diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py index 97923d892cc..c4b3c6466a5 100644 --- a/lib/galaxy/model/mapping.py +++ b/lib/galaxy/model/mapping.py @@ -958,45 +958,6 @@ model.FormDefinition.table = Table( Column("type", TrimmedString(255), index=True), Column("layout", JSONType())) -model.ExternalService.table = Table( - "external_service", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("name", TrimmedString(255), nullable=False), - Column("description", TEXT), - Column("external_service_type_id", TrimmedString(255), nullable=False), - Column("version", TrimmedString(255)), - Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True), - Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True), - Column("deleted", Boolean, index=True, default=False)) - -model.RequestType.table = Table( - "request_type", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("name", TrimmedString(255), nullable=False), - Column("desc", TEXT), - Column("request_form_id", Integer, ForeignKey("form_definition.id"), index=True), - Column("sample_form_id", Integer, ForeignKey("form_definition.id"), index=True), - Column("deleted", Boolean, index=True, default=False)) - -model.RequestTypeExternalServiceAssociation.table = Table( - "request_type_external_service_association", metadata, - Column("id", Integer, primary_key=True), - Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True), - Column("external_service_id", Integer, ForeignKey("external_service.id"), index=True)) - -model.RequestTypePermissions.table = Table( - "request_type_permissions", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("action", TEXT), - Column("request_type_id", Integer, ForeignKey("request_type.id"), nullable=True, index=True), - Column("role_id", Integer, ForeignKey("role.id"), index=True)) - model.FormValues.table = Table( "form_values", metadata, Column("id", Integer, primary_key=True), @@ -1005,97 +966,6 @@ model.FormValues.table = Table( Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True), Column("content", JSONType())) -model.Request.table = Table( - "request", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("name", TrimmedString(255), nullable=False), - Column("desc", TEXT), - Column("notification", JSONType()), - Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True), - Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True), - Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True), - Column("deleted", Boolean, index=True, default=False)) - -model.RequestEvent.table = Table( - "request_event", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("request_id", Integer, ForeignKey("request.id"), index=True), - Column("state", TrimmedString(255), index=True), - Column("comment", TEXT)) - -model.Sample.table = Table( - "sample", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("name", TrimmedString(255), nullable=False), - Column("desc", TEXT), - Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True), - Column("request_id", Integer, ForeignKey("request.id"), index=True), - Column("bar_code", TrimmedString(255), index=True), - Column("library_id", Integer, ForeignKey("library.id"), index=True), - Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True), - Column("deleted", Boolean, index=True, default=False), - Column("workflow", JSONType, nullable=True), - Column("history_id", Integer, ForeignKey("history.id"), nullable=True)) - -model.SampleState.table = Table( - "sample_state", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("name", TrimmedString(255), nullable=False), - Column("desc", TEXT), - Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True)) - -model.SampleEvent.table = Table( - "sample_event", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("sample_id", Integer, ForeignKey("sample.id"), index=True), - Column("sample_state_id", Integer, ForeignKey("sample_state.id"), index=True), - Column("comment", TEXT)) - -model.SampleDataset.table = Table( - "sample_dataset", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("sample_id", Integer, ForeignKey("sample.id"), index=True), - Column("name", TrimmedString(255), nullable=False), - Column("file_path", TEXT), - Column("status", TrimmedString(255), nullable=False), - Column("error_msg", TEXT), - Column("size", TrimmedString(255)), - Column("external_service_id", Integer, ForeignKey("external_service.id"), index=True)) - -model.Run.table = Table( - "run", metadata, - Column("id", Integer, primary_key=True), - Column("create_time", DateTime, default=now), - Column("update_time", DateTime, default=now, onupdate=now), - Column("form_definition_id", Integer, ForeignKey("form_definition.id"), index=True), - Column("form_values_id", Integer, ForeignKey("form_values.id"), index=True), - Column("deleted", Boolean, index=True, default=False), - Column("subindex", TrimmedString(255), index=True)) - -model.RequestTypeRunAssociation.table = Table( - "request_type_run_association", metadata, - Column("id", Integer, primary_key=True), - Column("request_type_id", Integer, ForeignKey("request_type.id"), index=True, nullable=False), - Column("run_id", Integer, ForeignKey("run.id"), index=True, nullable=False)) - -model.SampleRunAssociation.table = Table( - "sample_run_association", metadata, - Column("id", Integer, primary_key=True), - Column("sample_id", Integer, ForeignKey("sample.id"), index=True, nullable=False), - Column("run_id", Integer, ForeignKey("run.id"), index=True, nullable=False)) - model.Page.table = Table( "page", metadata, Column("id", Integer, primary_key=True), @@ -1440,80 +1310,11 @@ def simple_mapping(model, **kwds): mapper(model, model.table, properties=kwds) -mapper(model.Sample, model.Sample.table, properties=dict( - events=relation(model.SampleEvent, - backref="sample", - order_by=desc(model.SampleEvent.table.c.update_time)), - datasets=relation(model.SampleDataset, - backref="sample", - order_by=desc(model.SampleDataset.table.c.update_time)), - values=relation(model.FormValues, - primaryjoin=(model.Sample.table.c.form_values_id == model.FormValues.table.c.id)), - request=relation(model.Request, - primaryjoin=(model.Sample.table.c.request_id == model.Request.table.c.id)), - folder=relation(model.LibraryFolder, - primaryjoin=(model.Sample.table.c.folder_id == model.LibraryFolder.table.c.id)), - library=relation(model.Library, - primaryjoin=(model.Sample.table.c.library_id == model.Library.table.c.id)), - history=relation(model.History, - primaryjoin=(model.Sample.table.c.history_id == model.History.table.c.id)), -)) - mapper(model.FormValues, model.FormValues.table, properties=dict( form_definition=relation(model.FormDefinition, primaryjoin=(model.FormValues.table.c.form_definition_id == model.FormDefinition.table.c.id)) )) -mapper(model.Request, model.Request.table, properties=dict( - values=relation(model.FormValues, - primaryjoin=(model.Request.table.c.form_values_id == model.FormValues.table.c.id)), - type=relation(model.RequestType, - primaryjoin=(model.Request.table.c.request_type_id == model.RequestType.table.c.id)), - user=relation(model.User, - primaryjoin=(model.Request.table.c.user_id == model.User.table.c.id), - backref="requests"), - samples=relation(model.Sample, - primaryjoin=(model.Request.table.c.id == model.Sample.table.c.request_id), - order_by=asc(model.Sample.table.c.id)), - events=relation(model.RequestEvent, - backref="request", - order_by=desc(model.RequestEvent.table.c.update_time)) -)) - -mapper(model.RequestEvent, model.RequestEvent.table, properties=None) - -mapper(model.ExternalService, model.ExternalService.table, properties=dict( - form_definition=relation(model.FormDefinition, - primaryjoin=(model.ExternalService.table.c.form_definition_id == model.FormDefinition.table.c.id)), - form_values=relation(model.FormValues, - primaryjoin=(model.ExternalService.table.c.form_values_id == model.FormValues.table.c.id)) -)) - -mapper(model.RequestType, model.RequestType.table, properties=dict( - states=relation(model.SampleState, - backref="request_type", - primaryjoin=(model.RequestType.table.c.id == model.SampleState.table.c.request_type_id), - order_by=asc(model.SampleState.table.c.update_time)), - request_form=relation(model.FormDefinition, - primaryjoin=(model.RequestType.table.c.request_form_id == model.FormDefinition.table.c.id)), - sample_form=relation(model.FormDefinition, - primaryjoin=(model.RequestType.table.c.sample_form_id == model.FormDefinition.table.c.id)), -)) - -mapper(model.RequestTypeExternalServiceAssociation, model.RequestTypeExternalServiceAssociation.table, properties=dict( - request_type=relation(model.RequestType, - primaryjoin=((model.RequestTypeExternalServiceAssociation.table.c.request_type_id == model.RequestType.table.c.id)), - backref="external_service_associations"), - external_service=relation(model.ExternalService, - primaryjoin=(model.RequestTypeExternalServiceAssociation.table.c.external_service_id == model.ExternalService.table.c.id)) -)) - - -mapper(model.RequestTypePermissions, model.RequestTypePermissions.table, properties=dict( - request_type=relation(model.RequestType, backref="actions"), - role=relation(model.Role, backref="request_type_actions") -)) - mapper(model.FormDefinition, model.FormDefinition.table, properties=dict( current=relation(model.FormDefinitionCurrent, primaryjoin=(model.FormDefinition.table.c.form_definition_current_id == model.FormDefinitionCurrent.table.c.id)) @@ -1529,36 +1330,6 @@ mapper(model.FormDefinitionCurrent, model.FormDefinitionCurrent.table, propertie primaryjoin=(model.FormDefinitionCurrent.table.c.latest_form_id == model.FormDefinition.table.c.id)) )) -mapper(model.SampleEvent, model.SampleEvent.table, properties=dict( - state=relation(model.SampleState, - primaryjoin=(model.SampleEvent.table.c.sample_state_id == model.SampleState.table.c.id)), -)) - -mapper(model.SampleState, model.SampleState.table, properties=None) - -mapper(model.SampleDataset, model.SampleDataset.table, properties=dict( - external_service=relation(model.ExternalService, - primaryjoin=(model.SampleDataset.table.c.external_service_id == model.ExternalService.table.c.id)) -)) - - -mapper(model.SampleRunAssociation, model.SampleRunAssociation.table, properties=dict( - sample=relation(model.Sample, backref="runs", order_by=desc(model.Run.table.c.update_time)), - run=relation(model.Run, backref="samples", order_by=asc(model.Sample.table.c.id)) -)) - -mapper(model.RequestTypeRunAssociation, model.RequestTypeRunAssociation.table, properties=dict( - request_type=relation(model.RequestType, backref="run"), - run=relation(model.Run, backref="request_type") -)) - -mapper(model.Run, model.Run.table, properties=dict( - template=relation(model.FormDefinition, - primaryjoin=(model.Run.table.c.form_definition_id == model.FormDefinition.table.c.id)), - info=relation(model.FormValues, - primaryjoin=(model.Run.table.c.form_values_id == model.FormValues.table.c.id)) -)) - mapper(model.UserAddress, model.UserAddress.table, properties=dict( user=relation(model.User, primaryjoin=(model.UserAddress.table.c.user_id == model.User.table.c.id),