galaaz 0.4.5 → 0.4.6

data/lib/gknit/rb_engine.rb

@@ -0,0 +1,56 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2018 Rodrigo Botafogo. All Rights Reserved. Permission to use, copy, modify, 
+# and distribute this software and its documentation, without fee and without a signed 
+# licensing agreement, is hereby granted, provided that the above copyright notice, this 
+# paragraph and the following two paragraphs appear in all copies, modifications, and 
+# distributions.
+#
+# IN NO EVENT SHALL RODRIGO BOTAFOGO BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, 
+# INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING OUT OF THE USE OF 
+# THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF RODRIGO BOTAFOGO HAS BEEN ADVISED OF THE 
+# POSSIBILITY OF SUCH DAMAGE.
+#
+# RODRIGO BOTAFOGO SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, 
+# THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE 
+# SOFTWARE AND ACCOMPANYING DOCUMENTATION, IF ANY, PROVIDED HEREUNDER IS PROVIDED "AS IS". 
+# RODRIGO BOTAFOGO HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, 
+# OR MODIFICATIONS.
+##########################################################################################
+
+class RbEngine < KnitrEngine
+  include Singleton
+
+  attr_reader :engine
+
+  #--------------------------------------------------------------------------------------
+  # Ruby engine for processing Ruby chunks
+  #--------------------------------------------------------------------------------------
+
+  def initialize
+    
+    @engine = Proc.new do |options|
+
+      # the 'rb' engine has the code to be executed in the options.label
+      # argument
+      # options[['code']] = options[['label']]
+      options.code = options.label
+      # we do not want the code to be returned
+      options.echo = false
+      
+      GalaazUtil.exec_ruby(options)
+      
+    end
+
+    # Add the rb engine function for processing the rb block
+    add(rb: @engine)
+
+  end
+  
+end
+
+rb_engine = RbEngine.instance
+

data/lib/gknit/ruby_engine.rb

@@ -21,49 +21,26 @@
 # OR MODIFICATIONS.
 ##########################################################################################
 
-# Ruby engine for processing Ruby chunks
-eng_ruby = Proc.new do |options|
+class RubyEngine < KnitrEngine
+  include Singleton
 
-  begin
-    # read the chunk code
-    # code = R.paste(options.code, collapse: "\n") << 0
-    
-    # process the chunk options. Better to let interested methods process their
-    # options
-    KnitrEngine.process_options(options)
+  attr_reader :engine
 
-    tmp_fig = R.tempfile()
-     
-    # opens a device for the current chunk for plot recording. Knitr provides
-    # method chunck_device for that, but it is a non-exported method.  Galaaz
-    # does not yet provide a way to accessing non-exported methods, so, the ck_dv
-    # local method was developed that just calls chunk_device.
-    if (R._ck_dv(options.fig__width[1], options.fig__height[1], options.dev,
-                 options.dev__args, options.dpi, options, tmp_fig, record: true) << 0)
+  #--------------------------------------------------------------------------------------
+  # Ruby engine for processing Ruby chunks
+  #--------------------------------------------------------------------------------------
 
-      # chunk requires library 'showtext'.  Install and loads if not present
-      # FIXME: library showtext is giving error when trying to execute showtext beginning
-      if (!options[['fig.showtext']].is__null << 0) &&
-         options[['fig.showtext']] << 0
-        R.install_and_loads('showtext')
-        R.showtext
-      end
-      
-      dv = R.dev__cur
-    end
-    
-    # executes the code
-    res = GalaazUtil.exec_ruby(options)
+  def initialize
+
+    # call the RubyEngine initializer first so that @base_engine is defined
+    super
     
-    # formats and outputs the code and results
-    R.engine_output(options, out: res)
+    # Add the ruby engine function for processing the ruby block
+    add(ruby: @base_engine)
 
-  ensure
-    R.dev__off(dv)
   end
   
 end
 
-ruby_engine = KnitrEngine.new
-ruby_engine.add(ruby: eng_ruby)
+ruby_engine = RubyEngine.instance
 

data/lib/util/exec_ruby.rb

@@ -23,6 +23,52 @@
 
 require 'stringio'
 
+#----------------------------------------------------------------------------------------
+# Path StringIO puts... Already opened an issue in RC12
+#----------------------------------------------------------------------------------------
+
+class StringIO
+  
+  def puts(*args)
+
+    if args.empty?
+      write(DEFAULT_RECORD_SEPARATOR)
+    else
+      args.each do |arg|
+
+        # method to_s is not being called when the output is diverted
+        # need to fix it
+        if (arg.is_a? R::Object)
+          arg = arg.to_s
+        end
+        
+        if arg.nil?
+          line = ''
+        elsif Thread.guarding? arg
+          line = '[...]'
+        else
+          begin
+            arg = Truffle::Type.coerce_to(arg, Array, :to_ary)
+            Thread.recursion_guard arg do
+              arg.each { |a| puts a }
+            end
+            next
+          rescue
+            line = arg.to_s
+          end
+        end
+
+        write(line)
+        write(DEFAULT_RECORD_SEPARATOR) # unless line[-1] == ?\n
+      end
+    end
+
+    nil
+  end
+
+end
+
+
 #----------------------------------------------------------------------------------------
 # Class RubyChunk is used only as a context for all ruby chunks in the rmarkdown file.
 # This allows for chunks to access instance_variables (@)
@@ -30,6 +76,18 @@ require 'stringio'
 
 class RubyChunk
 
+  def self.init
+    @@outputs = R.list
+  end
+  
+  def self.get_outputs
+    @@outputs
+  end
+  
+  def self.outputs(obj)
+    @@outputs = R.c(@@outputs, obj)
+  end
+  
 end
 
 #----------------------------------------------------------------------------------------
@@ -53,39 +111,92 @@ module GalaazUtil
   # options[["eval"]], this is because eval is a Ruby function and doing options.eval
   # will call the eval method on options, which is not what we want
   #----------------------------------------------------------------------------------------
-  
+
   def self.exec_ruby(options)
 
+    RubyChunk.init
+    
     # read the chunk code
-    code = R.paste(options.code, collapse: "\n") << 0
+    code = R.paste(options.code, collapse: "\n") >> 0
+
+    # the output should be a list with the proper structure to pass to
+    # function engine_output.  We first add the souce code from the block to
+    # the list
+    out_list = R.list(R.structure(R.list(src: code), class: 'source')) if
+      options.echo >> 0
 
-    out_list = R.list
-    out_list["source"] = code if (options.echo << 0)
-    
     begin
-      # Set up standard output as a StringIO object.
+
+      # set $stdout to a new StringIO object so that everything that is
+      # output from instance_eval is captured and can be sent to the
+      # report
       $stdout = StringIO.new
-      RubyChunk.instance_eval(code) if (options[["eval"]] << 0)
+
+      # Execute the Ruby code in the scope of class RubyChunk. This is done
+      # so that instance variables created in one chunk can be used again on
+      # another chunk
+      RubyChunk.instance_eval(code) if (options[["eval"]] >> 0)
+      
+      # add the returned value to the list
+      # this should have captured everything in the evaluation code
+      # it is not working since at least RC10.
       out = $stdout.string
-      # KnitrEngine.capture_plot
       
+      out_list = R.c(out_list, out)
+      
+    rescue StandardError => e
+
+      # print the error message
+      if (options.message >> 0)
+        message = R.list(R.structure(R.list(message: e.message), class: 'message'))
+        out_list = R.c(out_list, message)
+      end
+
+      # Print the backtrace of the error message
+      if (options.warning >> 0)
+        bt = ""
+        e.backtrace.each { |line| bt << line + "\n"}
+        warning = R.list(R.structure(R.list(message: bt), class: 'message'))
+        out_list = R.c(out_list, warning)
+      end
+
+    rescue SyntaxError => e
+      STDERR.puts "A syntax error occured in ruby block '#{options.label >> 0}'"
+      raise SyntaxError.new(e)
+      
+    ensure
       # return $stdout to standard output
       $stdout = STDOUT
-      # return everything that was outputed
-      out_list["text"] = out
-    rescue StandardError => e
-      out_list["message"] = e.message if (options.message << 0)
-      out_list["warning"] = e.backtrace.inspect if (options.warning << 0)
     end
-
-    # TODO: check the name of procedures since communication is
-    # bidirectional.  The name parse_arg was done thinking only on
-    # the Ruby -> R direction.
-    # exec_ruby returns its output to an R script, so we need to pass
-    # the output (out_list) through parse_arg to make it available
-    # to R.
-    (options.include << 0)? R::Support.parse_arg(out_list) : nil
+    
+    (options.include >> 0)? out_list : R.list
     
   end
+  
+  #----------------------------------------------------------------------------------------
+  # Used by old gknit.  Will eventually be replaced by exe_ruby
+  #----------------------------------------------------------------------------------------
+
+  def self.exec_ruby_tor(code)
+
+    # the output should be a list with the proper structure to pass to
+    # function engine_output.
+    out_list = R.list(R.structure(R.list(src: code), class: 'source'))
+    
+    # Set up standard output as a StringIO object.
+    $stdout = StringIO.new
+    RubyChunk.instance_eval(code)
+
+    # this should have captured everything in the evaluation code
+    # it is not working since at least RC10.
+    out = $stdout.string
+
+    out_list = R.c(out_list, out)
+    
+    # return $stdout to standard output
+    $stdout = STDOUT
+    R::Support.parse_arg(out_list)
 
+  end
+  
 end

data/lib/util/inline_file.rb

@@ -38,8 +38,8 @@ module GalaazUtil
 
     filename << ".rb" if File.extname(filename) == ""
     file = "#{pwd}/#{filename}"
-    
-    if (relative == 'require ')
+
+    if (relative == false)
       $LOAD_PATH.each do |path|
         begin
           files = Dir.entries(path)
@@ -47,13 +47,13 @@ module GalaazUtil
           next
         end
 
-        if files != nil && files.include?("bigdecimal.rb")
+        if files != nil
           file = "#{path}/#{filename}"
-          break
+          break if File.exist?(file)
         end
       end
     end
-
+    
     if File.exist?(file)
       code = ""
       File.open(file, "r") do |fileObj|
@@ -61,10 +61,12 @@ module GalaazUtil
           code << line
         end
       end
-      code
+      
     else
-      raise Errno::ENOENT, "file #{filename} not found"
+      raise Errno::ENOENT, "file #{filename} not found in #{$LOAD_PATH}"
     end
+    
+    code
   end
   
 end

data/specs/all.rb

@@ -49,7 +49,12 @@ require_relative 'r_matrix.spec'
 # Specification for R::Dataframes
 require_relative 'r_dataframe.spec'
 
+# Specification for language features
+require_relative 'r_function.spec'
 require_relative 'r_formula.spec'
 
+# Test file generation
+require_relative 'r_devices.spec'
+
 # Testes for NSE
 # require_relative 'r_nse.spec'

data/specs/figures/bg.svg

@@ -0,0 +1,57 @@
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data/specs/figures/no_args.svg

@@ -0,0 +1,57 @@
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