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

Brandon Walts bwalts at ebi.ac.uk
Thu Nov 9 16:25:12 GMT 2017


Hi Francesco

We have just pushed a fix to the MySQLTransfer.pm runnable, so that it 
no longer locks tables by default. If you go to your eHive checkout and 
perform a git pull, you should get this fix.

Users who wish to retain the table locking behavior can switch it on by 
passing a parameter 'lock_tables=1' to MySQLTransfer.pm

Best
-Brandon


On 09/11/2017 16:20, Mateus Patricio wrote:
> 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
>
> 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
>
> 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 <mailto: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.
>>>
>>>
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>>
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