Address recent change in GTDB search API

bio-miga · Jan 16, 2025 · c2ccecd · c2ccecd
1 parent 1b624f6
commit c2ccecd
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Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/lib/miga/cli/action/download/gtdb.rb b/lib/miga/cli/action/download/gtdb.rb
@@ -23,8 +23,9 @@ def cli_name_modifiers(opt)
 
   def sanitize_cli
     cli.ensure_par(taxon: '-T')
-    unless cli[:taxon] =~ /^[a-z]__\S+$/
-      raise 'Taxon (-T) must be in GTDB format: s__Macondimonas_diazotrophica'
+    cli[:taxon].gsub!(' ', '%20')
+    unless cli[:taxon] =~ /^[a-z]__[\S ]+$/
+      raise 'Taxon (-T) must be in GTDB format: "s__Macondimonas diazotrophica"'
     end
     cli[:save_every] = 1 if cli[:dry]
   end

diff --git a/lib/miga/version.rb b/lib/miga/version.rb
@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 21, 4].freeze
+  VERSION = [1.3, 21, 5].freeze
 
   ##
   # Nickname for the current major.minor version.
   VERSION_NAME = 'mezzotint'
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 12, 23)
+  VERSION_DATE = Date.new(2025, 1, 16)
 
   ##
   # References of MiGA