Changes to mysqlimport

Owing to problems with BLOB data in some tables, we have had to change the way these tables are dumped, which in turn means a change to the mysqlimport parameters.

It has been necessary to escape the table fields when dumping the MySQL text files. Hence to import successfully, a field escape parameter needs to be specified when using mysqlimport, e.g.

mysqlimport -h your_host -u write_user -p write_pass -P 3306 –fields_escaped_by=\\ database_name /full/path/to/table_name.txt

Tables affected in Release 59 are:

* homo_sapiens_funcgen_59_37d.result_feature
* mus_musculus_funcgen_59_37l.result_feature
* ensembl_compara_59.conservation_scores

and the meta_conf__xml__dm and meta_template__xml__dm tables in all mart databases.

From release 60, all Ensembl mysql dumps will be done this way, so you will need to use the above parameters on all imports.

3 thoughts on “Changes to mysqlimport

  1. will anyone tell me that why can’t i see the newest data (e.g. homo_sapiens_core_61_37f) when i enter the ensembldb.ensembl.org(mysql -u anonymous -h ensembldb.ensembl.org)??….. ==

    Much obliged.

  2. Aha, forgive my silly question in my last comment…. i see now… i have to change the port 5306… like :mysql -uanonymous -h ensembdb.ensembl.org -P 5306 ==