Mercurial > repos > shellac > guppy_basecaller
diff env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyDatasetCollections.py @ 2:6af9afd405e9 draft
"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author | shellac |
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date | Thu, 14 May 2020 14:56:58 -0400 |
parents | 26e78fe6e8c4 |
children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/env/lib/python3.7/site-packages/bioblend/_tests/TestGalaxyDatasetCollections.py Thu May 14 14:56:58 2020 -0400 @@ -0,0 +1,135 @@ +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