DATAUP-765: assertify tests

src/biokbase/auth.py

@@ -54,26 +54,23 @@ def __init__(self, user_dict: dict):
         self.user_name = user_dict.get("user")
 
 
-def validate_token():
+def validate_token() -> bool:
     """
     Validates the currently set auth token. Returns True if valid, False otherwise.
     """
     headers = {"Authorization": get_auth_token()}
     r = requests.get(token_api_url + endpt_token, headers=headers)
-    if r.status_code == 200:
-        return True
-    else:
-        return False
+    return r.status_code == 200
 
 
-def set_environ_token(token: str) -> None:
+def set_environ_token(token: str | None) -> None:
     """
     Sets a login token in the local environment variable.
     """
     kbase_env.auth_token = token
 
 
-def get_auth_token() -> Optional[str]:
+def get_auth_token() -> str | None:
     """
     Returns the current login token being used, or None if one isn't set.
     """

src/biokbase/narrative/contents/narrativeio.py

@@ -99,15 +99,14 @@ def narrative_exists(self, ref):
         except WorkspaceError as err:
             if err.http_code == 404:
                 return False
-            else:
-                raise
+            raise
 
     def _validate_nar_type(self, t, ref):
         if not t.startswith(NARRATIVE_TYPE):
             err = "Expected a Narrative object"
             if ref is not None:
-                err += " with reference {}".format(ref)
-            err += ", got a {}".format(t)
+                err += f" with reference {ref}"
+            err += f", got a {t}"
             raise HTTPError(500, err)
 
     def read_narrative(self, ref, content=True, include_metadata=True):

src/biokbase/narrative/jobs/specmanager.py

@@ -140,7 +140,12 @@ def app_usage(self, app_id, tag="release"):
 
         return AppUsage(usage)
 
-    def check_app(self, app_id, tag="release", raise_exception=False):
+    def check_app(
+        self: "SpecManager",
+        app_id: str,
+        tag: str = "release",
+        raise_exception: bool = False,
+    ):
         """
         Checks if a method (and release tag) is available for running and such.
         If raise_exception==True, and either the tag or app_id are invalid, a ValueError is raised.

src/biokbase/narrative/tests/job_test_constants.py

@@ -1,14 +1,27 @@
 import copy
+from typing import Any
 
 from biokbase.narrative.jobs.job import TERMINAL_STATUSES
 
 from .util import ConfigTests
 
 config = ConfigTests()
-TEST_JOBS = config.load_json_file(config.get("jobs", "ee2_job_test_data_file"))
-
-
-def generate_error(job_id, err_type):
+TEST_JOBS: dict[str, dict] = config.load_json_file(
+    config.get("jobs", "ee2_job_test_data_file")
+)
+
+
+def generate_error(job_id: str, err_type: str) -> str:
+    """Given a job id and an error type, generate the appropriate error string.
+
+    :param job_id: job ID
+    :type job_id: str
+    :param err_type: error type
+    :type err_type: str
+    :raises KeyError: if the error type does not exist
+    :return: error string
+    :rtype: str
+    """
     user_id = None
     status = None
 
@@ -32,11 +45,25 @@ def generate_error(job_id, err_type):
     return error_strings[err_type]
 
 
-def get_test_job(job_id):
+def get_test_job(job_id: str) -> dict[str, Any]:
+    """Given a job ID, fetch the appropriate job.
+
+    :param job_id: job ID
+    :type job_id: str
+    :return: job data
+    :rtype: dict[str, Any]
+    """
     return copy.deepcopy(TEST_JOBS[job_id])
 
 
-def get_test_jobs(job_ids):
+def get_test_jobs(job_ids: list[str]) -> dict[str, dict[str, Any]]:
+    """Given a list of job IDs, fetch the appropriate jobs.
+
+    :param job_ids: list of job IDs
+    :type job_ids: list[str]
+    :return: dict of jobs keyed by job ID
+    :rtype: dict[str, dict[str, Any]]
+    """
     return {job_id: get_test_job(job_id) for job_id in job_ids}
 
 
@@ -93,16 +120,15 @@ def get_test_jobs(job_ids):
     BATCH_RETRY_ERROR,
 ]
 
-BATCH_PARENT_CHILDREN = [BATCH_PARENT] + BATCH_CHILDREN
+BATCH_PARENT_CHILDREN = [BATCH_PARENT, *BATCH_CHILDREN]
 
-JOB_TERMINAL_STATE = {
-    job_id: TEST_JOBS[job_id]["status"] in TERMINAL_STATUSES
-    for job_id in TEST_JOBS.keys()
+JOB_TERMINAL_STATE: dict[str, bool] = {
+    job_id: TEST_JOBS[job_id]["status"] in TERMINAL_STATUSES for job_id in TEST_JOBS
 }
 
-TERMINAL_JOBS = []
-ACTIVE_JOBS = []
-REFRESH_STATE = {}
+TERMINAL_JOBS: list[str] = []
+ACTIVE_JOBS: list[str] = []
+REFRESH_STATE: dict[str, bool] = {}
 for key, value in JOB_TERMINAL_STATE.items():
     if value:
         TERMINAL_JOBS.append(key)

src/biokbase/narrative/tests/narrative_mock/mockclients.py

@@ -81,7 +81,7 @@ def test_my_function(self):
     config = ConfigTests()
     _job_state_data = TEST_JOBS
 
-    def __init__(self, client_name=None, token=None):
+    def __init__(self, client_name=None, token=None) -> None:
         if token is not None:
             assert isinstance(token, str)
         self.client_name = client_name
@@ -326,9 +326,7 @@ def log_gen(log_params, total_lines=MAX_LOG_LINES):
             lines = []
             if skip < total_lines:
                 for i in range(total_lines - skip):
-                    lines.append(
-                        {"is_error": 0, "line": "This is line {}".format(i + skip)}
-                    )
+                    lines.append({"is_error": 0, "line": f"This is line {i + skip}"})
             return {"last_line_number": max(total_lines, skip), "lines": lines}
 
         if job_id == JOB_COMPLETED:
@@ -355,6 +353,7 @@ def log_gen(log_params, total_lines=MAX_LOG_LINES):
     def sync_call(self, call, params):
         if call == "NarrativeService.list_objects_with_sets":
             return self._mock_ns_list_objects_with_sets(params)
+        return None
 
     def _mock_ns_list_objects_with_sets(self, params):
         """
@@ -374,7 +373,7 @@ def _mock_ns_list_objects_with_sets(self, params):
         if params.get("workspaces"):
             ws_name = params["workspaces"][0]
         dp_id = 999
-        dp_ref = "{}/{}".format(ws_id, dp_id)
+        dp_ref = f"{ws_id}/{dp_id}"
 
         data = {
             "data": [
@@ -511,10 +510,7 @@ def _mock_ns_list_objects_with_sets(self, params):
             data["data"] = list(
                 filter(
                     lambda x: any(
-                        [
-                            x["object_info"][2].lower().startswith(t.lower())
-                            for t in types
-                        ]
+                        x["object_info"][2].lower().startswith(t.lower()) for t in types
                     ),
                     data["data"],
                 )
@@ -535,7 +531,8 @@ def get_failing_mock_client(client_name, token=None):
 
 
 class FailingMockClient:
-    def __init__(self, token=None):
+    def __init__(self, token=None) -> None:
+        # nothing to do here
         pass
 
     def check_workspace_jobs(self, params):
@@ -590,7 +587,7 @@ class assert_obj_method_called:
     )
     """
 
-    def __init__(self, target, method_name, call_status=True):
+    def __init__(self, target, method_name, call_status=True) -> None:
         self.target = target
         self.method_name = method_name
         self.call_status = call_status

src/biokbase/narrative/tests/narrative_mock/mockcomm.py

@@ -5,7 +5,7 @@ class MockComm:
     analyzed during the test.
     """
 
-    def __init__(self, *args, **kwargs):
+    def __init__(self, *args, **kwargs) -> None:
         """Mock the init"""
         self.messages = []
 

src/biokbase/narrative/tests/test_app_util.py

@@ -3,13 +3,10 @@
 """
 import copy
 import os
+import re
 from unittest import mock
 
 import pytest
-import re
-from biokbase.narrative.common.url_config import URLS
-from biokbase.workspace.client import Workspace
-
 from biokbase.narrative.app_util import (
     app_param,
     check_tag,
@@ -19,10 +16,11 @@
     map_outputs_from_state,
     transform_param_value,
 )
-
-from biokbase.narrative.tests.conftest import narrative_vcr as vcr
+from biokbase.narrative.common.url_config import URLS
 from biokbase.narrative.tests import util
+from biokbase.narrative.tests.conftest import narrative_vcr as vcr
 from biokbase.narrative.upa import is_upa
+from biokbase.workspace.client import Workspace
 
 config = util.ConfigTests()
 user_name = config.get("users", "test_user")
@@ -74,7 +72,7 @@ def set_ws_name(ws_name):
 ]
 
 
-@pytest.mark.parametrize("result,path,expected", get_result_sub_path_cases)
+@pytest.mark.parametrize(("result", "path", "expected"), get_result_sub_path_cases)
 def test_get_result_sub_path(result, path, expected):
     assert get_result_sub_path(result, path) == expected
 
@@ -275,7 +273,7 @@ def test_map_outputs_from_state_bad_spec(workspace_name):
 ]
 
 
-@pytest.mark.parametrize("field_type,spec_add,expect_add", app_param_cases)
+@pytest.mark.parametrize(("field_type", "spec_add", "expect_add"), app_param_cases)
 def test_app_param(field_type, spec_add, expect_add):
     spec_param = copy.deepcopy(base_app_param)
     expected = copy.deepcopy(base_expect)
@@ -307,7 +305,8 @@ def test_app_param(field_type, spec_add, expect_add):
 
 
 @pytest.mark.parametrize(
-    "transform_type,value,spec_param,expected", transform_param_value_simple_cases
+    ("transform_type", "value", "spec_param", "expected"),
+    transform_param_value_simple_cases,
 )
 def test_transform_param_value_simple(transform_type, value, spec_param, expected):
     assert transform_param_value(transform_type, value, spec_param) == expected
@@ -328,7 +327,7 @@ def test_transform_param_value_fail():
 ]
 
 
-@pytest.mark.parametrize("value,expected", textsubdata_cases)
+@pytest.mark.parametrize(("value", "expected"), textsubdata_cases)
 def test_transform_param_value_textsubdata(value, expected):
     spec = {"type": "textsubdata"}
     assert transform_param_value(None, value, spec) == expected
@@ -506,9 +505,6 @@ def get_workspace(_):
 
 
 class RefChainWorkspace:
-    def __init__(self):
-        pass
-
     def get_object_info3(self, params):
         """
         Makes quite a few assumptions about input, as it's used for a specific test.
@@ -568,7 +564,7 @@ def get_ref_path_mock_ws(name="workspace"):
 )
 @mock.patch("biokbase.narrative.app_util.clients.get", get_ref_path_mock_ws)
 def test_transform_param_value_upa_path(tf_type):
-    upa_path = f"69375/2/2;67729/2/2"
+    upa_path = "69375/2/2;67729/2/2"
     assert transform_param_value(tf_type, upa_path, None) == upa_path
 
 

src/biokbase/narrative/tests/test_appeditor.py

@@ -5,6 +5,7 @@
 import re
 import unittest
 
+import pytest
 from biokbase.narrative.appeditor import generate_app_cell
 
 from .util import ConfigTests
@@ -22,24 +23,26 @@ def setUpClass(cls):
 
     def test_gen_app_cell_post_validation(self):
         js = generate_app_cell(validated_spec=self.specs_list[0])
-        self.assertIsNotNone(js)
+        assert js is not None
 
     def test_gen_app_cell_pre_valid(self):
         js = generate_app_cell(
             spec_tuple=(json.dumps(self.spec_json), self.display_yaml)
         )
-        self.assertIsNotNone(js)
-        self.assertIsNotNone(js.data)
-        self.assertIn(
-            "A description string, with "quoted" values, shouldn't fail.",
-            js.data,
+        assert js is not None
+        assert js.data is not None
+        assert (
+            "A description string, with "quoted" values, shouldn't fail."
+            in js.data
         )
-        self.assertIn("Test Simple Inputs with "quotes"", js.data)
-        self.assertIn("A simple test spec with a single 'input'.", js.data)
+        assert "Test Simple Inputs with "quotes"" in js.data
+        assert "A simple test spec with a single 'input'." in js.data
 
     def test_gen_app_cell_fail_validation(self):
-        with self.assertRaisesRegexp(
+        with pytest.raises(
             Exception,
-            re.escape("Can't find sub-node [categories] within path [/] in spec.json"),
+            match=re.escape(
+                "Can't find sub-node [categories] within path [/] in spec.json"
+            ),
         ):
             generate_app_cell(spec_tuple=("{}", self.display_yaml))