workflow-to-galaxy 0.2.7
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- data/CHANGES +6 -0
- data/LICENSE +23 -0
- data/README +60 -0
- data/Rakefile +54 -0
- data/bin/workflow_to_galaxy.rb +110 -0
- data/doc/rdoc/classes/Generator.html +215 -0
- data/doc/rdoc/classes/WorkflowToGalaxy.html +105 -0
- data/doc/rdoc/created.rid +1 -0
- data/doc/rdoc/files/LICENSE.html +133 -0
- data/doc/rdoc/files/README.html +192 -0
- data/doc/rdoc/files/lib/workflow-to-galaxy/generator_rb.html +108 -0
- data/doc/rdoc/files/lib/workflow-to-galaxy_rb.html +108 -0
- data/doc/rdoc/fr_class_index.html +28 -0
- data/doc/rdoc/fr_file_index.html +30 -0
- data/doc/rdoc/fr_method_index.html +28 -0
- data/doc/rdoc/index.html +24 -0
- data/doc/rdoc/rdoc-style.css +208 -0
- data/lib/workflow-to-galaxy.rb +5 -0
- data/lib/workflow-to-galaxy/generator.rb +497 -0
- metadata +132 -0
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// ]]>
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<div id="fileHeader">
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<h1>workflow-to-galaxy.rb</h1>
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<table class="header-table">
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<tr class="top-aligned-row">
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<td><strong>Path:</strong></td>
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<td>lib/workflow-to-galaxy.rb
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</td>
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</tr>
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<tr class="top-aligned-row">
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<td><strong>Last Update:</strong></td>
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<td>Mon Dec 13 15:22:40 +0100 2010</td>
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<h3 class="section-bar">Required files</h3>
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<div class="name-list">
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workflow-to-galaxy/generator
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</div>
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</div>
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<div id="validator-badges">
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<p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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<title>Classes</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<div id="index-entries">
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<a href="classes/Generator.html">Generator</a><br />
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<a href="classes/WorkflowToGalaxy.html">WorkflowToGalaxy</a><br />
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</div>
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Files
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<title>Files</title>
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<h1 class="section-bar">Files</h1>
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<div id="index-entries">
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<a href="files/LICENSE.html">LICENSE</a><br />
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<a href="files/README.html">README</a><br />
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<a href="files/lib/workflow-to-galaxy_rb.html">lib/workflow-to-galaxy.rb</a><br />
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<a href="files/lib/workflow-to-galaxy/generator_rb.html">lib/workflow-to-galaxy/generator.rb</a><br />
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<title>Methods</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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<link rel="stylesheet" href="rdoc-style.css" type="text/css" />
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<body>
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<div id="index">
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<h1 class="section-bar">Methods</h1>
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<div id="index-entries">
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<a href="classes/Generator.html#M000002">generate_script (Generator)</a><br />
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<a href="classes/Generator.html#M000001">generate_xml (Generator)</a><br />
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</div>
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data/doc/rdoc/index.html
ADDED
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<!DOCTYPE html
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<!--
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workflow-to-galaxy Docs
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-->
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<title>workflow-to-galaxy Docs</title>
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<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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</head>
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<frame src="fr_method_index.html" name="Methods" />
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</html>
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body {
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font-size: 90%;
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margin: 0;
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margin-left: 40px;
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padding: 0;
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background: white;
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}
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h1,h2,h3,h4 { margin: 0; color: #efefef; background: transparent; }
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h1 { font-size: 150%; }
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a { background: #eef; color: #039; text-decoration: none; }
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text-decoration: none;
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}
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/* === Structural elements =================================== */
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div#index {
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margin: 0;
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margin-left: -40px;
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padding: 0;
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font-size: 90%;
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div#index a {
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div#classHeader, div#fileHeader {
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margin: 0;
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margin-left: -40px;
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div#bodyContent {
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div#description {
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/* --- Source code sections -------------------- */
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div.method-source-code pre { color: #ffdead; overflow: hidden; }
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/* --- Ruby keyword styles --------------------- */
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.standalone-code { background: #221111; color: #ffdead; overflow: hidden; }
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.ruby-comment { color: #b22222; font-weight: bold; background: transparent; }
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.ruby-regexp { color: #ffa07a; background: transparent; }
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.ruby-value { color: #7fffd4; background: transparent; }
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@@ -0,0 +1,497 @@
|
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1
|
+
#
|
|
2
|
+
# The Generator module contains two public methods that generate a Galaxy's tool
|
|
3
|
+
# XML and script files
|
|
4
|
+
#
|
|
5
|
+
module Generator
|
|
6
|
+
|
|
7
|
+
# private methods
|
|
8
|
+
private
|
|
9
|
+
|
|
10
|
+
# Used to create indentation when generating code
|
|
11
|
+
def indent(n)
|
|
12
|
+
ind = ""
|
|
13
|
+
n.times { ind += " " }
|
|
14
|
+
ind
|
|
15
|
+
end
|
|
16
|
+
|
|
17
|
+
# Galaxy's XML tool tag
|
|
18
|
+
def tool_begin_tag(out, name)
|
|
19
|
+
out.write("<tool id=\"#{name}_id\" name=\"#{name}\">\n")
|
|
20
|
+
end
|
|
21
|
+
|
|
22
|
+
# Galaxy's XML command tag
|
|
23
|
+
def command_tag(out, t2_workflow, script)
|
|
24
|
+
out.write indent(1) + "<command interpreter=\"ruby\">\n"
|
|
25
|
+
out.write indent(2) + script + "\n"
|
|
26
|
+
|
|
27
|
+
# inputs
|
|
28
|
+
t2_workflow.inputs.each do |i|
|
|
29
|
+
out.write indent(2) + "#if $#{i.name}_source.history_or_textfield == \"textfield\":\n"
|
|
30
|
+
out.write indent(3) + "false \"$#{i.name}_source.textfield_#{i.name}\"\n"
|
|
31
|
+
out.write indent(2) + "#else:\n"
|
|
32
|
+
out.write indent(3) + "true \"$#{i.name}_source.history_#{i.name}\"\n"
|
|
33
|
+
out.write indent(2) + "#end if\n"
|
|
34
|
+
end
|
|
35
|
+
|
|
36
|
+
# results as zip input
|
|
37
|
+
out.write indent(2) + "$results_as_zip\n"
|
|
38
|
+
|
|
39
|
+
# outputs
|
|
40
|
+
out.write indent(2)
|
|
41
|
+
t2_workflow.outputs.each do |o|
|
|
42
|
+
out.write "$#{o.name} "
|
|
43
|
+
end
|
|
44
|
+
|
|
45
|
+
# result zip output
|
|
46
|
+
out.write "$result_zip\n"
|
|
47
|
+
|
|
48
|
+
out.write indent(1) + "</command>\n"
|
|
49
|
+
end
|
|
50
|
+
|
|
51
|
+
|
|
52
|
+
# Galaxy's XML inputs tag
|
|
53
|
+
def inputs_tag(out, inputs)
|
|
54
|
+
out.write indent(1) + "<inputs>\n"
|
|
55
|
+
if inputs.size >= 1
|
|
56
|
+
inputs.each do |i|
|
|
57
|
+
out.write indent(2) + "<conditional name=\"#{i.name}_source\">\n"
|
|
58
|
+
out.write indent(3) + "<param name=\"history_or_textfield\" type=\"select\" label=\"Select source for #{i.name}\">\n"
|
|
59
|
+
out.write indent(4) + "<option value=\"history\">From history</option>\n"
|
|
60
|
+
out.write indent(4) + "<option value=\"textfield\" selected=\"true\">Type manually</option>\n"
|
|
61
|
+
out.write indent(3) + "</param>\n"
|
|
62
|
+
out.write indent(3) + "<when value=\"history\">\n"
|
|
63
|
+
out.write indent(4) + "<param name=\"history_#{i.name}\" type=\"data\" label=\"Select #{i.name}\"/>\n"
|
|
64
|
+
out.write indent(3) + "</when>\n"
|
|
65
|
+
out.write indent(3) + "<when value=\"textfield\">\n"
|
|
66
|
+
out.write indent(4) + "<param name=\"textfield_#{i.name}\" type=\"text\" area=\"True\" size=\"2x50\" "
|
|
67
|
+
if i.examples.size >= 1
|
|
68
|
+
# escape double quotes characters for galaxy's xml file
|
|
69
|
+
ex = i.examples[0].to_s.gsub('"', '"')
|
|
70
|
+
# convert newlines to HTML newlines to display in textareas inputs
|
|
71
|
+
ex = ex.gsub(/[\n]/, '
')
|
|
72
|
+
out.write "value=\"#{ex}\" "
|
|
73
|
+
end
|
|
74
|
+
out.write "label=\"Enter #{i.name}\"/>\n"
|
|
75
|
+
out.write indent(3) + "</when>\n"
|
|
76
|
+
out.write indent(2) + "</conditional>\n"
|
|
77
|
+
end
|
|
78
|
+
else
|
|
79
|
+
out.write indent(2) + "<param name=\"input\" type=\"select\" display=\"radio\" size=\"250\" label=\"This workflow has no inputs\" />\n"
|
|
80
|
+
end
|
|
81
|
+
|
|
82
|
+
# result as zip input
|
|
83
|
+
out.write indent(2) + "<param name=\"results_as_zip\" type=\"select\" label=\"Would you also like the raw results as a zip file\">\n"
|
|
84
|
+
out.write indent(3) + "<option value=\"yes\">Yes</option>\n"
|
|
85
|
+
out.write indent(3) + "<option value=\"no\" selected=\"true\">No</option>\n"
|
|
86
|
+
out.write indent(2) + "</param>\n"
|
|
87
|
+
|
|
88
|
+
out.write indent(1) + "</inputs>\n"
|
|
89
|
+
end
|
|
90
|
+
|
|
91
|
+
# Galaxy's XML outputs tag
|
|
92
|
+
def outputs_tag(out, outputs)
|
|
93
|
+
out.write indent(1) + "<outputs>\n"
|
|
94
|
+
outputs.each do |o|
|
|
95
|
+
out.write indent(2) + "<data format=\"tabular\" name=\"#{o.name}\" label=\"#{o.name}\"/>\n"
|
|
96
|
+
end
|
|
97
|
+
|
|
98
|
+
# result zip output
|
|
99
|
+
out.write indent(2) + "<data format=\"zip\" name=\"result_zip\" label=\"Compressed Results (zip)\">\n"
|
|
100
|
+
out.write indent(3) + "<filter>results_as_zip == \"yes\"</filter>\n"
|
|
101
|
+
out.write indent(2) + "</data>\n"
|
|
102
|
+
|
|
103
|
+
out.write indent(1) + "</outputs>\n"
|
|
104
|
+
end
|
|
105
|
+
|
|
106
|
+
# Galaxy's XML help tag
|
|
107
|
+
def help_tag(out, t2_workflow)
|
|
108
|
+
out.write indent(1) + "<help>\n"
|
|
109
|
+
out.write "**What it does**\n\n"
|
|
110
|
+
|
|
111
|
+
description = t2_workflow.description + "\n\n"
|
|
112
|
+
|
|
113
|
+
# Sometimes the workflow description contains HTML tags that are not allowed
|
|
114
|
+
# in Galaxy's xml interface specification and thus are removed! Same for
|
|
115
|
+
# HTML entities!
|
|
116
|
+
# TODO go through tags and find Galaxy's equivalent to include
|
|
117
|
+
description.gsub!(/<.*?>|&.*?;/, '')
|
|
118
|
+
|
|
119
|
+
# To remove ^M (cntl-v + cntl-m) characters that DOS files might have
|
|
120
|
+
description.gsub!(/\r/, '')
|
|
121
|
+
|
|
122
|
+
# TODO that works as a literal too but font changes to courier!
|
|
123
|
+
#out.write "::\n\n" # Start Galaxy's literal block to ignore indendation
|
|
124
|
+
|
|
125
|
+
# remove indendation from all description lines since Galaxy is confused by it
|
|
126
|
+
description.split(/[\n]/).each { |l| out.write "#{l.gsub(/^\s+/, '')}\n" }
|
|
127
|
+
|
|
128
|
+
# endline makes the following be parsed as a Galaxy GUI construct
|
|
129
|
+
out.write "\n"
|
|
130
|
+
|
|
131
|
+
# if at least one input add it to tool's UI help description
|
|
132
|
+
if t2_workflow.inputs.size >= 1
|
|
133
|
+
out.write "-----\n\n"
|
|
134
|
+
out.write "**Inputs**\n\n"
|
|
135
|
+
t2_workflow.inputs.each do |i|
|
|
136
|
+
out.write "- **#{i.name}** "
|
|
137
|
+
if i.descriptions.size >= 1
|
|
138
|
+
i.descriptions.each do |desc|
|
|
139
|
+
out.write desc.to_s + " "
|
|
140
|
+
end
|
|
141
|
+
end
|
|
142
|
+
if i.examples.size >= 1
|
|
143
|
+
out.write "Examples include:\n\n"
|
|
144
|
+
i.examples.each do |ex|
|
|
145
|
+
# some examples have a newline between them that breaks Galaxy's GUI
|
|
146
|
+
# so we substitute it with ' '
|
|
147
|
+
#out.write " - " + ex.to_s.gsub(/[\n]/, ' ') + "\n"
|
|
148
|
+
|
|
149
|
+
# We could substitute them with with 
 that works for HTML (e.g. wkf 1180)
|
|
150
|
+
# But if an example input is truly multiline then input descr. will
|
|
151
|
+
# display them all as separate inputs...
|
|
152
|
+
out.write " - " + ex.to_s.gsub(/[\n]/, '
 - ') + "\n"
|
|
153
|
+
|
|
154
|
+
# display example inputs as verbatim/literal so it is not our responsibility!!
|
|
155
|
+
# add indendation after each newline to specify the literal block
|
|
156
|
+
# TODO this looks ugly if we don't remove all the bullet points!
|
|
157
|
+
#out.write "::\n\n " + ex.to_s.gsub(/\n/, '
 ') + "\n"
|
|
158
|
+
end
|
|
159
|
+
end
|
|
160
|
+
out.write "\n"
|
|
161
|
+
end
|
|
162
|
+
out.write "\n"
|
|
163
|
+
end
|
|
164
|
+
|
|
165
|
+
# if at least one output add it to tool's UI help description
|
|
166
|
+
if t2_workflow.outputs.size >= 1
|
|
167
|
+
out.write "-----\n\n"
|
|
168
|
+
out.write "**Outputs**\n\n"
|
|
169
|
+
t2_workflow.outputs.each do |o|
|
|
170
|
+
out.write "- **#{o.name}** "
|
|
171
|
+
if o.descriptions.size >= 1
|
|
172
|
+
o.descriptions.each do |desc|
|
|
173
|
+
out.write desc.to_s + " "
|
|
174
|
+
end
|
|
175
|
+
end
|
|
176
|
+
if o.examples.size >= 1
|
|
177
|
+
out.write "Examples include:\n\n"
|
|
178
|
+
o.examples.each do |ex|
|
|
179
|
+
out.write " - " + ex.to_s + "\n"
|
|
180
|
+
end
|
|
181
|
+
end
|
|
182
|
+
out.write "\n"
|
|
183
|
+
end
|
|
184
|
+
out.write "\n"
|
|
185
|
+
end
|
|
186
|
+
|
|
187
|
+
out.write "-----\n\n"
|
|
188
|
+
out.write ".. class:: warningmark\n\n"
|
|
189
|
+
out.write "**Please note that some workflows are not up-to-date or have dependencies** " <<
|
|
190
|
+
"that cannot be met by the specific Taverna server that you specified during " <<
|
|
191
|
+
"generation of this tool. You can make sure that the workflow is valid " <<
|
|
192
|
+
"by running it in the Taverna Workbench first to confirm that it works " <<
|
|
193
|
+
"before running it via Galaxy.\n\n"
|
|
194
|
+
|
|
195
|
+
if t2_workflow.input_type == TavernaWorkflow::MY_EXPERIMENT
|
|
196
|
+
out.write "-----\n\n"
|
|
197
|
+
out.write ".. class:: warningmark\n\n"
|
|
198
|
+
out.write "**Please note that there might be some repetitions in the workflow description** " <<
|
|
199
|
+
"in some of the generated workflows. This is due to a backwards compatibility " <<
|
|
200
|
+
"issue on the myExperiment repository which keeps the old descriptions to make " <<
|
|
201
|
+
"sure that no information is lost.\n\n"
|
|
202
|
+
|
|
203
|
+
out.write "-----\n\n"
|
|
204
|
+
out.write ".. class:: infomark\n\n"
|
|
205
|
+
out.write "**For more information on that workflow please visit** #{t2_workflow.xml_uri.gsub(/(.*workflows\/\d+)[\/.].*/, '\1')}.\n\n"
|
|
206
|
+
end
|
|
207
|
+
|
|
208
|
+
out.write indent(1) + "</help>\n"
|
|
209
|
+
end
|
|
210
|
+
|
|
211
|
+
# Galaxy's XML tool tag close
|
|
212
|
+
def tool_end_tag(out)
|
|
213
|
+
out.write("</tool>\n")
|
|
214
|
+
end
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215
|
+
|
|
216
|
+
|
|
217
|
+
|
|
218
|
+
# Galaxy's script preample
|
|
219
|
+
def script_preample(out)
|
|
220
|
+
out.write("#!/usr/bin/env ruby\n\n")
|
|
221
|
+
out.write("require 'rubygems'\n")
|
|
222
|
+
out.write("require 't2-server'\n")
|
|
223
|
+
out.write("require 'open-uri'\n")
|
|
224
|
+
out.write("require 'zip/zipfilesystem'\n\n")
|
|
225
|
+
end
|
|
226
|
+
|
|
227
|
+
|
|
228
|
+
# Galaxy's script utility methods
|
|
229
|
+
# TODO: use ruby's flatten instead of our own !!!
|
|
230
|
+
def script_util_methods(out)
|
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231
|
+
|
|
232
|
+
out.write <<'UTIL_METHODS'
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|
233
|
+
|
|
234
|
+
# sends the zip file to specified output
|
|
235
|
+
def output_zip_file(uuid, zip_out)
|
|
236
|
+
File.open("/tmp/#{uuid}.zip") do |zip|
|
|
237
|
+
while data = zip.read(4096)
|
|
238
|
+
zip_out.write data
|
|
239
|
+
end
|
|
240
|
+
end
|
|
241
|
+
File.delete("/tmp/#{uuid}.zip")
|
|
242
|
+
end
|
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243
|
+
|
|
244
|
+
|
|
245
|
+
#
|
|
246
|
+
# replicates the directory result structure as constructed by the
|
|
247
|
+
# taverna server and recreates it in a zip File
|
|
248
|
+
#
|
|
249
|
+
def add_to_zip_file(output_dir, data_lists, zip_out)
|
|
250
|
+
zip_out.dir.mkdir("#{output_dir}")
|
|
251
|
+
data_lists.each_with_index do |item, index|
|
|
252
|
+
if item.instance_of? Array
|
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253
|
+
add_to_zip_file("#{output_dir}/#{index+1}", item, zip_out)
|
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254
|
+
else
|
|
255
|
+
zip_out.file.open("#{output_dir}/#{index+1}", "w") { |f| f.puts item }
|
|
256
|
+
end
|
|
257
|
+
end
|
|
258
|
+
end
|
|
259
|
+
|
|
260
|
+
|
|
261
|
+
# method that flattens the list of list of list ... result of get_output
|
|
262
|
+
def print_flattened_result(out, data_lists)
|
|
263
|
+
data_lists.each do |l|
|
|
264
|
+
if l.instance_of? Array
|
|
265
|
+
print_flattened_result(out, l)
|
|
266
|
+
else
|
|
267
|
+
out.puts l
|
|
268
|
+
end
|
|
269
|
+
end
|
|
270
|
+
end
|
|
271
|
+
|
|
272
|
+
|
|
273
|
+
#
|
|
274
|
+
# Method that acquires all the results of the specified output directory.
|
|
275
|
+
# If valid zip File is passed it also accumulates results as a zip file.
|
|
276
|
+
#
|
|
277
|
+
def get_outputs(run, refs, outfile, dir, zip_out=nil)
|
|
278
|
+
data_lists = run.get_output(dir, refs)
|
|
279
|
+
print_flattened_result(outfile, data_lists)
|
|
280
|
+
if zip_out
|
|
281
|
+
add_to_zip_file(dir, data_lists, zip_out)
|
|
282
|
+
end
|
|
283
|
+
end
|
|
284
|
+
|
|
285
|
+
|
|
286
|
+
#
|
|
287
|
+
# Sanitize all special characters in UI inputs that Galaxy substitutes for
|
|
288
|
+
# security reasons. This methods turns them back to their original values before
|
|
289
|
+
# using them (i.e. sending them to the taverna server
|
|
290
|
+
# NB: note that double quote is sanitized to "'" that is because the double code
|
|
291
|
+
# confuses the Taverna server ruby library. Apparently, this is not trivial
|
|
292
|
+
# to fix.
|
|
293
|
+
#
|
|
294
|
+
def sanitize(string)
|
|
295
|
+
string.gsub(/(__sq__|__dq__|__at__|__cr__|__cn__|__tc__|__gt__|__lt__|__ob__|__cb__|__oc__|__cc__)/) do
|
|
296
|
+
if $1 == '__sq__'
|
|
297
|
+
"'"
|
|
298
|
+
elsif $1 == '__dq__'
|
|
299
|
+
"'"
|
|
300
|
+
elsif $1 == '__cr__'
|
|
301
|
+
"\r"
|
|
302
|
+
elsif $1 == '__cn__'
|
|
303
|
+
"\n"
|
|
304
|
+
elsif $1 == '__tc__'
|
|
305
|
+
"\t"
|
|
306
|
+
elsif $1 == '__gt__'
|
|
307
|
+
'>'
|
|
308
|
+
elsif $1 == '__lt__'
|
|
309
|
+
'<'
|
|
310
|
+
elsif $1 == '__ob__'
|
|
311
|
+
'['
|
|
312
|
+
elsif $1 == '__cb__'
|
|
313
|
+
']'
|
|
314
|
+
elsif $1 == '__oc__'
|
|
315
|
+
'{'
|
|
316
|
+
elsif $1 == '__cc__'
|
|
317
|
+
'}'
|
|
318
|
+
else
|
|
319
|
+
'@'
|
|
320
|
+
end
|
|
321
|
+
end
|
|
322
|
+
end
|
|
323
|
+
|
|
324
|
+
#
|
|
325
|
+
# Deletes last new line of file if it exists! It is needed for t2 workflows that
|
|
326
|
+
# do not sanitize properly, i.e. via a user-provided beanshell script
|
|
327
|
+
#
|
|
328
|
+
def chomp_last_newline(file)
|
|
329
|
+
|
|
330
|
+
if File.file?(file) and File.size(file) > 1
|
|
331
|
+
f = open(file, "rb+")
|
|
332
|
+
f.seek(-1, File::SEEK_END)
|
|
333
|
+
f.truncate(File.size(file) - 1) if f.read(1) == "\n"
|
|
334
|
+
f.close
|
|
335
|
+
end
|
|
336
|
+
|
|
337
|
+
end
|
|
338
|
+
|
|
339
|
+
|
|
340
|
+
UTIL_METHODS
|
|
341
|
+
|
|
342
|
+
end
|
|
343
|
+
|
|
344
|
+
# Galaxy's script taverna 2 run
|
|
345
|
+
def script_create_t2_run(out, wkf, t2_uri)
|
|
346
|
+
if wkf.input_type == TavernaWorkflow::MY_EXPERIMENT
|
|
347
|
+
out.write "# use the uri reference to download the workflow locally\n"
|
|
348
|
+
out.write "wkf_file = URI.parse('#{wkf.xml_uri}')\n"
|
|
349
|
+
out.write "in_wkf = open(wkf_file)\n"
|
|
350
|
+
else # TavernaWorkflow::T2_FLOW
|
|
351
|
+
out.write "# uri contains local t2flow file\n"
|
|
352
|
+
out.write "in_wkf = open('#{wkf.xml_uri}')\n"
|
|
353
|
+
end
|
|
354
|
+
|
|
355
|
+
out.write <<CREATE_T2_RUN
|
|
356
|
+
|
|
357
|
+
wkf = in_wkf.read()
|
|
358
|
+
|
|
359
|
+
# create run
|
|
360
|
+
begin
|
|
361
|
+
run = T2Server::Run.create('#{t2_uri}', wkf)
|
|
362
|
+
rescue T2Server::T2ServerError => e
|
|
363
|
+
exit 1
|
|
364
|
+
end
|
|
365
|
+
|
|
366
|
+
CREATE_T2_RUN
|
|
367
|
+
|
|
368
|
+
end
|
|
369
|
+
|
|
370
|
+
|
|
371
|
+
# Galaxy's script input handling
|
|
372
|
+
def script_init_inputs(out, t2_workflow)
|
|
373
|
+
out.write "#\n"
|
|
374
|
+
out.write "# Get input arguments -- for each input a boolean specifies if it's from history\n"
|
|
375
|
+
out.write "# thus, for each t2_workflow input we have two arguments in the script!\n"
|
|
376
|
+
out.write "#\n"
|
|
377
|
+
t2_workflow.inputs.each_with_index do |input, i|
|
|
378
|
+
i_name = input.name.to_s
|
|
379
|
+
out.write "#{i_name}_from_history = ARGV[#{i*2}].chomp\n"
|
|
380
|
+
out.write "#{i_name}_tmp = ARGV[#{i*2+1}].chomp\n"
|
|
381
|
+
out.write "if #{i_name}_from_history == \"true\"\n"
|
|
382
|
+
out.write " chomp_last_newline(#{i_name}_tmp)\n"
|
|
383
|
+
out.write " run.upload_input_file('#{i_name}', #{i_name}_tmp)\n"
|
|
384
|
+
out.write "else\n"
|
|
385
|
+
out.write " run.set_input('#{i_name}', sanitize(#{i_name}_tmp))\n"
|
|
386
|
+
out.write "end\n"
|
|
387
|
+
end
|
|
388
|
+
|
|
389
|
+
# add code to handle results_as_zip input, i.e. create zip file
|
|
390
|
+
out.write "\n# get results_as_zip input and open zip file if appropriate\n"
|
|
391
|
+
# get argument index after workflow inputs
|
|
392
|
+
zip_index = t2_workflow.inputs.size * 2
|
|
393
|
+
out.write "zipped = ARGV[#{zip_index}].chomp == \"yes\"\n"
|
|
394
|
+
out.write 'zip_out = Zip::ZipFile.open("/tmp/#{run.uuid}.zip", Zip::ZipFile::CREATE) if zipped' + "\n"
|
|
395
|
+
|
|
396
|
+
end
|
|
397
|
+
|
|
398
|
+
|
|
399
|
+
# Galaxy's script starting taverna run
|
|
400
|
+
def script_start_run(out)
|
|
401
|
+
out.write <<START_RUN
|
|
402
|
+
|
|
403
|
+
|
|
404
|
+
# start run and wait until it is finished
|
|
405
|
+
run.start
|
|
406
|
+
run.wait(:progress => true)
|
|
407
|
+
|
|
408
|
+
START_RUN
|
|
409
|
+
end
|
|
410
|
+
|
|
411
|
+
|
|
412
|
+
# Galaxy's script output handling
|
|
413
|
+
def script_get_outputs(out, t2_workflow)
|
|
414
|
+
# outputs start after all inputs plus the results_as_zip input
|
|
415
|
+
outputs_start_index = t2_workflow.inputs.size * 2 + 1
|
|
416
|
+
outputs_end_index = outputs_start_index + t2_workflow.outputs.size - 1
|
|
417
|
+
out.write "# get output arguments and associated them with a file\n"
|
|
418
|
+
outputs_start_index.upto(outputs_end_index) do |o|
|
|
419
|
+
out.write "output#{o} = File.open(ARGV[#{o}], \"w\")\n"
|
|
420
|
+
out.write "begin\n"
|
|
421
|
+
out.write " get_outputs(run, false, output#{o}, '" + t2_workflow.outputs[o - outputs_start_index].name.to_s + "', zip_out)\n"
|
|
422
|
+
out.write "rescue Exception => err\n"
|
|
423
|
+
out.write " get_outputs(run, false, output#{o}, '" + t2_workflow.outputs[o - outputs_start_index].name.to_s + ".error', zip_out)\n"
|
|
424
|
+
out.write "ensure\n"
|
|
425
|
+
out.write " output#{o}.close\n"
|
|
426
|
+
out.write "end\n"
|
|
427
|
+
end
|
|
428
|
+
|
|
429
|
+
# close zip file if created when dealing with the inputs
|
|
430
|
+
#--
|
|
431
|
+
# ideally that would semantically belong to a separate method
|
|
432
|
+
out.write "\n# close zip_out (the newly created zip file) if opened\n"
|
|
433
|
+
out.write "zip_out.close if zip_out\n"
|
|
434
|
+
|
|
435
|
+
# dealing with zip output here -- zip arg index is outputs_end_index (last
|
|
436
|
+
# output) plus 1
|
|
437
|
+
out.write "\n# open galaxy zip output and write zip file\n"
|
|
438
|
+
out.write "if zipped\n"
|
|
439
|
+
out.write " galaxy_zip_out = File.open(ARGV[#{outputs_end_index+1}], \"w\")\n"
|
|
440
|
+
out.write " output_zip_file(run.uuid, galaxy_zip_out)\n"
|
|
441
|
+
out.write " galaxy_zip_out.close\n"
|
|
442
|
+
out.write "end\n"
|
|
443
|
+
|
|
444
|
+
end
|
|
445
|
+
|
|
446
|
+
|
|
447
|
+
# Galaxy's script cleaning taverna run
|
|
448
|
+
def script_finish_run(out)
|
|
449
|
+
out.write "\n# delete run\n"
|
|
450
|
+
out.write "run.delete\n"
|
|
451
|
+
end
|
|
452
|
+
|
|
453
|
+
|
|
454
|
+
|
|
455
|
+
|
|
456
|
+
|
|
457
|
+
# public methods from here onwards
|
|
458
|
+
public
|
|
459
|
+
|
|
460
|
+
# Generates the Galaxy tool's xml file responsible for the UI.
|
|
461
|
+
#
|
|
462
|
+
# :call-seq:
|
|
463
|
+
# Generator.generate_xml(my_exp_rest, xml_file) -> nil
|
|
464
|
+
#
|
|
465
|
+
# [+t2_workflow+] a _Workflow_ object as returned from <em>MyExperimentREST::Workflows.new.read(url)</em>
|
|
466
|
+
# [+xml_file+] a string containing the name of the generated XML file
|
|
467
|
+
# [+xml_out+] the file handler to write the generated XML tags
|
|
468
|
+
def generate_xml(t2_workflow, xml_file, xml_out)
|
|
469
|
+
tool_begin_tag(xml_out, t2_workflow.title)
|
|
470
|
+
command_tag(xml_out, t2_workflow, xml_file.gsub('.xml', '.rb'))
|
|
471
|
+
inputs_tag(xml_out, t2_workflow.inputs)
|
|
472
|
+
outputs_tag(xml_out, t2_workflow.outputs)
|
|
473
|
+
help_tag(xml_out, t2_workflow)
|
|
474
|
+
tool_end_tag(xml_out)
|
|
475
|
+
end
|
|
476
|
+
|
|
477
|
+
|
|
478
|
+
# Generates the Galaxy tool's script file responsible for talking to the
|
|
479
|
+
# taverna server
|
|
480
|
+
#
|
|
481
|
+
# :call-seq:
|
|
482
|
+
# Generator.generate_script(my_exp_rest, t2_server, script_file) -> nil
|
|
483
|
+
#
|
|
484
|
+
# [+my_exp_rest+] a _Workflow_ object as returned from <em>MyExperimentREST.ReadWorkflow.new(url)</em>
|
|
485
|
+
# [<tt>t2_server</tt>] a string containing the URL of the taverna 2 server
|
|
486
|
+
# [+script_out+] the file handler to write the generated script code
|
|
487
|
+
def generate_script(t2_workflow, t2_server, script_out)
|
|
488
|
+
script_preample(script_out)
|
|
489
|
+
script_util_methods(script_out)
|
|
490
|
+
script_create_t2_run(script_out, t2_workflow, t2_server)
|
|
491
|
+
script_init_inputs(script_out, t2_workflow)
|
|
492
|
+
script_start_run(script_out)
|
|
493
|
+
script_get_outputs(script_out, t2_workflow)
|
|
494
|
+
script_finish_run(script_out)
|
|
495
|
+
end
|
|
496
|
+
|
|
497
|
+
end
|