miga-base 0.7.10.0 → 0.7.10.2

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: f3b350bb3e5dce2f0f8d0006d7f0693ff746c157006890a1250f30d71d89a523
+  data.tar.gz: 1d94e39c61bfe191388d309eeb992b995350f6191dc74d5c7b15ae9741bcca09
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+  data.tar.gz: e8218114c0e89d80eab2b6cf7eba5a1de6f26b7d27e3560af1da12fdfc9037f3557a5994e1b982cff35635cea3d23e18ef234758ef8e12b86fb56f782a41ef89

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

@@ -19,6 +19,10 @@ class MiGA::Cli::Action::DerepWf < MiGA::Cli::Action
         'Use Average Amino Acid Identity (AAI) as genome similarity metric',
         'By default: Use Average Nucleotide Identity (ANI)'
       ) { cli[:metric] = :aai }
+      opt.on(
+        '--ani',
+        'Use Average Nucleotide Identity (ANI) as similarity metric (default)'
+      ) { cli[:metric] = :ani }
       opt.on(
         '--threshold FLOAT', Float,
         "Metric threshold (%) to dereplicate. By default: #{cli[:threshold]}"

data/lib/miga/daemon.rb

@@ -185,7 +185,7 @@ class MiGA::Daemon < MiGA::MiGA
     return if project.dataset_names.empty?
 
     # Double-check if all datasets are ready
-    return unless project.done_preprocessing?(false)
+    return unless project.done_preprocessing?
 
     # Queue project-level job
     to_run = project.next_task(nil, false)

data/lib/miga/dataset/result.rb

@@ -26,15 +26,24 @@ module MiGA::Dataset::Result
   # The values are symbols:
   # - empty: the dataset has no data
   # - inactive: the dataset is inactive
+  # - upstream: the task is upstream from dataset's input
   # - force: forced to ignore by metadata
   # - project: incompatible project
   # - noref: incompatible dataset, only for reference
   # - multi: incompatible dataset, only for multi
   # - nonmulti: incompatible dataset, only for nonmulti
+  # - complete: the task is already complete
   # - execute: do not ignore, execute the task
   def why_ignore(task)
-    if !active?
+    if !get_result(task).nil?
+      :complete
+    elsif !active?
       :inactive
+    elsif first_preprocessing.nil?
+      :empty
+    elsif @@PREPROCESSING_TASKS.index(task) <
+          @@PREPROCESSING_TASKS.index(first_preprocessing)
+      :upstream
     elsif !metadata["run_#{task}"].nil?
       metadata["run_#{task}"] ? :execute : :force
     elsif task == :taxonomy && project.metadata[:ref_project].nil?
@@ -56,7 +65,7 @@ module MiGA::Dataset::Result
   # initial input. Passes +save+ to #add_result.
   def first_preprocessing(save = false)
     @first_processing ||= @@PREPROCESSING_TASKS.find do |t|
-      !ignore_task?(t) && !add_result(t, save).nil?
+      !add_result(t, save).nil?
     end
   end
 
@@ -121,17 +130,12 @@ module MiGA::Dataset::Result
   # - complete: a task with registered results
   # - pending: a task queued to be performed
   def result_status(task)
-    if first_preprocessing.nil?
-      :ignore_empty
-    elsif !get_result(task).nil?
-      :complete
-    elsif @@PREPROCESSING_TASKS.index(task) <
-          @@PREPROCESSING_TASKS.index(first_preprocessing)
-      :-
-    elsif ignore_task?(task)
-      :"ignore_#{why_ignore task}"
-    else
-      :pending
+    reason = why_ignore(task)
+    case reason
+    when :upstream; :-
+    when :execute; :pending
+    when :complete; :complete
+    else; :"ignore_#{reason}"
     end
   end
 

data/lib/miga/lair.rb

@@ -111,7 +111,7 @@ class MiGA::Lair < MiGA::MiGA
 
         yield(project)
       elsif Dir.exist? f
-        each_project(f) { |project| yield(project) }
+        each_project(f) { |p| yield(p) }
       end
     end
   end

data/lib/miga/project/dataset.rb

@@ -134,12 +134,10 @@ module MiGA::Project::Dataset
   ##
   # Are all the datasets in the project preprocessed? Save intermediate results
   # if +save+ (until the first incomplete dataset is reached).
-  def done_preprocessing?(save = true)
-    dataset_names.each do |dn|
-      ds = dataset(dn)
-      return false if ds.is_ref? and not ds.done_preprocessing?(save)
+  def done_preprocessing?(save = false)
+    !each_dataset.any? do |d|
+      d.ref? && d.active? && !d.done_preprocessing?(save)
     end
-    true
   end
 
   ##

data/lib/miga/result/stats.rb

@@ -135,7 +135,7 @@ module MiGA::Result::Stats
       # Inactivate low-quality datasets
       min_qual = (project.metadata[:min_qual] || 50)
       if min_qual != 'no' && stats[:quality] < min_qual
-        source.inactivate! 'Low genome quality'
+        source.inactivate! 'Low quality genome'
       end
     end
     stats

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, 10, 0]
+  VERSION = [0.7, 10, 2]
 
   ##
   # Nickname for the current major.minor version.
@@ -16,7 +16,7 @@ module MiGA
 
   ##
   # Date of the current gem release.
-  VERSION_DATE = Date.new(2020, 6, 29)
+  VERSION_DATE = Date.new(2020, 6, 30)
 
   ##
   # Reference of MiGA.

data/test/project_test.rb

@@ -108,7 +108,7 @@ class ProjectTest < Test::Unit::TestCase
     d1 = p1.add_dataset('BAH')
     assert_not_predicate(p1, :done_preprocessing?)
     FileUtils.touch(File.join(p1.path, 'data', '90.stats', "#{d1.name}.done"))
-    assert_predicate(p1, :done_preprocessing?)
+    assert { p1.done_preprocessing? true }
     assert_nil(p1.next_inclade)
     p1.metadata[:type] = :clade
     assert_equal(:subclades, p1.next_inclade)

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.10.0
+  version: 0.7.10.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2020-06-29 00:00:00.000000000 Z
+date: 2020-06-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons