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TestGalaxyDatasetCollections.py
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TestGalaxyDatasetCollections.py
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from bioblend.galaxy import dataset_collections as 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=collections.CollectionDescription(
name="MyDatasetList",
elements=[
collections.HistoryDatasetElement(name="sample1", id=dataset1_id),
collections.HistoryDatasetElement(name="sample2", id=dataset2_id),
collections.HistoryDatasetElement(name="sample3", id=dataset3_id),
]
)
)
self.assertEqual(collection_response["name"], "MyDatasetList")
self.assertEqual(collection_response["collection_type"], "list")
elements = collection_response["elements"]
self.assertEqual(len(elements), 3)
self.assertEqual(elements[0]["element_index"], 0)
self.assertEqual(elements[0]["object"]["id"], dataset1_id)
self.assertEqual(elements[1]["object"]["id"], dataset2_id)
self.assertEqual(elements[2]["object"]["id"], dataset3_id)
self.assertEqual(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=collections.CollectionDescription(
name="MyListOfPairedDatasets",
type="list:paired",
elements=[
collections.CollectionElement(
name="sample1",
type="paired",
elements=[
collections.HistoryDatasetElement(name="forward", id=dataset1_id),
collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
]
),
collections.CollectionElement(
name="sample2",
type="paired",
elements=[
collections.HistoryDatasetElement(name="forward", id=dataset3_id),
collections.HistoryDatasetElement(name="reverse", id=dataset4_id),
]
),
]
)
)
self.assertEqual(collection_response["name"], "MyListOfPairedDatasets")
self.assertEqual(collection_response["collection_type"], "list:paired")
elements = collection_response["elements"]
self.assertEqual(len(elements), 2)
self.assertEqual(elements[0]["element_index"], 0)
created_pair1 = elements[0]["object"]
self.assertEqual(created_pair1["collection_type"], "paired")
self.assertEqual(len(created_pair1["elements"]), 2)
forward_element1 = created_pair1["elements"][0]
self.assertEqual(forward_element1["element_identifier"], "forward")
self.assertEqual(forward_element1["element_index"], 0)
forward_dataset1 = forward_element1["object"]
self.assertEqual(forward_dataset1["id"], dataset1_id)
self.assertEqual(elements[1]["element_index"], 1)
created_pair2 = elements[1]["object"]
self.assertEqual(created_pair2["collection_type"], "paired")
self.assertEqual(len(created_pair2["elements"]), 2)
reverse_element2 = created_pair2["elements"][1]
reverse_dataset2 = reverse_element2["object"]
self.assertEqual(reverse_element2["element_identifier"], "reverse")
self.assertEqual(reverse_element2["element_index"], 1)
self.assertEqual(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)
self.assertEqual(len(contents), 3)
self.assertEqual(contents[2]["id"], history_dataset_collection["id"])
self.assertEqual(contents[2]["name"], "MyTestPair")
self.assertEqual(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"]:
self.assertIn(key, show_response)
self.assertFalse(show_response["deleted"])
self.assertTrue(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"])
self.assertTrue(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"])
self.assertFalse(show_response["visible"])
def _create_pair_in_history(self, history_id):
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=collections.CollectionDescription(
name="MyTestPair",
type="paired",
elements=[
collections.HistoryDatasetElement(name="forward", id=dataset1_id),
collections.HistoryDatasetElement(name="reverse", id=dataset2_id),
]
)
)
return collection_response