miga-base 1.3.4.0 → 1.3.4.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 2bbf5a39c825a76578f7f5b9572fcd96ba8616f54204d6006a8dc8a43a1ed574
+  metadata.gz: 786b98a997a9145ad36a42404b756a65ca5f8abe628adf10e27960c58b7d5641
+  data.tar.gz: 95bc1da96a509cbe3c9334b78daf4ebaec9238693ef37fd5f417063943c9cf36
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data/lib/miga/cli/action/doctor.rb

@@ -26,7 +26,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
         '--only TASK',
         'Perform only the specified task (see --ignore)'
       ) do |v|
-        op_k = @@OPERATIONS.find { |_, i| i[0] == v.downcase }.first
+        op_k = @@OPERATIONS.find { |_, i| i[0] == v.downcase }&.first
+        op_k or raise "Unknown task: #{v}"
         @@OPERATIONS.each_key { |i| cli[i] = false }
         cli[op_k] = true
       end

data/lib/miga/remote_dataset.rb

@@ -178,9 +178,9 @@ class MiGA::RemoteDataset < MiGA::MiGA
     doc.scan(%r{<Taxon>(.*?)</Taxon>}m).map(&:first).each do |i|
       name = i.scan(%r{<ScientificName>(.*)</ScientificName>}).first.to_a.first
       rank = i.scan(%r{<Rank>(.*)</Rank>}).first.to_a.first
-      rank = nil if rank == 'no rank' or rank.empty?
-      rank = 'dataset' if lineage.empty? and rank.nil?
-      lineage[rank] = name unless rank.nil? or rank.nil?
+      rank = nil if rank.nil? || rank == 'no rank' || rank.empty?
+      rank = 'dataset' if lineage.size == 1 && rank.nil?
+      lineage[rank] = name unless rank.nil? || name.nil?
     end
     MiGA.DEBUG "Got lineage: #{lineage}"
     MiGA::Taxonomy.new(lineage)

data/lib/miga/result/stats.rb

@@ -231,9 +231,10 @@ module MiGA::Result::Stats
 
   # Fix estimates based on essential genes based on taxonomy
   def fix_essential_genes_by_domain
+    return if file_path(:raw_report)
+
     tax = source.metadata[:tax]
-    return if (!tax.nil? && !%w[Archaea Bacteria].include?(tax[:d])) ||
-       file_path(:raw_report)
+    return unless tax.nil? || %w[Archaea Bacteria].include?(tax[:d])
 
     domain = tax.nil? ? 'AB' : tax[:d][0]
     MiGA::MiGA.DEBUG "Fixing essential genes by domain"

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, 4, 0].freeze
+  VERSION = [1.3, 4, 2].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2023, 3, 30)
+  VERSION_DATE = Date.new(2023, 4, 7)
 
   ##
   # References of MiGA

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.4.0
+  version: 1.3.4.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-03-30 00:00:00.000000000 Z
+date: 2023-04-07 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons