1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/7073d786cad0/ changeset: 7073d786cad0 user: greg date: 2012-12-27 22:00:16 summary: Add the ability to view an SVG image of a workflow contained in a tool shed repository installed into a Galaxy instance. This feature is the same as the feature that has been available in the tool shed for some time. affected #: 14 files

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1,14 +1,14 @@ import os, shutil, tempfile, logging, string, threading, urllib2 from galaxy import util from galaxy.tools import parameters -from galaxy.util import inflector -from galaxy.util import json +from galaxy.util import inflector, json from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.webapps.community.util import container_util from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.tools.parameters import dynamic_options +from galaxy.tool_shed import encoding_util

from galaxy import eggs import pkg_resources @@ -176,7 +176,12 @@ containers_dict[ 'valid_tools' ] = valid_tools_root_folder # Workflows container. if workflows: - folder_id, workflows_root_folder = container_util.build_workflows_folder( trans, folder_id, workflows, repository_metadata, label='Workflows' ) + folder_id, workflows_root_folder = container_util.build_workflows_folder( trans=trans, + folder_id=folder_id, + workflows=workflows, + repository_metadata_id=None, + repository_id=repository_id, + label='Workflows' ) containers_dict[ 'workflows' ] = workflows_root_folder except Exception, e: log.debug( "Exception in build_repository_containers_for_galaxy: %s" % str( e ) ) @@ -252,7 +257,12 @@ # Workflows container. if metadata and 'workflows' in metadata: workflows = metadata[ 'workflows' ] - folder_id, workflows_root_folder = container_util.build_workflows_folder( trans, folder_id, workflows, repository_metadata, label='Workflows' ) + folder_id, workflows_root_folder = container_util.build_workflows_folder( trans=trans, + folder_id=folder_id, + workflows=workflows, + repository_metadata_id=repository_metadata.id, + repository_id=None, + label='Workflows' ) containers_dict[ 'workflows' ] = workflows_root_folder except Exception, e: log.debug( "Exception in build_repository_containers_for_tool_shed: %s" % str( e ) ) @@ -400,6 +410,25 @@ # tag for any tool in the repository. break return can_generate_dependency_metadata +def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ): + """ + Determine if repository's tool config file on disk can be used. This method is restricted to tool config files since, with the + exception of tool config files, multiple files with the same name will likely be in various directories in the repository and we're + comparing file names only (not relative paths). + """ + if not file_path or not os.path.exists( file_path ): + # The file no longer exists on disk, so it must have been deleted at some previous point in the change log. + return False + if changeset_revision == repository.tip( trans.app ): + return True + file_name = strip_path( file_path ) + latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision ) + can_use_disk_file = filecmp.cmp( file_path, latest_version_of_file ) + try: + os.unlink( latest_version_of_file ) + except: + pass + return can_use_disk_file 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 @@ -1339,6 +1368,16 @@ else: metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] return metadata_dict +def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): + """Return the absolute path to a specified disk file containe in a repository.""" + stripped_file_name = strip_path( file_name ) + file_path = None + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == stripped_file_name: + return os.path.abspath( os.path.join( root, name ) ) + return file_path def get_changectx_for_changeset( repo, changeset_revision, **kwd ): """Retrieve a specified changectx from a repository""" for changeset in repo.changelog: @@ -1487,14 +1526,14 @@ repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) ctx_rev = get_ctx_rev( tool_shed_url, name, owner, installed_changeset_revision ) print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name - repository = create_or_update_tool_shed_repository( app=self.app, + repository = create_or_update_tool_shed_repository( app=trans.app, name=name, description=None, installed_changeset_revision=changeset_revision, ctx_rev=ctx_rev, repository_clone_url=repository_clone_url, metadata_dict={}, - status=self.app.model.ToolShedRepository.installation_status.NEW, + status=trans.model.ToolShedRepository.installation_status.NEW, current_changeset_revision=None, owner=sowner, dist_to_shed=False ) @@ -1712,6 +1751,9 @@ 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 ) ) def get_repository_metadata_by_repository_id_changset_revision( trans, id, changeset_revision ): """Get a specified metadata record for a specified repository.""" return trans.sa_session.query( trans.model.RepositoryMetadata ) \ @@ -1822,6 +1864,10 @@ tool_path = shed_tool_conf_dict[ 'tool_path' ] break return tool_path +def get_tool_shed_repository_by_id( trans, repository_id ): + return trans.sa_session.query( trans.model.ToolShedRepository ) \ + .filter( trans.model.ToolShedRepository.table.c.id == trans.security.decode_id( repository_id ) ) \ + .first() def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current @@ -2110,6 +2156,46 @@ description = repository_dependencies_dict.get( 'description', None ) all_repository_dependencies[ 'description' ] = description return all_repository_dependencies +def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): + """ + Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision + 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. + """ + original_tool_data_path = trans.app.config.tool_data_path + repository = get_repository_in_tool_shed( trans, repository_id ) + repo_files_dir = repository.repo_path( trans.app ) + repo = hg.repository( get_configured_ui(), repo_files_dir ) + message = '' + tool = None + can_use_disk_file = False + tool_config_filepath = get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename ) + work_dir = tempfile.mkdtemp() + can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) + if can_use_disk_file: + trans.app.config.tool_data_path = work_dir + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) + if tool is not None: + invalid_files_and_errors_tups = check_tool_input_params( trans.app, + repo_files_dir, + tool_config_filename, + tool, + sample_files ) + if invalid_files_and_errors_tups: + message2 = generate_message_for_invalid_tools( trans, + invalid_files_and_errors_tups, + repository, + metadata_dict=None, + as_html=True, + displaying_invalid_tool=True ) + message = concat_messages( message, message2 ) + else: + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) + remove_dir( work_dir ) + 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 repository, tool, message def load_tool_from_config( app, full_path ): try: tool = app.toolbox.load_tool( full_path )

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -533,7 +533,7 @@ # The received id is a RepositoryMetadata object id, so we need to get the # associated Repository and redirect to view_or_manage_repository with the # changeset_revision. - repository_metadata = common.get_repository_metadata_by_id( trans, kwd[ 'id' ] ) + repository_metadata = suc.get_repository_metadata_by_id( trans, kwd[ 'id' ] ) repository = repository_metadata.repository kwd[ 'id' ] = trans.security.encode_id( repository.id ) kwd[ 'changeset_revision' ] = repository_metadata.changeset_revision @@ -615,7 +615,7 @@ ids = util.listify( id ) count = 0 for repository_metadata_id in ids: - repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) trans.sa_session.delete( repository_metadata ) trans.sa_session.flush() count += 1

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -113,25 +113,6 @@ repository_metadata.tool_versions = tool_versions_dict trans.sa_session.add( repository_metadata ) trans.sa_session.flush() -def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ): - """ - Determine if repository's tool config file on disk can be used. This method is restricted to tool config files since, with the - exception of tool config files, multiple files with the same name will likely be in various directories in the repository and we're - comparing file names only (not relative paths). - """ - if not file_path or not os.path.exists( file_path ): - # The file no longer exists on disk, so it must have been deleted at some previous point in the change log. - return False - if changeset_revision == repository.tip( trans.app ): - return True - file_name = suc.strip_path( file_path ) - latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision ) - can_use_disk_file = filecmp.cmp( file_path, latest_version_of_file ) - try: - os.unlink( latest_version_of_file ) - except: - pass - return can_use_disk_file def changeset_is_malicious( trans, id, changeset_revision, **kwd ): """Check the malicious flag in repository metadata for a specified change set""" repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) @@ -155,15 +136,6 @@ if user_email in admin_users: return True return False -def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ): - stripped_file_name = suc.strip_path( file_name ) - file_path = None - for root, dirs, files in os.walk( repo_files_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == stripped_file_name: - return os.path.abspath( os.path.join( root, name ) ) - return file_path def get_category( trans, id ): """Get a category from the database""" return trans.sa_session.query( trans.model.Category ).get( trans.security.decode_id( id ) ) @@ -249,9 +221,6 @@ def get_repository_by_name( trans, name ): """Get a repository from the database via name""" return trans.sa_session.query( trans.model.Repository ).filter_by( name=name ).one() -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 ) ) def get_repository_metadata_revisions_for_review( repository, reviewed=True ): repository_metadata_revisions = [] metadata_changeset_revision_hashes = [] @@ -425,46 +394,6 @@ if previous_changeset_revision in reviewed_revision_hashes: return True return False -def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): - """ - Return a loaded tool whose tool config file name (e.g., filtering.xml) is the value of tool_config_filename. The value of changeset_revision - 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. - """ - original_tool_data_path = trans.app.config.tool_data_path - repository = suc.get_repository_in_tool_shed( trans, repository_id ) - repo_files_dir = repository.repo_path( trans.app ) - repo = hg.repository( suc.get_configured_ui(), repo_files_dir ) - message = '' - tool = None - can_use_disk_file = False - tool_config_filepath = get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename ) - work_dir = tempfile.mkdtemp() - can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) - if can_use_disk_file: - trans.app.config.tool_data_path = work_dir - tool, valid, message, sample_files = suc.handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ) - if tool is not None: - invalid_files_and_errors_tups = suc.check_tool_input_params( trans.app, - repo_files_dir, - tool_config_filename, - tool, - sample_files ) - if invalid_files_and_errors_tups: - message2 = suc.generate_message_for_invalid_tools( trans, - invalid_files_and_errors_tups, - repository, - metadata_dict=None, - as_html=True, - displaying_invalid_tool=True ) - message = suc.concat_messages( message, message2 ) - else: - tool, message, sample_files = suc.handle_sample_files_and_load_tool_from_tmp_config( trans, repo, changeset_revision, tool_config_filename, work_dir ) - suc.remove_dir( work_dir ) - 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. - suc.reset_tool_data_tables( trans.app ) - return repository, tool, message def new_repository_dependency_metadata_required( trans, repository, metadata_dict ): """ Compare the last saved metadata for each repository dependency in the repository with the new

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1,18 +1,20 @@ -import os, logging, tempfile, shutil, ConfigParser +import os, logging, re, tempfile, shutil, ConfigParser from time import gmtime, strftime from datetime import date, datetime -from galaxy import util +from galaxy import util, web from galaxy.util.odict import odict -from galaxy.web.base.controller import * -from galaxy.web.form_builder import CheckboxField +from galaxy.web.base.controller import BaseUIController +from galaxy.web.form_builder import CheckboxField, SelectField, build_select_field from galaxy.webapps.community import model from galaxy.webapps.community.model import directory_hash_id -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 and_ +from galaxy.web.framework.helpers import grids +from galaxy.util import json +from galaxy.model.orm import and_, or_ import galaxy.util.shed_util_common as suc from galaxy.tool_shed import encoding_util +from galaxy.webapps.community.util import workflow_util import common +import galaxy.tools

from galaxy import eggs eggs.require('mercurial') @@ -157,7 +159,7 @@ model.User.table.c.email == column_filter ) ) class EmailAlertsColumn( grids.TextColumn ): def get_value( self, trans, grid, repository ): - if trans.user and repository.email_alerts and trans.user.email in from_json_string( repository.email_alerts ): + if trans.user and repository.email_alerts and trans.user.email in json.from_json_string( repository.email_alerts ): return 'yes' return '' class DeprecatedColumn( grids.TextColumn ): @@ -833,7 +835,7 @@ # Start building up the url to redirect back to the calling Galaxy instance. url = suc.url_join( galaxy_url, 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ - ( url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) + ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. if from_update_manager: @@ -1020,7 +1022,7 @@ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository, tool, message = common.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + repository, tool, message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) if message: status = 'error' tool_state = self.__new_state( trans ) @@ -1087,7 +1089,7 @@ is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = common.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = suc.get_repository_metadata_by_id( trans, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) kwd[ 'id' ] = repository_id @@ -1104,7 +1106,7 @@ encoded_repository_ids = [] changeset_revisions = [] for repository_metadata_id in util.listify( item_id ): - repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) new_kwd[ 'repository_ids' ] = encoded_repository_ids @@ -1172,7 +1174,7 @@ is_admin = trans.user_is_admin() if operation == "view_or_manage_repository": # The received id is a RepositoryMetadata id, so we have to get the repository id. - repository_metadata = common.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = suc.get_repository_metadata_by_id( trans, item_id ) repository_id = trans.security.encode_id( repository_metadata.repository.id ) repository = suc.get_repository_in_tool_shed( trans, repository_id ) kwd[ 'id' ] = repository_id @@ -1189,7 +1191,7 @@ encoded_repository_ids = [] changeset_revisions = [] for repository_metadata_id in util.listify( item_id ): - repository_metadata = common.get_repository_metadata_by_id( trans, item_id ) + repository_metadata = suc.get_repository_metadata_by_id( trans, item_id ) encoded_repository_ids.append( trans.security.encode_id( repository_metadata.repository.id ) ) changeset_revisions.append( repository_metadata.changeset_revision ) new_kwd = {} @@ -1245,6 +1247,10 @@ message=message, status=status ) @web.expose + def generate_workflow_image( self, trans, workflow_name, repository_metadata_id=None ): + """Return an svg image representation of a workflow dictionary created when the workflow was exported.""" + return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=repository_metadata_id, repository_id=None ) + @web.expose def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" params = util.Params( kwd ) @@ -1355,7 +1361,7 @@ repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, repository_metadata=repository_metadata, - toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, @@ -1418,7 +1424,7 @@ encoded_repository_ids.append( trans.security.encode_id( repository.id ) ) changeset_revisions.append( changeset_revision ) if encoded_repository_ids and changeset_revisions: - repo_info_dict = from_json_string( self.get_repository_information( trans, encoded_repository_ids, changeset_revisions ) ) + repo_info_dict = json.from_json_string( self.get_repository_information( trans, encoded_repository_ids, changeset_revisions ) ) else: repo_info_dict = {} return repo_info_dict @@ -1465,7 +1471,7 @@ if current_changeset_revision == changeset_revision: break if tool_version_dicts: - return to_json_string( tool_version_dicts ) + return json.to_json_string( tool_version_dicts ) return '' 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.""" @@ -1595,14 +1601,14 @@ # Redirect back to local Galaxy to perform install. url = suc.url_join( galaxy_url, 'admin_toolshed/prepare_for_install?tool_shed_url=%s&repository_ids=%s&changeset_revisions=%s' % \ - ( url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) + ( web.url_for( '/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join( util.listify( changeset_revisions ) ) ) ) return trans.response.send_redirect( url ) @web.expose def load_invalid_tool( self, trans, repository_id, tool_config, changeset_revision, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'error' ) - repository, tool, error_message = common.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + repository, tool, error_message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) tool_state = self.__new_state( trans ) is_malicious = common.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) invalid_file_tups = [] @@ -1701,7 +1707,7 @@ alerts_checked = CheckboxField.is_checked( alerts ) category_ids = util.listify( params.get( 'category_id', '' ) ) if repository.email_alerts: - email_alerts = from_json_string( repository.email_alerts ) + email_alerts = json.from_json_string( repository.email_alerts ) else: email_alerts = [] allow_push = params.get( 'allow_push', '' ) @@ -1776,12 +1782,12 @@ if alerts_checked: if user.email not in email_alerts: email_alerts.append( user.email ) - repository.email_alerts = to_json_string( email_alerts ) + repository.email_alerts = json.to_json_string( email_alerts ) flush_needed = True else: if user.email in email_alerts: email_alerts.remove( user.email ) - repository.email_alerts = to_json_string( email_alerts ) + repository.email_alerts = json.to_json_string( email_alerts ) flush_needed = True if flush_needed: trans.sa_session.add( repository ) @@ -1830,7 +1836,7 @@ repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, repository_metadata=repository_metadata, - toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) @@ -1913,7 +1919,7 @@ Only inputs on the first page will be initialized unless `all_pages` is True, in which case all inputs regardless of page are initialized. """ - state = DefaultToolState() + state = galaxy.tools.DefaultToolState() state.inputs = {} return state @web.json @@ -1939,7 +1945,7 @@ repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, repository_metadata=repository_metadata, - toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) @@ -2257,18 +2263,18 @@ for repository_id in repository_ids: repository = suc.get_repository_in_tool_shed( trans, repository_id ) if repository.email_alerts: - email_alerts = from_json_string( repository.email_alerts ) + email_alerts = json.from_json_string( repository.email_alerts ) else: email_alerts = [] if user.email in email_alerts: email_alerts.remove( user.email ) - repository.email_alerts = to_json_string( email_alerts ) + repository.email_alerts = json.to_json_string( email_alerts ) trans.sa_session.add( repository ) flush_needed = True total_alerts_removed += 1 else: email_alerts.append( user.email ) - repository.email_alerts = to_json_string( email_alerts ) + repository.email_alerts = json.to_json_string( email_alerts ) trans.sa_session.add( repository ) flush_needed = True total_alerts_added += 1 @@ -2424,7 +2430,7 @@ alerts = params.get( 'alerts', '' ) alerts_checked = CheckboxField.is_checked( alerts ) if repository.email_alerts: - email_alerts = from_json_string( repository.email_alerts ) + email_alerts = json.from_json_string( repository.email_alerts ) else: email_alerts = [] repository_dependencies = None @@ -2434,12 +2440,12 @@ if alerts_checked: if user.email not in email_alerts: email_alerts.append( user.email ) - repository.email_alerts = to_json_string( email_alerts ) + repository.email_alerts = json.to_json_string( email_alerts ) flush_needed = True else: if user.email in email_alerts: email_alerts.remove( user.email ) - repository.email_alerts = to_json_string( email_alerts ) + repository.email_alerts = json.to_json_string( email_alerts ) flush_needed = True if flush_needed: trans.sa_session.add( repository ) @@ -2460,7 +2466,7 @@ repository_dependencies = suc.get_repository_dependencies_for_changeset_revision( trans=trans, repository=repository, repository_metadata=repository_metadata, - toolshed_base_url=str( url_for( '/', qualified=True ) ).rstrip( '/' ), + toolshed_base_url=str( web.url_for( '/', qualified=True ) ).rstrip( '/' ), key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None ) @@ -2527,7 +2533,7 @@ guid = tool_metadata_dict[ 'guid' ] full_path_to_tool_config = os.path.abspath( relative_path_to_tool_config ) full_path_to_dir, tool_config_filename = os.path.split( full_path_to_tool_config ) - can_use_disk_file = common.can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) + can_use_disk_file = suc.can_use_tool_config_disk_file( trans, repository, repo, full_path_to_tool_config, changeset_revision ) if can_use_disk_file: trans.app.config.tool_data_path = work_dir tool, valid, message, sample_files = suc.handle_sample_files_and_load_tool_from_disk( trans, @@ -2576,7 +2582,26 @@ review_id=review_id, message=message, status=status ) - + @web.expose + def view_workflow( self, trans, workflow_name, repository_metadata_id, **kwd ): + """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if workflow_name: + workflow_name = encoding_util.tool_shed_decode( workflow_name ) + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) + changeset_revision = repository_metadata.changeset_revision + metadata = repository_metadata.metadata + return trans.fill_template( "/webapps/community/repository/view_workflow.mako", + repository=repository, + changeset_revision=changeset_revision, + repository_metadata_id=repository_metadata_id, + workflow_name=workflow_name, + metadata=metadata, + message=message, + status=status ) # ----- Utility methods -----

def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True,

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/controllers/workflow.py --- a/lib/galaxy/webapps/community/controllers/workflow.py +++ /dev/null @@ -1,411 +0,0 @@ -import pkg_resources -pkg_resources.require( "simplejson" ) -pkg_resources.require( "SVGFig" ) -import os, logging, ConfigParser, tempfile, shutil, svgfig -from galaxy.webapps.community import model -from galaxy.web.framework.helpers import time_ago, iff, grids -from galaxy.util.json import from_json_string, to_json_string -from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory -from galaxy.web.base.controller import * -from galaxy.tools import DefaultToolState -from galaxy.webapps.galaxy.controllers.workflow import attach_ordered_steps -import common -import galaxy.util.shed_util_common as suc -from galaxy.tool_shed import encoding_util - -class RepoInputDataModule( InputDataModule ): - - type = "data_input" - name = "Input dataset" - - @classmethod - def new( Class, trans, tools_metadata=None, tool_id=None ): - module = Class( trans ) - module.state = dict( name="Input Dataset" ) - return module - @classmethod - def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): - module = Class( trans ) - state = from_json_string( step_dict[ "tool_state" ] ) - module.state = dict( name=state.get( "name", "Input Dataset" ) ) - return module - @classmethod - def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): - module = Class( trans ) - module.state = dict( name="Input Dataset" ) - if step.tool_inputs and "name" in step.tool_inputs: - module.state[ 'name' ] = step.tool_inputs[ 'name' ] - return module - -class RepoToolModule( ToolModule ): - - type = "tool" - - def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ): - self.trans = trans - self.tools_metadata = tools_metadata - self.tool_id = tool_id - self.tool = None - self.errors = None - for tool_dict in tools_metadata: - if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: - repository, self.tool, message = common.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) - if message and self.tool is None: - self.errors = 'unavailable' - break - self.post_job_actions = {} - self.workflow_outputs = [] - self.state = None - @classmethod - def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): - module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) - module.state = module.tool.new_state( trans, all_pages=True ) - return module - @classmethod - def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): - tool_id = step_dict[ 'tool_id' ] - module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) - module.state = DefaultToolState() - if module.tool is not None: - module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) - module.errors = step_dict.get( "tool_errors", None ) - return module - @classmethod - def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): - module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) - module.state = DefaultToolState() - if module.tool: - module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) - else: - module.state.inputs = {} - module.errors = step.tool_errors - return module - def get_data_inputs( self ): - data_inputs = [] - def callback( input, value, prefixed_name, prefixed_label ): - if isinstance( input, DataToolParameter ): - data_inputs.append( dict( name=prefixed_name, - label=prefixed_label, - extensions=input.extensions ) ) - if self.tool: - visit_input_values( self.tool.inputs, self.state.inputs, callback ) - return data_inputs - def get_data_outputs( self ): - data_outputs = [] - if self.tool: - data_inputs = None - for name, tool_output in self.tool.outputs.iteritems(): - if tool_output.format_source != None: - # Default to special name "input" which remove restrictions on connections - formats = [ 'input' ] - if data_inputs == None: - data_inputs = self.get_data_inputs() - # Find the input parameter referenced by format_source - for di in data_inputs: - # Input names come prefixed with conditional and repeat names separated by '|', - # so remove prefixes when comparing with format_source. - if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: - formats = di[ 'extensions' ] - else: - formats = [ tool_output.format ] - for change_elem in tool_output.change_format: - for when_elem in change_elem.findall( 'when' ): - format = when_elem.get( 'format', None ) - if format and format not in formats: - formats.append( format ) - data_outputs.append( dict( name=name, extensions=formats ) ) - return data_outputs - -class RepoWorkflowModuleFactory( WorkflowModuleFactory ): - def __init__( self, module_types ): - self.module_types = module_types - def new( self, trans, type, tools_metadata=None, tool_id=None ): - """Return module for type and (optional) tool_id initialized with new / default state.""" - assert type in self.module_types - return self.module_types[type].new( trans, tool_id ) - def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): - """Return module initialized from the data in dictionary `step_dict`.""" - type = step_dict[ 'type' ] - assert type in self.module_types - return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) - def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): - """Return module initialized from the WorkflowStep object `step`.""" - type = step.type - return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) - -module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) - -class WorkflowController( BaseUIController ): - @web.expose - def view_workflow( self, trans, **kwd ): - repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) - workflow_name = kwd.get( 'workflow_name', '' ) - if workflow_name: - workflow_name = encoding_util.tool_shed_decode( workflow_name ) - message = kwd.get( 'message', '' ) - status = kwd.get( 'status', 'done' ) - repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id ) - repository = suc.get_repository_in_tool_shed( trans, trans.security.encode_id( repository_metadata.repository_id ) ) - return trans.fill_template( "/webapps/community/repository/view_workflow.mako", - repository=repository, - changeset_revision=repository_metadata.changeset_revision, - repository_metadata_id=repository_metadata_id, - workflow_name=workflow_name, - metadata=repository_metadata.metadata, - message=message, - status=status ) - @web.expose - def generate_workflow_image( self, trans, repository_metadata_id, workflow_name ): - repository_metadata = common.get_repository_metadata_by_id( trans, repository_metadata_id ) - repository_id = trans.security.encode_id( repository_metadata.repository_id ) - changeset_revision = repository_metadata.changeset_revision - metadata = repository_metadata.metadata - workflow_name = encoding_util.tool_shed_decode( workflow_name ) - # metadata[ 'workflows' ] is a list of tuples where each contained tuple is - # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - for workflow_tup in metadata[ 'workflows' ]: - workflow_dict = workflow_tup[1] - if workflow_dict[ 'name' ] == workflow_name: - break - if 'tools' in metadata: - tools_metadata = metadata[ 'tools' ] - else: - tools_metadata = [] - workflow, missing_tool_tups = self.__workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ) - data = [] - canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) - text = svgfig.SVG( "g" ) - connectors = svgfig.SVG( "g" ) - boxes = svgfig.SVG( "g" ) - svgfig.Text.defaults[ "font-size" ] = "10px" - in_pos = {} - out_pos = {} - margin = 5 - # Spacing between input/outputs. - line_px = 16 - # Store px width for boxes of each step. - widths = {} - max_width, max_x, max_y = 0, 0, 0 - for step in workflow.steps: - step.upgrade_messages = {} - module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) - tool_errors = module.type == 'tool' and not module.tool - module_data_inputs = self.__get_data_inputs( step, module ) - module_data_outputs = self.__get_data_outputs( step, module, workflow.steps ) - step_dict = { - 'id' : step.order_index, - 'data_inputs' : module_data_inputs, - 'data_outputs' : module_data_outputs, - 'position' : step.position, - 'tool_errors' : tool_errors - } - input_conn_dict = {} - for conn in step.input_connections: - input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) - step_dict[ 'input_connections' ] = input_conn_dict - data.append( step_dict ) - x, y = step.position[ 'left' ], step.position[ 'top' ] - count = 0 - module_name = self.__get_name( module, missing_tool_tups ) - max_len = len( module_name ) * 1.5 - text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) - y += 45 - for di in module_data_inputs: - cur_y = y + count * line_px - if step.order_index not in in_pos: - in_pos[ step.order_index ] = {} - in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) - text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) - count += 1 - max_len = max( max_len, len( di[ 'label' ] ) ) - if len( module.get_data_inputs() ) > 0: - y += 15 - for do in module_data_outputs: - cur_y = y + count * line_px - if step.order_index not in out_pos: - out_pos[ step.order_index ] = {} - out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) - text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) - count += 1 - max_len = max( max_len, len( do['name' ] ) ) - widths[ step.order_index ] = max_len * 5.5 - max_x = max( max_x, step.position[ 'left' ] ) - max_y = max( max_y, step.position[ 'top' ] ) - max_width = max( max_width, widths[ step.order_index ] ) - for step_dict in data: - tool_unavailable = step_dict[ 'tool_errors' ] - width = widths[ step_dict[ 'id' ] ] - x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] - if tool_unavailable: - fill = "#EBBCB2" - else: - fill = "#EBD9B2" - boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) - box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin - # Draw separator line. - if len( step_dict[ 'data_inputs' ] ) > 0: - box_height += 15 - sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 - text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) - # Define an input/output box. - boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) - for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): - in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] - # out_pos_index will be a step number like 1, 2, 3... - out_pos_index = output_dict[ 'id' ] - # out_pos_name will be a string like 'o', 'o2', etc. - out_pos_name = output_dict[ 'output_name' ] - if out_pos_index in out_pos: - # out_conn_index_dict will be something like: - # 7: {'o': (824.5, 618)} - out_conn_index_dict = out_pos[ out_pos_index ] - if out_pos_name in out_conn_index_dict: - out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ] - else: - # Take any key / value pair available in out_conn_index_dict. - # A problem will result if the dictionary is empty. - if out_conn_index_dict.keys(): - key = out_conn_index_dict.keys()[0] - out_conn_pos = out_pos[ out_pos_index ][ key ] - adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) - text.append( svgfig.SVG( "circle", - cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, - cy=out_conn_pos[ 1 ] - margin, - r = 5, - fill="#ffffff" ) ) - connectors.append( svgfig.Line( adjusted[ 0 ], - adjusted[ 1 ] - margin, - in_coords[ 0 ] - 10, - in_coords[ 1 ], - arrow_end = "true" ).SVG() ) - canvas.append( connectors ) - canvas.append( boxes ) - canvas.append( text ) - width, height = ( max_x + max_width + 50 ), max_y + 300 - canvas[ 'width' ] = "%s px" % width - canvas[ 'height' ] = "%s px" % height - canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) - trans.response.set_content_type( "image/svg+xml" ) - return canvas.standalone_xml() - def __get_name( self, module, missing_tool_tups ): - module_name = module.get_name() - if module.type == 'tool' and module_name == 'unavailable': - for missing_tool_tup in missing_tool_tups: - missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup - if missing_tool_id == module.tool_id: - module_name = '%s' % missing_tool_name - return module_name - def __get_data_inputs( self, step, module ): - if module.type == 'tool': - if module.tool: - return module.get_data_inputs() - else: - data_inputs = [] - for wfsc in step.input_connections: - data_inputs_dict = {} - data_inputs_dict[ 'extensions' ] = [ '' ] - data_inputs_dict[ 'name' ] = wfsc.input_name - data_inputs_dict[ 'label' ] = 'Unknown' - data_inputs.append( data_inputs_dict ) - return data_inputs - return module.get_data_inputs() - def __get_data_outputs( self, step, module, steps ): - if module.type == 'tool': - if module.tool: - return module.get_data_outputs() - else: - data_outputs = [] - data_outputs_dict = {} - data_outputs_dict[ 'extensions' ] = [ 'input' ] - found = False - for workflow_step in steps: - for wfsc in workflow_step.input_connections: - if step.name == wfsc.output_step.name: - data_outputs_dict[ 'name' ] = wfsc.output_name - found = True - break - if found: - break - if not found: - # We're at the last step of the workflow. - data_outputs_dict[ 'name' ] = 'output' - data_outputs.append( data_outputs_dict ) - return data_outputs - return module.get_data_outputs() - def __workflow_from_dict( self, trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): - """Creates and returns workflow object from a dictionary.""" - trans.workflow_building_mode = True - workflow = model.Workflow() - workflow.name = workflow_dict[ 'name' ] - workflow.has_errors = False - steps = [] - # Keep ids for each step that we need to use to make connections. - steps_by_external_id = {} - # Keep track of tools required by the workflow that are not available in - # the tool shed repository. Each tuple in the list of missing_tool_tups - # will be ( tool_id, tool_name, tool_version ). - missing_tool_tups = [] - # First pass to build step objects and populate basic values - for key, step_dict in workflow_dict[ 'steps' ].iteritems(): - # Create the model class for the step - step = model.WorkflowStep() - step.name = step_dict[ 'name' ] - step.position = step_dict[ 'position' ] - module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False ) - if module.type == 'tool' and module.tool is None: - # A required tool is not available in the current repository. - step.tool_errors = 'unavailable' - missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) - if missing_tool_tup not in missing_tool_tups: - missing_tool_tups.append( missing_tool_tup ) - module.save_to_step( step ) - if step.tool_errors: - workflow.has_errors = True - # Stick this in the step temporarily. - step.temp_input_connections = step_dict[ 'input_connections' ] - steps.append( step ) - steps_by_external_id[ step_dict[ 'id' ] ] = step - # Second pass to deal with connections between steps. - for step in steps: - # Input connections. - for input_name, conn_dict in step.temp_input_connections.iteritems(): - if conn_dict: - output_step = steps_by_external_id[ conn_dict[ 'id' ] ] - conn = model.WorkflowStepConnection() - conn.input_step = step - conn.input_name = input_name - conn.output_step = output_step - conn.output_name = conn_dict[ 'output_name' ] - step.input_connections.append( conn ) - del step.temp_input_connections - # Order the steps if possible. - attach_ordered_steps( workflow, steps ) - return workflow, missing_tool_tups - @web.expose - def import_workflow( self, trans, **kwd ): - repository_metadata_id = kwd.get( 'repository_metadata_id', '' ) - workflow_name = kwd.get( 'workflow_name', '' ) - if workflow_name: - workflow_name = encoding_util.tool_shed_decode( workflow_name ) - message = kwd.get( 'message', '' ) - status = kwd.get( 'status', 'done' ) - repository_metadata = get_repository_metadata_by_id( trans, repository_metadata_id ) - workflows = repository_metadata.metadata[ 'workflows' ] - workflow_data = None - for workflow_data in workflows: - if workflow_data[ 'name' ] == workflow_name: - break - if workflow_data: - if kwd.get( 'open_for_url', False ): - tmp_fd, tmp_fname = tempfile.mkstemp() - to_file = open( tmp_fname, 'wb' ) - to_file.write( to_json_string( workflow_data ) ) - return open( tmp_fname ) - galaxy_url = trans.get_cookie( name='toolshedgalaxyurl' ) - url = '%sworkflow/import_workflow?tool_shed_url=%s&repository_metadata_id=%s&workflow_name=%s' % \ - ( galaxy_url, url_for( '/', qualified=True ), repository_metadata_id, encoding_util.tool_shed_encode( workflow_name ) ) - return trans.response.send_redirect( url ) - return trans.response.send_redirect( web.url_for( controller='workflow', - action='view_workflow', - message=message, - status=status ) )

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/util/container_util.py --- a/lib/galaxy/webapps/community/util/container_util.py +++ b/lib/galaxy/webapps/community/util/container_util.py @@ -56,11 +56,12 @@

class InvalidTool( object ): """Invalid tool object""" - def __init__( self, id=None, tool_config=None, repository_id=None, changeset_revision=None ): + def __init__( self, id=None, tool_config=None, repository_id=None, changeset_revision=None, repository_installation_status=None ): self.id = id self.tool_config = tool_config self.repository_id = repository_id self.changeset_revision = changeset_revision + self.repository_installation_status = repository_installation_status

class ReadMe( object ): """Readme text object""" @@ -86,7 +87,7 @@ class Tool( object ): """Tool object""" def __init__( self, id=None, tool_config=None, tool_id=None, name=None, description=None, version=None, requirements=None, - repository_id=None, changeset_revision=None ): + repository_id=None, changeset_revision=None, repository_installation_status=None ): self.id = id self.tool_config = tool_config self.tool_id = tool_id @@ -96,6 +97,7 @@ self.requirements = requirements self.repository_id = repository_id self.changeset_revision = changeset_revision + self.repository_installation_status = repository_installation_status

class ToolDependency( object ): """Tool dependency object""" @@ -112,14 +114,17 @@ self.tool_dependency_id = tool_dependency_id

class Workflow( object ): - """Workflow object""" - def __init__( self, id=None, repository_metadata_id=None, workflow_name=None, steps=None, format_version=None, annotation=None ): + """Workflow object.""" + def __init__( self, id=None, workflow_name=None, steps=None, format_version=None, annotation=None, repository_metadata_id=None, repository_id=None ): + # When rendered in the tool shed, repository_metadata_id will have a value and repository_id will be None. When rendered in Galaxy, repository_id + # will have a value and repository_metadata_id will be None. self.id = id - self.repository_metadata_id = repository_metadata_id self.workflow_name = workflow_name self.steps = steps self.format_version = format_version self.annotation = annotation + self.repository_metadata_id = repository_metadata_id + self.repository_id = repository_id

def build_datatypes_folder( trans, folder_id, datatypes, label='Datatypes' ): """Return a folder hierarchy containing datatypes.""" @@ -163,12 +168,18 @@ invalid_tool_id += 1 if repository: repository_id = repository.id + if trans.webapp.name == 'galaxy': + repository_installation_status = repository.status + else: + repository_installation_status = None else: repository_id = None + repository_installation_status = None invalid_tool = InvalidTool( id=invalid_tool_id, tool_config=invalid_tool_config, repository_id=repository_id, - changeset_revision=changeset_revision ) + changeset_revision=changeset_revision, + repository_installation_status=repository_installation_status ) folder.invalid_tools.append( invalid_tool ) else: invalid_tools_root_folder = None @@ -249,8 +260,13 @@ folder.valid_tools.append( tool ) if repository: repository_id = repository.id + if trans.webapp.name == 'galaxy': + repository_installation_status = repository.status + else: + repository_installation_status = None else: - repository_id = '' + repository_id = None + repository_installation_status = None for tool_dict in tool_dicts: tool_id += 1 if 'requirements' in tool_dict: @@ -269,7 +285,8 @@ version=tool_dict[ 'version' ], requirements=requirements_str, repository_id=repository_id, - changeset_revision=changeset_revision ) + changeset_revision=changeset_revision, + repository_installation_status=repository_installation_status ) folder.valid_tools.append( tool ) else: tools_root_folder = None @@ -351,8 +368,13 @@ else: tool_dependencies_root_folder = None return folder_id, tool_dependencies_root_folder -def build_workflows_folder( trans, folder_id, workflows, repository_metadata, label='Workflows' ): - """Return a folder hierarchy containing invalid tools.""" +def build_workflows_folder( trans, folder_id, workflows, repository_metadata_id=None, repository_id=None, label='Workflows' ): + """ + Return a folder hierarchy containing workflow objects for each workflow dictionary in the received workflows list. When + this method is called from the tool shed, repository_metadata_id will have a value and repository_id will be None. When + this method is called from Galaxy, repository_id will have a value only if the repository is not currenlty being installed + and repository_metadata_id will be None. + """ if workflows: workflow_id = 0 folder_id += 1 @@ -363,11 +385,12 @@ # Insert a header row. workflow_id += 1 workflow = Workflow( id=workflow_id, - repository_metadata_id=None, workflow_name='Name', steps='steps', format_version='format-version', - annotation='annotation' ) + annotation='annotation', + repository_metadata_id=repository_metadata_id, + repository_id=repository_id ) folder.workflows.append( workflow ) for workflow_tup in workflows: workflow_dict=workflow_tup[ 1 ] @@ -378,11 +401,12 @@ steps = 'unknown' workflow_id += 1 workflow = Workflow( id=workflow_id, - repository_metadata_id=repository_metadata.id, workflow_name=workflow_dict[ 'name' ], steps=steps, format_version=workflow_dict[ 'format-version' ], - annotation=workflow_dict[ 'annotation' ] ) + annotation=workflow_dict[ 'annotation' ], + repository_metadata_id=repository_metadata_id, + repository_id=repository_id ) folder.workflows.append( workflow ) else: workflows_root_folder = None

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/community/util/workflow_util.py --- /dev/null +++ b/lib/galaxy/webapps/community/util/workflow_util.py @@ -0,0 +1,384 @@ +from galaxy import eggs +import pkg_resources + +pkg_resources.require( "SVGFig" ) + +import logging, svgfig +from galaxy.util import json +import galaxy.util.shed_util_common as suc +from galaxy.tool_shed import encoding_util +from galaxy.workflow.modules import InputDataModule, ToolModule, WorkflowModuleFactory +import galaxy.webapps.galaxy.controllers.workflow +import galaxy.tools +import galaxy.tools.parameters + +log = logging.getLogger( __name__ ) + +class RepoInputDataModule( InputDataModule ): + + type = "data_input" + name = "Input dataset" + + @classmethod + def new( Class, trans, tools_metadata=None, tool_id=None ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + return module + @classmethod + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata=None, secure=True ): + module = Class( trans ) + state = json.from_json_string( step_dict[ "tool_state" ] ) + module.state = dict( name=state.get( "name", "Input Dataset" ) ) + return module + @classmethod + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans ) + module.state = dict( name="Input Dataset" ) + if step.tool_inputs and "name" in step.tool_inputs: + module.state[ 'name' ] = step.tool_inputs[ 'name' ] + return module + +class RepoToolModule( ToolModule ): + + type = "tool" + + def __init__( self, trans, repository_id, changeset_revision, tools_metadata, tool_id ): + self.trans = trans + self.tools_metadata = tools_metadata + self.tool_id = tool_id + self.tool = None + self.errors = None + for tool_dict in tools_metadata: + if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: + if trans.webapp.name == 'community': + # We're in the tool shed. + repository, self.tool, message = suc.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) + if message and self.tool is None: + self.errors = 'unavailable' + break + else: + # We're in Galaxy. + self.tool = trans.app.toolbox.tools_by_id.get( self.tool_id, None ) + if self.tool is None: + self.errors = 'unavailable' + self.post_job_actions = {} + self.workflow_outputs = [] + self.state = None + @classmethod + def new( Class, trans, repository_id, changeset_revision, tools_metadata, tool_id=None ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) + module.state = module.tool.new_state( trans, all_pages=True ) + return module + @classmethod + def from_dict( Class, trans, repository_id, changeset_revision, step_dict, tools_metadata, secure=True ): + tool_id = step_dict[ 'tool_id' ] + module = Class( trans, repository_id, changeset_revision, tools_metadata, tool_id ) + module.state = galaxy.tools.DefaultToolState() + if module.tool is not None: + module.state.decode( step_dict[ "tool_state" ], module.tool, module.trans.app, secure=secure ) + module.errors = step_dict.get( "tool_errors", None ) + return module + @classmethod + def from_workflow_step( Class, trans, repository_id, changeset_revision, tools_metadata, step ): + module = Class( trans, repository_id, changeset_revision, tools_metadata, step.tool_id ) + module.state = galaxy.tools.DefaultToolState() + if module.tool: + module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) + else: + module.state.inputs = {} + module.errors = step.tool_errors + return module + def get_data_inputs( self ): + data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): + if isinstance( input, galaxy.tools.parameters.DataToolParameter ): + data_inputs.append( dict( name=prefixed_name, + label=prefixed_label, + extensions=input.extensions ) ) + if self.tool: + galaxy.tools.parameters.visit_input_values( self.tool.inputs, self.state.inputs, callback ) + return data_inputs + def get_data_outputs( self ): + data_outputs = [] + if self.tool: + data_inputs = None + for name, tool_output in self.tool.outputs.iteritems(): + if tool_output.format_source != None: + # Default to special name "input" which remove restrictions on connections + formats = [ 'input' ] + if data_inputs == None: + data_inputs = self.get_data_inputs() + # Find the input parameter referenced by format_source + for di in data_inputs: + # Input names come prefixed with conditional and repeat names separated by '|', + # so remove prefixes when comparing with format_source. + if di[ 'name' ] != None and di[ 'name' ].split( '|' )[ -1 ] == tool_output.format_source: + formats = di[ 'extensions' ] + else: + formats = [ tool_output.format ] + for change_elem in tool_output.change_format: + for when_elem in change_elem.findall( 'when' ): + format = when_elem.get( 'format', None ) + if format and format not in formats: + formats.append( format ) + data_outputs.append( dict( name=name, extensions=formats ) ) + return data_outputs + +class RepoWorkflowModuleFactory( WorkflowModuleFactory ): + def __init__( self, module_types ): + self.module_types = module_types + def new( self, trans, type, tools_metadata=None, tool_id=None ): + """Return module for type and (optional) tool_id initialized with new / default state.""" + assert type in self.module_types + return self.module_types[type].new( trans, tool_id ) + def from_dict( self, trans, repository_id, changeset_revision, step_dict, **kwd ): + """Return module initialized from the data in dictionary `step_dict`.""" + type = step_dict[ 'type' ] + assert type in self.module_types + return self.module_types[ type ].from_dict( trans, repository_id, changeset_revision, step_dict, **kwd ) + def from_workflow_step( self, trans, repository_id, changeset_revision, tools_metadata, step ): + """Return module initialized from the WorkflowStep object `step`.""" + type = step.type + return self.module_types[ type ].from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) + +module_factory = RepoWorkflowModuleFactory( dict( data_input=RepoInputDataModule, tool=RepoToolModule ) ) + +def generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=None ): + """ + Return an svg image representation of a workflow dictionary created when the workflow was exported. This method is called + from both Galaxy and the tool shed. When called from the tool shed, repository_metadata_id will have a value and repository_id + will be None. When called from Galaxy, repository_metadata_id will be None and repository_id will have a value. + """ + workflow_name = encoding_util.tool_shed_decode( workflow_name ) + if trans.webapp.name == 'community': + # We're in the tool shed. + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + metadata = repository_metadata.metadata + else: + # We're in Galaxy. + repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + changeset_revision = repository.changeset_revision + metadata = repository.metadata + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + for workflow_tup in metadata[ 'workflows' ]: + workflow_dict = workflow_tup[1] + if workflow_dict[ 'name' ] == workflow_name: + break + if 'tools' in metadata: + tools_metadata = metadata[ 'tools' ] + else: + tools_metadata = [] + workflow, missing_tool_tups = get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ) + data = [] + canvas = svgfig.canvas( style="stroke:black; fill:none; stroke-width:1px; stroke-linejoin:round; text-anchor:left" ) + text = svgfig.SVG( "g" ) + connectors = svgfig.SVG( "g" ) + boxes = svgfig.SVG( "g" ) + svgfig.Text.defaults[ "font-size" ] = "10px" + in_pos = {} + out_pos = {} + margin = 5 + # Spacing between input/outputs. + line_px = 16 + # Store px width for boxes of each step. + widths = {} + max_width, max_x, max_y = 0, 0, 0 + for step in workflow.steps: + step.upgrade_messages = {} + module = module_factory.from_workflow_step( trans, repository_id, changeset_revision, tools_metadata, step ) + tool_errors = module.type == 'tool' and not module.tool + module_data_inputs = get_workflow_data_inputs( step, module ) + module_data_outputs = get_workflow_data_outputs( step, module, workflow.steps ) + step_dict = { + 'id' : step.order_index, + 'data_inputs' : module_data_inputs, + 'data_outputs' : module_data_outputs, + 'position' : step.position, + 'tool_errors' : tool_errors + } + input_conn_dict = {} + for conn in step.input_connections: + input_conn_dict[ conn.input_name ] = dict( id=conn.output_step.order_index, output_name=conn.output_name ) + step_dict[ 'input_connections' ] = input_conn_dict + data.append( step_dict ) + x, y = step.position[ 'left' ], step.position[ 'top' ] + count = 0 + module_name = get_workflow_module_name( module, missing_tool_tups ) + max_len = len( module_name ) * 1.5 + text.append( svgfig.Text( x, y + 20, module_name, **{ "font-size": "14px" } ).SVG() ) + y += 45 + for di in module_data_inputs: + cur_y = y + count * line_px + if step.order_index not in in_pos: + in_pos[ step.order_index ] = {} + in_pos[ step.order_index ][ di[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, di[ 'label' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( di[ 'label' ] ) ) + if len( module.get_data_inputs() ) > 0: + y += 15 + for do in module_data_outputs: + cur_y = y + count * line_px + if step.order_index not in out_pos: + out_pos[ step.order_index ] = {} + out_pos[ step.order_index ][ do[ 'name' ] ] = ( x, cur_y ) + text.append( svgfig.Text( x, cur_y, do[ 'name' ] ).SVG() ) + count += 1 + max_len = max( max_len, len( do['name' ] ) ) + widths[ step.order_index ] = max_len * 5.5 + max_x = max( max_x, step.position[ 'left' ] ) + max_y = max( max_y, step.position[ 'top' ] ) + max_width = max( max_width, widths[ step.order_index ] ) + for step_dict in data: + tool_unavailable = step_dict[ 'tool_errors' ] + width = widths[ step_dict[ 'id' ] ] + x, y = step_dict[ 'position' ][ 'left' ], step_dict[ 'position' ][ 'top' ] + if tool_unavailable: + fill = "#EBBCB2" + else: + fill = "#EBD9B2" + boxes.append( svgfig.Rect( x - margin, y, x + width - margin, y + 30, fill=fill ).SVG() ) + box_height = ( len( step_dict[ 'data_inputs' ] ) + len( step_dict[ 'data_outputs' ] ) ) * line_px + margin + # Draw separator line. + if len( step_dict[ 'data_inputs' ] ) > 0: + box_height += 15 + sep_y = y + len( step_dict[ 'data_inputs' ] ) * line_px + 40 + text.append( svgfig.Line( x - margin, sep_y, x + width - margin, sep_y ).SVG() ) + # Define an input/output box. + boxes.append( svgfig.Rect( x - margin, y + 30, x + width - margin, y + 30 + box_height, fill="#ffffff" ).SVG() ) + for conn, output_dict in step_dict[ 'input_connections' ].iteritems(): + in_coords = in_pos[ step_dict[ 'id' ] ][ conn ] + # out_pos_index will be a step number like 1, 2, 3... + out_pos_index = output_dict[ 'id' ] + # out_pos_name will be a string like 'o', 'o2', etc. + out_pos_name = output_dict[ 'output_name' ] + if out_pos_index in out_pos: + # out_conn_index_dict will be something like: + # 7: {'o': (824.5, 618)} + out_conn_index_dict = out_pos[ out_pos_index ] + if out_pos_name in out_conn_index_dict: + out_conn_pos = out_pos[ out_pos_index ][ out_pos_name ] + else: + # Take any key / value pair available in out_conn_index_dict. + # A problem will result if the dictionary is empty. + if out_conn_index_dict.keys(): + key = out_conn_index_dict.keys()[0] + out_conn_pos = out_pos[ out_pos_index ][ key ] + adjusted = ( out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ], out_conn_pos[ 1 ] ) + text.append( svgfig.SVG( "circle", + cx=out_conn_pos[ 0 ] + widths[ output_dict[ 'id' ] ] - margin, + cy=out_conn_pos[ 1 ] - margin, + r = 5, + fill="#ffffff" ) ) + connectors.append( svgfig.Line( adjusted[ 0 ], + adjusted[ 1 ] - margin, + in_coords[ 0 ] - 10, + in_coords[ 1 ], + arrow_end = "true" ).SVG() ) + canvas.append( connectors ) + canvas.append( boxes ) + canvas.append( text ) + width, height = ( max_x + max_width + 50 ), max_y + 300 + canvas[ 'width' ] = "%s px" % width + canvas[ 'height' ] = "%s px" % height + canvas[ 'viewBox' ] = "0 0 %s %s" % ( width, height ) + trans.response.set_content_type( "image/svg+xml" ) + return canvas.standalone_xml() +def get_workflow_data_inputs( step, module ): + if module.type == 'tool': + if module.tool: + return module.get_data_inputs() + else: + data_inputs = [] + for wfsc in step.input_connections: + data_inputs_dict = {} + data_inputs_dict[ 'extensions' ] = [ '' ] + data_inputs_dict[ 'name' ] = wfsc.input_name + data_inputs_dict[ 'label' ] = 'Unknown' + data_inputs.append( data_inputs_dict ) + return data_inputs + return module.get_data_inputs() +def get_workflow_data_outputs( step, module, steps ): + if module.type == 'tool': + if module.tool: + return module.get_data_outputs() + else: + data_outputs = [] + data_outputs_dict = {} + data_outputs_dict[ 'extensions' ] = [ 'input' ] + found = False + for workflow_step in steps: + for wfsc in workflow_step.input_connections: + if step.name == wfsc.output_step.name: + data_outputs_dict[ 'name' ] = wfsc.output_name + found = True + break + if found: + break + if not found: + # We're at the last step of the workflow. + data_outputs_dict[ 'name' ] = 'output' + data_outputs.append( data_outputs_dict ) + return data_outputs + return module.get_data_outputs() +def get_workflow_from_dict( trans, workflow_dict, tools_metadata, repository_id, changeset_revision ): + """Return a workflow object from the dictionary object created when it was exported.""" + trans.workflow_building_mode = True + workflow = trans.model.Workflow() + workflow.name = workflow_dict[ 'name' ] + workflow.has_errors = False + steps = [] + # Keep ids for each step that we need to use to make connections. + steps_by_external_id = {} + # Keep track of tools required by the workflow that are not available in + # the tool shed repository. Each tuple in the list of missing_tool_tups + # will be ( tool_id, tool_name, tool_version ). + missing_tool_tups = [] + # First pass to build step objects and populate basic values + for key, step_dict in workflow_dict[ 'steps' ].iteritems(): + # Create the model class for the step + step = trans.model.WorkflowStep() + step.name = step_dict[ 'name' ] + step.position = step_dict[ 'position' ] + module = module_factory.from_dict( trans, repository_id, changeset_revision, step_dict, tools_metadata=tools_metadata, secure=False ) + if module.type == 'tool' and module.tool is None: + # A required tool is not available in the current repository. + step.tool_errors = 'unavailable' + missing_tool_tup = ( step_dict[ 'tool_id' ], step_dict[ 'name' ], step_dict[ 'tool_version' ] ) + if missing_tool_tup not in missing_tool_tups: + missing_tool_tups.append( missing_tool_tup ) + module.save_to_step( step ) + if step.tool_errors: + workflow.has_errors = True + # Stick this in the step temporarily. + step.temp_input_connections = step_dict[ 'input_connections' ] + steps.append( step ) + steps_by_external_id[ step_dict[ 'id' ] ] = step + # Second pass to deal with connections between steps. + for step in steps: + # Input connections. + for input_name, conn_dict in step.temp_input_connections.iteritems(): + if conn_dict: + output_step = steps_by_external_id[ conn_dict[ 'id' ] ] + conn = trans.model.WorkflowStepConnection() + conn.input_step = step + conn.input_name = input_name + conn.output_step = output_step + conn.output_name = conn_dict[ 'output_name' ] + step.input_connections.append( conn ) + del step.temp_input_connections + # Order the steps if possible. + galaxy.webapps.galaxy.controllers.workflow.attach_ordered_steps( workflow, steps ) + return workflow, missing_tool_tups +def get_workflow_module_name( module, missing_tool_tups ): + module_name = module.get_name() + if module.type == 'tool' and module_name == 'unavailable': + for missing_tool_tup in missing_tool_tups: + missing_tool_id, missing_tool_name, missing_tool_version = missing_tool_tup + if missing_tool_id == module.tool_id: + module_name = '%s' % missing_tool_name + break + return module_name \ No newline at end of file

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1,10 +1,10 @@ import urllib2, tempfile from admin import * -from galaxy.util.json import from_json_string, to_json_string +from galaxy.util import json import galaxy.util.shed_util as shed_util import galaxy.util.shed_util_common as suc from galaxy.tool_shed import encoding_util -from galaxy.webapps.community.util import container_util +from galaxy.webapps.community.util import container_util, workflow_util from galaxy import eggs, tools

eggs.require( 'mercurial' ) @@ -552,6 +552,11 @@ galaxy_url = url_for( '/', qualified=True ) url = suc.url_join( tool_shed_url, 'repository/find_workflows?galaxy_url=%s' % galaxy_url ) return trans.response.send_redirect( url ) + @web.expose + @web.require_admin + def generate_workflow_image( self, trans, workflow_name, repository_id=None ): + """Return an svg image representation of a workflow dictionary created when the workflow was exported.""" + return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=repository_id ) @web.json @web.require_admin def get_file_contents( self, trans, file_path ): @@ -576,7 +581,7 @@ raw_text = response.read() response.close() if len( raw_text ) > 2: - encoded_text = from_json_string( raw_text ) + encoded_text = json.from_json_string( raw_text ) text = encoding_util.tool_shed_decode( encoded_text ) else: text = '' @@ -586,6 +591,71 @@ return tool_version.get_version_ids( app, reverse=True ) @web.expose @web.require_admin + def import_workflow( self, trans, workflow_name, repository_id, **kwd ): + # FIXME: importing doesn't yet work... + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if workflow_name: + workflow_name = encoding_util.tool_shed_decode( workflow_name ) + repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + changeset_revision = repository.changeset_revision + metadata = repository.metadata + workflows = metadata[ 'workflows' ] + tools_metadata = metadata[ 'tools' ] + workflow_dict = None + for workflow_data_tuple in workflows: + # The value of workflow_data_tuple is ( relative_path_to_workflow_file, exported_workflow_dict ). + relative_path_to_workflow_file, exported_workflow_dict = workflow_data_tuple + if exported_workflow_dict[ 'name' ] == workflow_name: + # If the exported workflow is available on disk, import it. + if os.path.exists( relative_path_to_workflow_file ): + workflow_file = open( relative_path_to_workflow_file, 'rb' ) + workflow_data = workflow_file.read() + workflow_file.close() + workflow_dict = json.from_json_string( workflow_data ) + else: + # Use the current exported_workflow_dict. + workflow_dict = exported_workflow_dict + break + if workflow_dict: + # Create workflow if possible. If a required tool is not available in the local + # Galaxy instance, the tool information will be available in the step_dict. + src = None + workflow, missing_tool_tups = workflow_util.get_workflow_from_dict( trans, + workflow_dict, + tools_metadata, + repository_id, + changeset_revision ) + if workflow_name: + workflow.name = workflow_name + # Provide user feedback and show workflow list. + if workflow.has_errors: + message += "Imported, but some steps in this workflow have validation errors. " + status = "error" + if workflow.has_cycles: + message += "Imported, but this workflow contains cycles. " + status = "error" + else: + message += "Workflow <b>%s</b> imported successfully. " % workflow.name + if missing_tool_tups: + # TODO: rework this since it is used in the tool shed, but shoudn't be used in Galaxy. + name_and_id_str = '' + for missing_tool_tup in missing_tool_tups: + tool_id, tool_name, other = missing_tool_tup + name_and_id_str += 'name: %s, id: %s' % ( str( tool_id ), str( tool_name ) ) + log.debug( "The following tools required by this workflow are missing from this Galaxy instance: %s" % name_and_id_str ) + else: + message += 'The workflow named %s is not included in the metadata for revision %s of repository %s' % \ + ( str( workflow_name ), str( changeset_revision ), str( repository.name ) ) + status = 'error' + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repository', + id=repository_id, + message=message, + status=status ) ) + @web.expose + @web.require_admin def initiate_repository_installation( self, trans, shed_repository_ids, encoded_kwd, reinstalling=False ): tsr_ids = util.listify( shed_repository_ids ) tool_shed_repositories = [] @@ -728,7 +798,7 @@ text = response.read() response.close() if text: - tool_version_dicts = from_json_string( text ) + tool_version_dicts = json.from_json_string( text ) shed_util.handle_tool_versions( trans.app, tool_version_dicts, tool_shed_repository ) else: message += "Version information for the tools included in the <b>%s</b> repository is missing. " % name @@ -1084,7 +1154,7 @@ response = urllib2.urlopen( url ) raw_text = response.read() response.close() - repo_information_dict = from_json_string( raw_text ) + repo_information_dict = json.from_json_string( raw_text ) includes_tools = util.string_as_bool( repo_information_dict.get( 'includes_tools', False ) ) includes_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_repository_dependencies', False ) ) includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) @@ -1191,7 +1261,7 @@ response = urllib2.urlopen( url ) raw_text = response.read() response.close() - readme_files_dict = from_json_string( raw_text ) + readme_files_dict = json.from_json_string( raw_text ) # Since we are installing a new repository, no tool dependencies will be considered "missing". Most of the repository contents # are set to None since we don't yet know what they are. containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, @@ -1593,7 +1663,7 @@ text = response.read() response.close() if text: - tool_version_dicts = from_json_string( text ) + tool_version_dicts = json.from_json_string( text ) shed_util.handle_tool_versions( trans.app, tool_version_dicts, repository ) message = "Tool versions have been set for all included tools." status = 'done' @@ -1785,7 +1855,26 @@ tool_lineage=tool_lineage, message=message, status=status ) - + @web.expose + @web.require_admin + def view_workflow( self, trans, workflow_name=None, repository_id=None, **kwd ): + """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + if workflow_name: + workflow_name = encoding_util.tool_shed_decode( workflow_name ) + repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) + changeset_revision = repository.changeset_revision + metadata = repository.metadata + return trans.fill_template( "/admin/tool_shed_repository/view_workflow.mako", + repository=repository, + changeset_revision=changeset_revision, + repository_id=repository_id, + workflow_name=workflow_name, + metadata=metadata, + message=message, + status=status ) ## ---- Utility methods -------------------------------------------------------

def build_shed_tool_conf_select_field( trans ):

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -2,7 +2,7 @@ from elementtree.ElementTree import Element from galaxy import web from galaxy.tools.parameters import DataToolParameter, DummyDataset, RuntimeValue, check_param, visit_input_values -from galaxy.tools import DefaultToolState +import galaxy.tools from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string from galaxy.jobs.actions.post import ActionBox @@ -139,7 +139,7 @@ return dict( input=DataToolParameter( None, Element( "param", name="input", label=label, multiple=True, type="data", format=', '.join(filter_set) ), self.trans ) )

def get_runtime_state( self ): - state = DefaultToolState() + state = galaxy.tools.DefaultToolState() state.inputs = dict( input=None ) return state

@@ -149,7 +149,7 @@

def decode_runtime_state( self, trans, string ): fake_tool = Bunch( inputs = self.get_runtime_inputs() ) - state = DefaultToolState() + state = galaxy.tools.DefaultToolState() state.decode( string, fake_tool, trans.app ) return state

@@ -192,7 +192,7 @@ def from_dict( Class, trans, d, secure=True ): tool_id = d[ 'tool_id' ] module = Class( trans, tool_id ) - module.state = DefaultToolState() + module.state = galaxy.tools.DefaultToolState() if module.tool is not None: module.state.decode( d[ "tool_state" ], module.tool, module.trans.app, secure=secure ) module.errors = d.get( "tool_errors", None ) @@ -213,7 +213,7 @@ tool_id = tool.id if ( trans.app.toolbox and tool_id in trans.app.toolbox.tools_by_id ): module = Class( trans, tool_id ) - module.state = DefaultToolState() + module.state = galaxy.tools.DefaultToolState() module.state.inputs = module.tool.params_from_strings( step.tool_inputs, trans.app, ignore_errors=True ) module.errors = step.tool_errors # module.post_job_actions = step.post_job_actions

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 templates/admin/tool_shed_repository/view_workflow.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/view_workflow.mako @@ -0,0 +1,45 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/community/common/common.mako" import="*" /> +<%namespace file="/webapps/community/repository/common.mako" import="*" /> + +<% + from galaxy.web.framework.helpers import time_ago + from galaxy.tool_shed.encoding_util import tool_shed_encode +%> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/community/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<%def name="render_workflow( workflow_name, repository_id )"> + <% center_url = h.url_for( controller='admin_toolshed', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_id=repository_id ) %> + <iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe> +</%def> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <li><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='import_workflow', workflow_name=tool_shed_encode( workflow_name ), repository_id=repository_id )}">Import workflow to Galaxy</a></li> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolFormTitle">${workflow_name | h}</div> +<div class="form-row"> + <div class="toolParamHelp" style="clear: both;"> + (this page displays SVG graphics) + </div> +</div> +<br clear="left"/> + +${render_workflow( workflow_name, repository_id )}

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -231,6 +231,10 @@ folder_label = "%s<i> - this repository's tools require handling of these dependencies</i>" % folder_label col_span_str = 'colspan="4"' elif folder.workflows: + if folder.description: + folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) + else: + folder_label = "%s<i> - click the name to view an SVG image of the workflow</i>" % folder_label col_span_str = 'colspan="4"' %><td ${col_span_str} style="padding-left: ${folder_pad}px;"> @@ -439,7 +443,11 @@ <a class="action-button" href="${h.url_for( controller='repository', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">View tool metadata</a></div> %else: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">${tool.name | h}</a> + %if tool.repository_installation_status == trans.model.ToolShedRepository.installation_status.INSTALLED: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( tool.repository_id ), changeset_revision=tool.changeset_revision, tool_id=tool.tool_id )}">${tool.name | h}</a> + %else: + ${tool.name | h} + %endif %endif %else: ${tool.name | h} @@ -515,6 +523,13 @@ <% from galaxy.tool_shed.encoding_util import tool_shed_encode encoded_id = trans.security.encode_id( workflow.id ) + encoded_workflow_name = tool_shed_encode( workflow.workflow_name ) + if trans.webapp.name == 'community': + encoded_repository_metadata_id = trans.security.encode_id( workflow.repository_metadata_id ) + encoded_repository_id = None + else: + encoded_repository_metadata_id = None + encoded_repository_id = trans.security.encode_id( workflow.repository_id ) if row_is_header: cell_type = 'th' else: @@ -528,8 +543,12 @@ <${cell_type} style="padding-left: ${pad+20}px;"> %if row_is_header: ${workflow.workflow_name | h} + %elif trans.webapp.name == 'community' and encoded_repository_metadata_id: + <a href="${h.url_for( controller='repository', action='view_workflow', workflow_name=encoded_workflow_name, repository_metadata_id=encoded_repository_metadata_id )}">${workflow.workflow_name | h}</a> + %elif trans.webapp.name == 'galaxy' and encoded_repository_id: + <a href="${h.url_for( controller='admin_toolshed', action='view_workflow', workflow_name=encoded_workflow_name, repository_id=encoded_repository_id )}">${workflow.workflow_name | h}</a> %else: - <a href="${h.url_for( controller='workflow', action='view_workflow', repository_metadata_id=trans.security.encode_id( workflow.repository_metadata_id ), workflow_name=tool_shed_encode( workflow.workflow_name ) )}">${workflow.workflow_name | h}</a> + ${workflow.workflow_name | h} %endif </${cell_type}><${cell_type}>${workflow.steps | h}</${cell_type}> @@ -557,7 +576,7 @@ missing_repository_dependencies_root_folder = containers_dict.get( 'missing_repository_dependencies', None ) tool_dependencies_root_folder = containers_dict.get( 'tool_dependencies', None ) missing_tool_dependencies_root_folder = containers_dict.get( 'missing_tool_dependencies', None ) - valid_tools_root_folder = containers_dict.get( 'valid_tools', none ) + valid_tools_root_folder = containers_dict.get( 'valid_tools', None ) workflows_root_folder = containers_dict.get( 'workflows', None )

has_contents = datatypes_root_folder or invalid_tools_root_folder or valid_tools_root_folder or workflows_root_folder

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 templates/webapps/community/repository/view_workflow.mako --- a/templates/webapps/community/repository/view_workflow.mako +++ b/templates/webapps/community/repository/view_workflow.mako @@ -7,22 +7,23 @@ from galaxy.web.framework.helpers import time_ago from galaxy.tool_shed.encoding_util import tool_shed_encode

- in_tool_shed = trans.webapp.name == 'community' is_admin = trans.user_is_admin() is_new = repository.is_new( trans.app ) can_manage = is_admin or trans.user == repository.user - can_contact_owner = in_tool_shed and trans.user and trans.user != repository.user - can_push = in_tool_shed and trans.app.security_agent.can_push( trans.app, trans.user, repository ) + can_contact_owner = trans.user and trans.user != repository.user + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_upload = can_push - can_download = in_tool_shed and not is_new and ( not is_malicious or can_push ) - can_browse_contents = in_tool_shed and not is_new - can_rate = in_tool_shed and not is_new and trans.user and repository.user != trans.user - can_view_change_log = in_tool_shed and not is_new + can_download = not is_new and ( not is_malicious or can_push ) + can_browse_contents = not is_new + can_rate = not is_new and trans.user and repository.user != trans.user + can_view_change_log = not is_new if can_push: browse_label = 'Browse or delete repository tip files' else: browse_label = 'Browse repository tip files' - has_readme = metadata and 'readme' in metadata + has_readme = metadata and 'readme_files' in metadata + + # <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to Galaxy</a></li> %><%! @@ -34,57 +35,43 @@ %><%inherit file="${inherit(context)}"/>

-<%def name="render_workflow( repository_metadata_id, workflow_name )"> - <% center_url = h.url_for( controller='workflow', action='generate_workflow_image', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) ) %> +<%def name="render_workflow( workflow_name, repository_metadata_id )"> + <% center_url = h.url_for( controller='repository', action='generate_workflow_image', workflow_name=tool_shed_encode( workflow_name ), repository_metadata_id=repository_metadata_id, repository_id=None ) %><iframe name="galaxy_main" id="galaxy_main" frameborder="0" style="position: absolute; width: 100%; height: 100%;" src="${center_url}"></iframe></%def><br/><br/><ul class="manage-table-actions"> - %if in_tool_shed: - %if is_new and can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %else: - <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> - <div popupmenu="repository-${repository.id}-popup"> - %if can_upload: - <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> - %endif - %if can_manage: - <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> - %else: - <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> - %endif - %if can_view_change_log: - <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> - %endif - %if can_rate: - <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> - %endif - %if can_browse_contents: - <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> - %endif - %if can_contact_owner: - <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> - %endif - %if can_download: - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> - <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> - %endif - </div> - %endif + %if is_new and can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> %else: <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <li><a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', repository_metadata_id=repository_metadata_id, workflow_name=tool_shed_encode( workflow_name ) )}">Import workflow to local Galaxy</a></li> - <li><a class="action-button" href="${h.url_for( controller='repository', action='install_repositories_by_revision', repository_ids=trans.security.encode_id( repository.id ), changeset_revisions=changeset_revision )}">Install repository to local Galaxy</a></li> - </div> - <li><a class="action-button" id="toolshed-${repository.id}-popup" class="menubutton">Tool Shed Actions</a></li> - <div popupmenu="toolshed-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='repository', action='browse_valid_categories' )}">Browse valid repositories</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_tools' )}">Search for valid tools</a> - <a class="action-button" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a> + %if can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> + %endif + %if can_manage: + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">Manage repository</a> + %else: + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=repository.tip( trans.app ) )}">View repository</a> + %endif + %if can_view_change_log: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + %endif + %if can_rate: + <a class="action-button" href="${h.url_for( controller='repository', action='rate_repository', id=trans.app.security.encode_id( repository.id ) )}">Rate repository</a> + %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif + %if can_contact_owner: + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> + %endif + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> + %endif </div> %endif </ul> @@ -102,4 +89,4 @@ </div><br clear="left"/>

-${render_workflow( repository_metadata_id, workflow_name )} +${render_workflow( workflow_name, repository_metadata_id )}

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -454,9 +454,11 @@ ( self.security.encode_id( repository.id ), tool_xml_path, changeset_revision ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed ) - def load_workflow_image( self, repository, workflow_name, strings_displayed=[], strings_not_displayed=[] ): + def load_workflow_image_in_tool_shed( self, repository, workflow_name, strings_displayed=[], strings_not_displayed=[] ): + # FIXME: Can not always assume the first repository_metadata record is the correct one. + # TODO: Add a method for displaying a workflow image in Galaxy. metadata = self.get_repository_metadata( repository ) - url = '/workflow/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \ + url = '/repository/generate_workflow_image?repository_metadata_id=%s&workflow_name=%s' % \ ( self.security.encode_id( metadata[0].id ), tool_shed_encode( workflow_name ) ) self.visit_url( url ) self.check_for_strings( strings_displayed, strings_not_displayed )

diff -r 875ac898df00fd919b6b24f58562fadbf03dc5e1 -r 7073d786cad0f0d251d4ea9b2c42171f698cf953 test/tool_shed/functional/test_0060_workflows.py --- a/test/tool_shed/functional/test_0060_workflows.py +++ b/test/tool_shed/functional/test_0060_workflows.py @@ -46,7 +46,7 @@ workflow_filename, filepath=workflow_filepath, commit_message='Uploaded filtering workflow.' ) - self.load_workflow_image( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] ) + self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_displayed=[ '#EBBCB2' ] ) def test_0020_upload_tool( self ): '''Upload the missing tool for the workflow in the previous step, and verify that the error is no longer present.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name ) @@ -54,7 +54,7 @@ 'filtering/filtering_2.2.0.tar', commit_message="Uploaded filtering 2.2.0", remove_repo_files_not_in_tar='No' ) - self.load_workflow_image( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] ) + self.load_workflow_image_in_tool_shed( repository, workflow_name, strings_not_displayed=[ '#EBBCB2' ] ) def test_0025_verify_repository_metadata( self ): '''Verify that resetting the metadata does not change it.''' repository = test_db_util.get_repository_by_name_and_owner( repository_name, common.test_user_1_name )

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

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