It can happen that the JeDIS XMI store is corrupted by changed or incomplete preprocessing. It is quite tedious to iron out such cases because it is unknown which documents are affected and the reader will stop with exceptions.
Instead, let the reader skip corrupted documents and log a warning. Eventually, the corpus will be processed but the skipped documents will still habe in_process status in the CoStoSys subset table. Then we can re-preprocess those to fix the issues.