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 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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+
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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
data/README CHANGED
@@ -2,7 +2,7 @@
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  Authors:: Konstantinos Karasavvas
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- Gem Version:: 0.1.7
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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
@@ -23,9 +23,7 @@ description provided in the workflow itself in myExperiment.
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  == Usage
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- thin -p 9494 start
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-
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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 = '0.1.7'
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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_webapp.rb']
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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"
data/bin/t2-web ADDED
@@ -0,0 +1,43 @@
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+ #!/usr/bin/env ruby
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+
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+ require 'optparse'
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+ require 't2-web'
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+
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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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+
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+ # parse options (currently only displaying and passing all to thin!)
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+ opts.parse!
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+
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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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+
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+ # TODO: call webapp via rack and ruby rather than from the prompt!!
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+
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+ INSTALL_DIR = `gem environment gemdir`.chomp + "/gems/t2-web-#{T2Web::VERSION}/bin"
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+
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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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+
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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 ADDED
@@ -0,0 +1,3 @@
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+ module T2Web
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+ VERSION = "0.1.8"
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+ end
@@ -0,0 +1,185 @@
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+ <b>P70386</b>
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+ Q02527
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+ Q7M4L3
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+ Q9BT36
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+ Q9W5F1
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+ P05067
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+ P08592
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+ P12023
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+ Q9UCC8
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+ Q9UCD1
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+ Q9UQ58
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+ P15943
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+ Q06335
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+ Q06481
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+ Q13861
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+ Q14594
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+ Q14662
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+ Q7M4L3
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+ Q9W5F1
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+ P05067
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+ P08592
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+ P09000
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+ P12023
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+ P78438
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+ P97487
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+ P97942
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+ Q10651
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+ Q13764
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+ Q13778
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+ Q13793
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+ Q16011
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+ Q16014
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+ Q16019
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+ Q16020
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+ Q18583
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+ Q547B7
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+ Q6GSC0
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+ <b>P08396</b>
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+ Q60721
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+ Q62211
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+ Q62655
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+ Q64072
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+ Q80UE8
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+ Q99N33
@@ -0,0 +1,10 @@
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+ <b>GnT-III</b>
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+ GnT-III
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+ GnT-III
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+ GnT-III
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+ <b>gamma-actin</b>
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+ <b>APP</b>
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+ APP
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+ APP
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+ <b>UPS</b>
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+ <b>TFE</b>
@@ -0,0 +1 @@
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+ <b>path:hsa05016 Huntington's disease - Homo sapiens (human)</b>
@@ -0,0 +1,184 @@
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+ <b>100532726</b>
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+ 10105
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@@ -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
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  name: t2-web
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- version: !ruby/object:Gem::Version
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- hash: 21
3
+ version: !ruby/object:Gem::Version
4
+ version: 0.1.8
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  prerelease:
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- segments:
7
- - 0
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- - 1
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- - 7
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- version: 0.1.7
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6
  platform: ruby
12
- authors:
7
+ authors:
13
8
  - Kostas Karasavvas
14
9
  autorequire:
15
10
  bindir: bin
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11
  cert_chain: []
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-
18
- date: 2012-04-20 00:00:00 Z
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- dependencies:
20
- - !ruby/object:Gem::Dependency
12
+ date: 2012-05-03 00:00:00.000000000 Z
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+ dependencies:
14
+ - !ruby/object:Gem::Dependency
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15
  name: sinatra
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- prerelease: false
23
- requirement: &id001 !ruby/object:Gem::Requirement
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+ requirement: !ruby/object:Gem::Requirement
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  none: false
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- requirements:
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+ requirements:
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  - - ~>
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- - !ruby/object:Gem::Version
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- hash: 27
29
- segments:
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- - 1
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- - 3
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- - 0
20
+ - !ruby/object:Gem::Version
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21
  version: 1.3.0
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22
  type: :runtime
35
- version_requirements: *id001
36
- - !ruby/object:Gem::Dependency
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- name: haml
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23
  prerelease: false
39
- requirement: &id002 !ruby/object:Gem::Requirement
24
+ version_requirements: !ruby/object:Gem::Requirement
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25
  none: false
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- requirements:
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+ requirements:
42
27
  - - ~>
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- - !ruby/object:Gem::Version
44
- hash: 7
45
- segments:
46
- - 3
47
- - 1
48
- - 2
28
+ - !ruby/object:Gem::Version
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+ 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
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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
- requirement: &id003 !ruby/object:Gem::Requirement
40
+ version_requirements: !ruby/object:Gem::Requirement
56
41
  none: false
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- requirements:
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+ requirements:
58
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  - - ~>
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- - !ruby/object:Gem::Version
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- hash: 9
61
- segments:
62
- - 1
63
- - 6
64
- - 3
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
- requirement: &id004 !ruby/object:Gem::Requirement
56
+ version_requirements: !ruby/object:Gem::Requirement
72
57
  none: false
73
- requirements:
58
+ requirements:
74
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  - - ~>
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- - !ruby/object:Gem::Version
76
- hash: 5
77
- segments:
78
- - 0
79
- - 6
80
- - 1
60
+ - !ruby/object:Gem::Version
61
+ version: 1.6.3
62
+ - !ruby/object:Gem::Dependency
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+ name: t2-server
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+ requirement: !ruby/object:Gem::Requirement
65
+ none: false
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+ requirements:
67
+ - - ~>
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+ - !ruby/object:Gem::Version
81
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  version: 0.6.1
82
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  type: :runtime
83
- version_requirements: *id004
84
- - !ruby/object:Gem::Dependency
85
- name: myexperiment-rest
86
71
  prerelease: false
87
- requirement: &id005 !ruby/object:Gem::Requirement
72
+ version_requirements: !ruby/object:Gem::Requirement
73
+ none: false
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+ requirements:
75
+ - - ~>
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+ - !ruby/object:Gem::Version
77
+ version: 0.6.1
78
+ - !ruby/object:Gem::Dependency
79
+ name: myexperiment-rest
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+ 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
- version_requirements: *id005
100
- description: 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.
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
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  - 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
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  - public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/url
126
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  - public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/Pathway
@@ -262,6 +261,11 @@ files:
262
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  - public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/url
263
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  - 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
- hash: 3
310
- segments:
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
- hash: 3
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: 1.8.21
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 its myExperiment id, for ease of execution. The only requirement for the user is a web browser.
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
-