Hi Kevin,
If you installed Apollo from the installer, then you won't be able to
just modify the contents of the apollo.jar file, as the source code
isn't included. In that case, you'll want to check out the code from
CVS. For instructions, check out:
http://sourceforge.net/cvs/?group_id=27707
You'll want to look at the package:
apollo.dataadapter.ensj
In particular, you'll want to look at the EnsJAdapter and
EnsJConnectionUtil classes.
Once you've made the modification, you'll need to recompile the jar.
Cheers,
Ed
On Tue, 13 Jan 2009, Kevin Lam wrote:
Field Type Null Key Default Extra gene_id int(10) unsigned
PRI
auto_increment biotype varchar(40)
analysis_id int(11) YES MUL
seq_region_id int(10) unsigned
MUL 0
seq_region_start int(10) unsigned
0
seq_region_end int(10) unsigned
0
seq_region_strand tinyint(2)
0
display_xref_id int(10) unsigned YES MUL
source varchar(20)
confidence enum('KNOWN','NOVEL','PUTATIVE','PREDICTED') YES
description text YES
Hi Ed,
Thanks for the reply!
May I know where in the source do I find this?
Can I just unzip the ensj.jar file to edit this behaviour and zip it back up
as a jar and run it?
the above is what I got from mysql query 'describe gene'
so tecnically it should be schema 32 going by the logic u mentioned. I don't
mind hardcoding the schema version just to get it to work.
Cheers
Kevin
On Tue, Jan 13, 2009 at 2:32 AM, Ed Lee <[email protected]> wrote:
Hi Kevin,
I'm not familiar with the Ensembl schema at all, but looking at the code
it does the following to determine the schema version:
- Run MySQL query "describe gene"
- Look at the first column of the first row returned
- If its value equals "confidence" then set the schema to 32
- If its value equals "status" then set the schema to 34
- Look at the first column of any remainder rows returned
- If its value does not contain the substring "evision" then set
the schema to the integer value in the field
- Otherwise return 30
Steve Searle wrote the EnsJ adapter, so he might be able to give you
more insight on this.
Cheers,
Ed
On Mon, 12 Jan 2009, Kevin Lam wrote:
Hi,
I am using schema 32 for my db but apollo seems to think its schema 30..
is there a way to override this behaviour?
INFO : Setting schema to 30 for db fugu5_final on fugu-mysql.datastorage
port 3306
INFO : Done initialising driver
INFO : fetching genes...
INFO : Doing initial gene fetch
ERROR: Problem fetching data: Failed to execute sql against database
fugu5_final:SELECT g.gene_id, g.seq_region_id, g.seq_region_start,
g.seq_region_end, g.seq_region_strand, g.analysis_id, g.type as biotype,
NULL as source, g.display_xref_id, NULL as DESCRIPTION, gsi.stable_id,
gsi.version, gsi.created_date, gsi.modified_date, x.display_label,
exdb.db_name, exdb.status, NULL AS gene_status FROM gene g LEFT JOIN
gene_stable_id gsi ON gsi.gene_id=g.gene_id LEFT JOIN xref x ON
x.xref_id=g.display_xref_id LEFT JOIN external_db exdb ON
exdb.external_db_id=x.external_db_id WHERE g.seq_region_id = 3524 AND
g.seq_region_start <= 154185 AND g.seq_region_end >= 153186 AND
g.seq_region_start >= -111086 [39.2]; nested exception is:
java.sql.SQLException: Unknown column 'g.type' in 'field list'
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