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Source code for galaxy_test.api.test_libraries

import unittest

from galaxy.model.unittest_utils.store_fixtures import (
    one_ld_library_model_store_dict,
    TEST_LIBRARY_NAME,
)
from galaxy.util.unittest_utils import skip_if_github_down
from galaxy_test.base import api_asserts
from galaxy_test.base.decorators import requires_new_library
from galaxy_test.base.populators import (
    DatasetCollectionPopulator,
    DatasetPopulator,
    FILE_URL,
    LibraryPopulator,
    skip_without_asgi,
)
from ._framework import ApiTestCase


[docs]class TestLibrariesApi(ApiTestCase): dataset_populator: DatasetPopulator
[docs] 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)
[docs] @requires_new_library def test_create(self): data = dict(name="CreateTestLibrary") create_response = self._post("libraries", data=data, admin=True, json=True) self._assert_status_code_is(create_response, 200) library = create_response.json() self._assert_has_keys(library, "name") assert library["name"] == "CreateTestLibrary"
[docs] @skip_without_asgi @requires_new_library def test_create_from_store(self): response = self.library_populator.create_from_store(store_dict=one_ld_library_model_store_dict()) assert isinstance(response, list) assert len(response) == 1 library_summary = response[0] assert library_summary["name"] == TEST_LIBRARY_NAME assert "id" in library_summary ld = self.library_populator.get_library_contents_with_path(library_summary["id"], "/my cool name") assert ld
[docs] @requires_new_library def test_delete(self): library = self.library_populator.new_library("DeleteTestLibrary") create_response = self._delete(f"libraries/{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(f"libraries/{library['id']}", data=data, admin=True, json=True) library = create_response.json() self._assert_status_code_is(create_response, 200) assert library["deleted"] is False
[docs] 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(f"libraries/{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(f"libraries/{library['id']}", data=data, admin=False, anon=True, json=True) self._assert_status_code_is(create_response, 403)
[docs] @requires_new_library def test_update(self): library = self.library_populator.new_library("UpdateTestLibrary") data = dict(name="ChangedName", description="ChangedDescription", synopsis="ChangedSynopsis") create_response = self._patch(f"libraries/{library['id']}", data=data, admin=True, json=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"
[docs] @requires_new_library def test_update_non_admins_with_permission(self): library = self.library_populator.new_library("UpdateTestLibraryNonAdmin") library_id = library["id"] role_id = self.library_populator.user_private_role_id() data = dict(name="ChangedName", description="ChangedDescription", synopsis="ChangedSynopsis") # User has no permission by default create_response = self._patch(f"libraries/{library['id']}", data=data, json=True) self._assert_status_code_is(create_response, 403) # Grant modify permission self.library_populator.set_modify_permission(library_id, role_id) create_response = self._patch(f"libraries/{library['id']}", data=data, json=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"
[docs] @requires_new_library def test_create_private_library_legacy_permissions(self): library = self.library_populator.new_library("LegacyPermissionTestLibrary") 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) with self._different_user(): create_response = self._create_folder(library) self._assert_status_code_is(create_response, 403)
[docs] @requires_new_library 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_with_action(library_id, role_id, action="set_permissions") create_response = self._create_folder(library) self._assert_status_code_is(create_response, 200) with self._different_user(): create_response = self._create_folder(library) self._assert_status_code_is(create_response, 403)
[docs] @requires_new_library def test_get_library_current_permissions(self): library = self.library_populator.new_library("GetCurrentPermissionTestLibrary") library_id = library["id"] current = self.library_populator.get_permissions(library_id, scope="current") self._assert_has_keys( current, "access_library_role_list", "modify_library_role_list", "manage_library_role_list", "add_library_item_role_list", ) role_id = self.library_populator.user_private_role_id() self.library_populator.set_permissions_with_action(library_id, role_id, action="set_permissions") current = self.library_populator.get_permissions(library_id, scope="current") assert role_id in current["access_library_role_list"][0] assert role_id in current["modify_library_role_list"][0] assert role_id in current["manage_library_role_list"][0] assert role_id in current["add_library_item_role_list"][0]
[docs] @requires_new_library def test_get_library_available_permissions(self): library = self.library_populator.new_library("GetAvailablePermissionTestLibrary") library_id = library["id"] role_id = self.library_populator.user_private_role_id() # As we can manage this library our role will be available available = self.library_populator.get_permissions(library_id, scope="available") available_role_ids = [role["id"] for role in available["roles"]] assert role_id in available_role_ids
[docs] @requires_new_library def test_get_library_available_permissions_with_query(self): library = self.library_populator.new_library("GetAvailablePermissionWithQueryTestLibrary") library_id = library["id"] with self._different_user(): email = self.library_populator.user_email() # test at least 2 user roles should be available now available = self.library_populator.get_permissions(library_id, scope="available") available_role_ids = [role["id"] for role in available["roles"]] assert len(available_role_ids) > 1 # test query for specific role/email available = self.library_populator.get_permissions(library_id, scope="available", q=email) available_role_emails = [role["name"] for role in available["roles"]] assert available["total"] == 1 assert available_role_emails[0] == email
[docs] @requires_new_library def test_create_library_dataset_bootstrap_user(self, library_name="private_dataset", wait=True): library = self.library_populator.new_private_library(library_name) payload, files = self.library_populator.create_dataset_request(library, file_type="txt", contents="create_test") create_response = self.galaxy_interactor.post( "libraries/%s/contents" % library["id"], payload, files=files, key=self.master_api_key ) self._assert_status_code_is(create_response, 400)
[docs] @requires_new_library def test_create_dataset_denied(self): url, payload = self._create_dataset_kwargs() with self._different_user(): create_response = self._post(url, payload, json=True) self._assert_status_code_is(create_response, 403)
[docs] @requires_new_library def test_create_dataset_bootstrap_admin_user(self): url, payload = self._create_dataset_kwargs() with self._different_user(): create_response = self._post(url, payload, key=self.master_api_key, json=True) self._assert_status_code_is(create_response, 400)
def _create_dataset_kwargs(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"] return f"folders/{folder_id}/contents", {"from_hda_id": hda_id}
[docs] @requires_new_library 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_ld_raw(library["id"], library_dataset["id"]) api_asserts.assert_status_code_is(response, 403) api_asserts.assert_error_code_is(response, 403002)
[docs] @requires_new_library 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"] # Get library dataset (same as library_dataset) library_dataset_from_show = self.library_populator.show_ld(library["id"], library_dataset["id"]) assert library_dataset_from_show["id"] == library_dataset["id"] assert library_dataset_from_show["parent_library_id"] == library["id"] assert library_dataset_from_show["folder_id"] == library["root_folder_id"] # Get library dataset dataset association ldda = self.library_populator.show_ldda(library_dataset_from_show["ldda_id"]) assert ldda["library_dataset_id"] == library_dataset["id"] assert ldda["parent_library_id"] == library["id"] assert ldda["file_ext"] == "txt"
[docs] @requires_new_library 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": targets, "__files": {"files_0|file_data": open(self.test_data_resolver.get_filename("4.bed"))}, } self.dataset_populator.fetch(payload, wait=True) 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"
[docs] @requires_new_library 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": 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
[docs] @requires_new_library def test_fetch_single_url_to_folder(self): 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
[docs] @requires_new_library def test_fetch_single_url_with_invalid_datatype(self): _, 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."
[docs] @requires_new_library 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(f"libraries/{library['id']}/contents", payload) self._assert_status_code_is(create_response, 400) assert create_response.json() == "Requested extension 'xxx' unknown, cannot upload dataset."
[docs] @skip_if_github_down @requires_new_library 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": 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
[docs] @skip_if_github_down @requires_new_library 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": 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
[docs] @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": 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)
[docs] @requires_new_library 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(f"folders/{folder_id}/contents", payload, json=True) self._assert_status_code_is(create_response, 200) self._assert_has_keys(create_response.json(), "name", "id")
[docs] @requires_new_library 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(f"folders/{subfolder_id}/contents", payload, json=True) 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(f"folders/{folder_id}/contents") container_update_time = container_fetch_response.json()["folder_contents"][0]["update_time"] assert dataset_update_time == container_update_time, container_fetch_response
def _patch_library_dataset(self, library_dataset_id, data): create_response = self._patch(f"libraries/datasets/{library_dataset_id}", data=data, json=True) self._assert_status_code_is(create_response, 200) ld = create_response.json() library_id = ld["parent_library_id"] return self.library_populator.wait_on_library_dataset(library_id, ld["id"])
[docs] @requires_new_library def test_update_dataset_in_folder(self): ld = self._create_dataset_in_folder_in_library("ForUpdateDataset", content=">seq\nATGC", wait=True).json() data = { "name": "updated_name", "file_ext": "fasta", "misc_info": "updated_info", "genome_build": "updated_genome_build", } ld_updated = self._patch_library_dataset(ld["id"], data) self._assert_has_keys(ld_updated, "name", "file_ext", "misc_info", "genome_build")
[docs] @requires_new_library def test_update_dataset_tags(self): ld = self._create_dataset_in_folder_in_library("ForTagtestDataset", wait=True).json() data = {"tags": ["#Lancelot", "name:Holy Grail", "blue"]} ld_updated = self._patch_library_dataset(ld["id"], data) self._assert_has_keys(ld_updated, "tags") assert ld_updated["tags"] == "name:Lancelot, name:HolyGrail, blue"
[docs] @requires_new_library def test_invalid_update_dataset_in_folder(self): ld = self._create_dataset_in_folder_in_library("ForInvalidUpdateDataset", wait=True).json() data = {"file_ext": "nonexisting_type"} create_response = self._patch(f"libraries/datasets/{ld['id']}", data=data, json=True) self._assert_status_code_is(create_response, 400) assert "This Galaxy does not recognize the datatype of:" in create_response.json()["err_msg"]
[docs] @requires_new_library def test_detect_datatype_of_dataset_in_folder(self): ld = self._create_dataset_in_folder_in_library("ForDetectDataset", wait=True).json() data = {"file_ext": "data"} ld_updated = self._patch_library_dataset(ld["id"], data) self._assert_has_keys(ld_updated, "file_ext") assert ld_updated["file_ext"] == "data" data = {"file_ext": "auto"} ld_updated = self._patch_library_dataset(ld["id"], data) self._assert_has_keys(ld_updated, "file_ext") assert ld_updated["file_ext"] == "txt"
[docs] @requires_new_library def test_ldda_collection_import_to_history(self): self._import_to_history(visible=True)
[docs] @requires_new_library def test_ldda_collection_import_to_history_hide_source(self): self._import_to_history(visible=False)
[docs] @requires_new_library def test_import_paired_collection(self): ld = self._create_dataset_in_folder_in_library("ForHistoryImport").json() history_id = self.dataset_populator.new_history() url = f"histories/{history_id}/contents" collection_name = "Paired-end data (from library)" payload = { "name": collection_name, "collection_type": "list:paired", "type": "dataset_collection", "element_identifiers": [ { "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=True).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 = f"histories/{history_id}/contents" 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": [{"id": ld["id"], "name": element_identifer, "src": "ldda"}], "type": "dataset_collection", "elements": [], } new_collection = self._post(url, payload, json=True).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
[docs] @requires_new_library 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, wait=True ).json()["outputs"][0]["id"] payload = {"from_hdca_id": hdca_id, "create_type": "file", "folder_id": folder_id} create_response = self._post(f"libraries/{library['id']}/contents", payload) self._assert_status_code_is(create_response, 200)
[docs] @requires_new_library 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, wait=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(f"folders/{folder_id}/contents", payload, json=True) 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, wait=True).json()[ "outputs" ][0]["id"] payload = {"from_hdca_id": hdca_pair_id} create_response = self._post(f"folders/{folder_id}/contents", payload, json=True) 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(f"libraries/{library['id']}/contents", data=create_data) def _create_subfolder(self, containing_folder_id): create_data = dict( description="new subfolder desc", name="New Subfolder", ) return self._post(f"folders/{containing_folder_id}", data=create_data, json=True) def _create_dataset_in_folder_in_library(self, library_name, content="1 2 3", wait=False): 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=content, wait=wait)["id"] payload = {"from_hda_id": hda_id, "create_type": "file", "folder_id": folder_id} ld = self._post(f"libraries/{folder_id}/contents", payload) return ld