update bed file case for msg formatting purposes

Sage-Bionetworks · Nov 16, 2023 · f9f3e42 · f9f3e42
1 parent f48037e
commit f9f3e42
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/genie_registry/clinical.py b/genie_registry/clinical.py
@@ -1032,7 +1032,7 @@ def _cross_validate_bed_files_exist(self, clinicaldf) -> list:
                 **exception_params,
             )
             if not bed_files["files"]:
-                missing_files.append(f"{seq_assay_id}.bed")
+                missing_files.append(f"{seq_assay_id.upper()}.bed")
         return missing_files
 
     def _cross_validate_bed_files_exist_message(self, missing_bed_files: list) -> tuple:

diff --git a/tests/test_clinical.py b/tests/test_clinical.py
@@ -1094,7 +1094,7 @@ def get_cross_validate_bed_files_test_cases():
                 [{"name": "SAGE-1-1.bed", "path": ""}],
                 [{"name": "SAGE-1.bed", "path": ""}],
             ],
-            "expected_missing_files": ["sage-1-2.bed"],
+            "expected_missing_files": ["SAGE-1-2.bed"],
         },
         {
             "name": "no_match",
@@ -1106,7 +1106,7 @@ def get_cross_validate_bed_files_test_cases():
                 [{"name": "SAGE-1-1.bed", "path": ""}],
                 [{"name": "SAGE-1.bed", "path": ""}],
             ],
-            "expected_missing_files": ["sage-1-2.bed", "sage-1-3.bed"],
+            "expected_missing_files": ["SAGE-1-2.bed", "SAGE-1-3.bed"],
         },
         {
             "name": "no_bed_files",
@@ -1116,7 +1116,7 @@ def get_cross_validate_bed_files_test_cases():
             "test_ancillary_files": [
                 [{"name": "SAGE-1.txt", "path": ""}],
             ],
-            "expected_missing_files": ["sage-1-2.bed", "sage-1-3.bed"],
+            "expected_missing_files": ["SAGE-1-2.bed", "SAGE-1-3.bed"],
         },
     ]