sequenceserver 1.1.0.beta12 → 2.0.0.beta1

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Files changed (208) hide show
  1. checksums.yaml +4 -4
  2. data/.rspec +1 -0
  3. data/.travis.yml +5 -5
  4. data/README.md +86 -43
  5. data/bin/sequenceserver +29 -32
  6. data/lib/sequenceserver.rb +86 -123
  7. data/lib/sequenceserver/api_errors.rb +3 -1
  8. data/lib/sequenceserver/blast/hit.rb +48 -28
  9. data/lib/sequenceserver/blast/job.rb +28 -8
  10. data/lib/sequenceserver/blast/report.rb +52 -15
  11. data/lib/sequenceserver/database.rb +71 -0
  12. data/lib/sequenceserver/exceptions.rb +5 -10
  13. data/lib/sequenceserver/job.rb +8 -1
  14. data/lib/sequenceserver/links.rb +49 -17
  15. data/lib/sequenceserver/logger.rb +2 -2
  16. data/lib/sequenceserver/routes.rb +20 -14
  17. data/lib/sequenceserver/sys.rb +86 -0
  18. data/lib/sequenceserver/version.rb +1 -1
  19. data/public/css/sequenceserver.min.css +3 -3
  20. data/public/js/alignment_exporter.js +1 -1
  21. data/public/js/hsp.js +1 -1
  22. data/public/js/report.js +76 -63
  23. data/public/js/search.js +29 -6
  24. data/public/sequenceserver-report.min.js +4 -4
  25. data/public/sequenceserver-search.min.js +2 -2
  26. data/sequenceserver.gemspec +3 -2
  27. data/spec/blast_versions/blast_2.2.30/blast_2.2.30_spec.rb +228 -0
  28. data/spec/blast_versions/blast_2.2.30/import_spec_capybara_local_2.2.30.rb +53 -0
  29. data/spec/blast_versions/blast_2.2.31/blast_2.2.31_spec.rb +228 -0
  30. data/spec/blast_versions/blast_2.2.31/import_spec_capybara_local_2.2.31.rb +53 -0
  31. data/spec/{blast_spec.rb → blast_versions/blast_2.3.0/blast_2.3.0_spec.rb} +8 -37
  32. data/spec/blast_versions/blast_2.3.0/import_spec_capybara_local_2.3.0.rb +52 -0
  33. data/spec/blast_versions/blast_2.4.0/blast_2.4.0_spec.rb +228 -0
  34. data/spec/blast_versions/blast_2.4.0/import_spec_capybara_local_2.4.0.rb +52 -0
  35. data/spec/blast_versions/blast_2.5.0/blast_2.5.0_spec.rb +228 -0
  36. data/spec/blast_versions/blast_2.5.0/import_spec_capybara_local_2.5.0.rb +53 -0
  37. data/spec/blast_versions/blast_2.6.0/blast_2.6.0_spec.rb +228 -0
  38. data/spec/blast_versions/blast_2.6.0/import_spec_capybara_local_2.6.0.rb +52 -0
  39. data/spec/blast_versions/blast_2.7.1/blast_2.7.1_spec.rb +228 -0
  40. data/spec/blast_versions/blast_2.7.1/import_spec_capybara_local_2.7.1.rb +56 -0
  41. data/spec/blast_versions/blast_2.8.1/blast_2.8.1_spec.rb +228 -0
  42. data/spec/blast_versions/blast_2.8.1/import_spec_capybara_local_2.8.1.rb +55 -0
  43. data/spec/blast_versions/blast_2.9.0/blast_2.9.0_spec.rb +228 -0
  44. data/spec/blast_versions/blast_2.9.0/import_spec_capybara_local_2.9.0.rb +53 -0
  45. data/spec/blast_versions/diamond_0.9.24/diamond_0.9.24_spec.rb +176 -0
  46. data/spec/blast_versions/diamond_0.9.24/import_spec_capybara_local_0.9.24.rb +39 -0
  47. data/spec/capybara_spec.local.rb +190 -0
  48. data/spec/capybara_spec.rb +15 -13
  49. data/spec/config_spec.rb +1 -1
  50. data/spec/database/funky_ids/funky_ids.fa +2 -0
  51. data/spec/database/funky_ids/funky_ids.fa.nhd +8 -0
  52. data/spec/database/funky_ids/funky_ids.fa.nhi +0 -0
  53. data/spec/database/funky_ids/funky_ids.fa.nhr +0 -0
  54. data/spec/database/funky_ids/funky_ids.fa.nin +0 -0
  55. data/spec/database/funky_ids/funky_ids.fa.nog +0 -0
  56. data/spec/database/funky_ids/funky_ids.fa.nsd +15 -13
  57. data/spec/database/funky_ids/funky_ids.fa.nsi +0 -0
  58. data/spec/database/funky_ids/funky_ids.fa.nsq +0 -0
  59. data/spec/database_spec.rb +2 -2
  60. data/spec/dotdir/blast_2.2.30/blastn/BLASTN_XML_2.2.30.xml +1201 -0
  61. data/spec/dotdir/blast_2.2.30/blastn/job.yaml +8 -0
  62. data/spec/dotdir/blast_2.2.30/blastn_nohits/BLASTN_NO_HITS_XML_2.2.30.xml +866 -0
  63. data/spec/dotdir/blast_2.2.30/blastn_nohits/job.yaml +8 -0
  64. data/spec/dotdir/blast_2.2.30/blastp/BLASTP_XML_2.2.30.xml +1181 -0
  65. data/spec/dotdir/blast_2.2.30/blastp/job.yaml +8 -0
  66. data/spec/dotdir/blast_2.2.30/blastx/BLASTX_XML_2.2.30.xml +1181 -0
  67. data/spec/dotdir/blast_2.2.30/blastx/job.yaml +8 -0
  68. data/spec/dotdir/blast_2.2.30/tblastn/TBLASTN_XML_2.2.30.xml +1181 -0
  69. data/spec/dotdir/blast_2.2.30/tblastn/job.yaml +8 -0
  70. data/spec/dotdir/blast_2.2.30/tblastx/TBLASTX_XML_2.2.30.xml +8857 -0
  71. data/spec/dotdir/blast_2.2.30/tblastx/job.yaml +8 -0
  72. data/spec/dotdir/blast_2.2.31/blastn/BLASTN_XML_2.2.31.xml +1201 -0
  73. data/spec/dotdir/blast_2.2.31/blastn/job.yaml +8 -0
  74. data/spec/dotdir/blast_2.2.31/blastn_nohits/BLASTN_NO_HITS_XML_2.2.31.xml +866 -0
  75. data/spec/dotdir/blast_2.2.31/blastn_nohits/job.yaml +8 -0
  76. data/spec/dotdir/blast_2.2.31/blastp/BLASTP_XML_2.2.31.xml +1181 -0
  77. data/spec/dotdir/blast_2.2.31/blastp/job.yaml +8 -0
  78. data/spec/dotdir/blast_2.2.31/blastx/BLASTX_XML_2.2.31.xml +1181 -0
  79. data/spec/dotdir/blast_2.2.31/blastx/job.yaml +8 -0
  80. data/spec/dotdir/blast_2.2.31/tblastn/TBLASTN_XML_2.2.31.xml +1181 -0
  81. data/spec/dotdir/blast_2.2.31/tblastn/job.yaml +8 -0
  82. data/spec/dotdir/blast_2.2.31/tblastx/TBLASTX_XML_2.2.31.xml +8857 -0
  83. data/spec/dotdir/blast_2.2.31/tblastx/job.yaml +8 -0
  84. data/spec/dotdir/blast_2.3.0/blastn/BLASTN_XML_2.3.0.xml +1201 -0
  85. data/spec/dotdir/blast_2.3.0/blastn/job.yaml +8 -0
  86. data/spec/dotdir/blast_2.3.0/blastn_nohits/BLASTN_NO_HITS_XML_2.3.0.xml +866 -0
  87. data/spec/dotdir/blast_2.3.0/blastn_nohits/job.yaml +8 -0
  88. data/spec/dotdir/blast_2.3.0/blastp/BLASTP_XML_2.3.0.xml +1181 -0
  89. data/spec/dotdir/blast_2.3.0/blastp/job.yaml +8 -0
  90. data/spec/dotdir/blast_2.3.0/blastx/BLASTX_XML_2.3.0.xml +1181 -0
  91. data/spec/dotdir/blast_2.3.0/blastx/job.yaml +8 -0
  92. data/spec/dotdir/blast_2.3.0/tblastn/TBLASTN_XML_2.3.0.xml +1181 -0
  93. data/spec/dotdir/blast_2.3.0/tblastn/job.yaml +8 -0
  94. data/spec/dotdir/blast_2.3.0/tblastx/TBLASTX_XML_2.3.0.xml +8857 -0
  95. data/spec/dotdir/blast_2.3.0/tblastx/job.yaml +8 -0
  96. data/spec/dotdir/blast_2.4.0/blastn/BLASTN_XML_2.4.0.xml +1201 -0
  97. data/spec/dotdir/blast_2.4.0/blastn/TBLASTN_XML_2.4.0.xml +1181 -0
  98. data/spec/dotdir/blast_2.4.0/blastn/job.yaml +8 -0
  99. data/spec/dotdir/blast_2.4.0/blastn_nohits/BLASTN_NO_HITS_XML_2.4.0.xml +866 -0
  100. data/spec/dotdir/blast_2.4.0/blastn_nohits/job.yaml +8 -0
  101. data/spec/dotdir/blast_2.4.0/blastp/BLASTP_XML_2.4.0.xml +1181 -0
  102. data/spec/dotdir/blast_2.4.0/blastp/job.yaml +8 -0
  103. data/spec/dotdir/blast_2.4.0/blastx/BLASTX_XML_2.4.0.xml +1181 -0
  104. data/spec/dotdir/blast_2.4.0/blastx/job.yaml +8 -0
  105. data/spec/dotdir/blast_2.4.0/tblastn/TBLASTN_XML_2.4.0.xml +1181 -0
  106. data/spec/dotdir/blast_2.4.0/tblastn/job.yaml +8 -0
  107. data/spec/dotdir/blast_2.4.0/tblastx/TBLASTX_XML_2.4.0.xml +8857 -0
  108. data/spec/dotdir/blast_2.4.0/tblastx/job.yaml +8 -0
  109. data/spec/dotdir/blast_2.5.0/blastn/BLASTN_LONG_XML_2.5.0.xml +18813 -0
  110. data/spec/dotdir/blast_2.5.0/blastn/BLASTN_XML_2.5.0.xml +1201 -0
  111. data/spec/dotdir/blast_2.5.0/blastn/job.yaml +8 -0
  112. data/spec/dotdir/blast_2.5.0/blastn_nohits/BLASTN_NO_HITS_XML_2.5.0.xml +866 -0
  113. data/spec/dotdir/blast_2.5.0/blastn_nohits/job.yaml +8 -0
  114. data/spec/dotdir/blast_2.5.0/blastp/BLASTP +2161 -0
  115. data/spec/dotdir/blast_2.5.0/blastp/BLASTP_XML_2.5.0.xml +1181 -0
  116. data/spec/dotdir/blast_2.5.0/blastp/job.yaml +8 -0
  117. data/spec/dotdir/blast_2.5.0/blastx/BLASTX +28080 -0
  118. data/spec/dotdir/blast_2.5.0/blastx/BLASTX_XML_2.5.0.xml +1181 -0
  119. data/spec/dotdir/blast_2.5.0/blastx/job.yaml +8 -0
  120. data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN +29486 -0
  121. data/spec/dotdir/blast_2.5.0/tblastn/TBLASTN_XML_2.5.0.xml +1181 -0
  122. data/spec/dotdir/blast_2.5.0/tblastn/job.yaml +8 -0
  123. data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX +180859 -0
  124. data/spec/dotdir/blast_2.5.0/tblastx/TBLASTX_XML_2.5.0.xml +8857 -0
  125. data/spec/dotdir/blast_2.5.0/tblastx/job.yaml +8 -0
  126. data/spec/dotdir/blast_2.6.0/blastn/BLASTN_XML_2.6.0.xml +1201 -0
  127. data/spec/dotdir/blast_2.6.0/blastn/job.yaml +8 -0
  128. data/spec/dotdir/blast_2.6.0/blastn_nohits/BLASTN_NO_HITS_XML_2.6.0.xml +866 -0
  129. data/spec/dotdir/blast_2.6.0/blastn_nohits/job.yaml +8 -0
  130. data/spec/dotdir/blast_2.6.0/blastp/BLASTP_XML_2.6.0.xml +1181 -0
  131. data/spec/dotdir/blast_2.6.0/blastp/job.yaml +8 -0
  132. data/spec/dotdir/blast_2.6.0/blastx/BLASTX_XML_2.6.0.xml +1181 -0
  133. data/spec/dotdir/blast_2.6.0/blastx/job.yaml +8 -0
  134. data/spec/dotdir/blast_2.6.0/tblastn/TBLASTN_XML_2.6.0.xml +1181 -0
  135. data/spec/dotdir/blast_2.6.0/tblastn/job.yaml +8 -0
  136. data/spec/dotdir/blast_2.6.0/tblastx/TBLASTX_XML_2.6.0.xml +8857 -0
  137. data/spec/dotdir/blast_2.6.0/tblastx/job.yaml +8 -0
  138. data/spec/dotdir/blast_2.7.1/blastn/BLASTN_XML_2.7.1.xml +1201 -0
  139. data/spec/dotdir/blast_2.7.1/blastn/job.yaml +8 -0
  140. data/spec/dotdir/blast_2.7.1/blastn_nohits/BLASTN_NO_HITS_XML_2.7.1.xml +866 -0
  141. data/spec/dotdir/blast_2.7.1/blastn_nohits/job.yaml +8 -0
  142. data/spec/dotdir/blast_2.7.1/blastp/BLASTP_XML_2.7.1.xml +1181 -0
  143. data/spec/dotdir/blast_2.7.1/blastp/job.yaml +8 -0
  144. data/spec/dotdir/blast_2.7.1/blastx/BLASTX_XML_2.7.1.xml +1181 -0
  145. data/spec/dotdir/blast_2.7.1/blastx/job.yaml +8 -0
  146. data/spec/dotdir/blast_2.7.1/tblastn/TBLASTN_XML_2.7.1.xml +1181 -0
  147. data/spec/dotdir/blast_2.7.1/tblastn/job.yaml +8 -0
  148. data/spec/dotdir/blast_2.7.1/tblastx/TBLASTX_XML_2.7.1.xml +8857 -0
  149. data/spec/dotdir/blast_2.7.1/tblastx/job.yaml +8 -0
  150. data/spec/dotdir/blast_2.8.1/blastn/BLASTN_XML_2.8.1.xml +1201 -0
  151. data/spec/dotdir/blast_2.8.1/blastn/job.yaml +8 -0
  152. data/spec/dotdir/blast_2.8.1/blastn_nohits/BLASTN_NO_HITS_XML_2.8.1.xml +866 -0
  153. data/spec/dotdir/blast_2.8.1/blastn_nohits/job.yaml +8 -0
  154. data/spec/dotdir/blast_2.8.1/blastp/BLASTP_XML_2.8.1.xml +1181 -0
  155. data/spec/dotdir/blast_2.8.1/blastp/job.yaml +8 -0
  156. data/spec/dotdir/blast_2.8.1/blastx/BLASTX_XML_2.8.1.xml +1181 -0
  157. data/spec/dotdir/blast_2.8.1/blastx/job.yaml +8 -0
  158. data/spec/dotdir/blast_2.8.1/tblastn/TBLASTN_XML_2.8.1.xml +1181 -0
  159. data/spec/dotdir/blast_2.8.1/tblastn/job.yaml +8 -0
  160. data/spec/dotdir/blast_2.8.1/tblastx/TBLASTX_XML_2.8.1.xml +8857 -0
  161. data/spec/dotdir/blast_2.8.1/tblastx/job.yaml +8 -0
  162. data/spec/dotdir/blast_2.9.0/blastn/BLASTN_XML_2.9.0.xml +1201 -0
  163. data/spec/dotdir/blast_2.9.0/blastn/job.yaml +8 -0
  164. data/spec/dotdir/blast_2.9.0/blastn_nohits/BLASTN_NO_HITS_XML_2.9.0.xml +866 -0
  165. data/spec/dotdir/blast_2.9.0/blastn_nohits/job.yaml +8 -0
  166. data/spec/dotdir/blast_2.9.0/blastp/BLASTP_XML_2.9.0.xml +1181 -0
  167. data/spec/dotdir/blast_2.9.0/blastp/job.yaml +8 -0
  168. data/spec/dotdir/blast_2.9.0/blastx/BLASTX_XML_2.9.0.xml +1181 -0
  169. data/spec/dotdir/blast_2.9.0/blastx/job.yaml +8 -0
  170. data/spec/dotdir/blast_2.9.0/tblastn/TBLASTN_XML_2.9.0.xml +1181 -0
  171. data/spec/dotdir/blast_2.9.0/tblastn/job.yaml +8 -0
  172. data/spec/dotdir/blast_2.9.0/tblastx/TBLASTX_XML_2.9.0.xml +8857 -0
  173. data/spec/dotdir/blast_2.9.0/tblastx/job.yaml +8 -0
  174. data/spec/dotdir/diamond_0.9.24/blastp/DIAMOND_BLASTP_0.9.24.xml +1040 -0
  175. data/spec/dotdir/diamond_0.9.24/blastp/job.yaml +8 -0
  176. data/spec/dotdir/diamond_0.9.24/blastx/DIAMOND_BLASTX_0.9.24.xml +1040 -0
  177. data/spec/dotdir/diamond_0.9.24/blastx/job.yaml +8 -0
  178. data/spec/dotdir/diamond_0.9.24/blastx_nohits/DIAMOND_BLASTX_NOHITS_0.9.24.xml +41 -0
  179. data/spec/dotdir/diamond_0.9.24/blastx_nohits/job.yaml +8 -0
  180. data/spec/download_helper.rb +32 -0
  181. data/spec/import_spec_capybara_local.rb +61 -0
  182. data/spec/sequence_spec.rb +1 -2
  183. data/spec/sequences/Nucleotide_TP53_COX41.fasta +15 -0
  184. data/spec/sequences/Protein_TP53_COX41.fasta +12 -0
  185. data/spec/sequences/Query_1_SI2_2_0_06267.txt +6 -0
  186. data/spec/{nucleotide_query.fa → sequences/nucleotide_query.fa} +0 -0
  187. data/spec/sequences/problematic_query.fa +5 -0
  188. data/spec/sequences/protein_query.fa +9 -0
  189. data/spec/sequences/sample_query_fire_ant_obps.fa +44 -0
  190. data/spec/sequences/sequenceserver-SI2.2.0_06267.fa +5 -0
  191. data/spec/sequenceserver_spec.rb +3 -3
  192. data/spec/spec_helper.rb +59 -0
  193. metadata +185 -28
  194. data/spec/protein_query.fa +0 -21
  195. data/spec/sample_reports/blastn_sample/job.yaml +0 -10
  196. data/spec/sample_reports/blastn_sample/stdout +0 -144
  197. data/spec/sample_reports/blastp_sample/job.yaml +0 -10
  198. data/spec/sample_reports/blastp_sample/stdout +0 -1187
  199. data/spec/sample_reports/blastx_sample/job.yaml +0 -10
  200. data/spec/sample_reports/blastx_sample/stdout +0 -1191
  201. data/spec/sample_reports/no_hits_sample/job.yaml +0 -10
  202. data/spec/sample_reports/no_hits_sample/stdout +0 -130
  203. data/spec/sample_reports/tblastn_sample/job.yaml +0 -10
  204. data/spec/sample_reports/tblastn_sample/stdout +0 -1107
  205. data/spec/sample_reports/tblastx_sample/job.yaml +0 -10
  206. data/spec/sample_reports/tblastx_sample/stdout +0 -2422
  207. data/spec/sample_reports/with_hits_sample/job.yaml +0 -10
  208. data/spec/sample_reports/with_hits_sample/stdout +0 -1489

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