rbbt-util 5.27.9 → 5.28.0

checksums.yaml

@@ -1,7 +1,7 @@
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+  metadata.gz: fae2c7a6c6a64059a77fd43d0edf3c6b3a5835cea870b58ddf07a8e24deec18c
+  data.tar.gz: d92b6fbda894fd77dd5e69b391a1087e3401864f20a7422f92443fd01cc6b03b
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+  data.tar.gz: ca684d7817e67d324ae6767c8b802e2065855915cc541db5f65b070ef47d7862e98b0acc4e991cef38bd65e97ac1224bdcd03e1e4cc1211e937023bd1757e4a8

data/lib/rbbt/annotations/util.rb

@@ -74,7 +74,7 @@ module Annotated
 
     object = case
              when literal_pos
-               values[literal_pos]
+               values[literal_pos].tap{|o| o.force_encoding(Encoding.default_external)}
              else
                id.dup
              end
@@ -119,7 +119,7 @@ module Annotated
                fields = AnnotatedArray === annotations ? annotations.annotations : annotations.compact.first.annotations
                fields << :annotation_types
 
-             when (fields == [:literal] and not annotations.compact.empty?)
+             when (fields == [:literal] and ! annotations.compact.empty?)
                fields << :literal
 
              when (fields == [:all] && Annotated === annotations)

data/lib/rbbt/resource/path.rb

@@ -13,7 +13,7 @@ module Path
     string.resource = resource
     string.search_paths = search_paths
     string.search_order = search_order
-    string.libdir = libdir || Path.caller_lib_dir
+    string.libdir = libdir || Path.caller_lib_dir 
     string
   end
 
@@ -52,11 +52,11 @@ module Path
   def join(name)
     raise "Invalid path: #{ self }" if self.nil?
     new = if self.empty?
-            self.annotate name.to_s.dup
+            self.annotate name.to_s.dup.chomp
           else
-            self.annotate File.join(self, name.to_s)
+            self.annotate File.join(self, name.to_s.chomp)
           end
-    new.original = File.join(self.original, name.to_s) if self.original
+    new.original = File.join(self.original, name.to_s.chomp) if self.original
     new
   end
 

data/lib/rbbt/resource/util.rb

@@ -1,6 +1,6 @@
 module Path
 
-  def self.caller_lib_dir(file = nil, relative_to = 'lib')
+  def self.caller_lib_dir(file = nil, relative_to = ['lib', 'bin'])
     file = caller.reject{|l| 
       l =~ /rbbt\/(?:resource\.rb|workflow\.rb)/ or
       l =~ /rbbt\/resource\/path\.rb/ or
@@ -9,13 +9,14 @@ module Path
       l =~ /progress-monitor\.rb/ 
     }.first.sub(/\.rb[^\w].*/,'.rb') if file.nil?
 
+    relative_to = [relative_to] unless Array === relative_to
     file = File.expand_path(file)
-    return Path.setup(file) if File.exist? File.join(file, relative_to)
+    return Path.setup(file) if relative_to.select{|d| File.exist? File.join(file, d)}.any?
 
     while file != '/'
       dir = File.dirname file
 
-      return dir if File.exist? File.join(dir, relative_to)
+      return dir if relative_to.select{|d| File.exist? File.join(dir, d)}.any?
 
       file = File.dirname file
     end

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

@@ -727,6 +727,8 @@ module TSV
         Log.exception $!
         abort_stream(into, $!)
         raise $!
+      ensure
+        Log::ProgressBar.remove_bar(bar) if bar
       end
 
       into

data/lib/rbbt/util/misc.rb

@@ -2,6 +2,7 @@ require 'lockfile'
 require 'digest/md5'
 require 'cgi'
 require 'zlib'
+require 'etc'
 require 'rubygems/package'
 
 require 'rbbt/util/tar'

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

@@ -292,14 +292,21 @@ def self.add_libdir(dir=nil)
     end
   end
 
-  def self.bootstrap(elems, num = :current, options = {}, &block)
+  def self.bootstrap(elems, num = nil, options = {}, &block)
     IndiferentHash.setup options
+
+    num = Rbbt::Config.get :cpus, :default_bootstrap_cpus, :bootstrap_cpus if num == :current || num == nil if defined?(Rbbt::Config)
     num = :current if num.nil?
     cpus = case num
            when :current
-            n = 10
-            n = elems.length / 2 if n > elems.length/2
-            n
+             n = Etc.nprocessors
+             n = elems.length / 2 if n > elems.length/2
+
+             if $BOOTSTRAPPED_CURRENT && $BOOTSTRAPPED_CURRENT + n > Etc.nprocessors
+               1
+             else
+               n
+             end
            when String
              num.to_i
            when Integer
@@ -318,7 +325,12 @@ def self.add_libdir(dir=nil)
     respawn = options[:respawn] and options[:cpus] and options[:cpus].to_i > 1
 
     index = (0..elems.length-1).to_a.collect{|v| v.to_s }
+
     TSV.traverse index, options do |pos|
+      if num == :current
+        $BOOTSTRAPPED_CURRENT ||= n 
+        $BOOTSTRAPPED_CURRENT += 0 
+      end
       elem = elems[pos.to_i]
       elems.annotate elem if elems.respond_to? :annotate
       res = begin

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

@@ -401,7 +401,7 @@ module Misc
 
   def self.scan_version_text(text, cmd = nil)
     cmd = "NOCMDGIVE" if cmd.nil? || cmd.empty?
-    m = text.match(/(?:version.*?|#{cmd}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
+    m = text.match(/(?:version.*?|#{cmd}.*?|#{cmd.split(/[-_.]/).first}.*?|v)((?:\d+\.)*\d+(?:-[a-z_]+)?)/i)
     return nil if m.nil?
     m[1]
   end

data/lib/rbbt/util/open.rb

@@ -94,7 +94,8 @@ module Open
              end
 
     begin
-      wget_options = options.merge( '-O' => '-')
+      wget_options = options.dup
+      wget_options = wget_options.merge( '-O' => '-') unless options.include?('--output-document')
       wget_options[:pipe] = pipe unless pipe.nil?
       wget_options[:stderr] = stderr unless stderr.nil?
 
@@ -824,4 +825,8 @@ module Open
   def self.broken_link?(path)
     File.symlink?(path) && ! File.exists?(File.readlink(path))
   end
+
+  def self.download(url, path)
+    Open.wget(url, "--output-document" => path)
+  end
 end

data/share/rbbt_commands/app/start

@@ -15,6 +15,7 @@ $ rbbt app start [options]
 -Ho--Host* Host name
 -B--Bind* Bind IP
 -p--port* TCP port
+-w--workers* Number of workers for cluster mode (puma)
 -s--server* Server type:  thin, webrick, unicorn, etc
 -f--finder Start server with finder functionality
 -fs--file_server Activate file serving for resources
@@ -84,6 +85,12 @@ Misc.in_dir(app_dir) do
     end
   end
 
+  fixed_options = {}
+  options.each do |k,v| fixed_options[k.to_sym] = v end
+  options = fixed_options
+
+  options[:workers] = options[:workers].to_i if options[:workers]
+
   case server
   when 'passenger'
     system ENV, "env RBBT_LOG=0 passenger start -R '#{config_ru_file}' -p #{options[:Port] || "2887"}"
@@ -91,6 +98,7 @@ Misc.in_dir(app_dir) do
     system ENV, "puma '#{config_ru_file}' -p #{options[:Port] || "2887"} -w 3 -t 8:32 --preload"
   else
     options[:config] = config_ru_file
+    options[:threads] = "8:8"
     Rack::Server.start(options)
   end
 end

data/share/rbbt_commands/tsv/uncollapse

@@ -25,5 +25,4 @@ file = STDIN if file == '-'
 
 tsv = TSV.open file, :merge => true, :type => :double
 
-
 puts tsv.to_unmerged_expanded_s

data/share/rbbt_commands/workflow/server

@@ -123,15 +123,11 @@ TmpFile.with_file do |app_dir|
     else
       options[:config] = config_ru_file
 
-			clean_options = {}
-			options.each do |k,v|
-        begin
-          clean_options[k.to_sym] = v
-        rescue
-        end
-      end
+      fixed_options = {}
+      options.each do |k,v| fixed_options[k.to_sym] = v end
+      options = fixed_options
 
-      Rack::Server.start(clean_options)
+      Rack::Server.start(options)
     end
   end
 end

data/share/workflow_config.ru

@@ -43,7 +43,11 @@ etc_dir = Rbbt.etc
 load_file etc_dir['app.d/pre.rb'].find 
 
 app.get '/' do
-  redirect to(File.join('/', wf.to_s))
+  begin
+    template_render('main', params, 'main', :cache_type => :asynchronous)
+  rescue TemplateMissing
+    redirect to(File.join('/', wf.to_s))
+  end
 end
 
 #{{{ BASE

data/test/rbbt/test_resource.rb

@@ -69,11 +69,11 @@ class TestTSV < Test::Unit::TestCase
   end
 
   def test_libdir
-    assert File.exist? TestResource[].share.Rlib["util.R"].find :lib
-    assert File.exist? TestResource[].share.Rlib["util.R"].find 
+    assert File.exist?(TestResource[].share.Rlib["util.R"].find(:lib))
+    assert File.exist?(TestResource[].share.Rlib["util.R"].find)
   end
 
-  def test_server
+  def __test_server
     require 'rbbt/sources/organism'
     TmpFile.with_file :extension => 'gz' do |tmp|
       Organism.get_from_server("Hsa/b37/known_sites/dbsnp_138.vcf.gz", tmp, 'http://rbbt.bsc.es')

data/test/rbbt/util/test_misc.rb

@@ -690,5 +690,30 @@ Written by Mike Haertel and others, see
     EOF
     assert_equal "3.1", Misc.scan_version_text(txt, "grep")
   end
+
+  def test_bootstrap_current_only_once
+
+     
+    max = Etc.nprocessors * 10
+    TmpFile.with_file do |f|
+      RbbtSemaphore.with_semaphore(1) do |sem|
+        Misc.bootstrap (1..max).to_a do
+          Open.open(f, :mode => 'a') do |sin|
+            sin.puts Process.pid.to_s
+          end
+          Misc.bootstrap (1..10).to_a do
+            RbbtSemaphore.synchronize(sem) do
+              Open.open(f, :mode => 'a') do |sin|
+                sin.puts [Process.ppid.to_s, Process.pid.to_s] * ":"
+              end
+            end
+          end
+        end
+      end
+      assert_equal max * 10 + max, Open.read(f).split("\n").length
+      assert_equal Etc.nprocessors * 2, Open.read(f).split("\n").uniq.length
+    end
+
+  end
 end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.27.9
+  version: 5.28.0
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2020-07-09 00:00:00.000000000 Z
+date: 2020-07-23 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake