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commit/galaxy-central: jgoecks: Trackster: resolve name collision due to refactoring.
by commits-noreply＠bitbucket.org 24 Jul '14

24 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9d8967752787/ Changeset: 9d8967752787 User: jgoecks Date: 2014-07-24 15:26:39 Summary: Trackster: resolve name collision due to refactoring. Affected #: 1 file diff -r 6fbe4d95a8dc64bd222dbf1170bdadcc5321e855 -r 9d8967752787556b3d814e086fe2bd9eb1992170 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -103,8 +103,9 @@ var self = this, menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { - _.each(tracks, function(track) { + visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, + function(new_tracks) { + _.each(new_tracks, function(track) { view.add_drawable( tracks.object_from_template(track, view, view) ); }); }); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix missing import in the Tool Shed's ToolValidator.
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6fbe4d95a8dc/ Changeset: 6fbe4d95a8dc User: greg Date: 2014-07-23 22:31:59 Summary: Fix missing import in the Tool Shed's ToolValidator. Affected #: 1 file diff -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 -r 6fbe4d95a8dc64bd222dbf1170bdadcc5321e855 lib/tool_shed/tools/tool_validator.py --- a/lib/tool_shed/tools/tool_validator.py +++ b/lib/tool_shed/tools/tool_validator.py @@ -12,6 +12,7 @@ from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util +from tool_shed.util import xml_util log = logging.getLogger( __name__ ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ae881148949/ Changeset: 2ae881148949 User: dannon Date: 2014-07-23 21:41:14 Summary: Fix 'decod_id' invocation to use the correct function when deleting user addresses. Affected #: 1 file diff -r 053943b668af334c480b464fe7351b50284b7099 -r 2ae881148949596af9c30f2c559dc8f627dda402 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1514,7 +1514,7 @@ @web.expose def delete_address( self, trans, cntrller, address_id=None, user_id=None ): try: - user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decod_id( address_id ) ) + user_address = trans.sa_session.query( trans.app.model.UserAddress ).get( trans.security.decode_id( address_id ) ) except: message = 'Invalid address is (%s)' % address_id status = 'error' https://bitbucket.org/galaxy/galaxy-central/commits/4974ffd8b2cb/ Changeset: 4974ffd8b2cb User: dannon Date: 2014-07-23 21:42:23 Summary: Fix another variable definition issue in user address deletion. Affected #: 1 file diff -r 2ae881148949596af9c30f2c559dc8f627dda402 -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 lib/galaxy/webapps/galaxy/controllers/user.py --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1522,7 +1522,7 @@ user_address.deleted = True trans.sa_session.add( user_address ) trans.sa_session.flush() - 'Address (%s) deleted' % user_address.desc + message = 'Address (%s) deleted' % user_address.desc status = 'done' return trans.response.send_redirect( web.url_for( controller='user', action='manage_user_info', https://bitbucket.org/galaxy/galaxy-central/commits/7aade8875ea4/ Changeset: 7aade8875ea4 User: dannon Date: 2014-07-23 22:27:42 Summary: Merge. Affected #: 60 files diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -12,7 +12,6 @@ import tool_shed.repository_types.util as rt_util from tool_shed.util import common_util -from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import readme_util @@ -25,6 +24,7 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.grids import admin_toolshed_grids from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager @@ -256,17 +256,17 @@ dmh.remove_from_data_manager( tool_shed_repository ) if tool_shed_repository.includes_datatypes: # Deactivate proprietary datatypes. - installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, - tool_shed_repository, - repository_install_dir, - deactivate=True ) + cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, + repository_install_dir, + deactivate=True ) if installed_repository_dict: converter_path = installed_repository_dict.get( 'converter_path' ) if converter_path is not None: - datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True ) display_path = installed_repository_dict.get( 'display_path' ) if display_path is not None: - datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -195,6 +195,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, ExportsHistoryMixin, ImportsHistoryMixin ): + def __init__( self, app ): super( HistoryController, self ).__init__( app ) self.mgrs = util.bunch.Bunch( diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1,5 +1,6 @@ from sqlalchemy import desc, and_ from galaxy import model, web +from galaxy import managers from galaxy.web import error, url_for from galaxy.model.item_attrs import UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin @@ -285,6 +286,12 @@ _page_selection_grid = PageSelectionGrid() _visualization_selection_grid = VisualizationSelectionGrid() + def __init__( self, app ): + super( PageController, self ).__init__( app ) + self.mgrs = util.bunch.Bunch( + histories=managers.histories.HistoryManager() + ) + @web.expose @web.require_login() def list( self, trans, *args, **kwargs ): @@ -718,6 +725,7 @@ """ Returns html suitable for embedding in another page. """ + #TODO: should be moved to history controller and/or called via ajax from the template history = self.get_history( trans, id, False, True ) if not history: return None @@ -729,15 +737,22 @@ hda_dicts = [] datasets = self.get_history_datasets( trans, history ) - for hda in datasets: - hda_dict = self.get_hda_dict( trans, hda ) - hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) - hda_dicts.append( hda_dict ) - history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) - history_dict[ 'annotation' ] = history.annotation + #for hda in datasets: + # hda_dict = self.get_hda_dict( trans, hda ) + # hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) + # hda_dicts.append( hda_dict ) + #history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) + #history_dict[ 'annotation' ] = history.annotation + + # include all datasets: hidden, deleted, and purged + #TODO!: doubled query (hda_dictionaries + datasets) + history_data = self.mgrs.histories._get_history_data( trans, history ) + history_dictionary = history_data[ 'history' ] + hda_dictionaries = history_data[ 'contents' ] + history_dictionary[ 'annotation' ] = history.annotation filled = trans.fill_template( "history/embed.mako", item=history, item_data=datasets, - user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts ) + user_is_owner=user_is_owner, history_dict=history_dictionary, hda_dicts=hda_dictionaries ) return filled def _get_embed_html( self, trans, item_class, item_id ): diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1062,7 +1062,7 @@ action='browse_repositories', message=message, status=status ) ) - name = kwd.get( 'name', '' ) + name = kwd.get( 'name', '' ).strip() description = kwd.get( 'description', '' ) long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) @@ -1262,7 +1262,11 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) metadata = repository_metadata.metadata toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + # Initialize the repository dependency RelationBuilder. rb = relation_builder.RelationBuilder( trans.app, repository, repository_metadata, toolshed_base_url ) + # Work-around to ensure repositories that contain packages needed only for compiling + # a dependent package are included in the capsule. + rb.set_filter_dependencies_needed_for_compiling( False ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() if repository_dependencies: diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -245,9 +245,13 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, self.repository_id, self.changeset_revision ) - # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + # Get a dictionary of all repositories upon which the contents of the current + # repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) rb = RelationBuilder( self.app, repository, repository_metadata, toolshed_base_url ) + # Work-around to ensure repositories that contain packages needed only for compiling + # a dependent package are included in the capsule. + rb.set_filter_dependencies_needed_for_compiling( False ) repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/dependencies/repository/relation_builder.py --- a/lib/tool_shed/dependencies/repository/relation_builder.py +++ b/lib/tool_shed/dependencies/repository/relation_builder.py @@ -23,6 +23,11 @@ self.handled_key_rd_dicts = [] self.key_rd_dicts_to_be_processed = [] self.tool_shed_url = tool_shed_url + # This is a temporary work-around for handling repository dependencies that are needed + # only if compiling a dependent package. This value should be True unless exporting + # a repository capsule, in which case the set_filter_dependencies_needed_for_compiling() + # function is called. + self.filter_dependencies_needed_for_compiling = True def can_add_to_key_rd_dicts( self, key_rd_dict, key_rd_dicts ): """Handle the case where an update to the changeset revision was done.""" @@ -389,9 +394,12 @@ current_repository_key_rd_dicts = \ self.get_updated_changeset_revisions_for_repository_dependencies( current_repository_key_rd_dicts ) for key_rd_dict in current_repository_key_rd_dicts: - # Filter out repository dependencies that are required only if compiling the dependent - # repository's tool dependency. - key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict ) + if self.filter_dependencies_needed_for_compiling: + # Filter out repository dependencies that are required only if compiling the dependent + # repository's tool dependency. + # TODO: this temporary work-around should be removed when the underlying framework + # support for handling only_if_compiling_contained_td-flagged repositories is completed. + key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict ) if key_rd_dict: is_circular = False in_handled_key_rd_dicts = self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ) @@ -483,6 +491,9 @@ clean_key_rd_dicts.append( new_key_rd_dict ) return clean_key_rd_dicts + def set_filter_dependencies_needed_for_compiling( self, value ): + self.filter_dependencies_needed_for_compiling = asbool( value ) + def update_circular_repository_dependencies( self, repository_key, repository_dependency, repository_dependencies ): repository_dependency_as_key = self.get_repository_dependency_as_key( repository_dependency ) repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py @@ -0,0 +1,218 @@ +import logging +import os +import tempfile + +from galaxy.util import asbool + +from tool_shed.util import basic_util +from tool_shed.util import hg_util +from tool_shed.util import tool_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class CustomDatatypeLoader( object ): + + def __init__( self, app ): + self.app = app + + def alter_config_and_load_prorietary_datatypes( self, datatypes_config, relative_install_dir, + deactivate=False, override=True ): + """ + Parse a custom datatypes config (a datatypes_conf.xml file included in an installed + tool shed repository) and add information to appropriate element attributes that will + enable custom datatype class modules, datatypes converters and display applications + to be discovered and properly imported by the datatypes registry. The value of override + will be False when a tool shed repository is being installed. Since installation is + occurring after the datatypes registry has been initialized, the registry's contents + cannot be overridden by conflicting data types. + """ + tree, error_message = xml_util.parse_xml( datatypes_config ) + if tree is None: + return None, None + datatypes_config_root = tree.getroot() + registration = datatypes_config_root.find( 'registration' ) + if registration is None: + # We have valid XML, but not a valid custom datatypes definition. + return None, None + sniffers = datatypes_config_root.find( 'sniffers' ) + converter_path, display_path = self.get_converter_and_display_paths( registration, + relative_install_dir ) + if converter_path: + # Path to datatype converters + registration.attrib[ 'proprietary_converter_path' ] = converter_path + if display_path: + # Path to datatype display applications + registration.attrib[ 'proprietary_display_path' ] = display_path + relative_path_to_datatype_file_name = None + datatype_files = datatypes_config_root.find( 'datatype_files' ) + datatype_class_modules = [] + if datatype_files is not None: + # The <datatype_files> tag set contains any number of <datatype_file> tags. + # <datatype_files> + # <datatype_file name="gmap.py"/> + # <datatype_file name="metagenomics.py"/> + # </datatype_files> + # We'll add attributes to the datatype tag sets so that the modules can be properly imported + # by the datatypes registry. + for elem in datatype_files.findall( 'datatype_file' ): + datatype_file_name = elem.get( 'name', None ) + if datatype_file_name: + # Find the file in the installed repository. + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == datatype_file_name: + datatype_class_modules.append( os.path.join( root, name ) ) + break + break + if datatype_class_modules: + for relative_path_to_datatype_file_name in datatype_class_modules: + datatype_file_name_path, datatype_file_name = os.path.split( relative_path_to_datatype_file_name ) + for elem in registration.findall( 'datatype' ): + # Handle 'type' attribute which should be something like one of the following: + # type="gmap:GmapDB" + # type="galaxy.datatypes.gmap:GmapDB" + dtype = elem.get( 'type', None ) + if dtype: + fields = dtype.split( ':' ) + proprietary_datatype_module = fields[ 0 ] + if proprietary_datatype_module.find( '.' ) >= 0: + # Handle the case where datatype_module is "galaxy.datatypes.gmap". + proprietary_datatype_module = proprietary_datatype_module.split( '.' )[ -1 ] + # The value of proprietary_path must be an absolute path due to job_working_directory. + elem.attrib[ 'proprietary_path' ] = os.path.abspath( datatype_file_name_path ) + elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module + # Temporarily persist the custom datatypes configuration file so it can be loaded into the + # datatypes registry. + fd, proprietary_datatypes_config = tempfile.mkstemp( prefix="tmp-toolshed-acalpd" ) + os.write( fd, '<?xml version="1.0"?>\n' ) + os.write( fd, '<datatypes>\n' ) + os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) + if sniffers is not None: + os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) + os.write( fd, '</datatypes>\n' ) + os.close( fd ) + os.chmod( proprietary_datatypes_config, 0644 ) + # Load custom datatypes + self.app.datatypes_registry.load_datatypes( root_dir=self.app.config.root, + config=proprietary_datatypes_config, + deactivate=deactivate, + override=override ) + if deactivate: + # Reload the upload tool to eliminate deactivated datatype extensions from the file_type + # select list. + tool_util.reload_upload_tools( self.app ) + else: + self.append_to_datatypes_registry_upload_file_formats( registration ) + tool_util.reload_upload_tools( self.app ) + if datatype_files is not None: + try: + os.unlink( proprietary_datatypes_config ) + except: + pass + return converter_path, display_path + + def append_to_datatypes_registry_upload_file_formats( self, elem ): + # See if we have any datatypes that should be displayed in the upload tool's file_type select list. + for datatype_elem in elem.findall( 'datatype' ): + extension = datatype_elem.get( 'extension', None ) + display_in_upload = datatype_elem.get( 'display_in_upload', None ) + if extension is not None and display_in_upload is not None: + display_in_upload = asbool( str( display_in_upload ) ) + if display_in_upload and extension not in self.app.datatypes_registry.upload_file_formats: + self.app.datatypes_registry.upload_file_formats.append( extension ) + + def create_repository_dict_for_proprietary_datatypes( self, tool_shed, name, owner, installed_changeset_revision, + tool_dicts, converter_path=None, display_path=None ): + return dict( tool_shed=tool_shed, + repository_name=name, + repository_owner=owner, + installed_changeset_revision=installed_changeset_revision, + tool_dicts=tool_dicts, + converter_path=converter_path, + display_path=display_path ) + + def get_converter_and_display_paths( self, registration_elem, relative_install_dir ): + """ + Find the relative path to data type converters and display applications included + in installed tool shed repositories. + """ + converter_path = None + display_path = None + for elem in registration_elem.findall( 'datatype' ): + if not converter_path: + # If any of the <datatype> tag sets contain <converter> tags, set the converter_path + # if it is not already set. This requires developers to place all converters in the + # same subdirectory within the repository hierarchy. + for converter in elem.findall( 'converter' ): + converter_config = converter.get( 'file', None ) + if converter_config: + converter_config_file_name = basic_util.strip_path( converter_config ) + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == converter_config_file_name: + # The value of converter_path must be absolute due to job_working_directory. + converter_path = os.path.abspath( root ) + break + if converter_path: + break + if not display_path: + # If any of the <datatype> tag sets contain <display> tags, set the display_path + # if it is not already set. This requires developers to place all display acpplications + # in the same subdirectory within the repository hierarchy. + for display_app in elem.findall( 'display' ): + display_config = display_app.get( 'file', None ) + if display_config: + display_config_file_name = basic_util.strip_path( display_config ) + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == display_config_file_name: + # The value of display_path must be absolute due to job_working_directory. + display_path = os.path.abspath( root ) + break + if display_path: + break + if converter_path and display_path: + break + return converter_path, display_path + + def load_installed_datatype_converters( self, installed_repository_dict, deactivate=False ): + """Load or deactivate proprietary datatype converters.""" + self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, + installed_repository_dict=installed_repository_dict, + deactivate=deactivate ) + + def load_installed_datatypes( self, repository, relative_install_dir, deactivate=False ): + """ + Load proprietary datatypes and return information needed for loading custom + datatypes converters and display applications later. + """ + metadata = repository.metadata + repository_dict = None + datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) + if datatypes_config: + converter_path, display_path = \ + self.alter_config_and_load_prorietary_datatypes( datatypes_config, + relative_install_dir, + deactivate=deactivate ) + if converter_path or display_path: + # Create a dictionary of tool shed repository related information. + repository_dict = \ + self.create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, + name=repository.name, + owner=repository.owner, + installed_changeset_revision=repository.installed_changeset_revision, + tool_dicts=metadata.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) + return repository_dict + + def load_installed_display_applications( self, installed_repository_dict, deactivate=False ): + """Load or deactivate custom datatype display applications.""" + self.app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, + deactivate=deactivate ) diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -18,7 +18,6 @@ from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc @@ -26,6 +25,7 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder @@ -594,18 +594,19 @@ files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) # Load data types required by tools. + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) converter_path, display_path = \ - datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, files_dir, override=False ) + cdl.alter_config_and_load_prorietary_datatypes( datatypes_config, files_dir, override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = \ - datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - 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', [] ), - converter_path=converter_path, - display_path=display_path ) + cdl.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, + 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', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict ) diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -7,12 +7,12 @@ from galaxy import util from tool_shed.util import common_util from tool_shed.util import container_util -from tool_shed.util import datatype_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import xml_util from galaxy.model.orm import and_ +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager from tool_shed.galaxy_install.tools import data_manager @@ -114,17 +114,17 @@ else: repository_install_dir = os.path.abspath( relative_install_dir ) # Activate proprietary datatypes. - installed_repository_dict = datatype_util.load_installed_datatypes( self.app, - repository, - repository_install_dir, - deactivate=False ) + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) + installed_repository_dict = cdl.load_installed_datatypes( repository, + repository_install_dir, + deactivate=False ) if installed_repository_dict: converter_path = installed_repository_dict.get( 'converter_path' ) if converter_path is not None: - datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=False ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=False ) display_path = installed_repository_dict.get( 'display_path' ) if display_path is not None: - datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=False ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=False ) def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ @@ -732,22 +732,24 @@ self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) def load_proprietary_datatypes( self ): + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) for tool_shed_repository in self.context.query( self.install_model.ToolShedRepository ) \ - .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, - self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ - .order_by( self.install_model.ToolShedRepository.table.c.id ): + .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, + self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ + .order_by( self.install_model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = datatype_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=deactivate ) def purge_repository( self, repository ): """Purge a repository with status New (a white ghost) from the database.""" diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -14,6 +14,7 @@ from galaxy.util.odict import odict from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.tools import tool_panel_manager @@ -22,7 +23,6 @@ from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import datatype_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util @@ -492,6 +492,7 @@ 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: + 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: tool_shed_repository.includes_datatypes = True @@ -499,21 +500,27 @@ self.app.install_model.context.flush() work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" ) datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir ) - # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started - # after this installation completes. - converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir + # Load proprietary data types required by tools. The value of override is not + # important here since the Galaxy server will be started after this installation + #completes. + converter_path, display_path = \ + cdl.alter_config_and_load_prorietary_datatypes( datatypes_config, + repo_install_dir, + override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. - repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url, - name=tool_shed_repository.name, - owner=self.repository_owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + repository_dict = \ + cdl.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url, + name=tool_shed_repository.name, + owner=self.repository_owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters - self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict ) + self.app.datatypes_registry.load_datatype_converters( self.toolbox, + installed_repository_dict=repository_dict ) if display_path: # Load proprietary datatype display applications self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 lib/tool_shed/util/datatype_util.py --- a/lib/tool_shed/util/datatype_util.py +++ /dev/null @@ -1,187 +0,0 @@ -import logging -import os -import tempfile -from galaxy import eggs -from galaxy.util import asbool -from tool_shed.util import basic_util -from tool_shed.util import hg_util -from tool_shed.util import tool_util -from tool_shed.util import xml_util -import tool_shed.util.shed_util_common as suc - -log = logging.getLogger( __name__ ) - -def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=False, override=True ): - """ - Parse a proprietary datatypes config (a datatypes_conf.xml file included in an installed tool shed repository) and - add information to appropriate element attributes that will enable proprietary datatype class modules, datatypes converters - and display applications to be discovered and properly imported by the datatypes registry. The value of override will - be False when a tool shed repository is being installed. Since installation is occurring after the datatypes registry - has been initialized, the registry's contents cannot be overridden by conflicting data types. - """ - tree, error_message = xml_util.parse_xml( datatypes_config ) - if tree is None: - return None, None - datatypes_config_root = tree.getroot() - registration = datatypes_config_root.find( 'registration' ) - if registration is None: - # We have valid XML, but not a valid proprietary datatypes definition. - return None, None - sniffers = datatypes_config_root.find( 'sniffers' ) - converter_path, display_path = get_converter_and_display_paths( registration, relative_install_dir ) - if converter_path: - # Path to datatype converters - registration.attrib[ 'proprietary_converter_path' ] = converter_path - if display_path: - # Path to datatype display applications - registration.attrib[ 'proprietary_display_path' ] = display_path - relative_path_to_datatype_file_name = None - datatype_files = datatypes_config_root.find( 'datatype_files' ) - datatype_class_modules = [] - if datatype_files is not None: - # The <datatype_files> tag set contains any number of <datatype_file> tags. - # <datatype_files> - # <datatype_file name="gmap.py"/> - # <datatype_file name="metagenomics.py"/> - # </datatype_files> - # We'll add attributes to the datatype tag sets so that the modules can be properly imported by the datatypes registry. - for elem in datatype_files.findall( 'datatype_file' ): - datatype_file_name = elem.get( 'name', None ) - if datatype_file_name: - # Find the file in the installed repository. - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == datatype_file_name: - datatype_class_modules.append( os.path.join( root, name ) ) - break - break - if datatype_class_modules: - for relative_path_to_datatype_file_name in datatype_class_modules: - datatype_file_name_path, datatype_file_name = os.path.split( relative_path_to_datatype_file_name ) - for elem in registration.findall( 'datatype' ): - # Handle 'type' attribute which should be something like one of the following: - # type="gmap:GmapDB" - # type="galaxy.datatypes.gmap:GmapDB" - dtype = elem.get( 'type', None ) - if dtype: - fields = dtype.split( ':' ) - proprietary_datatype_module = fields[ 0 ] - if proprietary_datatype_module.find( '.' ) >= 0: - # Handle the case where datatype_module is "galaxy.datatypes.gmap". - proprietary_datatype_module = proprietary_datatype_module.split( '.' )[ -1 ] - # The value of proprietary_path must be an absolute path due to job_working_directory. - elem.attrib[ 'proprietary_path' ] = os.path.abspath( datatype_file_name_path ) - elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module - # Temporarily persist the proprietary datatypes configuration file so it can be loaded into the datatypes registry. - fd, proprietary_datatypes_config = tempfile.mkstemp( prefix="tmp-toolshed-acalpd" ) - os.write( fd, '<?xml version="1.0"?>\n' ) - os.write( fd, '<datatypes>\n' ) - os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) - if sniffers is not None: - os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) - os.write( fd, '</datatypes>\n' ) - os.close( fd ) - os.chmod( proprietary_datatypes_config, 0644 ) - # Load proprietary datatypes - app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) - if deactivate: - # Reload the upload tool to eliminate deactivated datatype extensions from the file_type select list. - tool_util.reload_upload_tools( app ) - else: - append_to_datatypes_registry_upload_file_formats( app, registration ) - tool_util.reload_upload_tools( app ) - if datatype_files is not None: - try: - os.unlink( proprietary_datatypes_config ) - except: - pass - return converter_path, display_path - -def append_to_datatypes_registry_upload_file_formats( app, elem ): - # See if we have any datatypes that should be displayed in the upload tool's file_type select list. - for datatype_elem in elem.findall( 'datatype' ): - extension = datatype_elem.get( 'extension', None ) - display_in_upload = datatype_elem.get( 'display_in_upload', None ) - if extension is not None and display_in_upload is not None: - display_in_upload = asbool( str( display_in_upload ) ) - if display_in_upload and extension not in app.datatypes_registry.upload_file_formats: - app.datatypes_registry.upload_file_formats.append( extension ) - -def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): - return dict( tool_shed=tool_shed, - repository_name=name, - repository_owner=owner, - installed_changeset_revision=installed_changeset_revision, - tool_dicts=tool_dicts, - converter_path=converter_path, - display_path=display_path ) - -def get_converter_and_display_paths( registration_elem, relative_install_dir ): - """Find the relative path to data type converters and display applications included in installed tool shed repositories.""" - converter_path = None - display_path = None - for elem in registration_elem.findall( 'datatype' ): - if not converter_path: - # If any of the <datatype> tag sets contain <converter> tags, set the converter_path - # if it is not already set. This requires developers to place all converters in the - # same subdirectory within the repository hierarchy. - for converter in elem.findall( 'converter' ): - converter_config = converter.get( 'file', None ) - if converter_config: - converter_config_file_name = basic_util.strip_path( converter_config ) - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == converter_config_file_name: - # The value of converter_path must be absolute due to job_working_directory. - converter_path = os.path.abspath( root ) - break - if converter_path: - break - if not display_path: - # If any of the <datatype> tag sets contain <display> tags, set the display_path - # if it is not already set. This requires developers to place all display acpplications - # in the same subdirectory within the repository hierarchy. - for display_app in elem.findall( 'display' ): - display_config = display_app.get( 'file', None ) - if display_config: - display_config_file_name = basic_util.strip_path( display_config ) - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == display_config_file_name: - # The value of display_path must be absolute due to job_working_directory. - display_path = os.path.abspath( root ) - break - if display_path: - break - if converter_path and display_path: - break - return converter_path, display_path - -def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ): - # Load or deactivate proprietary datatype converters - app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=installed_repository_dict, deactivate=deactivate ) - -def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ): - # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. - metadata = repository.metadata - repository_dict = None - datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) - if datatypes_config: - converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) - if converter_path or display_path: - # Create a dictionary of tool shed repository related information. - repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, - name=repository.name, - owner=repository.owner, - installed_changeset_revision=repository.installed_changeset_revision, - tool_dicts=metadata.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) - return repository_dict - -def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): - # Load or deactivate proprietary datatype display applications - app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -14,7 +14,7 @@ * @example * // Add to your models/views at the definition using chaining: * var MyModel = Backbone.Model.extend( LoggableMixin ).extend({ // ... }); - * + * * // or - more explicitly AFTER the definition: * var MyModel = Backbone.Model.extend({ * logger : console @@ -208,8 +208,23 @@ }; //============================================================================== -return { - LoggableMixin : LoggableMixin, - SessionStorageModel : SessionStorageModel, - HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin -};}); +function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){ + // usage: var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... }) ); + //NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that + + // simple reversal of param order on _.defaults() - to show mixins in top of definition + var args = Array.prototype.slice.call( arguments, 0 ), + lastArg = args.pop(); + args.unshift( lastArg ); + return _.defaults.apply( _, args ); +} + + +//============================================================================== + return { + LoggableMixin : LoggableMixin, + SessionStorageModel : SessionStorageModel, + HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin, + mixin : mixin + }; +}); diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 static/scripts/mvc/collection/collection-model.js --- /dev/null +++ b/static/scripts/mvc/collection/collection-model.js @@ -0,0 +1,250 @@ +define([ + "mvc/dataset/hda-model", + "mvc/base-mvc", + "utils/localization" +], function( HDA_MODEL, BASE_MVC, _l ){ +//============================================================================== +/** @class Backbone model for Dataset collection elements. + * DC Elements contain a sub-model named 'object'. This class moves that + * 'object' from the JSON in the attributes list to a full, instantiated + * sub-model found in this.object. This is done on intialization and + * everytime the 'change:object' event is fired. + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DatasetCollectionElement = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends DatasetCollectionElement.prototype */{ + //TODO:?? this model may be unneccessary - it reflects the api structure, but... + // if we munge the element with the element.object at parse, we can flatten the entire hierarchy + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + defaults : { + id : null, + model_class : 'DatasetCollectionElement', + element_identifier : null, + element_index : null, + element_type : null + }, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( model, options ){ + this.info( this + '.initialize:', model, options ); + options = options || {}; + //this._setUpListeners(); + + this.object = this._createObjectModel(); + this.on( 'change:object', function(){ + //console.log( 'change:object' ); +//TODO: prob. better to update the sub-model instead of re-creating it + this.object = this._createObjectModel(); + }); + }, + + _createObjectModel : function(){ + //console.log( '_createObjectModel', this.get( 'object' ), this.object ); + //TODO: same patterns as HDCA _createElementsModel - refactor to BASE_MVC.hasSubModel? + if( _.isUndefined( this.object ) ){ this.object = null; } + if( !this.get( 'object' ) ){ return this.object; } + + var object = this.get( 'object' ); + this.unset( 'object', { silent: true }); + + this.debug( 'DCE, element_type:', this.get( 'element_type' ) ); + switch( this.get( 'element_type' ) ){ + case 'dataset_collection': + this.object = new DatasetCollection( object ); + break; + case 'hda': + this.object = new HDA_MODEL.HistoryDatasetAssociation( object ); + break; + default: + throw new TypeError( 'Unknown element_type: ' + this.get( 'element_type' ) ); + } + return this.object; + }, + + /** String representation. */ + toString : function(){ + var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) ); + return ([ 'DatasetCollectionElement(', objStr, ')' ].join( '' )); + } +}); + + +//============================================================================== +/** @class Backbone collection for DCEs. + * NOTE: used *only* in second level of list:paired collections (a + * collection that contains collections) + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DatasetCollectionElementCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends DatasetCollectionElementCollection.prototype */{ + model: DatasetCollectionElement, + + // comment this out to suppress log output + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( models, options ){ + options = options || {}; + this.info( this + '.initialize:', models, options ); + //this._setUpListeners(); + }, + + /** String representation. */ + toString : function(){ + return ([ 'DatasetCollectionElementCollection(', this.length, ')' ].join( '' )); + } +}); + + +//============================================================================== +/** @class Backbone model for Dataset Collections. + * DCs contain a bbone collection named 'elements' using the class found in + * this.collectionClass (gen. DatasetCollectionElementCollection). DCs move + * that 'object' from the JSON in the attributes list to a full, instantiated + * collection found in this.elements. This is done on intialization and + * everytime the 'change:elements' event is fired. + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DatasetCollection = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends ListDatasetCollection.prototype */{ + + //logger : console, + + /** default attributes for a model */ + defaults : { + collection_type : 'list' + }, + + collectionClass : DatasetCollectionElementCollection, + + /** */ + initialize : function( model, options ){ + this.info( 'DatasetCollection.initialize:', model, options ); + //historyContent.HistoryContent.prototype.initialize.call( this, attrs, options ); + this.elements = this._createElementsModel(); +//TODO:?? no way to use parse here? + this.on( 'change:elements', function(){ + this.log( 'change:elements' ); +//TODO: prob. better to update the collection instead of re-creating it + this.elements = this._createElementsModel(); + }); + }, + + /** move elements model attribute to full collection */ + _createElementsModel : function(){ + this.log( '_createElementsModel', this.get( 'elements' ), this.elements ); +//TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel? + var elements = this.get( 'elements' ) || []; + this.info( 'elements:', elements ); + this.unset( 'elements', { silent: true }); + this.elements = new this.collectionClass( elements ); + return this.elements; + }, + + hasDetails : function(){ +//TODO: this is incorrect for (accidentally) empty collections + return this.elements.length !== 0; + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + var idAndName = [ this.get( 'id' ), this.get( 'name' ) || this.get( 'element_identifier' ) ]; + return 'DatasetCollection(' + ( idAndName.join(',') ) + ')'; + } +}); + + +//============================================================================== +/** @class Backbone collection for a collection of collection collections collecting correctly. */ +var DatasetCollectionCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend({ + + model: DatasetCollection, + + ///** logger used to record this.log messages, commonly set to console */ + //// comment this out to suppress log output + //logger : console, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( models, options ){ + options = options || {}; + this.info( 'DatasetCollectionCollection.initialize:', models, options ); + //this._setUpListeners(); + }, + + /** String representation. */ + toString : function(){ + return ([ 'DatasetCollectionCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//NOTE: the following prototypes may not be necessary - but I wanted to specifiy +// them (for now) and allow for the possibility of unique functionality +//============================================================================== +var ListDatasetCollection = DatasetCollection.extend( +/** @lends ListDatasetCollection.prototype */{ + + /** String representation. */ + toString : function(){ + return ([ 'ListDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== +var PairDatasetCollection = DatasetCollection.extend( +/** @lends ListDatasetCollection.prototype */{ + + /** String representation. */ + toString : function(){ + return ([ 'PairDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== +var ListPairedDatasetCollection = DatasetCollection.extend( +/** @lends ListDatasetCollection.prototype */{ + + // list:paired is the only collection that itself contains collections + //collectionClass : DatasetCollectionCollection, + + /** String representation. */ + toString : function(){ + return ([ 'ListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== + return { + DatasetCollectionElement : DatasetCollectionElement, + DatasetCollectionElementCollection : DatasetCollectionElementCollection, + DatasetCollection : DatasetCollection, + DatasetCollectionCollection : DatasetCollectionCollection, + ListDatasetCollection : ListDatasetCollection, + PairDatasetCollection : PairDatasetCollection, + ListPairedDatasetCollection : ListPairedDatasetCollection + }; +}); diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 static/scripts/mvc/collection/collection-panel.js --- /dev/null +++ b/static/scripts/mvc/collection/collection-panel.js @@ -0,0 +1,326 @@ +define([ + "mvc/collection/dataset-collection-base", + "mvc/dataset/hda-base", + "mvc/base-mvc", + "utils/localization" +], function( DC_BASE, HDA_BASE, BASE_MVC, _l ){ +/* ============================================================================= +TODO: + +============================================================================= */ +/** @class non-editable, read-only View/Controller for a dataset collection. + * @name CollectionPanel + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends CollectionPanel.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + tagName : 'div', + className : 'history-panel', + + /** (in ms) that jquery effects will use */ + fxSpeed : 'fast', + + // ......................................................................... SET UP + /** Set up the view, set up storage, bind listeners to HistoryContents events + * @param {Object} attributes optional settings for the panel + */ + initialize : function( attributes ){ + attributes = attributes || {}; + // set the logger if requested + if( attributes.logger ){ + this.logger = attributes.logger; + } + this.log( this + '.initialize:', attributes ); + + this.hasUser = attributes.hasUser; + this.HDAViewClass = attributes.HDAViewClass || HDA_BASE.HDABaseView; + }, + + /** create any event listeners for the panel + * @fires: rendered:initial on the first render + * @fires: empty-history when switching to a history with no HDAs or creating a new history + */ + _setUpListeners : function(){ + // debugging + //if( this.logger ){ + this.on( 'all', function( event ){ + this.log( this + '', arguments ); + }, this ); + //} + return this; + }, + + // ------------------------------------------------------------------------ history/hda event listening + /** listening for history and HDA events */ + _setUpModelEventHandlers : function(){ + return this; + }, + + // ------------------------------------------------------------------------ panel rendering + /** Render urls, historyPanel body, and hdas (if any are shown) + * @fires: rendered when the panel is attached and fully visible + * @see Backbone.View#render + */ + render : function( speed, callback ){ + this.log( 'render:', speed, callback ); + // send a speed of 0 to have no fade in/out performed + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + //console.debug( this + '.render, fxSpeed:', speed ); + var panel = this, + $newRender; + + // handle the possibility of no model (can occur if fetching the model returns an error) + if( !this.model ){ + return this; + } + $newRender = this.renderModel(); + + // fade out existing, swap with the new, fade in, set up behaviours + $( panel ).queue( 'fx', [ + function( next ){ + if( speed && panel.$el.is( ':visible' ) ){ + panel.$el.fadeOut( speed, next ); + } else { + next(); + } + }, + function( next ){ + // swap over from temp div newRender + panel.$el.empty(); + if( $newRender ){ + panel.$el.append( $newRender.children() ); + } + next(); + }, + function( next ){ + if( speed && !panel.$el.is( ':visible' ) ){ + panel.$el.fadeIn( speed, next ); + } else { + next(); + } + }, + function( next ){ + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + if( callback ){ callback.call( this ); } + panel.trigger( 'rendered', this ); + next(); + } + ]); + return this; + }, + + /** render with history data + * @returns {jQuery} dom fragment as temporary container to be swapped out later + */ + renderModel : function( ){ + // tmp div for final swap in render + var $newRender = $( '<div/>' ).append( CollectionPanel.templates.panel( this.model.toJSON() ) ); + this._setUpBehaviours( $newRender ); + this.renderContents( $newRender ); + return $newRender; + }, + + /** Set up HistoryPanel js/widget behaviours */ + _setUpBehaviours : function( $where ){ + //TODO: these should be either sub-MVs, or handled by events + $where = $where || this.$el; + $where.find( '[title]' ).tooltip({ placement: 'bottom' }); + return this; + }, + + // ------------------------------------------------------------------------ sub-$element shortcuts + /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ + $container : function(){ + return ( this.findContainerFn )?( this.findContainerFn.call( this ) ):( this.$el.parent() ); + }, + /** where hdaViews are attached */ + $datasetsList : function( $where ){ + return ( $where || this.$el ).find( '.datasets-list' ); + }, + + // ------------------------------------------------------------------------ sub-views + /** Set up/render a view for each HDA to be shown, init with model and listeners. + * HDA views are cached to the map this.hdaViews (using the model.id as key). + * @param {jQuery} $whereTo what dom element to prepend the HDA views to + * @returns the number of visible hda views + */ + renderContents : function( $whereTo ){ + //console.debug( 'renderContents, elements:', this.model.elements ); + $whereTo = $whereTo || this.$el; + + var panel = this, + contentViews = {}, + visibleContents = this.model.elements || []; + //this.log( 'renderContents, visibleContents:', visibleContents, $whereTo ); + + this.$datasetsList( $whereTo ).empty(); + if( visibleContents && visibleContents.length ){ + visibleContents.each( function( content ){ + var contentId = content.id, + contentView = panel._createContentView( content ); + contentViews[ contentId ] = contentView; + panel.attachContentView( contentView.render(), $whereTo ); + }); + } + this.contentViews = contentViews; + return this.contentViews; + }, + + /** + * @param {HistoryDatasetAssociation} content + */ + _createContentView : function( content ){ + //console.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); + var contentView = null, + ContentClass = this._getContentClass( content ); + //console.debug( 'content.object json:', JSON.stringify( content.object, null, ' ' ) ); + //console.debug( 'ContentClass:', ContentClass ); + //console.debug( 'content:', content ); + //console.debug( 'content.object:', content.object ); + contentView = new ContentClass({ + model : content.object, + linkTarget : this.linkTarget, + //draggable : true, + hasUser : this.hasUser, + logger : this.logger + }); + //this._setUpHdaListeners( contentView ); + return contentView; + }, + + _getContentClass : function( content ){ + switch( content.get( 'element_type' ) ){ + case 'hda': + return this.HDAViewClass; + case 'dataset_collection': + return DC_BASE.NestedDCEBaseView; + } + throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) ); + }, + +// /** Set up HistoryPanel listeners for HDAView events. Currently binds: +// * HDAView#body-visible, HDAView#body-hidden to store expanded states +// * @param {HDAView} hdaView HDAView (base or edit) to listen to +// */ +// _setUpHdaListeners : function( hdaView ){ +// var panel = this; +// hdaView.on( 'error', function( model, xhr, options, msg ){ +// panel.errorHandler( model, xhr, options, msg ); +// }); +// // maintain a list of hdas whose bodies are expanded +// hdaView.on( 'body-expanded', function( model ){ +// panel.storage.addExpandedHda( model ); +// }); +// hdaView.on( 'body-collapsed', function( id ){ +// panel.storage.removeExpandedHda( id ); +// }); +// return this; +// }, + + /** attach an contentView to the panel */ + attachContentView : function( contentView, $whereTo ){ + $whereTo = $whereTo || this.$el; + var $datasetsList = this.$datasetsList( $whereTo ); + $datasetsList.append( contentView.$el ); + return this; + }, + + // ------------------------------------------------------------------------ panel events + /** event map */ + events : { + 'click .panel-navigation-back' : 'close' + }, + + /** */ + close : function( event ){ + this.$el.remove(); + this.trigger( 'collection-close' ); + }, + + // ........................................................................ misc + /** Return a string rep of the history */ + toString : function(){ + return 'CollectionPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); + + +//------------------------------------------------------------------------------ TEMPLATES +var _panelTemplate = [ + '<div class="history-controls">', + '<div class="panel-navigation">', + '<a class="panel-navigation-back" href="javascript:void(0)">', _l( 'Back' ), '</a>', + '</div>', + + '<div class="history-title">', + '<% if( collection.name ){ %>', + '<div class="history-name"><%= collection.hid %> : <%= collection.name %></div>', + '<% } %>', + '</div>', + + //'<div class="history-subtitle clear">', + // '<% if( history.nice_size ){ %>', + // '<div class="history-size"><%= history.nice_size %></div>', + // '<% } %>', + // '<div class="history-secondary-actions"></div>', + //'</div>', + // + //'<% if( history.deleted ){ %>', + // '<div class="warningmessagesmall"><strong>', + // _l( 'You are currently viewing a deleted history!' ), + // '</strong></div>', + //'<% } %>', + // + //'<div class="message-container">', + // '<% if( history.message ){ %>', + // // should already be localized + // '<div class="<%= history.status %>message"><%= history.message %></div>', + // '<% } %>', + //'</div>', + // + //'<div class="quota-message errormessage">', + // _l( 'You are over your disk quota' ), '. ', + // _l( 'Tool execution is on hold until your disk usage drops below your allocated quota' ), '.', + //'</div>', + // + //'<div class="tags-display"></div>', + //'<div class="annotation-display"></div>', + //'<div class="history-dataset-actions">', + // '<div class="btn-group">', + // '<button class="history-select-all-datasets-btn btn btn-default"', + // 'data-mode="select">', _l( 'All' ), '</button>', + // '<button class="history-deselect-all-datasets-btn btn btn-default"', + // 'data-mode="select">', _l( 'None' ), '</button>', + // '</div>', + // '<button class="history-dataset-action-popup-btn btn btn-default">', + // _l( 'For all selected' ), '...</button>', + //'</div>', + '</div>', + // end history controls + + // where the datasets/hdas are added + '<div class="datasets-list"></div>' + +].join( '' ); + +CollectionPanel.templates = { + panel : function( JSON ){ + return _.template( _panelTemplate, JSON, { variable: 'collection' }); + } +}; + + +//============================================================================== + return { + CollectionPanel: CollectionPanel + }; +}); diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 static/scripts/mvc/collection/dataset-collection-base.js --- a/static/scripts/mvc/collection/dataset-collection-base.js +++ b/static/scripts/mvc/collection/dataset-collection-base.js @@ -1,328 +1,151 @@ define([ - "mvc/history/history-content-base-view", + "mvc/base-mvc", "utils/localization" -], function( historyContentBaseView, _l ){ +], function( BASE_MVC, _l ){ /* global Backbone, LoggableMixin */ //============================================================================== -/** @class Read only view for HistoryDatasetCollectionAssociation. - * @name HDABaseView +/** @class Read only view for DatasetCollection. + * @name DCBaseView * * @augments Backbone.View * @borrows LoggableMixin#logger as #logger * @borrows LoggableMixin#log as #log * @constructs */ -var DatasetCollectionBaseView = historyContentBaseView.HistoryContentBaseView.extend({ - className : "dataset hda history-panel-hda", - id : function(){ return 'hdca-' + this.model.get( 'id' ); }, +var DCBaseView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + /** */ + className : "dataset-collection", + /** */ + fxSpeed : 'fast', /** */ initialize : function( attributes ){ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } - this.log( this + '.initialize:', attributes ); - /** is the view currently in selection mode? */ - this.selectable = attributes.selectable || false; - //this.log( '\t selectable:', this.selectable ); - /** is the view currently selected? */ - this.selected = attributes.selected || false; - /** is the body of this collection view expanded/not? */ - this.expanded = attributes.expanded || false; + this.log( 'DCBaseView.initialize:', attributes ); }, - /** */ - render : function( fade ){ - var $newRender = this._buildNewRender(); - - this._queueNewRender( $newRender, fade ); - return this; - }, - - /** */ - _buildNewRender : function(){ - var $newRender = $( DatasetCollectionBaseView.templates.skeleton( this.model.toJSON() ) ); - $newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() ); - $newRender.children( '.dataset-body' ).replaceWith( this._render_body() ); - this._setUpBehaviors( $newRender ); - return $newRender; - }, - - /** */ - _queueNewRender : function( $newRender, fade ) { - fade = ( fade === undefined )?( true ):( fade ); - var view = this; - - // fade the old render out (if desired) - if( fade ){ - $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); }); - } - // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select - $( view ).queue( function( next ){ - this.$el.empty() - .attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) ) - .append( $newRender.children() ); - if( this.selectable ){ this.showSelector( 0 ); } - next(); - }); - // fade the new in - if( fade ){ - $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); }); - } - // trigger an event to know we're ready - $( view ).queue( function( next ){ - this.trigger( 'rendered', view ); - if( this.model.inReadyState() ){ - this.trigger( 'rendered:ready', view ); - } - if( this.draggable ){ this.draggableOn(); } - next(); - }); - }, - - // ................................................................................ titlebar buttons - /** Render icon-button group for the common, most easily accessed actions. - * @returns {jQuery} rendered DOM - */ - _render_titleButtons : function(){ - // render just the display for read-only - return [ ]; - }, - - // ......................................................................... state body renderers - /** Render the enclosing div of the collection body and, if expanded, the html in the body - * @returns {jQuery} rendered DOM - */ - _render_body : function(){ - var $body = $( '<div>Error: unknown state "' + this.model.get( 'state' ) + '".</div>' ), - // cheesy: get function by assumed matching name - renderFn = this[ '_render_body_' + this.model.get( 'state' ) ]; - if( _.isFunction( renderFn ) ){ - $body = renderFn.call( this ); - } - this._setUpBehaviors( $body ); - - // only render the body html if it's being shown - if( this.expanded ){ - $body.show(); - } - return $body; - }, - - /** set up js behaviors, event handlers for elements within the given container - * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) - */ - _setUpBehaviors : function( $container ){ - $container = $container || this.$el; - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - make_popup_menus( $container ); - $container.find( '[title]' ).tooltip({ placement : 'bottom' }); - }, - - // TODO: Eliminate duplication between following event map and one for HDAs. - - // ......................................................................... events - /** event map */ - events : { - // expand the body when the title is clicked or when in focus and space or enter is pressed - 'click .dataset-title-bar' : 'toggleBodyVisibility', - 'keydown .dataset-title-bar' : 'toggleBodyVisibility', - - // toggle selected state - 'click .dataset-selector' : 'toggleSelect' - }, - - /** Show or hide the body/details of history content. - * note: if the model does not have detailed data, fetch that data before showing the body - * @param {Event} event the event that triggered this (@link HDABaseView#events) - * @param {Boolean} expanded if true, expand; if false, collapse - * @fires body-expanded when a body has been expanded - * @fires body-collapsed when a body has been collapsed - */ - toggleBodyVisibility : function( event, expand ){ - // bail (with propagation) if keydown and not space or enter - var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( event && ( event.type === 'keydown' ) - && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ - return true; - } - - var $body = this.$el.find( '.dataset-body' ); - expand = ( expand === undefined )?( !$body.is( ':visible' ) ):( expand ); - if( expand ){ - this.expandBody(); - } else { - this.collapseBody(); - } - return false; - }, - - /** Render and show the full, detailed body of this view including extra data and controls. - * @fires body-expanded when a body has been expanded - */ - expandBody : function(){ - var contentView = this; - - function _renderBodyAndExpand(){ - contentView.$el.children( '.dataset-body' ).replaceWith( contentView._render_body() ); - contentView.$el.children( '.dataset-body' ).slideDown( contentView.fxSpeed, function(){ - contentView.expanded = true; - contentView.trigger( 'body-expanded', contentView.model ); - }); - } - // TODO: Fetch more details like HDA view... - _renderBodyAndExpand(); - }, - - /** Hide the body/details of an HDA. - * @fires body-collapsed when a body has been collapsed - */ - collapseBody : function(){ - var hdaView = this; - this.$el.children( '.dataset-body' ).slideUp( hdaView.fxSpeed, function(){ - hdaView.expanded = false; - hdaView.trigger( 'body-collapsed', hdaView.model.id ); - }); - }, - - /** Render an 'ok' collection. - * @param {jQuery} parent DOM to which to append this body - */ - _render_body_ok : function(){ - // most common state renderer and the most complicated - var $body = $( DatasetCollectionBaseView.templates.body( this.model.toJSON() ) ); - - // return shortened form if del'd (no display apps or peek?) - if( this.model.get( 'deleted' ) ){ - return $body; - } - - return $body; - }, - - // ......................................................................... selection - /** display a (fa-icon) checkbox on the left of the hda that fires events when checked - * Note: this also hides the primary actions - */ - showSelector : function(){ - // make sure selected state is represented properly - if( this.selected ){ - this.select( null, true ); - } - - this.selectable = true; - this.trigger( 'selectable', true, this ); - - this.$( '.dataset-primary-actions' ).hide(); - this.$( '.dataset-selector' ).show(); - }, - - /** remove the selection checkbox */ - hideSelector : function(){ - // reverse the process from showSelect - this.selectable = false; - this.trigger( 'selectable', false, this ); - - this.$( '.dataset-selector' ).hide(); - this.$( '.dataset-primary-actions' ).show(); - }, - - toggleSelector : function(){ - if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){ - this.showSelector(); - } else { - this.hideSelector(); - } - }, - - /** event handler for selection (also programmatic selection) - */ - select : function( event ){ - // switch icon, set selected, and trigger event - this.$el.find( '.dataset-selector span' ) - .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' ); - if( !this.selected ){ - this.trigger( 'selected', this, event ); - this.selected = true; - } - return false; - }, - - /** event handler for clearing selection (also programmatic deselection) - */ - deselect : function( event ){ - // switch icon, set selected, and trigger event - this.$el.find( '.dataset-selector span' ) - .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' ); - if( this.selected ){ - this.trigger( 'de-selected', this, event ); - this.selected = false; - } - return false; - }, - - toggleSelect : function( event ){ - if( this.selected ){ - this.deselect( event ); - } else { - this.select( event ); - } - }, +//TODO: render has been removed from the inheritance chain here, so this won't work when called as is // ......................................................................... misc /** String representation */ toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDCABaseView(' + modelString + ')'; + return 'DCBaseView(' + modelString + ')'; } }); -//------------------------------------------------------------------------------ TEMPLATES -//TODO: possibly break these out into a sep. module -var skeletonTemplate = _.template([ - '<div class="dataset hda">', - '<div class="dataset-warnings">', - '<% if ( collection.deleted ) { %>', - '<div class="dataset-deleted-msg warningmessagesmall"><strong>', - _l( 'This collection has been deleted.' ), +/** templates for DCBaseViews (skeleton and body) */ +DCBaseView.templates = (function(){ +// use closure to run underscore template fn only once at module load + var skeletonTemplate = _.template([ + '<div class="dataset hda">', + '<div class="dataset-warnings">', + '<% if ( collection.deleted ) { %>', + '<div class="dataset-deleted-msg warningmessagesmall"><strong>', + _l( 'This collection has been deleted.' ), + '</div>', + '<% } %>', + '<% if ( !collection.visible ) { %>', + '<div class="dataset-hidden-msg warningmessagesmall"><strong>', + _l( 'This collection has been hidden.' ), + '</div>', + '<% } %>', + '</div>', + '<div class="dataset-primary-actions"></div>', + '<div class="dataset-title-bar clear" tabindex="0">', + '<span class="dataset-state-icon state-icon"></span>', + '<div class="dataset-title">', + '<span class="dataset-name"><%- collection.name %></span>', '</div>', - '<% } %>', - '<% if ( !collection.visible ) { %>', - '<div class="dataset-hidden-msg warningmessagesmall"><strong>', - _l( 'This collection has been hidden.' ), - '</div>', - '<% } %>', - '</div>', - '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', - '<div class="dataset-primary-actions"></div>', - '<div class="dataset-title-bar clear" tabindex="0">', - '<span class="dataset-state-icon state-icon"></span>', - '<div class="dataset-title">', - '<span class="hda-hid"><%= collection.hid %></span> ', - '<span class="dataset-name"><%= collection.name %></span>', '</div>', - '</div>', - '<div class="dataset-body"></div>', - '</div>' -].join( '' )); + '<div class="dataset-body"></div>', + '</div>' + ].join( '' )); -var bodyTemplate = _.template([ - '<div class="dataset-body">', - '<div class="dataset-summary">', - _l( 'A dataset collection.' ), - '</div>' -].join( '' )); + var bodyTemplate = _.template([ + '<div class="dataset-body">', + '<div class="dataset-summary">', + _l( 'A dataset collection.' ), + '</div>' + ].join( '' )); -DatasetCollectionBaseView.templates = { // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within - skeleton : function( collectionJSON ){ - return skeletonTemplate({ _l: _l, collection: collectionJSON }); - }, - body : function( collectionJSON ){ - return bodyTemplate({ _l: _l, collection: collectionJSON }); - } -}; + return { + skeleton : function( collectionJSON ){ + return skeletonTemplate({ _l: _l, collection: collectionJSON }); + }, + body : function( collectionJSON ){ + return bodyTemplate({ _l: _l, collection: collectionJSON }); + } + }; +}()); + + +//TODO: unused +////============================================================================== +///** @class Read only view for DatasetCollectionElement. +// * @name DCEBaseView +// * +// * @augments Backbone.View +// * @borrows LoggableMixin#logger as #logger +// * @borrows LoggableMixin#log as #log +// * @constructs +// */ +//var NestedDCBaseView = DCBaseView.extend({ +// +// logger : console, +// +// /** */ +// initialize : function( attributes ){ +// if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } +// this.warn( this + '.initialize:', attributes ); +// DCBaseView.prototype.initialize.call( this, attributes ); +// }, +// +// _template : function(){ +// this.debug( this.model ); +// this.debug( this.model.toJSON() ); +// return NestedDCBaseView.templates.skeleton( this.model.toJSON() ); +// }, +// +// // ......................................................................... misc +// /** String representation */ +// toString : function(){ +// var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); +// return 'NestedDCBaseView(' + modelString + ')'; +// } +//}); +// +////------------------------------------------------------------------------------ TEMPLATES +////TODO: possibly break these out into a sep. module +//NestedDCBaseView.templates = (function(){ +// var skeleton = _.template([ +// '<div class="dataset hda history-panel-hda state-ok">', +// '<div class="dataset-primary-actions"></div>', +// '<div class="dataset-title-bar clear" tabindex="0">', +// '<div class="dataset-title">', +// '<span class="dataset-name"><%= collection.name %></span>', +// '</div>', +// '</div>', +// '</div>' +// ].join( '' )); +// // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within +// return { +// skeleton : function( json ){ +// return skeleton({ _l: _l, collection: json }); +// } +// }; +//}()); + //============================================================================== return { - DatasetCollectionBaseView : DatasetCollectionBaseView + DCBaseView : DCBaseView, + //NestedDCBaseView : NestedDCBaseView, }; }); diff -r 4974ffd8b2cb5ee994a0d517c2332261898d4d46 -r 7aade8875ea4dde276b33922bbc7fdbc0630a9f5 static/scripts/mvc/collection/dataset-collection-edit.js --- a/static/scripts/mvc/collection/dataset-collection-edit.js +++ b/static/scripts/mvc/collection/dataset-collection-edit.js @@ -1,75 +1,36 @@ define([ - "mvc/dataset/hda-model", + "mvc/dataset/states", "mvc/collection/dataset-collection-base", "utils/localization" -], function( hdaModel, datasetCollectionBase, _l ){ +], function( STATES, DC_BASE_VIEW, _l ){ //============================================================================== -/** @class Editing view for HistoryDatasetCollectionAssociation. +var _super = DC_BASE_VIEW.DCBaseView; +/** @class Editing view for DatasetCollection. * @name DatasetCollectionEditView * - * @augments DatasetCollectionBaseView + * @augments DCBaseView * @constructs */ -var DatasetCollectionEditView = datasetCollectionBase.DatasetCollectionBaseView.extend( { +var DCEditView = _super.extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, initialize : function( attributes ){ - datasetCollectionBase.DatasetCollectionBaseView.prototype.initialize.call( this, attributes ); - }, - - // ......................................................................... edit attr, delete - /** Render icon-button group for the common, most easily accessed actions. - * Overrides _render_titleButtons to include editing related buttons. - * @see DatasetCollectionBaseView#_render_titleButtons - * @returns {jQuery} rendered DOM - */ - _render_titleButtons : function(){ - // render the display, edit attr and delete icon-buttons - return datasetCollectionBase.DatasetCollectionBaseView.prototype._render_titleButtons.call( this ).concat([ - this._render_deleteButton() - ]); - }, - - /** Render icon-button to delete this hda. - * @returns {jQuery} rendered DOM - */ - _render_deleteButton : function(){ - // don't show delete if... - if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( !this.model.get( 'accessible' ) ) ){ - return null; - } - - var self = this, - deleteBtnData = { - title : _l( 'Delete' ), - classes : 'dataset-delete', - onclick : function() { - // ...bler... tooltips being left behind in DOM (hover out never called on deletion) - self.$el.find( '.icon-btn.dataset-delete' ).trigger( 'mouseout' ); - self.model[ 'delete' ](); - } - }; - if( this.model.get( 'deleted' ) ){ - deleteBtnData = { - title : _l( 'Dataset collection is already deleted' ), - disabled : true - }; - } - deleteBtnData.faIcon = 'fa-times'; - return faIconButton( deleteBtnData ); + _super.prototype.initialize.call( this, attributes ); }, // ......................................................................... misc /** string rep */ toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDCAEditView(' + modelString + ')'; + return 'DCEditView(' + modelString + ')'; } }); //============================================================================== return { - DatasetCollectionEditView : DatasetCollectionEditView + DCEditView : DCEditView }; }); This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for exporting repositories that contain package recipes that define additional packages needed only for compiling the dependent package.
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e45ed2368920/ Changeset: e45ed2368920 User: greg Date: 2014-07-23 22:19:39 Summary: Fix for exporting repositories that contain package recipes that define additional packages needed only for compiling the dependent package. Affected #: 3 files diff -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 -r e45ed2368920315ab1f9cfe28d81e07cefc5c955 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1262,7 +1262,11 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) metadata = repository_metadata.metadata toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + # Initialize the repository dependency RelationBuilder. rb = relation_builder.RelationBuilder( trans.app, repository, repository_metadata, toolshed_base_url ) + # Work-around to ensure repositories that contain packages needed only for compiling + # a dependent package are included in the capsule. + rb.set_filter_dependencies_needed_for_compiling( False ) # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() if repository_dependencies: diff -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 -r e45ed2368920315ab1f9cfe28d81e07cefc5c955 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -245,9 +245,13 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( self.app, self.repository_id, self.changeset_revision ) - # Get a dictionary of all repositories upon which the contents of the current repository_metadata record depend. + # Get a dictionary of all repositories upon which the contents of the current + # repository_metadata record depend. toolshed_base_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) rb = RelationBuilder( self.app, repository, repository_metadata, toolshed_base_url ) + # Work-around to ensure repositories that contain packages needed only for compiling + # a dependent package are included in the capsule. + rb.set_filter_dependencies_needed_for_compiling( False ) repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() repo = hg_util.get_repo_for_repository( self.app, repository=self.repository, diff -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 -r e45ed2368920315ab1f9cfe28d81e07cefc5c955 lib/tool_shed/dependencies/repository/relation_builder.py --- a/lib/tool_shed/dependencies/repository/relation_builder.py +++ b/lib/tool_shed/dependencies/repository/relation_builder.py @@ -23,6 +23,11 @@ self.handled_key_rd_dicts = [] self.key_rd_dicts_to_be_processed = [] self.tool_shed_url = tool_shed_url + # This is a temporary work-around for handling repository dependencies that are needed + # only if compiling a dependent package. This value should be True unless exporting + # a repository capsule, in which case the set_filter_dependencies_needed_for_compiling() + # function is called. + self.filter_dependencies_needed_for_compiling = True def can_add_to_key_rd_dicts( self, key_rd_dict, key_rd_dicts ): """Handle the case where an update to the changeset revision was done.""" @@ -389,9 +394,12 @@ current_repository_key_rd_dicts = \ self.get_updated_changeset_revisions_for_repository_dependencies( current_repository_key_rd_dicts ) for key_rd_dict in current_repository_key_rd_dicts: - # Filter out repository dependencies that are required only if compiling the dependent - # repository's tool dependency. - key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict ) + if self.filter_dependencies_needed_for_compiling: + # Filter out repository dependencies that are required only if compiling the dependent + # repository's tool dependency. + # TODO: this temporary work-around should be removed when the underlying framework + # support for handling only_if_compiling_contained_td-flagged repositories is completed. + key_rd_dict = self.filter_only_if_compiling_contained_td( key_rd_dict ) if key_rd_dict: is_circular = False in_handled_key_rd_dicts = self.in_key_rd_dicts( key_rd_dict, self.handled_key_rd_dicts ) @@ -483,6 +491,9 @@ clean_key_rd_dicts.append( new_key_rd_dict ) return clean_key_rd_dicts + def set_filter_dependencies_needed_for_compiling( self, value ): + self.filter_dependencies_needed_for_compiling = asbool( value ) + def update_circular_repository_dependencies( self, repository_key, repository_dependency, repository_dependencies ): repository_dependency_as_key = self.get_repository_dependency_as_key( repository_dependency ) repository_key_as_repository_dependency = repository_key.split( container_util.STRSEP ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Strip repository names when creating in the Tool Shed.
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b08a47eb8c3c/ Changeset: b08a47eb8c3c User: greg Date: 2014-07-23 19:40:23 Summary: Strip repository names when creating in the Tool Shed. Affected #: 1 file diff -r 598a4ec015f66237d41ed2176c673fd52b744f15 -r b08a47eb8c3c15022b9e3f7d9990d40fd0fa70c0 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -1062,7 +1062,7 @@ action='browse_repositories', message=message, status=status ) ) - name = kwd.get( 'name', '' ) + name = kwd.get( 'name', '' ).strip() description = kwd.get( 'description', '' ) long_description = kwd.get( 'long_description', '' ) category_ids = util.listify( kwd.get( 'category_id', '' ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: History/Collection/HDA MVC: refactoring; Base MVC: create mixin shortcut to extend, use with HistoryContentMixin; Pages: allow display of collections; HDAs: fix annotation default overwriting existing when only partial model is saved; Style: begin separation of collections styles and prep for DOM class renaming; pack scripts
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/598a4ec015f6/ Changeset: 598a4ec015f6 User: carlfeberhard Date: 2014-07-23 18:59:04 Summary: History/Collection/HDA MVC: refactoring; Base MVC: create mixin shortcut to extend, use with HistoryContentMixin; Pages: allow display of collections; HDAs: fix annotation default overwriting existing when only partial model is saved; Style: begin separation of collections styles and prep for DOM class renaming; pack scripts Affected #: 50 files diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -195,6 +195,7 @@ class HistoryController( BaseUIController, SharableMixin, UsesAnnotations, UsesItemRatings, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, ExportsHistoryMixin, ImportsHistoryMixin ): + def __init__( self, app ): super( HistoryController, self ).__init__( app ) self.mgrs = util.bunch.Bunch( diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1,5 +1,6 @@ from sqlalchemy import desc, and_ from galaxy import model, web +from galaxy import managers from galaxy.web import error, url_for from galaxy.model.item_attrs import UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin @@ -285,6 +286,12 @@ _page_selection_grid = PageSelectionGrid() _visualization_selection_grid = VisualizationSelectionGrid() + def __init__( self, app ): + super( PageController, self ).__init__( app ) + self.mgrs = util.bunch.Bunch( + histories=managers.histories.HistoryManager() + ) + @web.expose @web.require_login() def list( self, trans, *args, **kwargs ): @@ -718,6 +725,7 @@ """ Returns html suitable for embedding in another page. """ + #TODO: should be moved to history controller and/or called via ajax from the template history = self.get_history( trans, id, False, True ) if not history: return None @@ -729,15 +737,22 @@ hda_dicts = [] datasets = self.get_history_datasets( trans, history ) - for hda in datasets: - hda_dict = self.get_hda_dict( trans, hda ) - hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) - hda_dicts.append( hda_dict ) - history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) - history_dict[ 'annotation' ] = history.annotation + #for hda in datasets: + # hda_dict = self.get_hda_dict( trans, hda ) + # hda_dict[ 'annotation' ] = self.get_item_annotation_str( trans.sa_session, history.user, hda ) + # hda_dicts.append( hda_dict ) + #history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) + #history_dict[ 'annotation' ] = history.annotation + + # include all datasets: hidden, deleted, and purged + #TODO!: doubled query (hda_dictionaries + datasets) + history_data = self.mgrs.histories._get_history_data( trans, history ) + history_dictionary = history_data[ 'history' ] + hda_dictionaries = history_data[ 'contents' ] + history_dictionary[ 'annotation' ] = history.annotation filled = trans.fill_template( "history/embed.mako", item=history, item_data=datasets, - user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts ) + user_is_owner=user_is_owner, history_dict=history_dictionary, hda_dicts=hda_dictionaries ) return filled def _get_embed_html( self, trans, item_class, item_id ): diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -14,7 +14,7 @@ * @example * // Add to your models/views at the definition using chaining: * var MyModel = Backbone.Model.extend( LoggableMixin ).extend({ // ... }); - * + * * // or - more explicitly AFTER the definition: * var MyModel = Backbone.Model.extend({ * logger : console @@ -208,8 +208,23 @@ }; //============================================================================== -return { - LoggableMixin : LoggableMixin, - SessionStorageModel : SessionStorageModel, - HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin -};}); +function mixin( mixinHash1, /* mixinHash2, etc: ... variadic */ propsHash ){ + // usage: var NewModel = Something.extend( mixin( MyMixinA, MyMixinB, { ... }) ); + //NOTE: this does not combine any hashes (like events, etc.) and you're expected to handle that + + // simple reversal of param order on _.defaults() - to show mixins in top of definition + var args = Array.prototype.slice.call( arguments, 0 ), + lastArg = args.pop(); + args.unshift( lastArg ); + return _.defaults.apply( _, args ); +} + + +//============================================================================== + return { + LoggableMixin : LoggableMixin, + SessionStorageModel : SessionStorageModel, + HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin, + mixin : mixin + }; +}); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/collection-model.js --- /dev/null +++ b/static/scripts/mvc/collection/collection-model.js @@ -0,0 +1,250 @@ +define([ + "mvc/dataset/hda-model", + "mvc/base-mvc", + "utils/localization" +], function( HDA_MODEL, BASE_MVC, _l ){ +//============================================================================== +/** @class Backbone model for Dataset collection elements. + * DC Elements contain a sub-model named 'object'. This class moves that + * 'object' from the JSON in the attributes list to a full, instantiated + * sub-model found in this.object. This is done on intialization and + * everytime the 'change:object' event is fired. + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DatasetCollectionElement = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends DatasetCollectionElement.prototype */{ + //TODO:?? this model may be unneccessary - it reflects the api structure, but... + // if we munge the element with the element.object at parse, we can flatten the entire hierarchy + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + defaults : { + id : null, + model_class : 'DatasetCollectionElement', + element_identifier : null, + element_index : null, + element_type : null + }, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( model, options ){ + this.info( this + '.initialize:', model, options ); + options = options || {}; + //this._setUpListeners(); + + this.object = this._createObjectModel(); + this.on( 'change:object', function(){ + //console.log( 'change:object' ); +//TODO: prob. better to update the sub-model instead of re-creating it + this.object = this._createObjectModel(); + }); + }, + + _createObjectModel : function(){ + //console.log( '_createObjectModel', this.get( 'object' ), this.object ); + //TODO: same patterns as HDCA _createElementsModel - refactor to BASE_MVC.hasSubModel? + if( _.isUndefined( this.object ) ){ this.object = null; } + if( !this.get( 'object' ) ){ return this.object; } + + var object = this.get( 'object' ); + this.unset( 'object', { silent: true }); + + this.debug( 'DCE, element_type:', this.get( 'element_type' ) ); + switch( this.get( 'element_type' ) ){ + case 'dataset_collection': + this.object = new DatasetCollection( object ); + break; + case 'hda': + this.object = new HDA_MODEL.HistoryDatasetAssociation( object ); + break; + default: + throw new TypeError( 'Unknown element_type: ' + this.get( 'element_type' ) ); + } + return this.object; + }, + + /** String representation. */ + toString : function(){ + var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) ); + return ([ 'DatasetCollectionElement(', objStr, ')' ].join( '' )); + } +}); + + +//============================================================================== +/** @class Backbone collection for DCEs. + * NOTE: used *only* in second level of list:paired collections (a + * collection that contains collections) + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DatasetCollectionElementCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends DatasetCollectionElementCollection.prototype */{ + model: DatasetCollectionElement, + + // comment this out to suppress log output + /** logger used to record this.log messages, commonly set to console */ + //logger : console, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( models, options ){ + options = options || {}; + this.info( this + '.initialize:', models, options ); + //this._setUpListeners(); + }, + + /** String representation. */ + toString : function(){ + return ([ 'DatasetCollectionElementCollection(', this.length, ')' ].join( '' )); + } +}); + + +//============================================================================== +/** @class Backbone model for Dataset Collections. + * DCs contain a bbone collection named 'elements' using the class found in + * this.collectionClass (gen. DatasetCollectionElementCollection). DCs move + * that 'object' from the JSON in the attributes list to a full, instantiated + * collection found in this.elements. This is done on intialization and + * everytime the 'change:elements' event is fired. + * + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DatasetCollection = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends ListDatasetCollection.prototype */{ + + //logger : console, + + /** default attributes for a model */ + defaults : { + collection_type : 'list' + }, + + collectionClass : DatasetCollectionElementCollection, + + /** */ + initialize : function( model, options ){ + this.info( 'DatasetCollection.initialize:', model, options ); + //historyContent.HistoryContent.prototype.initialize.call( this, attrs, options ); + this.elements = this._createElementsModel(); +//TODO:?? no way to use parse here? + this.on( 'change:elements', function(){ + this.log( 'change:elements' ); +//TODO: prob. better to update the collection instead of re-creating it + this.elements = this._createElementsModel(); + }); + }, + + /** move elements model attribute to full collection */ + _createElementsModel : function(){ + this.log( '_createElementsModel', this.get( 'elements' ), this.elements ); +//TODO: same patterns as DatasetCollectionElement _createObjectModel - refactor to BASE_MVC.hasSubModel? + var elements = this.get( 'elements' ) || []; + this.info( 'elements:', elements ); + this.unset( 'elements', { silent: true }); + this.elements = new this.collectionClass( elements ); + return this.elements; + }, + + hasDetails : function(){ +//TODO: this is incorrect for (accidentally) empty collections + return this.elements.length !== 0; + }, + + // ........................................................................ misc + /** String representation */ + toString : function(){ + var idAndName = [ this.get( 'id' ), this.get( 'name' ) || this.get( 'element_identifier' ) ]; + return 'DatasetCollection(' + ( idAndName.join(',') ) + ')'; + } +}); + + +//============================================================================== +/** @class Backbone collection for a collection of collection collections collecting correctly. */ +var DatasetCollectionCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend({ + + model: DatasetCollection, + + ///** logger used to record this.log messages, commonly set to console */ + //// comment this out to suppress log output + //logger : console, + + /** Set up. + * @see Backbone.Collection#initialize + */ + initialize : function( models, options ){ + options = options || {}; + this.info( 'DatasetCollectionCollection.initialize:', models, options ); + //this._setUpListeners(); + }, + + /** String representation. */ + toString : function(){ + return ([ 'DatasetCollectionCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//NOTE: the following prototypes may not be necessary - but I wanted to specifiy +// them (for now) and allow for the possibility of unique functionality +//============================================================================== +var ListDatasetCollection = DatasetCollection.extend( +/** @lends ListDatasetCollection.prototype */{ + + /** String representation. */ + toString : function(){ + return ([ 'ListDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== +var PairDatasetCollection = DatasetCollection.extend( +/** @lends ListDatasetCollection.prototype */{ + + /** String representation. */ + toString : function(){ + return ([ 'PairDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== +var ListPairedDatasetCollection = DatasetCollection.extend( +/** @lends ListDatasetCollection.prototype */{ + + // list:paired is the only collection that itself contains collections + //collectionClass : DatasetCollectionCollection, + + /** String representation. */ + toString : function(){ + return ([ 'ListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== + return { + DatasetCollectionElement : DatasetCollectionElement, + DatasetCollectionElementCollection : DatasetCollectionElementCollection, + DatasetCollection : DatasetCollection, + DatasetCollectionCollection : DatasetCollectionCollection, + ListDatasetCollection : ListDatasetCollection, + PairDatasetCollection : PairDatasetCollection, + ListPairedDatasetCollection : ListPairedDatasetCollection + }; +}); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/collection-panel.js --- /dev/null +++ b/static/scripts/mvc/collection/collection-panel.js @@ -0,0 +1,326 @@ +define([ + "mvc/collection/dataset-collection-base", + "mvc/dataset/hda-base", + "mvc/base-mvc", + "utils/localization" +], function( DC_BASE, HDA_BASE, BASE_MVC, _l ){ +/* ============================================================================= +TODO: + +============================================================================= */ +/** @class non-editable, read-only View/Controller for a dataset collection. + * @name CollectionPanel + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( +/** @lends CollectionPanel.prototype */{ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + tagName : 'div', + className : 'history-panel', + + /** (in ms) that jquery effects will use */ + fxSpeed : 'fast', + + // ......................................................................... SET UP + /** Set up the view, set up storage, bind listeners to HistoryContents events + * @param {Object} attributes optional settings for the panel + */ + initialize : function( attributes ){ + attributes = attributes || {}; + // set the logger if requested + if( attributes.logger ){ + this.logger = attributes.logger; + } + this.log( this + '.initialize:', attributes ); + + this.hasUser = attributes.hasUser; + this.HDAViewClass = attributes.HDAViewClass || HDA_BASE.HDABaseView; + }, + + /** create any event listeners for the panel + * @fires: rendered:initial on the first render + * @fires: empty-history when switching to a history with no HDAs or creating a new history + */ + _setUpListeners : function(){ + // debugging + //if( this.logger ){ + this.on( 'all', function( event ){ + this.log( this + '', arguments ); + }, this ); + //} + return this; + }, + + // ------------------------------------------------------------------------ history/hda event listening + /** listening for history and HDA events */ + _setUpModelEventHandlers : function(){ + return this; + }, + + // ------------------------------------------------------------------------ panel rendering + /** Render urls, historyPanel body, and hdas (if any are shown) + * @fires: rendered when the panel is attached and fully visible + * @see Backbone.View#render + */ + render : function( speed, callback ){ + this.log( 'render:', speed, callback ); + // send a speed of 0 to have no fade in/out performed + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + //console.debug( this + '.render, fxSpeed:', speed ); + var panel = this, + $newRender; + + // handle the possibility of no model (can occur if fetching the model returns an error) + if( !this.model ){ + return this; + } + $newRender = this.renderModel(); + + // fade out existing, swap with the new, fade in, set up behaviours + $( panel ).queue( 'fx', [ + function( next ){ + if( speed && panel.$el.is( ':visible' ) ){ + panel.$el.fadeOut( speed, next ); + } else { + next(); + } + }, + function( next ){ + // swap over from temp div newRender + panel.$el.empty(); + if( $newRender ){ + panel.$el.append( $newRender.children() ); + } + next(); + }, + function( next ){ + if( speed && !panel.$el.is( ':visible' ) ){ + panel.$el.fadeIn( speed, next ); + } else { + next(); + } + }, + function( next ){ + //TODO: ideally, these would be set up before the fade in (can't because of async save text) + if( callback ){ callback.call( this ); } + panel.trigger( 'rendered', this ); + next(); + } + ]); + return this; + }, + + /** render with history data + * @returns {jQuery} dom fragment as temporary container to be swapped out later + */ + renderModel : function( ){ + // tmp div for final swap in render + var $newRender = $( '<div/>' ).append( CollectionPanel.templates.panel( this.model.toJSON() ) ); + this._setUpBehaviours( $newRender ); + this.renderContents( $newRender ); + return $newRender; + }, + + /** Set up HistoryPanel js/widget behaviours */ + _setUpBehaviours : function( $where ){ + //TODO: these should be either sub-MVs, or handled by events + $where = $where || this.$el; + $where.find( '[title]' ).tooltip({ placement: 'bottom' }); + return this; + }, + + // ------------------------------------------------------------------------ sub-$element shortcuts + /** the scroll container for this panel - can be $el, $el.parent(), or grandparent depending on context */ + $container : function(){ + return ( this.findContainerFn )?( this.findContainerFn.call( this ) ):( this.$el.parent() ); + }, + /** where hdaViews are attached */ + $datasetsList : function( $where ){ + return ( $where || this.$el ).find( '.datasets-list' ); + }, + + // ------------------------------------------------------------------------ sub-views + /** Set up/render a view for each HDA to be shown, init with model and listeners. + * HDA views are cached to the map this.hdaViews (using the model.id as key). + * @param {jQuery} $whereTo what dom element to prepend the HDA views to + * @returns the number of visible hda views + */ + renderContents : function( $whereTo ){ + //console.debug( 'renderContents, elements:', this.model.elements ); + $whereTo = $whereTo || this.$el; + + var panel = this, + contentViews = {}, + visibleContents = this.model.elements || []; + //this.log( 'renderContents, visibleContents:', visibleContents, $whereTo ); + + this.$datasetsList( $whereTo ).empty(); + if( visibleContents && visibleContents.length ){ + visibleContents.each( function( content ){ + var contentId = content.id, + contentView = panel._createContentView( content ); + contentViews[ contentId ] = contentView; + panel.attachContentView( contentView.render(), $whereTo ); + }); + } + this.contentViews = contentViews; + return this.contentViews; + }, + + /** + * @param {HistoryDatasetAssociation} content + */ + _createContentView : function( content ){ + //console.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); + var contentView = null, + ContentClass = this._getContentClass( content ); + //console.debug( 'content.object json:', JSON.stringify( content.object, null, ' ' ) ); + //console.debug( 'ContentClass:', ContentClass ); + //console.debug( 'content:', content ); + //console.debug( 'content.object:', content.object ); + contentView = new ContentClass({ + model : content.object, + linkTarget : this.linkTarget, + //draggable : true, + hasUser : this.hasUser, + logger : this.logger + }); + //this._setUpHdaListeners( contentView ); + return contentView; + }, + + _getContentClass : function( content ){ + switch( content.get( 'element_type' ) ){ + case 'hda': + return this.HDAViewClass; + case 'dataset_collection': + return DC_BASE.NestedDCEBaseView; + } + throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) ); + }, + +// /** Set up HistoryPanel listeners for HDAView events. Currently binds: +// * HDAView#body-visible, HDAView#body-hidden to store expanded states +// * @param {HDAView} hdaView HDAView (base or edit) to listen to +// */ +// _setUpHdaListeners : function( hdaView ){ +// var panel = this; +// hdaView.on( 'error', function( model, xhr, options, msg ){ +// panel.errorHandler( model, xhr, options, msg ); +// }); +// // maintain a list of hdas whose bodies are expanded +// hdaView.on( 'body-expanded', function( model ){ +// panel.storage.addExpandedHda( model ); +// }); +// hdaView.on( 'body-collapsed', function( id ){ +// panel.storage.removeExpandedHda( id ); +// }); +// return this; +// }, + + /** attach an contentView to the panel */ + attachContentView : function( contentView, $whereTo ){ + $whereTo = $whereTo || this.$el; + var $datasetsList = this.$datasetsList( $whereTo ); + $datasetsList.append( contentView.$el ); + return this; + }, + + // ------------------------------------------------------------------------ panel events + /** event map */ + events : { + 'click .panel-navigation-back' : 'close' + }, + + /** */ + close : function( event ){ + this.$el.remove(); + this.trigger( 'collection-close' ); + }, + + // ........................................................................ misc + /** Return a string rep of the history */ + toString : function(){ + return 'CollectionPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); + + +//------------------------------------------------------------------------------ TEMPLATES +var _panelTemplate = [ + '<div class="history-controls">', + '<div class="panel-navigation">', + '<a class="panel-navigation-back" href="javascript:void(0)">', _l( 'Back' ), '</a>', + '</div>', + + '<div class="history-title">', + '<% if( collection.name ){ %>', + '<div class="history-name"><%= collection.hid %> : <%= collection.name %></div>', + '<% } %>', + '</div>', + + //'<div class="history-subtitle clear">', + // '<% if( history.nice_size ){ %>', + // '<div class="history-size"><%= history.nice_size %></div>', + // '<% } %>', + // '<div class="history-secondary-actions"></div>', + //'</div>', + // + //'<% if( history.deleted ){ %>', + // '<div class="warningmessagesmall"><strong>', + // _l( 'You are currently viewing a deleted history!' ), + // '</strong></div>', + //'<% } %>', + // + //'<div class="message-container">', + // '<% if( history.message ){ %>', + // // should already be localized + // '<div class="<%= history.status %>message"><%= history.message %></div>', + // '<% } %>', + //'</div>', + // + //'<div class="quota-message errormessage">', + // _l( 'You are over your disk quota' ), '. ', + // _l( 'Tool execution is on hold until your disk usage drops below your allocated quota' ), '.', + //'</div>', + // + //'<div class="tags-display"></div>', + //'<div class="annotation-display"></div>', + //'<div class="history-dataset-actions">', + // '<div class="btn-group">', + // '<button class="history-select-all-datasets-btn btn btn-default"', + // 'data-mode="select">', _l( 'All' ), '</button>', + // '<button class="history-deselect-all-datasets-btn btn btn-default"', + // 'data-mode="select">', _l( 'None' ), '</button>', + // '</div>', + // '<button class="history-dataset-action-popup-btn btn btn-default">', + // _l( 'For all selected' ), '...</button>', + //'</div>', + '</div>', + // end history controls + + // where the datasets/hdas are added + '<div class="datasets-list"></div>' + +].join( '' ); + +CollectionPanel.templates = { + panel : function( JSON ){ + return _.template( _panelTemplate, JSON, { variable: 'collection' }); + } +}; + + +//============================================================================== + return { + CollectionPanel: CollectionPanel + }; +}); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/dataset-collection-base.js --- a/static/scripts/mvc/collection/dataset-collection-base.js +++ b/static/scripts/mvc/collection/dataset-collection-base.js @@ -1,328 +1,151 @@ define([ - "mvc/history/history-content-base-view", + "mvc/base-mvc", "utils/localization" -], function( historyContentBaseView, _l ){ +], function( BASE_MVC, _l ){ /* global Backbone, LoggableMixin */ //============================================================================== -/** @class Read only view for HistoryDatasetCollectionAssociation. - * @name HDABaseView +/** @class Read only view for DatasetCollection. + * @name DCBaseView * * @augments Backbone.View * @borrows LoggableMixin#logger as #logger * @borrows LoggableMixin#log as #log * @constructs */ -var DatasetCollectionBaseView = historyContentBaseView.HistoryContentBaseView.extend({ - className : "dataset hda history-panel-hda", - id : function(){ return 'hdca-' + this.model.get( 'id' ); }, +var DCBaseView = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + /** */ + className : "dataset-collection", + /** */ + fxSpeed : 'fast', /** */ initialize : function( attributes ){ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } - this.log( this + '.initialize:', attributes ); - /** is the view currently in selection mode? */ - this.selectable = attributes.selectable || false; - //this.log( '\t selectable:', this.selectable ); - /** is the view currently selected? */ - this.selected = attributes.selected || false; - /** is the body of this collection view expanded/not? */ - this.expanded = attributes.expanded || false; + this.log( 'DCBaseView.initialize:', attributes ); }, - /** */ - render : function( fade ){ - var $newRender = this._buildNewRender(); - - this._queueNewRender( $newRender, fade ); - return this; - }, - - /** */ - _buildNewRender : function(){ - var $newRender = $( DatasetCollectionBaseView.templates.skeleton( this.model.toJSON() ) ); - $newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() ); - $newRender.children( '.dataset-body' ).replaceWith( this._render_body() ); - this._setUpBehaviors( $newRender ); - return $newRender; - }, - - /** */ - _queueNewRender : function( $newRender, fade ) { - fade = ( fade === undefined )?( true ):( fade ); - var view = this; - - // fade the old render out (if desired) - if( fade ){ - $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); }); - } - // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select - $( view ).queue( function( next ){ - this.$el.empty() - .attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) ) - .append( $newRender.children() ); - if( this.selectable ){ this.showSelector( 0 ); } - next(); - }); - // fade the new in - if( fade ){ - $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); }); - } - // trigger an event to know we're ready - $( view ).queue( function( next ){ - this.trigger( 'rendered', view ); - if( this.model.inReadyState() ){ - this.trigger( 'rendered:ready', view ); - } - if( this.draggable ){ this.draggableOn(); } - next(); - }); - }, - - // ................................................................................ titlebar buttons - /** Render icon-button group for the common, most easily accessed actions. - * @returns {jQuery} rendered DOM - */ - _render_titleButtons : function(){ - // render just the display for read-only - return [ ]; - }, - - // ......................................................................... state body renderers - /** Render the enclosing div of the collection body and, if expanded, the html in the body - * @returns {jQuery} rendered DOM - */ - _render_body : function(){ - var $body = $( '<div>Error: unknown state "' + this.model.get( 'state' ) + '".</div>' ), - // cheesy: get function by assumed matching name - renderFn = this[ '_render_body_' + this.model.get( 'state' ) ]; - if( _.isFunction( renderFn ) ){ - $body = renderFn.call( this ); - } - this._setUpBehaviors( $body ); - - // only render the body html if it's being shown - if( this.expanded ){ - $body.show(); - } - return $body; - }, - - /** set up js behaviors, event handlers for elements within the given container - * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) - */ - _setUpBehaviors : function( $container ){ - $container = $container || this.$el; - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - make_popup_menus( $container ); - $container.find( '[title]' ).tooltip({ placement : 'bottom' }); - }, - - // TODO: Eliminate duplication between following event map and one for HDAs. - - // ......................................................................... events - /** event map */ - events : { - // expand the body when the title is clicked or when in focus and space or enter is pressed - 'click .dataset-title-bar' : 'toggleBodyVisibility', - 'keydown .dataset-title-bar' : 'toggleBodyVisibility', - - // toggle selected state - 'click .dataset-selector' : 'toggleSelect' - }, - - /** Show or hide the body/details of history content. - * note: if the model does not have detailed data, fetch that data before showing the body - * @param {Event} event the event that triggered this (@link HDABaseView#events) - * @param {Boolean} expanded if true, expand; if false, collapse - * @fires body-expanded when a body has been expanded - * @fires body-collapsed when a body has been collapsed - */ - toggleBodyVisibility : function( event, expand ){ - // bail (with propagation) if keydown and not space or enter - var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( event && ( event.type === 'keydown' ) - && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ - return true; - } - - var $body = this.$el.find( '.dataset-body' ); - expand = ( expand === undefined )?( !$body.is( ':visible' ) ):( expand ); - if( expand ){ - this.expandBody(); - } else { - this.collapseBody(); - } - return false; - }, - - /** Render and show the full, detailed body of this view including extra data and controls. - * @fires body-expanded when a body has been expanded - */ - expandBody : function(){ - var contentView = this; - - function _renderBodyAndExpand(){ - contentView.$el.children( '.dataset-body' ).replaceWith( contentView._render_body() ); - contentView.$el.children( '.dataset-body' ).slideDown( contentView.fxSpeed, function(){ - contentView.expanded = true; - contentView.trigger( 'body-expanded', contentView.model ); - }); - } - // TODO: Fetch more details like HDA view... - _renderBodyAndExpand(); - }, - - /** Hide the body/details of an HDA. - * @fires body-collapsed when a body has been collapsed - */ - collapseBody : function(){ - var hdaView = this; - this.$el.children( '.dataset-body' ).slideUp( hdaView.fxSpeed, function(){ - hdaView.expanded = false; - hdaView.trigger( 'body-collapsed', hdaView.model.id ); - }); - }, - - /** Render an 'ok' collection. - * @param {jQuery} parent DOM to which to append this body - */ - _render_body_ok : function(){ - // most common state renderer and the most complicated - var $body = $( DatasetCollectionBaseView.templates.body( this.model.toJSON() ) ); - - // return shortened form if del'd (no display apps or peek?) - if( this.model.get( 'deleted' ) ){ - return $body; - } - - return $body; - }, - - // ......................................................................... selection - /** display a (fa-icon) checkbox on the left of the hda that fires events when checked - * Note: this also hides the primary actions - */ - showSelector : function(){ - // make sure selected state is represented properly - if( this.selected ){ - this.select( null, true ); - } - - this.selectable = true; - this.trigger( 'selectable', true, this ); - - this.$( '.dataset-primary-actions' ).hide(); - this.$( '.dataset-selector' ).show(); - }, - - /** remove the selection checkbox */ - hideSelector : function(){ - // reverse the process from showSelect - this.selectable = false; - this.trigger( 'selectable', false, this ); - - this.$( '.dataset-selector' ).hide(); - this.$( '.dataset-primary-actions' ).show(); - }, - - toggleSelector : function(){ - if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){ - this.showSelector(); - } else { - this.hideSelector(); - } - }, - - /** event handler for selection (also programmatic selection) - */ - select : function( event ){ - // switch icon, set selected, and trigger event - this.$el.find( '.dataset-selector span' ) - .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' ); - if( !this.selected ){ - this.trigger( 'selected', this, event ); - this.selected = true; - } - return false; - }, - - /** event handler for clearing selection (also programmatic deselection) - */ - deselect : function( event ){ - // switch icon, set selected, and trigger event - this.$el.find( '.dataset-selector span' ) - .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' ); - if( this.selected ){ - this.trigger( 'de-selected', this, event ); - this.selected = false; - } - return false; - }, - - toggleSelect : function( event ){ - if( this.selected ){ - this.deselect( event ); - } else { - this.select( event ); - } - }, +//TODO: render has been removed from the inheritance chain here, so this won't work when called as is // ......................................................................... misc /** String representation */ toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDCABaseView(' + modelString + ')'; + return 'DCBaseView(' + modelString + ')'; } }); -//------------------------------------------------------------------------------ TEMPLATES -//TODO: possibly break these out into a sep. module -var skeletonTemplate = _.template([ - '<div class="dataset hda">', - '<div class="dataset-warnings">', - '<% if ( collection.deleted ) { %>', - '<div class="dataset-deleted-msg warningmessagesmall"><strong>', - _l( 'This collection has been deleted.' ), +/** templates for DCBaseViews (skeleton and body) */ +DCBaseView.templates = (function(){ +// use closure to run underscore template fn only once at module load + var skeletonTemplate = _.template([ + '<div class="dataset hda">', + '<div class="dataset-warnings">', + '<% if ( collection.deleted ) { %>', + '<div class="dataset-deleted-msg warningmessagesmall"><strong>', + _l( 'This collection has been deleted.' ), + '</div>', + '<% } %>', + '<% if ( !collection.visible ) { %>', + '<div class="dataset-hidden-msg warningmessagesmall"><strong>', + _l( 'This collection has been hidden.' ), + '</div>', + '<% } %>', + '</div>', + '<div class="dataset-primary-actions"></div>', + '<div class="dataset-title-bar clear" tabindex="0">', + '<span class="dataset-state-icon state-icon"></span>', + '<div class="dataset-title">', + '<span class="dataset-name"><%- collection.name %></span>', '</div>', - '<% } %>', - '<% if ( !collection.visible ) { %>', - '<div class="dataset-hidden-msg warningmessagesmall"><strong>', - _l( 'This collection has been hidden.' ), - '</div>', - '<% } %>', - '</div>', - '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', - '<div class="dataset-primary-actions"></div>', - '<div class="dataset-title-bar clear" tabindex="0">', - '<span class="dataset-state-icon state-icon"></span>', - '<div class="dataset-title">', - '<span class="hda-hid"><%= collection.hid %></span> ', - '<span class="dataset-name"><%= collection.name %></span>', '</div>', - '</div>', - '<div class="dataset-body"></div>', - '</div>' -].join( '' )); + '<div class="dataset-body"></div>', + '</div>' + ].join( '' )); -var bodyTemplate = _.template([ - '<div class="dataset-body">', - '<div class="dataset-summary">', - _l( 'A dataset collection.' ), - '</div>' -].join( '' )); + var bodyTemplate = _.template([ + '<div class="dataset-body">', + '<div class="dataset-summary">', + _l( 'A dataset collection.' ), + '</div>' + ].join( '' )); -DatasetCollectionBaseView.templates = { // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within - skeleton : function( collectionJSON ){ - return skeletonTemplate({ _l: _l, collection: collectionJSON }); - }, - body : function( collectionJSON ){ - return bodyTemplate({ _l: _l, collection: collectionJSON }); - } -}; + return { + skeleton : function( collectionJSON ){ + return skeletonTemplate({ _l: _l, collection: collectionJSON }); + }, + body : function( collectionJSON ){ + return bodyTemplate({ _l: _l, collection: collectionJSON }); + } + }; +}()); + + +//TODO: unused +////============================================================================== +///** @class Read only view for DatasetCollectionElement. +// * @name DCEBaseView +// * +// * @augments Backbone.View +// * @borrows LoggableMixin#logger as #logger +// * @borrows LoggableMixin#log as #log +// * @constructs +// */ +//var NestedDCBaseView = DCBaseView.extend({ +// +// logger : console, +// +// /** */ +// initialize : function( attributes ){ +// if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } +// this.warn( this + '.initialize:', attributes ); +// DCBaseView.prototype.initialize.call( this, attributes ); +// }, +// +// _template : function(){ +// this.debug( this.model ); +// this.debug( this.model.toJSON() ); +// return NestedDCBaseView.templates.skeleton( this.model.toJSON() ); +// }, +// +// // ......................................................................... misc +// /** String representation */ +// toString : function(){ +// var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); +// return 'NestedDCBaseView(' + modelString + ')'; +// } +//}); +// +////------------------------------------------------------------------------------ TEMPLATES +////TODO: possibly break these out into a sep. module +//NestedDCBaseView.templates = (function(){ +// var skeleton = _.template([ +// '<div class="dataset hda history-panel-hda state-ok">', +// '<div class="dataset-primary-actions"></div>', +// '<div class="dataset-title-bar clear" tabindex="0">', +// '<div class="dataset-title">', +// '<span class="dataset-name"><%= collection.name %></span>', +// '</div>', +// '</div>', +// '</div>' +// ].join( '' )); +// // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within +// return { +// skeleton : function( json ){ +// return skeleton({ _l: _l, collection: json }); +// } +// }; +//}()); + //============================================================================== return { - DatasetCollectionBaseView : DatasetCollectionBaseView + DCBaseView : DCBaseView, + //NestedDCBaseView : NestedDCBaseView, }; }); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/dataset-collection-edit.js --- a/static/scripts/mvc/collection/dataset-collection-edit.js +++ b/static/scripts/mvc/collection/dataset-collection-edit.js @@ -1,75 +1,36 @@ define([ - "mvc/dataset/hda-model", + "mvc/dataset/states", "mvc/collection/dataset-collection-base", "utils/localization" -], function( hdaModel, datasetCollectionBase, _l ){ +], function( STATES, DC_BASE_VIEW, _l ){ //============================================================================== -/** @class Editing view for HistoryDatasetCollectionAssociation. +var _super = DC_BASE_VIEW.DCBaseView; +/** @class Editing view for DatasetCollection. * @name DatasetCollectionEditView * - * @augments DatasetCollectionBaseView + * @augments DCBaseView * @constructs */ -var DatasetCollectionEditView = datasetCollectionBase.DatasetCollectionBaseView.extend( { +var DCEditView = _super.extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, initialize : function( attributes ){ - datasetCollectionBase.DatasetCollectionBaseView.prototype.initialize.call( this, attributes ); - }, - - // ......................................................................... edit attr, delete - /** Render icon-button group for the common, most easily accessed actions. - * Overrides _render_titleButtons to include editing related buttons. - * @see DatasetCollectionBaseView#_render_titleButtons - * @returns {jQuery} rendered DOM - */ - _render_titleButtons : function(){ - // render the display, edit attr and delete icon-buttons - return datasetCollectionBase.DatasetCollectionBaseView.prototype._render_titleButtons.call( this ).concat([ - this._render_deleteButton() - ]); - }, - - /** Render icon-button to delete this hda. - * @returns {jQuery} rendered DOM - */ - _render_deleteButton : function(){ - // don't show delete if... - if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ) - || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( !this.model.get( 'accessible' ) ) ){ - return null; - } - - var self = this, - deleteBtnData = { - title : _l( 'Delete' ), - classes : 'dataset-delete', - onclick : function() { - // ...bler... tooltips being left behind in DOM (hover out never called on deletion) - self.$el.find( '.icon-btn.dataset-delete' ).trigger( 'mouseout' ); - self.model[ 'delete' ](); - } - }; - if( this.model.get( 'deleted' ) ){ - deleteBtnData = { - title : _l( 'Dataset collection is already deleted' ), - disabled : true - }; - } - deleteBtnData.faIcon = 'fa-times'; - return faIconButton( deleteBtnData ); + _super.prototype.initialize.call( this, attributes ); }, // ......................................................................... misc /** string rep */ toString : function(){ var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); - return 'HDCAEditView(' + modelString + ')'; + return 'DCEditView(' + modelString + ')'; } }); //============================================================================== return { - DatasetCollectionEditView : DatasetCollectionEditView + DCEditView : DCEditView }; }); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/hdca-base.js --- /dev/null +++ b/static/scripts/mvc/collection/hdca-base.js @@ -0,0 +1,116 @@ +define([ + "mvc/base-mvc", + "mvc/collection/dataset-collection-base", + "mvc/history/history-content-base-view", + "utils/localization" +], function( BASE_MVC, DC_BASE, HISTORY_CONTENT_BASE_VIEW, _l ){ +/* global Backbone, LoggableMixin */ +//============================================================================== +var HCVMixin = HISTORY_CONTENT_BASE_VIEW.HistoryContentViewMixin, + _super = DC_BASE.DCBaseView; +/** @class Read only view for HistoryDatasetCollectionAssociation. + * @name + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var HDCABaseView = _super.extend( BASE_MVC.mixin( HCVMixin, { + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + /** */ + className : "dataset hda history-panel-hda", + + /** */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( this + '.initialize:', attributes ); + _super.prototype.initialize.call( this, attributes ); + HCVMixin.initialize.call( this, attributes ); + }, + + /** */ + _template : function(){ + return HDCABaseView.templates.skeleton( this.model.toJSON() ); + }, + + /** */ + events : _.extend( _.clone( HCVMixin.events ), { + }), + + /** */ + _renderBody : function(){ + // override this + var $body = $( _super.templates.body( this.model.toJSON() ) ); + if( this.expanded ){ + $body.show(); + } + return $body; + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'HDCABaseView(' + modelString + ')'; + } +})); + +/** templates for HDCAs (skeleton and body) */ +HDCABaseView.templates = HDCABaseView.prototype.templates = (function(){ +// use closure to run underscore template fn only once at module load + var skeletonTemplate = _.template([ + '<div class="dataset hda">', + '<div class="dataset-warnings">', + '<% if ( collection.deleted ) { %>', + '<div class="dataset-deleted-msg warningmessagesmall"><strong>', + _l( 'This collection has been deleted.' ), + '</div>', + '<% } %>', + '<% if ( !collection.visible ) { %>', + '<div class="dataset-hidden-msg warningmessagesmall"><strong>', + _l( 'This collection has been hidden.' ), + '</div>', + '<% } %>', + '</div>', + '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', + '<div class="dataset-primary-actions"></div>', + '<div class="dataset-title-bar clear" tabindex="0">', + '<span class="dataset-state-icon state-icon"></span>', + '<div class="dataset-title">', + '<span class="hda-hid"><%- collection.hid %></span> ', + '<span class="dataset-name"><%- collection.name %></span>', + '</div>', + '</div>', + '<div class="dataset-body"></div>', + '</div>' + ].join( '' )); + + var bodyTemplate = _.template([ + '<div class="dataset-body">', + '<div class="dataset-summary">', + _l( 'A dataset collection.' ), + '</div>' + ].join( '' )); + + // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within + return { + skeleton : function( collectionJSON ){ + return skeletonTemplate({ _l: _l, collection: collectionJSON }); + }, + body : function( collectionJSON ){ + return bodyTemplate({ _l: _l, collection: collectionJSON }); + } + }; +}()); + + +//============================================================================== + return { + HDCABaseView : HDCABaseView + }; +}); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/hdca-edit.js --- /dev/null +++ b/static/scripts/mvc/collection/hdca-edit.js @@ -0,0 +1,74 @@ +define([ + "mvc/dataset/states", + "mvc/collection/hdca-base", + "utils/localization" +], function( STATES, HDCA_BASE, _l ){ +//============================================================================== +var _super = HDCA_BASE.HDCABaseView; +/** @class Editing view for HistoryDatasetCollectionAssociation. + * @name DatasetCollectionEditView + * + * @augments HDCABaseView + * @constructs + */ +var HDCAEditView = _super.extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + initialize : function( attributes ){ + _super.prototype.initialize.call( this, attributes ); + }, + + // ......................................................................... edit attr, delete + /** Render icon-button group for the common, most easily accessed actions. + * Overrides _render_titleButtons to include editing related buttons. + * @returns {jQuery} rendered DOM + */ + _render_titleButtons : function(){ + this.log( this + '._render_titleButtons' ); + // render the display, edit attr and delete icon-buttons + return _super.prototype._render_titleButtons.call( this ) + .concat([ + this._render_deleteButton() + ]); + }, + + /** Render icon-button to delete this hda. + * @returns {jQuery} rendered DOM + */ + _render_deleteButton : function(){ + var self = this, + deleteBtnData = { + title : _l( 'Delete' ), + classes : 'dataset-delete', + onclick : function() { + // ...bler... tooltips being left behind in DOM (hover out never called on deletion) + self.$el.find( '.icon-btn.dataset-delete' ).trigger( 'mouseout' ); + self.model[ 'delete' ](); + } + }; + if( self.model.get( 'deleted' ) ){ + deleteBtnData = { + title : _l( 'Dataset collection is already deleted' ), + disabled : true + }; + } + deleteBtnData.faIcon = 'fa-times'; + return faIconButton( deleteBtnData ); + }, + + // ......................................................................... misc + /** string rep */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'HDCAEditView(' + modelString + ')'; + } +}); + +//============================================================================== + return { + HDCAEditView : HDCAEditView + }; +}); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/collection/hdca-model.js --- a/static/scripts/mvc/collection/hdca-model.js +++ b/static/scripts/mvc/collection/hdca-model.js @@ -1,69 +1,89 @@ define([ "mvc/history/history-content-base", + "mvc/collection/collection-model", "utils/localization" -], function( historyContent, _l ){ +], function( HISTORY_CONTENT, DC_MODEL, _l ){ //============================================================================== -var HistoryDatasetCollectionAssociation = historyContent.HistoryContent.extend( -/** @lends HistoryDatasetCollectionAssociation.prototype */{ - /** default attributes for a model */ - defaults : { - // parent (containing) history - history_id : null, - // often used with tagging - model_class : 'HistoryDatasetCollectionAssociation', - history_content_type : 'dataset_collection', - hid : 0, +var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin, +/** @class Backbone model for (generic) Dataset Collection within a History. + * @constructs + */ + HistoryDatasetCollection = DC_MODEL.DatasetCollection.extend( hcontentMixin ); - id : null, - name : '(unnamed dataset collection)', - // one of HistoryDatasetAssociation.STATES, calling them all 'ok' for now. - state : 'ok', - accessible : true, - deleted : false, - visible : true, +//NOTE: the following prototypes may not be necessary - but I wanted to specifiy +// them (for now) and allow for the possibility of unique functionality +//============================================================================== +var ListDC = DC_MODEL.ListDatasetCollection, +/** @class Backbone model for List Dataset Collection within a History. + * @constructs + */ + HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( +/** @lends HistoryListDatasetCollection.prototype */{ - purged : false, // Purged doesn't make sense for collections - at least right now. - - tags : [], - annotation : '' - }, - urls : function(){ + initialize : function( model, options ){ + ListDC.prototype.initialize.call( this, model, options ); + hcontentMixin.initialize.call( this, model, options ); + //TODO: in lieu of any state info for collections, show as 'ok' + this.set( 'state', 'ok', { silent: true }); }, - inReadyState : function(){ - return true; // TODO - }, - - // ........................................................................ search - /** what attributes of an collection will be used in a text search */ - searchAttributes : [ - 'name' - ], - - /** our attr keys don't often match the labels we display to the user - so, when using - * attribute specifiers ('name="bler"') in a term, allow passing in aliases for the - * following attr keys. - */ - searchAliases : { - title : 'name' - // TODO: Add tag... - }, - - // ........................................................................ misc - /** String representation */ + /** String representation. */ toString : function(){ - var nameAndId = this.get( 'id' ) || ''; - if( this.get( 'name' ) ){ - nameAndId = this.get( 'hid' ) + ' :"' + this.get( 'name' ) + '",' + nameAndId; - } - return 'HDCA-' + this.get( 'collection_type' ) + '(' + nameAndId + ')'; + return ([ 'HistoryListDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); } }); //============================================================================== +var PairDC = DC_MODEL.PairDatasetCollection, +/** @class Backbone model for Pair Dataset Collection within a History. + * @constructs + */ + HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend( +/** @lends HistoryPairDatasetCollection.prototype */{ + + initialize : function( model, options ){ + PairDC.prototype.initialize.call( this, model, options ); + hcontentMixin.initialize.call( this, model, options ); + //TODO: in lieu of any state info for collections, show as 'ok' + this.set( 'state', 'ok', { silent: true }); + }, + + /** String representation. */ + toString : function(){ + return ([ 'HistoryPairDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== +var ListPairedDC = DC_MODEL.ListPairedDatasetCollection, +/** @class Backbone model for List of Pairs Dataset Collection within a History. + * @constructs + */ + HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend( +/** @lends HistoryListPairedDatasetCollection.prototype */{ + + initialize : function( model, options ){ + ListPairedDC.prototype.initialize.call( this, model, options ); + hcontentMixin.initialize.call( this, model, options ); + //TODO: in lieu of any state info for collections, show as 'ok' + this.set( 'state', 'ok', { silent: true }); + }, + + /** String representation. */ + toString : function(){ + return ([ 'HistoryListPairedDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); + } +}); + + +//============================================================================== return { - HistoryDatasetCollectionAssociation : HistoryDatasetCollectionAssociation + HistoryDatasetCollection : HistoryDatasetCollection, + HistoryListDatasetCollection : HistoryListDatasetCollection, + HistoryPairDatasetCollection : HistoryPairDatasetCollection, + HistoryListPairedDatasetCollection : HistoryListPairedDatasetCollection }; }); diff -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 -r 598a4ec015f66237d41ed2176c673fd52b744f15 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -1,11 +1,12 @@ define([ - "mvc/dataset/hda-model", + "mvc/dataset/states", "mvc/history/history-content-base-view", "mvc/data", "utils/localization" -], function( hdaModel, historyContentBaseView, dataset, _l ){ +], function( STATES, HCONTENT_BASE_VIEW, DATA, _l ){ /* global Backbone */ //============================================================================== +var _super = HCONTENT_BASE_VIEW.HistoryContentBaseView; /** @class Read only view for HistoryDatasetAssociation. * @name HDABaseView * @@ -14,11 +15,11 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var HDABaseView = historyContentBaseView.HistoryContentBaseView.extend( +var HDABaseView = _super.extend( /** @lends HDABaseView.prototype */{ - ///** logger used to record this.log messages, commonly set to console */ - //// comment this out to suppress log output + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output //logger : console, tagName : "div", @@ -38,6 +39,8 @@ if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } this.log( this + '.initialize:', attributes ); + _super.prototype.initialize.call( this, attributes ); + /** list of rendering functions for the default, primary icon-buttons. */ this.defaultPrimaryActionButtonRenderers = [ this._render_showParamsButton @@ -46,15 +49,6 @@ /** where should pages from links be displayed? (default to new tab/window) */ this.linkTarget = attributes.linkTarget || '_blank'; - /** is the view currently in selection mode? */ - this.selectable = attributes.selectable || false; - //this.log( '\t selectable:', this.selectable ); - /** is the view currently selected? */ - this.selected = attributes.selected || false; - //this.log( '\t selected:', this.selected ); - /** is the body of this hda view expanded/not? */ - this.expanded = attributes.expanded || false; - //this.log( '\t expanded:', this.expanded ); /** is the body of this hda view expanded/not? */ this.draggable = attributes.draggable || false; //this.log( '\t draggable:', this.draggable ); @@ -86,77 +80,20 @@ // ......................................................................... render main /** Render this HDA, set up ui. * @param {Boolean} fade whether or not to fade out/in when re-rendering - * @fires rendered when rendered - * @fires rendered:ready when first rendered and NO running HDAs * @returns {Object} this HDABaseView */ render : function( fade ){ //HACK: hover exit doesn't seem to be called on prev. tooltips when RE-rendering - so: no tooltip hide // handle that here by removing previous view's tooltips this.$el.find("[title]").tooltip( "destroy" ); - // re-get web controller urls for functions relating to this hda. (new model data may have changed this) this.urls = this.model.urls(); - var $newRender = this._buildNewRender(); - this._queueNewRender( $newRender, fade ); - return this; - + return _super.prototype.render.call( this, fade ); }, - _buildNewRender : function(){ - // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. - var $newRender = $( HDABaseView.templates.skeleton( this.model.toJSON() ) ); - $newRender.find( '.dataset-primary-actions' ).append( this._render_titleButtons() ); - $newRender.children( '.dataset-body' ).replaceWith( this._render_body() ); - this._setUpBehaviors( $newRender ); - //this._renderSelectable( $newRender ); - return $newRender; - }, - - _queueNewRender : function( $newRender, fade ) { - fade = ( fade === undefined )?( true ):( fade ); - var view = this; - - // fade the old render out (if desired) - if( fade ){ - $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); }); - } - // empty the old render, update to any new HDA state, swap in the new render contents, handle multi-select - $( view ).queue( function( next ){ - this.$el.empty() - .attr( 'class', view.className ).addClass( 'state-' + view.model.get( 'state' ) ) - .append( $newRender.children() ); - if( this.selectable ){ this.showSelector( 0 ); } - next(); - }); - // fade the new in - if( fade ){ - $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); }); - } - // trigger an event to know we're ready - $( view ).queue( function( next ){ - this.trigger( 'rendered', view ); - if( this.model.inReadyState() ){ - this.trigger( 'rendered:ready', view ); - } - if( this.draggable ){ this.draggableOn(); } - next(); - }); - }, - - /** set up js behaviors, event handlers for elements within the given container - * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) - */ - _setUpBehaviors : function( $container ){ - $container = $container || this.$el; - // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) - make_popup_menus( $container ); - $container.find( '[title]' ).tooltip({ placement : 'bottom' }); - }, - // ................................................................................ titlebar buttons - /** Render icon-button group for the common, most easily accessed actions. + /** In this override, render the dataset display button * @returns {jQuery} rendered DOM */ _render_titleButtons : function(){ @@ -170,8 +107,8 @@ _render_displayButton : function(){ // don't show display if not viewable or not accessible // (do show if in error, running) - if( ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NOT_VIEWABLE ) - || ( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.DISCARDED ) + if( ( this.model.get( 'state' ) === STATES.NOT_VIEWABLE ) + || ( this.model.get( 'state' ) === STATES.DISCARDED ) || ( !this.model.get( 'accessible' ) ) ){ return null; } @@ -187,12 +124,12 @@ displayBtnData.title = _l( 'Cannot display datasets removed from disk' ); // disable if still uploading - } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.UPLOAD ){ + } else if( this.model.get( 'state' ) === STATES.UPLOAD ){ displayBtnData.disabled = true; displayBtnData.title = _l( 'This dataset must finish uploading before it can be viewed' ); // disable if still new - } else if( this.model.get( 'state' ) === hdaModel.HistoryDatasetAssociation.STATES.NEW ){ + } else if( this.model.get( 'state' ) === STATES.NEW ){ displayBtnData.disabled = true; displayBtnData.title = _l( 'This dataset is not yet viewable' ); @@ -211,9 +148,9 @@ title : "Data Viewer: " + self.model.get( 'name' ), type : "other", content : function( parent_elt ){ - var new_dataset = new dataset.TabularDataset({ id: self.model.get( 'id' ) }); + var new_dataset = new DATA.TabularDataset({ id: self.model.get( 'id' ) }); $.when( new_dataset.fetch() ).then( function(){ - dataset.createTabularDatasetChunkedView({ + DATA.createTabularDatasetChunkedView({ model: new_dataset, parent_elt: parent_elt, embedded: true, @@ -298,7 +235,7 @@ /** Render the enclosing div of the hda body and, if expanded, the html in the body * @returns {jQuery} rendered DOM */ - _render_body : function(){ + _renderBody : function(){ var $body = $( '<div>Error: unknown dataset state "' + this.model.get( 'state' ) + '".</div>' ), // cheesy: get function by assumed matching name renderFn = this[ '_render_body_' + this.model.get( 'state' ) ]; @@ -437,61 +374,23 @@ // ......................................................................... events /** event map */ - events : { - // expand the body when the title is clicked or when in focus and space or enter is pressed - 'click .dataset-title-bar' : 'toggleBodyVisibility', - 'keydown .dataset-title-bar' : 'toggleBodyVisibility', + events : _.extend( _.clone( _super.prototype.events ), { + }), - // dragging - don't work, originalEvent === null - //'dragstart .dataset-title-bar' : 'dragStartHandler', - //'dragend .dataset-title-bar' : 'dragEndHandler' - - // toggle selected state - 'click .dataset-selector' : 'toggleSelect' - }, - - /** Show or hide the body/details of history content. - * note: if the model does not have detailed data, fetch that data before showing the body - * @param {Event} event the event that triggered this (@link HDABaseView#events) - * @param {Boolean} expanded if true, expand; if false, collapse - * @fires body-expanded when a body has been expanded - * @fires body-collapsed when a body has been collapsed + /** Override for expanding hda details (within the panel) + * note: in this override, the fetch for details does *not* fire a change event (silent == true) + * @fires expanded when a body has been expanded */ - toggleBodyVisibility : function( event, expand ){ - // bail (with propagation) if keydown and not space or enter - var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; - if( event && ( event.type === 'keydown' ) - && !( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ - return true; - } - - var $body = this.$el.find( '.dataset-body' ); - expand = ( expand === undefined )?( !$body.is( ':visible' ) ):( expand ); - if( expand ){ - this.expandBody(); - } else { - this.collapseBody(); - } - return false; - }, - - /** Render and show the full, detailed body of this view including extra data and controls. - * @fires body-expanded when a body has been expanded - */ - expandBody : function(){ + expand : function(){ var hdaView = this; function _renderBodyAndExpand(){ - hdaView.$el.children( '.dataset-body' ).replaceWith( hdaView._render_body() ); + hdaView.$el.children( '.dataset-body' ).replaceWith( hdaView._renderBody() ); + //NOTE: needs to be set after the above or the slide will not show + hdaView.expanded = true; hdaView.$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){ - hdaView.expanded = true; - hdaView.trigger( 'body-expanded', hdaView.model ); + hdaView.trigger( 'expanded', hdaView.model ); }); - - //hdaView.render( false ).$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){ - // hdaView.expanded = true; - // hdaView.trigger( 'body-expanded', hdaView.model.get( 'id' ) ); - //}); } // fetch first if no details in the model if( this.model.inReadyState() && !this.model.hasDetails() ){ @@ -505,128 +404,6 @@ } }, - /** Hide the body/details of an HDA. - * @fires body-collapsed when a body has been collapsed - */ - collapseBody : function(){ - var hdaView = this; - this.$el.children( '.dataset-body' ).slideUp( hdaView.fxSpeed, function(){ - hdaView.expanded = false; - hdaView.trigger( 'body-collapsed', hdaView.model.id ); - }); - }, - - // ......................................................................... selection - /** display a (fa-icon) checkbox on the left of the hda that fires events when checked - * Note: this also hides the primary actions - */ - showSelector : function(){ - // make sure selected state is represented properly - if( this.selected ){ - this.select( null, true ); - } - - this.selectable = true; - this.trigger( 'selectable', true, this ); - - this.$( '.dataset-primary-actions' ).hide(); - this.$( '.dataset-selector' ).show(); - }, - - /** remove the selection checkbox */ - hideSelector : function(){ - // reverse the process from showSelect - this.selectable = false; - this.trigger( 'selectable', false, this ); - - this.$( '.dataset-selector' ).hide(); - this.$( '.dataset-primary-actions' ).show(); - }, - - toggleSelector : function(){ - if( !this.$el.find( '.dataset-selector' ).is( ':visible' ) ){ - this.showSelector(); - } else { - this.hideSelector(); - } - }, - - /** event handler for selection (also programmatic selection) - */ - select : function( event ){ - // switch icon, set selected, and trigger event - this.$el.find( '.dataset-selector span' ) - .removeClass( 'fa-square-o' ).addClass( 'fa-check-square-o' ); - if( !this.selected ){ - this.trigger( 'selected', this, event ); - this.selected = true; - } - return false; - }, - - /** event handler for clearing selection (also programmatic deselection) - */ - deselect : function( event ){ - // switch icon, set selected, and trigger event - this.$el.find( '.dataset-selector span' ) - .removeClass( 'fa-check-square-o' ).addClass( 'fa-square-o' ); - if( this.selected ){ - this.trigger( 'de-selected', this, event ); - this.selected = false; - } - return false; - }, - - toggleSelect : function( event ){ - if( this.selected ){ - this.deselect( event ); - } else { - this.select( event ); - } - }, - - // ......................................................................... drag/drop - draggableOn : function(){ - this.draggable = true; - //TODO: I have no idea why this doesn't work with the events hash or jq.on()... - //this.$el.find( '.dataset-title-bar' ) - // .attr( 'draggable', true ) - // .bind( 'dragstart', this.dragStartHandler, false ) - // .bind( 'dragend', this.dragEndHandler, false ); - this.dragStartHandler = _.bind( this._dragStartHandler, this ); - this.dragEndHandler = _.bind( this._dragEndHandler, this ); - - var titleBar = this.$el.find( '.dataset-title-bar' ).attr( 'draggable', true ).get(0); - titleBar.addEventListener( 'dragstart', this.dragStartHandler, false ); - titleBar.addEventListener( 'dragend', this.dragEndHandler, false ); - }, - draggableOff : function(){ - this.draggable = false; - var titleBar = this.$el.find( '.dataset-title-bar' ).attr( 'draggable', false ).get(0); - titleBar.removeEventListener( 'dragstart', this.dragStartHandler, false ); - titleBar.removeEventListener( 'dragend', this.dragEndHandler, false ); - }, - toggleDraggable : function(){ - if( this.draggable ){ - this.draggableOff(); - } else { - this.draggableOn(); - } - }, - _dragStartHandler : function( event ){ - //console.debug( 'dragStartHandler:', this, event, arguments ) - this.trigger( 'dragstart', this ); - event.dataTransfer.effectAllowed = 'move'; - //TODO: all except IE: should be 'application/json', IE: must be 'text' - event.dataTransfer.setData( 'text', JSON.stringify( this.model.toJSON() ) ); - return false; - }, - _dragEndHandler : function( event ){ - this.trigger( 'dragend', this ); - //console.debug( 'dragEndHandler:', event ) - return false; - }, - // ......................................................................... removal /** Remove this view's html from the DOM and remove all event listeners. * @param {Function} callback an optional function called when removal is done @@ -799,7 +576,7 @@ '</div>' ].join( '' )); -HDABaseView.templates = { +HDABaseView.templates = HDABaseView.prototype.templates = { // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within skeleton : function( hdaJSON ){ return skeletonTemplate({ _l: _l, hda: hdaJSON }); This diff is so big that we needed to truncate the remainder. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Add a CustomDatatypeLoader for Galaxy installs, eliminate the use of the tool shed's datatyps_util module.
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/74d7ff952ec9/ Changeset: 74d7ff952ec9 User: greg Date: 2014-07-23 17:26:49 Summary: Add a CustomDatatypeLoader for Galaxy installs, eliminate the use of the tool shed's datatyps_util module. Affected #: 7 files diff -r 053943b668af334c480b464fe7351b50284b7099 -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -12,7 +12,6 @@ import tool_shed.repository_types.util as rt_util from tool_shed.util import common_util -from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import readme_util @@ -25,6 +24,7 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.grids import admin_toolshed_grids from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager @@ -256,17 +256,17 @@ dmh.remove_from_data_manager( tool_shed_repository ) if tool_shed_repository.includes_datatypes: # Deactivate proprietary datatypes. - installed_repository_dict = datatype_util.load_installed_datatypes( trans.app, - tool_shed_repository, - repository_install_dir, - deactivate=True ) + cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, + repository_install_dir, + deactivate=True ) if installed_repository_dict: converter_path = installed_repository_dict.get( 'converter_path' ) if converter_path is not None: - datatype_util.load_installed_datatype_converters( trans.app, installed_repository_dict, deactivate=True ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True ) display_path = installed_repository_dict.get( 'display_path' ) if display_path is not None: - datatype_util.load_installed_display_applications( trans.app, installed_repository_dict, deactivate=True ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=True ) if remove_from_disk_checked: try: # Remove the repository from disk. diff -r 053943b668af334c480b464fe7351b50284b7099 -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/datatypes/custom_datatype_manager.py @@ -0,0 +1,218 @@ +import logging +import os +import tempfile + +from galaxy.util import asbool + +from tool_shed.util import basic_util +from tool_shed.util import hg_util +from tool_shed.util import tool_util +from tool_shed.util import shed_util_common as suc +from tool_shed.util import xml_util + +log = logging.getLogger( __name__ ) + + +class CustomDatatypeLoader( object ): + + def __init__( self, app ): + self.app = app + + def alter_config_and_load_prorietary_datatypes( self, datatypes_config, relative_install_dir, + deactivate=False, override=True ): + """ + Parse a custom datatypes config (a datatypes_conf.xml file included in an installed + tool shed repository) and add information to appropriate element attributes that will + enable custom datatype class modules, datatypes converters and display applications + to be discovered and properly imported by the datatypes registry. The value of override + will be False when a tool shed repository is being installed. Since installation is + occurring after the datatypes registry has been initialized, the registry's contents + cannot be overridden by conflicting data types. + """ + tree, error_message = xml_util.parse_xml( datatypes_config ) + if tree is None: + return None, None + datatypes_config_root = tree.getroot() + registration = datatypes_config_root.find( 'registration' ) + if registration is None: + # We have valid XML, but not a valid custom datatypes definition. + return None, None + sniffers = datatypes_config_root.find( 'sniffers' ) + converter_path, display_path = self.get_converter_and_display_paths( registration, + relative_install_dir ) + if converter_path: + # Path to datatype converters + registration.attrib[ 'proprietary_converter_path' ] = converter_path + if display_path: + # Path to datatype display applications + registration.attrib[ 'proprietary_display_path' ] = display_path + relative_path_to_datatype_file_name = None + datatype_files = datatypes_config_root.find( 'datatype_files' ) + datatype_class_modules = [] + if datatype_files is not None: + # The <datatype_files> tag set contains any number of <datatype_file> tags. + # <datatype_files> + # <datatype_file name="gmap.py"/> + # <datatype_file name="metagenomics.py"/> + # </datatype_files> + # We'll add attributes to the datatype tag sets so that the modules can be properly imported + # by the datatypes registry. + for elem in datatype_files.findall( 'datatype_file' ): + datatype_file_name = elem.get( 'name', None ) + if datatype_file_name: + # Find the file in the installed repository. + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == datatype_file_name: + datatype_class_modules.append( os.path.join( root, name ) ) + break + break + if datatype_class_modules: + for relative_path_to_datatype_file_name in datatype_class_modules: + datatype_file_name_path, datatype_file_name = os.path.split( relative_path_to_datatype_file_name ) + for elem in registration.findall( 'datatype' ): + # Handle 'type' attribute which should be something like one of the following: + # type="gmap:GmapDB" + # type="galaxy.datatypes.gmap:GmapDB" + dtype = elem.get( 'type', None ) + if dtype: + fields = dtype.split( ':' ) + proprietary_datatype_module = fields[ 0 ] + if proprietary_datatype_module.find( '.' ) >= 0: + # Handle the case where datatype_module is "galaxy.datatypes.gmap". + proprietary_datatype_module = proprietary_datatype_module.split( '.' )[ -1 ] + # The value of proprietary_path must be an absolute path due to job_working_directory. + elem.attrib[ 'proprietary_path' ] = os.path.abspath( datatype_file_name_path ) + elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module + # Temporarily persist the custom datatypes configuration file so it can be loaded into the + # datatypes registry. + fd, proprietary_datatypes_config = tempfile.mkstemp( prefix="tmp-toolshed-acalpd" ) + os.write( fd, '<?xml version="1.0"?>\n' ) + os.write( fd, '<datatypes>\n' ) + os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) + if sniffers is not None: + os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) + os.write( fd, '</datatypes>\n' ) + os.close( fd ) + os.chmod( proprietary_datatypes_config, 0644 ) + # Load custom datatypes + self.app.datatypes_registry.load_datatypes( root_dir=self.app.config.root, + config=proprietary_datatypes_config, + deactivate=deactivate, + override=override ) + if deactivate: + # Reload the upload tool to eliminate deactivated datatype extensions from the file_type + # select list. + tool_util.reload_upload_tools( self.app ) + else: + self.append_to_datatypes_registry_upload_file_formats( registration ) + tool_util.reload_upload_tools( self.app ) + if datatype_files is not None: + try: + os.unlink( proprietary_datatypes_config ) + except: + pass + return converter_path, display_path + + def append_to_datatypes_registry_upload_file_formats( self, elem ): + # See if we have any datatypes that should be displayed in the upload tool's file_type select list. + for datatype_elem in elem.findall( 'datatype' ): + extension = datatype_elem.get( 'extension', None ) + display_in_upload = datatype_elem.get( 'display_in_upload', None ) + if extension is not None and display_in_upload is not None: + display_in_upload = asbool( str( display_in_upload ) ) + if display_in_upload and extension not in self.app.datatypes_registry.upload_file_formats: + self.app.datatypes_registry.upload_file_formats.append( extension ) + + def create_repository_dict_for_proprietary_datatypes( self, tool_shed, name, owner, installed_changeset_revision, + tool_dicts, converter_path=None, display_path=None ): + return dict( tool_shed=tool_shed, + repository_name=name, + repository_owner=owner, + installed_changeset_revision=installed_changeset_revision, + tool_dicts=tool_dicts, + converter_path=converter_path, + display_path=display_path ) + + def get_converter_and_display_paths( self, registration_elem, relative_install_dir ): + """ + Find the relative path to data type converters and display applications included + in installed tool shed repositories. + """ + converter_path = None + display_path = None + for elem in registration_elem.findall( 'datatype' ): + if not converter_path: + # If any of the <datatype> tag sets contain <converter> tags, set the converter_path + # if it is not already set. This requires developers to place all converters in the + # same subdirectory within the repository hierarchy. + for converter in elem.findall( 'converter' ): + converter_config = converter.get( 'file', None ) + if converter_config: + converter_config_file_name = basic_util.strip_path( converter_config ) + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == converter_config_file_name: + # The value of converter_path must be absolute due to job_working_directory. + converter_path = os.path.abspath( root ) + break + if converter_path: + break + if not display_path: + # If any of the <datatype> tag sets contain <display> tags, set the display_path + # if it is not already set. This requires developers to place all display acpplications + # in the same subdirectory within the repository hierarchy. + for display_app in elem.findall( 'display' ): + display_config = display_app.get( 'file', None ) + if display_config: + display_config_file_name = basic_util.strip_path( display_config ) + for root, dirs, files in os.walk( relative_install_dir ): + if root.find( '.hg' ) < 0: + for name in files: + if name == display_config_file_name: + # The value of display_path must be absolute due to job_working_directory. + display_path = os.path.abspath( root ) + break + if display_path: + break + if converter_path and display_path: + break + return converter_path, display_path + + def load_installed_datatype_converters( self, installed_repository_dict, deactivate=False ): + """Load or deactivate proprietary datatype converters.""" + self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, + installed_repository_dict=installed_repository_dict, + deactivate=deactivate ) + + def load_installed_datatypes( self, repository, relative_install_dir, deactivate=False ): + """ + Load proprietary datatypes and return information needed for loading custom + datatypes converters and display applications later. + """ + metadata = repository.metadata + repository_dict = None + datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) + if datatypes_config: + converter_path, display_path = \ + self.alter_config_and_load_prorietary_datatypes( datatypes_config, + relative_install_dir, + deactivate=deactivate ) + if converter_path or display_path: + # Create a dictionary of tool shed repository related information. + repository_dict = \ + self.create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, + name=repository.name, + owner=repository.owner, + installed_changeset_revision=repository.installed_changeset_revision, + tool_dicts=metadata.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) + return repository_dict + + def load_installed_display_applications( self, installed_repository_dict, deactivate=False ): + """Load or deactivate custom datatype display applications.""" + self.app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, + deactivate=deactivate ) diff -r 053943b668af334c480b464fe7351b50284b7099 -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -18,7 +18,6 @@ from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import datatype_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc @@ -26,6 +25,7 @@ from tool_shed.util import tool_util from tool_shed.util import xml_util +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager from tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder import EnvFileBuilder @@ -594,18 +594,19 @@ files_dir = os.path.join( shed_config_dict[ 'tool_path' ], files_dir ) datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, files_dir ) # Load data types required by tools. + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) converter_path, display_path = \ - datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, files_dir, override=False ) + cdl.alter_config_and_load_prorietary_datatypes( datatypes_config, files_dir, override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = \ - datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, - 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', [] ), - converter_path=converter_path, - display_path=display_path ) + cdl.create_repository_dict_for_proprietary_datatypes( tool_shed=tool_shed, + 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', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters self.app.datatypes_registry.load_datatype_converters( self.app.toolbox, installed_repository_dict=repository_dict ) diff -r 053943b668af334c480b464fe7351b50284b7099 -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -7,12 +7,12 @@ from galaxy import util from tool_shed.util import common_util from tool_shed.util import container_util -from tool_shed.util import datatype_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import xml_util from galaxy.model.orm import and_ +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager from tool_shed.galaxy_install.tools import data_manager @@ -114,17 +114,17 @@ else: repository_install_dir = os.path.abspath( relative_install_dir ) # Activate proprietary datatypes. - installed_repository_dict = datatype_util.load_installed_datatypes( self.app, - repository, - repository_install_dir, - deactivate=False ) + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) + installed_repository_dict = cdl.load_installed_datatypes( repository, + repository_install_dir, + deactivate=False ) if installed_repository_dict: converter_path = installed_repository_dict.get( 'converter_path' ) if converter_path is not None: - datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=False ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=False ) display_path = installed_repository_dict.get( 'display_path' ) if display_path is not None: - datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=False ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=False ) def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ @@ -732,22 +732,24 @@ self.add_entry_to_installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) def load_proprietary_datatypes( self ): + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) for tool_shed_repository in self.context.query( self.install_model.ToolShedRepository ) \ - .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, - self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ - .order_by( self.install_model.ToolShedRepository.table.c.id ): + .filter( and_( self.install_model.ToolShedRepository.table.c.includes_datatypes==True, + self.install_model.ToolShedRepository.table.c.deleted==False ) ) \ + .order_by( self.install_model.ToolShedRepository.table.c.id ): relative_install_dir = self.get_repository_install_dir( tool_shed_repository ) if relative_install_dir: - installed_repository_dict = datatype_util.load_installed_datatypes( self.app, tool_shed_repository, relative_install_dir ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, relative_install_dir ) if installed_repository_dict: self.installed_repository_dicts.append( installed_repository_dict ) def load_proprietary_converters_and_display_applications( self, deactivate=False ): + cdl = custom_datatype_manager.CustomDatatypeLoader( self.app ) for installed_repository_dict in self.installed_repository_dicts: if installed_repository_dict[ 'converter_path' ]: - datatype_util.load_installed_datatype_converters( self.app, installed_repository_dict, deactivate=deactivate ) + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=deactivate ) if installed_repository_dict[ 'display_path' ]: - datatype_util.load_installed_display_applications( self.app, installed_repository_dict, deactivate=deactivate ) + cdl.load_installed_display_applications( installed_repository_dict, deactivate=deactivate ) def purge_repository( self, repository ): """Purge a repository with status New (a white ghost) from the database.""" diff -r 053943b668af334c480b464fe7351b50284b7099 -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 lib/tool_shed/galaxy_install/tool_migration_manager.py --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -14,6 +14,7 @@ from galaxy.util.odict import odict from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install.datatypes import custom_datatype_manager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager from tool_shed.galaxy_install.tools import tool_panel_manager @@ -22,7 +23,6 @@ from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import datatype_util from tool_shed.util import hg_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util @@ -492,6 +492,7 @@ 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: + 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: tool_shed_repository.includes_datatypes = True @@ -499,21 +500,27 @@ self.app.install_model.context.flush() work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-hrc" ) datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, repo_install_dir ) - # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started - # after this installation completes. - converter_path, display_path = datatype_util.alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir + # Load proprietary data types required by tools. The value of override is not + # important here since the Galaxy server will be started after this installation + #completes. + converter_path, display_path = \ + cdl.alter_config_and_load_prorietary_datatypes( datatypes_config, + repo_install_dir, + override=False ) if converter_path or display_path: # Create a dictionary of tool shed repository related information. - repository_dict = datatype_util.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url, - name=tool_shed_repository.name, - owner=self.repository_owner, - installed_changeset_revision=tool_shed_repository.installed_changeset_revision, - tool_dicts=metadata_dict.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) + repository_dict = \ + cdl.create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed_url, + name=tool_shed_repository.name, + owner=self.repository_owner, + installed_changeset_revision=tool_shed_repository.installed_changeset_revision, + tool_dicts=metadata_dict.get( 'tools', [] ), + converter_path=converter_path, + display_path=display_path ) if converter_path: # Load proprietary datatype converters - self.app.datatypes_registry.load_datatype_converters( self.toolbox, installed_repository_dict=repository_dict ) + self.app.datatypes_registry.load_datatype_converters( self.toolbox, + installed_repository_dict=repository_dict ) if display_path: # Load proprietary datatype display applications self.app.datatypes_registry.load_display_applications( installed_repository_dict=repository_dict ) diff -r 053943b668af334c480b464fe7351b50284b7099 -r 74d7ff952ec902e68cc99745fdcd3c14e86208b2 lib/tool_shed/util/datatype_util.py --- a/lib/tool_shed/util/datatype_util.py +++ /dev/null @@ -1,187 +0,0 @@ -import logging -import os -import tempfile -from galaxy import eggs -from galaxy.util import asbool -from tool_shed.util import basic_util -from tool_shed.util import hg_util -from tool_shed.util import tool_util -from tool_shed.util import xml_util -import tool_shed.util.shed_util_common as suc - -log = logging.getLogger( __name__ ) - -def alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=False, override=True ): - """ - Parse a proprietary datatypes config (a datatypes_conf.xml file included in an installed tool shed repository) and - add information to appropriate element attributes that will enable proprietary datatype class modules, datatypes converters - and display applications to be discovered and properly imported by the datatypes registry. The value of override will - be False when a tool shed repository is being installed. Since installation is occurring after the datatypes registry - has been initialized, the registry's contents cannot be overridden by conflicting data types. - """ - tree, error_message = xml_util.parse_xml( datatypes_config ) - if tree is None: - return None, None - datatypes_config_root = tree.getroot() - registration = datatypes_config_root.find( 'registration' ) - if registration is None: - # We have valid XML, but not a valid proprietary datatypes definition. - return None, None - sniffers = datatypes_config_root.find( 'sniffers' ) - converter_path, display_path = get_converter_and_display_paths( registration, relative_install_dir ) - if converter_path: - # Path to datatype converters - registration.attrib[ 'proprietary_converter_path' ] = converter_path - if display_path: - # Path to datatype display applications - registration.attrib[ 'proprietary_display_path' ] = display_path - relative_path_to_datatype_file_name = None - datatype_files = datatypes_config_root.find( 'datatype_files' ) - datatype_class_modules = [] - if datatype_files is not None: - # The <datatype_files> tag set contains any number of <datatype_file> tags. - # <datatype_files> - # <datatype_file name="gmap.py"/> - # <datatype_file name="metagenomics.py"/> - # </datatype_files> - # We'll add attributes to the datatype tag sets so that the modules can be properly imported by the datatypes registry. - for elem in datatype_files.findall( 'datatype_file' ): - datatype_file_name = elem.get( 'name', None ) - if datatype_file_name: - # Find the file in the installed repository. - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == datatype_file_name: - datatype_class_modules.append( os.path.join( root, name ) ) - break - break - if datatype_class_modules: - for relative_path_to_datatype_file_name in datatype_class_modules: - datatype_file_name_path, datatype_file_name = os.path.split( relative_path_to_datatype_file_name ) - for elem in registration.findall( 'datatype' ): - # Handle 'type' attribute which should be something like one of the following: - # type="gmap:GmapDB" - # type="galaxy.datatypes.gmap:GmapDB" - dtype = elem.get( 'type', None ) - if dtype: - fields = dtype.split( ':' ) - proprietary_datatype_module = fields[ 0 ] - if proprietary_datatype_module.find( '.' ) >= 0: - # Handle the case where datatype_module is "galaxy.datatypes.gmap". - proprietary_datatype_module = proprietary_datatype_module.split( '.' )[ -1 ] - # The value of proprietary_path must be an absolute path due to job_working_directory. - elem.attrib[ 'proprietary_path' ] = os.path.abspath( datatype_file_name_path ) - elem.attrib[ 'proprietary_datatype_module' ] = proprietary_datatype_module - # Temporarily persist the proprietary datatypes configuration file so it can be loaded into the datatypes registry. - fd, proprietary_datatypes_config = tempfile.mkstemp( prefix="tmp-toolshed-acalpd" ) - os.write( fd, '<?xml version="1.0"?>\n' ) - os.write( fd, '<datatypes>\n' ) - os.write( fd, '%s' % xml_util.xml_to_string( registration ) ) - if sniffers is not None: - os.write( fd, '%s' % xml_util.xml_to_string( sniffers ) ) - os.write( fd, '</datatypes>\n' ) - os.close( fd ) - os.chmod( proprietary_datatypes_config, 0644 ) - # Load proprietary datatypes - app.datatypes_registry.load_datatypes( root_dir=app.config.root, config=proprietary_datatypes_config, deactivate=deactivate, override=override ) - if deactivate: - # Reload the upload tool to eliminate deactivated datatype extensions from the file_type select list. - tool_util.reload_upload_tools( app ) - else: - append_to_datatypes_registry_upload_file_formats( app, registration ) - tool_util.reload_upload_tools( app ) - if datatype_files is not None: - try: - os.unlink( proprietary_datatypes_config ) - except: - pass - return converter_path, display_path - -def append_to_datatypes_registry_upload_file_formats( app, elem ): - # See if we have any datatypes that should be displayed in the upload tool's file_type select list. - for datatype_elem in elem.findall( 'datatype' ): - extension = datatype_elem.get( 'extension', None ) - display_in_upload = datatype_elem.get( 'display_in_upload', None ) - if extension is not None and display_in_upload is not None: - display_in_upload = asbool( str( display_in_upload ) ) - if display_in_upload and extension not in app.datatypes_registry.upload_file_formats: - app.datatypes_registry.upload_file_formats.append( extension ) - -def create_repository_dict_for_proprietary_datatypes( tool_shed, name, owner, installed_changeset_revision, tool_dicts, converter_path=None, display_path=None ): - return dict( tool_shed=tool_shed, - repository_name=name, - repository_owner=owner, - installed_changeset_revision=installed_changeset_revision, - tool_dicts=tool_dicts, - converter_path=converter_path, - display_path=display_path ) - -def get_converter_and_display_paths( registration_elem, relative_install_dir ): - """Find the relative path to data type converters and display applications included in installed tool shed repositories.""" - converter_path = None - display_path = None - for elem in registration_elem.findall( 'datatype' ): - if not converter_path: - # If any of the <datatype> tag sets contain <converter> tags, set the converter_path - # if it is not already set. This requires developers to place all converters in the - # same subdirectory within the repository hierarchy. - for converter in elem.findall( 'converter' ): - converter_config = converter.get( 'file', None ) - if converter_config: - converter_config_file_name = basic_util.strip_path( converter_config ) - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == converter_config_file_name: - # The value of converter_path must be absolute due to job_working_directory. - converter_path = os.path.abspath( root ) - break - if converter_path: - break - if not display_path: - # If any of the <datatype> tag sets contain <display> tags, set the display_path - # if it is not already set. This requires developers to place all display acpplications - # in the same subdirectory within the repository hierarchy. - for display_app in elem.findall( 'display' ): - display_config = display_app.get( 'file', None ) - if display_config: - display_config_file_name = basic_util.strip_path( display_config ) - for root, dirs, files in os.walk( relative_install_dir ): - if root.find( '.hg' ) < 0: - for name in files: - if name == display_config_file_name: - # The value of display_path must be absolute due to job_working_directory. - display_path = os.path.abspath( root ) - break - if display_path: - break - if converter_path and display_path: - break - return converter_path, display_path - -def load_installed_datatype_converters( app, installed_repository_dict, deactivate=False ): - # Load or deactivate proprietary datatype converters - app.datatypes_registry.load_datatype_converters( app.toolbox, installed_repository_dict=installed_repository_dict, deactivate=deactivate ) - -def load_installed_datatypes( app, repository, relative_install_dir, deactivate=False ): - # Load proprietary datatypes and return information needed for loading proprietary datatypes converters and display applications later. - metadata = repository.metadata - repository_dict = None - datatypes_config = hg_util.get_config_from_disk( suc.DATATYPES_CONFIG_FILENAME, relative_install_dir ) - if datatypes_config: - converter_path, display_path = alter_config_and_load_prorietary_datatypes( app, datatypes_config, relative_install_dir, deactivate=deactivate ) - if converter_path or display_path: - # Create a dictionary of tool shed repository related information. - repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=repository.tool_shed, - name=repository.name, - owner=repository.owner, - installed_changeset_revision=repository.installed_changeset_revision, - tool_dicts=metadata.get( 'tools', [] ), - converter_path=converter_path, - display_path=display_path ) - return repository_dict - -def load_installed_display_applications( app, installed_repository_dict, deactivate=False ): - # Load or deactivate proprietary datatype display applications - app.datatypes_registry.load_display_applications( installed_repository_dict=installed_repository_dict, deactivate=deactivate ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: More standardized (if still terse) exception handling in AuthenticationController.
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/053943b668af/ Changeset: 053943b668af User: jmchilton Date: 2014-07-23 16:16:08 Summary: More standardized (if still terse) exception handling in AuthenticationController. Affected #: 3 files diff -r f24d7ac8ee9549fc19435aa1448854e9024982ff -r 053943b668af334c480b464fe7351b50284b7099 lib/galaxy/exceptions/__init__.py --- a/lib/galaxy/exceptions/__init__.py +++ b/lib/galaxy/exceptions/__init__.py @@ -86,6 +86,11 @@ err_code = error_codes.USER_REQUEST_INVALID_PARAMETER +class AuthenticationFailed( MessageException ): + status_code = 401 + err_code = error_codes.USER_AUTHENTICATION_FAILED + + class AuthenticationRequired( MessageException ): status_code = 403 #TODO: as 401 and send WWW-Authenticate: ??? diff -r f24d7ac8ee9549fc19435aa1448854e9024982ff -r 053943b668af334c480b464fe7351b50284b7099 lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -60,6 +60,11 @@ "message": "Supplied incorrect or incompatible tool meta parameters." }, { + "name": "USER_AUTHENTICATION_FAILED", + "code": 401001, + "message": "Authentication failed, invalid credentials supplied." + }, + { "name": "USER_NO_API_KEY", "code": 403001, "message": "API authentication required for this request" diff -r f24d7ac8ee9549fc19435aa1448854e9024982ff -r 053943b668af334c480b464fe7351b50284b7099 lib/galaxy/webapps/galaxy/api/authenticate.py --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -12,11 +12,10 @@ """ from base64 import b64decode -from paste.httpexceptions import HTTPBadRequest from urllib import unquote -from galaxy import web -from galaxy.exceptions import ObjectNotFound +from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous +from galaxy import exceptions from galaxy.web.base.controller import BaseAPIController, CreatesApiKeysMixin import logging @@ -25,7 +24,7 @@ class AuthenticationController( BaseAPIController, CreatesApiKeysMixin ): - @web.expose_api_anonymous + @expose_api_anonymous def get_api_key( self, trans, **kwd ): """ def get_api_key( self, trans, **kwd ) @@ -43,7 +42,7 @@ if ( len( user ) is not 1 ): # DB is inconsistent and we have more users with same email - raise ObjectNotFound + raise exceptions.ObjectNotFound() else: user = user[0] is_valid_user = user.check_password( password ) @@ -54,8 +53,7 @@ key = self.create_api_key( trans, user ) return dict( api_key=key ) else: - trans.response.status = 500 - return "invalid password" + raise exceptions.AuthenticationFailed() def _decode_baseauth( self, encoded_str ): """ @@ -81,7 +79,7 @@ try: email, password = b64decode( split[ 0 ] ).split( ':' ) except: - raise HTTPBadRequest + raise exceptions.ActionInputError() # If there are only two elements, check the first and ensure it says # 'basic' so that we know we're about to decode the right thing. If not, @@ -91,13 +89,13 @@ try: email, password = b64decode( split[ 1 ] ).split( ':' ) except: - raise HTTPBadRequest + raise exceptions.ActionInputError() else: - raise HTTPBadRequest + raise exceptions.ActionInputError() # If there are more than 2 elements, something crazy must be happening. # Bail. else: - raise HTTPBadRequest + raise exceptions.ActionInputError() return unquote( email ), unquote( password ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Fixes in exception handlers in the Tool Shed's create_categories and create_users API modules.
by commits-noreply＠bitbucket.org 23 Jul '14

23 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f24d7ac8ee95/ Changeset: f24d7ac8ee95 User: greg Date: 2014-07-23 15:47:21 Summary: Fixes in exception handlers in the Tool Shed's create_categories and create_users API modules. Affected #: 2 files diff -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 -r f24d7ac8ee9549fc19435aa1448854e9024982ff lib/tool_shed/scripts/api/create_categories.py --- a/lib/tool_shed/scripts/api/create_categories.py +++ b/lib/tool_shed/scripts/api/create_categories.py @@ -44,7 +44,7 @@ response = submit( url, data, api_key ) except Exception, e: response = str( e ) - log.exception( str( e ) ) + print "Error attempting to create category using URL: ", url, " exception: ", str( e ) create_response_dict = dict( response=response ) create_response_dicts.append( create_response_dict ) diff -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 -r f24d7ac8ee9549fc19435aa1448854e9024982ff lib/tool_shed/scripts/api/create_users.py --- a/lib/tool_shed/scripts/api/create_users.py +++ b/lib/tool_shed/scripts/api/create_users.py @@ -47,7 +47,7 @@ response = submit( url, data, api_key ) except Exception, e: response = str( e ) - log.exception( str( e ) ) + print "Error attempting to create user using URL: ", url, " exception: ", str( e ) create_response_dict = dict( response=response ) create_response_dicts.append( create_response_dict ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Move some functions out of the Tool Shed's shed_util_common module.
by commits-noreply＠bitbucket.org 22 Jul '14

22 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0c62ccbc8624/ Changeset: 0c62ccbc8624 User: greg Date: 2014-07-22 22:46:30 Summary: Move some functions out of the Tool Shed's shed_util_common module. Affected #: 7 files diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -9,6 +9,7 @@ from time import strftime from galaxy import web +from galaxy.model.orm import and_ from galaxy.util import asbool from galaxy.util import CHUNK_SIZE from galaxy.util.odict import odict @@ -408,7 +409,7 @@ flush = True # Do not allow dependent repository revisions to be automatically installed if population # resulted in errors. - dependent_downloadable_revisions = suc.get_dependent_downloadable_revisions( self.app, repository_metadata ) + dependent_downloadable_revisions = self.get_dependent_downloadable_revisions( repository_metadata ) for dependent_downloadable_revision in dependent_downloadable_revisions: if dependent_downloadable_revision.downloadable: dependent_downloadable_revision.downloadable = False @@ -541,6 +542,66 @@ archives.append( archive_file_name ) return archives, error_message + def get_dependent_downloadable_revisions( self, repository_metadata ): + """ + Return all repository_metadata records that are downloadable and that depend upon the received + repository_metadata record. + """ + # This method is called only from the tool shed. + sa_session = self.app.model.context.current + rm_changeset_revision = repository_metadata.changeset_revision + rm_repository = repository_metadata.repository + rm_repository_name = str( rm_repository.name ) + rm_repository_owner = str( rm_repository.user.username ) + dependent_downloadable_revisions = [] + for repository in sa_session.query( self.app.model.Repository ) \ + .filter( and_( self.app.model.Repository.table.c.id != rm_repository.id, + self.app.model.Repository.table.c.deleted == False, + self.app.model.Repository.table.c.deprecated == False ) ): + downloadable_revisions = repository.downloadable_revisions + if downloadable_revisions: + for downloadable_revision in downloadable_revisions: + if downloadable_revision.has_repository_dependencies: + metadata = downloadable_revision.metadata + if metadata: + repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) + repository_dependencies_tups = repository_dependencies_dict.get( 'repository_dependencies', [] ) + for repository_dependencies_tup in repository_dependencies_tups: + tool_shed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td = \ + common_util.parse_repository_dependency_tuple( repository_dependencies_tup ) + if name == rm_repository_name and owner == rm_repository_owner: + # We've discovered a repository revision that depends upon the repository associated + # with the received repository_metadata record, but we need to make sure it depends + # upon the revision. + if changeset_revision == rm_changeset_revision: + dependent_downloadable_revisions.append( downloadable_revision ) + else: + # Make sure the defined changeset_revision is current. + defined_repository_metadata = \ + sa_session.query( self.app.model.RepositoryMetadata ) \ + .filter( self.app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) \ + .first() + if defined_repository_metadata is None: + # The defined changeset_revision is not associated with a repository_metadata + # record, so updates must be necessary. + defined_repository = suc.get_repository_by_name_and_owner( self.app, name, owner ) + defined_repo = hg_util.get_repo_for_repository( self.app, + repository=defined_repository, + repo_path=None, + create=False ) + updated_changeset_revision = \ + suc.get_next_downloadable_changeset_revision( defined_repository, + defined_repo, + changeset_revision ) + if updated_changeset_revision == rm_changeset_revision: + dependent_downloadable_revisions.append( downloadable_revision ) + return dependent_downloadable_revisions + def get_export_info_dict( self, export_info_file_path ): """ Parse the export_info.xml file contained within the capsule and return a dictionary diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -342,8 +342,8 @@ installed_rd_tups = [] missing_rd_tups = [] for tsr in repository.repository_dependencies: - prior_installation_required = suc.set_prior_installation_required( self.app, repository, tsr ) - only_if_compiling_contained_td = suc.set_only_if_compiling_contained_td( repository, tsr ) + prior_installation_required = self.set_prior_installation_required( repository, tsr ) + only_if_compiling_contained_td = self.set_only_if_compiling_contained_td( repository, tsr ) rd_tup = [ tsr.tool_shed, tsr.name, tsr.owner, @@ -957,6 +957,47 @@ return True return False + def set_only_if_compiling_contained_td( self, repository, required_repository ): + """ + Return True if the received required_repository is only needed to compile a tool + dependency defined for the received repository. + """ + # This method is called only from Galaxy when rendering repository dependencies + # for an installed tool shed repository. + # TODO: Do we need to check more than changeset_revision here? + required_repository_tup = [ required_repository.tool_shed, \ + required_repository.name, \ + required_repository.owner, \ + required_repository.changeset_revision ] + for tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: + partial_tup = tup[ 0:4 ] + if partial_tup == required_repository_tup: + return 'True' + return 'False' + + def set_prior_installation_required( self, repository, required_repository ): + """ + Return True if the received required_repository must be installed before the + received repository. + """ + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, + str( required_repository.tool_shed ) ) + required_repository_tup = [ tool_shed_url, + str( required_repository.name ), + str( required_repository.owner ), + str( required_repository.changeset_revision ) ] + # Get the list of repository dependency tuples associated with the received repository + # where prior_installation_required is True. + required_rd_tups_that_must_be_installed = repository.requires_prior_installation_of + for required_rd_tup in required_rd_tups_that_must_be_installed: + # Repository dependency tuples in metadata include a prior_installation_required value, + # so strip it for comparision. + partial_required_rd_tup = required_rd_tup[ 0:4 ] + if partial_required_rd_tup == required_repository_tup: + # Return the string value of prior_installation_required, which defaults to 'False'. + return str( required_rd_tup[ 4 ] ) + return 'False' + def update_existing_tool_dependency( self, repository, original_dependency_dict, new_dependencies_dict ): """ Update an exsiting tool dependency whose definition was updated in a change set diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py --- a/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py +++ b/lib/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py @@ -2,9 +2,9 @@ Class encapsulating the management of repository dependencies installed or being installed into Galaxy from the Tool Shed. """ - import json import logging +import os import urllib import urllib2 @@ -63,11 +63,10 @@ break if d_repository is None: # The dependent repository is not in the received list so look in the database. - d_repository = suc.get_or_create_tool_shed_repository( self.app, - d_toolshed, - d_name, - d_owner, - d_changeset_revision ) + d_repository = self.get_or_create_tool_shed_repository( d_toolshed, + d_name, + d_owner, + d_changeset_revision ) # Process each repository_dependency defined for the current dependent repository. for repository_dependency_components_list in val: required_repository = None @@ -87,11 +86,10 @@ break if required_repository is None: # The required repository is not in the received list so look in the database. - required_repository = suc.get_or_create_tool_shed_repository( self.app, - rd_toolshed, - rd_name, - rd_owner, - rd_changeset_revision ) + required_repository = self.get_or_create_tool_shed_repository( rd_toolshed, + rd_name, + rd_owner, + rd_changeset_revision ) # Ensure there is a repository_dependency relationship between d_repository and required_repository. rrda = None for rd in d_repository.repository_dependencies: @@ -257,6 +255,35 @@ self.build_repository_dependency_relationships( all_repo_info_dicts, all_created_or_updated_tool_shed_repositories ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts + def get_or_create_tool_shed_repository( self, tool_shed, name, owner, changeset_revision ): + """ + Return a tool shed repository database record defined by the combination of + tool shed, repository name, repository owner and changeset_revision or + installed_changeset_revision. A new tool shed repository record will be + created if one is not located. + """ + install_model = self.app.install_model + # We store the port in the database. + tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed ) + # This method is used only in Galaxy, not the tool shed. + repository = suc.get_repository_for_dependency_relationship( self.app, tool_shed, name, owner, changeset_revision ) + if not repository: + tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, tool_shed ) + repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) + ctx_rev = suc.get_ctx_rev( self.app, tool_shed_url, name, owner, changeset_revision ) + repository = suc.create_or_update_tool_shed_repository( app=self.app, + name=name, + description=None, + installed_changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=install_model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=None, + owner=owner, + dist_to_shed=False ) + return repository + def get_repository_dependencies_for_installed_tool_shed_repository( self, app, repository ): """ Send a request to the appropriate tool shed to retrieve the dictionary of repository dependencies defined diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -410,7 +410,7 @@ repo = hg_util.get_repo_for_repository( self.app, repository=repository, repo_path=None, create=False ) for changeset in repo.changelog: changeset_hash = str( repo.changectx( changeset ) ) - skip_tool_test = suc.get_skip_tool_test_by_changeset_revision( self.app, changeset_hash ) + skip_tool_test = self.get_skip_tool_test_by_changeset_revision( changeset_hash ) if skip_tool_test: # We found a skip_tool_test record associated with the changeset_revision, # so see if it has a valid repository_revision. @@ -521,6 +521,16 @@ return self.sa_session.query( self.app.model.Repository ) \ .filter( self.app.model.Repository.table.c.deleted == False ) + def get_skip_tool_test_by_changeset_revision( self, changeset_revision ): + """ + Return a skip_tool_test record whose initial_changeset_revision is the received + changeset_revision. + """ + # There should only be one, but we'll use first() so callers won't have to handle exceptions. + return self.sa_session.query( self.app.model.SkipToolTest ) \ + .filter( self.app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ + .first() + def new_datatypes_metadata_required( self, repository_metadata, metadata_dict ): """ Compare the last saved metadata for each datatype in the repository with the new metadata diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/tools/data_table_manager.py --- a/lib/tool_shed/tools/data_table_manager.py +++ b/lib/tool_shed/tools/data_table_manager.py @@ -2,8 +2,9 @@ import os import shutil +from xml.etree import ElementTree as XmlET + from tool_shed.util import hg_util -from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util log = logging.getLogger( __name__ ) @@ -14,6 +15,36 @@ def __init__( self, app ): self.app = app + def generate_repository_info_elem( self, tool_shed, repository_name, changeset_revision, owner, + parent_elem=None, **kwd ): + """Create and return an ElementTree repository info Element.""" + if parent_elem is None: + elem = XmlET.Element( 'tool_shed_repository' ) + else: + elem = XmlET.SubElement( parent_elem, 'tool_shed_repository' ) + tool_shed_elem = XmlET.SubElement( elem, 'tool_shed' ) + tool_shed_elem.text = tool_shed + repository_name_elem = XmlET.SubElement( elem, 'repository_name' ) + repository_name_elem.text = repository_name + repository_owner_elem = XmlET.SubElement( elem, 'repository_owner' ) + repository_owner_elem.text = owner + changeset_revision_elem = XmlET.SubElement( elem, 'installed_changeset_revision' ) + changeset_revision_elem.text = changeset_revision + #add additional values + #TODO: enhance additional values to allow e.g. use of dict values that will recurse + for key, value in kwd.iteritems(): + new_elem = XmlET.SubElement( elem, key ) + new_elem.text = value + return elem + + def generate_repository_info_elem_from_repository( self, tool_shed_repository, parent_elem=None, **kwd ): + return self.generate_repository_info_elem( tool_shed_repository.tool_shed, + tool_shed_repository.name, + tool_shed_repository.installed_changeset_revision, + tool_shed_repository.owner, + parent_elem=parent_elem, + **kwd ) + def get_tool_index_sample_files( self, sample_files ): """ Try to return the list of all appropriate tool data sample files included @@ -129,7 +160,7 @@ if path: file_elem.set( 'path', os.path.normpath( os.path.join( target_dir, os.path.split( path )[1] ) ) ) # Store repository info in the table tag set for trace-ability. - repo_elem = suc.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=elem ) + repo_elem = self.generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=elem ) if elems: # Remove old data_table os.unlink( tool_data_table_conf_filename ) diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -7,6 +7,18 @@ log = logging.getLogger( __name__ ) +def get_latest_changeset_revision( app, repository, repo ): + repository_tip = repository.tip( app ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + app.security.encode_id( repository.id ), + repository_tip ) + if repository_metadata and repository_metadata.downloadable: + return repository_tip + changeset_revisions = suc.get_ordered_metadata_changeset_revisions( repository, repo, downloadable=False ) + if changeset_revisions: + return changeset_revisions[ -1 ] + return hg_util.INITIAL_CHANGELOG_HASH + def get_latest_repository_metadata( app, decoded_repository_id, downloadable=False ): """Get last metadata defined for a specified repository from the database.""" sa_session = app.model.context.current @@ -15,7 +27,7 @@ if downloadable: changeset_revision = suc.get_latest_downloadable_changeset_revision( app, repository, repo ) else: - changeset_revision = suc.get_latest_changeset_revision( app, repository, repo ) + changeset_revision = get_latest_changeset_revision( app, repository, repo ) return suc.get_repository_metadata_by_changeset_revision( app, app.security.encode_id( repository.id ), changeset_revision ) diff -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a -r 0c62ccbc86246c9aebf8ff78c550234dfa6d5bd5 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -17,7 +17,6 @@ from tool_shed.util import encoding_util from tool_shed.util import hg_util -from xml.etree import ElementTree as XmlET from urllib2 import HTTPError log = logging.getLogger( __name__ ) @@ -165,35 +164,6 @@ components_list = [ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td ] return components_list -def generate_repository_info_elem( tool_shed, repository_name, changeset_revision, owner, parent_elem=None, **kwd ): - """Create and return an ElementTree repository info Element.""" - if parent_elem is None: - elem = XmlET.Element( 'tool_shed_repository' ) - else: - elem = XmlET.SubElement( parent_elem, 'tool_shed_repository' ) - tool_shed_elem = XmlET.SubElement( elem, 'tool_shed' ) - tool_shed_elem.text = tool_shed - repository_name_elem = XmlET.SubElement( elem, 'repository_name' ) - repository_name_elem.text = repository_name - repository_owner_elem = XmlET.SubElement( elem, 'repository_owner' ) - repository_owner_elem.text = owner - changeset_revision_elem = XmlET.SubElement( elem, 'installed_changeset_revision' ) - changeset_revision_elem.text = changeset_revision - #add additional values - #TODO: enhance additional values to allow e.g. use of dict values that will recurse - for key, value in kwd.iteritems(): - new_elem = XmlET.SubElement( elem, key ) - new_elem.text = value - return elem - -def generate_repository_info_elem_from_repository( tool_shed_repository, parent_elem=None, **kwd ): - return generate_repository_info_elem( tool_shed_repository.tool_shed, - tool_shed_repository.name, - tool_shed_repository.installed_changeset_revision, - tool_shed_repository.owner, - parent_elem=parent_elem, - **kwd ) - def generate_sharable_link_for_repository_in_tool_shed( repository, changeset_revision=None ): """Generate the URL for sharing a repository that is in the tool shed.""" base_url = url_for( '/', qualified=True ).rstrip( '/' ) @@ -291,61 +261,6 @@ return repository_metadata return None -def get_dependent_downloadable_revisions( app, repository_metadata ): - """ - Return all repository_metadata records that are downloadable and that depend upon the received - repository_metadata record. - """ - # This method is called only from the tool shed. - sa_session = app.model.context.current - rm_changeset_revision = repository_metadata.changeset_revision - rm_repository = repository_metadata.repository - rm_repository_name = str( rm_repository.name ) - rm_repository_owner = str( rm_repository.user.username ) - dependent_downloadable_revisions = [] - for repository in sa_session.query( app.model.Repository ) \ - .filter( and_( app.model.Repository.table.c.id != rm_repository.id, - app.model.Repository.table.c.deleted == False, - app.model.Repository.table.c.deprecated == False ) ): - downloadable_revisions = repository.downloadable_revisions - if downloadable_revisions: - for downloadable_revision in downloadable_revisions: - if downloadable_revision.has_repository_dependencies: - metadata = downloadable_revision.metadata - if metadata: - repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) - repository_dependencies_tups = repository_dependencies_dict.get( 'repository_dependencies', [] ) - for repository_dependencies_tup in repository_dependencies_tups: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - common_util.parse_repository_dependency_tuple( repository_dependencies_tup ) - if name == rm_repository_name and owner == rm_repository_owner: - # We've discovered a repository revision that depends upon the repository associated - # with the received repository_metadata record, but we need to make sure it depends - # upon the revision. - if changeset_revision == rm_changeset_revision: - dependent_downloadable_revisions.append( downloadable_revision ) - else: - # Make sure the defined changeset_revision is current. - defined_repository_metadata = \ - sa_session.query( app.model.RepositoryMetadata ) \ - .filter( app.model.RepositoryMetadata.table.c.changeset_revision == changeset_revision ) \ - .first() - if defined_repository_metadata is None: - # The defined changeset_revision is not associated with a repository_metadata - # record, so updates must be necessary. - defined_repository = get_repository_by_name_and_owner( app, name, owner ) - defined_repo = hg_util.get_repo_for_repository( app, - repository=defined_repository, - repo_path=None, - create=False ) - updated_changeset_revision = \ - get_next_downloadable_changeset_revision( defined_repository, - defined_repo, - changeset_revision ) - if updated_changeset_revision == rm_changeset_revision: - dependent_downloadable_revisions.append( downloadable_revision ) - return dependent_downloadable_revisions - def get_ids_of_tool_shed_repositories_being_installed( app, as_string=False ): installing_repository_ids = [] new_status = app.install_model.ToolShedRepository.installation_status.NEW @@ -365,18 +280,6 @@ return ','.join( installing_repository_ids ) return installing_repository_ids -def get_latest_changeset_revision( app, repository, repo ): - repository_tip = repository.tip( app ) - repository_metadata = get_repository_metadata_by_changeset_revision( app, - app.security.encode_id( repository.id ), - repository_tip ) - if repository_metadata and repository_metadata.downloadable: - return repository_tip - changeset_revisions = get_ordered_metadata_changeset_revisions( repository, repo, downloadable=False ) - if changeset_revisions: - return changeset_revisions[ -1 ] - return hg_util.INITIAL_CHANGELOG_HASH - def get_latest_downloadable_changeset_revision( app, repository, repo ): repository_tip = repository.tip( app ) repository_metadata = get_repository_metadata_by_changeset_revision( app, app.security.encode_id( repository.id ), repository_tip ) @@ -441,37 +344,11 @@ continue return key -def get_or_create_tool_shed_repository( app, tool_shed, name, owner, changeset_revision ): +def get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ): """ - Return a tool shed repository database record defined by the combination of - tool shed, repository name, repository owner and changeset_revision or - installed_changeset_revision. A new tool shed repository record will be - created if one is not located. + Return an ordered list of changeset_revisions that are associated with metadata + where order is defined by the repository changelog. """ - install_model = app.install_model - # We store the port in the database. - tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed ) - # This method is used only in Galaxy, not the tool shed. - repository = get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ) - if not repository: - tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, tool_shed ) - repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) - ctx_rev = get_ctx_rev( app, tool_shed_url, name, owner, changeset_revision ) - repository = create_or_update_tool_shed_repository( app=app, - name=name, - description=None, - installed_changeset_revision=changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=install_model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=None, - owner=owner, - dist_to_shed=False ) - return repository - -def get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ): - """Return an ordered list of changeset_revisions that are associated with metadata where order is defined by the repository changelog.""" if downloadable: metadata_revisions = repository.downloadable_revisions else: @@ -491,9 +368,11 @@ def get_prior_import_or_install_required_dict( app, tsr_ids, repo_info_dicts ): """ - This method is used in the Tool Shed when exporting a repository and its dependencies, and in Galaxy when a repository and its dependencies - are being installed. Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained - in the received list of tsr_ids and whose associated repository must be imported or installed prior to the repository associated with the tsr_id key. + This method is used in the Tool Shed when exporting a repository and its dependencies, + and in Galaxy when a repository and its dependencies are being installed. Return a + dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, + each of which is contained in the received list of tsr_ids and whose associated repository + must be imported or installed prior to the repository associated with the tsr_id key. """ # Initialize the dictionary. prior_import_or_install_required_dict = {} @@ -698,11 +577,14 @@ def get_repository_ids_requiring_prior_import_or_install( app, tsr_ids, repository_dependencies ): """ - This method is used in the Tool Shed when exporting a repository and its dependencies, and in Galaxy when a repository and its dependencies - are being installed. Inspect the received repository_dependencies and determine if the encoded id of each required repository is in the received - tsr_ids. If so, then determine whether that required repository should be imported / installed prior to its dependent repository. Return a list - of encoded repository ids, each of which is contained in the received list of tsr_ids, and whose associated repositories must be imported / installed - prior to the dependent repository associated with the received repository_dependencies. + This method is used in the Tool Shed when exporting a repository and its dependencies, + and in Galaxy when a repository and its dependencies are being installed. Inspect the + received repository_dependencies and determine if the encoded id of each required + repository is in the received tsr_ids. If so, then determine whether that required + repository should be imported / installed prior to its dependent repository. Return a + list of encoded repository ids, each of which is contained in the received list of tsr_ids, + and whose associated repositories must be imported / installed prior to the dependent + repository associated with the received repository_dependencies. """ prior_tsr_ids = [] if repository_dependencies: @@ -710,20 +592,32 @@ if key in [ 'description', 'root_key' ]: continue for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + tool_shed, \ + name, \ + owner, \ + changeset_revision, \ + prior_installation_required, \ + only_if_compiling_contained_td = \ common_util.parse_repository_dependency_tuple( rd_tup ) - # If only_if_compiling_contained_td is False, then the repository dependency is not required to be installed prior to the dependent - # repository even if prior_installation_required is True. This is because the only meaningful content of the repository dependency - # is its contained tool dependency, which is required in order to compile the dependent repository's tool dependency. In the scenario - # where the repository dependency is not installed prior to the dependent repository's tool dependency compilation process, the tool - # dependency compilation framework will install the repository dependency prior to compilation of the dependent repository's tool - # dependency. + # If only_if_compiling_contained_td is False, then the repository dependency + # is not required to be installed prior to the dependent repository even if + # prior_installation_required is True. This is because the only meaningful + # content of the repository dependency is its contained tool dependency, which + # is required in order to compile the dependent repository's tool dependency. + # In the scenario where the repository dependency is not installed prior to the + # dependent repository's tool dependency compilation process, the tool dependency + # compilation framework will install the repository dependency prior to compilation + # of the dependent repository's tool dependency. if not util.asbool( only_if_compiling_contained_td ): if util.asbool( prior_installation_required ): if is_tool_shed_client( app ): # We store the port, if one exists, in the database. tool_shed = common_util.remove_protocol_from_tool_shed_url( tool_shed ) - repository = get_repository_for_dependency_relationship( app, tool_shed, name, owner, changeset_revision ) + repository = get_repository_for_dependency_relationship( app, + tool_shed, + name, + owner, + changeset_revision ) else: repository = get_repository_by_name_and_owner( app, name, owner ) if repository: @@ -779,14 +673,6 @@ query = app.model.context.query( app.model.Repository ) return query -def get_skip_tool_test_by_changeset_revision( app, changeset_revision ): - """Return a skip_tool_test record whose initial_changeset_revision is the received changeset_revision.""" - # There should only be one, but we'll use first() so callers won't have to handle exceptions. - sa_session = app.model.context.current - return sa_session.query( app.model.SkipToolTest ) \ - .filter( app.model.SkipToolTest.table.c.initial_changeset_revision == changeset_revision ) \ - .first() - def get_tool_panel_config_tool_path_install_dir( app, repository ): """ Return shed-related tool panel config, the tool_path configured in it, and the relative path to @@ -1220,42 +1106,6 @@ text = re.sub( r'\.\. image:: (?!https?://)/?(.+)', r'.. image:: %s/\1' % route_to_images, text ) return text -def set_only_if_compiling_contained_td( repository, required_repository ): - """ - Return True if the received required_repository is only needed to compile a tool - dependency defined for the received repository. - """ - # This method is called only from Galaxy when rendering repository dependencies - # for an installed tool shed repository. - # TODO: Do we need to check more than changeset_revision here? - required_repository_tup = [ required_repository.tool_shed, \ - required_repository.name, \ - required_repository.owner, \ - required_repository.changeset_revision ] - for tup in repository.tuples_of_repository_dependencies_needed_for_compiling_td: - partial_tup = tup[ 0:4 ] - if partial_tup == required_repository_tup: - return 'True' - return 'False' - -def set_prior_installation_required( app, repository, required_repository ): - """Return True if the received required_repository must be installed before the received repository.""" - # This method is called only from Galaxy when rendering repository dependencies for an installed Tool Shed repository. - tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, str( required_repository.tool_shed ) ) - required_repository_tup = [ tool_shed_url, - str( required_repository.name ), - str( required_repository.owner ), - str( required_repository.changeset_revision ) ] - # Get the list of repository dependency tuples associated with the received repository where prior_installation_required is True. - required_rd_tups_that_must_be_installed = repository.requires_prior_installation_of - for required_rd_tup in required_rd_tups_that_must_be_installed: - # Repository dependency tuples in metadata include a prior_installation_required value, so strip it for comparision. - partial_required_rd_tup = required_rd_tup[ 0:4 ] - if partial_required_rd_tup == required_repository_tup: - # Return the string value of prior_installation_required, which defaults to 'False'. - return str( required_rd_tup[ 4 ] ) - return 'False' - def set_repository_attributes( app, repository, status, error_message, deleted, uninstalled, remove_from_disk=False ): if remove_from_disk: relative_install_dir = repository.repo_path( app ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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