cravat.us web services, unable to understand what to do

[dokadya]

I am following this website to get help regarding connection to cravat.us

with this website I have to connect so that I can submit job without opening my browser. in this website I am looking for web services section.

http://www.cravat.us/help.jsp?chapter=how_to_cite&article=

See the Image to understand the instructions :

https://drive.google.com/file/d/0B6DXP2pIxiX7R01JbmZtQ2RoMlk/edit?usp=sharing

They said create JSON object and all, I have create JSON object:

{
"analysis": "CHASM",
"analysistype" : "driver",
"chasmclassifier" : "Head and Neck",
"email" : "[email protected]"
"functionalannotation" : "on",
"hg18" : "off",
"inputfile" : "/media/storage1/SAMPLE_NAME_1.cravat",
"mupitinput" : "on",
"tsvreport" : "on"
}



How can i upload file ? Can I use just path to upload ?

What kind of script I have to write ? HTML form? PERL ?



See the link for my perl file:

https://drive.google.com/file/d/0B6DXP2pIxiX7eF9tWTZ5VDBoTzg/edit?usp=sharing

Like this I have created file but its not working. Please guide me.



Waiting for positive reply.

Thank You.

Chetan

[dokadya]

this is same question as explained in biostars.org
https://www.biostars.org/p/99365/

[slcrick]

Hi, this is Rick from In Silico Solutions, which maintains CRAVAT. Please see the following examples in Perl:

use LWP;
use URI;

my $browser = LWP::UserAgent->new();

#
# Job submission example, when the mutations are in a string
#
print "\n###### Submitting through GET #####\n";
my $urlSubmitGet = URI->new("http://www.cravat.us/rest/service/submit");
$urlSubmitGet->query_form(
'analyses' => 'CHASM',
'analysistype' => 'driver',
'chasmclassifier' => 'Ovary',
'email' => '[email protected]',
'functionalannotation' => 'off',
'hg18' => 'off',
'mutations' => 'TR1 chr22 30421786 + A T',
'mupitinput' => 'off',
'tsvreport' => 'off');
my $responseSubmitGet = $browser->get($urlSubmitGet);
print $responseSubmitGet->content, "\n";

#
# Job submission example, when the mutations are in a file
#
print "\n###### Submitting through POST #####\n";
my $urlSubmitPost = "http://www.cravat.us/rest/service/submit";
my $responseSubmitPost = $browser->post($urlSubmitPost,
Content_Type => 'form-data',
Content => [
'analyses' => 'CHASM',
'analysistype' => 'driver',
'chasmclassifier' => 'Ovary',
'email' => '[email protected]',
'functionalannotation' => 'off',
'hg18' => 'off',
'mupitinput' => 'off',
'tsvreport' => 'off',
'inputfile' => ['/home/testUser/mutations.txt']]);
print $responseSubmitPost->content, "\n";

#
# Job status checking example
#
print "##### Job Status Checking #####\n";
my $urlStatus = URI->new('http://www.cravat.us/rest/service/status');
$urlStatus->query_form('jobid' => 'testUser_20140430_110005');
my $responseStatus = $browser->get($urlStatus);
print $responseStatus->content, "\n";

Hope this helps and if you have any question, please let me know.