Skip to content

fix: misc cbioportal issues #612

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Dec 1, 2025
Merged

fix: misc cbioportal issues #612

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion chord_metadata_service/chord/export/cbioportal.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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:
Expand All @@ -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])
Expand Down
2 changes: 1 addition & 1 deletion chord_metadata_service/chord/export/views.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down