miga-base 0.7.23.0 → 0.7.24.0

data/lib/miga/common.rb

@@ -24,7 +24,7 @@ class MiGA::MiGA
   ##
   # Has MiGA been initialized?
   def self.initialized?
-    File.exist?(File.expand_path('.miga_rc', ENV['MIGA_HOME'])) and
+    File.exist?(File.expand_path('.miga_rc', ENV['MIGA_HOME'])) &&
       File.exist?(File.expand_path('.miga_daemon.json', ENV['MIGA_HOME']))
   end
 

data/lib/miga/common/with_option.rb

@@ -0,0 +1,83 @@
+# frozen_string_literal: true
+
+##
+# Helper module including specific functions to handle objects that
+# have configurable options. The class including this module must implement
+# the methods +.OPTIONS+, +#metadata+, and +#save+.
+module MiGA::Common::WithOption
+  def option(key)
+    assert_has_option(key)
+    opt = option_by_metadata(key)
+    value = opt.nil? ? option_by_default(key) : opt
+    value = value[self] if value.is_a?(Proc)
+    value
+  end
+
+  def set_option(key, value, from_string = false)
+    metadata[key] = assert_valid_option_value(key, value, from_string)
+    save
+    option(key)
+  end
+
+  def all_options
+    Hash[self.class.OPTIONS.each_key.map { |key| [key, option(key)] }]
+  end
+
+  def option?(key)
+    !self.class.OPTIONS[key.to_sym].nil?
+  end
+
+  def option_by_metadata(key)
+    metadata[key]
+  end
+
+  def option_by_default(key)
+    self.class.OPTIONS[key.to_sym][:default]
+  end
+
+  def assert_has_option(key)
+    opt = self.class.OPTIONS[key.to_sym]
+    raise "Unrecognized option: #{key}" if opt.nil?
+    opt
+  end
+
+  def assert_valid_option_value(key, value, from_string = false)
+    opt = assert_has_option(key)
+    value = option_from_string(key, value) if from_string
+
+    # nil is always valid, and so are supported tokens
+    return value if value.nil? || opt[:tokens]&.include?(value)
+
+    if opt[:type] && !value.is_a?(opt[:type])
+      raise "Invalid value type for #{key}: #{value.class}, not #{opt[:type]}"
+    end
+
+    if opt[:in] && !opt[:in].include?(value)
+      raise "Value out of range for #{key}: #{value}, not #{opt[:in]}"
+    end
+
+    value
+  end
+
+  def option_from_string(key, value)
+    opt = assert_has_option(key)
+
+    if ['', 'nil'].include?(value)
+      nil
+    elsif opt[:tokens]&.include?(value)
+      value
+    elsif opt[:type]&.equal?(Float)
+      raise "Not a float: #{value}" unless value =~ /^-?\.?\d/
+      value.to_f
+    elsif opt[:type]&.equal?(Integer)
+      raise "Not an integer: #{value}" unless value =~ /^-?\d/
+      value.to_i
+    elsif opt[:in]&.include?(true) && value == 'true'
+      true
+    elsif opt[:in]&.include?(false) && value == 'false'
+      false
+    else
+      value
+    end
+  end
+end

data/lib/miga/common/with_result.rb

@@ -86,7 +86,8 @@ module MiGA::Common::WithResult
         if res.nil?
           # Run if the step has not been calculated,
           # unless too many attempts were already made
-          if (metadata["_try_#{t}"] || 0) > (project.metadata[:max_try] || 10)
+          cur_try = metadata["_try_#{t}"] || 0
+          if cur_try > project.option(:max_try)
             inactivate! "Too many errors in step #{t}"
             false
           else

data/lib/miga/dataset/base.rb

@@ -1,7 +1,10 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
+
+require 'miga/common/with_option'
 
 class MiGA::Dataset < MiGA::MiGA
+  include MiGA::Common::WithOption
+
   # Class-level
   class << self
     def RESULT_DIRS
@@ -15,6 +18,10 @@ class MiGA::Dataset < MiGA::MiGA
     def PREPROCESSING_TASKS
       @@PREPROCESSING_TASKS
     end
+
+    def OPTIONS
+      @@OPTIONS
+    end
   end
 end
 
@@ -85,4 +92,15 @@ module MiGA::Dataset::Base
   # tasks are ignored for single-organism datasets or for unknwon types.
   @@ONLY_MULTI_TASKS = [:mytaxa]
   @@_ONLY_MULTI_TASKS_H = Hash[@@ONLY_MULTI_TASKS.map { |i| [i, true] }]
+
+  ##
+  # Options supported by datasets
+  @@OPTIONS = {
+    db_project: {
+      desc: 'Project to use as database', type: String
+    },
+    dist_req: {
+      desc: 'Run distances against these datasets', type: Array, default: []
+    }
+  }
 end

data/lib/miga/dataset/result.rb

@@ -50,7 +50,7 @@ module MiGA::Dataset::Result
       :upstream
     elsif !metadata["run_#{task}"].nil?
       metadata["run_#{task}"] ? :execute : :force
-    elsif task == :taxonomy && project.metadata[:ref_project].nil?
+    elsif task == :taxonomy && project.option(:ref_project).nil?
       :project
     elsif @@_EXCLUDE_NOREF_TASKS_H[task] && !ref?
       :noref

data/lib/miga/metadata.rb

@@ -56,24 +56,20 @@ class MiGA::Metadata < MiGA::MiGA
   ##
   # Save the metadata into #path
   def save
-    MiGA.DEBUG "Metadata.save #{path}"
+    return if self[:never_save]
+
+    MiGA::MiGA.DEBUG "Metadata.save #{path}"
     self[:updated] = Time.now.to_s
     json = to_json
-    sleeper = 0.0
-    slept = 0
-    while File.exist?(lock_file)
-      MiGA::MiGA.DEBUG "Waiting for lock: #{lock_file}"
-      sleeper += 0.1 if sleeper <= 10.0
-      sleep(sleeper.to_i)
-      slept += sleeper.to_i
-      raise "Lock detected for over 10 minutes: #{lock_file}" if slept > 600
-    end
-    FileUtils.touch lock_file
+    wait_for_lock
+    FileUtils.touch(lock_file)
     ofh = File.open("#{path}.tmp", 'w')
     ofh.puts json
     ofh.close
-    raise "Lock-racing detected for #{path}" unless
-      File.exist?("#{path}.tmp") and File.exist?(lock_file)
+
+    unless File.exist?("#{path}.tmp") && File.exist?(lock_file)
+      raise "Lock-racing detected for #{path}"
+    end
 
     File.rename("#{path}.tmp", path)
     File.unlink(lock_file)
@@ -154,4 +150,20 @@ class MiGA::Metadata < MiGA::MiGA
   def to_json
     MiGA::Json.generate(data)
   end
+
+  private
+
+  ##
+  # Wait for the lock to go away
+  def wait_for_lock
+    sleeper = 0.0
+    slept = 0.0
+    while File.exist?(lock_file)
+      MiGA::MiGA.DEBUG "Waiting for lock: #{lock_file}"
+      sleeper += 0.1 if sleeper <= 10.0
+      sleep(sleeper)
+      slept += sleeper
+      raise "Lock detected for over 10 minutes: #{lock_file}" if slept > 600
+    end
+  end
 end

data/lib/miga/project/base.rb

@@ -1,7 +1,10 @@
-# @package MiGA
-# @license Artistic-2.0
+# frozen_string_literal: true
+
+require 'miga/common/with_option'
 
 class MiGA::Project < MiGA::MiGA
+  include MiGA::Common::WithOption
+
   class << self
     ##
     # Does the project at +path+ exist?
@@ -33,6 +36,10 @@ class MiGA::Project < MiGA::MiGA
     def RESULT_DIRS
       @@RESULT_DIRS
     end
+
+    def OPTIONS
+      @@OPTIONS
+    end
   end
 end
 
@@ -108,4 +115,77 @@ module MiGA::Project::Base
   ##
   # Project-wide tasks for :clade projects
   @@INCLADE_TASKS = [:subclades, :ogs]
+
+  ##
+  # Options supported by projects
+  @@OPTIONS = {
+    ref_project: {
+      desc: 'Project with reference taxonomy', type: String
+    },
+    db_proj_dir: {
+      desc: 'Directory containing database projects', type: String
+    },
+    tax_pvalue: {
+      desc: 'Maximum p-value to transfer taxonomy', default: 0.05, type: Float,
+      in: 0.0..1.0
+    },
+    haai_p: {
+      desc: 'Value of aai.rb -p on hAAI', type: String,
+      default: proc { |project| project.clade? ? 'no' : 'blast+' },
+      in: %w[blast+ blast blat diamond no]
+    },
+    aai_p: {
+      desc: 'Value of aai.rb -p on AAI', default: 'blast+', type: String,
+      in: %w[blast+ blast blat diamond]
+    },
+    ani_p: {
+      desc: 'Value of ani.rb -p on ANI', default: 'blast+', type: String,
+      in: %w[blast+ blast blat fastani]
+    },
+    max_try: {
+      desc: 'Maximum number of task attempts', default: 10, type: Integer,
+      in: (0..1000)
+    },
+    aai_save_rbm: {
+      desc: 'Should RBMs be saved for OGS analysis?',
+      default: proc { |project| project.clade? },
+      in: [true, false]
+    },
+    ogs_identity: {
+      desc: 'Min RBM identity for OGS', default: 80.0, type: Float,
+      in: (0.0..100.0)
+    },
+    clean_ogs: {
+      desc: 'If false, keeps ABC files (clades only)', default: true,
+      in: [true, false]
+    },
+    run_clades: {
+      desc: 'Should clades be estimated from distances?', default: true,
+      in: [true, false]
+    },
+    gsp_ani: {
+      desc: 'ANI limit to propose gsp clades', default: 95.0, type: Float,
+      in: (0.0..100.0)
+    },
+    gsp_aai: {
+      desc: 'AAI limit to propose gsp clades', default: 90.0, type: Float,
+      in: (0.0..100.0)
+    },
+    gsp_metric: {
+      desc: 'Metric to propose clades', default: 'ani', type: String,
+      in: %w[ani aai]
+    },
+    ess_coll: {
+      desc: 'Collection of essential genes to use', default: 'dupont_2012',
+      type: String, in: %w[dupont_2012 lee_2019]
+    },
+    min_qual: {
+      desc: 'Minimum genome quality', default: 25.0, type: Float,
+      in: -Float::INFINITY..100.0, tokens: %w[no]
+    },
+    distances_checkpoint: {
+      desc: 'Number of comparisons before storing data', default: 10,
+      type: Integer, in: 1...Float::INFINITY
+    }
+  }
 end

data/lib/miga/project/result.rb

@@ -31,9 +31,9 @@ module MiGA::Project::Result
   ##
   # Is this +task+ to be bypassed?
   def ignore_task?(task)
-    metadata["run_#{task}"] == false ||
-      (!is_clade? && @@INCLADE_TASKS.include?(task) &&
-        metadata["run_#{task}"] != true)
+    return true if metadata["run_#{task}"] == false
+
+    !clade? && @@INCLADE_TASKS.include?(task) && metadata["run_#{task}"] != true
   end
 
   ##
@@ -74,7 +74,7 @@ module MiGA::Project::Result
       return r
     end
     return nil unless result_files_exist?(base, %w[.proposed-clades])
-    unless is_clade? ||
+    unless clade? ||
            result_files_exist?(
              base, %w[.pdf .classif .medoids .class.tsv .class.nwk]
            )

data/lib/miga/result/stats.rb

@@ -118,7 +118,7 @@ module MiGA::Result::Stats
 
   def compute_stats_essential_genes
     stats = {}
-    if source.is_multi?
+    if source.multi?
       stats = { median_copies: 0, mean_copies: 0 }
       File.open(file_path(:report), 'r') do |fh|
         fh.each_line do |ln|
@@ -151,7 +151,7 @@ module MiGA::Result::Stats
       source.save
 
       # Inactivate low-quality datasets
-      min_qual = (project.metadata[:min_qual] || 25)
+      min_qual = project.option(:min_qual)
       if min_qual != 'no' && stats[:quality] < min_qual
         source.inactivate! 'Low quality genome'
       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, 23, 0].freeze
+  VERSION = [0.7, 24, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -18,7 +18,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2021, 2, 9)
+  VERSION_DATE = Date.new(2021, 2, 16)
 
   ##
   # Reference of MiGA.

data/scripts/essential_genes.bash

@@ -24,8 +24,7 @@ fi
 mkdir "${DATASET}.ess"
 TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" \
   --metadata "type" | awk '{print $2}')
-COLL=$(miga about -P "$PROJECT" -m ess_coll)
-[[ "$COLL" == "?" ]] && COLL=dupont_2012
+COLL=$(miga option -P "$PROJECT" --key ess_coll)
 if [[ "$TYPE" == "metagenome" || "$TYPE" == "virome" ]] ; then
   FLAGS="--metagenome"
 else

data/scripts/ogs.bash

@@ -12,8 +12,7 @@ miga_start_project_step "$DIR"
 DS=$(miga ls -P "$PROJECT" --ref --no-multi)
 
 if [[ -n $DS ]] ; then
-  MIN_ID=$(miga about -P "$PROJECT" -m ogs_identity)
-  [[ $MIN_ID == "?" ]] && MIN_ID=80
+  MIN_ID=$(miga option -P "$PROJECT" --key ogs_identity)
   if [[ ! -s miga-project.ogs ]] ; then
     # Extract RBMs
     if [[ ! -s miga-project.abc ]] ; then
@@ -34,7 +33,7 @@ if [[ -n $DS ]] ; then
 
     # Estimate OGs and Clean RBMs
     ogs.mcl.rb -o miga-project.ogs --abc miga-project.abc -t "$CORES"
-    if [[ $(miga about -P "$PROJECT" -m clean_ogs) == "false" ]] ; then
+    if [[ $(miga option -P "$PROJECT" --key clean_ogs) == "false" ]] ; then
       gzip -9 miga-project.abc
     else
       rm miga-project.abc

data/test/dataset_test.rb

@@ -29,7 +29,7 @@ class DatasetTest < Test::Unit::TestCase
     assert_raise { MiGA::Dataset.new(project, 'dataset-1') }
     assert_equal(project, dataset.project)
     assert_equal('dataset0', dataset.name)
-    assert_predicate(dataset, :is_ref?)
+    assert_predicate(dataset, :ref?)
     assert_equal(MiGA::Metadata, dataset.metadata.class)
     assert_equal(:incomplete, dataset.status)
   end
@@ -38,14 +38,14 @@ class DatasetTest < Test::Unit::TestCase
     d2 = project.add_dataset('ds_save')
     assert_respond_to(d2, :save)
     d2.save
-    assert_not_predicate(d2, :is_multi?)
-    assert_not_predicate(d2, :is_nonmulti?)
+    assert_not_predicate(d2, :multi?)
+    assert_not_predicate(d2, :nonmulti?)
     assert_nil(d2.metadata[:type])
     d2.metadata[:type] = :metagenome
     d2.save
     assert_equal(:metagenome, d2.metadata[:type])
-    assert_predicate(d2, :is_multi?)
-    assert_not_predicate(d2, :is_nonmulti?)
+    assert_predicate(d2, :multi?)
+    assert_not_predicate(d2, :nonmulti?)
   end
 
   def test_remove

data/test/with_option_test.rb

@@ -0,0 +1,115 @@
+# frozen_string_literal: true
+
+require 'test_helper'
+require 'miga/common/with_option'
+
+class WithDaemonTest < Test::Unit::TestCase
+  include TestHelper
+
+  class TestWithOption < MiGA::MiGA
+    include MiGA::Common::WithOption
+
+    attr_reader :metadata, :saved
+
+    def initialize
+      @metadata = { range: 0.9 }
+      @saved = false
+    end
+
+    def self.OPTIONS
+      {
+        empty: {},
+        float: { type: Float },
+        range: { default: 1.0, in: -5.5..5.5, type: Float },
+        default: { default: 9, type: Integer },
+        token: { type: Integer, tokens: %w[yes no 0] },
+        proc: { default: proc { Date.today } },
+        bool: { in: [true, false] }
+      }
+    end
+
+    def save
+      @saved = true
+    end
+  end
+
+  def test_with_option
+    o = TestWithOption.new
+    assert_respond_to(o, :option)
+    assert_equal(1, o.metadata.size)
+  end
+
+  def test_option
+    o = TestWithOption.new
+    assert_equal(9, o.option(:default))
+    assert_nil(o.option(:bool))
+    assert_raise { o.option(:not_an_option) }
+    assert_nil(o.option(:empty))
+  end
+
+  def test_set_bool
+    o = TestWithOption.new
+    assert_nil(o.option(:bool))
+    assert(!o.saved)
+    assert_raise { o.set_option(:bool, 'true') }
+    assert_nil(o.option(:bool))
+    assert(!o.saved)
+    assert_equal(true, o.set_option(:bool, 'true', true))
+    assert(o.saved)
+    assert_equal(false, o.set_option(:bool, false))
+    assert_equal(false, o.set_option(:bool, 'false', true))
+    assert_nil(o.set_option(:bool, nil))
+  end
+
+  def test_set_empty
+    o = TestWithOption.new
+    assert_nil(o.option(:empty))
+    assert_equal('a', o.set_option(:empty, 'a'))
+    assert_equal('1', o.set_option(:empty, '1', true))
+  end
+
+  def test_all_options
+    o = TestWithOption.new
+    assert(o.all_options.is_a?(Hash))
+    assert_include(o.all_options.keys, :bool)
+    assert_nil(o.all_options[:bool])
+  end
+
+  def test_option?
+    o = TestWithOption.new
+    assert(o.option?(:range))
+    assert(!o.option?(:not_an_option))
+  end
+
+  def test_option_metadata
+    o = TestWithOption.new
+    assert_equal(0.9, o.option(:range))
+    assert_equal(1.0, o.set_option(:range, nil))
+    assert_equal(2.0, o.set_option(:range, 2.0))
+    assert_equal(3.0, o.set_option(:range, '3', true))
+  end
+
+  def test_option_range
+    o = TestWithOption.new
+    assert_raise { o.set_option(:range, 9.0) }
+    assert_raise { o.set_option(:range, 3) }
+    assert_raise { o.set_option(:range, true) }
+  end
+
+  def test_option_proc
+    o = TestWithOption.new
+    assert(o.option(:proc).is_a?(Date))
+    assert(o.set_option(:proc, 1).is_a?(Integer))
+    assert(o.set_option(:proc, nil).is_a?(Date))
+  end
+
+  def test_token
+    o = TestWithOption.new
+    assert_nil(o.option(:token))
+    assert_equal(1, o.set_option(:token, 1))
+    assert_equal(-2, o.set_option(:token, '-2', true))
+    assert_equal('yes', o.set_option(:token, 'yes'))
+    assert_equal('0', o.set_option(:token, '0', true))
+    assert_raise { o.set_option(:token, 'maybe') }
+  end
+end