Merge pull request #420 from VariantEffect/improve/estelle/350/surfaceValidationErrors

Show the variants that have problem in error message.

Author: EstelleDa

src/mavedb/lib/validation/dataframe/column.py

@@ -73,17 +73,38 @@ def validate_variant_formatting(column: pd.Series, prefixes: list[str], targets:
 
     # if there is more than one target, we expect variants to be fully qualified
     if fully_qualified:
-        if not all(len(str(v).split(":")) == 2 for v in variants):
+        invalid_fully_qualified = [f"{len(str(v).split(':'))} invalid fully qualified found from row {idx}"
+                                   for idx, v in enumerate(variants) if len(str(v).split(":")) != 2]
+        if invalid_fully_qualified:
             raise ValidationError(
-                f"variants in the provided column '{column.name}' were expected to be fully qualified, but are not described in relation to an accession"
+                f"variant column '{column.name}' has {len(invalid_fully_qualified)} unqualified variants.",
+                triggers=invalid_fully_qualified
             )
-        if len(set(str(v).split(":")[1][:2] for v in variants)) > 1:
-            raise ValidationError(f"variant column '{column.name}' has inconsistent variant prefixes")
-        if not all(str(v).split(":")[1][:2] in prefixes for v in variants):
-            raise ValidationError(f"variant column '{column.name}' has invalid variant prefixes")
-        if not all(str(v).split(":")[0] in targets for v in variants):
+
+        inconsistent_prefixes = [f"row {idx}: '{v}' uses inconsistent prefix '{str(v).split(':')[1][:2]}'"
+                                 for idx, v in enumerate(variants)
+                                 if len(set(str(v).split(":")[1][:2] for v in variants)) > 1]
+        if inconsistent_prefixes:
+            raise ValidationError(
+                f"variant column '{column.name}' has {len(inconsistent_prefixes)} inconsistent variant prefixes.",
+                triggers=inconsistent_prefixes
+            )
+
+        invalid_prefixes = [f"row {idx}: '{v}' uses invalid prefix '{str(v).split(':')[1][:2]}'"
+                            for idx, v in enumerate(variants) if str(v).split(":")[1][:2] not in prefixes]
+        if invalid_prefixes:
+            raise ValidationError(
+                f"variant column '{column.name}' has {len(invalid_prefixes)} invalid variant prefixes.",
+                triggers=invalid_prefixes
+            )
+
+        invalid_accessions = [f"accession identifier {str(v).split(':')[0]} from row {idx}, variant {v} not found"
+                              for idx, v in enumerate(variants) if str(v).split(":")[0] not in targets]
+        if invalid_accessions:
             raise ValidationError(
-                f"variant column '{column.name}' has invalid accession identifiers; some accession identifiers present in the score file were not added as targets"
+                f"variant column '{column.name}' has invalid accession identifiers; "
+                f"{len(invalid_accessions)} accession identifiers present in the score file were not added as targets.",
+                triggers=invalid_accessions
             )
 
     else: