From d2ed893a75e787d5ce6747af260904846015e212 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Thu, 4 Sep 2014 13:14:00 -0400 Subject: [PATCH 01/10] Encapsulate the Tool Shed's metadata generator. --- .../galaxy/api/tool_shed_repositories.py | 9 +- .../galaxy/controllers/admin_toolshed.py | 77 ++-- .../webapps/tool_shed/api/repositories.py | 31 +- .../webapps/tool_shed/controllers/hg.py | 16 +- .../tool_shed/controllers/repository.py | 25 +- .../webapps/tool_shed/controllers/upload.py | 5 +- lib/tool_shed/capsule/capsule_manager.py | 5 +- .../galaxy_install/install_manager.py | 48 +-- .../installed_repository_manager.py | 11 +- .../installed_repository_metadata_manager.py | 103 +++-- .../galaxy_install/tool_migration_manager.py | 38 +- lib/tool_shed/metadata/metadata_generator.py | 278 +++++++++----- .../metadata/repository_metadata_manager.py | 352 ++++++++---------- 13 files changed, 542 insertions(+), 456 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index 2193d082c3a..e5e54d44e83 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -417,12 +417,13 @@ class ToolShedRepositoriesController( BaseAPIController ): 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: - invalid_file_tups, metadata_dict = irmm.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + irmm.set_repository( repository ) + irmm.reset_all_metadata_on_installed_repository() + irmm_invalid_file_tups = irmm.get_invalid_file_tups() + if irmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + irmm_invalid_file_tups, repository, None, as_html=False ) diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 779255f5bd2..7761bafe25c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1732,20 +1732,21 @@ class AdminToolshed( AdminGalaxy ): tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: original_metadata_dict = repository.metadata - irmm = InstalledRepositoryMetadataManager( trans.app ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - irmm.update_in_shed_tool_config( repository ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + repository=repository, + changeset_revision=repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if irmm_metadata_dict != original_metadata_dict: + repository.metadata = irmm_metadata_dict + irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository %s.' % repository.name @@ -1938,22 +1939,24 @@ class AdminToolshed( AdminGalaxy ): dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) - irmm = InstalledRepositoryMetadataManager( trans.app, tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=latest_changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=repository.get_shed_config_dict( trans.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=True, - persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = metadata_dict.get( 'tool_panel_section', None ) + irmm = InstalledRepositoryMetadataManager( app=trans.app, + tpm=tpm, + repository=repository, + changeset_revision=latest_changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=repository.get_shed_config_dict( trans.app ), + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=True, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + if 'tools' in irmm_metadata_dict: + tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), @@ -1963,18 +1966,18 @@ class AdminToolshed( AdminGalaxy ): tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) new_data_managers = dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) - if 'repository_dependencies' in metadata_dict or 'tool_dependencies' in metadata_dict: - new_repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: + new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) - new_tool_dependencies_dict = metadata_dict.get( 'tool_dependencies', {} ) + new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False @@ -2017,7 +2020,7 @@ class AdminToolshed( AdminGalaxy ): updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include @@ -2033,12 +2036,12 @@ class AdminToolshed( AdminGalaxy ): proceed_to_install = True break if proceed_to_install: - encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( metadata_dict.get( 'tool_dependencies', {} ) ) + encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, - encoded_updated_metadata=encoding_util.tool_shed_encode( metadata_dict ), + encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, @@ -2047,7 +2050,7 @@ class AdminToolshed( AdminGalaxy ): # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, - updated_metadata_dict=metadata_dict, + updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index f886f3d6a7e..0d68c7c3dda 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -429,13 +429,13 @@ class RepositoriesController( BaseAPIController ): 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: - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + rmm.set_repository( repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) @@ -451,7 +451,11 @@ class RepositoriesController( BaseAPIController ): status = '%s : %s' % ( str( repository.name ), message ) results[ 'repository_status' ].append( status ) return results - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) results = dict( start_time=start_time, repository_status=[], @@ -511,12 +515,17 @@ class RepositoriesController( BaseAPIController ): results = dict( start_time=start_time, repository_status=[] ) try: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( trans.security.encode_id( repository.id ) ) - if invalid_file_tups: + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + resetting_all_metadata_on_repository=True, + updating_installed_repository=False, + persist=False ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, None, as_html=False ) diff --git a/lib/galaxy/webapps/tool_shed/controllers/hg.py b/lib/galaxy/webapps/tool_shed/controllers/hg.py index 33a41ad7ac3..48b850dceb6 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -1,6 +1,8 @@ import os, logging from galaxy import web from galaxy.web.base.controller import BaseUIController + +from tool_shed.util.common_util import generate_clone_url_for_repository_in_tool_shed from tool_shed.util.shed_util_common import get_repository_by_name_and_owner from tool_shed.util.hg_util import update_repository from tool_shed.metadata import repository_metadata_manager @@ -47,9 +49,19 @@ class HgController( BaseUIController ): # interface will result in a new head being created. repo = hg.repository( ui.ui(), repository.repo_path( trans.app ) ) update_repository( repo, ctx_rev=None ) + repository_clone_url = generate_clone_url_for_repository_in_tool_shed( trans.user, repository ) # Set metadata using the repository files on disk. - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - error_message, status = rmm.set_repository_metadata( trans.request.host, repository ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository, + changeset_revision=repository.tip( trans.app ), + repository_clone_url=repository_clone_url, + relative_install_dir=repository.repo_path( trans.app ), + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=False ) + error_message, status = rmm.set_repository_metadata( trans.request.host ) 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 --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 1f059b8d534..50b763e68d2 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2759,15 +2759,18 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): 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, trans.user ) - invalid_file_tups, metadata_dict = \ - rmm.reset_all_metadata_on_repository_in_tool_shed( id ) - if invalid_file_tups: - repository = suc.get_repository_in_tool_shed( trans.app, id ) + repository = suc.get_repository_in_tool_shed( trans.app, id ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + rmm.reset_all_metadata_on_repository_in_tool_shed() + rmm_metadata_dict = rmm.get_metadata_dict() + rmm_invalid_file_tups = rmm.get_invalid_file_tups() + if rmm_invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans.app, - invalid_file_tups, + rmm_invalid_file_tups, repository, - metadata_dict ) + rmm_metadata_dict ) status = 'error' else: message = "All repository metadata has been reset. " @@ -2849,10 +2852,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): if tip == repository.tip( trans.app ): message += 'No changes to repository. ' else: - rmm = repository_metadata_manager.RepositoryMetadataManager( trans.app, trans.user ) - status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, - **kwd ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) + status, error_message = rmm.set_repository_metadata_due_to_new_tip( trans.request.host, **kwd ) if error_message: message = error_message else: diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py index ec78a684398..62dbcb93581 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -263,10 +263,11 @@ class UploadController( BaseUIController ): ( 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, trans.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=trans.app, + user=trans.user, + repository=repository ) status, error_message = \ rmm.set_repository_metadata_due_to_new_tip( trans.request.host, - repository, content_alert_str=content_alert_str, **kwd ) if error_message: diff --git a/lib/tool_shed/capsule/capsule_manager.py b/lib/tool_shed/capsule/capsule_manager.py index fc723e0b3f5..15b6fb43d87 100644 --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -792,9 +792,10 @@ class ImportRepositoryManager( object ): results_dict[ 'ok' ] = False results_dict[ 'error_message' ] += error_message try: - rmm = repository_metadata_manager.RepositoryMetadataManager( self.app, self.user ) + rmm = repository_metadata_manager.RepositoryMetadataManager( app=self.app, + user=self.user, + repository=repository ) status, error_message = rmm.set_repository_metadata_due_to_new_tip( self.host, - repository, content_alert_str=content_alert_str ) if error_message: results_dict[ 'ok' ] = False diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py index d4c5a0003ba..466b51abb2c 100644 --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -510,31 +510,33 @@ class InstallRepositoryManager( object ): """ shed_config_dict = self.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ) tdtm = data_table_manager.ToolDataTableManager( self.app ) - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict=shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict=shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict # Update the tool_shed_repository.tool_shed_status column in the database. tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( self.app, tool_shed_repository ) if tool_shed_status_dict: tool_shed_repository.tool_shed_status = tool_shed_status_dict self.install_model.context.add( tool_shed_repository ) self.install_model.context.flush() - if 'tool_dependencies' in metadata_dict and not reinstalling: + if 'tool_dependencies' in irmm_metadata_dict and not reinstalling: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( self.app, tool_shed_repository, relative_install_dir, set_status=True ) - if 'sample_files' in metadata_dict: - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'sample_files' in irmm_metadata_dict: + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_data_table_conf_filename, tool_data_table_elems = \ tdtm.install_tool_data_tables( tool_shed_repository, tool_index_sample_files ) @@ -543,13 +545,13 @@ class InstallRepositoryManager( object ): None, self.app.config.shed_tool_data_table_config, persist=True ) - if 'tools' in metadata_dict: - tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) - sample_files = metadata_dict.get( 'sample_files', [] ) + if 'tools' in irmm_metadata_dict: + tool_panel_dict = self.tpm.generate_tool_panel_dict_for_new_install( irmm_metadata_dict[ 'tools' ], tool_section ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ str( s ) for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically generated select lists. repository_tools_tups = tdtm.handle_missing_data_table_entry( relative_install_dir, @@ -575,15 +577,15 @@ class InstallRepositoryManager( object ): shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=True ) - if 'data_manager' in metadata_dict: + if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata_dict, + irmm_metadata_dict, shed_config_dict, relative_install_dir, tool_shed_repository, repository_tools_tups ) - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: tool_shed_repository.status = self.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: tool_shed_repository.includes_datatypes = True @@ -604,7 +606,7 @@ class InstallRepositoryManager( object ): name=tool_shed_repository.name, owner=tool_shed_repository.owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff --git a/lib/tool_shed/galaxy_install/installed_repository_manager.py b/lib/tool_shed/galaxy_install/installed_repository_manager.py index 2ef682bb533..9437c983753 100644 --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -82,9 +82,12 @@ class InstalledRepositoryManager( object ): 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 ) - irmm = InstalledRepositoryMetadataManager( self.app, tpm ) - metadata = repository.metadata - repository_tools_tups = irmm.get_repository_tools_tups( metadata ) + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=tpm, + repository=repository, + changeset_revision=repository.changeset_revision, + metadata_dict=repository.metadata ) + repository_tools_tups = irmm.get_repository_tools_tups() # Reload tools into the appropriate tool panel section. tool_panel_dict = repository.metadata[ 'tool_panel_section' ] tpm.add_to_tool_panel( repository.name, @@ -101,7 +104,7 @@ class InstalledRepositoryManager( object ): data_manager_relative_install_dir = os.path.join( data_manager_relative_install_dir, repository.name ) dmh = data_manager.DataManagerHandler( self.app ) new_data_managers = dmh.install_data_managers( self.app.config.shed_data_manager_config_file, - metadata, + repository.metadata, repository.get_shed_config_dict( self.app ), data_manager_relative_install_dir, repository, diff --git a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py index a3541ace337..bf90c9cf854 100644 --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -19,9 +19,16 @@ log = logging.getLogger( __name__ ) class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, tpm=None ): - super( InstalledRepositoryMetadataManager, self ).__init__( app ) - self.app = app + def __init__( self, app, tpm=None, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( InstalledRepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=None ) if tpm is None: self.tpm = tool_panel_manager.ToolPanelManager( self.app ) else: @@ -53,15 +60,15 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ) return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.uninstalled == False ) - def get_repository_tools_tups( self, metadata_dict ): + def get_repository_tools_tups( self ): """ Return a list of tuples of the form (relative_path, guid, tool) for each tool defined in the received tool shed repository metadata. """ repository_tools_tups = [] - index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( metadata_dict.get( 'shed_config_filename' ) ) - if 'tools' in metadata_dict: - for tool_dict in metadata_dict[ 'tools' ]: + index, shed_conf_dict = self.tpm.get_shed_tool_conf_dict( self.metadata_dict.get( 'shed_config_filename' ) ) + if 'tools' in self.metadata_dict: + for tool_dict in self.metadata_dict[ 'tools' ]: load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) if shed_conf_dict.get( 'tool_path' ): load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) @@ -74,36 +81,21 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ) repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups - def reset_all_metadata_on_installed_repository( self, id ): + def reset_all_metadata_on_installed_repository( self ): """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" - invalid_file_tups = [] - metadata_dict = {} - repository = repository_util.get_installed_tool_shed_repository( self.app, id ) - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) - if relative_install_dir: - original_metadata_dict = repository.metadata - metadata_dict, invalid_file_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = repository.get_shed_config_dict( self.app ), - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - repository.metadata = metadata_dict - if metadata_dict != original_metadata_dict: - self.update_in_shed_tool_config( repository ) - self.app.install_model.context.add( repository ) + if self.relative_install_dir: + original_metadata_dict = self.repository.metadata + self.generate_metadata_for_changeset_revision() + if self.metadata_dict != original_metadata_dict: + self.repository.metadata = self.metadata_dict + self.update_in_shed_tool_config() + self.app.install_model.context.add( self.repository ) self.app.install_model.context.flush() - log.debug( 'Metadata has been reset on repository %s.' % repository.name ) + log.debug( 'Metadata has been reset on repository %s.' % self.repository.name ) else: - log.debug( 'Metadata did not need to be reset on repository %s.' % repository.name ) + log.debug( 'Metadata did not need to be reset on repository %s.' % self.repository.name ) else: - log.debug( 'Error locating installation directory for repository %s.' % repository.name ) - return invalid_file_tups, metadata_dict + log.debug( 'Error locating installation directory for repository %s.' % self.repository.name ) def reset_metadata_on_selected_repositories( self, user, **kwd ): """ @@ -119,19 +111,19 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ) for repository_id in repository_ids: try: repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) - owner = str( repository.owner ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_installed_repository( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_installed_repository() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % \ + ( str( repository.name ), str( repository.owner ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) @@ -146,32 +138,37 @@ class InstalledRepositoryMetadataManager( metadata_generator.MetadataGenerator ) status = 'error' return message, status - def tool_shed_from_repository_clone_url( self, repository_clone_url ): - """Given a repository clone URL, return the tool shed that contains the repository.""" - return common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + def set_repository( self, repository ): + super( InstalledRepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - def update_in_shed_tool_config( self, repository ): + def tool_shed_from_repository_clone_url( self ): + """Given a repository clone URL, return the tool shed that contains the repository.""" + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) + return common_util.remove_protocol_and_user_from_clone_url( cleaned_repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' ) + + def update_in_shed_tool_config( self ): """ A tool shed repository is being updated 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. """ - shed_conf_dict = repository.get_shed_config_dict( self.app ) + shed_conf_dict = self.repository.get_shed_config_dict( self.app ) shed_tool_conf = shed_conf_dict[ 'config_filename' ] tool_path = shed_conf_dict[ 'tool_path' ] - tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) - repository_tools_tups = self.get_repository_tools_tups( repository.metadata ) - clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) - cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) - tool_shed = self.tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner + tool_panel_dict = self.tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( self.repository ) + repository_tools_tups = self.get_repository_tools_tups() + clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + tool_shed = self.tool_shed_from_repository_clone_url() + owner = self.repository.owner if not owner: + cleaned_repository_clone_url = common_util.remove_protocol_and_user_from_clone_url( clone_url ) owner = suc.get_repository_owner( cleaned_repository_clone_url ) guid_to_tool_elem_dict = {} for tool_config_filename, guid, tool in repository_tools_tups: guid_to_tool_elem_dict[ guid ] = self.tpm.generate_tool_elem( tool_shed, - repository.name, - repository.changeset_revision, - repository.owner or '', + self.repository.name, + self.repository.changeset_revision, + self.repository.owner or '', tool_config_filename, tool, None ) diff --git a/lib/tool_shed/galaxy_install/tool_migration_manager.py b/lib/tool_shed/galaxy_install/tool_migration_manager.py index 39ada8ed05d..20e8e85b6cf 100644 --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -416,21 +416,23 @@ class ToolMigrationManager( object ): log.exception( "Exception attempting to filter and persist non-shed-related tool panel configs:\n%s" % str( e ) ) finally: lock.release() - irmm = InstalledRepositoryMetadataManager( self.app, self.tpm ) - metadata_dict, invalid_file_tups = \ - irmm.generate_metadata_for_changeset_revision( repository=tool_shed_repository, - changeset_revision=tool_shed_repository.changeset_revision, - repository_clone_url=repository_clone_url, - shed_config_dict = self.shed_config_dict, - relative_install_dir=relative_install_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=True ) - tool_shed_repository.metadata = metadata_dict + irmm = InstalledRepositoryMetadataManager( app=self.app, + tpm=self.tpm, + repository=tool_shed_repository, + changeset_revision=tool_shed_repository.changeset_revision, + repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, + relative_install_dir=relative_install_dir, + repository_files_dir=None, + resetting_all_metadata_on_repository=False, + updating_installed_repository=False, + persist=True ) + irmm.generate_metadata_for_changeset_revision() + irmm_metadata_dict = irmm.get_metadata_dict() + tool_shed_repository.metadata = irmm_metadata_dict self.app.install_model.context.add( tool_shed_repository ) self.app.install_model.context.flush() - has_tool_dependencies = self.__has_tool_dependencies( metadata_dict ) + has_tool_dependencies = self.__has_tool_dependencies( irmm_metadata_dict ) if has_tool_dependencies: # All tool_dependency objects must be created before the tools are processed even if no # tool dependencies will be installed. @@ -440,14 +442,14 @@ class ToolMigrationManager( object ): set_status=True ) else: tool_dependencies = None - if 'tools' in metadata_dict: + if 'tools' in irmm_metadata_dict: tdtm = data_table_manager.ToolDataTableManager( self.app ) - sample_files = metadata_dict.get( 'sample_files', [] ) + sample_files = irmm_metadata_dict.get( 'sample_files', [] ) sample_files = [ str( s ) for s in sample_files ] tool_index_sample_files = tdtm.get_tool_index_sample_files( sample_files ) tool_util.copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] - repository_tools_tups = irmm.get_repository_tools_tups( metadata_dict ) + repository_tools_tups = irmm.get_repository_tools_tups() if repository_tools_tups: # Handle missing data table entries for tool parameters that are dynamically # generated select lists. @@ -491,7 +493,7 @@ class ToolMigrationManager( object ): if installed_tool_dependency.status == self.app.install_model.ToolDependency.installation_status.ERROR: print '\nThe ToolMigrationManager returned the following error while installing tool dependency ', installed_tool_dependency.name, ':' print installed_tool_dependency.error_message, '\n\n' - if 'datatypes' in metadata_dict: + if 'datatypes' in irmm_metadata_dict: cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) tool_shed_repository.status = self.app.install_model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES if not tool_shed_repository.includes_datatypes: @@ -514,7 +516,7 @@ class ToolMigrationManager( object ): name=tool_shed_repository.name, owner=self.repository_owner, installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), + tool_dicts=irmm_metadata_dict.get( 'tools', [] ), converter_path=converter_path, display_path=display_path ) if converter_path: diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py index 05e82ed6026..81d5a62bdf9 100644 --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -27,31 +27,89 @@ log = logging.getLogger( __name__ ) class MetadataGenerator( object ): - def __init__( self, app ): + def __init__( self, app, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None, user=None ): self.app = app + self.user = user + self.repository = repository + if self.app.name == 'galaxy': + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.changeset_revision + else: + self.changeset_revision = changeset_revision + + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + if self.repository is not None: + self.shed_config_dict = self.repository.get_shed_config_dict( self.app ) + else: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_files_directory( self.app ) + if metadata_dict is None: + # Shed related tool panel configs are only relevant to Galaxy. + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + self.metadata_dict = metadata_dict + else: + # We're in the Tool Shed. + if changeset_revision is None and self.repository is not None: + self.changeset_revision = self.repository.tip( self.app ) + else: + self.changeset_revision = changeset_revision + if repository_clone_url is None and self.repository is not None: + self.repository_clone_url = \ + common_util.generate_clone_url_for_repository_in_tool_shed( self.user, self.repository ) + else: + self.repository_clone_url = repository_clone_url + if shed_config_dict is None: + self.shed_config_dict = {} + else: + self.shed_config_dict = shed_config_dict + if relative_install_dir is None and self.repository is not None: + relative_install_dir = self.repository.repo_path( self.app ) + if repository_files_dir is None and self.repository is not None: + repository_files_dir = self.repository.repo_path( self.app ) + if metadata_dict is None: + self.metadata_dict = {} + else: + self.metadata_dict = metadata_dict + self.relative_install_dir = relative_install_dir + self.repository_files_dir = repository_files_dir + self.resetting_all_metadata_on_repository = resetting_all_metadata_on_repository + self.updating_installed_repository = updating_installed_repository + self.persist = persist + self.invalid_file_tups = [] self.sa_session = app.model.context.current self.NOT_TOOL_CONFIGS = [ suc.DATATYPES_CONFIG_FILENAME, - rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, - rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, - suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] + rt_util.REPOSITORY_DEPENDENCY_DEFINITION_FILENAME, + rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, + suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME ] - def generate_data_manager_metadata( self, repository, repo_dir, data_manager_config_filename, metadata_dict, + def generate_data_manager_metadata( self, repo_dir, data_manager_config_filename, metadata_dict, shed_config_dict=None ): """ Update the received metadata_dict with information from the parsed data_manager_config_filename. """ if data_manager_config_filename is None: return metadata_dict - repo_path = repository.repo_path( self.app ) + repo_path = self.repository.repo_path( self.app ) try: # Galaxy Side. - repo_files_directory = repository.repo_files_directory( self.app ) + repo_files_directory = self.repository.repo_files_directory( self.app ) repo_dir = repo_files_directory - repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) except AttributeError: # Tool Shed side. repo_files_directory = repo_path - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( None, repository ) relative_data_manager_dir = util.relpath( os.path.split( data_manager_config_filename )[0], repo_dir ) rel_data_manager_config_filename = os.path.join( relative_data_manager_dir, os.path.split( data_manager_config_filename )[1] ) @@ -91,7 +149,7 @@ class MetadataGenerator( object ): # FIXME: default behavior is to fall back to tool.name. data_manager_name = data_manager_elem.get( 'name', data_manager_id ) version = data_manager_elem.get( 'version', DataManager.DEFAULT_VERSION ) - guid = self.generate_guid_for_object( repository_clone_url, DataManager.GUID_TYPE, data_manager_id, version ) + guid = self.generate_guid_for_object( DataManager.GUID_TYPE, data_manager_id, version ) data_tables = [] if tool_file is None: log.error( 'Data Manager entry is missing tool_file attribute in "%s".' % ( data_manager_config_filename ) ) @@ -130,8 +188,7 @@ class MetadataGenerator( object ): log.debug( 'Loaded Data Manager tool_files: %s' % ( tool_file ) ) return metadata_dict - def generate_datatypes_metadata( self, tv, repository, repository_clone_url, repository_files_dir, datatypes_config, - metadata_dict ): + def generate_datatypes_metadata( self, tv, repository_files_dir, datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree, error_message = xml_util.parse_xml( datatypes_config ) if tree is None: @@ -180,11 +237,11 @@ class MetadataGenerator( object ): 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 = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), full_path ) + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: guid = None else: - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) converter_dict = dict( tool_config=tool_config, guid=guid, target_datatype=target_datatype ) @@ -226,76 +283,70 @@ class MetadataGenerator( object ): valid_tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return valid_tool_dependencies_dict - def generate_guid_for_object( self, repository_clone_url, guid_type, obj_id, version ): - tmp_url = common_util.remove_protocol_and_user_from_clone_url( repository_clone_url ) + def generate_guid_for_object( self, guid_type, obj_id, version ): + tmp_url = common_util.remove_protocol_and_user_from_clone_url( self.repository_clone_url ) return '%s/%s/%s/%s' % ( tmp_url, guid_type, obj_id, version ) - def generate_metadata_for_changeset_revision( self, repository, changeset_revision, repository_clone_url, - shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, - resetting_all_metadata_on_repository=False, updating_installed_repository=False, - persist=False ): + def generate_metadata_for_changeset_revision( self ): """ Generate metadata for a repository using its files on disk. To generate metadata for changeset revisions older than the repository tip, the repository will have been cloned to a temporary location and updated to a specified changeset revision to access - that changeset revision's disk files, so the value of repository_files_dir will not - always be repository.repo_path( self.app ) (it could be an absolute path to a temporary - directory containing a clone). If it is an absolute path, the value of relative_install_dir + that changeset revision's disk files, so the value of self.repository_files_dir will not + always be self.repository.repo_path( self.app ) (it could be an absolute path to a temporary + directory containing a clone). If it is an absolute path, the value of self.relative_install_dir must contain repository.repo_path( self.app ). - The value of persist will be True when the installed repository contains a valid + The value of self.persist will be True when the installed repository contains a valid tool_data_table_conf.xml.sample file, in which case the entries should ultimately be persisted to the file referred to by self.app.config.shed_tool_data_table_config. """ tv = tool_validator.ToolValidator( self.app ) - if shed_config_dict is None: - shed_config_dict = {} - if updating_installed_repository: + if self.shed_config_dict is None: + self.shed_config_dict = {} + if self.updating_installed_repository: # Keep the original tool shed repository metadata if setting metadata on a repository # installed into a local Galaxy instance for which we have pulled updates. - original_repository_metadata = repository.metadata + original_repository_metadata = self.repository.metadata else: original_repository_metadata = None - readme_file_names = readme_util.get_readme_file_names( str( repository.name ) ) + readme_file_names = readme_util.get_readme_file_names( str( self.repository.name ) ) if self.app.name == 'galaxy': # Shed related tool panel configs are only relevant to Galaxy. - metadata_dict = { 'shed_config_filename' : shed_config_dict.get( 'config_filename' ) } + metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename' ) } else: metadata_dict = {} readme_files = [] - invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None original_tool_data_path = self.app.config.tool_data_path original_tool_data_table_config_path = self.app.config.tool_data_table_config_path - if resetting_all_metadata_on_repository: - if not relative_install_dir: - raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) + if self.resetting_all_metadata_on_repository: + if not self.relative_install_dir: + raise Exception( "The value of self.repository.repo_path must be set when resetting all metadata on a repository." ) # Keep track of the location where the repository is temporarily cloned so that we can - # strip the path when setting metadata. The value of repository_files_dir is the full - # path to the temporary directory to which the repository was cloned. - work_dir = repository_files_dir - files_dir = repository_files_dir + # strip the path when setting metadata. The value of self.repository_files_dir is the + # full path to the temporary directory to which self.repository was cloned. + work_dir = self.repository_files_dir + files_dir = self.repository_files_dir # Since we're working from a temporary directory, we can safely copy sample files included # in the repository to the repository root. - self.app.config.tool_data_path = repository_files_dir - self.app.config.tool_data_table_config_path = repository_files_dir + self.app.config.tool_data_path = self.repository_files_dir + self.app.config.tool_data_table_config_path = self.repository_files_dir else: # Use a temporary working directory to copy all sample files. work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-gmfcr" ) # All other files are on disk in the repository's repo_path, which is the value of - # relative_install_dir. - files_dir = relative_install_dir - if shed_config_dict.get( 'tool_path' ): - files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) + # self.relative_install_dir. + files_dir = self.relative_install_dir + if self.shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( self.shed_config_dict[ 'tool_path' ], files_dir ) self.app.config.tool_data_path = work_dir #FIXME: Thread safe? self.app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) if datatypes_config: metadata_dict = self.generate_datatypes_metadata( tv, - repository, - repository_clone_url, files_dir, datatypes_config, metadata_dict ) @@ -303,9 +354,8 @@ class MetadataGenerator( object ): # the repository's metadata. sample_file_metadata_paths, sample_file_copy_paths = \ self.get_sample_files_from_disk( repository_files_dir=files_dir, - tool_path=shed_config_dict.get( 'tool_path' ), - relative_install_dir=relative_install_dir, - resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) + tool_path=self.shed_config_dict.get( 'tool_path' ), + relative_install_dir=self.relative_install_dir ) if sample_file_metadata_paths: metadata_dict[ 'sample_files' ] = sample_file_metadata_paths # Copy all sample files included in the repository to a single directory location so we @@ -322,7 +372,7 @@ class MetadataGenerator( object ): shed_tool_data_table_config=self.app.config.shed_tool_data_table_config, persist=False ) if error_message: - invalid_file_tups.append( ( filename, error_message ) ) + self.invalid_file_tups.append( ( filename, error_message ) ) for root, dirs, files in os.walk( files_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: if '.hg' in dirs: @@ -333,18 +383,16 @@ class MetadataGenerator( object ): path_to_repository_dependencies_config = os.path.join( root, name ) metadata_dict, error_message = \ self.generate_repository_dependency_metadata( path_to_repository_dependencies_config, - metadata_dict, - updating_installed_repository=updating_installed_repository ) + metadata_dict ) if error_message: - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) readme_files.append( relative_path_to_readme ) # See if we have a tool config. elif name not in self.NOT_TOOL_CONFIGS and name.endswith( '.xml' ): @@ -365,12 +413,12 @@ class MetadataGenerator( object ): is_tool = element_tree_root.tag == 'tool' if is_tool: tool, valid, error_message = \ - tv.load_tool_from_config( self.app.security.encode_id( repository.id ), + tv.load_tool_from_config( self.app.security.encode_id( self.repository.id ), full_path ) if tool is None: if not valid: invalid_tool_configs.append( name ) - invalid_file_tups.append( ( name, error_message ) ) + self.invalid_file_tups.append( ( name, error_message ) ) else: invalid_files_and_errors_tups = \ tv.check_tool_input_params( files_dir, @@ -387,17 +435,15 @@ class MetadataGenerator( object ): relative_path_to_tool_config = \ self.get_relative_path_to_repository_file( root, name, - relative_install_dir, + self.relative_install_dir, work_dir, - shed_config_dict, - resetting_all_metadata_on_repository ) + self.shed_config_dict ) metadata_dict = self.generate_tool_metadata( relative_path_to_tool_config, tool, - repository_clone_url, metadata_dict ) else: for tup in invalid_files_and_errors_tups: - invalid_file_tups.append( tup ) + self.invalid_file_tups.append( tup ) # Find all exported workflows. elif name.endswith( '.ga' ): relative_path = os.path.join( root, name ) @@ -421,11 +467,10 @@ class MetadataGenerator( object ): metadata_dict ) # Handle any data manager entries data_manager_config = hg_util.get_config_from_disk( suc.REPOSITORY_DATA_MANAGER_CONFIG_FILENAME, files_dir ) - metadata_dict = self.generate_data_manager_metadata( repository, - files_dir, + metadata_dict = self.generate_data_manager_metadata( files_dir, data_manager_config, metadata_dict, - shed_config_dict=shed_config_dict ) + shed_config_dict=self.shed_config_dict ) if readme_files: metadata_dict[ 'readme_files' ] = readme_files @@ -433,21 +478,18 @@ class MetadataGenerator( object ): tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, files_dir ) if tool_dependencies_config: metadata_dict, error_message = \ - self.generate_tool_dependency_metadata( repository, - changeset_revision, - repository_clone_url, - tool_dependencies_config, + self.generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict, original_repository_metadata=original_repository_metadata ) if error_message: - invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) + self.invalid_file_tups.append( ( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, error_message ) ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs + self.metadata_dict = metadata_dict # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. self.app.config.tool_data_path = original_tool_data_path self.app.config.tool_data_table_config_path = original_tool_data_table_config_path basic_util.remove_dir( work_dir ) - return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( self, elem, valid_tool_dependencies_dict, invalid_tool_dependencies_dict ): """ @@ -475,8 +517,7 @@ class MetadataGenerator( object ): # where a tool dependency definition is considered invalid. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=False ) + only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': @@ -509,8 +550,7 @@ class MetadataGenerator( object ): # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) elif action_elem.tag == 'action': # # @@ -522,8 +562,7 @@ class MetadataGenerator( object ): # We have a complex repository dependency. repository_dependency_tup, repository_dependency_is_valid, error_message = \ self.handle_repository_elem( repository_elem=sub_action_elem, - only_if_compiling_contained_td=True, - updating_installed_repository=False ) + only_if_compiling_contained_td=True ) if requirements_dict: dependency_key = '%s/%s' % ( package_name, package_version ) if repository_dependency_is_valid: @@ -538,8 +577,7 @@ class MetadataGenerator( object ): repository_dependency_is_valid, \ error_message - def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict, - updating_installed_repository=False ): + def generate_repository_dependency_metadata( self, repository_dependencies_config, metadata_dict ): """ Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config. This method is called from the tool shed as well as from Galaxy. @@ -560,8 +598,7 @@ class MetadataGenerator( object ): for repository_elem in root.findall( 'repository' ): repository_dependency_tup, repository_dependency_is_valid, err_msg = \ self.handle_repository_elem( repository_elem, - only_if_compiling_contained_td=False, - updating_installed_repository=updating_installed_repository ) + only_if_compiling_contained_td=False ) if repository_dependency_is_valid: valid_repository_dependency_tups.append( repository_dependency_tup ) else: @@ -585,10 +622,10 @@ class MetadataGenerator( object ): metadata_dict[ 'repository_dependencies' ] = valid_repository_dependencies_dict return metadata_dict, error_message - def generate_tool_metadata( self, tool_config, tool, repository_clone_url, metadata_dict ): + def generate_tool_metadata( self, tool_config, tool, metadata_dict ): """Update the received metadata_dict with changes that have been applied to the received tool.""" # Generate the guid. - guid = suc.generate_tool_guid( repository_clone_url, tool ) + guid = suc.generate_tool_guid( self.repository_clone_url, tool ) # Handle tool.requirements. tool_requirements = [] for tool_requirement in tool.requirements: @@ -667,11 +704,10 @@ class MetadataGenerator( object ): metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict - def generate_tool_dependency_metadata( self, repository, changeset_revision, repository_clone_url, tool_dependencies_config, - metadata_dict, original_repository_metadata=None ): + def generate_tool_dependency_metadata( self, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the tag for - at least one tool in the repository, then update the received metadata_dict with information from the + at least one tool in self.repository, then update the received metadata_dict with information from the parsed tool_dependencies_config. """ error_message = '' @@ -738,7 +774,7 @@ class MetadataGenerator( object ): # into a Galaxy instance, so handle changes to tool dependencies appropriately. irm = self.app.installed_repository_manager updated_tool_dependency_names, deleted_tool_dependency_names = \ - irm.handle_existing_tool_dependencies_that_changed_in_update( repository, + irm.handle_existing_tool_dependencies_that_changed_in_update( self.repository, original_valid_tool_dependencies_dict, valid_tool_dependencies_dict ) metadata_dict[ 'tool_dependencies' ] = valid_tool_dependencies_dict @@ -769,9 +805,14 @@ class MetadataGenerator( object ): metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ] return metadata_dict - def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict, - resetting_all_metadata_on_repository ): - if resetting_all_metadata_on_repository: + def get_invalid_file_tups( self ): + return self.invalid_file_tups + + def get_metadata_dict( self ): + return self.metadata_dict + + def get_relative_path_to_repository_file( self, root, name, relative_install_dir, work_dir, shed_config_dict ): + if self.resetting_all_metadata_on_repository: full_path_to_file = os.path.join( root, name ) stripped_path_to_file = full_path_to_file.replace( work_dir, '' ) if stripped_path_to_file.startswith( '/' ): @@ -785,9 +826,8 @@ class MetadataGenerator( object ): relative_path_to_file = relative_path_to_file[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] return relative_path_to_file - def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None, - resetting_all_metadata_on_repository=False ): - if resetting_all_metadata_on_repository: + def get_sample_files_from_disk( self, repository_files_dir, tool_path=None, relative_install_dir=None ): + if self.resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip # it when setting metadata. work_dir = repository_files_dir @@ -797,7 +837,7 @@ class MetadataGenerator( object ): if root.find( '.hg' ) < 0: for name in files: if name.endswith( '.sample' ): - if resetting_all_metadata_on_repository: + if self.resetting_all_metadata_on_repository: full_path_to_sample_file = os.path.join( root, name ) stripped_path_to_sample_file = full_path_to_sample_file.replace( work_dir, '' ) if stripped_path_to_sample_file.startswith( '/' ): @@ -816,7 +856,7 @@ class MetadataGenerator( object ): sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths - def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False, updating_installed_repository=False ): + def handle_repository_elem( self, repository_elem, only_if_compiling_contained_td=False ): """ Process the received repository_elem which is a tag either from a repository_dependencies.xml file or a tool_dependencies.xml file. If the former, @@ -832,7 +872,7 @@ class MetadataGenerator( object ): changeset_revision = repository_elem.get( 'changeset_revision', None ) prior_installation_required = str( repository_elem.get( 'prior_installation_required', False ) ) if self.app.name == 'galaxy': - if updating_installed_repository: + if self.updating_installed_repository: pass else: # We're installing a repository into Galaxy, so make sure its contained repository @@ -889,12 +929,12 @@ class MetadataGenerator( object ): updated_changeset_revision ) if repository: return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed # repository, so it will not yet be installed. Return the tuple for later # installation. return repository_dependency_tup, is_valid, error_message - if updating_installed_repository: + if self.updating_installed_repository: # The repository dependency was included in an update to the installed repository, # so it will not yet be installed. Return the tuple for later installation. return repository_dependency_tup, is_valid, error_message @@ -1006,6 +1046,46 @@ class MetadataGenerator( object ): return False return True + def set_changeset_revision( self, changeset_revision ): + self.changeset_revision = changeset_revision + + def set_relative_install_dir( self, relative_install_dir ): + self.relative_install_dir = relative_install_dir + + def set_repository( self, repository, relative_install_dir=None, changeset_revision=None ): + self.repository = repository + # Shed related tool panel configs are only relevant to Galaxy. + if self.app.name == 'galaxy': + if relative_install_dir is None and self.repository is not None: + tool_path, relative_install_dir = self.repository.get_tool_relative_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.changeset_revision ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = repository.get_shed_config_dict( self.app ) + self.metadata_dict = { 'shed_config_filename' : self.shed_config_dict.get( 'config_filename', None ) } + else: + if relative_install_dir is None and self.repository is not None: + relative_install_dir = repository.repo_path( self.app ) + if changeset_revision is None and self.repository is not None: + self.set_changeset_revision( self.repository.tip( self.app ) ) + else: + self.set_changeset_revision( changeset_revision ) + self.shed_config_dict = {} + self.metadata_dict = {} + self.set_relative_install_dir( relative_install_dir ) + self.set_repository_files_dir() + self.resetting_all_metadata_on_repository = False + self.updating_installed_repository = False + self.persist = False + self.invalid_file_tups = [] + + def set_repository_clone_url( self, repository_clone_url ): + self.repository_clone_url = repository_clone_url + + def set_repository_files_dir( self, repository_files_dir=None ): + self.repository_files_dir = repository_files_dir + def update_repository_dependencies_metadata( self, metadata, repository_dependency_tups, is_valid, description ): if is_valid: repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) diff --git a/lib/tool_shed/metadata/repository_metadata_manager.py b/lib/tool_shed/metadata/repository_metadata_manager.py index ecc14b7832d..b8520110ec7 100644 --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -22,8 +22,16 @@ log = logging.getLogger( __name__ ) class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): - def __init__( self, app, user ): - super( RepositoryMetadataManager, self ).__init__( app ) + def __init__( self, app, user, repository=None, changeset_revision=None, repository_clone_url=None, + shed_config_dict=None, relative_install_dir=None, repository_files_dir=None, + resetting_all_metadata_on_repository=False, updating_installed_repository=False, + persist=False, metadata_dict=None ): + super( RepositoryMetadataManager, self ).__init__( app, repository, changeset_revision, + repository_clone_url, shed_config_dict, + relative_install_dir, repository_files_dir, + resetting_all_metadata_on_repository, + updating_installed_repository, persist, + metadata_dict=metadata_dict, user=user ) self.app = app self.user = user # Repository metadata comparisons for changeset revisions. @@ -62,7 +70,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): repositories_select_field.add_option( option_label, option_value ) return repositories_select_field - def clean_repository_metadata( self, id, changeset_revisions ): + def clean_repository_metadata( self, changeset_revisions ): # Delete all repository_metadata records associated with the repository that have # a changeset_revision that is not in changeset_revisions. We sometimes see multiple # records with the same changeset revision value - no idea how this happens. We'll @@ -71,7 +79,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): changeset_revisions_checked = [] for repository_metadata in \ self.sa_session.query( self.app.model.RepositoryMetadata ) \ - .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.app.security.decode_id( id ) ) \ + .filter( self.app.model.RepositoryMetadata.table.c.repository_id == self.repository.id ) \ .order_by( self.app.model.RepositoryMetadata.table.c.changeset_revision, self.app.model.RepositoryMetadata.table.c.update_time.desc() ): changeset_revision = repository_metadata.changeset_revision @@ -79,15 +87,14 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): self.sa_session.delete( repository_metadata ) self.sa_session.flush() - def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict, - current_changeset_revision, current_metadata_dict ): + def compare_changeset_revisions( self, ancestor_changeset_revision, ancestor_metadata_dict ): """ Compare the contents of two changeset revisions to determine if a new repository metadata revision should be created. """ # The metadata associated with ancestor_changeset_revision is ancestor_metadata_dict. - # This changeset_revision is an ancestor of current_changeset_revision which is associated - # with current_metadata_dict. A new repository_metadata record will be created only + # This changeset_revision is an ancestor of self.changeset_revision which is associated + # with self.metadata_dict. A new repository_metadata record will be created only # when this method returns the constant value self.NOT_EQUAL_AND_NOT_SUBSET. ancestor_datatypes = ancestor_metadata_dict.get( 'datatypes', [] ) ancestor_tools = ancestor_metadata_dict.get( 'tools', [] ) @@ -99,16 +106,16 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): ancestor_tool_dependencies = ancestor_metadata_dict.get( 'tool_dependencies', {} ) ancestor_workflows = ancestor_metadata_dict.get( 'workflows', [] ) ancestor_data_manager = ancestor_metadata_dict.get( 'data_manager', {} ) - current_datatypes = current_metadata_dict.get( 'datatypes', [] ) - current_tools = current_metadata_dict.get( 'tools', [] ) + current_datatypes = self.metadata_dict.get( 'datatypes', [] ) + current_tools = self.metadata_dict.get( 'tools', [] ) current_guids = [ tool_dict[ 'guid' ] for tool_dict in current_tools ] current_guids.sort() - current_readme_files = current_metadata_dict.get( 'readme_files', [] ) - current_repository_dependencies_dict = current_metadata_dict.get( 'repository_dependencies', {} ) + current_readme_files = self.metadata_dict.get( 'readme_files', [] ) + current_repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) current_repository_dependencies = current_repository_dependencies_dict.get( 'repository_dependencies', [] ) - current_tool_dependencies = current_metadata_dict.get( 'tool_dependencies', {} ) - current_workflows = current_metadata_dict.get( 'workflows', [] ) - current_data_manager = current_metadata_dict.get( 'data_manager', {} ) + current_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', {} ) + current_workflows = self.metadata_dict.get( 'workflows', [] ) + current_data_manager = self.metadata_dict.get( 'data_manager', {} ) # Handle case where no metadata exists for either changeset. no_datatypes = not ancestor_datatypes and not current_datatypes no_readme_files = not ancestor_readme_files and not current_readme_files @@ -334,7 +341,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): return self.SUBSET return self.NOT_EQUAL_AND_NOT_SUBSET - def create_or_update_repository_metadata( self, id, repository, changeset_revision, metadata_dict ): + def create_or_update_repository_metadata( self, changeset_revision, metadata_dict ): """Create or update a repository_metadatqa record in the tool shed.""" has_repository_dependencies = False has_repository_dependencies_only_if_compiling_contained_td = False @@ -364,7 +371,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): downloadable = True else: downloadable = False - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + self.app.security.encode_id( self.repository.id ), + changeset_revision ) if repository_metadata: # A repository metadata record already exists with the received changeset_revision, # so we don't need to check the skip_tool_test table. @@ -381,7 +390,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # need to update the skip_tool_test table. check_skip_tool_test = True repository_metadata = \ - self.app.model.RepositoryMetadata( repository_id=repository.id, + self.app.model.RepositoryMetadata( repository_id=self.repository.id, changeset_revision=changeset_revision, metadata=metadata_dict, downloadable=downloadable, @@ -407,7 +416,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # if it is contained in the skip_tool_test table. If it is, but is not associated # with a repository_metadata record, reset that skip_tool_test record to the newly # created repository_metadata record. - repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) + repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) skip_tool_test = self.get_skip_tool_test_by_changeset_revision( changeset_hash ) @@ -531,16 +540,16 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): .filter( self.app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ .first() - def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): + def new_datatypes_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each datatype in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if - the last saved metadata record can be updated for datatypes instead. + in self.metadata_dict to determine if a new repository_metadata table record is required + or if the last saved metadata record can be updated for datatypes instead. """ # Datatypes are stored in metadata as a list of dictionaries that looks like: # [{'dtype': 'galaxy.datatypes.data:Text', 'subclass': 'True', 'extension': 'acedb'}] - if 'datatypes' in metadata_dict: - current_datatypes = metadata_dict[ 'datatypes' ] + if 'datatypes' in self.metadata_dict: + current_datatypes = self.metadata_dict[ 'datatypes' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -564,37 +573,31 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for datatypes, so a new repository_metadata + # self.metadata_dict includes no metadata for datatypes, so a new repository_metadata # table record is not needed. return False - def new_metadata_required_for_utilities( self, repository, new_tip_metadata_dict ): + def new_metadata_required_for_utilities( self ): """ - Galaxy utilities currently consist of datatypes, repository_dependency definitions, - tools, tool_dependency definitions and exported Galaxy workflows. This method compares - the last stored repository_metadata record associated with the received repository against - the contents of the received new_tip_metadata_dict and returns True or False for the union - set of Galaxy utilities contained in both metadata dictionaries. The metadata contained - in new_tip_metadata_dict may not be a subset of that contained in the last stored - repository_metadata record associated with the received repository because one or more - Galaxy utilities may have been deleted from the repository in the new tip. + This method compares the last stored repository_metadata record associated with self.repository + against the contents of self.metadata_dict and returns True or False for the union set of Galaxy + utilities contained in both metadata dictionaries. The metadata contained in self.metadata_dict + may not be a subset of that contained in the last stored repository_metadata record associated with + self.repository because one or more Galaxy utilities may have been deleted from self.repository in + the new tip. """ repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) - datatypes_required = self.new_datatypes_metadata_required( repository_metadata, - new_tip_metadata_dict ) + datatypes_required = self.new_datatypes_metadata_required( repository_metadata ) # Uncomment the following if we decide that README files should affect how installable # repository revisions are defined. See the NOTE in the compare_readme_files() method. - # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata, - # new_tip_metadata_dict ) + # readme_files_required = sewlf.new_readme_files_metadata_required( repository_metadata ) repository_dependencies_required = \ - self.new_repository_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - tools_required = self.new_tool_metadata_required( repository_metadata, new_tip_metadata_dict ) - tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata, - new_tip_metadata_dict ) - workflows_required = self.new_workflow_metadata_required( repository_metadata, new_tip_metadata_dict ) + self.new_repository_dependency_metadata_required( repository_metadata ) + tools_required = self.new_tool_metadata_required( repository_metadata ) + tool_dependencies_required = self.new_tool_dependency_metadata_required( repository_metadata ) + workflows_required = self.new_workflow_metadata_required( repository_metadata ) if datatypes_required or \ repository_dependencies_required or \ tools_required or \ @@ -603,17 +606,17 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): return True return False - def new_readme_files_metadata_required( self, repository_metadata, metadata_dict ): + def new_readme_files_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each readme file in the repository with the new metadata - in metadata_dict to determine if a new repository_metadata table record is required or if the - last saved metadata record can be updated for readme files instead. + in self.metadata_dict to determine if a new repository_metadata table record is required or + if the last saved metadata record can be updated for readme files instead. """ # Repository README files are kind of a special case because they have no effect on reproducibility. # We'll simply inspect the file names to determine if any that exist in the saved metadata are - # eliminated from the new metadata in the received metadata_dict. - if 'readme_files' in metadata_dict: - current_readme_files = metadata_dict[ 'readme_files' ] + # eliminated from the new metadata in self.metadata_dict. + if 'readme_files' in self.metadata_dict: + current_readme_files = self.metadata_dict[ 'readme_files' ] if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -638,14 +641,14 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for readme_files, so a new repository_metadata + # self.metadata_dict includes no metadata for readme_files, so a new repository_metadata # table record is not needed. return False - def new_repository_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_repository_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each repository dependency in the repository - with the new metadata in metadata_dict to determine if a new repository_metadata + with the new metadata in self.metadata_dict to determine if a new repository_metadata table record is required or if the last saved metadata record can be updated for repository_dependencies instead. """ @@ -653,9 +656,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): metadata = repository_metadata.metadata if 'repository_dependencies' in metadata: saved_repository_dependencies = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] - new_repository_dependencies_metadata = metadata_dict.get( 'repository_dependencies', None ) + new_repository_dependencies_metadata = self.metadata_dict.get( 'repository_dependencies', None ) if new_repository_dependencies_metadata: - new_repository_dependencies = metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] + new_repository_dependencies = self.metadata_dict[ 'repository_dependencies' ][ 'repository_dependencies' ] # TODO: We used to include the following here to handle the case where repository # dependency definitions were deleted. However this erroneously returned True in # cases where is should not have done so. This usually occurred where multiple single @@ -682,21 +685,21 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): else: return False else: - if 'repository_dependencies' in metadata_dict: + if 'repository_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata record. return True else: - # The received metadata_dict includes no metadata for repository dependencies, so - # a new repository_metadata record is not needed. + # self.metadata_dict includes no metadata for repository dependencies, so a new repository_metadata + # record is not needed. return False - def new_tool_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool in the repository with the new metadata in - metadata_dict to determine if a new repository_metadata table record is required, or if + self.metadata_dict to determine if a new repository_metadata table record is required, or if the last saved metadata record can be updated instead. """ - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -704,9 +707,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): saved_tool_ids = [] # The metadata for one or more tools was successfully generated in the past # for this repository, so we first compare the version string for each tool id - # in metadata_dict with what was previously saved to see if we need to create + # in self.metadata_dict with what was previously saved to see if we need to create # a new table record or if we can simply update the existing record. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: for saved_tool_metadata_dict in metadata[ 'tools' ]: if saved_tool_metadata_dict[ 'id' ] not in saved_tool_ids: saved_tool_ids.append( saved_tool_metadata_dict[ 'id' ] ) @@ -714,10 +717,10 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): if new_tool_metadata_dict[ 'version' ] != saved_tool_metadata_dict[ 'version' ]: return True # So far, a new metadata record is not required, but we still have to check to see if - # any new tool ids exist in metadata_dict that are not in the saved metadata. We do + # any new tool ids exist in self.metadata_dict that are not in the saved metadata. We do # this because if a new tarball was uploaded to a repository that included tools, it # may have removed existing tool files if they were not included in the uploaded tarball. - for new_tool_metadata_dict in metadata_dict[ 'tools' ]: + for new_tool_metadata_dict in self.metadata_dict[ 'tools' ]: if new_tool_metadata_dict[ 'id' ] not in saved_tool_ids: return True return False @@ -733,22 +736,22 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # There is no stored repository metadata, so we need to create a new repository_metadata # table record. return True - # The received metadata_dict includes no metadata for tools, so a new repository_metadata table + # self.metadata_dict includes no metadata for tools, so a new repository_metadata table # record is not needed. return False - def new_tool_dependency_metadata_required( self, repository_metadata, metadata_dict ): + def new_tool_dependency_metadata_required( self, repository_metadata ): """ Compare the last saved metadata for each tool dependency in the repository with the new - metadata in metadata_dict to determine if a new repository_metadata table record is required - or if the last saved metadata record can be updated for tool_dependencies instead. + metadata in self.metadata_dict to determine if a new repository_metadata table record is + required or if the last saved metadata record can be updated for tool_dependencies instead. """ if repository_metadata: metadata = repository_metadata.metadata if metadata: if 'tool_dependencies' in metadata: saved_tool_dependencies = metadata[ 'tool_dependencies' ] - new_tool_dependencies = metadata_dict.get( 'tool_dependencies', None ) + new_tool_dependencies = self.metadata_dict.get( 'tool_dependencies', None ) if new_tool_dependencies: # TODO: We used to include the following here to handle the case where # tool dependency definitions were deleted. However, this erroneously @@ -777,22 +780,22 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # in the repository, so we can update the existing repository metadata. return False else: - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: # There is no saved repository metadata, so we need to create a new repository_metadata # record. return True else: - # The received metadata_dict includes no metadata for tool dependencies, so a new - # repository_metadata record is not needed. + # self.metadata_dict includes no metadata for tool dependencies, so a new repository_metadata + # record is not needed. return False - def new_workflow_metadata_required( self, repository_metadata, metadata_dict ): + def new_workflow_metadata_required( self, repository_metadata ): """ Currently everything about an exported workflow except the name is hard-coded, so there's no real way to differentiate versions of exported workflows. If this changes at some future time, this method should be enhanced accordingly. """ - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: if repository_metadata: # The repository has metadata, so update the workflows value - # no new record is needed. @@ -801,17 +804,17 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # There is no saved repository metadata, so we need to create a # new repository_metadata table record. return True - # The received metadata_dict includes no metadata for workflows, so a new + # self.metadata_dict includes no metadata for workflows, so a new # repository_metadata table record is not needed. return False - def reset_all_metadata_on_repository_in_tool_shed( self, id ): + def reset_all_metadata_on_repository_in_tool_shed( self ): """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( self.user, repository ) + log.debug( "Resetting all metadata on repository: %s" % self.repository.name ) + repo = hg_util.get_repo_for_repository( self.app, + repository=None, + repo_path=self.repository.repo_path( self.app ), + create=False ) # 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. @@ -822,33 +825,22 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): metadata_dict = None ancestor_changeset_revision = None ancestor_metadata_dict = None - invalid_file_tups = [] - for changeset in repository.get_changesets_for_setting_metadata( self.app ): + for changeset in self.repository.get_changesets_for_setting_metadata( self.app ): work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-ramorits" ) - current_changeset_revision = str( repo.changectx( changeset ) ) ctx = repo.changectx( changeset ) log.debug( "Cloning repository changeset revision: %s", str( ctx.rev() ) ) - cloned_ok, error_message = hg_util.clone_repository( repository_clone_url, work_dir, str( ctx.rev() ) ) + cloned_ok, error_message = hg_util.clone_repository( self.repository_clone_url, work_dir, str( ctx.rev() ) ) if cloned_ok: log.debug( "Generating metadata for changset revision: %s", str( ctx.rev() ) ) - current_metadata_dict, invalid_tups = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=current_changeset_revision, - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=work_dir, - resetting_all_metadata_on_repository=True, - updating_installed_repository=False, - persist=False ) - # We'll only display error messages for the repository tip (it may be better to display error - # messages for each installable changeset revision). - if current_changeset_revision == repository.tip( self.app ): - invalid_file_tups.extend( invalid_tups ) - if current_metadata_dict: + self.set_changeset_revision( str( repo.changectx( changeset ) ) ) + self.set_relative_install_dir( work_dir ) + self.set_repository_files_dir( work_dir ) + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: if metadata_changeset_revision is None and metadata_dict is None: # We're at the first change set in the change log. - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict if ancestor_changeset_revision: # Compare metadata from ancestor and current. The value of comparison will be one of: # self.NO_METADATA - no metadata for either ancestor or current, so continue from current @@ -856,66 +848,56 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # self.SUBSET - ancestor metadata is a subset of current metadata, so continue from current # self.NOT_EQUAL_AND_NOT_SUBSET - ancestor metadata is neither equal to nor a subset of current # metadata, so persist ancestor metadata. - comparison = self.compare_changeset_revisions( ancestor_changeset_revision, - ancestor_metadata_dict, - current_changeset_revision, - current_metadata_dict ) + comparison = self.compare_changeset_revisions( ancestor_changeset_revision, ancestor_metadata_dict ) if comparison in [ self.NO_METADATA, self.EQUAL, self.SUBSET ]: - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict elif comparison == self.NOT_EQUAL_AND_NOT_SUBSET: metadata_changeset_revision = ancestor_changeset_revision metadata_dict = ancestor_metadata_dict - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict else: # We're at the beginning of the change log. - ancestor_changeset_revision = current_changeset_revision - ancestor_metadata_dict = current_metadata_dict + ancestor_changeset_revision = self.changeset_revision + ancestor_metadata_dict = self.metadata_dict if not ctx.children(): - metadata_changeset_revision = current_changeset_revision - metadata_dict = current_metadata_dict + metadata_changeset_revision = self.changeset_revision + metadata_dict = self.metadata_dict # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None elif ancestor_metadata_dict: - # We reach here only if current_metadata_dict is empty and ancestor_metadata_dict is not. + # We reach here only if self.metadata_dict is empty and ancestor_metadata_dict is not. if not ctx.children(): # We're at the end of the change log. - repository_metadata = self.create_or_update_repository_metadata( id, - repository, - metadata_changeset_revision, - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( metadata_changeset_revision, metadata_dict ) changeset_revisions.append( metadata_changeset_revision ) ancestor_changeset_revision = None ancestor_metadata_dict = None basic_util.remove_dir( work_dir ) # Delete all repository_metadata records for this repository that do not have a changeset_revision # value in changeset_revisions. - self.clean_repository_metadata( id, changeset_revisions ) + self.clean_repository_metadata( changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset # revisions from the changelog. - self.reset_all_tool_versions( id, repo ) + self.reset_all_tool_versions( repo ) # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} - return invalid_file_tups, metadata_dict - def reset_all_tool_versions( self, id, repo ): + def reset_all_tool_versions( self, repo ): """Reset tool version lineage for those changeset revisions that include valid tools.""" + encoded_repository_id = self.app.security.encode_id( self.repository.id ) changeset_revisions_that_contain_tools = [] for changeset in repo.changelog: changeset_revision = str( repo.changectx( changeset ) ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) if repository_metadata: metadata = repository_metadata.metadata if metadata: @@ -926,7 +908,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): # { 'tool id' : 'parent tool id' } pairs for each tool in each changeset revision. for index, changeset_revision in enumerate( changeset_revisions_that_contain_tools ): tool_versions_dict = {} - repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, id, changeset_revision ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, + encoded_repository_id, + changeset_revision ) metadata = repository_metadata.metadata tool_dicts = metadata[ 'tools' ] if index == 0: @@ -937,7 +921,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): tool_versions_dict[ tool_dict[ 'guid' ] ] = tool_dict[ 'id' ] else: for tool_dict in tool_dicts: - parent_id = self.get_parent_id( id, + parent_id = self.get_parent_id( encoded_repository_id, tool_dict[ 'id' ], tool_dict[ 'version' ], tool_dict[ 'guid' ], @@ -962,11 +946,11 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): for repository_id in repository_ids: try: repository = suc.get_repository_in_tool_shed( self.app, repository_id ) - invalid_file_tups, metadata_dict = \ - self.reset_all_metadata_on_repository_in_tool_shed( repository_id ) - if invalid_file_tups: + self.set_repository( repository ) + self.reset_all_metadata_on_repository_in_tool_shed() + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, + self.invalid_file_tups, repository, None, as_html=False ) @@ -974,7 +958,7 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): unsuccessful_count += 1 else: log.debug( "Successfully reset metadata on repository %s owned by %s" % \ - ( str( repository.name ), str( repository.user.username ) ) ) + ( str( repository.name ), str( repository.user.username ) ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s" % str( repository.name ) ) @@ -989,75 +973,68 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): status = 'error' return message, status - def set_repository_metadata( self, host, repository, content_alert_str='', **kwd ): + def set_repository( self, repository ): + super( RepositoryMetadataManager, self ).set_repository( repository ) + self.repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( self.user, repository ) + + def set_repository_metadata( self, host, content_alert_str='', **kwd ): """ - Set metadata using the repository's current disk files, returning specific error + Set metadata using the self.repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset has problems. """ 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( self.user, repository ) - repo_dir = repository.repo_path( self.app ) + encoded_id = self.app.security.encode_id( self.repository.id ) + repo_dir = self.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 = \ - self.generate_metadata_for_changeset_revision( repository=repository, - changeset_revision=repository.tip( self.app ), - repository_clone_url=repository_clone_url, - relative_install_dir=repo_dir, - repository_files_dir=None, - resetting_all_metadata_on_repository=False, - updating_installed_repository=False, - persist=False ) - if metadata_dict: + self.generate_metadata_for_changeset_revision() + if self.metadata_dict: repository_metadata = None - repository_type_class = self.app.repository_types_registry.get_class_by_label( repository.type ) + repository_type_class = self.app.repository_types_registry.get_class_by_label( self.repository.type ) tip_only = isinstance( repository_type_class, TipOnly ) - if not tip_only and self.new_metadata_required_for_utilities( repository, metadata_dict ): + if not tip_only and self.new_metadata_required_for_utilities(): # Create a new repository_metadata table row. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) # If this is the first record stored for this repository, see if we need to send any email alerts. - if len( repository.downloadable_revisions ) == 1: + if len( self.repository.downloadable_revisions ) == 1: suc.handle_email_alerts( self.app, host, - repository, + self.repository, content_alert_str='', new_repo_alert=True, admin_only=False ) else: - # Update the latest stored repository metadata with the contents and attributes of metadata_dict. + # Update the latest stored repository metadata with the contents and attributes of self.metadata_dict. repository_metadata = metadata_util.get_latest_repository_metadata( self.app, - repository.id, + self.repository.id, downloadable=False ) if repository_metadata: - downloadable = metadata_util.is_downloadable( metadata_dict ) + downloadable = metadata_util.is_downloadable( self.metadata_dict ) # Update the last saved repository_metadata table row. - repository_metadata.changeset_revision = repository.tip( self.app ) - repository_metadata.metadata = metadata_dict + repository_metadata.changeset_revision = self.repository.tip( self.app ) + repository_metadata.metadata = self.metadata_dict repository_metadata.downloadable = downloadable - if 'datatypes' in metadata_dict: + if 'datatypes' in self.metadata_dict: repository_metadata.includes_datatypes = True else: repository_metadata.includes_datatypes = False # We don't store information about the special type of repository dependency that is needed only for # compiling a tool dependency defined for the dependent repository. - repository_dependencies_dict = metadata_dict.get( 'repository_dependencies', {} ) + repository_dependencies_dict = self.metadata_dict.get( 'repository_dependencies', {} ) repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ suc.get_repository_dependency_types( repository_dependencies ) repository_metadata.has_repository_dependencies = has_repository_dependencies - if 'tool_dependencies' in metadata_dict: + if 'tool_dependencies' in self.metadata_dict: repository_metadata.includes_tool_dependencies = True else: repository_metadata.includes_tool_dependencies = False - if 'tools' in metadata_dict: + if 'tools' in self.metadata_dict: repository_metadata.includes_tools = True else: repository_metadata.includes_tools = False - if 'workflows' in metadata_dict: + if 'workflows' in self.metadata_dict: repository_metadata.includes_workflows = True else: repository_metadata.includes_workflows = False @@ -1070,11 +1047,9 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): self.sa_session.flush() else: # There are no metadata records associated with the repository. - repository_metadata = self.create_or_update_repository_metadata( encoded_id, - repository, - repository.tip( self.app ), - metadata_dict ) - if 'tools' in metadata_dict and repository_metadata and status != 'error': + repository_metadata = self.create_or_update_repository_metadata( self.repository.tip( self.app ), + self.metadata_dict ) + if 'tools' in self.metadata_dict and repository_metadata and status != 'error': # Set tool versions on the new downloadable change set. The order of the list of changesets is # critical, so we use the repo's changelog. changeset_revisions = [] @@ -1083,25 +1058,22 @@ class RepositoryMetadataManager( metadata_generator.MetadataGenerator ): if suc.get_repository_metadata_by_changeset_revision( self.app, encoded_id, changeset_revision ): changeset_revisions.append( changeset_revision ) self.add_tool_versions( encoded_id, repository_metadata, changeset_revisions ) - elif len( repo ) == 1 and not invalid_file_tups: + elif len( repo ) == 1 and not self.invalid_file_tups: message = "Revision %s includes no Galaxy utilities for which metadata can " % \ - str( repository.tip( self.app ) ) + str( self.repository.tip( self.app ) ) message += "be defined so this revision cannot be automatically installed into a local Galaxy instance." status = "error" - if invalid_file_tups: + if self.invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( self.app, - invalid_file_tups, - repository, - metadata_dict ) + self.invalid_file_tups, + self.repository, + self.metadata_dict ) status = 'error' # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. self.app.tool_data_tables.data_tables = {} return message, status - 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, - repository, - content_alert_str=content_alert_str, - **kwd ) + def set_repository_metadata_due_to_new_tip( self, host, content_alert_str=None, **kwd ): + """Set metadata on the tip of self.repository in the tool shed.""" + error_message, status = self.set_repository_metadata( host, content_alert_str=content_alert_str, **kwd ) return status, error_message From 9e81adc5e6d32f726223720841cb5c863749e83e Mon Sep 17 00:00:00 2001 From: Lance Parsons Date: Thu, 4 Sep 2014 15:22:10 -0400 Subject: [PATCH 02/10] Allow local IGV users to visualize custom genomes --- display_applications/igv/bam.xml | 10 +++++++--- display_applications/igv/vcf.xml | 10 +++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/display_applications/igv/bam.xml b/display_applications/igv/bam.xml index c147894f1cd..1e7058e01c9 100644 --- a/display_applications/igv/bam.xml +++ b/display_applications/igv/bam.xml @@ -12,15 +12,19 @@ - ${dataset.dbkey in $site_dbkeys} - + ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys} + ${redirect_url} - $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bam_file.dbkey ) ] + #else: + $bam_file.dbkey + #end if <?xml version="1.0" encoding="utf-8"?> diff --git a/display_applications/igv/vcf.xml b/display_applications/igv/vcf.xml index 39d6700d503..a9276745b0c 100644 --- a/display_applications/igv/vcf.xml +++ b/display_applications/igv/vcf.xml @@ -12,15 +12,19 @@ - ${dataset.dbkey in $site_dbkeys} - + ${$site_id.startswith( 'local_' ) or $dataset.dbkey in $site_dbkeys} + ${redirect_url} - $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #if ($dataset.dbkey in $site_dbkeys) + $site_organisms[ $site_dbkeys.index( $bgzip_file.dbkey ) ] + #else: + $bgzip_file.dbkey + #end if <?xml version="1.0" encoding="utf-8"?> From 7ac2ae2f6d242233c850e1dafa1d373f877b41cf Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Fri, 12 Sep 2014 19:45:06 -0400 Subject: [PATCH 03/10] Prevent double submission of workflow. --- static/scripts/galaxy.base.js | 20 ++++++++++++++++++++ templates/webapps/galaxy/workflow/run.mako | 2 +- 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js index b2b621d9a2c..8e2e9c23347 100644 --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -593,6 +593,26 @@ function init_refresh_on_change () { }); }; + +// jQuery plugin to prevent double submission of forms +// Ref: http://stackoverflow.com/questions/2830542/prevent-double-submission-of-forms-in-jquery +jQuery.fn.preventDoubleSubmission = function() { + $(this).on('submit',function(e){ + var $form = $(this); + + if ($form.data('submitted') === true) { + // Previously submitted - don't submit again + e.preventDefault(); + } else { + // Mark it so that the next submit can be ignored + $form.data('submitted', true); + } + }); + + // Keep chainability + return this; +}; + $(document).ready( function() { // Refresh events for form fields. diff --git a/templates/webapps/galaxy/workflow/run.mako b/templates/webapps/galaxy/workflow/run.mako index 690d1ee21e1..6e42c5a9638 100644 --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -218,7 +218,7 @@ } }); }); - $("#tool_form").submit(function(e) { + $("#tool_form").preventDoubleSubmission().submit(function(e) { var matchLength = -1; $('span.multiinput_wrap select[name*="|input"]').each(function() { var value = $(this).val(); 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    ")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("None")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").off("change").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").off("click").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").off("click").click(function(){return confirm($(this).attr("confirm"))})}jQuery.fn.preventDoubleSubmission=function(){$(this).on("submit",function(b){var a=$(this);if(a.data("submitted")===true){b.preventDefault()}else{a.data("submitted",true)}});return this};$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip()}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file From 92f51b8eb9780890806eae80ac3e3175e5ec1d59 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 15 Sep 2014 14:58:14 -0400 Subject: [PATCH 05/10] Fix for handling unvalidated values in select lists. Addresses https://trello.com/c/5DKHp4ck --- lib/galaxy/tools/parameters/basic.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 225fc37f1b7..e3861c872d3 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -794,6 +794,8 @@ class SelectToolParameter( ToolParameter ): if value is not None: if not isinstance( value, list ): value = [ value ] + # We could have an unvalidated value here when e.g. running a workflow. + value = [ val.value if isinstance( val, UnvalidatedValue ) else val for val in value ] field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: From 430656023723571cdaf8fca3347ba2ad96081e32 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 15 Sep 2014 15:34:03 -0400 Subject: [PATCH 06/10] Remove unused "Main" versions of cleanup convenienence wrappers. --- scripts/cleanup_datasets/delete_datasets_main.sh | 4 ---- scripts/cleanup_datasets/delete_userless_histories_main.sh | 4 ---- scripts/cleanup_datasets/purge_datasets_main.sh | 4 ---- scripts/cleanup_datasets/purge_folders_main.sh | 4 ---- scripts/cleanup_datasets/purge_histories_main.sh | 4 ---- scripts/cleanup_datasets/purge_libraries_main.sh | 4 ---- 6 files changed, 24 deletions(-) delete mode 100644 scripts/cleanup_datasets/delete_datasets_main.sh delete mode 100644 scripts/cleanup_datasets/delete_userless_histories_main.sh delete mode 100644 scripts/cleanup_datasets/purge_datasets_main.sh delete mode 100644 scripts/cleanup_datasets/purge_folders_main.sh delete mode 100644 scripts/cleanup_datasets/purge_histories_main.sh delete mode 100644 scripts/cleanup_datasets/purge_libraries_main.sh diff --git a/scripts/cleanup_datasets/delete_datasets_main.sh b/scripts/cleanup_datasets/delete_datasets_main.sh deleted file mode 100644 index ea27a8940ad..00000000000 --- a/scripts/cleanup_datasets/delete_datasets_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -6 -r $@ >> ./scripts/cleanup_datasets/delete_datasets.log diff --git a/scripts/cleanup_datasets/delete_userless_histories_main.sh b/scripts/cleanup_datasets/delete_userless_histories_main.sh deleted file mode 100644 index fdfca81f9c8..00000000000 --- a/scripts/cleanup_datasets/delete_userless_histories_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -1 $@ >> ./scripts/cleanup_datasets/delete_userless_histories.log diff --git a/scripts/cleanup_datasets/purge_datasets_main.sh b/scripts/cleanup_datasets/purge_datasets_main.sh deleted file mode 100644 index 33f29b1487a..00000000000 --- a/scripts/cleanup_datasets/purge_datasets_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -3 -r $@ >> ./scripts/cleanup_datasets/purge_datasets.log diff --git a/scripts/cleanup_datasets/purge_folders_main.sh b/scripts/cleanup_datasets/purge_folders_main.sh deleted file mode 100644 index 3cc832c7b68..00000000000 --- a/scripts/cleanup_datasets/purge_folders_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -5 -r $@ >> ./scripts/cleanup_datasets/purge_folders.log diff --git a/scripts/cleanup_datasets/purge_histories_main.sh b/scripts/cleanup_datasets/purge_histories_main.sh deleted file mode 100644 index 29f8037705c..00000000000 --- a/scripts/cleanup_datasets/purge_histories_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -2 -r $@ >> ./scripts/cleanup_datasets/purge_histories.log diff --git a/scripts/cleanup_datasets/purge_libraries_main.sh b/scripts/cleanup_datasets/purge_libraries_main.sh deleted file mode 100644 index 83968f12c65..00000000000 --- a/scripts/cleanup_datasets/purge_libraries_main.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0`/../.. -python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 60 -4 -r $@ >> ./scripts/cleanup_datasets/purge_libraries.log From f7498a9b9253d9da6da81752b9db92e9960e25b4 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 15 Sep 2014 15:53:39 -0400 Subject: [PATCH 07/10] Remove old messaging code. --- run_galaxy_listener.sh | 4 - .../galaxy_messaging/client/amqp_publisher.py | 100 -------- .../client/galaxy_amq.ini.sample | 33 --- .../galaxy_messaging/client/report.bat.sample | 1 - .../galaxy_messaging/client/scan.bat.sample | 1 - .../galaxy_messaging/client/scan.sh.sample | 1 - scripts/galaxy_messaging/client/scanner.py | 92 ------- .../client/scanner_interface.py | 76 ------ .../galaxy_messaging/server/amqp_consumer.py | 164 ------------ .../galaxy_messaging/server/data_transfer.py | 239 ------------------ .../server/galaxydb_interface.py | 167 ------------ .../galaxy_messaging/server/setup_rabbitmq.py | 38 --- scripts/galaxy_messaging/server/xml_helper.py | 28 -- setup_rabbitmq.sh | 4 - 14 files changed, 948 deletions(-) delete mode 100644 run_galaxy_listener.sh delete mode 100644 scripts/galaxy_messaging/client/amqp_publisher.py delete mode 100644 scripts/galaxy_messaging/client/galaxy_amq.ini.sample delete mode 100644 scripts/galaxy_messaging/client/report.bat.sample delete mode 100644 scripts/galaxy_messaging/client/scan.bat.sample delete mode 100644 scripts/galaxy_messaging/client/scan.sh.sample delete mode 100644 scripts/galaxy_messaging/client/scanner.py delete mode 100644 scripts/galaxy_messaging/client/scanner_interface.py delete mode 100644 scripts/galaxy_messaging/server/amqp_consumer.py delete mode 100755 scripts/galaxy_messaging/server/data_transfer.py delete mode 100644 scripts/galaxy_messaging/server/galaxydb_interface.py delete mode 100644 scripts/galaxy_messaging/server/setup_rabbitmq.py delete mode 100644 scripts/galaxy_messaging/server/xml_helper.py delete mode 100644 setup_rabbitmq.sh diff --git a/run_galaxy_listener.sh b/run_galaxy_listener.sh deleted file mode 100644 index 754d7e34bfd..00000000000 --- a/run_galaxy_listener.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python scripts/galaxy_messaging/server/amqp_consumer.py --config-file=universe_wsgi.ini --http-server-section=server:main 2>&1 \ No newline at end of file diff --git a/scripts/galaxy_messaging/client/amqp_publisher.py b/scripts/galaxy_messaging/client/amqp_publisher.py deleted file mode 100644 index 4d822ff1140..00000000000 --- a/scripts/galaxy_messaging/client/amqp_publisher.py +++ /dev/null @@ -1,100 +0,0 @@ -''' -This script gets barcode data from a barcode scanner using serial communication -and sends the state representated by the barcode scanner & the barcode string -to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, -barcode & state. The state of the scanner should be set in the galaxy_amq.ini -file as a configuration variable. -''' - -import array -import ConfigParser -import optparse -import os -import serial -import sys -import time - -from galaxy import eggs -eggs.require("amqp") - -import amqp - - -xml = \ -''' - %(BARCODE)s - %(STATE)s - %(API_KEY)s - ''' - - -def handle_scan(states, amqp_config, barcode): - if states.get(barcode[:2], None): - values = dict( BARCODE=barcode[2:], - STATE=states.get(barcode[:2]), - API_KEY=amqp_config['api_key'] ) - print values - data = xml % values - print data - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'],) - - chan = conn.channel() - msg = amqp.Message(data, - content_type='text/plain', - application_headers={'msg_type': 'sample_state_update'}) - msg.properties["delivery_mode"] = 2 - chan.basic_publish(msg, - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) - chan.close() - conn.close() - -def recv_data(states, amqp_config, s): - while True: - bytes = s.inWaiting() - if bytes: - print '%i bytes recvd' % bytes - msg = s.read(bytes) - print msg - handle_scan(states, amqp_config, msg.strip()) - - -def main(): - parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', - dest='config_file', action='store') - parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', - dest='port', action='store') - (opts, args) = parser.parse_args() - config = ConfigParser.ConfigParser() - config.read(opts.config_file) - amqp_config = {} - states = {} - for option in config.options("galaxy:amqp"): - amqp_config[option] = config.get("galaxy:amqp", option) - # abort if api_key is not set in the config file - if not amqp_config['api_key']: - print 'Error: Set the api_key config variable in the config file before starting the amqp_publisher script.' - sys.exit( 1 ) - count = 1 - while True: - section = 'scanner%i' % count - if config.has_section(section): - states[config.get(section, 'prefix')] = config.get(section, 'state') - count = count + 1 - else: - break - print amqp_config - print states - s = serial.Serial(int(opts.port)) - print 'Port %s is open: %s' %( opts.port, s.isOpen()) - recv_data(states, amqp_config, s) - s.close() - print 'Port %s is open: %s' %( opts.port, s.isOpen()) - - -if __name__ == '__main__': - main() diff --git a/scripts/galaxy_messaging/client/galaxy_amq.ini.sample b/scripts/galaxy_messaging/client/galaxy_amq.ini.sample deleted file mode 100644 index 9526eac7cfd..00000000000 --- a/scripts/galaxy_messaging/client/galaxy_amq.ini.sample +++ /dev/null @@ -1,33 +0,0 @@ -# Galaxy Message Queue -# Galaxy uses AMQ protocol to receive messages from external sources like -# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -# For Galaxy to receive messages from a message queue the RabbitMQ server has -# to be set up with a user account and other parameters listed below. The 'host' -# and 'port' fields should point to where the RabbitMQ server is running. - -#[galaxy:amqp] -#host = 127.0.0.1 -#port = 5672 -#userid = galaxy -#password = galaxy -#virtual_host = galaxy_messaging_engine -#queue = galaxy_queue -#exchange = galaxy_exchange -#routing_key = bar_code_scanner -#api_key = - -# The following section(s) 'scanner#' is for specifying the state of the -# sample this scanner represents. This state name should be one of the -# possible states created for this request type in Galaxy -# If there multiple scanners attached to this host the add as many "scanner#" -# sections below each with the name & prefix of the bar code scanner and -# the state it represents -#[scanner1] -#name = -#state = -#prefix = - -#[scanner2] -#name = -#state = -#prefix = \ No newline at end of file diff --git a/scripts/galaxy_messaging/client/report.bat.sample b/scripts/galaxy_messaging/client/report.bat.sample deleted file mode 100644 index c35de51a8a8..00000000000 --- a/scripts/galaxy_messaging/client/report.bat.sample +++ /dev/null @@ -1 +0,0 @@ -python scanner.py -p 2 -c galaxy_amq.ini -r \ No newline at end of file diff --git a/scripts/galaxy_messaging/client/scan.bat.sample b/scripts/galaxy_messaging/client/scan.bat.sample deleted file mode 100644 index 7c5d6f8cedd..00000000000 --- a/scripts/galaxy_messaging/client/scan.bat.sample +++ /dev/null @@ -1 +0,0 @@ -python amqp_publisher.py -p 2 -c galaxy_amq.ini \ No newline at end of file diff --git a/scripts/galaxy_messaging/client/scan.sh.sample b/scripts/galaxy_messaging/client/scan.sh.sample deleted file mode 100644 index 59c61ea03e4..00000000000 --- a/scripts/galaxy_messaging/client/scan.sh.sample +++ /dev/null @@ -1 +0,0 @@ -python amqp_publisher.py -p 3 -c galaxy_amq.ini \ No newline at end of file diff --git a/scripts/galaxy_messaging/client/scanner.py b/scripts/galaxy_messaging/client/scanner.py deleted file mode 100644 index 2a7c5ea5fdb..00000000000 --- a/scripts/galaxy_messaging/client/scanner.py +++ /dev/null @@ -1,92 +0,0 @@ -import sys, os -import serial -import array -import time -import optparse -import ConfigParser, logging -from scanner_interface import ScannerInterface - -logging.basicConfig(level=logging.DEBUG) -log = logging.getLogger( 'Scanner' ) - -# command prefix: SYN M CR -cmd = [22, 77, 13] -response = { 6: 'ACK', 5: 'ENQ', 21: 'NAK' } -image_scanner_report = 'RPTSCN.' -get_prefix1 = 'PREBK2?.' -get_prefix2 = ':4820:PREBK2?.' -set_prefix = 'PREBK2995859.' -clear_prefix = 'PRECA2.' - -def get_prefix_cmd(name): - return ':' + name + ':' + 'PREBK2?.' - -def set_prefix_cmd(name, prefix): - prefix_str = '' - for c in prefix: - prefix_str = prefix_str + hex(ord(c))[2:] - return ':' + name + ':' + 'PREBK299' + prefix_str + '!' - -def read_config_file(config_file): - config = ConfigParser.ConfigParser() - config.read(config_file) - count = 1 - scanners_list = [] - while True: - section = 'scanner%i' % count - if config.has_section(section): - scanner = dict(name=config.get(section, 'name'), - prefix=config.get(section, 'prefix'), - state=config.get(section, 'state')) - scanners_list.append(scanner) - count = count + 1 - else: - return scanners_list - -def main(): - usage = "python %s -p PORT -c CONFIG_FILE [ OPTION ]" % sys.argv[0] - parser = optparse.OptionParser(usage=usage) - parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', - dest='port', action='store') - parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', - dest='config_file', action='store') - parser.add_option('-r', '--report', help='scanner report', - dest='report', action='store_true', default=False) - parser.add_option('-i', '--install', help='install the scanners', - dest='install', action='store_true', default=False) - (opts, args) = parser.parse_args() - # validate - if not opts.port: - parser.print_help() - sys.exit(0) - if ( opts.report or opts.install ) and not opts.config_file: - parser.print_help() - sys.exit(0) - - # create the scanner interface - si = ScannerInterface(opts.port) - if opts.install: - scanners_list = read_config_file(opts.config_file) - for scanner in scanners_list: - msg = set_prefix_cmd(scanner['name'], scanner['prefix']) - si.send(msg) - response = si.recv() - if not response: - log.error("Scanner %s could not be installed." % scanner['name']) - elif opts.report: - si.send(image_scanner_report) - rep = si.recv() - log.info(rep) - scanners_list = read_config_file(opts.config_file) - for scanner in scanners_list: - msg = get_prefix_cmd(scanner['name']) - si.send(msg) - response = si.recv() - if response: - log.info('PREFIX for scanner %s: %s' % (scanner['name'], chr(int(response[8:12][:2], 16))+chr(int(response[8:12][2:], 16)) )) - si.close() - - - -if __name__ == "__main__": - main() diff --git a/scripts/galaxy_messaging/client/scanner_interface.py b/scripts/galaxy_messaging/client/scanner_interface.py deleted file mode 100644 index 8598f002a8e..00000000000 --- a/scripts/galaxy_messaging/client/scanner_interface.py +++ /dev/null @@ -1,76 +0,0 @@ -import sys, os -import serial -import array -import time -import optparse -import ConfigParser -import logging - -logging.basicConfig(level=logging.INFO) -log = logging.getLogger( 'ScannerInterface' ) - -class ScannerInterface( object ): - cmdprefix = [22, 77, 13] - response = { 6: 'ACK', 5: 'ENQ', 21: 'NAK' } - - def __init__( self, port ): - if os.name in ['posix', 'mac']: - self.port = port - elif os.name == 'nt': - self.port = int(port) - if self.port: - self.open() - - def open(self): - try: - self.serial_conn = serial.Serial(self.port) - except serial.SerialException: - log.exception('Unable to open port: %s' % str(self.port)) - sys.exit(1) - log.debug('Port %s is open: %s' %( str(self.port), self.serial_conn.isOpen() ) ) - - def is_open(self): - return self.serial_conn.isOpen() - - def close(self): - self.serial_conn.close() - log.debug('Port %s is open: %s' %( str(self.port), self.serial_conn.isOpen() ) ) - - def send(self, msg): - message = self.cmdprefix + map(ord, msg) - byte_array = array.array('B', message) - log.debug('Sending message to %s: %s' % ( str(self.port), message) ) - bytes = self.serial_conn.write( byte_array.tostring() ) - log.debug('%i bytes out of %i bytes sent to the scanner' % ( bytes, len(message) ) ) - - def recv(self): - time.sleep(1) - self.serial_conn.flush() - nbytes = self.serial_conn.inWaiting() - log.debug('%i bytes received' % nbytes) - if nbytes: - msg = self.serial_conn.read(nbytes) - byte_array = map(ord, msg) - log.debug('Message received [%s]: %s' % (self.response.get(byte_array[len(byte_array)-2], byte_array[len(byte_array)-2]), - msg)) - return msg - else: - log.error('Error!') - return None - - def setup_recv(self, callback): - self.recv_callback = callback - - def wait(self): - nbytes = self.serial_conn.inWaiting() - if nbytes: - msg = self.serial_conn.read(nbytes) - byte_array = map(ord, msg) - log.debug('Message received [%s]: %s' % (self.response.get(byte_array[len(byte_array)-2], byte_array[len(byte_array)-2], - msg))) - if self.recv_callback: - self.recv_callback(msg) - return - - - diff --git a/scripts/galaxy_messaging/server/amqp_consumer.py b/scripts/galaxy_messaging/server/amqp_consumer.py deleted file mode 100644 index 464dfe0c0c3..00000000000 --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ /dev/null @@ -1,164 +0,0 @@ -''' -Galaxy Messaging with AMQP (RabbitMQ) -Galaxy uses AMQ protocol to receive messages from external sources like -bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -For Galaxy to receive messages from a message queue the RabbitMQ server has -to be set up with a user account and other parameters listed in the [galaxy_amqp] -section in the universe_wsgi.ini config file -Once the RabbitMQ server has been setup and started with the given parameters, -this script can be run to receive messages and update the Galaxy database accordingly -''' - -import ConfigParser -import sys, os -import optparse -import xml.dom.minidom -import subprocess -import urllib2 - -from xml_helper import get_value, get_value_index - -from galaxydb_interface import GalaxyDbInterface - -api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] -sys.path.extend( api_path ) -import common as api - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -from galaxy.web.api.requests import RequestsAPIController -import pkg_resources -pkg_resources.require( "amqp" ) -import amqp - -import logging -log = logging.getLogger("GalaxyAMQP") -log.setLevel(logging.DEBUG) -fh = logging.FileHandler("galaxy_listener.log") -fh.setLevel(logging.DEBUG) -formatter = logging.Formatter("%(asctime)s - %(name)s - %(message)s") -fh.setFormatter(formatter) -log.addHandler(fh) - -# data transfer script -data_transfer_script = os.path.join( os.getcwd(), - "scripts/galaxy_messaging/server/data_transfer.py" ) -global config -global config_file_name -global http_server_section - - -def start_data_transfer( message ): - # fork a new process to transfer datasets - cmd = '%s "%s" "%s" "%s"' % ( "python", - data_transfer_script, - message.body, - config_file_name ) # Galaxy config file name - pid = subprocess.Popen(cmd, shell=True).pid - log.debug('Started process (%i): %s' % (pid, str(cmd))) - -def update_sample_state( message ): - dom = xml.dom.minidom.parseString(message.body) - barcode = get_value(dom, 'barcode') - state = get_value(dom, 'state') - api_key = get_value(dom, 'api_key') - log.debug('Barcode: ' + barcode) - log.debug('State: ' + state) - log.debug('API Key: ' + api_key) - # validate - if not barcode or not state or not api_key: - log.debug( 'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.' ) - return - # update the sample state in Galaxy db - dbconnstr = config.get("app:main", "database_connection") - galaxydb = GalaxyDbInterface( dbconnstr ) - sample_id = galaxydb.get_sample_id( field_name='bar_code', value=barcode ) - if sample_id == -1: - log.debug( 'Invalid barcode.' ) - return - galaxydb.change_state(sample_id, state) - # after updating the sample state, update request status - request_id = galaxydb.get_request_id(sample_id) - update_request( api_key, request_id ) - -def update_request( api_key, request_id ): - encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) - data = dict( update_type=RequestsAPIController.update_types.REQUEST ) - url = "http://%s:%s/api/requests/%s" % ( config.get(http_server_section, "host"), - config.get(http_server_section, "port"), - encoded_request_id ) - log.debug( 'Updating request %i' % request_id ) - try: - retval = api.update( api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) - except Exception, e: - log.debug( 'ERROR(update_request (%s)): %s' % ( str((self.api_key, url, data)), str(e) ) ) - -def recv_callback( message ): - # check the meesage type. - msg_type = message.properties['application_headers'].get('msg_type') - log.debug( 'MESSAGE RECVD: ' + str( msg_type ) ) - if msg_type == 'data_transfer': - log.debug( 'DATA TRANSFER' ) - start_data_transfer( message ) - elif msg_type == 'sample_state_update': - log.debug( 'SAMPLE STATE UPDATE' ) - update_sample_state( message ) - -def main(): - parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='Galaxy configuration file', - dest='config_file', action='store') - parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', - dest='http_server_section', action='store') - (opts, args) = parser.parse_args() - log.debug( "GALAXY LISTENER PID: " + str(os.getpid()) + " - " + str( opts ) ) - # read the Galaxy config file - global config_file_name - config_file_name = opts.config_file - global config - config = ConfigParser.ConfigParser() - config.read( opts.config_file ) - global http_server_section - http_server_section = opts.http_server_section - amqp_config = {} - for option in config.options("galaxy_amqp"): - amqp_config[option] = config.get("galaxy_amqp", option) - log.debug( str( amqp_config ) ) - # connect - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host']) - chan = conn.channel() - chan.queue_declare( queue=amqp_config['queue'], - durable=True, - exclusive=True, - auto_delete=False) - chan.exchange_declare( exchange=amqp_config['exchange'], - type="direct", - durable=True, - auto_delete=False,) - chan.queue_bind( queue=amqp_config['queue'], - exchange=amqp_config['exchange'], - routing_key=amqp_config['routing_key']) - - chan.basic_consume( queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, - consumer_tag="testtag") - log.debug('Connected to rabbitmq server - '+amqp_config['host']+":"+amqp_config['port']) - while True: - chan.wait() - chan.basic_cancel("testtag") - chan.close() - conn.close() - -if __name__ == '__main__': - main() - - diff --git a/scripts/galaxy_messaging/server/data_transfer.py b/scripts/galaxy_messaging/server/data_transfer.py deleted file mode 100755 index 6eb90b95348..00000000000 --- a/scripts/galaxy_messaging/server/data_transfer.py +++ /dev/null @@ -1,239 +0,0 @@ -#!/usr/bin/env python -""" - -Data Transfer Script: Sequencer to Galaxy - -This script is called from Galaxy RabbitMQ listener ( amqp_consumer.py ) once -the lab admin starts the data transfer process using the user interface. - -Usage: - -python data_transfer.py - - -""" -import ConfigParser -import cookielib -import datetime -import logging -import optparse -import os -import shutil -import sys -import time -import time -import traceback -import urllib -import urllib2 -import xml.dom.minidom - - -from xml_helper import get_value, get_value_index - -log = logging.getLogger( "datatx_" + str( os.getpid() ) ) -log.setLevel( logging.DEBUG ) -fh = logging.FileHandler( "data_transfer.log" ) -fh.setLevel( logging.DEBUG ) -formatter = logging.Formatter( "%(asctime)s - %(name)s - %(message)s" ) -fh.setFormatter( formatter ) -log.addHandler( fh ) - -api_path = [ os.path.join( os.getcwd(), "scripts/api" ) ] -sys.path.extend( api_path ) -import common as api - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path - -from galaxy import eggs -from galaxy.model import SampleDataset -from galaxy.web.api.samples import SamplesAPIController -import pkg_resources -pkg_resources.require( "pexpect" ) -import pexpect - -log.debug(str(dir(api))) - -class DataTransfer( object ): - - def __init__( self, msg, config_file ): - log.info( msg ) - self.dom = xml.dom.minidom.parseString( msg ) - self.galaxy_host = get_value( self.dom, 'galaxy_host' ) - self.api_key = get_value( self.dom, 'api_key' ) - self.sequencer_host = get_value( self.dom, 'data_host' ) - self.sequencer_username = get_value( self.dom, 'data_user' ) - self.sequencer_password = get_value( self.dom, 'data_password' ) - self.request_id = get_value( self.dom, 'request_id' ) - self.sample_id = get_value( self.dom, 'sample_id' ) - self.library_id = get_value( self.dom, 'library_id' ) - self.folder_id = get_value( self.dom, 'folder_id' ) - self.dataset_files = [] - count=0 - while True: - dataset_id = get_value_index( self.dom, 'dataset_id', count ) - file = get_value_index( self.dom, 'file', count ) - name = get_value_index( self.dom, 'name', count ) - if file: - self.dataset_files.append( dict( name=name, - dataset_id=int( dataset_id ), - file=file ) ) - else: - break - count=count+1 - # read config variables - config = ConfigParser.ConfigParser() - retval = config.read( config_file ) - if not retval: - error_msg = 'FATAL ERROR: Unable to open config file %s.' % config_file - log.error( error_msg ) - sys.exit(1) - try: - self.config_id_secret = config.get( "app:main", "id_secret" ) - except ConfigParser.NoOptionError,e: - self.config_id_secret = "USING THE DEFAULT IS NOT SECURE!" - try: - self.import_dir = config.get( "app:main", "library_import_dir" ) - except ConfigParser.NoOptionError,e: - log.error( 'ERROR: library_import_dir config variable is not set in %s. ' % config_file ) - sys.exit( 1 ) - # create the destination directory within the import directory - self.server_dir = os.path.join( self.import_dir, - 'datatx_' + str( os.getpid() ) + '_' + datetime.date.today( ).strftime( "%d%b%Y" ) ) - try: - os.mkdir( self.server_dir ) - except Exception, e: - self.error_and_exit( str( e ) ) - - def start( self ): - ''' - This method executes the file transfer from the sequencer, adds the dataset - to the data library & finally updates the data transfer status in the db - ''' - # datatx - self.transfer_files() - # add the dataset to the given library - self.add_to_library() - # update the data transfer status in the db - self.update_status( SampleDataset.transfer_status.COMPLETE ) - # cleanup - #self.cleanup() - sys.exit( 0 ) - - def cleanup( self ): - ''' - remove the directory created to store the dataset files temporarily - before adding the same to the data library - ''' - try: - time.sleep( 60 ) - shutil.rmtree( self.server_dir ) - except: - self.error_and_exit() - - - def error_and_exit( self, msg='' ): - ''' - This method is called any exception is raised. This prints the traceback - and terminates this script - ''' - log.error( traceback.format_exc() ) - log.error( 'FATAL ERROR.' + msg ) - self.update_status( 'Error', 'All', msg ) - sys.exit( 1 ) - - def transfer_files( self ): - ''' - This method executes a scp process using pexpect library to transfer - the dataset file from the remote sequencer to the Galaxy server - ''' - def print_ticks( d ): - pass - for i, dataset_file in enumerate( self.dataset_files ): - self.update_status( SampleDataset.transfer_status.TRANSFERRING, dataset_file[ 'dataset_id' ] ) - try: - cmd = "scp %s@%s:'%s' '%s/%s'" % ( self.sequencer_username, - self.sequencer_host, - dataset_file[ 'file' ].replace( ' ', '\ ' ), - self.server_dir.replace( ' ', '\ ' ), - dataset_file[ 'name' ].replace( ' ', '\ ' ) ) - log.debug( cmd ) - output = pexpect.run( cmd, - events={ '.ssword:*': self.sequencer_password+'\r\n', - pexpect.TIMEOUT: print_ticks }, - timeout=10 ) - log.debug( output ) - path = os.path.join( self.server_dir, os.path.basename( dataset_file[ 'name' ] ) ) - if not os.path.exists( path ): - msg = 'Could not find the local file after transfer ( %s ).' % path - log.error( msg ) - raise Exception( msg ) - except Exception, e: - msg = traceback.format_exc() - self.update_status( 'Error', dataset_file['dataset_id'], msg) - - - def add_to_library( self ): - ''' - This method adds the dataset file to the target data library & folder - by opening the corresponding url in Galaxy server running. - ''' - self.update_status( SampleDataset.transfer_status.ADD_TO_LIBRARY ) - try: - data = {} - data[ 'folder_id' ] = 'F%s' % api.encode_id( self.config_id_secret, self.folder_id ) - data[ 'file_type' ] = 'auto' - data[ 'server_dir' ] = self.server_dir - data[ 'dbkey' ] = '' - data[ 'upload_option' ] = 'upload_directory' - data[ 'create_type' ] = 'file' - url = "http://%s/api/libraries/%s/contents" % ( self.galaxy_host, - api.encode_id( self.config_id_secret, self.library_id ) ) - log.debug( str( ( self.api_key, url, data ) ) ) - retval = api.submit( self.api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) - except Exception, e: - self.error_and_exit( str( e ) ) - - def update_status( self, status, dataset_id='All', msg='' ): - ''' - Update the data transfer status for this dataset in the database - ''' - try: - log.debug( 'Setting status "%s" for dataset "%s" of sample "%s"' % ( status, str( dataset_id ), str( self.sample_id) ) ) - sample_dataset_ids = [] - if dataset_id == 'All': - for dataset in self.dataset_files: - sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset[ 'dataset_id' ] ) ) - else: - sample_dataset_ids.append( api.encode_id( self.config_id_secret, dataset_id ) ) - # update the transfer status - data = {} - data[ 'update_type' ] = SamplesAPIController.update_types.SAMPLE_DATASET[0] - data[ 'sample_dataset_ids' ] = sample_dataset_ids - data[ 'new_status' ] = status - data[ 'error_msg' ] = msg - url = "http://%s/api/samples/%s" % ( self.galaxy_host, - api.encode_id( self.config_id_secret, self.sample_id ) ) - log.debug( str( ( self.api_key, url, data))) - retval = api.update( self.api_key, url, data, return_formatted=False ) - log.debug( str( retval ) ) - except urllib2.URLError, e: - log.debug( 'ERROR( sample_dataset_transfer_status ( %s ) ): %s' % ( url, str( e ) ) ) - log.error( traceback.format_exc() ) - except: - log.error( traceback.format_exc() ) - log.error( 'FATAL ERROR' ) - sys.exit( 1 ) - -if __name__ == '__main__': - log.info( 'STARTING %i %s' % ( os.getpid(), str( sys.argv ) ) ) - # - # Start the daemon - # - dt = DataTransfer( sys.argv[1], sys.argv[2]) - dt.start() - sys.exit( 0 ) - diff --git a/scripts/galaxy_messaging/server/galaxydb_interface.py b/scripts/galaxy_messaging/server/galaxydb_interface.py deleted file mode 100644 index 3040ed29abb..00000000000 --- a/scripts/galaxy_messaging/server/galaxydb_interface.py +++ /dev/null @@ -1,167 +0,0 @@ -#/usr/bin/python - -from datetime import datetime -import sys -import optparse -import os -import time -import logging - -assert sys.version_info[:2] >= ( 2, 4 ) -new_path = [ os.path.join( os.getcwd(), "lib" ) ] -new_path.extend( sys.path[1:] ) # remove scripts/ from the path -sys.path = new_path -from galaxy import eggs -from galaxy.model.custom_types import * -import pkg_resources -pkg_resources.require( "psycopg2" ) -import psycopg2 -pkg_resources.require( "SQLAlchemy >= 0.4" ) -from sqlalchemy import * -from sqlalchemy.orm import sessionmaker - -#logging.basicConfig(level=logging.DEBUG) -#log = logging.getLogger( 'GalaxyDbInterface' ) - -class GalaxyDbInterface(object): - - def __init__(self, dbstr): - self.dbstr = dbstr - self.db_engine = create_engine(self.dbstr) - self.db_engine.echo = False - self.metadata = MetaData(self.db_engine) - self.session = sessionmaker(bind=self.db_engine) - self.event_table = Table('sample_event', self.metadata, autoload=True ) - self.sample_table = Table('sample', self.metadata, autoload=True ) - self.sample_dataset_table = Table('sample_dataset', self.metadata, autoload=True ) - self.request_table = Table('request', self.metadata, autoload=True ) - self.request_event_table = Table('request_event', self.metadata, autoload=True ) - self.state_table = Table('sample_state', self.metadata, autoload=True ) - - def get_sample_id(self, field_name='bar_code', value=None): - if not value: - return -1 - sample_id = -1 - if field_name =='name': - stmt = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.name==value) - result = stmt.execute() - sample_id = result.fetchone()[0] - elif field_name == 'bar_code': - stmt = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.bar_code==value) - result = stmt.execute() - x = result.fetchone() - if x: - sample_id = x[0] - #log.debug('Sample ID: %i' % sample_id) - return sample_id - return -1 - - def get_request_id(self, sample_id): - query = select(columns=[self.sample_table.c.request_id], - whereclause=self.sample_table.c.id==sample_id) - request_id = query.execute().fetchall()[0][0] - return request_id - - def current_state(self, sample_id): - ''' - This method returns the current state of the sample for the given sample_id - ''' - stmt = select(columns=[self.event_table.c.sample_state_id], - whereclause=self.event_table.c.sample_id==sample_id, - order_by=self.event_table.c.update_time.desc()) - result = stmt.execute() - all_states = result.fetchall() - current_state_id = all_states[0][0] - return current_state_id - - def all_possible_states(self, sample_id): - subsubquery = select(columns=[self.sample_table.c.request_id], - whereclause=self.sample_table.c.id==sample_id) - self.request_id = subsubquery.execute().fetchall()[0][0] - #log.debug('REQUESTID: %i' % self.request_id) - subquery = select(columns=[self.request_table.c.request_type_id], - whereclause=self.request_table.c.id==self.request_id) - request_type_id = subquery.execute().fetchall()[0][0] - #log.debug('REQUESTTYPEID: %i' % request_type_id) - query = select(columns=[self.state_table.c.id, self.state_table.c.name], - whereclause=self.state_table.c.request_type_id==request_type_id, - order_by=self.state_table.c.id.asc()) - states = query.execute().fetchall() - #log.debug('POSSIBLESTATES: '+ str(states)) - return states - - def change_state(self, sample_id, new_state=None): - ''' - This method changes the state of the sample to the the 'new_state' - ''' - if not new_state: - return - new_state_id = -1 - # find the state_id for this new state in the list of possible states - possible_states = self.all_possible_states(sample_id) - for state_id, state_name in possible_states: - if new_state == state_name: - new_state_id = state_id - if new_state_id == -1: - return - #log.debug('Updating sample_id %i state to %s' % (sample_id, new_state)) - i = self.event_table.insert() - i.execute(update_time=datetime.utcnow(), - create_time=datetime.utcnow(), - sample_id=sample_id, - sample_state_id=int(new_state_id), - comment='Update by barcode scan') - # if all the samples for this request are in the final state - # then change the request state to 'Complete' - result = select(columns=[self.sample_table.c.id], - whereclause=self.sample_table.c.request_id==self.request_id).execute() - sample_id_list = result.fetchall() - request_complete = True - for sid in sample_id_list: - current_state_id = self.current_state(sid[0]) - if current_state_id != possible_states[-1][0]: - request_complete = False - break - if request_complete: - request_state = 'Complete' - #log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state)) - i = self.request_event_table.insert() - i.execute(update_time=datetime.utcnow(), - create_time=datetime.utcnow(), - request_id=self.request_id, - state=request_state, - comment='All samples of this request have finished processing.') - - def set_sample_dataset_status(self, id, new_status, msg=None): - u = self.sample_dataset_table.update(whereclause=self.sample_dataset_table.c.id==int(id)) - u.execute(status=new_status) - if new_status == 'Error': - u.execute(error_msg=msg) - else: - u.execute(error_msg='') - return - - - -if __name__ == '__main__': - print '''This file should not be run directly. To start the Galaxy AMQP Listener: - %sh run_galaxy_listener.sh''' - dbstr = 'postgres://postgres:postgres@localhost/g2' - - parser = optparse.OptionParser() - parser.add_option('-n', '--name', help='name of the sample field', dest='name', \ - action='store', default='bar_code') - parser.add_option('-v', '--value', help='value of the sample field', dest='value', \ - action='store') - parser.add_option('-s', '--state', help='new state of the sample', dest='state', \ - action='store') - (opts, args) = parser.parse_args() - - gs = GalaxyDbInterface(dbstr) - sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value) - gs.change_state(sample_id, opts.state) - - - diff --git a/scripts/galaxy_messaging/server/setup_rabbitmq.py b/scripts/galaxy_messaging/server/setup_rabbitmq.py deleted file mode 100644 index 68bb6dabd59..00000000000 --- a/scripts/galaxy_messaging/server/setup_rabbitmq.py +++ /dev/null @@ -1,38 +0,0 @@ -# -# Configuration script for RabbitMQ in Galaxy -# -# Requirements: -# - set the rabbitmqctl_path variable in the 'galaxy_amqp' section in Galaxy config file -# -# Usage: -# $ python setup_rabbitmq.py -# - -import os, sys, csv, ConfigParser - -def main( config_file ): - try: - config = ConfigParser.ConfigParser() - config.read( config_file ) - rabbitmqctl_path = config.get( 'galaxy_amqp', 'rabbitmqctl_path' ) - username = config.get( 'galaxy_amqp', 'userid' ) - password = config.get( 'galaxy_amqp', 'password' ) - virtual_host = config.get( 'galaxy_amqp', 'virtual_host' ) - except Exception, e: - print 'Fatal error:', str(e) - sys.exit(1) - - cmd_list = [ - 'add_user %s %s' % ( username, password ), - 'add_vhost %s' % virtual_host, - 'set_permissions -p %s %s ".*" ".*" ".*"' % ( virtual_host, username ) - ] - - for cmd in cmd_list: - retval = os.system( rabbitmqctl_path + ' ' + cmd ) - if retval: - print "Failed command: %s" % cmd - sys.exit(1) - -if __name__ == '__main__': - main( sys.argv[1] ) diff --git a/scripts/galaxy_messaging/server/xml_helper.py b/scripts/galaxy_messaging/server/xml_helper.py deleted file mode 100644 index 1b36ea66849..00000000000 --- a/scripts/galaxy_messaging/server/xml_helper.py +++ /dev/null @@ -1,28 +0,0 @@ -#======= XML helper methods ==================================================== - -import xml.dom.minidom - -def get_value( dom, tag_name ): - ''' - This method extracts the tag value from the xml message - ''' - nodelist = dom.getElementsByTagName( tag_name )[ 0 ].childNodes - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc - -def get_value_index( dom, tag_name, dataset_id ): - ''' - This method extracts the tag value from the xml message - ''' - try: - nodelist = dom.getElementsByTagName( tag_name )[ dataset_id ].childNodes - except: - return None - rc = "" - for node in nodelist: - if node.nodeType == node.TEXT_NODE: - rc = rc + node.data - return rc diff --git a/setup_rabbitmq.sh b/setup_rabbitmq.sh deleted file mode 100644 index 2ef96b5afb3..00000000000 --- a/setup_rabbitmq.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/sh - -cd `dirname $0` -python scripts/galaxy_messaging/server/setup_rabbitmq.py universe_wsgi.ini \ No newline at end of file From ce679acf892baad500551306604a3e5197fa38b6 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Tue, 16 Sep 2014 01:46:17 -0400 Subject: [PATCH 08/10] Ui: Unify checkboxes and radio buttons, extend functionality, Upload: Fix code style, ToolForm: Extend dataset filtering --- static/scripts/mvc/tools/tools-datasets.js | 23 +- static/scripts/mvc/tools/tools-form.js | 39 +-- static/scripts/mvc/tools/tools-jobs.js | 6 +- static/scripts/mvc/tools/tools-section.js | 6 +- .../scripts/mvc/tools/tools-select-dataset.js | 127 +++++----- static/scripts/mvc/tools/tools-template.js | 6 + static/scripts/mvc/tools/tools-tree.js | 44 +++- static/scripts/mvc/ui/ui-checkbox.js | 91 ------- static/scripts/mvc/ui/ui-misc.js | 8 +- static/scripts/mvc/ui/ui-options.js | 225 ++++++++++++++++++ static/scripts/mvc/ui/ui-radiobutton.js | 93 -------- static/scripts/mvc/ui/ui-select-default.js | 2 +- static/scripts/mvc/upload/upload-ftp.js | 18 +- static/scripts/mvc/upload/upload-row.js | 21 +- static/scripts/mvc/upload/upload-settings.js | 17 +- static/scripts/mvc/upload/upload-view.js | 3 +- .../packed/mvc/tools/tools-datasets.js | 2 +- static/scripts/packed/mvc/tools/tools-form.js | 2 +- static/scripts/packed/mvc/tools/tools-jobs.js | 2 +- .../scripts/packed/mvc/tools/tools-section.js | 2 +- .../packed/mvc/tools/tools-select-dataset.js | 2 +- .../packed/mvc/tools/tools-template.js | 2 +- static/scripts/packed/mvc/tools/tools-tree.js | 2 +- static/scripts/packed/mvc/ui/ui-checkbox.js | 1 - static/scripts/packed/mvc/ui/ui-misc.js | 2 +- .../scripts/packed/mvc/ui/ui-radiobutton.js | 1 - .../packed/mvc/ui/ui-select-default.js | 2 +- .../scripts/packed/mvc/upload/upload-ftp.js | 2 +- .../packed/mvc/upload/upload-settings.js | 2 +- static/style/blue/base.css | 2 +- static/style/src/less/ui.less | 2 +- 31 files changed, 410 insertions(+), 347 deletions(-) delete mode 100644 static/scripts/mvc/ui/ui-checkbox.js create mode 100644 static/scripts/mvc/ui/ui-options.js delete mode 100644 static/scripts/mvc/ui/ui-radiobutton.js delete mode 100644 static/scripts/packed/mvc/ui/ui-checkbox.js delete mode 100644 static/scripts/packed/mvc/ui/ui-radiobutton.js diff --git a/static/scripts/mvc/tools/tools-datasets.js b/static/scripts/mvc/tools/tools-datasets.js index e27f2e88c62..21fdcf31974 100644 --- a/static/scripts/mvc/tools/tools-datasets.js +++ b/static/scripts/mvc/tools/tools-datasets.js @@ -25,21 +25,26 @@ define([ 'mvc/history/history-contents' ], function( HISTORY_CONTENTS ){ }, // filter datasets by data type - filterType: function(filter_type) { - // return matched datasets - return this.currHistoryContents.filter( function( content ){ - // link details - var history_content_type = content.get( 'history_content_type' ); - var data_type = content.get( 'file_ext'); + filterType: function(options) { + options = options || {}; + return this.currHistoryContents.filter(function(content){ + // match datatypes + var found = false; + for (var i in options.data_types) { + if (content.get('data_type').indexOf(options.data_types[i]) != -1) { + found = true; + break; + } + } - // apply filter - return history_content_type === 'dataset';// && (data_type === filter_type || filter_type === ''); + // final match result + return (content.get('history_content_type') === options.content_type || !options.content_type) && + (found || !options.data_types) && !content.get('deleted'); }); }, // filter datasets by id filter: function(filter_id) { - // return matched datasets return _.first( this.currHistoryContents.filter( function( content ){ return content.get( 'id' ) === filter_id; }) ); } }); diff --git a/static/scripts/mvc/tools/tools-form.js b/static/scripts/mvc/tools/tools-form.js index c8d630e09f4..9b9a32446f3 100644 --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -56,6 +56,12 @@ define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', }); }, + // message + message: function(options) { + $(this.main_el).empty(); + $(this.main_el).append(ToolTemplate.message(options)); + }, + // reset form reset: function() { for (var i in this.element_list) { @@ -63,6 +69,20 @@ define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', } }, + // refresh + refresh: function() { + // recreate tree structure + this.tree.refresh(); + + // trigger change + for (var id in this.field_list) { + this.field_list[id].trigger('change'); + } + + // log + console.debug('tools-form::refresh() - Recreated tree structure. Refresh.'); + }, + // initialize tool form _initializeToolForm: function() { // link this @@ -135,10 +155,6 @@ define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', button_search.$el.hide(); } - // create message - self.message = new Ui.Message(); - self.portlet.append(self.message.$el); - // append form $(self.main_el).append(self.portlet.$el); @@ -174,22 +190,9 @@ define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', // trigger refresh self.refresh(); //self.job_handler.submit(); + self.tree.finalize(); } }); - }, - - // refresh - refresh: function() { - // recreate tree structure - this.tree.refresh(); - - // trigger change - for (var id in this.field_list) { - this.field_list[id].trigger('change'); - } - - // log - console.debug('tools-form::refresh() - Recreated tree structure. Refresh.'); } }); diff --git a/static/scripts/mvc/tools/tools-jobs.js b/static/scripts/mvc/tools/tools-jobs.js index ae31474dfbc..b55577aeb08 100644 --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -31,12 +31,16 @@ return Backbone.Model.extend({ // success handler function(response) { if (!response.outputs || response.outputs.length == 0) { - console.log(response); + console.debug(response); } + self.app.message({ + text : 'A job has been successfully added to the queue. You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from \'running\' to \'finished\' if completed successfully or \'error\' if problems were encountered.' + }); self._refreshHdas(); }, // error handler function(response) { + console.debug(response); if (response && response.message && response.message.data) { var error_messages = self.app.tree.match(response.message.data); for (var id in error_messages) { diff --git a/static/scripts/mvc/tools/tools-section.js b/static/scripts/mvc/tools/tools-section.js index 7006145ede7..8c870583841 100644 --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -16,13 +16,11 @@ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'm // set text this.$el.find('.ui-table-form-error-text').html(text); this.$el.find('.ui-table-form-error').fadeIn(); - this.$el.addClass('ui-table-row-error'); }, // reset reset: function() { this.$el.find('.ui-table-form-error').hide(); - this.$el.removeClass('ui-table-form-error'); }, // template @@ -35,7 +33,7 @@ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'm } // add error - $input.append('
    '); + $input.append('
    '); // add label if (options.label) { @@ -274,7 +272,7 @@ define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/ui/ui-tabs', 'm // dataset column case 'data_column': - field = this._field_data_colum(input_def); + field = this._field_select(input_def); break; // conditional select field diff --git a/static/scripts/mvc/tools/tools-select-dataset.js b/static/scripts/mvc/tools/tools-select-dataset.js index b34015aadce..6af97140561 100644 --- a/static/scripts/mvc/tools/tools-select-dataset.js +++ b/static/scripts/mvc/tools/tools-select-dataset.js @@ -6,54 +6,6 @@ var View = Backbone.View.extend({ initialize : function(app, options) { // link this var self = this; - - // get datasets - var datasets = app.datasets.filterType(); - - // configure options fields - var select_data = []; - for (var i in datasets) { - select_data.push({ - label: datasets[i].get('name'), - value: datasets[i].get('id') - }); - } - - // create select field - this.select = new Ui.Select.View({ - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - // create select field for multiple files - this.select_multiple = new Ui.Select.View({ - multiple : true, - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - - // create select field for multiple files - this.select_collection = new Ui.Select.View({ - data : select_data, - value : select_data[0].value, - onchange : function() { - self.trigger('change'); - } - }); - - // add change event. fires on trigger - this.on('change', function() { - if (options.onchange) { - options.onchange(self.value()); - } - }); // tabs this.tabs = new Tabs.View({ @@ -62,20 +14,66 @@ var View = Backbone.View.extend({ } }); - // add tab - this.tabs.add({ - id : 'single', - title : 'Select a dataset', - $el : this.select.$el + // + // datasets + // + var datasets = app.datasets.filterType({ + content_type : 'dataset', + data_types : options.extensions + }); + + // configure options fields + var dataset_options = []; + for (var i in datasets) { + dataset_options.push({ + label: datasets[i].get('name'), + value: datasets[i].get('id') + }); + } + + // select field + this.select_datasets = new Ui.Select.View({ + multiple : true, + data : dataset_options, + value : dataset_options[0] && dataset_options[0].value, + onchange : function() { + self.trigger('change'); + } }); // add tab this.tabs.add({ - id : 'multiple', - title : 'Select multiple datasets', - $el : this.select_multiple.$el + id : 'datasets', + title : 'Select datasets', + $el : this.select_datasets.$el }); - + + // + // collections + // + var collections = app.datasets.filterType({ + content_type : 'collection', + data_types : options.extensions + }); + + // configure options fields + var collection_options = []; + for (var i in collections) { + collection_options.push({ + label: collections[i].get('name'), + value: collections[i].get('id') + }); + } + + // create select field for collections + this.select_collection = new Ui.Select.View({ + data : collection_options, + value : collection_options[0] && collection_options[0].value, + onchange : function() { + self.trigger('change'); + } + }); + // add tab this.tabs.add({ id : 'collection', @@ -85,18 +83,23 @@ var View = Backbone.View.extend({ // add element this.setElement(this.tabs.$el); + + // add change event. fires on trigger + this.on('change', function() { + if (options.onchange) { + options.onchange(self.value()); + } + }); }, // value value : function (new_value) { var current_tab = this.tabs.current(); switch(current_tab) { - case 'multiple' : - return this.select_multiple.value(); - case 'collection' : + case 'datasets': + return this.select_datasets.value(); + case 'collection': return this.select_collection.value(); - default : - return this.select.value(); } }, diff --git a/static/scripts/mvc/tools/tools-template.js b/static/scripts/mvc/tools/tools-template.js index 261fe973426..7fc79acddb0 100644 --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -13,6 +13,12 @@ return { citations: function() { return '
    '; + }, + + message: function(options) { + return '
    ' + + '

    ' + options.text + '

    ' + + '
    '; } }; diff --git a/static/scripts/mvc/tools/tools-tree.js b/static/scripts/mvc/tools/tools-tree.js index 9d89831ff72..0e80c62b157 100644 --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -50,8 +50,8 @@ return Backbone.Model.extend({ // converter between raw dictionary and job dictionary function convert(identifier, head) { - for (var i in head) { - var node = head[i]; + for (var index in head) { + var node = head[index]; if (node.input) { // get node var input = node.input; @@ -68,9 +68,9 @@ return Backbone.Model.extend({ // handle repeats case 'repeat': var index = 0; - for (var j in node) { - if (j.indexOf('section') != -1) { - convert(job_input_id + '_' + index++, node[j]); + for (var i in node) { + if (i.indexOf('section') != -1) { + convert(job_input_id + '_' + index++, node[i]); } } break; @@ -83,20 +83,38 @@ return Backbone.Model.extend({ add (job_input_id + '|' + input.test_param.name, input.id, value); // find selected case - for (var j in input.cases) { - if (input.cases[j].value == value) { - convert(job_input_id, head[input.id + '-section-' + j]); + for (var i in input.cases) { + if (input.cases[i].value == value) { + convert(job_input_id, head[input.id + '-section-' + i]); break; } } break; // handle data inputs case 'data': - var value = { - id : self.app.field_list[input.id].value(), - src : 'hda' + // create array for dataset ids + var dataset_selection = null; + + // collect dataset ids from input field + var value = self.app.field_list[input.id].value(); + if (typeof value === 'string') { + dataset_selection = { + id : value, + src : 'hda' + }; + } else { + // create array of dataset dictionaries for api submission + dataset_selection = []; + for (var i in value) { + dataset_selection.push({ + id : value[i], + src : 'hda' + }); + } } - add(job_input_id, input.id, value); + + // add final array to job definition + add(job_input_id, input.id, dataset_selection); break; // handle boolean input case 'boolean': @@ -118,7 +136,7 @@ return Backbone.Model.extend({ // start conversion convert('', this.dict); - + console.log(this.job_def); // return result return this.job_def; }, diff --git a/static/scripts/mvc/ui/ui-checkbox.js b/static/scripts/mvc/ui/ui-checkbox.js deleted file mode 100644 index 14527bd1e6b..00000000000 --- a/static/scripts/mvc/ui/ui-checkbox.js +++ /dev/null @@ -1,91 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// plugin -var View = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - visible : true, - cls : '', - data : [], - id : Utils.uuid() - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // set initial value - if (this.options.value) { - this.value(this.options.value); - } - - // current value - this.current = this.options.value; - - // onchange event handler. fires on user activity. - var self = this; - this.$el.find('input').on('change', function() { - self.value(self._getValue()); - }); - }, - - // value - value : function (new_val) { - // get current value - var before = this.current; - - // set new value - if (new_val !== undefined) { - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); - this.current = new_val; - } - - // check value - var after = this.current; - if (after != before && this.options.onchange) { - this.options.onchange(this.current); - } - - // get and return value - return this.current; - }, - - // get value - _getValue: function() { - var selected = this.$el.find(':checked'); - var value = null; - if (selected.length > 0) { - value = selected.val(); - } - return value; - }, - - // element - _template: function(options) { - var tmpl = '
    '; - for (key in options.data) { - var pair = options.data[key]; - tmpl += '' + pair.label + '
    '; - } - tmpl += '
    '; - return tmpl; - } -}); - -return { - View : View -}; - -}); diff --git a/static/scripts/mvc/ui/ui-misc.js b/static/scripts/mvc/ui/ui-misc.js index 9d01406c76c..81966465995 100644 --- a/static/scripts/mvc/ui/ui-misc.js +++ b/static/scripts/mvc/ui/ui-misc.js @@ -1,6 +1,6 @@ // dependencies -define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-checkbox', 'mvc/ui/ui-radiobutton', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], - function(Utils, Select, Slider, Checkbox, RadioButton, ButtonMenu, Modal) { +define(['utils/utils', 'mvc/ui/ui-select-default', 'mvc/ui/ui-slider', 'mvc/ui/ui-options', 'mvc/ui/ui-button-menu', 'mvc/ui/ui-modal'], + function(Utils, Select, Slider, Options, ButtonMenu, Modal) { /** * This class contains backbone wrappers for basic ui elements such as Images, Labels, Buttons, Input fields etc. @@ -403,8 +403,8 @@ return { Label : Label, Message : Message, Modal : Modal, - RadioButton : RadioButton, - Checkbox : Checkbox, + RadioButton : Options.RadioButton, + Checkbox : Options.Checkbox, Searchbox : Searchbox, Select : Select, Hidden : Hidden, diff --git a/static/scripts/mvc/ui/ui-options.js b/static/scripts/mvc/ui/ui-options.js new file mode 100644 index 00000000000..c336554759c --- /dev/null +++ b/static/scripts/mvc/ui/ui-options.js @@ -0,0 +1,225 @@ +// dependencies +define(['utils/utils'], function(Utils) { + +/** base class for options based ui elements **/ +var OptionsBase = Backbone.View.extend({ + // settings + settings : { + multiple : false + }, + + // options + optionsDefault: { + value : [], + visible : true, + data : [], + id : Utils.uuid(), + empty : 'No data available' + }, + + // initialize + initialize: function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this._template(this.options)); + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } + + // initialize data + this.update(this.options.data); + + // set initial value + if (this.options.value) { + this.value(this.options.value); + } + + // add change event. fires on trigger + var self = this; + this.on('change', function() { + self._change(); + }); + }, + + // update options + update: function(options) { + // backup current value + var current = this._getValue(); + + // remove all options + this.$el.find('.ui-option').remove(); + + // add new options + for (var key in options) { + this.$el.append(this._templateOption(options[key])); + } + + // add change events + var self = this; + this.$el.find('input').on('change', function() { + self.value(self._getValue()); + self._change(); + }); + + // refresh + this._refresh(); + + // set previous value + this.value(current); + }, + + // check if selected value exists (or any if multiple) + exists: function(value) { + if (typeof value === 'string') { + value = [value]; + } + for (var i in value) { + if (this.$el.find('input[value="' + value[i] + '"]').length > 0) { + return true; + } + } + return false; + }, + + // first + first: function() { + var options = this.$el.find('input'); + if (options.length > 0) { + return options.val(); + } else { + return undefined; + } + }, + + // change + _change: function() { + if (this.options.onchange) { + this.options.onchange(this._getValue()); + } + }, + + // refresh + _refresh: function() { + // remove placeholder + this.$el.find('.ui-error').remove(); + + // count remaining options + var remaining = this.$el.find('input').length; + if (remaining == 0) { + this.$el.append(this._templateEmpty()); + } + }, + + // get value + _getValue: function() { + // get selected values + var selected = this.$el.find(':checked'); + if (selected.length == 0) { + return null; + } + + // return multiple or single value + if (this.settings.multiple) { + var values = []; + selected.each(function() { + values.push($(this).val()); + }); + return values; + } else { + return selected.val(); + } + }, + + // template for options + _templateEmpty: function() { + return '
    ' + this.options.empty + '
    '; + } +}); + +/** checkbox options field **/ +var Checkbox = {}; +Checkbox.View = OptionsBase.extend({ + // initialize + initialize: function(options) { + this.settings.multiple = true; + OptionsBase.prototype.initialize.call(this, options); + }, + + // value + value: function (new_val) { + // check if its an array + if (typeof new_val === 'string') { + new_val = [new_val]; + } + + // set new value + if (new_val !== undefined) { + // reset selection + this.$el.find('input').prop('checked', false); + + // update to new selection + for (var i in new_val) { + this.$el.find('input[value=' + new_val[i] + ']').prop('checked', true); + }; + } + + // get and return value + return this._getValue(); + }, + + // template for options + _templateOption: function(pair) { + return '
    ' + + '' + pair.label + '
    ' + + '
    '; + }, + + // template + _template: function() { + return '
    '; + } +}); + +/** radio button options field **/ +var RadioButton = {}; +RadioButton.View = OptionsBase.extend({ + // initialize + initialize: function(options) { + OptionsBase.prototype.initialize.call(this, options); + }, + + // value + value: function (new_val) { + // set new value + if (new_val !== undefined) { + this.$el.find('label').removeClass('active'); + this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); + } + + // get and return value + return this._getValue(); + }, + + // template for options + _templateOption: function(pair) { + return ''; + }, + + // template + _template: function() { + return '
    '; + } +}); + +return { + Checkbox : Checkbox, + RadioButton : RadioButton +}; + +}); diff --git a/static/scripts/mvc/ui/ui-radiobutton.js b/static/scripts/mvc/ui/ui-radiobutton.js deleted file mode 100644 index b0a82529414..00000000000 --- a/static/scripts/mvc/ui/ui-radiobutton.js +++ /dev/null @@ -1,93 +0,0 @@ -// dependencies -define(['utils/utils'], function(Utils) { - -// plugin -var View = Backbone.View.extend({ - // options - optionsDefault: { - value : '', - visible : true, - cls : '', - data : [], - id : Utils.uuid() - }, - - // initialize - initialize : function(options) { - // configure options - this.options = Utils.merge(options, this.optionsDefault); - - // create new element - this.setElement(this._template(this.options)); - - // hide input field - if (!this.options.visible) { - this.$el.hide(); - } - - // set initial value - if (this.options.value) { - this.value(this.options.value); - } - - // current value - this.current = this.options.value; - - // onchange event handler. fires on user activity. - var self = this; - this.$el.find('input').on('change', function() { - self.value(self._getValue()); - }); - }, - - // value - value : function (new_val) { - // get current value - var before = this.current; - - // set new value - if (new_val !== undefined) { - this.$el.find('label').removeClass('active'); - this.$el.find('[value="' + new_val + '"]').closest('label').addClass('active'); - this.current = new_val; - } - - // check value - var after = this.current; - if (after != before && this.options.onchange) { - this.options.onchange(this.current); - } - - // get and return value - return this.current; - }, - - // get value - _getValue: function() { - var selected = this.$el.find(':checked'); - var value = null; - if (selected.length > 0) { - value = selected.val(); - } - return value; - }, - - // element - _template: function(options) { - var tmpl = '
    '; - for (key in options.data) { - var pair = options.data[key]; - tmpl += ''; - } - tmpl += '
    '; - return tmpl; - } -}); - -return { - View : View -}; - -}); diff --git a/static/scripts/mvc/ui/ui-select-default.js b/static/scripts/mvc/ui/ui-select-default.js index 0cd03b2c67d..d8730aa27af 100644 --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -172,7 +172,7 @@ var View = Backbone.View.extend({ // check if selected value exists exists: function(value) { - return this.$select.find('option[value=' + value + ']').length > 0; + return this.$select.find('option[value="' + value + '"]').length > 0; }, // change diff --git a/static/scripts/mvc/upload/upload-ftp.js b/static/scripts/mvc/upload/upload-ftp.js index 42434478faf..96f86145161 100644 --- a/static/scripts/mvc/upload/upload-ftp.js +++ b/static/scripts/mvc/upload/upload-ftp.js @@ -31,10 +31,9 @@ return Backbone.View.extend({ // fill table _fill: function(ftp_files) { - if (ftp_files.length > 0) { // add table - this.$el.find('#upload-ftp-content').html($(this._template_table())); + this.$el.find('#upload-ftp-content').html($(this._templateTable())); // add files to table var size = 0; @@ -48,7 +47,7 @@ return Backbone.View.extend({ this.$el.find('#upload-ftp-disk').html(Utils.bytesToString (size, true)); } else { // add info - this.$el.find('#upload-ftp-content').html($(this._template_info())); + this.$el.find('#upload-ftp-content').html($(this._templateInfo())); } // hide spinner @@ -58,7 +57,7 @@ return Backbone.View.extend({ // add add: function(ftp_file) { // create new item - var $it = $(this._template_row(ftp_file)); + var $it = $(this._templateRow(ftp_file)); // append to table $(this.el).find('tbody').append($it); @@ -118,7 +117,7 @@ return Backbone.View.extend({ }, // template row - _template_row: function(options) { + _templateRow: function(options) { return '' + '
    ' + '

    ' + options.path + '

    ' + @@ -128,8 +127,7 @@ return Backbone.View.extend({ }, // load table template - _template_table: function() - { + _templateTable: function() { return 'Available files: ' + '' + '' + @@ -151,16 +149,14 @@ return Backbone.View.extend({ }, // load table template - _template_info: function() - { + _templateInfo: function() { return '
    ' + 'Your FTP directory does not contain any files.' + '
    '; }, // load html template - _template: function() - { + _template: function() { return '
    ' + '