rbbt-util 5.17.19 → 5.17.20

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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-  data.tar.gz: bb5058f3d0f22653fb8f01bcb2ff7660e581eb17
+  metadata.gz: 58cd900e8238a97baf230cbb81502f4c3aca35ba
+  data.tar.gz: fb08bda42782f76c8dd4a8b2b338d5ebc74a2038
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+  data.tar.gz: fa5201d4762db7bba332aa5d0fce2e41c540447793fda061436405e6af902d15ede743197481c2134df90081f889ba7e0636aea169aa0819763e8fdf96e41338

data/lib/rbbt/util/R/eval.rb

@@ -12,7 +12,7 @@ module Rserve
 end
 
 module R
-  SESSION = ENV["RServe-session"] || "Session-PID-" + Process.pid.to_s
+  SESSION = ENV["RServeSession"] || "Session-PID-" + Process.pid.to_s
 
   def self.socket_file
     @@socket_file ||= Rbbt.tmp.R_sockets[R::SESSION].find
@@ -22,6 +22,16 @@ module R
     @@lockfile ||= socket_file + '.lock'
   end
 
+  def self.semfile
+    if defined? @@semfile and not @@semfile.nil?
+      @@semfile 
+    else
+      @@semfile = File.basename(socket_file) + '.sem'
+      RbbtSemaphore.create_semaphore(@@semfile,1) 
+      @@semfile
+    end
+  end
+
   def self.workdir
     @@workdir ||= socket_file + '.wd'
   end
@@ -37,6 +47,7 @@ module R
       begin
         Process.kill :INT, @@instance_process
       rescue Exception
+        Log.warn "Error killing Rserve (#{@@instance_process}): #{$!.message}"
       end
     end
     FileUtils.rm_rf pid_file if File.exists? pid_file
@@ -103,8 +114,8 @@ module R
   end
 
   def self._eval(cmd)
-    Misc.lock lockfile do 
-      times = 2
+    RbbtSemaphore.synchronize(semfile) do 
+      times = 1
       begin
         instance.eval(cmd)
       rescue Rserve::Connection::EvalError

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

@@ -373,11 +373,14 @@ module Misc
       keys = []
       parts = []
       lines.each_with_index do |line,i|
-        key, *p = line.strip.split(sep, -1) 
-        keys[i] = key
-        parts[i] = p
+        if line.nil?
+          key, *p = line.strip.split(sep, -1) 
+          keys[i] = key
+          parts[i] = p
+        else
+        end
       end
-      sizes = parts.collect{|p| p.length }
+      sizes = parts.collect{|p| p.nil? ? 0 : p.length }
       last_min = nil
       while lines.compact.any?
         min = keys.compact.sort.first

data/lib/rbbt/workflow/accessor.rb

@@ -523,13 +523,16 @@ module Workflow
           case v
           when Symbol
             rec_dependency = (real_dependencies + real_dependencies.collect{|d| d.rec_dependencies}).flatten.compact.uniq.select{|d| d.task.name.to_sym == v }.first
-            raise "Dependency for parameter #{i} not found: #{v}" if rec_dependency.nil?
-            input_options = workflow.task_info(task)[:input_options][i] || {}
-            if input_options[:stream]
-              rec_dependency.run(true).grace unless rec_dependency.done? or rec_dependency.running?
-              _inputs[i] = rec_dependency
+            if rec_dependency.nil?
+              _inputs[i] = v
             else
-              _inputs[i] = rec_dependency.run
+              input_options = workflow.task_info(task)[:input_options][i] || {}
+              if input_options[:stream]
+                #rec_dependency.run(true).grace unless rec_dependency.done? or rec_dependency.running?
+                _inputs[i] = rec_dependency
+              else
+                _inputs[i] = rec_dependency.run
+              end
             end
           else
             _inputs[i] = v

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.19
+  version: 5.17.20
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-04-23 00:00:00.000000000 Z
+date: 2015-04-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake