rbbt-util 5.9.0 → 5.9.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 8809e7ff7afbc160340f326450273a14ca3ce286
-  data.tar.gz: 3de26d6f418fd60b21459b9cef3af0ed11844310
+  metadata.gz: 66364dac8f8a7eb98ad0b63b8d45405fd994a2ad
+  data.tar.gz: f1861d29eec6bc26661f829c80f1aa3367684a69
 SHA512:
-  metadata.gz: 8f3d7b38e869e5b88aa3005a6cdb1ffb96ca9eb8c8ef96625892ed3ba8a038422b9c7172806bda50fd1e1bdf4e014d75607ad0c8c4fe33a806e0498d3e4e6b88
-  data.tar.gz: c56376cae5c4fc796fedef603179fd4e1129581b7c495e6101705fe939f5facd1c5a200e500d592df10c26ec91466c118b79ca38efc2ad2b14aa9b414cf61be3
+  metadata.gz: ee58bf9d7f6abb6335f211e26ad2c3d84e6c6d3e56e0ed0279c00e8e6c5546f8065e5b14b6b881b7870e959f5c3f3f68f256f0685bf97de26aef09abf4bdef2e
+  data.tar.gz: 29cd31366e10b06ce60cd6df50d65067cce46450cddf188f6322fcd5a46c4c71b2a4669ef5521a1f6e21edea0967bf7b2b068e7acef6838bb08f833f377e8e13

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

@@ -91,7 +91,7 @@ module TSV
     q.init &block
 
     traverse_obj(obj, options) do |*p|
-      q.process p
+      q.process *p
     end
 
     q.join
@@ -119,8 +119,8 @@ module TSV
     into = Misc.process_options options, :into
 
     if into
-      callback = Proc.new do |*v|
-        store_into into, *v
+      callback = Proc.new do |e|
+        store_into into, e
       end
       options[:callback] = callback
     end

data/lib/rbbt/util/concurrency/processes.rb

@@ -84,7 +84,7 @@ class RbbtProcessQueue
     @callback_thread.raise Aborted if @callback_thread and @callback_thread.alive?
   end
 
-  def process(e)
+  def process(*e)
     @queue.push e
   end
 

data/lib/rbbt/util/concurrency/processes/worker.rb

@@ -14,7 +14,8 @@ class RbbtProcessQueue
           loop do
             p = @queue.pop
             raise p if Exception === p
-            res = @block.call p
+            raise p.first if Exception === p.first
+            res = @block.call *p
             @callback_queue.push res if @callback_queue
           end
 

data/lib/rbbt/util/concurrency/threads.rb

@@ -20,7 +20,6 @@ class RbbtThreadQueue
             loop do
               p = queue.pop
               p = Array === p ? p << mutex : [p,mutex]
-              p = [p, mutex].flatten(1) 
               block.call *p
             end
           rescue Exception

data/lib/rbbt/util/misc.rb

@@ -981,7 +981,11 @@ end
       else
         Log.warn("Insisting after exception: #{$!.message}")
       end
-      sleep sleep if sleep
+      if sleep and try > 0
+        sleep sleep
+      else
+        Thread.pass
+      end
       try += 1
       retry if try < times
       raise $!
@@ -1103,12 +1107,14 @@ end
     lockfile = Lockfile.new(lock_path)
 
     begin
-      if File.exists? lockfile and
-        Misc.hostname == (info = Open.open(lockfile){|f| YAML.load(f) })["host"] and 
-        info["pid"] and not Misc.pid_exists?(info["pid"])
+      Misc.insist 3 do
+        if File.exists? lockfile and
+          Misc.hostname == (info = Open.open(lockfile){|f| YAML.load(f) })["host"] and 
+          info["pid"] and not Misc.pid_exists?(info["pid"])
 
-        Log.info("Removing lockfile: #{lockfile}. This pid #{Process.pid}. Content: #{info.inspect}")
-        FileUtils.rm lockfile 
+          Log.info("Removing lockfile: #{lockfile}. This pid #{Process.pid}. Content: #{info.inspect}")
+          FileUtils.rm lockfile 
+        end
       end
     rescue
       Log.warn("Error checking lockfile #{lockfile}: #{$!.message}. Removing. Content: #{begin Open.read(lockfile) rescue "Could not open file" end}")

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

@@ -4,7 +4,7 @@ require 'rbbt/tsv/parallel'
 
 class TestTSVParallelThrough < Test::Unit::TestCase
 
-  def _test_traverse_tsv
+  def test_traverse_tsv
     require 'rbbt/sources/organism'
 
     head = 100
@@ -23,7 +23,29 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
   end
 
-  def _test_traverse_stream
+  def test_traverse_tsv_cpus
+    require 'rbbt/sources/organism'
+
+    head = 100
+
+    tsv = Organism.identifiers("Hsa").tsv :head => head
+    res = {}
+    TSV.traverse tsv do |k,v|
+       res[k] = v
+    end
+    assert_equal head, res.keys.compact.sort.length
+    assert res.values.compact.flatten.uniq.length > 0
+
+    tsv = Organism.identifiers("Hsa").tsv :head => head
+    TSV.traverse tsv, :into => res, :cpus => 5 do |k,v|
+      [k,v]
+    end
+
+    assert_equal head, res.keys.compact.sort.length
+    assert res.values.compact.flatten.uniq.length > 0
+  end
+
+  def test_traverse_stream
     require 'rbbt/sources/organism'
 
     head = 100
@@ -44,7 +66,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal head, res.keys.compact.sort.length
   end
 
-  def _test_traverse_stream_keys
+  def test_traverse_stream_keys
     require 'rbbt/sources/organism'
 
     head = 100
@@ -68,7 +90,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal res, Organism.identifiers("Hsa").tsv(:head => 100).keys
   end
   
-  def _test_traverse_array
+  def test_traverse_array
     require 'rbbt/sources/organism'
 
     array = []
@@ -90,7 +112,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal array, res
   end
 
-  def _test_traverse_array_threads
+  def test_traverse_array_threads
     require 'rbbt/sources/organism'
 
     array = []
@@ -111,7 +133,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
     assert_equal array.sort, res.sort
   end
 
-  def _test_traverse_array_cpus
+  def test_traverse_array_cpus
     require 'rbbt/sources/organism'
 
     array = []
@@ -129,7 +151,7 @@ class TestTSVParallelThrough < Test::Unit::TestCase
   def test_traverse_benchmark
     require 'rbbt/sources/organism'
 
-    head = 80_000
+    head = 8_000
 
     tsv = Organism.identifiers("Hsa").open
     Misc.benchmark do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.9.0
+  version: 5.9.1
 platform: ruby
 authors:
 - Miguel Vazquez