Merge pull request #18036 from mvdbeek/implicit_conversion_no_hid_fix (b97825b7) · Commits · NDIP / Galaxy

client/src/api/schema/schema.ts

+4 −3

Original line number	Diff line number	Diff line
		@@ -3751,7 +3751,7 @@ export interface components {
		* Element Type
		* @description The type of the element. Used to interpret the `object` field.
		*/
		element_type: components["schemas"]["DCEType"];
		element_type?: components["schemas"]["DCEType"] \| null;
		/**
		* Dataset Collection Element ID
		* @example 0123456789ABCDEF
		@@ -3767,10 +3767,11 @@ export interface components {
		* Object
		* @description The element's specific data depending on the value of `element_type`.
		*/
		object:
		object?:
		\| components["schemas"]["HDAObject"]
		\| components["schemas"]["HDADetailed"]
		\| components["schemas"]["DCObject"];
		\| components["schemas"]["DCObject"]
		\| null;
		};
		/**
		* DCEType

+5 −1

Original line number	Diff line number	Diff line
		@@ -842,7 +842,11 @@ class Data(metaclass=DataMeta):
		# Make the target datatype available to the converter
		params["__target_datatype__"] = target_type
		# Run converter, job is dispatched through Queue
		job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
		job, converted_datasets, *_ = converter.execute(
		trans, incoming=params, set_output_hid=visible, history=history, flush_job=False
		)
		for converted_dataset in converted_datasets.values():
		original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
		trans.app.job_manager.enqueue(job, tool=converter)
		if len(params) > 0:
		trans.log_event(f"Converter params: {str(params)}", tool_id=converter.id)

+1 −17

Original line number	Diff line number	Diff line
		@@ -11,7 +11,6 @@ from urllib.parse import quote_plus

		from galaxy.datatypes.data import Data
		from galaxy.model import DatasetInstance
		from galaxy.model.base import transaction
		from galaxy.schema.schema import DatasetState
		from galaxy.util import string_as_bool
		from galaxy.util.template import fill_template
		@@ -182,22 +181,7 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
		if target_ext and not converted_dataset:
		if isinstance(data, DisplayDataValueWrapper):
		data = data.value
		new_data = next(
		iter(
		data.datatype.convert_dataset(
		trans, data, target_ext, return_output=True, visible=False
		).values()
		)
		)
		new_data.hid = data.hid
		new_data.name = data.name
		trans.sa_session.add(new_data)
		assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
		parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False
		)
		trans.sa_session.add(assoc)
		with transaction(trans.sa_session):
		trans.sa_session.commit()
		data.datatype.convert_dataset(trans, data, target_ext, return_output=True, visible=False)
		elif converted_dataset and converted_dataset.state == DatasetState.ERROR:
		raise Exception(f"Dataset conversion failed for data parameter: {self.name}")
		return self.get_value(other_values, dataset_hash, user_hash, trans)

+2 −0

Original line number	Diff line number	Diff line
		@@ -85,5 +85,7 @@ class DatasetProtocol(

		def set_peek(self) -> None: ...

		def attach_implicitly_converted_dataset(self, session, new_dataset, target_ext: str) -> None: ...


		class DatasetHasHidProtocol(DatasetProtocol, HasHid, Protocol): ...

+4 −4

Original line number	Diff line number	Diff line
		@@ -95,7 +95,7 @@ class DatasetCollectionManager:
		# TODO: prebuild all required HIDs and send them in so no need to flush in between.
		dataset_collection = self.precreate_dataset_collection(
		structure,
		allow_unitialized_element=implicit_output_name is not None,
		allow_uninitialized_element=implicit_output_name is not None,
		completed_collection=completed_collection,
		implicit_output_name=implicit_output_name,
		)
		@@ -112,10 +112,10 @@ class DatasetCollectionManager:
		return instance

		def precreate_dataset_collection(
		self, structure, allow_unitialized_element=True, completed_collection=None, implicit_output_name=None
		self, structure, allow_uninitialized_element=True, completed_collection=None, implicit_output_name=None
		):
		has_structure = not structure.is_leaf and structure.children_known
		if not has_structure and allow_unitialized_element:
		if not has_structure and allow_uninitialized_element:
		dataset_collection = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
		elif not has_structure:
		collection_type_description = structure.collection_type_description
		@@ -143,7 +143,7 @@ class DatasetCollectionManager:
		element = model.DatasetCollectionElement.UNINITIALIZED_ELEMENT
		else:
		element = self.precreate_dataset_collection(
		substructure, allow_unitialized_element=allow_unitialized_element
		substructure, allow_uninitialized_element=allow_uninitialized_element
		)

		element = model.DatasetCollectionElement(