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import shutil
import tempfile
import pytest
from bioblend import (
ConnectionError,
galaxy,
)
from . import (
GalaxyTestBase,
test_util,
)
class TestGalaxyDatasets(GalaxyTestBase.GalaxyTestBase):
def setUp(self):
super().setUp()
self.history_id = self.gi.histories.create_history(name="TestDataset")["id"]
self.dataset_contents = "line 1\nline 2\rline 3\r\nline 4"
self.dataset_id = self._test_dataset(self.history_id, contents=self.dataset_contents)
self.gi.datasets.wait_for_dataset(self.dataset_id)
def tearDown(self):
self.gi.histories.delete_history(self.history_id, purge=True)
@test_util.skip_unless_galaxy("release_19.05")
def test_show_nonexistent_dataset(self):
with pytest.raises(ConnectionError):
self.gi.datasets.show_dataset("nonexistent_id")
def test_show_dataset(self):
self.gi.datasets.show_dataset(self.dataset_id)
def test_download_dataset(self):
with pytest.raises((TypeError, ConnectionError)):
self.gi.datasets.download_dataset(None) # type: ignore[call-overload]
expected_contents = ("\n".join(self.dataset_contents.splitlines()) + "\n").encode()
# download_dataset() with file_path=None is already tested in TestGalaxyTools.test_paste_content()
# self._wait_and_verify_dataset(self.dataset_id, expected_contents)
tempdir = tempfile.mkdtemp(prefix="bioblend_test_")
try:
downloaded_dataset = self.gi.datasets.download_dataset(
self.dataset_id, file_path=tempdir, maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT * 2
)
assert downloaded_dataset.startswith(tempdir)
with open(downloaded_dataset, "rb") as f:
assert f.read() == expected_contents
finally:
shutil.rmtree(tempdir)
with tempfile.NamedTemporaryFile(prefix="bioblend_test_") as f:
download_filename = self.gi.datasets.download_dataset(
self.dataset_id,
file_path=f.name,
use_default_filename=False,
maxwait=GalaxyTestBase.BIOBLEND_TEST_JOB_TIMEOUT,
)
assert download_filename == f.name
f.flush()
assert f.read() == expected_contents
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets(self):
datasets = self.gi.datasets.get_datasets()
dataset_ids = [dataset["id"] for dataset in datasets]
assert self.dataset_id in dataset_ids
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets_history(self):
datasets = self.gi.datasets.get_datasets(history_id=self.history_id)
assert len(datasets) == 1
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets_limit_offset(self):
datasets = self.gi.datasets.get_datasets(limit=1)
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, offset=1)
assert datasets == []
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets_name(self):
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, name="Pasted Entry")
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, name="Wrong Name")
assert datasets == []
@test_util.skip_unless_galaxy("release_20.05")
def test_get_datasets_time(self):
dataset = self.gi.datasets.show_dataset(self.dataset_id)
ct = dataset["create_time"]
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, create_time_min=ct)
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, create_time_max=ct)
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, create_time_min="2100-01-01T00:00:00")
assert datasets == []
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, create_time_max="2000-01-01T00:00:00")
assert datasets == []
ut = dataset["update_time"]
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, update_time_min=ut)
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, update_time_max=ut)
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, update_time_min="2100-01-01T00:00:00")
assert datasets == []
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, update_time_max="2000-01-01T00:00:00")
assert datasets == []
@test_util.skip_unless_galaxy("release_20.05")
def test_get_datasets_extension(self):
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, extension="txt")
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, extension="bam")
assert datasets == []
@test_util.skip_unless_galaxy("release_22.01")
def test_get_datasets_extension_list(self):
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, extension=["bam", "txt"])
assert len(datasets) == 1
@test_util.skip_unless_galaxy("release_20.05")
def test_get_datasets_state(self):
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, state="ok")
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, state="queued")
assert datasets == []
with pytest.raises(ConnectionError):
self.gi.datasets.get_datasets(history_id=self.history_id, state="nonexistent_state")
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, state=["ok", "queued"])
assert len(datasets) == 1
@test_util.skip_unless_galaxy("release_20.05")
def test_get_datasets_visible(self):
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, visible=True)
assert len(datasets) == 1
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, visible=False)
assert len(datasets) == 0
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets_ordering(self):
self.dataset_id2 = self._test_dataset(self.history_id, contents=self.dataset_contents)
self.gi.datasets.wait_for_dataset(self.dataset_id2)
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, order="create_time-dsc")
assert datasets[0]["id"] == self.dataset_id2
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, order="create_time-asc")
assert datasets[0]["id"] == self.dataset_id
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, order="hid-dsc")
assert datasets[0]["id"] == self.dataset_id2
datasets = self.gi.datasets.get_datasets(history_id=self.history_id, order="hid-asc")
assert datasets[0]["id"] == self.dataset_id
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets_deleted(self):
deleted_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, deleted=True)
assert deleted_datasets == []
self.gi.histories.delete_dataset(self.history_id, self.dataset_id)
deleted_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, deleted=True)
assert len(deleted_datasets) == 1
purged_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, purged=True)
assert purged_datasets == []
self.gi.histories.delete_dataset(self.history_id, self.dataset_id, purge=True)
purged_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, purged=True)
assert len(purged_datasets) == 1
@test_util.skip_unless_galaxy("release_19.05")
def test_get_datasets_tool_id_and_tag(self):
cat1_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, tool_id="cat1")
assert cat1_datasets == []
upload1_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, tool_id="upload1")
assert len(upload1_datasets) == 1
self.gi.histories.update_dataset(self.history_id, self.dataset_id, tags=["test"])
tagged_datasets = self.gi.datasets.get_datasets(history_id=self.history_id, tag="test")
assert len(tagged_datasets) == 1
def test_wait_for_dataset(self):
history_id = self.gi.histories.create_history(name="TestWaitForDataset")["id"]
dataset_contents = "line 1\nline 2\rline 3\r\nline 4"
dataset_id = self._test_dataset(history_id, contents=dataset_contents)
dataset = self.gi.datasets.wait_for_dataset(dataset_id)
assert dataset["state"] == "ok"
self.gi.histories.delete_history(history_id, purge=True)
@test_util.skip_unless_galaxy("release_19.05")
def test_dataset_permissions(self):
admin_user_id = self.gi.users.get_current_user()["id"]
username = test_util.random_string()
user_id = self.gi.users.create_local_user(username, f"{username}@example.org", test_util.random_string(20))[
"id"
]
user_api_key = self.gi.users.create_user_apikey(user_id)
anonymous_gi = galaxy.GalaxyInstance(url=self.gi.base_url, key=None)
user_gi = galaxy.GalaxyInstance(url=self.gi.base_url, key=user_api_key)
sharing_role = self.gi.roles.create_role("sharing_role", "sharing_role", [user_id, admin_user_id])["id"]
self.gi.datasets.publish_dataset(self.dataset_id, published=False)
with pytest.raises(ConnectionError):
anonymous_gi.datasets.show_dataset(self.dataset_id)
self.gi.datasets.publish_dataset(self.dataset_id, published=True)
# now dataset is public, i.e. accessible to anonymous users
assert anonymous_gi.datasets.show_dataset(self.dataset_id)["id"] == self.dataset_id
self.gi.datasets.publish_dataset(self.dataset_id, published=False)
with pytest.raises(ConnectionError):
user_gi.datasets.show_dataset(self.dataset_id)
self.gi.datasets.update_permissions(self.dataset_id, access_ids=[sharing_role], manage_ids=[sharing_role])
assert user_gi.datasets.show_dataset(self.dataset_id)["id"] == self.dataset_id
# anonymous access now fails because sharing is only with the shared user role
with pytest.raises(ConnectionError):
anonymous_gi.datasets.show_dataset(self.dataset_id)
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