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

[Jan Vogel]

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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