miga-base 1.3.10.3 → 1.3.11.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 0ce0666c34e0d79d39b9dfb3c695a48e17b11f066efff7185abd7f10b47d163b
+  metadata.gz: 0366c904edeefa13506aa8cc77fe1834e59d2cd30e7bd60dce822d981676b3fe
+  data.tar.gz: 7679c8d021c093cc1204384fe02f0126632dbc6735835ac31a19f8beaa8196e9
 SHA512:
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+  metadata.gz: bdc27c7a353300e6b61bacec87feea8b3d4f5337b46a6bfab62e1e6794777e2abf4bd4b79c2b1f2acb970997c2f9af0e21b62ea08daa16fd39be61eadd563be6
+  data.tar.gz: d5d0d9c245e9413d896fea2846f375109cbbe71e75235992164fe9647c9279a6f3adecc6c32eb70da65633f0ba56b604271bc66623cdf5c85d9e1bedb99f43e1

data/lib/miga/cli/action/get.rb

@@ -61,6 +61,10 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
         '--only-metadata',
         'Create datasets without input data but retrieve all metadata'
       ) { |v| cli[:only_md] = v }
+      opt.on(
+        '--bypass-metadata',
+        'Do not gather optional metadata such as the dataset taxonomy'
+      ) { |v| cli[:bypass_md] = v }
       opt.on(
         '--api-key STRING',
         'API key for the given universe'
@@ -75,6 +79,7 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
       rd = create_remote_dataset(sub_cli, p)
       next if rd.nil?
 
+      rd.metadata[:bypass_metadata] = true if sub_cli[:bypass_md]
       if sub_cli[:get_md]
         update_metadata(sub_cli, p, rd)
       else

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/remote_dataset.rb

@@ -188,6 +188,7 @@ class MiGA::RemoteDataset < MiGA::MiGA
   # Get metadata from the remote location.
   def get_metadata(metadata_def = {})
     metadata_def.each { |k, v| @metadata[k] = v }
+    return @metadata if @metadata[:bypass_metadata]
 
     case universe
     when :ebi, :ncbi, :web

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, 10, 3].freeze
+  VERSION = [1.3, 11, 1].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, 8)
+  VERSION_DATE = Date.new(2024, 3, 5)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.10.3
+  version: 1.3.11.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-08 00:00:00.000000000 Z
+date: 2024-03-05 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons