rbbt-util 5.21.94 → 5.21.95

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: a8627482cbd18d7d3a64ca31e0d6c1035f741523
+  data.tar.gz: 3ec4150b254df3faaec0645421da191703778eb5
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+  data.tar.gz: 0b76b13dc1a568c0238c40564f4f159713fa6a597bf27058face9d6c32fa9f255d06615143615f58e97dc6196c38ff6d0f6aed90df88e4edaaa060167cbdaaed

data/lib/rbbt/util/cmd.rb

@@ -32,6 +32,7 @@ module CMD
     log        = options.delete(:log)
     no_fail    = options.delete(:no_fail)
     no_wait    = options.delete(:no_wait)
+
     dont_close_in  = options.delete(:dont_close_in)
 
     log = true if log.nil?
@@ -127,12 +128,7 @@ module CMD
       sin.close
     end
 
-    if no_wait
-      pids = []
-    else
-      pids = [pid]
-    end
-
+    pids = [pid]
 
     if pipe
       err_thread = Thread.new do

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

@@ -79,7 +79,7 @@ module ConcurrentStream
       @threads.each do |t| 
         next if t == Thread.current
         begin
-          t.join unless FalseClass === t.status 
+          t.join #unless FalseClass === t.status 
         rescue Exception
           Log.warn "Exception joining thread in ConcurrenStream: #{filename}"
           raise $!
@@ -114,7 +114,6 @@ module ConcurrentStream
   end
 
   def join
-
     join_threads
     join_pids
 
@@ -126,26 +125,24 @@ module ConcurrentStream
     close unless closed?
   end
 
-  def abort_threads(exception)
+  def abort_threads(exception = nil)
+    return unless @threads and @threads.any?
     Log.low "Aborting threads (#{Thread.current.inspect}) #{@threads.collect{|t| t.inspect } * ", "}"
 
     @threads.each do |t| 
       next if t == Thread.current
-      Log.low "Aborting thread #{t.inspect}"
-      t.raise exception ? exception : Aborted.new 
-    end if @threads
+      Log.low "Aborting thread #{t.inspect} with exception: #{exception}"
+      t.raise((exception.nil? ? Aborted.new : exception))
+    end 
 
-    sleeped = false
     @threads.each do |t|
       next if t == Thread.current
       if t.alive? 
-        sleep 1 unless sleeped
-        sleeped = true
+        sleep 1
         Log.low "Kill thread #{t.inspect}"
         t.kill
       end
       begin
-        Log.low "Join thread #{t.inspect}"
         t.join unless t == Thread.current
       rescue Aborted
       rescue Exception
@@ -157,6 +154,7 @@ module ConcurrentStream
   def abort_pids
     @pids.each do |pid|
       begin 
+        Log.low "Killing PID #{pid} in ConcurrentStream #{filename}"
         Process.kill :INT, pid 
       rescue Errno::ESRCH
       end

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

@@ -361,6 +361,7 @@ module Misc
         FileUtils.mkdir_p File.dirname(tmp_path) unless File.directory? File.dirname(tmp_path)
         FileUtils.rm_f tmp_path if File.exist? tmp_path
         begin
+
           case
           when block_given?
             File.open(tmp_path, 'wb', &block)
@@ -372,7 +373,7 @@ module Misc
               f.sync = true
               while block = content.read(BLOCK_SIZE)
                 f.write block
-              end
+              end 
             end
           else
             File.open(tmp_path, 'wb') do |f|  end

data/lib/rbbt/util/tmpfile.rb

@@ -19,8 +19,7 @@ module TmpFile
   # up to +max+
   def self.random_name(s = "", max = 10000000)
     n = rand(max)
-    s << n.to_s
-    s
+    s + n.to_s
   end
 
   # Creates a random filename in the temporary directory
@@ -29,7 +28,8 @@ module TmpFile
   end
 
   def self.with_file(content = nil, erase = true, options = {})
-    tmpfile = tmp_file
+    prefix = options[:prefix] || ""
+    tmpfile = tmp_file prefix
     if options[:extension]
       tmpfile += ".#{options[:extension]}"
     end
@@ -48,7 +48,8 @@ module TmpFile
   end
 
   def self.with_dir(erase = true, options = {})
-    tmpdir = tmp_file
+    prefix = options[:prefix] || ""
+    tmpdir = tmp_file prefix
 
     FileUtils.mkdir_p tmpdir
 

data/lib/rbbt/workflow/accessor.rb

@@ -399,7 +399,7 @@ class Step
   end
 
   def aborted?
-    status == :aborted || nopid?
+    status == :aborted || (status != :noinfo && nopid?)
   end
 
   # {{{ INFO

data/share/Rlib/util.R

@@ -499,9 +499,10 @@ rbbt.heatmap <- function(filename, data, width=500, height=500, take_log=FALSE,
         data = data[, colSums(is.na(data))==0]
     }
 
+    rbbt.require('pls')
     data = stdize(data)
 
-    heatmap.2(data, margins = c(20,5), scale='column')
+    heatmap.2(data, scale='column', ...)
 
     dev.off();
     par(opar)

data/share/rbbt_commands/app/start

@@ -38,7 +38,11 @@ if options[:workdir]
   Workflow.workdir = options[:workdir]
 end
 
-options[:Port] ||= options[:port]
+options[:Port] = options["port"]
+options[:server] = options["server"]
+options[:Host] = options["Host"]
+options[:Bind = options["Bind"]
+
 options[:Host] ||= "0.0.0.0"
 options[:Bind] ||= "0.0.0.0"
 

data/share/rbbt_commands/tsv/read_excel

@@ -17,6 +17,7 @@ Use - to read from STDIN
 -f--fields* Fields
 -t--type* Type
 -m--merge Merge from multiple rows
+-z--zipped Assume data is zipped when merging (default is true)
 -s2--sep2* Second level separator. Default /[,|]\\s?/
 -h--help Print this help
 
@@ -34,6 +35,7 @@ excelfile = ARGV.first
 
 raise ParameterException, "No excel file given" if excelfile.nil?
 
+options[:zipped] ||= true if options[:merge]
 require 'rbbt/tsv/excel'
 puts TSV.excel(excelfile, options).to_s
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.21.94
+  version: 5.21.95
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-08-14 00:00:00.000000000 Z
+date: 2017-08-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -503,7 +503,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.12
+rubygems_version: 2.6.13
 signing_key: 
 specification_version: 4
 summary: Utilities for the Ruby Bioinformatics Toolkit (rbbt)