refactor: improve config

drs_filer/config.yaml

@@ -88,7 +88,8 @@ endpoints:
         updatedAt: "2020-01-01"
         environment: "ENV"
         version: "0.0.0"
-    url_prefix: http
-    external_host: 193.166.24.114
-    external_port: 8080
-    api_path: ga4gh/drs/v1
+    service:
+        url_prefix: http
+        external_host: 193.166.24.114
+        external_port: 8080
+        api_path: ga4gh/drs/v1

drs_filer/ga4gh/drs/endpoints/register_objects.py

@@ -35,21 +35,23 @@ def register_object(
         current_app.config['FOCA'].db.dbs['drsStore'].
         collections['objects'].client
     )
-    url_prefix = current_app.config['FOCA'].endpoints['url_prefix']
-    external_host = current_app.config['FOCA'].endpoints['external_host']
-    external_port = current_app.config['FOCA'].endpoints['external_port']
-    api_path = current_app.config['FOCA'].endpoints['api_path']
+    conf = current_app.config['FOCA'].endpoints
+
+    url_prefix = conf['service']['url_prefix']
+    external_host = conf['service']['external_host']
+    external_port = conf['service']['external_port']
+    api_path = conf['service']['api_path']
 
     # Set flags and parameters for POST/PUT routes
     replace = True
     was_replaced = False
     if object_id is None:
         replace = False
         id_length = (
-            current_app.config['FOCA'].endpoints['objects']['id_length']
+            conf['objects']['id_length']
         )
         id_charset: str = (
-            current_app.config['FOCA'].endpoints['objects']['id_charset']
+            conf['objects']['id_charset']
         )
         # evaluate character set expression or interpret literal string as set
         try:
@@ -120,11 +122,12 @@ def __add_access_ids(data: List) -> List:
     Returns:
         Access methods metadata complete with unique access identifiers.
     """
+    conf = current_app.config['FOCA'].endpoints
     id_charset = eval(
-        current_app.config['FOCA'].endpoints['access_methods']['id_charset']
+        conf['access_methods']['id_charset']
     )
     id_length = (
-        current_app.config['FOCA'].endpoints['access_methods']['id_length']
+        conf['access_methods']['id_length']
     )
     access_ids = []
     for method in data:

drs_filer/ga4gh/drs/endpoints/service_info.py

@@ -35,10 +35,10 @@ def __init__(self) -> None:
             conf_info: Service info details as per enpoints config.
         """
         conf = current_app.config['FOCA'].endpoints
-        self.url_prefix = conf['url_prefix']
-        self.host_name = conf['external_host']
-        self.external_port = conf['external_port']
-        self.api_path = conf['api_path']
+        self.url_prefix = conf['service']['url_prefix']
+        self.host_name = conf['service']['external_host']
+        self.external_port = conf['service']['external_port']
+        self.api_path = conf['service']['api_path']
         self.conf_info = conf['service_info']
         self.db_coll_info = (
             current_app.config['FOCA'].db.dbs['drsStore']

tests/ga4gh/drs/endpoints/test_register_objects.py

@@ -38,10 +38,12 @@
         "id_charset": 'string.digits',
         "id_length": 6
     },
-    "url_prefix": "http",
-    "external_host": "1.2.3.4",
-    "external_port": 8080,
-    "api_path": "ga4gh/drs/v1"
+    "service": {
+        "url_prefix": "http",
+        "external_host": "1.2.3.4",
+        "external_port": 8080,
+        "api_path": "ga4gh/drs/v1"
+    }
 }
 
 
@@ -70,7 +72,7 @@ def test_register_object_invalid_config():
     """
     app = Flask(__name__)
     endpoint_config = deepcopy(ENDPOINT_CONFIG)
-    del endpoint_config['url_prefix']
+    del endpoint_config['service']['url_prefix']
     app.config['FOCA'] = \
         Config(
             db=MongoConfig(**MONGO_CONFIG),

tests/ga4gh/drs/endpoints/test_service_info.py

@@ -68,10 +68,12 @@
         "id_length": 6
     },
     "service_info": deepcopy(SERVICE_INFO_CONFIG),
-    "url_prefix": "http",
-    "external_host": "1.2.3.4",
-    "external_port": 8080,
-    "api_path": "ga4gh/drs/v1"
+    "service": {
+        "url_prefix": "http",
+        "external_host": "1.2.3.4",
+        "external_port": 8080,
+        "api_path": "ga4gh/drs/v1"
+    }
 }
 SERVICE_CONFIG = {
     "url_prefix": "http",

tests/ga4gh/drs/test_server.py

@@ -83,10 +83,12 @@
         "id_length": 6
     },
     "service_info": deepcopy(SERVICE_INFO_CONFIG),
-    "url_prefix": "http",
-    "external_host": "1.2.3.4",
-    "external_port": 8080,
-    "api_path": "ga4gh/drs/v1"
+    "service": {
+        "url_prefix": "http",
+        "external_host": "1.2.3.4",
+        "external_port": 8080,
+        "api_path": "ga4gh/drs/v1"
+    }
 }
 
 data_objects_path = "tests/data_objects.json"

update-config-map.sh

@@ -31,9 +31,9 @@ echo "Current Kubernetes namespace: $NAMESPACE"; echo
 echo " * Getting current default configuration"
 
 APP_CONFIG=$(yq --arg HOST_NAME "$HOST_NAME" \
-    '.endpoints.url_prefix = "https" |
-     .endpoints.external_host = $HOST_NAME |
-     .endpoints.external_port = 443' \
+    '.endpoints.service.url_prefix = "https" |
+     .endpoints.service.external_host = $HOST_NAME |
+     .endpoints.service.external_port = 443' \
     "$APP_CONFIG_PATH") || exit 4
 
 echo " * Getting current configMap"