diff --git a/lib/galaxy_test/api/test_dataset_collections.py b/lib/galaxy_test/api/test_dataset_collections.py index 839fd296dd2..3f0e389e84b 100644 --- a/lib/galaxy_test/api/test_dataset_collections.py +++ b/lib/galaxy_test/api/test_dataset_collections.py @@ -88,8 +88,8 @@ class DatasetCollectionApiTestCase(ApiTestCase): assert pair_1_element["element_index"] == 0, pair_1_element pair_1_object = pair_1_element["object"] self._assert_has_keys(pair_1_object, "collection_type", "elements", "element_count") - self.assertEqual(pair_1_object["collection_type"], "paired") - self.assertEqual(pair_1_object["populated"], True) + assert pair_1_object["collection_type"] == "paired" + assert pair_1_object["populated"] is True pair_elements = pair_1_object["elements"] assert len(pair_elements) == 2 pair_1_element_1 = pair_elements[0] @@ -233,7 +233,7 @@ class DatasetCollectionApiTestCase(ApiTestCase): } self.dataset_populator.fetch(payload) hdca = self._assert_one_collection_created_in_history() - self.assertEqual(hdca["name"], "Test upload") + assert hdca["name"] == "Test upload" hdca_tags = hdca["tags"] assert len(hdca_tags) == 1 assert "name:collection1" in hdca_tags @@ -262,7 +262,7 @@ class DatasetCollectionApiTestCase(ApiTestCase): } self.dataset_populator.fetch(payload) hdca = self._assert_one_collection_created_in_history() - self.assertEqual(hdca["name"], "Test upload") + assert hdca["name"] == "Test upload" assert len(hdca["elements"]) == 1, hdca element0 = hdca["elements"][0] assert element0["element_identifier"] == "samp1" diff --git a/lib/galaxy_test/api/test_histories.py b/lib/galaxy_test/api/test_histories.py index 19090524b4d..3db663d5dd6 100644 --- a/lib/galaxy_test/api/test_histories.py +++ b/lib/galaxy_test/api/test_histories.py @@ -32,7 +32,7 @@ class BaseHistories: post_data = dict(name=name) create_response = self._post("histories", data=post_data).json() self._assert_has_keys(create_response, "name", "id") - self.assertEqual(create_response["name"], name) + assert create_response["name"] == name return create_response def _assert_history_length(self, history_id, n): @@ -56,14 +56,14 @@ class HistoriesApiTestCase(ApiTestCase, BaseHistories): # Make sure new history appears in index of user's histories. index_response = self._get("histories").json() indexed_history = [h for h in index_response if h["id"] == created_id][0] - self.assertEqual(indexed_history["name"], "TestHistory1") + assert indexed_history["name"] == "TestHistory1" def test_create_history_json(self): name = "TestHistoryJson" post_data = dict(name=name) create_response = self._post("histories", data=post_data, json=True).json() self._assert_has_keys(create_response, "name", "id") - self.assertEqual(create_response["name"], name) + assert create_response["name"] == name return create_response def test_show_history(self): diff --git a/lib/galaxy_test/api/test_history_contents.py b/lib/galaxy_test/api/test_history_contents.py index 50bb1ea9b25..000fc0b6a25 100644 --- a/lib/galaxy_test/api/test_history_contents.py +++ b/lib/galaxy_test/api/test_history_contents.py @@ -897,7 +897,7 @@ class HistoryContentsApiTestCase(ApiTestCase): ) self._assert_status_code_is(contents_response, 200) collection = contents_response.json()[0] - self.assertCountEqual(collection["elements_datatypes"], expected_datatypes) + assert sorted(collection["elements_datatypes"]) == sorted(expected_datatypes) class HistoryContentsApiNearTestCase(ApiTestCase): diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py index 92a8a30d960..65b913bc43c 100644 --- a/lib/galaxy_test/api/test_jobs.py +++ b/lib/galaxy_test/api/test_jobs.py @@ -943,7 +943,7 @@ steps: search_payload = self._search_payload(history_id=history_id, tool_id=tool_id, inputs=inputs) empty_search_response = self._post("jobs/search", data=search_payload) self._assert_status_code_is(empty_search_response, 200) - self.assertEqual(len(empty_search_response.json()), 0) + assert len(empty_search_response.json()) == 0 tool_response = self._post("tools", data=search_payload) self.dataset_populator.wait_for_tool_run(history_id, run_response=tool_response) self._search(search_payload, expected_search_count=1) diff --git a/lib/galaxy_test/api/test_pages.py b/lib/galaxy_test/api/test_pages.py index 2df2f28bd2c..2ff98839092 100644 --- a/lib/galaxy_test/api/test_pages.py +++ b/lib/galaxy_test/api/test_pages.py @@ -98,9 +98,9 @@ steps: self._assert_status_code_is(show_response, 200) show_json = show_response.json() self._assert_has_keys(show_json, "slug", "title", "id") - self.assertEqual(show_json["slug"], "invocation-report") - self.assertEqual(show_json["title"], "Invocation Report") - self.assertEqual(show_json["content_format"], "markdown") + assert show_json["slug"] == "invocation-report" + assert show_json["title"] == "Invocation Report" + assert show_json["content_format"] == "markdown" markdown_content = show_json["content"] assert "## Workflow Outputs" in markdown_content assert "## Workflow Inputs" in markdown_content @@ -307,10 +307,10 @@ steps: self._assert_status_code_is(show_response, 200) show_json = show_response.json() self._assert_has_keys(show_json, "slug", "title", "id") - self.assertEqual(show_json["slug"], "pagetoshow") - self.assertEqual(show_json["title"], "MY PAGE") - self.assertEqual(show_json["content"], "

Page!

") - self.assertEqual(show_json["content_format"], "html") + assert show_json["slug"] == "pagetoshow" + assert show_json["title"] == "MY PAGE" + assert show_json["content"] == "

Page!

" + assert show_json["content_format"] == "html" def test_403_on_unowner_show(self): response_json = self._create_valid_page_as("others_page_show@bx.psu.edu", "otherspageshow") diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py index fc8a9d4a66a..ba30ccb4fcc 100644 --- a/lib/galaxy_test/api/test_tools.py +++ b/lib/galaxy_test/api/test_tools.py @@ -347,8 +347,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): put_response.raise_for_status() response = get(user_info_url).json() - self.assertEqual(len(response["addresses"]), 1) - self.assertEqual(response["addresses"][0]["desc"], cool_name_with_quote) + assert len(response["addresses"]) == 1 + assert response["addresses"][0]["desc"] == cool_name_with_quote hda1 = self.dataset_populator.new_dataset(history_id, content="1\t2\t3", name=cool_name_with_quote) assert hda1["name"] == cool_name_with_quote @@ -549,7 +549,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) response = self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True) outputs = response["outputs"] - self.assertEqual(len(outputs), 2) + assert len(outputs) == 2 output_forward = outputs[0] output_reverse = outputs[1] output_forward_content = self.dataset_populator.get_history_dataset_content( @@ -605,7 +605,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): } response = self._run("__UNZIP_COLLECTION__", history_id, inputs, assert_ok=True) implicit_collections = response["implicit_collections"] - self.assertEqual(len(implicit_collections), 2) + assert len(implicit_collections) == 2 unzipped_hdca = self.dataset_populator.get_history_collection_details( history_id, hid=implicit_collections[0]["hid"] ) @@ -622,7 +622,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) response = self._run("__ZIP_COLLECTION__", history_id, inputs, assert_ok=True) output_collections = response["output_collections"] - self.assertEqual(len(output_collections), 1) + assert len(output_collections) == 1 self.dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True) zipped_hdca = self.dataset_populator.get_history_collection_details( history_id, hid=output_collections[0]["hid"] @@ -678,7 +678,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) response = self._run("__ZIP_COLLECTION__", history_id, inputs, assert_ok=True) implicit_collections = response["implicit_collections"] - self.assertEqual(len(implicit_collections), 1) + assert len(implicit_collections) == 1 self.dataset_populator.wait_for_job(response["jobs"][0]["id"], assert_ok=True) zipped_hdca = self.dataset_populator.get_history_collection_details( history_id, hid=implicit_collections[0]["hid"] @@ -694,7 +694,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): response = self.dataset_populator.run_exit_code_from_file(history_id, ok_hdca_id) mixed_implicit_collections = response["implicit_collections"] - self.assertEqual(len(mixed_implicit_collections), 1) + assert len(mixed_implicit_collections) == 1 mixed_hdca_hid = mixed_implicit_collections[0]["hid"] mixed_hdca = self.dataset_populator.get_history_collection_details( history_id, hid=mixed_hdca_hid, wait=False @@ -725,7 +725,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): response = self.dataset_populator.run_exit_code_from_file(history_id, ok_hdca_id) mixed_implicit_collections = response["implicit_collections"] - self.assertEqual(len(mixed_implicit_collections), 1) + assert len(mixed_implicit_collections) == 1 mixed_hdca_hid = mixed_implicit_collections[0]["hid"] mixed_hdca = self.dataset_populator.get_history_collection_details( history_id, hid=mixed_hdca_hid, wait=False @@ -774,7 +774,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): filter_output_collections = response["output_collections"] if batch: return response["implicit_collections"][0] - self.assertEqual(len(filter_output_collections), 1) + assert len(filter_output_collections) == 1 filtered_hid = filter_output_collections[0]["hid"] filtered_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=filtered_hid, wait=False) return filtered_hdca @@ -787,7 +787,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id) response = self._run("__APPLY_RULES__", history_id, inputs, assert_ok=True) output_collections = response["output_collections"] - self.assertEqual(len(output_collections), 1) + assert len(output_collections) == 1 output_hid = output_collections[0]["hid"] output_hdca = self.dataset_populator.get_history_collection_details(history_id, hid=output_hid, wait=False) example["check"](output_hdca, self.dataset_populator) @@ -874,10 +874,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): input1=dataset_to_param(new_dataset), ) outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "Cat1Test") + assert output1_content.strip() == "Cat1Test" @skip_without_tool("cat1") @uses_test_history(require_new=True) @@ -909,10 +909,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): input1=[dataset_to_param(new_dataset)], ) outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "Cat1Testlistified") + assert output1_content.strip() == "Cat1Testlistified" @skip_without_tool("multiple_versions") @uses_test_history(require_new=False) @@ -922,10 +922,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = self._run_and_get_outputs( tool_id="multiple_versions", history_id=history_id, tool_version=version ) - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), f"Version {version}") + assert output1_content.strip() == f"Version {version}" @skip_without_tool("multiple_versions") @uses_test_history(require_new=False) @@ -958,10 +958,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): input1={"batch": False, "values": [dataset_to_param(new_dataset)]}, ) outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "123") + assert output1_content.strip() == "123" @skip_without_tool("cat1") @uses_test_history(require_new=False) @@ -986,7 +986,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): assert_inputs(inputs, can_be_used=False) outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output1 = outputs[0] inputs_2 = dict( @@ -1175,7 +1175,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_has_keys(output_collection, "id", "name", "elements", "populated") assert not output_collection["populated"] assert len(output_collection["elements"]) == 0 - self.assertEqual(output_collection["name"], "Table split on first column") + assert output_collection["name"] == "Table split on first column" self.dataset_populator.wait_for_job(create["jobs"][0]["id"], assert_ok=True) get_collection_response = self._get( @@ -1186,7 +1186,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): output_collection = get_collection_response.json() self._assert_has_keys(output_collection, "id", "name", "elements", "populated") assert output_collection["populated"] - self.assertEqual(output_collection["name"], "Table split on first column") + assert output_collection["name"] == "Table split on first column" assert len(output_collection["elements"]) == 2 output_element_0 = output_collection["elements"][0] @@ -1228,7 +1228,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) output_content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(output_content, "Hello World\n") + assert output_content == "Hello World\n" def test_dynamic_tool_from_path(self): # Create tool. @@ -1244,7 +1244,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) output_content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(output_content, "Hello World 2\n") + assert output_content == "Hello World 2\n" def test_dynamic_tool_no_id(self): # Create tool. @@ -1257,7 +1257,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) output_content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(output_content, "Hello World 2\n") + assert output_content == "Hello World 2\n" def test_show_dynamic_tools(self): # Create tool. @@ -1316,10 +1316,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): new_dataset2 = self.dataset_populator.new_dataset(history_id, content="Cat2Test") inputs = {"input1": dataset_to_param(new_dataset1), "queries_0|input2": dataset_to_param(new_dataset2)} outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "Cat1Test\nCat2Test") + assert output1_content.strip() == "Cat1Test\nCat2Test" @skip_without_tool("mapper_two") @uses_test_history(require_new=False) @@ -1375,13 +1375,13 @@ class ToolsTestCase(ApiTestCase, TestsTools): def _check_cat1_multirun(self, history_id, inputs): outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 2) + assert len(outputs) == 2 output1 = outputs[0] output2 = outputs[1] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) - self.assertEqual(output1_content.strip(), "123") - self.assertEqual(output2_content.strip(), "456") + assert output1_content.strip() == "123" + assert output2_content.strip() == "456" @skip_without_tool("random_lines1") @uses_test_history(require_new=False) @@ -1422,7 +1422,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): "queries_0|input2": {"batch": True, "values": second_two}, } outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 2) + assert len(outputs) == 2 outputs_contents = [ self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs ] @@ -1440,7 +1440,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs_contents = [ self.dataset_populator.get_history_dataset_content(history_id, dataset=o).strip() for o in outputs ] - self.assertEqual(len(outputs), 4) + assert len(outputs) == 4 assert "123\n789" in outputs_contents assert "456\n0ab" in outputs_contents assert "123\n0ab" in outputs_contents @@ -1533,19 +1533,19 @@ class ToolsTestCase(ApiTestCase, TestsTools): implicit_collections = create["implicit_collections"] collections = create["output_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(implicit_collections), 0) - self.assertEqual(len(collections), 1) + assert len(jobs) == 1 + assert len(implicit_collections) == 0 + assert len(collections) == 1 output_collection = collections[0] return output_collection def _assert_elements_are(self, collection, *args): elements = collection["elements"] - self.assertEqual(len(elements), len(args)) + assert len(elements) == len(args) for index, element in enumerate(elements): arg = args[index] - self.assertEqual(arg, element["element_identifier"]) + assert arg == element["element_identifier"] return elements def _verify_element(self, history_id, element, **props): @@ -1555,14 +1555,14 @@ class ToolsTestCase(ApiTestCase, TestsTools): expected_contents = props["contents"] contents = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=object_id) - self.assertEqual(contents, expected_contents) + assert contents == expected_contents del props["contents"] if props: details = self.dataset_populator.get_history_dataset_details(history_id, dataset_id=object_id) for key, value in props.items(): - self.assertEqual(details[key], value) + assert details[key] == value def _setup_repeat_multirun(self): history_id = self.dataset_populator.new_history() @@ -1577,13 +1577,13 @@ class ToolsTestCase(ApiTestCase, TestsTools): def _check_repeat_multirun(self, history_id, inputs): outputs = self._cat1_outputs(history_id, inputs=inputs) - self.assertEqual(len(outputs), 2) + assert len(outputs) == 2 output1 = outputs[0] output2 = outputs[1] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) - self.assertEqual(output1_content.strip(), "Common\n123") - self.assertEqual(output2_content.strip(), "Common\n456") + assert output1_content.strip() == "Common\n123" + assert output2_content.strip() == "Common\n456" def _setup_two_multiruns(self): history_id = self.dataset_populator.new_history() @@ -1619,9 +1619,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 0) - self.assertEqual(len(outputs), 0) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 0 + assert len(outputs) == 0 + assert len(implicit_collections) == 1 empty_output = implicit_collections[0] assert empty_output["name"] == "Concatenate datasets on collection 1", empty_output @@ -1639,9 +1639,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(outputs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(outputs) == 2 + assert len(implicit_collections) == 1 output1 = outputs[0] output2 = outputs[1] output1_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output1) @@ -1658,9 +1658,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(outputs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(outputs) == 2 + assert len(implicit_collections) == 1 for output in outputs: assert output["file_ext"] == "txt", output @@ -1678,8 +1678,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("output_filter_with_input", history_id, inputs).json() jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 3) - self.assertEqual(len(implicit_collections), 3) + assert len(jobs) == 3 + assert len(implicit_collections) == 3 self._check_implicit_collection_populated(create) @skip_without_tool("output_filter_with_input_optional") @@ -1694,9 +1694,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("output_filter_with_input_optional", history_id, inputs).json() jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) + assert len(jobs) == 1 self.dataset_populator.wait_for_job(jobs[0]["id"], assert_ok=True) - self.assertEqual(len(implicit_collections), 1) + assert len(implicit_collections) == 1 self._check_implicit_collection_populated(create) @skip_without_tool("output_filter_with_input") @@ -1713,8 +1713,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("output_filter_with_input", history_id, inputs).json() jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 3) - self.assertEqual(len(implicit_collections), 2) + assert len(jobs) == 3 + assert len(implicit_collections) == 2 self._check_implicit_collection_populated(create) @skip_without_tool("Cut1") @@ -1730,9 +1730,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(outputs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(outputs) == 2 + assert len(implicit_collections) == 1 output1 = outputs[0] output2 = outputs[1] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) @@ -1749,14 +1749,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): inputs = {"input": {"batch": True, "values": [{"src": "hdca", "id": hdca_id}]}} create = self._run("collection_creates_dynamic_list_of_pairs", history_id, inputs).json() implicit_collections = create["implicit_collections"] - self.assertEqual(len(implicit_collections), 1) - self.assertEqual(implicit_collections[0]["collection_type"], "list:list:paired") - self.assertEqual(implicit_collections[0]["elements"][0]["object"]["element_count"], None) + assert len(implicit_collections) == 1 + assert implicit_collections[0]["collection_type"] == "list:list:paired" + assert implicit_collections[0]["elements"][0]["object"]["element_count"] is None self.dataset_populator.wait_for_job(create["jobs"][0]["id"], assert_ok=True) hdca = self._get(f"histories/{history_id}/contents/dataset_collections/{implicit_collections[0]['id']}").json() - self.assertEqual( - hdca["elements"][0]["object"]["elements"][0]["object"]["elements"][0]["element_identifier"], "forward" - ) + assert hdca["elements"][0]["object"]["elements"][0]["object"]["elements"][0]["element_identifier"] == "forward" def _bed_list(self, history_id): bed1_contents = open(self.get_filename("1.bed")).read() @@ -1778,15 +1776,15 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(outputs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(outputs) == 2 + assert len(implicit_collections) == 1 output1 = outputs[0] output2 = outputs[1] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) - self.assertEqual(output1_content.strip(), "forward") - self.assertEqual(output2_content.strip(), "reverse") + assert output1_content.strip() == "forward" + assert output2_content.strip() == "reverse" @skip_without_tool("identifier_single") @uses_test_history(require_new=False) @@ -1801,12 +1799,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "Plain HDA") + assert output1_content.strip() == "Plain HDA" @skip_without_tool("identifier_multiple") @uses_test_history(require_new=False) @@ -1828,12 +1826,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward\nreverse") + assert output1_content.strip() == "forward\nreverse" @skip_without_tool("identifier_in_conditional") @uses_test_history(require_new=False) @@ -1848,12 +1846,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward\nreverse") + assert output1_content.strip() == "forward\nreverse" @skip_without_tool("identifier_in_conditional") @uses_test_history(require_new=False) @@ -1871,12 +1869,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward\nreverse") + assert output1_content.strip() == "forward\nreverse" @skip_without_tool("identifier_multiple_in_repeat") @uses_test_history(require_new=False) @@ -1891,12 +1889,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward\nreverse") + assert output1_content.strip() == "forward\nreverse" @skip_without_tool("identifier_in_conditional") @uses_test_history(require_new=False) @@ -1913,15 +1911,15 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(outputs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(outputs) == 2 + assert len(implicit_collections) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward") + assert output1_content.strip() == "forward" output2 = outputs[1] output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) - self.assertEqual(output2_content.strip(), "reverse") + assert output2_content.strip() == "reverse" @skip_without_tool("identifier_multiple_in_conditional") @uses_test_history(require_new=False) @@ -1936,12 +1934,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward\nreverse") + assert output1_content.strip() == "forward\nreverse" @skip_without_tool("identifier_multiple_in_repeat") @uses_test_history(require_new=False) @@ -1956,12 +1954,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "forward\nreverse") + assert output1_content.strip() == "forward\nreverse" @skip_without_tool("identifier_single_in_repeat") @uses_test_history(require_new=False) @@ -1973,8 +1971,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = create_response.json() jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(implicit_collections) == 1 output_collection = implicit_collections[0] elements = output_collection["elements"] assert len(elements) == 2 @@ -1995,12 +1993,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "Normal HDA1") + assert output1_content.strip() == "Normal HDA1" @skip_without_tool("identifier_multiple") @uses_test_history(require_new=False) @@ -2014,12 +2012,12 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) - self.assertEqual(len(implicit_collections), 0) + assert len(jobs) == 1 + assert len(outputs) == 1 + assert len(implicit_collections) == 0 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "Normal HDA1\nNormal HDA2") + assert output1_content.strip() == "Normal HDA1\nNormal HDA2" @skip_without_tool("identifier_collection") @uses_test_history(require_new=False) @@ -2046,11 +2044,11 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = create_response.json() outputs = create["outputs"] jobs = create["jobs"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) + assert len(jobs) == 1 + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) - self.assertEqual(output1_content.strip(), "\n".join(d["name"] for d in element_identifiers)) + assert output1_content.strip() == "\n".join(d["name"] for d in element_identifiers) @skip_without_tool("identifier_in_actions") @uses_test_history(require_new=False) @@ -2101,8 +2099,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("collection_paired_structured_like", history_id, inputs, assert_ok=True) jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(implicit_collections) == 1 implicit_collection = implicit_collections[0] assert implicit_collection["collection_type"] == "list:paired", implicit_collection["collection_type"] outer_elements = implicit_collection["elements"] @@ -2120,8 +2118,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("collection_paired_conditional_structured_like", history_id, inputs, assert_ok=True) jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(implicit_collections) == 1 implicit_collection = implicit_collections[0] assert implicit_collection["collection_type"] == "list:paired", implicit_collection["collection_type"] outer_elements = implicit_collection["elements"] @@ -2132,9 +2130,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): outputs = create["outputs"] jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 4) - self.assertEqual(len(outputs), 4) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 4 + assert len(outputs) == 4 + assert len(implicit_collections) == 1 implicit_collection = implicit_collections[0] self._assert_has_keys(implicit_collection, "collection_type", "elements") assert implicit_collection["collection_type"] == "list:paired" @@ -2147,7 +2145,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): assert first_object["collection_type"] == "paired" assert len(first_object["elements"]) == 2 first_object_forward_element = first_object["elements"][0] - self.assertEqual(outputs[0]["id"], first_object_forward_element["object"]["id"]) + assert outputs[0]["id"] == first_object_forward_element["object"]["id"] @skip_without_tool("cat1") @uses_test_history(require_new=False) @@ -2165,17 +2163,17 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_status_code_is(response, 200) response_object = response.json() outputs = response_object["outputs"] - self.assertEqual(len(outputs), 2) + assert len(outputs) == 2 output1 = outputs[0] output2 = outputs[1] self.dataset_populator.wait_for_history(history_id) output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) - self.assertEqual(output1_content.strip(), "123\n789") - self.assertEqual(output2_content.strip(), "456\n0ab") + assert output1_content.strip() == "123\n789" + assert output2_content.strip() == "456\n0ab" - self.assertEqual(len(response_object["jobs"]), 2) - self.assertEqual(len(response_object["implicit_collections"]), 1) + assert len(response_object["jobs"]) == 2 + assert len(response_object["implicit_collections"]) == 1 @skip_without_tool("cat1") @uses_test_history(require_new=False) @@ -2190,13 +2188,13 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_status_code_is(response, 200) response_object = response.json() outputs = response_object["outputs"] - self.assertEqual(len(outputs), 4) + assert len(outputs) == 4 - self.assertEqual(len(response_object["jobs"]), 4) + assert len(response_object["jobs"]) == 4 implicit_collections = response_object["implicit_collections"] - self.assertEqual(len(implicit_collections), 1) + assert len(implicit_collections) == 1 implicit_collection = implicit_collections[0] - self.assertEqual(implicit_collection["collection_type"], "paired:paired") + assert implicit_collection["collection_type"] == "paired:paired" outer_elements = implicit_collection["elements"] assert len(outer_elements) == 2 @@ -2227,7 +2225,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): for (element, expected_contents) in expected_contents_list: dataset_id = element["object"]["id"] contents = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=dataset_id) - self.assertEqual(expected_contents, contents) + assert expected_contents == contents @skip_without_tool("cat1") @uses_test_history(require_new=False) @@ -2247,10 +2245,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_status_code_is(response, 200) response_object = response.json() outputs = response_object["outputs"] - self.assertEqual(len(outputs), 2) + assert len(outputs) == 2 - self.assertEqual(len(response_object["jobs"]), 2) - self.assertEqual(len(response_object["implicit_collections"]), 1) + assert len(response_object["jobs"]) == 2 + assert len(response_object["implicit_collections"]) == 1 @skip_without_tool("identifier_source") def test_default_identifier_source_map_over(self): @@ -2287,8 +2285,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("collection_creates_pair", history_id, inputs, assert_ok=True) jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) - self.assertEqual(len(implicit_collections), 1) + assert len(jobs) == 2 + assert len(implicit_collections) == 1 implicit_collection = implicit_collections[0] assert implicit_collection["collection_type"] == "list:paired", implicit_collection outer_elements = implicit_collection["elements"] @@ -2319,7 +2317,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): ] for i in range(4): contents = self.dataset_populator.get_history_dataset_content(history_id, dataset_id=pair_ids[i]) - self.assertEqual(expected_contents[i], contents) + assert expected_contents[i] == contents @skip_without_tool("cat1") def test_cannot_map_over_incompatible_collections(self): @@ -2436,8 +2434,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("multi_data_param", history_id, inputs, assert_ok=True) jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(implicit_collections), 2) + assert len(jobs) == 1 + assert len(implicit_collections) == 2 output_hdca = self.dataset_populator.get_history_collection_details( history_id, hid=implicit_collections[0]["hid"] ) @@ -2482,7 +2480,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): } create = self._run("column_multi_param", history_id, inputs, assert_ok=True) jobs = create["jobs"] - self.assertEqual(len(jobs), 1) + assert len(jobs) == 1 content = self.dataset_populator.get_history_dataset_content(history_id, hid=3) assert content.strip() == "hg17", content @@ -2496,8 +2494,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("multi_data_repeat", history_id, inputs, assert_ok=True) outputs = create["outputs"] jobs = create["jobs"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) + assert len(jobs) == 1 + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) assert output1_content.strip() == "123\n456", output1_content @@ -2512,8 +2510,8 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("multi_data_repeat", history_id, inputs, assert_ok=True) outputs = create["outputs"] jobs = create["jobs"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 1) + assert len(jobs) == 1 + assert len(outputs) == 1 output1 = outputs[0] output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) assert output1_content.strip() == "123\n456", output1_content @@ -2532,20 +2530,20 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("multi_data_param", history_id, inputs, assert_ok=True) outputs = create["outputs"] jobs = create["jobs"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 2) + assert len(jobs) == 1 + assert len(outputs) == 2 output1, output2 = outputs output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) - self.assertEqual(output1_content.strip(), "123\n456\nTestData123\nTestData123\nTestData123") - self.assertEqual(output2_content.strip(), "123\n456") + assert output1_content.strip() == "123\n456\nTestData123\nTestData123\nTestData123" + assert output2_content.strip() == "123\n456" def _check_simple_reduce_job(self, history_id, inputs): create = self._run("multi_data_param", history_id, inputs, assert_ok=True) outputs = create["outputs"] jobs = create["jobs"] - self.assertEqual(len(jobs), 1) - self.assertEqual(len(outputs), 2) + assert len(jobs) == 1 + assert len(outputs) == 2 output1, output2 = outputs output1_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output1) output2_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output2) @@ -2654,10 +2652,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) response = self._run("collection_cat_group_tag", history_id, inputs, assert_ok=True) outputs = response["outputs"] - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output = outputs[0] output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output) - self.assertEqual(output_content.strip(), "123\n456") + assert output_content.strip() == "123\n456" @skip_without_tool("collection_cat_group_tag_multiple") @uses_test_history(require_new=False) @@ -2670,10 +2668,10 @@ class ToolsTestCase(ApiTestCase, TestsTools): self.dataset_populator.wait_for_history(history_id, assert_ok=True) response = self._run("collection_cat_group_tag_multiple", history_id, inputs, assert_ok=True) outputs = response["outputs"] - self.assertEqual(len(outputs), 1) + assert len(outputs) == 1 output = outputs[0] output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output) - self.assertEqual(output_content.strip(), "123\n456\n456\n0ab") + assert output_content.strip() == "123\n456\n456\n0ab" @skip_without_tool("expression_forty_two") def test_galaxy_expression_tool_simplest(self): @@ -2682,7 +2680,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_status_code_is(run_response, 200) self.dataset_populator.wait_for_history(history_id, assert_ok=True) output_content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(output_content, "42") + assert output_content == "42" @skip_without_tool("expression_parse_int") def test_galaxy_expression_tool_simple(self): @@ -2694,7 +2692,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_status_code_is(run_response, 200) self.dataset_populator.wait_for_history(history_id, assert_ok=True) output_content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(output_content, "7") + assert output_content == "7" @skip_without_tool("expression_log_line_count") def test_galaxy_expression_metadata(self): @@ -2709,7 +2707,7 @@ class ToolsTestCase(ApiTestCase, TestsTools): self._assert_status_code_is(run_response, 200) self.dataset_populator.wait_for_history(history_id, assert_ok=True) output_content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(output_content, "3") + assert output_content == "3" @skip_without_tool("cat1") @uses_test_history(require_new=False) @@ -2981,9 +2979,9 @@ class ToolsTestCase(ApiTestCase, TestsTools): create = self._run("collection_paired_structured_like", history_id, inputs, assert_ok=True) jobs = create["jobs"] implicit_collections = create["implicit_collections"] - self.assertEqual(len(jobs), 2) + assert len(jobs) == 2 self.dataset_populator.wait_for_jobs(jobs, assert_ok=True) - self.assertEqual(len(implicit_collections), 1) + assert len(implicit_collections) == 1 implicit_collection = implicit_collections[0] assert implicit_collection["collection_type"] == "list:paired", implicit_collection["collection_type"] outer_elements = implicit_collection["elements"] diff --git a/lib/galaxy_test/api/test_tools_upload.py b/lib/galaxy_test/api/test_tools_upload.py index 80504673221..e56424425c1 100644 --- a/lib/galaxy_test/api/test_tools_upload.py +++ b/lib/galaxy_test/api/test_tools_upload.py @@ -51,22 +51,22 @@ class ToolsUploadTestCase(ApiTestCase): def test_upload_posix_newline_fixes_by_default(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content) - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS) + assert result_content == ONE_TO_SIX_WITH_TABS def test_fetch_posix_unaltered(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, api="fetch") - self.assertEqual(result_content, ONE_TO_SIX_ON_WINDOWS) + assert result_content == ONE_TO_SIX_ON_WINDOWS def test_upload_disable_posix_fix(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, to_posix_lines=None) - self.assertEqual(result_content, windows_content) + assert result_content == windows_content def test_fetch_post_lines_option(self): windows_content = ONE_TO_SIX_ON_WINDOWS result_content = self._upload_and_get_content(windows_content, api="fetch", to_posix_lines=True) - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS) + assert result_content == ONE_TO_SIX_WITH_TABS # Test how trailing new lines are added # - upload1 adds by default because to_posix_lines is on by default @@ -75,47 +75,47 @@ class ToolsUploadTestCase(ApiTestCase): def test_post_lines_trailing(self): input_content = ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE result_content = self._upload_and_get_content(input_content) - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS) + assert result_content == ONE_TO_SIX_WITH_TABS def test_post_lines_trailing_off(self): input_content = ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE result_content = self._upload_and_get_content(input_content, to_posix_lines=False) - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE) + assert result_content == ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE def test_fetch_post_lines_trailing_off_by_default(self): input_content = ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE result_content = self._upload_and_get_content(input_content, api="fetch") - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE) + assert result_content == ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE def test_fetch_post_lines_trailing_if_to_posix(self): input_content = ONE_TO_SIX_WITH_TABS_NO_TRAILING_NEWLINE result_content = self._upload_and_get_content(input_content, api="fetch", to_posix_lines=True) - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS) + assert result_content == ONE_TO_SIX_WITH_TABS def test_upload_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table) - self.assertEqual(result_content, table) + assert result_content == table def test_fetch_tab_to_space_off_by_default(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, api="fetch") - self.assertEqual(result_content, table) + assert result_content == table def test_upload_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, space_to_tab="Yes") - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS) + assert result_content == ONE_TO_SIX_WITH_TABS def test_fetch_tab_to_space(self): table = ONE_TO_SIX_WITH_SPACES result_content = self._upload_and_get_content(table, api="fetch", space_to_tab=True) - self.assertEqual(result_content, ONE_TO_SIX_WITH_TABS) + assert result_content == ONE_TO_SIX_WITH_TABS def test_fetch_tab_to_space_doesnt_swap_newlines(self): table = ONE_TO_SIX_WITH_SPACES_ON_WINDOWS result_content = self._upload_and_get_content(table, api="fetch", space_to_tab=True) - self.assertEqual(result_content, ONE_TO_SIX_ON_WINDOWS) + assert result_content == ONE_TO_SIX_ON_WINDOWS def test_fetch_compressed_with_explicit_type(self): fastqgz_path = TestDataResolver().get_filename("1.fastqsanger.gz") @@ -191,42 +191,42 @@ class ToolsUploadTestCase(ApiTestCase): rdata_path = TestDataResolver().get_filename("1.RData") with open(rdata_path, "rb") as fh: rdata_metadata = self._upload_and_get_details(fh, file_type="auto") - self.assertEqual(rdata_metadata["file_ext"], "rdata") + assert rdata_metadata["file_ext"] == "rdata" @skip_without_datatype("csv") def test_csv_upload(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, file_type="csv") - self.assertEqual(csv_metadata["file_ext"], "csv") + assert csv_metadata["file_ext"] == "csv" @skip_without_datatype("csv") def test_csv_upload_auto(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, file_type="auto") - self.assertEqual(csv_metadata["file_ext"], "csv") + assert csv_metadata["file_ext"] == "csv" @skip_without_datatype("csv") def test_csv_fetch(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, api="fetch", ext="csv", to_posix_lines=True) - self.assertEqual(csv_metadata["file_ext"], "csv") + assert csv_metadata["file_ext"] == "csv" @skip_without_datatype("csv") def test_csv_sniff_fetch(self): csv_path = TestDataResolver().get_filename("1.csv") with open(csv_path, "rb") as fh: csv_metadata = self._upload_and_get_details(fh, api="fetch", ext="auto", to_posix_lines=True) - self.assertEqual(csv_metadata["file_ext"], "csv") + assert csv_metadata["file_ext"] == "csv" @skip_without_datatype("tiff") def test_image_upload_auto(self): tiff_path = TestDataResolver().get_filename("1.tiff") with open(tiff_path, "rb") as fh: tiff_metadata = self._upload_and_get_details(fh, file_type="auto") - self.assertEqual(tiff_metadata["file_ext"], "tiff") + assert tiff_metadata["file_ext"] == "tiff" @uses_test_history(require_new=False) def test_newlines_stage_fetch(self, history_id): @@ -241,7 +241,7 @@ class ToolsUploadTestCase(ApiTestCase): dataset = datasets[0][0] content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset) # By default this appends the newline. - self.assertEqual(content, "This is a line of text.\n") + assert content == "This is a line of text.\n" @uses_test_history(require_new=False) def test_stage_object(self, history_id): @@ -251,7 +251,7 @@ class ToolsUploadTestCase(ApiTestCase): ) dataset = datasets[0][0] content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset) - self.assertEqual(content.strip(), '"randomstr"') + assert content.strip() == '"randomstr"' @uses_test_history(require_new=False) def test_stage_object_fetch(self, history_id): @@ -259,7 +259,7 @@ class ToolsUploadTestCase(ApiTestCase): inputs, datasets = stage_inputs(self.galaxy_interactor, history_id, job, use_path_paste=False) dataset = datasets[0][0] content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset) - self.assertEqual(content, '"randomstr"') + assert content == '"randomstr"' @uses_test_history(require_new=False) def test_newlines_stage_fetch_configured(self, history_id): @@ -277,7 +277,7 @@ class ToolsUploadTestCase(ApiTestCase): dataset = datasets[0][0] content = self.dataset_populator.get_history_dataset_content(history_id=history_id, dataset=dataset) # By default this appends the newline, but we disabled with 'to_posix_lines=False' above. - self.assertEqual(content, "This is a line of text.") + assert content == "This is a line of text." details = self.dataset_populator.get_history_dataset_details(history_id=history_id, dataset=dataset) assert details["genome_build"] == "hg19" diff --git a/lib/galaxy_test/api/test_users.py b/lib/galaxy_test/api/test_users.py index a1a986b61b6..ba890723692 100644 --- a/lib/galaxy_test/api/test_users.py +++ b/lib/galaxy_test/api/test_users.py @@ -52,7 +52,7 @@ class UsersApiTestCase(ApiTestCase): update_response = self.__update(user, username=new_name) self._assert_status_code_is(update_response, 200) update_json = update_response.json() - self.assertEqual(update_json["username"], new_name) + assert update_json["username"] == new_name # too short update_response = self.__update(user, username="") @@ -75,7 +75,7 @@ class UsersApiTestCase(ApiTestCase): update_response = put(update_url, data=json.dumps(dict(username=new_name))) self._assert_status_code_is(update_response, 200) update_json = update_response.json() - self.assertEqual(update_json["username"], new_name) + assert update_json["username"] == new_name def test_delete_user(self): user = self._setup_user(TEST_USER_EMAIL_DELETE) @@ -111,27 +111,27 @@ class UsersApiTestCase(ApiTestCase): user = self._setup_user(TEST_USER_EMAIL) url = self.__url("information/inputs", user) response = get(url).json() - self.assertEqual(response["username"], user["username"]) - self.assertEqual(response["email"], TEST_USER_EMAIL) + assert response["username"] == user["username"] + assert response["email"] == TEST_USER_EMAIL put(url, data=json.dumps(dict(username="newname", email="new@email.email"))) response = get(url).json() - self.assertEqual(response["username"], "newname") - self.assertEqual(response["email"], "new@email.email") + assert response["username"] == "newname" + assert response["email"] == "new@email.email" put(url, data=json.dumps(dict(username=user["username"], email=TEST_USER_EMAIL))) response = get(url).json() - self.assertEqual(response["username"], user["username"]) - self.assertEqual(response["email"], TEST_USER_EMAIL) + assert response["username"] == user["username"] + assert response["email"] == TEST_USER_EMAIL put(url, data=json.dumps({"address_0|desc": "_desc"})) response = get(url).json() - self.assertEqual(len(response["addresses"]), 1) - self.assertEqual(response["addresses"][0]["desc"], "_desc") + assert len(response["addresses"]) == 1 + assert response["addresses"][0]["desc"] == "_desc" def test_create_api_key(self): user = self._setup_user(TEST_USER_EMAIL) user_id = user["id"] response = self._put(f"users/{user_id}/api_key/inputs", admin=True) self._assert_status_code_is_ok(response) - self.assertEqual(response.json()["inputs"][0]["name"], "api-key") + assert response.json()["inputs"][0]["name"] == "api-key" @skip_without_tool("cat1") def test_favorites(self): @@ -140,7 +140,7 @@ class UsersApiTestCase(ApiTestCase): url = self._api_url(f"users/{user['id']}/favorites/tools", params=dict(key=self.master_api_key)) put_response = put(url, data=json.dumps({"object_id": "cat1"})) self._assert_status_code_is_ok(put_response) - self.assertEqual(put_response.json()["tools"][0], "cat1") + assert put_response.json()["tools"][0] == "cat1" # not implemented for workflows yet url = self._api_url(f"users/{user['id']}/favorites/workflows", params=dict(key=self.master_api_key)) put_response = put(url, data=json.dumps({"object_id": "14ds68f4sda68gf46dsag4"})) @@ -149,7 +149,7 @@ class UsersApiTestCase(ApiTestCase): url = self._api_url(f"users/{user['id']}/favorites/tools/cat1", params=dict(key=self.master_api_key)) delete_response = delete(url) self._assert_status_code_is_ok(delete_response) - self.assertEqual(delete_response.json()["tools"], []) + assert delete_response.json()["tools"] == [] # delete non-existing tool favorite url = self._api_url( f"users/{user['id']}/favorites/tools/madeuptoolthatdoes/not/exist/in/favs", diff --git a/lib/galaxy_test/api/test_workflow_extraction.py b/lib/galaxy_test/api/test_workflow_extraction.py index 4cb86862edb..67ef9bdaf60 100644 --- a/lib/galaxy_test/api/test_workflow_extraction.py +++ b/lib/galaxy_test/api/test_workflow_extraction.py @@ -32,7 +32,7 @@ class WorkflowExtractionApiTestCase(BaseWorkflowsApiTestCase): dataset_ids=input_hids, job_ids=[cat1_job_id], ) - self.assertEqual(downloaded_workflow["name"], "test import from history") + assert downloaded_workflow["name"] == "test import from history" self.__assert_looks_like_cat1_example_workflow(downloaded_workflow) @summarize_instance_history_on_error @@ -222,7 +222,7 @@ test_data: collection_step = self._get_steps_of_type(downloaded_workflow, "data_collection_input", expected_len=1)[0] collection_step_state = loads(collection_step["tool_state"]) - self.assertEqual(collection_step_state["collection_type"], "paired") + assert collection_step_state["collection_type"] == "paired" @skip_without_tool("cat_collection") def test_subcollection_mapping(self): @@ -264,7 +264,7 @@ test_data: collection_step = self._get_steps_of_type(downloaded_workflow, "data_collection_input", expected_len=1)[0] collection_step_state = loads(collection_step["tool_state"]) - self.assertEqual(collection_step_state["collection_type"], "list:paired") + assert collection_step_state["collection_type"] == "list:paired" @skip_without_tool("cat_list") @skip_without_tool("collection_creates_dynamic_nested") @@ -450,8 +450,8 @@ test_data: input1 = tool_step["input_connections"]["input1"] input2 = tool_step["input_connections"]["queries_0|input2"] - self.assertEqual(input_steps[0]["id"], input1["id"]) - self.assertEqual(input_steps[1]["id"], input2["id"]) + assert input_steps[0]["id"] == input1["id"] + assert input_steps[1]["id"] == input2["id"] def _history_contents(self, history_id=None): if history_id is None: @@ -484,7 +484,7 @@ test_data: collection_steps = self._get_steps_of_type(downloaded_workflow, "data_collection_input", expected_len=1) collection_step = collection_steps[0] collection_step_state = loads(collection_step["tool_state"]) - self.assertEqual(collection_step_state["collection_type"], "paired") + assert collection_step_state["collection_type"] == "paired" collect_step_idx = collection_step["id"] return collect_step_idx diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py index 92045bcad69..376fc1b8f9e 100644 --- a/lib/galaxy_test/api/test_workflows.py +++ b/lib/galaxy_test/api/test_workflows.py @@ -223,7 +223,7 @@ class BaseWorkflowsApiTestCase(ApiTestCase, RunsWorkflowFixtures): def _assert_history_job_count(self, history_id, n): jobs = self._history_jobs(history_id) - self.assertEqual(len(jobs), n) + assert len(jobs) == n def _download_workflow(self, workflow_id, style=None, history_id=None): return self.workflow_populator.download_workflow(workflow_id, style=style, history_id=history_id) @@ -314,7 +314,7 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase): workflow = show_response.json() self._assert_looks_like_instance_workflow_representation(workflow) assert len(workflow["steps"]) == 3 - self.assertEqual(sorted(step["id"] for step in workflow["steps"].values()), [0, 1, 2]) + assert sorted(step["id"] for step in workflow["steps"].values()) == [0, 1, 2] show_response = self._get(f"workflows/{workflow_id}", {"legacy": True}) workflow = show_response.json() @@ -322,7 +322,7 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase): assert len(workflow["steps"]) == 3 # Can't reay say what the legacy IDs are but must be greater than 3 because dummy # workflow was created first in this instance. - self.assertNotEqual(sorted(step["id"] for step in workflow["steps"].values()), [0, 1, 2]) + assert sorted(step["id"] for step in workflow["steps"].values()) != [0, 1, 2] def test_show_invalid_key_is_400(self): show_response = self._get(f"workflows/{self._random_key()}") @@ -768,8 +768,8 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase): assert order_index in uuids assert order_index in labels - self.assertEqual(uuids[order_index], step_dict["uuid"]) - self.assertEqual(labels[order_index], step_dict["label"]) + assert uuids[order_index] == step_dict["uuid"] + assert labels[order_index] == step_dict["label"] upload_response = self.__test_upload(workflow=original_workflow) workflow_id = upload_response.json()["id"] @@ -1347,7 +1347,7 @@ steps: def test_workflow_run_output_collections(self) -> None: with self.dataset_populator.test_history() as history_id: self._run_workflow(WORKFLOW_WITH_OUTPUT_COLLECTION, history_id=history_id) - self.assertEqual("a\nc\nb\nd\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0)) + assert "a\nc\nb\nd\n" == self.dataset_populator.get_history_dataset_content(history_id, hid=0) @skip_without_tool("job_properties") @skip_without_tool("identifier_multiple_in_conditional") @@ -1642,9 +1642,7 @@ steps: } invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id) self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id) - self.assertEqual( - "a\nc\nb\nd\ne\ng\nf\nh\n", self.dataset_populator.get_history_dataset_content(history_id, hid=0) - ) + assert "a\nc\nb\nd\ne\ng\nf\nh\n" == self.dataset_populator.get_history_dataset_content(history_id, hid=0) @skip_without_tool("cat_list") @skip_without_tool("collection_split_on_column") @@ -1655,7 +1653,7 @@ steps: last_item_hid = details["hid"] assert last_item_hid == 7, f"Expected 7 history items, got {last_item_hid}" content = self.dataset_populator.get_history_dataset_content(history_id, hid=0) - self.assertEqual("10.0\n30.0\n20.0\n40.0\n", content) + assert "10.0\n30.0\n20.0\n40.0\n" == content @skip_without_tool("collection_split_on_column") @skip_without_tool("min_repeat") @@ -1696,7 +1694,7 @@ steps: collection_details = self.dataset_populator.get_history_collection_details(history_id, hid=7) assert collection_details["populated_state"] == "ok" content = self.dataset_populator.get_history_dataset_content(history_id, hid=11) - self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0") + assert content.strip() == "samp1\t10.0\nsamp2\t20.0" @skip_without_tool("cat") @skip_without_tool("collection_split_on_column") @@ -1885,9 +1883,9 @@ outer_input: invocation_id = summary.invocation_id content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual( - "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", - content, + assert ( + content + == "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" ) steps = self.workflow_populator.get_invocation(invocation_id)["steps"] assert sum(1 for step in steps if step["subworkflow_invocation_id"] is None) == 3 @@ -2034,12 +2032,12 @@ test_data: """ summary = self._run_workflow(workflow_text, test_data=test_data, history_id=history_id) jobs = summary.jobs - assert len(jobs) == 4, "4 jobs expected, got %d jobs" % len(jobs) + assert len(jobs) == 4, f"4 jobs expected, got {len(jobs)} jobs" content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual( - "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", - content, + assert ( + content + == "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" ) run_test(NESTED_WORKFLOW_AUTO_LABELS_MODERN_SYNTAX) @@ -2080,7 +2078,7 @@ steps: invocation_id = self.__invoke_workflow(workflow_id, inputs=inputs, history_id=history_id) self.workflow_populator.wait_for_invocation_and_jobs(history_id, workflow_id, invocation_id) content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(content.strip(), "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0") + assert content.strip() == "samp1\t10.0\nsamp2\t20.0\nsamp1\t20.0\nsamp2\t40.0" @skip_without_tool("collection_paired_test") def test_workflow_flatten(self): @@ -2214,7 +2212,7 @@ steps: invocation_id = summary.invocation_id bco = self.workflow_populator.get_biocompute_object(invocation_id) self.workflow_populator.validate_biocompute_object(bco) - self.assertEqual(bco["provenance_domain"]["name"], "Simple Workflow") + assert bco["provenance_domain"]["name"] == "Simple Workflow" @skip_without_tool("__APPLY_RULES__") def test_workflow_run_apply_rules(self): @@ -2615,11 +2613,11 @@ test_data: wait=True, round_trip_format_conversion=True, ) - self.assertEqual( - "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", - self.dataset_populator.get_history_dataset_content(history_id), + assert ( + self.dataset_populator.get_history_dataset_content(history_id) + == "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" ) - # self.assertEqual("chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", self.dataset_populator.get_history_dataset_content(history_id)) + # assert self.dataset_populator.get_history_dataset_content(history_id) == "chr16\t142908\t143003\tCCDS10397.1_cds_0_0_chr16_142909_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" @skip_without_tool("cat_list") @skip_without_tool("random_lines1") @@ -2686,9 +2684,9 @@ outer_input: wait=True, round_trip_format_conversion=True, ) - self.assertEqual( - "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", - self.dataset_populator.get_history_dataset_content(history_id), + assert ( + self.dataset_populator.get_history_dataset_content(history_id) + == "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" ) @skip_without_tool("cat_list") @@ -2747,9 +2745,9 @@ outer_input: wait=True, round_trip_format_conversion=True, ) - self.assertEqual( - "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", - self.dataset_populator.get_history_dataset_content(history_id), + assert ( + self.dataset_populator.get_history_dataset_content(history_id) + == "chr6\t108722976\t108723115\tCCDS5067.1_cds_0_0_chr6_108722977_f\t0\t+\nchrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" ) @skip_without_tool("empty_list") @@ -2792,7 +2790,7 @@ input1: history_id=history_id, wait=True, ) - self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id)) + assert "0\n" == self.dataset_populator.get_history_dataset_content(history_id) @skip_without_tool("random_lines1") def test_change_datatype_collection_map_over(self): @@ -2889,7 +2887,7 @@ input1: wait=True, round_trip_format_conversion=True, ) - self.assertEqual("0\n", self.dataset_populator.get_history_dataset_content(history_id)) + assert "0\n" == self.dataset_populator.get_history_dataset_content(history_id) @skip_without_tool("cat") def test_cancel_new_workflow_when_history_deleted(self): @@ -3008,9 +3006,7 @@ input1: self.workflow_populator.wait_for_invocation_and_jobs(history_id, uploaded_workflow_id, invocation_id) invocation = self._invocation_details(uploaded_workflow_id, invocation_id) assert invocation["state"] == "scheduled" - self.assertEqual( - "reviewed\n1\nreviewed\n4\n", self.dataset_populator.get_history_dataset_content(history_id) - ) + assert "reviewed\n1\nreviewed\n4\n" == self.dataset_populator.get_history_dataset_content(history_id) @skip_without_tool("cat") def test_cancel_workflow_invocation(self): @@ -3406,7 +3402,7 @@ text_input: self.dataset_populator.wait_for_history(history_id, assert_ok=True) content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual("chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n", content) + assert "chrX\t152691446\t152691471\tCCDS14735.1_cds_0_0_chrX_152691447_f\t0\t+\n" == content def test_run_with_numeric_input_connection(self): history_id = self.dataset_populator.new_history() @@ -3612,10 +3608,8 @@ outer_input: for i, (item_one, item_two) in enumerate(zip(history_one_contents, history_two_contents)): assert ( item_one["dataset_id"] == item_two["dataset_id"] - ), 'Dataset ids should match, but "%s" and "%s" are not the same for History item %i.' % ( - item_one["dataset_id"], - item_two["dataset_id"], - i + 1, + ), 'Dataset ids should match, but "{}" and "{}" are not the same for History item {}.'.format( + item_one["dataset_id"], item_two["dataset_id"], i + 1 ) def test_cannot_run_inaccessible_workflow(self): @@ -3668,9 +3662,7 @@ outer_input: self.workflow_populator.invoke_workflow_and_wait( workflow_id, history_id=history_id, request=workflow_request ) - self.assertEqual( - "1 2 3\n4 5 6\n7 8 9\n0 a b\n", self.dataset_populator.get_history_dataset_content(history_id) - ) + assert "1 2 3\n4 5 6\n7 8 9\n0 a b\n" == self.dataset_populator.get_history_dataset_content(history_id) def test_workflow_stability(self): # Run this index stability test with following command: @@ -4858,10 +4850,10 @@ steps: t2 = self.dataset_populator.get_history_dataset_content(history_id, hid=10) t3 = self.dataset_populator.get_history_dataset_content(history_id, hid=13) t4 = self.dataset_populator.get_history_dataset_content(history_id, hid=16) - self.assertEqual(r1, t1) - self.assertEqual(r2, t2) - self.assertEqual(r3, t3) - self.assertEqual(r4, t4) + assert r1 == t1 + assert r2 == t2 + assert r3 == t3 + assert r4 == t4 @skip_without_tool("cat1") @skip_without_tool("addValue") @@ -4910,10 +4902,10 @@ steps: t2 = self.dataset_populator.get_history_dataset_content(history_id, hid=10) t3 = self.dataset_populator.get_history_dataset_content(history_id, hid=13) t4 = self.dataset_populator.get_history_dataset_content(history_id, hid=16) - self.assertEqual(r1, t1) - self.assertEqual(r2, t2) - self.assertEqual(r3, t3) - self.assertEqual(r4, t4) + assert r1 == t1 + assert r2 == t2 + assert r3 == t3 + assert r4 == t4 @skip_without_tool("validation_default") def test_parameter_substitution_sanitization(self): @@ -4921,9 +4913,7 @@ steps: run_workflow_response, history_id = self._run_validation_workflow_with_substitions(substitions) self.dataset_populator.wait_for_history(history_id, assert_ok=True) - self.assertEqual( - "__dq__ X echo __dq__moo\n", self.dataset_populator.get_history_dataset_content(history_id, hid=1) - ) + assert "__dq__ X echo __dq__moo\n" == self.dataset_populator.get_history_dataset_content(history_id, hid=1) @skip_without_tool("validation_repeat") def test_parameter_substitution_validation_value_errors_0(self): @@ -5014,7 +5004,7 @@ steps: ) workflow_request["parameters"] = params self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request) - self.assertEqual("2\n", self.dataset_populator.get_history_dataset_content(history_id)) + assert "2\n" == self.dataset_populator.get_history_dataset_content(history_id) @skip_without_tool("random_lines1") def test_run_replace_params_nested_normalized(self): @@ -5030,7 +5020,7 @@ steps: workflow_request["parameters"] = params workflow_request["parameters_normalized"] = False self.workflow_populator.invoke_workflow_and_wait(workflow_id, request=workflow_request) - self.assertEqual("2\n", self.dataset_populator.get_history_dataset_content(history_id)) + assert "2\n" == self.dataset_populator.get_history_dataset_content(history_id) @skip_without_tool("random_lines1") def test_run_replace_params_over_default(self): @@ -5512,7 +5502,7 @@ input_c: hda_summary = next(hc for hc in history_contents if hc["hid"] == hid) hda_info_response = self._get(f"{contents_url}/{hda_summary['id']}") self._assert_status_code_is(hda_info_response, 200) - self.assertEqual(hda_info_response.json()["metadata_data_lines"], lines) + assert hda_info_response.json()["metadata_data_lines"] == lines def __history_contents(self, history_id): contents_url = f"histories/{history_id}/contents" @@ -5606,7 +5596,4 @@ test_data: inputs=json.dumps({"input1": self._ds_entry(hda1)}), ) self.workflow_populator.invoke_workflow_and_wait(workflow_id, history_id=history_id, request=workflow_request) - self.assertEqual( - "Hello World Second!\nhello world 2\n", - self.dataset_populator.get_history_dataset_content(history_id), - ) + assert self.dataset_populator.get_history_dataset_content(history_id) == "Hello World Second!\nhello world 2\n" diff --git a/lib/galaxy_test/api/test_workflows_from_yaml.py b/lib/galaxy_test/api/test_workflows_from_yaml.py index 5fb4df0e7d0..6d70e55a296 100644 --- a/lib/galaxy_test/api/test_workflows_from_yaml.py +++ b/lib/galaxy_test/api/test_workflows_from_yaml.py @@ -78,13 +78,13 @@ input1: "hello world" round_trip_format_conversion=True, ) contents1 = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(contents1.strip(), "hello world\nhello world") + assert contents1.strip() == "hello world\nhello world" def test_outputs(self): workflow_id = self._upload_yaml_workflow(WORKFLOW_WITH_OUTPUTS, round_trip_format_conversion=True) workflow = self._get(f"workflows/{workflow_id}/download").json() - self.assertEqual(workflow["steps"]["1"]["workflow_outputs"][0]["output_name"], "out_file1") - self.assertEqual(workflow["steps"]["1"]["workflow_outputs"][0]["label"], "wf_output_1") + assert workflow["steps"]["1"]["workflow_outputs"][0]["output_name"] == "out_file1" + assert workflow["steps"]["1"]["workflow_outputs"][0]["label"] == "wf_output_1" workflow = self.workflow_populator.download_workflow(workflow_id, style="format2") def test_runtime_inputs(self): @@ -160,7 +160,7 @@ steps: assert subworkflow_connection["input_subworkflow_step_id"] == 0 # content = self.dataset_populator.get_history_dataset_content( history_id ) - # self.assertEqual("chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n", content) + # assert content == "chr5\t131424298\t131424460\tCCDS4149.1_cds_0_0_chr5_131424299_f\t0\t+\n" def test_subworkflow_duplicate(self): duplicate_subworkflow_invocate_wf = """ @@ -339,7 +339,7 @@ test_data: ) content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(content, "hello world\nhello world 2\n") + assert content == "hello world\nhello world 2\n" def test_workflow_import_tool(self): history_id = self.dataset_populator.new_history() @@ -347,7 +347,7 @@ test_data: jobs_descriptions = {"test_data": {"input1": "hello world"}} self._run_jobs(workflow_path, source_type="path", jobs_descriptions=jobs_descriptions, history_id=history_id) content = self.dataset_populator.get_history_dataset_content(history_id) - self.assertEqual(content, "hello world\nhello world 2\n") + assert content == "hello world\nhello world 2\n" def test_parameter_default_rep(self): workflow = self._upload_and_download(WORKFLOW_PARAMETER_INPUT_INTEGER_DEFAULT) diff --git a/lib/galaxy_test/selenium/test_admin_app.py b/lib/galaxy_test/selenium/test_admin_app.py index 6c06cb86798..358bcbbbdee 100644 --- a/lib/galaxy_test/selenium/test_admin_app.py +++ b/lib/galaxy_test/selenium/test_admin_app.py @@ -138,13 +138,13 @@ class AdminAppTestCase(SeleniumTestCase): self.sleep_for(self.wait_types.UX_TRANSITION) # Make sure the job lock has been toggled. new_label = lock_label.wait_for_text() - self.assertNotEqual(new_label, original_label) + assert new_label != original_label self.screenshot("admin_jobs_locked") lock_label.wait_for_and_click() self.sleep_for(self.wait_types.UX_TRANSITION) self.screenshot("admin_jobs_unlocked") # And confirm that it has toggled back to what it was. - self.assertEqual(lock_label.wait_for_text(), original_label) + assert lock_label.wait_for_text() == original_label @selenium_test def test_admin_server_display(self): diff --git a/lib/galaxy_test/selenium/test_custom_builds.py b/lib/galaxy_test/selenium/test_custom_builds.py index ee24f67e4f0..05890060007 100644 --- a/lib/galaxy_test/selenium/test_custom_builds.py +++ b/lib/galaxy_test/selenium/test_custom_builds.py @@ -27,9 +27,9 @@ class CustomBuildsTestcase(SharedStateSeleniumTestCase): actual_builds = self.get_custom_builds() intersection = set(actual_builds).intersection(expected_builds) if present: - self.assertEqual(intersection, set(expected_builds)) + assert intersection == set(expected_builds) else: - self.assertEqual(intersection, set()) + assert intersection == set() def _login(self): self.home() # ensure Galaxy is loaded diff --git a/lib/galaxy_test/selenium/test_histories_list.py b/lib/galaxy_test/selenium/test_histories_list.py index 79e8eccb780..9513d71d3a7 100644 --- a/lib/galaxy_test/selenium/test_histories_list.py +++ b/lib/galaxy_test/selenium/test_histories_list.py @@ -22,7 +22,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase): @retry_assertion_during_transitions def assert_history_name_switched(): - self.assertEqual(self.history_panel_name(), self.history2_name) + assert self.history_panel_name() == self.history2_name assert_history_name_switched() @@ -32,7 +32,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase): self.navigate_to_histories_page() self.click_grid_popup_option(self.history2_name, "View") history_name = self.wait_for_selector("[data-description='name display']") - self.assertEqual(history_name.text, self.history2_name) + assert history_name.text == self.history2_name @selenium_test def test_history_publish(self): @@ -155,7 +155,7 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase): # Filter out histories created by other tests actual_histories = [x for x in actual_histories if x in self.all_histories] - self.assertEqual(actual_histories, expected_histories) + assert actual_histories == expected_histories @selenium_test def test_standard_search(self): @@ -238,16 +238,16 @@ class SavedHistoriesTestCase(SharedStateSeleniumTestCase): if not sort_matters: actual_histories = set(actual_histories) expected_histories = set(expected_histories) - self.assertEqual(actual_histories, expected_histories) + assert actual_histories == expected_histories @retry_assertion_during_transitions def assert_histories_in_grid(self, expected_histories, present=True): actual_histories = self.get_histories() intersection = set(actual_histories).intersection(expected_histories) if present: - self.assertEqual(intersection, set(expected_histories)) + assert intersection == set(expected_histories) else: - self.assertEqual(intersection, set()) + assert intersection == set() def get_histories(self): return self.histories_get_history_names() diff --git a/lib/galaxy_test/selenium/test_history_panel.py b/lib/galaxy_test/selenium/test_history_panel.py index 9bb1903feb9..de9af89a399 100644 --- a/lib/galaxy_test/selenium/test_history_panel.py +++ b/lib/galaxy_test/selenium/test_history_panel.py @@ -244,7 +244,7 @@ class HistoryPanelTestCase(SeleniumTestCase): @retry_assertion_during_transitions def assert_name_changed(self): name = self.history_panel_name() - self.assertEqual(name, NEW_HISTORY_NAME) + assert name == NEW_HISTORY_NAME def _refresh(self): if self.is_beta_history(): diff --git a/lib/galaxy_test/selenium/test_invocation_grid.py b/lib/galaxy_test/selenium/test_invocation_grid.py index 29c82523fe5..d542e4bac08 100644 --- a/lib/galaxy_test/selenium/test_invocation_grid.py +++ b/lib/galaxy_test/selenium/test_invocation_grid.py @@ -47,4 +47,4 @@ class InvocationGridSeleniumTestCase(SeleniumTestCase, TestsGalaxyPagers): @retry_assertion_during_transitions def _assert_showing_n_invocations(self, n): - self.assertEqual(len(self.invocation_index_table_elements()), n) + assert len(self.invocation_index_table_elements()) == n diff --git a/lib/galaxy_test/selenium/test_library_landing.py b/lib/galaxy_test/selenium/test_library_landing.py index 4bc7badc8e4..69149278d6b 100644 --- a/lib/galaxy_test/selenium/test_library_landing.py +++ b/lib/galaxy_test/selenium/test_library_landing.py @@ -87,7 +87,7 @@ class LibraryLandingTestCase(SeleniumTestCase): @retry_assertion_during_transitions def _assert_names_are(self, expected_names): names = [e.find_element(self.by.CSS_SELECTOR, "td a").text for e in self.libraries_index_table_elements()] - self.assertEqual(names, expected_names) + assert names == expected_names @retry_assertion_during_transitions def _assert_at_least_one_library_displayed(self): @@ -95,7 +95,7 @@ class LibraryLandingTestCase(SeleniumTestCase): @retry_assertion_during_transitions def _assert_num_displayed_libraries_is(self, n): - self.assertEqual(n, self._num_displayed_libraries()) + assert n == self._num_displayed_libraries() def _num_displayed_libraries(self): return len(self.libraries_index_table_elements()) diff --git a/lib/galaxy_test/selenium/test_personal_information.py b/lib/galaxy_test/selenium/test_personal_information.py index de1925c17e6..19c733faadb 100644 --- a/lib/galaxy_test/selenium/test_personal_information.py +++ b/lib/galaxy_test/selenium/test_personal_information.py @@ -13,25 +13,25 @@ class ManageInformationTestCase(SeleniumTestCase): 'Not available.' """ self.login() - self.assertEqual(self.get_api_key(), "Not available.") + assert self.get_api_key() == "Not available." api_key = self.get_api_key() self.navigate_to_user_preferences() self.components.preferences.manage_api_key.wait_for_and_click() self.sleep_for(self.wait_types.UX_TRANSITION) api_key_input = self.components.preferences.api_key_input.wait_for_visible() # Assert that what's rendered on screen is what the API is returning - self.assertEqual(api_key_input.get_property("value"), api_key) + assert api_key_input.get_property("value") == api_key self.components.preferences.get_new_key.wait_for_and_click() self.sleep_for(self.wait_types.UX_TRANSITION) new_api_key = self.get_api_key() api_key_input = self.components.preferences.api_key_input.wait_for_visible() # And assert that this has now changed, and still renders correctly - self.assertEqual(new_api_key, api_key_input.get_property("value")) + assert new_api_key == api_key_input.get_property("value") @selenium_test def test_change_email(self): def assert_email(email_to_check): - self.assertTrue(email_to_check == self.components.preferences.current_email.wait_for_text()) + assert email_to_check == self.components.preferences.current_email.wait_for_text() email = self._get_random_email() self.register(email) @@ -46,7 +46,7 @@ class ManageInformationTestCase(SeleniumTestCase): new_email = self._get_random_email() # new email should be different from initially registered - self.assertTrue(email != new_email) + assert email != new_email email_input_field = self.components.preferences.email_input.wait_for_visible() self.clear_input_field_and_write(email_input_field, new_email) @@ -64,7 +64,7 @@ class ManageInformationTestCase(SeleniumTestCase): return self.components.preferences.username_input.wait_for_visible() def assert_public_name(expected_name): - self.assertTrue(expected_name == get_name_input_field().get_attribute("value")) + assert expected_name == get_name_input_field().get_attribute("value") public_name = "user-public-name" self.register(username=public_name) @@ -123,7 +123,7 @@ class ManageInformationTestCase(SeleniumTestCase): # check if address was saved correctly for input_field_label in address_fields.keys(): input_field = self.get_address_input_field(get_address_form(), input_field_label) - self.assertTrue(input_field.get_attribute("value") == address_fields[input_field_label]) + assert input_field.get_attribute("value") == address_fields[input_field_label] def navigate_to_manage_information(self): self.navigate_to_user_preferences() diff --git a/lib/galaxy_test/selenium/test_published_histories_grid.py b/lib/galaxy_test/selenium/test_published_histories_grid.py index ce4ec006f1c..3409d20bbf4 100644 --- a/lib/galaxy_test/selenium/test_published_histories_grid.py +++ b/lib/galaxy_test/selenium/test_published_histories_grid.py @@ -105,7 +105,7 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase): if tag_button_text == target_tag_button_text: break - self.assertEqual(tag_button_text, target_tag_button_text) + assert tag_button_text == target_tag_button_text tag_button.click() self.assert_grid_histories_are([self.history1_name, self.history3_name], False) @@ -139,16 +139,16 @@ class HistoryGridTestCase(SharedStateSeleniumTestCase): if not sort_matters: actual_histories = set(actual_histories) expected_histories = set(expected_histories) - self.assertEqual(actual_histories, expected_histories) + assert actual_histories == expected_histories @retry_assertion_during_transitions def assert_histories_in_grid(self, expected_histories, present=True): actual_histories = self.get_histories() intersection = set(actual_histories).intersection(expected_histories) if present: - self.assertEqual(intersection, set(expected_histories)) + assert intersection == set(expected_histories) else: - self.assertEqual(intersection, set()) + assert intersection == set() def set_filter(self, selector, value): filter_input = self.wait_for_selector_clickable(selector) diff --git a/lib/galaxy_test/selenium/test_sign_out.py b/lib/galaxy_test/selenium/test_sign_out.py index 9c953176a82..9902055b89f 100644 --- a/lib/galaxy_test/selenium/test_sign_out.py +++ b/lib/galaxy_test/selenium/test_sign_out.py @@ -17,7 +17,7 @@ class SignOutTestCase(SeleniumTestCase): self.components.sign_out.cancel_button.wait_for_and_click() assert self.is_logged_in() new_email = self.driver.find_element(By.ID, "user-preferences-current-email").text - self.assertTrue(email == new_email) + assert email == new_email self.components.preferences.sign_out.wait_for_and_click() self.components.sign_out.sign_out_button.wait_for_and_click() self.sleep_for(self.wait_types.UX_TRANSITION) diff --git a/lib/galaxy_test/selenium/test_tool_describing_tours.py b/lib/galaxy_test/selenium/test_tool_describing_tours.py index 7fdee274cdd..9d14e654bfb 100644 --- a/lib/galaxy_test/selenium/test_tool_describing_tours.py +++ b/lib/galaxy_test/selenium/test_tool_describing_tours.py @@ -70,7 +70,7 @@ class ToolDescribingToursTestCase(SeleniumTestCase): def _ensure_tdt_available(self): """Skip a test if the webhook TDT doesn't appear.""" response = self.api_get("webhooks", raw=True) - self.assertEqual(response.status_code, 200) + assert response.status_code == 200 data = response.json() webhooks = [x["id"] for x in data] if "tour_generator" not in webhooks: diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py index 28afa953a1e..3d81a77af47 100644 --- a/lib/galaxy_test/selenium/test_workflow_editor.py +++ b/lib/galaxy_test/selenium/test_workflow_editor.py @@ -724,7 +724,7 @@ steps: def assert_workflow_bookmarked_status(target_status): name_matches = [c.text == new_workflow_name for c in self.components.tool_panel.workflow_names.all()] status = any(name_matches) - self.assertTrue(status == target_status) + assert status == target_status new_workflow_name = self.workflow_create_new(clear_placeholder=True) diff --git a/lib/galaxy_test/selenium/test_workflow_management.py b/lib/galaxy_test/selenium/test_workflow_management.py index 1cf96bd8193..898b4625d5c 100644 --- a/lib/galaxy_test/selenium/test_workflow_management.py +++ b/lib/galaxy_test/selenium/test_workflow_management.py @@ -75,7 +75,7 @@ class WorkflowManagementTestCase(SeleniumTestCase, TestsGalaxyPagers, UsesWorkfl @retry_assertion_during_transitions def check_tags(): - self.assertEqual(self.workflow_index_tags(), ["cooltag"]) + assert self.workflow_index_tags() == ["cooltag"] check_tags() self.screenshot("workflow_manage_tags") diff --git a/lib/galaxy_test/selenium/test_workflow_run.py b/lib/galaxy_test/selenium/test_workflow_run.py index e3eac4b8d21..b04043f79bf 100644 --- a/lib/galaxy_test/selenium/test_workflow_run.py +++ b/lib/galaxy_test/selenium/test_workflow_run.py @@ -189,7 +189,7 @@ steps: ) self.workflow_run_wait_for_ok(hid=7) content = self.dataset_populator.get_history_dataset_content(history_id, hid=7) - self.assertEqual("10.0\n30.0\n20.0\n40.0\n", content) + assert "10.0\n30.0\n20.0\n40.0\n" == content @selenium_test @managed_history