miga-base 1.3.12.3 → 1.3.13.0
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- checksums.yaml +4 -4
- data/lib/miga/cli/action/get.rb +9 -0
- data/lib/miga/version.rb +1 -1
- metadata +1 -1
checksums.yaml
CHANGED
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@@ -1,7 +1,7 @@
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1
1
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---
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2
2
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SHA256:
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3
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-
metadata.gz:
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4
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-
data.tar.gz:
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3
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+
metadata.gz: 8659bae6ee7d40a76a464840a56b4aff77f9a848d777349e98d8c316717b0021
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4
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+
data.tar.gz: dab1cbd8ee24503b4dfbe0e8b034da195120251c258c798bbba92668a52d3cfa
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5
5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: '09a916e1db7bb4912111e83c2d832a779a245c8eb326aee3cfcead8611d484f737a1cbcae1a1279a2673a2f31a8252c859b533b7ae9b6c74c8881b41e63e7c40'
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7
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+
data.tar.gz: 43e7065632d2642abb0c6bb5fac8ae96e0696c0f48b128376fa5d1ac929c1c7b787df61af78bee5a4824049da7b2baf976f9bb3d3f083184ca02deefc166114e
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data/lib/miga/cli/action/get.rb
CHANGED
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@@ -5,6 +5,9 @@ require 'miga/cli/action'
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5
5
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require 'miga/remote_dataset'
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6
6
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7
7
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class MiGA::Cli::Action::Get < MiGA::Cli::Action
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8
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+
require 'miga/cli/action/download/base'
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9
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+
include MiGA::Cli::Action::Download::Base
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10
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+
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8
11
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def parse_cli
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9
12
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cli.defaults = {
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10
13
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query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
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@@ -69,12 +72,18 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
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69
72
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'--api-key STRING',
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70
73
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'API key for the given universe'
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71
74
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) { |v| cli[:api_key] = v }
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75
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+
opt.on(
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76
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+
'--ncbi-taxonomy-dump [path]',
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77
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+
'Path to an NCBI Taxonomy dump directory to query instead of API calls',
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78
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+
'If the path is not passed, the dump is automatically downloaded'
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79
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+
) { |v| cli[:ncbi_taxonomy_dump] = v || true }
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72
80
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end
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73
81
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end
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74
82
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75
83
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def perform
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76
84
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glob = get_sub_cli
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77
85
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p = cli.load_project
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86
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+
load_ncbi_taxonomy_dump
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78
87
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glob.each do |sub_cli|
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79
88
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rd = create_remote_dataset(sub_cli, p)
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80
89
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next if rd.nil?
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data/lib/miga/version.rb
CHANGED
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@@ -12,7 +12,7 @@ module MiGA
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12
12
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# - String indicating release status:
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13
13
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# - rc* release candidate, not released as gem
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14
14
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# - [0-9]+ stable release, released as gem
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15
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-
VERSION = [1.3,
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15
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+
VERSION = [1.3, 13, 0].freeze
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16
16
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17
17
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##
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18
18
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# Nickname for the current major.minor version.
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