[InterMine Dev] List non-matches

Paulo Nuin paulo.nuin at gmail.com
Mon Apr 12 20:16:57 BST 2021


Hi

> On Apr 12, 2021, at 11:07 AM, K.H. Reierskog <khr29 at cam.ac.uk> wrote:
> 
> Hello Paulo,
> 
> I checked these identifiers against Wormmine and 6 of them seem to just
> disappear from the IDresolver /ids/<uid>/results response. If I add
> identifiers I know don't exist, then those will show up as notFound, but
> the 6 identifiers below will still be missing from the response.
> 
> Bm3857a
> OVOC2812a
> Bm1727a
> Bm6280a
> Bm1294b
> Bm2929a
> 
> I did a keyword search for these and saw they were all CDS, but not
> available as Gene. If you take all of Paulo's identifiers and upload
> them setting *List type* to Protein, it will only match the 6 of them
> that are available as proteins.
> 
> It seems to me that the idresolver web service will ignore identifiers
> that match a class that is different from what is specified as `type`
> (List type dropdown in Bluegenes' upload page) when starting an ID
> resolution job. This must be a bug? It would make more sense to have the
> identifiers returned as notFound, just like the identifiers that don't
> match anything at all.


I don’t think it’s a bug per se, but it’s a nice feature to have, at least from WormMine perspective where some IDs overlap classes.

Cheers

Paulo


> 
> I can create an issue on the Intermine repo if Daniela agrees.
> 
> Cheers,
> 
> Kevin
> 
> On 4/9/21 3:22 PM, Paulo Nuin wrote:
>> Hi Kevin and Daniela
>> 
>> I understand it was never shown, but while discussing we thought it was something good to have. 
>> 
>> 
>> The XHR response is at the bottom of the message and the list of IDs, is this (I might be behind some commits on our Bluegenes install)
>> 
>> 
>> Bm1100
>> Bm1294b
>> Bm13855
>> Bm1727a
>> Bm17450
>> Bm1757
>> Bm1926
>> Bm2018
>> Bm2519
>> Bm2555
>> Bm2825
>> Bm2929a
>> Bm3456
>> Bm3857a
>> Bm5293
>> Bm5306
>> Bm5437
>> Bm5547
>> Bm6097
>> Bm6280a
>> Bm6970
>> Bm7141
>> Bm9770
>> OVOC11328
>> OVOC2812a
>> OVOC5021
>> OVOC8510
>> Bm1294b
>> Bm1727a
>> Bm2929a
>> Bm3857a
>> Bm6280a
>> OVOC2812a
>> 
>> Cheers
>> 
>> Paulo
>> 
>> 
>> 
>>> On Apr 9, 2021, at 4:10 AM, K.H. Reierskog <khr29 at cam.ac.uk <mailto:khr29 at cam.ac.uk>> wrote:
>>> 
>>> Bluegenes is supposed to show a *Not Found* tab, but I see it's missing
>>> in your screenshot. I tested entering nonexistent gene identifiers on
>>> Humanmine and Wormmine, and I do get the *Not Found* tab.
>>> 
>>> Could you open the network panel before clicking *Continue* on the
>>> upload page, filter to XHR, then copy the JSON response to `GET
>>> results?format=json`? Or share the identifiers you used that caused this?
>>> 
>>> Cheers,
>>> 
>>> Kevin
>>> 
>>> On 4/9/21 9:43 AM, daniela at intermine.org <mailto:daniela at intermine.org> wrote:
>>>> Hi Paulo,
>>>> I'm pretty sure that we have never shown the entities not matching.
>>>> But please, correct me if I'm wrong!
>>>> Do you want to add a ticket on github?
>>>> 
>>>> Thanks!
>>>> Daniela
>>>> 
>>>> 
>>>>> Hi everyone
>>>>> 
>>>>> We were doing some work on news lists on WormMine and one the things
>>>>> we concluded that the silent non-matches when creating lists. We were
>>>>> adding a short list (about 30 items), and about 2/3 matched, while the
>>>>> other 1/3 didn’t. We understand why it happens, as we had some mixed
>>>>> IDs the list, but for the end user, it might be quite frustrating in
>>>>> finding which IDs didn’t match. I don’t know if it’s possible to
>>>>> show the non-matched in the current web app, but I tried on Bluegenes
>>>>> and I see a warning for missed items, but I don’t actually see the
>>>>> items. Is that an issue with our current deployment or an issue with
>>>>> Bluegenes itself?
>>>>> 
>>>>> Thanks in advance
>>>>> 
>>>>> Cheers
>>>>> 
>>>>> Paulo
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> dev at lists.intermine.org <mailto:dev at lists.intermine.org>
>>>>> https://lists.intermine.org/mailman/listinfo/dev <https://lists.intermine.org/mailman/listinfo/dev>
>>>> _______________________________________________
>>>> dev mailing list
>>>> dev at lists.intermine.org <mailto:dev at lists.intermine.org>
>>>> https://lists.intermine.org/mailman/listinfo/dev <https://lists.intermine.org/mailman/listinfo/dev>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.intermine.org/pipermail/dev/attachments/20210412/f9569083/attachment-0001.html>


More information about the dev mailing list