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README.md

@@ -137,8 +137,9 @@ then run
 1. ``CREATE USER 'username'@'localhost' IDENTIFIED BY 'password';``
 2. ``GRANT ALL PRIVILEGES ON *.* TO 'username'@'localhost' WITH GRANT OPTION;``
 3. ``flush privileges;``
-
 More information https://dev.mysql.com/doc/refman/5.5/en/adding-users.html
+4. Set environment variable BIOM_MASS that holds user's password
+   ``export BIOM_MASS="password"``
 
 load_local_database.py script needs mysql.connect module.
 

database.py

@@ -1,14 +1,56 @@
-
 # Calls to obtain values from the data structures (to be populated by the local database next)
-
+import mysql.connector
+from mysql.connector import pooling
+import os
+import dbqueries
 import const
 
+# add increment for aggregations
 def add_key_increment(dictionary, key):
     if not key in dictionary:
         dictionary[key]=0
     dictionary[key]+=1
 
 class Data(object):
+
+    def __init__(self):
+        self.conn_pool = mysql.connector.connect(use_pure=False, pool_name="portal",
+                                                 pool_size=10,
+                                                 pool_reset_session=True,
+                                                 database='portal_ui',
+                                                 user='biom_mass',
+                                                 password=os.environ['BIOM_MASS'])
+
+    def __exit__(self):
+        self.conn_pool.close()
+
+    # get connection from pool
+    def get_pool(self):
+        conn = mysql.connector.connect(pool_name="portal")
+        cursor = conn.cursor(buffered=True,dictionary=True)
+        return conn, cursor
+
+    # release connection back to pool
+    def release_pool(self,conn,cursor):
+        cursor.close()
+        conn.close()
+
+    # runs query and returns results
+    def fetch_results(self,query):
+        conn,cursor=self.get_pool()
+        cursor.execute(query)
+        data=[row for row in cursor]
+        self.release_pool(conn,cursor)
+        return data
+
+    # get current version from db
+    def get_current_version(self):
+        version_data=self.fetch_results(dbqueries.version_query)
+        del  version_data[0]['updated']
+        del  version_data[0]['id']
+        return version_data[0]
+
+
     def load_data(self):
         self.data = const.DB()
 
@@ -78,9 +120,21 @@ def get_project_aggregations(self, projects):
 
         return project_aggregates
 
+
+   # get all  counts for front page summary from db
     def get_current_counts(self):
-        self.load_data()
-        return self.data.CURRENT_COUNTS
+        import schema
+
+        counts_data = self.fetch_results(dbqueries.all_counts_query)
+
+        return schema.Count(
+                    projects=counts_data[0]['total'],
+                    participants=counts_data[1]['total'],
+                    samples=counts_data[2]['total'],
+                    dataFormats=counts_data[3]['total'],
+                    rawFiles=counts_data[4]['total'],
+                    processedFiles=counts_data[5]['total'])
+
 
     def get_file_aggregations(self, files):
         import schema

dbqueries.py

@@ -0,0 +1,9 @@
+#  This file holds all queries run in database.py
+all_counts_query='''select count(id) as total from project
+                    union all select count(id) as total from participant
+                    union all select count(id) as total from sample
+                    union all select count(distinct data_format) as total from file_sample
+                    union all select count(id) as total from file_sample where  type="rawFiles"
+                    union all select count(id) as total from file_sample where type="processedFiles"'''
+
+version_query="select * from version order by updated desc limit 1"

load_local_database.py

@@ -23,7 +23,7 @@ def parse_arguments(args):
         required=False)
     parser.add_argument(
         "--key-file",
-        default="biom-mass-fdcadb440fdf.json",
+        default="/home/hutlab_public/compute_engine_service_account_key/biom-mass-8dc9ab934396.json",
         help="google project service account private key file path\n]",
         required=False)
     parser.add_argument(
@@ -256,7 +256,7 @@ def main():
            new_version = str(0.1)
 
     now = datetime.datetime.now()
-    release_date ="Date Release "+new_version+" "+ now.strftime("%b %d, %Y")
+    release_date ="Data Release "+new_version+" - "+ now.strftime("%b %d, %Y")
     commit ="commit_"+now.strftime("%m%d%Y")
     query_insert_version ='''INSERT INTO `version` (
            commit,

schema.py

@@ -427,5 +427,5 @@ def resolve_samples(self, info, namespace, workspace):
         json_result = query_firecloud.call_api(url)
         obj_result = utilities.json2obj(json.dumps(json_result))
         return obj_result
-
 
+

server.py

@@ -10,11 +10,13 @@
 import os
 
 import flask
+import flask_cors
 import flask_graphql
 import graphene
 
 import schema
 import const
+from database import data
 
 NAME = "firecloud_graphql"
 HOST = "0.0.0.0"
@@ -41,6 +43,8 @@ def process_query(request, schema):
 def main():
     # create the graphql flask app
     app = flask.Flask(NAME)
+    # allow initial OPTIONS requests
+    flask_cors.CORS(app)
 
     # add the root graphql queries
     @app.route('/graphql', methods=["POST"])
@@ -55,7 +59,7 @@ def get_schema(name):
     # add static endpoint for version/status
     @app.route('/status', methods=["GET"])
     def get_version():
-        return flask.jsonify(const.VERSION)
+        return flask.jsonify(data.get_current_version())
 
     # add end point for graphql gui
     app.add_url_rule('/test', view_func=flask_graphql.GraphQLView.as_view(