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import os
import tarfile
import tempfile
from inspect import signature
from typing import (
Any,
Dict,
Union,
)
from zipfile import ZipFile
from bioblend.galaxy import dataset_collections
from . import GalaxyTestBase
class TestGalaxyDatasetCollections(GalaxyTestBase.GalaxyTestBase):
def test_create_list_in_history(self):
history_id = self.gi.histories.create_history(name="TestDSListCreate")["id"]
dataset1_id = self._test_dataset(history_id)
dataset2_id = self._test_dataset(history_id)
dataset3_id = self._test_dataset(history_id)
collection_response = self.gi.histories.create_dataset_collection(
history_id=history_id,
collection_description=dataset_collections.CollectionDescription(
name="MyDatasetList",
elements=[
dataset_collections.HistoryDatasetElement(name="sample1", id=dataset1_id),
dataset_collections.HistoryDatasetElement(name="sample2", id=dataset2_id),
dataset_collections.HistoryDatasetElement(name="sample3", id=dataset3_id),
],
),
)
assert collection_response["name"] == "MyDatasetList"
assert collection_response["collection_type"] == "list"
elements = collection_response["elements"]
assert len(elements) == 3
assert elements[0]["element_index"] == 0
assert elements[0]["object"]["id"] == dataset1_id
assert elements[1]["object"]["id"] == dataset2_id
assert elements[2]["object"]["id"] == dataset3_id
assert elements[2]["element_identifier"] == "sample3"
def test_create_list_of_paired_datasets_in_history(self):
history_id = self.gi.histories.create_history(name="TestDSListCreate")["id"]
dataset1_id = self._test_dataset(history_id)
dataset2_id = self._test_dataset(history_id)
dataset3_id = self._test_dataset(history_id)
dataset4_id = self._test_dataset(history_id)
collection_response = self.gi.histories.create_dataset_collection(
history_id=history_id,
collection_description=dataset_collections.CollectionDescription(
name="MyListOfPairedDatasets",
type="list:paired",
elements=[
dataset_collections.CollectionElement(
name="sample1",
type="paired",
elements=[
dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
],
),
dataset_collections.CollectionElement(
name="sample2",
type="paired",
elements=[
dataset_collections.HistoryDatasetElement(name="forward", id=dataset3_id),
dataset_collections.HistoryDatasetElement(name="reverse", id=dataset4_id),
],
),
],
),
)
assert collection_response["name"] == "MyListOfPairedDatasets"
assert collection_response["collection_type"] == "list:paired"
elements = collection_response["elements"]
assert len(elements) == 2
assert elements[0]["element_index"] == 0
created_pair1 = elements[0]["object"]
assert created_pair1["collection_type"] == "paired"
assert len(created_pair1["elements"]) == 2
forward_element1 = created_pair1["elements"][0]
assert forward_element1["element_identifier"] == "forward"
assert forward_element1["element_index"] == 0
forward_dataset1 = forward_element1["object"]
assert forward_dataset1["id"] == dataset1_id
assert elements[1]["element_index"] == 1
created_pair2 = elements[1]["object"]
assert created_pair2["collection_type"] == "paired"
assert len(created_pair2["elements"]) == 2
reverse_element2 = created_pair2["elements"][1]
reverse_dataset2 = reverse_element2["object"]
assert reverse_element2["element_identifier"] == "reverse"
assert reverse_element2["element_index"] == 1
assert reverse_dataset2["id"] == dataset4_id
def test_collections_in_history_index(self):
history_id = self.gi.histories.create_history(name="TestHistoryDSIndex")["id"]
history_dataset_collection = self._create_pair_in_history(history_id)
contents = self.gi.histories.show_history(history_id, contents=True)
assert len(contents) == 3
assert contents[2]["id"] == history_dataset_collection["id"]
assert contents[2]["name"] == "MyTestPair"
assert contents[2]["collection_type"] == "paired"
def test_show_history_dataset_collection(self):
history_id = self.gi.histories.create_history(name="TestHistoryDSIndexShow")["id"]
history_dataset_collection = self._create_pair_in_history(history_id)
show_response = self.gi.histories.show_dataset_collection(history_id, history_dataset_collection["id"])
for key in ["collection_type", "elements", "name", "deleted", "visible"]:
assert key in show_response
assert not show_response["deleted"]
assert show_response["visible"]
def test_delete_history_dataset_collection(self):
history_id = self.gi.histories.create_history(name="TestHistoryDSDelete")["id"]
history_dataset_collection = self._create_pair_in_history(history_id)
self.gi.histories.delete_dataset_collection(history_id, history_dataset_collection["id"])
show_response = self.gi.histories.show_dataset_collection(history_id, history_dataset_collection["id"])
assert show_response["deleted"]
def test_update_history_dataset_collection(self):
history_id = self.gi.histories.create_history(name="TestHistoryDSDelete")["id"]
history_dataset_collection = self._create_pair_in_history(history_id)
self.gi.histories.update_dataset_collection(history_id, history_dataset_collection["id"], visible=False)
show_response = self.gi.histories.show_dataset_collection(history_id, history_dataset_collection["id"])
assert not show_response["visible"]
def test_show_dataset_collection(self):
history_id = self.gi.histories.create_history(name="TestDatasetCollectionShow")["id"]
dataset_collection1 = self._create_pair_in_history(history_id)
dataset_collection2 = self.gi.dataset_collections.show_dataset_collection(dataset_collection1["id"])
for key in (
"collection_type",
"deleted",
"id",
"hid",
"history_content_type",
"history_id",
"name",
"url",
"visible",
):
assert dataset_collection1[key] == dataset_collection2[key]
for element1, element2 in zip(dataset_collection1["elements"], dataset_collection2["elements"]):
assert element1["id"] == element2["id"]
assert element1.keys() == element2.keys()
for key in element1["object"].keys():
assert key in element2["object"].keys()
def test_download_dataset_collection(self):
history_id = self.gi.histories.create_history(name="TestDatasetCollectionDownload")["id"]
dataset_collection_id = self._create_pair_in_history(history_id)["id"]
self.gi.dataset_collections.wait_for_dataset_collection(dataset_collection_id)
tempdir = tempfile.mkdtemp(prefix="bioblend_test_dataset_collection_download_")
archive_path = os.path.join(tempdir, "dataset_collection")
archive_type = self.gi.dataset_collections.download_dataset_collection(
dataset_collection_id, file_path=archive_path
)["archive_type"]
expected_contents = signature(self._test_dataset).parameters["contents"].default + "\n"
extract_dir_path = os.path.join(tempdir, "extracted_files")
os.mkdir(extract_dir_path)
if archive_type == "zip":
archive: Union[ZipFile, tarfile.TarFile] = ZipFile(archive_path)
elif archive_type == "tgz":
archive = tarfile.open(archive_path)
archive.extractall(extract_dir_path)
for fname in os.listdir(extract_dir_path):
dataset_dir_path = os.path.join(extract_dir_path, fname)
file_path = os.path.join(dataset_dir_path, os.listdir(dataset_dir_path)[0])
with open(file_path) as f:
assert expected_contents == f.read()
archive.close()
def test_wait_for_dataset_collection(self):
history_id = self.gi.histories.create_history(name="TestDatasetCollectionWait")["id"]
dataset_collection_id = self._create_pair_in_history(history_id)["id"]
dataset_collection = self.gi.dataset_collections.wait_for_dataset_collection(dataset_collection_id)
for element in dataset_collection["elements"]:
assert element["object"]["state"] == "ok"
def _create_pair_in_history(self, history_id: str) -> Dict[str, Any]:
dataset1_id = self._test_dataset(history_id)
dataset2_id = self._test_dataset(history_id)
collection_response = self.gi.histories.create_dataset_collection(
history_id=history_id,
collection_description=dataset_collections.CollectionDescription(
name="MyTestPair",
type="paired",
elements=[
dataset_collections.HistoryDatasetElement(name="forward", id=dataset1_id),
dataset_collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
],
),
)
return collection_response
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