scicom 0.2.3.1-java → 0.3.0-java

data/doc/hearder.tex

@@ -0,0 +1,87 @@
+% !TEX TS-program = pdflatex
+% !TEX encoding = UTF-8 Unicode
+
+% This is a simple template for a LaTeX document using the "article" class.
+% See "book", "report", "letter" for other types of document.
+
+\documentclass[11pt]{report} % use larger type; default would be 10pt
+
+\usepackage[utf8]{inputenc} % set input encoding (not needed with XeLaTeX)
+
+%%% Examples of Article customizations
+% These packages are optional, depending whether you want the features they provide.
+% See the LaTeX Companion or other references for full information.
+
+%%% PAGE DIMENSIONS
+\usepackage{geometry} % to change the page dimensions
+\geometry{a4paper} % or letterpaper (US) or a5paper or....
+% \geometry{margin=2in} % for example, change the margins to 2 inches all round
+% \geometry{landscape} % set up the page for landscape
+%   read geometry.pdf for detailed page layout information
+
+\usepackage{graphicx} % support the \includegraphics command and options
+
+% \usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
+
+%%% PACKAGES
+\usepackage{booktabs} % for much better looking tables
+\usepackage{array} % for better arrays (eg matrices) in maths
+\usepackage{paralist} % very flexible & customisable lists (eg. enumerate/itemize, etc.)
+\usepackage{verbatim} % adds environment for commenting out blocks of text & for better verbatim
+\usepackage{subfig} % make it possible to include more than one captioned figure/table in a single float
+% These packages are all incorporated in the memoir class to one degree or another...
+
+\usepackage{color}
+\usepackage{xcolor}
+\usepackage{listings}
+
+\usepackage{caption}
+\DeclareCaptionFont{white}{\color{white}}
+\DeclareCaptionFormat{listing}{\colorbox{gray}{\parbox{\textwidth}{#1#2#3}}}
+\captionsetup[lstlisting]{format=listing,labelfont=white,textfont=white}
+
+\lstset{
+language=Ruby,
+basicstyle=\small\sffamily,
+numbers=left,
+numberstyle=\tiny,
+frame=tb,
+columns=fullflexible,
+showstringspaces=false
+}
+
+%%% HEADERS & FOOTERS
+\usepackage{fancyhdr} % This should be set AFTER setting up the page geometry
+\pagestyle{fancy} % options: empty , plain , fancy
+\renewcommand{\headrulewidth}{0pt} % customise the layout...
+\lhead{}\chead{}\rhead{}
+\lfoot{}\cfoot{\thepage}\rfoot{}
+
+%%% SECTION TITLE APPEARANCE
+\usepackage{sectsty}
+\allsectionsfont{\sffamily\mdseries\upshape} % (See the fntguide.pdf for font help)
+% (This matches ConTeXt defaults)
+
+%%% ToC (table of contents) APPEARANCE
+\usepackage[nottoc,notlof,notlot]{tocbibind} % Put the bibliography in the ToC
+\usepackage[titles,subfigure]{tocloft} % Alter the style of the Table of Contents
+\renewcommand{\cftsecfont}{\rmfamily\mdseries\upshape}
+\renewcommand{\cftsecpagefont}{\rmfamily\mdseries\upshape} % No bold!
+
+\newcommand{\del}[1]{}
+
+%%% END Article customizations
+
+%%% The "real" document content comes below...
+
+\title{SciCom Manual}
+\author{Rodrigo Botafogo}
+%\date{} % Activate to display a given date or no date (if empty),
+         % otherwise the current date is printed 
+         
+\begin{document}
+\maketitle
+
+\input{SciCom.tex}
+
+\end{document}

data/doc/hearder.tex~

@@ -0,0 +1,78 @@
+% !TEX TS-program = pdflatex
+% !TEX encoding = UTF-8 Unicode
+
+% This is a simple template for a LaTeX document using the "article" class.
+% See "book", "report", "letter" for other types of document.
+
+\documentclass[11pt]{report} % use larger type; default would be 10pt
+
+\usepackage[utf8]{inputenc} % set input encoding (not needed with XeLaTeX)
+
+%%% Examples of Article customizations
+% These packages are optional, depending whether you want the features they provide.
+% See the LaTeX Companion or other references for full information.
+
+%%% PAGE DIMENSIONS
+\usepackage{geometry} % to change the page dimensions
+\geometry{a4paper} % or letterpaper (US) or a5paper or....
+% \geometry{margin=2in} % for example, change the margins to 2 inches all round
+% \geometry{landscape} % set up the page for landscape
+%   read geometry.pdf for detailed page layout information
+
+\usepackage{graphicx} % support the \includegraphics command and options
+
+% \usepackage[parfill]{parskip} % Activate to begin paragraphs with an empty line rather than an indent
+
+%%% PACKAGES
+\usepackage{booktabs} % for much better looking tables
+\usepackage{array} % for better arrays (eg matrices) in maths
+\usepackage{paralist} % very flexible & customisable lists (eg. enumerate/itemize, etc.)
+\usepackage{verbatim} % adds environment for commenting out blocks of text & for better verbatim
+\usepackage{subfig} % make it possible to include more than one captioned figure/table in a single float
+% These packages are all incorporated in the memoir class to one degree or another...
+
+\usepackage{color}
+\usepackage{xcolor}
+\usepackage{listings}
+
+\usepackage{caption}
+\DeclareCaptionFont{white}{\color{white}}
+\DeclareCaptionFormat{listing}{\colorbox{gray}{\parbox{\textwidth}{#1#2#3}}}
+\captionsetup[lstlisting]{format=listing,labelfont=white,textfont=white}
+
+\lstset{
+language=Ruby,
+basicstyle=\small\sffamily,
+numbers=left,
+numberstyle=\tiny,
+frame=tb,
+columns=fullflexible,
+showstringspaces=false
+}
+
+%%% HEADERS & FOOTERS
+\usepackage{fancyhdr} % This should be set AFTER setting up the page geometry
+\pagestyle{fancy} % options: empty , plain , fancy
+\renewcommand{\headrulewidth}{0pt} % customise the layout...
+\lhead{}\chead{}\rhead{}
+\lfoot{}\cfoot{\thepage}\rfoot{}
+
+%%% SECTION TITLE APPEARANCE
+\usepackage{sectsty}
+\allsectionsfont{\sffamily\mdseries\upshape} % (See the fntguide.pdf for font help)
+% (This matches ConTeXt defaults)
+
+%%% ToC (table of contents) APPEARANCE
+\usepackage[nottoc,notlof,notlot]{tocbibind} % Put the bibliography in the ToC
+\usepackage[titles,subfigure]{tocloft} % Alter the style of the Table of Contents
+\renewcommand{\cftsecfont}{\rmfamily\mdseries\upshape}
+\renewcommand{\cftsecpagefont}{\rmfamily\mdseries\upshape} % No bold!
+
+%%% END Article customizations
+
+%%% The "real" document content comes below...
+
+\title{Brief Article}
+\author{The Author}
+%\date{} % Activate to display a given date or no date (if empty),
+         % otherwise the current date is printed 

data/lib/JRubyR/download_url_to_file.rb

@@ -0,0 +1,132 @@
+#!/usr/bin/env ruby
+#
+# Ruby script to download a number of files
+# from individual URLs via HTTP/HTTPS/FTP
+# specified in an external file.
+#
+# Author: Tobias Preuss
+# Revision: 2013-04-18 16:26 +0100 UTC
+# License: Creative Commons Attribution-ShareAlike 3.0 Unported
+ 
+require 'net/http'
+require 'net/ftp'
+require 'uri'
+require 'date'
+ 
+ 
+def create_directory(dirname)
+  unless Dir.exists?(dirname)
+    Dir.mkdir(dirname)
+  else
+    puts "Skipping creating directory " + dirname + ". It already exists."
+  end
+end
+ 
+def read_uris_from_file(file)
+  uris = Array.new
+  File.open(file).each do |line|
+    line = line.strip
+    next if line == nil || line.length == 0
+    parts = line.split(' ')
+    pair = Hash[ [:resource, :filename].zip(parts) ]
+    uris.push(pair)
+  end
+  uris
+end
+ 
+def download_resource(resource, filename)
+  uri = URI.parse(resource)
+  case uri.scheme.downcase
+  when /http|https/
+    http_download_uri(uri, filename)
+  when /ftp/
+    ftp_download_uri(uri, filename)
+  else
+    puts "Unsupported URI scheme for resource " + resource + "."
+  end
+end
+ 
+def http_download_uri(uri, filename)
+  puts "Starting HTTP download for: " + uri.to_s
+  http_object = Net::HTTP.new(uri.host, uri.port)
+  http_object.use_ssl = true if uri.scheme == 'https'
+  begin
+    http_object.start do |http|
+      request = Net::HTTP::Get.new uri.request_uri
+      http.read_timeout = 500
+      http.request request do |response|
+        open filename, 'w' do |io|
+          response.read_body do |chunk|
+            io.write chunk
+          end
+        end
+      end
+    end
+  rescue Exception => e
+    puts "=> Exception: '#{e}'. Skipping download."
+    return
+  end
+  puts "Stored download as " + filename + "."
+end
+ 
+def ftp_download_uri(uri, filename)
+  puts "Starting FTP download for: " + uri.to_s + "."
+  dirname = File.dirname(uri.path)
+  basename = File.basename(uri.path)
+  begin
+    Net::FTP.open(uri.host) do |ftp|
+      ftp.login
+      ftp.chdir(dirname)
+      ftp.getbinaryfile(basename)
+    end
+  rescue Exception => e
+    puts "=> Exception: '#{e}'. Skipping download."
+    return
+  end
+  puts "Stored download as " + filename + "."
+end
+ 
+def download_resources(pairs)
+  pairs.each do |pair|
+    filename = pair[:filename].to_s
+    resource = pair[:resource].to_s
+    unless File.exists?(filename)
+      download_resource(resource, filename)
+    else
+      puts "Skipping download for " + filename + ". It already exists."
+    end
+  end
+end
+ 
+ 
+def main
+  sources_file = ARGV.first
+  uris = read_uris_from_file(sources_file)
+ 
+  target_dir_name = Date.today.strftime('%y%m%d')
+  create_directory(target_dir_name)
+  Dir.chdir(target_dir_name)
+  puts "Changed directory: " + Dir.pwd
+ 
+  download_resources(uris)
+end
+ 
+ 
+if __FILE__ == $0
+  usage = <<-EOU
+
+usage: ruby #{File.basename($0)} sources.txt
+
+  The file sources.txt should contain an URL and the target file name.
+  The expected file format is:
+
+  http://www.domain.com/file target_file_name
+  ftp://www.domain.com/file target_file_name
+
+  EOU
+ 
+  abort usage if ARGV.length != 1
+ 
+  main
+ 
+end

data/lib/JRubyR/package.rb

@@ -0,0 +1,286 @@
+# -*- coding: utf-8 -*-
+
+##########################################################################################
+# @author Rodrigo Botafogo
+#
+# Copyright © 2013 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.
+##########################################################################################
+
+require 'net/http'
+require 'state_machine'
+require 'rexml/document'
+require 'observer'
+
+##########################################################################################
+#
+##########################################################################################
+
+module MergeObservable
+  include Observable
+
+  alias_method :old_notify, :notify_observers
+
+  def add_new_observer(observer)
+    @new_observers ||= Array.new
+    @new_observers << observer
+  end
+
+  def merge_observers
+    @new_observers ||= Array.new
+    @new_observers.each do |obs|
+      self.add_observer(obs)
+    end
+    @new_observers = nil 
+  end
+
+  def notify_observers(*args)
+    merge_observers
+    old_notify(*args)
+  end
+
+end
+
+##########################################################################################
+#
+##########################################################################################
+
+class PackageManager
+
+  ##########################################################################################
+  # Class to parse the maven-metadata.xml file for package management
+  ##########################################################################################
+  
+  class ParseXML
+    include MergeObservable
+    
+    #----------------------------------------------------------------------------------------
+    # Parse the input_file and send parsed events to the given state machine.  Results should
+    # be stored in the output_dir
+    #----------------------------------------------------------------------------------------
+    
+    def initialize(source)
+      @source = source
+    end
+    
+    #----------------------------------------------------------------------------------------
+    # start parsing the file.  This class will receive the events and redirect them to 
+    # listeners
+    #----------------------------------------------------------------------------------------
+    
+    def start
+      REXML::Document.parse_stream(@source, self)
+    end
+    
+    #----------------------------------------------------------------------------------------
+    # This method is necessary do ignore parsing events that are of no interest to our
+    # parsing.
+    #----------------------------------------------------------------------------------------
+    
+    def method_missing(*args)
+      # p args
+    end
+    
+    #----------------------------------------------------------------------------------------
+    # Called when receiving a tag_start event
+    #----------------------------------------------------------------------------------------
+    
+    def tag_start(name, attrs)
+      changed
+      notify_observers(:tag_start, name, attrs)
+    end
+    
+    #----------------------------------------------------------------------------------------
+    # Called when receiving a tag_end event
+    #----------------------------------------------------------------------------------------
+    
+    def tag_end(name)
+      changed
+      notify_observers(:tag_end, name, nil)
+    end
+    
+    #----------------------------------------------------------------------------------------
+    #
+    #----------------------------------------------------------------------------------------
+    
+    def text(text)
+      changed
+      notify_observers(:new_text, text, nil)
+    end
+    
+  end
+
+  ##########################################################################################
+  #
+  ##########################################################################################
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def initialize
+    @properties = Hash.new
+    super
+  end
+  
+  #----------------------------------------------------------------------------------------
+  # Machine starts in the metadata state.
+  #----------------------------------------------------------------------------------------
+
+  state_machine :state, initial: :metadata do
+
+    event :read_value do
+      transition :metadata => :reading
+    end
+
+    event :value_read do
+      transition :reading => :metadata
+    end
+
+    before_transition :on => :value_read, :do => :set_value
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+  
+  def set_value
+    @properties[@name] = @text
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+  
+  def tag_start(name, value)
+    @name = name
+    read_value
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def tag_end(name)
+    value_read
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def new_text(text)
+    @text = text
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def update(type, name, attrs)
+    
+    case type
+    when :tag_start
+      tag_start(name, attrs)
+    when :tag_end
+      tag_end(name)
+    when :new_text
+      new_text(name)
+    else
+      raise "Unknown type #{type}"
+    end
+
+  end
+
+  #----------------------------------------------------------------------------------------
+  #
+  #----------------------------------------------------------------------------------------
+
+  def http_download_uri(uri, filename)
+    puts "Starting HTTP download for: " + uri.to_s
+    http_object = Net::HTTP.new(uri.host, uri.port)
+    http_object.use_ssl = true if uri.scheme == 'https'
+    begin
+      http_object.start do |http|
+        request = Net::HTTP::Get.new uri.request_uri
+        http.read_timeout = 500
+        http.request request do |response|
+          open filename, 'wb' do |io|
+            response.read_body do |chunk|
+              io.write chunk
+            end
+          end
+        end
+      end
+    rescue Exception => e
+      puts "=> Exception: '#{e}'. Skipping download."
+      return
+    end
+    puts "Stored download as " + filename + "."
+  end
+  
+  #----------------------------------------------------------------------------------------
+  # Installs a new package
+  #----------------------------------------------------------------------------------------
+
+  def load_package(name)
+
+    # create the cran_dir if it does not already exists
+    Dir.mkdir(SciCom.cran_dir) if !Dir.exists?(SciCom.cran_dir)
+
+    # download address for Renjin packages
+    renjin_cran = 'http://nexus.bedatadriven.com/content/groups/public/org/renjin/cran/'
+
+    package = renjin_cran + name
+    spec = package + "/" + "maven-metadata.xml"
+    # read the maven-metadata specification
+    uri = URI(spec)
+
+    # parse the maven-metadata file
+    parse = ParseXML.new(Net::HTTP.get(uri))
+    parse.add_observer(self)
+    parse.start
+
+    download_dir = package + '/' + @properties['latest']
+    spec2 = download_dir + '/' + "maven-metadata.xml"
+
+    # parse the second maven-metadata file
+    uri = URI(spec2)
+    # download the spec file, so we know what version is actually installed
+    http_download_uri(uri, SciCom.cran_dir + "/#{name}.xml")
+
+    # need to clear the properties.  If the file has multiple properties with the same
+    # name, then only the last one will be kept.  This might be a problem, but for 
+    # now this does not seem to matter... We are only interested in the 'value'
+    # property that seems to always be the same for the 'pom' and 'jar' files.
+    @properties.clear
+    parse = ParseXML.new(Net::HTTP.get(uri))
+    parse.add_observer(self)
+    parse.start
+    
+    filename = '/' + name + '-' + @properties['value'] + ".jar"
+
+    download_file = download_dir + filename
+    target_file = SciCom.cran_dir + '/' + name + ".jar"
+
+    uri = URI.parse(download_file)
+    http_download_uri(uri, target_file)
+
+  end
+
+end