fix: missing/problematic clinvar version (#19)

bihealth · Jun 21, 2023 · b11a8a4 · b11a8a4
1 parent 1e46327
commit b11a8a4
Show file tree

Hide file tree

Showing 3 changed files with 14 additions and 35 deletions.
diff --git a/clinvar_tsv/__main__.py b/clinvar_tsv/__main__.py
@@ -182,7 +182,9 @@ def main(argv=None):
     parser_merge_tsvs.set_defaults(func=run_merge_tsvs)
 
     args = parser.parse_args(argv)
-    os.environ["CLINVAR_VERSION"] = args.clinvar_version
+    clinvar_version = os.environ.get("CLINVAR_VERSION", getattr(args, "clinvar_version", None))
+    if clinvar_version:
+        os.environ["CLINVAR_VERSION"] = clinvar_version
     return run(args)
 
 

diff --git a/requirements/test.txt b/requirements/test.txt
@@ -3,7 +3,7 @@
 # Base Requirements
 -r base.txt
 
-black ==22.3.0
+black ==23.3.0
 isort >=5.10.1, <6.0
 flake8 >=5.0.4, <6.0
 pytest

diff --git a/tests/test_merge_tsvs.py b/tests/test_merge_tsvs.py
@@ -31,10 +31,7 @@ def test_summarize_stratified_single(cvs_factory, rcva_factory, cva_factory):
         stratify_by_review_status=True,
     )
     expected = ReviewedPathogenicity(
-        review_statuses=(
-            ReviewStatus.SINGLE_SUBMITTER,
-            ReviewStatus.CRITERIA_PROVIDED,
-        ),
+        review_statuses=(ReviewStatus.SINGLE_SUBMITTER, ReviewStatus.CRITERIA_PROVIDED),
         pathogenicities=(Pathogenicity.LIKELY_BENIGN,),
     )
     assert result == expected
@@ -64,10 +61,7 @@ def test_summarize_unstratified_single(cvs_factory, rcva_factory, cva_factory):
         stratify_by_review_status=False,
     )
     expected = ReviewedPathogenicity(
-        review_statuses=(
-            ReviewStatus.SINGLE_SUBMITTER,
-            ReviewStatus.CRITERIA_PROVIDED,
-        ),
+        review_statuses=(ReviewStatus.SINGLE_SUBMITTER, ReviewStatus.CRITERIA_PROVIDED),
         pathogenicities=(Pathogenicity.LIKELY_BENIGN,),
     )
     assert result == expected
@@ -216,10 +210,7 @@ def test_summarize_stratified_lb_vus(cvs_factory, rcva_factory, cva_factory):
         stratify_by_review_status=True,
     )
     expected = ReviewedPathogenicity(
-        review_statuses=(
-            ReviewStatus.SINGLE_SUBMITTER,
-            ReviewStatus.CRITERIA_PROVIDED,
-        ),
+        review_statuses=(ReviewStatus.SINGLE_SUBMITTER, ReviewStatus.CRITERIA_PROVIDED),
         pathogenicities=(Pathogenicity.LIKELY_BENIGN,),
     )
     assert result == expected
@@ -320,10 +311,7 @@ def test_summarize_unstratified_lb_b(cvs_factory, rcva_factory, cva_factory):
             ReviewStatus.CRITERIA_PROVIDED,
             ReviewStatus.NO_CONFLICTS,
         ),
-        pathogenicities=(
-            Pathogenicity.BENIGN,
-            Pathogenicity.LIKELY_BENIGN,
-        ),
+        pathogenicities=(Pathogenicity.BENIGN, Pathogenicity.LIKELY_BENIGN),
     )
     assert result == expected
 
@@ -370,10 +358,7 @@ def test_summarize_unstratified_lp_p(cvs_factory, rcva_factory, cva_factory):
             ReviewStatus.CRITERIA_PROVIDED,
             ReviewStatus.NO_CONFLICTS,
         ),
-        pathogenicities=(
-            Pathogenicity.LIKELY_PATHOGENIC,
-            Pathogenicity.PATHOGENIC,
-        ),
+        pathogenicities=(Pathogenicity.LIKELY_PATHOGENIC, Pathogenicity.PATHOGENIC),
     )
     assert result == expected
 
@@ -440,8 +425,7 @@ def test_summarize_expert_panel(cvs_factory, rcva_factory, cva_factory):
                 ),
                 cv_assertions=(
                     cva_factory(
-                        review_status="reviewed by expert panel",
-                        pathogenicity="likely pathogenic",
+                        review_status="reviewed by expert panel", pathogenicity="likely pathogenic"
                     ),
                 ),
             ),
@@ -453,8 +437,7 @@ def test_summarize_expert_panel(cvs_factory, rcva_factory, cva_factory):
                 ),
                 cv_assertions=(
                     cva_factory(
-                        review_status="criteria provided, single submitter",
-                        pathogenicity="benign",
+                        review_status="criteria provided, single submitter", pathogenicity="benign"
                     ),
                 ),
             ),
@@ -483,22 +466,16 @@ def test_summarize_practice_guideline(cvs_factory, rcva_factory, cva_factory):
                 ),
                 cv_assertions=(
                     cva_factory(
-                        review_status="practice guideline",
-                        pathogenicity="likely pathogenic",
+                        review_status="practice guideline", pathogenicity="likely pathogenic"
                     ),
                 ),
             ),
             cvs_factory(
                 ref_cv_assertion=rcva_factory(
-                    gold_stars=3,
-                    review_status="reviewed by expert panel",
-                    pathogenicity="benign",
+                    gold_stars=3, review_status="reviewed by expert panel", pathogenicity="benign"
                 ),
                 cv_assertions=(
-                    cva_factory(
-                        review_status="reviewed by expert panel",
-                        pathogenicity="benign",
-                    ),
+                    cva_factory(review_status="reviewed by expert panel", pathogenicity="benign"),
                 ),
             ),
         ],