miga-base 1.3.12.3 → 1.3.13.0

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@@ -5,6 +5,9 @@ require 'miga/cli/action'
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  require 'miga/remote_dataset'
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  class MiGA::Cli::Action::Get < MiGA::Cli::Action
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+ require 'miga/cli/action/download/base'
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+ include MiGA::Cli::Action::Download::Base
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+
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  def parse_cli
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  cli.defaults = {
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  query: false, universe: :ncbi, db: :nuccore, get_md: false, only_md: false
@@ -69,12 +72,18 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
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  '--api-key STRING',
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  'API key for the given universe'
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  ) { |v| cli[:api_key] = v }
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+ opt.on(
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+ '--ncbi-taxonomy-dump [path]',
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+ 'Path to an NCBI Taxonomy dump directory to query instead of API calls',
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+ 'If the path is not passed, the dump is automatically downloaded'
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+ ) { |v| cli[:ncbi_taxonomy_dump] = v || true }
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  end
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  end
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  def perform
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  glob = get_sub_cli
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  p = cli.load_project
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+ load_ncbi_taxonomy_dump
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  glob.each do |sub_cli|
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  rd = create_remote_dataset(sub_cli, p)
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  next if rd.nil?
data/lib/miga/version.rb CHANGED
@@ -12,7 +12,7 @@ module MiGA
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  # - String indicating release status:
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  # - rc* release candidate, not released as gem
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  # - [0-9]+ stable release, released as gem
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- VERSION = [1.3, 12, 3].freeze
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+ VERSION = [1.3, 13, 0].freeze
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  ##
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  # Nickname for the current major.minor version.
metadata CHANGED
@@ -1,7 +1,7 @@
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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: 1.3.12.3
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+ version: 1.3.13.0
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  platform: ruby
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  authors:
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  - Luis M. Rodriguez-R