pbs_job 0.0.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.gitignore +6 -0
- data/Gemfile +4 -0
- data/LICENSE.txt +22 -0
- data/README.md +29 -0
- data/Rakefile +18 -0
- data/bin/pbs_job +107 -0
- data/lib/pbs_job/version.rb +3 -0
- data/lib/pbs_job.rb +4 -0
- data/pbs_job.gemspec +29 -0
- data/spec/pbs_job_spec.rb +128 -0
- data/spec/support/spec_helper.rb +21 -0
- data/templates/job.pbs.tt +4 -0
- data/templates/job.qsub.tt +3 -0
- data/templates/task.tt +6 -0
- metadata +160 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: fc1d00b54a1f3831231d2298367a8d6c04146b27
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data.tar.gz: d3d52813019b0a936c1cbb679f93db234ffb087a
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SHA512:
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metadata.gz: b57061cfd8bc858dce808277bbfe3353b663fd72f4a29f572ce8a01fa7aaa1ae4b99a47713a3b6090d03106aa48d39699b652bd1d10ebbd73649d734a893c8e9
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data.tar.gz: d3ba18b5ae94087a58b85210d55923e7467c89814a7378e098ffad66f39f237c69a6c27f3f9581675afc6cfbfc20f8e2ba5f511366321006996e0194831772ec
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data/.gitignore
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data/Gemfile
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data/LICENSE.txt
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Copyright (c) 2013 Dustin Morrill
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MIT License
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Permission is hereby granted, free of charge, to any person obtaining
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a copy of this software and associated documentation files (the
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"Software"), to deal in the Software without restriction, including
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without limitation the rights to use, copy, modify, merge, publish,
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distribute, sublicense, and/or sell copies of the Software, and to
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permit persons to whom the Software is furnished to do so, subject to
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the following conditions:
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The above copyright notice and this permission notice shall be
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included in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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data/README.md
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# PbsJob
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TODO: Write a gem description
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## Installation
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Add this line to your application's Gemfile:
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gem 'pbs_job'
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And then execute:
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$ bundle
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Or install it yourself as:
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$ gem install pbs_job
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## Usage
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TODO: Write usage instructions here
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## Contributing
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1. Fork it
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2. Create your feature branch (`git checkout -b my-new-feature`)
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3. Commit your changes (`git commit -am 'Add some feature'`)
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4. Push to the branch (`git push origin my-new-feature`)
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5. Create new Pull Request
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data/Rakefile
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#!/usr/bin/env rake
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require 'bundler'
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require 'rake/clean'
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require 'rake/testtask'
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include Rake::DSL
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Bundler::GemHelper.install_tasks
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Rake::TestTask.new do |t|
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t.libs << "lib" << 'spec/support'
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t.test_files = FileList['spec/**/*_spec.rb']
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t.verbose = false
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t.warning = false # pry-rescue has a lot of warnings
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end
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task :default => [:test]
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data/bin/pbs_job
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#!/usr/bin/env ruby
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require "rubygems"
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require 'thor'
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require 'date'
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module PbsJob
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class New < Thor::Group
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include Thor::Actions
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argument :name, :desc => 'Name of the new job.'
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argument :email_address, :desc => 'Email to which to send PBS alerts.'
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class_option(
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:link_results,
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{
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:desc => 'Directory to which to redirect results',
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:default => nil,
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:aliases => 'r'
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}
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)
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class_option(
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:script,
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{
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:desc => 'Type of script to make the task script',
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:default => '<script type>',
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:aliases => 's'
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}
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)
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def self.source_root
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File.expand_path('../../', __FILE__)
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end
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def gen_root
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empty_directory full_name
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end
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def qsub_script
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create_file_from_template 'job.qsub'
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end
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def pbs_script
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create_file_from_template 'job.pbs'
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end
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def task
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create_file_from_template 'task'
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end
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def results
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results_path = File.join full_name, 'results'
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if options[:link_results]
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create_link(results_path, options[:link_results])
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else
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empty_directory results_path
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end
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end
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def streams
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empty_directory streams_path
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end
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private
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def create_file_from_template(file_name)
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template(
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"templates/#{file_name}.tt",
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"#{full_name}/#{file_name}"
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)
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end
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# @returns [String] Name with date appended
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def full_name
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@full_name ||= -> do
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today = Date.today
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month = Date::MONTHNAMES[today.month].downcase
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"#{name}.#{month}#{today.day}_#{today.year}"
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end.call
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end
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def abs_job_root
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@abs_job_root ||= File.expand_path(full_name)
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end
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def streams_path
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@streams_path ||= File.join full_name, 'streams'
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end
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def abs_stream_prefix
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@abs_stream_prefix ||= File.join abs_job_root, streams_path, full_name
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end
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end
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class PbsJob < Thor
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map 'n' => :new
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register(
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New,
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'new',
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'new NAME EMAIL_ADDRESS [OPTIONS]',
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"Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS"
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)
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tasks["new"].options = New.class_options
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end
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end
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PbsJob::PbsJob.start(ARGV)
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data/lib/pbs_job.rb
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data/pbs_job.gemspec
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# coding: utf-8
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lib = File.expand_path('../lib', __FILE__)
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$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
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require 'pbs_job/version'
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Gem::Specification.new do |spec|
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spec.name = "pbs_job"
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spec.version = PbsJob::VERSION
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spec.authors = ["Dustin Morrill"]
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spec.email = ["morrill@ualberta.ca"]
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spec.description = %q{PBS/Torque job generator}
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spec.summary = %q{Creates a directory and file structure for a well organized PBS/Torque job.}
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spec.homepage = "https://github.com/dmorrill10/pbs_job"
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spec.license = "MIT"
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spec.files = `git ls-files`.split($/)
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spec.executables = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
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spec.test_files = spec.files.grep(%r{^(test|spec|features)/})
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spec.require_paths = ["lib"]
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spec.add_dependency 'thor', '~> 0.18.1'
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spec.add_development_dependency "bundler", '~> 1.3.5'
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spec.add_development_dependency 'bahia', '~> 0.7.2'
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spec.add_development_dependency 'rake', '~> 10.1.0'
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spec.add_development_dependency 'minitest', '~> 5.0.6'
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spec.add_development_dependency 'awesome_print', '~> 1.1.0'
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spec.add_development_dependency 'simplecov', '~> 0.7.1'
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end
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require_relative 'support/spec_helper'
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require "date"
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require 'tmpdir'
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describe 'pbs_job' do
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HELP = <<-HELP
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Commands:
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pbs_job help [COMMAND] # Describe available commands or ...
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pbs_job new NAME EMAIL_ADDRESS [OPTIONS] # Creates a new PBS job with the ...
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HELP
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NAME = 'test_job'
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EMAIL_ADDRESS = 'email@address'
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TODAY = Date.today
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MONTH = Date::MONTHNAMES[TODAY.month].downcase
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JOB_ROOT = "#{NAME}.#{MONTH}#{TODAY.day}_#{TODAY.year}"
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QSUB_SCRIPT = "#{JOB_ROOT}/job.qsub"
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PBS_SCRIPT = "#{JOB_ROOT}/job.pbs"
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TASK = "#{JOB_ROOT}/task"
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RESULTS = "#{JOB_ROOT}/results"
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STREAMS = "#{JOB_ROOT}/streams"
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it 'prints usage and options without arguments' do
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pbs_job
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stdout.must_equal HELP
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end
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it 'prints help' do
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pbs_job 'help'
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stdout.must_equal HELP
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end
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describe 'new' do
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it 'prints help' do
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pbs_job 'help new'
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stdout.must_equal <<-GEN_HELP
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Usage:
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pbs_job new NAME EMAIL_ADDRESS [OPTIONS]
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Options:
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r, [--link-results=LINK_RESULTS] # Directory to which to redirect results
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s, [--script=SCRIPT] # Type of script to make the task script
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# Default: <script type>
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Creates a new PBS job with the name NAME and arranges for PBS alerts to be sent to EMAIL_ADDRESS, customized by OPTIONS
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GEN_HELP
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end
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it 'requires name argument' do
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pbs_job 'new'
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stderr.must_equal "No value provided for required arguments 'name', 'email_address'\n"
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end
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it 'requires an email argument' do
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pbs_job "new #{NAME}"
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stderr.must_equal "No value provided for required arguments 'email_address'\n"
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end
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it 'creates a file structure for job components' do
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in_tmp_dir do
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pbs_job "new #{NAME} #{EMAIL_ADDRESS}"
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stdout.must_equal <<-DIR
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\e[1m\e[32m create\e[0m #{JOB_ROOT}
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\e[1m\e[32m create\e[0m #{QSUB_SCRIPT}
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\e[1m\e[32m create\e[0m #{PBS_SCRIPT}
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\e[1m\e[32m create\e[0m #{TASK}
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\e[1m\e[32m create\e[0m #{RESULTS}
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\e[1m\e[32m create\e[0m #{STREAMS}
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DIR
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File.directory?(JOB_ROOT).must_equal true
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File.file?(QSUB_SCRIPT).must_equal true
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File.file?(PBS_SCRIPT).must_equal true
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File.file?(TASK).must_equal true
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File.directory?(RESULTS).must_equal true
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File.directory?(STREAMS).must_equal true
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end
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end
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end
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describe 'script type option' do
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it '--script allows specification of the script type of task' do
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in_tmp_dir do
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pbs_job "new #{NAME} #{EMAIL_ADDRESS} --script=bash"
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stdout.must_equal <<-DIR
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\e[1m\e[32m create\e[0m #{JOB_ROOT}
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\e[1m\e[32m create\e[0m #{QSUB_SCRIPT}
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\e[1m\e[32m create\e[0m #{PBS_SCRIPT}
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\e[1m\e[32m create\e[0m #{TASK}
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\e[1m\e[32m create\e[0m #{RESULTS}
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\e[1m\e[32m create\e[0m #{STREAMS}
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DIR
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File.directory?(JOB_ROOT).must_equal true
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File.file?(QSUB_SCRIPT).must_equal true
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File.file?(PBS_SCRIPT).must_equal true
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File.file?(TASK).must_equal true
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File.directory?(RESULTS).must_equal true
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File.directory?(STREAMS).must_equal true
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end
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end
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end
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describe 'results link option' do
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it '--link-results allows redirection of results' do
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linked_results = '/scratch/results'
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in_tmp_dir do
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pbs_job "new #{NAME} #{EMAIL_ADDRESS} --link-results=#{linked_results}"
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stdout.must_equal <<-DIR
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\e[1m\e[32m create\e[0m #{JOB_ROOT}
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\e[1m\e[32m create\e[0m #{QSUB_SCRIPT}
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\e[1m\e[32m create\e[0m #{PBS_SCRIPT}
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\e[1m\e[32m create\e[0m #{TASK}
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\e[1m\e[32m create\e[0m #{RESULTS}
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\e[1m\e[32m create\e[0m #{STREAMS}
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DIR
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File.directory?(JOB_ROOT).must_equal true
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File.file?(QSUB_SCRIPT).must_equal true
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File.file?(PBS_SCRIPT).must_equal true
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File.file?(TASK).must_equal true
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File.symlink?(RESULTS).must_equal true
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File.readlink(RESULTS).must_equal linked_results
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File.directory?(STREAMS).must_equal true
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end
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end
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end
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def in_tmp_dir
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Dir.mktmpdir do |dir|
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Dir.chdir dir
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yield dir if block_given?
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end
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end
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end
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require 'simplecov'
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SimpleCov.start
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|
+
require 'minitest/autorun'
|
5
|
+
require 'minitest/spec'
|
6
|
+
|
7
|
+
begin
|
8
|
+
require 'awesome_print'
|
9
|
+
module Minitest::Assertions
|
10
|
+
def mu_pp(obj)
|
11
|
+
obj.awesome_inspect
|
12
|
+
end
|
13
|
+
end
|
14
|
+
rescue LoadError
|
15
|
+
end
|
16
|
+
|
17
|
+
require 'bahia'
|
18
|
+
|
19
|
+
class MiniTest::Spec
|
20
|
+
include Bahia
|
21
|
+
end
|
data/templates/task.tt
ADDED
metadata
ADDED
@@ -0,0 +1,160 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: pbs_job
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Dustin Morrill
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2013-07-25 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: thor
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - ~>
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: 0.18.1
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - ~>
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: 0.18.1
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: bundler
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - ~>
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: 1.3.5
|
34
|
+
type: :development
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - ~>
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: 1.3.5
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: bahia
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - ~>
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: 0.7.2
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - ~>
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: 0.7.2
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: rake
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - ~>
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: 10.1.0
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - ~>
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: 10.1.0
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: minitest
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ~>
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 5.0.6
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ~>
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 5.0.6
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: awesome_print
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - ~>
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: 1.1.0
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - ~>
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: 1.1.0
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: simplecov
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - ~>
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: 0.7.1
|
104
|
+
type: :development
|
105
|
+
prerelease: false
|
106
|
+
version_requirements: !ruby/object:Gem::Requirement
|
107
|
+
requirements:
|
108
|
+
- - ~>
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: 0.7.1
|
111
|
+
description: PBS/Torque job generator
|
112
|
+
email:
|
113
|
+
- morrill@ualberta.ca
|
114
|
+
executables:
|
115
|
+
- pbs_job
|
116
|
+
extensions: []
|
117
|
+
extra_rdoc_files: []
|
118
|
+
files:
|
119
|
+
- .gitignore
|
120
|
+
- Gemfile
|
121
|
+
- LICENSE.txt
|
122
|
+
- README.md
|
123
|
+
- Rakefile
|
124
|
+
- bin/pbs_job
|
125
|
+
- lib/pbs_job.rb
|
126
|
+
- lib/pbs_job/version.rb
|
127
|
+
- pbs_job.gemspec
|
128
|
+
- spec/pbs_job_spec.rb
|
129
|
+
- spec/support/spec_helper.rb
|
130
|
+
- templates/job.pbs.tt
|
131
|
+
- templates/job.qsub.tt
|
132
|
+
- templates/task.tt
|
133
|
+
homepage: https://github.com/dmorrill10/pbs_job
|
134
|
+
licenses:
|
135
|
+
- MIT
|
136
|
+
metadata: {}
|
137
|
+
post_install_message:
|
138
|
+
rdoc_options: []
|
139
|
+
require_paths:
|
140
|
+
- lib
|
141
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
142
|
+
requirements:
|
143
|
+
- - '>='
|
144
|
+
- !ruby/object:Gem::Version
|
145
|
+
version: '0'
|
146
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
147
|
+
requirements:
|
148
|
+
- - '>='
|
149
|
+
- !ruby/object:Gem::Version
|
150
|
+
version: '0'
|
151
|
+
requirements: []
|
152
|
+
rubyforge_project:
|
153
|
+
rubygems_version: 2.0.3
|
154
|
+
signing_key:
|
155
|
+
specification_version: 4
|
156
|
+
summary: Creates a directory and file structure for a well organized PBS/Torque job.
|
157
|
+
test_files:
|
158
|
+
- spec/pbs_job_spec.rb
|
159
|
+
- spec/support/spec_helper.rb
|
160
|
+
has_rdoc:
|