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)