t2-web 0.1.7 → 0.1.8

data/CHANGES

@@ -1,5 +1,8 @@
 = Changes log for the Taverna via the Web App
 
+== Version 0.1.8
+* Created executable to start the webapp
+
 == Version 0.1.7
 * The clean image is truncated/copied only once now -- needed to remove the bold tabs from the image
 * Fixed minor bug with displaying images -- incorrect truncation since there is an extra \n

data/README

@@ -2,7 +2,7 @@
 
 
 Authors::     Konstantinos Karasavvas
-Gem Version:: 0.1.7
+Gem Version:: 0.1.8
 Contact::     mailto:kostas.karasavvas@nbic.nl
 Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
 Copyright::   (c) 2012 Netherlands Bioinformatics Centre, The Netherlands
@@ -23,9 +23,7 @@ description provided in the workflow itself in myExperiment.
 
 == Usage
 
-  thin -p 9494 start
-
-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.
+  $ t2-web -p 9494 start
 
 
 

data/Rakefile

@@ -12,13 +12,13 @@ require 'rdoc/task'
 
 spec = Gem::Specification.new do |s|
   s.name = 't2-web'
-  s.version = '0.1.7'
+  s.version = '0.1.8'
   s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
   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.'
   s.description = s.summary
   s.author = 'Kostas Karasavvas'
   s.email = 'kostas.karasavvas@nbic.nl'
-  #s.executables = ['t2_webapp.rb']
+  s.executables = ['t2-web']
   s.files = %w(LICENSE README CHANGES Rakefile Gemfile Gemfile.lock) + Dir.glob("{bin,lib,doc,spec,public,views}/**/*")
   s.require_path = "lib"
   s.bindir = "bin"

data/bin/t2-web

@@ -0,0 +1,43 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 't2-web'
+
+# Set up and parse arguments
+opts = OptionParser.new do |opt|
+  opt.banner = "Usage: t2-web [options] start|stop|restart"
+  opt.separator("\nSupports the following options:")
+  opt.on("-d", "--daemonize", "Run daemonized in the background")
+  opt.on("-p", "--port PORT", "Use PORT (default: 3000)")
+  opt.on("-s", "--servers NUM", "Number of servers to start")
+  opt.on_tail("-v", "--version", "Show the version") do
+    puts "Taverna 2 Web Interface Generator version: #{T2Web::VERSION}"
+    exit
+  end
+  opt.on_tail("-h", "-?", "--help", "Show this message") do
+    puts opt
+    exit
+  end
+end
+
+# parse options (currently only displaying and passing all to thin!)
+opts.parse!
+
+if ARGV.size == 0
+  puts opts
+  exit
+end
+
+# TODO: call webapp via rack and ruby rather than from the prompt!!
+
+INSTALL_DIR = `gem environment gemdir`.chomp + "/gems/t2-web-#{T2Web::VERSION}/bin"
+
+# cd to proper dir and run thin $* for now
+success = `cd #{INSTALL_DIR} ; thin #{$*.join(' ')}`
+
+if success
+  puts "Running: thin #{$*.join(' ')} !"
+else
+  puts "Failed running: thin #{$*} !"
+end
+

data/lib/t2-web.rb

@@ -0,0 +1,3 @@
+module T2Web
+  VERSION = "0.1.8"
+end

data/public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/UniProtID

@@ -0,0 +1,185 @@
+<b>P70386</b>
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+P70386
+Q02527
+Q09327
+Q10470
+Q14CK5
+Q6IC49
+Q9UH32
+<b>A8K7C2</b>
+O73815
+P02571
+P02579
+P12714
+P14104
+P53478
+P60010
+P63259
+P63260
+P63261
+P99022
+Q5U032
+Q6P3K9
+Q7ZVI7
+Q96E67
+Q9P3X6
+Q9P3X7
+<b>P15943</b>
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+P15943
+Q06335
+Q06481
+Q13861
+Q14594
+Q14662
+Q71U10
+Q7M4L3
+Q9BT36
+Q9TVV0
+Q9U4H3
+Q9W5F1
+P05067
+P08592
+P09000
+P12023
+P78438
+P97487
+P97942
+Q10651
+Q13764
+Q13778
+Q13793
+Q16011
+Q16014
+Q16019
+Q16020
+Q18583
+Q547B7
+Q6GSC0
+Q8WZ99
+Q95ZX1
+Q99K32
+Q9BT38
+Q9UC33
+Q9UCA9
+Q9UCB6
+Q9UCC8
+Q9UCD1
+Q9UQ58
+<b>P08396</b>
+P08397
+P19356
+P22907
+P28789
+Q16012
+Q2VQW9
+<b>Q08AP2</b>
+Q08AP3
+Q15439
+Q15440
+Q15441
+Q60721
+Q60722
+Q62211
+Q62655
+Q64072
+Q80UE8
+Q99N33

data/public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/ValidatedProtein

@@ -0,0 +1,10 @@
+<b>GnT-III</b>
+GnT-III
+GnT-III
+GnT-III
+<b>gamma-actin</b>
+<b>APP</b>
+APP
+APP
+<b>UPS</b>
+<b>TFE</b>

data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/Pathway

@@ -0,0 +1 @@
+<b>path:hsa05016 Huntington's disease - Homo sapiens (human)</b>

data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/geneList

@@ -0,0 +1,184 @@
+<b>100532726</b>
+10105
+10126
+10476
+10488
+10540
+10891
+10975
+1173
+1175
+1211
+1212
+1213
+125965
+126328
+1327
+1329
+1337
+1339
+1340
+1345
+1346
+1347
+1349
+1350
+1351
+1385
+1387
+146754
+148327
+1537
+160
+161
+163
+1639
+170712
+1742
+2033
+23186
+23236
+246721
+25942
+25981
+27019
+27089
+27113
+2776
+2876
+2902
+2904
+291
+2911
+2915
+292
+293
+29796
+3064
+3065
+3066
+3092
+317
+341947
+3708
+374291
+387332
+440567
+4508
+4509
+4512
+4513
+4514
+4519
+4694
+4695
+4696
+4697
+4698
+4700
+4701
+4702
+4704
+4705
+4706
+4707
+4708
+4709
+4710
+4711
+4712
+4713
+4714
+4715
+4716
+4717
+4718
+4719
+4720
+4722
+4723
+4724
+4725
+4726
+4728
+4729
+4731
+4899
+498
+506
+509
+51079
+51164
+513
+514
+515
+516
+517
+518
+522
+5330
+5331
+5332
+539
+54205
+5430
+5431
+5432
+5433
+5434
+5435
+5436
+5437
+5438
+5439
+5440
+5441
+54539
+5468
+548644
+55081
+55567
+55967
+56901
+581
+5978
+627
+6389
+6390
+6391
+6392
+64446
+64764
+6647
+6648
+6667
+6874
+6875
+6908
+7019
+7052
+7157
+7350
+7381
+7384
+7385
+7386
+7388
+7416
+7417
+7419
+7802
+8218
+83447
+83544
+836
+841
+842
+84699
+84701
+9001
+90993
+9167
+9377
+9519
+9586

data/public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/url

@@ -0,0 +1 @@
+<b>http://soap.genome.jp/tmp/mark_pathway_www_api.13351787557631/hsa05016.png</b>

metadata

@@ -1,113 +1,108 @@
---- !ruby/object:Gem::Specification 
+--- !ruby/object:Gem::Specification
 name: t2-web
-version: !ruby/object:Gem::Version 
-  hash: 21
+version: !ruby/object:Gem::Version
+  version: 0.1.8
   prerelease: 
-  segments: 
-  - 0
-  - 1
-  - 7
-  version: 0.1.7
 platform: ruby
-authors: 
+authors:
 - Kostas Karasavvas
 autorequire: 
 bindir: bin
 cert_chain: []
-
-date: 2012-04-20 00:00:00 Z
-dependencies: 
-- !ruby/object:Gem::Dependency 
+date: 2012-05-03 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
   name: sinatra
-  prerelease: false
-  requirement: &id001 !ruby/object:Gem::Requirement 
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 27
-        segments: 
-        - 1
-        - 3
-        - 0
+      - !ruby/object:Gem::Version
         version: 1.3.0
   type: :runtime
-  version_requirements: *id001
-- !ruby/object:Gem::Dependency 
-  name: haml
   prerelease: false
-  requirement: &id002 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 7
-        segments: 
-        - 3
-        - 1
-        - 2
+      - !ruby/object:Gem::Version
+        version: 1.3.0
+- !ruby/object:Gem::Dependency
+  name: haml
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
         version: 3.1.2
   type: :runtime
-  version_requirements: *id002
-- !ruby/object:Gem::Dependency 
-  name: rest-client
   prerelease: false
-  requirement: &id003 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 9
-        segments: 
-        - 1
-        - 6
-        - 3
+      - !ruby/object:Gem::Version
+        version: 3.1.2
+- !ruby/object:Gem::Dependency
+  name: rest-client
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
         version: 1.6.3
   type: :runtime
-  version_requirements: *id003
-- !ruby/object:Gem::Dependency 
-  name: t2-server
   prerelease: false
-  requirement: &id004 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 5
-        segments: 
-        - 0
-        - 6
-        - 1
+      - !ruby/object:Gem::Version
+        version: 1.6.3
+- !ruby/object:Gem::Dependency
+  name: t2-server
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
         version: 0.6.1
   type: :runtime
-  version_requirements: *id004
-- !ruby/object:Gem::Dependency 
-  name: myexperiment-rest
   prerelease: false
-  requirement: &id005 !ruby/object:Gem::Requirement 
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.6.1
+- !ruby/object:Gem::Dependency
+  name: myexperiment-rest
+  requirement: !ruby/object:Gem::Requirement
     none: false
-    requirements: 
+    requirements:
     - - ~>
-      - !ruby/object:Gem::Version 
-        hash: 21
-        segments: 
-        - 0
-        - 3
-        - 3
+      - !ruby/object:Gem::Version
         version: 0.3.3
   type: :runtime
-  version_requirements: *id005
-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.
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 0.3.3
+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.
 email: kostas.karasavvas@nbic.nl
-executables: []
-
+executables:
+- t2-web
 extensions: []
-
-extra_rdoc_files: 
+extra_rdoc_files:
 - README
 - LICENSE
 - CHANGES
-files: 
+files:
 - LICENSE
 - README
 - CHANGES
@@ -116,11 +111,15 @@ files:
 - Gemfile.lock
 - bin/config.ru
 - bin/log/thin.log
+- bin/t2-web
 - bin/t2_webapp.rb
+- lib/t2-web.rb
 - public/t2web/scripts/results.js
 - public/t2web/scripts/form.js
 - public/t2web/scripts/jquery-1.6.1.js
 - public/t2web/scripts/jquery.tipsy.js
+- public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/ValidatedProtein
+- public/t2web/tmp/outputs/0b1e49dc-1028-4f11-8576-750e58d9d3c3/UniProtID
 - public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/image
 - public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/url
 - public/t2web/tmp/outputs/645e0cd3-b15c-419a-9aaf-cc252f698007/Pathway
@@ -262,6 +261,11 @@ files:
 - public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/url
 - public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/Pathway
 - public/t2web/tmp/outputs/c0881a86-9c9f-4a38-84cd-0a97ff6813a2/geneList
+- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/image
+- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/url
+- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/Pathway
+- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/clean_image
+- public/t2web/tmp/outputs/696393ef-e54a-4487-89a2-42d67a738bd3/geneList
 - public/t2web/tmp/outputs/d1461a45-200f-4f48-84a8-d01ca3e79b0b/ValidatedProtein
 - public/t2web/tmp/outputs/d1461a45-200f-4f48-84a8-d01ca3e79b0b/UniProtID
 - public/t2web/tmp/outputs/dcbec202-78b9-4a0f-ad2e-b1373190e21a/ValidatedProtein
@@ -295,36 +299,28 @@ files:
 - views/form.haml
 homepage: 
 licenses: []
-
 post_install_message: 
 rdoc_options: []
-
-require_paths: 
+require_paths:
 - lib
-required_ruby_version: !ruby/object:Gem::Requirement 
+required_ruby_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
-required_rubygems_version: !ruby/object:Gem::Requirement 
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
   none: false
-  requirements: 
-  - - ">="
-    - !ruby/object:Gem::Version 
-      hash: 3
-      segments: 
-      - 0
-      version: "0"
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
 requirements: []
-
 rubyforge_project: 
-rubygems_version: 1.8.21
+rubygems_version: 1.8.23
 signing_key: 
 specification_version: 3
-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.
+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.
 test_files: []
-