[ensembl-dev] Ensembl 90 archive site server error

[Steve Trevanion]

Hi Thomas,

Great to hear you've got this working.

Regards,

Steve

On 06/04/2018 22:26, Thomas Danhorn wrote:
> Great, thanks!  Yes am I using ensembldb.ensembl.org, and I figured 
> out the problem.  It used to be that the 'EntrezGene' database had 
> most if not all of the synonyms.  When this changed, I learned to 
> query all available databases, but promptly forgot to do that this 
> time around.  Your question prompted me to look at my script again and 
> remember this.  It appears to be working now.  Sorry for the confusion.
>
> Have a great weekend,
>
> Thomas
>
>
> On Fri, 6 Apr 2018, Steve Trevanion wrote:
>
>> 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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