[InterMine Dev] Logging messages from the rgd annotation parser

Vallejos, Andrew avallejos at mcw.edu
Fri Oct 21 19:28:27 BST 2011


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
>
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