lint - remove unused imports. black --line-len 100 -C

bcgsc · Jul 19, 2024 · e27e2d5 · e27e2d5
1 parent 9c1e70c
commit e27e2d5
Show file tree

Hide file tree

Showing 2 changed files with 11 additions and 41 deletions.
diff --git a/pori_python/ipr/main.py b/pori_python/ipr/main.py
@@ -74,10 +74,7 @@ def command_interface() -> None:
     parser.add_argument("--graphkb_url", default=None)
     parser.add_argument("--log_level", default="info", choices=LOG_LEVELS.keys())
     parser.add_argument(
-        "--therapeutics",
-        default=False,
-        help="Generate therapeutic options",
-        action="store_true",
+        "--therapeutics", default=False, help="Generate therapeutic options", action="store_true"
     )
     parser.add_argument(
         "--skip_comments",
@@ -86,9 +83,7 @@ def command_interface() -> None:
         help="Turn off generating the analyst comments section of the report",
     )
     parser.add_argument(
-        "-o",
-        "--output_json_path",
-        help="path to a JSON to output the report upload body",
+        "-o", "--output_json_path", help="path to a JSON to output the report upload body"
     )
     parser.add_argument(
         "-w",
@@ -370,10 +365,7 @@ def ipr_report(
     logger.info(f"annotating {len(structural_variants)} structural variants")
     gkb_matches.extend(
         annotate_positional_variants(
-            graphkb_conn,
-            structural_variants,
-            kb_disease_match,
-            show_progress=interactive,
+            graphkb_conn, structural_variants, kb_disease_match, show_progress=interactive
         )
     )
     logger.debug(f"\tgkb_matches: {len(gkb_matches)}")
@@ -389,10 +381,7 @@ def ipr_report(
     logger.info(f"annotating {len(expression_variants)} expression variants")
     gkb_matches.extend(
         annotate_expression_variants(
-            graphkb_conn,
-            expression_variants,
-            kb_disease_match,
-            show_progress=interactive,
+            graphkb_conn, expression_variants, kb_disease_match, show_progress=interactive
         )
     )
     logger.debug(f"\tgkb_matches: {len(gkb_matches)}")
@@ -429,10 +418,7 @@ def ipr_report(
     if generate_comments:
         comments = {
             "comments": summarize(
-                graphkb_conn,
-                gkb_matches,
-                disease_name=kb_disease_match,
-                variants=all_variants,
+                graphkb_conn, gkb_matches, disease_name=kb_disease_match, variants=all_variants
             )
         }
     else:

diff --git a/tests/test_ipr/test_upload.py b/tests/test_ipr/test_upload.py
@@ -4,8 +4,8 @@
 import pytest
 import sys
 import uuid
-from typing import Dict, Tuple
-from unittest.mock import MagicMock, patch
+from typing import Dict
+from unittest.mock import patch
 
 from pori_python.ipr.connection import IprConnection
 from pori_python.ipr.main import command_interface
@@ -41,10 +41,7 @@ def loaded_reports(tmp_path_factory) -> Dict:
             {"analysisRole": "expression (disease)", "name": "1"},
             {"analysisRole": "expression (primary site)", "name": "2"},
             {"analysisRole": "expression (biopsy site)", "name": "3"},
-            {
-                "analysisRole": "expression (internal pancancer cohort)",
-                "name": "4",
-            },
+            {"analysisRole": "expression (internal pancancer cohort)", "name": "4"},
         ],
         "patientId": patient_id,
         "project": "TEST",
@@ -66,20 +63,10 @@ def loaded_reports(tmp_path_factory) -> Dict:
         ),
         "kbDiseaseMatch": "colorectal cancer",
     }
-    json_file.write_text(
-        json.dumps(
-            json_contents,
-            allow_nan=False,
-        )
-    )
+    json_file.write_text(json.dumps(json_contents, allow_nan=False))
 
     json_contents["patientId"] = async_patient_id
-    async_json_file.write_text(
-        json.dumps(
-            json_contents,
-            allow_nan=False,
-        )
-    )
+    async_json_file.write_text(json.dumps(json_contents, allow_nan=False))
 
     argslist = [
         "ipr",
@@ -114,10 +101,7 @@ def loaded_reports(tmp_path_factory) -> Dict:
     loaded_report = ipr_conn.get(uri=f"reports?searchText={patient_id}")
     async_loaded_report = ipr_conn.get(uri=f"reports?searchText={async_patient_id}")
 
-    return {
-        "sync": (patient_id, loaded_report),
-        "async": (async_patient_id, async_loaded_report),
-    }
+    return {"sync": (patient_id, loaded_report), "async": (async_patient_id, async_loaded_report)}
 
 
 def get_section(loaded_report, section_name):