Added global variables for pathologies url and disabledAlgorithms.

docker/config/application.tmpl

@@ -76,3 +76,9 @@ services:
 
   keycloak:
     keycloakUrl: {{ .Env.KEYCLOAK_URL }}
+
+pathologies:
+  pathologiesUrl: "file:/opt/portal/api/pathologies.json"
+
+algorithms:
+  disabledAlgorithmsUrl: "file:/opt/portal/api/disabledAlgorithms.json"
\ No newline at end of file

pom.xml

@@ -268,6 +268,14 @@
                     <include>**/*.yml</include>    <!--  Only for development -->
                 </includes>
                 <filtering>true</filtering>
+
+            </resource>
+            <resource>
+                <directory>config</directory>
+                <includes>
+                    <include>*.json</include>
+                </includes>
+                <filtering>true</filtering>
             </resource>
         </resources>
 

src/main/java/eu/hbp/mip/configuration/SecurityConfiguration.java

@@ -6,6 +6,7 @@ import eu.hbp.mip.utils.CustomLoginUrlAuthenticationEntryPoint;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.boot.autoconfigure.security.oauth2.resource.AuthoritiesExtractor;
 import org.springframework.boot.autoconfigure.security.oauth2.resource.ResourceServerProperties;
@@ -70,6 +71,7 @@ public class SecurityConfiguration extends WebSecurityConfigurerAdapter {
 
     private static final Logger LOGGER = LoggerFactory.getLogger(SecurityConfiguration.class);
 
+    @Qualifier("oauth2ClientContext")
     @Autowired
     private OAuth2ClientContext oauth2ClientContext;
 

src/main/java/eu/hbp/mip/controllers/AlgorithmsApi.java

@@ -17,6 +17,7 @@ import eu.hbp.mip.utils.Logging;
 import io.swagger.annotations.Api;
 import io.swagger.annotations.ApiOperation;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.Resource;
 import org.springframework.http.ResponseEntity;
@@ -41,6 +42,7 @@ public class AlgorithmsApi {
 
     private static final Gson gson = new Gson();
 
+    @Qualifier("userInfo")
     @Autowired
     private UserInfo userInfo;
 
@@ -53,6 +55,9 @@ public class AlgorithmsApi {
     @Value("#{'${services.galaxy.galaxyApiKey}'}")
     private String galaxyApiKey;
 
+    @Value("#{'${services.algorithms.disabledAlgorithmsUrl}'}")
+    private String disabledAlgorithmsUrl;
+
     @ApiOperation(value = "List all algorithms", response = String.class)
     @RequestMapping(method = RequestMethod.GET)
     public ResponseEntity<List<AlgorithmDTO>> getAlgorithms() {
@@ -195,7 +200,7 @@ public class AlgorithmsApi {
      */
     List<String> getDisabledAlgorithms() throws IOException {
 
-        Resource resource = resourceLoader.getResource("file:/opt/portal/api/disabledAlgorithms.json");
+        Resource resource = resourceLoader.getResource(disabledAlgorithmsUrl);
 
         List<String> response = gson.fromJson(convertInputStreamToString(
                 resource.getInputStream()),

src/main/java/eu/hbp/mip/controllers/PathologiesApi.java

@@ -15,6 +15,7 @@ import eu.hbp.mip.utils.InputStreamConverter;
 import eu.hbp.mip.utils.Logging;
 import io.swagger.annotations.Api;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.Resource;
 import org.springframework.http.ResponseEntity;
@@ -35,6 +36,7 @@ public class PathologiesApi {
 
     private static final Gson gson = new Gson();
 
+    @Qualifier("userInfo")
     @Autowired
     private UserInfo userInfo;
 
@@ -42,32 +44,37 @@ public class PathologiesApi {
     @Value("#{'${hbp.authentication.enabled:1}'}")
     private boolean authenticationIsEnabled;
 
+    @Value("#{'${services.pathologies.pathologiesUrl}'}")
+    private String pathologiesUrl;
+
     @Autowired
     private CustomResourceLoader resourceLoader;
 
     @RequestMapping(name = "/pathologies", method = RequestMethod.GET)
     public ResponseEntity<String> getPathologies(Authentication authentication) {
-        Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Loading pathologies ...");
+        String endpoint = "(GET) /pathologies";
+        String username = userInfo.getUser().getUsername();
+        Logging.LogUserAction(username, endpoint, "Loading pathologies ...");
 
         // Load pathologies from file
-        Resource resource = resourceLoader.getResource("file:/opt/portal/api/pathologies.json");
+        Resource resource = resourceLoader.getResource(pathologiesUrl);
         List<PathologyDTO> allPathologies;
         try {
             allPathologies = gson.fromJson(InputStreamConverter.convertInputStreamToString(resource.getInputStream()), new TypeToken<List<PathologyDTO>>() {
             }.getType());
         } catch (IOException e) {
-            Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Unable to load pathologies");
+            Logging.LogUserAction(username, endpoint, "Unable to load pathologies");
             throw new BadRequestException("The pathologies could not be loaded.");
         }
 
         // If authentication is disabled return everything
         if (!authenticationIsEnabled) {
-            Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded " + allPathologies.size() + " pathologies");
+            Logging.LogUserAction(username, endpoint, "Successfully loaded " + allPathologies.size() + " pathologies");
             return ResponseEntity.ok().body(gson.toJson(allPathologies));
         }
 
-        Logging.LogUserAction(userInfo.getUser().getUsername(), "(GET) /pathologies", "Successfully loaded all authorized pathologies");
+        Logging.LogUserAction(username, endpoint, "Successfully loaded all authorized pathologies");
         return ResponseEntity.ok().body(ClaimUtils.getAuthorizedPathologies(
-                userInfo.getUser().getUsername(), authentication.getAuthorities(), allPathologies));
+                username, authentication.getAuthorities(), allPathologies));
     }
 }

src/main/resources/application.yml

@@ -21,7 +21,7 @@ spring:
 # HBP OAUTH2 LOGIN
 hbp:
   authentication:
-    enabled: true
+    enabled: 0
   client:
     clientId: "MIP"
     clientSecret: "dae83a6b-c769-4186-8383-f0984c6edf05"
@@ -71,5 +71,11 @@ services:
     galaxyUsername:  "admin"
     galaxyPassword:  "password"
 
-    keycloak:
-      keycloakUrl: 127.0.0.1
\ No newline at end of file
+  keycloak:
+   keycloakUrl: "127.0.0.1"
+
+  pathologies:
+    pathologiesUrl: "classPath:/pathologies.json"
+
+  algorithms:
+    disabledAlgorithmsUrl: "classPath:/disableAlgorithms.json"
\ No newline at end of file