ripe 0.1.0 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: f35a6d35553e2be4a3e844dabb53c32e2c1a1f6a
-  data.tar.gz: bf643294c8bfbe8deacd145beb0bb4d8de221451
+  metadata.gz: 2961c4cc93b7823c51c6ef1dc6d717b41de56d58
+  data.tar.gz: 5f80f681106b6b747f88fd9a3797ae661db7557f
 SHA512:
-  metadata.gz: 28e9487eebc73524e99974fb273ff106ee14c1b7cfcdb22159e2f4571a9abed6356490827261d9c95bbe04695e202906fee3ea22c82cb9baf797faa1354717df
-  data.tar.gz: 30708a13a9121c3aad6bb2ba23c12adec602468f632f5c4fd381d297c0919ce2b32f3f3670fa63994c6612e105d0fd87ecdee26205127f5884c94460554afb62
+  metadata.gz: 8b7edf637ca227eb6ac31ec0dd32bf7efbae0a54fda49e474f313850c554d45c55f03c767b315101f872cf11164c7a500f50b440fd9228f4afb2da42c34fa578
+  data.tar.gz: d8829b666f606a54c56c29e5a21a68ca04a177ce4a859fc83a8c9a0758c9d0f86d42e0ba671b31b996ac8313671e8bd849d731f2b8c420693cf0cc9096830534

data/.travis.yml

@@ -3,7 +3,8 @@ cache: bundler
 rvm:
   - 2.1.5
 script: bundle exec rake spec
+branches:
+  only:
+    - develop
 notifications:
   email: false
-  slack:
-    secure: "RlmKttTKbJlU1xu6blqP3HWwzH4KpvvdatvxkFWB1t3mBE3vRWC8FgiNpxYFs/6+TdctGOWRGW/i6CUaXbPwn3nyrlN+yxHmqNrJFg8dS2jQoM1/xBUZXdDhABMvw8qWzG26RSfGlvvO0P78rILawil+5/2z9e1XcUVmf0RL+gc="

data/Gemfile

@@ -1,6 +1,4 @@
 source 'https://rubygems.org'
 
-gem "codeclimate-test-reporter", group: :test, require: nil
-
 # Specify your gem's dependencies in ripe.gemspec
 gemspec

data/Guardfile

@@ -1,5 +1,6 @@
 guard :rspec, cmd: 'rspec' do
   watch(%r{^spec/.+_spec\.rb$})
-  watch(%r{^lib/ripe/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
-  watch('spec/spec_helper.rb')  { "spec" }
+  watch(%r{^lib/ripe/(.+)\.rb$}) { |m| "spec/lib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb') { "spec" }
+  watch('spec/testpack.rb') { "spec" }
 end

data/Rakefile

@@ -1,6 +1,5 @@
 require 'rspec/core/rake_task'
 require 'bundler/gem_tasks'
-require 'rdoc/task'
 
 # Default directory to look in is `/specs`
 # Run with `rake spec`
@@ -9,8 +8,4 @@ RSpec::Core::RakeTask.new(:spec) do |task|
 #  task.rspec_opts = ['--color', '--format', 'nested']
 end
 
-RDoc::Task.new(:rdoc         => 'rdoc',
-               :clobber_rdoc => 'rdoc:clean',
-               :rerdoc       => 'rdoc:force')
-
 # task :default => :spec

data/bin/ripe

@@ -1,31 +1,31 @@
 #!/usr/bin/env ruby
 
 require_relative '../lib/ripe'
+require_relative '../lib/ripe/dsl'
+require 'ripl' # REPL
+require 'hirb' # Pretty output for +ActiveRecord+ objects
 require 'thor'
 
 include Ripe
-
-# Look for workflows and blocks in ./.ripe wherever invoked, then in
-# directories specified in the $RIPELIB environment variable.
-$RIPELIBS = "#{ENV['PWD']}/.ripe:#{ENV['RIPELIB']}".split(/:/)
-
-def Task(handle, vars = {})
-  WorkingBlock.new($RIPELIBS.map{ |path| "#{path}/tasks/#{handle}.sh" }.select{ |path| File.exists? path }.first, vars)
-end
+include Ripe::DSL
 
 class CLI < Thor
   desc 'console', 'Enter ripe console'
   def console
-    require 'irb'
-    require 'irbtools'
+    repo = Repo.new
+    repo.attach
 
-    ARGV.clear # This is necessary because otherwise all arguments
-               # get sent to IRB
+    # Do not send arguments to the REPL
+    ARGV.clear
 
-    $ripe = Controller.new
-    $ripe.attach
+    Ripl.config[:prompt] = proc do
+      # This is the only place I could think of placing +Hirb#enable+.
+      Hirb.enable unless Hirb::View.enabled?
+      'ripe> '
+    end
 
-    IRB.start "ripe #{Ripe::VERSION}"
+    # Launch the REPL session in the context of +WorkerController+.
+    Ripl.start :binding => repo.controller.instance_eval { binding }
   end
 
   desc 'prepare SAMPLES', 'Prepare jobs from template workflow'
@@ -34,7 +34,7 @@ class CLI < Thor
   option :options, :aliases => '-o', :type => :string, :required => false,
     :desc => 'Options', :default => ''
   def prepare(*samples)
-    return if (samples.length == 0)
+    abort "No samples specified." if (samples.length == 0)
 
     additional_vars = options[:options].split(/,/).map do |pair|
       key, value = pair.split(/=/)
@@ -42,15 +42,16 @@ class CLI < Thor
     end
     additional_vars = additional_vars.inject(&:merge) || {}
 
-    # Expect $callback to be a lambda function that takes one argument (sample)
-    # and returns a Block, and $vars to be a dictionary mapping arguments to
-    # values (i.e. resource allocation)
-    workflows = $RIPELIBS.map{ |path| "#{path}/workflows/#{options[:workflow]}.rb" }
-    require_relative workflows.select{ |path| File.exists? path }.first
+    repo = Repo.new
+
+    filename = repo.library.find_workflow(options[:workflow])
+    abort "Could not find workflow #{@handle}." if filename == nil
+    require_relative filename # Imports +$workflow+ from the workflow component
 
-    $ripe = Controller.new
-    $ripe.attach_or_create # Create .ripe if it doesn't exist
-    $ripe.prepare(samples, $callback, $vars.merge(additional_vars))
+    repo.attach_or_create # Create .ripe if it doesn't exist
+    repo.controller.prepare(samples,
+                            $workflow.callback,
+                            $workflow.params.merge(additional_vars))
   end
 
   desc 'version', 'Retrieve ripe version'

data/lib/ripe/dsl/task_dsl.rb

@@ -0,0 +1,84 @@
+module Ripe
+
+  module DSL
+
+    ##
+    # Create a +WorkingBlock+ using a DSL.  It is syntactic sugar for
+    #
+    #    foo = WorkingBlock.new('/path/to/foo', {
+    #      param1: 'val1',
+    #      param2: 'val2',
+    #    })
+    #
+    # in the form of:
+    #
+    #    foo = task 'foo' do
+    #      param :param1, 'val1'
+    #      param :param2, 'val2'
+    #    end
+    #
+    #    foo = task 'foo' do |t|
+    #      t.param :param1, 'val1'
+    #      t.param :param2, 'val2'
+    #    end
+    #
+    # It internally uses +Ripe::DSL::TaskDSL+ to provide the DSL.
+    #
+    # @see Ripe::DSL::TaskDSL
+    # @see Ripe::DSL::WorkflowDSL
+    # @see Ripe::DSL::task
+    #
+    # @param handle [String] the name of the task
+    # @param block [Proc] executes block in the context of +TaskDSL+
+    # @return [WorkingBlock, nil]
+
+    def task(handle, &block)
+      filename = Repo.new.library.find_task(handle)
+      abort "Could not find task #{handle}." if filename == nil
+
+      params = TaskDSL.new(handle, &block).params
+      WorkingBlock.new(filename, params)
+    end
+
+    ##
+    # This class provides a DSL for defining a task.  It should only be called
+    # by #task.
+
+    class TaskDSL
+
+      attr_reader :params
+
+      ##
+      # Create a new +Task+ DSL
+      #
+      # @param handle [String] the name of the task
+      # @param block [Proc] executes block in the context of +TaskDSL+
+
+      def initialize(handle, &block)
+        @handle = handle
+        @params = {}
+
+        if block_given?
+          if block.arity == 1
+            yield self
+          else
+            instance_eval &block
+          end
+        end
+      end
+
+      ##
+      # Register a parameter
+      #
+      # @param key [Symbol] the parameter name
+      # @param value [String] its value
+
+      def param(key, value)
+        @params.merge!({ key => value })
+      end
+
+    end
+
+  end
+
+end

data/lib/ripe/dsl/workflow_dsl.rb

@@ -0,0 +1,92 @@
+module Ripe
+
+  module DSL
+
+    ##
+    # Create a +Workflow+ using a DSL.  It is syntactic sugar for
+    #
+    #    workflow 'foobar' do
+    #      param :node_count,    1
+    #      param :ppn,           8
+    #      param :project_name,  'abc-012-ab'
+    #      param :queue,         'queue'
+    #      param :walltime,      '12:00:00'
+    #
+    #      describe do |sample, params|
+    #        # task
+    #      end
+    #    end
+    #
+    # The block given in +describe+ has two mandatory arguments:
+    #   - sample: the name of the sample
+    #   - params: the parameters defined at the workflow-level
+    #
+    # It internally uses +Ripe::DSL::WorkflowDSL+ to provide the DSL.
+    #
+    # @see Ripe::DSL::TaskDSL
+    # @see Ripe::DSL::WorkflowDSL
+    # @see Ripe::DSL::workflow
+    #
+    # @param handle [String] the name of the workflow
+    # @param block [Proc] executes block in the context of +WorkflowDSL+
+
+    def workflow(handle, &block)
+      $workflow = WorkflowDSL.new(handle, &block)
+    end
+
+    ##
+    # This class provides a DSL for defining a workflow.  It should only be
+    # called by #workflow.
+
+    class WorkflowDSL
+
+      attr_reader :handle, :params, :callback
+
+      ##
+      # Create a new +Workflow+ DSL
+      #
+      # @param handle [String] the name of the workflow
+      # @param block [Proc] executes block in the context of +WorkflowDSL+
+
+      def initialize(handle, &block)
+        @handle = handle
+        @params = { handle: handle }
+        @callback = nil
+
+        if block_given?
+          if block.arity == 1
+            yield self
+          else
+            instance_eval &block
+          end
+        end
+      end
+
+      ##
+      # Register a parameter
+      #
+      # @param key [Symbol] the parameter name
+      # @param value [String] its value
+
+      def param(key, value)
+        @params.merge!({ key => value })
+      end
+
+      ##
+      # Describe the workflow in terms of a task.
+      #
+      # @see Ripe::WorkerController#prepare
+      #
+      # @param block [Proc] a callback function that takes as arguments the name
+      #   of sample and a hash of parameters provided by the workflow and by the
+      #   command line.
+
+      def describe(&block)
+        @callback = block
+      end
+
+    end
+
+  end
+
+end

data/lib/ripe/dsl.rb

@@ -0,0 +1,4 @@
+require_relative 'repo'
+require_relative 'working_block'
+require_relative 'dsl/task_dsl.rb'
+require_relative 'dsl/workflow_dsl.rb'

data/lib/ripe/library.rb

@@ -0,0 +1,61 @@
+module Ripe
+
+  ##
+  # This class represents a library containing all the components accessible
+  # to ripe (tasks and workflows) based on what is contained in the +RIPELIB+
+  # environment variable.
+
+  class Library
+
+    attr_reader :paths
+
+    ##
+    # Create a new library spanning all paths in the +RIPELIB+ environment
+    # variable.
+
+    def initialize
+      # Prepends the working directory to the list of paths so that the
+      # working directory is always looked in first.
+
+      @paths = "#{Dir.pwd}/#{Repo::REPOSITORY_PATH}:#{ENV['RIPELIB']}".split(/:/)
+    end
+
+    ##
+    # Search throughout the library for a task component by the name of
+    # +handle+.  When there is more than one match, give precendence to the
+    # component whose path is declared first.
+    #
+    # @param handle [String] Task to search for
+    # @return [String, nil] Return the full path of the component if found,
+    #   and +nil+ otherwise.
+
+    def find_task(handle)
+      search = @paths.map do |path|
+        filename = "#{path}/tasks/#{handle}.sh"
+        (File.exists? filename) ? filename : nil
+      end
+
+      search.compact.first
+    end
+
+    ##
+    # Search throughout the library for a workflow component by the name of
+    # +handle+.  When there is more than one match, give precendence to
+    # component whose path is declared first.
+    #
+    # @param handle [String] Workflow to search for
+    # @return [String, nil] Return the full path of the component if found,
+    #   and +nil+ otherwise.
+
+    def find_workflow(handle)
+      search = @paths.map do |path|
+        filename = "#{path}/workflows/#{handle}.rb"
+        (File.exists? filename) ? filename : nil
+      end
+
+      search.compact.first
+    end
+
+  end
+
+end

data/lib/ripe/repo.rb

@@ -0,0 +1,92 @@
+require 'active_record'
+require 'fileutils'
+require_relative 'block'
+require_relative 'worker'
+require_relative 'worker_controller'
+require_relative 'worker_migration'
+require_relative 'working_block'
+require_relative 'library'
+require_relative 'liquid_block'
+require_relative 'task'
+require_relative 'task_migration'
+
+module Ripe
+
+  ##
+  # This class represents a ripe session.  It is similar to the concept of a
+  # +git+ repository and is the starting point of the package.  It
+  # instantiates:
+  #
+  # * a library containing information as to where to retrieve ripe
+  #   components such as tasks and workflows;
+  # * a database that contains all worker metadata; and
+  # * a controller that communicates the database with the compute cluster
+  #   interface.
+  #
+  # @see Ripe::WorkerController
+  # @see Ripe::Library
+
+  class Repo
+
+    REPOSITORY_PATH = '.ripe'
+    DATABASE_PATH   = "#{REPOSITORY_PATH}/meta.db"
+    WORKERS_PATH    = "#{REPOSITORY_PATH}/workers"
+
+    attr_reader :library, :controller
+
+    ##
+    # Initialize a repository
+
+    def initialize
+      @has_repository = File.exists? REPOSITORY_PATH
+      @library        = Library.new
+      @controller     = WorkerController.instance
+    end
+
+    ##
+    # Attach to an existing database
+
+    def attach
+      ActiveRecord::Base.establish_connection({
+        adapter:  'sqlite3',
+        database: DATABASE_PATH,
+      })
+    end
+
+    ##
+    # Attach to an existing database, and creates one if none is found.
+
+    def attach_or_create
+      @has_repository ? attach : create
+    end
+
+    ##
+    # Create a database
+
+    def create
+      FileUtils.mkdir_p(REPOSITORY_PATH)
+      @has_repository = true
+
+      begin
+        attach
+
+        # Create the tables
+        WorkerMigration.up
+        TaskMigration.up
+      rescue
+        destroy
+      end
+    end
+
+    ##
+    # Destroy the ripe repository, including the database and the worker
+    # output.
+
+    def destroy
+      FileUtils.rm(DATABASE_PATH) if File.exists? DATABASE_PATH
+      FileUtils.rm(WORKERS_PATH)  if Dir.exists?  WORKERS_PATH
+    end
+
+  end
+
+end

data/lib/ripe/version.rb

@@ -1,3 +1,3 @@
 module Ripe
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end

data/lib/ripe/worker.rb

@@ -1,13 +1,14 @@
 require 'active_record'
 require 'fileutils'
 require_relative 'task'
+require_relative 'worker_controller'
 
 module Ripe
   class Worker < ActiveRecord::Base
     has_many :tasks, dependent: :destroy
 
     def dir
-      ".ripe/workers/#{self.id}"
+      "#{Repo::REPOSITORY_PATH}/workers/#{self.id}"
     end
 
     def sh
@@ -30,27 +31,14 @@ module Ripe
       FileUtils.rm_r dir if Dir.exists? dir
     end
 
-    def self.sync
-      WorkerController.instance.sync
-    end
-
-    def start!
-      raise "Worker #{id} could not be started: not prepared" unless self.status == 'prepared'
-      start
-    end
-
     def start
-      update(status: :queueing, moab_id: `qsub '#{self.sh}'`.strip.split(/\./).first) # Send to queue first
-    end
-
-    def cancel!
-      raise "Worker #{id} could not be cancelled: not started" unless ['queueing', 'idle', 'blocked', 'active'].include? self.status
-      cancel
+      raise "Worker #{id} could not be started: not prepared" unless self.status == 'prepared'
+      WorkerController.instance.start(self)
     end
 
     def cancel
-      `canceljob #{self.moab_id}`
-      update(status: :cancelled)
+      raise "Worker #{id} could not be cancelled: not started" unless ['queueing', 'idle', 'blocked', 'active'].include? self.status
+      WorkerController.instance.cancel(self)
     end
   end
 end

data/lib/ripe/worker_controller.rb

@@ -2,9 +2,28 @@ require 'singleton'
 require_relative 'worker'
 
 module Ripe
+
+  ##
+  # This class controls workers as well as their relationship with regards to
+  # the compute cluster: worker preparation, submission, cancellation as well
+  # as sync.
+
   class WorkerController
+
     include Singleton
 
+    ##
+    # Prepares workers by applying the workflow callback and its parameters to
+    # each sample.
+    #
+    # @see Ripe::DSL::WorkflowDSL#describe
+    #
+    # @param samples [List] list of samples to apply the callback to
+    # @param callback [Proc] a callback function that takes as arguments the name
+    #   of sample and a hash of parameters provided by the workflow and by the
+    #   command line.
+    # @param vars [Hash] a list of worker-wide parameters
+
     def prepare(samples, callback, vars = {})
       vars = {
         wd:        Dir.pwd,
@@ -78,6 +97,29 @@ module Ripe
       end
     end
 
+    ##
+    # Submit a job to the compute cluster system
+    #
+    # @param worker [Worker] the worker to submit
+
+    def start(worker)
+      worker.update(status: :queueing,
+                    moab_id: `qsub '#{worker.sh}'`.strip.split(/\./).first)
+    end
+
+    ##
+    # Cancel a job in the compute cluster system
+    #
+    # @param worker [Worker] the worker to cancel
+
+    def cancel(worker)
+      `canceljob #{worker.moab_id}`
+      worker.update(status: :cancelled)
+    end
+
+    ##
+    # Synchronize the status of jobs with the internal list of workers.
+
     def sync
       lists = {idle: '-i', blocked: '-b', active:  '-r'}
       lists = lists.map do |status, op|
@@ -134,5 +176,15 @@ module Ripe
         end
       end
     end
+
+    def list(n = 20)
+      Worker.last(n)
+    end
+
+    def edit(*args)
+      system("$EDITOR #{args.join(' ')}")
+    end
+
   end
+
 end

data/lib/ripe.rb

@@ -1,5 +1,5 @@
 require_relative 'ripe/version'
-require_relative 'ripe/controller'
+require_relative 'ripe/repo'
 
 module Ripe
   PATH = File.expand_path('..', File.dirname(__FILE__))

data/ripe.gemspec

@@ -20,17 +20,19 @@ Gem::Specification.new do |spec|
 
   spec.add_development_dependency "bundler", "~> 1.7"
   spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "yard", "~> 0.8"
   spec.add_development_dependency "rspec", "~> 3.2"
   spec.add_development_dependency "rspec-nc", "~> 0.2"
   spec.add_development_dependency "guard-rspec", "~> 4.5"
-  spec.add_development_dependency "rdoc", "~> 4.2"
+  spec.add_development_dependency "codeclimate-test-reporter", "~> 0.4"
 
   spec.add_runtime_dependency "activerecord", "~> 4.2"
   spec.add_runtime_dependency "fileutils", "~> 0.7"
   spec.add_runtime_dependency "liquid", "~> 3.0"
   spec.add_runtime_dependency "sqlite3", "~> 1.3"
+
+  spec.add_runtime_dependency "ripl", "~> 0.7"
   spec.add_runtime_dependency "hirb", "~> 0.7"
-  spec.add_runtime_dependency "irbtools", "~> 1.7"
+
   spec.add_runtime_dependency "thor", "~> 0.19"
-  spec.add_runtime_dependency "wirb", "~> 1.0"
 end

data/spec/library_spec.rb

@@ -0,0 +1,53 @@
+require 'spec_helper'
+
+describe Ripe::Library do
+  context 'when RIPELIB env is empty' do
+    before(:each) do
+      ENV['RIPELIB'] = ''
+      @library = Ripe::Library.new
+    end
+
+    it 'looks in the working directory' do
+      expect(@library.paths).to eql ["#{Dir.pwd}/#{Ripe::Repo::REPOSITORY_PATH}"]
+    end
+
+    it 'cannot resolve components of the test library' do
+      expect(@library.find_task('foo')).to eql nil
+      expect(@library.find_task('bar')).to eql nil
+      expect(@library.find_workflow('foobar')).to eql nil
+    end
+  end
+
+  context 'when RIPELIB contains the test library' do
+    before(:each) do
+      @test = Ripe::TestPack.new
+      ENV['RIPELIB'] = @test.path
+      @library = Ripe::Library.new
+    end
+
+    it 'looks in two directories' do
+      expect(@library.paths.length).to eql 2
+    end
+
+    it 'looks in the working directory first' do
+      # It looks in the working directory, and then in the directory
+      # specified in RIPELIB.
+      expect(@library.paths[0]).to eql "#{Dir.pwd}/#{Ripe::Repo::REPOSITORY_PATH}"
+      expect(@library.paths[1]).to eql @test.path
+    end
+
+    it 'resolves task components of the test library' do
+      expect(@library.find_task('foo')).to eql @test.tasks['foo']
+      expect(@library.find_task('bar')).to eql @test.tasks['bar']
+    end
+
+    it 'resolves workflows components of the test library' do
+      expect(@library.find_workflow('foobar')).to eql @test.workflows['foobar']
+    end
+
+    it 'cannot resolve non-existing componenets' do
+      expect(@library.find_task('other')).to eql nil
+      expect(@library.find_workflow('other')).to eql nil
+    end
+  end
+end

data/spec/spec_helper.rb

@@ -4,3 +4,4 @@ if !ENV['CODECLIMATE_REPO_TOKEN'].nil?
 end
 
 require_relative '../lib/ripe'
+require_relative 'testpack'

data/spec/testpack/case/Sample1/bar_output.txt

@@ -0,0 +1 @@
+One Bar

data/spec/testpack/case/Sample1/foo_input.txt

@@ -0,0 +1 @@
+One Foo

data/spec/testpack/case/Sample1/foo_output.txt

@@ -0,0 +1 @@
+One Foo For You

data/spec/testpack/case/Sample2/bar_output.txt

@@ -0,0 +1 @@
+Two Bar

data/spec/testpack/case/Sample2/foo_input.txt

@@ -0,0 +1 @@
+Two Foo

data/spec/testpack/case/Sample2/foo_output.txt

@@ -0,0 +1 @@
+Two Foo For You

data/spec/testpack/case/Sample3/bar_output.txt

@@ -0,0 +1 @@
+Three Bar

data/spec/testpack/case/Sample3/foo_input.txt

@@ -0,0 +1 @@
+Three Foo

data/spec/testpack/case/Sample3/foo_output.txt

@@ -0,0 +1 @@
+Three Foo For You

data/spec/testpack/ripe/tasks/bar.sh

@@ -0,0 +1,3 @@
+# Bar is the most important consequence of Foo.
+
+echo "$(cut -f1 "$INPUT_BAR") $BAR_MESSAGE" > "$OUTPUT_BAR"

data/spec/testpack/ripe/tasks/foo.sh

@@ -0,0 +1,3 @@
+# Foo is certainly one of the most important prerequisites to Bar.
+
+echo "$(cat "$INPUT_FOO") $FOO_MESSAGE" > "$OUTPUT_FOO"

data/spec/testpack/ripe/workflows/foobar.rb

@@ -0,0 +1,23 @@
+workflow 'foobar' do
+  param :node_count,    1
+  param :ppn,           8
+  param :project_name,  'abc-012-ab'
+  param :queue,         'queue'
+  param :walltime,      '12:00:00'
+
+  describe do |sample, params|
+    foo = task 'foo' do
+      param :input_foo,   "#{sample}/input_foo"
+      param :foo_message, 'FOO'
+      param :output_foo,  "#{sample}/output_foo"
+    end
+
+    bar = task 'bar' do
+      param :input_bar,   "#{sample}/input_bar"
+      param :bar_message, 'BAR'
+      param :output_bar,  "#{sample}/output_bar"
+    end
+
+    foo + bar
+  end
+end

data/spec/testpack.rb

@@ -0,0 +1,16 @@
+module Ripe
+  class TestPack
+    attr_reader :path, :tasks, :workflows
+
+    def initialize
+      @path = "#{Ripe::PATH}/spec/testpack/ripe"
+      @tasks = {
+        'foo' => "#{@path}/tasks/foo.sh",
+        'bar' => "#{@path}/tasks/bar.sh",
+      }
+      @workflows = {
+        'foobar' => "#{@path}/workflows/foobar.rb",
+      }
+    end
+  end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: ripe
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Nicolas De Jay
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-05-11 00:00:00.000000000 Z
+date: 2015-05-15 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
@@ -38,6 +38,20 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: yard
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '0.8'
 - !ruby/object:Gem::Dependency
   name: rspec
   requirement: !ruby/object:Gem::Requirement
@@ -81,19 +95,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '4.5'
 - !ruby/object:Gem::Dependency
-  name: rdoc
+  name: codeclimate-test-reporter
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.2'
+        version: '0.4'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '4.2'
+        version: '0.4'
 - !ruby/object:Gem::Dependency
   name: activerecord
   requirement: !ruby/object:Gem::Requirement
@@ -151,7 +165,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '1.3'
 - !ruby/object:Gem::Dependency
-  name: hirb
+  name: ripl
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
@@ -165,19 +179,19 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0.7'
 - !ruby/object:Gem::Dependency
-  name: irbtools
+  name: hirb
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '0.7'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
     - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.7'
+        version: '0.7'
 - !ruby/object:Gem::Dependency
   name: thor
   requirement: !ruby/object:Gem::Requirement
@@ -192,20 +206,6 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.19'
-- !ruby/object:Gem::Dependency
-  name: wirb
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
-  type: :runtime
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - "~>"
-      - !ruby/object:Gem::Version
-        version: '1.0'
 description: 
 email:
 - ndj+rubygems@pinkfilter.org
@@ -225,10 +225,14 @@ files:
 - bin/ripe
 - lib/ripe.rb
 - lib/ripe/block.rb
-- lib/ripe/controller.rb
+- lib/ripe/dsl.rb
+- lib/ripe/dsl/task_dsl.rb
+- lib/ripe/dsl/workflow_dsl.rb
+- lib/ripe/library.rb
 - lib/ripe/liquid_block.rb
 - lib/ripe/multi_block.rb
 - lib/ripe/parallel_block.rb
+- lib/ripe/repo.rb
 - lib/ripe/serial_block.rb
 - lib/ripe/task.rb
 - lib/ripe/task_migration.rb
@@ -240,8 +244,22 @@ files:
 - ripe.gemspec
 - share/moab.sh
 - spec/block_spec.rb
+- spec/library_spec.rb
 - spec/ripe_spec.rb
 - spec/spec_helper.rb
+- spec/testpack.rb
+- spec/testpack/case/Sample1/bar_output.txt
+- spec/testpack/case/Sample1/foo_input.txt
+- spec/testpack/case/Sample1/foo_output.txt
+- spec/testpack/case/Sample2/bar_output.txt
+- spec/testpack/case/Sample2/foo_input.txt
+- spec/testpack/case/Sample2/foo_output.txt
+- spec/testpack/case/Sample3/bar_output.txt
+- spec/testpack/case/Sample3/foo_input.txt
+- spec/testpack/case/Sample3/foo_output.txt
+- spec/testpack/ripe/tasks/bar.sh
+- spec/testpack/ripe/tasks/foo.sh
+- spec/testpack/ripe/workflows/foobar.rb
 homepage: https://github.com/ndejay/ripe
 licenses:
 - MIT
@@ -268,5 +286,20 @@ specification_version: 4
 summary: Abstraction layer between the MOAB/Torque stack and your pipeline.
 test_files:
 - spec/block_spec.rb
+- spec/library_spec.rb
 - spec/ripe_spec.rb
 - spec/spec_helper.rb
+- spec/testpack.rb
+- spec/testpack/case/Sample1/bar_output.txt
+- spec/testpack/case/Sample1/foo_input.txt
+- spec/testpack/case/Sample1/foo_output.txt
+- spec/testpack/case/Sample2/bar_output.txt
+- spec/testpack/case/Sample2/foo_input.txt
+- spec/testpack/case/Sample2/foo_output.txt
+- spec/testpack/case/Sample3/bar_output.txt
+- spec/testpack/case/Sample3/foo_input.txt
+- spec/testpack/case/Sample3/foo_output.txt
+- spec/testpack/ripe/tasks/bar.sh
+- spec/testpack/ripe/tasks/foo.sh
+- spec/testpack/ripe/workflows/foobar.rb
+has_rdoc: 

data/lib/ripe/controller.rb

@@ -1,52 +0,0 @@
-require 'active_record'
-require 'fileutils'
-require_relative 'block'
-require_relative 'worker'
-require_relative 'worker_controller'
-require_relative 'worker_migration'
-require_relative 'working_block'
-require_relative 'liquid_block'
-require_relative 'task'
-require_relative 'task_migration'
-
-module Ripe
-  class Controller
-    def initialize
-      @repository_path = '.ripe'
-      @has_repository = Dir.exists? @repository_path
-    end
-
-    def attach
-      ActiveRecord::Base.establish_connection({
-        adapter:  'sqlite3',
-        database: "#{@repository_path}/meta.db"
-      })
-    end
-
-    def attach_or_create
-      @has_repository ? attach : create
-    end
-
-    def create
-      FileUtils.mkdir_p(@repository_path)
-      @has_repository = true
-
-      begin
-        attach
-        WorkerMigration.up
-        TaskMigration.up
-      rescue
-        destroy
-      end
-    end
-
-    def destroy
-      FileUtils.rm("#{@repository_path}/meta.db") if File.exists? "#{@repository_path}/meta.db"
-      FileUtils.rm("#{@repository_path}/workers") if Dir.exists?  "#{@repository_path}/workers"
-    end
-
-    def prepare(samples, callback, vars = {})
-      WorkerController.instance.prepare(samples, callback, vars)
-    end
-  end
-end