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

    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.







    See the Image to understand the instructions :





    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:





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



    Waiting for positive reply.

    Thank You.

    Chetan

  • #2
    this is same question as explained in biostars.org

    Comment


    • #3
      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.

      Comment

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