From a88731ca3211faffaef49bd03ccc009c755b2f38 Mon Sep 17 00:00:00 2001 From: David Lougheed Date: Fri, 28 Nov 2025 17:13:23 -0500 Subject: [PATCH] fix: misc cbioportal issues --- chord_metadata_service/chord/export/cbioportal.py | 5 ++++- chord_metadata_service/chord/export/views.py | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/chord_metadata_service/chord/export/cbioportal.py b/chord_metadata_service/chord/export/cbioportal.py index 2a6f32b66..8a0ac3793 100644 --- a/chord_metadata_service/chord/export/cbioportal.py +++ b/chord_metadata_service/chord/export/cbioportal.py @@ -239,6 +239,8 @@ async def sample_export(results, file_handle: TextIO): - DRIVER_MUTATIONS """ + columns = ["individual_id", "id"] + samples = [] async for sample in results: if sample.individual_id is None: @@ -251,11 +253,12 @@ async def sample_export(results, file_handle: TextIO): "id": sanitize_id(sample.id) } if sample.sampled_tissue: + if "tissue_label" not in columns: + columns.append("tissue_label") sample_obj["tissue_label"] = sample.sampled_tissue.get("label", "") samples.append(sample_obj) - columns = list(samples[0].keys()) headers = biosample_to_sample_header(columns) file_handle.writelines([f"{line}\n" for line in headers]) diff --git a/chord_metadata_service/chord/export/views.py b/chord_metadata_service/chord/export/views.py index 56b56b1c7..7b50ef033 100644 --- a/chord_metadata_service/chord/export/views.py +++ b/chord_metadata_service/chord/export/views.py @@ -40,7 +40,7 @@ async def export(request: DrfRequest): res = await authz_middleware.async_evaluate_one(request, RESOURCE_EVERYTHING, P_EXPORT_DATA, mark_authz_done=True) if not res: - return Response(errors.forbidden_error("Fobidden"), status=status.HTTP_403_FORBIDDEN) + return Response(errors.forbidden_error("Forbidden"), status=status.HTTP_403_FORBIDDEN) # TODO: Schema for OpenAPI doc