[ensembl-dev] Patching an Ensembl compare database from 67 to 74

Will Chow wc2 at sanger.ac.uk
Fri Jan 17 10:08:11 GMT 2014


Hi Jan

I noticed warnings as well patching from 66->73 for compara for a few tables ( I don't quite remember which ones ).  

Of course this doesn't really help you or solve your issues, but since our group doesn't use those tables I just ignored the patch warnings and for our purposes, it seems to work.   I do notice in the meta table the patch keys for the updates are not there below e70 even though the patches are in the sql directory.

again doesn't really help you I guess.

Will

On 17 Jan 2014, at 06:49, Jan Vogel <jan.vogel at gmail.com> wrote:

> 
> Hi there, 
> 
> i'm trying to patch our ensembl 67 compara database up to schema 74. 
> 
> It fails :-( when applying the ensembl-compara/sql/patch_67_68.sql patch as in the 67 schema there are duplicate member ids in the sequence_exon_bounded table. Any idea how to fix this and patch my e67 up to e68 ? 
> 
> Thanks,
> 
>    Jan Vogel
> 
> 
> ERROR 1062 (23000) at line 28 in file: '/gnet/resfiles3/resapps/apps/ensembl/ensembl-74/ensembl-compara/sql/patch_67_68.sql': Duplicate entry '2012449' for key 'PRIMARY' : 
> 
> --------------
> SET session sql_mode='TRADITIONAL'
> --------------
> ……
> …..
> 
> 
> --------------
> ALTER TABLE sequence_exon_bounded 
> DROP PRIMARY KEY, DROP KEY member_id, 
> DROP COLUMN sequence_exon_bounded_id, 
> ADD PRIMARY KEY (member_id)
> --------------
> 
> Failed to apply patch 'patch_67_68.sql' to database 'ensembl_compara_67'!
> In non-interative mode; aborting current run at schema_patcher.pl line 643.
> 
> 
> Looking into the sequence_exon_bounded table, it looks that some member ids are duplicated: 
> 
> mysql> select count(distinct(member_id))  from sequence_exon_bounded limit 10 ; 
> +----------------------------+
> | count(distinct(member_id)) |
> +----------------------------+
> |                    1371152 | 
> +----------------------------+
> 1 row in set (10.55 sec)
> 
> mysql> select count(member_id)  from sequence_exon_bounded limit 10 ; 
> +------------------+
> | count(member_id) |
> +------------------+
> |          1373719 | 
> +------------------+
> 
> 
> 
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