FIX-11364 Proxy Controller and Monkifier

docs/deployment/customization/application.properties-Reference.md

@@ -826,3 +826,20 @@ Custom Buttons can be defined which will conditionally appear in all group compa
 ```
 download_custom_buttons_json=classpath:custom_buttons/download_custom_button_avm.json
 ```
+
+# Proxy Service
+cBioPortal can act as a proxy service so that users can run installations of different services behind firewalls that can't be reach by all users. To do this users set a proxy.routes.[name] property in the application.properties. This will create a proxy endpoint at /proxy/[name].
+
+As an example if you wanted to host genomenexus locally then you could set it in the following manner.
+
+```
+# Setup proxy routes
+proxy.routes.genomenexus=http://gn-spring-boot:8888
+proxy.routes.genomenexus38=http://gn-spring-boot-grch38:8888
+
+# GenomeNexus configuration
+genomenexus.url=/proxy/genomenexus
+genomenexus.url.grch38=/proxy/genomenexus38
+```
+
+NOTE: The proxy service is available to all logged in users and it is not recommended to be used on public non-secured instances of cBioPortal.

pom.xml

@@ -35,6 +35,7 @@
 		<!-- Version properties for dependencies that should have same version. -->
 		<!-- The rest can be set in the dependencyManagement section -->
 		<spring.social.version>1.1.6.RELEASE</spring.social.version>
+		<spring_cloud_gateway_mvc.version>4.1.5</spring_cloud_gateway_mvc.version>
 
 		<jackson.version>2.12.5</jackson.version>
 		<mysql-connector.version>8.0.28</mysql-connector.version>
@@ -385,6 +386,11 @@
             <artifactId>spring-boot-testcontainers</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+			<groupId>org.springframework.cloud</groupId>
+			<artifactId>spring-cloud-gateway-mvc</artifactId>
+			<version>${spring_cloud_gateway_mvc.version}</version>
+		</dependency>
     </dependencies>
 
     <dependencyManagement>

src/main/java/org/cbioportal/proxy/LegacyProxyController.java → src/main/java/org/cbioportal/proxy/APIProxyController.java

@@ -56,7 +56,7 @@
 
 @Controller
 @RequestMapping("/api/proxy")
-public class LegacyProxyController {
+public class APIProxyController {
 
     private String bitlyURL;
     private String sessionServiceURL;

src/main/java/org/cbioportal/proxy/Monkifier.java

@@ -2,7 +2,6 @@
 
 import jakarta.servlet.http.HttpServletRequest;
 import org.apache.commons.codec.binary.Base64;
-import org.springframework.stereotype.Component;
 import org.springframework.util.CollectionUtils;
 import org.springframework.web.util.UriComponentsBuilder;
 
@@ -11,32 +10,31 @@
 import java.util.Map;
 import java.util.stream.Collectors;
 
-@Component
 public class Monkifier {
-    public String decodeBase64(String value) {
+    public static String decodeBase64(String value) {
         return new String(Base64.decodeBase64(value.getBytes()));
     }
 
-    public String encodeBase64(String value) {
+    public static String encodeBase64(String value) {
         return value == null ? "": new String(Base64.encodeBase64(value.getBytes()));
     }
 
-    public String decodeQueryString(HttpServletRequest request) {
+    public static String decodeQueryString(HttpServletRequest request) {
         if (request.getQueryString() == null) {
             return null;
         }
 
-        return this.decodeQueryString(request.getParameterMap());
+        return decodeQueryString(request.getParameterMap());
     }
 
-    public String decodeQueryString(Map<String, String[]> encodedQueryParams) {
+    public static String decodeQueryString(Map<String, String[]> encodedQueryParams) {
         Map<String, List<String>> decodedQueryParams = encodedQueryParams
             .entrySet()
             .stream()
             .collect(
                 Collectors.toMap(
-                    e -> this.decodeBase64(e.getKey()),
-                    e -> Arrays.stream(e.getValue()).map(this::decodeBase64).collect(Collectors.toList())
+                    e -> Monkifier.decodeBase64(e.getKey()),
+                    e -> Arrays.stream(e.getValue()).map(Monkifier::decodeBase64).collect(Collectors.toList())
                 )
             );