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DIG-2086: specify fullSearch=true to enable full search #370

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Merged
daisieh merged 2 commits into from
Oct 7, 2025
Merged

DIG-2086: specify fullSearch=true to enable full search #370

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d90cec9
specify fullSearch=true to enable full search
daisieh Sep 26, 2025
55a48ac
Update htsget_server/beacon_openapi.yaml
daisieh Oct 7, 2025
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10 changes: 10 additions & 0 deletions htsget_server/beacon_openapi.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -147,6 +147,7 @@ paths:
- $ref: '#/components/parameters/genomicAlleleShortForm'
- $ref: '#/components/parameters/geneId'
- $ref: '#/components/parameters/filters'
- $ref: '#/components/parameters/fullSearch'
responses:
'200':
$ref: '#/components/responses/ResultsOKResponse'
Expand Down Expand Up @@ -202,6 +203,12 @@ components:
type: array
items:
type: string
fullSearch:
in: query
name: fullSearch
description: Set to true if a full beacon search is desired; default is to return estimated variant count.
schema:
type: boolean
geneId:
example: BRAF
in: query
Expand Down Expand Up @@ -709,6 +716,9 @@ components:
- requestedGranularity
RequestParameters:
properties:
fullSearch:
description: Set to true if full search of files is desired
type: boolean
alternateBases:
$ref: '#/components/schemas/AlternateBases'
aminoacidChange:
Expand Down
12 changes: 9 additions & 3 deletions htsget_server/beacon_operations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,8 @@ def get_search(
variant_max_length=None,
allele=None,
gene_id=None,
filters=None
filters=None,
full_search=False
):
req = {
"includeResultsetResponses": include_result_set_responses,
Expand Down Expand Up @@ -115,6 +116,8 @@ def get_search(
req['query']['requestParameters']['variant_max_length'] = variant_max_length
if variant_min_length is not None:
req['query']['requestParameters']['variant_min_length'] = variant_min_length
if full_search:
req['query']['requestParameters']['full_search'] = True

try:
result = search(req)
Expand Down Expand Up @@ -274,8 +277,11 @@ def search(raw_req):
"meta": meta,
"authed_programs": authed_programs
}
queue_id = add_to_queue(search_json)
response["beaconResultUrl"] = f"{HTSGET_URL}/beacon/v2/result/{queue_id}"

# only send to queue if a full search was requested:
if 'full_search' in actual_params and actual_params['full_search'] == True:
queue_id = add_to_queue(search_json)
response["beaconResultUrl"] = f"{HTSGET_URL}/beacon/v2/result/{queue_id}"

# set up quick beacon results:
response["estimatedSearchParameters"] = {
Expand Down