Merge branch 'feature/extract_patient_data' into 'dev'

retrieve_patient_data.py: Script used to export some filtered patient data

See merge request !616

server/web2py/applications/vidjil/scripts/retrieve_patient_data.py

+from __future__ import print_function
+from datetime import datetime
+import sys
+import tarfile
+import json
+
+if len(sys.argv) < 5 or sys.argv[1] == "-h" or sys.argv[1] == "--help" or sys.argv[1] is None:
+    print("Usage: %s <user id> <filter> <config_id> <outfile>\n\nGet a JSON output of all the patients accessible by the user with the specified config." % sys.argv[0])
+    exit(1)
+
+def get_json_patient(patient, config_id):
+    '''
+    Takes a row from the db.patient table and outputs a JSON on the patient.
+    '''
+    p = {}
+    p['id'] = patient.sample_set_id
+    p['last_name'] = patient.last_name
+    p['first_name'] = patient.first_name
+    p['birth'] = str(patient.birth)
+    p['info'] = patient.info
+
+    results = db(
+        (db.sequence_file.id == db.sample_set_membership.sequence_file_id)
+        & (db.sample_set_membership.sample_set_id == patient.sample_set_id)
+    ).select(
+        left=db.results_file.on(
+            (db.results_file.sequence_file_id==db.sequence_file.id)
+            & (db.results_file.config_id==str(config_id))
+            & (db.results_file.hidden == False)
+        ),
+        orderby = db.sequence_file.id
+    )
+
+    patient_results = []
+    for r in results:
+        info = {
+            'info': r.sequence_file.info,
+            'data': r.sequence_file.data_file,
+            'date': str(r.sequence_file.sampling_date),
+            'id': r.sequence_file.id,
+            'results': r.results_file.data_file,
+            'results_date': str(r.results_file.run_date),
+            'results_id': r.results_file.id
+        }
+        patient_results.append(info)
+
+    p['sequence_files'] = patient_results
+
+    return p
+    
+def get_patient_filtered_data(filter, config_id):
+    request.vars["type"] = defs.SET_TYPE_PATIENT
+    request.vars["filter"] = filter
+    execfile("applications/vidjil/controllers/sample_set.py", globals())
+    results = all()
+
+    patient_list = []
+
+    for patient in results['query']:
+        patient_list.append(get_json_patient(patient, config_id))
+
+    return json.dumps(patient_list)
+    
+if __name__ == '__main__':
+    auth.user = db.auth_user[int(sys.argv[1])]
+
+    # Override the function to prevent errors
+    auth.is_impersonating = lambda: False
+
+    f = open(sys.argv[4], 'w')
+    f.write(get_patient_filtered_data(sys.argv[2], int(sys.argv[3])))
+    f.close()