miga-base 1.3.8.2 → 1.3.9.1
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- checksums.yaml +4 -4
- data/README.md +2 -2
- data/lib/miga/cli/action/add_result.rb +22 -1
- data/lib/miga/cli/action/browse/about.html +4 -2
- data/lib/miga/cli/action/download/gtdb.rb +1 -1
- data/lib/miga/cli/action/download/ncbi.rb +43 -68
- data/lib/miga/cli/action/download/seqcode.rb +1 -2
- data/lib/miga/cli/action/ncbi_get.rb +1 -8
- data/lib/miga/cli/action/wf.rb +15 -6
- data/lib/miga/cli/objects_helper.rb +3 -0
- data/lib/miga/cli/opt_helper.rb +8 -2
- data/lib/miga/common/net.rb +100 -18
- data/lib/miga/dataset/base.rb +40 -12
- data/lib/miga/dataset/hooks.rb +8 -0
- data/lib/miga/dataset/result/ignore.rb +14 -2
- data/lib/miga/dataset/type.rb +51 -0
- data/lib/miga/dataset.rb +3 -22
- data/lib/miga/json.rb +9 -0
- data/lib/miga/project/base.rb +15 -9
- data/lib/miga/project.rb +7 -1
- data/lib/miga/remote_dataset/base.rb +117 -36
- data/lib/miga/remote_dataset/download.rb +121 -54
- data/lib/miga/remote_dataset.rb +34 -13
- data/lib/miga/result/stats.rb +2 -0
- data/lib/miga/result/versions.rb +23 -0
- data/lib/miga/result.rb +7 -1
- data/lib/miga/taxonomy/base.rb +3 -2
- data/lib/miga/version.rb +2 -2
- data/scripts/assembly.bash +15 -1
- data/scripts/cds.bash +9 -3
- data/scripts/distances.bash +103 -5
- data/scripts/essential_genes.bash +14 -1
- data/scripts/mytaxa.bash +18 -3
- data/scripts/mytaxa_scan.bash +16 -3
- data/scripts/read_quality.bash +6 -2
- data/scripts/ssu.bash +19 -1
- data/scripts/stats.bash +9 -3
- data/scripts/taxonomy.bash +98 -2
- data/scripts/trimmed_fasta.bash +10 -2
- data/scripts/trimmed_reads.bash +26 -6
- data/test/dataset_test.rb +17 -2
- data/test/hook_test.rb +3 -2
- data/test/net_test.rb +21 -5
- data/test/project_test.rb +13 -0
- data/test/remote_dataset_test.rb +106 -7
- data/test/result_test.rb +47 -21
- data/test/taxonomy_test.rb +9 -3
- data/utils/distance/runner.rb +3 -1
- data/utils/distances.rb +1 -1
- metadata +18 -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.
|
4
|
+
version: 1.3.9.1
|
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:
|
11
|
+
date: 2024-01-23 00:00:00.000000000 Z
|
12
12
|
dependencies:
|
13
13
|
- !ruby/object:Gem::Dependency
|
14
14
|
name: daemons
|
@@ -52,6 +52,20 @@ dependencies:
|
|
52
52
|
- - "~>"
|
53
53
|
- !ruby/object:Gem::Version
|
54
54
|
version: '1.3'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: net-http
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ">="
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :runtime
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ">="
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
55
69
|
- !ruby/object:Gem::Dependency
|
56
70
|
name: net-ftp
|
57
71
|
requirement: !ruby/object:Gem::Requirement
|
@@ -218,6 +232,7 @@ files:
|
|
218
232
|
- lib/miga/dataset/result/add.rb
|
219
233
|
- lib/miga/dataset/result/ignore.rb
|
220
234
|
- lib/miga/dataset/status.rb
|
235
|
+
- lib/miga/dataset/type.rb
|
221
236
|
- lib/miga/json.rb
|
222
237
|
- lib/miga/lair.rb
|
223
238
|
- lib/miga/metadata.rb
|
@@ -235,6 +250,7 @@ files:
|
|
235
250
|
- lib/miga/result/dates.rb
|
236
251
|
- lib/miga/result/source.rb
|
237
252
|
- lib/miga/result/stats.rb
|
253
|
+
- lib/miga/result/versions.rb
|
238
254
|
- lib/miga/sqlite.rb
|
239
255
|
- lib/miga/tax_dist.rb
|
240
256
|
- lib/miga/tax_index.rb
|