Class: Ms::Mascot::Submit

Inherits:
Tap::Mechanize::Request
  • Object
show all
Includes:
Validation
Defined in:
lib/ms/mascot/submit.rb

Overview

:startdoc::task submits a PMF or MS/MS search to Mascot

Submits a search request to Mascot using the mgf file and the search parameters in a static config file. Correctly formatting search config file is technical since it must contain the correct fields for Submit to recreate a Mascot HTTP search request.

The easiest way to capture search parameters in the correct format is to use TapHttpFrom the command line, invoke:

% tap server

Then visit ‘localhost:8080/capture/tutorial’ in a browser and apply the capture procedure to the Mascot search page. Once you have the .yml config file, use this command to submit a search.

% rap submit <mgf_file> --config <config_file> --: dump

A convenient aspect of this setup is that you can capure parameters once, then re-use them for a number of mgf files.

Note that the default Submit configuration uses parameters are typical for MS/MS searching of a human sample digested with trypsin. These values MUST be overridden and are only provided as a template (for those that want the adventure of manually making a config file).

Constant Summary collapse

SUCCESS_REGEXP =

Matches a successful search response. After the match:

$1:: the result file

/<A HREF="\.\.\/cgi\/master_results\.pl\?file=(.*?)">Click here to see Search Report<\/A>/
FAILURE_REGEXP =

Matches a failure response. After the match:

$1:: the failure message

/<BR>(.*)/m

Constants included from Validation

Validation::MASCOT_SWITCH

Instance Method Summary collapse

Instance Method Details

#parse_response_body(body) ⇒ Object

Processes the response body. Returns the result file if the body indicates a success, or nil if the body indicates a failure.



102
103
104
105
106
107
108
109
110
111
112
113
 
# File 'lib/ms/mascot/submit.rb', line 102

def parse_response_body(body)
  case body
  when SUCCESS_REGEXP
    log :success, $1
    $1
  when FAILURE_REGEXP 
    log :failure, $1.gsub("<BR>", "\n")
    nil
  else 
    raise "unparseable response: #{body}"
  end
end

#process(mgf_file) ⇒ Object 



83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
 
# File 'lib/ms/mascot/submit.rb', line 83

def process(mgf_file)
  File.open(mgf_file) do |io|
    # set filename for upload
    params = config[:params].to_hash
    params['FILE'] = io
  
    # submit request
    page = super(
      :request_method => 'POST',
      :uri => uri,
      :params => params
    )
    
    parse_response_body(page.body)
  end
end