[InterMine Dev] one more xpat q.

Julie Sullivan julie at flymine.org
Tue Aug 25 11:37:01 BST 2009


Sierra,

Your converter looks fine to me.  It's not immediately obvious how figure ids 
ended up in expression results.

If I were to guess, the problem is in the processXpatFig() method.  Maybe there 
is an extra tab in the files?

  1. I sometimes find logging items helpful:

	String xpatresId = line[0];
         String xpatfigId = line[1];
	LOG.error("This is my results id: " + xpatresId + ".This is my figure id: 
xpatfigId):

The log messages show up in intermine.log in whichever directory you are in.

  2.  Or you could throw an exception to stop the converter when a bad id is found:

	if (xpatresId.contains("ZDB-FIG")) {
		throw new RuntimeException("BAD results identifier:" + xpatresId);
	}

Once you identify a bad id (although I guess you already know that?), I'd take a 
look at the text file itself.  Maybe you can find some clues there.

  3. Have you set up a junit test for this converter?  It's a quick way to run 
the converter and see what it's producing.  Tests really make debugging a lot 
easier!

  4. There is one bug in the getStages() method on line 296.  You are putting 
the objects in the figures map instead of the stages map.

Let me know if you get stuck.

Cheers,
Julie

Sierra Moxon wrote:
> Ok, my load worked with expressions, results and figures.
> 
> One weird (maybe?) thing is that when I do a select * from 
> expressionresult, I see ZDB-FIG-ids in the primaryIdentifier column.
> I also see what I expect to see, ZDB-XPATRES-ids in the 
> primaryIdentifier column.
> 
> I have expression, expressionResult, expressionresultsfigures tables as 
> I expect.  expressionresultsfigures is populated with intermine ids as 
> expected.
> 
> Does this seem right to you?  Anything in particular I can do to speed 
> it up?  It takes 33 minutes to load all 3 files.
> 
> Attached is my parser and xml mapping.
> 
> Thanks again,
> Sierra
> 



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