Module: Encapsulator::CLI

Defined in:
lib/encapsulator/cli.rb

Class Method Summary collapse

Class Method Details

.decapsulate(capsule_name) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 69

def CLI.decapsulate capsule_name
	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", "--provider", "virtualbox", out: $stdout, err: $stdout)
	system("vagrant", "halt", out: $stdout, err: $stdout)
	puts 'you should find your capsule in the virtualbox GUI.'
end

.encapsulate(capsule_name, script) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 48

def CLI.encapsulate capsule_name, script
	ProvR.run_script script do
		v = Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json')
		system 'mkdir', '-p', '../.'+capsule_name
		Dir.chdir '../.'+capsule_name do
			puts "In directory #{Dir.pwd}..."
			File.open("Vagrantfile", "w+") do |f|
				puts 'Encapsulator will attempt to install the following packages:'
				v.packages_show
				script = CLI.vagrant capsule_name, v.install
	  		f.puts(script)
			end
			puts 'Provision script is ready...'
			puts 'getting your capsule ready, be patient...'
			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.'
	end
end

.get_jpg(script, all = false) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 93

def CLI.get_jpg script, all=false
  ProvR.run_script script do
		Encapsulator::RJSONParser.new('../'+script, all).read_json_file('ddg.json').jpg
	end
end

.get_png(script, all = false) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 99

def CLI.get_png script, all=false
  ProvR.run_script script do
		Encapsulator::RJSONParser.new('../'+script, all).read_json_file('ddg.json').png
	end
end

.get_svg(script, all = false) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 105

def CLI.get_svg script, all=false
  ProvR.run_script script do
		Encapsulator::RJSONParser.new('../'+script, all).read_json_file('ddg.json').svg
	end
end

.info(script) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 111

def CLI.info script
  ProvR.run_script script do
  	Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json').show
	end
end

.script_inputs(script, target_output, destination) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 117

def CLI.script_inputs script, target_output, destination
	inputs = nil
	destination = '../'+destination
	ProvR.run_script script do
		inputs = Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json').script_inputs target_output
		inputs.each do |path, file|
			next unless !file.include? destination
			dest_path = path.gsub '..', destination
			dest = file.gsub '..', destination
			system 'mkdir', '-p', dest_path
			system 'cp', '-f', file, dest
			puts "Saved input #{dest} for script #{target_output}.R"
		end
	end
end

.source_code(script, target_output, destination) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 78

def CLI.source_code script, target_output, destination
	ProvR.run_script script do
		script = Encapsulator::RJSONParser.new('../'+script).read_json_file('ddg.json').script target_output
	end
	if script.nil?
		abort "#{target_output} is not a valid output file."
	else
		File.open(destination, "w+") do |f|
			f.puts(script)
		end
    ProvR.tidy destination
		puts "Script written to #{destination}"
	end
end

.usage ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 3

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 [--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'
	puts '--decapsulate <user>/<project> download the coresponding capsule'
end

.vagrant(vm_name, install_instructions) ⇒ Object 



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# File 'lib/encapsulator/cli.rb', line 16

def CLI.vagrant vm_name, install_instructions
  provision = Array.new
  provision << '# -*- mode: ruby -*-'
  provision << '# vi: set ft=ruby :'
  provision << 'Vagrant.configure(2) do |config|'
  provision << "  "+'config.vm.box = "jhcook/fedora27"'
  provision << "  "+'config.vm.provider "virtualbox" do |vb|'
  provision << "  "+'vb.gui = true'
  provision << "  "+'vb.memory = 2048'
  provision << "  "+'vb.customize ["modifyvm", :id, "--cpuexecutioncap", "70"]'
  provision << "  "+'vb.cpus = 2'
  provision << "  "+"vb.name = \"#{vm_name.gsub '/', '_'}\""
  provision << 'end'
  provision << 'config.vm.provision "shell", inline: <<-SHELL'
	provision << "  "+'cp -a /vagrant/workspace/. /home/vagrant/Documents'
  provision << "  "+'sudo dnf -y -v install openssl-devel libxml2-devel'
  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'
  provision << "  "+'rm -rf ./atom.rpm'
  provision << install_instructions
	provision << " "+'wget https://download1.rstudio.org/rstudio-1.0.143-x86_64.rpm'
	provision << "  "+'sudo dnf -y -v install ./rstudio-1.0.143-x86_64.rpm'
	provision << "  "+'rm -rf ./rstudio-1.0.143-x86_64.rpm'
  provision << 'SHELL'
  provision << 'end'
end