rbbt-util 5.17.23 → 5.17.24

checksums.yaml

@@ -1,7 +1,7 @@
 ---
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+  metadata.gz: 1b5fa2c99f1f5a1055a498543a82cf6c2e411477
+  data.tar.gz: 8aa11e4383e4b2a5c7720c521d46192d2f0c282c
 SHA512:
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-  data.tar.gz: 9645b3c2c856cb2f9f8d2797090d20496bac1f5f15a9ef8d8c05339b1362f7bcf4fec500aa5029f8105c2d0a4075101ddfab8a3b99634d251b105766bd84ecd5
+  metadata.gz: af6894a3cf476efbf5b17447cf70376e37a2c648f8dfeba0acfe13e0272d8f487a7bda9114593497bf0c546d553923c96e74544a6e2d5359b47ec92e61aa0053
+  data.tar.gz: 257842a422857624986f833453280ee834a2d1547de0dd595ad191735bed123c746eb2a6a9f08098cb5a11ab9b59bc7dd308c839f8a54109c6d3f4bd295b2feb

data/lib/rbbt/persist.rb

@@ -295,11 +295,9 @@ module Persist
       end
 
     rescue Lockfile::StolenLockError
-      begin
-        Log.medium "Lockfile stolen: #{path}"
-        sleep 1 + rand(2)
-      rescue Exception
-      end
+      Log.medium "Lockfile stolen: #{path} - #{lock_filename}"
+      Log.exception $!
+      sleep 1 + rand(2)
       retry
     rescue Exception
       Log.medium "Error in persist: #{path}#{Open.exists?(path) ? Log.color(:red, " Erasing") : ""}"

data/lib/rbbt/tsv/util.rb

@@ -4,9 +4,11 @@ module TSV
   def self.reorder_stream(stream, positions, sep = "\t")
     Misc.open_pipe do |sin|
       line = stream.gets
+      line.strip! unless line.nil?
       while line =~ /^#\:/
         sin.puts line
         line = stream.gets
+        line.strip! unless line.nil?
       end
       while line  =~ /^#/
         if Hash === positions
@@ -19,6 +21,7 @@ module TSV
         end
         sin.puts "#" + line.sub!(/^#/,'').strip.split(sep).values_at(*positions).compact * sep
         line = stream.gets
+        line.strip! unless line.nil?
       end
       while line
         if Hash === positions
@@ -31,6 +34,7 @@ module TSV
         end
         sin.puts line.strip.split(sep).values_at(*positions) * sep
         line = stream.gets
+        line.strip! unless line.nil?
       end
     end
   end

data/lib/rbbt/util/R.rb

@@ -1,6 +1,8 @@
 require 'rbbt/util/cmd'
 require 'rbbt/tsv'
 require 'rbbt/util/R/eval'
+require 'rbbt/util/R/plot'
+require 'rbbt/util/R/model'
 
 module R
 

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

@@ -1,4 +1,3 @@
-require 'rbbt/util/R'
 
 module R
 

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

@@ -0,0 +1,109 @@
+module R
+  module SVG
+    def self.ggplotSVG(data, script = nil, width = nil, height = nil, options = {})
+      width ||= 3
+      height ||= 3
+      values = []
+
+      options = options.dup
+
+      sources = [:plot, Rbbt.share.Rlib["svg.R"].find(:lib), options[:source]].flatten.compact
+      options.delete :source
+
+      if data
+        data.each do |k,v|
+          v = Array === v ? v : [v]
+          next if v == "NA" or v.nil? or v.include? "NA" or v.include? nil
+          values = v
+          break
+        end
+        values = [values] unless Array === values
+        field_classes = values.collect do |v| 
+          case v
+          when FalseClass, TrueClass
+            "'logical'"
+          when Fixnum, Float
+            "'numeric'"
+          when String
+            if v.strip =~ /^[-+]?[\d\.]+$/
+              "'numeric'"
+            else
+              "'character'"
+            end
+          when Symbol
+            "'factor'"
+          else
+            ":NA"
+          end
+        end
+        options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')'
+
+        TmpFile.with_file nil, true, :extension => 'svg' do |tmpfile|
+          data.R <<-EOF, sources, options
+  plot = { #{script} }
+
+  rbbt.SVG.save('#{tmpfile}', plot, width = #{R.ruby2R width}, height = #{R.ruby2R height})
+  data = NULL
+          EOF
+        Open.read(tmpfile).gsub(/(glyph\d+-\d+)/, '\1-' + File.basename(tmpfile))
+        end
+      else
+
+        TmpFile.with_file nil, true, :extension => 'svg' do |tmpfile|
+          R.run <<-EOF, sources, options
+  plot = { #{script} }
+
+  rbbt.SVG.save('#{tmpfile}', plot, width = #{R.ruby2R width}, height = #{R.ruby2R height})
+  data = NULL
+          EOF
+          Open.read(tmpfile).gsub(/(glyph\d+-\d+)/, '\1-' + File.basename(tmpfile))
+        end
+      end
+    end
+  end
+
+  module PNG
+
+    def self.ggplotPNG(filename, data, script = nil, width = nil, height = nil, options = {})
+      width ||= 3
+      height ||= 3
+      values = []
+
+      sources = [:plot, options[:source]].flatten.compact
+
+      data.each do |k,v|
+        v = Array === v ? v : [v]
+        next if v == "NA" or v.nil? or v.include? "NA" or v.include? nil
+        values = v
+        break
+      end
+      values = [values] unless Array === values
+      field_classes = values.collect do |v| 
+        case v
+        when FalseClass, TrueClass
+          "'logical'"
+        when Fixnum, Float
+          "'numeric'"
+        when String
+          if v.strip =~ /^[-+]?[\d\.]+$/
+            "'numeric'"
+          else
+            "'character'"
+          end
+        when Symbol
+          "'factor'"
+        else
+          ":NA"
+        end
+      end
+      options[:R_open] ||= "colClasses=c('character'," + field_classes * ", " + ')'
+
+      data.R <<-EOF, :plot, options
+plot = { #{script} }
+
+ggsave('#{filename}', plot, width = #{R.ruby2R width}, height = #{R.ruby2R height})
+data = NULL
+      EOF
+    end
+  end
+end

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

@@ -3,26 +3,25 @@ module Misc
     if use
       Log.medium "Activating lockfile ids"
       Lockfile.dont_use_lock_id = false
-      Lockfile.refresh = 20 
-      Lockfile.max_age = 60 * 10
-      Lockfile.suspend = 10
+      #Lockfile.refresh = 20 
+      #Lockfile.max_age = 60
+      #Lockfile.suspend = 2
     else
       Log.medium "De-activating lockfile ids"
       Lockfile.dont_use_lock_id = true
-      Lockfile.refresh = 5
-      Lockfile.max_age = 30
-      Lockfile.suspend = 5
+      #Lockfile.refresh = 5
+      #Lockfile.max_age = 60 * 10
+      #Lockfile.suspend = 5
     end
 
-    Lockfile.refresh = 3
-    Lockfile.max_age = 10
+    Lockfile.refresh = 10
+    Lockfile.max_age = 60
     Lockfile.suspend = 2
   end
 
   self.use_lock_id = ENV["RBBT_NO_LOCKFILE_ID"] != "true"
 
   LOCK_MUTEX = Mutex.new
-  #def self.lock(file, unlock = true, options = {})
   def self.lock(file, unlock = true, options = {})
     unlock, options = true, unlock if Hash === unlock
     return yield if file.nil?
@@ -35,7 +34,12 @@ module Misc
       lockfile = options[:lock]
       lockfile.lock unless lockfile.locked?
     when FalseClass
+      lockfile = nil
       unlock = false
+    when Path, String
+      lock_path = options[:lock]
+      lockfile = Lockfile.new(lock_path, options)
+      lockfile.lock 
     else
       lock_path = File.expand_path(file + '.lock')
       lockfile = Lockfile.new(lock_path, options)

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

@@ -224,6 +224,9 @@ module Misc
     lock_options = lock_options[:lock] if Hash === lock_options[:lock]
     tmp_path = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_dir})
     tmp_path_lock = Persist.persistence_path(path, {:dir => Misc.sensiblewrite_lock_dir})
+
+    tmp_path_lock = nil if FalseClass === options[:lock]
+
     Misc.lock tmp_path_lock, lock_options do
 
       if Open.exists? path and not force
@@ -264,6 +267,7 @@ module Misc
         Open.rm path if File.exists? path
       rescue Exception
         Log.medium "Exception in sensiblewrite: #{$!.message} -- #{ Log.color :blue, path }"
+        Log.exception $!
         content.abort if content.respond_to? :abort
         Open.rm path if File.exists? path
         raise $!

data/lib/rbbt/util/open.rb

@@ -275,7 +275,7 @@ module Open
   end
 
   def self.lock(file, options = {}, &block)
-    if (dir_sub_path = find_repo_dir(file))
+    if file and (dir_sub_path = find_repo_dir(file))
       dir, sub_path = dir_sub_path
       repo = get_repo_from_dir(dir)
       Misc.lock_in_repo(repo, sub_path, &block)

data/lib/rbbt/workflow/accessor.rb

@@ -14,7 +14,18 @@ class Step
     jobs = [jobs] if Step === jobs
     begin
       threads = []
-      jobs.each do |j| threads << Thread.new{j.join} end
+
+      threads = jobs.collect do |j| 
+        Thread.new do
+          begin
+            j.join 
+          rescue Exception
+            Log.error "Exception waiting for job: #{Log.color :blue, j.path}"
+            raise $!
+          end
+        end
+      end
+
       threads.each{|t| t.join }
     rescue Exception
       threads.each{|t| t.exit }
@@ -65,10 +76,11 @@ class Step
   end
 
   def info_lock
-    @info_lock ||= begin
-                     path = Persist.persistence_path(info_file + '.lock', {:dir => Step.lock_dir})
-                     Lockfile.new path
-                   end
+    @info_lock = begin
+                   path = Persist.persistence_path(info_file + '.lock', {:dir => Step.lock_dir})
+                   Lockfile.new path, :refresh => false, :dont_use_lock_id => true
+                 end if @info_lock.nil?
+    @info_lock
   end
 
   def info(check_lock = true)
@@ -125,7 +137,7 @@ class Step
       i = info(false)
       i.merge! hash
       @info_cache = i
-      Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump(i), :force => true)
+      Misc.sensiblewrite(info_file, INFO_SERIALIAZER.dump(i), :force => true, :lock => false)
       @info_cache_time = Time.now
       value
     end
@@ -248,7 +260,9 @@ class Step
 
   def log(status, message = nil, &block)
     self.status = status
-    self.message Log.uncolor(message)
+    if message
+      self.message Log.uncolor(message)
+    end
     Step.log(status, message, path, &block)
   end
 
@@ -517,7 +531,6 @@ module Workflow
       when Array
         workflow, task, options = dependency
 
-        #options = dependency.last if Hash === dependency.last
         _inputs = IndiferentHash.setup(inputs.dup)
         options.each{|i,v|
           case v

data/share/Rlib/svg.R

@@ -0,0 +1,59 @@
+library(plyr)
+library(proto)
+library(ggplot2)
+library(gridSVG)
+library(grid)
+library(XML)
+library(ggthemes)
+library(Cairo)
+
+# Modified from http://aaronecay.com/blog/2014/02/tooltips-in-ggplot/
+
+rbbt.SVG.extract <- function(plot, size=NULL, prefix=NULL, ...){
+
+    if (is.null(prefix)) prefix = rbbt.random_string();
+    if (is.null(size)){
+        print(plot, type='cairo');
+        mysvg <- grid.export(prefix=prefix, ...)
+    }else{
+        base.size = 10 * (7/size)
+        resolution = 72 * (size/7)
+
+        if (length(plot$theme) == 0) plot <- plot + theme_gdocs();
+
+        plot$theme$text$size = base.size
+
+        print(plot, type='cairo')
+
+        mysvg <- grid.export(res=resolution, prefix=prefix, ...)
+    }
+
+    xml <- saveXML(mysvg$svg)
+    xml
+}
+
+rbbt.SVG.save <- function(filename, plot, width=NULL, height=NULL){
+    if (is.null(width)){
+        if (is.null(height)){
+            size = NULL
+        }else{
+            size=height
+        }
+    }else{
+        if (is.null(height)){
+            size = width
+        }else{
+            size=max(width, height)
+        }
+    }
+
+    xml = rbbt.SVG.extract(plot, size)
+    fileConn<-file(filename, 'w')
+    cat(xml, file=fileConn)
+    close(fileConn)
+}
+
+rbbt.SVG.save.fast <- function(filename, plot, width=3, height=3){
+    ggsave(file=filename, plot, width=width, height=height);
+}
+

data/share/rbbt_commands/app/template

@@ -3,7 +3,6 @@
 require 'rbbt/util/simpleopt'
 require 'rbbt/workflow'
 
-require 'zurb-foundation'
 require 'modular-scale'
 
 require 'rbbt/rest/main'

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.17.23
+  version: 5.17.24
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-14 00:00:00.000000000 Z
+date: 2015-05-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake
@@ -216,6 +216,7 @@ files:
 - lib/rbbt/util/R.rb
 - lib/rbbt/util/R/eval.rb
 - lib/rbbt/util/R/model.rb
+- lib/rbbt/util/R/plot.rb
 - lib/rbbt/util/chain_methods.rb
 - lib/rbbt/util/cmd.rb
 - lib/rbbt/util/color.rb
@@ -274,6 +275,7 @@ files:
 - lib/rbbt/workflow/task.rb
 - lib/rbbt/workflow/usage.rb
 - share/Rlib/plot.R
+- share/Rlib/svg.R
 - share/Rlib/util.R
 - share/config.ru
 - share/install/software/lib/install_helpers