style: drop all pylint disables

cumulus_etl/cli_utils.py

@@ -62,7 +62,7 @@ def make_export_dir(export_to: str | None = None) -> common.Directory:
     """Makes a temporary directory to drop exported ndjson files into"""
     # Handle the easy case -- just a random temp dir
     if not export_to:
-        return tempfile.TemporaryDirectory()  # pylint: disable=consider-using-with
+        return tempfile.TemporaryDirectory()
 
     # OK the user has a specific spot in mind. Let's do some quality checks. It must be local and empty.
 

cumulus_etl/deid/scrubber.py

@@ -44,7 +44,7 @@ async def scrub_bulk_data(input_dir: str) -> tempfile.TemporaryDirectory:
 
         :returns: a temporary directory holding the de-identified results, in FHIR ndjson format
         """
-        tmpdir = tempfile.TemporaryDirectory()  # pylint: disable=consider-using-with
+        tmpdir = tempfile.TemporaryDirectory()
         await mstool.run_mstool(input_dir, tmpdir.name)
         return tmpdir
 

cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py

@@ -63,7 +63,7 @@ async def covid_symptoms_extract(
         ctakes_json = await nlp.ctakes_extract(
             cache, ctakes_namespace, clinical_note, client=ctakes_http_client
         )
-    except Exception as exc:  # pylint: disable=broad-except
+    except Exception as exc:
         logging.warning(
             "Could not extract symptoms for docref %s (%s): %s", docref_id, type(exc).__name__, exc
         )
@@ -96,7 +96,7 @@ def is_covid_match(m: ctakesclient.typesystem.MatchText):
             model=polarity_model,
             client=cnlp_http_client,
         )
-    except Exception as exc:  # pylint: disable=broad-except
+    except Exception as exc:
         logging.warning(
             "Could not check polarity for docref %s (%s): %s", docref_id, type(exc).__name__, exc
         )

cumulus_etl/etl/tasks/basic_tasks.py

@@ -149,7 +149,7 @@ async def fetch_medication(self, resource: dict) -> dict | None:
 
         try:
             medication = await fhir.download_reference(self.task_config.client, reference)
-        except Exception as exc:  # pylint: disable=broad-except
+        except Exception as exc:
             logging.warning("Could not download Medication reference: %s", exc)
             self.summaries[1].had_errors = True
 

cumulus_etl/etl/tasks/nlp_task.py

@@ -94,7 +94,7 @@ async def read_notes(
                     warned_connection_error = True
                 self.add_error(orig_docref)
                 continue
-            except Exception as exc:  # pylint: disable=broad-except
+            except Exception as exc:
                 logging.warning("Error getting text for docref %s: %s", docref["id"], exc)
                 self.add_error(orig_docref)
                 continue

cumulus_etl/formats/base.py

@@ -62,7 +62,7 @@ def write_records(self, batch: Batch) -> bool:
         try:
             self._write_one_batch(batch)
             return True
-        except Exception:  # pylint: disable=broad-except
+        except Exception:
             logging.exception("Could not process data records")
             return False
 

cumulus_etl/formats/deltalake.py

@@ -139,15 +139,15 @@ def finalize(self) -> None:
             table = delta.DeltaTable.forPath(self.spark, full_path)
         except AnalysisException:
             return  # if the table doesn't exist because we didn't write anything, that's fine - just bail
-        except Exception:  # pylint: disable=broad-except
+        except Exception:
             logging.exception("Could not finalize Delta Lake table %s", self.dbname)
             return
 
         try:
             table.optimize().executeCompaction()  # pool small files for better query performance
             table.generate("symlink_format_manifest")
             table.vacuum()  # Clean up unused data files older than retention policy (default 7 days)
-        except Exception:  # pylint: disable=broad-except
+        except Exception:
             logging.exception("Could not finalize Delta Lake table %s", self.dbname)
 
     def _table_path(self, dbname: str) -> str:

cumulus_etl/loaders/fhir/ndjson_loader.py

@@ -67,7 +67,7 @@ async def load_all(self, resources: list[str]) -> common.Directory:
         # This uses more disk space temporarily (copied files will get deleted once the MS tool is done and this
         # TemporaryDirectory gets discarded), but that seems reasonable.
         print("Copying ndjson input files…")
-        tmpdir = tempfile.TemporaryDirectory()  # pylint: disable=consider-using-with
+        tmpdir = tempfile.TemporaryDirectory()
         filenames = common.ls_resources(input_root, set(resources), warn_if_empty=True)
         for filename in filenames:
             input_root.get(filename, f"{tmpdir.name}/")

cumulus_etl/loaders/i2b2/oracle/query.py

@@ -120,11 +120,11 @@ def where(expression=None) -> str:
     return "\n WHERE " + expression if expression else ""
 
 
-def AND(expression: str) -> str:  # pylint: disable=invalid-name
+def AND(expression: str) -> str:
     return f"\n AND ({expression})"
 
 
-def OR(expression: str) -> str:  # pylint: disable=invalid-name
+def OR(expression: str) -> str:
     return f"\n OR ({expression})"
 
 

cumulus_etl/nlp/extract.py

@@ -29,7 +29,7 @@ async def ctakes_extract(
     try:
         cached_response = common.read_json(full_path)
         result = ctakesclient.typesystem.CtakesJSON(source=cached_response)
-    except Exception:  # pylint: disable=broad-except
+    except Exception:
         result = await ctakesclient.client.extract(sentence, client=client)
         cache.makedirs(os.path.dirname(full_path))
         common.write_json(full_path, result.as_json())
@@ -58,7 +58,7 @@ async def list_polarity(
 
     try:
         result = [ctakesclient.typesystem.Polarity(x) for x in common.read_json(full_path)]
-    except Exception:  # pylint: disable=broad-except
+    except Exception:
         result = await ctakesclient.transformer.list_polarity(
             sentence, spans, client=client, model=model
         )

cumulus_etl/upload_notes/selector.py

@@ -43,7 +43,7 @@ def _create_docref_filter(
     else:
         # Just accept everything (we still want to read them though, to copy them to a possible export folder).
         # So this lambda just returns an iterator over its input.
-        return lambda x: iter(x)  # pylint: disable=unnecessary-lambda
+        return lambda x: iter(x)
 
 
 def _filter_real_docrefs(docrefs_csv: str, docrefs: Iterable[dict]) -> Iterator[dict]:

tests/covid_symptom/test_covid_results.py

@@ -92,10 +92,10 @@ async def test_ed_note_filtering_for_nlp(self, codings, expected):
     async def test_non_ed_visit_is_skipped_for_covid_symptoms(self):
         """Verify we ignore non ED visits for the covid symptoms NLP"""
         docref0 = i2b2_mock_data.documentreference()
-        docref0["type"]["coding"][0]["code"] = "NOTE:nope"  # pylint: disable=unsubscriptable-object
+        docref0["type"]["coding"][0]["code"] = "NOTE:nope"
         self.make_json("DocumentReference", "skipped", **docref0)
         docref1 = i2b2_mock_data.documentreference()
-        docref1["type"]["coding"][0]["code"] = "NOTE:149798455"  # pylint: disable=unsubscriptable-object
+        docref1["type"]["coding"][0]["code"] = "NOTE:149798455"
         self.make_json("DocumentReference", "present", **docref1)
 
         await covid_symptom.CovidSymptomNlpResultsTask(self.job_config, self.scrubber).run()

tests/ctakesmock.py

@@ -34,7 +34,7 @@ def setUp(self):
 
         CtakesMixin.ctakes_port += 1
         os.environ["URL_CTAKES_REST"] = f"http://localhost:{CtakesMixin.ctakes_port}/"
-        self.ctakes_overrides = tempfile.TemporaryDirectory()  # pylint: disable=consider-using-with
+        self.ctakes_overrides = tempfile.TemporaryDirectory()
         self._run_fake_ctakes_server(f"{self.ctakes_overrides.name}/symptoms.bsv")
 
         cnlp_patcher = mock.patch(
@@ -131,7 +131,7 @@ class FakeCTakesHandler(http.server.BaseHTTPRequestHandler):
     # We don't want that behavior, because if our mock code is misbehaving and not detecting an overrides file change,
     # if we time out a request on our end, it will look like a successful file change detection and mask a testing bug.
 
-    def do_POST(self):  # pylint: disable=invalid-name
+    def do_POST(self):
         """Serve a POST request."""
         self.server.was_called.value = 1  # signal to test framework that we were actually called
 

tests/formats/test_deltalake.py

@@ -27,7 +27,7 @@ class TestDeltaLake(utils.AsyncTestCase):
     @classmethod
     def setUpClass(cls):
         super().setUpClass()
-        output_tempdir = tempfile.TemporaryDirectory()  # pylint: disable=consider-using-with
+        output_tempdir = tempfile.TemporaryDirectory()
         cls.output_tempdir = output_tempdir
         cls.output_dir = output_tempdir.name
         cls.root = store.Root(output_tempdir.name)

tests/loaders/i2b2/test_i2b2_oracle_extract.py

@@ -15,7 +15,7 @@ class TestOracleExtraction(AsyncTestCase):
 
     def setUp(self) -> None:
         super().setUp()
-        self.maxDiff = None  # pylint: disable=invalid-name
+        self.maxDiff = None
 
         # Mock all the sql connection/cursor/execution stuff
         connect_patcher = mock.patch("cumulus_etl.loaders.i2b2.oracle.extract.connect")

tests/loaders/i2b2/test_i2b2_oracle_query.py

@@ -50,7 +50,7 @@ class TestOracleQueries(utils.AsyncTestCase):
 
     def setUp(self) -> None:
         super().setUp()
-        self.maxDiff = None  # pylint: disable=invalid-name
+        self.maxDiff = None
 
     def test_list_patient(self):
         common.print_header("# patient")

tests/loaders/i2b2/test_i2b2_transform.py

@@ -18,7 +18,6 @@ def test_to_fhir_patient(self):
         self.assertEqual(str(12345), subject["id"])
         self.assertEqual("2005-06-07", subject["birthDate"])
         self.assertEqual("female", subject["gender"])
-        # pylint: disable-next=unsubscriptable-object
         self.assertEqual("02115", subject["address"][0]["postalCode"])
 
     @ddt.data(

tests/loaders/ndjson/test_bulk_export.py

@@ -472,7 +472,7 @@ async def test_delay(self, mock_sleep):
             await self.export()
 
         # 86760 == 24 hours + six minutes
-        self.assertEqual(86760, self.exporter._total_wait_time)  # pylint: disable=protected-access
+        self.assertEqual(86760, self.exporter._total_wait_time)
 
         self.assertListEqual(
             [

tests/loaders/ndjson/test_ndjson_loader.py

@@ -21,7 +21,7 @@ class TestNdjsonLoader(AsyncTestCase):
 
     def setUp(self):
         super().setUp()
-        self.jwks_file = tempfile.NamedTemporaryFile()  # pylint: disable=consider-using-with
+        self.jwks_file = tempfile.NamedTemporaryFile()
         self.jwks_path = self.jwks_file.name
         self.jwks_file.write(b'{"fake":"jwks"}')
         self.jwks_file.flush()

tests/s3mock.py

@@ -54,7 +54,7 @@ def setUp(self):
 
         try:
             self.s3fs.mkdir(self.bucket)  # create the bucket as a quickstart
-        except Exception:  # pylint: disable=broad-except
+        except Exception:
             self._kill_moto_server()
             self.fail("Stale moto server")
 

tests/utils.py

@@ -57,7 +57,7 @@ def setUp(self):
 
     def make_tempdir(self) -> str:
         """Creates a temporary dir that will be automatically cleaned up"""
-        tempdir = tempfile.TemporaryDirectory()  # pylint: disable=consider-using-with
+        tempdir = tempfile.TemporaryDirectory()
         self.addCleanup(tempdir.cleanup)
         return tempdir.name
 
@@ -120,7 +120,7 @@ def setUp(self):
         filecmp.clear_cache()
 
         # you'll always want this when debugging
-        self.maxDiff = None  # pylint: disable=invalid-name
+        self.maxDiff = None
 
     def assert_etl_output_equal(self, left: str, right: str):
         """Compares the etl output with the expected json structure"""
@@ -188,7 +188,7 @@ def setUp(self):
         ).export(as_dict=True)
         self.fhir_jwks = {"keys": [jwk_token]}
 
-        self._fhir_jwks_file = tempfile.NamedTemporaryFile()  # pylint: disable=consider-using-with
+        self._fhir_jwks_file = tempfile.NamedTemporaryFile()
         self._fhir_jwks_file.write(json.dumps(self.fhir_jwks).encode("utf8"))
         self._fhir_jwks_file.flush()
         self.addCleanup(self._fhir_jwks_file.close)