ISA-tools/MAGEtoISAconverter — Issue #6: IndexOutOfBounds Error
Author: psm3426
Created: 2011-12-08 21:35:16+00:00
State: open

Hello. I've been running the JAR file on my local machine to convert some ArrayExpress Experiments and out of the 382 experiments that I ran, almost half of them had errors. When I looked at the messages sent by the compiler, many of them were the result of an IndexOutOfBounds Exception.

Most of these were thrown by line 125 of MAGETabSDRFLoader.java: Column scanName = columnOrders.remove(Utils.getIndexForValue("Scan Name", columnOrders));

When looking at the files in question, basically the "Scan Name" header didn't exist, causing the error.

I also occasionally saw the exception thrown by line 126 of MAGETabSDRFLoader.java: columnOrders.add(derivedArrayDataFileIndex - 1, scanName);

This was thrown because derivedArrayDataFileIndex had a value of -1 because the "Derived Array Data File" header was missing.

Could this be fixed please?