2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c1a640fa6b3d/ changeset: c1a640fa6b3d user: Brad Langhorst date: 2012-07-20 21:15:14 summary: copies the tags from a source history when a workflow is creating new histories to store results. moves tag copying logic into the model for TagAssociation class adds copy_tags_from method to history and storedworkflow classes affected #: 2 files diff -r 4c22a2fbf25a8ee05d870dcebe9f7b729fa22f07 -r c1a640fa6b3d4f0486d3a20b7f0eebb605c923db lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -434,7 +434,10 @@ # Copy annotation. self.copy_item_annotation( db_session, self.user, self, target_user, new_history ) - + + #Copy Tags + new_history.copy_tags_from(target_user=target_user, source_history=self) + # Copy HDAs. if activatable: hdas = self.activatable_datasets @@ -494,6 +497,12 @@ if nice_size: rval = galaxy.datatypes.data.nice_size( rval ) return rval + + def copy_tags_from(self,target_user,source_history): + for src_shta in source_history.tags: + new_shta = src_shta.copy() + new_shta.user = target_user + self.tags.append(new_shta) class HistoryUserShareAssociation( object ): def __init__( self ): @@ -1717,6 +1726,12 @@ self.published = False self.latest_workflow_id = None self.workflows = [] + + def copy_tags_from(self,target_user,source_workflow): + for src_swta in source_workflow.owner_tags: + new_swta = src_swta.copy() + new_swta.user = target_user + self.tags.append(new_swta) class Workflow( object ): def __init__( self ): @@ -2543,7 +2558,15 @@ self.user_tname = user_tname self.value = None self.user_value = None - + + def copy(self): + new_ta = type(self)() + new_ta.tag_id = self.tag_id + new_ta.user_tname = self.user_tname + new_ta.value = self.value + new_ta.user_value = self.user_value + return new_ta + class HistoryTagAssociation ( ItemTagAssociation ): pass diff -r 4c22a2fbf25a8ee05d870dcebe9f7b729fa22f07 -r c1a640fa6b3d4f0486d3a20b7f0eebb605c923db lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -508,7 +508,6 @@ trans.response.set_content_type("image/svg+xml") return self._workflow_to_svg_canvas( trans, stored ).standalone_xml() - @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): @@ -531,15 +530,8 @@ annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored ) if annotation_obj: self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation ) - # Clone tags. - for swta in stored.owner_tags: - new_swta = model.StoredWorkflowTagAssociation() - new_swta.tag = swta.tag - new_swta.user = trans.user - new_swta.user_tname = swta.user_tname - new_swta.user_value = swta.user_value - new_swta.value = swta.value - new_stored.tags.append( new_swta ) + new_stored.copy_tags_from(trans.user,stored) + if not owner: new_stored.name += " shared by '%s'" % stored.user.email new_stored.user = user @@ -1408,6 +1400,7 @@ mx_ds_name = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( single_input ).name nh_name = '%s on %s' % (nh_name, mx_ds_name) new_history = trans.app.model.History( user=trans.user, name=nh_name ) + new_history.copy_tags_from(trans.user, trans.get_history()) trans.sa_session.add( new_history ) target_history = new_history else: https://bitbucket.org/galaxy/galaxy-central/changeset/c81172ba88a7/ changeset: c81172ba88a7 user: dannon date: 2012-07-23 00:02:43 summary: Merge pull request #54 from bwlang - parent tag copying for multiple workflow run output histories. affected #: 2 files diff -r ed01365064b2644531c783f01a12b28384fd64ad -r c81172ba88a7d2ee619a32f6de8bdfdcfe5614e2 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -102,7 +102,7 @@ class Job( object ): """ - A job represents a request to run a tool given input datasets, tool + A job represents a request to run a tool given input datasets, tool parameters, and output datasets. """ states = Bunch( NEW = 'new', @@ -216,7 +216,7 @@ self.stdout = None self.stderr = None self.prepare_input_files_cmd = prepare_files_cmd - + def set_state( self, state ): self.state = state @@ -285,7 +285,7 @@ class JobExportHistoryArchive( object ): def __init__( self, job=None, history=None, dataset=None, compressed=False, \ - history_attrs_filename=None, datasets_attrs_filename=None, + history_attrs_filename=None, datasets_attrs_filename=None, jobs_attrs_filename=None ): self.job = job self.history = history @@ -378,7 +378,7 @@ self.datasets = [] self.galaxy_sessions = [] def _next_hid( self ): - # TODO: override this with something in the database that ensures + # TODO: override this with something in the database that ensures # better integrity if len( self.datasets ) == 0: return 1 @@ -435,6 +435,9 @@ # Copy annotation. self.copy_item_annotation( db_session, self.user, self, target_user, new_history ) + #Copy Tags + new_history.copy_tags_from(target_user=target_user, source_history=self) + # Copy HDAs. if activatable: hdas = self.activatable_datasets @@ -495,6 +498,12 @@ rval = galaxy.datatypes.data.nice_size( rval ) return rval + def copy_tags_from(self,target_user,source_history): + for src_shta in source_history.tags: + new_shta = src_shta.copy() + new_shta.user = target_user + self.tags.append(new_shta) + class HistoryUserShareAssociation( object ): def __init__( self ): self.history = None @@ -514,7 +523,7 @@ api_collection_visible_keys = ( 'id', 'name' ) api_element_visible_keys = ( 'id', 'name', 'description', 'type' ) private_id = None - types = Bunch( + types = Bunch( PRIVATE = 'private', SYSTEM = 'system', USER = 'user', @@ -657,7 +666,7 @@ self.external_filename = external_filename self._extra_files_path = extra_files_path self.file_size = file_size - + def get_file_name( self ): if not self.external_filename: assert self.id is not None, "ID must be set before filename used (commit the object)" @@ -961,17 +970,17 @@ session.flush() return None def get_metadata_dataset( self, trans, dataset_ext ): - """ - Returns an HDA that points to a metadata file which contains a + """ + Returns an HDA that points to a metadata file which contains a converted data with the requested extension. """ for name, value in self.metadata.items(): # HACK: MetadataFile objects do not have a type/ext, so need to use metadata name # to determine type. if dataset_ext == 'bai' and name == 'bam_index' and isinstance( value, trans.app.model.MetadataFile ): - # HACK: MetadataFile objects cannot be used by tools, so return + # HACK: MetadataFile objects cannot be used by tools, so return # a fake HDA that points to metadata file. - fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK, + fake_dataset = trans.app.model.Dataset( state=trans.app.model.Dataset.states.OK, external_filename=value.file_name ) fake_hda = trans.app.model.HistoryDatasetAssociation( dataset=fake_dataset ) return fake_hda @@ -1039,14 +1048,14 @@ return self.datatype.get_display_applications_by_dataset( self, trans ) class HistoryDatasetAssociation( DatasetInstance ): - def __init__( self, - hid = None, - history = None, - copied_from_history_dataset_association = None, - copied_from_library_dataset_dataset_association = None, + def __init__( self, + hid = None, + history = None, + copied_from_history_dataset_association = None, + copied_from_library_dataset_dataset_association = None, sa_session = None, **kwd ): - # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset + # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset # parameter is True so that the new object can be flushed. Is there a better way? DatasetInstance.__init__( self, sa_session=sa_session, **kwd ) self.hid = hid @@ -1055,18 +1064,18 @@ self.copied_from_history_dataset_association = copied_from_history_dataset_association self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association def copy( self, copy_children = False, parent_id = None ): - hda = HistoryDatasetAssociation( hid=self.hid, - name=self.name, - info=self.info, - blurb=self.blurb, - peek=self.peek, - tool_version=self.tool_version, - extension=self.extension, - dbkey=self.dbkey, - dataset = self.dataset, - visible=self.visible, - deleted=self.deleted, - parent_id=parent_id, + hda = HistoryDatasetAssociation( hid=self.hid, + name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + tool_version=self.tool_version, + extension=self.extension, + dbkey=self.dbkey, + dataset = self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, copied_from_history_dataset_association=self ) object_session( self ).add( hda ) object_session( self ).flush() @@ -1086,7 +1095,7 @@ # The replace_dataset param ( when not None ) refers to a LibraryDataset that is being replaced with a new version. library_dataset = replace_dataset else: - # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new + # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new # LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset. library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info ) object_session( self ).add( library_dataset ) @@ -1094,17 +1103,17 @@ if not user: # This should never happen since users must be authenticated to upload to a data library user = self.history.user - ldda = LibraryDatasetDatasetAssociation( name=self.name, + ldda = LibraryDatasetDatasetAssociation( name=self.name, info=self.info, - blurb=self.blurb, - peek=self.peek, - tool_version=self.tool_version, - extension=self.extension, - dbkey=self.dbkey, - dataset=self.dataset, + blurb=self.blurb, + peek=self.peek, + tool_version=self.tool_version, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, library_dataset=library_dataset, - visible=self.visible, - deleted=self.deleted, + visible=self.visible, + deleted=self.deleted, parent_id=parent_id, copied_from_history_dataset_association=self, user=user ) @@ -1202,7 +1211,7 @@ self.history_dataset_association = hda self.user = user self.site = site - + class HistoryDatasetAssociationSubset( object ): def __init__(self, hda, subset, location): self.hda = hda @@ -1252,7 +1261,7 @@ # inherited is not applicable at the library level. The get_contents # param is passed by callers that are inheriting a template - these # are usually new library datsets for which we want to include template - # fields on the upload form, but not necessarily the contents of the + # fields on the upload form, but not necessarily the contents of the # inherited template saved for the parent. info_association, inherited = self.get_info_association() if info_association: @@ -1271,7 +1280,7 @@ roles.append( lp.role ) return roles def get_display_name( self ): - # Library name can be either a string or a unicode object. If string, + # Library name can be either a string or a unicode object. If string, # convert to unicode object assuming 'utf-8' format. name = self.name if isinstance( name, str ): @@ -1329,7 +1338,7 @@ # not inherited ( we do not want to display the inherited contents ). # (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit # contents. We'll use this behavior until we hear from the community that - # contents should not be inherited. If we don't hear anything for a while, + # contents should not be inherited. If we don't hear anything for a while, # eliminate the old commented out behavior. #if not inherited and get_contents: if get_contents: @@ -1344,7 +1353,7 @@ # This needs to be a list return [ ld for ld in self.datasets if ld.library_dataset_dataset_association and not ld.library_dataset_dataset_association.dataset.deleted ] def get_display_name( self ): - # Library folder name can be either a string or a unicode object. If string, + # Library folder name can be either a string or a unicode object. If string, # convert to unicode object assuming 'utf-8' format. name = self.name if isinstance( name, str ): @@ -1451,7 +1460,7 @@ user=None, sa_session=None, **kwd ): - # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset + # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset # parameter in kwd is True so that the new object can be flushed. Is there a better way? DatasetInstance.__init__( self, sa_session=sa_session, **kwd ) if copied_from_history_dataset_association: @@ -1461,17 +1470,17 @@ self.library_dataset = library_dataset self.user = user def to_history_dataset_association( self, target_history, parent_id = None, add_to_history = False ): - hda = HistoryDatasetAssociation( name=self.name, + hda = HistoryDatasetAssociation( name=self.name, info=self.info, - blurb=self.blurb, - peek=self.peek, - tool_version=self.tool_version, - extension=self.extension, - dbkey=self.dbkey, - dataset=self.dataset, - visible=self.visible, - deleted=self.deleted, - parent_id=parent_id, + blurb=self.blurb, + peek=self.peek, + tool_version=self.tool_version, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, copied_from_library_dataset_dataset_association=self, history=target_history ) object_session( self ).add( hda ) @@ -1486,17 +1495,17 @@ object_session( self ).flush() return hda def copy( self, copy_children = False, parent_id = None, target_folder = None ): - ldda = LibraryDatasetDatasetAssociation( name=self.name, - info=self.info, - blurb=self.blurb, - peek=self.peek, - tool_version=self.tool_version, - extension=self.extension, - dbkey=self.dbkey, - dataset=self.dataset, - visible=self.visible, - deleted=self.deleted, - parent_id=parent_id, + ldda = LibraryDatasetDatasetAssociation( name=self.name, + info=self.info, + blurb=self.blurb, + peek=self.peek, + tool_version=self.tool_version, + extension=self.extension, + dbkey=self.dbkey, + dataset=self.dataset, + visible=self.visible, + deleted=self.deleted, + parent_id=parent_id, copied_from_library_dataset_dataset_association=self, folder=target_folder ) object_session( self ).add( ldda ) @@ -1534,7 +1543,7 @@ # See if we have any associated templatesThe get_contents # param is passed by callers that are inheriting a template - these # are usually new library datsets for which we want to include template - # fields on the upload form, but not necessarily the contents of the + # fields on the upload form, but not necessarily the contents of the # inherited template saved for the parent. info_association, inherited = self.get_info_association() if info_association: @@ -1546,7 +1555,7 @@ # not inherited ( we do not want to display the inherited contents ). # (gvk: 8/30/10) Based on conversations with Dan, we agreed to ALWAYS inherit # contents. We'll use this behavior until we hear from the community that - # contents should not be inherited. If we don't hear anything for a while, + # contents should not be inherited. If we don't hear anything for a while, # eliminate the old commented out behavior. #if not inherited and get_contents: if get_contents: @@ -1663,15 +1672,15 @@ self.message = message class GalaxySession( object ): - def __init__( self, - id=None, - user=None, - remote_host=None, - remote_addr=None, - referer=None, - current_history=None, - session_key=None, - is_valid=False, + def __init__( self, + id=None, + user=None, + remote_host=None, + remote_addr=None, + referer=None, + current_history=None, + session_key=None, + is_valid=False, prev_session_id=None ): self.id = id self.user = user @@ -1718,6 +1727,12 @@ self.latest_workflow_id = None self.workflows = [] + def copy_tags_from(self,target_user,source_workflow): + for src_swta in source_workflow.owner_tags: + new_swta = src_swta.copy() + new_swta.user = target_user + self.tags.append(new_swta) + class Workflow( object ): def __init__( self ): self.user = None @@ -1797,7 +1812,7 @@ raise # Return filename inside hashed directory return os.path.abspath( os.path.join( path, "metadata_%d.dat" % self.id ) ) - + class FormDefinition( object, APIItem ): # The following form_builder classes are supported by the FormDefinition class. @@ -1813,7 +1828,7 @@ def __init__( self, name=None, desc=None, fields=[], form_definition_current=None, form_type=None, layout=None ): self.name = name self.desc = desc - self.fields = fields + self.fields = fields self.form_definition_current = form_definition_current self.type = form_type self.layout = layout @@ -2012,7 +2027,7 @@ samples.append( sample ) return samples def send_email_notification( self, trans, common_state, final_state=False ): - # Check if an email notification is configured to be sent when the samples + # Check if an email notification is configured to be sent when the samples # are in this state if self.notification and common_state.id not in self.notification[ 'sample_states' ]: return @@ -2036,13 +2051,13 @@ All samples in state: %(sample_state)s """ - values = dict( user=self.user.email, - request_name=self.name, - request_type=self.type.name, - request_state=self.state, - num_samples=str( len( self.samples ) ), - sample_state=common_state.name, - create_time=self.create_time, + values = dict( user=self.user.email, + request_name=self.name, + request_type=self.type.name, + request_state=self.state, + num_samples=str( len( self.samples ) ), + sample_state=common_state.name, + create_time=self.create_time, submit_time=self.create_time ) body = body % values # check if this is the final state of the samples @@ -2207,7 +2222,7 @@ class Sample( object, APIItem ): # The following form_builder classes are supported by the Sample class. supported_field_types = [ CheckboxField, SelectField, TextField, WorkflowField, WorkflowMappingField, HistoryField ] - bulk_operations = Bunch( CHANGE_STATE = 'Change state', + bulk_operations = Bunch( CHANGE_STATE = 'Change state', SELECT_LIBRARY = 'Select data library and folder' ) api_collection_visible_keys = ( 'id', 'name' ) def __init__(self, name=None, desc=None, request=None, form_values=None, bar_code=None, library=None, folder=None, workflow=None, history=None): @@ -2290,8 +2305,8 @@ cmd = 'ssh %s "du -sh \'%s\'"' % ( login_str, filepath ) try: output = pexpect.run( cmd, - events={ '.ssword:*': scp_configs['password']+'\r\n', - pexpect.TIMEOUT:print_ticks}, + events={ '.ssword:*': scp_configs['password']+'\r\n', + pexpect.TIMEOUT:print_ticks}, timeout=10 ) except Exception, e: return error_msg @@ -2383,8 +2398,8 @@ self.run = run class UserAddress( object ): - def __init__( self, user=None, desc=None, name=None, institution=None, - address=None, city=None, state=None, postal_code=None, + def __init__( self, user=None, desc=None, name=None, institution=None, + address=None, city=None, state=None, postal_code=None, country=None, phone=None ): self.user = user self.desc = desc @@ -2493,8 +2508,8 @@ if not visualization: visualization = self.visualization - return VisualizationRevision( - visualization=visualization, + return VisualizationRevision( + visualization=visualization, title=self.title, dbkey=self.dbkey, config=self.config @@ -2544,6 +2559,14 @@ self.value = None self.user_value = None + def copy(self): + new_ta = type(self)() + new_ta.tag_id = self.tag_id + new_ta.user_tname = self.user_tname + new_ta.value = self.value + new_ta.user_value = self.user_value + return new_ta + class HistoryTagAssociation ( ItemTagAssociation ): pass @@ -2806,7 +2829,7 @@ if tva: return sa_session.query( app.model.ToolVersion ) \ .filter( app.model.ToolVersion.table.c.id == tva.tool_id ) \ - .first() + .first() return None def get_versions( self, app ): sa_session = app.model.context.current diff -r ed01365064b2644531c783f01a12b28384fd64ad -r c81172ba88a7d2ee619a32f6de8bdfdcfe5614e2 lib/galaxy/web/controllers/workflow.py --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -508,7 +508,6 @@ trans.response.set_content_type("image/svg+xml") return self._workflow_to_svg_canvas( trans, stored ).standalone_xml() - @web.expose @web.require_login( "use Galaxy workflows" ) def clone( self, trans, id ): @@ -531,15 +530,7 @@ annotation_obj = self.get_item_annotation_obj( trans.sa_session, stored.user, stored ) if annotation_obj: self.add_item_annotation( trans.sa_session, trans.get_user(), new_stored, annotation_obj.annotation ) - # Clone tags. - for swta in stored.owner_tags: - new_swta = model.StoredWorkflowTagAssociation() - new_swta.tag = swta.tag - new_swta.user = trans.user - new_swta.user_tname = swta.user_tname - new_swta.user_value = swta.user_value - new_swta.value = swta.value - new_stored.tags.append( new_swta ) + new_stored.copy_tags_from(trans.user,stored) if not owner: new_stored.name += " shared by '%s'" % stored.user.email new_stored.user = user @@ -918,11 +909,11 @@ # TODO: handle the case where the imported workflow requires tools that are not available in # the local Galaxy instance. pass - + # Provide user feedback. workflow_list_str = " <br>Return to <a href='%s'>workflow list." % url_for( action='list' ) if response.status != 200: - return trans.show_error_message( "There was a problem importing the workflow. Error: %s %s" % (response_data, workflow_list_str) ) + return trans.show_error_message( "There was a problem importing the workflow. Error: %s %s" % (response_data, workflow_list_str) ) if workflow.has_errors: return trans.show_warn_message( "Imported, but some steps in this workflow have validation errors. %s" % workflow_list_str ) if workflow.has_cycles: @@ -1408,6 +1399,7 @@ mx_ds_name = trans.sa_session.query(trans.app.model.HistoryDatasetAssociation).get( single_input ).name nh_name = '%s on %s' % (nh_name, mx_ds_name) new_history = trans.app.model.History( user=trans.user, name=nh_name ) + new_history.copy_tags_from(trans.user, trans.get_history()) trans.sa_session.add( new_history ) target_history = new_history else: @@ -1834,9 +1826,9 @@ trans.sa_session.flush() return stored, missing_tool_tups - - def _workflow_to_svg_canvas( self, trans, stored ): - + + def _workflow_to_svg_canvas( self, trans, stored ): + workflow = stored.latest_workflow data = [] Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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