rbbt-util 5.13.33 → 5.13.34

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: cff3c91f834c396cfbe8c0c9f65cd046aaff8ffc
+  metadata.gz: 1581db188b182a19a32b933fa09143b05a63f673
+  data.tar.gz: 4ff0988f92691a719fa4e5d255f5e91bde236ac5
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+  data.tar.gz: 3e46304432334c7fab8b8e95425794cec108b8dd80c4e598e5a7ad017eb31cd70c5a202997785ca1178a32dbb4fd839f50a2b4ca980b91f0ad1f8b0a656e5105

data/lib/rbbt/persist.rb

@@ -218,7 +218,7 @@ module Persist
 
     if stream
       if persist_options[:no_load] == :stream 
-        res = tee_stream(stream, path, type, stream.respond_to?(:callback)? stream.callback : nil, stream.respond_to?(:abort_callback)? stream.abort_callback : nil, lockfile)
+        res = tee_stream(stream, path, type, stream.respond_to?(:callback)? stream.callback : nil, stream.respond_to?(:abort_callback)? stream.abort_callback : nil)
         res.lockfile = lockfile
 
         raise KeepLocked.new res 

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

@@ -54,7 +54,7 @@ module Persist
 
     def write_and_read
       lock_filename = Persist.persistence_path(persistence_path + '.write', {:dir => TSV.lock_dir})
-      mutex.synchronize do
+      #mutex.synchronize do
         Misc.lock(lock_filename, true, :max_age => 600) do
           write if closed? or not write?
           res = begin
@@ -64,12 +64,12 @@ module Persist
                 end
           res
         end
-      end
+      #end
     end
 
     def write_and_close
       lock_filename = Persist.persistence_path(persistence_path + '.write', {:dir => TSV.lock_dir})
-      mutex.synchronize do
+      #mutex.synchronize do
         Misc.lock(lock_filename, true) do
           write if closed? or not write?
           res = begin
@@ -82,19 +82,19 @@ module Persist
                 end
           res
         end
-      end
+      #end
     end
 
     def read_and_close
-      mutex.synchronize do
-        read if closed? or not read?
-        res = begin
-                yield
-              ensure
-                close
-              end
-        res
-      end
+      #mutex.synchronize do
+      read if closed? or not read?
+      res = begin
+              yield
+            ensure
+              close
+            end
+      res
+      #end
     end
 
 

data/lib/rbbt/util/cmd.rb

@@ -186,6 +186,7 @@ module CMD
           end
 
           sin.close unless sin.closed?
+          in_content.join if in_content.respond_to? :join and not dont_close_in
           in_content.close unless in_content.closed? or dont_close_in
         rescue
           Process.kill "INT", pid

data/lib/rbbt/util/log.rb

@@ -17,7 +17,7 @@ module Log
                    end
 
   def self.ignore_stderr
-    LOG_MUTEX.synchronize do
+    #LOG_MUTEX.synchronize do
       backup_stderr = STDERR.dup
       File.open('/dev/null', 'w') do |f|
         STDERR.reopen(f)
@@ -28,7 +28,7 @@ module Log
           backup_stderr.close
         end
       end
-    end
+    #end
   end
 
   def self.get_level(level)

data/lib/rbbt/util/log/progress/report.rb

@@ -10,11 +10,11 @@ module Log
 
     def print(io, str)
       return if ENV["RBBT_NO_PROGRESS"] == "true"
-      LOG_MUTEX.synchronize do
+      #LOG_MUTEX.synchronize do
         STDERR.print str
         Log.logfile.puts str unless Log.logfile.nil?
         Log::LAST.replace "progress"
-      end
+      #end
     end
 
     attr_accessor :history, :mean_max
@@ -96,7 +96,7 @@ module Log
       else
         bars = BARS
       end
-      print(io, up_lines(bars.length) << Log.color(:yellow, "--Progress\n") << down_lines(bars.length)) 
+      print(io, up_lines(bars.length) << Log.color(:yellow, "...Progress\n") << down_lines(bars.length)) 
       print(io, up_lines(@depth) << report_msg << down_lines(@depth)) 
       @last_time = Time.now
       @last_count = ticks

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

@@ -12,7 +12,7 @@ module Misc
   class << self
     attr_accessor :sensiblewrite_dir
     def sensiblewrite_dir
-      @sensiblewrite_dir = Rbbt.tmp.sensiblewrite
+      @sensiblewrite_dir = Rbbt.tmp.sensiblewrite.find
     end
   end
 
@@ -171,7 +171,8 @@ module Misc
     else
       Log.medium "Consuming stream #{Misc.fingerprint io}"
       begin
-        while not io.closed? and block = io.read(2048)
+        into.sync == true if IO === into
+        while not io.closed? and block = io.read(2048 * 10)
           into << block if into
         end
         io.join if io.respond_to? :join
@@ -212,10 +213,12 @@ module Misc
     lock_options = Misc.pull_keys options, :lock
     lock_options = lock_options[:lock] if Hash === lock_options[:lock]
     return if Open.exists? path
-    tmp_path = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_lock_dir})
-    Misc.lock tmp_path, lock_options do
+    tmp_path = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_dir})
+    tmp_path_lock = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_lock_dir})
+    Misc.lock tmp_path_lock, lock_options do
       return if Open.exists? path
       if not Open.exists? path
+        FileUtils.mkdir_p File.dirname(tmp_path) unless File.directory? File.dirname(tmp_path)
         FileUtils.rm_f tmp_path if File.exists? tmp_path
         begin
           case

data/lib/rbbt/util/open.rb

@@ -367,9 +367,8 @@ module Open
            file_open(in_cache(url, wget_options), options[:grep], mode, options[:invert_grep])
          else
            io = wget(url, wget_options)
-           new, save = Misc.tee_stream io
-           add_cache(url, save, wget_options)
-           new
+           add_cache(url, io, wget_options)
+           file_open(in_cache(url, wget_options), options[:grep], mode, options[:invert_grep])
          end
     io = unzip(io)  if ((String === url and zip?(url))  and not options[:noz]) or options[:zip]
     io = gunzip(io) if ((String === url and gzip?(url)) and not options[:noz]) or options[:gzip]

data/lib/rbbt/workflow/step.rb

@@ -35,7 +35,7 @@ class Step
     @mutex = Mutex.new
     @info_mutex = Mutex.new
     @inputs = inputs || []
-    NamedArray.setup @inputs, task.inputs
+    NamedArray.setup @inputs, task.inputs if task
   end
 
   def inputs

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

@@ -140,7 +140,7 @@ class Step
           next if dependency.running?
           dependency.clean 
         else
-          dependency.clean if (dependency.error? or dependency.aborted? or dependency.status.nil?)# or not dependency.done?)
+          dependency.clean if (dependency.error? or dependency.aborted? or dependency.status.nil? or not (dependency.done? or dependency.running?))
         end
 
         unless dependency.started? #dependency.result or dependency.done?

data/share/rbbt_commands/system/status

@@ -59,20 +59,21 @@ end
 
 puts Log.color(:magenta, "# System report")
 puts
-sort_file = Proc.new do |f,i|
-  dir = f.split(/:\_/).first
-  
-  dir + i[:ctime].to_i.to_s
-end
-locks = Rbbt.lock_info
-if locks.any?
-  puts Log.color(:magenta, "Locks:")
-  #locks.sort_by{|f,i| i[:ctime] }.each do |file,info|
-  locks.sort_by(&sort_file).each do |file,info|
-    elapsed, pid, ppid = info.values_at :elapsed, :pid, :ppid
-    puts "  " << file + Log.color(:blue, " -- time: #{Misc.format_seconds elapsed}; ppid: #{ppid}; pid: #{pid_msg pid}")
+sort_files = Proc.new do |a,b|
+  fa,ia = a
+  fb,ib = b
+
+  dira = fa.split(/[:_][^\/>]*$/).first
+  dirb = fb.split(/[:_][^\/>]*$/).first
+
+  case dira <=> dirb
+  when -1
+    -1
+  when 1
+    1
+  else
+    ia[:ctime] <=> ib[:ctime]
   end
-  puts
 end
 
 
@@ -96,6 +97,16 @@ if sensiblewrites.any?
   puts
 end
 
+locks = Rbbt.lock_info
+if locks.any?
+  puts Log.color(:magenta, "Locks:")
+  locks.sort(&sort_files).each do |file,info|
+    elapsed, pid, ppid = info.values_at :elapsed, :pid, :ppid
+    puts "  " << file + Log.color(:blue, " -- time: #{Misc.format_seconds elapsed}; ppid: #{ppid}; pid: #{pid_msg pid}")
+  end
+  puts
+end
+
 exit 0 if workflow.nil?
 workflow = nil if workflow == ["all"]
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.13.33
+  version: 5.13.34
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-06 00:00:00.000000000 Z
+date: 2014-06-08 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake