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TASK-7482 - opencga junit tests failed #107

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Merged
pfurio merged 2 commits into from
Mar 27, 2025
Merged

TASK-7482 - opencga junit tests failed #107

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3b6ecb9
commons: Remove extra System.out . #TASK-7482
j-coll Mar 17, 2025
ed4feb8
lib: Throw exception on failed docker executions. #TASK-7482
j-coll Mar 17, 2025
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1 change: 0 additions & 1 deletion ...astore-mongodb/src/main/java/org/opencb/commons/datastore/mongodb/MongoDBNativeQuery.java
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Expand Up @@ -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;
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15 changes: 15 additions & 0 deletions commons-lib/src/main/java/org/opencb/commons/utils/DockerUtils.java
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Expand Up @@ -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;
}
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