diff env/lib/python3.9/site-packages/bioblend/_tests/TestGalaxyHistories.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/bioblend/_tests/TestGalaxyHistories.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,226 @@
+"""
+"""
+import os
+import shutil
+import tarfile
+import tempfile
+
+import bioblend.galaxy
+from . import GalaxyTestBase, test_util
+
+
+class TestGalaxyHistories(GalaxyTestBase.GalaxyTestBase):
+
+    def setUp(self):
+        super().setUp()
+        self.default_history_name = "buildbot - automated test"
+        self.history = self.gi.histories.create_history(name=self.default_history_name)
+
+    def test_create_history(self):
+        history_name = "another buildbot - automated test"
+        new_history = self.gi.histories.create_history(name=history_name)
+        self.assertIsNotNone(new_history['id'])
+        self.assertEqual(new_history['name'], history_name)
+        self.assertIsNotNone(new_history['url'])
+
+    def test_update_history(self):
+        new_name = 'buildbot - automated test renamed'
+        new_annotation = 'Annotation for %s' % new_name
+        new_tags = ['tag1', 'tag2']
+        updated_hist = self.gi.histories.update_history(self.history['id'], name=new_name, annotation=new_annotation, tags=new_tags)
+        if 'id' not in updated_hist:
+            updated_hist = self.gi.histories.show_history(self.history['id'])
+        self.assertEqual(self.history['id'], updated_hist['id'])
+        self.assertEqual(updated_hist['name'], new_name)
+        self.assertEqual(updated_hist['annotation'], new_annotation)
+        self.assertEqual(updated_hist['tags'], new_tags)
+
+    def test_publish_history(self):
+        # Verify that searching for published histories does not return the test history
+        published_histories = self.gi.histories.get_histories(published=True)
+        self.assertFalse(any(h['id'] == self.history['id'] for h in published_histories))
+        updated_hist = self.gi.histories.update_history(self.history['id'], published=True)
+        if 'id' not in updated_hist:
+            updated_hist = self.gi.histories.show_history(self.history['id'])
+        self.assertEqual(self.history['id'], updated_hist['id'])
+        self.assertTrue(updated_hist['published'])
+        # Verify that searching for published histories now returns the test history
+        published_histories = self.gi.histories.get_histories(published=True)
+        self.assertTrue(any(h['id'] == self.history['id'] for h in published_histories))
+        # Verify that get_published_histories as an anonymous user also returns the test history
+        anonymous_gi = bioblend.galaxy.GalaxyInstance(url=self.gi.base_url, key=None)
+        published_histories = anonymous_gi.histories.get_published_histories()
+        self.assertTrue(any(h['id'] == self.history['id'] for h in published_histories))
+        history_from_slug = anonymous_gi.histories.get_published_histories(slug=updated_hist['slug'])
+        self.assertTrue(len(history_from_slug) == 1)
+        self.assertEqual(self.history['id'], history_from_slug[0]['id'])
+
+    def test_get_histories(self):
+        # Make sure there's at least one value - the one we created
+        all_histories = self.gi.histories.get_histories()
+        self.assertGreater(len(all_histories), 0)
+
+        # Check whether name is correct, when searched by id
+        new_history = self.gi.histories.get_histories(history_id=self.history['id'])[0]
+        self.assertEqual(new_history['name'], self.default_history_name)
+
+        # Check whether id is present, when searched by name
+        histories = self.gi.histories.get_histories(name=self.default_history_name)
+        self.assertTrue(any(h['id'] == self.history['id'] for h in histories))
+
+        # TODO: check whether deleted history is returned correctly
+        # At the moment, get_histories() returns only not-deleted histories
+        # and get_histories(deleted=True) returns only deleted histories,
+        # so they are not comparable.
+        # In the future, according to https://trello.com/c/MoilsmVv/1673-api-incoherent-and-buggy-indexing-of-deleted-entities ,
+        # get_histories() will return both not-deleted and deleted histories
+        # and we can uncomment the following test.
+        # deleted_history = self.gi.histories.get_histories(deleted=True)
+        # self.assertGreaterEqual(len(all_histories), len(deleted_history))
+
+    def test_show_history(self):
+        history_data = self.gi.histories.show_history(self.history['id'])
+        self.assertEqual(self.history['id'], history_data['id'])
+        self.assertEqual(self.history['name'], history_data['name'])
+        self.assertEqual('new', history_data['state'])
+
+    def test_show_history_with_contents(self):
+        history_id = self.history["id"]
+        contents = self.gi.histories.show_history(history_id, contents=True)
+        # Empty history has no datasets, content length should be 0
+        self.assertEqual(len(contents), 0)
+        self._test_dataset(history_id)
+        contents = self.gi.histories.show_history(history_id, contents=True)
+        # history has 1 dataset, content length should be 1
+        self.assertEqual(len(contents), 1)
+        contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset'])
+        # filtering for dataset, content length should still be 1
+        self.assertEqual(len(contents), 1)
+        contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset_collection'])
+        # filtering for dataset collection but there's no collection in the history
+        self.assertEqual(len(contents), 0)
+        contents = self.gi.histories.show_history(history_id, contents=True, types=['dataset', 'dataset_collection'])
+        self.assertEqual(len(contents), 1)
+
+    def test_create_history_tag(self):
+        new_tag = 'tag1'
+        self.gi.histories.create_history_tag(self.history['id'], new_tag)
+        updated_hist = self.gi.histories.show_history(self.history['id'])
+        self.assertEqual(self.history['id'], updated_hist['id'])
+        self.assertIn(new_tag, updated_hist['tags'])
+
+    def test_show_dataset(self):
+        history_id = self.history["id"]
+        dataset1_id = self._test_dataset(history_id)
+        dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
+        for key in ["name", "hid", "id", "deleted", "history_id", "visible"]:
+            self.assertIn(key, dataset)
+        self.assertEqual(dataset["history_id"], history_id)
+        self.assertEqual(dataset["hid"], 1)
+        self.assertEqual(dataset["id"], dataset1_id)
+        self.assertEqual(dataset["deleted"], False)
+        self.assertEqual(dataset["visible"], True)
+
+    def test_show_dataset_provenance(self):
+        history_id = self.history["id"]
+        dataset1_id = self._test_dataset(history_id)
+        prov = self.gi.histories.show_dataset_provenance(history_id, dataset1_id)
+        for key in ["id", "job_id", "parameters", "stderr", "stdout", "tool_id"]:
+            self.assertIn(key, prov)
+
+    def test_delete_dataset(self):
+        history_id = self.history["id"]
+        dataset1_id = self._test_dataset(history_id)
+        self.gi.histories.delete_dataset(history_id, dataset1_id)
+        dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
+        self.assertTrue(dataset["deleted"])
+        self.assertFalse(dataset['purged'])
+
+    def test_purge_dataset(self):
+        history_id = self.history["id"]
+        dataset1_id = self._test_dataset(history_id)
+        self.gi.histories.delete_dataset(history_id, dataset1_id, purge=True)
+        dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
+        self.assertTrue(dataset["deleted"])
+        self.assertTrue(dataset['purged'])
+
+    def test_update_dataset(self):
+        history_id = self.history["id"]
+        dataset1_id = self._test_dataset(history_id)
+        updated_dataset = self.gi.histories.update_dataset(history_id, dataset1_id, visible=False)
+        if 'id' not in updated_dataset:
+            updated_dataset = self.gi.histories.show_dataset(history_id, dataset1_id)
+        self.assertFalse(updated_dataset["visible"])
+
+    def test_upload_dataset_from_library(self):
+        pass
+
+    # download_dataset() is already tested in TestGalaxyDatasets
+
+    def test_delete_history(self):
+        result = self.gi.histories.delete_history(self.history['id'])
+        self.assertTrue(result['deleted'])
+
+        all_histories = self.gi.histories.get_histories()
+        self.assertTrue(not any(d['id'] == self.history['id'] for d in all_histories))
+
+    def test_undelete_history(self):
+        self.gi.histories.delete_history(self.history['id'])
+        self.gi.histories.undelete_history(self.history['id'])
+        all_histories = self.gi.histories.get_histories()
+        self.assertTrue(any(d['id'] == self.history['id'] for d in all_histories))
+
+    def test_get_status(self):
+        state = self.gi.histories.get_status(self.history['id'])
+        self.assertEqual('new', state['state'])
+
+    def test_get_most_recently_used_history(self):
+        most_recently_used_history = self.gi.histories.get_most_recently_used_history()
+        # if the user has been created via the API, it does not have
+        # a session, therefore no history
+        if most_recently_used_history is not None:
+            self.assertIsNotNone(most_recently_used_history['id'])
+            self.assertIsNotNone(most_recently_used_history['name'])
+            self.assertIsNotNone(most_recently_used_history['state'])
+
+    def test_download_history(self):
+        jeha_id = self.gi.histories.export_history(
+            self.history['id'], wait=True, maxwait=60)
+        self.assertTrue(jeha_id)
+        tempdir = tempfile.mkdtemp(prefix='bioblend_test_')
+        temp_fn = os.path.join(tempdir, 'export.tar.gz')
+        try:
+            with open(temp_fn, 'wb') as fo:
+                self.gi.histories.download_history(self.history['id'], jeha_id,
+                                                   fo)
+            self.assertTrue(tarfile.is_tarfile(temp_fn))
+        finally:
+            shutil.rmtree(tempdir)
+
+    def test_import_history(self):
+        path = test_util.get_abspath(os.path.join('data', 'Galaxy-History-test.tar.gz'))
+        self.gi.histories.import_history(file_path=path)
+
+    def test_copy_dataset(self):
+        history_id = self.history["id"]
+        contents = "1\t2\t3"
+        dataset1_id = self._test_dataset(history_id, contents=contents)
+        self.history_id2 = self.gi.histories.create_history('TestCopyDataset')['id']
+        copied_dataset = self.gi.histories.copy_dataset(self.history_id2, dataset1_id)
+        expected_contents = ("\n".join(contents.splitlines()) + "\n").encode()
+        self._wait_and_verify_dataset(copied_dataset['id'], expected_contents)
+        self.gi.histories.delete_history(self.history_id2, purge=True)
+
+    @test_util.skip_unless_galaxy('release_20.09')
+    def test_update_dataset_datatype(self):
+        history_id = self.history["id"]
+        dataset1_id = self._test_dataset(history_id)
+        self._wait_and_verify_dataset(dataset1_id, b'1\t2\t3\n')
+        original_hda = self.gi.datasets.show_dataset(dataset1_id)
+        assert original_hda['extension'] == 'bed'
+        self.gi.histories.update_dataset(history_id, dataset1_id, datatype='tabular')
+        updated_hda = self.gi.datasets.show_dataset(dataset1_id)
+        assert updated_hda['extension'] == 'tabular'
+
+    def tearDown(self):
+        self.gi.histories.delete_history(self.history['id'], purge=True)