miga-base 1.3.8.2 → 1.3.9.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
1
  --- !ruby/object:Gem::Specification
2
2
  name: miga-base
3
3
  version: !ruby/object:Gem::Version
4
- version: 1.3.8.2
4
+ version: 1.3.9.0
5
5
  platform: ruby
6
6
  authors:
7
7
  - Luis M. Rodriguez-R
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2023-08-08 00:00:00.000000000 Z
11
+ date: 2024-01-22 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: daemons
@@ -218,6 +218,7 @@ files:
218
218
  - lib/miga/dataset/result/add.rb
219
219
  - lib/miga/dataset/result/ignore.rb
220
220
  - lib/miga/dataset/status.rb
221
+ - lib/miga/dataset/type.rb
221
222
  - lib/miga/json.rb
222
223
  - lib/miga/lair.rb
223
224
  - lib/miga/metadata.rb
@@ -235,6 +236,7 @@ files:
235
236
  - lib/miga/result/dates.rb
236
237
  - lib/miga/result/source.rb
237
238
  - lib/miga/result/stats.rb
239
+ - lib/miga/result/versions.rb
238
240
  - lib/miga/sqlite.rb
239
241
  - lib/miga/tax_dist.rb
240
242
  - lib/miga/tax_index.rb