miga-base 0.7.20.0 → 0.7.20.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: de9486ffe4bff4fd61295c004f36af331ce5a50645f4aa706076a38d3523ee38
-  data.tar.gz: 60ded180b92cfb27729a4844c00713b4e78bf08b6a1f8ebf30f6bdccd24eb769
+  metadata.gz: 76b06be04db6bb162666752f374da5a3adab38e010acf8a07f20fc2e8f97e75b
+  data.tar.gz: 6c4f9b9118b21b11921b4c0a70ae99f3b1728d5737175ca5b9f23088ff985063
 SHA512:
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-  data.tar.gz: 4ac7cf2785e42afd17f19749632e1deda80cecfa10103f64d4bc366a29e4a8acf9ead5e8a412ae1b11ba966c6dc9501017cb7dbee2572ebcbc835e9db0341a7b
+  metadata.gz: d90839141adeb99d0551d0228c7b5806b11a971852bf2ca8040f419af79330be47fc7abe7f1bffec35fe935b3857a1631c860d8e6aa877ba74eb1524d24f8153
+  data.tar.gz: baeee018956a1877065e2e9b5f689e1dc99af71cecc2705f951ab384b05b5760cffd7d85218068bb674541cb766a585add60c5b23a6209c15e2276b369d0f1b0

data/lib/miga/daemon.rb

@@ -103,7 +103,7 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Queue maintenance tasks as an analysis job
   def queue_maintenance
-    return if bypass_maintenance?
+    return if bypass_maintenance? || shutdown_when_done?
 
     say 'Queueing maintenance tasks'
     queue_job(:maintenance)
@@ -214,29 +214,38 @@ class MiGA::Daemon < MiGA::MiGA
     return nil unless get_job(job, ds).nil?
 
     ds_name = (ds.nil? ? 'miga-project' : ds.name)
-    say 'Queueing %s:%s' % [ds_name, job]
+    task_name = "#{project.metadata[:name][0..9]}:#{job}:#{ds_name}"
+    to_run = { ds: ds, ds_name: ds_name, job: job, task_name: task_name }
+    say 'Queueing %s:%s' % [to_run[:ds_name], to_run[:job]]
+    @jobs_to_run << to_run
+  end
+
+  ##
+  # Construct the command for the given job definition with current
+  # daemon settings
+  def job_cmd(to_run)
     vars = {
       'PROJECT' => project.path,
       'RUNTYPE' => runopts(:type),
       'CORES' => ppn,
       'MIGA' => MiGA::MiGA.root_path
     }
-    vars['DATASET'] = ds.name unless ds.nil?
-    log_dir = File.expand_path("daemon/#{job}", project.path)
-    Dir.mkdir(log_dir) unless Dir.exist? log_dir
-    task_name = "#{project.metadata[:name][0..9]}:#{job}:#{ds_name}"
-    to_run = { ds: ds, ds_name: ds_name, job: job, task_name: task_name }
-    to_run[:cmd] = runopts(:cmd).miga_variables(
-      script: MiGA::MiGA.script_path(job, miga: vars['MIGA'], project: project),
+    vars['DATASET'] = to_run[:ds].name unless to_run[:ds].nil?
+    log_dir = File.expand_path("daemon/#{to_run[:job]}", project.path)
+    FileUtils.mkdir_p(log_dir)
+    var_hsh = {
+      script: MiGA::MiGA.script_path(
+                to_run[:job], miga: vars['MIGA'], project: project
+              ),
       vars: vars.map do |k, v|
               runopts(:var).miga_variables(key: k, value: v)
             end.join(runopts(:varsep)),
       cpus: ppn,
-      log: File.expand_path("#{ds_name}.log", log_dir),
-      task_name: task_name,
-      miga: File.expand_path('bin/miga', MiGA::MiGA.root_path).shellescape
-    )
-    @jobs_to_run << to_run
+      log: File.join(log_dir, "#{to_run[:ds_name]}.log"),
+      task_name: to_run[:task_name],
+      miga: File.join(MiGA::MiGA.root_path, 'bin/miga').shellescape
+    }
+    runopts(:cmd).miga_variables(var_hsh)
   end
 
   ##
@@ -312,6 +321,7 @@ class MiGA::Daemon < MiGA::MiGA
   # Launch the job described by Hash +job+ to +hostk+-th host
   def launch_job(job, hostk = nil)
     # Execute job
+    job[:cmd] = job_cmd(job)
     case runopts(:type)
     when 'ssh'
       # Remote job

data/lib/miga/daemon/base.rb

@@ -93,7 +93,7 @@ module MiGA::Daemon::Base
   ##
   # Display log instead of the progress summary
   def show_log!
-    @show_log = true
+    @runopts[:show_log] = true
   end
 
   ##

data/lib/miga/project/dataset.rb

@@ -48,10 +48,11 @@ module MiGA::Project::Dataset
   # Add dataset identified by +name+ and return MiGA::Dataset.
   def add_dataset(name)
     unless metadata[:datasets].include? name
-      MiGA::Dataset.new(self, name)
+      ds = MiGA::Dataset.new(self, name)
       @metadata[:datasets] << name
       @dataset_names_hash = nil # Ensure loading even if +do_not_save+ is true
       save
+      # TODO redo_project_steps if ds.ref?
       pull_hook(:on_add_dataset, name)
     end
     dataset(name)

data/lib/miga/tax_index.rb

@@ -17,7 +17,7 @@ class MiGA::TaxIndex < MiGA::MiGA
   ##
   # Initialize an empty MiGA::TaxIndex
   def initialize
-    @root = MiGA::TaxIndexTaxon.new :root, 'biota'
+    @root = MiGA::TaxIndexTaxon.new(:root, 'biota')
     @datasets = []
   end
 
@@ -37,21 +37,22 @@ class MiGA::TaxIndex < MiGA::MiGA
   end
 
   ##
-  # Finds all the taxa in the collection at the +rank+ taxonomic rank.
+  # Finds all the taxa in the collection at the +rank+ taxonomic rank
   def taxa_by_rank(rank)
     rank = MiGA::Taxonomy.normalize_rank(rank)
     taxa = [@root]
     select = []
     loop do
       new_taxa = []
-      taxa.map { |tx| tx.children }.flatten.each do |ch|
+      taxa.map(&:children).flatten.each do |ch|
         if ch.rank == rank
           select << ch
-        elsif not ch.children.empty?
+        elsif !ch.children.empty?
           new_taxa << ch
         end
       end
-      break if new_taxa.empty?
+      taxa = new_taxa
+      break if taxa.empty?
     end
     select
   end
@@ -60,7 +61,8 @@ class MiGA::TaxIndex < MiGA::MiGA
   # Generate JSON String for the index.
   def to_json
     MiGA::Json.generate(
-      { root: root.to_hash, datasets: datasets.map { |d| d.name } }
+      root: root.to_hash,
+      datasets: datasets.map(&:name)
     )
   end
 
@@ -119,27 +121,33 @@ class MiGA::TaxIndexTaxon < MiGA::MiGA
   ##
   # Get the number of datasets in the taxon (including children).
   def datasets_count
-    children.map { |it| it.datasets_count }.reduce(datasets.size, :+)
+    children.map(&:datasets_count).reduce(datasets.size, :+)
   end
 
   ##
   # Get all the datasets in the taxon (including children).
   def all_datasets
-    children.map { |it| it.datasets }.reduce(datasets, :+)
+    children.map(&:datasets).reduce(datasets, :+)
   end
 
   ##
   # JSON String of the taxon.
   def to_json(*a)
-    { str: tax_str, datasets: datasets.map { |d| d.name },
-      children: children }.to_json(a)
+    {
+      str: tax_str,
+      datasets: datasets.map(&:name),
+      children: children
+    }.to_json(a)
   end
 
   ##
   # Hash representation of the taxon.
   def to_hash
-    { str: tax_str, datasets: datasets.map { |d| d.name },
-      children: children.map { |it| it.to_hash } }
+    {
+      str: tax_str,
+      datasets: datasets.map(&:name),
+      children: children.map(&:to_hash)
+    }
   end
 
   ##

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, 20, 0]
+  VERSION = [0.7, 20, 1]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 1, 7)
+  VERSION_DATE = Date.new(2021, 1, 10)
 
   ##
   # Reference of MiGA.

data/test/common_test.rb

@@ -72,4 +72,34 @@ class CommonTest < Test::Unit::TestCase
     assert_not_predicate('C3-PO', :miga_name?)
     assert_equal("123\n1\n", '1231'.wrap_width(3))
   end
+
+  def test_advance
+    m = MiGA::MiGA.new
+
+    # Check advance when missing total
+    o = capture_stderr { m.advance('x', 0) }.string
+    assert_match(/\] x *\r/, o)
+
+    # Initialize advance
+    o = capture_stderr { m.advance('x', 0, 10) }.string
+    assert_match(/\] x 0\.0% \(0\/10\) *\r/, o)
+
+    # Insufficient data for prediction
+    sleep(1)
+    o = capture_stderr { m.advance('x', 1, 10) }.string
+    assert_match(/\] x 10\.0% \(1\/10\) *\r/, o)
+
+    # Predict time
+    sleep(1)
+    o = capture_stderr { m.advance('x', 2, 10) }.string
+    assert_match(/\] x 20\.0% \(2\/10\) [7-9]s left *\r/, o)
+  end
+
+  def test_num_suffix
+    m = MiGA::MiGA.new
+    assert_equal('12', m.num_suffix(12))
+    assert_equal('1.5K', m.num_suffix(1.5e3))
+    assert_equal('1.0M', m.num_suffix(1024**2 + 1, true))
+    assert_equal('1.1G', m.num_suffix(1024**3))
+  end
 end

data/test/daemon_test.rb

@@ -48,7 +48,10 @@ class DaemonTest < Test::Unit::TestCase
     end
     assert_match(/Queueing #{ds.name}:d/, out.string)
     assert_equal(1, d.jobs_to_run.size)
-    assert_equal('echo project0:d:ds1 >/dev/null', d.jobs_to_run.first[:cmd])
+    assert_equal(
+      'echo project0:d:ds1 >/dev/null',
+      d.job_cmd(d.jobs_to_run.first)
+    )
     assert_equal(d.jobs_to_run.first, d.get_job(:d, ds))
   end
 
@@ -335,4 +338,17 @@ class DaemonTest < Test::Unit::TestCase
     capture_stderr { d.in_loop }
     assert_equal([], d.jobs_running)
   end
+
+  def test_show_log
+    d = daemon
+    assert(d.show_log?)
+    d.runopts(:show_log, false)
+    assert(!d.show_log?)
+    d.show_log!
+    assert(d.show_log?)
+    assert_equal($stderr, d.logfh)
+    d.show_summary!
+    assert(!d.show_log?)
+    assert_not_equal($stderr, d.logfh)
+  end
 end

data/test/tax_index_test.rb

@@ -35,4 +35,30 @@ class TaxIndexTest < Test::Unit::TestCase
     ti = MiGA::TaxIndex.new
     assert_equal("root:biota: 0\n", ti.to_tab)
   end
+
+  def test_tax_index_taxon
+    taxon = MiGA::TaxIndexTaxon.new(:root, 'biota')
+    assert_empty(taxon.datasets)
+    assert_equal('root:biota', taxon.to_hash[:str])
+    assert_equal(
+      '{"str":"root:biota","datasets":[],"children":[]}',
+      taxon.to_json
+    )
+    assert_empty(taxon.all_datasets)
+    assert_equal(0, taxon.datasets_count)
+  end
+
+  def test_taxa_by_rank
+    initialize_miga_home
+    d = dataset
+    d.metadata[:tax] = MiGA::Taxonomy.new('k:Fantasia g:Unicornia')
+
+    # Empty
+    ti = MiGA::TaxIndex.new
+    assert_empty(ti.taxa_by_rank(:genus))
+
+    # Unicorn
+    ti << d
+    assert_equal('Unicornia', ti.taxa_by_rank(:genus).first.name)
+  end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.20.0
+  version: 0.7.20.1
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-01-07 00:00:00.000000000 Z
+date: 2021-01-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons