t2-web 0.1.7 → 0.1.8
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- data/CHANGES +3 -0
- data/README +2 -4
- data/Rakefile +2 -2
- data/bin/t2-web +43 -0
- data/lib/t2-web.rb +3 -0
- data/public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/UniProtID +185 -0
- data/public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/ValidatedProtein +10 -0
- data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/Pathway +1 -0
- data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/clean_image +0 -0
- data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/geneList +184 -0
- data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/image +0 -0
- data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/url +1 -0
- metadata +92 -96
data/CHANGES
CHANGED
@@ -1,5 +1,8 @@
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= Changes log for the Taverna via the Web App
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== Version 0.1.8
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* Created executable to start the webapp
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== Version 0.1.7
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* The clean image is truncated/copied only once now -- needed to remove the bold tabs from the image
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* Fixed minor bug with displaying images -- incorrect truncation since there is an extra \n
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data/README
CHANGED
@@ -2,7 +2,7 @@
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Authors:: Konstantinos Karasavvas
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Gem Version:: 0.1.
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Gem Version:: 0.1.8
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Contact:: mailto:kostas.karasavvas@nbic.nl
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Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
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Copyright:: (c) 2012 Netherlands Bioinformatics Centre, The Netherlands
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@@ -23,9 +23,7 @@ description provided in the workflow itself in myExperiment.
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== Usage
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Run the above from the webapp's root directory to start the web application at port 9494 and wait for incoming requests. Uses rack's config.ru file.
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$ t2-web -p 9494 start
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data/Rakefile
CHANGED
@@ -12,13 +12,13 @@ require 'rdoc/task'
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spec = Gem::Specification.new do |s|
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s.name = 't2-web'
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s.version = '0.1.
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s.version = '0.1.8'
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s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
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s.summary = 'Web application that generates a Web UI form for a Taverna2 workflow, given its myExperiment id, for ease of execution. The only requirement for the user is a web browser.'
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s.description = s.summary
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s.author = 'Kostas Karasavvas'
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s.email = 'kostas.karasavvas@nbic.nl'
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s.executables = ['t2-web']
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s.files = %w(LICENSE README CHANGES Rakefile Gemfile Gemfile.lock) + Dir.glob("{bin,lib,doc,spec,public,views}/**/*")
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s.require_path = "lib"
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s.bindir = "bin"
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data/bin/t2-web
ADDED
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#!/usr/bin/env ruby
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require 'optparse'
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require 't2-web'
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# Set up and parse arguments
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opts = OptionParser.new do |opt|
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opt.banner = "Usage: t2-web [options] start|stop|restart"
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opt.separator("\nSupports the following options:")
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opt.on("-d", "--daemonize", "Run daemonized in the background")
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opt.on("-p", "--port PORT", "Use PORT (default: 3000)")
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opt.on("-s", "--servers NUM", "Number of servers to start")
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opt.on_tail("-v", "--version", "Show the version") do
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puts "Taverna 2 Web Interface Generator version: #{T2Web::VERSION}"
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exit
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end
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opt.on_tail("-h", "-?", "--help", "Show this message") do
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puts opt
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exit
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end
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end
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# parse options (currently only displaying and passing all to thin!)
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opts.parse!
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if ARGV.size == 0
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puts opts
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exit
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end
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# TODO: call webapp via rack and ruby rather than from the prompt!!
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INSTALL_DIR = `gem environment gemdir`.chomp + "/gems/t2-web-#{T2Web::VERSION}/bin"
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# cd to proper dir and run thin $* for now
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success = `cd #{INSTALL_DIR} ; thin #{$*.join(' ')}`
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if success
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puts "Running: thin #{$*.join(' ')} !"
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else
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puts "Failed running: thin #{$*} !"
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end
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data/lib/t2-web.rb
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64446
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64764
|
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+
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|
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7052
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|
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|
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|
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|
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9586
|
Binary file
|
@@ -0,0 +1 @@
|
|
1
|
+
<b>http://soap.genome.jp/tmp/mark_pathway_www_api.13351787557631/hsa05016.png</b>
|
metadata
CHANGED
@@ -1,113 +1,108 @@
|
|
1
|
-
--- !ruby/object:Gem::Specification
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
2
|
name: t2-web
|
3
|
-
version: !ruby/object:Gem::Version
|
4
|
-
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.1.8
|
5
5
|
prerelease:
|
6
|
-
segments:
|
7
|
-
- 0
|
8
|
-
- 1
|
9
|
-
- 7
|
10
|
-
version: 0.1.7
|
11
6
|
platform: ruby
|
12
|
-
authors:
|
7
|
+
authors:
|
13
8
|
- Kostas Karasavvas
|
14
9
|
autorequire:
|
15
10
|
bindir: bin
|
16
11
|
cert_chain: []
|
17
|
-
|
18
|
-
|
19
|
-
|
20
|
-
- !ruby/object:Gem::Dependency
|
12
|
+
date: 2012-05-03 00:00:00.000000000 Z
|
13
|
+
dependencies:
|
14
|
+
- !ruby/object:Gem::Dependency
|
21
15
|
name: sinatra
|
22
|
-
|
23
|
-
requirement: &id001 !ruby/object:Gem::Requirement
|
16
|
+
requirement: !ruby/object:Gem::Requirement
|
24
17
|
none: false
|
25
|
-
requirements:
|
18
|
+
requirements:
|
26
19
|
- - ~>
|
27
|
-
- !ruby/object:Gem::Version
|
28
|
-
hash: 27
|
29
|
-
segments:
|
30
|
-
- 1
|
31
|
-
- 3
|
32
|
-
- 0
|
20
|
+
- !ruby/object:Gem::Version
|
33
21
|
version: 1.3.0
|
34
22
|
type: :runtime
|
35
|
-
version_requirements: *id001
|
36
|
-
- !ruby/object:Gem::Dependency
|
37
|
-
name: haml
|
38
23
|
prerelease: false
|
39
|
-
|
24
|
+
version_requirements: !ruby/object:Gem::Requirement
|
40
25
|
none: false
|
41
|
-
requirements:
|
26
|
+
requirements:
|
42
27
|
- - ~>
|
43
|
-
- !ruby/object:Gem::Version
|
44
|
-
|
45
|
-
|
46
|
-
|
47
|
-
|
48
|
-
|
28
|
+
- !ruby/object:Gem::Version
|
29
|
+
version: 1.3.0
|
30
|
+
- !ruby/object:Gem::Dependency
|
31
|
+
name: haml
|
32
|
+
requirement: !ruby/object:Gem::Requirement
|
33
|
+
none: false
|
34
|
+
requirements:
|
35
|
+
- - ~>
|
36
|
+
- !ruby/object:Gem::Version
|
49
37
|
version: 3.1.2
|
50
38
|
type: :runtime
|
51
|
-
version_requirements: *id002
|
52
|
-
- !ruby/object:Gem::Dependency
|
53
|
-
name: rest-client
|
54
39
|
prerelease: false
|
55
|
-
|
40
|
+
version_requirements: !ruby/object:Gem::Requirement
|
56
41
|
none: false
|
57
|
-
requirements:
|
42
|
+
requirements:
|
58
43
|
- - ~>
|
59
|
-
- !ruby/object:Gem::Version
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
44
|
+
- !ruby/object:Gem::Version
|
45
|
+
version: 3.1.2
|
46
|
+
- !ruby/object:Gem::Dependency
|
47
|
+
name: rest-client
|
48
|
+
requirement: !ruby/object:Gem::Requirement
|
49
|
+
none: false
|
50
|
+
requirements:
|
51
|
+
- - ~>
|
52
|
+
- !ruby/object:Gem::Version
|
65
53
|
version: 1.6.3
|
66
54
|
type: :runtime
|
67
|
-
version_requirements: *id003
|
68
|
-
- !ruby/object:Gem::Dependency
|
69
|
-
name: t2-server
|
70
55
|
prerelease: false
|
71
|
-
|
56
|
+
version_requirements: !ruby/object:Gem::Requirement
|
72
57
|
none: false
|
73
|
-
requirements:
|
58
|
+
requirements:
|
74
59
|
- - ~>
|
75
|
-
- !ruby/object:Gem::Version
|
76
|
-
|
77
|
-
|
78
|
-
|
79
|
-
|
80
|
-
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: 1.6.3
|
62
|
+
- !ruby/object:Gem::Dependency
|
63
|
+
name: t2-server
|
64
|
+
requirement: !ruby/object:Gem::Requirement
|
65
|
+
none: false
|
66
|
+
requirements:
|
67
|
+
- - ~>
|
68
|
+
- !ruby/object:Gem::Version
|
81
69
|
version: 0.6.1
|
82
70
|
type: :runtime
|
83
|
-
version_requirements: *id004
|
84
|
-
- !ruby/object:Gem::Dependency
|
85
|
-
name: myexperiment-rest
|
86
71
|
prerelease: false
|
87
|
-
|
72
|
+
version_requirements: !ruby/object:Gem::Requirement
|
73
|
+
none: false
|
74
|
+
requirements:
|
75
|
+
- - ~>
|
76
|
+
- !ruby/object:Gem::Version
|
77
|
+
version: 0.6.1
|
78
|
+
- !ruby/object:Gem::Dependency
|
79
|
+
name: myexperiment-rest
|
80
|
+
requirement: !ruby/object:Gem::Requirement
|
88
81
|
none: false
|
89
|
-
requirements:
|
82
|
+
requirements:
|
90
83
|
- - ~>
|
91
|
-
- !ruby/object:Gem::Version
|
92
|
-
hash: 21
|
93
|
-
segments:
|
94
|
-
- 0
|
95
|
-
- 3
|
96
|
-
- 3
|
84
|
+
- !ruby/object:Gem::Version
|
97
85
|
version: 0.3.3
|
98
86
|
type: :runtime
|
99
|
-
|
100
|
-
|
87
|
+
prerelease: false
|
88
|
+
version_requirements: !ruby/object:Gem::Requirement
|
89
|
+
none: false
|
90
|
+
requirements:
|
91
|
+
- - ~>
|
92
|
+
- !ruby/object:Gem::Version
|
93
|
+
version: 0.3.3
|
94
|
+
description: Web application that generates a Web UI form for a Taverna2 workflow,
|
95
|
+
given its myExperiment id, for ease of execution. The only requirement for the user
|
96
|
+
is a web browser.
|
101
97
|
email: kostas.karasavvas@nbic.nl
|
102
|
-
executables:
|
103
|
-
|
98
|
+
executables:
|
99
|
+
- t2-web
|
104
100
|
extensions: []
|
105
|
-
|
106
|
-
extra_rdoc_files:
|
101
|
+
extra_rdoc_files:
|
107
102
|
- README
|
108
103
|
- LICENSE
|
109
104
|
- CHANGES
|
110
|
-
files:
|
105
|
+
files:
|
111
106
|
- LICENSE
|
112
107
|
- README
|
113
108
|
- CHANGES
|
@@ -116,11 +111,15 @@ files:
|
|
116
111
|
- Gemfile.lock
|
117
112
|
- bin/config.ru
|
118
113
|
- bin/log/thin.log
|
114
|
+
- bin/t2-web
|
119
115
|
- bin/t2_webapp.rb
|
116
|
+
- lib/t2-web.rb
|
120
117
|
- public/t2web/scripts/results.js
|
121
118
|
- public/t2web/scripts/form.js
|
122
119
|
- public/t2web/scripts/jquery-1.6.1.js
|
123
120
|
- public/t2web/scripts/jquery.tipsy.js
|
121
|
+
- public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/ValidatedProtein
|
122
|
+
- public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/UniProtID
|
124
123
|
- public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/image
|
125
124
|
- public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/url
|
126
125
|
- public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/Pathway
|
@@ -262,6 +261,11 @@ files:
|
|
262
261
|
- public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/url
|
263
262
|
- public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/Pathway
|
264
263
|
- public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/geneList
|
264
|
+
- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/image
|
265
|
+
- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/url
|
266
|
+
- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/Pathway
|
267
|
+
- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/clean_image
|
268
|
+
- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/geneList
|
265
269
|
- public/t2web/tmp/outputs/d1461a45-200f-4f48-84a8-d01ca3e79b0b/ValidatedProtein
|
266
270
|
- public/t2web/tmp/outputs/d1461a45-200f-4f48-84a8-d01ca3e79b0b/UniProtID
|
267
271
|
- public/t2web/tmp/outputs/dcbec202-78b9-4a0f-ad2e-b1373190e21a/ValidatedProtein
|
@@ -295,36 +299,28 @@ files:
|
|
295
299
|
- views/form.haml
|
296
300
|
homepage:
|
297
301
|
licenses: []
|
298
|
-
|
299
302
|
post_install_message:
|
300
303
|
rdoc_options: []
|
301
|
-
|
302
|
-
require_paths:
|
304
|
+
require_paths:
|
303
305
|
- lib
|
304
|
-
required_ruby_version: !ruby/object:Gem::Requirement
|
306
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
305
307
|
none: false
|
306
|
-
requirements:
|
307
|
-
- -
|
308
|
-
- !ruby/object:Gem::Version
|
309
|
-
|
310
|
-
|
311
|
-
- 0
|
312
|
-
version: "0"
|
313
|
-
required_rubygems_version: !ruby/object:Gem::Requirement
|
308
|
+
requirements:
|
309
|
+
- - ! '>='
|
310
|
+
- !ruby/object:Gem::Version
|
311
|
+
version: '0'
|
312
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
314
313
|
none: false
|
315
|
-
requirements:
|
316
|
-
- -
|
317
|
-
- !ruby/object:Gem::Version
|
318
|
-
|
319
|
-
segments:
|
320
|
-
- 0
|
321
|
-
version: "0"
|
314
|
+
requirements:
|
315
|
+
- - ! '>='
|
316
|
+
- !ruby/object:Gem::Version
|
317
|
+
version: '0'
|
322
318
|
requirements: []
|
323
|
-
|
324
319
|
rubyforge_project:
|
325
|
-
rubygems_version: 1.8.
|
320
|
+
rubygems_version: 1.8.23
|
326
321
|
signing_key:
|
327
322
|
specification_version: 3
|
328
|
-
summary: Web application that generates a Web UI form for a Taverna2 workflow, given
|
323
|
+
summary: Web application that generates a Web UI form for a Taverna2 workflow, given
|
324
|
+
its myExperiment id, for ease of execution. The only requirement for the user is
|
325
|
+
a web browser.
|
329
326
|
test_files: []
|
330
|
-
|