[ensembl-dev] Release 65 - 'not a valid species name' exception thrown by get_adaptor()
Andy Yates
ayates at ebi.ac.uk
Mon Jan 23 09:37:36 GMT 2012
Hi Giuseppe,
This looks more like an Ensembl Genomes error as I cannot find any compara database for release 12 on their public server. I will raise issue with them ASAP
Andy
Andrew Yates Ensembl Core Software Project Leader
EMBL-EBI Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK http://www.ensembl.org/
On 20 Jan 2012, at 20:49, Giuseppe G. wrote:
> Hi Andy,
>
> thanks for your reply. Unfortunately there are more problems. I'm not able anymore to create any genome DB adaptors for Ensemblgenomes families.
>
> When I do
> my $registry = 'Bio::EnsEMBL::Registry';
> $registry->load_registry_from_multiple_dbs(
> { #VERTEBRATES
> -host => 'ensembldb.ensembl.org',
> -user => 'anonymous',
> },
> { #EnsemblGenomes
> -host => 'mysql.ebi.ac.uk',
> -user => 'anonymous',
> -port => 4157,
> }
> );
> and any of
> my $genome_db_adaptor = $registry->get_adaptor('pan_homology', 'compara', 'GenomeDB');
> my $genome_db_adaptor = $registry->get_adaptor('metazoa', 'compara', 'GenomeDB');
> my $genome_db_adaptor = $registry->get_adaptor('protists', 'compara', 'GenomeDB');
>
> etc etc I will get the same exception we discussed earlier
>
> -------------------- WARNING ----------------------
> MSG: protists is not a valid species name (check DB and API version)
> FILE: Bio/EnsEMBL/Registry.pm LINE: 1159
> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 953
> Ensembl API version = 65
> ---------------------------------------------------
>
> -------------------- EXCEPTION --------------------
> MSG: Can not find internal name for species 'protists'
> STACK Bio::EnsEMBL::Registry::get_adaptor <MYPATH>/ensembl/modules/Bio/EnsEMBL/Registry.pm:955
> STACK toplevel <MYCODE>
> Ensembl API version = 65
> ---------------------------------------------------
>
> Can you help?
>
> Thanks
> Giuseppe
>
> On 20/01/12 17:34, Andy Yates wrote:
>> Hi Giuseppe,
>>
>> It is a strong response to the problem but we have seen an increase in the number of errors users are reporting that they cannot call a method on an undefined value. The hope is that this will help users diagnose the issues themselves. The problem we saw with implementing checks to solve this issue is that it is impossible to know if we are dealing with a mis-configured checkout of Ensembl (has a user checked out HEAD and looking for v66 DBs on our public servers) or a user who is intentionally going after this data. The errors give a clear message something is wrong with their setup.
>>
>> As for your situation I am sorry that this was such a breaking change for you. I'm glad that the proposed fixes have been able to get you back on track
>>
>> Best regards,
>>
>> Andy
>>
>> Andrew Yates Ensembl Core Software Project Leader
>> EMBL-EBI Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK http://www.ensembl.org/
>>
>> On 20 Jan 2012, at 17:23, Giuseppe G. wrote:
>>
>>> Hi Andy,
>>>
>>> I understand the problem however the solution seems i.m.o. a bit strong and the message returned by the warning a bit misleading for those with matching api/db version. Would it maybe be possible to do these version checks at the registry level rather than at the adaptor level? Anyway thank you for your suggestion, I will use that method you suggest from now on.
>>>
>>> Best,
>>> Giuseppe
>>>
>>> On 20/01/12 15:52, Andy Yates wrote:
>>>> Hi Giuseppe,
>>>>
>>>> I'm sorry that you are encountering this issue. The reason why this change was put into place was to avoid/inform users when they fail to connect to Ensembl with the correct database version. This is why the warning mentions that you should check the DB& API versions. Considering the amount of messages we get about this each release I am reluctant to revert this behaviour.
>>>>
>>>> If you want to check if a species is known you can do the following:
>>>>
>>>> my $species = 'ScerS288c';
>>>> my $type = 'core';
>>>> my $alias_exists = Bio::EnsEMBL::Registry->alias_exists($species);
>>>> if($alias_exists) {
>>>> my $a = Bio::EnsEMBL::Registry->get_adaptor($species, $type, 'Gene');
>>>> }
>>>>
>>>> Which would tell you if the species existed and then get the gene adaptor if it is available. You could also use:
>>>>
>>>> my $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $type, 1);
>>>> if($dba) {
>>>> my $a = $dba->get_GeneAdaptor();
>>>> }
>>>>
>>>> Both are valid& would not require you to do too much recoding.
>>>>
>>>> Hope this has helped you out
>>>>
>>>> Andy
>>>>
>>>> On 20 Jan 2012, at 12:34, Giuseppe G. wrote:
>>>>
>>>>> Hi again
>>>>>
>>>>> I'm on release 65, Bioperl 1.6.1.
>>>>>
>>>>> A line like the following
>>>>>
>>>>> my $gene_adaptor = $registry->get_adaptor('ScerS288c', 'core', 'Gene');
>>>>>
>>>>> will return the exception
>>>>>
>>>>> -------------------- WARNING ----------------------
>>>>> MSG: ScerS288c is not a valid species name (check DB and API version)
>>>>> FILE: Bio/EnsEMBL/Registry.pm LINE: 1159
>>>>> CALLED BY: Bio/EnsEMBL/Registry.pm LINE: 953
>>>>> Ensembl API version = 65
>>>>> ---------------------------------------------------
>>>>>
>>>>> -------------------- EXCEPTION --------------------
>>>>> MSG: Can not find internal name for species 'ScerS288c'
>>>>> STACK Bio::EnsEMBL::Registry::get_adaptor /home/giuseppe/src/ensembl/modules/Bio/EnsEMBL/Registry.pm:955
>>>>> STACK<MYCODE>
>>>>> Ensembl API version = 65
>>>>> ---------------------------------------------------
>>>>>
>>>>> instead of returning an undef.
>>>>>
>>>>> This happens whenever the query species is not contained in the genomeDB. So every time I try to get an adaptor with an unrecognised species (may be a typo, a strain name like Saccharomyces cerevisiae S288c, etc) I'll get this exception.
>>>>>
>>>>> The behaviour, up to v64, was different. I got an undefined $gene_adaptor and I could then go back to the taxon object and climb up the taxonomy to get the parent taxon (in the example case, 'Saccharomyces cerevisiae') and try once more to get a gene adaptor with the parent taxon binomial name.
>>>>>
>>>>> I *could* get round this exception by downloading all of the available binomal species names from a genome adaptor - comparing my species name against them, then trying to get the gene adaptor only if my species is in the genome adaptor array - however this is far from optimal (as I need to deal with EnsemblGenomes species names as well).
>>>>>
>>>>> Would it be possible to restore the former behaviour? Thanks a lot!
>>>>>
>>>>> Giuseppe
>>>>>
>>>>> --
>>>>>
>>>>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
>>>>>
>>>>> _______________________________________________
>>>>> Dev mailing list Dev at ensembl.org
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>>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>>
>>> --
>>>
>>> The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
>>
>>
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
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