Source code for galaxy_test.api.test_folder_contents

from typing import (
    Any,
    List,
    Optional,
)

from galaxy_test.base.populators import (
    DatasetCollectionPopulator,
    DatasetPopulator,
    LibraryPopulator,
)
from ._framework import ApiTestCase


[docs]class FolderContentsApiTestCase(ApiTestCase):
[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) self.history_id = self.dataset_populator.new_history() self.library = self.library_populator.new_private_library("FolderContentsTestsLibrary") self.root_folder_id = self._create_folder_in_library("Test Folder Contents")
[docs] def test_create_hda_with_ldda_message(self): hda_id = self._create_hda() ldda_message = "Test message" data = { "from_hda_id": hda_id, "ldda_message": ldda_message, } ldda = self._create_content_in_folder_with_payload(self.root_folder_id, data) self._assert_has_keys(ldda, "name", "id")
[docs] def test_create_hdca_with_ldda_message(self): contents = ["dataset01", "dataset02"] hdca_id = self._create_hdca_with_contents(contents) ldda_message = "Test message" data = { "from_hdca_id": hdca_id, "ldda_message": ldda_message, } lddas = self._create_content_in_folder_with_payload(self.root_folder_id, data) assert len(contents) == len(lddas)
[docs] def test_index(self): folder_id = self._create_folder_in_library("Test Folder Contents Index") self._create_dataset_in_folder(folder_id) response = self._get(f"folders/{folder_id}/contents") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == 1
[docs] def test_index_include_deleted(self): folder_name = "Test Folder Contents Index include deleted" folder_id = self._create_folder_in_library(folder_name) hda_id = self._create_dataset_in_folder(folder_id) self._delete_library_dataset(hda_id) response = self._get(f"folders/{folder_id}/contents") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == 0 include_deleted = True response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == 1 assert contents[0]["deleted"] is True
[docs] def test_index_limit_offset(self): folder_name = "Test Folder Contents Index limit" folder_id = self._create_folder_in_library(folder_name) num_subfolders = 5 for index in range(num_subfolders): self._create_subfolder_in(folder_id, name=f"Folder_{index}") num_datasets = 5 for _ in range(num_datasets): self._create_dataset_in_folder(folder_id) total_items = num_datasets + num_subfolders response = self._get(f"folders/{folder_id}/contents") self._assert_status_code_is(response, 200) original_contents = response.json()["folder_contents"] assert len(original_contents) == total_items limit = 7 response = self._get(f"folders/{folder_id}/contents?limit={limit}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == limit offset = 3 response = self._get(f"folders/{folder_id}/contents?offset={offset}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == total_items - offset limit = 4 offset = 4 response = self._get(f"folders/{folder_id}/contents?limit={limit}&offset={offset}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == limit expected_query_result = original_contents[offset : offset + limit] for index in range(limit): assert contents[index]["id"] == expected_query_result[index]["id"]
[docs] def test_index_search_text(self): folder_name = "Test Folder Contents Index search text" folder_id = self._create_folder_in_library(folder_name) dataset_names = ["AB", "BC", "ABC"] for name in dataset_names: self._create_dataset_in_folder(folder_id, name) subfolder_names = ["Folder_A", "Folder_C"] for name in subfolder_names: self._create_subfolder_in(folder_id, name) all_names = dataset_names + subfolder_names search_terms = ["A", "B", "C"] for search_text in search_terms: response = self._get(f"folders/{folder_id}/contents?search_text={search_text}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] matching_names = [name for name in all_names if search_text in name] assert len(contents) == len(matching_names)
[docs] def test_index_permissions_include_deleted(self): folder_name = "Test Folder Contents Index permissions include deteleted" folder_id = self._create_folder_in_library(folder_name) num_subfolders = 5 subfolder_ids: List[str] = [] deleted_subfolder_ids: List[str] = [] for index in range(num_subfolders): id = self._create_subfolder_in(folder_id, name=f"Folder_{index}") subfolder_ids.append(id) for index, subfolder_id in enumerate(subfolder_ids): if index % 2 == 0: self._delete_subfolder(subfolder_id) deleted_subfolder_ids.append(subfolder_id) num_datasets = 5 datasets_ids: List[str] = [] deleted_datasets_ids: List[str] = [] for _ in range(num_datasets): id = self._create_dataset_in_folder(folder_id) datasets_ids.append(id) for index, ldda_id in enumerate(datasets_ids): if index % 2 == 0: self._delete_library_dataset(ldda_id) deleted_datasets_ids.append(ldda_id) num_total_contents = num_subfolders + num_datasets num_non_deleted = num_total_contents - len(deleted_subfolder_ids) - len(deleted_datasets_ids) # Verify deleted contents are not listed include_deleted = False response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == num_non_deleted include_deleted = True # Admins can see everything... response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}", admin=True) self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == num_total_contents # Owner can see everything too response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == num_total_contents # Users with access but no modify permission can't see deleted with self._different_user(): different_user_role_id = self.dataset_populator.user_private_role_id() self._allow_library_access_to_user_role(different_user_role_id) with self._different_user(): response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_status_code_is(response, 200) contents = response.json()["folder_contents"] assert len(contents) == num_non_deleted
def _create_folder_in_library(self, name: str) -> Any: root_folder_id = self.library["root_folder_id"] return self._create_subfolder_in(root_folder_id, name) def _create_subfolder_in(self, folder_id: str, name: str) -> str: data = { "name": name, "description": f"The description of {name}", } create_response = self._post(f"folders/{folder_id}", data=data, json=True) self._assert_status_code_is(create_response, 200) folder = create_response.json() return folder["id"] def _create_dataset_in_folder(self, folder_id: str, name: Optional[str] = None) -> str: hda_id = self._create_hda(name) data = { "from_hda_id": hda_id, } ldda = self._create_content_in_folder_with_payload(folder_id, data) return ldda["id"] def _create_content_in_folder_with_payload(self, folder_id: str, payload) -> Any: create_response = self._post(f"folders/{folder_id}/contents", data=payload, json=True) self._assert_status_code_is(create_response, 200) return create_response.json() def _create_hda(self, name: Optional[str] = None) -> str: hda = self.dataset_populator.new_dataset(self.history_id, name=name) hda_id = hda["id"] return hda_id def _create_hdca_with_contents(self, contents: List[str]) -> str: hdca = self.dataset_collection_populator.create_list_in_history( self.history_id, contents=contents, direct_upload=True, wait=True ).json()["outputs"][0] hdca_id = hdca["id"] return hdca_id def _delete_library_dataset(self, ldda_id: str) -> None: delete_response = self._delete(f"libraries/datasets/{ldda_id}") self._assert_status_code_is(delete_response, 200) def _delete_subfolder(self, folder_id: str) -> None: delete_response = self._delete(f"folders/{folder_id}") self._assert_status_code_is(delete_response, 200) def _allow_library_access_to_user_role(self, role_id: str): library_id = self.library["id"] action = "set_permissions" data = { "access_ids[]": role_id, } response = self._post(f"libraries/{library_id}/permissions?action={action}", data=data, admin=True, json=True) self._assert_status_code_is(response, 200)