Added: Export to Opal only after all files are sent

CHANGELOG.md

@@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/)
 and this project adheres to [Semantic Versioning](http://semver.org/).
 
-## [1.1.0 - 2023-12-03]
+## [1.1.0 - 2023-12-20]
 ### Added
 - Java Opts
 - Divide Excel file in several files if number of rows is too large
@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 - Request Template
 - Query in body for CREATE_QUERY
 - ConverterGraph
+- Export to Opal only after all files are sent
 
 ### Changed
 - Move FHIR Packages to dktk-exporter

Dockerfile

@@ -1,14 +1,13 @@
 FROM eclipse-temurin:21-jre
 
-COPY target/exporter.jar /app/
-
-WORKDIR /app
-
 RUN apt-get update && apt-get upgrade -y && apt-get install python3-pip -y &&  \
     apt-get install libcurl4-openssl-dev libssl-dev -y && \
     python3 -m pip install obiba-opal && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
+COPY target/exporter.jar /app/
+
+WORKDIR /app
 
 CMD ["sh", "-c", "java $JAVA_OPTS -jar exporter.jar"]

src/main/java/de/samply/opal/CsvToOpalConverter.java

@@ -41,12 +41,21 @@ public Format getOutputFormat() {
 
     @Override
     protected Flux<Path> convert(Path input, ConverterTemplate template, Session session) {
+        session.addPath(input);
+        return Flux.just(input);
+    }
+
+    @Override
+    protected Runnable getSessionCompleter(ConverterTemplate template, Session session) {
+        return () -> session.getOpalPaths().forEach(path -> sendPathToOpal(path, session));
+    }
+
+    private void sendPathToOpal(Path input, Session session){
         try {
             opalEngine.sendPathToOpal(input, session);
         } catch (OpalEngineException e) {
             logger.error(ExceptionUtils.getStackTrace(e));
         }
-        return Flux.just(input);
     }
 
     @Override

src/main/java/de/samply/opal/Session.java

@@ -6,6 +6,8 @@
 import de.samply.template.token.TokenContext;
 
 import java.nio.file.Path;
+import java.util.HashSet;
+import java.util.Set;
 
 public class Session {
 
@@ -16,6 +18,7 @@ public class Session {
     private int maxNumberOfRetries;
     private String project;
     private final TokenContext tokenContext;
+    private final Set<Path> opalPaths = new HashSet<>();
 
     public Session(ConverterTemplate template, ConverterTemplateUtils converterTemplateUtils,
                    int timeoutInSeconds, int maxNumberOfRetries, TokenContext tokenContext) {
@@ -69,4 +72,12 @@ public void setMaxNumberOfRetries(int maxNumberOfRetries) {
         this.maxNumberOfRetries = maxNumberOfRetries;
     }
 
+    public void addPath (Path path){
+        this.opalPaths.add(path);
+    }
+
+    public Set<Path> getOpalPaths() {
+        return opalPaths;
+    }
+
 }