[InterMine Dev] setting residues in the direct loader

Richard Smith richard at flymine.org
Fri Apr 17 10:05:27 BST 2015

Hi Joe,
I would take a look at FastaLoaderTask.java which does the same thing. It
looks like it creates a PendingClob with a string of the sequence:

flymineSequence.setResidues(new PendingClob(sequence));

Which sources are you using a direct data loader for?  I'm interested to
know as I expect it to be faster only in certain circumstances.

I have a change which isn't quite ready yet that makes the
DirectDataLoader run primary key queries in batches (using a
ParallelBatchingFetcher). In my small test it was about 2x faster, but it
depends what percentage of the objects need merging.


> Hi Richard,
> I’m happily using the direct data loader now. but I realize there is one
> thing I can’t figure out tonight. I’m creating some objects with
> sequence, but it isn’t clear how to set the residues for these things.
> setResidues in Sequence.java expects a ClobAccess argument. But it’s not
> clear how to create one of these from scratch.
> Can you give me a pointer on this?
> Thanks,
> Joe

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