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Fasta query results: extra view parameters not showing up in header correctly #2016

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JoelRichardson opened this issue Feb 24, 2019 · 2 comments · Fixed by #2077
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@JoelRichardson
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JoelRichardson commented Feb 24, 2019

My question/issue is about adding multiple fields to the FASTA header lines.
I can add one field ok. But if I add another, only one of them makes it into the header.
Example: I want to add both the gene's symbol and name, but only name makes it in.

Here's my query, which returns the genomic sequence for Pax6 for strain A/J.

<query  model="genomic" view="Gene.id">
    <constraint path="Gene.canonical.primaryIdentifier" op="=" value="MGI:97490"/>
    <constraint path="Gene.strain.name" op="=" value="A/J"/>
</query>

I'm using the IOdocs interface. I leave Gene.length as a view column and then add Gene.canonical.symbol and Gene.canonical.name as additional view paths. The result only contains the name.

Thanks.

@julie-sullivan julie-sullivan changed the title Fasta query results: extra view parameters? Fasta query results: extra view parameters not showing up in header correctly Feb 25, 2019
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julie-sullivan commented Feb 25, 2019

Yes, I can replicate! That's a bug. Hopefully easy to fix. (famous last words)

Are the pathquery views being updated correctly? FastaQueryService.java#L57

@julie-sullivan julie-sullivan added this to the InterMine 4.1.0 milestone Jun 28, 2019
@julie-sullivan julie-sullivan added this to InterMine 4.1.0 (end of 2019) in Roadmap & release planning Jul 31, 2019
sergiocontrino added a commit to sergiocontrino/intermine that referenced this issue Aug 9, 2019
julie-sullivan pushed a commit that referenced this issue Sep 5, 2019
fixes #2016 (extra view parameters)
danielabutano pushed a commit that referenced this issue Sep 10, 2019
@danielabutano danielabutano reopened this Sep 16, 2019
@danielabutano
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danielabutano commented Sep 16, 2019

If I want to add an additional column in the view, I can modify the attribute view in the query and it works (it didn't before).
I can also use the view optional attribute (more than one)
&view=Gene.length&view=Gene.symbol
and it still works if you use curl or any browser's url address bar
beta.flymine.org/beta/service/query/results/fasta?query=<query model="genomic" view="Gene.id"><constraint path="Gene.chromosome.primaryIdentifier" op="=" value="X"/></query>&view=Gene.length&view=Gene.symbol
BUT IT DOESN'T WORK with iodocs

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4 participants