miga-base 1.3.13.7 → 1.3.13.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: 26c53b61236bb268538a557a66b6d041eaf1270d2b9c780351b543ccb9db61b7
+  metadata.gz: 843f35d4fa4d3543cc030db30b32ba87e40e21c967c4ecf3832973857e58dc05
+  data.tar.gz: e6f121106bce201cba4d6da053c1a07d977b12f5ee4d02d84c63ca204e4afa29
 SHA512:
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+  metadata.gz: de88c20be5deffa734c0fc692bde8ecc7f87c1bea571c125915b032232e1c9a54e41eb37f3c666f54a2adfd1be64adfb12ec61000553a3b1ace9ba70c7a3d048
+  data.tar.gz: d2ff4a70266159ccca8c1cff3dbaf0c52316e5608096014c04523e309f6ce768e1daa4f779275ef0293cb83d14af982d9c8a5412e1d433f25425f76adcac8261

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

@@ -73,7 +73,9 @@ module MiGA::Cli::Action::Doctor::Base
 
   ##
   # Reads all the distance estimates in +a+ -> * for +metric+ and
-  # returns them as a hash +{"b_name" => [val, sd, ...], ...}+
+  # returns them as a hash +{"b_name" => [val, sd, ...], ...}+ for
+  # rows with values other than the metric, or +{"b_name" => val}+ for
+  # rows with the metric only
   def read_bidirectional(a, metric)
     db_file = a.result(:distances)&.file_path("#{metric}_db") or return {}
     sql = "select seq2, #{metric}, sd, n, omega from #{metric}"

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

@@ -70,10 +70,10 @@ module MiGA::Cli::Action::Doctor::Distances
   #---- Auxuliary functions -----
 
   ##
-  # Make a temporal directory holding partial bidirectionality reports (one per thread)
-  # in a custom multi-JSON format. Requires a MiGA::Project +project+ and the iterator of
-  # the reference datasets +ref_ds+. Returns the path to the temporal directory created.
-  # Used by +check_bidir+
+  # Make a temporal directory holding partial bidirectionality reports (one per
+  # thread) in a custom multi-JSON format. Requires a MiGA::Project +project+
+  # and the iterator of the reference datasets +ref_ds+. Returns the path to the
+  # temporal directory created. Used by +check_bidir+
   def partial_bidir_tmp(project, ref_ds)
     n = ref_ds.size
 
@@ -106,9 +106,9 @@ module MiGA::Cli::Action::Doctor::Distances
   end
 
   ##
-  # Read partial temporal reports of bidirectionality (located in +tmp+), and return
-  # a two-deep hash with the final missingness report by metric (first key) and
-  # dataset name (second key). Used by +check_bidir+
+  # Read partial temporal reports of bidirectionality (located in +tmp+), and
+  # return a two-deep hash with the final missingness report by metric (first
+  # key) and dataset name (second key). Used by +check_bidir+
   def merge_bidir_tmp(tmp)
     dist = { aai: {}, ani: {} }
     cli[:threads].times do |i|

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

@@ -58,7 +58,7 @@ module MiGA::Cli::Action::Doctor::Operations
         unless ok
           cli.say "  > Registering again #{d.name}:#{r_k}   "
           d.add_result(r_k, true, force: true)
-          sr = d.result(:stats) and sr.remove!
+          d.result(:stats)&.remove!
         end
       end
     end

data/lib/miga/json.rb

@@ -3,7 +3,7 @@
 require 'json'
 begin
   require 'oj'
-  OJ.mimic_JSON()
+  Oj.mimic_JSON()
 rescue LoadError
   # Do nothing if not available
 end

data/lib/miga/result.rb

@@ -33,14 +33,26 @@ class MiGA::Result < MiGA::MiGA
     ##
     # Check if +path+ describes a result and otherwise create
     # it using the passed block. If +force+, ignore existing
-    # JSON in +path+ if any.
+    # JSON in +path+ if any, but it can rescue the versions 
+    # field from the old one if it exists and the new one doesn't
+    # contain such field.
     def create(path, force = false)
-      FileUtils.rm(path) if force && File.exist?(path)
-      r_pre = load(path)
-      return r_pre unless r_pre.nil?
+      # Deal with old results first
+      r_old = load(path)
+      return r_old if r_old && !force
 
+      # Create the new result using the block passed
+      FileUtils.rm(path) if r_old
       yield
-      load(path)
+
+      # Load and return
+      load(path).tap do |r_new|
+        # Rescue versions and start (if any and if necessary)
+        if r_old
+          %i[versions started].each { |i| r_new[i] ||= r_old[i] }
+          r_new[:versions] = (r_old[:versions] || {}).merge(r_new[:versions])
+        end
+      end
     end
   end
 

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 13, 7].freeze
+  VERSION = [1.3, 13, 9].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 3, 22)
+  VERSION_DATE = Date.new(2024, 3, 31)
 
   ##
   # References of MiGA

data/test/result_stats_test.rb

@@ -23,12 +23,12 @@ class ResultStatsTest < Test::Unit::TestCase
     File.open(fq, 'w') { |fh| fh.puts '@1', 'ACTAC', '+', '####' }
     touch_done(dir)
     r = dataset.add_result(:raw_reads)
-    assert_equal({}, r[:stats])
+    assert_equal({}, r.stats)
     r.compute_stats
-    assert_not_empty(r[:stats])
-    assert_equal(Hash, r[:stats].class)
-    assert_equal(1, r[:stats][:reads])
-    assert_equal([40.0, '%'], r[:stats][:g_c_content])
+    assert_not_empty(r.stats)
+    assert_equal(Hash, r.stats.class)
+    assert_equal(1, r.stats[:reads])
+    assert_equal([40.0, '%'], r.stats[:g_c_content])
   end
 
   def test_coupled_raw_reads
@@ -40,10 +40,10 @@ class ResultStatsTest < Test::Unit::TestCase
     touch_done(dir)
     r = dataset.add_result(:raw_reads)
     r.compute_stats
-    assert_not_empty(r[:stats])
-    assert_nil(r[:stats][:reads])
-    assert_equal(1, r[:stats][:read_pairs])
-    assert_equal([40.0, '%'], r[:stats][:reverse_g_c_content])
+    assert_not_empty(r.stats)
+    assert_nil(r.stats[:reads])
+    assert_equal(1, r.stats[:read_pairs])
+    assert_equal([40.0, '%'], r.stats[:reverse_g_c_content])
   end
 
   def test_trimmed_reads
@@ -51,9 +51,9 @@ class ResultStatsTest < Test::Unit::TestCase
     FileUtils.touch(file_path(dir, '.1.clipped.fastq'))
     touch_done(dir)
     r = dataset.add_result(:trimmed_reads)
-    assert_equal({}, r[:stats])
+    assert_equal({}, r.stats)
     r.compute_stats
-    assert_equal({}, r[:stats])
+    assert_equal({}, r.stats)
   end
 
   def test_read_quality
@@ -62,9 +62,9 @@ class ResultStatsTest < Test::Unit::TestCase
     Dir.mkdir(file_path(dir, '.fastqc'))
     touch_done(dir)
     r = dataset.add_result(:read_quality)
-    assert_equal({}, r[:stats])
+    assert_equal({}, r.stats)
     r.compute_stats
-    assert_equal({}, r[:stats])
+    assert_equal({}, r.stats)
   end
 
   def test_trimmed_fasta
@@ -133,10 +133,10 @@ class ResultStatsTest < Test::Unit::TestCase
     r = dataset.add_result(:taxonomy)
 
     # Test assertions
-    assert_nil(r[:stats][:closest_relative])
+    assert_nil(r.stats[:closest_relative])
     r.compute_stats
-    assert_equal('dad', r[:stats][:closest_relative])
-    assert_equal([100.0, '%'], r[:stats][:aai])
-    assert_equal(0.0, r[:stats][:phylum_pvalue])
+    assert_equal('dad', r.stats[:closest_relative])
+    assert_equal([100.0, '%'], r.stats[:aai])
+    assert_equal(0.0, r.stats[:phylum_pvalue])
   end
 end

data/test/result_test.rb

@@ -26,6 +26,30 @@ class ResultTest < Test::Unit::TestCase
     assert_instance_of(MiGA::Result, r)
   end
 
+  def test_overwrite_result
+    r = dataset.add_result(:trimmed_reads)
+    r[:ephemeral] = '@'
+    r[:versions] = { you: 'best' }
+    r.save
+
+    # Before reloading
+    assert_equal('@', r[:ephemeral])
+    assert_equal('best', r[:versions][:you])
+    assert_nil(r[:versions][:MiGA])
+
+    # After reloading (without forcing)
+    r = dataset.add_result(:trimmed_reads, true, force: false)
+    assert_equal('@', r[:ephemeral])
+    assert_equal('best', r[:versions][:you])
+    assert_nil(r[:versions][:MiGA])
+
+    # After reloading (with forcing)
+    r = dataset.add_result(:trimmed_reads, true, force: true)
+    assert_nil(r[:ephemeral])
+    assert_equal('best', r[:versions][:you])
+    assert_not_nil(r[:versions][:MiGA])
+  end
+
   def test_unlink
     r = project.add_result(:clade_finding)
     path = r.path

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.13.7
+  version: 1.3.13.9
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-03-22 00:00:00.000000000 Z
+date: 2024-03-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons