rbbt-util 5.28.1 → 5.28.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: 047125157bbeb36260736630c091dda1243a7856f88b01553c6ecec5177c1795
+  metadata.gz: 6bc94b86c69f95806ae280d76df8da7696f5df0f008a3791385e4ccf11b70977
+  data.tar.gz: f7763e2dd88ba121b8a625b846bf0f4f1efaba090b873f2947e0a83ae9dabff1
 SHA512:
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-  data.tar.gz: c5f52161994f7d6de86aba05544f05dfbe1fff765c587220adca9a917c6f7ebe410cfeae601996eaa790f9587468508a8750618a5c126b1ad5e07238bc4e34e1
+  metadata.gz: 59fd76fc00eeeb892ad53bbbc0757d5e17dde600f505d31e8dabe43e0184e5c5bfcef2ccc3f7aa9bc295e36251b9f864706bc0dcf357cc3606b73b1f25f7d672
+  data.tar.gz: ce4d345fc9876378b57ba8753d2a7dfd13b4fd23330246bc2385186f81344026cf415e7cc6eb86253f86e709e2061139930734b2c77b7329165ed2892e3e5d0a

data/lib/rbbt/tsv/parallel/traverse.rb

@@ -101,8 +101,8 @@ module TSV
         error = true
         raise $!
       ensure
-        Log::ProgressBar.remove_bar(bar) if bar
         join.call(error) if join
+        Log::ProgressBar.remove_bar(bar) if bar
       end
   end
 
@@ -137,8 +137,8 @@ module TSV
       error = true
       raise $!
     ensure
-      Log::ProgressBar.remove_bar(bar) if bar
       join.call(error) if join
+      Log::ProgressBar.remove_bar(bar) if bar
     end
   end
 
@@ -177,8 +177,8 @@ module TSV
       error = true
       raise $!
     ensure
-      Log::ProgressBar.remove_bar(bar) if bar
       join.call(error) if join
+      Log::ProgressBar.remove_bar(bar) if bar
     end
   end
 
@@ -219,8 +219,8 @@ module TSV
       error = true
       raise $!
     ensure
-      Log::ProgressBar.remove_bar(bar) if bar
       join.call(error) if join
+      Log::ProgressBar.remove_bar(bar) if bar
     end
   end
 
@@ -273,8 +273,8 @@ module TSV
       error = true
       raise $!
     ensure
-      Log::ProgressBar.remove_bar(bar) if bar
       join.call(error) if join
+      Log::ProgressBar.remove_bar(bar) if bar
     end
   end
 
@@ -318,8 +318,8 @@ module TSV
       error = true
       raise $!
     ensure
-      Log::ProgressBar.remove_bar(bar) if bar
       join.call(error) if join
+      Log::ProgressBar.remove_bar(bar) if bar
     end
   end
 
@@ -727,8 +727,6 @@ module TSV
         Log.exception $!
         abort_stream(into, $!)
         raise $!
-      ensure
-        Log::ProgressBar.remove_bar(bar) if bar
       end
 
       into

data/lib/rbbt/util/misc/inspect.rb

@@ -401,7 +401,7 @@ module Misc
 
   def self.scan_version_text(text, cmd = nil)
     cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
-    m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
+    m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.to_s.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
     return nil if m.nil?
     m[1]
   end

data/lib/rbbt/workflow/step/accessor.rb

@@ -208,7 +208,7 @@ class Step
   end
 
   def init_info(force = false)
-    return nil if @exec or info_file.nil? or (Open.exists?(info_file) and ! force)
+    return nil if @exec || info_file.nil? || (Open.exists?(info_file) && ! force)
     Open.lock(info_file, :lock => info_lock) do
       i = {:status => :waiting, :pid => Process.pid, :path => path}
       i[:dependencies] = dependencies.collect{|dep| [dep.task_name, dep.name, dep.path]} if dependencies

data/lib/rbbt/workflow/step/dependencies.rb

@@ -24,7 +24,7 @@ class Step
           Log.medium "Not duplicating stream #{stream_key}"
           STREAM_CACHE[stream_key] = stream
         when File
-          if Open.exists? current.path 
+          if Open.exists?(current.path)
             Log.medium "Reopening file #{stream_key}"
             Open.open(current.path)
           else
@@ -97,7 +97,7 @@ class Step
       end
 
       job.dup_inputs unless status == 'done' or job.started?
-      job.init_info unless status == 'noinfo' or status == 'done' or job.started?
+      job.init_info(status == 'noinfo') unless status == 'waiting' || status == 'done' || job.started?
 
       canfail = ComputeDependency === job && job.canfail?
     end

data/test/rbbt/tsv/parallel/test_traverse.rb

@@ -202,7 +202,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     stream = datafile_test('identifiers').open 
     dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
     dumper.init
-    TSV.traverse stream, :head => head, :into => dumper do |k,v|
+    TSV.traverse stream, :head => head, :into => dumper, :bar => true do |k,v|
       k = k.first
       [k,v]
     end
@@ -212,6 +212,26 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.size
   end
 
+  def test_traverse_into_dumper_error_bar
+    require 'rbbt/sources/organism'
+
+    head = 2_000
+
+    stream = datafile_test('identifiers').open 
+    dumper = TSV::Dumper.new datafile_test('identifiers').tsv_options
+    dumper.init
+    TSV.traverse stream, :head => head, :into => dumper, :bar => true do |k,v|
+      k = k.first
+      raise 
+      [k,v]
+    end
+
+    assert_raise do 
+      res = TSV.open(dumper.stream)
+    end
+
+  end
+
   def test_traverse_into_dumper_threads
     require 'rbbt/sources/organism'
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.28.1
+  version: 5.28.2
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-27 00:00:00.000000000 Z
+date: 2020-08-12 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake