t2-web 0.1.6 → 0.1.7

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.
Files changed (17) hide show
  1. data/CHANGES +4 -0
  2. data/README +1 -1
  3. data/Rakefile +1 -1
  4. data/bin/t2_webapp.rb +2 -2
  5. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/Pathway +1 -0
  6. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/clean_image +0 -0
  7. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/geneList +184 -0
  8. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/image +0 -0
  9. data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/url +1 -0
  10. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/Pathway +1 -0
  11. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/clean_image +0 -0
  12. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/geneList +184 -0
  13. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/image +0 -0
  14. data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/url +1 -0
  15. data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/UniProtID +185 -0
  16. data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/ValidatedProtein +10 -0
  17. metadata +15 -3
data/CHANGES CHANGED
@@ -1,5 +1,9 @@
1
1
  = Changes log for the Taverna via the Web App
2
2
 
3
+ == 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
5
+ * Fixed minor bug with displaying images -- incorrect truncation since there is an extra \n
6
+
3
7
  == Version 0.1.6
4
8
  * Now, for some list disambiguation, the first element of top level lists are in bold
5
9
  * Increased side frames slightly
data/README CHANGED
@@ -2,7 +2,7 @@
2
2
 
3
3
 
4
4
  Authors:: Konstantinos Karasavvas
5
- Gem Version:: 0.1.6
5
+ Gem Version:: 0.1.7
6
6
  Contact:: mailto:kostas.karasavvas@nbic.nl
7
7
  Licence:: MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
8
8
  Copyright:: (c) 2012 Netherlands Bioinformatics Centre, The Netherlands
data/Rakefile CHANGED
@@ -12,7 +12,7 @@ require 'rdoc/task'
12
12
 
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  spec = Gem::Specification.new do |s|
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  s.name = 't2-web'
15
- s.version = '0.1.6'
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+ s.version = '0.1.7'
16
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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
data/bin/t2_webapp.rb CHANGED
@@ -345,8 +345,8 @@ END
345
345
  if mime_type =~ /image\/png|image\/jpg|image\/gif|image\/bmp|application\/octet-stream/
346
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  # clean image from <b></b> --- will not be needed after we deal with 'typing' properly t2-server-0.9.x
347
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  if mime_type =~ /octet-stream/
348
- unless File.file?("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
349
- new_length = File.size?(display_file) - 3 - 4 # for <b> and </b> respectively
348
+ unless File.file?("#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
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+ new_length = File.size?(display_file) - 3 - 5 # for <b> and </b>\n respectively
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  %x( dd if="#{display_file}" of="#{settings.public_folder}/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}" bs=1 skip=3 count="#{new_length}" )
351
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  end
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  generate_image_result("/#{WEB_APP_NAME}/tmp/outputs/#{run_uuid}/clean_#{t2_output}")
data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/Pathway ADDED
@@ -0,0 +1 @@
1
+ <b>path:hsa05016 Huntington's disease - Homo sapiens (human)</b>
data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/geneList ADDED
@@ -0,0 +1,184 @@
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+ <b>100532726</b>
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data/public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/url ADDED
@@ -0,0 +1 @@
1
+ <b>http://soap.genome.jp/tmp/mark_pathway_www_api.133491304616025/hsa05016.png</b>
data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/Pathway ADDED
@@ -0,0 +1 @@
1
+ <b>path:hsa05016 Huntington's disease - Homo sapiens (human)</b>
data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/geneList ADDED
@@ -0,0 +1,184 @@
1
+ <b>100532726</b>
2
+ 10105
3
+ 10126
4
+ 10476
5
+ 10488
6
+ 10540
7
+ 10891
8
+ 10975
9
+ 1173
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+ 1175
11
+ 1211
12
+ 1212
13
+ 1213
14
+ 125965
15
+ 126328
16
+ 1327
17
+ 1329
18
+ 1337
19
+ 1339
20
+ 1340
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+ 1345
22
+ 1346
23
+ 1347
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+ 1349
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+ 1350
26
+ 1351
27
+ 1385
28
+ 1387
29
+ 146754
30
+ 148327
31
+ 1537
32
+ 160
33
+ 161
34
+ 163
35
+ 1639
36
+ 170712
37
+ 1742
38
+ 2033
39
+ 23186
40
+ 23236
41
+ 246721
42
+ 25942
43
+ 25981
44
+ 27019
45
+ 27089
46
+ 27113
47
+ 2776
48
+ 2876
49
+ 2902
50
+ 2904
51
+ 291
52
+ 2911
53
+ 2915
54
+ 292
55
+ 293
56
+ 29796
57
+ 3064
58
+ 3065
59
+ 3066
60
+ 3092
61
+ 317
62
+ 341947
63
+ 3708
64
+ 374291
65
+ 387332
66
+ 440567
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+ 4508
68
+ 4509
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+ 4512
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+ 4513
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+ 4514
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+ 4519
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+ 4694
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+ 4695
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+ 4696
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+ 4697
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+ 4698
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+ 4700
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+ 4701
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+ 4702
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+ 4704
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+ 4705
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+ 4706
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+ 4707
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+ 4708
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+ 4709
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+ 4710
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+ 4711
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+ 4712
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+ 4713
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+ 4714
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+ 4715
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+ 4716
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+ 4717
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+ 4718
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+ 4719
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+ 4720
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+ 4723
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+ 4724
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+ 4725
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+ 4726
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+ 4728
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+ 498
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+ 506
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+ 509
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+ 514
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+ 515
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+ 516
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+ 517
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+ 522
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+ 5330
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+ 5331
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+ 539
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+ 5430
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+ 5431
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+ 5432
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+ 5433
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+ 55081
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+ 55567
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+ 55967
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+ 56901
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+ 581
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+ 5978
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+ 627
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+ 6389
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+ 6390
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+ 6391
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+ 6392
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+ 64446
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+ 64764
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+ 6647
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+ 6648
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+ 6667
155
+ 6874
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+ 6875
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+ 6908
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+ 7019
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+ 7052
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+ 7157
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+ 7350
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+ 7381
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+ 7384
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+ 7385
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+ 7386
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+ 7388
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+ 7416
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+ 7417
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+ 7419
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+ 7802
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+ 8218
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+ 83544
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+ 836
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+ 841
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+ 842
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+ 84699
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+ 84701
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+ 9001
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+ 90993
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+ 9167
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+ 9377
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+ 9519
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+ 9586
data/public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/url ADDED
@@ -0,0 +1 @@
1
+ <b>http://soap.genome.jp/tmp/mark_pathway_www_api.133491773910665/hsa05016.png</b>
data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/UniProtID ADDED
@@ -0,0 +1,185 @@
1
+ <b>P70386</b>
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+ Q02527
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+ Q09327
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+ Q10470
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+ Q14CK5
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+ Q6IC49
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+ Q9UH32
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+ P70386
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+ Q02527
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+ Q09327
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+ Q14CK5
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+ Q6IC49
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+ Q9UH32
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+ <b>A8K7C2</b>
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+ P02571
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data/public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/ValidatedProtein ADDED
@@ -0,0 +1,10 @@
1
+ <b>GnT-III</b>
2
+ GnT-III
3
+ GnT-III
4
+ GnT-III
5
+ <b>gamma-actin</b>
6
+ <b>APP</b>
7
+ APP
8
+ APP
9
+ <b>UPS</b>
10
+ <b>TFE</b>
metadata CHANGED
@@ -1,13 +1,13 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: t2-web
3
3
  version: !ruby/object:Gem::Version
4
- hash: 23
4
+ hash: 21
5
5
  prerelease:
6
6
  segments:
7
7
  - 0
8
8
  - 1
9
- - 6
10
- version: 0.1.6
9
+ - 7
10
+ version: 0.1.7
11
11
  platform: ruby
12
12
  authors:
13
13
  - Kostas Karasavvas
@@ -146,6 +146,11 @@ files:
146
146
  - public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopContributingConcepts
147
147
  - public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/TopMatchingConcepts
148
148
  - public/t2web/tmp/outputs/f5d66ef2-8ca7-436e-aa74-73375121bc5a/SummedSimilarity
149
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/image
150
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/url
151
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/Pathway
152
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/clean_image
153
+ - public/t2web/tmp/outputs/46c02da9-0577-4cbe-9ba5-d8fdfe649328/geneList
149
154
  - public/t2web/tmp/outputs/1dbfe89e-527b-4bbd-9aff-e2acb0250480/image
150
155
  - public/t2web/tmp/outputs/1dbfe89e-527b-4bbd-9aff-e2acb0250480/url
151
156
  - public/t2web/tmp/outputs/1dbfe89e-527b-4bbd-9aff-e2acb0250480/Pathway
@@ -190,6 +195,11 @@ files:
190
195
  - public/t2web/tmp/outputs/17a9e3a7-01e8-4906-bb4e-17afc495c3f2/UniProtID
191
196
  - public/t2web/tmp/outputs/dc51d833-8d87-4e89-8343-46bca8898345/ValidatedProtein
192
197
  - public/t2web/tmp/outputs/dc51d833-8d87-4e89-8343-46bca8898345/UniProtID
198
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/image
199
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/url
200
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/Pathway
201
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/clean_image
202
+ - public/t2web/tmp/outputs/3527c902-497c-40fd-baed-68de0ad42e67/geneList
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  - public/t2web/tmp/outputs/98992f59-65d0-4f07-a35d-c9cdc5a8ce82/image
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  - public/t2web/tmp/outputs/98992f59-65d0-4f07-a35d-c9cdc5a8ce82/url
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  - public/t2web/tmp/outputs/98992f59-65d0-4f07-a35d-c9cdc5a8ce82/Pathway
@@ -256,6 +266,8 @@ files:
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  - public/t2web/tmp/outputs/d1461a45-200f-4f48-84a8-d01ca3e79b0b/UniProtID
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  - public/t2web/tmp/outputs/dcbec202-78b9-4a0f-ad2e-b1373190e21a/ValidatedProtein
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  - public/t2web/tmp/outputs/dcbec202-78b9-4a0f-ad2e-b1373190e21a/UniProtID
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+ - public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/ValidatedProtein
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+ - public/t2web/tmp/outputs/57e79763-5f5a-408b-b454-7e9aca4da68a/UniProtID
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  - public/t2web/tmp/outputs/ecc62b90-7989-4165-addd-0b53581a9627/image
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  - public/t2web/tmp/outputs/ecc62b90-7989-4165-addd-0b53581a9627/url
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  - public/t2web/tmp/outputs/ecc62b90-7989-4165-addd-0b53581a9627/Pathway