rebrand to medic etl toolkit and byte compile groovy just once

Author: nr23730

.github/workflows/docker-image.yml

@@ -28,5 +28,5 @@ jobs:
         uses: docker/build-push-action@v7
         with:
           push: true
-          tags: ghcr.io/itcr-uni-luebeck/obds2openehr:latest
+          tags: ghcr.io/skfit-uni-luebeck/medic-etl-toolkit:latest
           platforms: linux/amd64,linux/arm64/v8

Dockerfile

@@ -1,12 +1,12 @@
 FROM busybox:uclibc AS wget
 FROM docker.io/maven:3-eclipse-temurin-25 as build
-COPY $PWD /openehr-obds
-WORKDIR /openehr-obds
+COPY $PWD /medic-etl-toolkit
+WORKDIR /medic-etl-toolkit
 RUN mvn -DskipTests clean package
 
 FROM gcr.io/distroless/java25-debian13
 COPY --from=wget /bin/wget /bin/wget
 COPY --from=wget /bin/sh /bin/sh
-COPY --from=build /openehr-obds/target/openehr-obds-*-jar-with-dependencies.jar /app/openehr-obds.jar
-ENTRYPOINT ["java", "-jar", "/app/openehr-obds.jar"]
+COPY --from=build /medic-etl-toolkit/target/medic-etl-toolkit-*-jar-with-dependencies.jar /app/medic-etl-toolkit.jar
+ENTRYPOINT ["java", "-jar", "/app/medic-etl-toolkit.jar"]
 HEALTHCHECK CMD /bin/wget -q -O - http://localhost:4567/health || exit 1

README.md

@@ -1,14 +1,16 @@
-# oBDS 2 openEHR
+# MeDIC-ETL-Toolkit
 
-This project is used to map [oBDS](https://www.basisdatensatz.de/basisdatensatz) (German oncological basis data set) data to openEHR using a FHIR Terminology Server and CentraXX MDR. The target openEHR templates are available [here](https://ckm.highmed.org/ckm/projects/1246.152.61).
+A toolkit for mapping various data formats to openEHR. It reads json/xml files from kafka, transforms them using groovy scripts to openEHR compositions, which then will be uploaded to the openEHR repository.
+
+This project was initially created to map [oBDS](https://www.basisdatensatz.de/basisdatensatz) (German oncological basis data set) data to openEHR using a FHIR Terminology Server and CentraXX MDR. The target openEHR templates are available [here](https://ckm.highmed.org/ckm/projects/1246.152.61).
 
 ## Get started
 
 To get started, copy the `settings.yaml.example` file to `settings.yaml`. This avoids future conflicts within the git tree. The parameters need to be tailored to your environment.
 
 ### Running in container
 
-oBDS 2 openEHR is also available as a container. The image is available at `ghcr.io/skfit-uni-luebeck/obds2openehr:latest`. There are native builds available for `linux/amd64` and `linux/arm64/v8`.
+MeDIC-ETL-Toolkit is also available as a container. The image is available at `ghcr.io/skfit-uni-luebeck/medic-etl-toolkit:latest`. There are native builds available for `linux/amd64` and `linux/arm64/v8`.
 There is also a compose file available.
 
 ## Citation

compose.yml

@@ -1,6 +1,6 @@
 version: "3"
 services:
-  openehr-obds:
+  medic-etl-toolkit:
     restart: unless-stopped
     build: ./
     command: "/app/settings.yml"

pom.xml

@@ -5,7 +5,7 @@
     <modelVersion>4.0.0</modelVersion>
 
     <groupId>de.uksh.medic.etl</groupId>
-    <artifactId>openehr-obds</artifactId>
+    <artifactId>medic-etl-toolkit</artifactId>
     <version>0.1-SNAPSHOT</version>
 
     <properties>
@@ -18,7 +18,7 @@
         <maven-surefire-plugin.version>3.5.5</maven-surefire-plugin.version>
         <coveralls-maven-plugin.version>4.3.0</coveralls-maven-plugin.version>
         <maven-source-plugin.version>3.4.0</maven-source-plugin.version>
-        <exec.mainClass>de.uksh.medic.etl.OpenEhrObds</exec.mainClass>
+        <exec.mainClass>de.uksh.medic.etl.MedicEtlToolkit</exec.mainClass>
     </properties>
 
     <dependencies>
@@ -197,7 +197,7 @@
                     </descriptorRefs>
                     <archive>
                         <manifest>
-                            <mainClass>de.uksh.medic.etl.OpenEhrObds</mainClass>
+                            <mainClass>de.uksh.medic.etl.MedicEtlToolkit</mainClass>
                         </manifest>
                     </archive>
                 </configuration>

…/java/de/uksh/medic/etl/OpenEhrObds.java …a/de/uksh/medic/etl/MedicEtlToolkit.javasrc/main/java/de/uksh/medic/etl/OpenEhrObds.java renamed to src/main/java/de/uksh/medic/etl/MedicEtlToolkit.java src/main/java/de/uksh/medic/etl/OpenEhrObds.java renamed to src/main/java/de/uksh/medic/etl/MedicEtlToolkit.java

@@ -34,7 +34,8 @@
 import de.uksh.medic.etl.settings.ServerCheckSettings;
 import de.uksh.medic.etl.settings.Settings;
 import groovy.lang.Binding;
-import groovy.lang.GroovyShell;
+import groovy.lang.GroovyClassLoader;
+import groovy.lang.Script;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileInputStream;
@@ -83,14 +84,16 @@
 import org.openehr.schemas.v1.OPERATIONALTEMPLATE;
 import org.tinylog.Logger;
 
-public final class OpenEhrObds {
+public final class MedicEtlToolkit {
 
     private static final Cache<String, Object> SPEED = Caffeine.newBuilder()
             .expireAfterWrite(60, TimeUnit.SECONDS).build();
     private static final Map<String, Map<String, MappingAttributes>> FHIR_ATTRIBUTES = new HashMap<>();
     private static final Map<String, Object> OPENEHR_ATTRIBUTES = new HashMap<>();
     private static final Map<String, MappingAttributes> AQLS = new HashMap<>();
     private static final Map<String, EHRParser> PARSERS = new HashMap<>();
+    private static final Map<String, Class<? extends Script>> GROOVY_SCRIPTS = new HashMap<>();
+    private static GroovyClassLoader groovyClassLoader;
     private static Integer i = 0;
     private static final int DEFAULT_RECONNECT_DELAY_MS = 1000;
     private static final int MAX_RECONNECT_DELAY_MS = 30000;
@@ -101,7 +104,7 @@ public final class OpenEhrObds {
     private static IGenericClient fc;
     private static IGenericClient fhirTsClient;
 
-    private OpenEhrObds() {
+    private MedicEtlToolkit() {
     }
 
     @SuppressWarnings({ "IllegalCatch", "MethodLength" })
@@ -194,7 +197,7 @@ public static void main(String[] args) throws IOException, KeyStoreException, Ge
             return "{\"msgsPerMinute\": " + SPEED.estimatedSize() + ", \"cacheSize\": " + fr.getCacheSize() + "}";
         });
 
-        Logger.info("OpenEhrObds started!");
+        Logger.info("MedicEtlToolkit started!");
 
         if (Settings.getKafka().getUrl() == null || Settings.getKafka().getUrl().isEmpty()) {
             Logger.debug("Kafka URL not set, loading local file");
@@ -352,6 +355,25 @@ private static void initializeAttribute(Mapping m, ObjectMapper mapper) {
             XmlOptions opts = new XmlOptions();
             opts.setSaveSyntheticDocumentElement(new QName("http://schemas.openehr.org/v1", "template"));
             PARSERS.put(m.getTemplateId(), new EHRParser(template.xmlText(opts)));
+
+            // Pre-compile Groovy script for this template
+            if (Settings.getDev()) {
+                return;
+            }
+            File groovyFile = new File("scripts", m.getTemplateId() + ".groovy");
+            if (!groovyFile.exists()) {
+                return;
+            }
+            if (groovyClassLoader == null) {
+                groovyClassLoader = new GroovyClassLoader();
+            }
+            try {
+                Class<? extends Script> scriptClass = groovyClassLoader.parseClass(groovyFile);
+                GROOVY_SCRIPTS.put(m.getTemplateId(), scriptClass);
+                Logger.info("Pre-compiled Groovy script for template: {}", m.getTemplateId());
+            } catch (IOException e) {
+                Logger.error("Failed to pre-compile Groovy script for template {}: {}", m.getTemplateId(), e);
+            }
         }
 
         if (m.getSource() == null) {
@@ -407,26 +429,35 @@ private static void initializeAttribute(Mapping m, ObjectMapper mapper) {
     @SuppressWarnings({ "IllegalCatch" })
     public static Object localMap(Set<Entry<String, Object>> xmlSet, String templateId, String path,
             Map<String, Object> cache) {
-        Binding b = new Binding();
-        GroovyShell s = new GroovyShell(b);
-        b.setVariable("xmlSet", xmlSet);
-        b.setVariable("path", path);
-        b.setVariable("fhirClient", fc);
-        b.setVariable("fhirResolver", fr);
-        b.setVariable("openEhrClient", openEhrClient);
-        b.setVariable("utils", um);
-        b.setVariable("cache", cache);
-
         if (Settings.getDev()) {
+            Binding b = new Binding();
+            b.setVariable("xmlSet", xmlSet);
+            b.setVariable("path", path);
+            b.setVariable("fhirClient", fc);
+            b.setVariable("fhirResolver", fr);
+            b.setVariable("openEhrClient", openEhrClient);
+            b.setVariable("utils", um);
+            b.setVariable("cache", cache);
             return Mapper.javaMap(xmlSet, path, fc, fr, openEhrClient, um, cache);
         } else {
-            try {
-                File groovyFile = new File("scripts", templateId + ".groovy");
-                if (groovyFile.exists()) {
-                    return s.evaluate(groovyFile);
+            // Use pre-compiled script instance
+            Class<? extends Script> scriptClass = GROOVY_SCRIPTS.get(templateId);
+            if (scriptClass != null) {
+                try {
+                    Script script = scriptClass.getDeclaredConstructor().newInstance();
+                    Binding b = new Binding();
+                    b.setVariable("xmlSet", xmlSet);
+                    b.setVariable("path", path);
+                    b.setVariable("fhirClient", fc);
+                    b.setVariable("fhirResolver", fr);
+                    b.setVariable("openEhrClient", openEhrClient);
+                    b.setVariable("utils", um);
+                    b.setVariable("cache", cache);
+                    script.setBinding(b);
+                    return script.run();
+                } catch (Exception e) {
+                    throw new ProcessingException(e);
                 }
-            } catch (Exception e) {
-                throw new ProcessingException(e);
             }
         }
 

src/main/java/de/uksh/medic/etl/settings/Settings.java

@@ -9,7 +9,7 @@
 import java.util.Map;
 
 /**
- * Settings for OpenEhrObds.
+ * Settings for MedicEtlToolkit.
  */
 @JsonInclude(JsonInclude.Include.NON_NULL)
 public final class Settings {

src/main/resources/tinylogPROD.properties

@@ -1,8 +1,11 @@
-locale = de_DE
-level = info
-writer1 = console
-writer2 = rolling file
-writer2.file = log_{date}.txt
-writer2.charset = UTF-8
-writer2.policies = daily: 00:00
-writer.backups = 100
+writer1          = console
+writer1.format   = {date: yyyy-MM-dd HH:mm:ss.SSS} {level}: {message}{exception}
+
+writer2          = rolling file
+writer2.level    = info
+writer2.format   = {date: yyyy-MM-dd HH:mm:ss.SSS} {level}: {message}{exception}
+writer2.file     = /log/log_{pid}_{count}.txt
+writer2.charset  = UTF-8
+writer2.policies = startup, daily: 03:00
+writer2.backups  = 30
+writer2.convert  = gzip