[ensembl-dev] Ensembl 90 archive site server error

[Steve Trevanion]

Hi Thomas,

We have put in the permanent (hopefully) fix for the search issue.

Can you send me any specific details of the missing synonyms so that I 
can see if there is a problem on ensembldb.ensembl.org (I assume you are 
getting them from there) ?

Regards,

Steve


On 02/04/2018 16:58, Thomas Danhorn wrote:
> Thanks Steve!  The website error message did indeed disappear, but the 
> real issue is the API access to the synonymns, which still does not work.
>
> I cannot easily test release 91 right now (some issue with library and 
> perl module versions, which I have to figure out), but I have tested 
> 84 and 78 (both of which I have used previously), and they both work 
> fine (in fact, I get a couple of extra synonymns now). I was able to 
> download mouse synonyms from relaease 90 back in August, so it used to 
> work then for that release.  This leads me to believe that the issue 
> is limited to release 90 and is "new" in the sense that it used to 
> work al least some months ago (when 90 was current).
>
> Thank you for your help,
>
> Thomas
>
>
> On Sat, 31 Mar 2018, Steve Trevanion wrote:
>
>> Hi Thomas,
>>
>> I have put in a temporary fix for the search archive which I hope 
>> will stand up for a few days. A permanent fix requires action from 
>> our systems team; I have let them know about the issue but it will be 
>> next week before they can look at it.
>>
>> I doubt that the API problem you are seeing is related to the archive 
>> search issue. Is it a new problem ? Do you also see this if you use 
>> the current (91) version ?
>>
>> Regards,
>>
>> Steve
>>
>>
>> On 30/03/2018 07:00, Thomas Danhorn wrote:
>>> Dear developers,
>>>
>>> When I search for something (e.g. ENSG00000000003) on 
>>> http://aug2017.archive.ensembl.org/ (the Ensembl 90 archive site), I 
>>> get a message on pink background, "Search server failed to respond", 
>>> evn though I get search results like I would expect. The main web 
>>> site and its US mirrors do not give this error message, and neither 
>>> does the archive site for Ensembl 89 (may2017), so this is lilely 
>>> specific to the archive for 90.
>>>
>>> When I try do download synonyms for Ensembl genes using version 90 
>>> of the Perl API, however, it silently fails, i.e. it appears like 
>>> there are no synonyms (even though the gene record on the web site 
>>> shows that there should be some), and I see warnings or errors.  I 
>>> have done this for a couple thousand genes.  (Interestingly, 
>>> ENSG00000015479 does give "ALS21, MPD2, VCPDM" as sysnonyms, but 
>>> none of the other genes do -- different source?)  I tried both mouse 
>>> and human genes, and I suspect this issue is related to the error 
>>> message on the web site described above.
>>>
>>> I have retried several times (both the web search and Perl API), and 
>>> the problem has persisted for more than 7 hours now, so this does 
>>> not appear to be a momentary glitch.  I would greatly appreciate if 
>>> someone could look into this.
>>>
>>> Thank you very much,
>>>
>>> Thomas
>>>
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>
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