miga-base 1.3.11.0 → 1.3.12.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: e09fb9877dfe796856db08b80ac176033025603a49ca5222fda69942544c99ff
+  metadata.gz: 45ab052e74f73fe87a2383443285dae3fb218c659618c1d2d7278ff8bb0de6f4
+  data.tar.gz: 553c70d1a5c15093686260a0dec176a0f8ecd196f0884218484ff9964e416661
 SHA512:
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-  data.tar.gz: f26bc6e99d591a60603c06de28f6b622ac13ed9e4d17acce43f532a3d29bed930e013aa7bd84b93aa1f9ca272c4427ea4bce7afe8e0bd5fbeef4174b75d40142
+  metadata.gz: 27a87882655d6875f482042d388273ce46135329919f9738913022af6fd97f411e9db6238b4bd7fbcc50d7d605da51f447d85b68ff77758cf324ce9e59c7e592
+  data.tar.gz: 116737b9a5ca99d97a8ad8f704a5df9146177c2d9603c8c4b19e631baa52e60183888369dcec96f671238f6ad934ce8c6324bc368aaff8bc8645f3b1d3dee247

data/lib/miga/cli/action/download/base.rb

@@ -68,6 +68,10 @@ module MiGA::Cli::Action::Download::Base
       '-R', '--remote-list PATH',
       'Path to an output file with the list of all datasets listed remotely'
     ) { |v| cli[:remote_list] = v }
+    opt.on(
+      '--ncbi-taxonomy-dump STRING',
+      'Path to an NCBI Taxonomy dump directory to query instead of API calls'
+    ) { |v| cli[:ncbi_taxonomy_dump] = v }
   end
 
   def generic_perform
@@ -82,6 +86,7 @@ module MiGA::Cli::Action::Download::Base
   def load_tasks
     sanitize_cli
     p = cli.load_project
+    load_ncbi_taxonomy_dump
     ds = remote_list
     ds = discard_excluded(ds)
     ds = exclude_newer(ds)
@@ -89,6 +94,14 @@ module MiGA::Cli::Action::Download::Base
     [p, ds]
   end
 
+  def load_ncbi_taxonomy_dump
+    return unless cli[:ncbi_taxonomy_dump]
+
+    cli.say "Reading NCBI Taxonomy dump: #{cli[:ncbi_taxonomy_dump]}"
+    MiGA::RemoteDataset.use_ncbi_taxonomy_dump(cli[:ncbi_taxonomy_dump], cli)
+  end
+
+
   def finalize_tasks(d, downloaded)
     cli.say "Datasets listed: #{d.size}"
     act = cli[:dry] ? 'to download' : 'downloaded'

data/lib/miga/cli/action/download/ncbi.rb

@@ -26,10 +26,6 @@ module MiGA::Cli::Action::Download::Ncbi
     opt.on('--ncbi-list-json STRING', '::HIDE::') do |v|
       cli[:ncbi_list_json] = v
     end
-    opt.on(
-      '--ncbi-taxonomy-dump STRING',
-      'Path to an NCBI Taxonomy dump directory to query instead of API calls'
-    ) { |v| cli[:ncbi_taxonomy_dump] = v }
   end
 
   def cli_name_modifiers(opt)
@@ -55,11 +51,6 @@ module MiGA::Cli::Action::Download::Ncbi
   end
 
   def remote_list
-    if cli[:ncbi_taxonomy_dump]
-      cli.say "Reading NCBI Taxonomy dump: #{cli[:ncbi_taxonomy_dump]}"
-      MiGA::RemoteDataset.use_ncbi_taxonomy_dump(cli[:ncbi_taxonomy_dump], cli)
-    end
-
     if cli[:ncbi_list_json] && File.size?(cli[:ncbi_list_json])
       return read_ncbi_list_json(cli[:ncbi_list_json])
     end

data/lib/miga/dataset.rb

@@ -3,7 +3,7 @@
 # @package MiGA
 # @license Artistic-2.0
 
-require'set'
+require 'set'
 require 'miga/metadata'
 require 'miga/dataset/result'
 require 'miga/dataset/status'

data/lib/miga/remote_dataset/base.rb

@@ -21,7 +21,7 @@ module MiGA::RemoteDataset::Base
   @@_NCBI_DATASETS = 'https://api.ncbi.nlm.nih.gov/datasets/v2alpha/'
   @@_EUTILS        = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/'
   @@_EBI_API       = 'https://www.ebi.ac.uk/Tools/'
-  @@_GTDB_API      = 'https://api.gtdb.ecogenomic.org/'
+  @@_GTDB_API      = 'https://gtdb-api.ecogenomic.org/'
   @@_SEQCODE_API   = 'https://disc-genomics.uibk.ac.at/seqcode/'
   @@_EUTILS_BUILD  = lambda { |service, q|
     q[:api_key] = ENV['NCBI_API_KEY'] if ENV['NCBI_API_KEY']

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 11, 0].freeze
+  VERSION = [1.3, 12, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 2, 11)
+  VERSION_DATE = Date.new(2024, 3, 8)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.11.0
+  version: 1.3.12.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-11 00:00:00.000000000 Z
+date: 2024-03-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons