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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