Aphl mergeback

.github/workflows/check-pr.yaml

@@ -13,4 +13,4 @@ jobs:
               distribution: temurin
               java-version: 21
          - name: Run Checks
-           run: mvn --batch-mode --no-transfer-progress --update-snapshots verify
+           run: ./mvnw -T 4 --batch-mode --no-transfer-progress --update-snapshots verify

.github/workflows/publish-snapshot-vsm-operations.yml

@@ -0,0 +1,40 @@
+name: Publish Snapshot VSM Operations
+on:
+  push:
+    branches:
+      - vsm_operations
+jobs:
+  maven:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Add SHORT_SHA env property with commit short sha
+        run: echo "SHORT_SHA=`echo ${GITHUB_SHA} | cut -c1-8`" >> $GITHUB_ENV
+      - uses: actions/checkout@v3
+        with:
+          submodules: true
+      - uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 11
+          server-id: ossrh
+          server-username: MAVEN_USERNAME
+          server-password: MAVEN_PASSWORD
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ vars.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+      - name: Install
+        run: ./scripts/install.sh
+      - name: Build and push
+        uses: docker/build-push-action@v4
+        with:
+          context: .
+          push: true
+          platforms: linux/amd64,linux/arm64
+          tags: alphora/cqf-ruler:cqf-ruler-vsm
+          build-args: COMMIT_HASH=${{ env.SHORT_SHA }}
+          cache-from: type=gha
+          cache-to: type=gha,mode=max

.github/workflows/publish-snapshot.yml

@@ -21,7 +21,7 @@ jobs:
               server-username: MAVEN_USERNAME
               server-password: MAVEN_PASSWORD
          - name: Publish snapshot
-           run: mvn --batch-mode -no-transfer-progress --update-snapshots deploy
+           run: ./mvnw -T 4 --batch-mode -no-transfer-progress --update-snapshots deploy
            env:
               MAVEN_USERNAME: ${{ vars.OSSRH_USERNAME }}
               MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}

Dockerfile

@@ -4,13 +4,15 @@ ARG COMMIT_HASH
 LABEL COMMIT_HASH ${COMMIT_HASH}
 ENV COMMIT_HASH ${COMMIT_HASH}
 
+ENV VERSION=0.15.0-SNAPSHOT
 RUN apt-get update && apt-get upgrade -y && rm -rf /var/lib/apt/lists/*
 RUN groupadd -r cqfruler && useradd -r -g cqfruler cqfruler
 USER cqfruler
 WORKDIR /home/cqfruler
 
 RUN mkdir server
 RUN mkdir plugin
-COPY ./server/target/cqf-ruler-server-*.war server/ROOT.war
+COPY /server/target/cqf-ruler-server-${VERSION}.war server/ROOT.war
+
 EXPOSE 8080
 CMD ["java", "-cp", "server/ROOT.war", "-Dloader.path=WEB-INF/classes,WEB-INF/lib,WEB-INF/lib-provided,plugin", "org.springframework.boot.loader.PropertiesLauncher"]

core/src/main/java/org/opencds/cqf/ruler/utility/SemanticVersion.java

@@ -0,0 +1,42 @@
+package org.opencds.cqf.ruler.utility;
+
+import java.util.List;
+import java.util.Comparator;
+
+public class SemanticVersion {
+	public static Comparator<String> getVersionComparator() {
+		return new VersionComparator();
+	}
+
+	public static String findHighestVersion(List<String> versions) {
+		String highestVersion = null;
+		Comparator<String> versionComparator = new VersionComparator();
+
+		for (String version : versions) {
+			if (highestVersion == null || versionComparator.compare(version, highestVersion) > 0) {
+				highestVersion = version;
+			}
+		}
+
+		return highestVersion;
+	}
+
+	public static class VersionComparator implements Comparator<String> {
+		@Override
+		public int compare(String v1, String v2) {
+			String[] v1Parts = v1.split("\\.");
+			String[] v2Parts = v2.split("\\.");
+
+			for (int i = 0; i < Math.max(v1Parts.length, v2Parts.length); i++) {
+				int num1 = i < v1Parts.length ? Integer.parseInt(v1Parts[i]) : 0;
+				int num2 = i < v2Parts.length ? Integer.parseInt(v2Parts[i]) : 0;
+
+				if (num1 != num2) {
+					return num1 - num2;
+				}
+			}
+
+			return 0;
+		}
+	}
+}

core/src/test/java/org/opencds/cqf/ruler/ExampleServerDstu2IT.java

@@ -23,7 +23,8 @@
 				"hapi.fhir.fhir_version=dstu2",
 				"spring.datasource.url=jdbc:h2:mem:dbr2",
 				"hapi.fhir.cr.enabled=false",
-				"spring.main.allow-bean-definition-overriding=true"
+				"spring.main.allow-bean-definition-overriding=true",
+				"spring.jpa.properties.hibernate.search.backend.directory.root=target/lucenefiles-dstu2",
 		})
 public class ExampleServerDstu2IT {
 

core/src/test/java/org/opencds/cqf/ruler/ExampleServerDstu3IT.java

@@ -1,8 +1,18 @@
 package org.opencds.cqf.ruler;
 
 import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertFalse;
+import static org.junit.jupiter.api.Assertions.assertTrue;
 
+import ca.uhn.fhir.cr.config.RepositoryConfig;
+import ca.uhn.fhir.model.primitive.IdDt;
+import ca.uhn.fhir.rest.api.CacheControlDirective;
+import org.apache.commons.io.FileUtils;
+import org.hl7.fhir.dstu3.model.Bundle;
+import org.hl7.fhir.dstu3.model.MeasureReport;
+import org.hl7.fhir.dstu3.model.Parameters;
 import org.hl7.fhir.dstu3.model.Patient;
+import org.hl7.fhir.dstu3.model.StringType;
 import org.hl7.fhir.instance.model.api.IIdType;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
@@ -15,21 +25,41 @@
 import ca.uhn.fhir.rest.client.api.IGenericClient;
 import ca.uhn.fhir.rest.client.api.ServerValidationModeEnum;
 import ca.uhn.fhir.rest.client.interceptor.LoggingInterceptor;
+import org.springframework.core.io.ClassPathResource;
 import org.springframework.test.annotation.DirtiesContext;
 import org.springframework.test.context.junit.jupiter.SpringExtension;
 
+import java.io.File;
+import java.io.IOException;
+import java.util.Collection;
+import java.util.List;
+
 @ExtendWith(SpringExtension.class)
-@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT, classes = {Application.class, JpaStarterWebsocketDispatcherConfig.class}, properties = {
+@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT,
+	classes = {
+		Application.class,
+		JpaStarterWebsocketDispatcherConfig.class
+	}, properties =
+	{
+		"spring.profiles.include=storageSettingsTest",
 		"spring.datasource.url=jdbc:h2:mem:dbr3",
 		"hapi.fhir.fhir_version=dstu3",
+		"hapi.fhir.cr_enabled=true",
+		"hapi.fhir.mdm_enabled=false",
+		"spring.batch.enabled=false",
 		"hapi.fhir.subscription.websocket_enabled=true",
 		"hapi.fhir.allow_external_references=true",
 		"hapi.fhir.allow_placeholder_references=true",
-		"spring.main.allow-bean-definition-overriding=true"})
-class ExampleServerDstu3IT {
-	private IGenericClient ourClient;
+		"hapi.fhir.enable_repository_validating_interceptor=true",
+		"spring.main.allow-bean-definition-overriding=true",
+		"spring.jpa.properties.hibernate.search.backend.directory.root=target/lucenefiles-dstu3",
+	})
 
-	@Autowired
+
+class ExampleServerDstu3IT implements IServerSupport {
+
+	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerDstu3IT.class);
+	private IGenericClient ourClient;
 	private FhirContext ourCtx;
 
 	@Autowired
@@ -38,7 +68,6 @@ class ExampleServerDstu3IT {
 	@LocalServerPort
 	private int port;
 
-
 	@BeforeEach
 	void beforeEach() {
 		ourCtx = FhirContext.forDstu3();
@@ -52,6 +81,7 @@ void beforeEach() {
 	@Test
 	@DirtiesContext
 	void testCreateAndRead() {
+
 		String methodName = "testCreateResourceConditional";
 
 		Patient pt = new Patient();

core/src/test/java/org/opencds/cqf/ruler/ExampleServerR4IT.java

@@ -40,7 +40,8 @@
 				// Override is currently required when using MDM as the construction of the MDM
 				// beans are ambiguous as they are constructed multiple places. This is evident
 				// when running in a spring boot environment
-				"spring.main.allow-bean-definition-overriding=true"
+				"spring.main.allow-bean-definition-overriding=true",
+				"spring.jpa.properties.hibernate.search.backend.directory.root=target/lucenefiles-r4",
 		})
 public class ExampleServerR4IT implements IServerSupport {
 	private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ExampleServerR4IT.class);

core/src/test/java/org/opencds/cqf/ruler/ExampleServerR5IT.java

@@ -23,7 +23,8 @@
 		"hapi.fhir.fhir_version=r5",
 		"hapi.fhir.subscription.websocket_enabled=true",
 		"hapi.fhir.mdm_enabled=false",
-		"spring.main.allow-bean-definition-overriding=true"
+		"spring.main.allow-bean-definition-overriding=true",
+		"spring.jpa.properties.hibernate.search.backend.directory.root=target/lucenefiles-dstu2",
 })
 public class ExampleServerR5IT {
 

example/README.md

@@ -19,6 +19,10 @@ This system is very basic. It does not support runtime addition or removal of pl
 
 NOTE: This plugin is for demonstration purposes only. It's never intended to be published
 
+## Build
+
+Use `mvn package` to build the jar files
+
 ## Docker
 
 The Dockerfile builds on top of the base cqf-ruler image and simply copies the jar into the `plugin` directory of the image.

external/pom.xml

@@ -15,6 +15,7 @@
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
 		</dependency>
+
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-storage</artifactId>