[InterMine Dev] Logging messages from the rgd annotation parser

julie at flymine.org julie at flymine.org
Fri Oct 21 19:52:50 BST 2011


good point, will do.

> Can I configure the property in the project xml file?  I am trying to
> not have to create 3 annotation sources (gene, qtl, sslp) for each
> ontology.
>
> -----Original Message-----
> From: www-data [mailto:www-data at flymine.org] On Behalf Of
> julie at flymine.org
> Sent: Friday, October 21, 2011 1:28 PM
> To: Vallejos, Andrew
> Cc: dev at intermine.org
> Subject: RE: [InterMine Dev] Logging messages from the rgd annotation
> parser
>
> In the next release I'll add a setting to the config to toggle between
> these two values.
>
>> My code is pretty strait forward.  I simply uncommented line 193 and
>> commented line 194. (Those are the lines in the GoConverter.java
>> anyway.)
>>
>> -----Original Message-----
>> From: dev-bounces at intermine.org [mailto:dev-bounces at intermine.org] On
>> Behalf Of Julie Sullivan
>> Sent: Thursday, October 20, 2011 2:59 AM
>> To: dev at intermine.org
>> Subject: Re: [InterMine Dev] Logging messages from the rgd annotation
>> parser
>>
>> Andrew
>>
>> Your syntax is correct.  You might not have your logger set to be
>> "verbose", eg.
>> it only prints the important messages.  Try either setting the
> priority
>> to show
>> all messages, or use a higher level of message:
>>
>> 	 LOG.error("TYPE " + type);
>>
>> http://logging.apache.org/log4j/1.2/manual.html has a list of the
> levels
>> in order:
>>
>> 	TRACE,
>> 	DEBUG,
>> 	INFO,
>> 	WARN,
>> 	ERROR and
>> 	FATAL
>>
>> However, if you are testing the GO annotation loader, it might be
>> quicker and
>> easier to use the test in go-annotation/test.  You can print out log
>> messages
>> directly to the console as well as view the objects the loader
> created.
>>
>> Cheers
>> Julie
>>
>> On 19/10/11 22:05, Vallejos, Andrew wrote:
>>> Hi,
>>>
>>>
>>>
>>> I'm trying to get the annotation loader to use the 12th column to
>>> determine the type.  Unfortunately, the annotation loader just loads
>>> everything as a gene.  Also, I cannot get the annotation java file to
>>> log any messages.
>>>
>>>
>>>
>>> // LOG is the Logger object
>>>
>>> // type is a String value from array[11], or the 12th column of the
>> data
>>> line being processed.
>>>
>>> LOG.info("TYPE " + type); yields no TYPE messages in my interine.log
>>> file or screen output.
>>>
>>>
>>>
>>> How do I send messages to the log file?
>>>
>>>
>>>
>>> Thanks,
>>>
>>>
>>>
>>> Andrew
>>>
>>>
>>>
>>> ======================
>>>
>>> Andrew Vallejos M.S.
>>>
>>> Web Developer II
>>>
>>> Biotechnology and Bioengineering Center
>>>
>>> Medical College of Wisconsin
>>>
>>> 414-955-4104
>>>
>>> avallejos at mcw.edu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> dev at intermine.org
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>> _______________________________________________
>> dev mailing list
>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>>
>
>
>




More information about the dev mailing list