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

[Chris Mungall]

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 Oh crud -- that page is out of date.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 didn't like the look of it", kind; the others have been superseded  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
>>>>
>>>>
>>>
>>
>>
>>
>