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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_index(self):
self.library_populator.new_library("TestIndexLibraries")
libraries = self.library_populator.get_libraries()
assert len(libraries) > 0
[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(
f"libraries/{library['id']}/contents", 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, json=True)
self._assert_status_code_is(create_response, 400)
assert create_response.json()["err_msg"] == "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,
}
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",
"message": "update message",
}
ld_updated = self._patch_library_dataset(ld["id"], data)
for key, value in data.items():
assert ld_updated[key] == value
[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, json=True)
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, json=True)
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/{library['id']}/contents", payload, json=True)
ld.raise_for_status()
return ld