July 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 21 Jul '14

21 Jul '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c118476b5823/ Changeset: c118476b5823 User: jgoecks Date: 2014-07-21 16:19:14 Summary: Use jquery to remove event handler. Affected #: 1 file diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r c118476b5823c676267dbe5d48f7105711e3c15d static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -356,7 +356,7 @@ buttons: { "Cancel": function() { Galaxy.modal.hide(); }, "Leave without Saving" : function() { - window.onbeforeunload = undefined; + $(window).off('beforeunload'); window.location = galaxy_config.root + 'visualization'; }, "Save" : function() { https://bitbucket.org/galaxy/galaxy-central/commits/bca25a3bc9c7/ Changeset: bca25a3bc9c7 User: jgoecks Date: 2014-07-21 16:26:18 Summary: Trackster: remove bottom label track because it is redundant. Affected #: 1 file diff -r c118476b5823c676267dbe5d48f7105711e3c15d -r bca25a3bc9c7618eb37fb467ae32564fa213aac5 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -885,8 +885,6 @@ }); }); }); - // Another label track at bottom - this.nav_labeltrack = $("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container); // Navigation at top this.nav_container = $("<div/>").addClass("trackster-nav-container").prependTo(this.top_container); this.nav = $("<div/>").addClass("trackster-nav").appendTo(this.nav_container); @@ -1042,7 +1040,7 @@ // Dragging in the top label track allows selecting a region to zoom in on selected region. this.top_labeltrack.bind( "dragstart", function( e, d ) { return $("<div/>").addClass('zoom-area').css( - "height", view.browser_content_div.height() + view.top_labeltrack.height() + view.nav_labeltrack.height() + 1 + "height", view.browser_content_div.height() + view.top_labeltrack.height() + 1 ).appendTo( $(this) ); }).bind( "drag", function( e, d ) { $( d.proxy ).css({ left: Math.min( e.pageX, d.startX ) - view.container.offset().left, width: Math.abs( e.pageX - d.startX ) }); @@ -1091,7 +1089,6 @@ */ this.add_label_track( new LabelTrack( this, { content_div: this.top_labeltrack } ) ); - this.add_label_track( new LabelTrack( this, { content_div: this.nav_labeltrack } ) ); $(window).bind("resize", function() { // Stop previous timer. https://bitbucket.org/galaxy/galaxy-central/commits/f9b47a91b7f2/ Changeset: f9b47a91b7f2 User: jgoecks Date: 2014-07-21 16:27:44 Summary: Trackster: some fixes for vertical position element. Affected #: 1 file diff -r bca25a3bc9c7618eb37fb467ae32564fa213aac5 -r f9b47a91b7f2611c87c9dc7a0ceafc733f6bc181 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1062,11 +1062,9 @@ view.request_redraw(); }); + // FIXME: this is still wonky for embedded visualizations. + /* // For vertical alignment, track mouse with simple line. - // Fixes needed for this to work: - // (a) make work with embedded visualizations; - // (b) seems to get stuck on tile overlaps. - /* var mouse_tracker_div = $('<div/>').addClass('mouse-pos').appendTo(parent_element); // Show tracker only when hovering over view. @@ -1075,9 +1073,8 @@ mouse_tracker_div.show(); parent_element.mousemove(function(e) { mouse_tracker_div.css({ - // -1 makes it appear next to the mouse w/o obscuring clicking - // and dragging on view elements. - left: e.pageX - 1 + // -1 makes line appear next to the mouse w/o preventing mouse actions. + left: e.pageX - parent_element.offset().left - 1 }); }); }, https://bitbucket.org/galaxy/galaxy-central/commits/972a80267009/ Changeset: 972a80267009 User: jgoecks Date: 2014-07-21 19:23:41 Summary: Trackster: do not reset overview when changing chromosome. Affected #: 1 file diff -r f9b47a91b7f2611c87c9dc7a0ceafc733f6bc181 -r 972a80267009126e558ba14142df48b897db48c8 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1287,7 +1287,6 @@ } } - view.reset_overview(); view.request_redraw(); } }, https://bitbucket.org/galaxy/galaxy-central/commits/e9de99ef7710/ Changeset: e9de99ef7710 User: jgoecks Date: 2014-07-21 19:42:14 Summary: Automated merge Affected #: 19 files diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -413,12 +413,12 @@ # Make sure the current user's API key proves he is an admin user in this Galaxy instance. if not trans.user_is_admin(): raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' ) - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=False ) + irmm = InstalledRepositoryMetadataManager( trans.app ) + query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: repository_id = trans.security.encode_id( repository.id ) try: - irmm = InstalledRepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b 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 @@ -30,6 +30,7 @@ from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -244,10 +245,10 @@ if kwd.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. - tool_util.remove_from_tool_panel( trans.app, - tool_shed_repository, - shed_tool_conf, - uninstall=remove_from_disk_checked ) + tpm = tool_panel_manager.ToolPanelManager( trans.app ) + tpm.remove_from_tool_panel( tool_shed_repository, + shed_tool_conf, + uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: data_manager_util.remove_from_data_manager( trans.app, tool_shed_repository ) if tool_shed_repository.includes_datatypes: @@ -1336,13 +1337,14 @@ # its repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools_for_display_in_tool_panel: + tpm = tool_panel_manager.ToolPanelManager( trans.app ) # Handle the selected tool panel location for loading tools included in the tool shed repository. tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( toolbox=trans.app.toolbox, - metadata=metadata, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_selection( toolbox=trans.app.toolbox, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) if tool_section is not None: # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't... tool_panel_section_id = str( tool_section.id ) @@ -1706,13 +1708,13 @@ @web.expose @web.require_admin def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): + irmm = InstalledRepositoryMetadataManager( trans.app ) if 'reset_metadata_on_selected_repositories_button' in kwd: - irmm = InstalledRepositoryMetadataManager( trans.app ) message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field( trans ) return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, @@ -1942,19 +1944,19 @@ updating_installed_repository=True, persist=True ) if 'tools' in metadata_dict: + tpm = tool_panel_manager.ToolPanelManager( trans.app ) tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) - tool_util.add_to_tool_panel( app=trans.app, - repository_name=str( repository.name ), - repository_clone_url=repository_clone_url, - changeset_revision=str( repository.installed_changeset_revision ), - repository_tools_tups=repository_tools_tups, - owner=str( repository.owner ), - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=False ) + tpm.add_to_tool_panel( repository_name=str( repository.name ), + repository_clone_url=repository_clone_url, + changeset_revision=str( repository.installed_changeset_revision ), + repository_tools_tups=repository_tools_tups, + owner=str( repository.owner ), + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=False ) # Add new Data Manager entries if 'data_manager' in metadata_dict: new_data_managers = data_manager_util.install_data_managers( trans.app, diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -392,7 +392,8 @@ my_writable = True handled_repository_ids = [] repository_ids = [] - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False ) # Make sure repositories of type tool_dependency_definition are first in the list. for repository in query: if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: @@ -426,13 +427,12 @@ This param can be used as an alternative to the above encoded_ids_to_skip. """ - def handle_repository( trans, repository, results ): + def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, repository_id ) + rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, @@ -451,7 +451,7 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -473,7 +473,7 @@ my_writable = util.asbool( payload.get( 'my_writable', False ) ) else: my_writable = True - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False ) # First reset metadata on all repositories of type repository_dependency_definition. for repository in query: encoded_id = trans.security.encode_id( repository.id ) @@ -481,7 +481,7 @@ log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ ( str( repository.id ), str( encoded_ids_to_skip ) ) ) elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) + results = handle_repository( trans, rmm, repository, results ) # Now reset metadata on all remaining repositories. for repository in query: encoded_id = trans.security.encode_id( repository.id ) @@ -489,7 +489,7 @@ log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ ( str( repository.id ), str( encoded_ids_to_skip ) ) ) elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) + results = handle_repository( trans, rmm, repository, results ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time return json.dumps( results, sort_keys=True, indent=4 ) @@ -511,10 +511,9 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, - trans.security.encode_id( repository.id ) ) + rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -348,13 +348,16 @@ @web.expose @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) if 'reset_metadata_on_selected_repositories_button' in kwd: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) + message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans ) + repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids', + multiple=True, + display='checkboxes', + my_writable=False ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -48,8 +48,8 @@ repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - error_message, status = rmm.set_repository_metadata( trans.request.host, trans.user, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2753,9 +2753,9 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, id, **kwd ) + rmm.reset_all_metadata_on_repository_in_tool_shed( id, **kwd ) if invalid_file_tups: repository = suc.get_repository_in_tool_shed( trans.app, id ) message = tool_util.generate_message_for_invalid_tools( trans.app, @@ -2774,13 +2774,16 @@ @web.expose def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ): + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) if 'reset_metadata_on_selected_repositories_button' in kwd: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) + message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans, my_writable=True ) + repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids', + multiple=True, + display='checkboxes', + my_writable=True ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, @@ -2840,9 +2843,8 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - trans.user, repository, **kwd ) if error_message: diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -262,10 +262,9 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - trans.user, repository, content_alert_str=content_alert_str, **kwd ) diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -727,9 +727,8 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - self.user, repository, content_alert_str=content_alert_str ) if error_message: diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -33,6 +33,7 @@ from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -535,7 +536,8 @@ self.app.config.shed_tool_data_table_config, persist=True ) if 'tools' in metadata_dict: - tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + tpm = tool_panel_manager.ToolPanelManager( self.app ) + tool_panel_dict = tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) @@ -555,16 +557,18 @@ sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the # local Galaxy instance. - tool_util.copy_sample_files( self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - tool_util.add_to_tool_panel( app=self.app, - repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) + tool_util.copy_sample_files( self.app, + sample_files, + tool_path=tool_path, + sample_files_copied=sample_files_copied ) + tpm.add_to_tool_panel( repository_name=tool_shed_repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=tool_shed_repository.owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) if 'data_manager' in metadata_dict: new_data_managers = data_manager_util.install_data_managers( self.app, self.app.config.shed_data_manager_config_file, @@ -644,10 +648,11 @@ tool_shed_url = installation_dict[ 'tool_shed_url' ] # Handle contained tools. if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section_label or tool_panel_section_id ): + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_section = \ - tool_util.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: tool_panel_section_key = None tool_section = None diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -11,11 +11,11 @@ from tool_shed.util import datatype_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util from tool_shed.util import xml_util from galaxy.model.orm import and_ from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -80,19 +80,19 @@ repository.deleted = False repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: + tpm = tool_panel_manager.ToolPanelManager( self.app ) metadata = repository.metadata repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] - tool_util.add_to_tool_panel( self.app, - repository.name, - repository_clone_url, - repository.installed_changeset_revision, - repository_tools_tups, - repository.owner, - shed_tool_conf, - tool_panel_dict, - new_install=False ) + tpm.add_to_tool_panel( repository.name, + repository_clone_url, + repository.installed_changeset_revision, + repository_tools_tups, + repository.owner, + shed_tool_conf, + tool_panel_dict, + new_install=False ) if repository.includes_data_managers: tp, data_manager_relative_install_dir = repository.get_tool_relative_path( self.app ) # Hack to add repository.name here, which is actually the root of the installed repository diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -3,6 +3,7 @@ from galaxy import util from galaxy.util import inflector +from galaxy.web.form_builder import SelectField from tool_shed.metadata import metadata_generator @@ -19,6 +20,32 @@ super( InstalledRepositoryMetadataManager, self ).__init__( app ) self.app = app + def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes' ): + """Generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + query = self.get_query_for_setting_metadata_on_repositories( order=True ) + for repository in query: + owner = str( repository.owner ) + option_label = '%s (%s)' % ( str( repository.name ), owner ) + option_value = '%s' % self.app.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field + + def get_query_for_setting_metadata_on_repositories( self, order=True ): + """ + Return a query containing repositories for resetting metadata. The order parameter + is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from the Galaxy API, order is False. + """ + if order: + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) \ + .order_by( self.app.install_model.ToolShedRepository.table.c.name, + self.app.install_model.ToolShedRepository.table.c.owner ) + else: + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) + def reset_all_metadata_on_installed_repository( self, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/repair_repository_manager.py --- a/lib/tool_shed/galaxy_install/repair_repository_manager.py +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -5,13 +5,14 @@ from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import shed_util_common as suc from tool_shed.util import repository_maintenance_util from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util + class RepairRepositoryManager(): @@ -119,10 +120,11 @@ tool_panel_section_id = section_dict[ 'id' ] tool_panel_section_name = section_dict[ 'name' ] if tool_panel_section_id: + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_panel_section = \ - tool_util.get_or_create_tool_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=tool_panel_section_name ) + tpm.get_or_create_tool_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=tool_panel_section_name ) else: tool_dependencies = None repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=self.app, @@ -156,15 +158,17 @@ log.debug( error_message ) repair_dict [ repository.name ] = error_message elif repository.status not in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED ]: - shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = \ + suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( self.app.toolbox, - metadata, - no_changes_checked=True, - tool_panel_section_id=None, - new_tool_panel_section_label=None ) + tpm.handle_tool_panel_selection( self.app.toolbox, + metadata, + no_changes_checked=True, + tool_panel_section_id=None, + new_tool_panel_section_label=None ) else: # The tools will be loaded outside of any sections in the tool panel. tool_panel_section_key = None diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py --- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py +++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py @@ -10,11 +10,12 @@ from galaxy.util import asbool +from tool_shed.galaxy_install.tools import tool_panel_manager + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import shed_util_common as suc -from tool_shed.util import tool_util log = logging.getLogger( __name__ ) @@ -216,19 +217,20 @@ if can_update_db_record: # The database record for the tool shed repository currently being processed can be updated. # Get the repository metadata to see where it was previously located in the tool panel. + tpm = tool_panel_manager.ToolPanelManager( self.app ) if repository_db_record and repository_db_record.metadata: tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( toolbox=self.app.toolbox, - metadata=repository_db_record.metadata, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_selection( toolbox=self.app.toolbox, + metadata=repository_db_record.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: # We're installing a new tool shed repository that does not yet have a database record. tool_panel_section_key, tool_section = \ - tool_util.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) tool_shed_repository = \ suc.create_or_update_tool_shed_repository( app=self.app, name=name, diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -14,6 +14,7 @@ from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.util import basic_util from tool_shed.util import common_util @@ -30,23 +31,31 @@ class ToolMigrationManager( object ): - def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ): + def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, + install_dependencies ): """ - Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool - panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. + Check tool settings in tool_shed_install_config and install all repositories + that are not already installed. The tool panel configuration file is the received + migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. """ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config - # If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message. + self.tpm = tool_panel_manager.ToolPanelManager( self.app ) + # If install_dependencies is True but tool_dependency_dir is not set, do not attempt + # to install but print informative error message. if install_dependencies and app.config.tool_dependency_dir is None: - message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini ' - message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.' + message = 'You are attempting to install tool dependencies but do not have a value ' + message += 'for "tool_dependency_dir" set in your universe_wsgi.ini file. Set this ' + message += 'location value to the path where you want tool dependencies installed and ' + message += 'rerun the migration script.' raise Exception( message ) - # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). + # Get the local non-shed related tool panel configs (there can be more than one, and the + # default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) - # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. + # Set the location where the repositories will be installed by retrieving the tool_path + # setting from migrated_tools_config. tree, error_message = xml_util.parse_xml( migrated_tools_config ) if tree is None: print error_message @@ -66,21 +75,24 @@ self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url ) self.repository_owner = common_util.REPOSITORY_OWNER index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config ) - # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in - # tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk. - # The default behavior is that the tool shed is down. + # Since tool migration scripts can be executed any number of times, we need to + # make sure the appropriate tools are defined in tool_conf.xml. If no tools + # associated with the migration stage are defined, no repositories will be installed + # on disk. The default behavior is that the tool shed is down. tool_shed_accessible = False tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app ) if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, - tool_panel_configs, - latest_migration_script_number ) + tool_shed_accessible, missing_tool_configs_dict = \ + common_util.check_for_missing_tools( app, + tool_panel_configs, + latest_migration_script_number ) else: - # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but - # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in - # the database. + # It doesn't matter if the tool shed is accessible since there are no migrated + # tools defined in the local Galaxy instance, but we have to set the value of + # tool_shed_accessible to True so that the value of migrate_tools.version can + # be correctly set in the database. tool_shed_accessible = True missing_tool_configs_dict = odict() if tool_shed_accessible: @@ -93,15 +105,18 @@ if missing_tool_configs_dict: for proprietary_tool_conf in self.proprietary_tool_confs: # Create a backup of the tool configuration in the un-migrated state. - shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, latest_migration_script_number ) ) + shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, + latest_migration_script_number ) ) for repository_elem in root: # Make sure we have a valid repository tag. if self.__is_valid_repository_tag( repository_elem ): - # Get all repository dependencies for the repository defined by the current repository_elem. Repository dependency - # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository - # dependency that contains a tool. The repository dependency can only contain items that are not loaded into the Galaxy - # tool panel (e.g., tool dependency definitions, custom datatypes, etc). This restriction must be followed down the - # entire dependency hierarchy. + # Get all repository dependencies for the repository defined by the + # current repository_elem. Repository dependency definitions contained + # in tool shed repositories with migrated tools must never define a + # relationship to a repository dependency that contains a tool. The + # repository dependency can only contain items that are not loaded into + # the Galaxy tool panel (e.g., tool dependency definitions, custom datatypes, + # etc). This restriction must be followed down the entire dependency hierarchy. name = repository_elem.get( 'name' ) changeset_revision = repository_elem.get( 'changeset_revision' ) tool_shed_accessible, repository_dependencies_dict = \ @@ -110,30 +125,38 @@ name, self.repository_owner, changeset_revision ) - # Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database. - created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name, - changeset_revision, - repository_dependencies_dict ) + # Make sure all repository dependency records exist (as tool_shed_repository + # table rows) in the Galaxy database. + created_tool_shed_repositories = \ + self.create_or_update_tool_shed_repository_records( name, + changeset_revision, + repository_dependencies_dict ) # Order the repositories for proper installation. This process is similar to the # process used when installing tool shed repositories, but does not handle managing # tool panel sections and other components since repository dependency definitions # contained in tool shed repositories with migrated tools must never define a relationship # to a repository dependency that contains a tool. - ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories, - repository_dependencies_dict ) + ordered_tool_shed_repositories = \ + self.order_repositories_for_installation( created_tool_shed_repositories, + repository_dependencies_dict ) for tool_shed_repository in ordered_tool_shed_repositories: - is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository ) + is_repository_dependency = self.__is_repository_dependency( name, + changeset_revision, + tool_shed_repository ) self.install_repository( repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=is_repository_dependency ) else: - message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number ) - message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names ) + message = "\nNo tools associated with migration stage %s are defined in your " % \ + str( latest_migration_script_number ) + message += "file%s named %s,\nso no repositories will be installed on disk.\n" % \ + ( plural, file_names ) print message else: - message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number ) + message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % \ + str( latest_migration_script_number ) message += "Try again later.\n" print message @@ -354,16 +377,21 @@ repo_install_dir = relative_install_dir if not is_repository_dependency: for tool_elem in repository_elem: - # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> + # The tool_elem looks something like this: + # <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: tool_panel_dict_for_tool_config = \ - tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) + self.tpm.generate_tool_panel_dict_for_tool_config( guid, + tool_config, + tool_sections=tool_sections ) # The tool-panel_dict has the following structure. - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, + # {<Tool guid> : [{ tool_config : <tool_config_file>, + # id: <ToolSection id>, + # version : <ToolSection version>, # name : <TooSection name>}]} for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v @@ -433,15 +461,14 @@ tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if not is_repository_dependency: - tool_util.add_to_tool_panel( self.app, - tool_shed_repository.name, - repository_clone_url, - tool_shed_repository.installed_changeset_revision, - repository_tools_tups, - self.repository_owner, - self.migrated_tools_config, - tool_panel_dict=tool_panel_dict_for_display, - new_install=True ) + self.tpm.add_to_tool_panel( tool_shed_repository.name, + repository_clone_url, + tool_shed_repository.installed_changeset_revision, + repository_tools_tups, + self.repository_owner, + self.migrated_tools_config, + tool_panel_dict=tool_panel_dict_for_display, + new_install=True ) if install_dependencies and tool_dependencies and has_tool_dependencies: # Install tool dependencies. suc.update_tool_shed_repository_status( self.app, diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/galaxy_install/tools/tool_panel_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py @@ -0,0 +1,465 @@ +import logging +import os + +import galaxy.tools +from galaxy.tools.search import ToolBoxSearch +from xml.etree import ElementTree as XmlET + +from tool_shed.util import basic_util +from tool_shed.util import common_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class ToolPanelManager( object ): + + def __init__( self, app ): + self.app = app + + def add_to_shed_tool_config( self, shed_tool_conf_dict, elem_list ): + # A tool shed repository is being installed so change the shed_tool_conf file. Parse the + # config file to generate the entire list of config_elems instead of using the in-memory list + # since it will be a subset of the entire list if one or more repositories have been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + # Add the elements to the in-memory list of config_elems. + for elem_entry in elem_list: + config_elems.append( elem_entry ) + # Persist the altered shed_tool_config file. + suc.config_elems_to_xml_file( self.app, config_elems, shed_tool_conf, tool_path ) + + def add_to_tool_panel( self, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, + shed_tool_conf, tool_panel_dict, new_install=True ): + """A tool shed repository is being installed or updated so handle tool panel alterations accordingly.""" + # We need to change the in-memory version and the file system version of the shed_tool_conf file. + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + tool_path = shed_tool_conf_dict[ 'tool_path' ] + # Generate the list of ElementTree Element objects for each section or tool. + elem_list = self.generate_tool_panel_elem_list( repository_name, + repository_clone_url, + changeset_revision, + tool_panel_dict, + repository_tools_tups, + owner=owner ) + if new_install: + # Add the new elements to the shed_tool_conf file on disk. + self.add_to_shed_tool_config( shed_tool_conf_dict, elem_list ) + # Use the new elements to add entries to the + config_elems = shed_tool_conf_dict[ 'config_elems' ] + for config_elem in elem_list: + # Add the new elements to the in-memory list of config_elems. + config_elems.append( config_elem ) + # Load the tools into the in-memory tool panel. + if config_elem.tag == 'section': + self.app.toolbox.load_section_tag_set( config_elem, tool_path, load_panel_dict=True ) + elif config_elem.tag == 'workflow': + self.app.toolbox.load_workflow_tag_set( config_elem, + self.app.toolbox.tool_panel, + self.app.toolbox.integrated_tool_panel, + load_panel_dict=True ) + elif config_elem.tag == 'tool': + guid = config_elem.get( 'guid' ) + self.app.toolbox.load_tool_tag_set( config_elem, + self.app.toolbox.tool_panel, + self.app.toolbox.integrated_tool_panel, + tool_path, + load_panel_dict=True, + guid=guid ) + # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. + shed_tool_conf_dict[ 'config_elems' ] = config_elems + self.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + if self.app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + self.app.toolbox.write_integrated_tool_panel_config_file() + self.app.toolbox_search = ToolBoxSearch( self.app.toolbox ) + + def generate_tool_panel_dict_for_new_install( self, tool_dicts, tool_section=None ): + """ + When installing a repository that contains tools, all tools must currently be defined + within the same tool section in the tool panel or outside of any sections. + """ + tool_panel_dict = {} + if tool_section: + section_id = tool_section.id + section_name = tool_section.name + section_version = tool_section.version or '' + else: + section_id = '' + section_name = '' + section_version = '' + for tool_dict in tool_dicts: + if tool_dict.get( 'add_to_tool_panel', True ): + guid = tool_dict[ 'guid' ] + tool_config = tool_dict[ 'tool_config' ] + tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ tool_section_dict ] + return tool_panel_dict + + def generate_tool_panel_dict_for_tool_config( self, guid, tool_config, tool_sections=None ): + """ + Create a dictionary of the following type for a single tool config file name. + The intent is to call this method for every tool config in a repository and + append each of these as entries to a tool panel dictionary for the repository. + This enables each tool to be loaded into a different section in the tool panel. + {<Tool guid> : + [{ tool_config : <tool_config_file>, + id: <ToolSection id>, + version : <ToolSection version>, + name : <TooSection name>}]} + """ + tool_panel_dict = {} + file_name = basic_util.strip_path( tool_config ) + tool_section_dicts = self. generate_tool_section_dicts( tool_config=file_name, + tool_sections=tool_sections ) + tool_panel_dict[ guid ] = tool_section_dicts + return tool_panel_dict + + def generate_tool_panel_elem_list( self, repository_name, repository_clone_url, changeset_revision, + tool_panel_dict, repository_tools_tups, owner='' ): + """Generate a list of ElementTree Element objects for each section or tool.""" + elem_list = [] + tool_elem = None + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + if not owner: + owner = suc.get_repository_owner( cleaned_repository_clone_url ) + tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' ) + for guid, tool_section_dicts in tool_panel_dict.items(): + for tool_section_dict in tool_section_dicts: + tool_section = None + inside_section = False + section_in_elem_list = False + if tool_section_dict[ 'id' ]: + inside_section = True + # Create a new section element only if we haven't already created it. + for index, elem in enumerate( elem_list ): + if elem.tag == 'section': + section_id = elem.get( 'id', None ) + if section_id == tool_section_dict[ 'id' ]: + section_in_elem_list = True + tool_section = elem + break + if tool_section is None: + tool_section = self.generate_tool_section_element_from_dict( tool_section_dict ) + # Find the tuple containing the current guid from the list of repository_tools_tups. + for repository_tool_tup in repository_tools_tups: + tool_file_path, tup_guid, tool = repository_tool_tup + if tup_guid == guid: + break + if inside_section: + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + tool_section ) + else: + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + None ) + if inside_section: + if section_in_elem_list: + elem_list[ index ] = tool_section + else: + elem_list.append( tool_section ) + else: + elem_list.append( tool_elem ) + return elem_list + + def generate_tool_section_dicts( self, tool_config=None, tool_sections=None ): + tool_section_dicts = [] + if tool_config is None: + tool_config = '' + if tool_sections: + for tool_section in tool_sections: + # The value of tool_section will be None if the tool is displayed outside + # of any sections in the tool panel. + if tool_section: + section_id = tool_section.id or '' + section_version = tool_section.version or '' + section_name = tool_section.name or '' + else: + section_id = '' + section_version = '' + section_name = '' + tool_section_dicts.append( dict( tool_config=tool_config, + id=section_id, + version=section_version, + name=section_name ) ) + else: + tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) + return tool_section_dicts + + def generate_tool_section_element_from_dict( self, tool_section_dict ): + # The value of tool_section_dict looks like the following. + # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} + if tool_section_dict[ 'id' ]: + # Create a new tool section. + tool_section = XmlET.Element( 'section' ) + tool_section.attrib[ 'id' ] = tool_section_dict[ 'id' ] + tool_section.attrib[ 'name' ] = tool_section_dict[ 'name' ] + tool_section.attrib[ 'version' ] = tool_section_dict[ 'version' ] + else: + tool_section = None + return tool_section + + def get_or_create_tool_section( self, toolbox, tool_panel_section_id, new_tool_panel_section_label=None ): + tool_panel_section_key = str( tool_panel_section_id ) + if tool_panel_section_key in toolbox.tool_panel: + # Appending a tool to an existing section in toolbox.tool_panel + tool_section = toolbox.tool_panel[ tool_panel_section_key ] + log.debug( "Appending to tool panel section: %s" % str( tool_section.name ) ) + else: + # Appending a new section to toolbox.tool_panel + if new_tool_panel_section_label is None: + # This might add an ugly section label to the tool panel, but, oh well... + new_tool_panel_section_label = tool_panel_section_id + elem = XmlET.Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section_label + elem.attrib[ 'id' ] = tool_panel_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + toolbox.tool_panel[ tool_panel_section_key ] = tool_section + log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) + return tool_panel_section_key, tool_section + + def handle_tool_panel_section( self, toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None ): + """Return a ToolSection object retrieved from the current in-memory tool_panel.""" + # If tool_panel_section_id is received, the section exists in the tool panel. In this + # case, the value of the received tool_panel_section_id must be the id retrieved from a + # tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label + # is received, a new section will be added to the tool panel. + if new_tool_panel_section_label: + section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) + tool_panel_section_key, tool_section = \ + self.get_or_create_tool_section( toolbox, + tool_panel_section_id=section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + elif tool_panel_section_id: + tool_panel_section_key = str( tool_panel_section_id ) + tool_section = toolbox.tool_panel[ tool_panel_section_key ] + else: + return None, None + return tool_panel_section_key, tool_section + + def handle_tool_panel_selection( self, toolbox, metadata, no_changes_checked, tool_panel_section_id, + new_tool_panel_section_label ): + """ + Handle the selected tool panel location for loading tools included in tool shed + repositories when installing or reinstalling them. + """ + # Get the location in the tool panel in which each tool was originally loaded. + tool_section = None + tool_panel_section_key = None + if 'tools' in metadata: + # This forces everything to be loaded into the same section (or no section) + # in the tool panel. + if no_changes_checked: + # Make sure the no_changes check box overrides the new_tool_panel_section_label + # if the user checked the check box and entered something into the field. + new_tool_panel_section_label = None + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if not tool_panel_dict: + tool_panel_dict = self.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + else: + tool_panel_dict = self.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + if tool_panel_dict: + # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_id = tool_section_dict[ 'id' ] + original_section_name = tool_section_dict[ 'name' ] + if original_section_id: + tool_panel_section_key, tool_section = \ + self.get_or_create_tool_section( toolbox, + tool_panel_section_id=original_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + else: + # The user elected to change the tool panel section to contain the tools. + tool_panel_section_key, tool_section = \ + self.handle_tool_panel_section( toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + return tool_section, tool_panel_section_key + + def remove_from_shed_tool_config( self, shed_tool_conf_dict, guids_to_remove ): + # A tool shed repository is being uninstalled so change the shed_tool_conf file. + # Parse the config file to generate the entire list of config_elems instead of + # using the in-memory list since it will be a subset of the entire list if one + # or more repositories have been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove all of the appropriate tool sub-elements from the section element. + config_elem.remove( tool_elem ) + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + if config_elem.get( 'guid' ) in guids_to_remove: + config_elems_to_remove.append( config_elem ) + for config_elem in config_elems_to_remove: + config_elems.remove( config_elem ) + # Persist the altered in-memory version of the tool config. + suc.config_elems_to_xml_file( self.app, config_elems, shed_tool_conf, tool_path ) + + def remove_from_tool_panel( self, repository, shed_tool_conf, uninstall ): + """ + A tool shed repository is being deactivated or uninstalled, so handle tool panel + alterations accordingly. + """ + # Determine where the tools are currently defined in the tool panel and store this + # information so the tools can be displayed in the same way when the repository is + # activated or reinstalled. + tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( self.app, repository ) + repository.metadata[ 'tool_panel_section' ] = tool_panel_dict + self.app.install_model.context.add( repository ) + self.app.install_model.context.flush() + # Create a list of guids for all tools that will be removed from the in-memory tool panel + # and config file on disk. + guids_to_remove = [ k for k in tool_panel_dict.keys() ] + # Remove the tools from the toolbox's tools_by_id dictionary. + for guid_to_remove in guids_to_remove: + if guid_to_remove in self.app.toolbox.tools_by_id: + del self.app.toolbox.tools_by_id[ guid_to_remove ] + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + if uninstall: + # Remove from the shed_tool_conf file on disk. + self.remove_from_shed_tool_config( shed_tool_conf_dict, guids_to_remove ) + config_elems = shed_tool_conf_dict[ 'config_elems' ] + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + # Get the section key for the in-memory tool panel. + section_key = str( config_elem.get( "id" ) ) + # Generate the list of tool elements to remove. + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + if tool_elem in config_elem: + # Remove the tool sub-element from the section element. + config_elem.remove( tool_elem ) + # Remove the tool from the section in the in-memory tool panel. + if section_key in self.app.toolbox.tool_panel: + tool_section = self.app.toolbox.tool_panel[ section_key ] + guid = tool_elem.get( 'guid' ) + tool_key = 'tool_%s' % str( guid ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = self.app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in tool_section.elems: + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + replacement_tool_version = None + # Since we are going to remove the tool from the section, replace it with the + # newest loaded version of the tool. + for available_tool_version in available_tool_versions: + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_section_elems_index, key in enumerate( tool_section.elems.keys() ): + if key == tool_key: + break + # Remove the tool from the tool section. + del tool_section.elems[ tool_key ] + # Add the replacement tool at the same location in the tool section. + tool_section.elems.insert( tool_section_elems_index, + replacement_tool_key, + replacement_tool_version ) + else: + del tool_section.elems[ tool_key ] + else: + del tool_section.elems[ tool_key ] + if uninstall: + # Remove the tool from the section in the in-memory integrated tool panel. + if section_key in self.app.toolbox.integrated_tool_panel: + tool_section = self.app.toolbox.integrated_tool_panel[ section_key ] + tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) + if tool_key in tool_section.elems: + del tool_section.elems[ tool_key ] + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + guid = config_elem.get( 'guid' ) + if guid in guids_to_remove: + tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = self.app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in self.app.toolbox.tool_panel: + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + replacement_tool_version = None + # Since we are going to remove the tool from the section, replace it with + # the newest loaded version of the tool. + for available_tool_version in available_tool_versions: + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in self.app.toolbox.tool_panel.keys() or not available_tool_section_id: + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_panel_index, key in enumerate( self.app.toolbox.tool_panel.keys() ): + if key == tool_key: + break + # Remove the tool from the tool panel. + del self.app.toolbox.tool_panel[ tool_key ] + # Add the replacement tool at the same location in the tool panel. + self.app.toolbox.tool_panel.insert( tool_panel_index, + replacement_tool_key, + replacement_tool_version ) + else: + del self.app.toolbox.tool_panel[ tool_key ] + else: + del self.app.toolbox.tool_panel[ tool_key ] + if uninstall: + if tool_key in self.app.toolbox.integrated_tool_panel: + del self.app.toolbox.integrated_tool_panel[ tool_key ] + config_elems_to_remove.append( config_elem ) + for config_elem in config_elems_to_remove: + # Remove the element from the in-memory list of elements. + config_elems.remove( config_elem ) + # Update the config_elems of the in-memory shed_tool_conf_dict. + shed_tool_conf_dict[ 'config_elems' ] = config_elems + self.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + self.app.toolbox_search = ToolBoxSearch( self.app.toolbox ) + if uninstall and self.app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + self.app.toolbox.write_integrated_tool_panel_config_file() diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -2,11 +2,13 @@ import os import tempfile +from galaxy import util from galaxy.util import inflector -from galaxy import util +from galaxy.web.form_builder import SelectField from tool_shed.metadata import metadata_generator from tool_shed.repository_types.metadata import TipOnly +from tool_shed.repository_types import util as rt_util from tool_shed.util import basic_util from tool_shed.util import common_util @@ -20,9 +22,10 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app ): + def __init__( self, app, user ): super( RepositoryMetadataManager, self ).__init__( app ) self.app = app + self.user = user # Repository metadata comparisons for changeset revisions. self.EQUAL = 'equal' self.NO_METADATA = 'no metadata' @@ -47,6 +50,18 @@ self.sa_session.add( repository_metadata ) self.sa_session.flush() + def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes', + my_writable=False ): + """Generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=True ) + for repository in query: + owner = str( repository.user.username ) + option_label = '%s (%s)' % ( str( repository.name ), owner ) + option_value = '%s' % self.app.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field + def clean_repository_metadata( self, id, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple @@ -458,6 +473,54 @@ # The tool did not change through all of the changeset revisions. return old_id + def get_query_for_setting_metadata_on_repositories( self, my_writable=False, order=True ): + """ + Return a query containing repositories for resetting metadata. The order parameter + is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from the Tool Shed API, order is False. + """ + # When called from the Tool Shed API, the metadata is reset on all repositories of types + # repository_suite_definition and tool_dependency_definition in addition to other selected + # repositories. + if my_writable: + username = self.user.username + clause_list = [] + for repository in self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ): + # Always reset metadata on all repositories of types repository_suite_definition and + # tool_dependency_definition. + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: + clause_list.append( self.app.model.Repository.table.c.id == repository.id ) + else: + allow_push = repository.allow_push( self.app ) + if allow_push: + # Include all repositories that are writable by the current user. + allow_push_usernames = allow_push.split( ',' ) + if username in allow_push_usernames: + clause_list.append( self.app.model.Repository.table.c.id == repository.id ) + if clause_list: + if order: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( or_( *clause_list ) ) \ + .order_by( self.app.model.Repository.table.c.name, + self.app.model.Repository.table.c.user_id ) + else: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( or_( *clause_list ) ) + else: + # Return an empty query. + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.id == -1 ) + else: + if order: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ) \ + .order_by( self.app.model.Repository.table.c.name, + self.app.model.Repository.table.c.user_id ) + else: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ) + def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): """ Compare the last saved metadata for each datatype in the repository with the new metadata @@ -732,13 +795,13 @@ # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, user, id ): + def reset_all_metadata_on_repository_in_tool_shed( self, id ): """Reset all metadata on a single repository in a tool shed.""" repository = suc.get_repository_in_tool_shed( self.app, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -875,7 +938,7 @@ self.sa_session.add( repository_metadata ) self.sa_session.flush() - def reset_metadata_on_selected_repositories( self, user, **kwd ): + def reset_metadata_on_selected_repositories( self, **kwd ): """ Inspect the repository changelog to reset metadata for all appropriate changeset revisions. This method is called from both Galaxy and the Tool Shed. @@ -892,7 +955,7 @@ repository = suc.get_repository_in_tool_shed( self.app, repository_id ) owner = str( repository.user.username ) invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( user, repository_id ) + self.reset_all_metadata_on_repository_in_tool_shed( self.user, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, invalid_file_tups, @@ -918,7 +981,7 @@ status = 'error' return message, status - def set_repository_metadata( self, host, user, repository, content_alert_str='', **kwd ): + def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. @@ -926,7 +989,7 @@ message = '' status = 'done' encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) repo_dir = repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) metadata_dict, invalid_file_tups = \ @@ -1027,10 +1090,9 @@ tool_util.reset_tool_data_tables( self.app ) return message, status - def set_repository_metadata_due_to_new_tip( self, host, user, repository, content_alert_str=None, **kwd ): + def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): """Set metadata on the repository tip in the tool shed.""" error_message, status = self.set_repository_metadata( host, - user, repository, content_alert_str=content_alert_str, **kwd ) diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -84,20 +84,6 @@ '${host}' """ -def build_repository_ids_select_field( trans, name='repository_ids', multiple=True, display='checkboxes', my_writable=False ): - """Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata.""" - repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) - query = get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=True ) - for repository in query: - if trans.webapp.name == 'tool_shed': - owner = str( repository.user.username ) - else: - owner = str( repository.owner ) - option_label = '%s (%s)' % ( str( repository.name ), owner ) - option_value = '%s' % trans.security.encode_id( repository.id ) - repositories_select_field.add_option( option_label, option_value ) - return repositories_select_field - def build_tool_dependencies_select_field( app, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ): """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository.""" tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display ) @@ -645,66 +631,6 @@ prior_import_or_install_required_dict[ encoded_repository_id ] = prior_import_or_install_ids return prior_import_or_install_required_dict -def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=True ): - """ - Return a query containing repositories for resetting metadata. This method is called from both the - Tool Shed and Galaxy. The my_writable parameter is ignored unless called from the Tool Shed, and the - order parameter is used for displaying the list of repositories ordered alphabetically for display on - a page. When called from either the Tool Shed or Galaxy API, order is False. - """ - if trans.webapp.name == 'tool_shed': - # When called from the Tool Shed API, the metadata is reset on all repositories of types - # repository_suite_definition and tool_dependency_definition in addition to other selected - # repositories. - if my_writable: - username = trans.user.username - clause_list = [] - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ): - # Always reset metadata on all repositories of types repository_suite_definition and - # tool_dependency_definition. - if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: - clause_list.append( trans.model.Repository.table.c.id == repository.id ) - else: - allow_push = repository.allow_push( trans.app ) - if allow_push: - # Include all repositories that are writable by the current user. - allow_push_usernames = allow_push.split( ',' ) - if username in allow_push_usernames: - clause_list.append( trans.model.Repository.table.c.id == repository.id ) - if clause_list: - if order: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( or_( *clause_list ) ) \ - .order_by( trans.model.Repository.table.c.name, - trans.model.Repository.table.c.user_id ) - else: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( or_( *clause_list ) ) - else: - # Return an empty query. - return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.id == -1 ) - else: - if order: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) \ - .order_by( trans.model.Repository.table.c.name, - trans.model.Repository.table.c.user_id ) - else: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) - else: - # We're in Galaxy. - if order: - return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) \ - .order_by( trans.install_model.ToolShedRepository.table.c.name, - trans.install_model.ToolShedRepository.table.c.owner ) - else: - return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repo_info_tuple_contents( repo_info_tuple ): """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: diff -r 972a80267009126e558ba14142df48b897db48c8 -r e9de99ef77105d221df55771724ca56b86485a4b lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -19,69 +19,6 @@ log = logging.getLogger( __name__ ) -def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): - # A tool shed repository is being installed so change the shed_tool_conf file. Parse the - # config file to generate the entire list of config_elems instead of using the in-memory list - # since it will be a subset of the entire list if one or more repositories have been deactivated. - shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] - tool_path = shed_tool_conf_dict[ 'tool_path' ] - config_elems = [] - tree, error_message = xml_util.parse_xml( shed_tool_conf ) - if tree: - root = tree.getroot() - for elem in root: - config_elems.append( elem ) - # Add the elements to the in-memory list of config_elems. - for elem_entry in elem_list: - config_elems.append( elem_entry ) - # Persist the altered shed_tool_config file. - suc.config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) - -def add_to_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, - shed_tool_conf, tool_panel_dict, new_install=True ): - """A tool shed repository is being installed or updated so handle tool panel alterations accordingly.""" - # We need to change the in-memory version and the file system version of the shed_tool_conf file. - index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( app, shed_tool_conf ) - tool_path = shed_tool_conf_dict[ 'tool_path' ] - # Generate the list of ElementTree Element objects for each section or tool. - elem_list = generate_tool_panel_elem_list( repository_name, - repository_clone_url, - changeset_revision, - tool_panel_dict, - repository_tools_tups, - owner=owner ) - if new_install: - # Add the new elements to the shed_tool_conf file on disk. - add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ) - # Use the new elements to add entries to the - config_elems = shed_tool_conf_dict[ 'config_elems' ] - for config_elem in elem_list: - # Add the new elements to the in-memory list of config_elems. - config_elems.append( config_elem ) - # Load the tools into the in-memory tool panel. - if config_elem.tag == 'section': - app.toolbox.load_section_tag_set( config_elem, tool_path, load_panel_dict=True ) - elif config_elem.tag == 'workflow': - app.toolbox.load_workflow_tag_set( config_elem, - app.toolbox.tool_panel, - app.toolbox.integrated_tool_panel, - load_panel_dict=True ) - elif config_elem.tag == 'tool': - guid = config_elem.get( 'guid' ) - app.toolbox.load_tool_tag_set( config_elem, - app.toolbox.tool_panel, - app.toolbox.integrated_tool_panel, - tool_path, - load_panel_dict=True, - guid=guid ) - # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. - shed_tool_conf_dict[ 'config_elems' ] = config_elems - app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - if app.config.update_integrated_tool_panel: - # Write the current in-memory version of the integrated_tool_panel.xml file to disk. - app.toolbox.write_integrated_tool_panel_config_file() - app.toolbox_search = ToolBoxSearch( app.toolbox ) - def build_shed_tool_conf_select_field( app ): """Build a SelectField whose options are the keys in app.toolbox.shed_tool_confs.""" options = [] @@ -192,142 +129,6 @@ message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) return message -def generate_tool_panel_dict_for_new_install( tool_dicts, tool_section=None ): - """ - When installing a repository that contains tools, all tools must currently be defined - within the same tool section in the tool panel or outside of any sections. - """ - tool_panel_dict = {} - if tool_section: - section_id = tool_section.id - section_name = tool_section.name - section_version = tool_section.version or '' - else: - section_id = '' - section_name = '' - section_version = '' - for tool_dict in tool_dicts: - if tool_dict.get( 'add_to_tool_panel', True ): - guid = tool_dict[ 'guid' ] - tool_config = tool_dict[ 'tool_config' ] - tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) - if guid in tool_panel_dict: - tool_panel_dict[ guid ].append( tool_section_dict ) - else: - tool_panel_dict[ guid ] = [ tool_section_dict ] - return tool_panel_dict - -def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=None ): - """ - Create a dictionary of the following type for a single tool config file name. - The intent is to call this method for every tool config in a repository and - append each of these as entries to a tool panel dictionary for the repository. - This allows for each tool to be loaded into a different section in the tool panel. - {<Tool guid> : - [{ tool_config : <tool_config_file>, - id: <ToolSection id>, - version : <ToolSection version>, - name : <TooSection name>}]} - """ - tool_panel_dict = {} - file_name = basic_util.strip_path( tool_config ) - tool_section_dicts = generate_tool_section_dicts( tool_config=file_name, tool_sections=tool_sections ) - tool_panel_dict[ guid ] = tool_section_dicts - return tool_panel_dict - -def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, - repository_tools_tups, owner='' ): - """Generate a list of ElementTree Element objects for each section or tool.""" - elem_list = [] - tool_elem = None - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) - if not owner: - owner = suc.get_repository_owner( cleaned_repository_clone_url ) - tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' ) - for guid, tool_section_dicts in tool_panel_dict.items(): - for tool_section_dict in tool_section_dicts: - tool_section = None - inside_section = False - section_in_elem_list = False - if tool_section_dict[ 'id' ]: - inside_section = True - # Create a new section element only if we haven't already created it. - for index, elem in enumerate( elem_list ): - if elem.tag == 'section': - section_id = elem.get( 'id', None ) - if section_id == tool_section_dict[ 'id' ]: - section_in_elem_list = True - tool_section = elem - break - if tool_section is None: - tool_section = generate_tool_section_element_from_dict( tool_section_dict ) - # Find the tuple containing the current guid from the list of repository_tools_tups. - for repository_tool_tup in repository_tools_tups: - tool_file_path, tup_guid, tool = repository_tool_tup - if tup_guid == guid: - break - if inside_section: - tool_elem = suc.generate_tool_elem( tool_shed, - repository_name, - changeset_revision, - owner, - tool_file_path, - tool, - tool_section ) - else: - tool_elem = suc.generate_tool_elem( tool_shed, - repository_name, - changeset_revision, - owner, - tool_file_path, - tool, - None ) - if inside_section: - if section_in_elem_list: - elem_list[ index ] = tool_section - else: - elem_list.append( tool_section ) - else: - elem_list.append( tool_elem ) - return elem_list - -def generate_tool_section_dicts( tool_config=None, tool_sections=None ): - tool_section_dicts = [] - if tool_config is None: - tool_config = '' - if tool_sections: - for tool_section in tool_sections: - # The value of tool_section will be None if the tool is displayed outside - # of any sections in the tool panel. - if tool_section: - section_id = tool_section.id or '' - section_version = tool_section.version or '' - section_name = tool_section.name or '' - else: - section_id = '' - section_version = '' - section_name = '' - tool_section_dicts.append( dict( tool_config=tool_config, - id=section_id, - version=section_version, - name=section_name ) ) - else: - tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) - return tool_section_dicts - -def generate_tool_section_element_from_dict( tool_section_dict ): - # The value of tool_section_dict looks like the following. - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} - if tool_section_dict[ 'id' ]: - # Create a new tool section. - tool_section = XmlET.Element( 'section' ) - tool_section.attrib[ 'id' ] = tool_section_dict[ 'id' ] - tool_section.attrib[ 'name' ] = tool_section_dict[ 'name' ] - tool_section.attrib[ 'version' ] = tool_section_dict[ 'version' ] - else: - tool_section = None - return tool_section - def get_headers( fname, sep, count=60, is_multi_byte=False ): """Returns a list with the first 'count' lines split by 'sep'.""" headers = [] @@ -341,26 +142,6 @@ break return headers -def get_or_create_tool_section( toolbox, tool_panel_section_id, new_tool_panel_section_label=None ): - tool_panel_section_key = str( tool_panel_section_id ) - if tool_panel_section_key in toolbox.tool_panel: - # Appending a tool to an existing section in toolbox.tool_panel - tool_section = toolbox.tool_panel[ tool_panel_section_key ] - log.debug( "Appending to tool panel section: %s" % str( tool_section.name ) ) - else: - # Appending a new section to toolbox.tool_panel - if new_tool_panel_section_label is None: - # This might add an ugly section label to the tool panel, but, oh well... - new_tool_panel_section_label = tool_panel_section_id - elem = XmlET.Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section_label - elem.attrib[ 'id' ] = tool_panel_section_id - elem.attrib[ 'version' ] = '' - tool_section = galaxy.tools.ToolSection( elem ) - toolbox.tool_panel[ tool_panel_section_key ] = tool_section - log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) - return tool_panel_section_key, tool_section - def get_tool_path_install_dir( partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems ): for elem in config_elems: if elem.tag == 'tool': @@ -514,63 +295,6 @@ error = True return error, message -def handle_tool_panel_selection( toolbox, metadata, no_changes_checked, tool_panel_section_id, new_tool_panel_section_label ): - """ - Handle the selected tool panel location for loading tools included in tool shed repositories when installing - or reinstalling them. - """ - # Get the location in the tool panel in which each tool was originally loaded. - tool_section = None - tool_panel_section_key = None - if 'tools' in metadata: - # This forces everything to be loaded into the same section (or no section) in the tool panel. - if no_changes_checked: - # Make sure the no_changes check box overrides the new_tool_panel_section_label if the user checked the check - # box and entered something into the field. - new_tool_panel_section_label = None - if 'tool_panel_section' in metadata: - tool_panel_dict = metadata[ 'tool_panel_section' ] - if not tool_panel_dict: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - else: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - if tool_panel_dict: - # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] - original_section_id = tool_section_dict[ 'id' ] - original_section_name = tool_section_dict[ 'name' ] - if original_section_id: - tool_panel_section_key, tool_section = \ - get_or_create_tool_section( toolbox, - tool_panel_section_id=original_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - else: - # The user elected to change the tool panel section to contain the tools. - tool_panel_section_key, tool_section = handle_tool_panel_section( toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - return tool_section, tool_panel_section_key - -def handle_tool_panel_section( toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None ): - """Return a ToolSection object retrieved from the current in-memory tool_panel.""" - # If tool_panel_section_id is received, the section exists in the tool panel. In this - # case, the value of the received tool_panel_section_id must be the id retrieved from a - # tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label - # is received, a new section will be added to the tool panel. - if new_tool_panel_section_label: - section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) - tool_panel_section_key, tool_section = \ - get_or_create_tool_section( toolbox, - tool_panel_section_id=section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - elif tool_panel_section_id: - tool_panel_section_key = str( tool_panel_section_id ) - tool_section = toolbox.tool_panel[ tool_panel_section_key ] - else: - return None, None - return tool_panel_section_key, tool_section - def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ): """ Using the list of tool_version_dicts retrieved from the tool shed (one per changeset @@ -741,170 +465,6 @@ if isinstance( tool.tool_action, UploadToolAction ): app.toolbox.reload_tool_by_id( tool_id ) -def remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ): - # A tool shed repository is being uninstalled so change the shed_tool_conf file. - # Parse the config file to generate the entire list of config_elems instead of - # using the in-memory list since it will be a subset of the entire list if one - # or more repositories have been deactivated. - shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] - tool_path = shed_tool_conf_dict[ 'tool_path' ] - config_elems = [] - tree, error_message = xml_util.parse_xml( shed_tool_conf ) - if tree: - root = tree.getroot() - for elem in root: - config_elems.append( elem ) - config_elems_to_remove = [] - for config_elem in config_elems: - if config_elem.tag == 'section': - tool_elems_to_remove = [] - for tool_elem in config_elem: - if tool_elem.get( 'guid' ) in guids_to_remove: - tool_elems_to_remove.append( tool_elem ) - for tool_elem in tool_elems_to_remove: - # Remove all of the appropriate tool sub-elements from the section element. - config_elem.remove( tool_elem ) - if len( config_elem ) < 1: - # Keep a list of all empty section elements so they can be removed. - config_elems_to_remove.append( config_elem ) - elif config_elem.tag == 'tool': - if config_elem.get( 'guid' ) in guids_to_remove: - config_elems_to_remove.append( config_elem ) - for config_elem in config_elems_to_remove: - config_elems.remove( config_elem ) - # Persist the altered in-memory version of the tool config. - suc.config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) - -def remove_from_tool_panel( app, repository, shed_tool_conf, uninstall ): - """ - A tool shed repository is being deactivated or uninstalled, so handle tool panel - alterations accordingly. - """ - # Determine where the tools are currently defined in the tool panel and store this - # information so the tools can be displayed in the same way when the repository is - # activated or reinstalled. - tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( app, repository ) - repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - app.install_model.context.add( repository ) - app.install_model.context.flush() - # Create a list of guids for all tools that will be removed from the in-memory tool panel - # and config file on disk. - guids_to_remove = [ k for k in tool_panel_dict.keys() ] - # Remove the tools from the toolbox's tools_by_id dictionary. - for guid_to_remove in guids_to_remove: - if guid_to_remove in app.toolbox.tools_by_id: - del app.toolbox.tools_by_id[ guid_to_remove ] - index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( app, shed_tool_conf ) - if uninstall: - # Remove from the shed_tool_conf file on disk. - remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ) - config_elems = shed_tool_conf_dict[ 'config_elems' ] - config_elems_to_remove = [] - for config_elem in config_elems: - if config_elem.tag == 'section': - # Get the section key for the in-memory tool panel. - section_key = str( config_elem.get( "id" ) ) - # Generate the list of tool elements to remove. - tool_elems_to_remove = [] - for tool_elem in config_elem: - if tool_elem.get( 'guid' ) in guids_to_remove: - tool_elems_to_remove.append( tool_elem ) - for tool_elem in tool_elems_to_remove: - if tool_elem in config_elem: - # Remove the tool sub-element from the section element. - config_elem.remove( tool_elem ) - # Remove the tool from the section in the in-memory tool panel. - if section_key in app.toolbox.tool_panel: - tool_section = app.toolbox.tool_panel[ section_key ] - guid = tool_elem.get( 'guid' ) - tool_key = 'tool_%s' % str( guid ) - # Get the list of versions of this tool that are currently available in the toolbox. - available_tool_versions = app.toolbox.get_loaded_tools_by_lineage( guid ) - if tool_key in tool_section.elems: - if available_tool_versions: - available_tool_versions.reverse() - replacement_tool_key = None - replacement_tool_version = None - # Since we are going to remove the tool from the section, replace it with the - # newest loaded version of the tool. - for available_tool_version in available_tool_versions: - available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() - if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: - replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) - replacement_tool_version = available_tool_version - break - if replacement_tool_key and replacement_tool_version: - # Get the index of the tool_key in the tool_section. - for tool_section_elems_index, key in enumerate( tool_section.elems.keys() ): - if key == tool_key: - break - # Remove the tool from the tool section. - del tool_section.elems[ tool_key ] - # Add the replacement tool at the same location in the tool section. - tool_section.elems.insert( tool_section_elems_index, - replacement_tool_key, - replacement_tool_version ) - else: - del tool_section.elems[ tool_key ] - else: - del tool_section.elems[ tool_key ] - if uninstall: - # Remove the tool from the section in the in-memory integrated tool panel. - if section_key in app.toolbox.integrated_tool_panel: - tool_section = app.toolbox.integrated_tool_panel[ section_key ] - tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) - if tool_key in tool_section.elems: - del tool_section.elems[ tool_key ] - if len( config_elem ) < 1: - # Keep a list of all empty section elements so they can be removed. - config_elems_to_remove.append( config_elem ) - elif config_elem.tag == 'tool': - guid = config_elem.get( 'guid' ) - if guid in guids_to_remove: - tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) - # Get the list of versions of this tool that are currently available in the toolbox. - available_tool_versions = app.toolbox.get_loaded_tools_by_lineage( guid ) - if tool_key in app.toolbox.tool_panel: - if available_tool_versions: - available_tool_versions.reverse() - replacement_tool_key = None - replacement_tool_version = None - # Since we are going to remove the tool from the section, replace it with - # the newest loaded version of the tool. - for available_tool_version in available_tool_versions: - available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() - if available_tool_version.id in app.toolbox.tool_panel.keys() or not available_tool_section_id: - replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) - replacement_tool_version = available_tool_version - break - if replacement_tool_key and replacement_tool_version: - # Get the index of the tool_key in the tool_section. - for tool_panel_index, key in enumerate( app.toolbox.tool_panel.keys() ): - if key == tool_key: - break - # Remove the tool from the tool panel. - del app.toolbox.tool_panel[ tool_key ] - # Add the replacement tool at the same location in the tool panel. - app.toolbox.tool_panel.insert( tool_panel_index, replacement_tool_key, replacement_tool_version ) - else: - del app.toolbox.tool_panel[ tool_key ] - else: - del app.toolbox.tool_panel[ tool_key ] - if uninstall: - if tool_key in app.toolbox.integrated_tool_panel: - del app.toolbox.integrated_tool_panel[ tool_key ] - config_elems_to_remove.append( config_elem ) - for config_elem in config_elems_to_remove: - # Remove the element from the in-memory list of elements. - config_elems.remove( config_elem ) - # Update the config_elems of the in-memory shed_tool_conf_dict. - shed_tool_conf_dict[ 'config_elems' ] = config_elems - app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - app.toolbox_search = ToolBoxSearch( app.toolbox ) - if uninstall and app.config.update_integrated_tool_panel: - # Write the current in-memory version of the integrated_tool_panel.xml file to disk. - app.toolbox.write_integrated_tool_panel_config_file() - def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. app.tool_data_tables.data_tables = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Some code cleanup for setting metadata on tool shed repositories.
by commits-noreply＠bitbucket.org 21 Jul '14

21 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0eaf1edd08e3/ Changeset: 0eaf1edd08e3 User: greg Date: 2014-07-21 19:38:43 Summary: Some code cleanup for setting metadata on tool shed repositories. Affected #: 11 files diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -413,12 +413,12 @@ # Make sure the current user's API key proves he is an admin user in this Galaxy instance. if not trans.user_is_admin(): raise HTTPForbidden( detail='You are not authorized to reset metadata on repositories installed into this Galaxy instance.' ) - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=False ) + irmm = InstalledRepositoryMetadataManager( trans.app ) + query = irmm.get_query_for_setting_metadata_on_repositories( order=False ) # Now reset metadata on all remaining repositories. for repository in query: repository_id = trans.security.encode_id( repository.id ) try: - irmm = InstalledRepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d 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 @@ -1708,13 +1708,13 @@ @web.expose @web.require_admin def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): + irmm = InstalledRepositoryMetadataManager( trans.app ) if 'reset_metadata_on_selected_repositories_button' in kwd: - irmm = InstalledRepositoryMetadataManager( trans.app ) message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans ) + repositories_select_field = irmm.build_repository_ids_select_field( trans ) return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -392,7 +392,8 @@ my_writable = True handled_repository_ids = [] repository_ids = [] - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False ) # Make sure repositories of type tool_dependency_definition are first in the list. for repository in query: if repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: @@ -426,13 +427,12 @@ This param can be used as an alternative to the above encoded_ids_to_skip. """ - def handle_repository( trans, repository, results ): + def handle_repository( trans, rmm, repository, results ): log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, repository_id ) + rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, @@ -451,7 +451,7 @@ status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -473,7 +473,7 @@ my_writable = util.asbool( payload.get( 'my_writable', False ) ) else: my_writable = True - query = suc.get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=False ) + query = rmm.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=False ) # First reset metadata on all repositories of type repository_dependency_definition. for repository in query: encoded_id = trans.security.encode_id( repository.id ) @@ -481,7 +481,7 @@ log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ ( str( repository.id ), str( encoded_ids_to_skip ) ) ) elif repository.type == rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) + results = handle_repository( trans, rmm, repository, results ) # Now reset metadata on all remaining repositories. for repository in query: encoded_id = trans.security.encode_id( repository.id ) @@ -489,7 +489,7 @@ log.debug( "Skipping repository with id %s because it is in encoded_ids_to_skip %s" % \ ( str( repository.id ), str( encoded_ids_to_skip ) ) ) elif repository.type != rt_util.TOOL_DEPENDENCY_DEFINITION and repository.id not in handled_repository_ids: - results = handle_repository( trans, repository, results ) + results = handle_repository( trans, rmm, repository, results ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time return json.dumps( results, sort_keys=True, indent=4 ) @@ -511,10 +511,9 @@ results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, - trans.security.encode_id( repository.id ) ) + rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -348,13 +348,16 @@ @web.expose @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) if 'reset_metadata_on_selected_repositories_button' in kwd: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) + message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: message = util.restore_text( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans ) + repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids', + multiple=True, + display='checkboxes', + my_writable=False ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -48,8 +48,8 @@ repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - error_message, status = rmm.set_repository_metadata( trans.request.host, trans.user, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) if status == 'ok' and error_message: log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ ( str( repository.name ), str( repository.user.username ), error_message ) ) diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2753,9 +2753,9 @@ def reset_all_metadata( self, trans, id, **kwd ): """Reset all metadata on the complete changelog for a single repository in the tool shed.""" # This method is called only from the ~/templates/webapps/tool_shed/repository/manage_repository.mako template. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.user, id, **kwd ) + rmm.reset_all_metadata_on_repository_in_tool_shed( id, **kwd ) if invalid_file_tups: repository = suc.get_repository_in_tool_shed( trans.app, id ) message = tool_util.generate_message_for_invalid_tools( trans.app, @@ -2774,13 +2774,16 @@ @web.expose def reset_metadata_on_my_writable_repositories_in_tool_shed( self, trans, **kwd ): + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) if 'reset_metadata_on_selected_repositories_button' in kwd: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) - message, status = rmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) + message, status = rmm.reset_metadata_on_selected_repositories( **kwd ) else: message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repositories_select_field = suc.build_repository_ids_select_field( trans, my_writable=True ) + repositories_select_field = rmm.build_repository_ids_select_field( name='repository_ids', + multiple=True, + display='checkboxes', + my_writable=True ) return trans.fill_template( '/webapps/tool_shed/common/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, @@ -2840,9 +2843,8 @@ if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - trans.user, repository, **kwd ) if error_message: diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/galaxy/webapps/tool_shed/controllers/upload.py --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -262,10 +262,9 @@ ( len( files_to_remove ), upload_point ) else: message += " %d files were removed from the repository root. " % len( files_to_remove ) - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - trans.user, repository, content_alert_str=content_alert_str, **kwd ) diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -727,9 +727,8 @@ results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app ) + rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - self.user, repository, content_alert_str=content_alert_str ) if error_message: diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -3,6 +3,7 @@ from galaxy import util from galaxy.util import inflector +from galaxy.web.form_builder import SelectField from tool_shed.metadata import metadata_generator @@ -19,6 +20,32 @@ super( InstalledRepositoryMetadataManager, self ).__init__( app ) self.app = app + def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes' ): + """Generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + query = self.get_query_for_setting_metadata_on_repositories( order=True ) + for repository in query: + owner = str( repository.owner ) + option_label = '%s (%s)' % ( str( repository.name ), owner ) + option_value = '%s' % self.app.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field + + def get_query_for_setting_metadata_on_repositories( self, order=True ): + """ + Return a query containing repositories for resetting metadata. The order parameter + is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from the Galaxy API, order is False. + """ + if order: + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) \ + .order_by( self.app.install_model.ToolShedRepository.table.c.name, + self.app.install_model.ToolShedRepository.table.c.owner ) + else: + return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ + .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) + def reset_all_metadata_on_installed_repository( self, id ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -2,11 +2,13 @@ import os import tempfile +from galaxy import util from galaxy.util import inflector -from galaxy import util +from galaxy.web.form_builder import SelectField from tool_shed.metadata import metadata_generator from tool_shed.repository_types.metadata import TipOnly +from tool_shed.repository_types import util as rt_util from tool_shed.util import basic_util from tool_shed.util import common_util @@ -20,9 +22,10 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app ): + def __init__( self, app, user ): super( RepositoryMetadataManager, self ).__init__( app ) self.app = app + self.user = user # Repository metadata comparisons for changeset revisions. self.EQUAL = 'equal' self.NO_METADATA = 'no metadata' @@ -47,6 +50,18 @@ self.sa_session.add( repository_metadata ) self.sa_session.flush() + def build_repository_ids_select_field( self, name='repository_ids', multiple=True, display='checkboxes', + my_writable=False ): + """Generate the current list of repositories for resetting metadata.""" + repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) + query = self.get_query_for_setting_metadata_on_repositories( my_writable=my_writable, order=True ) + for repository in query: + owner = str( repository.user.username ) + option_label = '%s (%s)' % ( str( repository.name ), owner ) + option_value = '%s' % self.app.security.encode_id( repository.id ) + repositories_select_field.add_option( option_label, option_value ) + return repositories_select_field + def clean_repository_metadata( self, id, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple @@ -458,6 +473,54 @@ # The tool did not change through all of the changeset revisions. return old_id + def get_query_for_setting_metadata_on_repositories( self, my_writable=False, order=True ): + """ + Return a query containing repositories for resetting metadata. The order parameter + is used for displaying the list of repositories ordered alphabetically for display on + a page. When called from the Tool Shed API, order is False. + """ + # When called from the Tool Shed API, the metadata is reset on all repositories of types + # repository_suite_definition and tool_dependency_definition in addition to other selected + # repositories. + if my_writable: + username = self.user.username + clause_list = [] + for repository in self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ): + # Always reset metadata on all repositories of types repository_suite_definition and + # tool_dependency_definition. + if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: + clause_list.append( self.app.model.Repository.table.c.id == repository.id ) + else: + allow_push = repository.allow_push( self.app ) + if allow_push: + # Include all repositories that are writable by the current user. + allow_push_usernames = allow_push.split( ',' ) + if username in allow_push_usernames: + clause_list.append( self.app.model.Repository.table.c.id == repository.id ) + if clause_list: + if order: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( or_( *clause_list ) ) \ + .order_by( self.app.model.Repository.table.c.name, + self.app.model.Repository.table.c.user_id ) + else: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( or_( *clause_list ) ) + else: + # Return an empty query. + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.id == -1 ) + else: + if order: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ) \ + .order_by( self.app.model.Repository.table.c.name, + self.app.model.Repository.table.c.user_id ) + else: + return self.sa_session.query( self.app.model.Repository ) \ + .filter( self.app.model.Repository.table.c.deleted == False ) + def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): """ Compare the last saved metadata for each datatype in the repository with the new metadata @@ -732,13 +795,13 @@ # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, user, id ): + def reset_all_metadata_on_repository_in_tool_shed( self, id ): """Reset all metadata on a single repository in a tool shed.""" repository = suc.get_repository_in_tool_shed( self.app, id ) log.debug( "Resetting all metadata on repository: %s" % repository.name ) repo_dir = repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) # The list of changeset_revisions refers to repository_metadata records that have been created # or updated. When the following loop completes, we'll delete all repository_metadata records # for this repository that do not have a changeset_revision value in this list. @@ -875,7 +938,7 @@ self.sa_session.add( repository_metadata ) self.sa_session.flush() - def reset_metadata_on_selected_repositories( self, user, **kwd ): + def reset_metadata_on_selected_repositories( self, **kwd ): """ Inspect the repository changelog to reset metadata for all appropriate changeset revisions. This method is called from both Galaxy and the Tool Shed. @@ -892,7 +955,7 @@ repository = suc.get_repository_in_tool_shed( self.app, repository_id ) owner = str( repository.user.username ) invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( user, repository_id ) + self.reset_all_metadata_on_repository_in_tool_shed( self.user, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, invalid_file_tups, @@ -918,7 +981,7 @@ status = 'error' return message, status - def set_repository_metadata( self, host, user, repository, content_alert_str='', **kwd ): + def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. @@ -926,7 +989,7 @@ message = '' status = 'done' encoded_id = self.app.security.encode_id( repository.id ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) repo_dir = repository.repo_path( self.app ) repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_dir, create=False ) metadata_dict, invalid_file_tups = \ @@ -1027,10 +1090,9 @@ tool_util.reset_tool_data_tables( self.app ) return message, status - def set_repository_metadata_due_to_new_tip( self, host, user, repository, content_alert_str=None, **kwd ): + def set_repository_metadata_due_to_new_tip( self, host, repository, content_alert_str=None, **kwd ): """Set metadata on the repository tip in the tool shed.""" error_message, status = self.set_repository_metadata( host, - user, repository, content_alert_str=content_alert_str, **kwd ) diff -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 -r 0eaf1edd08e3b79ebbbe68921baef2f94bb4804d lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -84,20 +84,6 @@ '${host}' """ -def build_repository_ids_select_field( trans, name='repository_ids', multiple=True, display='checkboxes', my_writable=False ): - """Method called from both Galaxy and the Tool Shed to generate the current list of repositories for resetting metadata.""" - repositories_select_field = SelectField( name=name, multiple=multiple, display=display ) - query = get_query_for_setting_metadata_on_repositories( trans, my_writable=my_writable, order=True ) - for repository in query: - if trans.webapp.name == 'tool_shed': - owner = str( repository.user.username ) - else: - owner = str( repository.owner ) - option_label = '%s (%s)' % ( str( repository.name ), owner ) - option_value = '%s' % trans.security.encode_id( repository.id ) - repositories_select_field.add_option( option_label, option_value ) - return repositories_select_field - def build_tool_dependencies_select_field( app, tool_shed_repository, name, multiple=True, display='checkboxes', uninstalled_only=False ): """Method called from Galaxy to generate the current list of tool dependency ids for an installed tool shed repository.""" tool_dependencies_select_field = SelectField( name=name, multiple=multiple, display=display ) @@ -645,66 +631,6 @@ prior_import_or_install_required_dict[ encoded_repository_id ] = prior_import_or_install_ids return prior_import_or_install_required_dict -def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, order=True ): - """ - Return a query containing repositories for resetting metadata. This method is called from both the - Tool Shed and Galaxy. The my_writable parameter is ignored unless called from the Tool Shed, and the - order parameter is used for displaying the list of repositories ordered alphabetically for display on - a page. When called from either the Tool Shed or Galaxy API, order is False. - """ - if trans.webapp.name == 'tool_shed': - # When called from the Tool Shed API, the metadata is reset on all repositories of types - # repository_suite_definition and tool_dependency_definition in addition to other selected - # repositories. - if my_writable: - username = trans.user.username - clause_list = [] - for repository in trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ): - # Always reset metadata on all repositories of types repository_suite_definition and - # tool_dependency_definition. - if repository.type in [ rt_util.REPOSITORY_SUITE_DEFINITION, rt_util.TOOL_DEPENDENCY_DEFINITION ]: - clause_list.append( trans.model.Repository.table.c.id == repository.id ) - else: - allow_push = repository.allow_push( trans.app ) - if allow_push: - # Include all repositories that are writable by the current user. - allow_push_usernames = allow_push.split( ',' ) - if username in allow_push_usernames: - clause_list.append( trans.model.Repository.table.c.id == repository.id ) - if clause_list: - if order: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( or_( *clause_list ) ) \ - .order_by( trans.model.Repository.table.c.name, - trans.model.Repository.table.c.user_id ) - else: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( or_( *clause_list ) ) - else: - # Return an empty query. - return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.id == -1 ) - else: - if order: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) \ - .order_by( trans.model.Repository.table.c.name, - trans.model.Repository.table.c.user_id ) - else: - return trans.sa_session.query( trans.model.Repository ) \ - .filter( trans.model.Repository.table.c.deleted == False ) - else: - # We're in Galaxy. - if order: - return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) \ - .order_by( trans.install_model.ToolShedRepository.table.c.name, - trans.install_model.ToolShedRepository.table.c.owner ) - else: - return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ - .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repo_info_tuple_contents( repo_info_tuple ): """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a ToolPanelManager for Galaxy installs from the Tool Shed.
by commits-noreply＠bitbucket.org 21 Jul '14

21 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8bf7a37c694/ Changeset: f8bf7a37c694 User: greg Date: 2014-07-21 17:36:29 Summary: Add a ToolPanelManager for Galaxy installs from the Tool Shed. Affected #: 9 files diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 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 @@ -30,6 +30,7 @@ from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -244,10 +245,10 @@ if kwd.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. - tool_util.remove_from_tool_panel( trans.app, - tool_shed_repository, - shed_tool_conf, - uninstall=remove_from_disk_checked ) + tpm = tool_panel_manager.ToolPanelManager( trans.app ) + tpm.remove_from_tool_panel( tool_shed_repository, + shed_tool_conf, + uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: data_manager_util.remove_from_data_manager( trans.app, tool_shed_repository ) if tool_shed_repository.includes_datatypes: @@ -1336,13 +1337,14 @@ # its repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools_for_display_in_tool_panel: + tpm = tool_panel_manager.ToolPanelManager( trans.app ) # Handle the selected tool panel location for loading tools included in the tool shed repository. tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( toolbox=trans.app.toolbox, - metadata=metadata, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_selection( toolbox=trans.app.toolbox, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) if tool_section is not None: # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't... tool_panel_section_id = str( tool_section.id ) @@ -1942,19 +1944,19 @@ updating_installed_repository=True, persist=True ) if 'tools' in metadata_dict: + tpm = tool_panel_manager.ToolPanelManager( trans.app ) tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) repository_tools_tups = suc.get_repository_tools_tups( trans.app, metadata_dict ) - tool_util.add_to_tool_panel( app=trans.app, - repository_name=str( repository.name ), - repository_clone_url=repository_clone_url, - changeset_revision=str( repository.installed_changeset_revision ), - repository_tools_tups=repository_tools_tups, - owner=str( repository.owner ), - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=False ) + tpm.add_to_tool_panel( repository_name=str( repository.name ), + repository_clone_url=repository_clone_url, + changeset_revision=str( repository.installed_changeset_revision ), + repository_tools_tups=repository_tools_tups, + owner=str( repository.owner ), + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=False ) # Add new Data Manager entries if 'data_manager' in metadata_dict: new_data_managers = data_manager_util.install_data_managers( trans.app, diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -33,6 +33,7 @@ from tool_shed.galaxy_install.tool_dependencies.recipe.install_environment import InstallEnvironment from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import StepManager from tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager import TagManager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -535,7 +536,8 @@ self.app.config.shed_tool_data_table_config, persist=True ) if 'tools' in metadata_dict: - tool_panel_dict = tool_util.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) + tpm = tool_panel_manager.ToolPanelManager( self.app ) + tool_panel_dict = tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tool_util.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) @@ -555,16 +557,18 @@ sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the # local Galaxy instance. - tool_util.copy_sample_files( self.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) - tool_util.add_to_tool_panel( app=self.app, - repository_name=tool_shed_repository.name, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - repository_tools_tups=repository_tools_tups, - owner=tool_shed_repository.owner, - shed_tool_conf=shed_tool_conf, - tool_panel_dict=tool_panel_dict, - new_install=True ) + tool_util.copy_sample_files( self.app, + sample_files, + tool_path=tool_path, + sample_files_copied=sample_files_copied ) + tpm.add_to_tool_panel( repository_name=tool_shed_repository.name, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + repository_tools_tups=repository_tools_tups, + owner=tool_shed_repository.owner, + shed_tool_conf=shed_tool_conf, + tool_panel_dict=tool_panel_dict, + new_install=True ) if 'data_manager' in metadata_dict: new_data_managers = data_manager_util.install_data_managers( self.app, self.app.config.shed_data_manager_config_file, @@ -644,10 +648,11 @@ tool_shed_url = installation_dict[ 'tool_shed_url' ] # Handle contained tools. if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section_label or tool_panel_section_id ): + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_section = \ - tool_util.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: tool_panel_section_key = None tool_section = None diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -11,11 +11,11 @@ from tool_shed.util import datatype_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util from tool_shed.util import xml_util from galaxy.model.orm import and_ from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager log = logging.getLogger( __name__ ) @@ -80,19 +80,19 @@ repository.deleted = False repository.status = self.install_model.ToolShedRepository.installation_status.INSTALLED if repository.includes_tools_for_display_in_tool_panel: + tpm = tool_panel_manager.ToolPanelManager( self.app ) metadata = repository.metadata repository_tools_tups = suc.get_repository_tools_tups( self.app, metadata ) # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] - tool_util.add_to_tool_panel( self.app, - repository.name, - repository_clone_url, - repository.installed_changeset_revision, - repository_tools_tups, - repository.owner, - shed_tool_conf, - tool_panel_dict, - new_install=False ) + tpm.add_to_tool_panel( repository.name, + repository_clone_url, + repository.installed_changeset_revision, + repository_tools_tups, + repository.owner, + shed_tool_conf, + tool_panel_dict, + new_install=False ) if repository.includes_data_managers: tp, data_manager_relative_install_dir = repository.get_tool_relative_path( self.app ) # Hack to add repository.name here, which is actually the root of the installed repository diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/galaxy_install/repair_repository_manager.py --- a/lib/tool_shed/galaxy_install/repair_repository_manager.py +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -5,13 +5,14 @@ from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import shed_util_common as suc from tool_shed.util import repository_maintenance_util from tool_shed.util import tool_dependency_util -from tool_shed.util import tool_util + class RepairRepositoryManager(): @@ -119,10 +120,11 @@ tool_panel_section_id = section_dict[ 'id' ] tool_panel_section_name = section_dict[ 'name' ] if tool_panel_section_id: + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_panel_section_key, tool_panel_section = \ - tool_util.get_or_create_tool_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=tool_panel_section_name ) + tpm.get_or_create_tool_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=tool_panel_section_name ) else: tool_dependencies = None repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=self.app, @@ -156,15 +158,17 @@ log.debug( error_message ) repair_dict [ repository.name ] = error_message elif repository.status not in [ self.app.install_model.ToolShedRepository.installation_status.INSTALLED ]: - shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) + shed_tool_conf, tool_path, relative_install_dir = \ + suc.get_tool_panel_config_tool_path_install_dir( self.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: + tpm = tool_panel_manager.ToolPanelManager( self.app ) tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( self.app.toolbox, - metadata, - no_changes_checked=True, - tool_panel_section_id=None, - new_tool_panel_section_label=None ) + tpm.handle_tool_panel_selection( self.app.toolbox, + metadata, + no_changes_checked=True, + tool_panel_section_id=None, + new_tool_panel_section_label=None ) else: # The tools will be loaded outside of any sections in the tool panel. tool_panel_section_key = None diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py --- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py +++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py @@ -10,11 +10,12 @@ from galaxy.util import asbool +from tool_shed.galaxy_install.tools import tool_panel_manager + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import shed_util_common as suc -from tool_shed.util import tool_util log = logging.getLogger( __name__ ) @@ -216,19 +217,20 @@ if can_update_db_record: # The database record for the tool shed repository currently being processed can be updated. # Get the repository metadata to see where it was previously located in the tool panel. + tpm = tool_panel_manager.ToolPanelManager( self.app ) if repository_db_record and repository_db_record.metadata: tool_section, tool_panel_section_key = \ - tool_util.handle_tool_panel_selection( toolbox=self.app.toolbox, - metadata=repository_db_record.metadata, - no_changes_checked=no_changes_checked, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_selection( toolbox=self.app.toolbox, + metadata=repository_db_record.metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: # We're installing a new tool shed repository that does not yet have a database record. tool_panel_section_key, tool_section = \ - tool_util.handle_tool_panel_section( self.app.toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) + tpm.handle_tool_panel_section( self.app.toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) tool_shed_repository = \ suc.create_or_update_tool_shed_repository( app=self.app, name=name, diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -14,6 +14,7 @@ from tool_shed.galaxy_install import install_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager +from tool_shed.galaxy_install.tools import tool_panel_manager from tool_shed.util import basic_util from tool_shed.util import common_util @@ -30,23 +31,31 @@ class ToolMigrationManager( object ): - def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, install_dependencies ): + def __init__( self, app, latest_migration_script_number, tool_shed_install_config, migrated_tools_config, + install_dependencies ): """ - Check tool settings in tool_shed_install_config and install all repositories that are not already installed. The tool - panel configuration file is the received migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. + Check tool settings in tool_shed_install_config and install all repositories + that are not already installed. The tool panel configuration file is the received + migrated_tools_config, which is the reserved file named migrated_tools_conf.xml. """ self.app = app self.toolbox = self.app.toolbox self.migrated_tools_config = migrated_tools_config - # If install_dependencies is True but tool_dependency_dir is not set, do not attempt to install but print informative error message. + self.tpm = tool_panel_manager.ToolPanelManager( self.app ) + # If install_dependencies is True but tool_dependency_dir is not set, do not attempt + # to install but print informative error message. if install_dependencies and app.config.tool_dependency_dir is None: - message = 'You are attempting to install tool dependencies but do not have a value for "tool_dependency_dir" set in your universe_wsgi.ini ' - message += 'file. Set this location value to the path where you want tool dependencies installed and rerun the migration script.' + message = 'You are attempting to install tool dependencies but do not have a value ' + message += 'for "tool_dependency_dir" set in your universe_wsgi.ini file. Set this ' + message += 'location value to the path where you want tool dependencies installed and ' + message += 'rerun the migration script.' raise Exception( message ) - # Get the local non-shed related tool panel configs (there can be more than one, and the default name is tool_conf.xml). + # Get the local non-shed related tool panel configs (there can be more than one, and the + # default name is tool_conf.xml). self.proprietary_tool_confs = self.non_shed_tool_panel_configs self.proprietary_tool_panel_elems = self.get_proprietary_tool_panel_elems( latest_migration_script_number ) - # Set the location where the repositories will be installed by retrieving the tool_path setting from migrated_tools_config. + # Set the location where the repositories will be installed by retrieving the tool_path + # setting from migrated_tools_config. tree, error_message = xml_util.parse_xml( migrated_tools_config ) if tree is None: print error_message @@ -66,21 +75,24 @@ self.tool_shed = common_util.remove_protocol_and_port_from_tool_shed_url( self.tool_shed_url ) self.repository_owner = common_util.REPOSITORY_OWNER index, self.shed_config_dict = suc.get_shed_tool_conf_dict( app, self.migrated_tools_config ) - # Since tool migration scripts can be executed any number of times, we need to make sure the appropriate tools are defined in - # tool_conf.xml. If no tools associated with the migration stage are defined, no repositories will be installed on disk. - # The default behavior is that the tool shed is down. + # Since tool migration scripts can be executed any number of times, we need to + # make sure the appropriate tools are defined in tool_conf.xml. If no tools + # associated with the migration stage are defined, no repositories will be installed + # on disk. The default behavior is that the tool shed is down. tool_shed_accessible = False tool_panel_configs = common_util.get_non_shed_tool_panel_configs( app ) if tool_panel_configs: # The missing_tool_configs_dict contents are something like: # {'emboss_antigenic.xml': [('emboss', '5.0.0', 'package', '\nreadme blah blah blah\n')]} - tool_shed_accessible, missing_tool_configs_dict = common_util.check_for_missing_tools( app, - tool_panel_configs, - latest_migration_script_number ) + tool_shed_accessible, missing_tool_configs_dict = \ + common_util.check_for_missing_tools( app, + tool_panel_configs, + latest_migration_script_number ) else: - # It doesn't matter if the tool shed is accessible since there are no migrated tools defined in the local Galaxy instance, but - # we have to set the value of tool_shed_accessible to True so that the value of migrate_tools.version can be correctly set in - # the database. + # It doesn't matter if the tool shed is accessible since there are no migrated + # tools defined in the local Galaxy instance, but we have to set the value of + # tool_shed_accessible to True so that the value of migrate_tools.version can + # be correctly set in the database. tool_shed_accessible = True missing_tool_configs_dict = odict() if tool_shed_accessible: @@ -93,15 +105,18 @@ if missing_tool_configs_dict: for proprietary_tool_conf in self.proprietary_tool_confs: # Create a backup of the tool configuration in the un-migrated state. - shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, latest_migration_script_number ) ) + shutil.copy( proprietary_tool_conf, '%s-pre-stage-%04d' % ( proprietary_tool_conf, + latest_migration_script_number ) ) for repository_elem in root: # Make sure we have a valid repository tag. if self.__is_valid_repository_tag( repository_elem ): - # Get all repository dependencies for the repository defined by the current repository_elem. Repository dependency - # definitions contained in tool shed repositories with migrated tools must never define a relationship to a repository - # dependency that contains a tool. The repository dependency can only contain items that are not loaded into the Galaxy - # tool panel (e.g., tool dependency definitions, custom datatypes, etc). This restriction must be followed down the - # entire dependency hierarchy. + # Get all repository dependencies for the repository defined by the + # current repository_elem. Repository dependency definitions contained + # in tool shed repositories with migrated tools must never define a + # relationship to a repository dependency that contains a tool. The + # repository dependency can only contain items that are not loaded into + # the Galaxy tool panel (e.g., tool dependency definitions, custom datatypes, + # etc). This restriction must be followed down the entire dependency hierarchy. name = repository_elem.get( 'name' ) changeset_revision = repository_elem.get( 'changeset_revision' ) tool_shed_accessible, repository_dependencies_dict = \ @@ -110,30 +125,38 @@ name, self.repository_owner, changeset_revision ) - # Make sure all repository dependency records exist (as tool_shed_repository table rows) in the Galaxy database. - created_tool_shed_repositories = self.create_or_update_tool_shed_repository_records( name, - changeset_revision, - repository_dependencies_dict ) + # Make sure all repository dependency records exist (as tool_shed_repository + # table rows) in the Galaxy database. + created_tool_shed_repositories = \ + self.create_or_update_tool_shed_repository_records( name, + changeset_revision, + repository_dependencies_dict ) # Order the repositories for proper installation. This process is similar to the # process used when installing tool shed repositories, but does not handle managing # tool panel sections and other components since repository dependency definitions # contained in tool shed repositories with migrated tools must never define a relationship # to a repository dependency that contains a tool. - ordered_tool_shed_repositories = self.order_repositories_for_installation( created_tool_shed_repositories, - repository_dependencies_dict ) + ordered_tool_shed_repositories = \ + self.order_repositories_for_installation( created_tool_shed_repositories, + repository_dependencies_dict ) for tool_shed_repository in ordered_tool_shed_repositories: - is_repository_dependency = self.__is_repository_dependency( name, changeset_revision, tool_shed_repository ) + is_repository_dependency = self.__is_repository_dependency( name, + changeset_revision, + tool_shed_repository ) self.install_repository( repository_elem, tool_shed_repository, install_dependencies, is_repository_dependency=is_repository_dependency ) else: - message = "\nNo tools associated with migration stage %s are defined in your " % str( latest_migration_script_number ) - message += "file%s named %s,\nso no repositories will be installed on disk.\n" % ( plural, file_names ) + message = "\nNo tools associated with migration stage %s are defined in your " % \ + str( latest_migration_script_number ) + message += "file%s named %s,\nso no repositories will be installed on disk.\n" % \ + ( plural, file_names ) print message else: - message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % str( latest_migration_script_number ) + message = "\nThe main Galaxy tool shed is not currently available, so skipped migration stage %s.\n" % \ + str( latest_migration_script_number ) message += "Try again later.\n" print message @@ -354,16 +377,21 @@ repo_install_dir = relative_install_dir if not is_repository_dependency: for tool_elem in repository_elem: - # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> + # The tool_elem looks something like this: + # <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) guid = self.get_guid( repository_clone_url, relative_install_dir, tool_config ) # See if tool_config is defined inside of a section in self.proprietary_tool_panel_elems. is_displayed, tool_sections = self.get_containing_tool_sections( tool_config ) if is_displayed: tool_panel_dict_for_tool_config = \ - tool_util.generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=tool_sections ) + self.tpm.generate_tool_panel_dict_for_tool_config( guid, + tool_config, + tool_sections=tool_sections ) # The tool-panel_dict has the following structure. - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, + # {<Tool guid> : [{ tool_config : <tool_config_file>, + # id: <ToolSection id>, + # version : <ToolSection version>, # name : <TooSection name>}]} for k, v in tool_panel_dict_for_tool_config.items(): tool_panel_dict_for_display[ k ] = v @@ -433,15 +461,14 @@ tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if not is_repository_dependency: - tool_util.add_to_tool_panel( self.app, - tool_shed_repository.name, - repository_clone_url, - tool_shed_repository.installed_changeset_revision, - repository_tools_tups, - self.repository_owner, - self.migrated_tools_config, - tool_panel_dict=tool_panel_dict_for_display, - new_install=True ) + self.tpm.add_to_tool_panel( tool_shed_repository.name, + repository_clone_url, + tool_shed_repository.installed_changeset_revision, + repository_tools_tups, + self.repository_owner, + self.migrated_tools_config, + tool_panel_dict=tool_panel_dict_for_display, + new_install=True ) if install_dependencies and tool_dependencies and has_tool_dependencies: # Install tool dependencies. suc.update_tool_shed_repository_status( self.app, diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/galaxy_install/tools/tool_panel_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/tools/tool_panel_manager.py @@ -0,0 +1,465 @@ +import logging +import os + +import galaxy.tools +from galaxy.tools.search import ToolBoxSearch +from xml.etree import ElementTree as XmlET + +from tool_shed.util import basic_util +from tool_shed.util import common_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class ToolPanelManager( object ): + + def __init__( self, app ): + self.app = app + + def add_to_shed_tool_config( self, shed_tool_conf_dict, elem_list ): + # A tool shed repository is being installed so change the shed_tool_conf file. Parse the + # config file to generate the entire list of config_elems instead of using the in-memory list + # since it will be a subset of the entire list if one or more repositories have been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + # Add the elements to the in-memory list of config_elems. + for elem_entry in elem_list: + config_elems.append( elem_entry ) + # Persist the altered shed_tool_config file. + suc.config_elems_to_xml_file( self.app, config_elems, shed_tool_conf, tool_path ) + + def add_to_tool_panel( self, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, + shed_tool_conf, tool_panel_dict, new_install=True ): + """A tool shed repository is being installed or updated so handle tool panel alterations accordingly.""" + # We need to change the in-memory version and the file system version of the shed_tool_conf file. + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + tool_path = shed_tool_conf_dict[ 'tool_path' ] + # Generate the list of ElementTree Element objects for each section or tool. + elem_list = self.generate_tool_panel_elem_list( repository_name, + repository_clone_url, + changeset_revision, + tool_panel_dict, + repository_tools_tups, + owner=owner ) + if new_install: + # Add the new elements to the shed_tool_conf file on disk. + self.add_to_shed_tool_config( shed_tool_conf_dict, elem_list ) + # Use the new elements to add entries to the + config_elems = shed_tool_conf_dict[ 'config_elems' ] + for config_elem in elem_list: + # Add the new elements to the in-memory list of config_elems. + config_elems.append( config_elem ) + # Load the tools into the in-memory tool panel. + if config_elem.tag == 'section': + self.app.toolbox.load_section_tag_set( config_elem, tool_path, load_panel_dict=True ) + elif config_elem.tag == 'workflow': + self.app.toolbox.load_workflow_tag_set( config_elem, + self.app.toolbox.tool_panel, + self.app.toolbox.integrated_tool_panel, + load_panel_dict=True ) + elif config_elem.tag == 'tool': + guid = config_elem.get( 'guid' ) + self.app.toolbox.load_tool_tag_set( config_elem, + self.app.toolbox.tool_panel, + self.app.toolbox.integrated_tool_panel, + tool_path, + load_panel_dict=True, + guid=guid ) + # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. + shed_tool_conf_dict[ 'config_elems' ] = config_elems + self.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + if self.app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + self.app.toolbox.write_integrated_tool_panel_config_file() + self.app.toolbox_search = ToolBoxSearch( self.app.toolbox ) + + def generate_tool_panel_dict_for_new_install( self, tool_dicts, tool_section=None ): + """ + When installing a repository that contains tools, all tools must currently be defined + within the same tool section in the tool panel or outside of any sections. + """ + tool_panel_dict = {} + if tool_section: + section_id = tool_section.id + section_name = tool_section.name + section_version = tool_section.version or '' + else: + section_id = '' + section_name = '' + section_version = '' + for tool_dict in tool_dicts: + if tool_dict.get( 'add_to_tool_panel', True ): + guid = tool_dict[ 'guid' ] + tool_config = tool_dict[ 'tool_config' ] + tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) + if guid in tool_panel_dict: + tool_panel_dict[ guid ].append( tool_section_dict ) + else: + tool_panel_dict[ guid ] = [ tool_section_dict ] + return tool_panel_dict + + def generate_tool_panel_dict_for_tool_config( self, guid, tool_config, tool_sections=None ): + """ + Create a dictionary of the following type for a single tool config file name. + The intent is to call this method for every tool config in a repository and + append each of these as entries to a tool panel dictionary for the repository. + This enables each tool to be loaded into a different section in the tool panel. + {<Tool guid> : + [{ tool_config : <tool_config_file>, + id: <ToolSection id>, + version : <ToolSection version>, + name : <TooSection name>}]} + """ + tool_panel_dict = {} + file_name = basic_util.strip_path( tool_config ) + tool_section_dicts = self. generate_tool_section_dicts( tool_config=file_name, + tool_sections=tool_sections ) + tool_panel_dict[ guid ] = tool_section_dicts + return tool_panel_dict + + def generate_tool_panel_elem_list( self, repository_name, repository_clone_url, changeset_revision, + tool_panel_dict, repository_tools_tups, owner='' ): + """Generate a list of ElementTree Element objects for each section or tool.""" + elem_list = [] + tool_elem = None + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + if not owner: + owner = suc.get_repository_owner( cleaned_repository_clone_url ) + tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' ) + for guid, tool_section_dicts in tool_panel_dict.items(): + for tool_section_dict in tool_section_dicts: + tool_section = None + inside_section = False + section_in_elem_list = False + if tool_section_dict[ 'id' ]: + inside_section = True + # Create a new section element only if we haven't already created it. + for index, elem in enumerate( elem_list ): + if elem.tag == 'section': + section_id = elem.get( 'id', None ) + if section_id == tool_section_dict[ 'id' ]: + section_in_elem_list = True + tool_section = elem + break + if tool_section is None: + tool_section = self.generate_tool_section_element_from_dict( tool_section_dict ) + # Find the tuple containing the current guid from the list of repository_tools_tups. + for repository_tool_tup in repository_tools_tups: + tool_file_path, tup_guid, tool = repository_tool_tup + if tup_guid == guid: + break + if inside_section: + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + tool_section ) + else: + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + None ) + if inside_section: + if section_in_elem_list: + elem_list[ index ] = tool_section + else: + elem_list.append( tool_section ) + else: + elem_list.append( tool_elem ) + return elem_list + + def generate_tool_section_dicts( self, tool_config=None, tool_sections=None ): + tool_section_dicts = [] + if tool_config is None: + tool_config = '' + if tool_sections: + for tool_section in tool_sections: + # The value of tool_section will be None if the tool is displayed outside + # of any sections in the tool panel. + if tool_section: + section_id = tool_section.id or '' + section_version = tool_section.version or '' + section_name = tool_section.name or '' + else: + section_id = '' + section_version = '' + section_name = '' + tool_section_dicts.append( dict( tool_config=tool_config, + id=section_id, + version=section_version, + name=section_name ) ) + else: + tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) + return tool_section_dicts + + def generate_tool_section_element_from_dict( self, tool_section_dict ): + # The value of tool_section_dict looks like the following. + # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} + if tool_section_dict[ 'id' ]: + # Create a new tool section. + tool_section = XmlET.Element( 'section' ) + tool_section.attrib[ 'id' ] = tool_section_dict[ 'id' ] + tool_section.attrib[ 'name' ] = tool_section_dict[ 'name' ] + tool_section.attrib[ 'version' ] = tool_section_dict[ 'version' ] + else: + tool_section = None + return tool_section + + def get_or_create_tool_section( self, toolbox, tool_panel_section_id, new_tool_panel_section_label=None ): + tool_panel_section_key = str( tool_panel_section_id ) + if tool_panel_section_key in toolbox.tool_panel: + # Appending a tool to an existing section in toolbox.tool_panel + tool_section = toolbox.tool_panel[ tool_panel_section_key ] + log.debug( "Appending to tool panel section: %s" % str( tool_section.name ) ) + else: + # Appending a new section to toolbox.tool_panel + if new_tool_panel_section_label is None: + # This might add an ugly section label to the tool panel, but, oh well... + new_tool_panel_section_label = tool_panel_section_id + elem = XmlET.Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section_label + elem.attrib[ 'id' ] = tool_panel_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + toolbox.tool_panel[ tool_panel_section_key ] = tool_section + log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) + return tool_panel_section_key, tool_section + + def handle_tool_panel_section( self, toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None ): + """Return a ToolSection object retrieved from the current in-memory tool_panel.""" + # If tool_panel_section_id is received, the section exists in the tool panel. In this + # case, the value of the received tool_panel_section_id must be the id retrieved from a + # tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label + # is received, a new section will be added to the tool panel. + if new_tool_panel_section_label: + section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) + tool_panel_section_key, tool_section = \ + self.get_or_create_tool_section( toolbox, + tool_panel_section_id=section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + elif tool_panel_section_id: + tool_panel_section_key = str( tool_panel_section_id ) + tool_section = toolbox.tool_panel[ tool_panel_section_key ] + else: + return None, None + return tool_panel_section_key, tool_section + + def handle_tool_panel_selection( self, toolbox, metadata, no_changes_checked, tool_panel_section_id, + new_tool_panel_section_label ): + """ + Handle the selected tool panel location for loading tools included in tool shed + repositories when installing or reinstalling them. + """ + # Get the location in the tool panel in which each tool was originally loaded. + tool_section = None + tool_panel_section_key = None + if 'tools' in metadata: + # This forces everything to be loaded into the same section (or no section) + # in the tool panel. + if no_changes_checked: + # Make sure the no_changes check box overrides the new_tool_panel_section_label + # if the user checked the check box and entered something into the field. + new_tool_panel_section_label = None + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if not tool_panel_dict: + tool_panel_dict = self.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + else: + tool_panel_dict = self.generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) + if tool_panel_dict: + # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_id = tool_section_dict[ 'id' ] + original_section_name = tool_section_dict[ 'name' ] + if original_section_id: + tool_panel_section_key, tool_section = \ + self.get_or_create_tool_section( toolbox, + tool_panel_section_id=original_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + else: + # The user elected to change the tool panel section to contain the tools. + tool_panel_section_key, tool_section = \ + self.handle_tool_panel_section( toolbox, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + return tool_section, tool_panel_section_key + + def remove_from_shed_tool_config( self, shed_tool_conf_dict, guids_to_remove ): + # A tool shed repository is being uninstalled so change the shed_tool_conf file. + # Parse the config file to generate the entire list of config_elems instead of + # using the in-memory list since it will be a subset of the entire list if one + # or more repositories have been deactivated. + shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] + tool_path = shed_tool_conf_dict[ 'tool_path' ] + config_elems = [] + tree, error_message = xml_util.parse_xml( shed_tool_conf ) + if tree: + root = tree.getroot() + for elem in root: + config_elems.append( elem ) + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + # Remove all of the appropriate tool sub-elements from the section element. + config_elem.remove( tool_elem ) + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + if config_elem.get( 'guid' ) in guids_to_remove: + config_elems_to_remove.append( config_elem ) + for config_elem in config_elems_to_remove: + config_elems.remove( config_elem ) + # Persist the altered in-memory version of the tool config. + suc.config_elems_to_xml_file( self.app, config_elems, shed_tool_conf, tool_path ) + + def remove_from_tool_panel( self, repository, shed_tool_conf, uninstall ): + """ + A tool shed repository is being deactivated or uninstalled, so handle tool panel + alterations accordingly. + """ + # Determine where the tools are currently defined in the tool panel and store this + # information so the tools can be displayed in the same way when the repository is + # activated or reinstalled. + tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( self.app, repository ) + repository.metadata[ 'tool_panel_section' ] = tool_panel_dict + self.app.install_model.context.add( repository ) + self.app.install_model.context.flush() + # Create a list of guids for all tools that will be removed from the in-memory tool panel + # and config file on disk. + guids_to_remove = [ k for k in tool_panel_dict.keys() ] + # Remove the tools from the toolbox's tools_by_id dictionary. + for guid_to_remove in guids_to_remove: + if guid_to_remove in self.app.toolbox.tools_by_id: + del self.app.toolbox.tools_by_id[ guid_to_remove ] + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( self.app, shed_tool_conf ) + if uninstall: + # Remove from the shed_tool_conf file on disk. + self.remove_from_shed_tool_config( shed_tool_conf_dict, guids_to_remove ) + config_elems = shed_tool_conf_dict[ 'config_elems' ] + config_elems_to_remove = [] + for config_elem in config_elems: + if config_elem.tag == 'section': + # Get the section key for the in-memory tool panel. + section_key = str( config_elem.get( "id" ) ) + # Generate the list of tool elements to remove. + tool_elems_to_remove = [] + for tool_elem in config_elem: + if tool_elem.get( 'guid' ) in guids_to_remove: + tool_elems_to_remove.append( tool_elem ) + for tool_elem in tool_elems_to_remove: + if tool_elem in config_elem: + # Remove the tool sub-element from the section element. + config_elem.remove( tool_elem ) + # Remove the tool from the section in the in-memory tool panel. + if section_key in self.app.toolbox.tool_panel: + tool_section = self.app.toolbox.tool_panel[ section_key ] + guid = tool_elem.get( 'guid' ) + tool_key = 'tool_%s' % str( guid ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = self.app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in tool_section.elems: + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + replacement_tool_version = None + # Since we are going to remove the tool from the section, replace it with the + # newest loaded version of the tool. + for available_tool_version in available_tool_versions: + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_section_elems_index, key in enumerate( tool_section.elems.keys() ): + if key == tool_key: + break + # Remove the tool from the tool section. + del tool_section.elems[ tool_key ] + # Add the replacement tool at the same location in the tool section. + tool_section.elems.insert( tool_section_elems_index, + replacement_tool_key, + replacement_tool_version ) + else: + del tool_section.elems[ tool_key ] + else: + del tool_section.elems[ tool_key ] + if uninstall: + # Remove the tool from the section in the in-memory integrated tool panel. + if section_key in self.app.toolbox.integrated_tool_panel: + tool_section = self.app.toolbox.integrated_tool_panel[ section_key ] + tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) + if tool_key in tool_section.elems: + del tool_section.elems[ tool_key ] + if len( config_elem ) < 1: + # Keep a list of all empty section elements so they can be removed. + config_elems_to_remove.append( config_elem ) + elif config_elem.tag == 'tool': + guid = config_elem.get( 'guid' ) + if guid in guids_to_remove: + tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) + # Get the list of versions of this tool that are currently available in the toolbox. + available_tool_versions = self.app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in self.app.toolbox.tool_panel: + if available_tool_versions: + available_tool_versions.reverse() + replacement_tool_key = None + replacement_tool_version = None + # Since we are going to remove the tool from the section, replace it with + # the newest loaded version of the tool. + for available_tool_version in available_tool_versions: + available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() + if available_tool_version.id in self.app.toolbox.tool_panel.keys() or not available_tool_section_id: + replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) + replacement_tool_version = available_tool_version + break + if replacement_tool_key and replacement_tool_version: + # Get the index of the tool_key in the tool_section. + for tool_panel_index, key in enumerate( self.app.toolbox.tool_panel.keys() ): + if key == tool_key: + break + # Remove the tool from the tool panel. + del self.app.toolbox.tool_panel[ tool_key ] + # Add the replacement tool at the same location in the tool panel. + self.app.toolbox.tool_panel.insert( tool_panel_index, + replacement_tool_key, + replacement_tool_version ) + else: + del self.app.toolbox.tool_panel[ tool_key ] + else: + del self.app.toolbox.tool_panel[ tool_key ] + if uninstall: + if tool_key in self.app.toolbox.integrated_tool_panel: + del self.app.toolbox.integrated_tool_panel[ tool_key ] + config_elems_to_remove.append( config_elem ) + for config_elem in config_elems_to_remove: + # Remove the element from the in-memory list of elements. + config_elems.remove( config_elem ) + # Update the config_elems of the in-memory shed_tool_conf_dict. + shed_tool_conf_dict[ 'config_elems' ] = config_elems + self.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + self.app.toolbox_search = ToolBoxSearch( self.app.toolbox ) + if uninstall and self.app.config.update_integrated_tool_panel: + # Write the current in-memory version of the integrated_tool_panel.xml file to disk. + self.app.toolbox.write_integrated_tool_panel_config_file() diff -r cbca66cc16bfed165f3b38399857ad0b85d14489 -r f8bf7a37c69469d3b4350e0d6b1965cc87dc7a49 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -19,69 +19,6 @@ log = logging.getLogger( __name__ ) -def add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ): - # A tool shed repository is being installed so change the shed_tool_conf file. Parse the - # config file to generate the entire list of config_elems instead of using the in-memory list - # since it will be a subset of the entire list if one or more repositories have been deactivated. - shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] - tool_path = shed_tool_conf_dict[ 'tool_path' ] - config_elems = [] - tree, error_message = xml_util.parse_xml( shed_tool_conf ) - if tree: - root = tree.getroot() - for elem in root: - config_elems.append( elem ) - # Add the elements to the in-memory list of config_elems. - for elem_entry in elem_list: - config_elems.append( elem_entry ) - # Persist the altered shed_tool_config file. - suc.config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) - -def add_to_tool_panel( app, repository_name, repository_clone_url, changeset_revision, repository_tools_tups, owner, - shed_tool_conf, tool_panel_dict, new_install=True ): - """A tool shed repository is being installed or updated so handle tool panel alterations accordingly.""" - # We need to change the in-memory version and the file system version of the shed_tool_conf file. - index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( app, shed_tool_conf ) - tool_path = shed_tool_conf_dict[ 'tool_path' ] - # Generate the list of ElementTree Element objects for each section or tool. - elem_list = generate_tool_panel_elem_list( repository_name, - repository_clone_url, - changeset_revision, - tool_panel_dict, - repository_tools_tups, - owner=owner ) - if new_install: - # Add the new elements to the shed_tool_conf file on disk. - add_to_shed_tool_config( app, shed_tool_conf_dict, elem_list ) - # Use the new elements to add entries to the - config_elems = shed_tool_conf_dict[ 'config_elems' ] - for config_elem in elem_list: - # Add the new elements to the in-memory list of config_elems. - config_elems.append( config_elem ) - # Load the tools into the in-memory tool panel. - if config_elem.tag == 'section': - app.toolbox.load_section_tag_set( config_elem, tool_path, load_panel_dict=True ) - elif config_elem.tag == 'workflow': - app.toolbox.load_workflow_tag_set( config_elem, - app.toolbox.tool_panel, - app.toolbox.integrated_tool_panel, - load_panel_dict=True ) - elif config_elem.tag == 'tool': - guid = config_elem.get( 'guid' ) - app.toolbox.load_tool_tag_set( config_elem, - app.toolbox.tool_panel, - app.toolbox.integrated_tool_panel, - tool_path, - load_panel_dict=True, - guid=guid ) - # Replace the old list of in-memory config_elems with the new list for this shed_tool_conf_dict. - shed_tool_conf_dict[ 'config_elems' ] = config_elems - app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - if app.config.update_integrated_tool_panel: - # Write the current in-memory version of the integrated_tool_panel.xml file to disk. - app.toolbox.write_integrated_tool_panel_config_file() - app.toolbox_search = ToolBoxSearch( app.toolbox ) - def build_shed_tool_conf_select_field( app ): """Build a SelectField whose options are the keys in app.toolbox.shed_tool_confs.""" options = [] @@ -192,142 +129,6 @@ message += "%s%s%s - %s%s" % ( bold_start, tool_file, bold_end, correction_msg, new_line ) return message -def generate_tool_panel_dict_for_new_install( tool_dicts, tool_section=None ): - """ - When installing a repository that contains tools, all tools must currently be defined - within the same tool section in the tool panel or outside of any sections. - """ - tool_panel_dict = {} - if tool_section: - section_id = tool_section.id - section_name = tool_section.name - section_version = tool_section.version or '' - else: - section_id = '' - section_name = '' - section_version = '' - for tool_dict in tool_dicts: - if tool_dict.get( 'add_to_tool_panel', True ): - guid = tool_dict[ 'guid' ] - tool_config = tool_dict[ 'tool_config' ] - tool_section_dict = dict( tool_config=tool_config, id=section_id, name=section_name, version=section_version ) - if guid in tool_panel_dict: - tool_panel_dict[ guid ].append( tool_section_dict ) - else: - tool_panel_dict[ guid ] = [ tool_section_dict ] - return tool_panel_dict - -def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=None ): - """ - Create a dictionary of the following type for a single tool config file name. - The intent is to call this method for every tool config in a repository and - append each of these as entries to a tool panel dictionary for the repository. - This allows for each tool to be loaded into a different section in the tool panel. - {<Tool guid> : - [{ tool_config : <tool_config_file>, - id: <ToolSection id>, - version : <ToolSection version>, - name : <TooSection name>}]} - """ - tool_panel_dict = {} - file_name = basic_util.strip_path( tool_config ) - tool_section_dicts = generate_tool_section_dicts( tool_config=file_name, tool_sections=tool_sections ) - tool_panel_dict[ guid ] = tool_section_dicts - return tool_panel_dict - -def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, - repository_tools_tups, owner='' ): - """Generate a list of ElementTree Element objects for each section or tool.""" - elem_list = [] - tool_elem = None - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) - if not owner: - owner = suc.get_repository_owner( cleaned_repository_clone_url ) - tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' ) - for guid, tool_section_dicts in tool_panel_dict.items(): - for tool_section_dict in tool_section_dicts: - tool_section = None - inside_section = False - section_in_elem_list = False - if tool_section_dict[ 'id' ]: - inside_section = True - # Create a new section element only if we haven't already created it. - for index, elem in enumerate( elem_list ): - if elem.tag == 'section': - section_id = elem.get( 'id', None ) - if section_id == tool_section_dict[ 'id' ]: - section_in_elem_list = True - tool_section = elem - break - if tool_section is None: - tool_section = generate_tool_section_element_from_dict( tool_section_dict ) - # Find the tuple containing the current guid from the list of repository_tools_tups. - for repository_tool_tup in repository_tools_tups: - tool_file_path, tup_guid, tool = repository_tool_tup - if tup_guid == guid: - break - if inside_section: - tool_elem = suc.generate_tool_elem( tool_shed, - repository_name, - changeset_revision, - owner, - tool_file_path, - tool, - tool_section ) - else: - tool_elem = suc.generate_tool_elem( tool_shed, - repository_name, - changeset_revision, - owner, - tool_file_path, - tool, - None ) - if inside_section: - if section_in_elem_list: - elem_list[ index ] = tool_section - else: - elem_list.append( tool_section ) - else: - elem_list.append( tool_elem ) - return elem_list - -def generate_tool_section_dicts( tool_config=None, tool_sections=None ): - tool_section_dicts = [] - if tool_config is None: - tool_config = '' - if tool_sections: - for tool_section in tool_sections: - # The value of tool_section will be None if the tool is displayed outside - # of any sections in the tool panel. - if tool_section: - section_id = tool_section.id or '' - section_version = tool_section.version or '' - section_name = tool_section.name or '' - else: - section_id = '' - section_version = '' - section_name = '' - tool_section_dicts.append( dict( tool_config=tool_config, - id=section_id, - version=section_version, - name=section_name ) ) - else: - tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) - return tool_section_dicts - -def generate_tool_section_element_from_dict( tool_section_dict ): - # The value of tool_section_dict looks like the following. - # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} - if tool_section_dict[ 'id' ]: - # Create a new tool section. - tool_section = XmlET.Element( 'section' ) - tool_section.attrib[ 'id' ] = tool_section_dict[ 'id' ] - tool_section.attrib[ 'name' ] = tool_section_dict[ 'name' ] - tool_section.attrib[ 'version' ] = tool_section_dict[ 'version' ] - else: - tool_section = None - return tool_section - def get_headers( fname, sep, count=60, is_multi_byte=False ): """Returns a list with the first 'count' lines split by 'sep'.""" headers = [] @@ -341,26 +142,6 @@ break return headers -def get_or_create_tool_section( toolbox, tool_panel_section_id, new_tool_panel_section_label=None ): - tool_panel_section_key = str( tool_panel_section_id ) - if tool_panel_section_key in toolbox.tool_panel: - # Appending a tool to an existing section in toolbox.tool_panel - tool_section = toolbox.tool_panel[ tool_panel_section_key ] - log.debug( "Appending to tool panel section: %s" % str( tool_section.name ) ) - else: - # Appending a new section to toolbox.tool_panel - if new_tool_panel_section_label is None: - # This might add an ugly section label to the tool panel, but, oh well... - new_tool_panel_section_label = tool_panel_section_id - elem = XmlET.Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section_label - elem.attrib[ 'id' ] = tool_panel_section_id - elem.attrib[ 'version' ] = '' - tool_section = galaxy.tools.ToolSection( elem ) - toolbox.tool_panel[ tool_panel_section_key ] = tool_section - log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) - return tool_panel_section_key, tool_section - def get_tool_path_install_dir( partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems ): for elem in config_elems: if elem.tag == 'tool': @@ -514,63 +295,6 @@ error = True return error, message -def handle_tool_panel_selection( toolbox, metadata, no_changes_checked, tool_panel_section_id, new_tool_panel_section_label ): - """ - Handle the selected tool panel location for loading tools included in tool shed repositories when installing - or reinstalling them. - """ - # Get the location in the tool panel in which each tool was originally loaded. - tool_section = None - tool_panel_section_key = None - if 'tools' in metadata: - # This forces everything to be loaded into the same section (or no section) in the tool panel. - if no_changes_checked: - # Make sure the no_changes check box overrides the new_tool_panel_section_label if the user checked the check - # box and entered something into the field. - new_tool_panel_section_label = None - if 'tool_panel_section' in metadata: - tool_panel_dict = metadata[ 'tool_panel_section' ] - if not tool_panel_dict: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - else: - tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) - if tool_panel_dict: - # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] - original_section_id = tool_section_dict[ 'id' ] - original_section_name = tool_section_dict[ 'name' ] - if original_section_id: - tool_panel_section_key, tool_section = \ - get_or_create_tool_section( toolbox, - tool_panel_section_id=original_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - else: - # The user elected to change the tool panel section to contain the tools. - tool_panel_section_key, tool_section = handle_tool_panel_section( toolbox, - tool_panel_section_id=tool_panel_section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - return tool_section, tool_panel_section_key - -def handle_tool_panel_section( toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None ): - """Return a ToolSection object retrieved from the current in-memory tool_panel.""" - # If tool_panel_section_id is received, the section exists in the tool panel. In this - # case, the value of the received tool_panel_section_id must be the id retrieved from a - # tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label - # is received, a new section will be added to the tool panel. - if new_tool_panel_section_label: - section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) - tool_panel_section_key, tool_section = \ - get_or_create_tool_section( toolbox, - tool_panel_section_id=section_id, - new_tool_panel_section_label=new_tool_panel_section_label ) - elif tool_panel_section_id: - tool_panel_section_key = str( tool_panel_section_id ) - tool_section = toolbox.tool_panel[ tool_panel_section_key ] - else: - return None, None - return tool_panel_section_key, tool_section - def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ): """ Using the list of tool_version_dicts retrieved from the tool shed (one per changeset @@ -741,170 +465,6 @@ if isinstance( tool.tool_action, UploadToolAction ): app.toolbox.reload_tool_by_id( tool_id ) -def remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ): - # A tool shed repository is being uninstalled so change the shed_tool_conf file. - # Parse the config file to generate the entire list of config_elems instead of - # using the in-memory list since it will be a subset of the entire list if one - # or more repositories have been deactivated. - shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] - tool_path = shed_tool_conf_dict[ 'tool_path' ] - config_elems = [] - tree, error_message = xml_util.parse_xml( shed_tool_conf ) - if tree: - root = tree.getroot() - for elem in root: - config_elems.append( elem ) - config_elems_to_remove = [] - for config_elem in config_elems: - if config_elem.tag == 'section': - tool_elems_to_remove = [] - for tool_elem in config_elem: - if tool_elem.get( 'guid' ) in guids_to_remove: - tool_elems_to_remove.append( tool_elem ) - for tool_elem in tool_elems_to_remove: - # Remove all of the appropriate tool sub-elements from the section element. - config_elem.remove( tool_elem ) - if len( config_elem ) < 1: - # Keep a list of all empty section elements so they can be removed. - config_elems_to_remove.append( config_elem ) - elif config_elem.tag == 'tool': - if config_elem.get( 'guid' ) in guids_to_remove: - config_elems_to_remove.append( config_elem ) - for config_elem in config_elems_to_remove: - config_elems.remove( config_elem ) - # Persist the altered in-memory version of the tool config. - suc.config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) - -def remove_from_tool_panel( app, repository, shed_tool_conf, uninstall ): - """ - A tool shed repository is being deactivated or uninstalled, so handle tool panel - alterations accordingly. - """ - # Determine where the tools are currently defined in the tool panel and store this - # information so the tools can be displayed in the same way when the repository is - # activated or reinstalled. - tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( app, repository ) - repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - app.install_model.context.add( repository ) - app.install_model.context.flush() - # Create a list of guids for all tools that will be removed from the in-memory tool panel - # and config file on disk. - guids_to_remove = [ k for k in tool_panel_dict.keys() ] - # Remove the tools from the toolbox's tools_by_id dictionary. - for guid_to_remove in guids_to_remove: - if guid_to_remove in app.toolbox.tools_by_id: - del app.toolbox.tools_by_id[ guid_to_remove ] - index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( app, shed_tool_conf ) - if uninstall: - # Remove from the shed_tool_conf file on disk. - remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ) - config_elems = shed_tool_conf_dict[ 'config_elems' ] - config_elems_to_remove = [] - for config_elem in config_elems: - if config_elem.tag == 'section': - # Get the section key for the in-memory tool panel. - section_key = str( config_elem.get( "id" ) ) - # Generate the list of tool elements to remove. - tool_elems_to_remove = [] - for tool_elem in config_elem: - if tool_elem.get( 'guid' ) in guids_to_remove: - tool_elems_to_remove.append( tool_elem ) - for tool_elem in tool_elems_to_remove: - if tool_elem in config_elem: - # Remove the tool sub-element from the section element. - config_elem.remove( tool_elem ) - # Remove the tool from the section in the in-memory tool panel. - if section_key in app.toolbox.tool_panel: - tool_section = app.toolbox.tool_panel[ section_key ] - guid = tool_elem.get( 'guid' ) - tool_key = 'tool_%s' % str( guid ) - # Get the list of versions of this tool that are currently available in the toolbox. - available_tool_versions = app.toolbox.get_loaded_tools_by_lineage( guid ) - if tool_key in tool_section.elems: - if available_tool_versions: - available_tool_versions.reverse() - replacement_tool_key = None - replacement_tool_version = None - # Since we are going to remove the tool from the section, replace it with the - # newest loaded version of the tool. - for available_tool_version in available_tool_versions: - available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() - if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: - replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) - replacement_tool_version = available_tool_version - break - if replacement_tool_key and replacement_tool_version: - # Get the index of the tool_key in the tool_section. - for tool_section_elems_index, key in enumerate( tool_section.elems.keys() ): - if key == tool_key: - break - # Remove the tool from the tool section. - del tool_section.elems[ tool_key ] - # Add the replacement tool at the same location in the tool section. - tool_section.elems.insert( tool_section_elems_index, - replacement_tool_key, - replacement_tool_version ) - else: - del tool_section.elems[ tool_key ] - else: - del tool_section.elems[ tool_key ] - if uninstall: - # Remove the tool from the section in the in-memory integrated tool panel. - if section_key in app.toolbox.integrated_tool_panel: - tool_section = app.toolbox.integrated_tool_panel[ section_key ] - tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) - if tool_key in tool_section.elems: - del tool_section.elems[ tool_key ] - if len( config_elem ) < 1: - # Keep a list of all empty section elements so they can be removed. - config_elems_to_remove.append( config_elem ) - elif config_elem.tag == 'tool': - guid = config_elem.get( 'guid' ) - if guid in guids_to_remove: - tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) - # Get the list of versions of this tool that are currently available in the toolbox. - available_tool_versions = app.toolbox.get_loaded_tools_by_lineage( guid ) - if tool_key in app.toolbox.tool_panel: - if available_tool_versions: - available_tool_versions.reverse() - replacement_tool_key = None - replacement_tool_version = None - # Since we are going to remove the tool from the section, replace it with - # the newest loaded version of the tool. - for available_tool_version in available_tool_versions: - available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() - if available_tool_version.id in app.toolbox.tool_panel.keys() or not available_tool_section_id: - replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) - replacement_tool_version = available_tool_version - break - if replacement_tool_key and replacement_tool_version: - # Get the index of the tool_key in the tool_section. - for tool_panel_index, key in enumerate( app.toolbox.tool_panel.keys() ): - if key == tool_key: - break - # Remove the tool from the tool panel. - del app.toolbox.tool_panel[ tool_key ] - # Add the replacement tool at the same location in the tool panel. - app.toolbox.tool_panel.insert( tool_panel_index, replacement_tool_key, replacement_tool_version ) - else: - del app.toolbox.tool_panel[ tool_key ] - else: - del app.toolbox.tool_panel[ tool_key ] - if uninstall: - if tool_key in app.toolbox.integrated_tool_panel: - del app.toolbox.integrated_tool_panel[ tool_key ] - config_elems_to_remove.append( config_elem ) - for config_elem in config_elems_to_remove: - # Remove the element from the in-memory list of elements. - config_elems.remove( config_elem ) - # Update the config_elems of the in-memory shed_tool_conf_dict. - shed_tool_conf_dict[ 'config_elems' ] = config_elems - app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - app.toolbox_search = ToolBoxSearch( app.toolbox ) - if uninstall and app.config.update_integrated_tool_panel: - # Write the current in-memory version of the integrated_tool_panel.xml file to disk. - app.toolbox.write_integrated_tool_panel_config_file() - def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. app.tool_data_tables.data_tables = {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a missing function to the ToolValidator.
by commits-noreply＠bitbucket.org 18 Jul '14

18 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cbca66cc16bf/ Changeset: cbca66cc16bf User: greg Date: 2014-07-18 22:44:54 Summary: Add a missing function to the ToolValidator. Affected #: 2 files diff -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff -r cbca66cc16bfed165f3b38399857ad0b85d14489 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -149,6 +149,45 @@ return tmp_filename return None + def get_list_of_copied_sample_files( self, repo, ctx, dir ): + """ + Find all sample files (files in the repository with the special .sample extension) + in the reversed repository manifest up to ctx. Copy each discovered file to dir and + return the list of filenames. If a .sample file was added in a changeset and then + deleted in a later changeset, it will be returned in the deleted_sample_files list. + The caller will set the value of app.config.tool_data_path to dir in order to load + the tools and generate metadata for them. + """ + deleted_sample_files = [] + sample_files = [] + for changeset in hg_util.reversed_upper_bounded_changelog( repo, ctx ): + changeset_ctx = repo.changectx( changeset ) + for ctx_file in changeset_ctx.files(): + ctx_file_name = basic_util.strip_path( ctx_file ) + # If we decide in the future that files deleted later in the changelog should + # not be used, we can use the following if statement. if ctx_file_name.endswith( '.sample' ) + # and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: + if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: + fctx = hg_util.get_file_context_from_ctx( changeset_ctx, ctx_file ) + if fctx in [ 'DELETED' ]: + # Since the possibly future used if statement above is commented out, the + # same file that was initially added will be discovered in an earlier changeset + # in the change log and fall through to the else block below. In other words, + # if a file named blast2go.loc.sample was added in change set 0 and then deleted + # in changeset 3, the deleted file in changeset 3 will be handled here, but the + # later discovered file in changeset 0 will be handled in the else block below. + # In this way, the file contents will always be found for future tools even though + # the file was deleted. + if ctx_file_name not in deleted_sample_files: + deleted_sample_files.append( ctx_file_name ) + else: + sample_files.append( ctx_file_name ) + tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) + fh = open( tmp_ctx_file_name, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return sample_files, deleted_sample_files + def handle_sample_files_and_load_tool_from_disk( self, repo_files_dir, repository_id, tool_config_filepath, work_dir ): """ Copy all sample files from disk to a temporary directory since the sample files may @@ -172,7 +211,7 @@ ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) # We're not currently doing anything with the returned list of deleted_sample_files here. It is # intended to help handle sample files that are in the manifest, but have been deleted from disk. - sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + sample_files, deleted_sample_files = self.get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) if sample_files: self.app.config.tool_data_path = work_dir if 'tool_data_table_conf.xml.sample' in sample_files: diff -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff -r cbca66cc16bfed165f3b38399857ad0b85d14489 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -341,45 +341,6 @@ break return headers -def get_list_of_copied_sample_files( repo, ctx, dir ): - """ - Find all sample files (files in the repository with the special .sample extension) - in the reversed repository manifest up to ctx. Copy each discovered file to dir and - return the list of filenames. If a .sample file was added in a changeset and then - deleted in a later changeset, it will be returned in the deleted_sample_files list. - The caller will set the value of app.config.tool_data_path to dir in order to load - the tools and generate metadata for them. - """ - deleted_sample_files = [] - sample_files = [] - for changeset in hg_util.reversed_upper_bounded_changelog( repo, ctx ): - changeset_ctx = repo.changectx( changeset ) - for ctx_file in changeset_ctx.files(): - ctx_file_name = basic_util.strip_path( ctx_file ) - # If we decide in the future that files deleted later in the changelog should - # not be used, we can use the following if statement. if ctx_file_name.endswith( '.sample' ) - # and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: - if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: - fctx = hg_util.get_file_context_from_ctx( changeset_ctx, ctx_file ) - if fctx in [ 'DELETED' ]: - # Since the possibly future used if statement above is commented out, the - # same file that was initially added will be discovered in an earlier changeset - # in the change log and fall through to the else block below. In other words, - # if a file named blast2go.loc.sample was added in change set 0 and then deleted - # in changeset 3, the deleted file in changeset 3 will be handled here, but the - # later discovered file in changeset 0 will be handled in the else block below. - # In this way, the file contents will always be found for future tools even though - # the file was deleted. - if ctx_file_name not in deleted_sample_files: - deleted_sample_files.append( ctx_file_name ) - else: - sample_files.append( ctx_file_name ) - tmp_ctx_file_name = os.path.join( dir, ctx_file_name.replace( '.sample', '' ) ) - fh = open( tmp_ctx_file_name, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return sample_files, deleted_sample_files - def get_or_create_tool_section( toolbox, tool_panel_section_id, new_tool_panel_section_label=None ): tool_panel_section_key = str( tool_panel_section_id ) if tool_panel_section_key in toolbox.tool_panel: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add a ToolValidator to validate tools contained in tool shed repositories.
by commits-noreply＠bitbucket.org 18 Jul '14

18 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/24437efed65c/ Changeset: 24437efed65c User: greg Date: 2014-07-18 22:38:57 Summary: Add a ToolValidator to validate tools contained in tool shed repositories. Affected #: 6 files diff -r cd5d9bf32d865657208b0b657b08c9142b357e25 -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -20,6 +20,7 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager +from tool_shed.tools import tool_validator from tool_shed.util import basic_util from tool_shed.util import common_util @@ -1164,10 +1165,10 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository, tool, message = tool_util.load_tool_from_changeset_revision( trans.app, - repository_id, - changeset_revision, - tool_config ) + tv = tool_validator.ToolValidator( trans.app ) + repository, tool, message = tv.load_tool_from_changeset_revision( repository_id, + changeset_revision, + tool_config ) if message: status = 'error' tool_state = tool_util.new_state( trans, tool, invalid=False ) @@ -2147,18 +2148,17 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'error' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans.app, - repository_id, - changeset_revision, - tool_config ) + tv = tool_validator.ToolValidator( trans.app ) + repository, tool, error_message = tv.load_tool_from_changeset_revision( repository_id, + changeset_revision, + tool_config ) tool_state = tool_util.new_state( trans, tool, invalid=True ) invalid_file_tups = [] if tool: - invalid_file_tups = tool_util.check_tool_input_params( trans.app, - repository.repo_path( trans.app ), - tool_config, - tool, - [] ) + invalid_file_tups = tv.check_tool_input_params( repository.repo_path( trans.app ), + tool_config, + tool, + [] ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, invalid_file_tups, @@ -3397,6 +3397,7 @@ metadata = repository_metadata.metadata if metadata: if 'tools' in metadata: + tv = tool_validator.ToolValidator( trans.app ) for tool_metadata_dict in metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: work_dir = tempfile.mkdtemp() @@ -3404,29 +3405,26 @@ 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 = tool_util.can_use_tool_config_disk_file( trans.app, - repository, - repo, - full_path_to_tool_config, - changeset_revision ) + can_use_disk_file = tv.can_use_tool_config_disk_file( 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 = \ - tool_util.handle_sample_files_and_load_tool_from_disk( trans.app, - repo_files_dir, - repository_id, - full_path_to_tool_config, - work_dir ) + tv.handle_sample_files_and_load_tool_from_disk( repo_files_dir, + repository_id, + full_path_to_tool_config, + work_dir ) if message: status = 'error' else: tool, message, sample_files = \ - tool_util.handle_sample_files_and_load_tool_from_tmp_config( trans.app, - repo, - repository_id, - changeset_revision, - tool_config_filename, - work_dir ) + tv.handle_sample_files_and_load_tool_from_tmp_config( repo, + repository_id, + changeset_revision, + tool_config_filename, + work_dir ) if message: status = 'error' basic_util.remove_dir( work_dir ) diff -r cd5d9bf32d865657208b0b657b08c9142b357e25 -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -10,6 +10,7 @@ from galaxy.web import url_for from tool_shed.repository_types import util as rt_util +from tool_shed.tools import tool_validator from tool_shed.util import basic_util from tool_shed.util import common_util @@ -128,7 +129,7 @@ log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, repository, repository_clone_url, repository_files_dir, datatypes_config, + def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) @@ -178,7 +179,7 @@ tool_config_path = hg_util.get_config_from_disk( tool_config, repository_files_dir ) full_path = os.path.abspath( tool_config_path ) tool, valid, error_message = \ - tool_util.load_tool_from_config( self.app, self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) if tool is None: guid = None else: @@ -245,6 +246,7 @@ tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ + tv = tool_validator.ToolValidator( self.app ) if shed_config_dict is None: shed_config_dict = {} if updating_installed_repository: @@ -290,7 +292,8 @@ # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: - metadata_dict = self.generate_datatypes_metadata( repository, + metadata_dict = self.generate_datatypes_metadata( tv, + repository, repository_clone_url, files_dir, datatypes_config, @@ -361,20 +364,18 @@ is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tool_util.load_tool_from_config( self.app, - self.app.security.encode_id( repository.id ), - full_path ) + tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ - tool_util.check_tool_input_params( self.app, - files_dir, - name, - tool, - sample_file_copy_paths ) + tv.check_tool_input_params( files_dir, + name, + tool, + sample_file_copy_paths ) can_set_metadata = True for tup in invalid_files_and_errors_tups: if name in tup: diff -r cd5d9bf32d865657208b0b657b08c9142b357e25 -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff lib/tool_shed/tools/tool_validator.py --- /dev/null +++ b/lib/tool_shed/tools/tool_validator.py @@ -0,0 +1,289 @@ +import filecmp +import logging +import os +import tempfile + +from galaxy.tools import parameters +from galaxy.tools.parameters import dynamic_options + +from tool_shed.util import basic_util +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import tool_util + +log = logging.getLogger( __name__ ) + + +class ToolValidator( object ): + + def __init__( self, app ): + self.app = app + + def can_use_tool_config_disk_file( self, 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( self.app ): + return True + file_name = basic_util.strip_path( file_path ) + latest_version_of_file = \ + self.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( self, repo_dir, tool_config_name, tool, sample_files ): + """ + Check all of the tool's input parameters, looking for any that are dynamically + generated using external data files to make sure the files exist. + """ + invalid_files_and_errors_tups = [] + correction_msg = '' + for input_param in tool.input_params: + if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: + # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, + # make sure all requirements exist. + options = input_param.dynamic_options or input_param.options + if options and isinstance( options, dynamic_options.DynamicOptions ): + if options.tool_data_table or options.missing_tool_data_table_name: + # Make sure the repository contains a tool_data_table_conf.xml.sample file. + sample_tool_data_table_conf = hg_util.get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) + if sample_tool_data_table_conf: + error, correction_msg = \ + tool_util.handle_sample_tool_data_table_conf_file( self.app, sample_tool_data_table_conf ) + if error: + invalid_files_and_errors_tups.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) + else: + options.missing_tool_data_table_name = None + else: + correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " + correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " + correction_msg += "that includes the required entry to correct this error.<br/>" + invalid_tup = ( tool_config_name, correction_msg ) + if invalid_tup not in invalid_files_and_errors_tups: + invalid_files_and_errors_tups.append( invalid_tup ) + if options.index_file or options.missing_index_file: + # Make sure the repository contains the required xxx.loc.sample file. + index_file = options.index_file or options.missing_index_file + index_file_name = basic_util.strip_path( index_file ) + sample_found = False + for sample_file in sample_files: + sample_file_name = basic_util.strip_path( sample_file ) + if sample_file_name == '%s.sample' % index_file_name: + options.index_file = index_file_name + options.missing_index_file = None + if options.tool_data_table: + options.tool_data_table.missing_index_file = None + sample_found = True + break + if not sample_found: + correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file_name ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % \ + str( index_file_name ) + invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) + return invalid_files_and_errors_tups + + def concat_messages( self, msg1, msg2 ): + if msg1: + if msg2: + message = '%s %s' % ( msg1, msg2 ) + else: + message = msg1 + elif msg2: + message = msg2 + else: + message = '' + return message + + def copy_disk_sample_files_to_dir( self, repo_files_dir, dest_path ): + """ + Copy all files currently on disk that end with the .sample extension to the + directory to which dest_path refers. + """ + sample_files = [] + for root, dirs, files in os.walk( repo_files_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name.endswith( '.sample' ): + relative_path = os.path.join( root, name ) + tool_util.copy_sample_file( self.app, relative_path, dest_path=dest_path ) + sample_files.append( name ) + return sample_files + + def get_latest_tool_config_revision_from_repository_manifest( self, repo, filename, changeset_revision ): + """ + Get the latest revision of a tool config file named filename from the repository + manifest up to the value of changeset_revision. This method is restricted to tool_config + files rather than any file since it is likely that, with the exception of tool config + files, multiple files will have the same name in various directories within the repository. + """ + stripped_filename = basic_util.strip_path( filename ) + for changeset in hg_util.reversed_upper_bounded_changelog( repo, changeset_revision ): + manifest_ctx = repo.changectx( changeset ) + for ctx_file in manifest_ctx.files(): + ctx_file_name = basic_util.strip_path( ctx_file ) + if ctx_file_name == stripped_filename: + try: + fctx = manifest_ctx[ ctx_file ] + except LookupError: + # The ctx_file may have been moved in the change set. For example, + # 'ncbi_blastp_wrapper.xml' was moved to 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml', + # so keep looking for the file until we find the new location. + continue + fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-gltcrfrm" ) + tmp_filename = fh.name + fh.close() + fh = open( tmp_filename, 'wb' ) + fh.write( fctx.data() ) + fh.close() + return tmp_filename + return None + + def handle_sample_files_and_load_tool_from_disk( self, repo_files_dir, repository_id, tool_config_filepath, work_dir ): + """ + Copy all sample files from disk to a temporary directory since the sample files may + be in multiple directories. + """ + message = '' + sample_files = self.copy_disk_sample_files_to_dir( repo_files_dir, work_dir ) + if sample_files: + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + error, message = tool_util.handle_sample_tool_data_table_conf_file( self.app, tool_data_table_config ) + tool, valid, message2 = self.load_tool_from_config( repository_id, tool_config_filepath ) + message = self.concat_messages( message, message2 ) + return tool, valid, message, sample_files + + def handle_sample_files_and_load_tool_from_tmp_config( self, repo, repository_id, changeset_revision, + tool_config_filename, work_dir ): + tool = None + message = '' + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) + # We're not currently doing anything with the returned list of deleted_sample_files here. It is + # intended to help handle sample files that are in the manifest, but have been deleted from disk. + sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + if sample_files: + self.app.config.tool_data_path = work_dir + if 'tool_data_table_conf.xml.sample' in sample_files: + # Load entries into the tool_data_tables if the tool requires them. + tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) + if tool_data_table_config: + error, message = tool_util.handle_sample_tool_data_table_conf_file( self.app, tool_data_table_config ) + if error: + log.debug( message ) + manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) + if manifest_ctx and ctx_file: + tool, message2 = self.load_tool_from_tmp_config( repo, repository_id, manifest_ctx, ctx_file, work_dir ) + message = self.concat_messages( message, message2 ) + return tool, message, sample_files + + def load_tool_from_changeset_revision( self, 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) + changeset 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 = self.app.config.tool_data_path + repository = suc.get_repository_in_tool_shed( self.app, repository_id ) + repo_files_dir = repository.repo_path( self.app ) + repo = hg_util.get_repo_for_repository( self.app, repository=None, repo_path=repo_files_dir, create=False ) + message = '' + tool = None + can_use_disk_file = False + tool_config_filepath = suc.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename ) + work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ltfcr" ) + can_use_disk_file = self.can_use_tool_config_disk_file( repository, + repo, + tool_config_filepath, + changeset_revision ) + if can_use_disk_file: + self.app.config.tool_data_path = work_dir + tool, valid, message, sample_files = \ + self.handle_sample_files_and_load_tool_from_disk( repo_files_dir, + repository_id, + tool_config_filepath, + work_dir ) + if tool is not None: + invalid_files_and_errors_tups = \ + self.check_tool_input_params( repo_files_dir, + tool_config_filename, + tool, + sample_files ) + if invalid_files_and_errors_tups: + message2 = tool_util.generate_message_for_invalid_tools( self.app, + invalid_files_and_errors_tups, + repository, + metadata_dict=None, + as_html=True, + displaying_invalid_tool=True ) + message = self.concat_messages( message, message2 ) + else: + tool, message, sample_files = \ + self.handle_sample_files_and_load_tool_from_tmp_config( repo, + repository_id, + changeset_revision, + tool_config_filename, + work_dir ) + basic_util.remove_dir( work_dir ) + self.app.config.tool_data_path = original_tool_data_path + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + tool_util.reset_tool_data_tables( self.app ) + return repository, tool, message + + def load_tool_from_config( self, repository_id, full_path ): + try: + tool = self.app.toolbox.load_tool( full_path, repository_id=repository_id ) + valid = True + error_message = None + except KeyError, e: + tool = None + valid = False + error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) + error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' + error_message += 'this error. ' + except Exception, e: + tool = None + valid = False + error_message = str( e ) + return tool, valid, error_message + + def load_tool_from_tmp_config( self, repo, repository_id, ctx, ctx_file, work_dir ): + tool = None + message = '' + tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) + if tmp_tool_config: + element_tree, error_message = xml_util.parse_xml( tmp_tool_config ) + if element_tree is None: + return tool, message + element_tree_root = element_tree.getroot() + # Look for code files required by the tool config. + tmp_code_files = [] + for code_elem in element_tree_root.findall( 'code' ): + code_file_name = code_elem.get( 'file' ) + tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) + if tmp_code_file_name: + tmp_code_files.append( tmp_code_file_name ) + tool, valid, message = self.load_tool_from_config( repository_id, tmp_tool_config ) + for tmp_code_file in tmp_code_files: + try: + os.unlink( tmp_code_file ) + except: + pass + try: + os.unlink( tmp_tool_config ) + except: + pass + return tool, message diff -r cd5d9bf32d865657208b0b657b08c9142b357e25 -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -1,14 +1,11 @@ -import filecmp import logging import os import shutil -import tempfile import galaxy.tools from galaxy import util from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.tools import parameters -from galaxy.tools.parameters import dynamic_options from galaxy.tools.search import ToolBoxSearch from galaxy.util.expressions import ExpressionContext from galaxy.web.form_builder import SelectField @@ -112,107 +109,6 @@ select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] ) return select_field -def can_use_tool_config_disk_file( app, 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( app ): - return True - file_name = basic_util.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 sure the files exist. - """ - invalid_files_and_errors_tups = [] - correction_msg = '' - for input_param in tool.input_params: - if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, - # make sure all requirements exist. - options = input_param.dynamic_options or input_param.options - if options and isinstance( options, dynamic_options.DynamicOptions ): - if options.tool_data_table or options.missing_tool_data_table_name: - # Make sure the repository contains a tool_data_table_conf.xml.sample file. - sample_tool_data_table_conf = hg_util.get_config_from_disk( 'tool_data_table_conf.xml.sample', repo_dir ) - if sample_tool_data_table_conf: - error, correction_msg = handle_sample_tool_data_table_conf_file( app, sample_tool_data_table_conf ) - if error: - invalid_files_and_errors_tups.append( ( 'tool_data_table_conf.xml.sample', correction_msg ) ) - else: - options.missing_tool_data_table_name = None - else: - correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " - correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " - correction_msg += "that includes the required entry to correct this error.<br/>" - invalid_tup = ( tool_config_name, correction_msg ) - if invalid_tup not in invalid_files_and_errors_tups: - invalid_files_and_errors_tups.append( invalid_tup ) - if options.index_file or options.missing_index_file: - # Make sure the repository contains the required xxx.loc.sample file. - index_file = options.index_file or options.missing_index_file - index_file_name = basic_util.strip_path( index_file ) - sample_found = False - for sample_file in sample_files: - sample_file_name = basic_util.strip_path( sample_file ) - if sample_file_name == '%s.sample' % index_file_name: - options.index_file = index_file_name - options.missing_index_file = None - if options.tool_data_table: - options.tool_data_table.missing_index_file = None - sample_found = True - break - if not sample_found: - correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file_name ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % \ - str( index_file_name ) - invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) - return invalid_files_and_errors_tups - -def concat_messages( msg1, msg2 ): - if msg1: - if msg2: - message = '%s %s' % ( msg1, msg2 ) - else: - message = msg1 - elif msg2: - message = msg2 - else: - message = '' - return message - -def copy_disk_sample_files_to_dir( app, repo_files_dir, dest_path ): - """ - Copy all files currently on disk that end with the .sample extension to the - directory to which dest_path refers. - """ - sample_files = [] - for root, dirs, files in os.walk( repo_files_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name.endswith( '.sample' ): - relative_path = os.path.join( root, name ) - copy_sample_file( app, relative_path, dest_path=dest_path ) - sample_files.append( name ) - return sample_files - def copy_sample_file( app, filename, dest_path=None ): """ Copy xxx.sample to dest_path/xxx.sample and dest_path/xxx. The default value for dest_path @@ -445,35 +341,6 @@ break return headers -def get_latest_tool_config_revision_from_repository_manifest( repo, filename, changeset_revision ): - """ - Get the latest revision of a tool config file named filename from the repository - manifest up to the value of changeset_revision. This method is restricted to tool_config - files rather than any file since it is likely that, with the exception of tool config - files, multiple files will have the same name in various directories within the repository. - """ - stripped_filename = basic_util.strip_path( filename ) - for changeset in hg_util.reversed_upper_bounded_changelog( repo, changeset_revision ): - manifest_ctx = repo.changectx( changeset ) - for ctx_file in manifest_ctx.files(): - ctx_file_name = basic_util.strip_path( ctx_file ) - if ctx_file_name == stripped_filename: - try: - fctx = manifest_ctx[ ctx_file ] - except LookupError: - # The ctx_file may have been moved in the change set. For example, - # 'ncbi_blastp_wrapper.xml' was moved to 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml', - # so keep looking for the file until we find the new location. - continue - fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-gltcrfrm" ) - tmp_filename = fh.name - fh.close() - fh = open( tmp_filename, 'wb' ) - fh.write( fctx.data() ) - fh.close() - return tmp_filename - return None - def get_list_of_copied_sample_files( repo, ctx, dir ): """ Find all sample files (files in the repository with the special .sample extension) @@ -664,45 +531,6 @@ repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups, sample_files_copied -def handle_sample_files_and_load_tool_from_disk( app, repo_files_dir, repository_id, tool_config_filepath, work_dir ): - """ - Copy all sample files from disk to a temporary directory since the sample files may - be in multiple directories. - """ - message = '' - sample_files = copy_disk_sample_files_to_dir( app, repo_files_dir, work_dir ) - if sample_files: - if 'tool_data_table_conf.xml.sample' in sample_files: - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) - error, message = handle_sample_tool_data_table_conf_file( app, tool_data_table_config ) - tool, valid, message2 = load_tool_from_config( app, repository_id, tool_config_filepath ) - message = concat_messages( message, message2 ) - return tool, valid, message, sample_files - -def handle_sample_files_and_load_tool_from_tmp_config( app, repo, repository_id, changeset_revision, - tool_config_filename, work_dir ): - tool = None - message = '' - ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - # We're not currently doing anything with the returned list of deleted_sample_files here. It is - # intended to help handle sample files that are in the manifest, but have been deleted from disk. - sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) - if sample_files: - app.config.tool_data_path = work_dir - if 'tool_data_table_conf.xml.sample' in sample_files: - # Load entries into the tool_data_tables if the tool requires them. - tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) - if tool_data_table_config: - error, message = handle_sample_tool_data_table_conf_file( app, tool_data_table_config ) - if error: - log.debug( message ) - manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) - if manifest_ctx and ctx_file: - tool, message2 = load_tool_from_tmp_config( app, repo, repository_id, manifest_ctx, ctx_file, work_dir ) - message = concat_messages( message, message2 ) - return tool, message, sample_files - def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ Parse the incoming filename and add new entries to the in-memory @@ -911,107 +739,6 @@ # Default to copying the file if none of the above are true. return True -def load_tool_from_changeset_revision( app, 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 = app.config.tool_data_path - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repo_files_dir = repository.repo_path( app ) - repo = hg_util.get_repo_for_repository( app, repository=None, repo_path=repo_files_dir, create=False ) - message = '' - tool = None - can_use_disk_file = False - tool_config_filepath = suc.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename ) - work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ltfcr" ) - can_use_disk_file = can_use_tool_config_disk_file( app, - repository, - repo, - tool_config_filepath, - changeset_revision ) - if can_use_disk_file: - app.config.tool_data_path = work_dir - tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( app, - repo_files_dir, - repository_id, - tool_config_filepath, - work_dir ) - if tool is not None: - invalid_files_and_errors_tups = check_tool_input_params( app, - repo_files_dir, - tool_config_filename, - tool, - sample_files ) - if invalid_files_and_errors_tups: - message2 = generate_message_for_invalid_tools( app, - 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( app, - repo, - repository_id, - changeset_revision, - tool_config_filename, - work_dir ) - basic_util.remove_dir( work_dir ) - 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( app ) - return repository, tool, message - -def load_tool_from_config( app, repository_id, full_path ): - try: - tool = app.toolbox.load_tool( full_path, repository_id=repository_id ) - valid = True - error_message = None - except KeyError, e: - tool = None - valid = False - error_message = 'This file requires an entry for "%s" in the tool_data_table_conf.xml file. Upload a file ' % str( e ) - error_message += 'named tool_data_table_conf.xml.sample to the repository that includes the required entry to correct ' - error_message += 'this error. ' - except Exception, e: - tool = None - valid = False - error_message = str( e ) - return tool, valid, error_message - -def load_tool_from_tmp_config( app, repo, repository_id, ctx, ctx_file, work_dir ): - tool = None - message = '' - tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) - if tmp_tool_config: - element_tree, error_message = xml_util.parse_xml( tmp_tool_config ) - if element_tree is None: - return tool, message - element_tree_root = element_tree.getroot() - # Look for code files required by the tool config. - tmp_code_files = [] - for code_elem in element_tree_root.findall( 'code' ): - code_file_name = code_elem.get( 'file' ) - tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) - if tmp_code_file_name: - tmp_code_files.append( tmp_code_file_name ) - tool, valid, message = load_tool_from_config( app, repository_id, tmp_tool_config ) - for tmp_code_file in tmp_code_files: - try: - os.unlink( tmp_code_file ) - except: - pass - try: - os.unlink( tmp_tool_config ) - except: - pass - return tool, message - def new_state( trans, tool, invalid=False ): """Create a new `DefaultToolState` for the received tool. Only inputs on the first page will be initialized.""" state = galaxy.tools.DefaultToolState() diff -r cd5d9bf32d865657208b0b657b08c9142b357e25 -r 24437efed65c4db4b22b25df6b6d307ac5dcb2ff lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -1,5 +1,6 @@ import logging import os + import galaxy.tools import galaxy.tools.parameters import galaxy.webapps.galaxy.controllers.workflow @@ -9,9 +10,12 @@ from galaxy.workflow.modules import InputDataModule from galaxy.workflow.modules import ToolModule from galaxy.workflow.modules import WorkflowModuleFactory -import tool_shed.util.shed_util_common as suc + +from tool_shed.tools import tool_validator + from tool_shed.util import encoding_util from tool_shed.util import metadata_util +from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util eggs.require( "SVGFig" ) @@ -57,14 +61,14 @@ self.tool_id = tool_id self.tool = None self.errors = None + self.tv = tool_validator.ToolValidator( trans.app ) if trans.webapp.name == 'tool_shed': # We're in the tool shed. for tool_dict in tools_metadata: if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: - repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans.app, - repository_id, - changeset_revision, - tool_dict[ 'tool_config' ] ) + repository, self.tool, message = self.tv.load_tool_from_changeset_revision( repository_id, + changeset_revision, + tool_dict[ 'tool_config' ] ) if message and self.tool is None: self.errors = 'unavailable' break Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: As much as possible, eliminate the use of trans in the tool shed's tool_util.py module.
by commits-noreply＠bitbucket.org 18 Jul '14

18 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd5d9bf32d86/ Changeset: cd5d9bf32d86 User: greg Date: 2014-07-18 20:41:44 Summary: As much as possible, eliminate the use of trans in the tool shed's tool_util.py module. Affected #: 4 files diff -r 5242547f33ed801a83837de5d507cc4b4c2eb6ff -r cd5d9bf32d865657208b0b657b08c9142b357e25 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 @@ -244,7 +244,10 @@ if kwd.get( 'deactivate_or_uninstall_repository_button', False ): if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle tool panel alterations. - tool_util.remove_from_tool_panel( trans, tool_shed_repository, shed_tool_conf, uninstall=remove_from_disk_checked ) + tool_util.remove_from_tool_panel( trans.app, + tool_shed_repository, + shed_tool_conf, + uninstall=remove_from_disk_checked ) if tool_shed_repository.includes_data_managers: data_manager_util.remove_from_data_manager( trans.app, tool_shed_repository ) if tool_shed_repository.includes_datatypes: @@ -1116,9 +1119,9 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repositories', **kwd ) ) - shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) + shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf ) - tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) + tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) if len( repo_info_dicts ) == 1: # If we're installing or updating a single repository, see if it contains a readme or # dependencies that we can display. @@ -1636,7 +1639,7 @@ original_section_name = '' else: original_section_name = '' - tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans ) + tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ @@ -1652,7 +1655,7 @@ no_changes_check_box = None original_section_name = '' tool_panel_section_select_field = None - shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans ) + shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) dd = dependency_display.DependencyDisplayer( trans.app ) containers_dict = \ dd.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, diff -r 5242547f33ed801a83837de5d507cc4b4c2eb6ff -r cd5d9bf32d865657208b0b657b08c9142b357e25 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1164,7 +1164,10 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository, tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + repository, tool, message = tool_util.load_tool_from_changeset_revision( trans.app, + repository_id, + changeset_revision, + tool_config ) if message: status = 'error' tool_state = tool_util.new_state( trans, tool, invalid=False ) @@ -2144,7 +2147,10 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'error' ) render_repository_actions_for = kwd.get( 'render_repository_actions_for', 'tool_shed' ) - repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config ) + repository, tool, error_message = tool_util.load_tool_from_changeset_revision( trans.app, + repository_id, + changeset_revision, + tool_config ) tool_state = tool_util.new_state( trans, tool, invalid=True ) invalid_file_tups = [] if tool: @@ -3398,7 +3404,7 @@ 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 = tool_util.can_use_tool_config_disk_file( trans, + can_use_disk_file = tool_util.can_use_tool_config_disk_file( trans.app, repository, repo, full_path_to_tool_config, @@ -3406,7 +3412,7 @@ if can_use_disk_file: trans.app.config.tool_data_path = work_dir tool, valid, message, sample_files = \ - tool_util.handle_sample_files_and_load_tool_from_disk( trans, + tool_util.handle_sample_files_and_load_tool_from_disk( trans.app, repo_files_dir, repository_id, full_path_to_tool_config, @@ -3415,7 +3421,7 @@ status = 'error' else: tool, message, sample_files = \ - tool_util.handle_sample_files_and_load_tool_from_tmp_config( trans, + tool_util.handle_sample_files_and_load_tool_from_tmp_config( trans.app, repo, repository_id, changeset_revision, diff -r 5242547f33ed801a83837de5d507cc4b4c2eb6ff -r cd5d9bf32d865657208b0b657b08c9142b357e25 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -65,7 +65,10 @@ if config_elem.tag == 'section': app.toolbox.load_section_tag_set( config_elem, tool_path, load_panel_dict=True ) elif config_elem.tag == 'workflow': - app.toolbox.load_workflow_tag_set( config_elem, app.toolbox.tool_panel, app.toolbox.integrated_tool_panel, load_panel_dict=True ) + app.toolbox.load_workflow_tag_set( config_elem, + app.toolbox.tool_panel, + app.toolbox.integrated_tool_panel, + load_panel_dict=True ) elif config_elem.tag == 'tool': guid = config_elem.get( 'guid' ) app.toolbox.load_tool_tag_set( config_elem, @@ -82,12 +85,12 @@ app.toolbox.write_integrated_tool_panel_config_file() app.toolbox_search = ToolBoxSearch( app.toolbox ) -def build_shed_tool_conf_select_field( trans ): - """Build a SelectField whose options are the keys in trans.app.toolbox.shed_tool_confs.""" +def build_shed_tool_conf_select_field( app ): + """Build a SelectField whose options are the keys in app.toolbox.shed_tool_confs.""" options = [] - for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: + for shed_tool_conf_dict in app.toolbox.shed_tool_confs: shed_tool_conf_filename = shed_tool_conf_dict[ 'config_filename' ] - if shed_tool_conf_filename != trans.app.config.migrated_tools_config: + if shed_tool_conf_filename != app.config.migrated_tools_config: if shed_tool_conf_filename.startswith( './' ): option_label = shed_tool_conf_filename.replace( './', '', 1 ) else: @@ -98,10 +101,10 @@ select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] ) return select_field -def build_tool_panel_section_select_field( trans ): +def build_tool_panel_section_select_field( app ): """Build a SelectField whose options are the sections of the current in-memory toolbox.""" options = [] - for k, v in trans.app.toolbox.tool_panel.items(): + for k, v in app.toolbox.tool_panel.items(): if isinstance( v, galaxy.tools.ToolSection ): options.append( ( v.name, v.id ) ) select_field = SelectField( name='tool_panel_section_id', display='radio' ) @@ -109,19 +112,23 @@ select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] ) return select_field -def can_use_tool_config_disk_file( trans, repository, repo, file_path, changeset_revision ): +def can_use_tool_config_disk_file( app, 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). + 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. + # 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 ): + if changeset_revision == repository.tip( app ): return True file_name = basic_util.strip_path( file_path ) - latest_version_of_file = get_latest_tool_config_revision_from_repository_manifest( repo, file_name, changeset_revision ) + 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 ) @@ -131,14 +138,15 @@ def check_tool_input_params( app, repo_dir, tool_config_name, tool, sample_files ): """ - Check all of the tool's input parameters, looking for any that are dynamically generated using external data files to make - sure the files exist. + Check all of the tool's input parameters, looking for any that are dynamically + generated using external data files to make sure the files exist. """ invalid_files_and_errors_tups = [] correction_msg = '' for input_param in tool.input_params: if isinstance( input_param, parameters.basic.SelectToolParameter ) and input_param.is_dynamic: - # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, make sure all requirements exist. + # If the tool refers to .loc files or requires an entry in the tool_data_table_conf.xml, + # make sure all requirements exist. options = input_param.dynamic_options or input_param.options if options and isinstance( options, dynamic_options.DynamicOptions ): if options.tool_data_table or options.missing_tool_data_table_name: @@ -151,8 +159,9 @@ else: options.missing_tool_data_table_name = None else: - correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. Upload a file named tool_data_table_conf.xml.sample " - correction_msg += "to the repository that includes the required entry to correct this error.<br/>" + correction_msg = "This file requires an entry in the tool_data_table_conf.xml file. " + correction_msg += "Upload a file named tool_data_table_conf.xml.sample to the repository " + correction_msg += "that includes the required entry to correct this error.<br/>" invalid_tup = ( tool_config_name, correction_msg ) if invalid_tup not in invalid_files_and_errors_tups: invalid_files_and_errors_tups.append( invalid_tup ) @@ -172,7 +181,8 @@ break if not sample_found: correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file_name ) - correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) + correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % \ + str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) return invalid_files_and_errors_tups @@ -188,15 +198,18 @@ message = '' return message -def copy_disk_sample_files_to_dir( trans, repo_files_dir, dest_path ): - """Copy all files currently on disk that end with the .sample extension to the directory to which dest_path refers.""" +def copy_disk_sample_files_to_dir( app, repo_files_dir, dest_path ): + """ + Copy all files currently on disk that end with the .sample extension to the + directory to which dest_path refers. + """ sample_files = [] for root, dirs, files in os.walk( repo_files_dir ): if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): relative_path = os.path.join( root, name ) - copy_sample_file( trans.app, relative_path, dest_path=dest_path ) + copy_sample_file( app, relative_path, dest_path=dest_path ) sample_files.append( name ) return sample_files @@ -239,7 +252,8 @@ if is_data_index_sample_file( filename ): copy_sample_file( app, filename, dest_path=dest_path ) -def generate_message_for_invalid_tools( app, invalid_file_tups, repository, metadata_dict, as_html=True, displaying_invalid_tool=False ): +def generate_message_for_invalid_tools( app, invalid_file_tups, repository, metadata_dict, as_html=True, + displaying_invalid_tool=False ): if as_html: new_line = '<br/>' bold_start = '<b>' @@ -270,8 +284,10 @@ sample_ext = '%s.sample' % missing_file else: sample_ext = missing_file - correction_msg = "This file refers to a missing file %s%s%s. " % ( bold_start, str( missing_file ), bold_end ) - correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % ( bold_start, sample_ext, bold_end ) + correction_msg = "This file refers to a missing file %s%s%s. " % \ + ( bold_start, str( missing_file ), bold_end ) + correction_msg += "Upload a file named %s%s%s to the repository to correct this error." % \ + ( bold_start, sample_ext, bold_end ) else: if as_html: correction_msg = exception_msg @@ -282,8 +298,8 @@ def generate_tool_panel_dict_for_new_install( tool_dicts, tool_section=None ): """ - When installing a repository that contains tools, all tools must currently be defined within the same tool section in the tool - panel or outside of any sections. + When installing a repository that contains tools, all tools must currently be defined + within the same tool section in the tool panel or outside of any sections. """ tool_panel_dict = {} if tool_section: @@ -307,10 +323,15 @@ def generate_tool_panel_dict_for_tool_config( guid, tool_config, tool_sections=None ): """ - Create a dictionary of the following type for a single tool config file name. The intent is to call this method for every tool config - in a repository and append each of these as entries to a tool panel dictionary for the repository. This allows for each tool to be - loaded into a different section in the tool panel. - {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} + Create a dictionary of the following type for a single tool config file name. + The intent is to call this method for every tool config in a repository and + append each of these as entries to a tool panel dictionary for the repository. + This allows for each tool to be loaded into a different section in the tool panel. + {<Tool guid> : + [{ tool_config : <tool_config_file>, + id: <ToolSection id>, + version : <ToolSection version>, + name : <TooSection name>}]} """ tool_panel_dict = {} file_name = basic_util.strip_path( tool_config ) @@ -318,7 +339,8 @@ tool_panel_dict[ guid ] = tool_section_dicts return tool_panel_dict -def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, repository_tools_tups, owner='' ): +def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, + repository_tools_tups, owner='' ): """Generate a list of ElementTree Element objects for each section or tool.""" elem_list = [] tool_elem = None @@ -349,9 +371,21 @@ if tup_guid == guid: break if inside_section: - tool_elem = suc.generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ) + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + tool_section ) else: - tool_elem = suc.generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, None ) + tool_elem = suc.generate_tool_elem( tool_shed, + repository_name, + changeset_revision, + owner, + tool_file_path, + tool, + None ) if inside_section: if section_in_elem_list: elem_list[ index ] = tool_section @@ -367,7 +401,8 @@ tool_config = '' if tool_sections: for tool_section in tool_sections: - # The value of tool_section will be None if the tool is displayed outside of any sections in the tool panel. + # The value of tool_section will be None if the tool is displayed outside + # of any sections in the tool panel. if tool_section: section_id = tool_section.id or '' section_version = tool_section.version or '' @@ -376,7 +411,10 @@ section_id = '' section_version = '' section_name = '' - tool_section_dicts.append( dict( tool_config=tool_config, id=section_id, version=section_version, name=section_name ) ) + tool_section_dicts.append( dict( tool_config=tool_config, + id=section_id, + version=section_version, + name=section_name ) ) else: tool_section_dicts.append( dict( tool_config=tool_config, id='', version='', name='' ) ) return tool_section_dicts @@ -409,9 +447,10 @@ def get_latest_tool_config_revision_from_repository_manifest( repo, filename, changeset_revision ): """ - Get the latest revision of a tool config file named filename from the repository manifest up to the value of changeset_revision. - This method is restricted to tool_config files rather than any file since it is likely that, with the exception of tool config files, - multiple files will have the same name in various directories within the repository. + Get the latest revision of a tool config file named filename from the repository + manifest up to the value of changeset_revision. This method is restricted to tool_config + files rather than any file since it is likely that, with the exception of tool config + files, multiple files will have the same name in various directories within the repository. """ stripped_filename = basic_util.strip_path( filename ) for changeset in hg_util.reversed_upper_bounded_changelog( repo, changeset_revision ): @@ -422,8 +461,9 @@ try: fctx = manifest_ctx[ ctx_file ] except LookupError: - # The ctx_file may have been moved in the change set. For example, 'ncbi_blastp_wrapper.xml' was moved to - # 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml', so keep looking for the file until we find the new location. + # The ctx_file may have been moved in the change set. For example, + # 'ncbi_blastp_wrapper.xml' was moved to 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml', + # so keep looking for the file until we find the new location. continue fh = tempfile.NamedTemporaryFile( 'wb', prefix="tmp-toolshed-gltcrfrm" ) tmp_filename = fh.name @@ -436,10 +476,12 @@ def get_list_of_copied_sample_files( repo, ctx, dir ): """ - Find all sample files (files in the repository with the special .sample extension) in the reversed repository manifest up to ctx. Copy - each discovered file to dir and return the list of filenames. If a .sample file was added in a changeset and then deleted in a later - changeset, it will be returned in the deleted_sample_files list. The caller will set the value of app.config.tool_data_path to dir in - order to load the tools and generate metadata for them. + Find all sample files (files in the repository with the special .sample extension) + in the reversed repository manifest up to ctx. Copy each discovered file to dir and + return the list of filenames. If a .sample file was added in a changeset and then + deleted in a later changeset, it will be returned in the deleted_sample_files list. + The caller will set the value of app.config.tool_data_path to dir in order to load + the tools and generate metadata for them. """ deleted_sample_files = [] sample_files = [] @@ -447,16 +489,20 @@ changeset_ctx = repo.changectx( changeset ) for ctx_file in changeset_ctx.files(): ctx_file_name = basic_util.strip_path( ctx_file ) - # If we decide in the future that files deleted later in the changelog should not be used, we can use the following if statement. - # if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: + # If we decide in the future that files deleted later in the changelog should + # not be used, we can use the following if statement. if ctx_file_name.endswith( '.sample' ) + # and ctx_file_name not in sample_files and ctx_file_name not in deleted_sample_files: if ctx_file_name.endswith( '.sample' ) and ctx_file_name not in sample_files: fctx = hg_util.get_file_context_from_ctx( changeset_ctx, ctx_file ) if fctx in [ 'DELETED' ]: - # Since the possibly future used if statement above is commented out, the same file that was initially added will be - # discovered in an earlier changeset in the change log and fall through to the else block below. In other words, if - # a file named blast2go.loc.sample was added in change set 0 and then deleted in changeset 3, the deleted file in changeset - # 3 will be handled here, but the later discovered file in changeset 0 will be handled in the else block below. In this - # way, the file contents will always be found for future tools even though the file was deleted. + # Since the possibly future used if statement above is commented out, the + # same file that was initially added will be discovered in an earlier changeset + # in the change log and fall through to the else block below. In other words, + # if a file named blast2go.loc.sample was added in change set 0 and then deleted + # in changeset 3, the deleted file in changeset 3 will be handled here, but the + # later discovered file in changeset 0 will be handled in the else block below. + # In this way, the file contents will always be found for future tools even though + # the file was deleted. if ctx_file_name not in deleted_sample_files: deleted_sample_files.append( ctx_file_name ) else: @@ -522,14 +568,14 @@ """Return a ToolVersionAssociation if one exists that associates the two received tool_versions""" context = app.install_model.context return context.query( app.install_model.ToolVersionAssociation ) \ - .filter( and_( app.install_model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id, - app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id ) ) \ - .first() + .filter( and_( app.install_model.ToolVersionAssociation.table.c.parent_id == parent_tool_version.id, + app.install_model.ToolVersionAssociation.table.c.tool_id == tool_version.id ) ) \ + .first() def get_version_lineage_for_tool( app, repository_id, repository_metadata, guid ): """ - Return the tool version lineage chain in descendant order for the received guid contained in the received - repsitory_metadata.tool_versions. + Return the tool version lineage chain in descendant order for the received + guid contained in the received repsitory_metadata.tool_versions. """ repository = suc.get_repository_by_id( app, repository_id ) repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) @@ -563,9 +609,10 @@ def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ): """ - Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the - tool_data_table_conf.xml file. This method is called only from Galaxy (not the tool shed) when a repository is being installed - or reinstalled. + Inspect each tool to see if any have input parameters that are dynamically + generated select lists that require entries in the tool_data_table_conf.xml + file. This method is called only from Galaxy (not the tool shed) when a + repository is being installed or reinstalled. """ missing_data_table_entry = False for index, repository_tools_tup in enumerate( repository_tools_tups ): @@ -574,7 +621,8 @@ missing_data_table_entry = True break if missing_data_table_entry: - # The repository must contain a tool_data_table_conf.xml.sample file that includes all required entries for all tools in the repository. + # The repository must contain a tool_data_table_conf.xml.sample file that includes + # all required entries for all tools in the repository. sample_tool_data_table_conf = hg_util.get_config_from_disk( 'tool_data_table_conf.xml.sample', relative_install_dir ) if sample_tool_data_table_conf: # Add entries to the ToolDataTableManager's in-memory data_tables dictionary. @@ -591,8 +639,9 @@ def handle_missing_index_file( app, tool_path, sample_files, repository_tools_tups, sample_files_copied ): """ - Inspect each tool to see if it has any input parameters that are dynamically generated select lists that depend on a .loc file. - This method is not called from the tool shed, but from Galaxy when a repository is being installed. + Inspect each tool to see if it has any input parameters that are dynamically + generated select lists that depend on a .loc file. This method is not called + from the tool shed, but from Galaxy when a repository is being installed. """ for index, repository_tools_tup in enumerate( repository_tools_tups ): tup_path, guid, repository_tool = repository_tools_tup @@ -615,53 +664,60 @@ repository_tools_tups[ index ] = ( tup_path, guid, repository_tool ) return repository_tools_tups, sample_files_copied -def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, repository_id, tool_config_filepath, work_dir ): - # Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories. +def handle_sample_files_and_load_tool_from_disk( app, repo_files_dir, repository_id, tool_config_filepath, work_dir ): + """ + Copy all sample files from disk to a temporary directory since the sample files may + be in multiple directories. + """ message = '' - sample_files = copy_disk_sample_files_to_dir( trans, repo_files_dir, work_dir ) + sample_files = copy_disk_sample_files_to_dir( app, repo_files_dir, work_dir ) if sample_files: if 'tool_data_table_conf.xml.sample' in sample_files: # Load entries into the tool_data_tables if the tool requires them. tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) - error, message = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - tool, valid, message2 = load_tool_from_config( trans.app, repository_id, tool_config_filepath ) + error, message = handle_sample_tool_data_table_conf_file( app, tool_data_table_config ) + tool, valid, message2 = load_tool_from_config( app, repository_id, tool_config_filepath ) message = concat_messages( message, message2 ) return tool, valid, message, sample_files -def handle_sample_files_and_load_tool_from_tmp_config( trans, repo, repository_id, changeset_revision, tool_config_filename, work_dir ): +def handle_sample_files_and_load_tool_from_tmp_config( app, repo, repository_id, changeset_revision, + tool_config_filename, work_dir ): tool = None message = '' ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - # We're not currently doing anything with the returned list of deleted_sample_files here. It is intended to help handle sample files that are in - # the manifest, but have been deleted from disk. + # We're not currently doing anything with the returned list of deleted_sample_files here. It is + # intended to help handle sample files that are in the manifest, but have been deleted from disk. sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) if sample_files: - trans.app.config.tool_data_path = work_dir + app.config.tool_data_path = work_dir if 'tool_data_table_conf.xml.sample' in sample_files: # Load entries into the tool_data_tables if the tool requires them. tool_data_table_config = os.path.join( work_dir, 'tool_data_table_conf.xml' ) if tool_data_table_config: - error, message = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) + error, message = handle_sample_tool_data_table_conf_file( app, tool_data_table_config ) if error: log.debug( message ) manifest_ctx, ctx_file = hg_util.get_ctx_file_path_from_manifest( tool_config_filename, repo, changeset_revision ) if manifest_ctx and ctx_file: - tool, message2 = load_tool_from_tmp_config( trans, repo, repository_id, manifest_ctx, ctx_file, work_dir ) + tool, message2 = load_tool_from_tmp_config( app, repo, repository_id, manifest_ctx, ctx_file, work_dir ) message = concat_messages( message, message2 ) return tool, message, sample_files def handle_sample_tool_data_table_conf_file( app, filename, persist=False ): """ - Parse the incoming filename and add new entries to the in-memory app.tool_data_tables dictionary. If persist is True (should only occur - if call is from the Galaxy side, not the tool shed), the new entries will be appended to Galaxy's shed_tool_data_table_conf.xml file on disk. + Parse the incoming filename and add new entries to the in-memory + app.tool_data_tables dictionary. If persist is True (should only occur + if call is from the Galaxy side, not the tool shed), the new entries will + be appended to Galaxy's shed_tool_data_table_conf.xml file on disk. """ error = False message = '' try: - new_table_elems, message = app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, - tool_data_path=app.config.tool_data_path, - shed_tool_data_table_config=app.config.shed_tool_data_table_config, - persist=persist ) + new_table_elems, message = \ + app.tool_data_tables.add_new_entries_from_config_file( config_filename=filename, + tool_data_path=app.config.tool_data_path, + shed_tool_data_table_config=app.config.shed_tool_data_table_config, + persist=persist ) if message: error = True except Exception, e: @@ -709,9 +765,10 @@ def handle_tool_panel_section( toolbox, tool_panel_section_id=None, new_tool_panel_section_label=None ): """Return a ToolSection object retrieved from the current in-memory tool_panel.""" - # If tool_panel_section_id is received, the section exists in the tool panel. In this case, the value of the - # received tool_panel_section_id must be the id retrieved from a tool panel config (e.g., tool_conf.xml, which - # may have getext). If new_tool_panel_section_label is received, a new section will be added to the tool panel. + # If tool_panel_section_id is received, the section exists in the tool panel. In this + # case, the value of the received tool_panel_section_id must be the id retrieved from a + # tool panel config (e.g., tool_conf.xml, which may have getext). If new_tool_panel_section_label + # is received, a new section will be added to the tool panel. if new_tool_panel_section_label: section_id = str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) tool_panel_section_key, tool_section = \ @@ -727,8 +784,9 @@ def handle_tool_versions( app, tool_version_dicts, tool_shed_repository ): """ - Using the list of tool_version_dicts retrieved from the tool shed (one per changeset revison up to the currently installed changeset revision), - create the parent / child pairs of tool versions. Each dictionary contains { tool id : parent tool id } pairs. + Using the list of tool_version_dicts retrieved from the tool shed (one per changeset + revison up to the currently installed changeset revision), create the parent / child + pairs of tool versions. Each dictionary contains { tool id : parent tool id } pairs. """ context = app.install_model.context for tool_version_dict in tool_version_dicts: @@ -802,9 +860,10 @@ #store repository info in the table tagset for traceability repo_elem = suc.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=elem ) if elems: - os.unlink( tool_data_table_conf_filename ) #remove old data_table - app.tool_data_tables.to_xml_file( tool_data_table_conf_filename, elems ) #persist new data_table content - + # Remove old data_table + os.unlink( tool_data_table_conf_filename ) + # Persist new data_table content. + app.tool_data_tables.to_xml_file( tool_data_table_conf_filename, elems ) return tool_data_table_conf_filename, elems @@ -829,10 +888,11 @@ def is_data_index_sample_file( file_path ): """ - Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when a tool shed repository is being installed - into a Galaxy instance. + Attempt to determine if a .sample file is appropriate for copying to ~/tool-data when + a tool shed repository is being installed into a Galaxy instance. """ - # Currently most data index files are tabular, so check that first. We'll assume that if the file is tabular, it's ok to copy. + # Currently most data index files are tabular, so check that first. We'll assume that + # if the file is tabular, it's ok to copy. if is_column_based( file_path ): return True # If the file is any of the following, don't copy it. @@ -851,7 +911,7 @@ # Default to copying the file if none of the above are true. return True -def load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_config_filename ): +def load_tool_from_changeset_revision( app, 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) @@ -859,31 +919,35 @@ 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.app, repository_id ) - repo_files_dir = repository.repo_path( trans.app ) - repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_files_dir, create=False ) + original_tool_data_path = app.config.tool_data_path + repository = suc.get_repository_in_tool_shed( app, repository_id ) + repo_files_dir = repository.repo_path( app ) + repo = hg_util.get_repo_for_repository( app, repository=None, repo_path=repo_files_dir, create=False ) message = '' tool = None can_use_disk_file = False tool_config_filepath = suc.get_absolute_path_to_file_in_repository( repo_files_dir, tool_config_filename ) work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ltfcr" ) - can_use_disk_file = can_use_tool_config_disk_file( trans, repository, repo, tool_config_filepath, changeset_revision ) + can_use_disk_file = can_use_tool_config_disk_file( app, + 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, + app.config.tool_data_path = work_dir + tool, valid, message, sample_files = handle_sample_files_and_load_tool_from_disk( app, repo_files_dir, repository_id, tool_config_filepath, work_dir ) if tool is not None: - invalid_files_and_errors_tups = check_tool_input_params( trans.app, + invalid_files_and_errors_tups = check_tool_input_params( app, repo_files_dir, tool_config_filename, tool, sample_files ) if invalid_files_and_errors_tups: - message2 = generate_message_for_invalid_tools( trans.app, + message2 = generate_message_for_invalid_tools( app, invalid_files_and_errors_tups, repository, metadata_dict=None, @@ -891,16 +955,16 @@ displaying_invalid_tool=True ) message = concat_messages( message, message2 ) else: - tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( trans, + tool, message, sample_files = handle_sample_files_and_load_tool_from_tmp_config( app, repo, repository_id, changeset_revision, tool_config_filename, work_dir ) basic_util.remove_dir( work_dir ) - trans.app.config.tool_data_path = original_tool_data_path + 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 ) + reset_tool_data_tables( app ) return repository, tool, message def load_tool_from_config( app, repository_id, full_path ): @@ -920,7 +984,7 @@ error_message = str( e ) return tool, valid, error_message -def load_tool_from_tmp_config( trans, repo, repository_id, ctx, ctx_file, work_dir ): +def load_tool_from_tmp_config( app, repo, repository_id, ctx, ctx_file, work_dir ): tool = None message = '' tmp_tool_config = hg_util.get_named_tmpfile_from_ctx( ctx, ctx_file, work_dir ) @@ -936,7 +1000,7 @@ tmp_code_file_name = hg_util.copy_file_from_manifest( repo, ctx, code_file_name, work_dir ) if tmp_code_file_name: tmp_code_files.append( tmp_code_file_name ) - tool, valid, message = load_tool_from_config( trans.app, repository_id, tmp_tool_config ) + tool, valid, message = load_tool_from_config( app, repository_id, tmp_tool_config ) for tmp_code_file in tmp_code_files: try: os.unlink( tmp_code_file ) @@ -966,7 +1030,11 @@ def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. - # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} + # {<Tool guid> : + # [{ tool_config : <tool_config_file>, + # id: <ToolSection id>, + # version : <ToolSection version>, + # name : <TooSection name>}]} # But not like this. # { id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>} if not tool_section_dict: @@ -985,10 +1053,11 @@ if isinstance( tool.tool_action, UploadToolAction ): app.toolbox.reload_tool_by_id( tool_id ) -def remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ): - # A tool shed repository is being uninstalled so change the shed_tool_conf file. Parse the config file to generate the entire list - # of config_elems instead of using the in-memory list since it will be a subset of the entire list if one or more repositories have - # been deactivated. +def remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ): + # A tool shed repository is being uninstalled so change the shed_tool_conf file. + # Parse the config file to generate the entire list of config_elems instead of + # using the in-memory list since it will be a subset of the entire list if one + # or more repositories have been deactivated. shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] tool_path = shed_tool_conf_dict[ 'tool_path' ] config_elems = [] @@ -1016,26 +1085,31 @@ for config_elem in config_elems_to_remove: config_elems.remove( config_elem ) # Persist the altered in-memory version of the tool config. - suc.config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path ) + suc.config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) -def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ): - """A tool shed repository is being deactivated or uninstalled, so handle tool panel alterations accordingly.""" - # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed - # in the same way when the repository is activated or reinstalled. - tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( trans.app, repository ) +def remove_from_tool_panel( app, repository, shed_tool_conf, uninstall ): + """ + A tool shed repository is being deactivated or uninstalled, so handle tool panel + alterations accordingly. + """ + # Determine where the tools are currently defined in the tool panel and store this + # information so the tools can be displayed in the same way when the repository is + # activated or reinstalled. + tool_panel_dict = suc.generate_tool_panel_dict_from_shed_tool_conf_entries( app, repository ) repository.metadata[ 'tool_panel_section' ] = tool_panel_dict - trans.install_model.context.add( repository ) - trans.install_model.context.flush() - # Create a list of guids for all tools that will be removed from the in-memory tool panel and config file on disk. + app.install_model.context.add( repository ) + app.install_model.context.flush() + # Create a list of guids for all tools that will be removed from the in-memory tool panel + # and config file on disk. guids_to_remove = [ k for k in tool_panel_dict.keys() ] # Remove the tools from the toolbox's tools_by_id dictionary. for guid_to_remove in guids_to_remove: - if guid_to_remove in trans.app.toolbox.tools_by_id: - del trans.app.toolbox.tools_by_id[ guid_to_remove ] - index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( trans.app, shed_tool_conf ) + if guid_to_remove in app.toolbox.tools_by_id: + del app.toolbox.tools_by_id[ guid_to_remove ] + index, shed_tool_conf_dict = suc.get_shed_tool_conf_dict( app, shed_tool_conf ) if uninstall: # Remove from the shed_tool_conf file on disk. - remove_from_shed_tool_config( trans, shed_tool_conf_dict, guids_to_remove ) + remove_from_shed_tool_config( app, shed_tool_conf_dict, guids_to_remove ) config_elems = shed_tool_conf_dict[ 'config_elems' ] config_elems_to_remove = [] for config_elem in config_elems: @@ -1052,18 +1126,19 @@ # Remove the tool sub-element from the section element. config_elem.remove( tool_elem ) # Remove the tool from the section in the in-memory tool panel. - if section_key in trans.app.toolbox.tool_panel: - tool_section = trans.app.toolbox.tool_panel[ section_key ] + if section_key in app.toolbox.tool_panel: + tool_section = app.toolbox.tool_panel[ section_key ] guid = tool_elem.get( 'guid' ) tool_key = 'tool_%s' % str( guid ) # Get the list of versions of this tool that are currently available in the toolbox. - available_tool_versions = trans.app.toolbox.get_loaded_tools_by_lineage( guid ) + available_tool_versions = app.toolbox.get_loaded_tools_by_lineage( guid ) if tool_key in tool_section.elems: if available_tool_versions: available_tool_versions.reverse() replacement_tool_key = None replacement_tool_version = None - # Since we are going to remove the tool from the section, replace it with the newest loaded version of the tool. + # Since we are going to remove the tool from the section, replace it with the + # newest loaded version of the tool. for available_tool_version in available_tool_versions: available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() if available_tool_version.id in tool_section.elems.keys() or section_key == available_tool_section_id: @@ -1078,15 +1153,17 @@ # Remove the tool from the tool section. del tool_section.elems[ tool_key ] # Add the replacement tool at the same location in the tool section. - tool_section.elems.insert( tool_section_elems_index, replacement_tool_key, replacement_tool_version ) + tool_section.elems.insert( tool_section_elems_index, + replacement_tool_key, + replacement_tool_version ) else: del tool_section.elems[ tool_key ] else: del tool_section.elems[ tool_key ] if uninstall: # Remove the tool from the section in the in-memory integrated tool panel. - if section_key in trans.app.toolbox.integrated_tool_panel: - tool_section = trans.app.toolbox.integrated_tool_panel[ section_key ] + if section_key in app.toolbox.integrated_tool_panel: + tool_section = app.toolbox.integrated_tool_panel[ section_key ] tool_key = 'tool_%s' % str( tool_elem.get( 'guid' ) ) if tool_key in tool_section.elems: del tool_section.elems[ tool_key ] @@ -1098,46 +1175,47 @@ if guid in guids_to_remove: tool_key = 'tool_%s' % str( config_elem.get( 'guid' ) ) # Get the list of versions of this tool that are currently available in the toolbox. - available_tool_versions = trans.app.toolbox.get_loaded_tools_by_lineage( guid ) - if tool_key in trans.app.toolbox.tool_panel: + available_tool_versions = app.toolbox.get_loaded_tools_by_lineage( guid ) + if tool_key in app.toolbox.tool_panel: if available_tool_versions: available_tool_versions.reverse() replacement_tool_key = None replacement_tool_version = None - # Since we are going to remove the tool from the section, replace it with the newest loaded version of the tool. + # Since we are going to remove the tool from the section, replace it with + # the newest loaded version of the tool. for available_tool_version in available_tool_versions: available_tool_section_id, available_tool_section_name = available_tool_version.get_panel_section() - if available_tool_version.id in trans.app.toolbox.tool_panel.keys() or not available_tool_section_id: + if available_tool_version.id in app.toolbox.tool_panel.keys() or not available_tool_section_id: replacement_tool_key = 'tool_%s' % str( available_tool_version.id ) replacement_tool_version = available_tool_version break if replacement_tool_key and replacement_tool_version: # Get the index of the tool_key in the tool_section. - for tool_panel_index, key in enumerate( trans.app.toolbox.tool_panel.keys() ): + for tool_panel_index, key in enumerate( app.toolbox.tool_panel.keys() ): if key == tool_key: break # Remove the tool from the tool panel. - del trans.app.toolbox.tool_panel[ tool_key ] + del app.toolbox.tool_panel[ tool_key ] # Add the replacement tool at the same location in the tool panel. - trans.app.toolbox.tool_panel.insert( tool_panel_index, replacement_tool_key, replacement_tool_version ) + app.toolbox.tool_panel.insert( tool_panel_index, replacement_tool_key, replacement_tool_version ) else: - del trans.app.toolbox.tool_panel[ tool_key ] + del app.toolbox.tool_panel[ tool_key ] else: - del trans.app.toolbox.tool_panel[ tool_key ] + del app.toolbox.tool_panel[ tool_key ] if uninstall: - if tool_key in trans.app.toolbox.integrated_tool_panel: - del trans.app.toolbox.integrated_tool_panel[ tool_key ] + if tool_key in app.toolbox.integrated_tool_panel: + del app.toolbox.integrated_tool_panel[ tool_key ] config_elems_to_remove.append( config_elem ) for config_elem in config_elems_to_remove: # Remove the element from the in-memory list of elements. config_elems.remove( config_elem ) # Update the config_elems of the in-memory shed_tool_conf_dict. shed_tool_conf_dict[ 'config_elems' ] = config_elems - trans.app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict - trans.app.toolbox_search = ToolBoxSearch( trans.app.toolbox ) - if uninstall and trans.app.config.update_integrated_tool_panel: + app.toolbox.shed_tool_confs[ index ] = shed_tool_conf_dict + app.toolbox_search = ToolBoxSearch( app.toolbox ) + if uninstall and app.config.update_integrated_tool_panel: # Write the current in-memory version of the integrated_tool_panel.xml file to disk. - trans.app.toolbox.write_integrated_tool_panel_config_file() + app.toolbox.write_integrated_tool_panel_config_file() def reset_tool_data_tables( app ): # Reset the tool_data_tables to an empty dictionary. diff -r 5242547f33ed801a83837de5d507cc4b4c2eb6ff -r cd5d9bf32d865657208b0b657b08c9142b357e25 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -61,7 +61,10 @@ # We're in the tool shed. for tool_dict in tools_metadata: if self.tool_id in [ tool_dict[ 'id' ], tool_dict[ 'guid' ] ]: - repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans, repository_id, changeset_revision, tool_dict[ 'tool_config' ] ) + repository, self.tool, message = tool_util.load_tool_from_changeset_revision( trans.app, + repository_id, + changeset_revision, + tool_dict[ 'tool_config' ] ) if message and self.tool is None: self.errors = 'unavailable' break Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for bug introduced when I eliminated the use of trans from the tool shed's review_util.py module.
by commits-noreply＠bitbucket.org 18 Jul '14

18 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5242547f33ed/ Changeset: 5242547f33ed User: greg Date: 2014-07-18 12:50:16 Summary: Fix for bug introduced when I eliminated the use of trans from the tool shed's review_util.py module. Affected #: 1 file diff -r 6609ad71320787b849d6d68522b9f346090706c5 -r 5242547f33ed801a83837de5d507cc4b4c2eb6ff lib/tool_shed/util/review_util.py --- a/lib/tool_shed/util/review_util.py +++ b/lib/tool_shed/util/review_util.py @@ -41,8 +41,8 @@ def get_component_by_name( app, name ): """Get a component from the database via a name.""" sa_session = app.model.context.current - return sa_session.query( app.app.model.Component ) \ - .filter( app.app.model.Component.table.c.name==name ) \ + return sa_session.query( app.model.Component ) \ + .filter( app.model.Component.table.c.name==name ) \ .first() def get_component_review_by_repository_review_id_component_id( app, repository_review_id, component_id ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Update embedded visualizations to work with recent refactoring.
by commits-noreply＠bitbucket.org 17 Jul '14

17 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6609ad713207/ Changeset: 6609ad713207 User: jgoecks Date: 2014-07-17 22:53:04 Summary: Update embedded visualizations to work with recent refactoring. Affected #: 2 files diff -r 6cdc306ec75b37c5dbd8f0472d73956b60186926 -r 6609ad71320787b849d6d68522b9f346090706c5 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -566,6 +566,7 @@ }); return { + TracksterUI: TracksterUI, GalaxyApp : TracksterView }; diff -r 6cdc306ec75b37c5dbd8f0472d73956b60186926 -r 6609ad71320787b849d6d68522b9f346090706c5 templates/webapps/galaxy/visualization/display.mako --- a/templates/webapps/galaxy/visualization/display.mako +++ b/templates/webapps/galaxy/visualization/display.mako @@ -60,13 +60,12 @@ "libs/backbone/backbone": { exports: "Backbone" }, } }); - require( ["base", "viz/visualization", "viz/trackster_ui", "viz/trackster/tracks"], - function( base, visualization, trackster_ui, tracks ) { + require( ["viz/trackster"], function(trackster) { // FIXME: deliberate global required for now due to requireJS integration. view = null; - - var ui = new (trackster_ui.TracksterUI)( "${h.url_for('/')}" ) + + var ui = new (trackster.TracksterUI)( "${h.url_for('/')}" ) container_element = $("#${trans.security.encode_id( visualization.id )}"); $(function() { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: jgoecks: Remove duplicated function definition.
by commits-noreply＠bitbucket.org 17 Jul '14

17 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cdc306ec75b/ Changeset: 6cdc306ec75b User: jgoecks Date: 2014-07-17 22:34:20 Summary: Remove duplicated function definition. Affected #: 1 file diff -r 1d578ea7ba67cedd9e8ce193c4cfdb581224a3df -r 6cdc306ec75b37c5dbd8f0472d73956b60186926 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -34,24 +34,6 @@ // trackster viewer define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], function(_, base, tracks, visualization) { -/** - * Returns an IconButtonMenuView for the provided configuration. - * Configuration is a list of dictionaries where each dictionary - * defines an icon button. Each dictionary must have the following - * elements: icon_class, title, and on_click. - */ -var create_icon_buttons_menu = function(config, global_config) { - if (!global_config) { global_config = {}; } - - // Create and initialize menu. - var buttons = new IconButtonCollection( - _.map(config, function(button_config) { - return new IconButton(_.extend(button_config, global_config)); - }) - ); - - return new IconButtonMenuView( {collection: buttons} ); -}; /** * User interface controls for trackster Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 17 Jul '14

17 Jul '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/68f8568c9519/ Changeset: 68f8568c9519 User: jgoecks Date: 2014-07-17 21:44:45 Summary: Trackster: remove unused requirements. Affected #: 1 file diff -r f65eb16fdf1e0b7a6f3483373c32765107c3b2b6 -r 68f8568c95195600cb38adab95cf9fcf7d617aa3 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -1,13 +1,10 @@ -define( ["base","libs/underscore","viz/trackster/slotting", "viz/trackster/painters", "viz/trackster/tracks", "viz/visualization" ], - function( base, _, slotting, painters, tracks, visualization ) { +define( ["base","libs/underscore", "viz/trackster/tracks", "viz/visualization" ], + function( base, _, tracks, visualization ) { /************************************************************************ * Functions used for creating and managing the Trackster user interface. ************************************************************************/ -var object_from_template = tracks.object_from_template; - - /** * Returns an IconButtonMenuView for the provided configuration. * Configuration is a list of dictionaries where each dictionary @@ -96,7 +93,7 @@ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { _.each(tracks, function(track) { - view.add_drawable( object_from_template(track, view, view) ); + view.add_drawable( tracks.object_from_template(track, view, view) ); }); }); } }, @@ -263,7 +260,7 @@ drawable_type, drawable; for (var i = 0; i < drawables_config.length; i++) { - view.add_drawable( object_from_template( drawables_config[i], view, view ) ); + view.add_drawable( tracks.object_from_template( drawables_config[i], view, view ) ); } } @@ -367,7 +364,7 @@ }); return { - object_from_template: object_from_template, + object_from_template: tracks.object_from_template, TracksterUI: TracksterUI }; https://bitbucket.org/galaxy/galaxy-central/commits/40d27b0ba43a/ Changeset: 40d27b0ba43a User: jgoecks Date: 2014-07-17 22:23:17 Summary: Trackster: merge all top-level UI code into the same file for simplicity. Affected #: 4 files diff -r 68f8568c95195600cb38adab95cf9fcf7d617aa3 -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ /dev/null @@ -1,1 +0,0 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.config.get_value("name"):null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.config.get_value("name"),dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(f.extend(p,{header:false}));l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].config.get_value("name")===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});this.set_up_router({view:l});return l},set_up_router:function(k){new h.TrackBrowserRouter(k);Backbone.history.start()},init_keyboard_nav:function(k){$(document).keyup(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file diff -r 68f8568c95195600cb38adab95cf9fcf7d617aa3 -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -1,3 +1,7 @@ +/** + * Top-level trackster code, used for creating/loading visualizations and user interface elements. + */ + // global variables var ui = null; var view = null; @@ -28,15 +32,374 @@ }); // trackster viewer -define( ["libs/backbone/backbone", "viz/trackster_ui"], function(backbone, trackster_ui) { +define( ["libs/underscore", "base", "viz/trackster/tracks", "viz/visualization"], + function(_, base, tracks, visualization) { +/** + * Returns an IconButtonMenuView for the provided configuration. + * Configuration is a list of dictionaries where each dictionary + * defines an icon button. Each dictionary must have the following + * elements: icon_class, title, and on_click. + */ +var create_icon_buttons_menu = function(config, global_config) { + if (!global_config) { global_config = {}; } -var TracksterView = Backbone.View.extend( + // Create and initialize menu. + var buttons = new IconButtonCollection( + _.map(config, function(button_config) { + return new IconButton(_.extend(button_config, global_config)); + }) + ); + + return new IconButtonMenuView( {collection: buttons} ); +}; + +/** + * User interface controls for trackster + */ +var TracksterUI = base.Base.extend({ + initialize: function( baseURL ) { + this.baseURL = baseURL; + }, + + /** + * Save visualization, returning a Deferred object for the remote call to save. + */ + save_viz: function() { + // show dialog + Galaxy.modal.show({title: "Saving...", body: "progress" }); + + // Save bookmarks. + var bookmarks = []; + $(".bookmark").each(function() { + bookmarks.push({ + position: $(this).children(".position").text(), + annotation: $(this).children(".annotation").text() + }); + }); + + // FIXME: give unique IDs to Drawables and save overview as ID. + var overview_track_name = (view.overview_drawable ? view.overview_drawable.config.get_value('name') : null), + viz_config = { + 'view': view.to_dict(), + 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, + 'bookmarks': bookmarks + }; + + // Make call to save visualization. + return $.ajax({ + url: galaxy_config.root + "visualization/save", + type: "POST", + dataType: "json", + data: { + 'id' : view.vis_id, + 'title' : view.config.get_value('name'), + 'dbkey' : view.dbkey, + 'type' : 'trackster', + 'vis_json' : JSON.stringify(viz_config) + } + }).success(function(vis_info) { + Galaxy.modal.hide(); + view.vis_id = vis_info.vis_id; + view.has_changes = false; + + // Needed to set URL when first saving a visualization. + window.history.pushState({}, "", vis_info.url + window.location.hash); + }).error(function() { + // show dialog + Galaxy.modal.show({ + title : "Could Not Save", + body : "Could not save visualization. Please try again later.", + buttons : { "Cancel": function() { Galaxy.modal.hide(); } } + }); + }); + }, + + /** + * Create button menu + */ + createButtonMenu: function() { + var self = this, + menu = create_icon_buttons_menu([ + { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { + visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { + _.each(tracks, function(track) { + view.add_drawable( tracks.object_from_template(track, view, view) ); + }); + }); + } }, + { icon_class: 'block--plus', title: 'Add group', on_click: function() { + view.add_drawable( new tracks.DrawableGroup(view, view, { name: "New Group" }) ); + } }, + { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() { + // HACK -- use style to determine if panel is hidden and hide/show accordingly. + force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); + } }, + { + icon_class: 'globe', + title: 'Circster', + on_click: function() { + window.location = self.baseURL + 'visualization/circster?id=' + view.vis_id; + } + }, + { icon_class: 'disk--arrow', title: 'Save', on_click: function() { + self.save_viz(); + } }, + { + icon_class: 'cross-circle', + title: 'Close', + on_click: function() { + self.handle_unsaved_changes(view); + } + } + ], + { + tooltip_config: { placement: 'bottom' } + }); + this.buttonMenu = menu; + return menu; + }, + + /** + * Use a popup to select a dataset of create bookmarks from + */ + add_bookmarks: function() { + var self = this, + baseURL = this.baseURL; + + // show modal while loading history + Galaxy.modal.show({title: "Select dataset for new bookmarks", body: "progress" }); + + $.ajax({ + url: this.baseURL + "/visualization/list_histories", + data: { "f-dbkey": view.dbkey }, + error: function() { alert( "Grid failed" ); }, + success: function(table_html) { + + // show modal to select bookmarks + Galaxy.modal.show( + { + title : "Select dataset for new bookmarks", + body : table_html, + buttons : + { + "Cancel": function() + { + Galaxy.modal.hide(); + }, + + "Insert": function() + { + // Just use the first selected + $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function() + { + var data, id = $(this).val(); + if ($(this).attr("name") === "id") + data = { hda_id: id }; + else + data = { ldda_id: id}; + + $.ajax({ + url: this.baseURL + "/visualization/bookmarks_from_dataset", + data: data, + dataType: "json" + }).then( function(data) { + for( i = 0; i < data.data.length; i++ ) { + var row = data.data[i]; + self.add_bookmark( row[0], row[1] ); + } + }); + }); + Galaxy.modal.hide(); + } + } + }); + } + }); + }, + + /** + * Add bookmark. + */ + add_bookmark: function(position, annotation, editable) { + // Create HTML. + var bookmarks_container = $("#right .unified-panel-body"), + new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container); + + var position_div = $("<div/>").addClass("position").appendTo(new_bookmark), + position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() { + view.go_to(position); + return false; + }), + annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark); + + // If editable, enable bookmark deletion and annotation editing. + if (editable) { + var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){ + // Remove bookmark. + new_bookmark.slideUp("fast"); + new_bookmark.remove(); + view.has_changes = true; + return false; + }), + delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container); + annotation_div.make_text_editable({ + num_rows: 3, + use_textarea: true, + help_text: "Edit bookmark note" + }).addClass("annotation"); + } + + view.has_changes = true; + return new_bookmark; + }, + + /** + * Create a complete Trackster visualization. Returns view. + */ + create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) { + + // Create view. + var self = this, + view = new tracks.TracksterView(_.extend(view_config, {header: false})); + view.editor = true; + $.when( view.load_chroms_deferred ).then(function(chrom_info) { + // Viewport config. + if (viewport_config) { + var chrom = viewport_config.chrom, + start = viewport_config.start, + end = viewport_config.end, + overview_drawable_name = viewport_config.overview; + + if (chrom && (start !== undefined) && end) { + view.change_chrom(chrom, start, end); + } + else { + // No valid viewport, so use first chromosome. + view.change_chrom(chrom_info[0].chrom); + } + } + else { + // No viewport, so use first chromosome. + view.change_chrom(chrom_info[0].chrom); + } + + // Add drawables to view. + if (drawables_config) { + // FIXME: can from_dict() be used to create view and add drawables? + var drawable_config, + drawable_type, + drawable; + for (var i = 0; i < drawables_config.length; i++) { + view.add_drawable( tracks.object_from_template( drawables_config[i], view, view ) ); + } + } + + // Set overview. + var overview_drawable; + for (var i = 0; i < view.drawables.length; i++) { + if (view.drawables[i].config.get_value('name') === overview_drawable_name) { + view.set_overview(view.drawables[i]); + break; + } + } + + // Load bookmarks. + if (bookmarks_config) { + var bookmark; + for (var i = 0; i < bookmarks_config.length; i++) { + bookmark = bookmarks_config[i]; + self.add_bookmark(bookmark['position'], bookmark['annotation'], editable); + } + } + + // View has no changes as of yet. + view.has_changes = false; + }); + + // Final initialization. + this.set_up_router({view: view}); + + return view; + }, + + /** + * Set up location router to use hashes as track browser locations. + */ + set_up_router : function(options) + { + new visualization.TrackBrowserRouter(options); + Backbone.history.start(); + }, + + /** + * Set up keyboard navigation for a visualization. + */ + init_keyboard_nav: function(view) { + // Keyboard navigation. Scroll ~7% of height when scrolling up/down. + $(document).keyup(function(e) { + // Do not navigate if arrow keys used in input element. + if ($(e.srcElement).is(':input')) { + return; + } + + // Key codes: left == 37, up == 38, right == 39, down == 40 + switch(e.which) { + case 37: + view.move_fraction(0.25); + break; + case 38: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); + break; + case 39: + view.move_fraction(-0.25); + break; + case 40: + var change = Math.round(view.viewport_container.height()/15.0); + view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20); + break; + } + }); + }, + + /** + * Handle unsaved changes in visualization. + */ + handle_unsaved_changes: function(view) { + if (view.has_changes) { + var self = this; + Galaxy.modal.show({ + title: "Close visualization", + body: "There are unsaved changes to your visualization which will be lost if you do not save them.", + buttons: { + "Cancel": function() { Galaxy.modal.hide(); }, + "Leave without Saving" : function() { + window.onbeforeunload = undefined; + window.location = galaxy_config.root + 'visualization'; + }, + "Save" : function() { + $.when(self.save_viz()).then(function() { + window.location = galaxy_config.root + 'visualization'; + }); + } + } + }); + + } + else { + window.location = galaxy_config.root + 'visualization'; + } + } + +}); + +var TracksterView = base.Backbone.View.extend( { // initalize trackster initialize : function () { // load ui - ui = new trackster_ui.TracksterUI(galaxy_config.root); + ui = new TracksterUI(galaxy_config.root); // create button menu ui.createButtonMenu(); @@ -197,7 +560,7 @@ url: galaxy_config.root + "api/datasets/" + galaxy_config.app.add_dataset, data: { hda_ldda: 'hda', data_type: 'track_config' }, dataType: "json", - success: function(track_data) { view.add_drawable( trackster_ui.object_from_template(track_data, view, view) ); } + success: function(track_data) { view.add_drawable( tracks.object_from_template(track_data, view, view) ); } }); // initialize icons @@ -220,10 +583,8 @@ } }); -// return return { GalaxyApp : TracksterView }; -// done }); \ No newline at end of file diff -r 68f8568c95195600cb38adab95cf9fcf7d617aa3 -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -877,7 +877,7 @@ this.content_div = this.viewport_container; is_container(this.viewport_container, view); // Introduction div shown when there are no tracks. - this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container).hide(); + this.intro_div = $("<div/>").addClass("intro").appendTo(this.viewport_container); var add_tracks_button = $("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function () { visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { _.each(tracks, function(track) { diff -r 68f8568c95195600cb38adab95cf9fcf7d617aa3 -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ /dev/null @@ -1,371 +0,0 @@ -define( ["base","libs/underscore", "viz/trackster/tracks", "viz/visualization" ], - function( base, _, tracks, visualization ) { - -/************************************************************************ - * Functions used for creating and managing the Trackster user interface. - ************************************************************************/ - -/** - * Returns an IconButtonMenuView for the provided configuration. - * Configuration is a list of dictionaries where each dictionary - * defines an icon button. Each dictionary must have the following - * elements: icon_class, title, and on_click. - */ -var create_icon_buttons_menu = function(config, global_config) { - if (!global_config) { global_config = {}; } - - // Create and initialize menu. - var buttons = new IconButtonCollection( - _.map(config, function(button_config) { - return new IconButton(_.extend(button_config, global_config)); - }) - ); - - return new IconButtonMenuView( {collection: buttons} ); -}; - - -var TracksterUI = base.Base.extend({ - - initialize: function( baseURL ) { - this.baseURL = baseURL; - }, - - /** - * Save visualization, returning a Deferred object for the remote call to save. - */ - save_viz: function() { - // show dialog - Galaxy.modal.show({title: "Saving...", body: "progress" }); - - // Save bookmarks. - var bookmarks = []; - $(".bookmark").each(function() { - bookmarks.push({ - position: $(this).children(".position").text(), - annotation: $(this).children(".annotation").text() - }); - }); - - // FIXME: give unique IDs to Drawables and save overview as ID. - var overview_track_name = (view.overview_drawable ? view.overview_drawable.config.get_value('name') : null), - viz_config = { - 'view': view.to_dict(), - 'viewport': { 'chrom': view.chrom, 'start': view.low , 'end': view.high, 'overview': overview_track_name }, - 'bookmarks': bookmarks - }; - - // Make call to save visualization. - return $.ajax({ - url: galaxy_config.root + "visualization/save", - type: "POST", - dataType: "json", - data: { - 'id' : view.vis_id, - 'title' : view.config.get_value('name'), - 'dbkey' : view.dbkey, - 'type' : 'trackster', - 'vis_json' : JSON.stringify(viz_config) - } - }).success(function(vis_info) { - Galaxy.modal.hide(); - view.vis_id = vis_info.vis_id; - view.has_changes = false; - - // Needed to set URL when first saving a visualization. - window.history.pushState({}, "", vis_info.url + window.location.hash); - }).error(function() { - // show dialog - Galaxy.modal.show({ - title : "Could Not Save", - body : "Could not save visualization. Please try again later.", - buttons : { "Cancel": function() { Galaxy.modal.hide(); } } - }); - }); - }, - - /** - * Create button menu - */ - createButtonMenu: function() { - var self = this, - menu = create_icon_buttons_menu([ - { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { - _.each(tracks, function(track) { - view.add_drawable( tracks.object_from_template(track, view, view) ); - }); - }); - } }, - { icon_class: 'block--plus', title: 'Add group', on_click: function() { - view.add_drawable( new tracks.DrawableGroup(view, view, { name: "New Group" }) ); - } }, - { icon_class: 'bookmarks', title: 'Bookmarks', on_click: function() { - // HACK -- use style to determine if panel is hidden and hide/show accordingly. - force_right_panel(($("div#right").css("right") == "0px" ? "hide" : "show")); - } }, - { - icon_class: 'globe', - title: 'Circster', - on_click: function() { - window.location = self.baseURL + 'visualization/circster?id=' + view.vis_id; - } - }, - { icon_class: 'disk--arrow', title: 'Save', on_click: function() { - self.save_viz(); - } }, - { - icon_class: 'cross-circle', - title: 'Close', - on_click: function() { - self.handle_unsaved_changes(view); - } - } - ], - { - tooltip_config: { placement: 'bottom' } - }); - this.buttonMenu = menu; - return menu; - }, - - /** - * Use a popup to select a dataset of create bookmarks from - */ - add_bookmarks: function() { - var self = this, - baseURL = this.baseURL; - - // show modal while loading history - Galaxy.modal.show({title: "Select dataset for new bookmarks", body: "progress" }); - - $.ajax({ - url: this.baseURL + "/visualization/list_histories", - data: { "f-dbkey": view.dbkey }, - error: function() { alert( "Grid failed" ); }, - success: function(table_html) { - - // show modal to select bookmarks - Galaxy.modal.show( - { - title : "Select dataset for new bookmarks", - body : table_html, - buttons : - { - "Cancel": function() - { - Galaxy.modal.hide(); - }, - - "Insert": function() - { - // Just use the first selected - $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function() - { - var data, id = $(this).val(); - if ($(this).attr("name") === "id") - data = { hda_id: id }; - else - data = { ldda_id: id}; - - $.ajax({ - url: this.baseURL + "/visualization/bookmarks_from_dataset", - data: data, - dataType: "json" - }).then( function(data) { - for( i = 0; i < data.data.length; i++ ) { - var row = data.data[i]; - self.add_bookmark( row[0], row[1] ); - } - }); - }); - Galaxy.modal.hide(); - } - } - }); - } - }); - }, - - /** - * Add bookmark. - */ - add_bookmark: function(position, annotation, editable) { - // Create HTML. - var bookmarks_container = $("#right .unified-panel-body"), - new_bookmark = $("<div/>").addClass("bookmark").appendTo(bookmarks_container); - - var position_div = $("<div/>").addClass("position").appendTo(new_bookmark), - position_link = $("<a href=''/>").text(position).appendTo(position_div).click(function() { - view.go_to(position); - return false; - }), - annotation_div = $("<div/>").text(annotation).appendTo(new_bookmark); - - // If editable, enable bookmark deletion and annotation editing. - if (editable) { - var delete_icon_container = $("<div/>").addClass("delete-icon-container").prependTo(new_bookmark).click(function (){ - // Remove bookmark. - new_bookmark.slideUp("fast"); - new_bookmark.remove(); - view.has_changes = true; - return false; - }), - delete_icon = $("<a href=''/>").addClass("icon-button delete").appendTo(delete_icon_container); - annotation_div.make_text_editable({ - num_rows: 3, - use_textarea: true, - help_text: "Edit bookmark note" - }).addClass("annotation"); - } - - view.has_changes = true; - return new_bookmark; - }, - - /** - * Create a complete Trackster visualization. Returns view. - */ - create_visualization: function(view_config, viewport_config, drawables_config, bookmarks_config, editable) { - - // Create view. - var self = this, - view = new tracks.TracksterView(_.extend(view_config, {header: false})); - view.editor = true; - $.when( view.load_chroms_deferred ).then(function(chrom_info) { - // Viewport config. - if (viewport_config) { - var chrom = viewport_config.chrom, - start = viewport_config.start, - end = viewport_config.end, - overview_drawable_name = viewport_config.overview; - - if (chrom && (start !== undefined) && end) { - view.change_chrom(chrom, start, end); - } - else { - // No valid viewport, so use first chromosome. - view.change_chrom(chrom_info[0].chrom); - } - } - else { - // No viewport, so use first chromosome. - view.change_chrom(chrom_info[0].chrom); - } - - // Add drawables to view. - if (drawables_config) { - // FIXME: can from_dict() be used to create view and add drawables? - var drawable_config, - drawable_type, - drawable; - for (var i = 0; i < drawables_config.length; i++) { - view.add_drawable( tracks.object_from_template( drawables_config[i], view, view ) ); - } - } - - // Set overview. - var overview_drawable; - for (var i = 0; i < view.drawables.length; i++) { - if (view.drawables[i].config.get_value('name') === overview_drawable_name) { - view.set_overview(view.drawables[i]); - break; - } - } - - // Load bookmarks. - if (bookmarks_config) { - var bookmark; - for (var i = 0; i < bookmarks_config.length; i++) { - bookmark = bookmarks_config[i]; - self.add_bookmark(bookmark['position'], bookmark['annotation'], editable); - } - } - - // View has no changes as of yet. - view.has_changes = false; - }); - - // Final initialization. - this.set_up_router({view: view}); - - return view; - }, - - /** - * Set up location router to use hashes as track browser locations. - */ - set_up_router : function(options) - { - new visualization.TrackBrowserRouter(options); - Backbone.history.start(); - }, - - /** - * Set up keyboard navigation for a visualization. - */ - init_keyboard_nav: function(view) { - // Keyboard navigation. Scroll ~7% of height when scrolling up/down. - $(document).keyup(function(e) { - // Do not navigate if arrow keys used in input element. - if ($(e.srcElement).is(':input')) { - return; - } - - // Key codes: left == 37, up == 38, right == 39, down == 40 - switch(e.which) { - case 37: - view.move_fraction(0.25); - break; - case 38: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTop( view.viewport_container.scrollTop() - 20); - break; - case 39: - view.move_fraction(-0.25); - break; - case 40: - var change = Math.round(view.viewport_container.height()/15.0); - view.viewport_container.scrollTop( view.viewport_container.scrollTop() + 20); - break; - } - }); - }, - - /** - * Handle unsaved changes in visualization. - */ - handle_unsaved_changes: function(view) { - if (view.has_changes) { - var self = this; - Galaxy.modal.show({ - title: "Close visualization", - body: "There are unsaved changes to your visualization which will be lost if you do not save them.", - buttons: { - "Cancel": function() { Galaxy.modal.hide(); }, - "Leave without Saving" : function() { - window.onbeforeunload = undefined; - window.location = galaxy_config.root + 'visualization'; - }, - "Save" : function() { - $.when(self.save_viz()).then(function() { - window.location = galaxy_config.root + 'visualization'; - }); - } - } - }); - - } - else { - window.location = galaxy_config.root + 'visualization'; - } - } - -}); - -return { - object_from_template: tracks.object_from_template, - TracksterUI: TracksterUI -}; - -}); https://bitbucket.org/galaxy/galaxy-central/commits/1d578ea7ba67/ Changeset: 1d578ea7ba67 User: jgoecks Date: 2014-07-17 22:23:33 Summary: Automated merge. Affected #: 4 files diff -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 -r 1d578ea7ba67cedd9e8ce193c4cfdb581224a3df 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 @@ -169,7 +169,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems " @@ -806,7 +806,7 @@ tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) if tool_dependency_ids: # We need a tool_shed_repository, so get it from one of the tool_dependencies. - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] ) tool_shed_repository = tool_dependency.tool_shed_repository else: # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a @@ -830,7 +830,7 @@ elif operation == 'uninstall': tool_dependencies_for_uninstallation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.INSTALLED, trans.install_model.ToolDependency.installation_status.ERROR ]: tool_dependencies_for_uninstallation.append( tool_dependency ) @@ -845,7 +845,7 @@ if trans.app.config.tool_dependency_dir: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) @@ -889,7 +889,7 @@ repository_id = kwd.get( 'repository_id', None ) if tool_dependency_ids: # We need a tool_shed_repository, so get it from one of the tool_dependencies. - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_ids[ 0 ] ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] ) tool_shed_repository = tool_dependency.tool_shed_repository else: # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a @@ -914,7 +914,7 @@ if trans.app.config.tool_dependency_dir: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) @@ -1849,7 +1849,7 @@ tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: - tool_dependency = tool_dependency_util.get_tool_dependency( trans, tool_dependency_id ) + tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) tool_dependencies.append( tool_dependency ) tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository if kwd.get( 'uninstall_tool_dependencies_button', False ): diff -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 -r 1d578ea7ba67cedd9e8ce193c4cfdb581224a3df lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1347,7 +1347,7 @@ match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - ok, match_tuples = search_util.search_repository_metadata( trans, + ok, match_tuples = search_util.search_repository_metadata( trans.app, exact_matches_checked, tool_ids=tool_ids, tool_names=tool_names, @@ -1437,9 +1437,14 @@ match_tuples = [] ok = True if workflow_names: - ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=workflow_names ) + ok, match_tuples = search_util.search_repository_metadata( trans.app, + exact_matches_checked, + workflow_names=workflow_names ) else: - ok, match_tuples = search_util.search_repository_metadata( trans, exact_matches_checked, workflow_names=[], all_workflows=True ) + ok, match_tuples = search_util.search_repository_metadata( trans.app, + exact_matches_checked, + workflow_names=[], + all_workflows=True ) if ok: kwd[ 'match_tuples' ] = match_tuples if trans.webapp.name == 'galaxy': diff -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 -r 1d578ea7ba67cedd9e8ce193c4cfdb581224a3df lib/tool_shed/util/search_util.py --- a/lib/tool_shed/util/search_util.py +++ b/lib/tool_shed/util/search_util.py @@ -81,15 +81,17 @@ match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return match_tuples -def search_repository_metadata( trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): +def search_repository_metadata( app, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', + workflow_names='', all_workflows=False ): + sa_session=app.model.context.current match_tuples = [] ok = True if tool_ids or tool_names or tool_versions: - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ - .join( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): + for repository_metadata in sa_session.query( app.model.RepositoryMetadata ) \ + .filter( app.model.RepositoryMetadata.table.c.includes_tools == True ) \ + .join( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.deleted == False, + app.model.Repository.table.c.deprecated == False ) ): metadata = repository_metadata.metadata if metadata: tools = metadata.get( 'tools', [] ) @@ -140,11 +142,11 @@ else: ok = False elif workflow_names or all_workflows: - for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ - .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ - .join( trans.model.Repository ) \ - .filter( and_( trans.model.Repository.table.c.deleted == False, - trans.model.Repository.table.c.deprecated == False ) ): + for repository_metadata in sa_session.query( app.model.RepositoryMetadata ) \ + .filter( app.model.RepositoryMetadata.table.c.includes_workflows == True ) \ + .join( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.deleted == False, + app.model.Repository.table.c.deprecated == False ) ): metadata = repository_metadata.metadata if metadata: # metadata[ 'workflows' ] is a list of tuples where each contained tuple is diff -r 40d27b0ba43a746aeecd8e78891c270bcb513ca8 -r 1d578ea7ba67cedd9e8ce193c4cfdb581224a3df lib/tool_shed/util/tool_dependency_util.py --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -128,9 +128,9 @@ platform_dict[ 'architecture' ] = machine.lower() return platform_dict -def get_tool_dependency( trans, id ): +def get_tool_dependency( app, id ): """Get a tool_dependency from the database via id""" - return trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) ) + return app.install_model.context.query( app.install_model.ToolDependency ).get( app.security.decode_id( id ) ) def get_tool_dependency_by_name_type_repository( app, repository, name, type ): context = app.install_model.context Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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