rbbt-util 5.19.11 → 5.19.12

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: d033f774277a3c6644e82ccb1d904d394dd68fe8
-  data.tar.gz: 654e1dabdcabf1bd94d5ad4bc48f1284ffc26007
+  metadata.gz: 9d50592693c2e72df449b2bed576cfce4a6791d5
+  data.tar.gz: 31f019642b140c119e08c2e4eb465b6775f4e89b
 SHA512:
-  metadata.gz: 9595ff8109bcdaac80a1e2f04eb4516814586de65605a4721ece5f9754d8dcdec31176db1933bf397c2c16d6b99bd66c3c4d638a1c722f45a07b55ea412d2ef5
-  data.tar.gz: 7c7d186eedf2bf54debecde2057523fb433c7c9c6fcd12fc46a15f14298c614cc497b569b7d40870f3ecda8081b01a1b2948b62e56f59370b921964df48812c5
+  metadata.gz: ad859664ea8715a701c3273bc536af07fb139b80c71e69be3a0bf55d53882c0fe821fbbe87da5369a2ad81deceb14fb8866d5ba6d58f377ed92557e5bdf30922
+  data.tar.gz: 9ead4f2c55309687b45f0877a3700c06883bab045c1f7f0013d2656f0f6de53a830c111772b07176db49e2f4c3d9de3594e66c2f1d05a5f9405984a082f42df6

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

@@ -44,13 +44,16 @@ module R
         end
 
         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))
+
+          Open.read(tmpfile).gsub(/(glyph\d+-\d+)/, '\1-' + File.basename(tmpfile))
+
         end
       else
 
@@ -68,7 +71,6 @@ module R
   end
 
   module PNG
-
     def self.ggplotPNG(filename, data, script = nil, width = nil, height = nil, options = {})
       width ||= 3
       height ||= 3
@@ -107,6 +109,51 @@ module R
 plot = { #{script} }
 
 ggsave('#{filename}', plot, width = #{R.ruby2R width}, height = #{R.ruby2R height})
+data = NULL
+      EOF
+    end
+
+    def self.plot(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 * ", " + ')' if field_classes.any?
+
+      data.R <<-EOF, :plot, options
+png("#{ filename }", #{ width }, #{ height })
+{ #{script} }
+dev.off()
 data = NULL
       EOF
     end

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

@@ -43,8 +43,14 @@ module Log
         @mean_max = mean if mean > @mean_max
       end
 
-      str = "#{ Log.color :blue, thr.to_i.to_s } per sec."
-      str << " #{ Log.color :yellow, mean.to_i.to_s } avg. #{Log.color :yellow, @mean_max.to_i.to_s} max." if @mean_max > 0
+      if mean.nil? or mean.to_i > 1
+        str = "#{ Log.color :blue, thr.to_i.to_s } per sec."
+        str << " #{ Log.color :yellow, mean.to_i.to_s } avg. #{Log.color :yellow, @mean_max.to_i.to_s} max." if @mean_max > 0
+      else
+        str = "#{ Log.color :blue, (1/thr).ceil.to_s } secs each"
+        str << " #{ Log.color :yellow, (1/mean).ceil.to_s } avg. #{Log.color :yellow, (1/@mean_max).ceil.to_s} min." if @mean_max > 0
+      end
+
       str
     end
 

data/lib/rbbt/util/simpleopt/parse.rb

@@ -41,7 +41,12 @@ module SOPT
     info = {}
 
     inputs = []
-    opt_str.split(/[:\n]+/).each do |entry|
+    if opt_str.include? "\n"
+      re = /\n+/
+    else
+      re = /:/
+    end
+    opt_str.split(re).each do |entry|
       entry.strip!
       next if entry.empty?
       names, _sep, description = entry.partition /\s+/

data/lib/rbbt/workflow/usage.rb

@@ -19,7 +19,9 @@ module Task
       puts
     end
 
+    selects = []
     if inputs.any?
+      inputs.zip(input_types.values_at(*inputs)).select{|i,t| t.to_sym == :select and input_options[i][:select_options] }.each{|i,t| selects << [i, input_options[i][:select_options]]  }
       puts SOPT.input_doc(inputs, input_types, input_descriptions, input_defaults, true)
       puts
     end
@@ -30,6 +32,7 @@ module Task
       seen = []
       task_inputs = dep_inputs deps, workflow
       task_inputs.each do |task,new_inputs|
+        task.inputs.zip(task.input_types.values_at(*task.inputs)).select{|i,t| t.to_sym == :select and task.input_options[i][:select_options] }.each{|i,t| selects << [i, task.input_options[i][:select_options]]  }
         puts "  #{Log.color :yellow, task.name.to_s}:"
         puts
         puts SOPT.input_doc(new_inputs, task.input_types, task.input_descriptions, task.input_defaults, true)
@@ -39,6 +42,15 @@ module Task
 
     puts Log.color(:magenta, "Returns: ") << Log.color(:blue, result_type.to_s) << "\n"
     puts
+    
+    if selects.any?
+      puts Log.color(:magenta, "Input options: ") << Log.color(:blue, result_type.to_s) << "\n"
+      puts
+      selects.each do |input,options|
+        puts Log.color(:blue, input.to_s + ": ") << Misc.format_paragraph(options.collect{|o| o.to_s} * ", ") << "\n"
+        puts
+      end
+    end
   end
 end
 

data/share/rbbt_commands/app/start

@@ -3,7 +3,36 @@
 require 'rbbt-util'
 require 'rbbt/util/simpleopt'
 
-options = SOPT.get "-e--environment*:-p--port*:-s--server*:-f--finder:-R--Rserve_session*:-ho--host*:--views*"
+#options = SOPT.get "-e--environment*:-p--port*:-s--server*:-f--finder:-R--Rserve_session*:-ho--host*:--views*"
+
+$0 = "rbbt #{$previous_commands*""} #{ File.basename(__FILE__) }" if $previous_commands
+
+options = SOPT.setup <<EOF
+Description
+
+$ rbbt command command [options] <filename.tsv|->
+
+Use - to read from STDIN
+
+-h--help Print this help
+-e--environment* Execution environment: production or development
+-ho--host* Host name
+-p--port* TCP port
+-s--server* Server type:  thin, webrick, unicorn, etc
+-f--finder Start server with finder functionality
+-R--Rserve_session* Rserve session to use, otherwise start new one
+--views* Directory with view templates
+EOF
+
+if options[:help]
+  if defined? rbbt_usage
+    rbbt_usage 
+  else
+    puts SOPT.usage
+  end
+  exit 0
+end
+
 options[:Port] ||= options[:port]
 options[:Host] ||= "0.0.0.0"
 options[:Bind] ||= "0.0.0.0"
@@ -32,3 +61,14 @@ Misc.in_dir(app_dir) do
     Rack::Server.start(options)
   end
 end
+
+
+
+
+#!/usr/bin/env ruby
+
+require 'rbbt-util'
+require 'rbbt/util/simpleopt'
+
+
+

data/share/rbbt_commands/app/template

@@ -22,6 +22,7 @@ template = template.sub('.haml','')
 
 ENV["RBBT_FINDER"] = "true" if options.include?(:finder)
 ENV["RServe-session"] = options[:RServe_session] 
+ENV["RACK_ENV"] = options[:environment] if options.include?(:environment)
 
 raise rbbt_usage unless template
 
@@ -45,7 +46,7 @@ app.helpers Sinatra::RbbtMiscHelpers
 app.helpers Sinatra::RbbtToolHelper
 
 app.get '/' do
-  template_render(template, @clean_params)
+  template_render(template, @clean_params, "Template cache", :cache_type => :asynchronous)
 end
 app.instance_eval Rbbt.etc['app.d/base.rb'].read
 app.use Rack::Deflater

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-util
 version: !ruby/object:Gem::Version
-  version: 5.19.11
+  version: 5.19.12
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-01-21 00:00:00.000000000 Z
+date: 2016-01-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rake