[ensembl-dev] skip lock tables for ensembl-compara

[Mateus Patricio]

Hi Francesco,

So what’s happening here is that you are trying to lock a table in one of our servers.

That can be fixed by telling mysqldump to avoid locking the table. (Like you initially suspected)

You could do that directly on the eHive runnable "ehive/master/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm”

The dump command is constructed at:
https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117 <https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L117>

I would suggest you to create a new entry to “mode_options”:
https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112 <https://github.com/Ensembl/ensembl-hive/blob/6c4877d4eda1bf0469c29bdbe58932671848cc20/modules/Bio/EnsEMBL/Hive/RunnableDB/MySQLTransfer.pm#L112>

So that you could access directly from your pipeline config file, by setting something like:

>         {   -logic_name    => 'copy_ncbi_table',
>             -module        => 'Bio::EnsEMBL::Hive::RunnableDB::MySQLTransfer',
>             -parameters    => {
>                 'src_db_conn'   => '#ncbi_db#',
>                 'mode'          => ’SKIP_LOCK',
>                 'filter_cmd'    => 'sed "s/ENGINE=MyISAM/ENGINE=InnoDB/"',
>             },
>         },

Please let me know if that doesn’t work.

Cheers,

Mateus.




> On 9 Nov 2017, at 15:44, Francesco Lamanna <francesco.lamanna at gmail.com> wrote:
> 
> Hi Mateus,
> 
> thank you for your answer.
> 
> I am using 'ncbi_db'   => 'mysql://anonymous@ensembldb.ensembl.org/ensembl_compara_90 <http://anonymous@ensembldb.ensembl.org/ensembl_compara_90>' to conncect to ncbi_db (I used the same value as in the NoMasterProteinTrees_conf.pm example).
> 
> The failing analysis is copy_ncbi_table(9).
> 
> Cheers,
> Francesco.
> 
> 2017-11-09 16:29 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk <mailto:mateus at ebi.ac.uk>>:
> Hi Francesco,
> 
> Looks like your pipeline is using the user anonymous to connect to the database.
> 
> I would suggest that you add the skip option within your runnable.
> 
> Which analysis is actually failing?
> 
> Cheers,
> 
> Mateus.
> 
> 
>> On 8 Nov 2017, at 17:36, Francesco Lamanna <francesco.lamanna at gmail.com <mailto:francesco.lamanna at gmail.com>> wrote:
>> 
>> Hello,
>> 
>> I am trying to apply the ProteinTrees pipeline to a set of Ensembl and non-Ensembl genomes. 
>> 
>> When running the pipeline without a master database (via beekeeper.pl <http://beekeeper.pl/>) I get the following error:
>> 
>> ensembl_compara_90 ncbi_taxa_node  | sed "s/ENGINE=MyISAM/ENGINE=InnoDB/" |  mysql -h127.0.0.1 -P3306 -uroot -p$EHIVE_TMP_PASSWORD_0 hd_cc141_test_protein_trees_no_master_90' resulted in an error code=2
>> stderr is: mysql: [Warning] Using a password on the command line interface can be insecure.
>> mysqldump: Got error: 1044: Access denied for user 'anonymous'@'%' to database 'ensembl_compara_90' when doing LOCK TABLES 
>> 
>> 
>> Is there a way to pass --skip-lock-tables to the pipeline (e.g. in the conf file) in order to be able to dump the database?
>> 
>> Thanks,
>> Francesco.
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev <http://lists.ensembl.org/mailman/listinfo/dev>
>> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org <mailto:Dev at ensembl.org>
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev <http://lists.ensembl.org/mailman/listinfo/dev>
> Ensembl Blog: http://www.ensembl.info/ <http://www.ensembl.info/>
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20171109/80a4e966/attachment.html>