sequenceserver 2.0.0.rc3 → 2.0.0.rc8

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Files changed (473) hide show
  1. checksums.yaml +4 -4
  2. data/bin/chromedriver +0 -0
  3. data/bin/geckodriver +0 -0
  4. data/bin/sequenceserver +39 -29
  5. data/lib/sequenceserver.rb +48 -22
  6. data/lib/sequenceserver/blast/job.rb +11 -1
  7. data/lib/sequenceserver/database.rb +7 -168
  8. data/lib/sequenceserver/exceptions.rb +14 -0
  9. data/lib/sequenceserver/makeblastdb.rb +323 -0
  10. data/lib/sequenceserver/routes.rb +6 -1
  11. data/lib/sequenceserver/sequence.rb +1 -1
  12. data/lib/sequenceserver/version.rb +1 -1
  13. data/public/css/sequenceserver.css +10 -3
  14. data/public/css/sequenceserver.min.css +1 -1
  15. data/public/js/error_modal.js +27 -29
  16. data/public/js/hit.js +14 -5
  17. data/public/js/jquery_world.js +1 -1
  18. data/public/js/query.js +31 -15
  19. data/public/js/report.js +13 -6
  20. data/public/js/search.js +44 -24
  21. data/public/js/sequence_modal.js +10 -5
  22. data/public/js/sidebar.js +52 -28
  23. data/public/sequenceserver-report.min.js +17 -17
  24. data/public/sequenceserver-search.min.js +2 -2
  25. data/views/layout.erb +5 -1
  26. data/views/report.erb +1 -1
  27. data/views/search.erb +1 -1
  28. metadata +9 -450
  29. data/.bootstrap/config.json +0 -433
  30. data/.codeclimate.yml +0 -31
  31. data/.csslintrc +0 -2
  32. data/.eslintignore +0 -1
  33. data/.eslintrc.json +0 -36
  34. data/.gitignore +0 -56
  35. data/.mailmap +0 -5
  36. data/.rspec +0 -3
  37. data/.rubocop.yml +0 -61
  38. data/.travis.yml +0 -74
  39. data/AppImage/recipe.yml +0 -15
  40. data/AppImage/sequenceserver.desktop +0 -8
  41. data/AppImage/sequenceserver.png +0 -0
  42. data/AppImage/sequenceserver.sh +0 -16
  43. data/Dockerfile +0 -23
  44. data/LICENSE.txt +0 -661
  45. data/LICENSE/Apache.txt +0 -176
  46. data/LICENSE/d3.txt +0 -26
  47. data/README.md +0 -161
  48. data/package.json +0 -48
  49. data/public/vendor/.dependencies.json +0 -18
  50. data/public/vendor/.loaderversions +0 -1
  51. data/public/vendor/github/components/jquery@2.1.4/.gitignore +0 -1
  52. data/public/vendor/github/components/jquery@2.1.4/.jspm-hash +0 -1
  53. data/public/vendor/github/components/jquery@2.1.4/.jspm.json +0 -37
  54. data/public/vendor/github/components/jqueryui@1.11.4/.gitignore +0 -4
  55. data/public/vendor/github/components/jqueryui@1.11.4/.jspm-hash +0 -1
  56. data/public/vendor/github/components/jqueryui@1.11.4/.jspm.json +0 -136
  57. data/public/vendor/github/components/jqueryui@1.11.4/ui/.jshintrc +0 -24
  58. data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm-hash +0 -1
  59. data/public/vendor/github/jspm/nodelibs-buffer@0.1.0/.jspm.json +0 -10
  60. data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm-hash +0 -1
  61. data/public/vendor/github/jspm/nodelibs-events@0.1.1/.jspm.json +0 -10
  62. data/public/vendor/github/jspm/nodelibs-fs@0.1.2/.jspm-hash +0 -1
  63. data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm-hash +0 -1
  64. data/public/vendor/github/jspm/nodelibs-module@0.1.0/.jspm.json +0 -3
  65. data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm-hash +0 -1
  66. data/public/vendor/github/jspm/nodelibs-path@0.1.0/.jspm.json +0 -10
  67. data/public/vendor/github/jspm/nodelibs-process@0.1.1/.jspm-hash +0 -1
  68. data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm-hash +0 -1
  69. data/public/vendor/github/jspm/nodelibs-stream@0.1.0/.jspm.json +0 -10
  70. data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm-hash +0 -1
  71. data/public/vendor/github/jspm/nodelibs-util@0.1.0/.jspm.json +0 -10
  72. data/public/vendor/github/mbostock/d3@3.5.6/.jspm-hash +0 -1
  73. data/public/vendor/github/mbostock/d3@3.5.6/.jspm.json +0 -76
  74. data/public/vendor/github/nicgirault/circosJs@1.7.0/.gitignore +0 -10
  75. data/public/vendor/github/nicgirault/circosJs@1.7.0/.jspm-hash +0 -1
  76. data/public/vendor/github/systemjs/plugin-css@0.1.15/.gitignore +0 -1
  77. data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm-hash +0 -1
  78. data/public/vendor/github/systemjs/plugin-css@0.1.15/.jspm.json +0 -4
  79. data/public/vendor/github/systemjs/plugin-json@0.1.0/.jspm-hash +0 -1
  80. data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm-hash +0 -1
  81. data/public/vendor/github/twbs/bootstrap@3.3.5/.jspm.json +0 -100
  82. data/public/vendor/npm/amdefine@1.0.0/.jspm-hash +0 -1
  83. data/public/vendor/npm/amdefine@1.0.0/.jspm.json +0 -55
  84. data/public/vendor/npm/babel-core@5.8.23/.jspm-hash +0 -1
  85. data/public/vendor/npm/babel-runtime@5.8.20/.jspm-hash +0 -1
  86. data/public/vendor/npm/babel-runtime@5.8.20/.npmignore +0 -2
  87. data/public/vendor/npm/base62@0.1.1/.jspm-hash +0 -1
  88. data/public/vendor/npm/base62@0.1.1/.jspm.json +0 -49
  89. data/public/vendor/npm/base62@0.1.1/.travis.yml +0 -4
  90. data/public/vendor/npm/base64-js@0.0.8/.jspm-hash +0 -1
  91. data/public/vendor/npm/base64-js@0.0.8/.jspm.json +0 -77
  92. data/public/vendor/npm/base64-js@0.0.8/.travis.yml +0 -5
  93. data/public/vendor/npm/buffer@3.4.3/.jspm-hash +0 -1
  94. data/public/vendor/npm/buffer@3.4.3/.jspm.json +0 -105
  95. data/public/vendor/npm/buffer@3.4.3/.npmignore +0 -1
  96. data/public/vendor/npm/buffer@3.4.3/.travis.yml +0 -8
  97. data/public/vendor/npm/buffer@3.4.3/.zuul.yml +0 -20
  98. data/public/vendor/npm/core-js@1.1.2/.eslintrc +0 -36
  99. data/public/vendor/npm/core-js@1.1.2/.gitattributes +0 -1
  100. data/public/vendor/npm/core-js@1.1.2/.jspm-hash +0 -1
  101. data/public/vendor/npm/core-js@1.1.2/.npmignore +0 -10
  102. data/public/vendor/npm/core-js@1.1.2/.travis.yml +0 -3
  103. data/public/vendor/npm/core-util-is@1.0.1/.jspm-hash +0 -1
  104. data/public/vendor/npm/core-util-is@1.0.1/.jspm.json +0 -58
  105. data/public/vendor/npm/envify@3.4.0/.jspm-hash +0 -1
  106. data/public/vendor/npm/envify@3.4.0/.jspm.json +0 -72
  107. data/public/vendor/npm/envify@3.4.0/.npmignore +0 -2
  108. data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm-hash +0 -1
  109. data/public/vendor/npm/esprima-fb@13001.1001.0-dev-harmony-fb/.jspm.json +0 -102
  110. data/public/vendor/npm/events@1.0.2/.jspm-hash +0 -1
  111. data/public/vendor/npm/events@1.0.2/.jspm.json +0 -67
  112. data/public/vendor/npm/events@1.0.2/.npmignore +0 -1
  113. data/public/vendor/npm/events@1.0.2/.travis.yml +0 -7
  114. data/public/vendor/npm/events@1.0.2/.zuul.yml +0 -12
  115. data/public/vendor/npm/font-awesome@4.4.0/.jspm-hash +0 -1
  116. data/public/vendor/npm/font-awesome@4.4.0/.jspm.json +0 -81
  117. data/public/vendor/npm/font-awesome@4.4.0/.npmignore +0 -42
  118. data/public/vendor/npm/ieee754@1.1.6/.jspm-hash +0 -1
  119. data/public/vendor/npm/ieee754@1.1.6/.jspm.json +0 -70
  120. data/public/vendor/npm/ieee754@1.1.6/.travis.yml +0 -7
  121. data/public/vendor/npm/ieee754@1.1.6/.zuul.yml +0 -20
  122. data/public/vendor/npm/inherits@2.0.1/.jspm-hash +0 -1
  123. data/public/vendor/npm/inherits@2.0.1/.jspm.json +0 -60
  124. data/public/vendor/npm/is-array@1.0.1/.jepso-ci.json +0 -3
  125. data/public/vendor/npm/is-array@1.0.1/.jspm-hash +0 -1
  126. data/public/vendor/npm/is-array@1.0.1/.jspm.json +0 -42
  127. data/public/vendor/npm/is-array@1.0.1/.npmignore +0 -0
  128. data/public/vendor/npm/isarray@0.0.1/.jspm-hash +0 -1
  129. data/public/vendor/npm/isarray@0.0.1/.jspm.json +0 -51
  130. data/public/vendor/npm/jstransform@10.1.0/.jshintrc +0 -28
  131. data/public/vendor/npm/jstransform@10.1.0/.jspm-hash +0 -1
  132. data/public/vendor/npm/jstransform@10.1.0/.jspm.json +0 -95
  133. data/public/vendor/npm/jstransform@10.1.0/.npmignore +0 -4
  134. data/public/vendor/npm/jstransform@10.1.0/.travis.yml +0 -8
  135. data/public/vendor/npm/path-browserify@0.0.0/.jspm-hash +0 -1
  136. data/public/vendor/npm/path-browserify@0.0.0/.jspm.json +0 -56
  137. data/public/vendor/npm/process@0.10.1/.jspm-hash +0 -1
  138. data/public/vendor/npm/react@0.13.3/.jspm-hash +0 -1
  139. data/public/vendor/npm/react@0.13.3/.jspm.json +0 -77
  140. data/public/vendor/npm/readable-stream@1.1.13/.jspm-hash +0 -1
  141. data/public/vendor/npm/readable-stream@1.1.13/.jspm.json +0 -95
  142. data/public/vendor/npm/readable-stream@1.1.13/.npmignore +0 -5
  143. data/public/vendor/npm/source-map@0.1.31/.jspm-hash +0 -1
  144. data/public/vendor/npm/source-map@0.1.31/.jspm.json +0 -133
  145. data/public/vendor/npm/source-map@0.1.31/.npmignore +0 -2
  146. data/public/vendor/npm/source-map@0.1.31/.travis.yml +0 -4
  147. data/public/vendor/npm/stream-browserify@1.0.0/.jspm-hash +0 -1
  148. data/public/vendor/npm/stream-browserify@1.0.0/.jspm.json +0 -77
  149. data/public/vendor/npm/stream-browserify@1.0.0/.travis.yml +0 -4
  150. data/public/vendor/npm/string_decoder@0.10.31/.jspm-hash +0 -1
  151. data/public/vendor/npm/string_decoder@0.10.31/.jspm.json +0 -58
  152. data/public/vendor/npm/string_decoder@0.10.31/.npmignore +0 -2
  153. data/public/vendor/npm/through@2.3.8/.jspm-hash +0 -1
  154. data/public/vendor/npm/through@2.3.8/.jspm.json +0 -72
  155. data/public/vendor/npm/through@2.3.8/.travis.yml +0 -5
  156. data/public/vendor/npm/underscore@1.8.3/.jspm-hash +0 -1
  157. data/public/vendor/npm/underscore@1.8.3/.jspm.json +0 -74
  158. data/public/vendor/npm/util@0.10.3/.jspm-hash +0 -1
  159. data/public/vendor/npm/util@0.10.3/.jspm.json +0 -58
  160. data/public/vendor/npm/util@0.10.3/.npmignore +0 -1
  161. data/public/vendor/npm/util@0.10.3/.travis.yml +0 -8
  162. data/public/vendor/npm/util@0.10.3/.zuul.yml +0 -10
  163. data/public/vendor/npm/webshim@1.15.8/.gitattributes +0 -12
  164. data/public/vendor/npm/webshim@1.15.8/.jspm-hash +0 -1
  165. data/public/vendor/npm/webshim@1.15.8/.jspm.json +0 -92
  166. data/public/vendor/npm/webshim@1.15.8/.npmignore +0 -16
  167. data/public/vendor/npm/webshim@1.15.8/.project +0 -12
  168. data/public/vendor/npm/webshim@1.15.8/demos/demos/filereader/upload/.keep +0 -0
  169. data/sequenceserver.gemspec +0 -55
  170. data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +0 -228
  171. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +0 -583
  172. data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +0 -228
  173. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +0 -587
  174. data/spec/blast_versions/blast_2.3.0/blast_2.3.0_spec.rb +0 -229
  175. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +0 -587
  176. data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +0 -228
  177. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +0 -588
  178. data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +0 -228
  179. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +0 -587
  180. data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +0 -228
  181. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +0 -587
  182. data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +0 -228
  183. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +0 -587
  184. data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +0 -228
  185. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +0 -587
  186. data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +0 -228
  187. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +0 -585
  188. data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +0 -176
  189. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +0 -237
  190. data/spec/capybara_spec.rb +0 -334
  191. data/spec/config_spec.rb +0 -87
  192. data/spec/database/funky_ids/funky_ids.fa +0 -16
  193. data/spec/database/funky_ids/funky_ids.fa.nhd +0 -8
  194. data/spec/database/funky_ids/funky_ids.fa.nhi +0 -0
  195. data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
  196. data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
  197. data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
  198. data/spec/database/funky_ids/funky_ids.fa.nsd +0 -15
  199. data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
  200. data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
  201. data/spec/database/funky_sequences/README.md +0 -14
  202. data/spec/database/funky_sequences/funky_aa_sequences.fa +0 -7
  203. data/spec/database/funky_sequences/funky_aa_sequences.fa.phd +0 -3
  204. data/spec/database/funky_sequences/funky_aa_sequences.fa.phi +0 -0
  205. data/spec/database/funky_sequences/funky_aa_sequences.fa.phr +0 -0
  206. data/spec/database/funky_sequences/funky_aa_sequences.fa.pin +0 -0
  207. data/spec/database/funky_sequences/funky_aa_sequences.fa.pog +0 -0
  208. data/spec/database/funky_sequences/funky_aa_sequences.fa.psd +0 -6
  209. data/spec/database/funky_sequences/funky_aa_sequences.fa.psi +0 -0
  210. data/spec/database/funky_sequences/funky_aa_sequences.fa.psq +0 -0
  211. data/spec/database/funky_sequences/funky_na_sequences.fa +0 -2
  212. data/spec/database/funky_sequences/funky_na_sequences.fa.nhr +0 -0
  213. data/spec/database/funky_sequences/funky_na_sequences.fa.nin +0 -0
  214. data/spec/database/funky_sequences/funky_na_sequences.fa.nog +0 -0
  215. data/spec/database/funky_sequences/funky_na_sequences.fa.nsd +0 -2
  216. data/spec/database/funky_sequences/funky_na_sequences.fa.nsi +0 -0
  217. data/spec/database/funky_sequences/funky_na_sequences.fa.nsq +0 -0
  218. data/spec/database/ox_parse_error/query.fa +0 -1
  219. data/spec/database/ox_parse_error/rand1.fa +0 -2
  220. data/spec/database/ox_parse_error/rand1.fa.nhd +0 -1
  221. data/spec/database/ox_parse_error/rand1.fa.nhi +0 -0
  222. data/spec/database/ox_parse_error/rand1.fa.nhr +0 -0
  223. data/spec/database/ox_parse_error/rand1.fa.nin +0 -0
  224. data/spec/database/ox_parse_error/rand1.fa.nog +0 -0
  225. data/spec/database/ox_parse_error/rand1.fa.nsd +0 -2
  226. data/spec/database/ox_parse_error/rand1.fa.nsi +0 -0
  227. data/spec/database/ox_parse_error/rand1.fa.nsq +0 -0
  228. data/spec/database/ox_parse_error/rand2.fa +0 -2
  229. data/spec/database/ox_parse_error/rand2.fa.nhd +0 -1
  230. data/spec/database/ox_parse_error/rand2.fa.nhi +0 -0
  231. data/spec/database/ox_parse_error/rand2.fa.nhr +0 -0
  232. data/spec/database/ox_parse_error/rand2.fa.nin +0 -0
  233. data/spec/database/ox_parse_error/rand2.fa.nog +0 -0
  234. data/spec/database/ox_parse_error/rand2.fa.nsd +0 -2
  235. data/spec/database/ox_parse_error/rand2.fa.nsi +0 -0
  236. data/spec/database/ox_parse_error/rand2.fa.nsq +0 -0
  237. data/spec/database/ox_parse_error_unique_ids/query.fa +0 -1
  238. data/spec/database/ox_parse_error_unique_ids/rand1.fa +0 -2
  239. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhd +0 -1
  240. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhi +0 -0
  241. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nhr +0 -0
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  243. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nog +0 -0
  244. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsd +0 -2
  245. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsi +0 -0
  246. data/spec/database/ox_parse_error_unique_ids/rand1.fa.nsq +0 -0
  247. data/spec/database/ox_parse_error_unique_ids/rand2.fa +0 -2
  248. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhd +0 -1
  249. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhi +0 -0
  250. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nhr +0 -0
  251. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nin +0 -0
  252. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nog +0 -0
  253. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsd +0 -2
  254. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsi +0 -0
  255. data/spec/database/ox_parse_error_unique_ids/rand2.fa.nsq +0 -0
  256. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa +0 -6
  257. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhd +0 -1
  258. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhi +0 -0
  259. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nhr +0 -0
  260. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nin +0 -0
  261. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nog +0 -0
  262. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsd +0 -2
  263. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsi +0 -0
  264. data/spec/database/pipe_in_seqid/pipe_in_seqid.fa.nsq +0 -0
  265. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +0 -8
  266. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
  267. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  268. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  269. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
  270. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd +0 -16
  271. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +0 -0
  272. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
  273. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +0 -8
  274. data/spec/database/sample/links.rb +0 -23
  275. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +0 -6449
  276. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phd +0 -1189
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