Re: [mart-dev] Mis-configuration in the IKMC Mart - help...

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Re: [mart-dev] Mis-configuration in the IKMC Mart - help...

Syed Haider
Hi Darren,

please scroll down to see the reply,

On 01/06/2010 09:31, Darren Oakley wrote:
> Hi All,
>
> I've just had an email from a user who is having problems accessing one of our marts via an R package (biomaRt).  I tried to use the same package but it looks like we've got a slight mis-configuration on our server - in the registry, all of our 'host' directives are set the the hostname of the machine the mart is running on ('hpgen-1-14') - not what is configured in the registry file:

You need to set proxy="80" in the settings.conf, that should do the
trick. I am assuming these marts in your registry file have
martDBLocation type connections and point to a database locally.

Best
Syed


>
> http://www.i-dcc.org/biomart/martservice?type=registry
>
> compared to the attached XML at the base of this email...
>
> Any idea how I can fix this one?
>
> Thanks,
>
> Daz
>
> P.S. On a side note - is there any chance we can get the IKMC mart added to the biomart central portal too for easier access to our data too?
>
> ---
>
> <?xml version="1.0" encoding="UTF-8"?>
> <!DOCTYPE MartRegistry>
> <MartRegistry>
>
>      <MartDBLocation
>          name            = "ikmc"
>          displayName     = "IKMC Genes and Products"
>          databaseType    = "mysql"
>          host            = "web-mii-shap.internal.sanger.ac.uk"
>          port            = "3303"
>          database        = "ikmc_mart_alt"
>          schema          = "ikmc_mart_alt"
>          user            = "ikmc"
>          password        = "ikmc"
>          visible         = "1"
>          default         = ""
>          includeDatasets = ""
>          martUser        = ""
>      />
>
>      <MartURLLocation
>        name                = "biomart"
>        database            = "biomart"
>        default             = ""
>        displayName         = "MGI (Jackson Laboratory US)"
>        host                = "www.biomart.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "markers"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
>      <MartURLLocation
>        name                = "htgt"
>        database            = "htgt_mart"
>        default             = ""
>        displayName         = "WTSI Mouse Genetics Programme (Sanger UK)"
>        host                = "www.sanger.ac.uk"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "htgt_targ"
>        martUser            = ""
>        path                = "/htgt/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
>      <MartURLLocation
>        name                = "emma_biomart"
>        database            = "emma_biomart"
>        default             = ""
>        displayName         = "The European Mouse Mutant Archive (EMMA)"
>        host                = "www.emmanet.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = ""
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
>      <MartURLLocation
>        name                = "Eurexpress Biomart"
>        database            = "ee_biomart_test5"
>        default             = ""
>        displayName         = "Eurexpress"
>        host                = "biomart.eurexpress.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "template"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
>      <MartURLLocation
>        name                = "europhenomeannotations"
>        database            = "europhenome_annotation_1_3_3_20100414"
>        default             = ""
>        displayName         = "Europhenome"
>        host                = "www.europhenome.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "europhenome"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
>      <MartURLLocation
>        name                = "ensembl"
>        default             = ""
>        displayName         = "Ensembl Gene (Sanger UK)"
>        host                = "www.biomart.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "mmusculus_gene_ensembl"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
>      <MartURLLocation
>        name                = "sequence"
>        default             = ""
>        displayName         = "Ensembl Sequence (Sanger UK)"
>        host                = "www.biomart.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "mmusculus_genomic_sequence"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = ""
>      />
>      <MartURLLocation
>        name                = "ontology"
>        default             = ""
>        displayName         = "Ensembl Ontology (Sanger UK)"
>        host                = "www.biomart.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "closure_biological_process,closure_cellular_component,closure_molecular_function"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = ""
>      />
>      <MartURLLocation
>        name                = "genomic_features"
>        default             = ""
>        displayName         = "Ensembl Genomic Features (Sanger UK)"
>        host                = "www.biomart.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "mmus_karyotype_start,mmus_karyotype_end,mmus_marker_start,mmus_marker_end"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = ""
>      />
>      <MartURLLocation
>        name                = "vega"
>        default             = ""
>        displayName         = "Vega (Sanger UK)"
>        host                = "www.biomart.org"
>        proxy               = "http://wwwcache.sanger.ac.uk:3128"
>        includeDatasets     = "mmusculus_gene_vega"
>        martUser            = ""
>        path                = "/biomart/martservice"
>        port                = "80"
>        serverVirtualSchema = "default"
>        visible             = "1"
>      />
> </MartRegistry>
>
>
>
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Re: Mis-configuration in the IKMC Mart - help...

Darren Oakley
Hi Syed,

Thanks for that - it wasn't the full solution (as it turns out), but it lead me to it. :)

I was foolishly setting the 'severHost' directive (in settings.conf) to the hostname!!!  Added the proxy setting and the correct serverHost and it's working happily now.

Thanks,

Daz

On 3 Jun 2010, at 15:43, Syed Haider wrote:

> Hi Darren,
>
> please scroll down to see the reply,
>
> On 01/06/2010 09:31, Darren Oakley wrote:
>> Hi All,
>>
>> I've just had an email from a user who is having problems accessing one of our marts via an R package (biomaRt).  I tried to use the same package but it looks like we've got a slight mis-configuration on our server - in the registry, all of our 'host' directives are set the the hostname of the machine the mart is running on ('hpgen-1-14') - not what is configured in the registry file:
>
> You need to set proxy="80" in the settings.conf, that should do the trick. I am assuming these marts in your registry file have martDBLocation type connections and point to a database locally.
>
> Best
> Syed
>
>
>>
>> http://www.i-dcc.org/biomart/martservice?type=registry
>>
>> compared to the attached XML at the base of this email...
>>
>> Any idea how I can fix this one?
>>
>> Thanks,
>>
>> Daz
>>
>> P.S. On a side note - is there any chance we can get the IKMC mart added to the biomart central portal too for easier access to our data too?
>>
>> ---
>>
>> <?xml version="1.0" encoding="UTF-8"?>
>> <!DOCTYPE MartRegistry>
>> <MartRegistry>
>>
>>     <MartDBLocation
>>         name            = "ikmc"
>>         displayName     = "IKMC Genes and Products"
>>         databaseType    = "mysql"
>>         host            = "web-mii-shap.internal.sanger.ac.uk"
>>         port            = "3303"
>>         database        = "ikmc_mart_alt"
>>         schema          = "ikmc_mart_alt"
>>         user            = "ikmc"
>>         password        = "ikmc"
>>         visible         = "1"
>>         default         = ""
>>         includeDatasets = ""
>>         martUser        = ""
>>     />
>>
>>     <MartURLLocation
>>       name                = "biomart"
>>       database            = "biomart"
>>       default             = ""
>>       displayName         = "MGI (Jackson Laboratory US)"
>>       host                = "www.biomart.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "markers"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>>     <MartURLLocation
>>       name                = "htgt"
>>       database            = "htgt_mart"
>>       default             = ""
>>       displayName         = "WTSI Mouse Genetics Programme (Sanger UK)"
>>       host                = "www.sanger.ac.uk"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "htgt_targ"
>>       martUser            = ""
>>       path                = "/htgt/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>>     <MartURLLocation
>>       name                = "emma_biomart"
>>       database            = "emma_biomart"
>>       default             = ""
>>       displayName         = "The European Mouse Mutant Archive (EMMA)"
>>       host                = "www.emmanet.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = ""
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>>     <MartURLLocation
>>       name                = "Eurexpress Biomart"
>>       database            = "ee_biomart_test5"
>>       default             = ""
>>       displayName         = "Eurexpress"
>>       host                = "biomart.eurexpress.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "template"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>>     <MartURLLocation
>>       name                = "europhenomeannotations"
>>       database            = "europhenome_annotation_1_3_3_20100414"
>>       default             = ""
>>       displayName         = "Europhenome"
>>       host                = "www.europhenome.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "europhenome"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>>     <MartURLLocation
>>       name                = "ensembl"
>>       default             = ""
>>       displayName         = "Ensembl Gene (Sanger UK)"
>>       host                = "www.biomart.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "mmusculus_gene_ensembl"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>>     <MartURLLocation
>>       name                = "sequence"
>>       default             = ""
>>       displayName         = "Ensembl Sequence (Sanger UK)"
>>       host                = "www.biomart.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "mmusculus_genomic_sequence"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = ""
>>     />
>>     <MartURLLocation
>>       name                = "ontology"
>>       default             = ""
>>       displayName         = "Ensembl Ontology (Sanger UK)"
>>       host                = "www.biomart.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "closure_biological_process,closure_cellular_component,closure_molecular_function"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = ""
>>     />
>>     <MartURLLocation
>>       name                = "genomic_features"
>>       default             = ""
>>       displayName         = "Ensembl Genomic Features (Sanger UK)"
>>       host                = "www.biomart.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "mmus_karyotype_start,mmus_karyotype_end,mmus_marker_start,mmus_marker_end"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = ""
>>     />
>>     <MartURLLocation
>>       name                = "vega"
>>       default             = ""
>>       displayName         = "Vega (Sanger UK)"
>>       host                = "www.biomart.org"
>>       proxy               = "http://wwwcache.sanger.ac.uk:3128"
>>       includeDatasets     = "mmusculus_gene_vega"
>>       martUser            = ""
>>       path                = "/biomart/martservice"
>>       port                = "80"
>>       serverVirtualSchema = "default"
>>       visible             = "1"
>>     />
>> </MartRegistry>
>>
>>
>>



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