From 3b6ecb9273e5e3c6d8412187f81522587db6e8ef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= <jacobo167@gmail.com>
Date: Mon, 17 Mar 2025 09:00:09 +0000
Subject: [PATCH 1/2] commons: Remove extra System.out . #TASK-7482

---
 .../org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java | 1 -
 1 file changed, 1 deletion(-)

diff --git a/commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java b/commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java
index ce2f71d06..0876bacdd 100644
--- a/commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java
+++ b/commons-datastore/commons-datastore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java
@@ -118,7 +118,6 @@ public <T> MongoDBIterator<T> aggregate(ClientSession clientSession, List<? exte
         // we need to be sure that the List is mutable
         List<Bson> bsonOperations = new ArrayList<>(operations);
         parseQueryOptions(bsonOperations, options);
-        System.out.println("bsonOperations = " + bsonOperations);
         MongoDBIterator<T> iterator = null;
         if (bsonOperations.size() > 0) {
             long numMatches = -1;

From ed4feb832265ae709fe25406483d7c585c3c4527 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jacobo=20Coll=20Morag=C3=B3n?= <jacobo167@gmail.com>
Date: Mon, 17 Mar 2025 09:00:44 +0000
Subject: [PATCH 2/2] lib: Throw exception on failed docker executions.
 #TASK-7482

---
 .../org/opencb/commons/utils/DockerUtils.java     | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java b/commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java
index 1332b41ec..6d1c9574c 100644
--- a/commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java
+++ b/commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java
@@ -203,6 +203,21 @@ public static String run(String image, List<AbstractMap.SimpleEntry<String, Stri
         // Execute command
         Command cmd = new Command(commandLine);
         cmd.run();
+        if (cmd.getExitValue() != 0) {
+            String stderr = cmd.getError();
+            int maxOutputContext = 1024;
+            if (stderr.length() > maxOutputContext) {
+                int length = stderr.length();
+                stderr = " ... (length: " + length + ") " + stderr.substring(length - maxOutputContext);
+            }
+            String stdout = cmd.getOutput();
+            if (stdout.length() > maxOutputContext) {
+                int length = stdout.length();
+                stdout = " ... (length: " + length + ") " + stdout.substring(length - maxOutputContext);
+            }
+            throw new IOException("Docker command failed with exit value " + cmd.getExitValue()
+                    + ": stdout:" + stdout + " stderr:" + stderr);
+        }
 
         return commandLine;
     }