bio-commandeer 0.0.1

checksums.yaml

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+  data.tar.gz: cb1e3b28ff63aa29bcc50fc8a5180ea3f968ac12
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data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - jruby-19mode # JRuby in 1.9 mode
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem 'bio-logger', '~>1.0'
+gem 'systemu', '~>2.6'
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.8"
+  gem "rdoc", "~> 3.12"
+  gem "jeweler", "~> 2.0"
+  gem "bundler", "~> 1.3"
+end

data/LICENSE.txt

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+Copyright (c) 2013 Ben J. Woodcroft
+
+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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+# bio-commandeer
+
+[![Build Status](https://secure.travis-ci.org/wwood/bioruby-commandeer.png)](http://travis-ci.org/wwood/bioruby-commandeer)
+
+`Bio::Commandeer` provides a dead simple method of running shell commands from within Ruby:
+
+```ruby
+require 'bio-commandeer'
+Bio::Commandeer.run 'echo 5' #=> "5\n"
+```
+The real advantage of bio-commandeer is that when something goes wrong, it tells you; you don't have go looking for the error. Take for instance this simple script:
+```ruby
+#!/usr/bin/env ruby
+require 'bio-commandeer'
+print Bio::Commandeer.run('echo 5')
+print Bio::Commandeer.run('cat /not_a_file')
+```
+The output is:
+```sh
+5
+<snip>/lib/bio-commandeer/commandeer.rb:32:in `run': Command returned non-zero exit status (1), likely indicating failure. Command run was cat /not_a_file and the STDERR was: (Bio::CommandFailedException)
+cat: /not_a_file: No such file or directory
+	from spec/eg.rb:4:in `<main>'
+```
+When a command fails (as detected through a non-zero exit status), then a `Bio::CommandFailedException` exception is thrown. While you can catch these exceptions with begin/rescue, often the best to do is fail, especially if you are writing quick one-off scripts.
+
+Of course, when running commands such as this, take care not to trust the input directly from the command line, and especially not from a website. When in doubt, use `inspect` around the arguments to make sure that you don't run into [little bobby tables](http://xkcd.com/327).
+
+Note: this software is under active development! Currently it is perhaps overly opinionated and as such not overly flexible.
+
+## Installation
+
+```sh
+gem install bio-commandeer
+```
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-commandeer)
+
+## Copyright
+
+Copyright (c) 2014 Ben J. Woodcroft. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "bio-commandeer"
+  gem.homepage = "http://github.com/wwood/bioruby-commandeer"
+  gem.license = "MIT"
+  gem.summary = %Q{dead simple method of running shell commands from within Ruby}
+  gem.description = %Q{A dead simple method of running shell commands from within Ruby, by applying opinion}
+  gem.email = "donttrustben near gmail.com"
+  gem.authors = ["Ben J. Woodcroft"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+RSpec::Core::RakeTask.new(:rcov) do |spec|
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.rcov = true
+end
+
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bio-commandeer #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/lib/bio-commandeer.rb

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+
+
+require 'bio-logger'
+Bio::Log::LoggerPlus.new('bio-commandeer')
+module Bio
+  module CommandeerLogging
+    def log
+      Bio::Log::LoggerPlus['bio-commandeer']
+    end
+  end
+end
+
+
+require 'bio-commandeer/commandeer.rb'

data/lib/bio-commandeer/commandeer.rb

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+require 'systemu'
+
+module Bio
+  # See #run
+  class Commandeer
+    include Bio::CommandeerLogging
+
+    # Run a command line program, and be opinionated about how to handle failure
+    #
+    # command is a string of the command to be run
+    # * options is a hash, with keys:
+    # :stdin: a string that is the stdin
+    # :log: turn on logging
+    def self.run(command, options={})
+      if options[:log]
+        log_name = 'bio-commandeer'
+        @log = Bio::Log::LoggerPlus[log_name]
+        if @log.nil? or @log.outputters.empty?
+          @log = Bio::Log::LoggerPlus.new(log_name)
+          Bio::Log::CLI.configure(log_name)
+        end
+
+        @log.info "Running command: #{command}"
+      end
+      status, stdout, stderr = systemu command, :stdin => options[:stdin]
+
+      if @log
+        @log.info "Command finished with exitstatus #{status.exitstatus}"
+      end
+
+      if status.exitstatus != 0
+        raise Bio::CommandFailedException, "Command returned non-zero exit status (#{status.exitstatus}), likely indicating failure. Command run was #{command} and the STDERR was:\n#{stderr}"
+      end
+
+      return stdout
+    end
+  end
+
+  class CommandFailedException < Exception; end
+end

data/spec/bio-commandeer_spec.rb

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+require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
+
+describe "BioCommandeer" do
+  it "should return stdout" do
+    Bio::Commandeer.run("echo 1 3").should == "1 3\n"
+  end
+
+  it 'should raise when exit status the command fails' do
+    expect {Bio::Commandeer.run("cat /definitelyNotAFile")}.to raise_error
+  end
+end

data/spec/spec_helper.rb

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+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'rspec'
+require 'bio-commandeer'
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

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+--- !ruby/object:Gem::Specification
+name: bio-commandeer
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Ben J. Woodcroft
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-01-12 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  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'
+- !ruby/object:Gem::Dependency
+  name: systemu
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.6'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.8'
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '2.0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.3'
+description: A dead simple method of running shell commands from within Ruby, by applying
+  opinion
+email: donttrustben near gmail.com
+executables: []
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+files:
+- ".document"
+- ".rspec"
+- ".travis.yml"
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/bio-commandeer.rb
+- lib/bio-commandeer/commandeer.rb
+- spec/bio-commandeer_spec.rb
+- spec/spec_helper.rb
+homepage: http://github.com/wwood/bioruby-commandeer
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.2.0.rc.1
+signing_key: 
+specification_version: 4
+summary: dead simple method of running shell commands from within Ruby
+test_files: []