Hi Scott,
You can turn on debugging info by changing the following line in
the $APOLLO_ROOT/conf/log4j.properties:
log4j.rootLogger=INFO,stdout
to
log4j.rootLogger=DEBUG,stdout
It should should you all the SQL statements that are being run.
I'm surprised that it's not working with the suggested change, so perhaps
you could provide me with a dump of the data (or access to the database)
along with the style/tiers file you're using I can investigate this
further.
Cheers,
Ed
On Wed, 10 Jun 2009, Scott Cain wrote:
Hi Ed,
I tried that, as well as BLASTN: and BLASTN:na. How do you turn on
logging on the command line so I can try to figure out what is happen?
Also, can you suggest a way to modify the analysis table row to make
it more likely to work?
Thanks,
Scott
On Wed, Jun 10, 2009 at 5:15 PM, Ed Lee<[email protected]> wrote:
Hey Scott,
Try using "BLASTN" as the resulttype instead of "BLASTN:BLASTN".
Cheers,
Ed
On Tue, 9 Jun 2009, Scott Cain wrote:
Hi Ed,
How does the tiers file field "resulttype" map to Chado?
Specifically, I'm trying to use the conf below to extract blast
results from chado where the analysis table row for these results look
like this:
analysis_id | name | program | programversion | sourcename
-------------+--------+---------+----------------+------------
44 | BLASTN | BLASTN | null |
[Tier]
tiername : BLASTN
visible : true
expanded : true
[Type]
tiername : BLASTN
typename : BLASTN:BLASTN
resulttype : BLASTN:BLASTN
color : 204,0,51
usescore : false
minscore : 0
maxscore : 100
glyph : DrawableResultFeatureSet
column : SCORE
column : expect
column : query_frame
column : GENOMIC_RANGE
column : MATCH_RANGE
column : GENOMIC_LENGTH
column : MATCH_LENGTH
sortbycolumn : GENOMIC_RANGE
groupby : HOMOLOGY
weburl :
freshdate: 26-NOV-2007
Thanks,
Scott
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain
dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
--
------------------------------------------------------------------------
Scott Cain, Ph. D. scott at scottcain dot net
GMOD Coordinator (http://gmod.org/) 216-392-3087
Ontario Institute for Cancer Research
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