Merge pull request #14167 from mvdbeek/fix_folder_import (0304821e) · Commits · NDIP / Galaxy

lib/galaxy/webapps/galaxy/api/common.py

+1 −8

Original line number	Diff line number	Diff line
		@@ -31,12 +31,6 @@ SerializationKeysQueryParam: Optional[str] = Query(
		description="Comma-separated list of keys to be passed to the serializer",
		)

		SerializationDefaultViewQueryParam: Optional[str] = Query(
		None,
		title="Default View",
		description="The item view that will be used in case no particular view was specified.",
		)

		FilterQueryQueryParam: Optional[List[str]] = Query(
		default=None,
		title="Filter Query",
		@@ -67,9 +61,8 @@ def parse_serialization_params(
		def query_serialization_params(
		view: Optional[str] = SerializationViewQueryParam,
		keys: Optional[str] = SerializationKeysQueryParam,
		default_view: Optional[str] = SerializationDefaultViewQueryParam,
		) -> SerializationParams:
		return parse_serialization_params(view=view, keys=keys, default_view=default_view, format=format)
		return parse_serialization_params(view=view, keys=keys)


		def get_value_filter_query_params(

lib/galaxy/webapps/galaxy/api/history_contents.py

+1 −1

Original line number	Diff line number	Diff line
		@@ -587,7 +587,7 @@ class FastAPIHistoryContents:
		),
		serialization_params: SerializationParams = Depends(query_serialization_params),
		payload: CreateHistoryContentPayload = Body(...),
		) -> AnyHistoryContentItem:
		) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
		"""Create a new `HDA` or `HDCA` in the given History."""
		payload.type = type or payload.type
		return self.service.create(trans, history_id, payload, serialization_params)

lib/galaxy/webapps/galaxy/services/history_contents.py

+3 −4

Original line number	Diff line number	Diff line
		@@ -511,7 +511,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
		history_id: EncodedDatabaseIdField,
		payload: CreateHistoryContentPayload,
		serialization_params: SerializationParams,
		) -> AnyHistoryContentItem:
		) -> Union[AnyHistoryContentItem, List[AnyHistoryContentItem]]:
		"""
		Create a new HDA or HDCA.

		@@ -520,6 +520,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
		"""
		history = self.history_manager.get_owned(self.decode_id(history_id), trans.user, current_history=trans.history)

		serialization_params.default_view = "detailed"
		history_content_type = payload.type
		if history_content_type == HistoryContentType.dataset:
		source = payload.source
		@@ -1334,7 +1335,7 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
		history, add_to_history=True
		)
		hda_dict = self.hda_serializer.serialize_to_view(
		hda, user=trans.user, trans=trans, default_view="detailed", **serialization_params.dict()
		hda, user=trans.user, trans=trans, **serialization_params.dict()
		)
		rval.append(hda_dict)
		else:
		@@ -1368,7 +1369,6 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto
		return None

		trans.sa_session.flush()
		serialization_params.default_view = "detailed"
		return self.hda_serializer.serialize_to_view(hda, user=trans.user, trans=trans, **serialization_params.dict())

		def __create_hda_from_ldda(self, trans, history: History, ldda_id: EncodedDatabaseIdField):
		@@ -1465,7 +1465,6 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto

		# if the consumer specified keys or view, use the secondary serializer
		if serialization_params.view or serialization_params.keys:
		serialization_params.default_view = "detailed"
		return self.hdca_serializer.serialize_to_view(
		dataset_collection_instance, user=trans.user, trans=trans, **serialization_params.dict()
		)

lib/galaxy_test/api/test_folders.py

+16 −1

Original line number	Diff line number	Diff line
		from galaxy_test.base.populators import LibraryPopulator
		from galaxy_test.base.populators import (
		DatasetPopulator,
		LibraryPopulator,
		)
		from ._framework import ApiTestCase


		class FoldersApiTestCase(ApiTestCase):
		def setUp(self):
		super().setUp()
		self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
		self.library_populator = LibraryPopulator(self.galaxy_interactor)
		self.library = self.library_populator.new_library("FolderTestsLibrary")

		@@ -78,6 +82,17 @@ class FoldersApiTestCase(ApiTestCase):
		undeleted_folder = undelete_response.json()
		assert undeleted_folder["deleted"] is False

		def test_import_folder_to_history(self):
		library, response = self.library_populator.fetch_single_url_to_folder()
		dataset = self.library_populator.get_library_contents_with_path(library["id"], "/4.bed")
		with self.dataset_populator.test_history() as history_id:
		create_data = {"source": "library_folder", "content": dataset["folder_id"]}
		create_response = self._post(f"histories/{history_id}/contents", create_data, json=True)
		create_response.raise_for_status()
		datasets = create_response.json()
		assert len(datasets) == 1
		assert datasets[0]["name"] == "4.bed"

		def test_update_deleted_raise_403(self):
		folder = self._create_folder("Test Update Deleted Folder")
		folder_id = folder["id"]

lib/galaxy_test/api/test_libraries.py

+3 −28

Original line number	Diff line number	Diff line
		@@ -10,15 +10,13 @@ from galaxy.model.unittest_utils.store_fixtures import (
		from galaxy_test.base.populators import (
		DatasetCollectionPopulator,
		DatasetPopulator,
		FILE_URL,
		LibraryPopulator,
		skip_if_github_down,
		skip_without_asgi,
		)
		from ._framework import ApiTestCase

		FILE_URL = "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed"
		FILE_MD5 = "37b59762b59fff860460522d271bc111"


		class LibrariesApiTestCase(ApiTestCase):
		def setUp(self):
		@@ -268,38 +266,15 @@ class LibrariesApiTestCase(ApiTestCase):
		assert dataset["file_size"] == 61, dataset

		def test_fetch_single_url_to_folder(self):
		library, response = self._fetch_single_url_to_folder()
		library, response = self.library_populator.fetch_single_url_to_folder()
		dataset = self.library_populator.get_library_contents_with_path(library["id"], "/4.bed")
		assert dataset["file_size"] == 61, dataset

		def test_fetch_single_url_with_invalid_datatype(self):
		_, response = self._fetch_single_url_to_folder("xxx", assert_ok=False)
		_, response = self.library_populator.fetch_single_url_to_folder("xxx", assert_ok=False)
		self._assert_status_code_is(response, 400)
		assert response.json()["err_msg"] == "Requested extension 'xxx' unknown, cannot upload dataset."

		def _fetch_single_url_to_folder(self, file_type="auto", assert_ok=True):
		history_id, library, destination = self._setup_fetch_to_folder("single_url")
		items = [
		{
		"src": "url",
		"url": FILE_URL,
		"MD5": FILE_MD5,
		"ext": file_type,
		}
		]
		targets = [
		{
		"destination": destination,
		"items": items,
		}
		]
		payload = {
		"history_id": history_id, # TODO: Shouldn't be needed :(
		"targets": targets,
		"validate_hashes": True,
		}
		return library, self.dataset_populator.fetch(payload, assert_ok=assert_ok)

		def test_legacy_upload_unknown_datatype(self):
		library = self.library_populator.new_private_library("ForLegacyUpload")
		folder_response = self._create_folder(library)