The loop query doesn't work

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The loop query doesn't work

Chen, Yian
Hi,

I found that the loop constraint doesn't work now.

For example, I tried the following query in FlyMine:
<query name="" model="genomic" view="Gene.primaryIdentifier Gene.symbol
Gene.interactions.participant2.primaryIdentifier
Gene.interactions.participant2.symbol
Gene.interactions.participant2.interactions.participant2.primaryIdentifier
Gene.interactions.participant2.interactions.participant2.symbol"
longDescription="For a specified gene, show physical and genetic
interaction partners.  Optionally constrain to show just physical or
genetic interactions or interactions determined by a specific method."
sortOrder="Gene.primaryIdentifier asc" constraintLogic="A and B">
   <constraint path="Gene" code="A" op="LOOKUP" value="notch"
extraValue="D. melanogaster"/>
   <constraint path="Gene" code="B" op="!="
loopPath="Gene.interactions.participant2.interactions.participant2"/>
</query>

And I got the following error message:
XML is not well formatted. Got <query model="genomic"
view="Gene.primaryIdentifier Gene.symbol
Gene.interactions.participant2.primaryIdentifier
Gene.interactions.participant2.symbol
Gene.interactions.participant2.interactions.participant2.primaryIdentifier
Gene.interactions.participant2.interactions.participant2.symbol"
sortOrder="Gene.primaryIdentifier ASC" constraintLogic="A and B"
 ><constraint path="Gene" op="LOOKUP" value="notch" extraValue="D.
melanogaster" code="A" /><constraint path="Gene" op="!=" code="B"
/></query>.

I guess the loop constraint was not processed correctly and it was
truncated.

Thanks in advance,

Yi-An Chen


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Re: The loop query doesn't work

Rachel Lyne-2
Dear Chen,

Thanks for reporting this - yes it does appear to be broken.  We are
looking into it and will let you know when it's fixed,


Best Wishes,


Rachel.




On 25/06/2019 05:19, Chen, Yi-An wrote:

> Hi,
>
> I found that the loop constraint doesn't work now.
>
> For example, I tried the following query in FlyMine:
> <query name="" model="genomic" view="Gene.primaryIdentifier
> Gene.symbol Gene.interactions.participant2.primaryIdentifier
> Gene.interactions.participant2.symbol
> Gene.interactions.participant2.interactions.participant2.primaryIdentifier
> Gene.interactions.participant2.interactions.participant2.symbol"
> longDescription="For a specified gene, show physical and genetic
> interaction partners.  Optionally constrain to show just physical or
> genetic interactions or interactions determined by a specific method."
> sortOrder="Gene.primaryIdentifier asc" constraintLogic="A and B">
>   <constraint path="Gene" code="A" op="LOOKUP" value="notch"
> extraValue="D. melanogaster"/>
>   <constraint path="Gene" code="B" op="!="
> loopPath="Gene.interactions.participant2.interactions.participant2"/>
> </query>
>
> And I got the following error message:
> XML is not well formatted. Got <query model="genomic"
> view="Gene.primaryIdentifier Gene.symbol
> Gene.interactions.participant2.primaryIdentifier
> Gene.interactions.participant2.symbol
> Gene.interactions.participant2.interactions.participant2.primaryIdentifier
> Gene.interactions.participant2.interactions.participant2.symbol"
> sortOrder="Gene.primaryIdentifier ASC" constraintLogic="A and B"
> ><constraint path="Gene" op="LOOKUP" value="notch" extraValue="D.
> melanogaster" code="A" /><constraint path="Gene" op="!=" code="B"
> /></query>.
>
> I guess the loop constraint was not processed correctly and it was
> truncated.
>
> Thanks in advance,
>
> Yi-An Chen
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

--
Rachel Lyne, Ph.D.
Cambridge Systems Biology Centre,
University of Cambridge,
Tennis Court Road,
Cambridge,
CB2 1QR

+44 (0)1223 (7)60224

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