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Query should handle 401 unauthorized exceptions from Katsu gracefully #56

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Oct 21, 2024
Merged

Query should handle 401 unauthorized exceptions from Katsu gracefully #56

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42 changes: 28 additions & 14 deletions query_server/query_operations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -199,6 +199,22 @@ def fix_dicts(to_fix):
else:
return to_fix

# Helper function to format the response from a query into a format the data portal understands
def format_query_response(donors, genomic_query, summary_stats, page, page_size):
# Determine which part of the filtered donors to send back
full_data = {
'results': donors[(page*page_size):((page+1)*page_size)],
'genomic': genomic_query,
'count': len(donors),
'summary': summary_stats
}
# full_data['genomic_query_info'] = genomic_query_info

# Add prev and next parameters to the repsonse, appending a session ID.
# Essentially we want to go session ID -> list of donors
# and then paginate the list of donors, calling donors_with_clinical_data on each before returning
return fix_dicts(full_data), 200

@app.route('/query')
def query(treatment="", primary_site="", drug_name="", systemic_therapy_type="", chrom="", gene="", page=0, page_size=10, assembly="hg38", exclude_cohorts=[], session_id=""):
# Add a service token to the headers so that other services will know this is from the query service:
Expand Down Expand Up @@ -233,7 +249,17 @@ def query(treatment="", primary_site="", drug_name="", systemic_therapy_type="",
params[param[1]] = param[0]

full_url = f"{url}?{urllib.parse.urlencode(params, doseq=True)}"
donors = safe_get_request_json(requests.get(full_url, headers=headers), 'Katsu explorer donors')['items']
donors_req = requests.get(full_url, headers=headers)
if not donors_req.ok:
if donors_req.status_code == 401:
# 401 Unauthorized: the user is not allowed to view any donors at this site
# The rest of the code should just pass quietly
return format_query_response([], [], get_summary_stats([], {}, {}), page, page_size)
else:
err_msg = f"Could not got Katsu donors response: {donors_req.status_code} {donors_req.text}"
logger.error(err_msg)
raise Exception(err_msg)
donors = donors_req.json()['items']

# Filter on excluded cohorts
donors = [donor for donor in donors if donor['program_id'] not in exclude_cohorts]
Expand Down Expand Up @@ -317,19 +343,7 @@ def query(treatment="", primary_site="", drug_name="", systemic_therapy_type="",
# TODO: Cache the above list of donor IDs and summary statistics
summary_stats = get_summary_stats(donors, summary_info['primary_site'], summary_info['treatment_type'])

# Determine which part of the filtered donors to send back
full_data = {
'results': [donor for donor in donors[(page*page_size):((page+1)*page_size)]],
'genomic': genomic_query,
'count': len(donors),
'summary': summary_stats
}
# full_data['genomic_query_info'] = genomic_query_info

# Add prev and next parameters to the repsonse, appending a session ID.
# Essentially we want to go session ID -> list of donors
# and then paginate the list of donors, calling donors_with_clinical_data on each before returning
return fix_dicts(full_data), 200
return format_query_response(donors, genomic_query, summary_stats, page, page_size)

@app.route('/genomic_completeness')
def genomic_completeness():
Expand Down