[Ontology-editors] [Software-group] obo2obo failing

[Mike Cherry]

I changed the OSL script and see exactly the same errors on both  
Solaris and MacOS.  ??

Parse Done!
Exception in thread "main" java.lang.StackOverflowError

However, maybe this is a hint.  I tried OBO-Edit 2.000-beta39 and with  
-Xmx2048M in the vmoptions file there was the same behavior.  However  
with I decreased the memory to 512M it worked?

All works with the file from Feb 5th.

-Mike


On Feb 10, 2009, at 3:37 AM, Midori Harris wrote:

> I've fixed the go_write file (will commit later today, probably by  
> the time you get to email) and updated the documentation. Can't help  
> with the innards of obo2obo, unfortunately!
>
> m
>
> On Mon, 9 Feb 2009, Chris Mungall wrote:
>
>>
>> OK, but I think we need to fix the obo file too. Can we do this  
>> with obo2obo or shall I write a perl script? Should be a 2-liner
>>
>> I'm thinking that perhaps the comments issue is not linked to  
>> obo2obo failing on production, as I can't reproduce Mike's error:
>>
>>> /Applications/OBO-Edit1/obo2obo -formatversion OBO_1_0  
>>> obo_format_1_2/gene_ontology.1_2.obo -writecomments -o /tmp/ 
>>> gene_ontology.1_0.obo -runscript ~/Eclipse/workspace/OBO-Edit/docs/ 
>>> examplescripts/strip_disjoint_and_replaced_by_tags.osl
>>> args[0] = |-formatversion|
>>> args[1] = |OBO_1_0|
>>> args[2] = |obo_format_1_2/gene_ontology.1_2.obo|
>>> args[3] = |-writecomments|
>>> args[4] = |-o|
>>> args[5] = |/tmp/gene_ontology.1_0.obo|
>>> args[6] = |-runscript|
>>> args[7] = |/Users/cjm/Eclipse/workspace/OBO-Edit/docs/ 
>>> examplescripts/strip_disjoint_and_replaced_by_tags.osl|
>>> Allowdangling = false
>>> Parse Done!
>>> About to write files..., session object count = 28093
>>> writePath = null
>>> savePath = [/tmp/gene_ontology.1_0.obo]
>>
>> This is on revision 1.188 of the file
>>
>> This is running the release version of obo2obo from OE1.1, using  
>> the osl script from svn head (the same script did not seem to be  
>> distributed with OE1). This is on OS X so I have a file
>> 	more /Applications/OBO-Edit1/obo2obo.vmoptions
>> 	 -Xmx512M
>>
>> I believe this is OS X specific, I think for running obo2obo on  
>> linux the best thing to do is edit the obo2obo file and set -Xmx
>>
>> ...but I have a feeling we did this previously for obo2obo on  
>> production..?
>>
>> Might be an idea to check the actual version used into cvs
>>
>> On Feb 9, 2009, at 10:50 AM, Midori Harris wrote:
>>
>>> Oh crud -- that page is out of date. The only comments we type in  
>>> nowadays are the first, i.e. "this term was made obsolete because  
>>> we didn't like the look of it", kind; the others have been  
>>> superseded in the OBO format 1.2 files by the 'consider' and  
>>> 'replaced_by' tags. For the 1.0 format files, comments are created  
>>> by the obo2obo utility as Mike's cronjob runs it.
>>> I'm on my way out now, but will work on that doc page tomorrow.
>>> m
>>> On Mon, 9 Feb 2009, Tanya Berardini wrote:
>>>> Is there something I could be doing to help sort this out?  I did  
>>>> several
>>>> term obsoletions on both Thursday and Friday, following the  
>>>> protocol and
>>>> format outlined in http://geneontology.org/GO.usage.shtml#obs.  I  
>>>> was
>>>> editing and saving in OE1.101.
>>>> Cheers,
>>>> Tanya
>>>> On Mon, Feb 9, 2009 at 9:19 AM, Chris Mungall  
>>>> <cjm at berkeleybop.org> wrote:
>>>>> one possibility is that we have just gone over some kind of size  
>>>>> threshold.
>>>>> If so we have to up the memory. This can be done directly in the  
>>>>> obo2obo
>>>>> script
>>>>> however, I have a suspicion this may be some oddity to do with the
>>>>> -writecomments required for 1.2 to 1.0. On friday some  
>>>>> obsoletions in the
>>>>> ontology were accidentally made 1.0-style, this may be confusing  
>>>>> obo2obo.
>>>>> Let's sort that out first and see if that works
>>>>> On Feb 9, 2009, at 9:12 AM, Mike Cherry wrote:
>>>>> Hi,
>>>>>> the obo2obo command is failing.  It worked last week,  
>>>>>> specifically it
>>>>>> worked on version 1.185 of the gene_ontology.1_2.obo file.   
>>>>>> With version
>>>>>> 1.188 it doesn't work.
>>>>>> Here is the command.
>>>>>> obo2obo -formatversion OBO_1_0 /tmp/gene_ontology.1_2.obo - 
>>>>>> writecomments
>>>>>> -o /tmp/gene_ontology.1_0.obo -runscript
>>>>>> /share/go/bin/oboedit/current/docs/examplescripts/ 
>>>>>> strip_disjoint_and_replaced_by_tags.osl
>>>>>> ;
>>>>>> The error message on failng is just:
>>>>>> Exception in thread "main" java.lang.StackOverflowError
>>>>>> It there something wrong with that OBO file?
>>>>>> -Mike
>>>>>> _______________________________________________
>>>>>> Software-group mailing list
>>>>>> Software-group at geneontology.org
>>>>>> http://fafner.stanford.edu/mailman/listinfo/software-group
>>
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