thehyve · tgreenwood · Jun 11, 2024 · Jun 11, 2024 · Jul 18, 2024 · Aug 13, 2024
diff --git a/README.adoc b/README.adoc
@@ -2238,10 +2238,10 @@ The data models for these metadata are defined using the {SHACL}[Shapes Constrai
 * The customisable data model includes the custom (shared)
   metadata entities, custom controlled vocabulary types,
   and custom properties of the system entities.
-  The default custom data model is defined in link:projects/saturn/vocabulary.ttl[vocabulary.ttl].
+  The default custom data model is defined in link:projects/saturn/src/main/resources/vocabulary.ttl[vocabulary.ttl].
   This data model can be overriden by a data more suitable for your organisation.
 
-A schematic overview of the default data model in link:projects/saturn/vocabulary.ttl[vocabulary.ttl]:
+A schematic overview of the default data model in link:projects/saturn/src/main/resources/vocabulary.ttl[vocabulary.ttl]:
 
 image:docs/images/diagrams/CDR data model.png[CDR data model]
 
@@ -2462,8 +2462,8 @@ use `--set-file` option:
 +
 This should also restart the Saturn pod. If not, trigger the restart manually.
 +
-For local development - replace vocabulary file in link:projects/saturn/vocabulary.ttl[projects/saturn/vocabulary.ttl]
-and views configuration in link:projects/saturn/views.ttl[projects/saturn/views.ttl].
+For local development - replace vocabulary file in link:projects/saturn/src/main/resources/vocabulary.ttl[vocabulary.ttl]
+and views configuration in link:projects/saturn/src/main/resources/views.yaml[views.yaml].
 Restart Saturn run.
 +
 . Load data for new entities or properties.
@@ -2474,7 +2474,7 @@ Restart Saturn run.
 
 For controlled vocabulary types, e.g., _Gender_ and _Species_ in the example, you should insert the allowed values in the database by uploading
 a taxonomies file using the <<RDF metadata>> API.
-An example taxonomy is in link:projects/saturn/taxonomies.ttl[taxonomies.ttl].
+An example taxonomy is in link:projects/saturn/src/main/resources/taxonomies.ttl[taxonomies.ttl].
 
 It is preferred to use existing standard taxonomies and labels.
 If that is not possible, please define your own namespaces for
@@ -2526,7 +2526,7 @@ ncbitaxon:10090 a example:Species ;
 
 For the metadata pages in the user interface, a view configuration needs to be created
 that specifies the tables and columns.
-An example can be found in link:projects/saturn/views.yaml[views.yaml]
+An example can be found in link:projects/saturn/src/main/resources/views.yaml[views.yaml]
 
 
 

diff --git a/charts/fairspace/templates/project/stateful-set.yaml b/charts/fairspace/templates/project/stateful-set.yaml
@@ -100,16 +100,16 @@ spec:
 {{- end }}
           livenessProbe:
             httpGet:
-              path:  /liveness
+              path:  /actuator/health/liveness
               port: 8091
             initialDelaySeconds: {{ .Values.saturn.livenessProbe.initialDelaySeconds }}
             periodSeconds: {{ .Values.saturn.livenessProbe.periodSeconds }}
             successThreshold: {{ .Values.saturn.livenessProbe.successThreshold }}
             timeoutSeconds: {{ .Values.saturn.livenessProbe.timeoutSeconds }}
           readinessProbe:
             httpGet:
-              path:  /api/health/
-              port: 8090
+              path:  /actuator/health/readiness
+              port: 8091
             periodSeconds: {{ .Values.saturn.readinessProbe.periodSeconds }}
             successThreshold: {{ .Values.saturn.readinessProbe.successThreshold }}
             timeoutSeconds: {{ .Values.saturn.readinessProbe.timeoutSeconds }}
@@ -222,4 +222,4 @@ spec:
       storageClassName: {{ index .Values "saturn" "persistence" "extra-file-storage" "storageClass" | quote }}
   {{- end }}
 {{- end }}
-{{- end }}
+{{- end }}
diff --git a/projects/mercury/package.json b/projects/mercury/package.json
@@ -7,8 +7,8 @@
     "dev-be": "concurrently \"yarn localdevelopment\" \"yarn saturn\" \"yarn pluto\"",
     "dev-fe": "yarn build && yarn start",
     "localdevelopment": "cd ../../local-development && docker compose up",
-    "saturn": "wait-on http://localhost:5100/ && wait-on tcp:9432 && cd ../saturn/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew run",
-    "pluto": "wait-on http://localhost:8090/api/health/ && cd ../pluto/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun --args='--spring.profiles.active=local'",
+    "saturn": "wait-on http://localhost:5100/ && wait-on tcp:9432 && cd ../saturn/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun",
+    "pluto": "wait-on http://localhost:8091/actuator/health/ && cd ../pluto/ && KEYCLOAK_CLIENT_SECRET=********** ./gradlew bootRun --args='--spring.profiles.active=local'",
     "start": "craco start",
     "build": "yarn check-format && craco build",
     "test": "craco test --env=jsdom",

diff --git a/projects/pluto/src/main/resources/application-local.yml b/projects/pluto/src/main/resources/application-local.yml
@@ -4,7 +4,7 @@ pluto:
   domains:
     - http://localhost:8080
   force-https: false
-  downstreamServiceHealthUrl: http://localhost:8090/api/health/
+  downstreamServiceHealthUrl: http://localhost:8091/actuator/health/
   oauth2:
     base-url: http://localhost:5100
     realm: fairspace

diff --git a/projects/saturn/application.yaml b/projects/saturn/application.yaml
diff --git a/projects/saturn/build.gradle b/projects/saturn/build.gradle
@@ -1,7 +1,7 @@
 buildscript {
     ext {
-        jena_version = '4.10.0' // todo: upgrade to 5+ (FAIRSPC-69)
-        milton_version = '3.1.1.488' // Milton >= 4 is migrated to Jakarta EE 9, which is not compatible with Jena < 5 (no stable release of Jena 5 yet). To be updated when Jena 5 is released.
+        jena_version = '5.1.0'
+        milton_version = '4.0.2.2101'
         mockitoVersion = '5.11.0'
         jacksonVersion = '2.15.3' // check what version is used by Jena
         postgresqlVersion = '42.7.2'
@@ -10,6 +10,8 @@ buildscript {
 
 plugins {
     id 'java'
+    id 'org.springframework.boot' version '3.3.0'
+    id 'io.spring.dependency-management' version '1.1.5'
     id "io.freefair.lombok" version "8.6"
     id 'application'
     id 'jacoco'
@@ -26,7 +28,7 @@ compileJava {
 }
 
 application {
-    mainClassName = "io.fairspace.saturn.App"
+    mainClassName = "io.fairspace.saturn.SaturnApplication"
     applicationDefaultJvmArgs = ['-XX:+ShowCodeDetailsInExceptionMessages']
 }
 
@@ -38,53 +40,47 @@ repositories {
     }
 }
 
-lombok.version = "1.18.30"
+lombok.version = "1.18.32"
 
 jacoco.toolVersion = "0.8.11"
 
 dependencies {
-//    implementation fileTree(dir: 'libs', include: '*.jar') // jena-fuseki-server-*.jar jena-text-es-*.jar
-    implementation "org.apache.jena:jena-fuseki-main:${jena_version}"
+    implementation 'org.springframework.boot:spring-boot-starter-oauth2-resource-server'
+    implementation 'org.springframework.boot:spring-boot-starter-security'
+    implementation 'org.springframework.boot:spring-boot-starter-web'
+    implementation 'org.springframework.boot:spring-boot-starter-validation'
+    implementation 'org.springframework.boot:spring-boot-starter-actuator'
+
     implementation "org.apache.jena:jena-text:${jena_version}"
     implementation "io.milton:milton-server-ce:${milton_version}"
+
     implementation "com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:${jacksonVersion}"
     implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${jacksonVersion}"
-    implementation "com.sparkjava:spark-core:2.9.4"
+
     implementation 'com.pivovarit:throwing-function:1.5.1'
     implementation 'com.google.guava:guava:33.0.0-jre'
-//    implementation 'jakarta.servlet:jakarta.servlet-api:6.0.0' // To be updated when Jena 5 is released.
     implementation('com.io-informatics.oss:jackson-jsonld:0.1.1') {
         exclude group: 'com.github.jsonld-java'
     }
     implementation('org.bouncycastle:bcprov-jdk15on:1.70')
 
     implementation 'org.apache.logging.log4j:log4j-layout-template-json:2.23.0'
 
-    implementation 'org.eclipse.jetty:jetty-proxy:9.4.54.v20240208'
-
-    implementation 'org.keycloak:keycloak-jetty94-adapter:23.0.7'
     implementation 'org.keycloak:keycloak-admin-client:23.0.7'
     implementation 'org.keycloak:keycloak-policy-enforcer:23.0.7'
 
     implementation "org.postgresql:postgresql:${postgresqlVersion}"
     implementation "com.zaxxer:HikariCP:5.1.0"
 
-    runtimeOnly 'org.apache.logging.log4j:log4j-api:2.23.0'
-    runtimeOnly 'org.apache.logging.log4j:log4j-core:2.23.0'
-    runtimeOnly 'org.apache.logging.log4j:log4j-slf4j2-impl:2.23.0'
-
     testImplementation "junit:junit:4.13.2"
     testImplementation "org.mockito:mockito-core:${mockitoVersion}"
+    testImplementation 'org.springframework.boot:spring-boot-starter-test'
+    testImplementation 'org.junit.vintage:junit-vintage-engine:5.10.2'
     testImplementation "org.testcontainers:postgresql:1.19.6"
     testImplementation('com.github.stefanbirkner:system-rules:1.19.0') {
         exclude group: 'junit', module:'junit-dep'
     }
 
-    constraints {
-//        implementation('com.fasterxml.jackson.core:jackson-databind:2.9.10.1') {
-//            because 'previous versions have security vulnerabilities'
-//        }
-    }
 }
 
 jacocoTestReport {
@@ -117,4 +113,5 @@ test {
     // They also blocks usage of testing library mocking environment variables,
     // That is why this additional arg for tests is needed
     jvmArgs = ['--add-opens', 'java.base/java.util=ALL-UNNAMED']
+    useJUnitPlatform()
 }
diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/App.java b/projects/saturn/src/main/java/io/fairspace/saturn/App.java
diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/SaturnApplication.java b/projects/saturn/src/main/java/io/fairspace/saturn/SaturnApplication.java
@@ -0,0 +1,12 @@
+package io.fairspace.saturn;
+
+import org.springframework.boot.SpringApplication;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+
+@SpringBootApplication
+public class SaturnApplication {
+
+    public static void main(String[] args) {
+        SpringApplication.run(SaturnApplication.class, args);
+    }
+}
diff --git a/projects/saturn/src/main/java/io/fairspace/saturn/audit/Audit.java b/projects/saturn/src/main/java/io/fairspace/saturn/audit/Audit.java
@@ -2,10 +2,11 @@
 
 import java.util.Objects;
 
-import org.apache.logging.log4j.*;
+import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.apache.logging.log4j.ThreadContext;
 
-import static io.fairspace.saturn.auth.RequestContext.getAccessToken;
+import static io.fairspace.saturn.auth.RequestContext.getClaims;
 
 public class Audit {
     private static final Logger log = LogManager.getLogger("audit");
@@ -19,16 +20,18 @@ public static void audit(String event, Object... params) {
             }
         }
 
-        var token = getAccessToken();
+        var claims = getClaims();
+        String preferredUsername = claims.getPreferredUsername();
 
-        if (token.getPreferredUsername() != null) {
-            ThreadContext.put("user_name", token.getPreferredUsername());
+        if (preferredUsername != null) {
+            ThreadContext.put("user_name", preferredUsername);
         }
 
-        if (token.getEmail() != null) {
-            ThreadContext.put("user_email", token.getEmail());
+        String email = claims.getEmail();
+        if (email != null) {
+            ThreadContext.put("user_email", email);
         }
-        ThreadContext.put("user_id", token.getSubject());
+        ThreadContext.put("user_id", claims.getSubject());
 
         log.trace(event);