fix exception handling when one score fails matching

pgscatalog.match/src/pgscatalog/match/cli/match_cli.py

@@ -9,7 +9,7 @@
 
 import polars as pl
 
-from ..lib import (
+from .. import (
     VariantFrame,
     ScoringFileFrame,
     match_variants,

pgscatalog.match/src/pgscatalog/match/lib/matchresult.py

@@ -272,6 +272,7 @@ def write_scorefiles(
             _ = self.label(**kwargs)  # self.df gets updated
 
         if not self._filtered:
+            # score_df = original scoring file variants
             _ = self.filter(score_df=score_df, min_overlap=min_overlap)
 
         # a summary log contains up to one variant (the best match) for each variant
@@ -296,12 +297,20 @@ def write_scorefiles(
         self.summary_log = self.summary_log.collect()
 
         # error at the end, to allow logs to be generated
-        if not all(x[1] for x in self.filter_summary.iter_rows()):
-            logger.warning(f"{self.filter_summary}")
-            [
-                x.unlink() for xs in outfs for x in xs
-            ]  # don't provide dodgy scoring files
-            raise MatchRateError(
+        for x in self.filter_summary.iter_rows():
+            try:
+                if not x[1]:
+                    raise MatchRateError("Fails matching")
+            except MatchRateError:
+                # we reported the exception, but it's fine
+                logger.warning(f"Score {x[0]} matching failed with match rate {x[2]}")
+                continue
+            else:
+                logger.info(f"Score {x[0]} matching passed with match rate {x[2]}")
+
+        # unless everything is bad!
+        if not any(x[1] for x in self.filter_summary.iter_rows()):
+            raise ZeroMatchesError(
                 f"All scores fail to meet match threshold {min_overlap}"
             )
 

pgscatalog.match/tests/test_match_cli.py

@@ -4,7 +4,7 @@
 from unittest.mock import patch
 import pytest
 
-from pgscatalog.core import ZeroMatchesError, MatchRateError
+from pgscatalog.core import ZeroMatchesError
 from pgscatalog.match.cli.match_cli import run_match
 
 
@@ -124,8 +124,11 @@ def test_only_match(tmp_path_factory, good_scorefile, good_variants):
     assert "0.ipc.zst" in os.listdir(outdir)
 
 
-def test_strict_match(tmp_path_factory, good_scorefile, good_variants):
-    """Test matching well with extremely strict overlap to trigger a MatchRateError"""
+def test_stringent_match(tmp_path_factory, good_scorefile, good_variants):
+    """Test matching well with stringent match rate.
+
+    Some scores pass, some fail, but the application exits successfully.
+    """
     outdir = tmp_path_factory.mktemp("outdir")
 
     args = [
@@ -140,20 +143,26 @@ def test_strict_match(tmp_path_factory, good_scorefile, good_variants):
             "--outdir",
             str(outdir),
             "--min_overlap",
-            "1.0",
+            "0.9",
         )
     ]
     flargs = list(itertools.chain(*args))
 
-    with pytest.raises(MatchRateError):
-        with patch("sys.argv", flargs):
-            run_match()
+    with patch("sys.argv", flargs):
+        run_match()
 
     assert (outdir / "test_log.csv.gz").exists()
     assert (outdir / "test_summary.csv").exists()
-    assert not (outdir / "test_ALL_recessive_0.scorefile.gz").exists()
-    assert not (outdir / "test_ALL_dominant_0.scorefile.gz").exists()
-    assert not (outdir / "test_ALL_additive_0.scorefile.gz").exists()
+
+    with open(outdir / "test_summary.csv") as f:
+        summary = list(csv.DictReader(f))
+        # at least one score fails matching
+        assert any([x["score_pass"] == "false" for x in summary])
+        # and at least one score passes matching
+        assert any([x["score_pass"] == "true" for x in summary])
+
+    # but scoring files are still written because at least one score passed
+    assert (outdir / "test_ALL_additive_0.scorefile.gz").exists()
 
 
 def test_match_fail(tmp_path_factory, bad_scorefile, good_variants):

pgscatalog.match/tests/test_merge_cli.py

@@ -4,7 +4,7 @@
 
 from glob import glob
 
-from pgscatalog.core import MatchRateError
+from pgscatalog.core import ZeroMatchesError
 from pgscatalog.match.cli.merge_cli import run_merge
 
 
@@ -120,7 +120,7 @@ def test_splitcombine_output(tmp_path_factory, good_scorefile, match_ipc):
 
 
 def test_strict_merge(tmp_path_factory, good_scorefile, match_ipc):
-    """Test merging with extremely strict overlap to trigger a MatchRateError"""
+    """Test merging with extremely strict overlap to trigger a ZeroMatchesError"""
     outdir = tmp_path_factory.mktemp("outdir")
 
     args = [
@@ -140,6 +140,6 @@ def test_strict_merge(tmp_path_factory, good_scorefile, match_ipc):
     ]
     flargs = list(itertools.chain(*args))
 
-    with pytest.raises(MatchRateError):
+    with pytest.raises(ZeroMatchesError):
         with patch("sys.argv", flargs):
             run_merge()