condor-job 1.3.13

data/.gitignore

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+*.gem
+*.rbc
+.bundle
+.config
+.yardoc
+Gemfile.lock
+InstalledFiles
+_yardoc
+coverage
+doc/
+lib/bundler/man
+pkg
+rdoc
+spec/reports
+test/tmp
+test/version_tmp
+tmp
+vendor/bundle
+cinput*

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in condor-job.gemspec
+gemspec

data/LICENSE.txt

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+Copyright (c) 2013 Jonatan Hejzlar
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# Condor::Job
+
+TODO: Write a gem description
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'condor-job'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install condor-job
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Contributing
+
+1. Fork it
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create new Pull Request

data/Rakefile

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+require "bundler/gem_tasks"
+
+require 'rake/testtask'
+
+Rake::TestTask.new do |t|
+  t.libs = ["lib/condor"]
+  t.warning = true
+  t.verbose = true
+  t.test_files = FileList['test/test_*.rb']
+end

data/condor-job.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'condor-job/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = "condor-job"
+  spec.version       = Condor::VERSION
+  spec.authors       = ["Jonatan Hejzlar"]
+  spec.email         = ["hea@ujv.cz"]
+  spec.description   = "Gem for condor execution of bash jobs"
+  spec.summary       = "Gem for condor execution of bash jobs"
+  spec.homepage      = ""
+  spec.license       = "MIT"
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ["lib"]
+
+  spec.add_development_dependency "bundler", "~> 1.3"
+  spec.add_development_dependency "rake"
+  spec.add_runtime_dependency "nokogiri"
+  spec.add_runtime_dependency "activesupport"
+end

data/lib/condor-job/job.rb

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+require_relative "version"
+
+module Condor
+  
+  class Job
+    
+    attr_reader :priority, :id, :cmd, :dir, :job_data
+    attr_reader :finished
+
+    def initialize(cmd = nil, options = {})
+      options ||= {}
+      @priority = options.delete(:priority)
+      @avoid_finalize = !!options.delete(:no_finalizer)
+      @home = `echo $HOME`.strip
+      @home = nil if (@home || '').empty?
+      @dir = options.delete(:directory) || Dir.pwd
+      @id = options.delete(:id)
+      @finished = false
+      @job_data = nil
+      @base_name = options.delete(:base_name) || "#{@dir}/cinput"
+      @suppress_numbering = options.delete(:simple)
+      
+      options.empty? or raise "Unknown options: #{options.keys.inspect}"
+
+      if @id
+        @cmd = nil
+        update
+      else
+        @id = nil
+        @cmd = []
+        @cmd << "#!/bin/bash"
+        @cmd << "# encoding: UTF-8"
+        @cmd << "source /etc/profile"
+        @cmd << "source #{@home}/.profile" if @home and File.exist?("#{@home}/.profile")
+        @cmd << "source #{@home}/.rvm/scripts/rvm" if @home and File.exist?("#{@home}/.rvm/scripts/rvm")        
+        @cmd += [cmd].flatten
+      end
+      
+      ObjectSpace.define_finalizer(self, proc { finalize_job }) unless @avoid_finalize
+    end
+
+    def run(set_dir = nil)
+      @dir = set_dir || @dir
+      name = if @suppress_numbering
+        "#{@base_name}"
+      else
+        # get condor input file number
+        num = (Dir["#{@base_name}*"].map{|x| File.basename(x).sub(@base_name,'').to_i}.max or 0) + 1
+        "#{@base_name}#{num}"
+      end
+      
+      @input, @log, @error, @output, @bash = ['.inp','.log','.error','.output',''].map{|x| "#{name}#{x}"}
+
+      # create bash executable file to run
+      File.open(@bash,'w'){|f| f.puts @cmd * "\n"}
+      `chmod +x #{@bash}`
+
+      input = []
+      input << "Executable = #{@bash}"
+      input << "Universe = vanilla"
+      input << "Log = #{name}.log"
+      input << "Error = #{name}.error"
+      input << "Environment = HOME=#{@home}" if @home
+      input << "Initialdir = #{@dir}"
+      input << "Output = #{@output}"
+      input << "Requirements = OpSys == \"LINUX\""
+      input << "Queue"
+
+      File.open(@input, 'w'){|f| f.puts input * "\n"}
+      if submit_output = `condor_submit #{@input}`.strip.split.last
+        @id = submit_output + '0'
+        set_priority
+        update(true)
+        @executed = true
+      else
+        @id = nil
+        @executed = false
+        @job_data = nil
+      end        
+    end
+
+    def cleanup
+      [@input, @log, @error, @output, @bash].each{|x| `rm #{x}` if x and File.exists?(x)} if @id
+    end
+
+    def priority=(val)
+      @priority = val
+      set_priority
+    end
+
+    def done?; @finished; end
+    def running?; @job_data ? (@job_data.job_status == '2') : false; end
+    def idle?; @job_data ? (@job_data.job_status == '1') : false; end
+    def held?; @job_data ? (@job_data.job_status == '5') : false; end
+    def runtime; @job_data ? Time.at(@job_data.server_time.to_f - @job_data.job_start_date.to_f).utc.strftime("%H:%M:%S") : nil; end
+    def alive?; @id and !@finished; end
+
+    def error; IO.read(@error); end
+    def input; IO.read(@input); end
+    def log; IO.read(@log); end
+    def output; IO.read(@output); end
+    def bash; IO.read(@bash); end
+
+    # update job information
+    def update(force = false)
+      Condor::Queue.load(force)
+      return nil if !@id
+      if @job_data = Condor::Queue[@id]
+        return self
+      else
+        @finished = true 
+        return nil
+      end
+    end
+    
+    def remove
+      `condor_rm #{@id}` if @id
+    end
+
+    def finalize_job
+      unless @avoid_finalize
+        remove if !done?
+        cleanup
+      end
+    end
+
+  private
+
+    def set_priority
+      `condor_prio -p #{@priority} #{@id}` if alive?
+    end
+    
+  end
+end

data/lib/condor-job/pool.rb

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+module Condor
+  class Pool
+    attr_reader :jobs
+    attr_reader :waiting
+
+    def initialize
+      @jobs = []
+      @waiting = {}
+    end
+
+    # run command, given job dependencies
+    def add(cmd, dep = nil, priority = nil, dir = nil)
+      return if !cmd or cmd.empty?
+      c = Job.new(cmd, :priority => priority, :directory => dir)
+      if [dep].flatten.compact.empty?
+        c.run
+      else
+        @waiting[c] = [dep].flatten.compact
+      end
+      @jobs << c
+      update
+      return c
+    end
+
+    def update
+      Condor::Queue.load(true)
+      @jobs.each do |j|
+        j.update
+        next if !(deps = @waiting[j])
+        if deps.all?(&:done?)
+          j.run
+          @waiting.delete(j)
+        end
+      end
+    end
+
+    def finalize
+      while alive?
+        sleep 2
+        update
+      end
+      @jobs.each{|x| x.cleanup}
+      @jobs = []
+    end
+
+    def alive?
+      return true if !@waiting.empty?
+      @jobs.any?(&:done?)
+    end
+  end
+end

data/lib/condor-job/queue.rb

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+require 'nokogiri'
+require 'active_support/inflector'
+require 'singleton'
+require 'ostruct'
+
+module Condor
+  
+  class Queue
+    
+    include Singleton
+    
+    def self.load(force = false)
+      instance.load(force)
+    end
+    
+    def self.[](job_id)
+      instance[job_id]
+    end
+    
+    def [](job_id)
+      @queue.detect{|job| job_id == job.global_job_id.split('#')[1]}
+    end
+    
+    def initialize
+      load
+    end
+    
+    def load(force = false)
+      @queue = nil if force
+      @queue ||= begin
+        queue = []
+      
+        data = `condor_q -global -xml 2>&1`
+        n_retries = 0
+        while data.include?("condor_collector") # retry!
+          data = `condor_q -global -xml 2>&1`
+          sleep rand
+          (n_retries += 1) < 10 or raise "Could not retrieve the queue!"
+        end
+      
+        xml = Nokogiri::XML("<condor>#{data}</condor>")
+        xml.root.css("c").each do |e|
+          job = {}
+          e.css("a").each do |ee|
+            key = ee.attributes["n"].to_s
+            if ee.children.first
+              val = ee.children.first.text
+              job[key.underscore] = val
+            end
+          end
+
+          queue << QueueEntry.new(job)
+        end
+        @queue = queue
+      end
+      @queue
+    end
+    
+  end
+  
+  class QueueEntry < OpenStruct
+
+  end
+  
+end

data/lib/condor-job/version.rb

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+module Condor
+  VERSION = "1.3.13"
+end

data/lib/condor-job.rb

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+require_relative 'condor-job/queue.rb'
+require_relative 'condor-job/pool.rb'
+require_relative 'condor-job/job.rb'

data/test/test_basic.rb

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+require 'minitest/autorun'
+require 'minitest/unit'
+require 'minitest/pride'
+
+require 'rubygems'
+require 'bundler/setup'
+require_relative '../lib/condor-job'
+
+class TestBasic < MiniTest::Unit::TestCase
+
+  def test_simple_run
+    puts "Running a simple job"
+    j = Condor::Job.new 'echo "hello"'
+    j.run
+    while !j.done?
+      j.update
+      sleep 2
+      if j.running?
+        puts "running #{j.runtime} @ #{j.job_data.remote_host}"
+      elsif j.held?
+        puts "held : #{j.job_data.hold_reason}"
+	#break
+      elsif j.idle?
+        puts "idle"
+      end
+    end
+
+    puts "output: #{j.output}, error: #{j.error}"
+  end
+
+  def test_pool
+    puts "Pool test"
+    c = Condor::Pool.new
+    job = c.add ['echo "hi there"', 'sleep 2']
+    job1 = c.add 'echo "reply"', job
+    job2 = c.add 'echo "priority reply"', job, 1
+    c.add 'echo "wait for all reply"', [job1, job2]
+    puts "Waiting for the pool"
+    c.finalize
+  end
+  
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: condor-job
+version: !ruby/object:Gem::Version
+  version: 1.3.13
+  prerelease: 
+platform: ruby
+authors:
+- Jonatan Hejzlar
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-01-01 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.3'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: nokogiri
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+description: Gem for condor execution of bash jobs
+email:
+- hea@ujv.cz
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .gitignore
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- condor-job.gemspec
+- lib/condor-job.rb
+- lib/condor-job/job.rb
+- lib/condor-job/pool.rb
+- lib/condor-job/queue.rb
+- lib/condor-job/version.rb
+- test/test_basic.rb
+homepage: ''
+licenses:
+- MIT
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.28
+signing_key: 
+specification_version: 3
+summary: Gem for condor execution of bash jobs
+test_files:
+- test/test_basic.rb