][ 'indexes' ][ label ] = 'Generate' + if label not in trans.app.tool_data_tables.data_tables: + indextable[ genome ][ 'indexes' ][ label ] = 'Disabled' + else: + for row in trans.app.tool_data_tables.data_tables[ label ].data: + if genome in row or row[0].startswith( genome ): + indextable[ genome ][ 'indexes' ][ label ] = 'Generated' jobgrid = [] sa_session = trans.app.model.context.current jobs = sa_session.query( model.GenomeIndexToolData ).order_by( model.GenomeIndexToolData.created_time.desc() ).filter_by( user_id=trans.get_user().id ).group_by( model.GenomeIndexToolData.deferred ).limit( 20 ).all() @@ -65,7 +68,8 @@ jobtype = 'index' indexers = ', '.join( params['indexes'] ) jobgrid.append( dict( jobtype=jobtype, indexers=indexers, rowclass=state, deferred=job.deferred.id, state=state, intname=job.deferred.params[ 'intname' ], dbkey=job.deferred.params[ 'dbkey' ] ) ) - return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, genomes=genomes ) + styles = dict( Generate=self.jobstyles['new'], Generated=self.jobstyles['ok'], Disabled=self.jobstyles['error'] ) + return trans.fill_template( '/admin/data_admin/local_data.mako', jobgrid=jobgrid, indextable=indextable, labels=labels, dbkeys=dbkeys, styles=styles, indexfuncs=indexfuncs ) @web.expose @web.require_admin diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -655,7 +655,7 @@ 'name': module.get_name(), 'tool_id': module.get_tool_id(), 'tool_state': module.get_state(), - 'tooltip': module.get_tooltip(), + 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), 'form_html': module.get_config_form(), @@ -732,7 +732,7 @@ 'tool_id': module.get_tool_id(), 'name': module.get_name(), 'tool_state': module.get_state(), - 'tooltip': module.get_tooltip(), + 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), 'tool_errors': module.get_errors(), 'data_inputs': module.get_data_inputs(), 'data_outputs': module.get_data_outputs(), diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -1,15 +1,13 @@ -import os, string, socket, logging, simplejson, binascii +import os, string, socket, logging, simplejson, binascii, tempfile from time import strftime from datetime import * from galaxy.datatypes.checkers import * from galaxy.tools import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.hash_util import * -from galaxy.util.shed_util import clone_repository, copy_sample_file, generate_datatypes_metadata, generate_tool_dependency_metadata, generate_tool_metadata -from galaxy.util.shed_util import generate_workflow_metadata, get_changectx_for_changeset, get_config, get_config_from_disk, get_configured_ui -from galaxy.util.shed_util import get_named_tmpfile_from_ctx, get_sample_files_from_disk, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH -from galaxy.util.shed_util import make_tmp_directory, NOT_TOOL_CONFIGS, reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path, to_html_escaped -from galaxy.util.shed_util import to_html_str, update_repository +from galaxy.util.shed_util import clone_repository, generate_metadata_for_changeset_revision, get_changectx_for_changeset, get_config_from_disk +from galaxy.util.shed_util import get_configured_ui, get_named_tmpfile_from_ctx, handle_sample_tool_data_table_conf_file, INITIAL_CHANGELOG_HASH +from galaxy.util.shed_util import reset_tool_data_tables, reversed_upper_bounded_changelog, strip_path from galaxy.web.base.controller import * from galaxy.webapps.community import model from galaxy.model.orm import * @@ -107,11 +105,8 @@ trans.sa_session.flush() return item_rating -## ---- Utility methods ------------------------------------------------------- - 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. + # 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 ) @@ -120,57 +115,24 @@ 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. + # 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 ] ) + 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 build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True ): - """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository.""" - repo = hg.repository( get_configured_ui(), repository.repo_path ) - options = [] - changeset_tups = [] - refresh_on_change_values = [] - for repository_metadata in repository.downloadable_revisions: - changeset_revision = repository_metadata.changeset_revision - ctx = get_changectx_for_changeset( repo, changeset_revision ) - if ctx: - rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) - else: - rev = '-1' - label = "-1:%s" % changeset_revision - changeset_tups.append( ( rev, label, changeset_revision ) ) - refresh_on_change_values.append( changeset_revision ) - # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. - for changeset_tup in sorted( changeset_tups ): - # Display the latest revision first. - options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) - if add_id_to_name: - name = 'changeset_revision_%d' % repository.id - else: - name = 'changeset_revision' - select_field = SelectField( name=name, - refresh_on_change=True, - refresh_on_change_values=refresh_on_change_values ) - for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option( option_tup[0], option_tup[1], selected=selected ) - return select_field -def changeset_is_downloadable( metadata_dict ): - # A RepositoryMetadata record will be created if metadata_dict includes only invalid stuff like 'invalid_tools', but in this case - # it won't be downloadable. - return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict 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 ) @@ -188,60 +150,12 @@ if user_email in admin_users: return True return False -def check_tool_input_params( trans, repo_dir, tool_config, tool, sample_files, invalid_files ): - """ - Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make - sure the files exist. - """ - can_set_metadata = True - correction_msg = '' - for input_param in tool.input_params: - if isinstance( input_param, tools.parameters.basic.SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options: - if options.tool_data_table or options.missing_tool_data_table_name: - # Make sure the repository contains a tool_data_table_conf.xml.sample file. - sample_tool_data_table_conf = get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) - if sample_tool_data_table_conf: - error, correction_msg = handle_sample_tool_data_table_conf_file( trans, sample_tool_data_table_conf ) - if error: - can_set_metadata = False - invalid_files.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) - else: - options.missing_tool_data_table_name = None - else: - can_set_metadata = False - correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " - correction_msg += "to the repository that includes the required entry to correct this error.<br/>" - invalid_files.append( ( tool_config, correction_msg ) ) - if options.index_file or options.missing_index_file: - # Make sure the repository contains the required xxx.loc.sample file. - index_file = options.index_file or options.missing_index_file - index_file_name = strip_path( index_file ) - sample_found = False - for sample_file in sample_files: - sample_file_name = strip_path( sample_file ) - if sample_file_name == '%s.sample' % index_file_name: - options.index_file = index_file_name - options.missing_index_file = None - if options.tool_data_table: - options.tool_data_table.missing_index_file = None - sample_found = True - break - if not sample_found: - can_set_metadata = False - correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) - invalid_files.append( ( tool_config, correction_msg ) ) - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( trans.app ) - return can_set_metadata, invalid_files def clean_repository_metadata( trans, id, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have a changeset_revision that is not in changeset_revisions. # 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 = [] + 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, @@ -251,6 +165,9 @@ 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 @@ -369,14 +286,19 @@ return file_path return None def create_or_update_repository_metadata( trans, id, repository, changeset_revision, metadata_dict ): + downloadable = is_downloadable( metadata_dict ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: repository_metadata.metadata = metadata_dict + repository_metadata.downloadable = downloadable else: - repository_metadata = trans.model.RepositoryMetadata( repository.id, changeset_revision, metadata_dict ) - repository_metadata.downloadable = changeset_is_downloadable( metadata_dict ) + repository_metadata = trans.model.RepositoryMetadata( repository_id=repository.id, + changeset_revision=changeset_revision, + metadata=metadata_dict, + downloadable=downloadable ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() + return repository_metadata def generate_clone_url( trans, repository_id ): """Generate the URL for cloning a repository.""" repository = get_repository( trans, repository_id ) @@ -387,69 +309,6 @@ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) -def generate_metadata_for_changeset_revision( trans, repository_files_dir, repository_clone_url ): - """ - 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). - """ - metadata_dict = {} - invalid_files = [] - invalid_tool_configs = [] - tool_dependencies_config = None - datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repository_files_dir ) - if datatypes_config: - metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) - sample_files = get_sample_files_from_disk( repository_files_dir ) - 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 ): - if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: - if '.hg' in dirs: - dirs.remove( '.hg' ) - for name in files: - # Find all tool configs. - if name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): - full_path = os.path.abspath( os.path.join( root, name ) ) - if not ( check_binary( full_path ) or check_image( full_path ) or check_gzip( full_path )[ 0 ] - or check_bz2( full_path )[ 0 ] or check_zip( full_path ) ): - try: - # Make sure we're looking at a tool config and not a display application config or something else. - element_tree = util.parse_xml( full_path ) - element_tree_root = element_tree.getroot() - is_tool = element_tree_root.tag == 'tool' - except Exception, e: - print "Error parsing %s", full_path, ", exception: ", str( e ) - is_tool = False - if is_tool: - try: - tool = trans.app.toolbox.load_tool( full_path ) - tool_config = os.path.join( root, name ) - except Exception, e: - tool = None - invalid_tool_configs.append( name ) - if tool is not None: - can_set_metadata, invalid_files = check_tool_input_params( trans, repository_files_dir, tool_config, tool, sample_files, invalid_files ) - if can_set_metadata: - metadata_dict = generate_tool_metadata( tool_config, tool, repository_clone_url, metadata_dict ) - # Find all exported workflows - elif name.endswith( '.ga' ): - relative_path = os.path.join( root, name ) - fp = open( relative_path, 'rb' ) - workflow_text = fp.read() - fp.close() - exported_workflow_dict = from_json_string( workflow_text ) - if 'a_galaxy_workflow' in exported_workflow_dict and exported_workflow_dict[ 'a_galaxy_workflow' ] == 'true': - 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 ) - 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 - return metadata_dict, invalid_files def generate_tool_guid( trans, repository, tool ): """ Generate a guid for the received tool. The form of the guid is @@ -588,10 +447,23 @@ .first() def get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ): """Get metadata for a specified repository change set from the database""" - return trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), - trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ - .first() + # Make sure there are no duplicate records, and return the single unique record for the changeset_revision. Duplicate records were somehow + # creatd in the past. This may or may not be resolved, so when it is confirmed that the cause of duplicate records has been corrected, tweak + # this method accordingly. + all_metadata_records = trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( and_( trans.model.RepositoryMetadata.table.c.repository_id == trans.security.decode_id( id ), + trans.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) ) \ + .order_by( trans.model.RepositoryMetadata.table.c.update_time.desc() ) \ + .all() + if len( all_metadata_records ) > 1: + # Delete all recrds older than the last one updated. + for repository_metadata in all_metadata_records[ 1: ]: + trans.sa_session.delete( repository_metadata ) + trans.sa_session.flush() + return all_metadata_records[ 0 ] + elif all_metadata_records: + return all_metadata_records[ 0 ] + return None def get_repository_metadata_by_id( trans, id ): """Get repository metadata from the database""" return trans.sa_session.query( trans.model.RepositoryMetadata ).get( trans.security.decode_id( id ) ) @@ -700,6 +572,8 @@ util.send_mail( frm, to, subject, body, trans.app.config ) except Exception, e: log.exception( "An error occurred sending a tool shed repository update alert by email." ) +def is_downloadable( metadata_dict ): + return 'datatypes' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict def load_tool( trans, config_file ): """Load a single tool from the file named by `config_file` and return an instance of `Tool`.""" # Parse XML configuration file and get the root element @@ -762,7 +636,7 @@ ctx = get_changectx_for_changeset( repo, changeset_revision ) tool = None message = '' - work_dir = make_tmp_directory() + 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 @@ -913,7 +787,7 @@ print "Cloning repository revision: ", 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_files = generate_metadata_for_changeset_revision( trans, work_dir, repository_clone_url ) + current_metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, work_dir, repository_clone_url ) if current_metadata_dict: if not metadata_changeset_revision and not metadata_dict: # We're at the first change set in the change log. @@ -935,7 +809,7 @@ elif comparison == 'not equal and not subset': metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = current_changeset_revision ancestor_metadata_dict = current_metadata_dict @@ -947,7 +821,7 @@ metadata_changeset_revision = current_changeset_revision metadata_dict = current_metadata_dict # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None @@ -958,7 +832,7 @@ metadata_dict = ancestor_metadata_dict if not ctx.children(): # We're at the end of the change log. - create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) + repository_metadata = create_or_update_repository_metadata( trans, id, repository, metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None @@ -968,8 +842,9 @@ except: pass # Delete all repository_metadata records for this repository that do not have a changeset_revision value in changeset_revisions. - clean_repository_metadata( trans, id, changeset_revisions ) - add_repository_metadata_tool_versions( trans, id, 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 ) 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 @@ -980,46 +855,60 @@ repository_clone_url = generate_clone_url( trans, trans.security.encode_id( repository.id ) ) repo_dir = repository.repo_path repo = hg.repository( get_configured_ui(), repo_dir ) - metadata_dict, invalid_files = generate_metadata_for_changeset_revision( trans, repo_dir, repository_clone_url ) + metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( trans.app, repo_dir, repository_clone_url ) 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 = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - try: - trans.sa_session.flush() - # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: - handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) - except TypeError, e: - message = "Unable to save metadata for this repository, exception: %s" % str( e ) - status = 'error' + repository_metadata = create_or_update_repository_metadata( trans, + trans.security.encode_id( repository.id ), + repository, + repository.tip, + metadata_dict ) + # If this is the first record stored for this repository, see if we need to send any email alerts. + if len( repository.downloadable_revisions ) == 1: + handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: repository_metadata = get_latest_repository_metadata( trans, repository.id ) if repository_metadata: + downloadable = is_downloadable( metadata_dict ) # Update the last saved repository_metadata table row. repository_metadata.changeset_revision = repository.tip repository_metadata.metadata = metadata_dict - repository_metadata.downloadable = changeset_is_downloadable( metadata_dict ) + repository_metadata.downloadable = downloadable trans.sa_session.add( repository_metadata ) trans.sa_session.flush() else: # There are no tools in the repository, and we're setting metadata on the repository tip. - repository_metadata = trans.model.RepositoryMetadata( repository.id, repository.tip, metadata_dict ) - trans.sa_session.add( repository_metadata ) - trans.sa_session.flush() - elif len( repo ) == 1 and not invalid_files: + repository_metadata = create_or_update_repository_metadata( trans, + trans.security.encode_id( repository.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: + 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 ) + 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." status = "error" - if invalid_files: + if invalid_file_tups: if metadata_dict: message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip ) message += "Correct the following problems if necessary and reset metadata.<br/>" else: message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip ) message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.<br/>" - for itc_tup in invalid_files: + for itc_tup in invalid_file_tups: tool_file, exception_msg = itc_tup if exception_msg.find( 'No such file or directory' ) >= 0: exception_items = exception_msg.split() diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -9,8 +9,8 @@ from galaxy.web.framework.helpers import time_ago, iff, grids 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, make_tmp_directory, NOT_TOOL_CONFIGS -from galaxy.util.shed_util import open_repository_files_folder, reversed_lower_upper_bounded_changelog, strip_path +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.tool_shed.encoding_util import * from common import * @@ -113,7 +113,7 @@ grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): """Display a SelectField whose options are the changeset_revision strings of all downloadable_revisions of this repository.""" - select_field = build_changeset_revision_select_field( trans, repository ) + select_field = build_changeset_revision_select_field( trans, repository, downloadable_only=False ) if len( select_field.options ) > 1: return select_field.get_html() return repository.revision @@ -268,7 +268,7 @@ grids.GridColumn.__init__( self, col_name ) def get_value( self, trans, grid, repository ): """Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository.""" - select_field = build_changeset_revision_select_field( trans, repository ) + select_field = build_changeset_revision_select_field( trans, repository, downloadable_only=True ) if len( select_field.options ) > 1: return select_field.get_html() return repository.revision @@ -1346,19 +1346,14 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) 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_files, deleted_sample_files = generate_metadata_for_changeset_revision( trans, - repo, - repository_id, - ctx, - changeset_revision, - repo_dir, - updating_tip=changeset_revision==repository.tip ) - for invalid_file_tup in invalid_files: + 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: @@ -1554,7 +1549,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -1657,7 +1653,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) return trans.fill_template( '/webapps/community/repository/preview_tools_in_changeset.mako', repository=repository, repository_metadata_id=repository_metadata_id, @@ -2128,7 +2125,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) revision_label = get_revision_label( trans, repository, changeset_revision ) repository_metadata = get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -2185,7 +2183,8 @@ changeset_revision_select_field = build_changeset_revision_select_field( trans, repository, selected_value=changeset_revision, - add_id_to_name=False ) + add_id_to_name=False, + downloadable_only=False ) return trans.fill_template( "/webapps/community/repository/view_tool_metadata.mako", repository=repository, tool=tool, @@ -2197,3 +2196,42 @@ webapp=webapp, message=message, status=status ) + +# ----- Utility methods ----- +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, downloadable_only=False ): + """Build a SelectField whose options are the changeset_rev strings of all downloadable revisions of the received repository.""" + repo = hg.repository( get_configured_ui(), repository.repo_path ) + options = [] + changeset_tups = [] + refresh_on_change_values = [] + if downloadable_only: + repository_metadata_revisions = repository.downloadable_revisions + else: + repository_metadata_revisions = repository.metadata_revisions + for repository_metadata in repository_metadata_revisions: + changeset_revision = repository_metadata.changeset_revision + ctx = get_changectx_for_changeset( repo, changeset_revision ) + if ctx: + rev = '%04d' % ctx.rev() + label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + else: + rev = '-1' + label = "-1:%s" % changeset_revision + changeset_tups.append( ( rev, label, changeset_revision ) ) + refresh_on_change_values.append( changeset_revision ) + # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, + # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. + for changeset_tup in sorted( changeset_tups ): + # Display the latest revision first. + options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) + if add_id_to_name: + name = 'changeset_revision_%d' % repository.id + else: + name = 'changeset_revision' + select_field = SelectField( name=name, + refresh_on_change=True, + refresh_on_change_values=refresh_on_change_values ) + for option_tup in options: + selected = selected_value and option_tup[1] == selected_value + select_field.add_option( option_tup[0], option_tup[1], selected=selected ) + return select_field diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/webapps/community/model/__init__.py --- a/lib/galaxy/webapps/community/model/__init__.py +++ b/lib/galaxy/webapps/community/model/__init__.py @@ -166,12 +166,13 @@ fp.close() class RepositoryMetadata( object ): - def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False ): + def __init__( self, repository_id=None, changeset_revision=None, metadata=None, tool_versions=None, malicious=False, downloadable=False ): self.repository_id = repository_id self.changeset_revision = changeset_revision self.metadata = metadata or dict() self.tool_versions = tool_versions or dict() self.malicious = malicious + self.downloadable = downloadable class ItemRatingAssociation( object ): def __init__( self, id=None, user=None, item=None, rating=0, comment='' ): diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -49,7 +49,7 @@ return self.name def get_tool_id( self ): return None - def get_tooltip( self ): + def get_tooltip( self, static_path='' ): return None ## ---- Configuration time ----------------------------------------------- @@ -258,8 +258,8 @@ return self.state.encode( self.tool, self.trans.app, secure=secure ) def get_errors( self ): return self.errors - def get_tooltip( self ): - return self.tool.help + def get_tooltip( self, static_path='' ): + return self.tool.help.render( static_path=static_path ) def get_data_inputs( self ): data_inputs = [] def callback( input, value, prefixed_name, prefixed_label ): diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/admin/data_admin/betajob.mako --- a/templates/admin/data_admin/betajob.mako +++ /dev/null @@ -1,35 +0,0 @@ -<%inherit file="/base.mako"/> -<%namespace file="/message.mako" import="render_msg" /> -<%namespace file="/library/common/common.mako" import="common_javascripts" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False - self.active_view="user" - self.overlay_visible=False - self.has_accessible_datasets = False -%> -</%def> -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "autocomplete_tagging" )} -</%def> -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js("jquery.autocomplete", "autocomplete_tagging" )} -</%def> -## -## Override methods from base.mako and base_panels.mako -## -<p class="panel-error-message">This feature requires that enable_beta_job_managers be set to True in your Galaxy configuration.</p> \ No newline at end of file diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/admin/data_admin/generic_error.mako --- /dev/null +++ b/templates/admin/data_admin/generic_error.mako @@ -0,0 +1,35 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/library/common/common.mako" import="common_javascripts" /> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/galaxy/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False + self.active_view="user" + self.overlay_visible=False + self.has_accessible_datasets = False +%> +</%def> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "autocomplete_tagging" )} +</%def> +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js("jquery.autocomplete", "autocomplete_tagging" )} +</%def> +## +## Override methods from base.mako and base_panels.mako +## +<p class="panel-error-message">${message}</p> \ No newline at end of file diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/admin/data_admin/local_data.mako --- a/templates/admin/data_admin/local_data.mako +++ b/templates/admin/data_admin/local_data.mako @@ -44,6 +44,7 @@ td, th { padding-left: 10px; padding-right: 10px; } td.state-color-new { text-decoration: underline; } td.panel-done-message { background-image: none; padding: 0px 10px 0px 10px; } + td.panel-error-message { background-image: none; padding: 0px 10px 0px 10px; } </style><div class="toolForm"> %if message: @@ -52,19 +53,23 @@ <div class="toolFormTitle">Currently tracked builds <a class="action-button" href="${h.url_for( controller='data_admin', action='add_genome' )}">Add new</a></div><div class="toolFormBody"><h2>Locally cached data:</h2> - <h3>NOTE: Indexers queued here will not be reflected in the table until Galaxy is restarted.</h3> + <h3>NOTE: Indexes generated here will not be reflected in the table until Galaxy is restarted.</h3><table id="locfiles"> - <tr><th>Database ID</th><th>Name</th><th>Bowtie</th><th>Bowtie 2</th><th>BWA</th><th>Sam</th><th>Picard</th><th>PerM</th></tr> - %for dbkey in sorted(genomes.keys()): + <tr> + <th>DB Key</th> + <th>Name</th> + %for label in labels: + <th>${labels[label]}</th> + %endfor + </tr> + %for dbkey in sorted(dbkeys): <tr><td>${dbkey}</td> - <td>${genomes[dbkey]['name']}</td> - <td id="${dbkey}-bowtie" class="indexcell ${genomes[dbkey]['bowtie_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie_indexes']['state']}</td> - <td id="${dbkey}-bowtie2" class="indexcell ${genomes[dbkey]['bowtie2_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bowtie2" data-dbkey="${dbkey}">${genomes[dbkey]['bowtie2_indexes']['state']}</td> - <td id="${dbkey}-bwa" class="indexcell ${genomes[dbkey]['bwa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="bwa" data-dbkey="${dbkey}">${genomes[dbkey]['bwa_indexes']['state']}</td> - <td id="${dbkey}-sam" class="indexcell ${genomes[dbkey]['sam_fa_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="sam" data-dbkey="${dbkey}">${genomes[dbkey]['sam_fa_indexes']['state']}</td> - <td id="${dbkey}-picard" class="indexcell ${genomes[dbkey]['srma_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="picard" data-dbkey="${dbkey}">${genomes[dbkey]['srma_indexes']['state']}</td> - <td id="${dbkey}-perm" class="indexcell ${genomes[dbkey]['perm_base_indexes']['style']}" data-fapath="${genomes[dbkey]['fapath']}" data-longname="${genomes[dbkey]['name']}" data-index="perm" data-dbkey="${dbkey}">${genomes[dbkey]['perm_base_indexes']['state']}</td> + <td>${indextable[dbkey]['name']}</td> + %for label in labels: + <td id="${dbkey}-${indexfuncs[label]}" class="indexcell ${styles[indextable[dbkey]['indexes'][label]]}" data-fapath="${indextable[dbkey]['path']}" data-longname="${indextable[dbkey]['name']}" data-index="${indexfuncs[label]}" data-dbkey="${dbkey}">${indextable[dbkey]['indexes'][label]}</td> + %endfor + </tr> %endfor </table> @@ -124,6 +129,7 @@ jsondata["name"] = $('#job-' + jobid).attr('data-name'); jsondata["dbkey"] = $('#job-' + jobid).attr('data-dbkey'); jsondata["indexes"] = $('#job-' + jobid).attr('data-indexes'); + tdid = jq(jsondata["dbkey"] + '-' + jsondata["indexes"]); newhtml = makeNewHTML(jsondata); $('#job-' + jobid).replaceWith(newhtml); if ($.inArray(jsondata["status"], finalstates) == -1) { @@ -133,7 +139,7 @@ }); } if (jsondata["status"] == 'done' || jsondata["status"] == 'ok') { - elem = $('#' + jsondata["dbkey"] + '-' + jsondata["indexes"]); + elem = $(tdid); elem.html('Generated'); elem.attr('class', 'indexcell panel-done-message'); } @@ -156,5 +162,8 @@ } }); }); - + + function jq(id) { + return '#' + id.replace(/(:|\.)/g,'\\$1'); + } </script> \ No newline at end of file diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako --- a/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako +++ b/templates/webapps/community/admin/reset_metadata_on_selected_repositories.mako @@ -43,14 +43,17 @@ ${render_msg( message, status )} %endif +<div class="warningmessage"> + Resetting metadata may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. + Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not be helpful. Watch + the tool shed paster log to pass the time if necessary. +</div> + <div class="toolForm"><div class="toolFormTitle">Reset all metadata on each selected repository</div><form name="reset_metadata_on_selected_repositories" id="reset_metadata_on_selected_repositories" action="${h.url_for( controller='admin', action='reset_metadata_on_selected_repositories' )}" method="post" ><div class="form-row"> - Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. Resetting metadata - may take a while because this process clones each change set in each selected repository's change log to a temporary location on disk. - Wait until this page redirects after clicking the <b>Reset metadata on selected repositories</b> button, as doing anything else will not - be helpful. Watch the tool shed paster log to pass the time if necessary. + Check each repository for which you want to reset metadata. Repository names are followed by owners in parentheses. </div><div style="clear: both"></div><div class="form-row"> diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 templates/webapps/community/repository/tool_form.mako --- a/templates/webapps/community/repository/tool_form.mako +++ b/templates/webapps/community/repository/tool_form.mako @@ -186,12 +186,15 @@ <div class="toolHelp"><div class="toolHelpBody"><% + tool_help = tool.help + # Help is Mako template, so render using current static path. + tool_help = tool_help.render( static_path=h.url_for( '/static' ) ) # Convert to unicode to display non-ascii characters. - if type( tool.help ) is not unicode: - tool.help = unicode( tool.help, 'utf-8') + if type( tool_help ) is not unicode: + tool_help = unicode( tool_help, 'utf-8') %> - ${tool.help} - </div> + ${tool_help} + </div></div> %endif %else: diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 test/functional/test_library_templates.py --- a/test/functional/test_library_templates.py +++ b/test/functional/test_library_templates.py @@ -398,7 +398,7 @@ folder_id=self.security.encode_id( folder3.id ), upload_option='import_from_history', hda_ids=self.security.encode_id( hda.id ), - strings_displayed=[ '<input type="hidden" name="%s" value="Option1"/>' % select_field_name ] ) + strings_displayed=[ '<select name="%s" last_selected_value="Option1">' % select_field_name ] ) ldda = get_latest_ldda_by_name( filename ) assert ldda is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda from the database' self.browse_library( cntrller='library_admin', diff -r d960803cbacc5cdeea67ffa9a26010adba1120d6 -r 761c58466d97ba0d29af670daabc256aacf4dbb8 tools/new_operations/operation_filter.py --- a/tools/new_operations/operation_filter.py +++ b/tools/new_operations/operation_filter.py @@ -3,6 +3,9 @@ from galaxy import eggs from galaxy import jobs from galaxy.tools.parameters import DataToolParameter + +from galaxy.jobs.handler import JOB_ERROR + # Older py compatibility try: set() @@ -63,8 +66,8 @@ raise Exception( stderr ) except Exception, exc: - data.blurb = jobs.JOB_ERROR - data.state = jobs.JOB_ERROR + data.blurb = JOB_ERROR + data.state = JOB_ERROR ## def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): ## pass https://bitbucket.org/galaxy/galaxy-central/changeset/713ee9f0ae6a/ changeset: 713ee9f0ae6a user: dannon date: 2012-08-13 19:22:51 summary: Merge pull request. affected #: 5 files diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -544,7 +544,10 @@ else: return False -class Group( object ): +class Group( object, APIItem ): + api_collection_visible_keys = ( 'id', 'name' ) + api_element_visible_keys = ( 'id', 'name' ) + def __init__( self, name = None ): self.name = name self.deleted = False diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/api/group_roles.py --- /dev/null +++ b/lib/galaxy/web/api/group_roles.py @@ -0,0 +1,124 @@ +""" +API operations on Group objects. +""" +import logging +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy import web + +log = logging.getLogger( __name__ ) + +class GroupRolesAPIController( BaseAPIController ): + + @web.expose_api + @web.require_admin + def index( self, trans, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/roles + Displays a collection (list) of groups. + """ + decoded_group_id = trans.security.decode_id( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + rval = [] + try: + for gra in group.roles: + role = gra.role + encoded_id = trans.security.encode_id( role.id ) + rval.append( dict( id = encoded_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=encoded_id, ) ) ) + except Exception, e: + rval = "Error in group API at listing roles" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 + return rval + + @web.expose_api + @web.require_admin + def show( self, trans, id, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/roles/{encoded_role_id} + Displays information about a group role. + """ + role_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_role_id = trans.security.decode_id( role_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) + for gra in group.roles: + if gra.role == role: + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) # TODO Fix This + if not item: + item = "role %s not in group %s" % (role.name,group.name) + except Exception, e: + item = "Error in group_role API group %s role %s" % (group.name, role.name) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def update( self, trans, id, group_id, **kwd ): + """ + PUT /api/groups/{encoded_group_id}/roles/{encoded_role_id} + Adds a role to a group + """ + role_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_role_id = trans.security.decode_id( role_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) + for gra in group.roles: + if gra.role == role: + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) + if not item: + gra = trans.app.model.GroupRoleAssociation( group, role ) + # Add GroupRoleAssociation + trans.sa_session.add( gra ) + trans.sa_session.flush() + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) + except Exception, e: + item = "Error in group_role API Adding role %s to group %s" % (role.name,group.name) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def delete( self, trans, id, group_id, **kwd ): + """ + DELETE /api/groups/{encoded_group_id}/roles/{encoded_role_id} + Removes a role from a group + """ + role_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_role_id = trans.security.decode_id( role_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + role = trans.sa_session.query( trans.app.model.Role ).get( decoded_role_id ) + for gra in group.roles: + if gra.role == role: + trans.sa_session.delete( gra ) + trans.sa_session.flush() + item = dict( id = role_id, + name = role.name, + url = url_for( 'group_role', group_id=group_id, id=role_id) ) + if not item: + item = "role %s not in group %s" % (role.name,group.name) + except Exception, e: + item = "Error in group_role API Removing role %s from group %s" % (role.name,group.name) + log.error(item + ": %s" % str(e)) + return item diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/api/group_users.py --- /dev/null +++ b/lib/galaxy/web/api/group_users.py @@ -0,0 +1,124 @@ +""" +API operations on Group objects. +""" +import logging +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy import web + +log = logging.getLogger( __name__ ) + +class GroupUsersAPIController( BaseAPIController ): + + @web.expose_api + @web.require_admin + def index( self, trans, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/users + Displays a collection (list) of groups. + """ + decoded_group_id = trans.security.decode_id( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + rval = [] + try: + for uga in group.users: + user = uga.user + encoded_id = trans.security.encode_id( user.id ) + rval.append( dict( id = encoded_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=encoded_id, ) ) ) + except Exception, e: + rval = "Error in group API at listing users" + log.error( rval + ": %s" % str(e) ) + trans.response.status = 500 + return rval + + @web.expose_api + @web.require_admin + def show( self, trans, id, group_id, **kwd ): + """ + GET /api/groups/{encoded_group_id}/users/{encoded_user_id} + Displays information about a group user. + """ + user_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_user_id = trans.security.decode_id( user_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) + for uga in group.users: + if uga.user == user: + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) # TODO Fix This + if not item: + item = "user %s not in group %s" % (user.email,group.name) + except Exception, e: + item = "Error in group_user API group %s user %s" % (group.name, user.email) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def update( self, trans, id, group_id, **kwd ): + """ + PUT /api/groups/{encoded_group_id}/users/{encoded_user_id} + Adds a user to a group + """ + user_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_user_id = trans.security.decode_id( user_id ) + item = None + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) + for uga in group.users: + if uga.user == user: + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) + if not item: + uga = trans.app.model.UserGroupAssociation( user, group ) + # Add UserGroupAssociations + trans.sa_session.add( uga ) + trans.sa_session.flush() + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) + except Exception, e: + item = "Error in group_user API Adding user %s to group %s" % (user.email,group.name) + log.error(item + ": %s" % str(e)) + return item + + @web.expose_api + @web.require_admin + def delete( self, trans, id, group_id, **kwd ): + """ + DELETE /api/groups/{encoded_group_id}/users/{encoded_user_id} + Removes a user from a group + """ + user_id = id + decoded_group_id = trans.security.decode_id( group_id ) + decoded_user_id = trans.security.decode_id( user_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + user = trans.sa_session.query( trans.app.model.User ).get( decoded_user_id ) + for uga in group.users: + if uga.user == user: + trans.sa_session.delete( uga ) + trans.sa_session.flush() + item = dict( id = user_id, + email = user.email, + url = url_for( 'group_user', group_id=group_id, id=user_id) ) + if not item: + item = "user %s not in group %s" % (user.email,group.name) + except Exception, e: + item = "Error in group_user API Removing user %s from group %s" % (user.email,group.name) + log.error(item + ": %s" % str(e)) + return item diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/api/groups.py --- /dev/null +++ b/lib/galaxy/web/api/groups.py @@ -0,0 +1,128 @@ +""" +API operations on Group objects. +""" +import logging +from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy import web + + +log = logging.getLogger( __name__ ) + + +class GroupAPIController( BaseAPIController ): + + @web.expose_api + @web.require_admin + def index( self, trans, **kwd ): + """ + GET /api/groups + Displays a collection (list) of groups. + """ + rval = [] + for group in trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.deleted == False ): + if trans.user_is_admin(): + item = group.get_api_value( value_mapper={ 'id': trans.security.encode_id } ) + encoded_id = trans.security.encode_id( group.id ) + item['url'] = url_for( 'group', id=encoded_id ) + rval.append( item ) + return rval + + @web.expose_api + def create( self, trans, payload, **kwd ): + """ + POST /api/groups + Creates a new group. + """ + log.info("groups payload%s\n" % (payload)) + if not trans.user_is_admin(): + trans.response.status = 403 + return "You are not authorized to create a new group." + name = payload.get( 'name', None ) + if not name: + trans.response.status = 400 + return "Enter a valid name" + if trans.sa_session.query( trans.app.model.Group ).filter( trans.app.model.Group.table.c.name==name ).first(): + trans.response.status = 400 + return "A group with that name already exists" + + group = trans.app.model.Group( name=name ) + trans.sa_session.add( group ) + user_ids = payload.get( 'user_ids', [] ) + for i in user_ids: + log.info("user_id: %s\n" % (i )) + log.info("%s %s\n" % (i, trans.security.decode_id( i ) )) + users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ] + role_ids = payload.get( 'role_ids', [] ) + roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ] + trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users ) + """ + # Create the UserGroupAssociations + for user in users: + trans.app.security_agent.associate_user_group( user, group ) + # Create the GroupRoleAssociations + for role in roles: + trans.app.security_agent.associate_group_role( group, role ) + """ + trans.sa_session.flush() + encoded_id = trans.security.encode_id( group.id ) + item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) + item['url'] = url_for( 'group', id=encoded_id ) + return [ item ] + + @web.expose_api + @web.require_admin + def show( self, trans, id, **kwd ): + """ + GET /api/groups/{encoded_group_id} + Displays information about a group. + """ + group_id = id + try: + decoded_group_id = trans.security.decode_id( group_id ) + except TypeError: + trans.response.status = 400 + return "Malformed group id ( %s ) specified, unable to decode." % str( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + item = group.get_api_value( view='element', value_mapper={ 'id': trans.security.encode_id } ) + item['url'] = url_for( 'group', id=group_id ) + item['users_url'] = url_for( 'group_users', group_id=group_id ) + item['roles_url'] = url_for( 'group_roles', group_id=group_id ) + return item + + @web.expose_api + @web.require_admin + def update( self, trans, id, payload, **kwd ): + """ + PUT /api/groups/{encoded_group_id} + Modifies a group. + """ + group_id = id + try: + decoded_group_id = trans.security.decode_id( group_id ) + except TypeError: + trans.response.status = 400 + return "Malformed group id ( %s ) specified, unable to decode." % str( group_id ) + try: + group = trans.sa_session.query( trans.app.model.Group ).get( decoded_group_id ) + except: + group = None + if not group: + trans.response.status = 400 + return "Invalid group id ( %s ) specified." % str( group_id ) + name = payload.get( 'name', None ) + if name: + group.name = name + trans.sa_session.add(group) + user_ids = payload.get( 'user_ids', [] ) + users = [ trans.sa_session.query( trans.model.User ).get( trans.security.decode_id( i ) ) for i in user_ids ] + role_ids = payload.get( 'role_ids', [] ) + roles = [ trans.sa_session.query( trans.model.Role ).get( trans.security.decode_id( i ) ) for i in role_ids ] + trans.app.security_agent.set_entity_group_associations( groups=[ group ], roles=roles, users=users,delete_existing_assocs=False ) + trans.sa_session.flush() + diff -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 -r 713ee9f0ae6a005d8a283427c496c27f9f83c43b lib/galaxy/web/buildapp.py --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -122,6 +122,18 @@ 'permissions', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'user', + 'users', + controller='group_users', + name_prefix='group_', + path_prefix='/api/groups/:group_id', + parent_resources=dict( member_name='group', collection_name='groups' ) ) + webapp.api_mapper.resource( 'role', + 'roles', + controller='group_roles', + name_prefix='group_', + path_prefix='/api/groups/:group_id', + parent_resources=dict( member_name='group', collection_name='groups' ) ) webapp.api_mapper.resource( 'dataset', 'datasets', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) @@ -129,6 +141,7 @@ webapp.api_mapper.resource( 'form', 'forms', path_prefix='/api' ) webapp.api_mapper.resource( 'request_type', 'request_types', path_prefix='/api' ) webapp.api_mapper.resource( 'role', 'roles', path_prefix='/api' ) + webapp.api_mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) webapp.api_mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.api_mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) https://bitbucket.org/galaxy/galaxy-central/changeset/966a9b393b85/ changeset: 966a9b393b85 branch: add_requirement_tags_for_plink user: dannon date: 2012-08-13 19:23:54 summary: Branch close affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 13 Aug '12

13 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/afbff82a32e9/ changeset: afbff82a32e9 user: dannon date: 2012-08-13 18:59:17 summary: Fix convert_newlines and sep2tabs to return '0' lines in the event of an empty file, instead of blowing up. affected #: 1 file diff -r bb76489b554107f534df7e0f829e60308fea719a -r afbff82a32e98e9261b52c5415377c0ee5ecee1d lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -91,15 +91,16 @@ """ fd, temp_name = tempfile.mkstemp() fp = os.fdopen( fd, "wt" ) - for i, line in enumerate( file( fname, "U" ) ): + i = 0 + for i, line in enumerate( file( fname, "U" ), 1 ): fp.write( "%s\n" % line.rstrip( "\r\n" ) ) fp.close() if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. - return ( i + 1, None ) + return ( i, None ) else: - return ( i + 1, temp_name ) + return ( i, temp_name ) def sep2tabs( fname, in_place=True, patt="\\s+" ): """ @@ -115,7 +116,8 @@ regexp = re.compile( patt ) fd, temp_name = tempfile.mkstemp() fp = os.fdopen( fd, "wt" ) - for i, line in enumerate( file( fname ) ): + i = 0 + for i, line in enumerate( file( fname ), 1): line = line.rstrip( '\r\n' ) elems = regexp.split( line ) fp.write( "%s\n" % '\t'.join( elems ) ) @@ -123,9 +125,9 @@ if in_place: shutil.move( temp_name, fname ) # Return number of lines in file. - return ( i + 1, None ) + return ( i, None ) else: - return ( i + 1, temp_name ) + return ( i, temp_name ) def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ): """ https://bitbucket.org/galaxy/galaxy-central/changeset/fbefa0369895/ changeset: fbefa0369895 user: dannon date: 2012-08-13 19:00:09 summary: Whitespace cleanup. affected #: 1 file diff -r afbff82a32e98e9261b52c5415377c0ee5ecee1d -r fbefa03698959fc15d06d74ad9a2cf24f6001e63 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -8,7 +8,7 @@ from galaxy.datatypes.binary import unsniffable_binary_formats log = logging.getLogger(__name__) - + def get_test_fname(fname): """Returns test data filename""" path, name = os.path.split(__file__) @@ -79,7 +79,7 @@ def convert_newlines( fname, in_place=True ): """ - Converts in place a file from universal line endings + Converts in place a file from universal line endings to Posix line endings. >>> fname = get_test_fname('temp.txt') @@ -159,7 +159,7 @@ def get_headers( fname, sep, count=60, is_multi_byte=False ): """ Returns a list with the first 'count' lines split by 'sep' - + >>> fname = get_test_fname('complete.bed') >>> get_headers(fname,'\\t') [['chr7', '127475281', '127491632', 'NM_000230', '0', '+', '127486022', '127488767', '0', '3', '29,172,3225,', '0,10713,13126,'], ['chr7', '127486011', '127488900', 'D49487', '0', '+', '127486022', '127488767', '0', '2', '155,490,', '0,2399']] @@ -175,12 +175,12 @@ if idx == count: break return headers - + def is_column_based( fname, sep='\t', skip=0, is_multi_byte=False ): """ - Checks whether the file is column based with respect to a separator + Checks whether the file is column based with respect to a separator (defaults to tab separator). - + >>> fname = get_test_fname('test.gff') >>> is_column_based(fname) True @@ -288,7 +288,7 @@ """ Some classes may not have a sniff function, which is ok. In fact, the Tabular and Text classes are 2 examples of classes that should never have - a sniff function. Since these classes are default classes, they contain + a sniff function. Since these classes are default classes, they contain few rules to filter out data of other formats, so they should be called from this function after all other datatypes in sniff_order have not been successfully discovered. @@ -333,7 +333,7 @@ is_compressed = check_compressed_function( filename ) if is_compressed: break #found compression type - if is_compressed: + if is_compressed: if ext in AUTO_DETECT_EXTENSIONS: check_exts = COMPRESSION_DATATYPES[ compressed_type ] elif ext in COMPRESSED_EXTENSIONS: @@ -347,7 +347,7 @@ keep_compressed = True is_valid = True break - + if not is_compressed: is_valid = True elif not keep_compressed: @@ -373,13 +373,13 @@ def handle_uploaded_dataset_file( filename, datatypes_registry, ext = 'auto', is_multi_byte = False ): is_valid, ext = handle_compressed_file( filename, datatypes_registry, ext = ext ) - + if not is_valid: raise InappropriateDatasetContentError, 'The compressed uploaded file contains inappropriate content.' - + if ext in AUTO_DETECT_EXTENSIONS: ext = guess_ext( filename, sniff_order = datatypes_registry.sniff_order, is_multi_byte=is_multi_byte ) - + if check_binary( filename ): if ext not in unsniffable_binary_formats and not datatypes_registry.get_datatype_by_extension( ext ).sniff( filename ): raise InappropriateDatasetContentError, 'The binary uploaded file contains inappropriate content.' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Aug '12

10 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/05c643a133ec/ changeset: 05c643a133ec user: fubar date: 2012-08-11 01:36:29 summary: Unicode/raw for re.sub string in rgFastQC.py affected #: 1 file diff -r 0a800e817e84abba99331e784f622dd3ce54e900 -r 05c643a133ec9421c252647fb1eedc96f2940da5 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -56,7 +56,7 @@ cl.append('-c %s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = re.sub('[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) + fastqinfilename = re.sub(ru'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name) https://bitbucket.org/galaxy/galaxy-central/changeset/bb76489b5541/ changeset: bb76489b5541 user: fubar date: 2012-08-11 01:42:48 summary: Added unicode and raw flags to the re.sub string - not tested with unicode name yet.. affected #: 1 file diff -r 05c643a133ec9421c252647fb1eedc96f2940da5 -r bb76489b554107f534df7e0f829e60308fea719a tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -56,7 +56,7 @@ cl.append('-c %s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = re.sub(ru'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) + fastqinfilename = re.sub(ur'[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Aug '12

10 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/48560a3547e2/ changeset: 48560a3547e2 user: fubar date: 2012-08-11 01:21:45 summary: Add - and . to re.sub exclusion list for user supplied filename at Scott's suggestion and use _ as a substitute for all other characters so 'cd \/; rm -rf' becomes 'cd_____rm_-rf' FastQC wrapper should now be reasonably hard to pervert but user filenames will be at least vaguely recognizable... affected #: 1 file diff -r 18462a6cbf46566307eaa4fd33c8891b5979d699 -r 48560a3547e2bc8691f16d525fac117befe58829 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -1,4 +1,7 @@ """ +# added sanitizer for user supplied name +# removed shell and make cl a sequence for Popen call +# ross lazarus August 10 2012 in response to anon insecurity report wrapper for fastqc called as @@ -53,7 +56,7 @@ cl.append('-c %s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = re.sub('[^a-zA-Z0-9_]+', '', os.path.basename(self.opts.inputfilename)) + fastqinfilename = re.sub('[^a-zA-Z0-9_\-\.]', '_', os.path.basename(self.opts.inputfilename)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name) https://bitbucket.org/galaxy/galaxy-central/changeset/0a800e817e84/ changeset: 0a800e817e84 user: fubar date: 2012-08-11 01:22:57 summary: Branch merge affected #: 9 files diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -40,7 +40,18 @@ if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - # Append commands to copy job outputs based on from_work_dir attribute. + # -- Append commands to copy job outputs based on from_work_dir attribute. -- + + # Set up dict of dataset id --> output path; output path can be real or + # false depending on outputs_to_working_directory + output_paths = {} + for dataset_path in job_wrapper.get_output_fnames(): + path = dataset_path.real_path + if self.app.config.outputs_to_working_directory: + path = dataset_path.false_path + output_paths[ dataset_path.dataset_id ] = path + + # Walk job's output associations to find and use from_work_dir attributes. job = job_wrapper.get_job() job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) for dataset_assoc in job.output_datasets + job.output_library_datasets: @@ -53,12 +64,13 @@ # Copy from working dir to HDA. # TODO: move instead of copy to save time? source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir ) + destination = output_paths[ dataset.dataset_id ] if in_directory( source_file, job_wrapper.working_directory ): try: - commands += "; cp %s %s" % ( source_file, dataset.file_name ) - log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) ) + commands += "; cp %s %s" % ( source_file, destination ) + log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) except ( IOError, OSError ): - log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) ) + log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, destination ) ) else: # Security violation. log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -112,16 +112,30 @@ class Client(object): """ """ - def __init__(self, remote_host, job_id): + """ + """ + def __init__(self, remote_host, job_id, private_key=None): if not remote_host.endswith("/"): remote_host = remote_host + "/" + ## If we don't have an explicit private_key defined, check for + ## one embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_key_format = "https?://(.*)@.*/?" + private_key_match= re.match(private_key_format, remote_host) + if not private_key and private_key_match: + private_key = private_key_match.group(1) + remote_host = remote_host.replace("%s@" % private_key, '', 1) self.remote_host = remote_host self.job_id = job_id + self.private_key = private_key def url_open(self, request, data): return urllib2.urlopen(request, data) def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key data = urllib.urlencode(args) url = self.remote_host + command + "?" + data return url diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1083,7 +1083,9 @@ help_pages = self.help.findall( "page" ) help_header = self.help.text try: - self.help = Template( util.rst_to_html(self.help.text) ) + self.help = Template( util.rst_to_html(self.help.text), input_encoding='utf-8', + output_encoding='utf-8', default_filters=[ 'decode.utf8' ], + encoding_errors='replace' ) except: log.exception( "error in help for tool %s" % self.name ) # Multiple help page case @@ -1093,7 +1095,10 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer ) ) + self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer, + input_encoding='utf-8', output_encoding='utf-8', + default_filters=[ 'decode.utf8' ], + encoding_errors='replace' ) ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml +++ b/tools/rgenetics/rgCaCo.xml @@ -1,4 +1,5 @@ <tool id="rgCaCo1" name="Case Control:"> + <requirements><requirement type="package">plink</requirement></requirements><description>for unrelated subjects</description><command interpreter="python"> rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml +++ b/tools/rgenetics/rgClean.xml @@ -1,4 +1,5 @@ <tool id="rgClean1" name="Clean genotypes:"> + <requirements><requirement type="package">plink</requirement></requirements><description>filter markers, subjects</description><command interpreter="python"> diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml +++ b/tools/rgenetics/rgGLM.xml @@ -1,4 +1,5 @@ <tool id="rgGLM1" name="Linear Models:" version="0.2"> + <requirements><requirement type="package">plink</requirement></requirements><description>for genotype data</description><code file="rgGLM_code.py"/><command interpreter="python"> diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 tools/rgenetics/rgLDIndep.xml --- a/tools/rgenetics/rgLDIndep.xml +++ b/tools/rgenetics/rgLDIndep.xml @@ -1,4 +1,5 @@ <tool id="rgLDIndep1" name="LD Independent:"> + <requirements><requirement type="package">plink</requirement></requirements><code file="rgLDIndep_code.py"/><description>filter high LD pairs - decrease redundancy</description> diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -1,5 +1,6 @@ <tool id="rgQC1" name="QC reports:"> - + <requirements><requirement type="package">plink</requirement></requirements> + <description>Marker and Subject measures</description><command interpreter="python"> diff -r 48560a3547e2bc8691f16d525fac117befe58829 -r 0a800e817e84abba99331e784f622dd3ce54e900 tools/rgenetics/rgTDT.xml --- a/tools/rgenetics/rgTDT.xml +++ b/tools/rgenetics/rgTDT.xml @@ -1,4 +1,6 @@ <tool id="rgTDT1" name="Transmission Distortion:"> + <requirements><requirement type="package">plink</requirement></requirements> + <description>for family data</description><command interpreter="python"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Aug '12

10 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b612d9dcca9f/ changeset: b612d9dcca9f user: jmchilton date: 2012-08-10 00:25:35 summary: Implement a mechanism to secure access to lwr. If enabled on the server, a private token must be passed along with all interactions. This token may be specified as part of the job runner url as such: wintool = lwr://https://token@host:8913/ This token will not protect the client against a rouge server that has exploited say a DNS spoofing vulnerability. It is only meant as a mechanism for the lwr to ensure the client is authorized. This feature should be used in conjunction with SSL to prevent a "man-in-middle" from intercepting this token. affected #: 1 file diff -r 3b5db939aebe61addd6f0b8d0c14267cf16c4144 -r b612d9dcca9fd75f7dc9592cd64e385d3300e0bb lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -112,16 +112,30 @@ class Client(object): """ """ - def __init__(self, remote_host, job_id): + """ + """ + def __init__(self, remote_host, job_id, private_key=None): if not remote_host.endswith("/"): remote_host = remote_host + "/" + ## If we don't have an explicit private_key defined, check for + ## one embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_key_format = "https?://(.*)@.*/?" + private_key_match= re.match(private_key_format, remote_host) + if not private_key and private_key_match: + private_key = private_key_match.group(1) + remote_host = remote_host.replace("%s@" % private_key, '', 1) self.remote_host = remote_host self.job_id = job_id + self.private_key = private_key def url_open(self, request, data): return urllib2.urlopen(request, data) def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key data = urllib.urlencode(args) url = self.remote_host + command + "?" + data return url https://bitbucket.org/galaxy/galaxy-central/changeset/b24c67866f49/ changeset: b24c67866f49 user: natefoo date: 2012-08-10 20:35:44 summary: Merged in jmchilton/galaxy-central-lwr-enhancement-1 (pull request #57) affected #: 1 file diff -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 -r b24c67866f4942fddf50be60aa66b39f34643a55 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -112,16 +112,30 @@ class Client(object): """ """ - def __init__(self, remote_host, job_id): + """ + """ + def __init__(self, remote_host, job_id, private_key=None): if not remote_host.endswith("/"): remote_host = remote_host + "/" + ## If we don't have an explicit private_key defined, check for + ## one embedded in the URL. A URL of the form + ## https://moo@cow:8913 will try to contact https://cow:8913 + ## with a private key of moo + private_key_format = "https?://(.*)@.*/?" + private_key_match= re.match(private_key_format, remote_host) + if not private_key and private_key_match: + private_key = private_key_match.group(1) + remote_host = remote_host.replace("%s@" % private_key, '', 1) self.remote_host = remote_host self.job_id = job_id + self.private_key = private_key def url_open(self, request, data): return urllib2.urlopen(request, data) def __build_url(self, command, args): + if self.private_key: + args["private_key"] = self.private_key data = urllib.urlencode(args) url = self.remote_host + command + "?" + data return url Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 10 Aug '12

10 Aug '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/06b31a61793c/ changeset: 06b31a61793c branch: add_requirement_tags_for_plink user: jmchilton date: 2012-02-06 22:43:05 summary: Adding plink requirement tag for various rgenetics tools requiring plink. affected #: 6 files diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml +++ b/tools/rgenetics/rgCaCo.xml @@ -1,4 +1,5 @@ <tool id="rgCaCo1" name="Case Control:"> + <requirements><requirement type="package">plink</requirement></requirements><description>for unrelated subjects</description><command interpreter="python"> rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml +++ b/tools/rgenetics/rgClean.xml @@ -1,4 +1,5 @@ <tool id="rgClean1" name="Clean genotypes:"> + <requirements><requirement type="package">plink</requirement></requirements><description>filter markers, subjects</description><command interpreter="python"> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml +++ b/tools/rgenetics/rgGLM.xml @@ -1,4 +1,5 @@ <tool id="rgGLM1" name="Linear Models:" version="0.2"> + <requirements><requirement type="package">plink</requirement></requirements><description>for genotype data</description><code file="rgGLM_code.py"/><command interpreter="python"> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgLDIndep.xml --- a/tools/rgenetics/rgLDIndep.xml +++ b/tools/rgenetics/rgLDIndep.xml @@ -1,4 +1,5 @@ <tool id="rgLDIndep1" name="LD Independent:"> + <requirements><requirement type="package">plink</requirement></requirements><code file="rgLDIndep_code.py"/><description>filter high LD pairs - decrease redundancy</description> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -1,5 +1,6 @@ <tool id="rgQC1" name="QC reports:"> - + <requirements><requirement type="package">plink</requirement></requirements> + <description>Marker and Subject measures</description><command interpreter="python"> diff -r 74b6319b38b4b3876d0b81ef1296bb5afc729cc1 -r 06b31a61793c6e3b8ab39676ded73f6af95212f7 tools/rgenetics/rgTDT.xml --- a/tools/rgenetics/rgTDT.xml +++ b/tools/rgenetics/rgTDT.xml @@ -1,4 +1,6 @@ <tool id="rgTDT1" name="Transmission Distortion:"> + <requirements><requirement type="package">plink</requirement></requirements> + <description>for family data</description><command interpreter="python"> https://bitbucket.org/galaxy/galaxy-central/changeset/4b0d6a9ecef8/ changeset: 4b0d6a9ecef8 user: natefoo date: 2012-08-10 20:33:59 summary: Merged in jmchilton/umn-galaxy-central/add_requirement_tags_for_plink (pull request #35) affected #: 6 files diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgCaCo.xml --- a/tools/rgenetics/rgCaCo.xml +++ b/tools/rgenetics/rgCaCo.xml @@ -1,4 +1,5 @@ <tool id="rgCaCo1" name="Case Control:"> + <requirements><requirement type="package">plink</requirement></requirements><description>for unrelated subjects</description><command interpreter="python"> rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout' diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgClean.xml --- a/tools/rgenetics/rgClean.xml +++ b/tools/rgenetics/rgClean.xml @@ -1,4 +1,5 @@ <tool id="rgClean1" name="Clean genotypes:"> + <requirements><requirement type="package">plink</requirement></requirements><description>filter markers, subjects</description><command interpreter="python"> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgGLM.xml --- a/tools/rgenetics/rgGLM.xml +++ b/tools/rgenetics/rgGLM.xml @@ -1,4 +1,5 @@ <tool id="rgGLM1" name="Linear Models:" version="0.2"> + <requirements><requirement type="package">plink</requirement></requirements><description>for genotype data</description><code file="rgGLM_code.py"/><command interpreter="python"> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgLDIndep.xml --- a/tools/rgenetics/rgLDIndep.xml +++ b/tools/rgenetics/rgLDIndep.xml @@ -1,4 +1,5 @@ <tool id="rgLDIndep1" name="LD Independent:"> + <requirements><requirement type="package">plink</requirement></requirements><code file="rgLDIndep_code.py"/><description>filter high LD pairs - decrease redundancy</description> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgQC.xml --- a/tools/rgenetics/rgQC.xml +++ b/tools/rgenetics/rgQC.xml @@ -1,5 +1,6 @@ <tool id="rgQC1" name="QC reports:"> - + <requirements><requirement type="package">plink</requirement></requirements> + <description>Marker and Subject measures</description><command interpreter="python"> diff -r 35c524274296c33320190a017bc316b57cb4f759 -r 4b0d6a9ecef858e507df4fa04fd8d8c37d542958 tools/rgenetics/rgTDT.xml --- a/tools/rgenetics/rgTDT.xml +++ b/tools/rgenetics/rgTDT.xml @@ -1,4 +1,6 @@ <tool id="rgTDT1" name="Transmission Distortion:"> + <requirements><requirement type="package">plink</requirement></requirements> + <description>for family data</description><command interpreter="python"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Explicitly specify encodings for tool help templates to avoid unicode/ascii confusion.
by Bitbucket 10 Aug '12

10 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/35c524274296/ changeset: 35c524274296 user: jgoecks date: 2012-08-10 18:26:43 summary: Explicitly specify encodings for tool help templates to avoid unicode/ascii confusion. affected #: 1 file diff -r 7ac62afbcdf2b983e002b79e52753f9cf142db60 -r 35c524274296c33320190a017bc316b57cb4f759 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1083,7 +1083,9 @@ help_pages = self.help.findall( "page" ) help_header = self.help.text try: - self.help = Template( util.rst_to_html(self.help.text) ) + self.help = Template( util.rst_to_html(self.help.text), input_encoding='utf-8', + output_encoding='utf-8', default_filters=[ 'decode.utf8' ], + encoding_errors='replace' ) except: log.exception( "error in help for tool %s" % self.name ) # Multiple help page case @@ -1093,7 +1095,10 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer ) ) + self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer, + input_encoding='utf-8', output_encoding='utf-8', + default_filters=[ 'decode.utf8' ], + encoding_errors='replace' ) ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Make from_work_dir attribute work when outputs_to_working_directory is True.
by Bitbucket 10 Aug '12

10 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7ac62afbcdf2/ changeset: 7ac62afbcdf2 user: jgoecks date: 2012-08-10 15:58:59 summary: Make from_work_dir attribute work when outputs_to_working_directory is True. affected #: 1 file diff -r 18462a6cbf46566307eaa4fd33c8891b5979d699 -r 7ac62afbcdf2b983e002b79e52753f9cf142db60 lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -40,7 +40,18 @@ if job_wrapper.dependency_shell_commands: commands = "; ".join( job_wrapper.dependency_shell_commands + [ commands ] ) - # Append commands to copy job outputs based on from_work_dir attribute. + # -- Append commands to copy job outputs based on from_work_dir attribute. -- + + # Set up dict of dataset id --> output path; output path can be real or + # false depending on outputs_to_working_directory + output_paths = {} + for dataset_path in job_wrapper.get_output_fnames(): + path = dataset_path.real_path + if self.app.config.outputs_to_working_directory: + path = dataset_path.false_path + output_paths[ dataset_path.dataset_id ] = path + + # Walk job's output associations to find and use from_work_dir attributes. job = job_wrapper.get_job() job_tool = self.app.toolbox.tools_by_id.get( job.tool_id, None ) for dataset_assoc in job.output_datasets + job.output_library_datasets: @@ -53,12 +64,13 @@ # Copy from working dir to HDA. # TODO: move instead of copy to save time? source_file = os.path.join( os.path.abspath( job_wrapper.working_directory ), hda_tool_output.from_work_dir ) + destination = output_paths[ dataset.dataset_id ] if in_directory( source_file, job_wrapper.working_directory ): try: - commands += "; cp %s %s" % ( source_file, dataset.file_name ) - log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) ) + commands += "; cp %s %s" % ( source_file, destination ) + log.debug( "Copying %s to %s as directed by from_work_dir" % ( source_file, destination ) ) except ( IOError, OSError ): - log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, dataset.file_name ) ) + log.debug( "Could not copy %s to %s as directed by from_work_dir" % ( source_file, destination ) ) else: # Security violation. log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: Added sanitisation of the only user controllable parameter and removed use of shell in subprocess.popen to
by Bitbucket 10 Aug '12

10 Aug '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/18462a6cbf46/ changeset: 18462a6cbf46 user: fubar date: 2012-08-10 12:53:00 summary: Added sanitisation of the only user controllable parameter and removed use of shell in subprocess.popen to improve security and reduce breakage risk from ugly filenames pointed out by A Nonymous in https://bitbucket.org/galaxy/galaxy-central/issue/793/rgenetics-rgfastqcpy-… affected #: 2 files diff -r c6e1ef62c40b6c212210356fa59222b60645070b -r 18462a6cbf46566307eaa4fd33c8891b5979d699 tools/rgenetics/rgFastQC.py --- a/tools/rgenetics/rgFastQC.py +++ b/tools/rgenetics/rgFastQC.py @@ -13,8 +13,13 @@ """ - -import os,sys,subprocess,optparse,shutil,tempfile +import re +import os +import sys +import subprocess +import optparse +import shutil +import tempfile from rgutils import getFileString class FastQC(): @@ -38,25 +43,26 @@ """ serr = '' - dummy,tlog = tempfile.mkstemp(prefix='rgFastQClog') + dummy,tlog = tempfile.mkstemp(prefix='rgFastQC',suffix=".log",dir=self.opts.outputdir) sout = open(tlog, 'w') fastq = os.path.basename(self.opts.input) - cl = [self.opts.executable,'-o %s' % self.opts.outputdir] + cl = [self.opts.executable,'--outdir=%s' % self.opts.outputdir] if self.opts.informat in ['sam','bam']: cl.append('-f %s' % self.opts.informat) if self.opts.contaminants <> None : cl.append('-c %s' % self.opts.contaminants) # patch suggested by bwlang https://bitbucket.org/galaxy/galaxy-central/pull-request/30 # use a symlink in a temporary directory so that the FastQC report reflects the history input file name - fastqinfilename = os.path.basename(self.opts.inputfilename).replace(' ','_') + fastqinfilename = re.sub('[^a-zA-Z0-9_]+', '', os.path.basename(self.opts.inputfilename)) link_name = os.path.join(self.opts.outputdir, fastqinfilename) os.symlink(self.opts.input, link_name) cl.append(link_name) - p = subprocess.Popen(' '.join(cl), shell=True, stderr=sout, stdout=sout, cwd=self.opts.outputdir) + sout.write('# FastQC cl = %s\n' % ' '.join(cl)) + sout.flush() + p = subprocess.Popen(cl, shell=False, stderr=sout, stdout=sout, cwd=self.opts.outputdir) retval = p.wait() sout.close() runlog = open(tlog,'r').readlines() - os.unlink(tlog) os.unlink(link_name) flist = os.listdir(self.opts.outputdir) # fastqc plays games with its output directory name. eesh odpath = None diff -r c6e1ef62c40b6c212210356fa59222b60645070b -r 18462a6cbf46566307eaa4fd33c8891b5979d699 tools/rgenetics/rgFastQC.xml --- a/tools/rgenetics/rgFastQC.xml +++ b/tools/rgenetics/rgFastQC.xml @@ -1,5 +1,5 @@ -<tool name="Fastqc: Fastqc QC" id="fastqc" version="0.5"> - <description>using FastQC from Babraham</description> +<tool name="FastQC:Read QC" id="fastqc" version="0.51"> + <description>reports using FastQC</description><command interpreter="python"> rgFastQC.py -i "$input_file" -d "$html_file.files_path" -o "$html_file" -n "$out_prefix" -f "$input_file.ext" -j "$input_file.name" -e "${GALAXY_DATA_INDEX_DIR}/shared/jars/FastQC/fastqc" #if $contaminants.dataset and str($contaminants) > '' @@ -21,7 +21,7 @@ help="tab delimited file with 2 columns: name and sequence. For example: Illumina Small RNA RT Primer CAAGCAGAAGACGGCATACGA"/></inputs><outputs> - <data format="html" name="html_file" label="${out_prefix}_${on_string}.html" /> + <data format="html" name="html_file" label="${out_prefix}_${input_file.name}.html" /></outputs><tests><test> @@ -51,15 +51,18 @@ - Export of results to an HTML based permanent report - Offline operation to allow automated generation of reports without running the interactive application -**FastQC documentation** -This is a Galaxy interface to the external package FastQC_. -Specific documentation on FastQC can be found on that site. +----- + + +.. class:: infomark + +**FastQC** + +This is a Galaxy wrapper. It merely exposes the external package FastQC_ which is documented at FastQC_ +Kindly acknowledge it as well as this tool if you use it. FastQC incorporates the Picard-tools_ libraries for sam/bam processing. - .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ - .. _Picard-tools: http://picard.sourceforge.net/index.shtml - The contaminants file parameter was borrowed from the independently developed fastqcwrapper contributed to the Galaxy Community Tool Shed by J. Johnson. @@ -69,7 +72,10 @@ **Inputs and outputs** -This wrapper will accept any fastq file as well as sam or bam as the primary file to check. +FastQC_ is the best place to look for documentation - it's very good. +A summary follows below for those in a tearing hurry. + +This wrapper will accept a Galaxy fastq, sam or bam as the input read file to check. It will also take an optional file containing a list of contaminants information, in the form of a tab-delimited file with 2 columns, name and sequence. @@ -88,6 +94,8 @@ - Kmer Content All except Basic Statistics and Overrepresented sequences are plots. + .. _FastQC: http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/ + .. _Picard-tools: http://picard.sourceforge.net/index.shtml </help></tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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galaxy-commits August 2012