miga-base 1.3.20.7 → 1.3.20.9

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 2c6360afd316cce82e4e86fbf6add9fcf77e8d42b8f3310639be4d96f8b9c195
-  data.tar.gz: dba1b714a536d2a99fe6101ba2406eab9e8d91d32a813f6a00670195ac0bd841
+  metadata.gz: 1fc1b49c630d4e619c3394850d15b692cab359f617970ce6f3235e8f6c373d6c
+  data.tar.gz: 2c2c6bb6ee77b873993a6ecea24047ca854acd31e88a43ee9588c350df0a719b
 SHA512:
-  metadata.gz: 78f8a407b258726b64d4fcc1c124a614ae7a0b0f9401669b3fbeae6912045ba0c7dac5af73d20359bb0c073bba20c87d4a3efcbb0c81b06cedc1c65ce2e0feba
-  data.tar.gz: eeb2acbcb111419f6c7427a08a29095f075ba6b548a9a56ec8689d8ad72a188db6a3277c861c1baaebc5a9492f64d459f1f1c8be62d5231feaf7bb5d2544b2ec
+  metadata.gz: 86a62582ae62601a5c3e3935b5bae8046e97a19b53624827d20a8728066ec68360664042a213ee094346e7dba63d8765a044cbc413bcafc3bd8f841579371c1f
+  data.tar.gz: 7ad47d39abd7c257c23b8bdf825135a51dd8e9fa2c96cc14881a16e5a8e03264d9541381796616462c8e6bf3b4a85cfd5ff0528539447e2f3e487aceafa6bb48

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

@@ -92,13 +92,15 @@ module MiGA::Cli::Action::Doctor::Distances
 
     # Check first if a previous run is complete (and recover it)
     tmp = File.join(project.path, 'doctor-bidirectional.tmp')
-    tmp_done = File.join(tmp, 'read-done.txt')
-    if File.size?(tmp_done) &&
-          File.readlines(tmp_done)[0].chomp.to_i == chunks
-      return tmp
+    tmp_chunks = File.join(tmp, 'chunks.txt')
+    tmp_chunks_val = [chunks, 0]
+    if File.size?(tmp_chunks)
+      tmp_chunks_val = File.readlines(tmp_chunks).map(&:chomp).map(&:to_i)
     end
+    chunks = tmp_chunks_val[0]
+    FileUtils.rm_rf(tmp) unless tmp_chunks_val[1] == n
 
-    # Read data first (threaded)
+    # Read data (threaded)
     FileUtils.mkdir_p(tmp)
     chunks_e = 0 .. chunks - 1
     MiGA::Parallel.distribute(chunks_e, cli[:threads]) do |chunk, k, thr|
@@ -121,7 +123,7 @@ module MiGA::Cli::Action::Doctor::Distances
     cli.say
 
     # Save information to indicate that the run is complete and return
-    File.open(tmp_done, 'w') { |fh| fh.puts chunks }
+    File.open(tmp_chunks, 'w') { |fh| fh.puts(chunks, n) }
     return tmp
   end
 
@@ -130,7 +132,7 @@ module MiGA::Cli::Action::Doctor::Distances
   # fill databases with missing values. Returns the names of the datasets fixed
   # as a Set.
   def merge_bidir_tmp(tmp)
-    tmp_done = File.join(tmp, 'read-done.txt')
+    tmp_done = File.join(tmp, 'chunks.txt')
     chunks = File.readlines(tmp_done)[0].chomp.to_i
 
     lower_triangle = []
@@ -139,18 +141,22 @@ module MiGA::Cli::Action::Doctor::Distances
     end
     MiGA::Parallel.distribute(lower_triangle, cli[:threads]) do |cell, k, thr|
       cli.advance('Writing:', k, lower_triangle.size, false) if thr == 0
+      done_f = File.join(tmp, "#{cell[0]}-#{cell[1]}.txt")
+      next if File.exist?(done_f)
+
       fixed_ds = merge_bidir_tmp_pair(tmp, cell[0], cell[1])
-      File.open(File.join(tmp, "#{cell[0]}-#{cell[1]}.txt"), 'w') do |fh|
-        fixed_ds.each { |ds| fh.puts ds }
-      end
+      File.open("#{done_f}.tmp", 'w') { |fh| fixed_ds.each { |ds| fh.puts ds } }
+      File.rename("#{done_f}.tmp", done_f)
     end
     cli.advance('Writing:', lower_triangle.size, lower_triangle.size, false)
     cli.say
     lower_triangle.map do |cell|
       Set.new.tap do |y|
-        File.open(File.join(tmp, "#{cell[0]}-#{cell[1]}.txt"), 'r') do |fh|
-          fh.each { |ln| y << ln.chomp }
-        end
+        file = File.join(tmp, "#{cell[0]}-#{cell[1]}.txt")
+        raise MiGA::Error.new(
+          "Expected file missing, probably due to a thread failure: #{file}"
+        ) unless File.exist?(file)
+        File.open(file, 'r') { |fh| fh.each { |ln| y << ln.chomp } }
       end
     end.inject(Set.new, :+)
   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, 20, 7].freeze
+  VERSION = [1.3, 20, 9].freeze
 
   ##
   # Nickname for the current major.minor version.

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.20.7
+  version: 1.3.20.9
 platform: ruby
 authors:
 - Luis M. Rodriguez-R