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_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)