Module: GalaazUtil

Defined in:
lib/util/exec_ruby.rb,
lib/util/inline_file.rb

Overview

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.

Author:

  • Rodrigo Botafogo

Class Method Summary collapse

Class Method Details

.exec_ruby(options) ⇒ R::List

Executes the ruby code with the given options. The options are:

  • options.code: the ruby code
  • options[["eval"]]: evaluate if true
  • options.echo: if true, show the source code of the chunk in the output
  • options.message: if true, show error message if any exception in the ruby code
  • options.warning: if true, show stack trace from the ruby code
  • options.include: if true, include the code output Note that we need to access the 'eval' element of the list by indexing as 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

Parameters:

  • options (R::List) —

    An R list of options

Returns:

  • (R::List) —

    an R list with everything that needs to be outputed.



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# File 'lib/util/exec_ruby.rb', line 130

def self.exec_ruby(options)

  # RubyChunk.init

  # Read chunk code via a temp file (avoids result-protocol limits on long strings). Use Dir.tmpdir
  # so gknit works without /dev/shm (macOS, sandboxes, minimal containers).
  chunk_code_file = File.join(Dir.tmpdir, "galaaz_chunk_code_#{Process.pid}_#{Thread.current.object_id}.txt")
  path_lit = ::R::Support.parse_arg(chunk_code_file)
  begin
    R.bridge.eval_r("writeLines(paste(#{options.r_interop}[['code']], collapse='\\n'), #{path_lit})")
    code = File.read(chunk_code_file)
  ensure
    File.unlink(chunk_code_file) if chunk_code_file && File.file?(chunk_code_file)
  end
  # If the string arrived with literal \n (e.g. from R→Ruby transport), convert to real newlines so eval does not hit "unexpected backslash"
  code = code.gsub("\\n", "\n") if code.is_a?(String)
  # the output should be a list with the proper structure to pass to
  # function engine_output.  We first add the source code from the block to
  # the list. Pass src as a character vector of lines (not one string with \n)
  # so knitr preserves line breaks and indentation in the rendered chunk.
  if knitr_option_trueish?(options, 'echo', default: true)
    src_lines = code.lines.map(&:chomp)
    src_lines = [" "] if src_lines.empty?
    out_list = R.list(R.structure(R.list(src: R.c(*src_lines)), class: 'source'))
  else
    out_list = R.list
  end

  begin

    # 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

    # 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
    # RChunk.instance_eval(code) if (options[["eval"]].unboxed_get(0))
    eval(code, RCbinding, __FILE__, __LINE__ + 1) if knitr_option_trueish?(options, 'eval', default: true)
    
    # 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
    
    out_list = R.c(out_list, out)
    
  rescue StandardError => e
    begin
      label = options['label'].unboxed_get(0).to_s
      GknitDiagnostics.record(chunk_label: label, error: e) if defined?(GknitDiagnostics)
    rescue StandardError
      nil
    end

    # Use R's simpleMessage/simpleWarning so knitr's engine_output can call conditionMessage() on them
    # g_simpleMessage transforms "; " to newlines then calls simpleMessage (defined in R engine setup)
    if knitr_option_trueish?(options, 'message', default: true)
      msg_cond = R.g_simpleMessage(e.message.to_s)
      out_list = R.c(out_list, msg_cond)
    end

    if knitr_option_trueish?(options, 'warning', default: true)
      bt = ""
      e.backtrace.each { |line| bt << line + "\n"}
      warn_cond = R.g_simpleWarning(bt)
      out_list = R.c(out_list, warn_cond)
    end

  rescue SyntaxError => e
    STDERR.puts "A syntax error occured in ruby block '#{options['label'].unboxed_get(0)}'"
    raise SyntaxError.new(e)
    
  ensure
    # return $stdout to standard output
    $stdout = STDOUT
  end
  
  # include=FALSE must still execute code (knitr semantics). Output suppression is handled
  # at engine emission stage, not here.
  out_list
  
end

.inline_file(filename, relative, pwd = Dir.pwd) ⇒ Object

========================================================================================

Opens the given filename for reading and returns the file content so that it can be printed as a code chunk in rmarkdown

Parameters:

  • filename (String) —

    the name of the file to be found. If the file has no extension then '.rb' is assumed

  • relative (String) —

    containing either 'require_relative ' or 'require '. In the first case looks on the current directory, on the latter, searches the $LOAD_PATH

  • pwd (String) (defaults to: Dir.pwd) —

    Directory to look at when 'require_relative ', by default, its the pwd directory



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# File 'lib/util/inline_file.rb', line 70

def self.inline_file(filename, relative, pwd = Dir.pwd)
  file = inline_file_path(filename, relative, pwd)
  code = ""
  File.open(file, "r") do |fileObj|
    while (line = fileObj.gets)
      code << line
    end
  end
  code
end

.inline_file_path(filename, relative, pwd = Dir.pwd) ⇒ String

========================================================================================

Resolves the path of the file (same logic as inline_file) and returns it. Does not read the file. Use this when the content will be read by R (e.g. readLines) to avoid embedding file content in R code.

Parameters:

  • filename (String) —

    same as inline_file

  • relative (String) —

    same as inline_file

  • pwd (String) (defaults to: Dir.pwd) —

    same as inline_file

Returns:

  • (String) —

    resolved absolute path

Raises:

  • (Errno::ENOENT) 


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# File 'lib/util/inline_file.rb', line 35

def self.inline_file_path(filename, relative, pwd = Dir.pwd)
  f = filename.dup
  f << ".rb" if File.extname(f) == ""
  file = "#{pwd}/#{f}"

  if (relative == false) && !R.file__exists(file).unboxed_get(0)
    $LOAD_PATH.each do |path|
      begin
        files = Dir.entries(path)
      rescue Errno::ENOENT
        next
      end

      if files != nil
        file = "#{path}/#{f}"
        break if (R.file__exists(file).unboxed_get(0))
      end
    end
  end

  raise Errno::ENOENT, "file #{filename} not found in #{$LOAD_PATH}" unless R.file__exists(file).unboxed_get(0)
  file
end

.knitr_logical_trueish?(opt) ⇒ Boolean

Knitr chunk options are often R logical NA ("inherit global default"). Those must not be treated as false (see R::Vector#unboxed_get: NA → nil). Defaults match knitr: eval/echo/include/message/warning TRUE.

Returns:

  • (Boolean) 


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# File 'lib/util/exec_ruby.rb', line 101

def self.knitr_logical_trueish?(opt)
  return true if opt.nil?
  return opt if opt == true || opt == false

  raw = opt.unboxed_get(0) if opt.respond_to?(:unboxed_get)
  return true if raw.nil?
  return raw if raw == true || raw == false
  return raw != 0 if raw.is_a?(Numeric)
  return !raw.to_s.strip.casecmp('FALSE').zero? if raw.respond_to?(:to_s)

  true
end

.knitr_option_trueish?(options, key, default: true) ⇒ Boolean

Read a logical-ish knitr option directly from the options list on the R side. This avoids wrapper-shape differences when values arrive as handles/lists via NewBridge.

Returns:

  • (Boolean) 


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# File 'lib/util/exec_ruby.rb', line 83

def self.knitr_option_trueish?(options, key, default: true)
  return default unless options && options.respond_to?(:r_interop)

  key_esc = key.to_s.gsub("'", "\\\\'")
  txt = R.bridge.eval_r("as.character(#{options.r_interop}[['#{key_esc}']])").to_s
  token = txt.sub(/\A\[\d+\]\s*/, '').gsub('"', '').strip.upcase
  return true if token == 'TRUE'
  return false if token == 'FALSE'
  return default if token == '' || token == 'NA' || token == 'NULL'
  return token.to_f != 0.0 if token.match?(/\A-?(?:\d+(?:\.\d*)?|\.\d+)(?:[eE][+-]?\d+)?\z/)

  default
rescue StandardError
  default
end