[InterMine Dev] About the ObjectStoreQueryDurationException

Chen Yian chenyian at nibio.go.jp
Fri Mar 15 09:15:00 GMT 2013

Hi Fengyuan,

Do you mean the properties file at ~/.intermine folder ?
I've tired to add the property and rebuilt my application but I still 
got a blank result, after the "building table" message (when tried to 
run a long query).
By the way, I also noticed that the property os.query.max-time has 
already set in the "default.intermine.webapp.properties" file.
Did I misunderstand anything?



(2013/03/15 1:58), Fengyuan Hu wrote:
> Hi Chen,
> You can tweak "os.query.max-time" in MINE.properties to filter out 
> long queries (e.g. os.query.max-time=10000000). The webapp should be 
> able to catch it and show a warning. Could you give a try?
> Cheers
> Fengyuan
> On 13/03/13 01:54, Chen Yian wrote:
>> Hi Fengyuan,
>> Thanks for your reply.
>> I'm sorry I forgot to attach the query, it is as follow:
>> <query model="genomic" 
>> view="Gene.goAnnotation.subject.primaryIdentifier 
>> Gene.goAnnotation.subject.name Gene.goAnnotation.subject.symbol
>> Gene.goAnnotation.ontologyTerm.identifier 
>> Gene.goAnnotation.ontologyTerm.name Gene.pathways.identifier 
>> Gene.pathways.name
>> Gene.proteins.primaryIdentifier Gene.proteins.primaryAccession 
>> Gene.proteins.name Gene.proteins.organism.name
>> Gene.proteins.proteinDomainRegions.proteinDomain.primaryIdentifier 
>> Gene.proteins.proteinDomainRegions.proteinDomain.name
>> Gene.proteins.proteinDomainRegions.proteinDomain.shortName 
>> Gene.proteins.proteinDomainRegions.proteinDomain.type
>> Gene.proteins.structuralDomains.cathClassification.level 
>> Gene.proteins.structuralDomains.cathClassification.cathCode
>> Gene.proteins.structuralDomains.cathClassification.description" 
>> sortOrder="Gene.goAnnotation.subject.primaryIdentifier ASC" ></query>
>> Though some classes or attributes are TargetMine specific, but I 
>> think it may not be difficult to image how the query was.
>> I understand most of  the case Postgres may take care the thread, and 
>> close it,
>> I just wonder if it is possible to execute something like 
>> pg_cancel_backend when we throw an exception and decide to quit?
>> By the way, I also think we should catch the exception, log the query 
>> and response to the user with some warning.
>> What do you think?
>> All the best,
>> Chen
>> (2013/03/13 1:34), Fengyuan Hu wrote:
>>> Hi Chen,
>>> Sorry you had the problem. Postgres will normally take some time to 
>>> close the threads, for a large query, it's suppose to take longer, 
>>> and it's bad at estimating running time of a query.
>>> It's a bit hard for us to investigate further without accessing your 
>>> mine from outside world. Could send us an example of the query?
>>> Cheers
>>> Fengyuan
>>> On 12/03/13 09:22, Chen Yian wrote:
>>>> Hi all,
>>>> Someone constructed an improper query which associated with many 
>>>> classes and without any constraint.
>>>> Since the query could be expected to return several million results,
>>>> when it was executed I got the ObjectStoreQueryDurationException 
>>>> finally.
>>>> Though the system threw the Exception and stopped working for the 
>>>> query, PostgreSQL was still running.
>>>> These threads occupied all resources for a while and some of them 
>>>> even hang.
>>>> Probably the problem itself is related to PostgreSQL,
>>>> but is there any suggestion for preventing this kind of 'accident'?
>>>> Best,
>>>> Chen
>>>> _______________________________________________
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>>>> dev at intermine.org
>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev

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