miga-base 1.3.13.2 → 1.3.13.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 1fb9ba522229fa36265c9f5b261c57c44f98e0d31275acd7903c0e4e79f9791a
+  metadata.gz: bdf054cb57b5a84d9ffb450b440a4dc6310e8aaf826d9b2160f0eecabce16385
+  data.tar.gz: 237517417fa21ad566df29aa9da67a8307b8b6a3988b0fae16fd4b594d2cc6f8
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+  metadata.gz: aae8695fab93405b5bb96063c35b12218eed2c78fcea1b2f308589bf29e600c7fbd89515cff59fc1b378b090b0786d55d627444d88810c7c25b202c0d772a310
+  data.tar.gz: 923d60bb47caeab98c9b062dc8af575e8dbe2950cf0602e123cfe8e7533ccdb0aaa5034d1bf0006d5e5f418f7004777c08f861a1e2eb9d143a79044ece69a2d3

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/cli/action/get.rb

@@ -77,6 +77,9 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
         'Path to an NCBI Taxonomy dump directory to query instead of API calls',
         'If the path is not passed, the dump is automatically downloaded'
       ) { |v| cli[:ncbi_taxonomy_dump] = v || true }
+      opt.on(
+        '--ignore-file', '::HIDE::' # Only for internal use
+      ) { |v| cli[:ignore_file] = v }
     end
   end
 
@@ -100,9 +103,10 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
   private
 
   def get_sub_cli
-    return [cli] if cli[:file].nil?
+    return [cli] if cli[:file].nil? || cli[:ignore_file]
 
     glob = []
+    cli_default = cli.original_argv + ['--ignore-file']
     File.open(cli[:file], 'r') do |fh|
       h = nil
       fh.each do |ln|
@@ -110,7 +114,7 @@ class MiGA::Cli::Action::Get < MiGA::Cli::Action
         if h.nil?
           h = r
         else
-          argv_i = [self.name]
+          argv_i = cli_default.dup
           h.each_with_index do |field, k|
             case field.downcase
             when *%w[query ignore-dup get-metadata only-metadata]

data/lib/miga/cli.rb

@@ -19,9 +19,13 @@ class MiGA::Cli < MiGA::MiGA
   attr_accessor :task
 
   ##
-  # The CLI parameters (except the task), and Array of String
+  # The unparsed CLI parameters (except the task), an Array of String
   attr_accessor :argv
 
+  ##
+  # The original ARGV passed to the CLI, an Array of String
+  attr_accessor :original_argv
+
   ##
   # Action to launch, an object inheriting from MiGA::Cli::Action
   attr_accessor :action
@@ -62,6 +66,7 @@ class MiGA::Cli < MiGA::MiGA
     @data = {}
     @defaults = { verbose: false, tabular: false }
     @opt_common = true
+    @original_argv = argv.dup
     @objects = {}
     if argv[0].nil? or argv[0].to_s[0] == '-'
       @task = :generic

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, 2].freeze
+  VERSION = [1.3, 13, 4].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, 15)
+  VERSION_DATE = Date.new(2024, 3, 20)
 
   ##
   # References of MiGA

data/scripts/aai_distances.bash

@@ -24,10 +24,8 @@ function aai_tsv {
   echo "a b value sd n omega" | tr " " "\\t"
   if [[ ${#DS[@]} -gt 40000 ]] ; then
     # Use comparisons in strictly one direction only for huge projects
-    foreach_database_aai \
-      | awk -F"\t" 'BEGIN { OFS="\t" }
-          { if ($1 > $2) { a=$1; $1=$2; $2=a; } } { print $0 }' \
-      | sort -k 1,2 -u
+    # (assuming the distances are truly bidirectional!)
+    foreach_database_aai | awk -F"\t" '$1 >= $2'
   else
     foreach_database_aai
   fi

data/scripts/haai_distances.bash

@@ -12,6 +12,9 @@ miga_start_project_step "$DIR"
 # Cleanup databases
 ruby -I "$MIGA/lib" "$MIGA/utils/cleanup-databases.rb" "$PROJECT" "$CORES"
 
+# Ensure bidirectional reference distances
+miga doctor -P "$PROJECT" --only bidirectional -v -t "$CORES"
+
 # No real need for hAAI distributions at all
 echo -n "" > miga-project.log
 echo -n "" > miga-project.txt

data/scripts/project_stats.bash

@@ -9,9 +9,9 @@ DIR="$PROJECT/data/90.stats"
 # Initialize
 miga_start_project_step "$DIR"
 
-# Execute doctor
+# Execute doctor (bidirectional is checked in haai_distances)
 echo "# Doctor"
-miga doctor -P "$PROJECT" -t "$CORES" -v
+miga doctor -P "$PROJECT" -t "$CORES" -v --ignore bidirectional
 
 # Index taxonomy
 echo "# Index taxonomy"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.13.2
+  version: 1.3.13.4
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-15 00:00:00.000000000 Z
+date: 2024-03-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons