JSON auto-import may create duplicate library plates, pools, flow cells and sequencing runs

[Nicklas Nordborg]

If there is more than one JSON file that references the same non-existing item (Library plate, Pool or FlowCell lookup via ExternalRef) the importer may create multiple items with the same ExternalRef. This first import will be successful for all JSON files. If there are more JSON files later that also reference any of the duplicate items, the new files will not be possible to import. They will stop with an error message about the duplicate items.

[Nicklas Nordborg]

In 7253:

Fixes #1497: JSON auto-import may create duplicate library plates, pools, flow cells and sequencing runs

We can't keep the result from parsing the JSON in the JsonAutoImporter.autoConfirm() method when executing the JsonAutoImporter.startNextStep() method. After the autoConfirm() all files think that they need to create new items. The startNextStep() processes each file in a separate transaction. After the first file has been processed and imported, the rest of the files will see (if they are re-parsed) the newly created items and link to them instead of creating new items.