miga-base 1.3.13.1 → 1.3.13.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: e3c8217b95cae01a70b7248f33790b672b18fd4c3c739437f49f37c7520ece66
-  data.tar.gz: e86e9bb0d8e6beebaf838bc42233ddd9cda5343756853d44ee5873df4d62426d
+  metadata.gz: 278d0637c00542b14f71285b198201a37a287aecef2392bcf77d915c0be9bd52
+  data.tar.gz: 97012a85b2e4f1baf6e5ded3ec8a454d3dbbf76e556b42eff1b216c0f7735a7a
 SHA512:
-  metadata.gz: 1b2550a8b834a611533d079fc5b5a46b770ba321ae4b062a3e451e752eb3b39d50828ac12261e5a446a5626b904a50b69c7b095cc0d89873bb01fba11b6e1d35
-  data.tar.gz: 4781f1f57b21bf75de2724243751c091f14071ce5a7b3de1505f7cb197175189d6ea11da62b845b5132746bed5fee9250c27cf4c6776875a1d4dfcd0b7751d0b
+  metadata.gz: dfae6fff930fcfef0517988855007fb62b65106cc52d6857dc7f384a8f4d967f5c6d0084809607921529649cc5237f6adc1c95a6e0f80604c4201bbc9539666e
+  data.tar.gz: 5d825d4f6e0da2a47b4b287b494a4609cadc76bea390b415db9c7a8c18320a442022eaf801384ec43afd8424739d53e86ba2b2dfd67dd775d5f03adc2b8f1699

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

@@ -12,8 +12,7 @@ module MiGA::Cli::Action::Doctor::Base
   # list, and therefore the databases need to be cleaned.
   # This is a subtask of +check_dist+
   def check_dist_eval(cli, p, res)
-    notok = {}
-    fix = {}
+    y = { notok: Set.new, fix: Set.new }
     Zlib::GzipReader.open(res.file_path(:matrix)) do |fh|
       lineno = 0
       fh.each_line do |ln|
@@ -23,16 +22,11 @@ module MiGA::Cli::Action::Doctor::Base
         names = [r[0], r[1]]
         next unless names.any? { |i| p.dataset(i).nil? }
 
-        names.each do |i|
-          if p.dataset(i).nil? || !p.dataset(i).active?
-            notok[i] = true
-          else
-            fix[i] = true
-          end
-        end
+        names.each { |i| y[p.dataset(i)&.active? ? :fix : :notok] << i }
       end
     end
-    [notok.keys, fix.keys]
+    # The code below is more readable than `y.values.map(&:to_a)`
+    [y[:notok].to_a, y[:fix].to_a]
   end
 
   ##
@@ -43,8 +37,8 @@ module MiGA::Cli::Action::Doctor::Base
     return if fix.empty?
 
     cli.say("- Fixing #{fix.size} datasets")
-    fix.each do |d_n|
-      cli.say "  > Fixing #{d_n}."
+    fix.each_with_index do |d_n, k|
+      cli.advance('  > Fixing', k + 1, fix.size, false)
       p.dataset(d_n).cleanup_distances!
     end
   end

data/lib/miga/dataset/result.rb

@@ -97,15 +97,14 @@ module MiGA::Dataset::Result
 
   ##
   # Clean-up all the stored distances, removing values for datasets no longer in
-  # the project as reference datasets.
-  def cleanup_distances!
+  # the project as reference datasets. All metrics are processed unless +metric+
+  # is passed (Array[Symbol], including :haai, :aai, :ani)
+  def cleanup_distances!(metrics = %i[haai aai ani])
     return if get_result(:distances).nil?
 
     require 'miga/sqlite'
-    ref = project.datasets.select(&:ref?).select(&:active?).map(&:name)
-    %i[haai aai ani].each do |metric|
-      cleanup_distances_by_metric!(ref, metric)
-    end
+    ref = project.dataset_ref_active.map(&:name)
+    metrics.each { |metric| cleanup_distances_by_metric!(ref, metric) }
   end
 
   private

data/lib/miga/project/dataset.rb

@@ -31,6 +31,22 @@ module MiGA::Project::Dataset
     @dataset_names_set ||= Set.new(dataset_names)
   end
 
+  ##
+  # Cache for the special set of datasets which are both reference and
+  # active, returned as an Array. Use carefully, as it doesn't get
+  # recalculated upon dataset (in)activation once loaded. To force
+  # recalculating, use +dataset_ref_active!+
+  def dataset_ref_active
+    @dataset_ref_active ||= dataset_ref_active!
+  end
+
+  ##
+  # Force recalculation of +dataset_ref_active+ and returns the Array
+  # of MiGA::Dataset objects
+  def dataset_ref_active!
+    @dataset_ref_active = datasets.select(&:ref?).select(&:active?)
+  end
+
   ##
   # Returns MiGA::Dataset
   def dataset(name)
@@ -60,6 +76,7 @@ module MiGA::Project::Dataset
       @metadata[:datasets] << name
       @dataset_names_hash[name] = true if @dataset_names_hash
       @dataset_names_set << name if @dataset_names_set
+      @dataset_ref_active = nil
       save
       if d.ref? && d.active?
         recalculate_tasks("Reference dataset added: #{d.name}")
@@ -75,6 +92,9 @@ module MiGA::Project::Dataset
     d = dataset(name)
     return nil if d.nil?
 
+    @dataset_names_hash = nil
+    @dataset_names_set  = nil
+    @dataset_ref_active = nil
     self.metadata[:datasets].delete(name)
     save
     if d.ref? && d.active?

data/lib/miga/remote_dataset/download.rb

@@ -186,7 +186,6 @@ class MiGA::RemoteDataset
     # Looks for the entry +id+ in +dbfrom+, and returns the linked
     # identifier in +db+ (or nil).
     def ncbi_map(id, dbfrom, db)
-      attempts = 0
       doc = download(:ncbi_map, dbfrom, id, :json, nil, db: db)
       return if doc.empty?
 

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, 13, 1].freeze
+  VERSION = [1.3, 13, 3].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, 3, 11)
+  VERSION_DATE = Date.new(2024, 3, 18)
 
   ##
   # References of MiGA

data/utils/distance/commands.rb

@@ -27,7 +27,7 @@ module MiGA::DistanceRunner::Commands
     # Launch comparisons
     pending_targets(targets, :aai).each do |target|
       # Full AAI
-      target_cds = target.result(:cds).file_path(:proteins) or next
+      target_cds = target.result(:cds)&.file_path(:proteins) or next
       aairb_cmd(
         tmp_file('proteins.fa'), target_cds,
         dataset.name, target.name, tmp_dbs[:aai], checkpoint: :aai

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.13.1
+  version: 1.3.13.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-11 00:00:00.000000000 Z
+date: 2024-03-18 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons