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Add fixes for things that changed with the Katsu UUID fix #6

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merged 1 commit into from
Dec 19, 2023
Merged

Add fixes for things that changed with the Katsu UUID fix #6

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27 changes: 13 additions & 14 deletions query_server/query_operations.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,8 @@ def get_donors_from_katsu(url, param_name, parameter_list):
'page_size': PAGE_SIZE
}
treatments = requests.get(f"{url}?{urllib.parse.urlencode(parameters)}", headers=request.headers)
results = safe_get_request_json(treatments, f'Katsu {param_name}')['results']
results = safe_get_request_json(treatments, f'Katsu {param_name}')['items']
permissible_donors |= set([result['submitter_donor_id'] for result in results])
print(permissible_donors)
return permissible_donors

def add_or_increment(dict, key):
Expand All @@ -59,7 +58,7 @@ def get_summary_stats(donors, headers):
# Perform (and cache) summary statistics
diagnoses = requests.get(f"{config.KATSU_URL}/v2/authorized/primary_diagnoses/?page_size={PAGE_SIZE}",
headers=headers)
diagnoses = safe_get_request_json(diagnoses, 'Katsu diagnoses')['results']
diagnoses = safe_get_request_json(diagnoses, 'Katsu diagnoses')['items']
# This search is inefficient O(m*n)
# Should find a better way (Preferably SQL again)
donor_date_of_births = {}
Expand Down Expand Up @@ -100,7 +99,7 @@ def get_summary_stats(donors, headers):
# http://candig.docker.internal:8008/v2/authorized/treatments/
treatments = requests.get(f"{config.KATSU_URL}/v2/authorized/treatments/?page_size={PAGE_SIZE}",
headers=headers)
treatments = safe_get_request_json(treatments, 'Katsu treatments')['results']
treatments = safe_get_request_json(treatments, 'Katsu treatments')['items']
treatment_type_count = {}
for treatment in treatments:
# This search is inefficient O(m*n)
Expand Down Expand Up @@ -198,11 +197,9 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm
r = safe_get_request_json(requests.get(f"{url}?{urllib.parse.urlencode(params)}",
# Reuse their bearer token
headers=request.headers), 'Katsu Donors')
donors = r['results']
donors = r['items']

# Filter on excluded cohorts
print(str(donors))
print(str(exclude_cohorts))
donors = [donor for donor in donors if donor['program_id'] not in exclude_cohorts]

# Will need to look into how to go about this -- ideally we implement this into the SQL in Katsu's side
Expand Down Expand Up @@ -276,14 +273,16 @@ def query(treatment="", primary_site="", chemotherapy="", immunotherapy="", horm

# Determine which part of the filtered donors to send back
ret_donors = [donor['submitter_donor_id'] for donor in donors[(page*page_size):((page+1)*page_size)]]
ret_programs = [donor['program_id'] for donor in donors[(page*page_size):((page+1)*page_size)]]
full_data = {'results' : []}
if len(donors) > 0:
params = {
'page_size': page_size,
'donors': ','.join(ret_donors)
}
r = requests.get(f"{config.KATSU_URL}/v2/authorized/donor_with_clinical_data/?{urllib.parse.urlencode(params)}",
headers=request.headers)
full_data = safe_get_request_json(r, 'Katsu donor clinical data')
for i, donor_id in enumerate(ret_donors):
donor_id_url = urllib.parse.quote(donor_id)
program_id_url = urllib.parse.quote(ret_programs[i])
print('asdf')
r = requests.get(f"{config.KATSU_URL}/v2/authorized/donor_with_clinical_data/program/{program_id_url}/donor/{donor_id_url}",
headers=request.headers)
full_data['results'].append(safe_get_request_json(r, 'Katsu donor clinical data'))
else:
full_data = {'results': []}
full_data['genomic'] = genomic_query
Expand Down