osc_machete_rails 1.2.0

data/lib/osc_machete_rails/workflow.rb

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+module OscMacheteRails
+  # A plugin to maintain a workflow for Jobs.
+  module Workflow
+
+    # Registers a workflow relationship and sets up a hook to additional builder methods.
+    #
+    # @param [Symbol] jobs_active_record_relation_symbol The Job Identifier
+    def has_machete_workflow_of(jobs_active_record_relation_symbol)
+      # yes, this is magic mimicked from http://guides.rubyonrails.org/plugins.html
+      #  and http://yehudakatz.com/2009/11/12/better-ruby-idioms/
+      cattr_accessor :jobs_active_record_relation_symbol
+      self.jobs_active_record_relation_symbol = jobs_active_record_relation_symbol
+
+      # separate modules to group common methods for readability purposes
+      # both builder methods and status methods need the jobs relation so
+      # we include that first
+      self.send :include, OscMacheteRails::Workflow::JobsRelation
+      self.send :include, OscMacheteRails::Workflow::BuilderMethods
+      self.send :include, OscMacheteRails::Workflow::StatusMethods
+    end
+
+    # The module defining the active record relation of the jobs
+    module JobsRelation
+      # Assign the active record relation of this instance to the
+      def jobs_active_record_relation
+        self.send self.class.jobs_active_record_relation_symbol
+      end
+    end
+
+    # depends on jobs_active_record_relation being defined
+    module BuilderMethods
+      # Methods run when this module is included
+      def self.included(obj)
+        # before we destroy ActiveRecord we stop all jobs and delete staging dir
+        # prepend: true tells this to run before any of the jobs are destroyed
+        # so we can stop them first and recover if there is a problem
+        if obj.respond_to?(:before_destroy)
+          obj.before_destroy prepend: true do |sim|
+            sim.stop ? sim.delete_staging : false
+          end
+        end
+      end
+
+      def ood_dataroot
+        if defined? OodAppkit
+          OodAppkit.dataroot
+        elsif ENV['OOD_DATAROOT'] || ENV['RAILS_DATAROOT']
+          Pathname.new(ENV['OOD_DATAROOT'] || ENV['RAILS_DATAROOT'])
+        else
+          raise "no ood_dataroot specified"
+        end
+      end
+
+      #
+      # @example Underscore a class
+      #   FlowratePerformanceRun => flowrate_performance_run
+      #
+      # @return [String] The template name
+      def staging_template_name
+        self.class.name.underscore
+      end
+
+      # Returns the name of a staging directory that has been underscored and pluralized.
+      #
+      # @example
+      #   Simulation => simulations
+      # @example
+      #   FlowratePerformanceRun => flowrate_performance_runs
+      #
+      # @return [String] The staging template directory name
+      def staging_target_dir_name
+        staging_template_name.pluralize
+      end
+
+      # Gets the staging target directory path.
+      # Joins the AwesimRails.dataroot and the staging target directory name.
+      #
+      # @raise [Exception] "override staging_target_dir or include awesim_rails gem"
+      #
+      # @return [String] The staging target directory path.
+      def staging_target_dir(dataroot: ood_dataroot)
+        Pathname.new(dataroot).join(staging_target_dir_name)
+      end
+
+      # Gets the staging template directory path.
+      # Joins the { rails root }/jobs/{ staging_template_name } into a path.
+      #
+      # @return [String] The staging template directory path.
+      def staging_template_dir
+        Rails.root.join("jobs", staging_template_name)
+      end
+
+      # Creates a new staging target job directory on the system
+      # Copies the staging template directory to the staging target job directory
+      #
+      # @return [Pathname] The staged directory path.
+      def stage
+        staged_dir = OSC::Machete::JobDir.new(staging_target_dir).new_jobdir
+        FileUtils.mkdir_p staged_dir
+        FileUtils.cp_r staging_template_dir.to_s + "/.", staged_dir
+
+        staged_dir
+      end
+
+      # Deletes the staged directory if it exists
+      def delete_staging
+        FileUtils.rm_rf(staged_dir) if respond_to?(:staged_dir) && staged_dir
+      end
+
+      # Stops all jobs, updating each active job to status "failed"
+      # returns true if all jobs were stopped, false otherwise
+      def stop
+        jobs_active_record_relation.to_a.each(&:stop)
+
+        true
+      rescue PBS::Error => e
+        msg = "A PBS::Error occurred when trying to stop jobs for simulation #{id}: #{e.message}"
+        errors[:base] << msg
+        Rails.logger.error(msg)
+
+        false
+      end
+
+      # Creates a new location and renders the mustache files
+      #
+      # @param [String] staged_dir The staging target directory path.
+      # @param [Hash] template_view The template options to be rendered.
+      #
+      # @return [Location] The location of the staged and rendered template.
+      def render_mustache_files(staged_dir, template_view)
+        OSC::Machete::Location.new(staged_dir).render(template_view)
+      end
+
+      # Actions to perform after staging
+      #
+      # @param [String] staged_dir The staged directory path.
+      def after_stage(staged_dir)
+      end
+
+      # Unimplemented method for building jobs.
+      #
+      # @param [String] staged_dir The staged directory path.
+      # @param [Array, Nil] jobs An array of jobs to be built.
+      #
+      # @raise [NotImplementedError] The method is currently not implemented
+      def build_jobs(staged_dir, jobs = [])
+        raise NotImplementedError, "Objects including OSC::Machete::SimpleJob::Workflow must implement build_jobs"
+      end
+
+      # Call the #submit method on each job in a hash.
+      #
+      # @param [Hash] jobs A Hash of Job objects to be submitted.
+      def submit_jobs(jobs)
+        jobs.each(&:submit)
+        true
+      rescue OSC::Machete::Job::ScriptMissingError => e
+        stop_machete_jobs(jobs)
+
+        msg = "A OSC::Machete::Job::ScriptMissingError occurred when submitting jobs for simulation #{id}: #{e.message}"
+        errors[:base] << msg
+        Rails.logger.error(msg)
+        false
+      rescue PBS::Error => e
+        stop_machete_jobs(jobs)
+
+        msg = "A PBS::Error occurred when submitting jobs for simulation #{id}: #{e.message}"
+        errors[:base] << msg
+        Rails.logger.error(msg)
+
+        false
+      end
+
+      # given an array of OSC::Machete::Job objects, qdel them all and handle
+      # any errors. not to be confused with #stop which stops all actual jobs of
+      # the workflow
+      def stop_machete_jobs(jobs)
+        jobs.each do |job|
+          begin
+            job.delete
+          rescue PBS::Error
+            msg = "A PBS::Error occurred when deleting a job from the batch system with pbsid: #{job.pbsid} and message: #{e.message}"
+            errors[:base] << msg
+            Rails.logger.error(msg)
+          end
+        end
+      end
+
+      # Saves a Hash of jobs to a staged directory
+      #
+      # @param [Hash] jobs A Hash of Job objects to be saved.
+      # @param [Location] staged_dir The staged directory as Location object.
+      def save_jobs(jobs, staged_dir)
+        self.staged_dir = staged_dir.to_s if self.respond_to?(:staged_dir=)
+        self.save if self.id.nil? || self.respond_to?(:staged_dir=)
+
+        jobs.each do |job|
+          self.jobs_active_record_relation.create(job: job)
+        end
+      end
+
+      # Perform the submit actions.
+      #
+      # Sets the staged_dir
+      # Renders the mustache files.
+      # Calls after_stage.
+      # Calls build_jobs.
+      # Submits the jobs.
+      # Saves the jobs.
+      #
+      # @param [Hash, nil] template_view (self) The template options to be rendered.
+      def submit(template_view=self)
+        staged_dir = stage
+        render_mustache_files(staged_dir, template_view)
+        after_stage(staged_dir)
+        jobs = build_jobs(staged_dir)
+        if submit_jobs(jobs)
+          save_jobs(jobs, staged_dir)
+        else
+          FileUtils.rm_rf staged_dir.to_s
+          false
+        end
+      end
+    end
+
+    # depends on jobs_active_record_relation being defined
+    module StatusMethods
+      delegate :not_submitted?, :submitted?, :completed?, :passed?, :failed?, :active?, to: :status
+
+      # Reduce the jobs to a single OSC::Machete:Status value
+      #
+      # Assumes `jobs_active_record_relation` is a Statusable ActiveRecord
+      # model. Get array of status values (one for each job) and then add them
+      # together to get one value. OSC::Machete::Status#+ is overridden to 
+      # return the highest precendent status value when adding two together.
+      #
+      # FIXME: it might be clearer in code to use `max` instead of `+` i.e.
+      # statuses.reduce(&:max) and rename OSC::Machete::Status#+.
+      #
+      # @return [OSC::Machete::Status] a single value representing the status 
+      def status
+        statuses = jobs_active_record_relation.to_a.map(&:status)
+        statuses.empty? ? OSC::Machete::Status.not_submitted : statuses.reduce(&:+)
+      end
+    end
+
+    # extend Active Record with the has_workflow_of method
+    ActiveRecord::Base.extend OscMacheteRails::Workflow if defined? ActiveRecord::Base
+  end
+end

data/lib/osc_machete_rails.rb

@@ -0,0 +1,12 @@
+require "osc/machete"
+require "osc_machete_rails/engine"
+require "osc_machete_rails/statusable"
+require "osc_machete_rails/workflow"
+require "osc_machete_rails/helper"
+
+module OscMacheteRails
+  mattr_accessor :update_status_of_all_active_jobs_on_each_request
+
+  # make OSC::Machete::SimpleJob an alias of this module for backwards compatibility
+  OSC::Machete::SimpleJob = self
+end

data/lib/tasks/osc_machete_rails_tasks.rake

@@ -0,0 +1,4 @@
+# desc "Explaining what the task does"
+# task :osc_machete_rails do
+#   # Task goes here
+# end

data/test/dummy/README.rdoc

@@ -0,0 +1,28 @@
+== README
+
+This README would normally document whatever steps are necessary to get the
+application up and running.
+
+Things you may want to cover:
+
+* Ruby version
+
+* System dependencies
+
+* Configuration
+
+* Database creation
+
+* Database initialization
+
+* How to run the test suite
+
+* Services (job queues, cache servers, search engines, etc.)
+
+* Deployment instructions
+
+* ...
+
+
+Please feel free to use a different markup language if you do not plan to run
+<tt>rake doc:app</tt>.

data/test/dummy/Rakefile

@@ -0,0 +1,6 @@
+# Add your own tasks in files placed in lib/tasks ending in .rake,
+# for example lib/tasks/capistrano.rake, and they will automatically be available to Rake.
+
+require File.expand_path('../config/application', __FILE__)
+
+Dummy::Application.load_tasks

data/test/dummy/app/assets/javascripts/application.js

@@ -0,0 +1,13 @@
+// This is a manifest file that'll be compiled into application.js, which will include all the files
+// listed below.
+//
+// Any JavaScript/Coffee file within this directory, lib/assets/javascripts, vendor/assets/javascripts,
+// or vendor/assets/javascripts of plugins, if any, can be referenced here using a relative path.
+//
+// It's not advisable to add code directly here, but if you do, it'll appear at the bottom of the
+// compiled file.
+//
+// Read Sprockets README (https://github.com/sstephenson/sprockets#sprockets-directives) for details
+// about supported directives.
+//
+//= require_tree .

data/test/dummy/app/assets/javascripts/simulations.js

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+// Place all the behaviors and hooks related to the matching controller here.
+// All this logic will automatically be available in application.js.

data/test/dummy/app/assets/stylesheets/application.css

@@ -0,0 +1,13 @@
+/*
+ * This is a manifest file that'll be compiled into application.css, which will include all the files
+ * listed below.
+ *
+ * Any CSS and SCSS file within this directory, lib/assets/stylesheets, vendor/assets/stylesheets,
+ * or vendor/assets/stylesheets of plugins, if any, can be referenced here using a relative path.
+ *
+ * You're free to add application-wide styles to this file and they'll appear at the top of the
+ * compiled file, but it's generally better to create a new file per style scope.
+ *
+ *= require_self
+ *= require_tree .
+ */

data/test/dummy/app/assets/stylesheets/simulations.css

@@ -0,0 +1,4 @@
+/*
+  Place all the styles related to the matching controller here.
+  They will automatically be included in application.css.
+*/

data/test/dummy/app/controllers/application_controller.rb

@@ -0,0 +1,5 @@
+class ApplicationController < ActionController::Base
+  # Prevent CSRF attacks by raising an exception.
+  # For APIs, you may want to use :null_session instead.
+  protect_from_forgery with: :exception
+end

data/test/dummy/app/controllers/simulations_controller.rb

@@ -0,0 +1,103 @@
+class SimulationsController < ApplicationController
+  before_action :set_simulation, only: [:show, :edit, :update, :destroy, :submit, :copy]
+
+  # GET /simulations
+  # GET /simulations.json
+  def index
+    @simulations = Simulation.preload(:simulation_jobs).all
+  end
+
+  # GET /simulations/1
+  # GET /simulations/1.json
+  def show
+  end
+
+  # GET /simulations/new
+  def new
+    @simulation = Simulation.new
+  end
+
+  # GET /simulations/1/edit
+  def edit
+  end
+
+  # POST /simulations
+  # POST /simulations.json
+  def create
+    @simulation = Simulation.new(simulation_params)
+
+    respond_to do |format|
+      if @simulation.save
+        format.html { redirect_to @simulation, notice: 'Simulation was successfully created.' }
+        format.json { render :show, status: :created, location: @simulation }
+      else
+        format.html { render :new }
+        format.json { render json: @simulation.errors, status: :unprocessable_entity }
+      end
+    end
+  end
+
+  # PATCH/PUT /simulations/1
+  # PATCH/PUT /simulations/1.json
+  def update
+    respond_to do |format|
+      if @simulation.update(simulation_params)
+        format.html { redirect_to @simulation, notice: 'Simulation was successfully updated.' }
+        format.json { render :show, status: :ok, location: @simulation }
+      else
+        format.html { render :edit }
+        format.json { render json: @simulation.errors, status: :unprocessable_entity }
+      end
+    end
+  end
+
+  # DELETE /simulations/1
+  # DELETE /simulations/1.json
+  def destroy
+    respond_to do |format|
+      if @simulation.destroy
+        format.html { redirect_to simulations_url, notice: 'Simulation was successfully destroyed.' }
+        format.json { head :no_content }
+      else
+        format.html { render :show, status: 500, alert: 'A problem occurred when trying to destroy the simulation.' }
+        format.json { render json: @simulation.errors, status: 500 }
+      end
+    end
+  end
+
+  # PUT /simulations/1/submit
+  # PUT /simulations/1/submit.json
+  def submit
+    respond_to do |format|
+
+      if @simulation.submitted?
+        format.html { redirect_to simulations_url, alert: 'Simulation has already been submitted.' }
+        format.json { head :no_content }
+      elsif @simulation.submit
+        format.html { redirect_to simulations_url, notice: 'Simulation was successfully submitted.' }
+        format.json { head :no_content }
+      else
+        format.html { render :show, status: 500, alert: 'A problem occurred when trying to submit the simulation.' }
+        format.json { render json: @simulation.errors, status: 500 }
+      end
+    end
+  end
+
+  # PUT /simulations/1/copy
+  def copy
+    @simulation = @simulation.copy
+
+    render template: "simulations/edit"
+  end
+
+  private
+    # Use callbacks to share common setup or constraints between actions.
+    def set_simulation
+      @simulation = Simulation.preload(:simulation_jobs).find(params[:id])
+    end
+
+    # Only allow a trusted parameter "white list" through.
+    def simulation_params
+      params.require(:simulation).permit!
+    end
+end

data/test/dummy/app/helpers/application_helper.rb

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+module ApplicationHelper
+end

data/test/dummy/app/helpers/simulations_helper.rb

@@ -0,0 +1,2 @@
+module SimulationsHelper
+end

data/test/dummy/app/models/simulation.rb

@@ -0,0 +1,26 @@
+class Simulation < ActiveRecord::Base
+  has_many :simulation_jobs, dependent: :destroy
+  has_machete_workflow_of :simulation_jobs
+
+
+  # Name that defines the template/target dirs
+  def staging_template_name
+    "simulation"
+  end
+
+  # Define tasks to do after staging template directory typically copy over
+  # uploaded files here
+  # def after_stage(staged_dir)
+  #   # CODE HERE
+  # end
+
+  # Build an array of Machete jobs that are then submitted to the batch server
+  def build_jobs(staged_dir, job_list = [])
+    job_list << OSC::Machete::Job.new(script: staged_dir.join("main.sh"))
+  end
+
+  # Make copy of workflow
+  def copy
+    self.dup
+  end
+end

data/test/dummy/app/models/simulation_job.rb

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+class SimulationJob < ActiveRecord::Base
+  # Here we test the deprecated include method instead of the new
+  # OscMacheteRails::Statusable
+  # We will want both to work...
+  include OSC::Machete::SimpleJob::Statusable
+
+  belongs_to :simulation
+
+  before_destroy { |j| j.job.delete(rmdir: true) if j.job }
+
+  # Determine if the results are valid
+  # def results_valid?
+  #   # CODE GOES HERE
+  # end
+end

data/test/dummy/app/views/layouts/application.html.erb

@@ -0,0 +1,14 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <title>Dummy</title>
+  <%= stylesheet_link_tag    "application", media: "all", "data-turbolinks-track" => true %>
+  <%= javascript_include_tag "application", "data-turbolinks-track" => true %>
+  <%= csrf_meta_tags %>
+</head>
+<body>
+
+<%= yield %>
+
+</body>
+</html>

data/test/dummy/app/views/simulations/_form.html.erb

@@ -0,0 +1,15 @@
+<%# Uses rails_bootstrap_form gem. API at: https://github.com/bootstrap-ruby/rails-bootstrap-forms %>
+<%= bootstrap_form_for(simulation) do |f| %>
+  <%= f.alert_message "Please fix the errors below." %>
+
+  <%= f.text_field :name %>
+  <%= f.text_field :pressure %>
+
+  <%= f.submit 'Save', class: 'btn btn-primary' %>
+  <%= f.button 'Reset', type: :reset, class: 'btn btn-default' %>
+
+  <hr>
+
+  <%= link_to 'Back', simulations_path, class: 'btn btn-default' %>
+  <%= link_to 'Show', simulation, class: 'btn btn-primary' unless simulation.new_record? %>
+<% end %>

data/test/dummy/app/views/simulations/edit.html.erb

@@ -0,0 +1,5 @@
+<div class="page-header">
+  <h2>Editing Simulation</h2>
+</div>
+
+<%= render 'form', simulation: @simulation %>

data/test/dummy/app/views/simulations/index.html.erb

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+<div class="page-header">
+  <h2>Listing Simulations</h2>
+</div>
+
+<table class="table">
+  <thead>
+    <tr>
+      <th>#</th>
+      <th>Status</th>
+      <th>Name</th>
+      <th>Pressure</th>
+      <th colspan="4"></th>
+    </tr>
+  </thead>
+
+  <tbody>
+    <% @simulations.each do |simulation| %>
+      <tr>
+        <td><%= simulation.id %></td>
+        <td><%= status_label(simulation) %></td>
+        <td><%= simulation.name %></td>
+        <td><%= simulation.pressure %></td>
+        <td><%= link_to 'Submit', submit_simulation_path(simulation), method: :put, class: 'btn btn-success btn-sm' unless simulation.submitted? %></td>
+        <td><%= link_to 'Show', simulation, class: 'btn btn-primary btn-sm' %></td>
+        <td><%= link_to 'Edit', edit_simulation_path(simulation), class: 'btn btn-default btn-sm' unless simulation.submitted? %></td>
+        <td><%= link_to 'Copy', copy_simulation_path(simulation), method: :put, class: 'btn btn-default btn-sm' %></td>
+        <td><%= link_to 'Destroy', simulation, method: :delete, class: 'btn btn-danger btn-sm', data: { confirm: 'Are you sure?' } %></td>
+      </tr>
+    <% end %>
+  </tbody>
+</table>
+
+<br>
+
+<%= link_to 'New Simulation', new_simulation_path %>

data/test/dummy/app/views/simulations/new.html.erb

@@ -0,0 +1,5 @@
+<div class="page-header">
+    <h2>New Simulation</h2>
+</div>
+
+<%= render 'form', simulation: @simulation %>

data/test/dummy/app/views/simulations/show.html.erb

@@ -0,0 +1,16 @@
+<div class="page-header">
+    <h2>Showing Simulation</h2>
+</div>
+
+<p>
+  <strong>Name:</strong>
+  <%= @simulation.name %>
+</p>
+
+<p>
+  <strong>Pressure:</strong>
+  <%= @simulation.pressure %>
+</p>
+
+<%= link_to 'Back', simulations_path, class: 'btn btn-default' %>
+<%= link_to 'Edit', edit_simulation_path(@simulation), class: 'btn btn-default' %>

data/test/dummy/bin/bundle

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+#!/usr/bin/env ruby
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../Gemfile', __FILE__)
+load Gem.bin_path('bundler', 'bundle')

data/test/dummy/bin/rails

@@ -0,0 +1,4 @@
+#!/usr/bin/env ruby
+APP_PATH = File.expand_path('../../config/application',  __FILE__)
+require_relative '../config/boot'
+require 'rails/commands'

data/test/dummy/bin/rake

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+#!/usr/bin/env ruby
+require_relative '../config/boot'
+require 'rake'
+Rake.application.run

data/test/dummy/config/application.rb

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+require File.expand_path('../boot', __FILE__)
+
+require 'rails/all'
+
+Bundler.require(*Rails.groups)
+require "osc_machete_rails"
+
+module Dummy
+  class Application < Rails::Application
+    # Settings in config/environments/* take precedence over those specified here.
+    # Application configuration should go into files in config/initializers
+    # -- all .rb files in that directory are automatically loaded.
+
+    # Set Time.zone default to the specified zone and make Active Record auto-convert to this zone.
+    # Run "rake -D time" for a list of tasks for finding time zone names. Default is UTC.
+    # config.time_zone = 'Central Time (US & Canada)'
+
+    # The default locale is :en and all translations from config/locales/*.rb,yml are auto loaded.
+    # config.i18n.load_path += Dir[Rails.root.join('my', 'locales', '*.{rb,yml}').to_s]
+    # config.i18n.default_locale = :de
+  end
+end
+

data/test/dummy/config/boot.rb

@@ -0,0 +1,5 @@
+# Set up gems listed in the Gemfile.
+ENV['BUNDLE_GEMFILE'] ||= File.expand_path('../../../../Gemfile', __FILE__)
+
+require 'bundler/setup' if File.exists?(ENV['BUNDLE_GEMFILE'])
+$LOAD_PATH.unshift File.expand_path('../../../../lib', __FILE__)