Warning

This document is for an in-development version of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy_test.api.test_folder_contents

from typing import (
    Any,
    List,
    Optional,
    Tuple,
)

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


[docs]class TestFolderContentsApi(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) self.library = self.library_populator.new_private_library("FolderContentsTestsLibrary") self.root_folder_id = self._create_folder_in_library("Test Folder Contents")
[docs] @requires_new_library def test_create_hda_with_ldda_message(self, history_id): hda_id = self._create_hda(history_id) 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] @requires_new_library def test_create_hdca_with_ldda_message(self, history_id): contents = ["dataset01", "dataset02"] hdca_id = self._create_hdca_with_contents(history_id, 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] @requires_new_library def test_index(self, history_id): folder_id = self._create_folder_in_library("Test Folder Contents Index") self._create_subfolder_in(folder_id) self._create_dataset_in_folder(history_id, folder_id) response = self._get(f"folders/{folder_id}/contents") self._assert_index_count_is_correct(response, expected_contents_count=2)
[docs] @requires_new_library def test_index_include_deleted(self, history_id): folder_name = "Test Folder Contents Index include deleted" folder_id = self._create_folder_in_library(folder_name) sub_folder_id = self._create_subfolder_in(folder_id) ldda_id, _ = self._create_dataset_in_folder(history_id, folder_id) self._delete_library_dataset(ldda_id) self._delete_subfolder(sub_folder_id) response = self._get(f"folders/{folder_id}/contents") self._assert_index_count_is_correct(response, expected_contents_count=0) include_deleted = True response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") index_response = self._assert_index_count_is_correct(response, expected_contents_count=2) for content in index_response["folder_contents"]: assert content["deleted"] is True
[docs] @requires_new_library def test_index_pagination(self, history_id): folder_name = "Test Folder Contents Pagination" 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(history_id, folder_id) total_items = num_datasets + num_subfolders response = self._get(f"folders/{folder_id}/contents") index_response = self._assert_index_count_is_correct(response, expected_contents_count=total_items) original_contents = index_response["folder_contents"] limit = 7 response = self._get(f"folders/{folder_id}/contents?limit={limit}") index_response = self._assert_index_count_is_correct( response, expected_contents_count=limit, expected_total_count=total_items ) limit = 20 response = self._get(f"folders/{folder_id}/contents?limit={limit}") index_response = self._assert_index_count_is_correct(response, expected_contents_count=total_items) offset = 3 response = self._get(f"folders/{folder_id}/contents?offset={offset}") index_response = self._assert_index_count_is_correct( response, expected_contents_count=total_items - offset, expected_total_count=total_items ) offset = 20 response = self._get(f"folders/{folder_id}/contents?offset={offset}") index_response = self._assert_index_count_is_correct( response, expected_contents_count=0, expected_total_count=total_items ) limit = 4 offset = 4 response = self._get(f"folders/{folder_id}/contents?limit={limit}&offset={offset}") index_response = self._assert_index_count_is_correct( response, expected_contents_count=limit, expected_total_count=total_items ) contents = index_response["folder_contents"] expected_query_result = original_contents[offset : offset + limit] for index in range(limit): assert contents[index]["id"] == expected_query_result[index]["id"] limit = 20 offset = 6 response = self._get(f"folders/{folder_id}/contents?limit={limit}&offset={offset}") actual_limit = limit if limit < total_items else total_items - offset index_response = self._assert_index_count_is_correct( response, expected_contents_count=actual_limit, expected_total_count=total_items ) contents = index_response["folder_contents"] expected_query_result = original_contents[offset : offset + actual_limit] for index in range(actual_limit): assert contents[index]["id"] == expected_query_result[index]["id"]
[docs] @requires_new_library def test_index_search_text(self, history_id): folder_name = "Test Folder Contents Index search text" folder_id = self._create_folder_in_library(folder_name) dataset_names = ["AB", "BX", "abx"] for name in dataset_names: self._create_dataset_in_folder(history_id, folder_id, name) subfolder_names = ["Folder_a", "Folder_X"] for name in subfolder_names: self._create_subfolder_in(folder_id, name) all_names = dataset_names + subfolder_names search_terms = ["A", "B", "X"] for search_text in search_terms: matching_names = [name for name in all_names if search_text.casefold() in name.casefold()] response = self._get(f"folders/{folder_id}/contents?search_text={search_text}") index_response = self._assert_index_count_is_correct(response, expected_contents_count=len(matching_names)) contents = index_response["folder_contents"] for content in contents: assert search_text.casefold() in content["name"].casefold()
[docs] @requires_new_library def test_index_permissions(self, history_id): folder_name = "Test Folder Contents Index permissions" folder_id = self._create_folder_in_library(folder_name) _, hda_id = self._create_dataset_in_folder(history_id, folder_id) self._make_dataset_private(hda_id) # Owner can access response = self._get(f"folders/{folder_id}/contents") self._assert_index_count_is_correct(response, expected_contents_count=1) # Admins can access response = self._get(f"folders/{folder_id}/contents", admin=True) self._assert_index_count_is_correct(response, expected_contents_count=1) # Other users can't access with self._different_user(): # Without access to the parent library the user gets a 404... should it be a 403 instead? response = self._get(f"folders/{folder_id}/contents") self._assert_status_code_is(response, 404) # Grant library access to this user different_user_role_id = self.dataset_populator.user_private_role_id() self._allow_library_access_to_user_role(different_user_role_id) # Runs as admin # The user can access the library folder but not the private dataset in it response = self._get(f"folders/{folder_id}/contents") self._assert_index_count_is_correct(response, expected_contents_count=0) # Grant access to this user self._allow_dataset_access(hda_id) response = self._get(f"folders/{folder_id}/contents") self._assert_index_count_is_correct(response, expected_contents_count=1)
[docs] @requires_new_library def test_index_permissions_include_deleted(self, history_id) -> None: folder_name = "Test Folder Contents Index permissions include deleted" 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): ldda_id = self._create_subfolder_in(folder_id, name=f"Folder_{index}") subfolder_ids.append(ldda_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 ldda_ids: List[str] = [] deleted_ldda_ids: List[str] = [] for _ in range(num_datasets): ldda_id, _ = self._create_dataset_in_folder(history_id, folder_id) ldda_ids.append(ldda_id) for index, ldda_id in enumerate(ldda_ids): if index % 2 == 0: self._delete_library_dataset(ldda_id) deleted_ldda_ids.append(ldda_id) num_total_contents = num_subfolders + num_datasets num_non_deleted = num_total_contents - len(deleted_subfolder_ids) - len(deleted_ldda_ids) # Verify deleted contents are not listed include_deleted = False response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_index_count_is_correct(response, expected_contents_count=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_index_count_is_correct(response, expected_contents_count=num_total_contents) # Owner can see everything too response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_index_count_is_correct(response, expected_contents_count=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) # Runs as admin response = self._get(f"folders/{folder_id}/contents?include_deleted={include_deleted}") self._assert_index_count_is_correct(response, expected_contents_count=num_non_deleted)
[docs] @requires_new_library def test_index_order_by(self, history_id): folder_name = "Test Folder Contents Index Order By" folder_id = self._create_folder_in_library(folder_name) subfolder_names = ["Folder_A", "Folder_B", "Folder_C"] subfolder_descriptions = ["Description Z", "Description Y", "Description X"] for index, name in enumerate(subfolder_names): self._create_subfolder_in(folder_id, name, subfolder_descriptions[index]) dataset_names = ["a", "b", "c"] ldda_messages = ["Message Z", "Message Y", "Message X"] dataset_sizes = [50, 100, 10] file_types = ["txt", "csv", "json"] for index, name in enumerate(dataset_names): self._create_dataset_in_folder( history_id, folder_id, name, content=f"{'0' * dataset_sizes[index]}", ldda_message=ldda_messages[index], file_type=file_types[index], ) # Wait for datasets to finish upload self.dataset_populator.wait_for_history(history_id) # Folders always have priority (they show-up before any dataset regardless of the sorting) and they # can only be sorted by name, description and update_time, the other sorting attributes are ignored sort_desc = False order_by = "name" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "a", "b", "c"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "description" expected_order_by_name = ["Folder_C", "Folder_B", "Folder_A", "c", "b", "a"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "type" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "b", "c", "a"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "size" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "c", "a", "b"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "update_time" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "a", "b", "c"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) sort_desc = True order_by = "name" expected_order_by_name = ["Folder_C", "Folder_B", "Folder_A", "c", "b", "a"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "description" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "a", "b", "c"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "type" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "a", "c", "b"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "size" expected_order_by_name = ["Folder_A", "Folder_B", "Folder_C", "b", "a", "c"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name) order_by = "update_time" expected_order_by_name = ["Folder_C", "Folder_B", "Folder_A", "c", "b", "a"] self._assert_folder_order_by_is_expected(folder_id, order_by, sort_desc, expected_order_by_name)
def _assert_folder_order_by_is_expected( self, folder_id: str, order_by: str, sort_desc: str, expected_order_by_name: List[str] ): response = self._get(f"folders/{folder_id}/contents?order_by={order_by}&sort_desc={sort_desc}") index_response = self._assert_index_count_is_correct( response, expected_contents_count=len(expected_order_by_name) ) for index, item in enumerate(index_response["folder_contents"]): assert item["name"] == expected_order_by_name[index] def _assert_index_count_is_correct( self, raw_response, expected_contents_count: int, expected_total_count: Optional[int] = None ) -> dict: self._assert_status_code_is(raw_response, 200) if expected_total_count is None: expected_total_count = expected_contents_count index_response = raw_response.json() metadata = index_response["metadata"] contents = index_response["folder_contents"] assert metadata["total_rows"] == expected_total_count, "Expected total rows doesn't match" assert len(contents) == expected_contents_count, "Expected number of contents doesn't match" return index_response def _create_folder_in_library(self, name: str) -> str: 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: Optional[str] = None, description: Optional[str] = None ) -> str: data = { "name": name or "Test Folder", "description": description or 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, history_id: str, folder_id: str, name: Optional[str] = None, content: Optional[str] = None, ldda_message: Optional[str] = None, **kwds, ) -> Tuple[str, str]: """Returns a tuple with the LDDA ID and the underlying HDA ID""" hda_id = self._create_hda(history_id, name, content, **kwds) data = { "from_hda_id": hda_id, "ldda_message": ldda_message or "Test msg", } ldda = self._create_content_in_folder_with_payload(folder_id, data) return ldda["id"], hda_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, history_id: str, name: Optional[str] = None, content: Optional[str] = None, **kwds) -> str: hda = self.dataset_populator.new_dataset(history_id, name=name, content=content, **kwds) hda_id = hda["id"] return hda_id def _create_hdca_with_contents(self, history_id: str, contents: List[str]) -> str: hdca = self.dataset_collection_populator.create_list_in_history( 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) def _allow_dataset_access(self, dataset_id: str): payload = {"action": "remove_restrictions"} update_response = self._put(f"datasets/{dataset_id}/permissions", payload, admin=True, json=True) self._assert_status_code_is_ok(update_response) def _make_dataset_private(self, dataset_id: str): payload = {"action": "make_private"} update_response = self._put(f"datasets/{dataset_id}/permissions", payload, json=True) self._assert_status_code_is_ok(update_response)