libis-rosetta_checker 1.0.0

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data/.rspec ADDED
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+ --format documentation
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+ --color
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+ --require spec_helper
data/.travis.yml ADDED
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+ sudo: false
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+ language: ruby
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+ rvm:
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+ - 2.4.0
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+ before_install: gem install bundler -v 1.16.0
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+ # Contributor Covenant Code of Conduct
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+
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+ ## Our Pledge
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+
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+ In the interest of fostering an open and welcoming environment, we as
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+ contributors and maintainers pledge to making participation in our project and
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+ our community a harassment-free experience for everyone, regardless of age, body
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+ size, disability, ethnicity, gender identity and expression, level of experience,
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+ nationality, personal appearance, race, religion, or sexual identity and
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+ orientation.
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+
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+ ## Our Standards
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+
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+ Examples of behavior that contributes to creating a positive environment
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+ include:
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+
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+ * Using welcoming and inclusive language
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+ * Being respectful of differing viewpoints and experiences
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+ * Gracefully accepting constructive criticism
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+ * Focusing on what is best for the community
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+ * Showing empathy towards other community members
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+
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+ Examples of unacceptable behavior by participants include:
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+
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+ * The use of sexualized language or imagery and unwelcome sexual attention or
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+ advances
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+ * Trolling, insulting/derogatory comments, and personal or political attacks
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+ * Public or private harassment
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+ * Publishing others' private information, such as a physical or electronic
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+ address, without explicit permission
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+ * Other conduct which could reasonably be considered inappropriate in a
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+ professional setting
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+
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+ ## Our Responsibilities
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+
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+ Project maintainers are responsible for clarifying the standards of acceptable
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+ behavior and are expected to take appropriate and fair corrective action in
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+ response to any instances of unacceptable behavior.
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+
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+ Project maintainers have the right and responsibility to remove, edit, or
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+ reject comments, commits, code, wiki edits, issues, and other contributions
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+ that are not aligned to this Code of Conduct, or to ban temporarily or
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+ permanently any contributor for other behaviors that they deem inappropriate,
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+ threatening, offensive, or harmful.
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+
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+ ## Scope
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+
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+ This Code of Conduct applies both within project spaces and in public spaces
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+ when an individual is representing the project or its community. Examples of
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+ representing a project or community include using an official project e-mail
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+ address, posting via an official social media account, or acting as an appointed
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+ representative at an online or offline event. Representation of a project may be
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+ further defined and clarified by project maintainers.
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+
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+ ## Enforcement
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+
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+ Instances of abusive, harassing, or otherwise unacceptable behavior may be
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+ reported by contacting the project team at kris.dekeyser@libis.be. All
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+ complaints will be reviewed and investigated and will result in a response that
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+ is deemed necessary and appropriate to the circumstances. The project team is
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+ obligated to maintain confidentiality with regard to the reporter of an incident.
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+ Further details of specific enforcement policies may be posted separately.
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+
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+ Project maintainers who do not follow or enforce the Code of Conduct in good
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+ faith may face temporary or permanent repercussions as determined by other
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+ members of the project's leadership.
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+
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+ ## Attribution
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+
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+ This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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+ available at [http://contributor-covenant.org/version/1/4][version]
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+
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+ [homepage]: http://contributor-covenant.org
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+ [version]: http://contributor-covenant.org/version/1/4/
data/Gemfile ADDED
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+ source "https://rubygems.org"
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+
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+ git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
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+
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+ # Specify your gem's dependencies in libis-rosetta_checker.gemspec
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+ gemspec
data/LICENSE.txt ADDED
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2017 LIBIS (Kris Dekeyser)
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
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+ in the Software without restriction, including without limitation the rights
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+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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+ copies of the Software, and to permit persons to whom the Software is
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+ furnished to do so, subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in
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+ all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.
data/README.md ADDED
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+ # Libis::RosettaChecker
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+
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+ Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/libis/rosetta_checker`. To experiment with that code, run `bin/console` for an interactive prompt.
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+
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+ TODO: Delete this and the text above, and describe your gem
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+
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+ ## Installation
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+
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+ Add this line to your application's Gemfile:
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+
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+ ```ruby
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+ gem 'libis-rosetta_checker'
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+ ```
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+
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+ And then execute:
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+
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+ $ bundle
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+
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+ Or install it yourself as:
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+
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+ $ gem install libis-rosetta_checker
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+
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+ ## Usage
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+
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+ TODO: Write usage instructions here
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+
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+ ## Development
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+
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+ After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
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+
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+ To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
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+
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+ ## Contributing
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+
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+ Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/libis-rosetta_checker. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
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+
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+ ## License
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+
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+ The gem is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
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+
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+ ## Code of Conduct
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+
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+ Everyone interacting in the Libis::RosettaChecker project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/libis-rosetta_checker/blob/master/CODE_OF_CONDUCT.md).
data/Rakefile ADDED
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+ require "bundler/gem_tasks"
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+ require "rspec/core/rake_task"
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+
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+ RSpec::Core::RakeTask.new(:spec)
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+
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+ task :default => :spec
data/bin/console ADDED
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+ #!/usr/bin/env ruby
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+
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+ require "bundler/setup"
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+ require "libis/rosetta_checker"
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+
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+ # You can add fixtures and/or initialization code here to make experimenting
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+ # with your gem easier. You can also use a different console, if you like.
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+
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+ # (If you use this, don't forget to add pry to your Gemfile!)
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+ # require "pry"
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+ # Pry.start
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+
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+ require "irb"
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+ IRB.start(__FILE__)
data/bin/setup ADDED
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+ #!/usr/bin/env bash
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+ set -euo pipefail
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+ IFS=$'\n\t'
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+ set -vx
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+
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+ bundle install
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+
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+ # Do any other automated setup that you need to do here
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+ #!/usr/bin/env ruby
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+
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+ require "bundler/setup"
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+ require "libis/rosetta_checker"
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+
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+ Libis::RosettaChecker.run
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+ require 'optionparser'
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+ require 'digest'
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+ require 'bzip2/ffi'
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+ require 'zip'
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+ require 'oci8'
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+ require 'logging'
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+ require 'pathname'
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+ require 'csv'
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+
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+ require_relative 'sub_command'
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+ require_relative 'options/files_to_ingest_cleanup'
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+
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+ module Libis
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+ module RosettaChecker
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+ class FilesToIngestCleanup < SubCommand
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+
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+ def self.short_desc
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+ 'Report on files that are/are not ingested'.freeze
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+ end
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+
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+ def self.command
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+ 'files2ingest'.freeze
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+ end
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+
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+ def self.options_class
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+ FilesToIngestCleanupOptions
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+ end
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+
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+ def self.run
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+ super do |cfg|
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+ self.new(cfg).run(ARGV)
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+ end
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+ end
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+
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+ attr_accessor :cfg, :logger, :connection, :cursor, :report
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+
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+ def initialize(cfg)
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+ @cfg = cfg
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+
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+ setup_logging
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+
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+ setup_db
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+ end
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+
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+ def finalize
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+ cursor.close if cursor
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+ connection.logoff if connection
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+ end
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+
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+ def run(argv)
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+ raise ArgumentError, 'Need to specify at least a directory/file to parse' unless argv.size > 0
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+ while (dir = argv.shift)
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+ process_dir dir
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+ next if argv.empty?
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+ self.class.parse_options(argv)
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+ setup_logging
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+ end
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+ end
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+
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+ protected
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+
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+ SQL_DATA = %w'ie_id rep_id fl_id original_name owner label group_id entity_type user_c'
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+ CSV_HEADER = %w'parent_type parent file size md5 found name_match' + SQL_DATA
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+
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+ LOG_PATTERN = "[%d #%p] %-5l : %m\n".freeze
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+
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+ MSG_CALC_FC = ' - Calculating filesize and checksum'.freeze
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+ MSG_CHCK_DB = ' - Checking file in DB'.freeze
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+ MSG_DEFLATE = ' - Deflating'.freeze
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+
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+ FIND_SQL = <<-SQL
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+ SELECT
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+ CONCAT(sp.VALUE, ps.INDEX_LOCATION) as path,
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+ ps.FILE_SIZE as filesize,
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+ ps.CHECK_SUM_TYPE as checksum_type,
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+ ps.CHECK_SUM as checksum,
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+ sr.FILEORIGINALNAME as original_name,
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+ ps.STORED_ENTITY_ID as fl_id,
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+ cr.PID as rep_id,
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+ ci.PID as ie_id,
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+ ci.OWNER as owner,
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+ ci.LABEL as label,
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+ cf.GROUPID as group_id,
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+ ci.ENTITYTYPE as entity_type,
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+ ci.PARTITIONC as user_c
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+ FROM
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+ V2KU_PER00.PERMANENT_INDEX ps
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+ LEFT JOIN V2KU_SHR00.STORAGE_PARAMETER sp ON sp.STORAGE_ID = ps.STORAGE_ID
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+ LEFT JOIN V2KU_REP00.HDESTREAMREF sr ON sr.PID = ps.STORED_ENTITY_ID
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+ LEFT JOIN V2KU_REP00.HDECONTROL cf ON cf.PID = ps.STORED_ENTITY_ID
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+ LEFT JOIN V2KU_REP00.HDECONTROL cr ON cr.PID = cf.PARENTID
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+ LEFT JOIN V2KU_REP00.HDECONTROL ci ON ci.PID = cr.PARENTID
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+ WHERE
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+ sp."KEY" = 'DIR_ROOT'
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+ AND ps.FILE_SIZE = :filesize
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+ AND ps.CHECK_SUM = :checksum
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+ AND ps.CHECK_SUM_TYPE = 'MD5'
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+ AND cf.OBJECTTYPE = 'FILE'
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+ AND cr.OBJECTTYPE = 'REPRESENTATION'
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+ AND ci.OBJECTTYPE = 'INTELLECTUAL_ENTITY'
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+ SQL
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+
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+ def setup_logging
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+ Logging.logger.root.level = :info
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+ @logger = Logging.logger[self.class.command]
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+ @logger.appenders = [Logging.appenders.stdout]
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+ Logging.appenders.stdout.level = (@cfg.quiet ? :warn : :info)
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+ @cfg.log_file = nil if @cfg.log_file&.chomp&.strip&.empty?
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+ @logger.add_appenders Logging.appenders.file(
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+ @cfg.log_file,
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+ truncate: false,
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+ layout: Logging.layouts.pattern(pattern: LOG_PATTERN)
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+ ) if @cfg.log_file
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+ end
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+
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+ def setup_db
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+ @connection = OCI8.new(@cfg.dbuser, @cfg.dbpass, @cfg.dburl)
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+ @cursor = @connection.parse(FIND_SQL)
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+ @cursor.prefetch_rows = 10
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+ end
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+
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+ def process_dir(dir)
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+ if File.directory?(dir)
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+ unless Dir.exist?(dir)
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+ logger.error "Directory '#{dir}' does not exist"
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+ return nil
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+ end
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+ unless File.readable?(dir)
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+ logger.error "Directory '#{dir}' cannot be read"
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+ return nil
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+ end
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+ logger.info "Processing dir '#{dir}'"
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+ Dir.entries(dir).each do |entry|
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+ next if %w'. ..'.include? entry
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+ path = File.join dir, entry
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+ begin
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+ process_dir path if @cfg.recursive
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+ next
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+ end if File.directory?(path)
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+ process_file path
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+ end
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+ elsif dir[0] == '@'
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+ file = to_file(dir[1..-1])
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+ return nil unless file
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+ logger.info "Processing input file '#{file}'"
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+ File.open(file, 'r').each_line do |line|
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+ process_file(line.chomp, File.dirname(file))
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+ end
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+ elsif File.file?(dir)
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+ process_file(dir)
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+ else
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+ raise ArgumentError, "Argument '#{dir}' should refer to an existing and readable file or directory"
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+ end
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+ end
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+
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+ def to_file(file, *search_dirs)
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+ if File.exist?(file)
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+ return file if File.readable?(file)
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+ logger.error "File '#{file}' cannot be read"
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+ return nil
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+ end
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+ search_dirs.each do |dir|
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+ f = File.join(dir, file)
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+ if File.exist? f
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+ return f if File.readable?(f)
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+ logger.error "File '#{f}' cannot be read"
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+ return nil
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+ end
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+ end
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+ logger.error "File '#{file}' does not exist"
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+ nil
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+ end
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+
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+ def process_file(_file, *search_dir)
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+ file = to_file(_file, *search_dir)
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+ return unless file
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+
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+ if File.directory?(file)
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+ process_dir(file)
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+ return
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+ end
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+
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+ info = {
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+ parent_type: 'D',
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+ parent: File.dirname(file),
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+ file: File.basename(file)
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+ }
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+
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+ logger.info "- #{file}"
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+ if File.extname(file) == '.bz2'
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+ logger.info MSG_DEFLATE
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+ info[:size] = 0
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+ reader = Bzip2::FFI::Reader.open file
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+ md5 = Digest::MD5.new
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+ logger.info MSG_CALC_FC
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+ while (data = reader.read 2048000) do
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+ info[:size] += data.length
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+ md5 << data
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+ end
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+ reader.close
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+ info[:parent_type] = 'F'
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+ info[:parent] = file
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+ info[:file] = File.basename file, '.bz2'
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+ info[:md5] = md5.hexdigest
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+ check_file info
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+ elsif File.extname(file) == '.zip'
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+ logger.info ' - Unpacking'.freeze
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+ info[:parent_type] = 'Z'
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+ info[:parent] = file
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+ Zip::File.open(file) do |zip|
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+ zip.each do |entry|
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+ next if entry.directory?
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+ info[:file] = entry.name
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+ logger.info "- #{file}/#{entry.name}"
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+ logger.info MSG_CALC_FC
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+ info[:size] = 0
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+ md5 = Digest::MD5.new
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+ reader = entry.get_input_stream
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+ while (data = reader.read 2048000) do
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+ info[:size] += data.length
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+ md5 << data
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+ end
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+ reader.close
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+ info[:md5] = md5.hexdigest
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+ check_file info
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+ end
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+ end
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+ else
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+ begin
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+ logger.info MSG_CALC_FC
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+ info[:size] = File.size file
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+ info[:md5] = Digest::MD5.file file
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+ check_file info
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+ rescue Exception
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+ logger.error "Could not access file '#{file}'"
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+ end
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+ end
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+ end
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+
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+ def check_file(info)
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+ logger.info MSG_CHCK_DB
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+
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+ cursor.bind_param(':filesize', info[:size].to_i)
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+ cursor.bind_param(':checksum', info[:md5].to_s)
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+
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+ cursor.exec
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+
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+ while (found = cursor.fetch_hash)
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+ SQL_DATA.each {|x| info[x.to_sym] = found[x.upcase]}
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+ logger.info " found match: #{info[:ie_id]}/#{info[:rep_id]}/#{info[:fl_id]}"
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+ if info[:original_name] =~ Regexp.new(info[:file].split(/[ #._-]/).join('.*'))
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+ logger.info " name matches: #{info[:original_name]}"
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+ info[:name_match] = true
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+ else
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+ info[:name_match] = false
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+ end
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+
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+ end
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+
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+ info[:found] = cursor.row_count
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+
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+ to_report(info)
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+
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+ end
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+
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+ def to_report(info = nil)
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+ return unless @cfg.report
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+ unless @report
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+ @report ||= CSV.open(@cfg.report_file, 'wb')
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+ @report << CSV_HEADER
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+ end
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+ @report << CSV_HEADER.map {|x| info[x.to_sym]} if info
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+ end
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+
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+ end
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+ end
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+ end