fix: updating model catalog example

examples/modelcatalog/config.yaml

@@ -23,7 +23,7 @@ firebase:
 
 endpoint:
   url: http://endpoint.mint.isi.edu/modelCatalog-1.4.0
-  prefix: https://w3id.org/okn/i/masd
+  prefix: https://w3id.org/okn/i/mint
   graph_base: http://endpoint.mint.isi.edu/modelCatalog-1.4.0/data/
 
 custom_queries_directory: examples/modelcatalog/custom_queries

examples/modelcatalog/custom_queries/custom_modelconfigurationsetups.rq

@@ -67,6 +67,8 @@ WHERE {
             ?region ?region_p ?region_o .
             OPTIONAL {
                 ?region_o ?sub_region_p ?sub_region_o
+                FILTER (?sub_region_p != <https://w3id.org/okn/o/sdm#geo>) .
+
             }
             FILTER (?region_p != <https://w3id.org/okn/o/sdm#geo>)
        }

examples/modelcatalog/custom_queries/custom_modelconfigurationsetups_variable.rq

@@ -7,7 +7,9 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 
 CONSTRUCT {
     ?setup ?predicate ?prop .
-    ?prop a ?type
+    ?prop a ?type .
+    ?region ?region_p ?region_o .
+    ?region_o ?sub_region_p ?sub_region_o .
 }
 WHERE {
         GRAPH ?_g_iri {
@@ -28,9 +30,20 @@ WHERE {
                   FILTER REGEX(?variableLabel, ?_label, "i")
                 }
             }
-            ?setup ?predicate ?prop
-            OPTIONAL {
-             ?prop a ?type
+            {
+                ?setup ?predicate ?prop
+                OPTIONAL {
+                 ?prop a ?type
+                }
+            }
+            UNION {
+                ?setup sdm:hasRegion ?region .
+                ?region ?region_p ?region_o .
+                FILTER (?region_p != <https://w3id.org/okn/o/sdm#geo>) .
+                OPTIONAL {
+                    ?region_o ?sub_region_p ?sub_region_o .
+                    FILTER (?sub_region_p != <https://w3id.org/okn/o/sdm#geo>)
+                }
             }
       }
 }

src/main/java/edu/isi/oba/Mapper.java

@@ -143,13 +143,12 @@ private void add_user_path(Path pathGenerator) {
         userProperties.put("password", password);
 
         Schema userSchema = new Schema();
-        userSchema.setName("ObaUser");
+        userSchema.setName("User");
         userSchema.setType("object");
         userSchema.setProperties(userProperties);
-        userSchema.setXml(new XML().name("User"));
         schemas.put("User", userSchema);
 
-        this.paths.addPathItem("/user/login", pathGenerator.user_login(userSchema));
+        this.paths.addPathItem("/user/login", pathGenerator.user_login(userSchema.getName()));
     }
 
     private List<OWLClass> add_owlclass_to_openapi(Query query, Path pathGenerator, OWLOntology ontology,

src/main/java/edu/isi/oba/Path.java

@@ -56,12 +56,14 @@ public PathItem generate_plural(String schemaName, String schemaURI){
   }
 
 
-  public PathItem user_login(Schema schema) {
-    List<Parameter> parameters = new ArrayList<>();
+  public PathItem user_login(String schema_name) {
     ApiResponses apiResponses = new ApiResponses();
 
     final RequestBody requestBody = new RequestBody();
 
+    String ref_text = "#/components/schemas/" + schema_name;
+    Schema schema = new Schema().$ref(ref_text);
+
     MediaType mediaType = new MediaType().schema(schema);
     Content content = new Content().addMediaType("application/json", mediaType);
     requestBody.setContent(content);
@@ -84,11 +86,10 @@ public PathItem user_login(Schema schema) {
             .content(new Content().addMediaType("application/json", new MediaType().schema(new StringSchema()))));
 
     Map<String,Object> extensions = new HashMap<String, Object>();
-    extensions.put("x-openapi-router-controller", "openapi_server.controllers.default_controller");
+    extensions.put("x-openapi-router-controller", "openapi_server.controllers.user_controller");
     Operation operation = new Operation()
             .description("Login the user")
             .extensions(extensions)
-            .operationId("user_login_get")
             .requestBody(requestBody)
             .responses(apiResponses);
     return new PathItem().post(operation);

src/main/resources/servers/python/.openapi-generator/template/static_files/user_controller.py

@@ -4,8 +4,10 @@
 import json
 import requests
 from werkzeug.exceptions import Unauthorized
-
+import connexion
 from openapi_server.settings import FIREBASE_KEY
+from openapi_server.models.user import User
+
 JWT_ISSUER = 'com.zalando.connexion'
 JWT_SECRET = 'change_this'
 JWT_LIFETIME_SECONDS = 60000000
@@ -39,7 +41,7 @@ def auth_with_password(email, password):
 
     return response.ok
 
-def user_login_get(username, password):  # noqa: E501
+def user_login_post():  # noqa: E501
     """Logs user into the system
 
      # noqa: E501
@@ -51,7 +53,9 @@ def user_login_get(username, password):  # noqa: E501
 
     :rtype: str
     """
-    if not auth_with_password(username, password):
+    if connexion.request.is_json:
+        user = User.from_dict(connexion.request.get_json())  # noqa: E501
+    if not auth_with_password(user.username, user.password):
         return "Invalid User or Password", 401, {}
 
 
@@ -60,16 +64,14 @@ def user_login_get(username, password):  # noqa: E501
         "iss": JWT_ISSUER,
         "iat": int(timestamp),
         "exp": int(timestamp + JWT_LIFETIME_SECONDS),
-        "sub": str(username),
+        "sub": str(user.username),
     }
 
     access_token = jwt.encode(payload, JWT_SECRET, algorithm=JWT_ALGORITHM)
     return {
-        "access_token": access_token,
-        "token_type": "bearer",
-        "expires_in": JWT_LIFETIME_SECONDS,
-        "refresh_token": "IwOGYzYTlmM2YxOTQ5MGE3YmNmMDFkNTVk",
-        "scope": "create"
-    }, 200, {'X-Expires-After': JWT_LIFETIME_SECONDS, 'X-Rate-Limit': 1000}
-
-
+               "access_token": access_token,
+               "token_type": "bearer",
+               "expires_in": JWT_LIFETIME_SECONDS,
+               "refresh_token": "IwOGYzYTlmM2YxOTQ5MGE3YmNmMDFkNTVk",
+               "scope": "create"
+           }, 200, {'X-Expires-After': JWT_LIFETIME_SECONDS, 'X-Rate-Limit': 1000}