Re: [Obo-format] .obo rules ?

[mark g. <mg...@fr...>]

nonetheless it would be good to see what in your obo caused obo to  
barf with an uninformative error message - null pointer - in other  
words obo needs to check for that null and give an informative error  
message - so it would be good for you to pass on the failing obo so  
the obo code can become more robust - thanks - mark


On Feb 19, 2008, at 7:16 PM, azu...@it... wrote:

> Hey Mark, no worries, I think I've just figured it out, still playing
> with it.  The .obo was at the URL, but should be good now.  Thanks !
> J
>
>> yikes null pointer exception is rather uninformative
>> i think youve hit a shortcoming in error reportin in obo
>> can you email me the obo file and ill give it a try
>> im in berkeley at the moment and away rest of week so may not be able
>> to get to this til next week - sorry
>>
>> On Feb 15, 2008, at 7:48 PM, azu...@it... wrote:
>>
>>> Hi Mark,
>>>
>>> Karen wants some data displayed but not editable, but the amount of
>>> data is too large for our current un-editable fields, so I'm  
>>> trying to
>>> put it in a .obo file, but I don't understand why it's not working.
>>> I'm getting :
>>>
>>> 2008-02-15 16:45:19,513 [main] ERROR  
>>> dataadapter.OntologyDataAdapter -
>>> got obo data adapter exception:
>>> org.bbop.dataadapter.DataAdapterException: Load error message Load
>>> error cause java.lang.NullPointerException
>>> THIS IS FATAL!
>>> Can not load ontologies. Phenote must exit.
>>> Consider clearing out bad file from ~/.phenote/obo-files
>>> 2008-02-15 16:45:19,515 [main] FATAL  
>>> dataadapter.OntologyDataAdapter -
>>> got obo data adapter exception:
>>> org.bbop.dataadapter.DataAdapterException: Load error message Load
>>> error cause java.lang.NullPointerException
>>> THIS IS FATAL!
>>> Can not load ontologies. Phenote must exit.
>>> Consider clearing out bad file from ~/.phenote/obo-files
>>>
>>>
>>> I've added this to the worm.cfg (haven't svn commit since it doesn't
>>> work)
>>>
>>>   <field name="WS_current info" datatag="WS_currentinfo"
>>> enable="true" groups="default">
>>>          <ontology name="ws_variation" file="http://
>>> tazendra.caltech.edu/~azurebrd/var/work/phenote/wb_variation.obo"/>
>>>          <!--<ontology name="ws_variation" file="http://
>>> tazendra.caltech.edu/~azurebrd/cgi-bin/forms/person_obo.cgi"/>-->
>>>   </field>
>>>
>>>
>>> If I use the commented-out obo it loads fine, so there seems to be
>>> something wrong with the obo file.  Can you tell what's wrong with
>>> it ?
>>>
>>> Thanks,
>>> J
>>>
>