sequenceserver 1.0.0.pre.5 → 1.0.0

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Files changed (221) hide show
  1. checksums.yaml +4 -4
  2. data/.bootstrap/README.mkd +2 -0
  3. data/.bootstrap/config.json +416 -0
  4. data/.gitignore +56 -0
  5. data/.mailmap +5 -0
  6. data/.rspec +2 -0
  7. data/.rubocop.yml +51 -0
  8. data/.travis.yml +18 -0
  9. data/COPYRIGHT.txt +13 -0
  10. data/Gruntfile.js +133 -0
  11. data/LICENSE.txt +638 -46
  12. data/{LICENSE.Apache.txt → LICENSE/Apache.txt} +0 -0
  13. data/LICENSE/d3.txt +26 -0
  14. data/Rakefile +13 -0
  15. data/bin/sequenceserver +27 -4
  16. data/lib/sequenceserver.rb +26 -13
  17. data/lib/sequenceserver/database.rb +19 -8
  18. data/lib/sequenceserver/exceptions.rb +9 -1
  19. data/package.json +29 -0
  20. data/public/css/custom.css +10 -2
  21. data/public/dist/css/sequenceserver.min.css +1 -1
  22. data/public/dist/css/sequenceserver.min.css.gz +0 -0
  23. data/public/dist/js/sequenceserver.min.js +1 -1
  24. data/public/dist/js/sequenceserver.min.js.gz +0 -0
  25. data/public/js/jquery.t.js +2 -2
  26. data/public/js/sequence.js +4 -1
  27. data/public/js/sequenceserver.js +23 -20
  28. data/sequenceserver.gemspec +3 -6
  29. data/spec/blast_spec.rb +297 -0
  30. data/spec/capybara_spec.rb +51 -0
  31. data/spec/config_spec.rb +87 -0
  32. data/spec/database/funky_ids/funky_ids.fa +12 -0
  33. data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
  34. data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
  35. data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
  36. data/spec/database/funky_ids/funky_ids.fa.nsd +11 -0
  37. data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
  38. data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
  39. data/spec/database/sample/links.rb +23 -0
  40. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta +6449 -0
  41. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.phr +0 -0
  42. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pin +0 -0
  43. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.pog +0 -0
  44. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psd +2378 -0
  45. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psi +0 -0
  46. data/spec/database/sample/proteins/Solenopsis_invicta/Sinvicta2-2-3.prot.subset.fasta.psq +0 -0
  47. data/spec/database/sample/si_uniprot_idmap.yml +14180 -0
  48. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta +5486 -0
  49. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nhr +0 -0
  50. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nin +0 -0
  51. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nog +0 -0
  52. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd +946 -0
  53. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsi +0 -0
  54. data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsq +0 -0
  55. data/spec/database/unformatted/Cardiocondyla_obscurior/Cobs1.4.proteins.fa +148303 -0
  56. data/spec/database/without_parse_seqids/without_parse_seqids.fa +10 -0
  57. data/spec/database/without_parse_seqids/without_parse_seqids.fa.phr +0 -0
  58. data/spec/database/without_parse_seqids/without_parse_seqids.fa.pin +0 -0
  59. data/spec/database/without_parse_seqids/without_parse_seqids.fa.psq +0 -0
  60. data/spec/database_spec.rb +129 -0
  61. data/spec/empty_config.yml +0 -0
  62. data/spec/routes_spec.rb +103 -0
  63. data/spec/sample.conf +2 -0
  64. data/spec/sample_reports/blastn_sample.asn +144 -0
  65. data/spec/sample_reports/blastp_sample.asn +1187 -0
  66. data/spec/sample_reports/blastx_sample.asn +1191 -0
  67. data/spec/sample_reports/no_hits_sample.asn +130 -0
  68. data/spec/sample_reports/tblastn_sample.asn +1107 -0
  69. data/spec/sample_reports/tblastx_sample.asn +2422 -0
  70. data/spec/sample_reports/with_hits_sample.asn +1489 -0
  71. data/spec/sequence_spec.rb +100 -0
  72. data/spec/sequenceserver_spec.rb +108 -0
  73. data/spec/spec_helper.rb +11 -0
  74. data/views/result.erb +55 -33
  75. data/views/search.erb +28 -23
  76. metadata +63 -151
  77. data/public/dist/js/webshims/shims/FlashCanvas/canvas2png.js +0 -1
  78. data/public/dist/js/webshims/shims/FlashCanvas/flashcanvas.js +0 -1
  79. data/public/dist/js/webshims/shims/FlashCanvas/flashcanvas.swf +0 -0
  80. data/public/dist/js/webshims/shims/FlashCanvasPro/canvas2png.js +0 -1
  81. data/public/dist/js/webshims/shims/FlashCanvasPro/flash10canvas.swf +0 -0
  82. data/public/dist/js/webshims/shims/FlashCanvasPro/flash9canvas.swf +0 -0
  83. data/public/dist/js/webshims/shims/FlashCanvasPro/flashcanvas.js +0 -1
  84. data/public/dist/js/webshims/shims/canvas-blob.js +0 -1
  85. data/public/dist/js/webshims/shims/color-picker.js +0 -2
  86. data/public/dist/js/webshims/shims/combos/1.js +0 -6
  87. data/public/dist/js/webshims/shims/combos/10.js +0 -2
  88. data/public/dist/js/webshims/shims/combos/11.js +0 -2
  89. data/public/dist/js/webshims/shims/combos/12.js +0 -6
  90. data/public/dist/js/webshims/shims/combos/13.js +0 -1
  91. data/public/dist/js/webshims/shims/combos/14.js +0 -1
  92. data/public/dist/js/webshims/shims/combos/15.js +0 -2
  93. data/public/dist/js/webshims/shims/combos/16.js +0 -7
  94. data/public/dist/js/webshims/shims/combos/17.js +0 -2
  95. data/public/dist/js/webshims/shims/combos/18.js +0 -3
  96. data/public/dist/js/webshims/shims/combos/2.js +0 -7
  97. data/public/dist/js/webshims/shims/combos/21.js +0 -2
  98. data/public/dist/js/webshims/shims/combos/22.js +0 -1
  99. data/public/dist/js/webshims/shims/combos/23.js +0 -6
  100. data/public/dist/js/webshims/shims/combos/25.js +0 -2
  101. data/public/dist/js/webshims/shims/combos/27.js +0 -1
  102. data/public/dist/js/webshims/shims/combos/28.js +0 -1
  103. data/public/dist/js/webshims/shims/combos/29.js +0 -1
  104. data/public/dist/js/webshims/shims/combos/3.js +0 -1
  105. data/public/dist/js/webshims/shims/combos/30.js +0 -2
  106. data/public/dist/js/webshims/shims/combos/31.js +0 -1
  107. data/public/dist/js/webshims/shims/combos/33.js +0 -1
  108. data/public/dist/js/webshims/shims/combos/34.js +0 -1
  109. data/public/dist/js/webshims/shims/combos/4.js +0 -1
  110. data/public/dist/js/webshims/shims/combos/5.js +0 -2
  111. data/public/dist/js/webshims/shims/combos/6.js +0 -2
  112. data/public/dist/js/webshims/shims/combos/7.js +0 -7
  113. data/public/dist/js/webshims/shims/combos/8.js +0 -7
  114. data/public/dist/js/webshims/shims/combos/9.js +0 -2
  115. data/public/dist/js/webshims/shims/combos/97.js +0 -1
  116. data/public/dist/js/webshims/shims/combos/98.js +0 -1
  117. data/public/dist/js/webshims/shims/combos/99.js +0 -1
  118. data/public/dist/js/webshims/shims/details.js +0 -1
  119. data/public/dist/js/webshims/shims/dom-extend.js +0 -1
  120. data/public/dist/js/webshims/shims/es5.js +0 -1
  121. data/public/dist/js/webshims/shims/es6.js +0 -1
  122. data/public/dist/js/webshims/shims/excanvas.js +0 -1
  123. data/public/dist/js/webshims/shims/filereader-xhr.js +0 -1
  124. data/public/dist/js/webshims/shims/form-combat.js +0 -1
  125. data/public/dist/js/webshims/shims/form-core.js +0 -1
  126. data/public/dist/js/webshims/shims/form-datalist-lazy.js +0 -1
  127. data/public/dist/js/webshims/shims/form-datalist.js +0 -1
  128. data/public/dist/js/webshims/shims/form-fixrangechange.js +0 -1
  129. data/public/dist/js/webshims/shims/form-inputmode.js +0 -1
  130. data/public/dist/js/webshims/shims/form-message.js +0 -1
  131. data/public/dist/js/webshims/shims/form-native-extend.js +0 -1
  132. data/public/dist/js/webshims/shims/form-number-date-api.js +0 -1
  133. data/public/dist/js/webshims/shims/form-number-date-ui.js +0 -1
  134. data/public/dist/js/webshims/shims/form-shim-extend.js +0 -1
  135. data/public/dist/js/webshims/shims/form-shim-extend2.js +0 -1
  136. data/public/dist/js/webshims/shims/form-validation.js +0 -1
  137. data/public/dist/js/webshims/shims/form-validators.js +0 -1
  138. data/public/dist/js/webshims/shims/forms-picker.js +0 -1
  139. data/public/dist/js/webshims/shims/geolocation.js +0 -1
  140. data/public/dist/js/webshims/shims/i18n/formcfg-ar.js +0 -1
  141. data/public/dist/js/webshims/shims/i18n/formcfg-ch-CN.js +0 -1
  142. data/public/dist/js/webshims/shims/i18n/formcfg-cs.js +0 -1
  143. data/public/dist/js/webshims/shims/i18n/formcfg-de.js +0 -1
  144. data/public/dist/js/webshims/shims/i18n/formcfg-el.js +0 -1
  145. data/public/dist/js/webshims/shims/i18n/formcfg-en.js +0 -1
  146. data/public/dist/js/webshims/shims/i18n/formcfg-es.js +0 -1
  147. data/public/dist/js/webshims/shims/i18n/formcfg-fa.js +0 -1
  148. data/public/dist/js/webshims/shims/i18n/formcfg-fr.js +0 -1
  149. data/public/dist/js/webshims/shims/i18n/formcfg-he.js +0 -1
  150. data/public/dist/js/webshims/shims/i18n/formcfg-hi.js +0 -1
  151. data/public/dist/js/webshims/shims/i18n/formcfg-hu.js +0 -1
  152. data/public/dist/js/webshims/shims/i18n/formcfg-it.js +0 -1
  153. data/public/dist/js/webshims/shims/i18n/formcfg-ja.js +0 -1
  154. data/public/dist/js/webshims/shims/i18n/formcfg-lt.js +0 -1
  155. data/public/dist/js/webshims/shims/i18n/formcfg-nl.js +0 -1
  156. data/public/dist/js/webshims/shims/i18n/formcfg-pl.js +0 -1
  157. data/public/dist/js/webshims/shims/i18n/formcfg-pt-BR.js +0 -1
  158. data/public/dist/js/webshims/shims/i18n/formcfg-pt-PT.js +0 -1
  159. data/public/dist/js/webshims/shims/i18n/formcfg-pt.js +0 -1
  160. data/public/dist/js/webshims/shims/i18n/formcfg-ru.js +0 -1
  161. data/public/dist/js/webshims/shims/i18n/formcfg-sv.js +0 -1
  162. data/public/dist/js/webshims/shims/i18n/formcfg-zh-CN.js +0 -1
  163. data/public/dist/js/webshims/shims/i18n/formcfg-zh-TW.js +0 -1
  164. data/public/dist/js/webshims/shims/jme/alternate-media.js +0 -1
  165. data/public/dist/js/webshims/shims/jme/base.js +0 -1
  166. data/public/dist/js/webshims/shims/jme/controls.css +0 -1
  167. data/public/dist/js/webshims/shims/jme/jme.eot +0 -0
  168. data/public/dist/js/webshims/shims/jme/jme.svg +0 -36
  169. data/public/dist/js/webshims/shims/jme/jme.ttf +0 -0
  170. data/public/dist/js/webshims/shims/jme/jme.woff +0 -0
  171. data/public/dist/js/webshims/shims/jme/mediacontrols-lazy.js +0 -1
  172. data/public/dist/js/webshims/shims/jme/mediacontrols.js +0 -1
  173. data/public/dist/js/webshims/shims/jme/playlist.js +0 -1
  174. data/public/dist/js/webshims/shims/jpicker/images/AlphaBar.png +0 -0
  175. data/public/dist/js/webshims/shims/jpicker/images/Bars.png +0 -0
  176. data/public/dist/js/webshims/shims/jpicker/images/Maps.png +0 -0
  177. data/public/dist/js/webshims/shims/jpicker/images/NoColor.png +0 -0
  178. data/public/dist/js/webshims/shims/jpicker/images/bar-opacity.png +0 -0
  179. data/public/dist/js/webshims/shims/jpicker/images/map-opacity.png +0 -0
  180. data/public/dist/js/webshims/shims/jpicker/images/mappoint.gif +0 -0
  181. data/public/dist/js/webshims/shims/jpicker/images/picker.gif +0 -0
  182. data/public/dist/js/webshims/shims/jpicker/images/preview-opacity.png +0 -0
  183. data/public/dist/js/webshims/shims/jpicker/images/rangearrows.gif +0 -0
  184. data/public/dist/js/webshims/shims/jpicker/jpicker.css +0 -1
  185. data/public/dist/js/webshims/shims/matchMedia.js +0 -3
  186. data/public/dist/js/webshims/shims/mediacapture-picker.js +0 -1
  187. data/public/dist/js/webshims/shims/mediacapture.js +0 -1
  188. data/public/dist/js/webshims/shims/mediaelement-core.js +0 -1
  189. data/public/dist/js/webshims/shims/mediaelement-debug.js +0 -1
  190. data/public/dist/js/webshims/shims/mediaelement-jaris.js +0 -1
  191. data/public/dist/js/webshims/shims/mediaelement-native-fix.js +0 -1
  192. data/public/dist/js/webshims/shims/mediaelement-yt.js +0 -1
  193. data/public/dist/js/webshims/shims/moxie/flash/Moxie.cdn.swf +0 -0
  194. data/public/dist/js/webshims/shims/moxie/flash/Moxie.min.swf +0 -0
  195. data/public/dist/js/webshims/shims/moxie/js/moxie-html4.js +0 -3
  196. data/public/dist/js/webshims/shims/moxie/js/moxie-swf.js +0 -2
  197. data/public/dist/js/webshims/shims/picture.js +0 -1
  198. data/public/dist/js/webshims/shims/plugins/jquery.ui.position.js +0 -11
  199. data/public/dist/js/webshims/shims/range-ui.js +0 -1
  200. data/public/dist/js/webshims/shims/sizzle.js +0 -11
  201. data/public/dist/js/webshims/shims/sticky.js +0 -1
  202. data/public/dist/js/webshims/shims/styles/color-picker.png +0 -0
  203. data/public/dist/js/webshims/shims/styles/forms-ext.css +0 -1
  204. data/public/dist/js/webshims/shims/styles/forms-picker.css +0 -1
  205. data/public/dist/js/webshims/shims/styles/progress.gif +0 -0
  206. data/public/dist/js/webshims/shims/styles/progress.png +0 -0
  207. data/public/dist/js/webshims/shims/styles/shim-ext.css +0 -1
  208. data/public/dist/js/webshims/shims/styles/shim.css +0 -1
  209. data/public/dist/js/webshims/shims/styles/transparent.png +0 -0
  210. data/public/dist/js/webshims/shims/styles/widget.eot +0 -0
  211. data/public/dist/js/webshims/shims/styles/widget.svg +0 -12
  212. data/public/dist/js/webshims/shims/styles/widget.ttf +0 -0
  213. data/public/dist/js/webshims/shims/styles/widget.woff +0 -0
  214. data/public/dist/js/webshims/shims/swf/JarisFLVPlayer.swf +0 -0
  215. data/public/dist/js/webshims/shims/swfmini-embed.js +0 -1
  216. data/public/dist/js/webshims/shims/swfmini.js +0 -6
  217. data/public/dist/js/webshims/shims/track-ui.js +0 -1
  218. data/public/dist/js/webshims/shims/track.js +0 -1
  219. data/public/dist/js/webshims/shims/url.js +0 -1
  220. data/public/dist/js/webshims/shims/usermedia-core.js +0 -1
  221. data/public/dist/js/webshims/shims/usermedia-shim.js +0 -1
data/spec/database/sample/transcripts/Solenopsis_invicta/Sinvicta2-2-3.cdna.subset.fasta.nsd ADDED
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