[ensembl-dev] Ensembl 90 archive site server error

Thomas Danhorn danhornt at njhealth.org
Mon Apr 2 16:58:23 BST 2018


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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