Class: Ms::Mascot::Export

Inherits:
Tap::Http::Submit
  • Object
show all
Defined in:
lib/ms/mascot/export.rb

Overview

:startdoc::manifest exports results from a search

Constant Summary collapse

DEFAULT_URI =

The MatrixScience public search site

"http://www.matrixscience.com/cgi/export_dat_2.pl"
DEFAULT_PARAMS =

Parameters for a typical export

{
  "pep_expect"=>"1",
  "prot_mass"=>"1",
  "protein_master"=>"1",
  "_server_mudpit_switch"=>"0.000000001",
  "pep_exp_mz"=>"1",
  "do_export"=>"1",
  "pep_delta"=>"1",
  "export_format"=>"XML",
  "prot_acc"=>"1",
  "pep_score"=>"1",
  "show_format"=>"1",
  "_showsubsets"=>"0",
  "_show_decoy_report"=>"",
  "pep_scan_title"=>"1",
  "pep_miss"=>"1",
  "pep_calc_mr"=>"1",
  "pep_exp_mr"=>"1",
  "prot_score"=>"1",
  "pep_query"=>"1",
  "peptide_master"=>"1",
  "prot_matches"=>"1",
  "_onlyerrortolerant"=>"",
  "_showallfromerrortolerant"=>"",
  "prot_hit_num"=>"1",
  "search_master"=>"1",
  "_sigthreshold"=>"0.05",
  "show_params"=>"1",
  "show_mods"=>"1",
  "show_header"=>"1",
  "pep_isbold"=>"1",
  "pep_seq"=>"1",
  "pep_exp_z"=>"1",
  "prot_desc"=>"1",
  "_ignoreionsscorebelow"=>"0",
  "REPORT"=>"AUTO",
  "pep_rank"=>"1",
  "pep_var_mod"=>"1",
  "_noerrortolerant"=>""
}
DEFAULT_HEADERS =

Typical headers for an export

{
  "Keep-Alive"=>"300",
  "Accept-Encoding"=>"gzip,deflate",
  "Accept-Language"=>"en-us,en;q=0.5",
  "Content-Type"=> "multipart/form-data; boundary=---------------------------168072824752491622650073",
  "Accept-Charset"=>"ISO-8859-1,utf-8;q=0.7,*;q=0.7",
  "Accept"=>"text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8",
  "Connection"=>"keep-alive"
}

Instance Method Summary collapse

Instance Method Details

#process(result_filepath) ⇒ Object 



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# File 'lib/ms/mascot/export.rb', line 71

def process(result_filepath)
  # duplicate the configurations
  request = {}
  config.each_pair do |key, value|
    request[key] = value.kind_of?(Hash) ? value.dup : value
  end
  
  # set filename for export
  request[:params]['file'] = result_filepath
  
  super(request)
end