miga-base 0.7.18.0 → 0.7.18.4

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 78b020bda6120b5a284100b9544d7a488d385630f21b5d6d5e2bb9b365c832fb
-  data.tar.gz: d8332711fdf86308726700654ee8db91bb097f022a26e1240e62d107efa833a1
+  metadata.gz: 1a0c77da5b4e0cfaee8d470f669d0589f00949c686868780c9c8ee2eb68cd9cd
+  data.tar.gz: 9f78d665d2559eacc0a19dd16d8b3cd712a512909db8c1a7af1dcb0edd7302d4
 SHA512:
-  metadata.gz: 8b766a40acf37193204e6369e07f2ecba1a67aa6141133654ab69f89b2ba9a63a959bd3f5b7fd21c56542eea7e3174cc342b05dc76b73ed27c6a2b273c546ca9
-  data.tar.gz: 6f8d791b9bf443a1eb43198625ebce48501ebaa3680be0c4cef55931b176fd2365407865e6e43cd549217ada6c67e5c86b156bd0816b80f91c388af812af810c
+  metadata.gz: 0f2ad1f0efb0712fac07ffb62198695be09a27a0f2e3346c97532331973cae21cbede3002c8e0c935945cccdcbbf6027e6297f2621fe8add53f4b47b3fbb2e18
+  data.tar.gz: 31e5c848db45f20b5a5358b602ee08ad285ba44bb40f20265792a8331067ba51c1cba4e78b6f260264a6bd480d95447e10031005e3b8d18a336ad93f467695c7

data/lib/miga/cli/action/run.rb

@@ -59,7 +59,7 @@ class MiGA::Cli::Action::Run < MiGA::Cli::Action
            "MIGA=#{miga.shellescape}", "CORES=#{cli[:thr]}"]
     obj = cli.load_project_or_dataset
     klass = obj.class
-    virtual_task = [:p, :d].include?(cli[:result])
+    virtual_task = %i[p d maintenance].include?(cli[:result])
     cmd << "DATASET=#{obj.name.shellescape}" if obj.is_a? MiGA::Dataset
     if klass.RESULT_DIRS[cli[:result]].nil? and not virtual_task
       raise "Unsupported #{klass.to_s.sub(/.*::/, '')} result: #{cli[:result]}."

data/lib/miga/common.rb

@@ -74,10 +74,13 @@ class MiGA::MiGA
     @_advance_time[:n] = n
 
     # Report
-    adv_vals = [100.0 * n / total, num_suffix(n, bin), num_suffix(total, bin)]
     adv =
-      total.nil? ? (n == 0 ? '' : num_suffix(n, bin)) :
-        ('%.1f%% (%s/%s)' % adv_vals)
+      if total.nil?
+        (n == 0 ? '' : num_suffix(n, bin))
+      else
+        vals = [100.0 * n / total, num_suffix(n, bin), num_suffix(total, bin)]
+        ('%.1f%% (%s/%s)' % vals)
+      end
     left =
       if @_advance_time[:avg].nil?
         ''

data/lib/miga/common/with_daemon.rb

@@ -158,7 +158,7 @@ module MiGA::Common::WithDaemon
   # Returns the status of the daemon with +opts+
   def status(opts = [], wait = true)
     if active?
-      say "Running with pid #{File.read(pid_file)}"
+      say "Running with pid #{File.size?(pid_file) ? File.read(pid_file) : '?'}"
     else
       say 'Not running'
     end

data/lib/miga/daemon.rb

@@ -182,6 +182,7 @@ class MiGA::Daemon < MiGA::MiGA
     unless show_log?
       n = project.dataset_names.count
       k = jobs_to_run.size + jobs_running.size
+      k -= 1 unless get_job(:maintenance).nil?
       advance('Datasets:', n - k, n, false)
       miga_say if k == 0
     end
@@ -274,10 +275,10 @@ class MiGA::Daemon < MiGA::MiGA
     # Avoid single datasets hogging resources
     @jobs_to_run.rotate! rand(jobs_to_run.size)
 
-    # Prioritize project-wide jobs
-    project_jobs = @jobs_to_run.select { |i| i[:ds].nil? }
-    @jobs_to_run.delete_if { |i| i[:ds].nil? }
-    @jobs_to_run.prepend(*project_jobs)
+    # Prioritize: Project-wide > MiGA Online queries > Other datasets
+    @jobs_to_run.sort_by! do |job|
+      job[:ds].nil? ? 1 : job[:ds_name] =~ /^qG_/ ? 2 : 3
+    end
 
     # Launch as many +jobs_to_run+ as possible
     while (hostk = next_host)

data/lib/miga/dataset.rb

@@ -7,7 +7,11 @@ require 'miga/metadata'
 require 'miga/dataset/result'
 require 'miga/dataset/status'
 require 'miga/dataset/hooks'
-require 'miga/sqlite'
+
+# This library is only required by +#closest_relatives+, so it is now
+# being loaded on call instead to allow most of miga-base to work without
+# issue in systems with problematic SQLite3 installations.
+# require 'miga/sqlite'
 
 ##
 # Dataset representation in MiGA
@@ -190,6 +194,7 @@ class MiGA::Dataset < MiGA::MiGA
     r = result(ref_project ? :taxonomy : :distances)
     return nil if r.nil?
 
+    require 'miga/sqlite'
     MiGA::SQLite.new(r.file_path(:aai_db)).run(
       'SELECT seq2, aai FROM aai WHERE seq2 != ? ' \
       'GROUP BY seq2 ORDER BY aai DESC LIMIT ?', [name, how_many]

data/lib/miga/dataset/result.rb

@@ -1,8 +1,12 @@
-require 'miga/sqlite'
 require 'miga/result'
 require 'miga/dataset/base'
 require 'miga/common/with_result'
 
+# This library is only required by +#cleanup_distances!+, so it is now
+# being loaded on call instead to allow most of miga-base to work without
+# issue in systems with problematic SQLite3 installations.
+# require 'miga/sqlite'
+
 ##
 # Helper module including specific functions to add dataset results
 module MiGA::Dataset::Result
@@ -144,9 +148,10 @@ module MiGA::Dataset::Result
   # the project as reference datasets.
   def cleanup_distances!
     r = get_result(:distances)
-    ref = project.datasets.select(&:ref?).select(&:active?).map(&:name)
     return if r.nil?
 
+    require 'miga/sqlite'
+    ref = project.datasets.select(&:ref?).select(&:active?).map(&:name)
     %i[haai_db aai_db ani_db].each do |db_type|
       db = r.file_path(db_type)
       next if db.nil? || !File.size?(db)

data/lib/miga/version.rb

@@ -8,7 +8,7 @@ module MiGA
   # - Float representing the major.minor version.
   # - Integer representing gem releases of the current version.
   # - Integer representing minor changes that require new version number.
-  VERSION = [0.7, 18, 0]
+  VERSION = [0.7, 18, 4]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 12, 27)
+  VERSION_DATE = Date.new(2021, 1, 1)
 
   ##
   # Reference of MiGA.

data/scripts/miga.bash

@@ -11,17 +11,17 @@ function exists { [[ -e "$1" ]] ; }
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
 
 if [[ "$SCRIPT" != "d" && "$SCRIPT" != "p" ]] ; then
-  echo '############'
-  echo -n "Date: " ; miga date
-  echo "Hostname: $(hostname)"
-  echo "MiGA: $MIGA"
-  echo "Task: $SCRIPT"
-  echo "Project: $PROJECT"
+  echo ""
+  echo "######[ $SCRIPT ]######"
+  echo "# Date: $(miga date)"
+  echo "# Host: $(hostname)"
+  echo "# MiGA: $MIGA"
+  echo "# Project: $PROJECT"
   if [[ -n $DATASET ]] ; then
-    echo "Dataset: $DATASET"
+    echo "# Dataset: $DATASET"
     miga edit -P "$PROJECT" -D "$DATASET" -m "_step=$SCRIPT"
   fi
-  echo '------------'
+  echo '#------------'
 fi
 
 true

data/utils/cleanup-databases.rb

@@ -5,21 +5,17 @@ require 'miga'
 
 ARGV[1] or abort "Usage: #{$0} path/to/project threads"
 
-$stderr.puts 'Cleaning databases...'
 p = MiGA::Project.load(ARGV[0])
-ds_names = p.dataset_names
+dsn = p.dataset_names
 thr = ARGV[1].to_i
 
-pc = [0] + (1..100).map { |i| ds_names.size * i / 100 }
-$stderr.puts (('.' * 9 + '|') * 10) + ' 100%'
+m = MiGA::MiGA.new
+m.say 'Cleaning Databases'
 
 (0..thr - 1).each do |t|
   fork do
-    ds_names.each_with_index do |i, idx|
-      while t == 0 and idx + 1 > pc.first
-        $stderr.print '#'
-        pc.shift
-      end
+    dsn.each_with_index do |i, idx|
+      m.advance('Dataset:', dsn.size, idx + 1) if t == 0
       next unless (idx % thr) == t
 
       d = p.dataset(i)
@@ -30,4 +26,6 @@ $stderr.puts (('.' * 9 + '|') * 10) + ' 100%'
   end
 end
 Process.waitall
-$stderr.puts ' Done'
+m.advance('Dataset:', dsn.size, dsn.size)
+m.say
+

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.18.0
+  version: 0.7.18.4
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-12-27 00:00:00.000000000 Z
+date: 2021-01-01 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons