myexperiment-rest 0.2.6

Sign up to get free protection for your applications and to get access to all the features.
Files changed (55) hide show
  1. data/CHANGES +9 -0
  2. data/LICENSE +23 -0
  3. data/README +33 -0
  4. data/Rakefile +45 -0
  5. data/bin/get_workflow_data.rb +31 -0
  6. data/doc/classes/MyExperimentREST.html +113 -0
  7. data/doc/classes/MyExperimentREST/IOData.html +169 -0
  8. data/doc/classes/MyExperimentREST/IOData.src/M000003.html +20 -0
  9. data/doc/classes/MyExperimentREST/ReadWorkflow.html +184 -0
  10. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000002.html +39 -0
  11. data/doc/classes/MyExperimentREST/ReadWorkflow.src/M000005.html +41 -0
  12. data/doc/classes/MyExperimentREST/TavernaIOData.html +167 -0
  13. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000006.html +20 -0
  14. data/doc/classes/MyExperimentREST/TavernaIOData.src/M000007.html +20 -0
  15. data/doc/classes/MyExperimentREST/TavernaWorkflow.html +209 -0
  16. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000005.html +23 -0
  17. data/doc/classes/MyExperimentREST/TavernaWorkflow.src/M000006.html +22 -0
  18. data/doc/classes/MyExperimentREST/Workflow.html +172 -0
  19. data/doc/classes/MyExperimentREST/Workflow.src/M000001.html +21 -0
  20. data/doc/classes/MyExperimentREST/Workflows.html +167 -0
  21. data/doc/classes/MyExperimentREST/Workflows.src/M000004.html +41 -0
  22. data/doc/classes/TestReadWorkflow.html +167 -0
  23. data/doc/classes/TestReadWorkflow.src/M000001.html +18 -0
  24. data/doc/classes/TestReadWorkflow.src/M000002.html +24 -0
  25. data/doc/classes/TestReadWorkflow.src/M000003.html +20 -0
  26. data/doc/classes/TestReadWorkflow.src/M000004.html +20 -0
  27. data/doc/created.rid +1 -0
  28. data/doc/files/bin/get_workflow_data_rb.html +116 -0
  29. data/doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html +110 -0
  30. data/doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
  31. data/doc/files/lib/myexperiment-rest_rb.html +108 -0
  32. data/doc/files/test/test_read_workflow_rb.html +122 -0
  33. data/doc/fr_class_index.html +31 -0
  34. data/doc/fr_file_index.html +29 -0
  35. data/doc/fr_method_index.html +32 -0
  36. data/doc/index.html +24 -0
  37. data/doc/rdoc-style.css +208 -0
  38. data/doc/rdoc/classes/MyExperimentREST.html +117 -0
  39. data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html +178 -0
  40. data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html +223 -0
  41. data/doc/rdoc/classes/MyExperimentREST/Workflows.html +199 -0
  42. data/doc/rdoc/created.rid +1 -0
  43. data/doc/rdoc/files/CHANGES.html +121 -0
  44. data/doc/rdoc/files/LICENSE.html +133 -0
  45. data/doc/rdoc/files/README.html +148 -0
  46. data/doc/rdoc/files/lib/myexperiment-rest/myexperiment_rest_rb.html +110 -0
  47. data/doc/rdoc/files/lib/myexperiment-rest_rb.html +108 -0
  48. data/doc/rdoc/fr_class_index.html +30 -0
  49. data/doc/rdoc/fr_file_index.html +31 -0
  50. data/doc/rdoc/fr_method_index.html +29 -0
  51. data/doc/rdoc/index.html +24 -0
  52. data/doc/rdoc/rdoc-style.css +208 -0
  53. data/lib/myexperiment-rest.rb +5 -0
  54. data/lib/myexperiment-rest/myexperiment_rest.rb +146 -0
  55. metadata +133 -0
data/doc/rdoc/classes/MyExperimentREST.html ADDED
@@ -0,0 +1,117 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>Module: MyExperimentREST</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
+ <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
18
+
19
+ function toggleCode( id ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
22
+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
24
+ else
25
+ return false;
26
+
27
+ elemStyle = elem.style;
28
+
29
+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
34
+
35
+ return true;
36
+ }
37
+
38
+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
41
+ // ]]>
42
+ </script>
43
+
44
+ </head>
45
+ <body>
46
+
47
+
48
+
49
+ <div id="classHeader">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Module</strong></td>
53
+ <td class="class-name-in-header">MyExperimentREST</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../files/lib/myexperiment-rest_rb.html">
59
+ lib/myexperiment-rest.rb
60
+ </a>
61
+ <br />
62
+ <a href="../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
63
+ lib/myexperiment-rest/myexperiment_rest.rb
64
+ </a>
65
+ <br />
66
+ </td>
67
+ </tr>
68
+
69
+ </table>
70
+ </div>
71
+ <!-- banner header -->
72
+
73
+ <div id="bodyContent">
74
+
75
+
76
+
77
+ <div id="contextContent">
78
+
79
+
80
+
81
+ </div>
82
+
83
+
84
+ </div>
85
+
86
+
87
+ <!-- if includes -->
88
+
89
+ <div id="section">
90
+
91
+ <div id="class-list">
92
+ <h3 class="section-bar">Classes and Modules</h3>
93
+
94
+ Class <a href="MyExperimentREST/TavernaIOData.html" class="link">MyExperimentREST::TavernaIOData</a><br />
95
+ Class <a href="MyExperimentREST/TavernaWorkflow.html" class="link">MyExperimentREST::TavernaWorkflow</a><br />
96
+ Class <a href="MyExperimentREST/Workflows.html" class="link">MyExperimentREST::Workflows</a><br />
97
+
98
+ </div>
99
+
100
+
101
+
102
+
103
+
104
+
105
+
106
+ <!-- if method_list -->
107
+
108
+
109
+ </div>
110
+
111
+
112
+ <div id="validator-badges">
113
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
114
+ </div>
115
+
116
+ </body>
117
+ </html>
data/doc/rdoc/classes/MyExperimentREST/TavernaIOData.html ADDED
@@ -0,0 +1,178 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>Class: MyExperimentREST::TavernaIOData</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
18
+
19
+ function toggleCode( id ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
22
+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
24
+ else
25
+ return false;
26
+
27
+ elemStyle = elem.style;
28
+
29
+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
34
+
35
+ return true;
36
+ }
37
+
38
+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
41
+ // ]]>
42
+ </script>
43
+
44
+ </head>
45
+ <body>
46
+
47
+
48
+
49
+ <div id="classHeader">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">MyExperimentREST::TavernaIOData</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
59
+ lib/myexperiment-rest/myexperiment_rest.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
64
+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
67
+ <td>
68
+ Object
69
+ </td>
70
+ </tr>
71
+ </table>
72
+ </div>
73
+ <!-- banner header -->
74
+
75
+ <div id="bodyContent">
76
+
77
+
78
+
79
+ <div id="contextContent">
80
+
81
+ <div id="description">
82
+ <p>
83
+ Contains all available information about an input or output: name,
84
+ descriptions and examples. The last two are lists.
85
+ </p>
86
+
87
+ </div>
88
+
89
+
90
+ </div>
91
+
92
+ <div id="method-list">
93
+ <h3 class="section-bar">Methods</h3>
94
+
95
+ <div class="name-list">
96
+ <a href="#M000003">new</a>&nbsp;&nbsp;
97
+ </div>
98
+ </div>
99
+
100
+ </div>
101
+
102
+
103
+ <!-- if includes -->
104
+
105
+ <div id="section">
106
+
107
+
108
+
109
+
110
+
111
+ <div id="attribute-list">
112
+ <h3 class="section-bar">Attributes</h3>
113
+
114
+ <div class="name-list">
115
+ <table>
116
+ <tr class="top-aligned-row context-row">
117
+ <td class="context-item-name">descriptions</td>
118
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
119
+ <td class="context-item-desc"></td>
120
+ </tr>
121
+ <tr class="top-aligned-row context-row">
122
+ <td class="context-item-name">examples</td>
123
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
124
+ <td class="context-item-desc"></td>
125
+ </tr>
126
+ <tr class="top-aligned-row context-row">
127
+ <td class="context-item-name">name</td>
128
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
129
+ <td class="context-item-desc"></td>
130
+ </tr>
131
+ </table>
132
+ </div>
133
+ </div>
134
+
135
+
136
+
137
+ <!-- if method_list -->
138
+ <div id="methods">
139
+ <h3 class="section-bar">Public Class methods</h3>
140
+
141
+ <div id="method-M000003" class="method-detail">
142
+ <a name="M000003"></a>
143
+
144
+ <div class="method-heading">
145
+ <a href="#M000003" class="method-signature">
146
+ <span class="method-name">new</span><span class="method-args">(name, descriptions, examples)</span>
147
+ </a>
148
+ </div>
149
+
150
+ <div class="method-description">
151
+ <p><a class="source-toggle" href="#"
152
+ onclick="toggleCode('M000003-source');return false;">[Source]</a></p>
153
+ <div class="method-source-code" id="M000003-source">
154
+ <pre>
155
+ <span class="ruby-comment cmt"># File lib/myexperiment-rest/myexperiment_rest.rb, line 136</span>
156
+ 136: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">descriptions</span>, <span class="ruby-identifier">examples</span>)
157
+ 137: <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
158
+ 138: <span class="ruby-ivar">@descriptions</span> = <span class="ruby-identifier">descriptions</span>
159
+ 139: <span class="ruby-ivar">@examples</span> = <span class="ruby-identifier">examples</span>
160
+ 140: <span class="ruby-keyword kw">end</span>
161
+ </pre>
162
+ </div>
163
+ </div>
164
+ </div>
165
+
166
+
167
+ </div>
168
+
169
+
170
+ </div>
171
+
172
+
173
+ <div id="validator-badges">
174
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
175
+ </div>
176
+
177
+ </body>
178
+ </html>
data/doc/rdoc/classes/MyExperimentREST/TavernaWorkflow.html ADDED
@@ -0,0 +1,223 @@
1
+ <?xml version="1.0" encoding="iso-8859-1"?>
2
+ <!DOCTYPE html
3
+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
4
+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
5
+
6
+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
7
+ <head>
8
+ <title>Class: MyExperimentREST::TavernaWorkflow</title>
9
+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
10
+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
11
+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
12
+ <script type="text/javascript">
13
+ // <![CDATA[
14
+
15
+ function popupCode( url ) {
16
+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
17
+ }
18
+
19
+ function toggleCode( id ) {
20
+ if ( document.getElementById )
21
+ elem = document.getElementById( id );
22
+ else if ( document.all )
23
+ elem = eval( "document.all." + id );
24
+ else
25
+ return false;
26
+
27
+ elemStyle = elem.style;
28
+
29
+ if ( elemStyle.display != "block" ) {
30
+ elemStyle.display = "block"
31
+ } else {
32
+ elemStyle.display = "none"
33
+ }
34
+
35
+ return true;
36
+ }
37
+
38
+ // Make codeblocks hidden by default
39
+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
40
+
41
+ // ]]>
42
+ </script>
43
+
44
+ </head>
45
+ <body>
46
+
47
+
48
+
49
+ <div id="classHeader">
50
+ <table class="header-table">
51
+ <tr class="top-aligned-row">
52
+ <td><strong>Class</strong></td>
53
+ <td class="class-name-in-header">MyExperimentREST::TavernaWorkflow</td>
54
+ </tr>
55
+ <tr class="top-aligned-row">
56
+ <td><strong>In:</strong></td>
57
+ <td>
58
+ <a href="../../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
59
+ lib/myexperiment-rest/myexperiment_rest.rb
60
+ </a>
61
+ <br />
62
+ </td>
63
+ </tr>
64
+
65
+ <tr class="top-aligned-row">
66
+ <td><strong>Parent:</strong></td>
67
+ <td>
68
+ Object
69
+ </td>
70
+ </tr>
71
+ </table>
72
+ </div>
73
+ <!-- banner header -->
74
+
75
+ <div id="bodyContent">
76
+
77
+
78
+
79
+ <div id="contextContent">
80
+
81
+ <div id="description">
82
+ <p>
83
+ Contains all available information about a workflow: <em>input_type</em>,
84
+ <em>xml_uri</em>, <em>title</em>, <em>description</em>, <em>inputs</em> and
85
+ <em>outputs</em>. The <em>xml_uri</em> specifies the XML description on
86
+ myExperiment and not the XML of the workflow itself. <em>input_type</em>
87
+ specifies the kind of input. Currently, either &quot;myexperiment&quot;
88
+ (myExperiment&#8216;s xml uri) or &quot;t2flow&quot; (filename)
89
+ </p>
90
+
91
+ </div>
92
+
93
+
94
+ </div>
95
+
96
+ <div id="method-list">
97
+ <h3 class="section-bar">Methods</h3>
98
+
99
+ <div class="name-list">
100
+ <a href="#M000002">new</a>&nbsp;&nbsp;
101
+ </div>
102
+ </div>
103
+
104
+ </div>
105
+
106
+
107
+ <!-- if includes -->
108
+
109
+ <div id="section">
110
+
111
+
112
+ <div id="constants-list">
113
+ <h3 class="section-bar">Constants</h3>
114
+
115
+ <div class="name-list">
116
+ <table summary="Constants">
117
+ <tr class="top-aligned-row context-row">
118
+ <td class="context-item-name">MY_EXPERIMENT</td>
119
+ <td>=</td>
120
+ <td class="context-item-value">'myexperiment'</td>
121
+ <td width="3em">&nbsp;</td>
122
+ <td class="context-item-desc">
123
+ possible input types
124
+
125
+ </td>
126
+ </tr>
127
+ <tr class="top-aligned-row context-row">
128
+ <td class="context-item-name">T2_FLOW</td>
129
+ <td>=</td>
130
+ <td class="context-item-value">'t2flow'</td>
131
+ </tr>
132
+ </table>
133
+ </div>
134
+ </div>
135
+
136
+
137
+
138
+ <div id="attribute-list">
139
+ <h3 class="section-bar">Attributes</h3>
140
+
141
+ <div class="name-list">
142
+ <table>
143
+ <tr class="top-aligned-row context-row">
144
+ <td class="context-item-name">description</td>
145
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
146
+ <td class="context-item-desc"></td>
147
+ </tr>
148
+ <tr class="top-aligned-row context-row">
149
+ <td class="context-item-name">input_type</td>
150
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
151
+ <td class="context-item-desc"></td>
152
+ </tr>
153
+ <tr class="top-aligned-row context-row">
154
+ <td class="context-item-name">inputs</td>
155
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
156
+ <td class="context-item-desc"></td>
157
+ </tr>
158
+ <tr class="top-aligned-row context-row">
159
+ <td class="context-item-name">outputs</td>
160
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
161
+ <td class="context-item-desc"></td>
162
+ </tr>
163
+ <tr class="top-aligned-row context-row">
164
+ <td class="context-item-name">title</td>
165
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
166
+ <td class="context-item-desc"></td>
167
+ </tr>
168
+ <tr class="top-aligned-row context-row">
169
+ <td class="context-item-name">xml_uri</td>
170
+ <td class="context-item-value">&nbsp;[R]&nbsp;</td>
171
+ <td class="context-item-desc"></td>
172
+ </tr>
173
+ </table>
174
+ </div>
175
+ </div>
176
+
177
+
178
+
179
+ <!-- if method_list -->
180
+ <div id="methods">
181
+ <h3 class="section-bar">Public Class methods</h3>
182
+
183
+ <div id="method-M000002" class="method-detail">
184
+ <a name="M000002"></a>
185
+
186
+ <div class="method-heading">
187
+ <a href="#M000002" class="method-signature">
188
+ <span class="method-name">new</span><span class="method-args">(input_type, xml_uri, title, description, inputs, outputs)</span>
189
+ </a>
190
+ </div>
191
+
192
+ <div class="method-description">
193
+ <p><a class="source-toggle" href="#"
194
+ onclick="toggleCode('M000002-source');return false;">[Source]</a></p>
195
+ <div class="method-source-code" id="M000002-source">
196
+ <pre>
197
+ <span class="ruby-comment cmt"># File lib/myexperiment-rest/myexperiment_rest.rb, line 114</span>
198
+ 114: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">input_type</span>, <span class="ruby-identifier">xml_uri</span>, <span class="ruby-identifier">title</span>, <span class="ruby-identifier">description</span>, <span class="ruby-identifier">inputs</span>, <span class="ruby-identifier">outputs</span>)
199
+ 115: <span class="ruby-ivar">@input_type</span> = <span class="ruby-identifier">input_type</span>
200
+ 116: <span class="ruby-ivar">@xml_uri</span> = <span class="ruby-identifier">xml_uri</span>
201
+ 117: <span class="ruby-ivar">@title</span> = <span class="ruby-identifier">title</span>
202
+ 118: <span class="ruby-ivar">@description</span> = <span class="ruby-identifier">description</span>
203
+ 119: <span class="ruby-ivar">@inputs</span> = <span class="ruby-identifier">inputs</span>
204
+ 120: <span class="ruby-ivar">@outputs</span> = <span class="ruby-identifier">outputs</span>
205
+ 121: <span class="ruby-keyword kw">end</span>
206
+ </pre>
207
+ </div>
208
+ </div>
209
+ </div>
210
+
211
+
212
+ </div>
213
+
214
+
215
+ </div>
216
+
217
+
218
+ <div id="validator-badges">
219
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
220
+ </div>
221
+
222
+ </body>
223
+ </html>