Update SMILE dependencies to 2.0.0.RELEASE (#81)

* Update to java21 General updates: - Support java21 - Spring framework and spring boot updates - Updated test layer to junit-jupiter - Updated circleci config Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com> * Update SMILE dependencies to 2.0.0.RELEASE Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com> --------- Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>
mskcc · Nov 15, 2024 · 27cacfe · 27cacfe
1 parent 8dea13d
commit 27cacfe
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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:

diff --git a/Dockerfile b/Dockerfile
@@ -1,11 +1,11 @@
-FROM maven:3.6.1-jdk-11-slim
+FROM maven:3.8.8
 # create working directory and set
 RUN mkdir /label-generator
 ADD . /label-generator
 WORKDIR /label-generator
 RUN mvn clean install
 
 # copy jar and set entrypoint
-FROM openjdk:11-slim
+FROM openjdk:21
 COPY --from=0 /label-generator/target/smile_label_generator.jar /label-generator/smile_label_generator.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>
@@ -29,21 +29,20 @@
   </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 and shared entities dependency versions -->
     <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>
     <!-- smile server model module -->
     <smile_server.group>com.github.mskcc.smile-server</smile_server.group>
-    <smile_server.version>1.6.0.RELEASE</smile_server.version>
+    <smile_server.version>2.0.0.RELEASE</smile_server.version>
   </properties>
 
   <dependencies>
@@ -72,20 +71,21 @@
     </dependency>
     <!-- testing -->
     <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
+      <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.springframework</groupId>
-      <artifactId>spring-test</artifactId>
-      <version>${spring.version}</version>
+      <groupId>org.springframework.boot</groupId>
+      <artifactId>spring-boot-test</artifactId>
+      <version>${spring.boot.version}</version>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.mockito</groupId>
       <artifactId>mockito-core</artifactId>
-      <version>3.3.3</version>
       <scope>test</scope>
       <type>jar</type>
     </dependency>
@@ -99,19 +99,7 @@
     <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>
-    </dependency>
-    <dependency>
-      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-lang3</artifactId>
-      <version>3.11</version>
+      <version>1.5.3</version>
     </dependency>
   </dependencies>
 
@@ -144,10 +132,10 @@
       <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/LabelGenMessageHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/LabelGenMessageHandlingServiceImpl.java
@@ -39,31 +39,31 @@
 @Service
 public class LabelGenMessageHandlingServiceImpl implements MessageHandlingService {
 
-    @Value("${igo.cmo_label_generator_topic}")
+    @Value("${igo.cmo_label_generator_topic:}")
     private String CMO_LABEL_GENERATOR_TOPIC;
 
-    @Value("${igo.cmo_promoted_label_topic}")
+    @Value("${igo.cmo_promoted_label_topic:}")
     private String CMO_PROMOTED_LABEL_TOPIC;
 
-    @Value("${igo.new_request_topic}")
+    @Value("${igo.new_request_topic:}")
     private String IGO_NEW_REQUEST_TOPIC;
 
-    @Value("${igo.promoted_request_topic}")
+    @Value("${igo.promoted_request_topic:}")
     private String IGO_PROMOTED_REQUEST_TOPIC;
 
-    @Value("${igo.cmo_sample_label_update_topic}")
+    @Value("${igo.cmo_sample_label_update_topic:}")
     private String CMO_LABEL_UPDATE_TOPIC;
 
-    @Value("${smile.sample_update_topic}")
+    @Value("${smile.sample_update_topic:}")
     private String IGO_SAMPLE_UPDATE_TOPIC;
 
-    @Value("${num.new_request_handler_threads}")
+    @Value("${num.new_request_handler_threads:1}")
     private int NUM_NEW_REQUEST_HANDLERS;
 
-    @Value("${num.promoted_request_handler_threads}")
+    @Value("${num.promoted_request_handler_threads:1}")
     private int NUM_PROMOTED_REQUEST_HANDLERS;
 
-    @Value("${request_reply.patient_samples_topic}")
+    @Value("${request_reply.patient_samples_topic:}")
     private String PATIENT_SAMPLES_REQUEST_TOPIC;
 
     @Autowired

diff --git a/src/main/java/org/mskcc/smile/service/impl/RequestReplyHandlingServiceImpl.java b/src/main/java/org/mskcc/smile/service/impl/RequestReplyHandlingServiceImpl.java
@@ -32,13 +32,13 @@
 @Service
 public class RequestReplyHandlingServiceImpl implements RequestReplyHandlingService {
 
-    @Value("${request_reply.cmo_label_generator_topic}")
+    @Value("${request_reply.cmo_label_generator_topic:}")
     private String CMO_LABEL_GENERATOR_REQREPLY_TOPIC;
 
-    @Value("${request_reply.patient_samples_topic}")
+    @Value("${request_reply.patient_samples_topic:}")
     private String PATIENT_SAMPLES_REQUEST_TOPIC;
 
-    @Value("${num.new_request_handler_threads}")
+    @Value("${num.new_request_handler_threads:1}")
     private int NUM_NEW_REQUEST_HANDLERS;
 
     @Autowired

diff --git a/src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java b/src/test/java/org/mskcc/smile/CmoLabelGeneratorServiceTest.java
@@ -7,9 +7,8 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import junit.framework.Assert;
-import org.junit.Test;
-import org.junit.runner.RunWith;
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
 import org.mskcc.smile.commons.enums.NucleicAcid;
 import org.mskcc.smile.commons.enums.SpecimenType;
 import org.mskcc.smile.config.TestConfiguration;
@@ -19,13 +18,11 @@
 import org.mskcc.smile.model.igo.IgoSampleManifest;
 import org.mskcc.smile.service.CmoLabelGeneratorService;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.ComponentScan;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.context.annotation.Import;
 
-@ContextConfiguration(classes = TestConfiguration.class)
-@RunWith(SpringJUnit4ClassRunner.class)
-@ComponentScan("org.mskcc.smile.service")
+@SpringBootTest(classes = LabelGeneratorTestApp.class)
+@Import(TestConfiguration.class)
 public class CmoLabelGeneratorServiceTest {
     private final ObjectMapper mapper = new ObjectMapper();
 
@@ -40,7 +37,7 @@ public class CmoLabelGeneratorServiceTest {
      */
     @Test
     public void testMockedRequestJsonDataLoading() {
-        Assert.assertNotNull(mockedRequestJsonDataMap);
+        Assertions.assertNotNull(mockedRequestJsonDataMap);
     }
 
     /**
@@ -52,7 +49,7 @@ public void testValidRequestJson() throws Exception {
         MockJsonTestData requestJson = mockedRequestJsonDataMap
                 .get("mockIncomingRequest1JsonDataWith2T2N");
         String modifiedRequestJson = requestJson.getJsonString();
-        Assert.assertNotNull(modifiedRequestJson);
+        Assertions.assertNotNull(modifiedRequestJson);
     }
 
     /**
@@ -89,12 +86,12 @@ public void testCmoLabelGenForSampleUpdate() throws JsonProcessingException,
         String newCmoLabel = cmoLabelGeneratorService.generateCmoSampleLabel(
                 updatedSample, existingSamples);
         // if the cmo label before the update is C-MP789JR-X001-d
-        Assert.assertEquals("C-MP789JR-P003-d02", newCmoLabel);
+        Assertions.assertEquals("C-MP789JR-P003-d02", newCmoLabel);
 
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
-        Assert.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
-        Assert.assertEquals(sampleStatus.getValidationReport(), (new HashMap()).toString());
+        Assertions.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
+        Assertions.assertEquals(sampleStatus.getValidationReport(), (new HashMap()).toString());
     }
 
     /**
@@ -135,12 +132,12 @@ public void testCmoLabelGenForSampleWithPatientCorrection()
                 updatedSample, existingSamples);
 
         // if the cmo label before the update is C-MP789JR-X001-d
-        Assert.assertEquals("C-newPatient-X003-d02", newCmoLabel);
+        Assertions.assertEquals("C-newPatient-X003-d02", newCmoLabel);
 
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
-        Assert.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
-        Assert.assertEquals(sampleStatus.getValidationReport(), (new HashMap()).toString());
+        Assertions.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
+        Assertions.assertEquals(sampleStatus.getValidationReport(), (new HashMap()).toString());
     }
 
     /**
@@ -180,13 +177,13 @@ public void testCmoLabelGenForExistingSampleWithPatientCorrection()
                 updatedSample, existingSamples);
 
         // if the cmo label before the update is C-MP789JR-X001-d
-        Assert.assertEquals("C-newPatient-X001-d02", newCmoLabel);
+        Assertions.assertEquals("C-newPatient-X001-d02", newCmoLabel);
 
 
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
-        Assert.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
-        Assert.assertEquals(sampleStatus.getValidationReport(), (new HashMap()).toString());
+        Assertions.assertEquals(Boolean.TRUE, sampleStatus.getValidationStatus());
+        Assertions.assertEquals(sampleStatus.getValidationReport(), (new HashMap()).toString());
     }
 
     /**
@@ -226,12 +223,12 @@ public void testCmoLabelGenForSampleWithOtherSpecimenType()
         // should return null string
         String newCmoLabel = cmoLabelGeneratorService.generateCmoSampleLabel(
                 updatedSample, existingSamples);
-        Assert.assertEquals("C-MP789JR-F001-d01", newCmoLabel);
+        Assertions.assertEquals("C-MP789JR-F001-d01", newCmoLabel);
 
         Status sampleStatus = cmoLabelGeneratorService.generateSampleStatus(
                 updatedSample, existingSamples);
-        Assert.assertEquals(Boolean.FALSE, sampleStatus.getValidationStatus());
-        Assert.assertNotSame(sampleStatus.getValidationReport(), (new HashMap()).toString());
+        Assertions.assertEquals(Boolean.FALSE, sampleStatus.getValidationStatus());
+        Assertions.assertNotSame(sampleStatus.getValidationReport(), (new HashMap()).toString());
     }
 
     @Test
@@ -245,7 +242,7 @@ public void testCmoCelllineLabelGenerationUpdates() {
         String sampleLabel =  cmoLabelGeneratorService.generateCmoSampleLabel(requestId,
                 sample, existingSamples);
         String sampleExpectedLabel = "AMP1-86793T";
-        Assert.assertEquals("AMP1-86793T", sampleLabel);
+        Assertions.assertEquals("AMP1-86793T", sampleLabel);
 
         // test label generated with new investigator id and assert
         // that the sample would require a label update
@@ -254,9 +251,9 @@ public void testCmoCelllineLabelGenerationUpdates() {
         String sampleUpdatedInvestigatorIdLabel = cmoLabelGeneratorService.generateCmoSampleLabel(requestId,
                 sampleUpdatedInvestigatorId, existingSamples);
         String expectedLabelWithInvestiagorIdUpdate = "MIP2-86793T";
-        Assert.assertEquals(expectedLabelWithInvestiagorIdUpdate, sampleUpdatedInvestigatorIdLabel);
+        Assertions.assertEquals(expectedLabelWithInvestiagorIdUpdate, sampleUpdatedInvestigatorIdLabel);
         // assert that the sample would require a label update
-        Assert.assertTrue(cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(
+        Assertions.assertTrue(cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(
                 sampleUpdatedInvestigatorIdLabel, sampleLabel));
 
         // test label generated with same investigator id as original sample
@@ -265,16 +262,16 @@ public void testCmoCelllineLabelGenerationUpdates() {
                 SpecimenType.CELLLINE, NucleicAcid.CFDNA, "AMP1");
         String sampleUpdatedNaExtractLabel = cmoLabelGeneratorService.generateCmoSampleLabel(requestId,
                 sampleUpdatedNaExtract, existingSamples);
-        Assert.assertEquals(sampleExpectedLabel, sampleUpdatedNaExtractLabel);
-        Assert.assertFalse(cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(
+        Assertions.assertEquals(sampleExpectedLabel, sampleUpdatedNaExtractLabel);
+        Assertions.assertFalse(cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(
                 sampleUpdatedNaExtractLabel, sampleExpectedLabel));
     }
 
     @Test
     public void testDefaultSampleTypeAbbreviation() {
         String sampleTypeAbbrev = cmoLabelGeneratorService.resolveSampleTypeAbbreviation("RapidAutopsy",
                 "Cerebrospinal Fluid", "Other");
-        Assert.assertTrue(sampleTypeAbbrev.equals("F"));
+        Assertions.assertTrue(sampleTypeAbbrev.equals("F"));
     }
 
     private IgoSampleManifest getSampleMetadata(String igoId, String cmoPatientId,

diff --git a/src/test/java/org/mskcc/smile/LabelGeneratorTestApp.java b/src/test/java/org/mskcc/smile/LabelGeneratorTestApp.java
@@ -0,0 +1,23 @@
+package org.mskcc.smile;
+
+import org.mskcc.cmo.messaging.Gateway;
+import org.mskcc.smile.service.impl.LabelGenMessageHandlingServiceImpl;
+import org.mskcc.smile.service.impl.RequestReplyHandlingServiceImpl;
+import org.springframework.boot.autoconfigure.SpringBootApplication;
+import org.springframework.boot.test.mock.mockito.MockBean;
+
+/**
+ *
+ * @author laptop
+ */
+@SpringBootApplication(scanBasePackages = {"org.mskcc.smile.service", "org.mskcc.smile.commons.*"})
+public class LabelGeneratorTestApp {
+    @MockBean
+    public Gateway messagingGateway;
+
+    @MockBean
+    public LabelGenMessageHandlingServiceImpl labelGenMessageHandlingServiceImpl;
+
+    @MockBean
+    public RequestReplyHandlingServiceImpl requestReplyMessageHandlingServiceImpl;
+}