[BioC] too many biomaRt connections

[Steffen]

Hi Kasper,

That's correct.  biomaRt is made to do batch queries and users should 
try to avoid using it in loops.

Cheers,
Steffen

Kasper Daniel Hansen wrote:
> Steffen will know more about this, but it is well known that when you  
> access the Mart servers that you should collect all your queries into  
> one big query, so not do something like
>    for ( g in genes)
>      getInfo(g)
> but instead do something like
>    getInfo(genes)
>
> So try to collect everything into a few big queries, instead of doing  
> "thousands of queries" in a day.
>
> You also have the option of downloading the entire database and access  
> it locally. That way there is no limit, but it requires some work
>
> It is not uncommon for these large databases to have some usage limits.
>
> Kasper
>
> On Apr 9, 2008, at 12:09 PM, Elizabeth Purdom wrote:
>
>   
>> Hi,
>> I am using biomaRt to get information regarding genes. I use it pretty
>> frequently and recently have gotten the error:
>>
>> Too many connections at
>> /ebi/www/biomart/www/biomart-perl-06/lib/BioMart/Configuration/ 
>> DBLocation.pm
>> line 98
>>
>> I assume that I've hit some sort of wall in terms of how often I have
>> queried the database?
>>
>> I don't really use biomart except through R; at what point do you get
>> booted off and what can I do to regain access? I often run queries  
>> on a
>> few hundred genes and don't think twice about rerunning such a query  
>> or
>> running several such queries in a day plus I use functions that call  
>> on
>> biomaRt repeatedly that I also apply to around 100 genes. So I could
>> easily send a thousand queries in a day. I can be more careful, but it
>> would be useful to know what the limits are. And does it matter how  
>> many
>> times you call a 'mart<-useMart(...)' command? (lately, I've been
>> calling it frequently rather than using the one I've already opened,
>> largely through programming laziness).
>>
>> By the way, it took me quite some time to track down the error,  
>> because
>> I was using getGene which just gave me the confusing error:
>> "Error: ncol(result) == length(attributes) is not TRUE"
>> I think this must be because something like try(...) is used within
>> getBM() and so the output is the error message which is then  
>> transferred
>> down the line and at some point causes a problem when the function  
>> tries
>> to bundle it into a data.frame, etc.
>>
>> Thanks,
>> Elizabeth
>>
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>
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