Update to Java21 (#62) (#64)

* Update to Java21 (#62) General changes: - updated spring boot, spring versions - updated test framework to junit-jupiter - updated maven compiler - updated other dependencies as needed to support java21 Update messaging lib and commons versions Signed-off-by: Angelica Ochoa <[email protected]> * Bug fix: always publish requests or samples even when validation fails (#65) Signed-off-by: Angelica Ochoa <[email protected]> * patch for writing validation report as string (#66) * Fix test layer (#67) Signed-off-by: Angelica Ochoa <[email protected]> * Update SMILE dependencies to 2.0.0.RELEASE (#68) Signed-off-by: Angelica Ochoa <[email protected]> --------- Signed-off-by: Angelica Ochoa <[email protected]>
mskcc · Nov 15, 2024 · 30f3f2a · 30f3f2a
1 parent b120d8b
commit 30f3f2a
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Showing 11 changed files with 218 additions and 156 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,11 +1,11 @@
 defaults: &defaults
     docker:
-        - image: cimg/openjdk:8.0.275
+        - image: cimg/openjdk:21.0
 
 version: 2.1
 
 orbs:
-  maven: circleci/maven@1.0.3
+  maven: circleci/maven@1.4.1
 
 jobs:
   run_checkstyle:
@@ -25,7 +25,7 @@ jobs:
               git checkout ${SMILE_COMMONS_VERSION}
       - run:
           name: "Build project..."
-          command: mvn clean install
+          command: mvn clean install -U
       - run:
           name: "Run checkstyle plugin..."
           command: mvn checkstyle:checkstyle

diff --git a/Dockerfile b/Dockerfile
@@ -1,9 +1,9 @@
-FROM maven:3.6.1-jdk-11-slim
+FROM maven:3.8.8
 RUN mkdir /request-filter
 ADD . /request-filter
 WORKDIR /request-filter
 RUN mvn clean install
 
-FROM openjdk:11-slim
+FROM openjdk:21
 COPY --from=0 /request-filter/target/smile_request_filter.jar /request-filter/smile_request_filter.jar
 ENTRYPOINT ["java"]
diff --git a/jitpack.yml b/jitpack.yml
@@ -0,0 +1,9 @@
+jdk:
+  - openjdk21
+
+before_install:
+   - sdk install maven 3.8.8
+   - sdk use maven 3.8.8
+   - sdk install java 21.0.2-open
+   - sdk use java 21.0.2-open
+   - sdk update
diff --git a/pom.xml b/pom.xml
@@ -11,7 +11,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.3.3.RELEASE</version>
+    <version>3.3.3</version>
   </parent>
 
   <repositories>
@@ -29,18 +29,17 @@
   </pluginRepositories>
 
   <properties>
-    <java.version>1.8</java.version>
-    <maven.compiler.version>1.8</maven.compiler.version>
-    <spring.version>5.2.6.RELEASE</spring.version>
-    <spring.boot.version>2.3.3.RELEASE</spring.boot.version>
-    <slf4j.version>1.7.30</slf4j.version>
-    <jackson.version>2.11.2</jackson.version>
+    <java.version>21</java.version>
+    <maven.compiler.version>3.11.0</maven.compiler.version>
+    <spring.version>6.1.12</spring.version>
+    <spring.boot.version>3.3.3</spring.boot.version>
+    <jackson.version>2.17.2</jackson.version>
     <!-- smile messaging -->
     <smile_messaging_java.group>com.github.mskcc</smile_messaging_java.group>
-    <smile_messaging_java.version>1.4.1.RELEASE</smile_messaging_java.version>
+    <smile_messaging_java.version>2.0.0.RELEASE</smile_messaging_java.version>
     <!-- smile commons centralized config properties -->
     <smile_commons.group>com.github.mskcc</smile_commons.group>
-    <smile_commons.version>1.4.1.RELEASE</smile_commons.version>
+    <smile_commons.version>2.0.0.RELEASE</smile_commons.version>
   </properties>
 
   <dependencies>
@@ -58,20 +57,22 @@
     </dependency>
     <!-- testing -->
     <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-test</artifactId>
+      <version>${spring.boot.version}</version>
       <scope>test</scope>
+      <type>jar</type>
     </dependency>
     <dependency>
-      <groupId>org.springframework</groupId>
-      <artifactId>spring-test</artifactId>
-      <version>${spring.version}</version>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+      <version>5.10.3</version>
       <scope>test</scope>
+      <type>jar</type>
     </dependency>
     <dependency>
       <groupId>org.mockito</groupId>
       <artifactId>mockito-core</artifactId>
-      <version>3.3.3</version>
       <scope>test</scope>
       <type>jar</type>
     </dependency>
@@ -85,19 +86,12 @@
     <dependency>
       <groupId>org.skyscreamer</groupId>
       <artifactId>jsonassert</artifactId>
-      <version>1.5.0</version>
-    </dependency>
-    <!-- string utils -->
-    <dependency>
-      <groupId>com.google.guava</groupId>
-      <artifactId>guava</artifactId>
-      <version>19.0</version>
-      <type>jar</type>
+      <version>1.5.3</version>
     </dependency>
     <dependency>
-      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-lang3</artifactId>
-      <version>3.11</version>
+      <groupId>commons-logging</groupId>
+      <artifactId>commons-logging</artifactId>
+      <version>1.3.4</version>
     </dependency>
   </dependencies>
 
@@ -130,10 +124,10 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-compiler-plugin</artifactId>
-        <version>3.6.1</version>
+        <version>${maven.compiler.version}</version>
         <configuration>
-          <source>${maven.compiler.version}</source>
-          <target>${maven.compiler.version}</target>
+          <source>${java.version}</source>
+          <target>${java.version}</target>
           <compilerArgument>-Xlint:deprecation</compilerArgument>
         </configuration>
       </plugin>

diff --git a/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/PromotedRequestMsgHandlingServiceImpl.java
@@ -1,8 +1,8 @@
 package org.mskcc.smile.service.impl;
 
+import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.nats.client.Message;
-import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.Map;
 import java.util.concurrent.BlockingQueue;
@@ -29,16 +29,16 @@
 @Service
 public class PromotedRequestMsgHandlingServiceImpl implements PromotedRequestMsgHandlingService {
 
-    @Value("${igo.validate_promoted_request_topic}")
+    @Value("${igo.validate_promoted_request_topic:}")
     private String VALIDATE_PROMOTED_REQUEST_TOPIC;
 
-    @Value("${igo.cmo_promoted_label_topic}")
+    @Value("${igo.cmo_promoted_label_topic:}")
     private String CMO_PROMOTED_LABEL_TOPIC;
 
-    @Value("${igo.promoted_request_topic}")
+    @Value("${igo.promoted_request_topic:}")
     private String IGO_PROMOTED_REQUEST_TOPIC;
 
-    @Value("${num.promoted_request_handler_threads}")
+    @Value("${num.promoted_request_handler_threads:1}")
     private int NUM_PROMOTED_REQUEST_HANDLERS;
 
     @Autowired
@@ -75,14 +75,16 @@ public void run() {
                                 validRequestChecker.generatePromotedRequestValidationMap(requestJson);
                         Map<String, Object> requestStatus =
                                 mapper.convertValue(promotedRequestJsonMap.get("status"), Map.class);
+                        String requestWithStatus = updateJsonWithValidationMap(requestJson, requestStatus);
+
                         if ((Boolean) requestStatus.get("validationStatus")) {
                             // if request is cmo then publish to CMO_PROMOTED_LABEL_TOPIC
                             // otherwise publish to IGO_PROMOTED_REQUEST_TOPIC
                             String topic = validRequestChecker.isCmo(requestJson)
                                     ? CMO_PROMOTED_LABEL_TOPIC : IGO_PROMOTED_REQUEST_TOPIC;
                             String requestId = validRequestChecker.getRequestId(requestJson);
                             LOG.info("Promoted request passed sanity checks - publishing to: " + topic);
-                            messagingGateway.publish(requestId, topic, requestJson);
+                            messagingGateway.publish(requestId, topic, requestWithStatus);
                         }
                     }
                     if (interrupted && promotedRequestQueue.isEmpty()) {
@@ -162,4 +164,19 @@ public void onMessage(Message msg, Object message) {
             }
         });
     }
+
+    /**
+     * Updates the input json with the validation map provided.
+     * The validation map contains the validation report and validation status.
+     * @param inputJson
+     * @param validationMap
+     * @return String
+     * @throws JsonProcessingException
+     */
+    private String updateJsonWithValidationMap(String inputJson, Map<String, Object> validationMap)
+            throws JsonProcessingException {
+        Map<String, Object> inputJsonMap = mapper.readValue(inputJson, Map.class);
+        inputJsonMap.put("status", validationMap);
+        return mapper.writeValueAsString(inputJsonMap);
+    }
 }
diff --git a/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java b/src/main/java/org/mskcc/smile/service/impl/RequestFilterMsgHandlingServiceIml.java
@@ -2,7 +2,6 @@
 
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.nats.client.Message;
-import java.io.IOException;
 import java.nio.charset.StandardCharsets;
 import java.util.concurrent.BlockingQueue;
 import java.util.concurrent.CountDownLatch;
@@ -28,16 +27,16 @@
 @Service
 public class RequestFilterMsgHandlingServiceIml implements RequestFilterMessageHandlingService {
 
-    @Value("${igo.request_filter_topic}")
+    @Value("${igo.request_filter_topic:}")
     private String IGO_REQUEST_FILTER_TOPIC;
 
-    @Value("${igo.cmo_label_generator_topic}")
+    @Value("${igo.cmo_label_generator_topic:}")
     private String CMO_LABEL_GENERATOR_TOPIC;
 
-    @Value("${igo.new_request_topic}")
+    @Value("${igo.new_request_topic:}")
     private String IGO_NEW_REQUEST_TOPIC;
 
-    @Value("${num.new_request_handler_threads}")
+    @Value("${num.new_request_handler_threads:1}")
     private int NUM_NEW_REQUEST_HANDLERS;
 
     @Autowired
@@ -79,25 +78,27 @@ public void run() {
                             if (passCheck) {
                                 LOG.info("Request'" + requestId + "' passed sanity check, publishing to: "
                                         + CMO_LABEL_GENERATOR_TOPIC);
-                                // even if sanity check passed there might still be information worth
-                                // reporting from the sample-level validation reports
-                                messagingGateway.publish(requestId,
-                                    CMO_LABEL_GENERATOR_TOPIC,
-                                    filteredRequestJson);
                             } else {
-                                LOG.error("Sanity check failed on request: " + requestId);
+                                LOG.error("Sanity check failed on request: " + filteredRequestJson);
                             }
+                            // even if sanity check failed there might still be information worth
+                            // reporting from the sample-level validation reports
+                            messagingGateway.publish(requestId,
+                                    CMO_LABEL_GENERATOR_TOPIC,
+                                    filteredRequestJson);
                         } else {
                             LOG.info("Handling non-CMO request...");
                             if (passCheck) {
                                 LOG.info("Request '" + requestId + "' passed sanity check, publishing to: "
                                         + IGO_NEW_REQUEST_TOPIC);
-                                messagingGateway.publish(requestId,
-                                        IGO_NEW_REQUEST_TOPIC,
-                                        filteredRequestJson);
                             } else {
-                                LOG.error("Sanity check failed on request: " + requestId);
+                                LOG.error("Sanity check failed on request: " + filteredRequestJson);
                             }
+                            // even if sanity check failed there might still be information worth
+                            // reporting from the sample-level validation reports
+                            messagingGateway.publish(requestId,
+                                    IGO_NEW_REQUEST_TOPIC,
+                                    filteredRequestJson);
                         }
                         // data dog log message
                         String ddogLogMessage = validRequestChecker.generateValidationReport(