from base import api from base.populators import ( DatasetCollectionPopulator, DatasetPopulator, LibraryPopulator, TestsDatasets, wait_on_state ) class LibrariesApiTestCase(api.ApiTestCase, TestsDatasets): def setUp(self): super(LibrariesApiTestCase, self).setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor) self.library_populator = LibraryPopulator(self) def test_create(self): data = dict(name="CreateTestLibrary") create_response = self._post("libraries", data=data, admin=True) self._assert_status_code_is(create_response, 200) library = create_response.json() self._assert_has_keys(library, "name") assert library["name"] == "CreateTestLibrary" def test_delete(self): library = self.library_populator.new_library("DeleteTestLibrary") create_response = self._delete("libraries/%s" % library["id"], admin=True) self._assert_status_code_is(create_response, 200) library = create_response.json() self._assert_has_keys(library, "deleted") assert library["deleted"] is True # Test undeleting data = dict(undelete='true') create_response = self._delete("libraries/%s" % library["id"], data=data, admin=True) library = create_response.json() self._assert_status_code_is(create_response, 200) assert library["deleted"] is False def test_nonadmin(self): # Anons can't create libs data = dict(name="CreateTestLibrary") create_response = self._post("libraries", data=data, admin=False, anon=True) self._assert_status_code_is(create_response, 403) # Anons can't delete libs library = self.library_populator.new_library("AnonDeleteTestLibrary") create_response = self._delete("libraries/%s" % library["id"], admin=False, anon=True) self._assert_status_code_is(create_response, 403) # Anons can't update libs data = dict(name="ChangedName", description="ChangedDescription", synopsis='ChangedSynopsis') create_response = self._patch("libraries/%s" % library["id"], data=data, admin=False, anon=True) self._assert_status_code_is(create_response, 403) def test_update(self): library = self.library_populator.new_library("UpdateTestLibrary") data = dict(name='ChangedName', description='ChangedDescription', synopsis='ChangedSynopsis') create_response = self._patch("libraries/%s" % library["id"], data=data, admin=True) self._assert_status_code_is(create_response, 200) library = create_response.json() self._assert_has_keys(library, 'name', 'description', 'synopsis') assert library['name'] == 'ChangedName' assert library['description'] == 'ChangedDescription' assert library['synopsis'] == 'ChangedSynopsis' def test_create_private_library_permissions(self): library = self.library_populator.new_library("PermissionTestLibrary") library_id = library["id"] role_id = self.library_populator.user_private_role_id() self.library_populator.set_permissions(library_id, role_id) create_response = self._create_folder(library) self._assert_status_code_is(create_response, 200) def test_create_dataset_denied(self): library = self.library_populator.new_private_library("ForCreateDatasets") folder_response = self._create_folder(library) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] history_id = self.dataset_populator.new_history() hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] with self._different_user(): payload = {'from_hda_id': hda_id} create_response = self._post("folders/%s/contents" % folder_id, payload) self._assert_status_code_is(create_response, 403) def test_create_dataset(self): library = self.library_populator.new_private_library("ForCreateDatasets") payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test") create_response = self._post("libraries/%s/contents" % library["id"], payload, files=files) self._assert_status_code_is(create_response, 200) library_datasets = create_response.json() assert len(library_datasets) == 1 library_dataset = library_datasets[0] def show(): return self._get("libraries/%s/contents/%s" % (library["id"], library_dataset["id"])) wait_on_state(show, assert_ok=True) library_dataset = show().json() self._assert_has_keys(library_dataset, "peek", "data_type") assert library_dataset["peek"].find("create_test") >= 0 assert library_dataset["file_ext"] == "txt", library_dataset["file_ext"] def test_create_dataset_in_folder(self): library = self.library_populator.new_private_library("ForCreateDatasets") folder_response = self._create_folder(library) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] history_id = self.dataset_populator.new_history() hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] payload = {'from_hda_id': hda_id} create_response = self._post("folders/%s/contents" % folder_id, payload) self._assert_status_code_is(create_response, 200) self._assert_has_keys(create_response.json(), "name", "id") def test_update_dataset_in_folder(self): library = self.library_populator.new_private_library("ForUpdateDataset") folder_response = self._create_folder(library) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] history_id = self.dataset_populator.new_history() hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] payload = {'from_hda_id': hda_id, 'create_type': 'file', 'folder_id': folder_id} ld = self._post("libraries/%s/contents" % folder_id, payload) data = {'name': 'updated_name', 'file_ext': 'fastq', 'misc_info': 'updated_info', 'genome_build': 'updated_genome_build'} create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data) self._assert_status_code_is(create_response, 200) self._assert_has_keys(create_response.json(), "name", "file_ext", "misc_info", "genome_build") def test_invalid_update_dataset_in_folder(self): library = self.library_populator.new_private_library("ForInvalidUpdateDataset") folder_response = self._create_folder(library) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] history_id = self.dataset_populator.new_history() hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3")['id'] payload = {'from_hda_id': hda_id, 'create_type': 'file', 'folder_id': folder_id} ld = self._post("libraries/%s/contents" % folder_id, payload) data = {'file_ext': 'nonexisting_type'} create_response = self._patch("libraries/datasets/%s" % ld.json()["id"], data=data) self._assert_status_code_is(create_response, 400) assert 'This Galaxy does not recognize the datatype of:' in create_response.json()['err_msg'] def test_create_datasets_in_library_from_collection(self): library = self.library_populator.new_private_library("ForCreateDatasetsFromCollection") folder_response = self._create_folder(library) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] history_id = self.dataset_populator.new_history() hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["xxx", "yyy"]).json()["id"] payload = {'from_hdca_id': hdca_id, 'create_type': 'file', 'folder_id': folder_id} create_response = self._post("libraries/%s/contents" % library['id'], payload) self._assert_status_code_is(create_response, 200) def test_create_datasets_in_folder_from_collection(self): library = self.library_populator.new_private_library("ForCreateDatasetsFromCollection") history_id = self.dataset_populator.new_history() hdca_id = self.dataset_collection_populator.create_list_in_history(history_id, contents=["xxx", "yyy"]).json()["id"] folder_response = self._create_folder(library) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] payload = {'from_hdca_id': hdca_id} create_response = self._post("folders/%s/contents" % folder_id, payload) self._assert_status_code_is(create_response, 200) assert len(create_response.json()) == 2 # Also test that anything different from a flat dataset collection list # is refused hdca_pair_id = self.dataset_collection_populator.create_list_of_pairs_in_history(history_id).json()['id'] payload = {'from_hdca_id': hdca_pair_id} create_response = self._post("folders/%s/contents" % folder_id, payload) self._assert_status_code_is(create_response, 501) assert create_response.json()['err_msg'] == 'Cannot add nested collections to library. Please flatten your collection first.' def _create_folder(self, library): create_data = dict( folder_id=library["root_folder_id"], create_type="folder", name="New Folder", ) return self._post("libraries/%s/contents" % library["id"], data=create_data)