Merge pull request #98 from pbashyal-nmdp/set-feature-service-url

WIP: Set feature service url

Author: chrisammon3000

gfe-db/pipeline/jobs/build/run.sh

@@ -90,6 +90,14 @@ else
 	ALIGNFLAG=""
 fi
 
+# Check for FEATURE_SERVICE_URL
+if [[ -z "${FEATURE_SERVICE_URL}" ]]; then
+	echo "No FEATURE_SERVICE_URL set, building GFEs with default feature service."
+else
+	echo "Using Feature Service: ${FEATURE_SERVICE_URL}"
+fi
+
+
 # Build csv files
 RELEASES=$(echo "${RELEASES}" | sed s'/"//'g | sed s'/,/ /g')
 # exit 1 # TODO test state machine error handling
@@ -134,7 +142,8 @@ for release in ${RELEASES}; do
 		$ALIGNFLAG \
 		$MEM_PROFILE_FLAG \
 		-v \
-		-l $LIMIT
+		-l $LIMIT \
+		-u $FEATURE_SERVICE_URL
     build_exit_status=$?
     echo "Build exit status (1:CRITICAL, 2:WARNING): $build_exit_status"
 

gfe-db/pipeline/jobs/build/src/app.py

@@ -528,6 +528,13 @@ def process_allele(allele, alignments_dict, csv_path=None):
                         nargs='?',
                         action="store")
 
+    parser.add_argument("-u", "--feature-service-url",
+                        required=False,
+                        help="URL of Feature Service to retrieve/populate",
+                        default="https://feature-service.nmdp.org/",
+                        nargs='?',
+                        action="store")
+
     args = parser.parse_args()
 
     logging.debug(f'Input args: {vars(args)}')
@@ -574,9 +581,10 @@ def process_allele(allele, alignments_dict, csv_path=None):
 
     alleles = parse_dat(data_dir, dbversion)
 
-    ard = pyard.init(dbversion, data_dir="/tmp/gfe-pyard/", load_mac=False)
+    ard = pyard.init(dbversion, data_dir="/tmp/gfe-pyard", load_mac=False)
 
     gfe_maker = GFE(
+        url=args.feature_service_url,
         verbose=verbose, 
         verbosity=verbosity,
         load_features=False,