Merge pull request #25 from statgen/status

Data collection counts at status endpoint

README.md

@@ -84,7 +84,7 @@ venv/bin/flask load-genes \
 
 venv/bin/flask load-snv 2 data/basis/vcfs/*.vcf.gz
 
-venv/bin/flask load-qc-metrics
+venv/bin/flask load-qc-metrics \
 	data/basis/qc_metrics/metrics.json.gz
 ```
 

bravo_api/__init__.py

@@ -1,5 +1,5 @@
 from logging.config import dictConfig
-from os import getenv
+from os import getenv, getcwd
 from flask import Flask
 from flask_cors import CORS
 from flask_pymongo import PyMongo
@@ -43,14 +43,15 @@ def version():
 
 
 def create_app(test_config=None):
-    instance_path = getenv('BRAVO_API_INSTANCE_DIR', None)
+    instance_path = getenv('BRAVO_API_INSTANCE_DIR', getcwd())
     app = Flask(__name__,
                 instance_relative_config=True,
                 instance_path=instance_path)
 
     app.version = pkg_resources.read_text(__package__, 'VERSION').strip()
 
     if test_config is None:
+        print(getcwd())
         app.config.from_object('bravo_api.default_config')
         app.config.from_envvar('BRAVO_API_CONFIG_FILE', silent=True)
     else:

bravo_api/blueprints/status/status.py

@@ -3,6 +3,7 @@
 import sys
 from flask import Blueprint, Response, current_app, jsonify, make_response
 
+
 bp = Blueprint('status', __name__)
 logger = logging.getLogger(__name__)
 
@@ -38,11 +39,33 @@ def usage() -> Response:
     result = current_app.cache.get('usage')
     if result is None:
         result = usage_stats(current_app.mmongo.db)
-        current_app.cache.set('usage', result, timeout=3600)
-        logger.debug("Usage result updated")
+        current_app.cache.set('usage', result, timeout=0)
+    return make_response(jsonify(result))
+
+
+@bp.route('/counts', methods=['GET'])
+def counts() -> Response:
+    result = current_app.cache.get('counts')
+    if result is None:
+        snv_count = count_collection(current_app.mmongo.db.snv)
+        transcript_count = count_collection(current_app.mmongo.db.transcripts)
+        gene_count = count_collection(current_app.mmongo.db.genes)
+
+        result = {'snvs': snv_count, 'transcripts': transcript_count, 'genes': gene_count}
+
+        current_app.cache.set('counts', result, timeout=3600)
+        logger.debug('variant counts updated')
     return make_response(jsonify(result))
 
 
+def count_collection(collection: pymongo.collection.Collection) -> int:
+    """
+    Count (estimate) the number of snv in backing database
+    """
+    result = collection.estimated_document_count()
+    return result
+
+
 def usage_stats(db: pymongo.database.Database) -> dict:
     """
     Given a mongo database, run queries to compile statistics about user usage of API.

bravo_api/blueprints/structvar/structvar.py

@@ -67,7 +67,8 @@ def sv_region(structvars: pymongo.collection.Collection,
                     ]}
                 ]}
             ]}
-         }
+         },
+        {'$project': {'_id': 0}}
     ]
 
     cursor = structvars.aggregate(pipeline)