Changeset 84


Ignore:
Timestamp:
Jan 28, 2011, 4:45:13 PM (6 years ago)
Author:
kostas.karasavvas@…
Message:

updated test files for new generated output

File:
1 edited

Legend:

Unmodified
Added
Removed
  • galaxy-taverna/workflow-to-galaxy/test/Expected_BioAID_ProteinDiscovery_rb

    r75 r84  
    2626
    2727#
    28 # Sanitize single and double quotes in str. E.g. galaxy substitutes them to
    29 # __sq__ and __dq__ respectively. This methods turns them back to their
    30 # original values before using them
     28# Sanitize single quotes, double quotes, at symbol and newline in str. E.g. Galaxy
     29# substitutes them to __sq__, __dq__, __at__ and __cr____cn__ respectively. This
     30# methods turns them back to their original values before using them (i.e.
     31# sending them to the taverna server
    3132#
    3233def sanitize(string)
    33   string.gsub(/(__sq__|__dq__|__at__)/) do
     34  string.gsub(/(__sq__|__dq__|__at__|__cr____cn__)/) do
    3435    if $1 == '__sq__'
    3536      "'"
    3637    elsif $1 == '__dq__'
    3738      '\"'
     39    elsif $1 == '__cr____cn__'
     40      '
'
    3841    else
    3942      '@'
     
    4144  end
    4245end
     46
     47#
     48# Deletes last new line of file if it exists! It is needed for t2 workflows that
     49# do not sanitize properly, i.e. via a user-provided beanshell script
     50#
     51def chomp_last_newline(file)
     52
     53  if File.file?(file) and File.size(file) > 1
     54    f = open(file, "rb+")
     55    f.seek(-1, File::SEEK_END)
     56    f.truncate(File.size(file) - 1) if f.read(1) == "\n"
     57    f.close
     58  end
     59
     60end
     61
    4362
    4463
     
    6079Query_tmp = ARGV[1].chomp
    6180if Query_from_history == "true"
     81  chomp_last_newline(Query_tmp)
    6282  run.upload_input_file('Query', Query_tmp)
    6383else
     
    6787maxHits_parameter_tmp = ARGV[3].chomp
    6888if maxHits_parameter_from_history == "true"
     89  chomp_last_newline(maxHits_parameter_tmp)
    6990  run.upload_input_file('maxHits_parameter', maxHits_parameter_tmp)
    7091else
     
    7899# get output arguments and associated them with a file
    79100output4 = File.open(ARGV[4], "w")
    80 get_outputs(run, false, output4, 'ValidatedProtein')
     101begin
     102  get_outputs(run, false, output4, 'ValidatedProtein')
     103rescue Exception => err
     104  get_outputs(run, false, output4, 'ValidatedProtein.error')
     105end
    81106output5 = File.open(ARGV[5], "w")
    82 get_outputs(run, false, output5, 'UniProtID')
     107begin
     108  get_outputs(run, false, output5, 'UniProtID')
     109rescue Exception => err
     110  get_outputs(run, false, output5, 'UniProtID.error')
     111end
    83112
    84113# delete run
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