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

[Midori Harris]

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 Oh crud -- that page is out of date.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 look of it", kind; the others have been superseded in the OBO format 1.2 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
>>>>> 
>>>>> 
>>>> 
>>> 
>>> 
>>> 
>