miga-base 1.3.10.2 → 1.3.11.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 601e480270ea7f04ff3f5057fa5f031146ac2e73247a7c191ea391a17e971bfc
-  data.tar.gz: 1577f19ec6b7798305a847da42556a16ff9e6a144c2e317e3349a8b49a0069fd
+  metadata.gz: 4d513b44448defe8d433ed9c6f573dcc84df356c610598e3b2bbaea370c9f459
+  data.tar.gz: e09fb9877dfe796856db08b80ac176033025603a49ca5222fda69942544c99ff
 SHA512:
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-  data.tar.gz: b7ab71aa3a78d32861e1e9f6ff685424530093fd485185be722c6cc139a81d30692e00ccb6cbad4799bbcbd077ce32c7693db8336c98e8dfe0b18196748af174
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+  data.tar.gz: f26bc6e99d591a60603c06de28f6b622ac13ed9e4d17acce43f532a3d29bed930e013aa7bd84b93aa1f9ca272c4427ea4bce7afe8e0bd5fbeef4174b75d40142

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/metadata.rb

@@ -103,7 +103,7 @@ class MiGA::Metadata < MiGA::MiGA
   # Delete file at #path
   def remove!
     MiGA.DEBUG "Metadata.remove! #{path}"
-    File.unlink(path)
+    File.unlink(path) if File.exist?(path)
     nil
   end
 

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, 2].freeze
+  VERSION = [1.3, 11, 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, 6)
+  VERSION_DATE = Date.new(2024, 2, 11)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.10.2
+  version: 1.3.11.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-06 00:00:00.000000000 Z
+date: 2024-02-11 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons