add results counts on phenotype api

nlp/apis/phenotype_apis.py

@@ -196,8 +196,24 @@ def get_paged_phenotype_results(job_id: int, phenotype_final_str: str):
         if phenotype_final_str == 't' or phenotype_final_str == 'true' or phenotype_final_str == 'yes':
             phenotype_final = True
         last_id = request.args.get('last_id', '')
-        results = paged_phenotype_results(str(job_id), phenotype_final, last_id)
+        res = paged_phenotype_results(str(job_id), phenotype_final, last_id)
 
-        return json.dumps(results, indent=4, default=str)
+        return json.dumps(res, indent=4, default=str)
+    except Exception as e:
+        return "Failed to get job status" + str(e)
+
+
+@phenotype_app.route('/phenotype_subjects/<int:job_id>/<string:phenotype_final_str>', methods=['GET'])
+@auto.doc(groups=['public', 'private', 'phenotypes'])
+def get_phenotype_subjects(job_id: int, phenotype_final_str: str):
+    """GET phenotype_subjects"""
+    try:
+        phenotype_final = False
+        phenotype_final_str = phenotype_final_str.strip().lower()
+        if phenotype_final_str == 't' or phenotype_final_str == 'true' or phenotype_final_str == 'yes':
+            phenotype_final = True
+        res = phenotype_subjects(str(job_id), phenotype_final)
+
+        return json.dumps(res, indent=4, default=str)
     except Exception as e:
         return "Failed to get job status" + str(e)

nlp/data_access/__init__.py

@@ -2,6 +2,6 @@
 from .jobs import *
 from .pipeline_config import get_pipeline_config, PipelineConfig, insert_pipeline_config
 from .base_model import *
-from .results import job_results, paged_phenotype_results
+from .results import job_results, paged_phenotype_results, phenotype_subjects
 from .phenotype import *
 from .measurement_model import *

nlp/data_access/results.py

@@ -195,6 +195,41 @@ def paged_phenotype_results(job_id: str, phenotype_final: bool, last_id: str = '
     return obj
 
 
+def phenotype_subjects(job_id: str, phenotype_final: bool):
+    client = MongoClient(util.mongo_host, util.mongo_port)
+    db = client[util.mongo_db]
+    results = []
+    # db.phenotype_results.aggregate([  {"$match":{"job_id":{"$eq":10201}, "phenotype_final":{"$eq":true}}},
+    #  {"$group" : {_id:"$subject", count:{$sum:1}}} ])
+    try:
+        q = [
+            {
+                "$match": {
+                    "phenotype_final": {
+                        "$eq": phenotype_final
+                    },
+                    "job_id": {
+                        "$eq": int(job_id)
+                    }
+                }},
+            {
+                "$group": {
+                    "_id": "$subject",
+                    "count": {
+                        "$sum": 1
+                    }
+                }
+            }
+        ]
+        results = list(db.phenotype_results.aggregate(q))
+    except Exception as e:
+        traceback.print_exc(file=sys.stdout)
+    finally:
+        client.close()
+
+    return results
+
+
 def remove_tmp_file(filename):
     if filename:
         os.remove(filename)