[biomart-users] Errors when using Perl API

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[biomart-users] Errors when using Perl API

Julien Fumey
Hi everyone,
i am trying to configure the Biomart's Perl API with EnsEMBL release 73.
I am coming across some errors for which i can't find the origin :
Use of uninitialized value in lc at /biomart-perl/lib/BioMart/Configurator.pm line 367.
Use of uninitialized value in lc at /biomart-perl/lib/BioMart/Configurator.pm line 460.

Setting possible links between datasets
....(scanning) 0%      WARNING: Pointer attributes from closure_GO will not be available as closure_GO not in registry

default ... ENSEMBL GENES 73 (SANGER UK) ...   .......... drerio_gene_ensembl ....................... (WEB) www.biomart.org:80 ............ File does not exist: Could not retrieve valid XML for SCHEMA: ensembl_mart_73    DATASET: drerio_gene_ensembl at /biomart-perl/lib/BioMart/Configurator.pm line 170



Furthermore i cannot add ontology's servers in the XML registry file resulting in the following error :

Can not add dataset 'closure_EFO', already added
 
Please note that it was working a few months ago with previous EnsEMBL release.
Thanks.

Julien Fumey

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Re: [biomart-users] Errors when using Perl API

Arek Kasprzyk
Hi Julien,
I am not sure what's going on there so I will let somebody else comment on that.

Just wondering if you would not be better off using web services instead of perl API? 
(it is faster and you will not need any configuration steps)


Please see 


It is also possible to create web servcie queries from MView user interface by clicking 'XML' button

a





On 23 September 2013 12:00, Julien Fumey <[hidden email]> wrote:
Hi everyone,
i am trying to configure the Biomart's Perl API with EnsEMBL release 73.
I am coming across some errors for which i can't find the origin :
Use of uninitialized value in lc at /biomart-perl/lib/BioMart/Configurator.pm line 367.
Use of uninitialized value in lc at /biomart-perl/lib/BioMart/Configurator.pm line 460.

Setting possible links between datasets
....(scanning) 0%      WARNING: Pointer attributes from closure_GO will not be available as closure_GO not in registry

default ... ENSEMBL GENES 73 (SANGER UK) ...   .......... drerio_gene_ensembl ....................... (WEB) www.biomart.org:80 ............ File does not exist: Could not retrieve valid XML for SCHEMA: ensembl_mart_73    DATASET: drerio_gene_ensembl at /biomart-perl/lib/BioMart/Configurator.pm line 170



Furthermore i cannot add ontology's servers in the XML registry file resulting in the following error :

Can not add dataset 'closure_EFO', already added
 
Please note that it was working a few months ago with previous EnsEMBL release.
Thanks.

Julien Fumey

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Re: [biomart-users] Errors when using Perl API

Rhoda Kinsella
Hi Julien
We came across a similar error recently when we upgraded the perl version
we were using. To get rid of the error, you need to modify the lines of
code in the Configurator.pm where it is complains when trying to deal with
a lowercase undefined value (i.e. line 367 and 460) This is what I did:

In biomart-perl/lib/BioMart/Configurator.pm

I modified the lines 367 and 460. An example of what I did can be seen below.

Modified from:
                     'name' => lc($xmlAttribute->{'internalName'}),
To:

                     'name' => lc($xmlAttribute->{'internalName'} || ""),



The ontology issue may be related to a problem with your registry.xml
file. If you send it to me I can take a look.
I hope that helps,
Regards
Rhoda


> Hi Julien,
> I am not sure what's going on there so I will let somebody else comment on
> that.
>
> Just wondering if you would not be better off using web services instead
> of
> perl API?
> (it is faster and you will not need any configuration steps)
>
>
> Please see
>
> http://www.biomart.org/martservice.html
>
> It is also possible to create web servcie queries from MView user
> interface
> by clicking 'XML' button
>
> a
>
>
>
>
>
> On 23 September 2013 12:00, Julien Fumey
> <[hidden email]>wrote:
>
>>  Hi everyone,
>> i am trying to configure the Biomart's Perl API with EnsEMBL release 73.
>> I am coming across some errors for which i can't find the origin :
>> Use of uninitialized value in lc at
>> /biomart-perl/lib/BioMart/Configurator.pm line 367.
>> Use of uninitialized value in lc at
>> /biomart-perl/lib/BioMart/Configurator.pm line 460.
>>
>> Setting possible links between datasets
>> ....(scanning) 0%      WARNING: Pointer attributes from closure_GO will
>> not be available as closure_GO not in registry
>>
>> default ... ENSEMBL GENES 73 (SANGER UK) ...   ..........
>> drerio_gene_ensembl ....................... (WEB)
>> www.biomart.org:80............ File does not exist: Could not retrieve
>> valid XML for SCHEMA:
>> ensembl_mart_73    DATASET: drerio_gene_ensembl at
>> /biomart-perl/lib/BioMart/Configurator.pm line 170
>>
>>
>> Furthermore i cannot add ontology's servers in the XML registry file
>> resulting in the following error :
>>
>> Can not add dataset 'closure_EFO', already added
>>
>>>
>> Please note that it was working a few months ago with previous EnsEMBL
>> release.
>> Thanks.
>>
>> Julien Fumey
>>
>> --
>> You received this message because you are subscribed to the Google
>> Groups
>> "biomart-users" group.
>> To unsubscribe from this group and stop receiving emails from it, send
>> an
>> email to [hidden email].
>> Visit this group at http://groups.google.com/group/biomart-users.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>
> --
> You received this message because you are subscribed to the Google Groups
> "biomart-users" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [hidden email].
> Visit this group at http://groups.google.com/group/biomart-users.
> For more options, visit https://groups.google.com/groups/opt_out.
>

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