class ConfigurationDecodeIntegrationTestCase(integration_util.IntegrationTestCase): def setUp(self): super().setUp() self.library_populator = LibraryPopulator(self.galaxy_interactor) def test_admin_decode_id(self): new_lib = self.library_populator.new_library('DecodeTestLibrary') decode_response = self._get("configuration/decode/" + new_lib["id"], admin=True) response_id = decode_response.json()["decoded_id"] decoded_library_id = self._app.security.decode_id(new_lib["id"]) assert decoded_library_id == response_id # fake valid folder id by prepending F valid_encoded_folder_id = 'F' + new_lib["id"] folder_decode_response = self._get("configuration/decode/" + valid_encoded_folder_id, admin=True) folder_response_id = folder_decode_response.json()["decoded_id"] assert decoded_library_id == folder_response_id
class ConfigurationApiTestCase(ApiTestCase): def setUp(self): super(ConfigurationApiTestCase, self).setUp() self.library_populator = LibraryPopulator(self.galaxy_interactor) def test_normal_user_configuration(self): config = self._get_configuration() assert_has_keys(config, *TEST_KEYS_FOR_ALL_USERS) assert_not_has_keys(config, *TEST_KEYS_FOR_ADMIN_ONLY) def test_admin_user_configuration(self): config = self._get_configuration(admin=True) assert_has_keys(config, *TEST_KEYS_FOR_ALL_USERS) assert_has_keys(config, *TEST_KEYS_FOR_ADMIN_ONLY) def test_admin_decode_id(self): new_lib = self.library_populator.new_library('DecodeTestLibrary') decode_response = self._get("configuration/decode/" + new_lib["id"], admin=True) response_id = decode_response.json()["decoded_id"] decoded_library_id = self.security.decode_id(new_lib["id"]) assert decoded_library_id == response_id # fake valid folder id by prepending F valid_encoded_folder_id = 'F' + new_lib["id"] folder_decode_response = self._get("configuration/decode/" + valid_encoded_folder_id, admin=True) folder_response_id = folder_decode_response.json()["decoded_id"] assert decoded_library_id == folder_response_id def test_normal_user_decode_id(self): decode_response = self._get("configuration/decode/badhombre", admin=False) self._assert_status_code_is(decode_response, 403) def _get_configuration(self, data={}, admin=False): response = self._get("configuration", data=data, admin=admin) self._assert_status_code_is(response, 200) configuration = response.json() return configuration
class LibrariesApiTestCase(ApiTestCase, TestsDatasets): def setUp(self): super().setUp() self.dataset_populator = DatasetPopulator(self.galaxy_interactor) self.dataset_collection_populator = DatasetCollectionPopulator( self.galaxy_interactor) self.library_populator = LibraryPopulator(self.galaxy_interactor) 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_show_private_dataset_permissions(self): library, library_dataset = self.library_populator.new_library_dataset_in_private_library( "ForCreateDatasets", wait=True) with self._different_user(): response = self.library_populator.show_ldda( library["id"], library_dataset["id"]) # TODO: this should really be 403 and a proper JSON exception. self._assert_status_code_is(response, 400) def test_create_dataset(self): library, library_dataset = self.library_populator.new_library_dataset_in_private_library( "ForCreateDatasets", wait=True) 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_fetch_upload_to_folder(self): history_id, library, destination = self._setup_fetch_to_folder( "flat_zip") items = [{ "src": "files", "dbkey": "hg19", "info": "my cool bed", "created_from_basename": "4.bed" }] targets = [{"destination": destination, "items": items}] payload = { "history_id": history_id, # TODO: Shouldn't be needed :( "targets": json.dumps(targets), "__files": { "files_0|file_data": open(self.test_data_resolver.get_filename("4.bed")) }, } self.dataset_populator.fetch(payload) dataset = self.library_populator.get_library_contents_with_path( library["id"], "/4.bed") assert dataset["file_size"] == 61, dataset assert dataset["genome_build"] == "hg19", dataset assert dataset["misc_info"] == "my cool bed", dataset assert dataset["file_ext"] == "bed", dataset assert dataset["created_from_basename"] == "4.bed" def test_fetch_zip_to_folder(self): history_id, library, destination = self._setup_fetch_to_folder( "flat_zip") bed_test_data_path = self.test_data_resolver.get_filename("4.bed.zip") targets = [{ "destination": destination, "items_from": "archive", "src": "files", }] payload = { "history_id": history_id, # TODO: Shouldn't be needed :( "targets": json.dumps(targets), "__files": { "files_0|file_data": open(bed_test_data_path, 'rb') } } self.dataset_populator.fetch(payload) dataset = self.library_populator.get_library_contents_with_path( library["id"], "/4.bed") assert dataset["file_size"] == 61, dataset def test_fetch_single_url_to_folder(self): library, response = self._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) 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": json.dumps(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) self._assert_status_code_is(folder_response, 200) folder_id = folder_response.json()[0]['id'] payload = { 'folder_id': folder_id, 'create_type': 'file', 'file_type': 'xxx', 'upload_option': 'upload_file', 'files_0|url_paste': FILE_URL, } create_response = self._post("libraries/%s/contents" % library['id'], payload) self._assert_status_code_is(create_response, 400) assert create_response.json( ) == "Requested extension 'xxx' unknown, cannot upload dataset." def test_fetch_failed_validation(self): # Exception handling is really rough here - we should be creating a dataset in error instead # of just failing the job like this. history_id, library, destination = self._setup_fetch_to_folder( "single_url") items = [{ "src": "url", "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed", "MD5": "37b59762b59fff860460522d271bc112", "name": "4.bed", }] targets = [{ "destination": destination, "items": items, }] payload = { "history_id": history_id, # TODO: Shouldn't be needed :( "targets": json.dumps(targets), "validate_hashes": True } tool_response = self.dataset_populator.fetch(payload, assert_ok=False) job = self.dataset_populator.check_run(tool_response) self.dataset_populator.wait_for_job(job["id"]) job = tool_response.json()["jobs"][0] details = self.dataset_populator.get_job_details(job["id"]).json() assert details["state"] == "ok", details dataset = self.library_populator.get_library_contents_with_path( library["id"], "/4.bed") assert dataset["state"] == "error", dataset def test_fetch_url_archive_to_folder(self): history_id, library, destination = self._setup_fetch_to_folder( "single_url") targets = [{ "destination": destination, "items_from": "archive", "src": "url", "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/4.bed.zip", }] payload = { "history_id": history_id, # TODO: Shouldn't be needed :( "targets": json.dumps(targets), } self.dataset_populator.fetch(payload) dataset = self.library_populator.get_library_contents_with_path( library["id"], "/4.bed") assert dataset["file_size"] == 61, dataset @unittest.skip # reference URLs changed, checksums now invalid. def test_fetch_bagit_archive_to_folder(self): history_id, library, destination = self._setup_fetch_to_folder( "bagit_archive") example_bag_path = self.test_data_resolver.get_filename( "example-bag.zip") targets = [{ "destination": destination, "items_from": "bagit_archive", "src": "files", }] payload = { "history_id": history_id, # TODO: Shouldn't be needed :( "targets": json.dumps(targets), "__files": { "files_0|file_data": open(example_bag_path) }, } self.dataset_populator.fetch(payload) dataset = self.library_populator.get_library_contents_with_path( library["id"], "/README.txt") assert dataset["file_size"] == 66, dataset dataset = self.library_populator.get_library_contents_with_path( library["id"], "/bdbag-profile.json") assert dataset["file_size"] == 723, dataset def _setup_fetch_to_folder(self, test_name): return self.library_populator.setup_fetch_to_folder(test_name) 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_create_dataset_in_subfolder(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'] subfolder_response = self._create_subfolder(folder_id) self._assert_status_code_is(folder_response, 200) print(subfolder_response.json()) subfolder_id = subfolder_response.json()['id'] history_id = self.dataset_populator.new_history() hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3 sub")['id'] payload = {'from_hda_id': hda_id} create_response = self._post("folders/%s/contents" % subfolder_id, payload) self._assert_status_code_is(create_response, 200) self._assert_has_keys(create_response.json(), "name", "id") dataset_update_time = create_response.json()['update_time'] container_fetch_response = self.galaxy_interactor.get( "folders/%s/contents" % folder_id) container_update_time = container_fetch_response.json( )['folder_contents'][0]['update_time'] assert dataset_update_time == container_update_time, container_fetch_response def test_update_dataset_in_folder(self): ld = self._create_dataset_in_folder_in_library("ForUpdateDataset") 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_update_dataset_tags(self): ld = self._create_dataset_in_folder_in_library("ForTagtestDataset") data = {"tags": ["#Lancelot", "name:Holy Grail", "blue"]} 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(), "tags") assert create_response.json( )["tags"] == "name:Lancelot, name:HolyGrail, blue" def test_invalid_update_dataset_in_folder(self): ld = self._create_dataset_in_folder_in_library( "ForInvalidUpdateDataset") 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_detect_datatype_of_dataset_in_folder(self): ld = self._create_dataset_in_folder_in_library("ForDetectDataset") # Wait for metadata job to finish. time.sleep(2) data = {'file_ext': 'data'} 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(), "file_ext") assert create_response.json()["file_ext"] == "data" # Wait for metadata job to finish. time.sleep(2) data = {'file_ext': 'auto'} 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(), "file_ext") assert create_response.json()["file_ext"] == "txt" def test_ldda_collection_import_to_history(self): self._import_to_history(visible=True) def test_ldda_collection_import_to_history_hide_source(self): self._import_to_history(visible=False) def test_import_paired_collection(self): ld = self._create_dataset_in_folder_in_library( "ForHistoryImport").json() history_id = self.dataset_populator.new_history() url = "histories/%s/contents" % history_id collection_name = 'Paired-end data (from library)' payload = { 'name': collection_name, 'collection_type': 'list:paired', "type": "dataset_collection", 'element_identifiers': json.dumps([{ 'src': 'new_collection', 'name': 'pair1', 'collection_type': 'paired', 'element_identifiers': [{ 'name': 'forward', 'src': 'ldda', 'id': ld['id'] }, { 'name': 'reverse', 'src': 'ldda', 'id': ld['id'] }] }]) } new_collection = self._post(url, payload).json() assert new_collection['name'] == collection_name pair = new_collection['elements'][0] assert pair['element_identifier'] == 'pair1' assert pair['object']['elements'][0]['object'][ 'history_id'] == history_id def _import_to_history(self, visible=True): ld = self._create_dataset_in_folder_in_library( "ForHistoryImport").json() history_id = self.dataset_populator.new_history() url = "histories/%s/contents" % history_id collection_name = 'new_collection_name' element_identifer = 'new_element_identifier' payload = { "collection_type": "list", "history_content_type": "dataset_collection", "model_class": "HistoryDatasetCollectionAssociation", "history_id": history_id, "name": collection_name, "hide_source_items": not visible, "element_identifiers": json.dumps([{ "id": ld['id'], "name": element_identifer, "src": "ldda" }]), "type": "dataset_collection", "elements": [] } new_collection = self._post(url, payload).json() assert new_collection['name'] == collection_name assert new_collection['element_count'] == 1 element = new_collection['elements'][0] assert element['element_identifier'] == element_identifer assert element['object']['visible'] == visible 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"], direct_upload=True).json()["outputs"][0]["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"], direct_upload=True).json()["outputs"][0]["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()["outputs"][0]['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) def _create_subfolder(self, containing_folder_id): create_data = dict( description="new subfolder desc", name="New Subfolder", ) return self._post("folders/%s" % containing_folder_id, data=create_data) def _create_dataset_in_folder_in_library(self, library_name): library = self.library_populator.new_private_library(library_name) 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) return ld
class FoldersApiTestCase(ApiTestCase): def setUp(self): super().setUp() self.library_populator = LibraryPopulator(self.galaxy_interactor) self.library = self.library_populator.new_library("FolderTestsLibrary") def test_create(self): folder = self._create_folder("Test Create Folder") self._assert_valid_folder(folder) def test_create_without_name_raises_400(self): root_folder_id = self.library["root_folder_id"] data = { "description": "Description only", } create_response = self._post(f"folders/{root_folder_id}", data=data, admin=True) self._assert_status_code_is(create_response, 400) def test_permissions(self): folder = self._create_folder("Test Permissions Folder") folder_id = folder["id"] empty_permissions = self._get_permissions(folder_id) self._assert_permissions_empty(empty_permissions) role_id = self.library_populator.user_private_role_id() action = "set_permissions" data = { "add_ids[]": [role_id], "manage_ids[]": role_id, # string-lists also supported "modify_ids[]": [role_id] } response = self._post( f"folders/{folder_id}/permissions?action={action}", data=data, admin=True) self._assert_status_code_is(response, 200) new_permissions = response.json() permissions = self._get_permissions(folder_id) assert permissions == new_permissions self._assert_permissions_contains_role(permissions, role_id) def test_update(self): folder = self._create_folder("Test Update Folder") folder_id = folder["id"] updated_name = "UPDATED" updated_desc = "UPDATED DESCRIPTION" data = { "name": updated_name, "description": updated_desc, } patch_response = self._patch(f"folders/{folder_id}", data=data, admin=True) self._assert_status_code_is(patch_response, 200) updated_folder = patch_response.json() self._assert_valid_folder(updated_folder) assert updated_folder["name"] == updated_name assert updated_folder["description"] == updated_desc def test_delete(self): folder = self._create_folder("Test Delete Folder") folder_id = folder["id"] deleted_folder = self._delete_folder(folder_id) assert deleted_folder["deleted"] is True def test_undelete(self): folder = self._create_folder("Test Undelete Folder") folder_id = folder["id"] deleted_folder = self._delete_folder(folder_id) assert deleted_folder["deleted"] is True undelete = True undelete_response = self._delete( f"folders/{folder_id}?undelete={undelete}", admin=True) self._assert_status_code_is(undelete_response, 200) undeleted_folder = undelete_response.json() assert undeleted_folder["deleted"] is False def test_update_deleted_raise_403(self): folder = self._create_folder("Test Update Deleted Folder") folder_id = folder["id"] deleted_folder = self._delete_folder(folder_id) assert deleted_folder["deleted"] is True data = { "name": "test", } patch_response = self._patch(f"folders/{folder_id}", data=data, admin=True) self._assert_status_code_is(patch_response, 403) def _create_folder(self, name: str): root_folder_id = self.library["root_folder_id"] data = { "name": name, "description": f"The description of {name}", } create_response = self._post(f"folders/{root_folder_id}", data=data, admin=True) self._assert_status_code_is(create_response, 200) folder = create_response.json() return folder def _delete_folder(self, folder_id): delete_response = self._delete(f"folders/{folder_id}", admin=True) self._assert_status_code_is(delete_response, 200) deleted_folder = delete_response.json() return deleted_folder def _get_permissions(self, folder_id): response = self._get(f"folders/{folder_id}/permissions", admin=True) self._assert_status_code_is(response, 200) permissions = response.json() self._assert_valid_permissions(permissions) return permissions def _assert_valid_folder(self, folder): self._assert_has_keys(folder, "id", "name", "model_class", "parent_id", "item_count", "genome_build", "update_time", "deleted", "library_path", "parent_library_id") def _assert_valid_permissions(self, permissions): self._assert_has_keys( permissions, "modify_folder_role_list", "manage_folder_role_list", "add_library_item_role_list", ) def _assert_permissions_empty(self, permissions): assert permissions["modify_folder_role_list"] == [] assert permissions["manage_folder_role_list"] == [] assert permissions["add_library_item_role_list"] == [] def _assert_permissions_contains_role(self, permissions, role_id): assert role_id in permissions["modify_folder_role_list"][0] assert role_id in permissions["manage_folder_role_list"][0] assert role_id in permissions["add_library_item_role_list"][0]