miga-base 1.3.8.2 → 1.3.9.0

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Files changed (50) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +2 -2
  3. data/lib/miga/cli/action/add_result.rb +22 -1
  4. data/lib/miga/cli/action/browse/about.html +4 -2
  5. data/lib/miga/cli/action/download/gtdb.rb +1 -1
  6. data/lib/miga/cli/action/download/ncbi.rb +43 -68
  7. data/lib/miga/cli/action/download/seqcode.rb +1 -2
  8. data/lib/miga/cli/action/ncbi_get.rb +1 -8
  9. data/lib/miga/cli/action/wf.rb +15 -6
  10. data/lib/miga/cli/objects_helper.rb +3 -0
  11. data/lib/miga/cli/opt_helper.rb +8 -2
  12. data/lib/miga/common/net.rb +100 -18
  13. data/lib/miga/dataset/base.rb +40 -12
  14. data/lib/miga/dataset/hooks.rb +8 -0
  15. data/lib/miga/dataset/result/ignore.rb +14 -2
  16. data/lib/miga/dataset/type.rb +51 -0
  17. data/lib/miga/dataset.rb +3 -22
  18. data/lib/miga/json.rb +9 -0
  19. data/lib/miga/project/base.rb +15 -9
  20. data/lib/miga/project.rb +7 -1
  21. data/lib/miga/remote_dataset/base.rb +117 -36
  22. data/lib/miga/remote_dataset/download.rb +121 -54
  23. data/lib/miga/remote_dataset.rb +34 -13
  24. data/lib/miga/result/stats.rb +2 -0
  25. data/lib/miga/result/versions.rb +23 -0
  26. data/lib/miga/result.rb +7 -1
  27. data/lib/miga/taxonomy/base.rb +3 -2
  28. data/lib/miga/version.rb +2 -2
  29. data/scripts/assembly.bash +15 -1
  30. data/scripts/cds.bash +9 -3
  31. data/scripts/distances.bash +103 -5
  32. data/scripts/essential_genes.bash +14 -1
  33. data/scripts/mytaxa.bash +18 -3
  34. data/scripts/mytaxa_scan.bash +16 -3
  35. data/scripts/read_quality.bash +6 -2
  36. data/scripts/ssu.bash +19 -1
  37. data/scripts/stats.bash +9 -3
  38. data/scripts/taxonomy.bash +98 -2
  39. data/scripts/trimmed_fasta.bash +10 -2
  40. data/scripts/trimmed_reads.bash +26 -6
  41. data/test/dataset_test.rb +17 -2
  42. data/test/hook_test.rb +3 -2
  43. data/test/net_test.rb +21 -5
  44. data/test/project_test.rb +13 -0
  45. data/test/remote_dataset_test.rb +106 -7
  46. data/test/result_test.rb +47 -21
  47. data/test/taxonomy_test.rb +9 -3
  48. data/utils/distance/runner.rb +3 -1
  49. data/utils/distances.rb +1 -1
  50. metadata +4 -2
metadata CHANGED
@@ -1,14 +1,14 @@
1
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  --- !ruby/object:Gem::Specification
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  name: miga-base
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  version: !ruby/object:Gem::Version
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- version: 1.3.8.2
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+ version: 1.3.9.0
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  platform: ruby
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  authors:
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  - Luis M. Rodriguez-R
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2023-08-08 00:00:00.000000000 Z
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+ date: 2024-01-22 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: daemons
@@ -218,6 +218,7 @@ files:
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  - lib/miga/dataset/result/add.rb
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  - lib/miga/dataset/result/ignore.rb
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  - lib/miga/dataset/status.rb
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+ - lib/miga/dataset/type.rb
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  - lib/miga/json.rb
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  - lib/miga/lair.rb
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  - lib/miga/metadata.rb
@@ -235,6 +236,7 @@ files:
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  - lib/miga/result/dates.rb
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  - lib/miga/result/source.rb
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  - lib/miga/result/stats.rb
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+ - lib/miga/result/versions.rb
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  - lib/miga/sqlite.rb
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  - lib/miga/tax_dist.rb
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  - lib/miga/tax_index.rb