[InterMine Dev] List non-matches

K.H. Reierskog khr29 at cam.ac.uk
Mon Apr 12 18:07:50 BST 2021


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 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> 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 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
>>>> _______________________________________________
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>>>> dev at lists.intermine.org
>>>> https://lists.intermine.org/mailman/listinfo/dev
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