Fix exit() errors and and __main__ section

deploy/conf.py

@@ -74,7 +74,7 @@
 #
 # Database connection
 #
-database_host = '127.0.0.1'
+database_host = 'mongo'
 database_port = 27017
 database_user = 'root'
 database_password = 'example'
@@ -126,4 +126,4 @@
 #
 # Ontologies
 #
-ontologies_folder = "ontologies"
+ontologies_folder = "ontologies"

deploy/docker-compose.yml

@@ -7,6 +7,29 @@ networks:
 
 services:
 
+  ###########################################
+  # beacon-ri-tools
+  ###########################################
+
+  beacon-ri-tools:
+    image: beacon2ri/beacon_reference_implementation:v2.0.0
+    hostname: beacon-ri-tools
+    networks:
+      - beacon-priv 
+    tty: true
+
+  ###########################################
+  # training-ui
+  ###########################################
+
+  training-ui:
+    image: beacon2ri/training_ui:v0.1
+    hostname: beacon_training_ui    
+    ports:
+      - 8080:8080
+    networks:
+      - beacon-priv
+
   ###########################################
   # MongoDB Database
   ###########################################
@@ -22,8 +45,8 @@ services:
       MONGO_INITDB_DATABASE: beacon
     volumes:
       - ./mongo-init/:/docker-entrypoint-initdb.d/:ro
-    # networks:
-    #   - beacon-priv
+    networks:
+      - beacon-priv
 
   mongo-express:
     image: mongo-express
@@ -34,8 +57,8 @@ services:
       ME_CONFIG_MONGODB_ADMINUSERNAME: root
       ME_CONFIG_MONGODB_ADMINPASSWORD: example
       ME_CONFIG_MONGODB_URL: mongodb://root:example@mongo:27017/
-    # networks:
-    #   - beacon-priv
+    networks:
+      - beacon-priv
 
   ###########################################
   # Beacon
@@ -55,9 +78,9 @@ services:
       - ./ontologies:/beacon/ontologies
     ports:
       - "5050:5050"
-    # networks:
-    #   - beacon-priv
-    #   - pub
+    networks:
+      - beacon-priv
+      - pub
     working_dir: '/beacon'
     entrypoint: ['python','-m','beacon']
     # entrypoint: ['/bin/sleep','100000000']
@@ -75,9 +98,9 @@ services:
       - ./logger.yml:/beacon/logger.yml
     ports:
       - "5051:5051"
-    # networks:
-    #   - beacon-priv
-    #   - pub
+    networks:
+      - beacon-priv
+      - pub
     #entrypoint: ['/bin/sleep','100000000']
     working_dir: '/beacon'
     entrypoint: ['python','-m', 'permissions']
@@ -110,9 +133,9 @@ services:
       - ./beacon-realm.json:/tmp/beacon-realm.json
     ports:
       - "8080:8080"
-    # networks:
-    #   - pub
-    #   - idp-priv
+    networks:
+      - pub
+      - idp-priv 
     depends_on:
       - idp-db
 
@@ -124,5 +147,5 @@ services:
       - POSTGRES_DB=keycloak
       - POSTGRES_USER=admin
       - POSTGRES_PASSWORD=secret
-    # networks:
-    #   - idp-priv
+    networks:
+      - idp-priv 

deploy/extract_filtering_terms.py

@@ -1,7 +1,8 @@
+import re
+import sys
 import os.path
 import urllib.request
 from typing import List, Dict, Optional
-import re
 from urllib.error import HTTPError
 
 import requests
@@ -165,6 +166,8 @@ def get_properties_of_document(document, prefix="") -> List[str]:
                 properties.append(prefix + '.' + key if prefix else key)
             elif isinstance(value, int):
                 properties.append(prefix + '.' + key if prefix else key)
+            elif isinstance(value, float):
+                properties.append(prefix + '.' + key if prefix else key)                
             elif isinstance(value, str):
                 properties.append(prefix + '.' + key if prefix else key)
             elif isinstance(value, list):
@@ -173,10 +176,10 @@ def get_properties_of_document(document, prefix="") -> List[str]:
                 properties += get_properties_of_document(value, prefix + '.' + key if prefix else key)
             else:
                 print('Unknown type:', value, ' (', type(value), ')')
-                exit(0)
+                sys.exit(0)
     else:
         print('Unknown type2:', document, ' (', type(document), ')')
-        exit(0)
+        sys.exit(0)
     return properties
 
 
@@ -210,6 +213,6 @@ def insert_all_alphanumeric_terms_used():
         if len(terms) > 0:
             client.beacon.filtering_terms.insert_many(terms)
 
-
-insert_all_ontology_terms_used()
-insert_all_alphanumeric_terms_used()
+if __name__=='__main__':
+    insert_all_ontology_terms_used()
+    insert_all_alphanumeric_terms_used()