Merge pull request #12 from bcgsc/improvement/lint_typing

Improvement/lint typing

pori_python/__init__.py

@@ -1 +1 @@
-from . import graphkb, ipr
+from . import graphkb, ipr  # noqa: F401

pori_python/graphkb/genes.py

@@ -226,11 +226,9 @@ def get_preferred_gene_name(
 def get_cancer_predisposition_info(
     conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
 ) -> Tuple[List[str], Dict[str, str]]:
-    newval = get_gene_linked_cancer_predisposition_info(conn, source)
-    genes = newval[0]
-    allvardata = newval[1]
+    genes, allvardata = get_gene_linked_cancer_predisposition_info(conn, source)
     variants = {key: allvardata[key][0] for key in allvardata.keys()}
-    return newval[0], variants
+    return genes, variants
 
 
 def get_gene_linked_cancer_predisposition_info(
@@ -322,11 +320,9 @@ def get_gene_linked_cancer_predisposition_info(
 def get_pharmacogenomic_info(
     conn: GraphKBConnection, source: str = PREFERRED_GENE_SOURCE
 ) -> Tuple[List[str], Dict[str, str]]:
-    newval = get_gene_linked_pharmacogenomic_info(conn, source)
-    genes = newval[0]
-    allvardata = newval[1]
+    genes, allvardata = get_gene_linked_pharmacogenomic_info(conn, source)
     variants = {key: allvardata[key][0] for key in allvardata.keys()}
-    return newval[0], variants
+    return genes, variants
 
 
 def get_gene_linked_pharmacogenomic_info(

pori_python/graphkb/util.py

@@ -1,6 +1,5 @@
 import requests
 from requests.adapters import HTTPAdapter
-from requests.packages.urllib3.util.retry import Retry
 
 import hashlib
 import json
@@ -9,6 +8,7 @@
 import time
 from datetime import datetime
 from typing import Any, Dict, Iterable, List, Optional, Union, cast
+from urllib3.util.retry import Retry
 
 from .constants import DEFAULT_LIMIT, DEFAULT_URL, TYPES_TO_NOTATION, AA_3to1_MAPPING
 from .types import OntologyTerm, ParsedVariant, PositionalVariant, Record

pori_python/ipr/main.py

@@ -463,7 +463,7 @@ def ipr_report(
     if ipr_upload:
         try:
             logger.info(f"Uploading to IPR {ipr_conn.url}")
-            ipr_result = ipr_conn.upload_report(output, async_upload, mins_to_wait)
+            ipr_result = ipr_conn.upload_report(output, mins_to_wait, async_upload)
             logger.info(ipr_result)
             output.update(ipr_result)
         except Exception as err:

tests/test_graphkb/test_statement.py

@@ -2,15 +2,18 @@
 import pytest
 from unittest.mock import Mock
 
-from pori_python.graphkb import statement
-
-from .test_match import (  # noqa - 'F401 imported but unused' is being fooled by pytest conventions
-    conn,
-)
+from pori_python.graphkb import GraphKBConnection, statement
 
 EXCLUDE_INTEGRATION_TESTS = os.environ.get("EXCLUDE_INTEGRATION_TESTS") == "1"
 
 
+@pytest.fixture(scope="module")
+def conn() -> GraphKBConnection:
+    conn = GraphKBConnection()
+    conn.login(os.environ["GRAPHKB_USER"], os.environ["GRAPHKB_PASS"])
+    return conn
+
+
 @pytest.fixture()
 def graphkb_conn():
     def make_rid_list(*values):