rbbt-util 5.6.9 → 5.6.10

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 3a45eff8cafc9d26b4eb4e6c670af1d2fe17ec0d
-  data.tar.gz: e889c0fafcc84778750f7093ed9a1a408de7c31f
+  metadata.gz: b271b167bce0dcfd0cdd1c72e569633f410f02a0
+  data.tar.gz: a0ded4de2b73712c66255e3ecaf2ee18198d4178
 SHA512:
-  metadata.gz: f7dccdd9729516b74d7ab8ab162d7290e5b4e4485efc1839bea45bba479b088641b988320f994fd0e4ee0d27a29fa1f671a7a7fd171261ab9ceaea50479a5bf6
-  data.tar.gz: 5e1531954628ba52e9afd7f57690af8f3955c7bbab949235ca2c537a71270677ac19eaf64d16d8f168f7322b5c09b29c0dfdd7aac0fb857ad4774d3e99d31c98
+  metadata.gz: 09962fd13e045bcf3f97b1655d41e1262e9216c454c7af0c3b207ec61f640ffac382e84dbaa995c45b25efd85bf32a56b2b3068ff75146b6125e54ac668c89ac
+  data.tar.gz: 174808a701eba99667b447e8bfee0cc5bd0fbd4f29047b53de0358d8dd9ec75130340c63ed1861f6e9a63c018cbe4b48ca38ac74a50e19139501f8f72396b797

data/bin/rbbt

@@ -109,7 +109,6 @@ begin
   exit 0
 
 rescue ParameterException
-  ddd "EXCEPTION"
   puts
   rbbt_usage
   print_error($!.message, $!.backtrace)

data/lib/rbbt/persist.rb

@@ -275,9 +275,11 @@ module Persist
 
             Log.medium "Persist create: #{ path } - #{persist_options.inspect[0..100]}"
             res = yield
+
             Misc.lock(path) do
               save_file(path, type, res)
             end
+
             res
           end
         rescue

data/lib/rbbt/persist/tsv/leveldb.rb

@@ -13,7 +13,6 @@ module Persist
 
       database.extend Persist::LevelDBAdapter unless Persist::LevelDBAdapter === database
       database.persistence_path ||= path
-      ddd database
 
       database
     end

data/lib/rbbt/util/filecache.rb

@@ -76,7 +76,7 @@ module FileCache
       path = FileCache.path(filename)
       Open.write(path, content)
       result_files[id] = path
-    end
+    end if missing.any?
 
     result_files
   end

data/lib/rbbt/util/misc.rb

@@ -26,6 +26,7 @@ module LaterString
   end
 end
 
+Lockfile.refresh = false if ENV["RBBT_NO_LOCKFILE_REFRESH"] == "true"
 module Misc
 
   def self.correct_icgc_mutation(pos, ref, mut_str)
@@ -945,12 +946,11 @@ end
 
     begin
       lockfile.lock do 
-        yield file, *args
+        res = yield file, *args
       end
     rescue Interrupt
       Log.error "Process #{Process.pid} interrupted while in lock: #{ lock_path }"
       raise $!
-    ensure
     end
 
     res

data/lib/rbbt/util/tar.rb

@@ -42,7 +42,6 @@ module Misc
     tar.rewind
 
     string = tar.string
-    ddd string.size
 
     #chunk_size = 1024
     #Zlib::GzipWriter.wrap(gz) do |writer|

data/lib/rbbt/workflow/accessor.rb

@@ -280,7 +280,7 @@ module Workflow
 
   def rec_input_types(taskname)
     [taskname].concat(rec_dependencies(taskname)).inject({}){|acc, tn| acc.merge tasks[tn.to_sym].input_types}.
-      tap{|h| IndiferentHash.setup(h)}
+      tap{|h| IndiferentHash.setup(h) }
   end
 
   def rec_input_descriptions(taskname)

data/lib/rbbt/workflow/step.rb

@@ -166,6 +166,7 @@ class Step
       set_info :done, (done_time = Time.now)
       set_info :time_elapsed, done_time - start_time
       Log.medium("Completed task #{task.name || ""} [#{Process.pid}]: #{ path }")
+
       res
     end
 

data/share/rbbt_commands/workflow/task

@@ -274,7 +274,8 @@ if options.delete(:list_job_files)
 end
 
 if job_file = options.delete(:job_file)
-  out.puts job.file(job_file).read
+  file = job.file(job_file)
+  out.puts Path === file ? file.read : file
   exit 0
 end
 

data/test/rbbt/util/test_misc.rb

@@ -1,5 +1,3 @@
-#ENV['LOCKFILE_DEBUG'] = "true";; require 'lockfile'
-
 require File.expand_path(File.dirname(__FILE__) + '/../../test_helper')
 require 'rbbt/util/misc'
 require 'test/unit'

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.6.9
+  version: 5.6.10
 platform: ruby
 authors:
 - Miguel Vazquez