sequenceserver 1.1.0.beta2 → 1.1.0.beta3

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Files changed (63) hide show
  1. checksums.yaml +4 -4
  2. data/.travis.yml +16 -5
  3. data/README.md +3 -0
  4. data/lib/sequenceserver/api_errors.rb +67 -0
  5. data/lib/sequenceserver/blast/constants.rb +1 -1
  6. data/lib/sequenceserver/blast/formatter.rb +4 -2
  7. data/lib/sequenceserver/blast/job.rb +17 -62
  8. data/lib/sequenceserver/blast/report.rb +15 -2
  9. data/lib/sequenceserver/blast.rb +1 -0
  10. data/lib/sequenceserver/exceptions.rb +2 -3
  11. data/lib/sequenceserver/job.rb +72 -44
  12. data/lib/sequenceserver/routes.rb +29 -25
  13. data/lib/sequenceserver/version.rb +1 -1
  14. data/lib/sequenceserver.rb +32 -20
  15. data/public/js/errormodal.js +55 -0
  16. data/public/js/report.js +6 -2
  17. data/public/js/sequenceserver.js +0 -12
  18. data/public/sequenceserver-report.min.js +15 -15
  19. data/public/sequenceserver-search.min.js +3 -3
  20. data/sequenceserver.gemspec +2 -1
  21. data/spec/capybara_spec.rb +120 -21
  22. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhd +8 -0
  23. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhi +0 -0
  24. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nhr +0 -0
  25. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nin +0 -0
  26. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nog +0 -0
  27. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsd +16 -0
  28. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsi +0 -0
  29. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.fasta.nsq +0 -0
  30. data/spec/database/sample/genome/Solenopsis_invicta/Solenopsis_invicta_gnG_subset.txt +8 -0
  31. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phd +9140 -0
  32. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phi +0 -0
  33. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.phr +0 -0
  34. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pin +0 -0
  35. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.pog +0 -0
  36. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psd +18280 -0
  37. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psi +0 -0
  38. data/spec/database/sample/proteins/uniprot/2018-04-Swiss-Prot_insecta.fasta.psq +0 -0
  39. data/spec/database/sample/proteins/uniprot/URL +1 -0
  40. data/spec/nucleotide_query.fa +21 -0
  41. data/spec/protein_query.fa +21 -0
  42. data/spec/routes_spec.rb +2 -0
  43. data/spec/sample_reports/blastn_sample/job.yaml +1 -0
  44. data/spec/sample_reports/blastn_sample/{rfile → stdout} +0 -0
  45. data/spec/sample_reports/blastp_sample/job.yaml +1 -0
  46. data/spec/sample_reports/blastp_sample/{rfile → stdout} +0 -0
  47. data/spec/sample_reports/blastx_sample/job.yaml +1 -0
  48. data/spec/sample_reports/blastx_sample/{rfile → stdout} +0 -0
  49. data/spec/sample_reports/no_hits_sample/job.yaml +1 -0
  50. data/spec/sample_reports/no_hits_sample/{rfile → stdout} +0 -0
  51. data/spec/sample_reports/tblastn_sample/job.yaml +1 -0
  52. data/spec/sample_reports/tblastn_sample/{rfile → stdout} +0 -0
  53. data/spec/sample_reports/tblastx_sample/job.yaml +1 -0
  54. data/spec/sample_reports/tblastx_sample/{rfile → stdout} +0 -0
  55. data/spec/sample_reports/with_hits_sample/job.yaml +1 -0
  56. data/spec/sample_reports/with_hits_sample/{rfile → stdout} +0 -0
  57. data/spec/sequenceserver_spec.rb +1 -1
  58. data/spec/spec_helper.rb +2 -16
  59. data/views/layout.erb +0 -45
  60. metadata +55 -16
  61. data/lib/sequenceserver/blast/exceptions.rb +0 -27
  62. data/views/400.erb +0 -29
  63. data/views/500.erb +0 -41

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