From d73389ff9bc66418b1ce57926995262a49299a0c Mon Sep 17 00:00:00 2001
From: Sam Leeflang <sam.leeflang@naturalis.nl>
Date: Mon, 29 Jan 2024 11:45:47 +0100
Subject: [PATCH] Try with buffered outputstream and add java opts to docker

---
 Dockerfile                                    |  2 +-
 .../translator/repository/BatchInserter.java  | 26 +++++++------------
 2 files changed, 11 insertions(+), 17 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index f0e77a9..4b41849 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -16,4 +16,4 @@ RUN true
 COPY --chown=java:java --from=builder application/application/ ./
 USER 1000
 
-ENTRYPOINT ["java", "org.springframework.boot.loader.launch.JarLauncher"]
+ENTRYPOINT ["java", "$JAVA_OPTS", "org.springframework.boot.loader.launch.JarLauncher"]
diff --git a/src/main/java/eu/dissco/core/translator/repository/BatchInserter.java b/src/main/java/eu/dissco/core/translator/repository/BatchInserter.java
index d7c2eae..2c4a1cf 100644
--- a/src/main/java/eu/dissco/core/translator/repository/BatchInserter.java
+++ b/src/main/java/eu/dissco/core/translator/repository/BatchInserter.java
@@ -2,10 +2,10 @@
 
 import com.fasterxml.jackson.databind.JsonNode;
 import eu.dissco.core.translator.exception.DisscoRepositoryException;
+import java.io.BufferedOutputStream;
+import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
-import java.io.PipedInputStream;
-import java.io.PipedOutputStream;
 import java.nio.charset.StandardCharsets;
 import java.sql.SQLException;
 import java.util.List;
@@ -41,23 +41,16 @@ private static String cleanString(JsonNode jsonNode) {
 
   public void batchCopy(String tableName, List<Pair<String, JsonNode>> dbRecords)
       throws DisscoRepositoryException {
-    try (var outputStream = new ByteArrayOutputStream();
-        var in = new PipedInputStream();
-        var out = new PipedOutputStream(in)) {
+    byte[] buffer = new byte[2048];
+    try (var baos = new ByteArrayOutputStream();
+        var bos = new BufferedOutputStream(baos, buffer.length)) {
       for (var dbRecord : dbRecords) {
-        outputStream.write(getCsvRow(dbRecord));
+        bos.write(getCsvRow(dbRecord));
       }
-      try (in) {
-        new Thread(() -> {
-          try (out) {
-            outputStream.writeTo(out);
-          } catch (IOException e) {
-            log.error("Error writing to pipe", e);
-          }
-        }).start();
-
+      try (ByteArrayInputStream bais =
+          new ByteArrayInputStream(baos.toByteArray())) {
         copyManager.copyIn("COPY " + tableName
-            + " FROM stdin DELIMITER ','", in);
+            + " FROM stdin DELIMITER ','", bais);
       }
     } catch (IOException | SQLException e) {
       throw new DisscoRepositoryException(
@@ -66,4 +59,5 @@ public void batchCopy(String tableName, List<Pair<String, JsonNode>> dbRecords)
     }
   }
 
+
 }