From f9f3e4208574cb381a3161d64722f73825eacfd3 Mon Sep 17 00:00:00 2001 From: rxu17 <26471741+rxu17@users.noreply.github.com> Date: Wed, 15 Nov 2023 21:07:56 -0800 Subject: [PATCH] update bed file case for msg formatting purposes --- genie_registry/clinical.py | 2 +- tests/test_clinical.py | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/genie_registry/clinical.py b/genie_registry/clinical.py index d649bee7..e20dac75 100644 --- 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 index 1c09c106..91815c97 100644 --- 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"], }, ]