lint

Author: cmungall

src/semsql/builder/builder.py

@@ -28,7 +28,9 @@ class DockerConfig:
     memory: str = None
 
 
-def make(target: str, docker_config: Optional[DockerConfig] = None, prefix_csv_path = None):
+def make(
+    target: str, docker_config: Optional[DockerConfig] = None, prefix_csv_path=None
+):
     """
     Builds a target such as a SQLite file using the build.Makefile
 
@@ -93,7 +95,7 @@ def download_obo_sqlite(ontology: str, destination: str):
     db = f"{ontology}.db"
     url = f"https://s3.amazonaws.com/bbop-sqlite/{db}.gz"
     logging.info(f"Downloading from {url}")
-    r = requests.get(url, allow_redirects=True)
+    r = requests.get(url, allow_redirects=True, timeout=3600)
     destination_gzip = f"{destination}.gz"
     open(destination_gzip, "wb").write(r.content)
     with gzip.open(destination_gzip, "rb") as f_in:

src/semsql/builder/cli.py

@@ -33,11 +33,7 @@ def main(verbose: int, quiet: bool):
     show_default=True,
     help="Uses ODK docker image",
 )
-@click.option(
-    "--prefix-csv-path",
-    "-P",
-    help="path to csv of prefix expansions"
-)
+@click.option("--prefix-csv-path", "-P", help="path to csv of prefix expansions")
 def make(path, docker, **kwargs):
     """
     Makes a specified target, such as a db file

src/semsql/builder/registry/registry_schema.py

@@ -326,7 +326,6 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
 
 # Enumerations
 class FormatEnum(EnumDefinitionImpl):
-
     n3 = PermissibleValue(text="n3", description="n3")
 
     _defn = EnumDefinition(
@@ -335,7 +334,6 @@ class FormatEnum(EnumDefinitionImpl):
 
 
 class CompressionEnum(EnumDefinitionImpl):
-
     gzip = PermissibleValue(text="gzip", description="gzip")
 
     _defn = EnumDefinition(