Hi Leandro,
I was just trying to understand the use case, i got it. The reason we
have the webservice and Perl returning similar string like datastructure
is to aim for a coherent results structure across all API end-points. I
agree there are several ways to publishing the results in other formats
e.g arrays, hashes, JSON etc that offers great interoperability with
various languages. Your suggestions are very valuable and have been
taken on board for the ongoing new libraries, where we intend to offer
these as extensions.
thanks
Syed
On 14/07/2010 15:32, Leandro Hermida 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
