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DIG-1803, DIG-1810: query fixes #55

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merged 4 commits into from
Oct 18, 2024
Merged

DIG-1803, DIG-1810: query fixes #55

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2595394
[wip]
OrdiNeu Sep 17, 2024
a236153
Add link to API in readme
kcranston Oct 10, 2024
47416a5
query needs to default to giant page size
daisieh Oct 17, 2024
ffdc3e9
update query param names
daisieh Oct 18, 2024
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2 changes: 2 additions & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@

Query API for Katsu and HTSGet that allows for caching and pagination of calls.

[openapi spec on Swagger](https://editor.swagger.io/?url=https://raw.githubusercontent.com/CanDIG/query/main/query_server/openapi.yaml)

## Stack

- [Flask](http://flask.pocoo.org/)
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13 changes: 8 additions & 5 deletions query_server/query_operations.py
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Expand Up @@ -224,7 +224,9 @@ def query(treatment="", primary_site="", drug_name="", systemic_therapy_type="",
(systemic_therapy_type, "systemic_therapy_type"),
(exclude_cohorts, "exclude_cohorts")
]
params = {}
params = {
'page_size': PAGE_SIZE
}
for param in param_mapping:
if param[0] == "" or param[0] == []:
continue
Expand Down Expand Up @@ -430,7 +432,7 @@ def discovery_programs():
return fix_dicts(ret_val), 200

@app.route('/discovery/query')
def discovery_query(treatment="", primary_site="", systemic_therapy="", systemic_therapy_type="", chrom="", gene="", assembly="hg38", exclude_cohorts=[]):
def discovery_query(treatment="", primary_site="", drug_name="", chrom="", gene="", assembly="hg38", exclude_cohorts=[]):
url = f"{config.KATSU_URL}/v3/explorer/donors/"
headers = {}
for k in request.headers.keys():
Expand All @@ -440,11 +442,12 @@ def discovery_query(treatment="", primary_site="", systemic_therapy="", systemic
param_mapping = [
(treatment, "treatment_type"),
(primary_site, "primary_site"),
(systemic_therapy, "systemic_therapy_drug_name"),
(systemic_therapy_type, "systemic_therapy_type"),
(drug_name, "systemic_therapy_drug_name"),
(exclude_cohorts, "exclude_cohorts")
]
params = {}
params = {
"page_size": PAGE_SIZE
}
for param in param_mapping:
if param[0] == "" or param[0] == []:
continue
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