Merge pull request #107 from opencb/TASK-7482

TASK-7482 - opencga junit tests failed

Author: pfurio

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;

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;
     }