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hotfix: Add try catches for timeout errors #198

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hotfix: Add try catches for timeout errors #198

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469866a
add catches for timeout errors
mshadbolt Mar 17, 2026
33abbc4
remove non connection trycatch
mshadbolt Mar 17, 2026
cdfc003
change to exceptions instead of logging
mshadbolt Mar 17, 2026
4fdf6c2
remove len
mshadbolt Mar 17, 2026
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13 changes: 11 additions & 2 deletions htsget_ingest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,6 +11,7 @@
from clinical_etl.schema import openapi_to_jsonschema
import jsonschema
from candigv2_logging.logging import CanDIGLogger
from requests.exceptions import ConnectTimeout


logger = CanDIGLogger(__file__)
Expand Down Expand Up @@ -311,9 +312,15 @@ def parse_s3_url(url):
data["object"] = object[0]
if len(object) > 1:
data["object"] = object[0]
response, status_code = get_s3_url(s3_endpoint=data["endpoint"], bucket=data["bucket"], object_id=data["object"], access_key=None, secret_key=None, region=None, public=True)
try:
response, status_code = get_s3_url(s3_endpoint=data["endpoint"], bucket=data["bucket"], object_id=data["object"], access_key=None, secret_key=None, region=None, public=True)
except ConnectTimeout as e:
raise Exception(f"Could not read {data["object"]}: {e}")
else:
response, status_code = get_s3_url(s3_endpoint=data["endpoint"], bucket=data["bucket"], object_id=data["object"], access_key=None, secret_key=None, region=None, public=False)
try:
response, status_code = get_s3_url(s3_endpoint=data["endpoint"], bucket=data["bucket"], object_id=data["object"], access_key=None, secret_key=None, region=None, public=False)
except ConnectTimeout as e:
raise Exception(f"Could not read {data["object"]}: {e}")

if status_code == 500:
raise Exception(response["error"])
Expand Down Expand Up @@ -509,6 +516,7 @@ def check_genomic_data(dataset, token):
result["errors"][program_id].append({analysis["analysis_id"]: sample_errors})
if len(result["errors"][program_id]) == 0:
result["errors"].pop(program_id)

if len(result["errors"]) == 0:
return by_program, 200
return result, 400
Expand Down Expand Up @@ -541,5 +549,6 @@ def main():
result, status_code = htsget_ingest(result)
print(json.dumps(result, indent=4))


if __name__ == "__main__":
main()
2 changes: 1 addition & 1 deletion requirements.txt
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
requests==2.32.4
requests-mock>=1.12.1
candigv2-authx@git+https://github.com/CanDIG/candigv2-authx.git@v2.8.7
clinical_etl@git+https://github.com/CanDIG/clinical_ETL_code.git@v3.2.0
clinical_etl@git+https://github.com/CanDIG/clinical_ETL_code.git@v3.4.0
candigv2-logging@git+https://github.com/CanDIG/candigv2-logging.git@v1.0.3
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