miga-base 1.3.13.3 → 1.3.13.5

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 278d0637c00542b14f71285b198201a37a287aecef2392bcf77d915c0be9bd52
-  data.tar.gz: 97012a85b2e4f1baf6e5ded3ec8a454d3dbbf76e556b42eff1b216c0f7735a7a
+  metadata.gz: a1685116a04fec8af54d7f61494d8465fe51ae333620b36e5733094dfe3cb084
+  data.tar.gz: 3b88d700bab3819fc510e433855c86c1dad22a237364397e0cc32cec79caa673
 SHA512:
-  metadata.gz: dfae6fff930fcfef0517988855007fb62b65106cc52d6857dc7f384a8f4d967f5c6d0084809607921529649cc5237f6adc1c95a6e0f80604c4201bbc9539666e
-  data.tar.gz: 5d825d4f6e0da2a47b4b287b494a4609cadc76bea390b415db9c7a8c18320a442022eaf801384ec43afd8424739d53e86ba2b2dfd67dd775d5f03adc2b8f1699
+  metadata.gz: 341e70012a81c98836843ca5ff286b293f9cd5ae381636b7936943bad6118bbacd4af7e854dfaf944ee19aa56a975290a0734e791c29fca94a7df03c73d6e481
+  data.tar.gz: ab555131f4e7863b0409c2d89f6d493b539482afb075e19b172755d645ecd736491266f0a74dace121583c356a3b94216f605ab419268b84517488d7c2d4c458

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

@@ -37,10 +37,11 @@ module MiGA::Cli::Action::Doctor::Base
     return if fix.empty?
 
     cli.say("- Fixing #{fix.size} datasets")
-    fix.each_with_index do |d_n, k|
-      cli.advance('  > Fixing', k + 1, fix.size, false)
+    MiGA::Parallel.distribute(fix, cli[:threads]) do |d_n, idx, thr|
+      cli.advance('  > Fixing', idx + 1, fix.size, false) if thr == 0
       p.dataset(d_n).cleanup_distances!
     end
+    cli.say
   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/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, 3].freeze
+  VERSION = [1.3, 13, 5].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, 18)
+  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: 1.3.13.3
+  version: 1.3.13.5
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-18 00:00:00.000000000 Z
+date: 2024-03-20 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons