Merge pull request #56 from HHS/update-gcm-to-4.2.1

Update gcm to 4.2.1
HHS · Jun 14, 2024 · b2b37a6 · b2b37a6
2 parents 8a46c03 + 48ba562
commit b2b37a6
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Showing 21 changed files with 245 additions and 53 deletions.
diff --git a/.github/workflows/dev_build.yml b/.github/workflows/dev_build.yml
@@ -11,8 +11,6 @@ name: GCM Taskit Development Build
 on:
   push:
     branches: [ "dev" ]
-  pull_request:
-    branches: [ "dev" ]
 
 jobs:
   dev-build:
@@ -28,9 +26,10 @@ jobs:
         distribution: 'temurin'
         cache: maven
 
-    - name: Get GCM Version
+    - name: Get GCM and Taskit Version
       run: |
         echo "gcm_version=v$(mvn help:evaluate -Dexpression=gcm.version -q -DforceStdout --file pom.xml)" >> "$GITHUB_ENV"
+        echo "taskit_version=v$(mvn help:evaluate -Dexpression=taskit.version -q -DforceStdout --file pom.xml)" >> "$GITHUB_ENV"
 
     - name: Checkout GCM
       if: ${{ endsWith(env.gcm_version, 'SNAPSHOT') }}
@@ -40,10 +39,6 @@ jobs:
         path: gcm
         ref: dev
 
-    - name: Get Taskit Version
-      run: |
-        echo "taskit_version=v$(mvn help:evaluate -Dexpression=taskit.version -q -DforceStdout --file pom.xml)" >> "$GITHUB_ENV"
-
     - name: Checkout Taskit
       if: ${{ endsWith(env.taskit_version, 'SNAPSHOT') }}
       uses: actions/checkout@v4

diff --git a/.github/workflows/dev_pr_build.yml b/.github/workflows/dev_pr_build.yml
@@ -0,0 +1,80 @@
+# This workflow will build a Java project with Maven, and cache/restore any dependencies to improve the workflow execution time
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-java-with-maven
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: GCM Taskit Development PR Build
+
+on:
+  pull_request:
+    branches-ignore: [ "main" ]
+
+jobs:
+  dev-build:
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout GCM Taskit
+      uses: actions/checkout@v4
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v4
+      with:
+        java-version: '17'
+        distribution: 'temurin'
+        cache: maven
+
+    - name: Get GCM and Taskit Version
+      run: |
+        echo "gcm_version=v$(mvn help:evaluate -Dexpression=gcm.version -q -DforceStdout --file pom.xml)" >> "$GITHUB_ENV"
+        echo "taskit_version=v$(mvn help:evaluate -Dexpression=taskit.version -q -DforceStdout --file pom.xml)" >> "$GITHUB_ENV"
+
+    - name: Checkout GCM
+      if: ${{ endsWith(env.gcm_version, 'SNAPSHOT') }}
+      uses: actions/checkout@v4
+      with:
+        repository: HHS/ASPR-8
+        path: gcm
+        ref: dev
+
+    - name: Checkout Taskit
+      if: ${{ endsWith(env.taskit_version, 'SNAPSHOT') }}
+      uses: actions/checkout@v4
+      with:
+        repository: HHS/ASPR-ms-taskit
+        path: taskit
+        ref: dev
+
+    - name: Get Util Version
+      if: ${{ endsWith(env.gcm_version, 'SNAPSHOT') }}
+      run: |
+        echo "util_version=v$(mvn help:evaluate -Dexpression=util.version -q -DforceStdout --file gcm/pom.xml)" >> "$GITHUB_ENV"
+
+    - name: Checkout Util
+      if: ${{ endsWith(env.util_version, 'SNAPSHOT') }}
+      uses: actions/checkout@v4
+      with:
+        repository: HHS/ASPR-ms-util
+        path: util
+        ref: dev
+
+    - name: Build Util
+      if: ${{ endsWith(env.util_version, 'SNAPSHOT') }}
+      run: mvn clean install -DskipTests --file util/pom.xml
+
+    - name: Build GCM
+      if: ${{ endsWith(env.gcm_version, 'SNAPSHOT') }}
+      run: mvn clean install -DskipTests --file gcm/simulation/pom.xml
+
+    - name: Build Taskit
+      if: ${{ endsWith(env.taskit_version, 'SNAPSHOT') }}
+      run: mvn clean install -DskipTests --file taskit/pom.xml
+
+    - name: Build GCM Taskit
+      run: mvn clean install --file pom.xml
+
+    # Optional: Uploads the full dependency graph to GitHub to improve the quality of Dependabot alerts this repository can receive
+   # - name: Update dependency graph
+     # uses: advanced-security/maven-dependency-submission-action@571e99aab1055c2e71a1e2309b9691de18d6b7d6
diff --git a/pom.xml b/pom.xml
@@ -50,7 +50,7 @@
 
     <!-- Properties -->
     <properties>
-        <revision>2.8.1</revision>
+        <revision>2.8.2</revision>
 
         <!-- basic project properties -->
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -62,15 +62,15 @@
         <maven-surefire-plugin.version>3.2.5</maven-surefire-plugin.version>
         <maven-failsafe-plugin.version>3.2.5</maven-failsafe-plugin.version>
         <maven-source-plugin.version>3.3.1</maven-source-plugin.version>
-        <maven-install-plugin.version>3.1.1</maven-install-plugin.version>
-        <maven-deploy-plugin.version>3.1.1</maven-deploy-plugin.version>
+        <maven-install-plugin.version>3.1.2</maven-install-plugin.version>
+        <maven-deploy-plugin.version>3.1.2</maven-deploy-plugin.version>
         <maven-javadoc-plugin.version>3.6.3</maven-javadoc-plugin.version>
         <maven-gpg-plugin.version>3.2.4</maven-gpg-plugin.version>
         <central-publishing-maven-plugin.version>0.4.0</central-publishing-maven-plugin.version>
 
         <!-- dependency versions -->
         <taskit.version>4.0.2</taskit.version>
-        <gcm.version>4.2.0</gcm.version>
+        <gcm.version>4.2.1</gcm.version>
         <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
         <junit-jupiter-engine.version>5.10.2</junit-jupiter-engine.version>
     </properties>
@@ -110,7 +110,6 @@
         <dependency>
             <groupId>gov.hhs.aspr.ms.gcm</groupId>
             <artifactId>simulation</artifactId>
-            <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>org.jacoco</groupId>
@@ -411,4 +410,4 @@
             </build>
         </profile>
     </profiles>
-</project>
+</project>
diff --git a/protobuf/src/main/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/nucleus/NucleusTranslator.java b/protobuf/src/main/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/nucleus/NucleusTranslator.java
@@ -3,6 +3,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.input.ExperimentParameterDataInput;
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.input.SimulationStateInput;
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.testsupport.translationSpecs.ExampleDimensionTranslationSpec;
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.nucleus.translationSpecs.DimensionTranslationSpec;
@@ -51,6 +52,19 @@ private static Translator.Builder builder() {
 
                     translationEngineBuilder.addFieldToIncludeDefaultValue(
                             SimulationStateInput.getDescriptor().findFieldByName("startTime"));
+
+                    translationEngineBuilder.addFieldToIncludeDefaultValue(
+                            ExperimentParameterDataInput.getDescriptor().findFieldByName("threadCount"))
+                    .addFieldToIncludeDefaultValue(
+                            ExperimentParameterDataInput.getDescriptor().findFieldByName("startRecordingIsScheduled"))
+                    .addFieldToIncludeDefaultValue(
+                            ExperimentParameterDataInput.getDescriptor().findFieldByName("simulationHaltTime"))
+                    .addFieldToIncludeDefaultValue(
+                            ExperimentParameterDataInput.getDescriptor().findFieldByName("haltOnException"))
+                    .addFieldToIncludeDefaultValue(
+                            ExperimentParameterDataInput.getDescriptor().findFieldByName("experimentProgressLogPath"))
+                    .addFieldToIncludeDefaultValue(
+                            ExperimentParameterDataInput.getDescriptor().findFieldByName("continueFromProgressLog"));                    
                 });
 
         return builder;

diff --git a/...n/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/stochastics/StochasticsTranslator.java b/...n/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/stochastics/StochasticsTranslator.java
@@ -4,6 +4,7 @@
 import java.util.List;
 
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.translationSpecs.RandomNumberGeneratorIdTranslationSpec;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.translationSpecs.SimpleRandomNumberGeneratorIdTranslationSpec;
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.translationSpecs.StochasticsPluginDataTranslationSpec;
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.translationSpecs.TestRandomGeneratorIdTranslationSpec;
 import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.translationSpecs.WellStateTranslationSpec;
@@ -27,6 +28,8 @@ private StochasticsTranslator() {
         list.add(new WellStateTranslationSpec());
         list.add(new RandomNumberGeneratorIdTranslationSpec());
         list.add(new TestRandomGeneratorIdTranslationSpec());
+        list.add(new SimpleRandomNumberGeneratorIdTranslationSpec());
+
 
         return list;
     }

diff --git a/...uf/plugins/stochastics/translationSpecs/SimpleRandomNumberGeneratorIdTranslationSpec.java b/...uf/plugins/stochastics/translationSpecs/SimpleRandomNumberGeneratorIdTranslationSpec.java
@@ -0,0 +1,38 @@
+package gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.translationSpecs;
+
+import gov.hhs.aspr.ms.gcm.simulation.plugins.reports.support.SimpleReportLabel;
+import gov.hhs.aspr.ms.gcm.simulation.plugins.stochastics.support.SimpleRandomNumberGeneratorId;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.reports.support.input.SimpleReportLabelInput;
+import gov.hhs.aspr.ms.gcm.taskit.protobuf.plugins.stochastics.support.input.SimpleRandomNumberGeneratorIdInput;
+import gov.hhs.aspr.ms.taskit.protobuf.ProtobufTranslationSpec;
+
+/**
+ * TranslationSpec that defines how to convert between
+ * {@linkplain SimpleReportLabelInput} and {@linkplain SimpleReportLabel}
+ */
+public class SimpleRandomNumberGeneratorIdTranslationSpec
+        extends ProtobufTranslationSpec<SimpleRandomNumberGeneratorIdInput, SimpleRandomNumberGeneratorId> {
+
+    @Override
+    protected SimpleRandomNumberGeneratorId convertInputObject(SimpleRandomNumberGeneratorIdInput inputObject) {
+        return new SimpleRandomNumberGeneratorId(this.translationEngine.getObjectFromAny(inputObject.getValue()));
+    }
+
+    @Override
+    protected SimpleRandomNumberGeneratorIdInput convertAppObject(SimpleRandomNumberGeneratorId appObject) {
+        return SimpleRandomNumberGeneratorIdInput.newBuilder()
+                .setValue(this.translationEngine.getAnyFromObject(appObject.getValue()))
+                .build();
+    }
+
+    @Override
+    public Class<SimpleRandomNumberGeneratorId> getAppObjectClass() {
+        return SimpleRandomNumberGeneratorId.class;
+    }
+
+    @Override
+    public Class<SimpleRandomNumberGeneratorIdInput> getInputObjectClass() {
+        return SimpleRandomNumberGeneratorIdInput.class;
+    }
+
+}
diff --git a/...obuf/src/main/proto/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/stochastics/support.proto b/...obuf/src/main/proto/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/stochastics/support.proto
@@ -11,6 +11,11 @@ message RandomNumberGeneratorIdInput {
     google.protobuf.Any id = 1;
 }
 
+message SimpleRandomNumberGeneratorIdInput {
+    google.protobuf.Any value = 1;
+}
+
+
 message WellStateInput {
     int64 seed = 1;
     optional int32 index = 2;

diff --git a/protobuf/src/test/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/nucleus/IT_NucleusTranslator.java b/protobuf/src/test/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/nucleus/IT_NucleusTranslator.java
@@ -19,14 +19,14 @@
 
 public class IT_NucleusTranslator {
     Path basePath = ResourceHelper.getResourceDir(this.getClass());
-    Path filePath = ResourceHelper.makeOutputDir(basePath, "test-output");
+    Path filePath = ResourceHelper.createDirectory(basePath, "test-output");
 
     @Test
     @UnitTestForCoverage
     public void testSimulationStateTranslator() {
         String fileName = "simulationState.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(
@@ -57,7 +57,7 @@ public void testSimulationStateTranslator() {
     public void testExperimentParameterDataTranslator() {
         String fileName = "experimentParameterData.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(

diff --git a/...s/aspr/ms/gcm/taskit/protobuf/plugins/globalproperties/IT_GlobalPropertiesTranslator.java b/...s/aspr/ms/gcm/taskit/protobuf/plugins/globalproperties/IT_GlobalPropertiesTranslator.java
@@ -26,14 +26,14 @@
 
 public class IT_GlobalPropertiesTranslator {
     Path basePath = ResourceHelper.getResourceDir(this.getClass());
-    Path filePath = ResourceHelper.makeOutputDir(basePath, "test-output");
+    Path filePath = ResourceHelper.createDirectory(basePath, "test-output");
 
     @Test
     @UnitTestForCoverage
     public void testGlobalPropertiesPluginDataIntegration() {
         String fileName = "globalPropertiesPluginData.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         ProtobufTranslationEngine protobufTranslationEngine = ProtobufTranslationEngine.builder()
                 .addTranslator(GlobalPropertiesTranslator.getTranslator())
@@ -68,7 +68,7 @@ public void testGlobalPropertiesPluginDataIntegration() {
     public void testGlobalPropertyReportPluginDataIntegration() {
         String fileName = "propertyReport.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         ProtobufTranslationEngine protobufTranslationEngine = ProtobufTranslationEngine.builder()
                 .addTranslator(GlobalPropertiesTranslator.getTranslator())

diff --git a/...src/test/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/groups/IT_GroupsTranslator.java b/...src/test/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/groups/IT_GroupsTranslator.java
@@ -34,14 +34,14 @@
 
 public class IT_GroupsTranslator {
     Path basePath = ResourceHelper.getResourceDir(this.getClass());
-    Path filePath = ResourceHelper.makeOutputDir(basePath, "test-output");
+    Path filePath = ResourceHelper.createDirectory(basePath, "test-output");
 
     @Test
     @UnitTestForCoverage
     public void testGroupsTranslator() {
         String fileName = "groupsPluginData.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         ProtobufTranslationEngine protobufTranslationEngine = ProtobufTranslationEngine.builder()
                 .addTranslator(GroupsTranslator.getTranslator())
@@ -99,7 +99,7 @@ public void testGroupsTranslator() {
     public void testGroupPropertyReportTranslatorSpec() {
         String fileName = "propertyReport.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         ProtobufTranslationEngine protobufTranslationEngine = ProtobufTranslationEngine.builder()
                 .addTranslator(GroupsTranslator.getTranslator())

diff --git a/...st/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/materials/IT_MaterialsTranslator.java b/...st/java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/materials/IT_MaterialsTranslator.java
@@ -32,14 +32,14 @@
 
 public class IT_MaterialsTranslator {
     Path basePath = ResourceHelper.getResourceDir(this.getClass());
-    Path filePath = ResourceHelper.makeOutputDir(basePath, "test-output");
+    Path filePath = ResourceHelper.createDirectory(basePath, "test-output");
 
     @Test
     @UnitTestForCoverage
     public void testMaterialsTranslator() {
         String fileName = "materialsPluginData.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(ProtobufTranslationEngine.builder()
@@ -76,7 +76,7 @@ public void testMaterialsTranslator() {
     public void testBatchStatusReportPluginDataTranslatorSpec() {
         String fileName = "batchStatusReport.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(ProtobufTranslationEngine.builder()
@@ -116,7 +116,7 @@ public void testBatchStatusReportPluginDataTranslatorSpec() {
     public void testMaterialsProducerPropertyReportPluginDataTranslatorSpec() {
         String fileName = "materialsProducerPropertyReport.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(ProtobufTranslationEngine.builder()
@@ -155,7 +155,7 @@ public void testMaterialsProducerPropertyReportPluginDataTranslatorSpec() {
     public void testMaterialsProducerResourceReportPluginDataTranslatorSpec() {
         String fileName = "materialsProducerResourceReport.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(ProtobufTranslationEngine.builder()
@@ -194,7 +194,7 @@ public void testMaterialsProducerResourceReportPluginDataTranslatorSpec() {
     public void testStageReportPluginDataTranslatorSpec() {
         String fileName = "stageReport.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(ProtobufTranslationEngine.builder()

diff --git a/.../java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/partitions/IT_PartitionsTranslator.java b/.../java/gov/hhs/aspr/ms/gcm/taskit/protobuf/plugins/partitions/IT_PartitionsTranslator.java
@@ -18,14 +18,14 @@
 
 public class IT_PartitionsTranslator {
     Path basePath = ResourceHelper.getResourceDir(this.getClass());
-    Path filePath = ResourceHelper.makeOutputDir(basePath, "test-output");
+    Path filePath = ResourceHelper.createDirectory(basePath, "test-output");
 
     @Test
     @UnitTestForCoverage
     public void testGroupsTranslator() {
         String fileName = "partitionsPluginData.json";
 
-        ResourceHelper.createOutputFile(filePath, fileName);
+        ResourceHelper.createFile(filePath, fileName);
 
         TranslationController translatorController = TranslationController.builder()
                 .addTranslationEngine(ProtobufTranslationEngine.builder()