encapsulator 0.1.0 → 0.1.1

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -4,47 +4,51 @@
 
 ## Installation
 
+```
+gem install encapsulator
+```
+
+## Building from source
+
 ### Fedora 25
 
 ```
-sudo dnf install ruby
-gem install json rgl rake bundler
-git clone https://github.com/tfjmp/encapsulator.git
-cd encapsulator
-rake install
-encapsulator --install fedora
-encapsulator -h
+$ sudo dnf install ruby
+$ gem install encapsulator
+$ encapsulator --install fedora
+$ encapsulator -h
 ```
 
 ### Ubuntu
 
 ```
-sudo apt install ruby
-gem install json rgl rake bundler
-git clone https://github.com/tfjmp/encapsulator.git
-cd encapsulator
-rake install
-encapsulator --install ubuntu
-encapsulator -h
+$ sudo apt install ruby
+$ gem install encapsulator
+$ encapsulator --install ubuntu
+$ encapsulator -h
 ```
 
 ### MacOS
 
 ```
-brew install ruby
-gem install json rgl rake bundler
-git clone https://github.com/tfjmp/encapsulator.git
-cd encapsulator
-rake install
-encapsulator --install mac
-encapsulator -h
+$ brew install ruby
+$ gem install encapsulator
+$ encapsulator --install mac
+$ encapsulator -h
 ```
 
 ## USAGE
 
 ```
-# extract info from ddg.json
-encapsulator --info <your_RDT_prov.json>
-# select an output node to generate the code to be generate
-encapsulator --code <your_RDT_prov.json> <output_node_name> <new R script>
+# see
+$ encapsulator -h
+--version display encapsulator version
+--info <path to R script> display information about the R script
+--jpg [--all] <path to R script> output graph as jpg
+--png [--all] <path to R script> output graph as png
+--svg [--all] <path to R script> output graph as svg
+--code <path to R script> <output> [output] ... [output] create the source necessary to generate the specified output
+--run <path to R script> run the provided r script
+--encapsulate <user>/<project> <script> <output> [output] ... [output] create the specified capsule
+--decapsulate <user>/<project> download the coresponding capsule
 ```

data/bin/encapsulator

@@ -2,7 +2,9 @@
 
 require "encapsulator"
 
-if ARGV[0] == '--info'
+if ARGV[0] == '-v' || ARGV[0] == '--version'
+	puts Encapsulator::VERSION
+elsif ARGV[0] == '--info'
 	Encapsulator::CLI::info ARGV[1]
 elsif ARGV[0] == '--encapsulate'
 	system 'rm', '-rf', '.'+ARGV[1]
@@ -21,11 +23,23 @@ elsif ARGV[0] == '--encapsulate'
 elsif ARGV[0] == '--decapsulate'
   decapsulate ARGV[1]
 elsif ARGV[0] == '--jpg'
-  Encapsulator::CLI::get_jpg ARGV[1]
+	if ARGV[1] == '--all'
+		Encapsulator::CLI::get_jpg ARGV[2], true
+	else
+		Encapsulator::CLI::get_jpg ARGV[1]
+	end
 elsif ARGV[0] == '--png'
-  Encapsulator::CLI::get_png ARGV[1]
+	if ARGV[1] == '--all'
+		Encapsulator::CLI::get_png ARGV[2], true
+	else
+		Encapsulator::CLI::get_png ARGV[1]
+	end
 elsif ARGV[0] == '--svg'
-  Encapsulator::CLI::get_svg ARGV[1]
+	if ARGV[1] == '--all'
+		Encapsulator::CLI::get_svg ARGV[2], true
+	else
+		Encapsulator::CLI::get_svg ARGV[1]
+	end
 elsif ARGV[0] == '--code'
 	out_path = '.encapsulator'
 	system 'rm', '-rf', out_path

data/lib/encapsulator/cli.rb

@@ -2,10 +2,11 @@ module Encapsulator
   module CLI
     def CLI.usage
       puts "USAGE\n\n"
+      puts '--version display encapsulator version'
       puts '--info <path to R script> display information about the provenance graph'
-      puts '--jpg <path to R script> output graph as jpg'
-      puts '--png <path to R script> output graph as png'
-      puts '--svg <path to R script> output graph as svg'
+      puts '--jpg [--all] <path to R script> output graph as jpg'
+      puts '--png [--all] <path to R script> output graph as png'
+      puts '--svg [--all] <path to R script> output graph as svg'
       puts '--code <path to R script> <output> [output] ... [output] create the source necessary to generate the specified output'
       puts '--run <path to R script> run the provided r script'
     	puts '--encapsulate <user>/<project> <script> <output> [output] ... [output] create the specified capsule'
@@ -17,7 +18,7 @@ module Encapsulator
       provision << '# -*- mode: ruby -*-'
       provision << '# vi: set ft=ruby :'
       provision << 'Vagrant.configure(2) do |config|'
-      provision << "  "+'config.vm.box = "jhcook/fedora25"'
+      provision << "  "+'config.vm.box = "jhcook/fedora27"'
       provision << "  "+'config.vm.provider "virtualbox" do |vb|'
       provision << "  "+'vb.gui = true'
       provision << "  "+'vb.memory = 2048'
@@ -31,6 +32,7 @@ module Encapsulator
       provision << "  "+'sudo dnf -y -v install libcurl libcurl-devel'
       provision << "  "+'sudo dnf -y -v install perl-CPAN'
       provision << "  "+'sudo dnf -y -v install ruby'
+      provision << "  "+'sudo dnf -y -v install R'
       provision << "  "+'wget https://atom.io/download/rpm'
       provision << "  "+'mv ./rpm ./atom.rpm'
       provision << "  "+'sudo dnf -y -v install ./atom.rpm'
@@ -57,7 +59,7 @@ module Encapsulator
     			end
     			puts 'Provision script is ready...'
     			puts 'getting your capsule ready, be patient...'
-    			system("vagrant", "up", out: $stdout, err: $stdout)
+    			system("vagrant", "up", "--provider", "virtualbox", out: $stdout, err: $stdout)
     			system("vagrant", "halt", out: $stdout, err: $stdout)
     		end
     		puts 'Your capsule should be visible in the virtualbox interface.'
@@ -68,7 +70,7 @@ module Encapsulator
     	puts "looking for the capsule #{vm}..."
     	system("vagrant", "init", capsule_name, out: $stdout, err: $stdout)
     	puts 'getting your capsule ready, be patient...'
-    	system("vagrant", "up", out: $stdout, err: $stdout)
+    	system("vagrant", "up", "--provider", "virtualbox", out: $stdout, err: $stdout)
     	system("vagrant", "halt", out: $stdout, err: $stdout)
     	puts 'you should find your capsule in the virtualbox GUI.'
     end
@@ -88,21 +90,21 @@ module Encapsulator
     	end
     end
 
-    def CLI.get_jpg script
+    def CLI.get_jpg script, all=false
       ProvR.run_script script do
-    		Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json').jpg
+    		Encapsulator::RJSONParser.new('../'+script, all).read_json_file('ddg.json').jpg
     	end
     end
 
-    def CLI.get_png script
+    def CLI.get_png script, all=false
       ProvR.run_script script do
-    		Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json').png
+    		Encapsulator::RJSONParser.new('../'+script, all).read_json_file('ddg.json').png
     	end
     end
 
-    def CLI.get_svg script
+    def CLI.get_svg script, all=false
       ProvR.run_script script do
-    		Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json').svg
+    		Encapsulator::RJSONParser.new('../'+script, all).read_json_file('ddg.json').svg
     	end
     end
 

data/lib/encapsulator/installer.rb

@@ -4,6 +4,11 @@ module Encapsulator
       system 'wget', 'http://download.virtualbox.org/virtualbox/5.1.22/VirtualBox-5.1-5.1.22_115126_fedora25-1.x86_64.rpm', out: $stdout, err: $stdout
       system 'sudo', 'dnf', '-y', '-v', 'install', './VirtualBox-5.1-5.1.22_115126_fedora25-1.x86_64.rpm', out: $stdout, err: $stdout
       system 'sudo', 'dnf', '-y', '-v', 'install', 'vagrant', out: $stdout, err: $stdout
+      system 'sudo', 'dnf', '-y', '-v', 'install', 'openssl-devel', out: $stdout, err: $stdout
+      system 'sudo', 'dnf', '-y', '-v', 'install', 'libcurl-devel', out: $stdout, err: $stdout
+      system 'sudo', 'dnf', '-y', '-v', 'install', 'libxml-devel', out: $stdout, err: $stdout
+      system 'sudo', 'dnf', '-y', '-v', 'install', 'libxml2-devel', out: $stdout, err: $stdout
+      system 'sudo', 'dnf', '-y', '-v', 'install', 'R', out: $stdout, err: $stdout
     end
 
     def self.install_ubuntu

data/lib/encapsulator/provr.rb

@@ -1,19 +1,27 @@
+require 'fileutils'
+
 module Encapsulator
   module ProvR
     def ProvR.run script
-    	require 'rinruby'
+      FileUtils.mkdir_p './prov'
+      require 'rinruby'
       r = RinRuby.new(echo: false)
+      r.eval "chooseCRANmirror(ind=81)"
       r.eval "install.packages('devtools')"
-    	r.eval "require('devtools')"
-    	r.eval "install_github('provtools/provR', ref='dev')"
-    	r.eval "require('provR')"
-      r.eval "prov.capture('#{script}', save=TRUE)"
+      r.eval "require('devtools')"
+      r.eval "install_github('provtools/provR', ref='dev')"
+      r.eval "require('provR')"
+      r.eval "prov.capture('#{script}')"
+      r.eval "f <- file('./prov/ddg.json')"
+      r.eval "writeLines(prov.json(), f)"
+      r.eval "close(f)"
     end
 
     def ProvR.tidy script
       require 'rinruby'
       r = RinRuby.new(echo: false)
-    	r.eval "install.packages('formatR', repos = 'http://cran.rstudio.com')"
+      r.eval "chooseCRANmirror(ind=81)"
+      r.eval "install.packages('formatR', repos = 'http://cran.rstudio.com')"
       r.eval "require('formatR')"
       r.eval "tidy_file('#{script}')"
     end
@@ -24,7 +32,7 @@ module Encapsulator
     		run script
     		$ran_script = true
     	end
-    	prov_folder = script.gsub('.R', '_ddg')
+    	prov_folder = './prov'
     	Dir.chdir prov_folder do
     		yield
     	end

data/lib/encapsulator/rjson_parser.rb

@@ -14,8 +14,9 @@ module Encapsulator
     attr_reader :libraries
     attr_reader :packages
     attr_reader :file
+    attr_reader :informed
 
-    def initialize r_file
+    def initialize r_file, informed=false
       @dg = RGL::DirectedAdjacencyGraph.new # initialise the graph structure
       @map = Hash.new(0)
       @files = Hash.new
@@ -24,6 +25,7 @@ module Encapsulator
       @libraries = Hash.new
       @packages = Hash.new
       @script = IO.readlines(r_file)
+      @informed = informed
     end
 
     def get_operation start_line, end_line
@@ -53,7 +55,7 @@ module Encapsulator
     end
 
     def wasInformedBy k, v
-      #@dg.add_edge v['prov:informed'], v['prov:informant']
+      @dg.add_edge v['prov:informed'], v['prov:informant'] unless !informed
     end
 
     def wasAssociatedWith k, v
@@ -110,15 +112,21 @@ module Encapsulator
     end
 
     def svg
-      @dg.write_to_graphic_file('svg')
+      Dir.chdir('..') do
+        @dg.write_to_graphic_file('svg')
+      end
     end
 
     def jpg
-      @dg.write_to_graphic_file('jpg')
+      Dir.chdir('..') do
+        @dg.write_to_graphic_file('jpg')
+      end
     end
 
     def png
-      @dg.write_to_graphic_file('png')
+      Dir.chdir('..') do
+        @dg.write_to_graphic_file('png')
+      end
     end
 
 		def get_list file

data/lib/encapsulator/version.rb

@@ -1,3 +1,3 @@
 module Encapsulator
-  VERSION = "0.1.0"
+  VERSION = "0.1.1"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: encapsulator
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.1.1
 platform: ruby
 authors:
 - Thomas Pasquier
@@ -10,7 +10,7 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-09-15 00:00:00.000000000 Z
+date: 2018-03-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rgl
@@ -121,7 +121,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.6.11
+rubygems_version: 2.6.14
 signing_key: 
 specification_version: 4
 summary: encapsulator for R.