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Miscellaneous indexing fixes #380

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Merged
daisieh merged 2 commits into from
Dec 2, 2025
Merged

Miscellaneous indexing fixes #380

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84e9a2c
return better errors
daisieh Dec 1, 2025
f64ff1a
Update htsget_operations.py
daisieh Dec 2, 2025
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7 changes: 7 additions & 0 deletions htsget_server/database.py
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Original file line number Diff line number Diff line change
Expand Up @@ -575,6 +575,13 @@ def create_pos_buckets_for_variantfile(obj):
session.bulk_insert_mappings(PositionBucketVariantFileAssociation, pbvfs_to_add)
session.commit()

with Session() as session:
new_variantfile = session.query(VariantFile).filter_by(id=variantfile_id).one_or_none()
if new_variantfile is not None:
new_variantfile.indexed = 1
session.add(new_variantfile)
session.commit()
Comment on lines +579 to +583
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@OrdiNeu OrdiNeu Dec 2, 2025

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If the new variantfile doesn't exist in the database, should it create a new entry?

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@daisieh daisieh Dec 2, 2025

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I don't think so: this is actually the second time we look up a variantfile in this method; the first time is at the top, and that time it returns None:

        if new_variantfile is None:
            logger.debug(f"couldn't find variantfile {variantfile_id}")
            return None # we can't work on nonexistent variantfiles


return None


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4 changes: 2 additions & 2 deletions htsget_server/htsget_operations.py
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Expand Up @@ -352,8 +352,8 @@ def _get_experiment(id_=None):
elif drs_obj["type"] == "read":
result["reads"].append(drs_obj["name"])
return result, 200
else:
return resp.text, resp.status_code
return f"{id_} is not an Experiment", 404
return resp.text, resp.status_code


def _get_htsget_url(id, reference_name, slice_start, slice_end, file_type, data=True):
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