rm noqa e501s that arent needed

src/therapy/database.py

@@ -68,12 +68,12 @@ def __init__(self, db_url: str = "", region_name: str = "us-east-2") -> None:
             if aws_env not in VALID_AWS_ENV_NAMES:
                 raise DatabaseException(
                     f"{AWS_ENV_VAR_NAME} must be one of {VALID_AWS_ENV_NAMES}"
-                )  # noqa: E501
+                )
 
             skip_confirmation = environ.get(SKIP_AWS_DB_ENV_NAME)
             if (not skip_confirmation) or (
                 skip_confirmation and skip_confirmation != "true"
-            ):  # noqa: E501
+            ):
                 confirm_aws_db_use(environ[AWS_ENV_VAR_NAME])
 
             boto_params = {"region_name": region_name}

src/therapy/etl/chembl.py

@@ -190,7 +190,7 @@ def _load_meta(self) -> None:
         """Add ChEMBL metadata."""
         metadata = SourceMeta(
             data_license="CC BY-SA 3.0",
-            data_license_url="https://creativecommons.org/licenses/by-sa/3.0/",  # noqa: E501
+            data_license_url="https://creativecommons.org/licenses/by-sa/3.0/",
             version=self._version,
             data_url=bioversions.resolve("chembl").homepage,
             rdp_url="http://reusabledata.org/chembl.html",

src/therapy/etl/guidetopharmacology.py

@@ -29,7 +29,7 @@ def _download_data(self) -> None:
             assert self._ligands_file.exists()
         if not self._mapping_file.exists():
             self._http_download(
-                "https://www.guidetopharmacology.org/DATA/ligand_id_mapping.tsv",  # noqa: E501
+                "https://www.guidetopharmacology.org/DATA/ligand_id_mapping.tsv",
                 self._mapping_file,
             )
             assert self._mapping_file.exists()
@@ -78,7 +78,7 @@ def _extract_data(self, use_existing: bool = False) -> None:
                     )
                 check_mapping_file = (
                     self._src_dir / f"{prefix}_ligand_id_mapping_{version}.tsv"
-                )  # noqa: E501
+                )
                 if check_mapping_file.exists():
                     self._version = version
                     self._ligands_file = ligands_file
@@ -95,7 +95,7 @@ def _extract_data(self, use_existing: bool = False) -> None:
             self._ligands_file = self._src_dir / f"{prefix}_ligands_{self._version}.tsv"
             self._mapping_file = (
                 self._src_dir / f"{prefix}_ligand_id_mapping_{self._version}.tsv"
-            )  # noqa: E501
+            )
             if not (self._ligands_file.exists() and self._mapping_file.exists()):
                 self._download_data()
                 assert self._ligands_file.exists()
@@ -176,11 +176,11 @@ def _transform_ligands(self, data: Dict) -> None:
                 if row[8]:
                     associated_with.append(
                         f"{NamespacePrefix.PUBCHEMSUBSTANCE.value}:{row[8]}"
-                    )  # noqa: E501
+                    )
                 if row[9]:
                     associated_with.append(
                         f"{NamespacePrefix.PUBCHEMCOMPOUND.value}:{row[9]}"
-                    )  # noqa: E501
+                    )
                 if row[10]:
                     associated_with.append(f"{NamespacePrefix.UNIPROT.value}:{row[10]}")
                 if row[16]:
@@ -202,7 +202,7 @@ def _transform_ligands(self, data: Dict) -> None:
                 if row[20]:
                     associated_with.append(
                         f"{NamespacePrefix.INCHIKEY.value}:{row[20]}"
-                    )  # noqa: E501
+                    )
 
                 if associated_with:
                     params["associated_with"] = associated_with

src/therapy/etl/hemonc.py

@@ -33,7 +33,7 @@ def get_latest_version(self) -> str:
         """
         response = requests.get(
             "https://dataverse.harvard.edu/api/datasets/export?persistentId=doi:10.7910/DVN/9CY9C6&exporter=dataverse_json"
-        )  # noqa: E501
+        )
         try:
             response.raise_for_status()
         except requests.HTTPError as e:

src/therapy/etl/rxnorm.py

@@ -63,7 +63,7 @@ def _create_drug_form_yaml(self) -> None:
         """Create a YAML file containing RxNorm drug form values."""
         self._drug_forms_file = (
             self._src_dir / f"rxnorm_drug_forms_{self._version}.yaml"
-        )  # noqa: E501
+        )
         dfs = []
         with open(self._src_file) as f:  # type: ignore
             data = csv.reader(f, delimiter="|")

src/therapy/schemas.py

@@ -615,7 +615,7 @@ class NormalizationService(BaseNormalizationService):
                         "data_license": "custom",
                         "data_license_url": "https://www.nlm.nih.gov/databases/download/terms_and_conditions.html",  # noqa: E501
                         "version": "20200327",
-                        "data_url": "ftp://ftp.nlm.nih.gov/nlmdata/.chemidlease/",  # noqa: E501
+                        "data_url": "ftp://ftp.nlm.nih.gov/nlmdata/.chemidlease/",
                         "rdp_url": None,
                         "data_license_attributes": {
                             "non_commercial": False,

tests/unit/test_chembl.py

@@ -238,7 +238,7 @@ def test_meta_info(chembl):
     assert response.source_meta_.version == "31"
     assert response.source_meta_.data_url.startswith(
         "ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb"
-    )  # noqa: E501
+    )
     assert response.source_meta_.rdp_url == "http://reusabledata.org/chembl.html"
     assert response.source_meta_.data_license_attributes == {
         "non_commercial": False,

tests/unit/test_chemidplus.py

@@ -205,11 +205,11 @@ def test_meta(chemidplus):
     assert (
         response.source_meta_.data_license_url
         == "https://www.nlm.nih.gov/databases/download/terms_and_conditions.html"
-    )  # noqa: E501
+    )
     assert isodate.parse_date(response.source_meta_.version)
     assert (
         response.source_meta_.data_url == "ftp://ftp.nlm.nih.gov/nlmdata/.chemidlease/"
-    )  # noqa: E501
+    )
     assert response.source_meta_.rdp_url is None
     assert response.source_meta_.data_license_attributes == {
         "non_commercial": False,

tests/unit/test_disease_indication.py

@@ -11,7 +11,7 @@
 RUN_TEST = (
     os.environ.get("THERAPY_TEST", "").lower() == "true"
     and AWS_ENV_VAR_NAME not in os.environ
-)  # noqa: E501
+)
 
 
 class TestDiseaseIndication(DiseaseIndicationBase):

tests/unit/test_drugbank.py

@@ -201,7 +201,7 @@ def test_meta_info(drugbank):
     assert (
         response.data_license_url
         == "https://creativecommons.org/publicdomain/zero/1.0/"
-    )  # noqa: E501
+    )
     assert re.match(r"[0-9]+\.[0-9]+\.[0-9]", response.version)
     assert response.data_url == "https://go.drugbank.com/releases/latest#open-data"
     assert response.rdp_url == "http://reusabledata.org/drugbank.html"

tests/unit/test_drugsatfda.py

@@ -448,12 +448,12 @@ def test_meta(drugsatfda):
     assert (
         response.source_meta_.data_license_url
         == "https://creativecommons.org/publicdomain/zero/1.0/legalcode"
-    )  # noqa: E501
+    )
     assert isodate.parse_date(response.source_meta_.version)
     assert (
         response.source_meta_.data_url
         == "https://open.fda.gov/apis/drug/drugsfda/download/"
-    )  # noqa: E501
+    )
     assert response.source_meta_.rdp_url is None
     assert response.source_meta_.data_license_attributes == {
         "non_commercial": False,

tests/unit/test_hemonc.py

@@ -218,12 +218,12 @@ def test_metadata(hemonc):
     assert (
         response.data_license_url
         == "https://creativecommons.org/licenses/by/4.0/legalcode"
-    )  # noqa: E501
+    )
     assert isodate.parse_date(response.version)
     assert (
         response.data_url
         == "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/9CY9C6"
-    )  # noqa: E501
+    )
     assert response.rdp_url is None
     assert response.data_license_attributes == {
         "non_commercial": False,

tests/unit/test_query.py

@@ -772,14 +772,14 @@ def test_service_meta(search_handler, normalize_handler):
     assert service_meta.name == "thera-py"
     assert service_meta.version >= "0.2.13"
     assert isinstance(service_meta.response_datetime, datetime)
-    assert service_meta.url == "https://github.com/cancervariants/therapy-normalization"  # noqa: E501
+    assert service_meta.url == "https://github.com/cancervariants/therapy-normalization"
 
     response = normalize_handler.normalize(query)
     service_meta = response.service_meta_
     assert service_meta.name == "thera-py"
     assert service_meta.version >= "0.2.13"
     assert isinstance(service_meta.response_datetime, datetime)
-    assert service_meta.url == "https://github.com/cancervariants/therapy-normalization"  # noqa: E501
+    assert service_meta.url == "https://github.com/cancervariants/therapy-normalization"
 
 
 def test_broken_db_handling(normalize_handler):