Re: [Obo-phenotype] URGENT: Fwd: [ obo-Phenotypic quality (PATO) requests-3296336 ] rev.1.289 of quality.obo introduced a parent-children LOOP!

[Hilmar L. <hl...@ne...>]

Hi George et al -

is it possible to catch this beforehand with a simple unit test? It  
seems less than ideal to rely on users of the ontology to find out  
whether the ontology is free of this issue or not.

	-hilmar

On Jun 9, 2011, at 9:37 AM, George Gkoutos wrote:

>
> Hi Igor,
>
> thank you for reporting this. I have now committed a new version -  
> could you please let me know if it is OK now ?
>
> Best wishes,
>
> George
>
>
> On 9 Jun 2011, at 13:52, Igor Rodchenkov wrote:
>
>> Hi George,
>>
>> We have the same problem emerged again: quality.obo, since rev.  
>> 1.304, has introduced loops in the child term hierarchy (see below,  
>> similar issue with rev. 1.289 has been already fixed)!
>> Rev. 1.303 works ok.
>>
>> I am sure (prom previous experience), this also breaks EBI OLS  
>> (Ontology Lookup Service) builds (they can see it in the logs...)
>>
>> PS:
>> Anush, the version of BioPAX validator that you use fails because  
>> of the ontology file (it always tries to get the latest OBO file  
>> from internet, which is currently invalid.)
>>
>>
>> Best regards,
>> Igor Rodchenkov, Ph.D
>> University of Toronto
>> baderlab.org biopax.org pathwaycommons.org cytoscape.org
>>
>>
>>
>> On Tue, May 3, 2011 at 9:57 AM, George Gkoutos <gg...@ca...>  
>> wrote:
>> Hi Igor,
>>
>> many thanks for reporting this.
>>
>> It is now fixed.
>>
>> Best wishes,
>>
>> George
>>
>> On 2 May 2011, at 20:24, Igor Rodchenkov wrote:
>>
>>>
>>> ---------- Forwarded message ----------
>>> From: SourceForge.net <no...@so...>
>>> Date: Mon, May 2, 2011 at 1:20 PM
>>> Subject: [ obo-Phenotypic quality (PATO) requests-3296336 ] rev. 
>>> 1.289 of quality.obo introduced a parent-children LOOP!
>>> To: no...@so...
>>>
>>>
>>> Phenotypic quality (PATO) requests item #3296336, was opened at  
>>> 2011-05-02 13:20
>>> Message generated for change (Tracker Item Submitted) made by rodche
>>> You can respond by visiting:
>>> https://sourceforge.net/tracker/?func=detail&atid=595654&aid=3296336&group_id=76834
>>>
>>> Please note that this message will contain a full copy of the  
>>> comment thread,
>>> including the initial issue submission, for this request,
>>> not just the latest update.
>>> Category: None
>>> Group: phenotype
>>> Status: Open
>>> Resolution: None
>>> Priority: 5
>>> Private: No
>>> Submitted By: Igor Rodchenkov (rodche)
>>> Assigned to: Nobody/Anonymous (nobody)
>>> Summary: rev.1.289 of quality.obo introduced a parent-children LOOP!
>>>
>>> Initial Comment:
>>> The latest commit/revision 1.289 of the quality.obo probably  
>>> breaks the ontology, making it not DAG anymore. rev.1.288 work ok.  
>>> I think so because the same ontology manager software (using  
>>> oboedit 1.101 and ols-1.18 libs) still loads the previous version  
>>> but not the latest:
>>>
>>> Unfortunately, I cannot point to the term(s)  that cause this,  
>>> but, believe, one can easily trace it down by comparing the two  
>>> revisions of quality.obo.
>>>
>>> excerpt from my failure logs:
>>> ...
>>> Caused by: java.lang.StackOverflowError
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        at  
>>> uk 
>>> .ac 
>>> .ebi 
>>> .ols 
>>> .loader 
>>> .parser.AbstractParser.computeChildPaths(AbstractParser.java:97)
>>>        ... etc..
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> You can respond by visiting:
>>> https://sourceforge.net/tracker/?func=detail&atid=595654&aid=3296336&group_id=76834
>>>
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>>
>> ---------------------------------------------------
>> Dr. G.V.Gkoutos
>>
>> University of Cambridge
>> Department of Genetics
>> Downing Site, Downing Street
>> Cambridge, CB2 3EH
>>
>> Tel: +44 [0] 01223 766336
>>
>> email: gg...@ca...
>> url: http://www.gen.cam.ac.uk
>>
>> ------------------------------------------------------
>>
>>
>>
>>
>>
>>
>
> ---------------------------------------------------
> Dr. G.V.Gkoutos
>
> University of Cambridge
> Department of Genetics
> Downing Site, Downing Street
> Cambridge, CB2 3EH
>
> Tel: +44 [0] 01223 766336
>
> email: gg...@ca...
> url: http://www.gen.cam.ac.uk
>
> ------------------------------------------------------
>
>
>
>
>
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-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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