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Check if score set has variants before mapping, return error if not #25

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merged 2 commits into from
Nov 21, 2024
Merged

Check if score set has variants before mapping, return error if not #25

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85c25b8
Check if score set has variants before mapping, return error if no va…
sallybg Oct 14, 2024
2813d84
Do not map score sets without variants in API function
sallybg Oct 18, 2024
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8 changes: 8 additions & 0 deletions src/api/routers/map.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,14 @@ async def map_scoreset(urn: str) -> ScoresetMapping:
msg = f"Unable to acquire resource from MaveDB: {e}"
raise HTTPException(status_code=500, detail=msg) from e

if not records:
return JSONResponse(
content=ScoresetMapping(
metadata=metadata,
error_message="Score set contains no variants to map",
).model_dump(exclude_none=True)
)

try:
alignment_result = align(metadata, True)
except BlatNotFoundError as e:
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14 changes: 14 additions & 0 deletions src/dcd_mapping/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -321,6 +321,20 @@ async def map_scoreset_urn(
_logger.critical(msg)
click.echo(f"Error: {msg}")
raise e

if not records:
_emit_info("Score set contains no variants to map", silent, logging.ERROR)
final_output = write_scoreset_mapping_to_json(
urn,
ScoresetMapping(
metadata=metadata,
error_message="Score set contains no variants to map",
),
output_path,
)
_emit_info(f"Score set mapping output saved to: {final_output}.", silent)
return

await map_scoreset(
metadata, records, output_path, vrs_version, prefer_genomic, silent
)
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