Changeset 81


Ignore:
Timestamp:
Jan 28, 2011, 2:23:01 PM (6 years ago)
Author:
kostas.karasavvas@…
Message:

v0.2.2 -- allows multi-line input in Galaxy and properly sanitises Galaxy's newline (crcn) to \n before sending to the taverna server

Location:
galaxy-taverna/workflow-to-galaxy
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • galaxy-taverna/workflow-to-galaxy/Rakefile

    r79 r81  
    1313spec = Gem::Specification.new do |s|
    1414  s.name = 'workflow-to-galaxy'
    15   s.version = '0.2.1'
     15  s.version = '0.2.2'
    1616  s.has_rdoc = true
    1717  s.extra_rdoc_files = ['README', 'LICENSE']
  • galaxy-taverna/workflow-to-galaxy/lib/workflow-to-galaxy/generator.rb

    r80 r81  
    5050        out.write indent(3) + "</when>\n"
    5151        out.write indent(3) + "<when value=\"textfield\">\n"
    52         out.write indent(4) + "<param name=\"textfield_#{i.name}\" type=\"text\" size=\"30\" "
     52        out.write indent(4) + "<param name=\"textfield_#{i.name}\" type=\"text\" area=\"True\" size=\"2x50\" "
    5353        if i.examples.size >= 1
    54           # escape double quotes characters for galaxy's xml file
     54          # escape double quotes characters and add <BR> for newlines for galaxy's xml file
    5555          ex = i.examples[0].to_s.gsub('"', '&quot;')
     56          # convert newlines to HTML newlines to display in textareas inputs
     57          ex = ex.gsub(/[\n]/, '&#xA;')
    5658          out.write "value=\"#{ex}\" "         
    5759        end
     
    151153              "before running it via Galaxy.\n\n"
    152154
     155    out.write "-----\n\n"
     156    out.write ".. class:: warningmark\n\n"
     157    out.write "**Please note that there might be some repetitions in the workflow description** " <<
     158              "in some of the generated workflows. This is due to a backwards compatibility " <<
     159              "issue on the myExperiment repository which keeps the old descriptions to make " <<
     160              "sure that no information is lost.\n\n"
    153161
    154162    out.write "-----\n\n"
     
    197205
    198206#
    199 # Sanitize single and double quotes in str. E.g. galaxy substitutes them to
    200 # __sq__ and __dq__ respectively. This methods turns them back to their
    201 # original values before using them
     207# Sanitize single quotes, double quotes, at symbol and newline in str. E.g. Galaxy
     208# substitutes them to __sq__, __dq__, __at__ and __cr____cn__ respectively. This
     209# methods turns them back to their original values before using them (i.e.
     210# sending them to the taverna server
    202211#
    203212def sanitize(string)
    204   string.gsub(/(__sq__|__dq__|__at__)/) do
     213  string.gsub(/(__sq__|__dq__|__at__|__cr____cn__)/) do
    205214    if $1 == '__sq__'
    206215      "'"
    207216    elsif $1 == '__dq__'
    208217      '\\\"'
     218    elsif $1 == '__cr____cn__'
     219      '\n'
    209220    else
    210221      '@'
Note: See TracChangeset for help on using the changeset viewer.