miga-base 0.7.3.1 → 0.7.4.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  data.tar.gz: 9b6751862e49aee3980133dc16d85d51d973111ad5db9eb15dcbb369972e548d
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data/lib/miga/cli/action/doctor/base.rb

@@ -0,0 +1,79 @@
+
+require 'miga/cli/action'
+require 'sqlite3'
+
+class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
+end
+
+module MiGA::Cli::Action::Doctor::Base
+  ##
+  # Check the database in +db_file+ maintains integrity for the
+  # tables saving +metric+ (:ani or :aai)
+  def check_sqlite3_database(db_file, metric)
+    SQLite3::Database.new(db_file) do |conn|
+      conn.execute("select count(*) from #{metric}").first
+    end
+  rescue SQLite3::SQLException
+    yield
+  end
+
+  ##
+  # Scans the all-vs-all matrix registered in +res+ (MiGA::Result) in search of
+  # pairs where one or both datasets are missing or inactive in the project +p+
+  # (MiGA::Project), and report progress through +cli+ (MiGA::Cli).
+  # Returns an Array with two arrays: the first a list of dataset names that are
+  # no longer registered in the project or are currently inactive, and the
+  # second a list of dataset names that have registered pairs with the first
+  # 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 = {}
+    Zlib::GzipReader.open(res.file_path(:matrix)) do |fh|
+      lineno = 0
+      fh.each_line do |ln|
+        next if (lineno += 1) == 1
+        r = ln.split("\t")
+        next unless [1, 2].map { |i| p.dataset(r[i]).nil? }.any?
+        [1, 2].each do |i|
+          if p.dataset(r[i]).nil? || !p.dataset(r[i]).active?
+            notok[r[i]] = true
+          else
+            fix[r[i]] = true
+          end
+        end
+      end
+    end
+    [notok.keys, fix.keys]
+  end
+
+  ##
+  # Cleanup distance databases for datasets names in +fix+ (Array: String)
+  # from project +p+ (MiGA::Project), and report through +cli+ (MiGA::Cli).
+  # This is a subtask of +check_dist+
+  def check_dist_fix(cli, p, fix)
+    return if fix.empty?
+    cli.say("- Fixing #{fix.size} datasets")
+    fix.each do |d_n|
+      cli.say "  > Fixing #{d_n}."
+      p.dataset(d_n).cleanup_distances!
+    end
+  end
+
+  ##
+  # Recompute +res+ (MiGA::Result) if +notok+ (Array: String) has any dataset
+  # names registered, and report through +cli+ (MiGA::Cli).
+  # This is a subtask of +check_dist+
+  def check_dist_recompute(cli, res, notok)
+    return if notok.empty?
+    cli.say '- Unregistered datasets detected: '
+    if notok.size <= 5
+      notok.each { |i| cli.say "  > #{i}" }
+    else
+      cli.say "  > #{notok.size}, including #{notok.first}"
+    end
+    cli.say '- Removing tables, recompute'
+    res.remove!
+  end
+end
+

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

@@ -1,15 +1,15 @@
 # @package MiGA
 # @license Artistic-2.0
 
-require 'miga/cli/action'
-require 'sqlite3'
+require 'miga/cli/action/doctor/base'
 
 class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
+  include MiGA::Cli::Action::Doctor::Base
 
   def parse_cli
-    @@OPERATIONS.keys.each { |i| cli.defaults = { i => true } }
+    cli.defaults = Hash[@@OPERATIONS.keys.map { |i| [i, true] }]
     cli.parse do |opt|
-      operation_n = Hash[@@OPERATIONS.map { |k,v| [v[0], k] }]
+      operation_n = Hash[@@OPERATIONS.map { |k, v| [v[0], k] }]
       cli.opt_object(opt, [:project])
       opt.on(
         '--ignore TASK1,TASK2', Array,
@@ -21,20 +21,12 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
         'Perform only the specified task (see --ignore)'
       ) do |v|
         op_k = @@OPERATIONS.find { |_, i| i[0] == v.downcase }.first
-        @@OPERATIONS.keys.each { |i| cli[i] = false }
+        @@OPERATIONS.each_key { |i| cli[i] = false }
         cli[op_k] = true
       end
     end
   end
 
-  def check_sqlite3_database(db_file, metric)
-    SQLite3::Database.new(db_file) do |conn|
-      conn.execute("select count(*) from #{metric}").first
-    end
-  rescue SQLite3::SQLException
-    yield
-  end
-
   def perform
     p = cli.load_project
     @@OPERATIONS.keys.each do |k|
@@ -43,7 +35,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
   end
 
   @@OPERATIONS = {
-    db: ['databases', 'Check database files integrity'],
+    status: ['status', 'Update metadata status of all datasets'],
+    db: ['databases', 'Check integrity of database files'],
     dist: ['distances', 'Check distance summary tables'],
     files: ['files', 'Check for outdated files'],
     cds: ['cds', 'Check for gzipped genes and proteins'],
@@ -52,34 +45,52 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     start: ['start', 'Check for lingering .start files'],
     tax: ['taxonomy', 'Check for taxonomy consistency (not yet implemented)']
   }
+
   class << self
+    ##
+    # All supported operations
     def OPERATIONS
       @@OPERATIONS
     end
   end
 
+  ##
+  # Perform status operation with MiGA::Cli +cli+
+  def check_status(cli)
+    cli.say 'Updating metadata status'
+    cli.load_project.each_dataset { |d| d.recalculate_status }
+  end
+
+  ##
+  # Perform databases operation with MiGA::Cli +cli+
   def check_db(cli)
-    cli.say 'Checking databases integrity'
+    cli.say 'Checking integrity of databases'
     cli.load_project.each_dataset do |d|
-      [:distances, :taxonomy].each do |r_key|
+      %i[distances taxonomy].each do |r_key|
         r = d.result(r_key) or next
-        {haai_db: :aai, aai_db: :aai, ani_db: :ani}.each do |db_key, metric|
+        { haai_db: :aai, aai_db: :aai, ani_db: :ani }.each do |db_key, metric|
           db_file = r.file_path(db_key) or next
           check_sqlite3_database(db_file, metric) do
-            cli.say(
-              "  > Removing #{db_key} #{r_key} table for #{d.name}")
+            cli.say("  > Removing #{db_key} #{r_key} table for #{d.name}")
             [db_file, r.path(:done), r.path].each do |f|
               File.unlink(f) if File.exist? f
-            end # each |f|
-          end # check_sqlite3_database
-        end # each |db_key, metric|
-      end # each |r_key|
-    end # each |d|
+            end
+            # /each |f|
+          end
+          # /check_sqlite3_database
+        end
+        # /each |db_key, metric|
+      end
+      # /each |r_key|
+    end
+    # /each |d|
   end
 
+  ##
+  # Perform distances operation with MiGA::Cli +cli+
   def check_dist(cli)
     p = cli.load_project
-    [:ani, :aai].each do |dist|
+    %i[ani aai].each do |dist|
       res = p.result("#{dist}_distances")
       next if res.nil?
       cli.say "Checking #{dist} table for consistent datasets"
@@ -89,6 +100,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     end
   end
 
+  ##
+  # Perform files operation with MiGA::Cli +cli+
   def check_files(cli)
     cli.say 'Looking for outdated files in results'
     p = cli.load_project
@@ -110,12 +123,14 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     end
   end
 
+  ##
+  # Perform cds operation with MiGA::Cli +cli+
   def check_cds(cli)
     cli.say 'Looking for unzipped genes or proteins'
     cli.load_project.each_dataset do |d|
       res = d.result(:cds) or next
       changed = false
-      [:genes, :proteins, :gff3, :gff2, :tab].each do |f|
+      %i[genes proteins gff3 gff2 tab].each do |f|
         file = res.file_path(f) or next
         if file !~ /\.gz/
           cli.say "  > Gzipping #{d.name} #{f}"
@@ -131,6 +146,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     end
   end
 
+  ##
+  # Perform essential-genes operation with MiGA::Cli +cli+
   def check_ess(cli)
     cli.say 'Looking for unarchived essential genes'
     cli.load_project.each_dataset do |d|
@@ -150,6 +167,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     end
   end
 
+  ##
+  # Perform mytaxa-scan operation with MiGA::Cli +cli+
   def check_mts(cli)
     cli.say 'Looking for unarchived MyTaxa Scan runs'
     cli.load_project.each_dataset do |d|
@@ -166,8 +185,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
         end
         fix = true
       end
-      %w[blast mytaxain wintax gene_ids region_ids].each do |ext|
-        file = res.file_path(ext.to_sym)
+      %i[blast mytaxain wintax gene_ids region_ids].each do |ext|
+        file = res.file_path(ext)
         unless file.nil?
           FileUtils.rm(file) if File.exist? file
           fix = true
@@ -180,6 +199,8 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     end
   end
 
+  ##
+  # Perform start operation with MiGA::Cli +cli+
   def check_start(cli)
     cli.say 'Looking for legacy .start files lingering'
     cli.load_project.each_dataset do |d|
@@ -192,52 +213,12 @@ class MiGA::Cli::Action::Doctor < MiGA::Cli::Action
     end
   end
 
+  ##
+  # Perform taxonomy operation with MiGA::Cli +cli+
   def check_tax(cli)
-    #cli.say 'o Checking for taxonomy/distances consistency'
+    # cli.say 'o Checking for taxonomy/distances consistency'
     # TODO: Find 95%ANI clusters with entries from different species
-  end
-
-  private
-
-  def check_dist_eval(cli, p, res)
-    notok = {}
-    fix = {}
-    Zlib::GzipReader.open(res.file_path(:matrix)) do |fh|
-      lineno = 0
-      fh.each_line do |ln|
-        next if (lineno += 1) == 1
-        r = ln.split("\t")
-        next unless [1, 2].map { |i| p.dataset(r[i]).nil? }.any?
-        [1, 2].each do |i|
-          if p.dataset(r[i]).nil?
-            notok[r[i]] = true
-          else
-            fix[r[i]] = true
-          end
-        end
-      end
-    end
-    [notok, fix]
-  end
-
-  def check_dist_fix(cli, p, fix)
-    return if fix.empty?
-    cli.say("- Fixing #{fix.size} datasets")
-    fix.keys.each do |d_n|
-      cli.say "  > Fixing #{d_n}."
-      p.dataset(d_n).cleanup_distances!
-    end
-  end
-
-  def check_dist_recompute(cli, p, notok)
-    return if notok.empty?
-    cli.say '- Unregistered datasets detected: '
-    if notok.size <= 5
-      notok.keys.each { |i| cli.say "  > #{i}" }
-    else
-      cli.say "  > #{notok.size}, including #{notok.keys.first}"
-    end
-    cli.say '- Removing tables, recompute'
-    res.remove!
+    # TODO: Find different 95%ANI clusters with genomes from the same species
+    # TODO: Find AAI values too high or too low for each LCA rank
   end
 end

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

@@ -12,12 +12,25 @@ class MiGA::Cli::Action::Edit < MiGA::Cli::Action
         '-m', '--metadata STRING',
         'Metadata as key-value pairs separated by = and delimited by comma',
         'Values are saved as strings except for booleans (true / false) or nil'
-        ){ |v| cli[:metadata] = v }
+      ) { |v| cli[:metadata] = v }
+      opt.on(
+        '--activate',
+        'Activate dataset; requires -D'
+      ) { |v| cli[:activate] = v }
+      opt.on(
+        '--inactivate',
+        'Inactivate dataset; requires -D'
+      ) { |v| cli[:activate] = !v }
     end
   end
 
   def perform
     obj = cli.load_project_or_dataset
+    unless cli[:activate].nil?
+      cli.ensure_par({ dataset: '-D' },
+        '%<name>s is mandatory with --[in-]activate: please provide %<flag>s')
+      cli[:activate] ? obj.activate! : obj.inactivate!
+    end
     cli.add_metadata(obj)
     obj.save
   end

data/lib/miga/daemon/base.rb

@@ -14,19 +14,21 @@ module MiGA::Daemon::Base
     k = k.to_sym
     unless v.nil?
       case k
-      when :latency, :maxjobs, :ppn, :format_version
+      when :latency, :maxjobs, :ppn, :format_version, :verbosity
         v = v.to_i
+        if !force && v == 0 && k != :verbosity
+          raise "Daemon's #{k} cannot be set to zero"
+        end
       when :shutdown_when_done
         v = !!v
       when :nodelist
         if v =~ /^\$/
-          vv = ENV[v.sub('$','')] or raise "Unset environment variable: #{v}"
+          vv = ENV[v.sub('$', '')] or raise "Unset environment variable: #{v}"
           v = vv
         end
         say "Reading node list: #{v}"
         v = File.readlines(v).map(&:chomp)
       end
-      raise "Daemon's #{k} cannot be set to zero." if !force and v == 0
       @runopts[k] = v
     end
     @runopts[k]
@@ -34,24 +36,43 @@ module MiGA::Daemon::Base
 
   ##
   # Returns Integer indicating the number of seconds to sleep between checks
-  def latency() runopts(:latency); end
+  def latency
+    runopts(:latency)
+  end
 
   ##
   # Returns Integer indicating the maximum number of concurrent jobs to run
-  def maxjobs() runopts(:maxjobs); end
+  def maxjobs
+    runopts(:maxjobs)
+  end
 
   ##
   # Returns the path to the list of execution hostnames
-  def nodelist() runopts(:nodelist); end
+  def nodelist
+    runopts(:nodelist)
+  end
 
   ##
   # Returns Integer indicating the number of CPUs per job
-  def ppn() runopts(:ppn); end
+  def ppn
+    runopts(:ppn)
+  end
 
   ##
   # Returns Boolean indicating if the daemon should shutdown when processing is
   # complete
-  def shutdown_when_done?() !!runopts(:shutdown_when_done); end
+  def shutdown_when_done?
+    !!runopts(:shutdown_when_done)
+  end
 
+  ##
+  # Returns the level of verbosity for the daemon as an Integer, or 1 if unset.
+  # Verbosity levels are:
+  # 0: No output
+  # 1: General daemon and job information
+  # 2: Same, and indicate when each task is performed (even if nothing happens)
+  # 3: Same, and indicate when each loop begins and ends
+  def verbosity
+    runopts(:verbosity) || 1
+  end
 end
-

data/lib/miga/daemon.rb

@@ -45,8 +45,9 @@ class MiGA::Daemon < MiGA::MiGA
     @project = project
     @runopts = {}
     json ||= File.join(project.path, 'daemon/daemon.json')
+    default_json = File.expand_path('.miga_daemon.json', ENV['MIGA_HOME'])
     MiGA::Json.parse(
-      json, default: File.expand_path('.miga_daemon.json', ENV['MIGA_HOME'])
+      json, default: File.exist?(default_json) ? default_json : nil
     ).each { |k,v| runopts(k, v) }
     update_format_0
     @jobs_to_run = []
@@ -77,29 +78,54 @@ class MiGA::Daemon < MiGA::MiGA
   end
 
   ##
-  # Run one loop step. Returns a Boolean indicating if the loop should continue.
+  # Run one loop step. Returns a Boolean indicating if the loop should continue
   def daemon_loop
-    project.load
+    l_say(3, 'Daemon loop start')
+    reload_project
     check_datasets
     check_project
-    if shutdown_when_done? and jobs_running.size + jobs_to_run.size == 0
-      say 'Nothing else to do, shutting down.'
+    if shutdown_when_done? && jobs_running.size + jobs_to_run.size == 0
+      say 'Nothing else to do, shutting down'
       return false
     end
     flush!
-    if loop_i >= 12
-      say 'Probing running jobs'
-      @loop_i = 0
+    if loop_i % 12 == 0
       purge!
+      recalculate_status!
     end
-    report_status
+    save_status
     sleep(latency)
+    l_say(3, 'Daemon loop end')
     true
   end
 
+  def recalculate_status!
+    project.each_dataset(&:recalculate_status)
+  end
+
+  ##
+  # Send +msg+ to +say+ as long as +level+ is at most +verbosity+
+  def l_say(level, *msg)
+    say(*msg) if verbosity >= level
+  end
+
+  ##
+  # Same as +l_say+ with +level = 1+
+  def say(*msg)
+    super(*msg) if verbosity >= 1
+  end
+
+  ##
+  # Reload the project's metadata
+  def reload_project
+    l_say(2, 'Reloading project')
+    project.load
+  end
+
   ##
   # Report status in a JSON file.
-  def report_status
+  def save_status
+    l_say(2, 'Saving current status')
     MiGA::Json.generate(
       { jobs_running: @jobs_running, jobs_to_run: @jobs_to_run },
       File.join(daemon_home, 'status.json')
@@ -134,7 +160,9 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Traverse datasets
   def check_datasets
-    project.each_dataset do |n, ds|
+    l_say(2, 'Checking datasets')
+    project.each_dataset do |ds|
+      next unless ds.status == :incomplete
       to_run = ds.next_preprocessing(false)
       queue_job(:d, ds) unless to_run.nil?
     end
@@ -144,6 +172,7 @@ class MiGA::Daemon < MiGA::MiGA
   # Check if all reference datasets are pre-processed. If yes, check the
   # project-level tasks
   def check_project
+    l_say(2, 'Checking project')
     return if project.dataset_names.empty?
     return unless project.done_preprocessing?(false)
     to_run = project.next_task(nil, false)
@@ -199,6 +228,7 @@ class MiGA::Daemon < MiGA::MiGA
   # possible respecting #maxjobs or #nodelist (if set).
   def flush!
     # Check for finished jobs
+    l_say(2, 'Checking for finished jobs')
     @jobs_running.select! do |job|
       ongoing = case job[:job].to_s
       when 'd'
@@ -211,8 +241,10 @@ class MiGA::Daemon < MiGA::MiGA
       say "Completed pid:#{job[:pid]} for #{job[:task_name]}" unless ongoing
       ongoing
     end
+
     # Avoid single datasets hogging resources
     @jobs_to_run.rotate! rand(jobs_to_run.size)
+
     # Launch as many +jobs_to_run+ as possible
     while hostk = next_host
       break if jobs_to_run.empty?
@@ -233,6 +265,7 @@ class MiGA::Daemon < MiGA::MiGA
   ##
   # Remove dead jobs.
   def purge!
+    say 'Probing running jobs'
     @jobs_running.select! do |job|
       `#{runopts(:alive).miga_variables(pid: job[:pid])}`.chomp.to_i == 1
     end

data/lib/miga/dataset/status.rb

@@ -4,7 +4,7 @@ module MiGA::Dataset::Status
   ##
   # Returns the status of the dataset. If the status is not yet defined,
   # it recalculates it and, if +save+ is true, saves it in metadata.
-  # Return values are:
+  # Return symbols are:
   # - +:inactive+ The dataset is currently inactive
   # - +:incomplete+ The dataset is not yet fully processed
   # - +:complete+ The dataset is fully processed
@@ -14,12 +14,13 @@ module MiGA::Dataset::Status
   end
 
   ##
-  # Identify the current status instead of relying on metadata, and save
-  # it if +save+ is true. Return codes are the same as +status+.
+  # Identify the current status and save it if +save+ and the status changed.
+  # Return symbols are the same as +status+.
   def recalculate_status(save = true)
+    old_status = metadata[:status]
     metadata[:status] =
-      !active? ? :inactive : done_preprocessing? ? :complete : :incomplete
-    self.save if save
+      !active? ? 'inactive' : done_preprocessing? ? 'complete' : 'incomplete'
+    self.save if save && (old_status.nil? || old_status != metadata[:status])
     metadata[:status].to_sym
   end
 end

data/lib/miga/project/dataset.rb

@@ -35,16 +35,12 @@ module MiGA::Project::Dataset
   end
 
   ##
-  # Iterate through datasets, with one or two variables passed to +blk+.
-  # If one, the dataset MiGA::Dataset object is passed. If two, the name and
-  # the dataset object are passed.
+  # Iterate through datasets (MiGA::Dataset)
   def each_dataset(&blk)
-    metadata[:datasets].each do |name|
-      if blk.arity == 1
-        blk.call(dataset(name))
-      else
-        blk.call(name, dataset(name))
-      end
+    if block_given?
+      metadata[:datasets].each { |name| blk.call(dataset(name)) }
+    else
+      to_enum(:each_dataset)
     end
   end
 
@@ -140,9 +136,7 @@ module MiGA::Project::Dataset
   # - 2: To do.
   def profile_datasets_advance
     advance = []
-    self.each_dataset_profile_advance do |ds_adv|
-      advance << ds_adv
-    end
+    each_dataset_profile_advance { |adv| advance << adv }
     advance
   end
 
@@ -154,4 +148,3 @@ module MiGA::Project::Dataset
   end
 
 end
-

data/lib/miga/version.rb

@@ -10,7 +10,7 @@ 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, 3, 1]
+  VERSION = [0.7, 4, 0]
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 4, 23)
+  VERSION_DATE = Date.new(2020, 4, 28)
 
   ##
   # Reference of MiGA.

data/test/daemon_test.rb

@@ -88,7 +88,7 @@ class DaemonTest < Test::Unit::TestCase
     assert_equal(11, d.loop_i)
     out = capture_stderr { d.in_loop }.string
     assert_match(/Probing running jobs/, out)
-    assert_equal(0, d.loop_i)
+    assert_equal(12, d.loop_i)
   end
 
   def test_start
@@ -109,6 +109,7 @@ class DaemonTest < Test::Unit::TestCase
     assert_match(/Sending termination message/, out)
     assert_path_not_exist(d.pid_file)
     assert_path_exist(d.output_file)
+    assert_equal(1, d.verbosity)
     l = File.readlines(d.output_file)
     {
       0 => /-{20}\n/,
@@ -312,6 +313,26 @@ class DaemonTest < Test::Unit::TestCase
     assert_equal(1, d1.jobs_to_run.size)
   end
 
+  def test_verbosity
+    d1 = $d1
+    d1.runopts(:verbosity, 0)
+    out = capture_stderr { d1.in_loop }.string
+    assert_empty(out)
+
+    d1.runopts(:verbosity, 1)
+    helper_datasets_with_results.first.inactivate!
+    out = capture_stderr { d1.check_project }
+    assert_match(/Queueing miga-project:p/, out.string)
+
+    d1.runopts(:verbosity, 2)
+    out = capture_stderr { d1.in_loop }.string
+    assert_match(/Reloading project/, out)
+
+    d1.runopts(:verbosity, 3)
+    out = capture_stderr { d1.in_loop }.string
+    assert_match(/Daemon loop start/, out)
+  end
+
   def helper_daemon_launch_job
     omit_if($jruby_tests, 'JRuby doesn\'t implement fork.')
     d1 = $d1
@@ -324,5 +345,4 @@ class DaemonTest < Test::Unit::TestCase
     assert_equal(0, d1.jobs_to_run.size, 'There should be nothing running')
     assert_equal(1, d1.jobs_running.size, 'There should be one job running')
   end
-
 end

data/test/project_test.rb

@@ -58,7 +58,6 @@ class ProjectTest < Test::Unit::TestCase
     assert_equal([d], p.datasets)
     assert_equal(['d1'], p.dataset_names)
     p.each_dataset { |ds| assert_equal(d, ds) }
-    p.each_dataset { |n, ds| assert_equal(n, ds.name) }
     dr = p.unlink_dataset('d1')
     assert_equal(d, dr)
     assert_equal([], p.datasets)

data/test/tax_dist_test.rb

@@ -40,12 +40,12 @@ class TaxDistTest < Test::Unit::TestCase
   def test_aai_taxtest
     distant_intax = MiGA::TaxDist.aai_taxtest(35.0, :intax, engine: :diamond)
     assert_equal(:root, distant_intax[:most_likely][0])
-    assert_nil(distant_intax[:probably])
+    assert_equal(:d, distant_intax[:probably][0])
     assert_nil(distant_intax[:possibly_even])
 
     distant_intax = MiGA::TaxDist.aai_taxtest(35.0, :intax, engine: :blast)
     assert_equal(:root, distant_intax[:most_likely][0])
-    assert_nil(distant_intax[:probably])
+    assert_equal(:d, distant_intax[:probably][0])
     assert_nil(distant_intax[:possibly_even])
 
     close_intax = MiGA::TaxDist.aai_taxtest(99.0, :intax, engine: :diamond)

data/utils/index_metadata.rb

@@ -16,14 +16,13 @@ def searchable(db, d, k, v)
     d.name, k.to_s, " #{v.to_s.downcase.gsub(/[^A-Za-z0-9\-]+/, ' ')} "
 end
 
-p.each_dataset do |name, d|
+p.each_dataset do |d|
   next unless d.is_ref?
   next unless d.is_active?
   searchable(db, d, :name, d.name)
   d.metadata.each do |k, v|
     next if [:created, :updated].include? k
-    v = v.sorted_ranks.map{ |r| r[1] }.join(" ") if k==:tax
+    v = v.sorted_ranks.map{ |r| r[1] }.join(' ') if k == :tax
     searchable(db, d, k, v)
   end
 end
-

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.3.1
+  version: 0.7.4.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-04-23 00:00:00.000000000 Z
+date: 2020-04-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -124,6 +124,7 @@ files:
 - lib/miga/cli/action/date.rb
 - lib/miga/cli/action/derep_wf.rb
 - lib/miga/cli/action/doctor.rb
+- lib/miga/cli/action/doctor/base.rb
 - lib/miga/cli/action/edit.rb
 - lib/miga/cli/action/files.rb
 - lib/miga/cli/action/find.rb