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

Tue Feb 10 10:36:53 PST 2009

Hi Midori,

Yes, I understand now. If you could add that little bit of instruction below
to the web docs, that would be brilliant.

T

On Tue, Feb 10, 2009 at 10:27 AM, Midori Harris <midori at ebi.ac.uk> wrote:

> Hi Tanya,
>
> In the brave new world with tags, we don't have to put the suggested terms
> in comments at all any more. Instead, we set 'consider' and 'replaced_by'
> terms in OE (works in OE1 or OE2, as long as you save in OBO format version
> 1.2, which we all do anyway). Drag a 'live' term and drop it onto an
> obsolete term, and a little menu pops up with just the 'set consider term'
> and 'set replacement term' options.
>
> The OBO format 1.0 files still use text comments, but they're generated by
> obo2obo magic.
>
> I can demo sometime if that's still all confusing.
>
> m
>
>
> On Tue, 10 Feb 2009, Tanya Berardini wrote:
>
>  Hi Midori,
>>
>> Thanks for fixing the documentation.  I'm still confused about how to add
>> the comments to the file.  Can one do this in OE1?  If so, how?  Or is
>> this
>> a new feature of OE2?  If so, how does one do it there?  Or does this
>> involve editing the flat file?
>>
>> Thanks,
>>
>> Tanya
>>
>> On Tue, Feb 10, 2009 at 3:37 AM, Midori Harris <midori at ebi.ac.uk> 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
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>
>>
>>
>>

-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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