miga-base 0.7.20.1 → 0.7.21.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 6c4f9b9118b21b11921b4c0a70ae99f3b1728d5737175ca5b9f23088ff985063
+  metadata.gz: ed3a4b61cfc055c8f305438f304257116b7ec3fe92e10af4d00150d6835cf079
+  data.tar.gz: 9cad53f9a308fbb96d0264932348543339a3d03e096695217b2af85f5b2ac89f
 SHA512:
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-  data.tar.gz: baeee018956a1877065e2e9b5f689e1dc99af71cecc2705f951ab384b05b5760cffd7d85218068bb674541cb766a585add60c5b23a6209c15e2276b369d0f1b0
+  metadata.gz: 1507b05bdc37fe6b8f7dc1b7531042d225dc2e79112b3fb9dcb1e4a558e38321a1a8a1203024cb6f956623be928c676fa3c9c1fb971190e2ef6e26328a97d5e5
+  data.tar.gz: 570bd7b58bc0a6262ef77b1be1a797783b423d76f474fa4840eb146fdbc5fefc12dc5d8abd34f72c4dc7a7cc8ad000fe80005c33af8c9dbcb4232a757f01e07a

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

@@ -20,6 +20,6 @@ class MiGA::Cli::Action::AddResult < MiGA::Cli::Action
     obj = cli.load_project_or_dataset
     cli.say "Registering result: #{cli[:result]}"
     r = obj.add_result(cli[:result], true, force: cli[:force])
-    raise "Cannot add result, incomplete expected files." if r.nil?
+    raise 'Cannot add result, incomplete expected files' if r.nil?
   end
 end

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

@@ -11,16 +11,8 @@ class MiGA::Cli::Action::NextStep < MiGA::Cli::Action
   end
 
   def perform
-    p = cli.load_project
-    n = nil
-    if cli[:dataset].nil?
-      n = p.next_distances(false)
-      n ||= p.next_inclade(false)
-    else
-      d = cli.load_dataset
-      n = d.next_preprocessing if d.is_active?
-    end
-    n ||= '?'
-    cli.puts n
+    obj = cli.load_project_or_dataset
+    n = obj.next_task
+    cli.puts(n || '?')
   end
 end

data/lib/miga/common/with_result.rb

@@ -1,6 +1,8 @@
 ##
 # Helper module including specific functions to handle objects that
-# have results.
+# have results. The class including this module must implement methods
+# +.RESULT_DIRS+, +#ignore_task?+, +#metadata+, +#project+,
+# and +#inactivate!+.
 module MiGA::Common::WithResult
   ##
   # Result directories as a Hash
@@ -68,4 +70,40 @@ module MiGA::Common::WithResult
   def get_result(task)
     add_result(task, false)
   end
+
+  ##
+  # Get the next task from +tasks+, saving intermediate results if +save+.
+  # If +tasks+ is +nil+ (default), it uses the entire list of tasks.
+  # Returns a Symbol.
+  def next_task(tasks = nil, save = false)
+    tasks ||= result_dirs.keys
+    tasks.find do |t|
+      if ignore_task?(t)
+        # Do not run if this step is to be ignored
+        false
+      else
+        res = add_result(t, save)
+        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)
+            inactivate! "Too many errors in step #{t}"
+            false
+          else
+            true
+          end
+        else
+          # Run if the step is ready but has to be recalculated
+          res.recalculate? ? true : false
+        end
+      end
+    end
+  end
+
+  ##
+  # Mark all results for recalculation
+  def recalculate_tasks(reason = nil)
+    each_result { |res| res.recalculate!(reason).save }
+  end
+
 end

data/lib/miga/dataset.rb

@@ -107,6 +107,7 @@ class MiGA::Dataset < MiGA::MiGA
     metadata[:warn] = "Inactive: #{reason}" unless reason.nil?
     metadata[:inactive] = true
     metadata.save
+    project.recalculate_tasks('Reference dataset inactivated') if ref?
     pull_hook :on_inactivate
   end
 
@@ -116,6 +117,7 @@ class MiGA::Dataset < MiGA::MiGA
     metadata[:inactive] = nil
     metadata[:warn] = nil if metadata[:warn] && metadata[:warn] =~ /^Inactive: /
     metadata.save
+    project.recalculate_tasks('Reference dataset activated') if ref?
     pull_hook :on_activate
   end
 

data/lib/miga/dataset/result.rb

@@ -77,19 +77,8 @@ module MiGA::Dataset::Result
   # Returns the key symbol of the next task that needs to be executed or nil.
   # Passes +save+ to #add_result.
   def next_preprocessing(save = false)
-    first = first_preprocessing(save) or return nil
-    @@PREPROCESSING_TASKS[@@PREPROCESSING_TASKS.index(first)..-1].find do |t|
-      if ignore_task? t
-        false
-      elsif add_result(t, save).nil?
-        if (metadata["_try_#{t}"] || 0) > (project.metadata[:max_try] || 10)
-          inactivate! "Too many errors in step #{t}"
-          false
-        else
-          true
-        end
-      end
-    end
+    first_preprocessing(save) if save
+    next_task(nil, save)
   end
 
   ##

data/lib/miga/project.rb

@@ -97,13 +97,28 @@ class MiGA::Project < MiGA::MiGA
 
   ##
   # Is this a clade project?
-  def is_clade?
+  def clade?
     type == :clade
   end
 
+  ##
+  # Same as active? For backward compatibility
+  alias is_clade? clade?
+
   ##
   # Is this a project for multi-organism datasets?
-  def is_multi?
+  def multi?
     @@KNOWN_TYPES[type][:multi]
   end
+
+  ##
+  # Same as multi? For backward compatibility
+  alias is_multi? multi?
+
+  ##
+  # Is this project active? Currently a dummy function, returns
+  # always true.
+  def active?
+    true
+  end
 end

data/lib/miga/project/base.rb

@@ -50,14 +50,11 @@ module MiGA::Project::Base
     07.annotation/01.function/01.essential
     07.annotation/01.function/02.ssu
     07.annotation/02.taxonomy/01.mytaxa
-    07.annotation/03.qa 07.annotation/03.qa/01.checkm
-    07.annotation/03.qa/02.mytaxa_scan
+    07.annotation/03.qa 07.annotation/03.qa/02.mytaxa_scan
     08.mapping 08.mapping/01.read-ctg 08.mapping/02.read-gene
     09.distances 09.distances/01.haai 09.distances/02.aai
     09.distances/03.ani 09.distances/04.ssu 09.distances/05.taxonomy
     10.clades 10.clades/01.find 10.clades/02.ani 10.clades/03.ogs
-    10.clades/04.phylogeny 10.clades/04.phylogeny/01.essential
-    10.clades/04.phylogeny/02.core 10.clades/05.metadata
     90.stats
   ]
 

data/lib/miga/project/dataset.rb

@@ -48,11 +48,11 @@ module MiGA::Project::Dataset
   # Add dataset identified by +name+ and return MiGA::Dataset.
   def add_dataset(name)
     unless metadata[:datasets].include? name
-      ds = MiGA::Dataset.new(self, name)
+      d = 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?
+      recalculate_tasks('New reference dataset added') if d.ref? && d.active?
       pull_hook(:on_add_dataset, name)
     end
     dataset(name)
@@ -66,6 +66,7 @@ module MiGA::Project::Dataset
 
     self.metadata[:datasets].delete(name)
     save
+    recalculate_tasks('Reference dataset unlinked') if d.ref? && d.active?
     pull_hook(:on_unlink_dataset, name)
     d
   end

data/lib/miga/project/result.rb

@@ -23,6 +23,11 @@ module MiGA::Project::Result
     self
   end
 
+  ##
+  # Do nothing, only to comply with MiGA::Common::WithResult
+  def inactivate!(reason = nil)
+  end
+
   ##
   # Is this +task+ to be bypassed?
   def ignore_task?(task)
@@ -45,17 +50,6 @@ module MiGA::Project::Result
     next_task(@@INCLADE_TASKS, save)
   end
 
-  ##
-  # Get the next task from +tasks+, saving intermediate results if +save+.
-  # If +tasks+ is +nil+ (default), it uses the entire list of tasks.
-  # Returns a Symbol.
-  def next_task(tasks = nil, save = true)
-    tasks ||= @@DISTANCE_TASKS + @@INCLADE_TASKS
-    tasks.find do |t|
-      ignore_task?(t) ? false : add_result(t, save).nil?
-    end
-  end
-
   private
 
   ##

data/lib/miga/result.rb

@@ -59,9 +59,25 @@ class MiGA::Result < MiGA::MiGA
   end
 
   ##
-  # Register the result as cleaned
+  # Register the result as cleaned, returns self
   def clean!
     self[:clean] = true
+    self
+  end
+
+  ##
+  # Is the result marked to be recalculated? Returns Boolean
+  def recalculate?
+    !!self[:recalculate]
+  end
+
+  ##
+  # Mark the result to be recalculated, returns self
+  def recalculate!(reason = nil)
+    self[:recalculate] = true
+    self[:recalculate_why] = reason
+    self[:recalculate_when] = Time.now.to_s
+    self
   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, 1]
+  VERSION = [0.7, 21, 0]
 
   ##
   # 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, 10)
+  VERSION_DATE = Date.new(2021, 1, 13)
 
   ##
   # Reference of MiGA.

data/test/hook_test.rb

@@ -107,10 +107,10 @@ class HookTest < Test::Unit::TestCase
         File.join(project.path, 'data', '90.stats', "miga-project.#{ext}")
       )
     end
-    assert_equal(:project_stats, project.next_task(nil, false))
+    assert_equal(:project_stats, project.next_task)
     assert_equal(:test, $res)
     assert_equal(1, $counter)
-    assert_equal(:haai_distances, project.next_task)
+    assert_equal(:haai_distances, project.next_task(nil, true))
     assert_equal(:project_stats, $res)
     assert_equal(2, $counter)
   end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 0.7.20.1
+  version: 0.7.21.0
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire:
 bindir: bin
 cert_chain: []
-date: 2021-01-10 00:00:00.000000000 Z
+date: 2021-01-13 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons