On 14/07/2010 15:46, Leandro Hermida wrote:
Hi again,
In the new BioMart 0.8 will the SOAP and REST APIs have:
- an option to return results in JSON or other serialized data structure form?
tentative yes for results request. For all other API call (meta data
calls), a definite yes. For the former, there is very little point to
e.g wrap 1000 bytes of gene ids in 20,000 bytes of JSON.
- an option to return results sorted by some attribute(s)?
no, thats a post processing option and tends to be very expensive as it
needs all results to be collected in the first place. we can make it
optional though. BioMart web interface would have this option for sure.
- an option to return results with LIMITs in full form i.e. start_row,
end_row (for paging)?
you will have limit as offset of zero. e.g you can retrieve, first 100,
first 1000, first 10000 and so on.
HTH,
Syed
best,
Leandro
On Wed, Jul 14, 2010 at 4:32 PM, Leandro Hermida
<[email protected]> wrote:
Hi Syed,
Since none of the BioMart APIs actually return results in a data
structure (it only returns formatted files like TSV, etc) I was trying
to be helpful and show other developers on this forum how they can go
about populating a Perl data structure from the results returned by
BioMart.
It's not obvious after reading the docs and when you get started how
you need to do this, one initially expects in the APIs that there
would be for e.g. in the Perl API some method call ->getResults()
which returns an @array of arrayrefs structure or in the REST API that
there would be an option to return for e.g. a JSON serialized data
structure that can be unserialized into a native data structure for
the language you are using.
best,
Leandro
On Wed, Jul 14, 2010 at 3:21 PM, Syed Haider<[email protected]> wrote:
Hi Leandro,
this is the only method that returns the results. What exactly are you after
?
Best
Syed
On 14/07/2010 13:14, Leandro Hermida wrote:
Sorry forgot to post what I did before! For those of your who use the
Biomart APIs and want to get results back into a Perl data structures,
here is the approach I use:
If using the Perl API:
use BioMart::Initializer;
use BioMart::Query;
use BioMart::QueryRunner;
my $bm_initializer = BioMart::Initializer->new(
registryFile => "/path/to/myRegistry.xml",
action => 'update',
);
my $bm_query = BioMart::Query->new(
registry => $bm_initializer->getRegistry(),
virtualSchemaName => 'default'
);
$bm_query->setDataset('my_dataset');
$bm_query->addFilter('attr1', ['Q6LTE1']);
$bm_query->addAttribute('attr2');
$bm_query->addAttribute('attr3');
$bm_query->formatter('TSV');
my $bm_query_runner=BioMart::QueryRunner->new();
$bm_query_runner->uniqueRowsOnly(1);
$bm_query_runner->execute($bm_query);
open(RESULTS, '+>', \my $results) or die "$!\n";
$bm_query_runner->printResults(\*RESULTS);
seek(RESULTS, 0, 0);
while (<RESULTS>) {
chomp;
my @row_fields = split /\t/;
# build up a data structure or processed your fields here...
}
close(RESULTS);
Using the REST API:
use LWP::UserAgent ();
my $query_xml =<<XML;
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName="default" formatter="TSV" header="0"
uniqueRows="1" count="" datasetConfigVersion="0.7">
<Dataset name="my_dataset" interface="default">
<Filter name="attr1" value="Q6LTE1"/>
<Attribute name="attr2" />
<Attribute name="attr3" />
</Dataset>
</Query>
XML
my $ua = LWP::UserAgent->new();
my $response =
$ua->post('http://myserver.mydomain:9002/biomart/martservice',
[ query => $query_xml ]);
if ($response->is_success and $response->decoded_content !~
/BioMart::Exception/i) {
open(RESULTS, '<', \$response->decoded_content) or die "$!\n";
while (<RESULTS>) {
chomp;
my @row_fields = split /\t/;
# build up a data structure or processed your fields here...
}
close(RESULTS);
}
else {
die $response->decoded_content, "\n";
}
On Thu, Jun 10, 2010 at 12:03 AM, Syed Haider<[email protected]>
wrote:
Hi Leandro,
The datastructures representation of results is not returned by the API.
If
you are feeling adventurous please feel free to look into the
lib/BioMart/Formatter/ directory for the appropriate formatter that you
are
interested in.
Best
Syed
On 09/06/2010 17:51, Leandro Hermida wrote:
Hi,
I was wondering if there is a way using the Perl API to get results in a
Perl data structure and, if possible, row by row. For example each row
returned as an array or arrayref. It seems inefficient to take
printResults() and have to break everything up again when I know
somewhere
in the Perl API it was doing the reverse...
thanks,
Leandro
