miga-base 0.7.23.0 → 0.7.24.0

data/utils/cleanup-databases.rb

@@ -19,7 +19,7 @@ m.say 'Cleaning Databases'
       next unless (idx % thr) == t
 
       d = p.dataset(i)
-      next unless d.is_ref? and d.is_active?
+      next unless d.ref? && d.active?
 
       d.cleanup_distances!
     end
@@ -28,4 +28,3 @@ end
 Process.waitall
 m.advance('Dataset:', dsn.size, dsn.size)
 m.say
-

data/utils/distance/commands.rb

@@ -9,7 +9,7 @@ module MiGA::DistanceRunner::Commands
     return y unless y.nil? || y.zero?
 
     # Try hAAI (except in clade projects)
-    unless @ref_project.is_clade?
+    unless @ref_project.clade?
       y = haai(target)
       return y unless y.nil? || y.zero?
     end
@@ -75,7 +75,7 @@ module MiGA::DistanceRunner::Commands
     v = `aai.rb -1 "#{f1}" -2 "#{f2}" -S "#{db}" \
           --name1 "#{n1}" --name2 "#{n2}" \
           -t "#{o[:thr]}" -a --lookup-first "--#{o[:aai_save_rbm]}" \
-          -p "#{o[:aai_p] || 'blast+'}"`.chomp
+          -p "#{o[:aai_p]}"`.chomp
     (v.nil? || v.empty?) ? 0 : v.to_f
   end
 

data/utils/distance/database.rb

@@ -66,7 +66,7 @@ module MiGA::DistanceRunner::Database
     return y unless y.nil? || y.zero?
 
     # Check if self.dataset <- target is done (another thread)
-    if dataset.is_ref? && project.path == ref_project.path
+    if dataset.ref? && project.path == ref_project.path
       y = data_from_db(
         target.name, dataset.name, ref_db(metric, target.name), metric
       )

data/utils/distance/pipeline.rb

@@ -31,10 +31,8 @@ module MiGA::DistanceRunner::Pipeline
 
   # Run distances against datasets listed in metadata's +:dist_req+
   def distances_by_request(metric)
-    return unless dataset.metadata[:dist_req]
-
     $stderr.puts 'Running distances by request'
-    dataset.metadata[:dist_req].each do |target|
+    dataset.option(:dist_req).each do |target|
       ds = ref_project.dataset(target) and send(metric, ds)
     end
   end
@@ -112,7 +110,7 @@ module MiGA::DistanceRunner::Pipeline
     $stderr.puts 'Transferring taxonomy'
     return if tax.nil?
 
-    pval = (project.metadata[:tax_pvalue] || 0.05).to_f
+    pval = project.option(:tax_pvalue)
     tax_a = tax
             .select { |i| i[1] != '?' && i[2] <= pval }
             .map { |i| i[0, 2].join(':') }

data/utils/distance/runner.rb

@@ -21,47 +21,39 @@ class MiGA::DistanceRunner
     @home = File.expand_path('data/09.distances', project.path)
 
     # Default opts
-    if project.metadata[:aai_save_rbm] == false
-      @opts[:aai_save_rbm] ||= 'no-save-rbm'
-    end
-    @opts[:aai_save_rbm] ||= ENV.fetch('MIGA_AAI_SAVE_RBM') do
-      project.is_clade? ? 'save-rbm' : 'no-save-rbm'
-    end
+    @opts[:aai_save_rbm] =
+      project.option(:aai_save_rbm) ? 'save-rbm' : 'no-save-rbm'
     @opts[:thr] ||= ENV.fetch('CORES') { 2 }.to_i
-    if opts[:run_taxonomy] and project.metadata[:ref_project]
-      ref_path = project.metadata[:ref_project]
+    if opts[:run_taxonomy] && project.option(:ref_project)
+      ref_path = project.option(:ref_project)
       @home = File.expand_path('05.taxonomy', @home)
       @ref_project = MiGA::Project.load(ref_path)
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
-    elsif !opts[:run_taxonomy] and dataset.metadata[:db_project]
-      ref_path = dataset.metadata[:db_project]
-      if project.metadata[:db_proj_dir]
-        ref_path = File.expand_path(ref_path, project.metadata[:db_proj_dir])
+    elsif !opts[:run_taxonomy] && dataset.option(:db_project)
+      ref_path = dataset.option(:db_project)
+      if project.option(:db_proj_dir)
+        ref_path = File.expand_path(ref_path, project.option(:db_proj_dir))
       end
       @ref_project = MiGA::Project.load(ref_path)
       raise "Cannot load reference project: #{ref_path}" if @ref_project.nil?
     else
       @ref_project = project
     end
-    [:haai_p, :aai_p, :ani_p, :distances_checkpoint].each do |m|
-      @opts[m] ||= ref_project.metadata[m]
+    %i[haai_p aai_p ani_p distances_checkpoint].each do |m|
+      @opts[m] ||= ref_project.option(m)
     end
-    @opts[:aai_p] ||= 'blast+'
-    @opts[:ani_p] ||= 'blast+'
-    @opts[:distances_checkpoint] ||= 10
-    @opts[:distances_checkpoint] = @opts[:distances_checkpoint].to_i
     $stderr.puts "Options: #{opts}"
   end
 
   # Launch the appropriate analysis
   def go!
     $stderr.puts "Launching analysis"
-    return if dataset.is_multi?
+    return if dataset.multi?
 
     Dir.mktmpdir do |tmp_dir|
       @tmp = tmp_dir
       create_temporals
-      opts[:run_taxonomy] ? go_taxonomy! : dataset.is_ref? ? go_ref! : go_query!
+      opts[:run_taxonomy] ? go_taxonomy! : dataset.ref? ? go_ref! : go_query!
     end
   end
 
@@ -73,7 +65,7 @@ class MiGA::DistanceRunner
 
     # first-come-first-serve traverse
     ref_project.each_dataset do |ds|
-      next if !ds.is_ref? or ds.is_multi? or ds.result(:essential_genes).nil?
+      next if !ds.ref? or ds.multi? or ds.result(:essential_genes).nil?
 
       puts "[ #{Time.now} ] #{ds.name}"
       ani_after_aai(ds)
@@ -88,7 +80,7 @@ class MiGA::DistanceRunner
   def go_query!
     $stderr.puts 'Launching analysis for query dataset'
     # Check if project is ready
-    tsk = ref_project.is_clade? ? [:subclades, :ani] : [:clade_finding, :aai]
+    tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])
     return if res.nil?
 
@@ -137,7 +129,7 @@ class MiGA::DistanceRunner
   # Launch analysis for taxonomy jobs
   def go_taxonomy!
     $stderr.puts 'Launching taxonomy analysis'
-    return unless project.metadata[:ref_project]
+    return unless project.option(:ref_project)
 
     go_query! # <- yeah, it's actually the same, just different ref_project
   end

data/utils/index_metadata.rb

@@ -17,8 +17,7 @@ def searchable(db, d, k, v)
 end
 
 p.each_dataset do |d|
-  next unless d.is_ref?
-  next unless d.is_active?
+  next unless d.ref? && d.active?
 
   searchable(db, d, :name, d.name)
   d.metadata.each do |k, v|

data/utils/subclade/runner.rb

@@ -18,19 +18,18 @@ class MiGA::SubcladeRunner
       @step == :clade_finding ? '01.find.running' : '02.ani.running'
     )
     @opts[:thr] ||= ENV.fetch('CORES') { 2 }.to_i
-    @opts[:run_clades] = !!@project.metadata.data.fetch(:run_clades) { true }
-    @opts[:gsp_ani] = @project.metadata.data.fetch(:gsp_ani) { 95.0 }.to_f
-    @opts[:gsp_aai] = @project.metadata.data.fetch(:gsp_aai) { 90.0 }.to_f
-    @opts[:gsp_metric] =
-      @project.metadata.data.fetch(:gsp_metric) { 'ani' }.to_s
+    @opts[:run_clades] = @project.option(:run_clades)
+    @opts[:gsp_ani] = @project.option(:gsp_ani)
+    @opts[:gsp_aai] = @project.option(:gsp_aai)
+    @opts[:gsp_metric] = @project.option(:gsp_metric)
   end
 
   # Launch the appropriate analysis
   def go!
     return if project.type == :metagenomes
 
-    unless @project.dataset_names.any? { |i| @project.dataset(i).is_ref? }
-      FileUtils.touch(File.expand_path('miga-project.empty', @home))
+    unless @project.dataset_names.any? { |i| @project.dataset(i).ref? }
+      FileUtils.touch(File.join(@home, 'miga-project.empty'))
       return
     end
     Dir.chdir home
@@ -44,15 +43,15 @@ class MiGA::SubcladeRunner
   # Launch analysis for clade_finding
   def go_clade_finding!
     cluster_species
-    unless project.is_clade?
-      subclades :aai
+    unless project.clade?
+      subclades(:aai)
       compile
     end
   end
 
   # Launch analysis for subclades
   def go_subclades!
-    subclades :ani
+    subclades(:ani)
     compile
   end
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.23.0
+  version: 0.7.24.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-02-09 00:00:00.000000000 Z
+date: 2021-02-16 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons
@@ -152,6 +152,7 @@ files:
 - lib/miga/cli/action/ncbi_get.rb
 - lib/miga/cli/action/new.rb
 - lib/miga/cli/action/next_step.rb
+- lib/miga/cli/action/option.rb
 - lib/miga/cli/action/preproc_wf.rb
 - lib/miga/cli/action/quality_wf.rb
 - lib/miga/cli/action/rm.rb
@@ -174,6 +175,7 @@ files:
 - lib/miga/common/path.rb
 - lib/miga/common/with_daemon.rb
 - lib/miga/common/with_daemon_class.rb
+- lib/miga/common/with_option.rb
 - lib/miga/common/with_result.rb
 - lib/miga/daemon.rb
 - lib/miga/daemon/base.rb
@@ -247,6 +249,7 @@ files:
 - test/taxonomy_test.rb
 - test/test_helper.rb
 - test/with_daemon_test.rb
+- test/with_option_test.rb
 - utils/adapters.fa
 - utils/cleanup-databases.rb
 - utils/core-pan-plot.R
@@ -566,7 +569,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.1.2
+rubygems_version: 3.1.4
 signing_key:
 specification_version: 4
 summary: MiGA