Alt-Ids intended to be unique per sample may repeat

[dmcmanam]

We see some repeat Alt-ids in the database due to the code below in PromoteBanked.java returning the same value in two consecutive calls.

String uuid;
try {
        uuid = uuidGen.integerToUUID(Integer.parseInt(util.getNextBankedId()), 32);
} catch (Exception e) {
        throw new LimsException("UUID generation failed for sample due to " + e.getMessage());
}

the uuidGen.integerToUUID() does return distinct values from 1-100million so it appears the call to util.getNextBankedId() can, when called consecutively, return the same value.

[jfkonecn]

Is this bug still an issue for you?

I was trying to see if I could build and debug that line of code.
I might be wrong, but it seems like some of the libraries required to build this repo are not available publicly.
I also don't do a lot of Java development so I could be doing something wrong on my end.

Anyway, if this is still an issue for you, my guess is that it's a race condition.
Here's a code snippet I wanted to use on the call to "util.getNextBankedId()".
Maybe it'll help you get to the bottom of it.

The results are random, but it always results in ID duplication in a few of the threads.

import java.util.concurrent.Semaphore;

class EvilRaceConditionClass {
    private int evilMutableInt;

    public int getNextBankedId() {
        evilMutableInt++;
        try {
            // simulate a non trivial method that will 
            // force more than one cpu core to be used
            Thread.sleep(1);
        } catch (InterruptedException e) {
            e.printStackTrace();
        }
        return evilMutableInt;
    }
}

class RunnableRaceCondition extends Thread {
    private final int id;
    private final Semaphore semaphore;
    private final EvilRaceConditionClass evil;

    RunnableRaceCondition(int id, Semaphore semaphore, EvilRaceConditionClass evil) {
        this.id = id;
        this.semaphore = semaphore;
        this.evil = evil;
    }

    @Override
    public void run() {
        try {
            // hold all the threads here so that they try to hit getNextBankedId at the same time
            semaphore.acquire();
        } catch (Exception e) {
            e.printStackTrace();
        }
        var nextId = evil.getNextBankedId();
        System.out.println("Thread ID:" + id + " completed with ID:" + nextId);
    }
}

class Main {
    public static void main(String[] args) {
        int totalThreads = 10;
        var semaphore = new Semaphore(totalThreads);
        var evil = new EvilRaceConditionClass();
        var threads = new RunnableRaceCondition[totalThreads];

        for (int i = 0; i < totalThreads; i++) {
            threads[i] = new RunnableRaceCondition(i, semaphore, evil);
        }
            
        for (Thread thread : threads) {
            thread.start();
        }

        semaphore.release(totalThreads);

        for (Thread thread : threads) {
            try {
                thread.join();
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
}

Here's an example output for the code snippet:

Thread ID:1 completed with ID:10
Thread ID:6 completed with ID:10
Thread ID:5 completed with ID:10
Thread ID:4 completed with ID:10
Thread ID:2 completed with ID:10
Thread ID:0 completed with ID:10
Thread ID:3 completed with ID:10
Thread ID:9 completed with ID:10
Thread ID:7 completed with ID:10
Thread ID:8 completed with ID:10