rbbt-util 5.33.20 → 5.33.21

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 87f3c2c6750c49c90cce3fd4f8e24d270d471538f65374e388ec6ac83bf7134c
-  data.tar.gz: fb4909c5ef2ab2a751271f1f49db270ea1f91c4a84ed26504ddebebf23aae75a
+  metadata.gz: 563841b942e1b0cf4a97bed6900bd51c96df63ec993d3a5280faadbf7b8eb753
+  data.tar.gz: c2cd78f5dfe5061f97021fd2121dd415d7b6c36c1fef2fc9f496c2cc985e4c4d
 SHA512:
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-  data.tar.gz: a7f50b0bb6829c781c9b8081b63464997f1d2aa1e8ab68871af6d13799867f4f136385b704e1bf5badce2ed03171db421ba5f9452d491b02c96aa8fe36d8eeea
+  metadata.gz: 6382e73cdb35ff7ab7dcd3de894a192353c39edef06ddaeb030ec376089b638acb0f62f468153433dfb0e3b0242a44146bfaeb1770ef35ee7175200caeea5e12
+  data.tar.gz: '08b8ce8d556f25269c671b6307972669927b468975c77d188b572e2285627968989a2db68de7fa2983908cb7d4cf3a236f0908a78d3917ea46ad84f82c60f536'

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

@@ -92,7 +92,6 @@ module Misc
       ConcurrentStream.setup sout, :pids => [pid]
     else
 
-
       ConcurrentStream.setup sin, :pair => sout
       ConcurrentStream.setup sout, :pair => sin
 
@@ -782,4 +781,13 @@ module Misc
     ConcurrentStream.setup out, :threads => monitor_thread
   end
 
+  def self.open_gz_pipe
+    sout = Misc.open_pipe do |sin|
+      yield sin
+      sin.close
+    end
+
+    Open.gzip(sout)
+  end
+
 end

data/lib/rbbt/util/open.rb

@@ -748,6 +748,7 @@ module Open
           raise $!
         end
         content.close
+        content.join if content.respond_to? :join
       end
     end
 

data/lib/rbbt/workflow.rb

@@ -414,7 +414,7 @@ module Workflow
     end if task.required_inputs
 
     if missing_inputs.length == 1
-      raise ParameterException, "Input #{missing_inputs.first} is required but was not provided or is nil"
+      raise ParameterException, "Input '#{missing_inputs.first}' is required but was not provided or is nil"
     end
 
     if missing_inputs.length > 1

data/share/rbbt_commands/hpc/list

@@ -356,5 +356,5 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 end
 
 puts 
-puts "Found #{count} jobs"
+puts Log.color :clear, "Found #{count} jobs"
 

data/share/rbbt_commands/lsf/list

@@ -356,5 +356,5 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 end
 
 puts 
-puts "Found #{count} jobs"
+puts Log.color :clear, "Found #{count} jobs"
 

data/share/rbbt_commands/slurm/list

@@ -356,5 +356,5 @@ workdir.glob("**/command.batch").sort_by{|f| File.mtime(f)}.each do |fcmd|
 end
 
 puts 
-puts "Found #{count} jobs"
+puts Log.color :clear, "Found #{count} jobs"
 

data/share/rbbt_commands/workflow/task

@@ -469,7 +469,7 @@ begin
   end
 
   if options.delete(:printpath)
-    job.join
+    job.join if job.running?
     raise job.messages.last if (job.error? || job.aborted?) && job.messages
     if Open.remote? job.path
       puts job.url + Log.color(:blue, "?_format=raw")

data/test/rbbt/util/misc/test_pipes.rb

@@ -284,4 +284,41 @@ line4
       end
     end
   end
+
+  def test_gz_pipe
+    text =<<-EOF
+line1
+line2
+line3
+line4
+    EOF
+
+    TmpFile.with_file nil, :extension => 'txt.gz' do |file|
+      sout = Misc.open_gz_pipe do |sin|
+        text.split("\n").each do |line|
+          sin.puts line
+        end
+      end
+
+      Open.mkdir File.basename(file)
+      thr1 = Misc.consume_stream(sout, true, file)
+      thr1.join
+      assert Open.gzip?(file)
+      assert_equal text, Open.read(file)
+    end
+  end
+
+  def test_open_pipe_error
+    sout = Misc.open_pipe do |sin|
+      10.times do |i|
+        sin.puts "line #{i}"
+      end
+      raise
+    end
+
+    TmpFile.with_file do |tmp|
+      #Misc.consume_stream(sout, false, tmp)
+      Open.write(tmp, sout)
+    end
+  end
 end

data/test/rbbt/util/test_open.rb

@@ -186,6 +186,6 @@ class TestOpen < Test::Unit::TestCase
     end
 
   end
-  
+
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.33.20
+  version: 5.33.21
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2022-05-30 00:00:00.000000000 Z
+date: 2022-06-03 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake