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Code committed and applied to test. The test url is:
http://tesuque.stanford.edu:9999/pubtest
We have a new link from the Phenotype detail page: "Attach
Germplasm".
2006-03-29 00:13:39 UTC in Generic Model Organism System Database
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Hmm... I'll drop the test for replaced_by. It seems to be
causing more problems, and it's not really that helpful. If
one is trying to unobsolete a gene, then that should
automatically clear out the replaced_by.
Change committed, but I'll do some internal testing first
before closing this bug.
2006-03-24 19:34:41 UTC in Generic Model Organism System Database
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Closing bug; fixed.
2006-03-24 01:29:09 UTC in Generic Model Organism System Database
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Ok, found this out. There was some check added at r2393
that causes this problem. The log message at that time was
that we didn't want to automatically clear the replaced_by
when unobsoleting a gene, and the error message is supposed
to indicate that the clearing of replaced_by had to be done
first.
I'm not sure if this is a feature we should still keep...
2006-03-24 01:28:29 UTC in Generic Model Organism System Database
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The proposed fix needs clarification. This sounds that it
needs something multistage:
To attach a germplasm to a phenotype:
1. First choose the germplasm.
2. Next, given that germplasm, present a list of
possible pub references.
3. Finally, confirm and add.
Does this sound right? The requirements below sound like I
need to make this...
2006-03-22 00:13:50 UTC in Generic Model Organism System Database
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Fixed in r3370:
http://aztec.stanford.edu/cgi-bin/pub-trac.cgi/changeset/3370
This fix should be in test:
http://tesuque.stanford.edu:9999/pubtest
Please tell me if it looks ok now. Hope this helps!
2006-03-22 00:02:10 UTC in Generic Model Organism System Database
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Needs further discussion. Fixing this properly seems to
involve fixing the gene/term relationship and making genes
isa term, rather than term isa gene.
2006-03-21 19:58:25 UTC in Generic Model Organism System Database
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Note to self: check the name and type constraints on AddTerm
and see if it's being overly restrictive.
2006-03-21 19:54:57 UTC in Generic Model Organism System Database
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The problem is that the related gene band is not filtering
out bad hits. See the PAP1 example at:
http://tesuque.stanford.edu:8080/pub/DisplayArticle?article_id=25043.
2006-03-21 19:53:08 UTC in Generic Model Organism System Database
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the only thing left to do here is to sort hits by year.
2006-03-21 19:49:39 UTC in Generic Model Organism System Database
