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monarch-initiative / phenogrid

The phenogrid widget
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Replace the species "compare" in phenogrid #253

Closed frdougal closed 7 years ago

frdougal commented 8 years ago

The phenogrid displays the text "Species: compare" in the hoverbox for a column when the user accesses phenogrid through the Analyze interface (see below). The text should correspond to its actual species represented by the gene in the column.

column_hover
frdougal commented 8 years ago

@jmcmurry @harryhoch My changes are deployed to beta.monarchinitiative.org (which looks like it is down as of 10:26 AM EST July 25 Jeremy said he took beta down). I tested my changes and I noticed a problem with the data returned by /compare. The /compare code (used by the Analyze page) and the /simsearch/phenotype (used by the Disease page) handle the taxa differently. The /simsearch/phenotype properly handles the taxon by assigning each column a species. The compare code only assigns a taxon if the column is a human gene (see screenshot).

At this point my code behaves correctly, but the data returned by /compare is incomplete. Should I add an issue on the monarch-app issue tracker requesting the /compare code to add the taxon information for non-humans?

screen shot 2016-07-25 at 10 20 42 am

harryhoch commented 8 years ago

so in #4 above it does not have the taxon for 19090, where it should, as it does for #5? looks like a bug to me...

frdougal commented 8 years ago

@harryhoch That's correct. I deliberately mixed human and non-human genes into the Analyze "Gene IDs" text box. The only ones returning taxon data are the human genes.

frdougal commented 8 years ago

@harryhoch @yuanzhou this appears to have been reported by Zhou: https://github.com/monarch-initiative/monarch-app/issues/1024. I followed the thread, but I don't see a resolution.

yuanzhou commented 8 years ago

@cborromeo @harryhoch as far as I can remember, the issue #1024 was not fully addressed. It was addressed for a short time of period then I encountered that "Not specified" again later. And I also remembered that I had the same issue several months ago. It should a data issue since the taxon needs to be returned from owlsim.

kshefchek commented 8 years ago

This will be fixed with https://github.com/monarch-initiative/monarch-app/pull/1315

harryhoch commented 7 years ago

I think this is fixed