myexperiment-rest 0.2.6 → 0.2.7

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data/CHANGES CHANGED
@@ -1,7 +1,12 @@
1
1
  = Changes log for the MyExperiment via REST Gem
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2
 
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+ == Version 0.2.7
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+ * Minor clean up of get_workflow_data.rb and documentation.
5
+ * Added libxml-ruby dependency in gem specification.
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+
7
+
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8
  == Version 0.2.6
4
- * Added dependency in gem specification.
9
+ * Added rest-client dependency version in gem specification.
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10
 
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11
 
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  == Version 0.2.5
data/README CHANGED
@@ -1,7 +1,7 @@
1
1
  = MyExperiment Interaction via REST
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2
 
3
3
  Authors:: Konstantinos Karasavvas
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- Gem Version:: 0.2.6
4
+ Gem Version:: 0.2.7
5
5
  Contact:: mailto:kostas.karasavvas@nbic.nl
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6
  Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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7
  Copyright:: (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
@@ -25,9 +25,9 @@ how you can use the library.
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25
 
26
26
  == Installation
27
27
 
28
- [sudo] gem install myexperiment-rest
28
+ [sudo] gem install myexperiment-rest
29
29
 
30
30
 
31
31
  == References
32
32
 
33
- myExperiment:: http://www.myexperiment.org
33
+ myExperiment:: http://www.myexperiment.org
data/Rakefile CHANGED
@@ -12,7 +12,7 @@ require 'rake/testtask'
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12
 
13
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  spec = Gem::Specification.new do |s|
14
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  s.name = 'myexperiment-rest'
15
- s.version = '0.2.6'
15
+ s.version = '0.2.7'
16
16
  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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17
  s.summary = 'This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.'
18
18
  s.description = s.summary
@@ -22,7 +22,8 @@ spec = Gem::Specification.new do |s|
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22
  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec}/**/*")
23
23
  s.require_path = "lib"
24
24
  s.bindir = "bin"
25
- s.add_dependency 'rest-client'
25
+ s.add_dependency 'rest-client', '>= 1.6.3'
26
+ s.add_dependency 'libxml-ruby', '>= 2.0.5'
26
27
  end
27
28
 
28
29
  Rake::GemPackageTask.new(spec) do |p|
@@ -5,11 +5,9 @@ require "myexperiment-rest"
5
5
 
6
6
  include MyExperimentREST
7
7
 
8
- if ARGV[0] == nil
9
- wkf = Workflows.new.read('http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_221429.xml?version=3')
10
- else
11
- wkf = Workflows.new.read(ARGV[0])
12
- end
8
+ my_exp_workflow = ARGV[0] || "http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_221429.xml?version=3"
9
+ wkf = Workflows.new.read(my_exp_workflow)
10
+
13
11
 
14
12
 
15
13
  puts wkf.input_type
data/doc/created.rid CHANGED
@@ -1 +1 @@
1
- Thu, 19 May 2011 18:29:06 +0200
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+ Thu, 21 Jul 2011 18:40:11 +0200
@@ -0,0 +1,148 @@
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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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>File: README</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
20
+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ 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
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+
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+ // ]]>
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+ </script>
43
+
44
+ </head>
45
+ <body>
46
+
47
+
48
+
49
+ <div id="fileHeader">
50
+ <h1>README</h1>
51
+ <table class="header-table">
52
+ <tr class="top-aligned-row">
53
+ <td><strong>Path:</strong></td>
54
+ <td>README
55
+ </td>
56
+ </tr>
57
+ <tr class="top-aligned-row">
58
+ <td><strong>Last Update:</strong></td>
59
+ <td>Wed Jul 20 19:31:37 +0200 2011</td>
60
+ </tr>
61
+ </table>
62
+ </div>
63
+ <!-- banner header -->
64
+
65
+ <div id="bodyContent">
66
+
67
+
68
+
69
+ <div id="contextContent">
70
+
71
+ <div id="description">
72
+ <h1>MyExperiment Interaction via REST</h1>
73
+ <table>
74
+ <tr><td valign="top">Authors:</td><td>Konstantinos Karasavvas
75
+
76
+ </td></tr>
77
+ <tr><td valign="top">Gem Version:</td><td>0.2.6
78
+
79
+ </td></tr>
80
+ <tr><td valign="top">Contact:</td><td><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a>
81
+
82
+ </td></tr>
83
+ <tr><td valign="top">Licence:</td><td>MIT (See LICENCE or <a
84
+ href="http://www.opensource.org/licenses/mit-license">www.opensource.org/licenses/mit-license</a>)
85
+
86
+ </td></tr>
87
+ <tr><td valign="top">Copyright:</td><td>(c) 2010 Netherlands Bioinformatics Centre, The Netherlands
88
+
89
+ </td></tr>
90
+ </table>
91
+ <h2>Description</h2>
92
+ <p>
93
+ This is a simple library to access data on myExperiment via its REST API.
94
+ </p>
95
+ <h2>Features/Problems</h2>
96
+ <p>
97
+ Only a subset of myExperiment workflow data can be currently accessed.
98
+ </p>
99
+ <h2>Usage</h2>
100
+ <p>
101
+ There is an example script inside the <tt>bin</tt> directory that
102
+ demonstrates how you can use the library.
103
+ </p>
104
+ <h2>Installation</h2>
105
+ <dl>
106
+ <dt>sudo</dt><dd>gem install myexperiment-rest
107
+
108
+ </dd>
109
+ </dl>
110
+ <h2>References</h2>
111
+ <table>
112
+ <tr><td valign="top">myExperiment:</td><td><a href="http://www.myexperiment.org">www.myexperiment.org</a>
113
+
114
+ </td></tr>
115
+ </table>
116
+
117
+ </div>
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+
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+
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+ </div>
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+
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+
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+
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+ </div>
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+
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+
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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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+ </div>
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+
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+ </body>
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+ </html>
@@ -20,11 +20,6 @@
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  <div id="index">
21
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  <h1 class="section-bar">Classes</h1>
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  <div id="index-entries">
23
- <a href="classes/MyExperimentREST.html">MyExperimentREST</a><br />
24
- <a href="classes/MyExperimentREST/TavernaIOData.html">MyExperimentREST::TavernaIOData</a><br />
25
- <a href="classes/MyExperimentREST/TavernaWorkflow.html">MyExperimentREST::TavernaWorkflow</a><br />
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- <a href="classes/MyExperimentREST/Workflows.html">MyExperimentREST::Workflows</a><br />
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- <a href="classes/TestReadWorkflow.html">TestReadWorkflow</a><br />
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  </div>
29
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  </div>
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  </body>
@@ -20,9 +20,7 @@
20
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  <div id="index">
21
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  <h1 class="section-bar">Files</h1>
22
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  <div id="index-entries">
23
- <a href="files/bin/get_workflow_data_rb.html">bin/get_workflow_data.rb</a><br />
24
- <a href="files/lib/myexperiment-rest/myexperiment_rest_rb.html">lib/myexperiment-rest/myexperiment_rest.rb</a><br />
25
- <a href="files/test/test_read_workflow_rb.html">test/test_read_workflow.rb</a><br />
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+ <a href="files/README.html">README</a><br />
26
24
  </div>
27
25
  </div>
28
26
  </body>
@@ -20,12 +20,6 @@
20
20
  <div id="index">
21
21
  <h1 class="section-bar">Methods</h1>
22
22
  <div id="index-entries">
23
- <a href="classes/MyExperimentREST/TavernaIOData.html#M000006">new (MyExperimentREST::TavernaIOData)</a><br />
24
- <a href="classes/MyExperimentREST/TavernaWorkflow.html#M000005">new (MyExperimentREST::TavernaWorkflow)</a><br />
25
- <a href="classes/MyExperimentREST/Workflows.html#M000004">read (MyExperimentREST::Workflows)</a><br />
26
- <a href="classes/TestReadWorkflow.html#M000001">setup (TestReadWorkflow)</a><br />
27
- <a href="classes/TestReadWorkflow.html#M000002">test_workflow_values (TestReadWorkflow)</a><br />
28
- <a href="classes/TestReadWorkflow.html#M000003">test_workflows_ios (TestReadWorkflow)</a><br />
29
23
  </div>
30
24
  </div>
31
25
  </body>
data/doc/index.html CHANGED
@@ -19,6 +19,6 @@
19
19
  <frame src="fr_class_index.html" name="Classes" />
20
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  <frame src="fr_method_index.html" name="Methods" />
21
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  </frameset>
22
- <frame src="files/test/test_read_workflow_rb.html" name="docwin" />
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+ <frame src="files/README.html" name="docwin" />
23
23
  </frameset>
24
24
  </html>
data/doc/rdoc/created.rid CHANGED
@@ -1 +1 @@
1
- Wed, 20 Jul 2011 19:32:01 +0200
1
+ Fri, 22 Jul 2011 12:32:40 +0200
@@ -56,7 +56,7 @@
56
56
  </tr>
57
57
  <tr class="top-aligned-row">
58
58
  <td><strong>Last Update:</strong></td>
59
- <td>Wed Jul 20 19:30:21 +0200 2011</td>
59
+ <td>Fri Jul 22 12:32:28 +0200 2011</td>
60
60
  </tr>
61
61
  </table>
62
62
  </div>
@@ -70,9 +70,18 @@
70
70
 
71
71
  <div id="description">
72
72
  <h1>Changes log for the MyExperiment via REST Gem</h1>
73
+ <h2>Version 0.2.7</h2>
74
+ <ul>
75
+ <li>Minor clean up of get_workflow_data.rb and documentation.
76
+
77
+ </li>
78
+ <li>Added libxml-ruby dependency in gem specification.
79
+
80
+ </li>
81
+ </ul>
73
82
  <h2>Version 0.2.6</h2>
74
83
  <ul>
75
- <li>Added dependency in gem specification.
84
+ <li>Added rest-client dependency version in gem specification.
76
85
 
77
86
  </li>
78
87
  </ul>
@@ -56,7 +56,7 @@
56
56
  </tr>
57
57
  <tr class="top-aligned-row">
58
58
  <td><strong>Last Update:</strong></td>
59
- <td>Wed Jul 20 19:31:37 +0200 2011</td>
59
+ <td>Fri Jul 22 12:29:57 +0200 2011</td>
60
60
  </tr>
61
61
  </table>
62
62
  </div>
@@ -74,7 +74,7 @@
74
74
  <tr><td valign="top">Authors:</td><td>Konstantinos Karasavvas
75
75
 
76
76
  </td></tr>
77
- <tr><td valign="top">Gem Version:</td><td>0.2.6
77
+ <tr><td valign="top">Gem Version:</td><td>0.2.7
78
78
 
79
79
  </td></tr>
80
80
  <tr><td valign="top">Contact:</td><td><a href="mailto:kostas.karasavvas@nbic.nl">kostas.karasavvas@nbic.nl</a>
@@ -102,11 +102,9 @@ There is an example script inside the <tt>bin</tt> directory that
102
102
  demonstrates how you can use the library.
103
103
  </p>
104
104
  <h2>Installation</h2>
105
- <dl>
106
- <dt>sudo</dt><dd>gem install myexperiment-rest
107
-
108
- </dd>
109
- </dl>
105
+ <pre>
106
+ [sudo] gem install myexperiment-rest
107
+ </pre>
110
108
  <h2>References</h2>
111
109
  <table>
112
110
  <tr><td valign="top">myExperiment:</td><td><a href="http://www.myexperiment.org">www.myexperiment.org</a>
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: myexperiment-rest
3
3
  version: !ruby/object:Gem::Version
4
- hash: 27
4
+ hash: 25
5
5
  prerelease:
6
6
  segments:
7
7
  - 0
8
8
  - 2
9
- - 6
10
- version: 0.2.6
9
+ - 7
10
+ version: 0.2.7
11
11
  platform: ruby
12
12
  authors:
13
13
  - Konstantinos Karasavvas
@@ -15,7 +15,7 @@ autorequire:
15
15
  bindir: bin
16
16
  cert_chain: []
17
17
 
18
- date: 2011-07-20 00:00:00 Z
18
+ date: 2011-07-22 00:00:00 Z
19
19
  dependencies:
20
20
  - !ruby/object:Gem::Dependency
21
21
  name: rest-client
@@ -25,12 +25,30 @@ dependencies:
25
25
  requirements:
26
26
  - - ">="
27
27
  - !ruby/object:Gem::Version
28
- hash: 3
28
+ hash: 9
29
29
  segments:
30
- - 0
31
- version: "0"
30
+ - 1
31
+ - 6
32
+ - 3
33
+ version: 1.6.3
32
34
  type: :runtime
33
35
  version_requirements: *id001
36
+ - !ruby/object:Gem::Dependency
37
+ name: libxml-ruby
38
+ prerelease: false
39
+ requirement: &id002 !ruby/object:Gem::Requirement
40
+ none: false
41
+ requirements:
42
+ - - ">="
43
+ - !ruby/object:Gem::Version
44
+ hash: 5
45
+ segments:
46
+ - 2
47
+ - 0
48
+ - 5
49
+ version: 2.0.5
50
+ type: :runtime
51
+ version_requirements: *id002
34
52
  description: This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.
35
53
  email: kostas.karasavvas@nbic.nl
36
54
  executables:
@@ -76,6 +94,7 @@ files:
76
94
  - doc/index.html
77
95
  - doc/files/test/test_read_workflow_rb.html
78
96
  - doc/files/bin/get_workflow_data_rb.html
97
+ - doc/files/README.html
79
98
  - doc/files/lib/myexperiment-rest/my_experiment_rest_rb.html
80
99
  - doc/files/lib/myexperiment-rest/myexperiment_rest_rb.html
81
100
  - doc/files/lib/myexperiment-rest_rb.html