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'
>>
>> Note: This message may contain confidential information. If this Email/Fax
>> has been sent to you by mistake, please notify the sender and delete it
>> immediately. Thank you.
>> _______________________________________________
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>>
>>
>>
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