rjobs 0.1.0.alpha

data/.codeintel/config

@@ -0,0 +1,26 @@
+{
+    "PHP": {
+        "php": '/usr/bin/php',
+        "phpExtraPaths": [],
+        "phpConfigFile": 'php.ini'
+    },
+    "JavaScript": {
+        "javascriptExtraPaths": []
+    },
+    "Perl": {
+        "perl": "/usr/bin/perl",
+        "perlExtraPaths": []
+    },
+    "Ruby": {
+        "ruby": "/Users/merlin/.rvm/rubies/ruby-1.9.2-p290/bin/ruby",
+        "rubyExtraPaths": []
+    },
+    "Python": {
+        "python": '/usr/bin/python',
+        "pythonExtraPaths": []
+    },
+    "Python3": {
+        "python": '/usr/bin/python3',
+        "pythonExtraPaths": []
+    }
+}

data/.gitignore

@@ -0,0 +1,7 @@
+*.swp
+*.gem
+.bundle
+Gemfile.lock
+pkg/*
+tmp/*
+vendor/*

data/Gemfile

@@ -0,0 +1,4 @@
+source "http://rubygems.org"
+
+# Specify your gem's dependencies in rjobs.gemspec
+gemspec

data/Guardfile

@@ -0,0 +1,15 @@
+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+guard 'cucumber' do
+  watch(%r{^features/.+\.feature$})
+  watch(%r{^features/support/.+$})          { 'features' }
+  watch(%r{^features/step_definitions/(.+)_steps\.rb$}) { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'features' }
+end
+
+
+guard 'rspec' do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/(.+)\.rb$}) {|m| "spec/lib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb') { "spec" }
+end

data/README.md

@@ -0,0 +1 @@
+This is the readme file

data/Rakefile

@@ -0,0 +1,34 @@
+require "bundler/gem_tasks"
+
+
+desc 'List all defined steps'
+task :steps do
+  require 'hirb'
+  extend Hirb::Console
+  puts "CUCUMBER steps:"
+  puts ""
+  #step_definition_dir = "features/step_definitions"
+  step_definition_dir = "."
+  #step_definition_dir = "/Users/merlin/.rvm/gems/ruby-1.9.2-p290/gems/aruba-0.4.7/lib/aruba/"
+
+  Dir.glob(File.join(step_definition_dir,'**/*.rb')).each do |step_file|
+
+    puts "File: #{step_file}"
+    puts ""
+    results = []
+    File.new(step_file).read.each_line.each_with_index do |line, number|
+
+      next unless line =~ /^\s*(?:Given|When|Then)\s+|\//
+        res = /(?:Given|When|Then)[\s\(]*\/(.*)\/([imxo]*)[\s\)]*do\s*(?:$|\|(.*)\|)/.match(line)
+      next unless res
+      matches = res.captures
+      results << OpenStruct.new(
+        :steps => matches[0],
+        :modifier => matches[1],
+        :args => matches[2]
+      )
+        end
+      table results, :resize => false, :fields=>[:steps, :modifier, :args]
+      puts ""
+  end
+end

data/bin/rjharvest

@@ -0,0 +1,34 @@
+#!/usr/bin/env ruby
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../lib') unless $LOAD_PATH.include?(File.dirname(__FILE__) + '/../lib')
+
+require 'trollop'
+require "rjobs/jobs_file"
+require "rjobs/job"
+require "rjobs/job_handler"
+require 'rjobs/cli_helper'
+include  Rjobs::CliHelper   
+
+p = Trollop::Parser.new do
+  banner <<-EOS
+Harvest all finished jobs described in the jobs file.
+
+Usage:
+       rjharvest [options] <filename>
+where [options] are:
+EOS
+  
+end
+
+opts = Trollop::with_standard_exception_handling p do
+  o = p.parse ARGV
+  raise Trollop::HelpNeeded if ARGV.empty? # show help screen
+end
+
+jobs_file = ARGV[0]
+
+jobs = get_jobs_info(jobs_file)
+jobs.each do |job| 
+  Rjobs::JobHandler.get_job_results(job)        
+end        
+

data/bin/rjstatus

@@ -0,0 +1,35 @@
+#!/usr/bin/env ruby
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../lib') unless $LOAD_PATH.include?(File.dirname(__FILE__) + '/../lib')
+
+require 'trollop'
+require "rjobs/jobs_file"
+require "rjobs/job"
+require "rjobs/job_handler"
+require 'rjobs/cli_helper'
+include  Rjobs::CliHelper   
+
+p = Trollop::Parser.new do
+  banner <<-EOS
+Get the status of jobs described in the jobs file.
+
+Usage:
+       rjstatus [options] <filename>
+where [options] are:
+EOS
+  
+end
+
+opts = Trollop::with_standard_exception_handling p do
+  o = p.parse ARGV
+  raise Trollop::HelpNeeded if ARGV.empty? # show help screen
+end
+
+jobs_file = ARGV[0]
+
+jobs = get_jobs_info(jobs_file)
+
+jobs.each do |job|        
+  puts "#{job.name} - #{job.status_with_color}"
+end
+

data/bin/rjsubmit

@@ -0,0 +1,49 @@
+#!/usr/bin/env ruby
+
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../lib') unless $LOAD_PATH.include?(File.dirname(__FILE__) + '/../lib')
+
+require 'trollop'
+require "rjobs/jobs_file"
+require "rjobs/job_input_file"
+require "rjobs/job"
+require "rjobs/job_handler"
+require 'rjobs/cli_helper'
+include  Rjobs::CliHelper   
+
+p = Trollop::Parser.new do
+  banner <<-EOS
+Submit jobs described in the YAML input file.
+
+Usage:
+      rjsubmit [options] <filename>
+where [options] are:
+EOS
+  
+end
+
+opts = Trollop::with_standard_exception_handling p do
+  o = p.parse ARGV
+  raise Trollop::HelpNeeded if ARGV.empty? # show help screen
+end
+
+
+jobs_input_file = ARGV[0]
+
+jif = Rjobs::JobInputFile.new(jobs_input_file)
+jobs = []
+length = jif.jobIdTo.length
+(jif.jobIdFrom .. jif.jobIdTo).each do |id| 
+  j = Rjobs::Job.new()
+  j.name = "%s%0#{length}d" % [jif.jobName,id]
+  j.command = jif.command
+  jobs << j        
+end
+
+jobs.each do |job|        
+  Rjobs::JobHandler.submit_job(job)        
+end
+
+jf = Rjobs::JobsFile.new()
+jf.write(jif.jobName+".rjobs",jobs)
+
+puts "#{jobs.count} job(s) submited.".green

data/features/harvest.feature

@@ -0,0 +1,32 @@
+Feature: Submit
+  As a user
+  I want to harvest jobs' results
+  So that I can analyse it later
+  
+  Scenario: Have a harvest command
+    When I successfully run `rjharvest`
+    Then the output should contain "rjharvest [options] <filename>"
+  
+
+
+  Scenario: Submit a job input files will return a jobs result file
+    Given a file named "VAA.rjobs" with:
+    """
+    VAA1 1
+    VAA2 2
+    VAA3 3
+    VAA4 4
+    VAA5 5
+    VAA6 6
+    VAA7 7
+    """
+    When I successfully run `rjharvest VAA.rjobs`
+    Then show me the output
+    Then a file named "VAA1.out" should exist    
+    And the file "VAA1.out" should match /Hello world/
+    # And a file named "VAA.out" should exist    
+    # And the file "VAA.out" should match /Hello World/
+
+       
+  
+  

data/features/listJobs.feature

@@ -0,0 +1,22 @@
+Feature: List Jobs
+	As a user
+	I want to have a function to list all jobs
+	So as I can see a list of jobs
+
+	Background:
+
+
+	Scenario: list all jobs
+		Given a file named "test_jobs.rjob" with:
+		"""
+		VAA1 1
+		VAA2 2
+		VAA3 3
+		VAA4 4
+		VAA5 5
+		VAA6 6
+		VAA7 7
+		"""
+		When I successfully run `rjstatus test_jobs.rjob`    
+		Then each line of the output should match /VAA\d+ - (Finished|Failed|Not Exist)/
+		And show me the output

data/features/step_definitions/listJobs_steps.rb

@@ -0,0 +1,19 @@
+require 'rjobs/process'
+require 'rjobs/job_handler'
+require 'cucumber/rspec/doubles'
+require 'aruba/api'
+require 'aruba/hooks'
+require 'aruba/reporting'
+
+World(Aruba::Api)
+
+Then /^show me the output$/ do
+  puts all_stdout
+end
+
+Then /^each line of the output should match \/([^\/]*)\/$/ do |expected|
+    all_stdout.split("\n").each do |line|
+      # puts line
+      line.should match expected
+    end
+end

data/features/step_definitions/submit_steps.rb

@@ -0,0 +1,2 @@
+
+

data/features/submit.feature

@@ -0,0 +1,27 @@
+Feature: Submit
+  As a user
+  I want to submit jobs
+  So that jobs can be run on the xgrid
+  
+  Scenario: Have a submit command
+    When I successfully run `rjsubmit`
+    Then the output should contain "rjsubmit [options] <filename>"
+  
+
+
+  Scenario: Submit a job input files will return a jobs file
+    Given a file named "VAA.myJobs" with:
+    """
+    JobName: VAA
+    JobId: 1-10
+    Command: ~/plays/cpp/testGrid/a.out
+    """
+    When I successfully run `rjsubmit VAA.myJobs`
+    Then show me the output
+    Then a file named "VAA.rjobs" should exist    
+    And the file "VAA.rjobs" should match /(VAA\d+\t\d+\n)+/
+    
+
+       
+  
+  

data/features/support/env.rb

@@ -0,0 +1,6 @@
+require 'aruba'
+require 'cucumber/rspec/doubles'
+
+ENV["RAILS_ENV"] ||= "cucumber"
+ENV['PATH'] = "#{File.expand_path(File.dirname(__FILE__) + '/../../bin')}#{File::PATH_SEPARATOR}#{ENV['PATH']}"
+$LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib') unless $LOAD_PATH.include?(File.dirname(__FILE__) + '/../../lib')

data/features/support/setup.rb

@@ -0,0 +1 @@
+require 'aruba/cucumber'

data/lib/rjobs.rb

@@ -0,0 +1,5 @@
+require "rjobs/version"
+
+module Rjobs
+    # Your code goes here...
+end

data/lib/rjobs/cli_helper.rb

@@ -0,0 +1,14 @@
+module Rjobs
+  module CliHelper
+    def get_jobs_info(jobs_file)
+      jf = JobsFile.new(jobs_file)
+      jobs= []
+      jf.ids.each_with_index do |jobId,index|
+        job = Rjobs::Job.new(jobId, Rjobs::JobHandler.get_job_attributes(jobId))
+        job.name = jf.job_names[index]
+        jobs << job
+      end
+      jobs
+    end
+  end
+end

data/lib/rjobs/color_helper.rb

@@ -0,0 +1,12 @@
+class String
+  def colorize(text, color_code)
+    "#{color_code}#{text}e[0m"
+  end
+
+  def red 
+    colorize(self, "e[31m") 
+  end
+  def green 
+    colorize(self, "e[32m")
+  end
+end

data/lib/rjobs/command_builder.rb

@@ -0,0 +1,23 @@
+module Rjobs
+  class CommandBuilder
+    attr_accessor :command, :params    
+    def initialize(command = "", params = "")
+      @command = command
+      @params = params
+    end
+
+    def build()
+      cmd = []
+      cmd <<  @command
+      @params.each do |key, value|
+        if value == ""
+          cmd << "#{key}"
+        else
+          cmd << "-#{key}"
+          cmd << value
+        end        
+      end
+      cmd.join(" ")
+    end
+  end
+end

data/lib/rjobs/job.rb

@@ -0,0 +1,53 @@
+require 'plist'
+require 'rjobs/command_builder'
+require 'colorize'
+
+module Rjobs
+  class Job
+    attr_accessor :id, :name, :status
+    attr_writer :params, :command
+
+    def initialize(id=0,xml="")
+      @id = id
+      parse(xml)
+      @params= {}
+      @command = ""
+    end
+    
+    def xml=(xml)
+      parse(xml)
+    end
+
+    def command
+      cb = Rjobs::CommandBuilder.new(@command,@params)
+      cb.build
+    end
+    
+    def status_with_color
+      case @status
+      when /Finished/
+        @status.green
+      when /Failed/
+        @status.light_red
+      when /Not Exist/
+        @status.red
+      else
+        @status
+      end
+    end
+
+
+    private
+    def parse(xml)
+      return if xml.empty?
+      result = Plist::parse_xml(xml)
+      @name = result['jobAttributes'].nil? ? "" : result['jobAttributes']['name']      
+      @status = result['jobAttributes'].nil? ? "Not Exist" : result['jobAttributes']['jobStatus']      
+      
+    end
+
+
+
+  end
+end
+