add: custom query

config.yaml

@@ -20,31 +20,31 @@ firebase:
   key:
 
 
-custom_queries:
-  /custom/configurationsetups:
-    get:
-      description: Gets a list of all ConfigurationSetup entities
-      parameters:
-        - description: Username to query
-          in: query
-          name: username
-          required: false
-          schema:
-            type: string
-        - description: Filter by label
-          in: query
-          name: label
-          required: false
-          schema:
-            type: string
-      responses:
-        200:
-          content:
-            application/json:
-              schema:
-                items:
-                  $ref: '#/components/schemas/ConfigurationSetup'
-                type: array
-          description: Successful response - returns an array of ConfigurationSetup
-            entities.
-      summary: List all ConfigurationSetup entities
+custom_paths:
+    /custom/configurationsetups:
+      get:
+        description: Gets a list of all ConfigurationSetup entities
+        parameters:
+          - description: Username to query
+            in: query
+            name: username
+            required: false
+            schema:
+              type: string
+          - description: Filter by label
+            in: query
+            name: label
+            required: false
+            schema:
+              type: string
+        responses:
+          '200':
+            content:
+              application/json:
+                schema:
+                  items:
+                    $ref: '#/components/schemas/ConfigurationSetup'
+                  type: array
+            description: Successful response - returns an array of ConfigurationSetup
+              entities.
+        summary: List all ConfigurationSetup entities

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

@@ -4,6 +4,7 @@
 import edu.isi.oba.config.RelationConfig;
 import edu.isi.oba.config.YamlConfig;
 import io.swagger.v3.oas.models.OpenAPI;
+import io.swagger.v3.oas.models.PathItem;
 import io.swagger.v3.parser.OpenAPIV3Parser;
 import org.apache.commons.io.FileUtils;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -13,15 +14,11 @@
 import java.io.*;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
+import java.util.*;
 
 import org.apache.commons.cli.*;
 
 class Oba {
-
   public static void main(String[] args) throws Exception {
     final String base_project_dir = "./tools/base_project/";
 
@@ -34,11 +31,14 @@ public static void main(String[] args) throws Exception {
     python_copy_base_project(base_project_dir, destination_dir);
     //read ontologies and get schema and paths
     List<Mapper> mappers = get_mappers(config_data);
+    //obtain custom paths
+    LinkedHashMap<String, PathItem> custom_paths = config_data.getCustom_paths();
+
     //get base of openapi
     OpenAPI openapi_base = new OpenAPIV3Parser().read(config_data.getOpenapi_base());
     //obtain the output directory to write the openapi specification
     //write the openapi specification
-    generate_openapi_spec(openapi_base, mappers, destination_dir);
+    generate_openapi_spec(openapi_base, mappers, destination_dir, custom_paths);
   }
 
   /**
@@ -73,10 +73,10 @@ private static void python_copy_base_project(String base_project_dir, String des
     FileUtils.copyDirectory(baseProject.toFile(), destinationProject.toFile());
   }
 
-  private static void generate_openapi_spec(OpenAPI openapi_base, List<Mapper> mappers, String dir) throws IOException {
+  private static void generate_openapi_spec(OpenAPI openapi_base, List<Mapper> mappers, String dir, LinkedHashMap<String, PathItem> custom_paths) throws IOException {
     String destinationProjectDirectory = dir;
     Path destinationProject = Paths.get(destinationProjectDirectory);
-    Serializer serializer = new Serializer(mappers, destinationProject, openapi_base);
+    Serializer serializer = new Serializer(mappers, destinationProject, openapi_base, custom_paths);
     SerializerPython serializer_python = new SerializerPython(mappers, destinationProject, openapi_base);
   }
 

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

@@ -18,7 +18,7 @@
 
 class Serializer {
   //TODO: validate the yaml
-  public  Serializer(List<Mapper> mappers, java.nio.file.Path dir, OpenAPI openAPI) throws IOException {
+  public  Serializer(List<Mapper> mappers, java.nio.file.Path dir, OpenAPI openAPI, LinkedHashMap<String, PathItem> custom_paths) throws IOException {
     Map<String, Object> extensions = new HashMap<String, Object>();
     final String openapi_file = "openapi.yaml";
 
@@ -37,6 +37,12 @@ public  Serializer(List<Mapper> mappers, java.nio.file.Path dir, OpenAPI openAPI
       components.securitySchemes(securitySchemes);
     }
 
+    //add custom paths
+    custom_paths.forEach((k, v) -> {
+      System.out.println("inserting custom query " + k);
+      paths.addPathItem(k, v);
+    });
+
     openAPI.setPaths(paths);
     openAPI.components(components);
 

src/main/java/edu/isi/oba/config/YamlConfig.java

@@ -1,6 +1,10 @@
 package edu.isi.oba.config;
 
 
+import io.swagger.v3.oas.models.PathItem;
+import io.swagger.v3.oas.models.Paths;
+
+import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
@@ -17,6 +21,8 @@ public class YamlConfig {
   public EndpointConfig endpoint;
   public FirebaseConfig firebase;
   public Map<String, List<RelationConfig>> relations;
+  private LinkedHashMap<String, PathItem> custom_paths = null;
+
 
   public String getOutput_dir() {
     return output_dir;
@@ -81,5 +87,14 @@ public Map<String, List<RelationConfig>> getRelations() {
   public void setRelations(Map<String, List<RelationConfig>> relations) {
     this.relations = relations;
   }
+
+
+  public LinkedHashMap<String, PathItem> getCustom_paths() {
+    return custom_paths;
+  }
+
+  public void setCustom_paths(LinkedHashMap<String, PathItem> custom_paths) {
+    this.custom_paths = custom_paths;
+  }
 }