libis-rosetta_checker 1.0.0
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 +14 -0
- data/.idea/libis-rosetta_checker.iml +28 -0
- data/.idea/misc.xml +4 -0
- data/.idea/modules.xml +8 -0
- data/.idea/workspace.xml +764 -0
- data/.rspec +3 -0
- data/.travis.yml +5 -0
- data/CODE_OF_CONDUCT.md +74 -0
- data/Gemfile +6 -0
- data/LICENSE.txt +21 -0
- data/README.md +43 -0
- data/Rakefile +6 -0
- data/bin/console +14 -0
- data/bin/setup +8 -0
- data/exe/rosetta_checker +6 -0
- data/lib/libis/rosetta_checker/files_to_ingest_cleanup.rb +277 -0
- data/lib/libis/rosetta_checker/options/files_to_ingest_cleanup.rb +106 -0
- data/lib/libis/rosetta_checker/sub_command.rb +60 -0
- data/lib/libis/rosetta_checker/version.rb +5 -0
- data/lib/libis/rosetta_checker.rb +46 -0
- data/libis-rosetta_checker.gemspec +42 -0
- metadata +194 -0
data/.rspec
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data/.travis.yml
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data/CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct
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## Our Pledge
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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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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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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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Examples of unacceptable behavior by participants include:
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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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## Our Responsibilities
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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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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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## Scope
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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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## Enforcement
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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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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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## Attribution
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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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[homepage]: http://contributor-covenant.org
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[version]: http://contributor-covenant.org/version/1/4/
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data/Gemfile
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data/LICENSE.txt
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The MIT License (MIT)
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Copyright (c) 2017 LIBIS (Kris Dekeyser)
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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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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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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.
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data/README.md
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# Libis::RosettaChecker
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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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TODO: Delete this and the text above, and describe your gem
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## Installation
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Add this line to your application's Gemfile:
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```ruby
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gem 'libis-rosetta_checker'
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```
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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 libis-rosetta_checker
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## Usage
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TODO: Write usage instructions here
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## Development
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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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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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## Contributing
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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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## License
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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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## Code of Conduct
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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).
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data/bin/console
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#!/usr/bin/env ruby
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require "bundler/setup"
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require "libis/rosetta_checker"
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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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# (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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require "irb"
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IRB.start(__FILE__)
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data/bin/setup
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data/exe/rosetta_checker
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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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require_relative 'sub_command'
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require_relative 'options/files_to_ingest_cleanup'
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module Libis
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module RosettaChecker
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class FilesToIngestCleanup < SubCommand
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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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def self.command
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'files2ingest'.freeze
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end
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def self.options_class
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FilesToIngestCleanupOptions
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end
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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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attr_accessor :cfg, :logger, :connection, :cursor, :report
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def initialize(cfg)
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@cfg = cfg
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setup_logging
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setup_db
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end
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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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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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protected
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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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LOG_PATTERN = "[%d #%p] %-5l : %m\n".freeze
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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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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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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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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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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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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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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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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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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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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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|
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reader = Bzip2::FFI::Reader.open file
|
194
|
+
md5 = Digest::MD5.new
|
195
|
+
logger.info MSG_CALC_FC
|
196
|
+
while (data = reader.read 2048000) do
|
197
|
+
info[:size] += data.length
|
198
|
+
md5 << data
|
199
|
+
end
|
200
|
+
reader.close
|
201
|
+
info[:parent_type] = 'F'
|
202
|
+
info[:parent] = file
|
203
|
+
info[:file] = File.basename file, '.bz2'
|
204
|
+
info[:md5] = md5.hexdigest
|
205
|
+
check_file info
|
206
|
+
elsif File.extname(file) == '.zip'
|
207
|
+
logger.info ' - Unpacking'.freeze
|
208
|
+
info[:parent_type] = 'Z'
|
209
|
+
info[:parent] = file
|
210
|
+
Zip::File.open(file) do |zip|
|
211
|
+
zip.each do |entry|
|
212
|
+
next if entry.directory?
|
213
|
+
info[:file] = entry.name
|
214
|
+
logger.info "- #{file}/#{entry.name}"
|
215
|
+
logger.info MSG_CALC_FC
|
216
|
+
info[:size] = 0
|
217
|
+
md5 = Digest::MD5.new
|
218
|
+
reader = entry.get_input_stream
|
219
|
+
while (data = reader.read 2048000) do
|
220
|
+
info[:size] += data.length
|
221
|
+
md5 << data
|
222
|
+
end
|
223
|
+
reader.close
|
224
|
+
info[:md5] = md5.hexdigest
|
225
|
+
check_file info
|
226
|
+
end
|
227
|
+
end
|
228
|
+
else
|
229
|
+
begin
|
230
|
+
logger.info MSG_CALC_FC
|
231
|
+
info[:size] = File.size file
|
232
|
+
info[:md5] = Digest::MD5.file file
|
233
|
+
check_file info
|
234
|
+
rescue Exception
|
235
|
+
logger.error "Could not access file '#{file}'"
|
236
|
+
end
|
237
|
+
end
|
238
|
+
end
|
239
|
+
|
240
|
+
def check_file(info)
|
241
|
+
logger.info MSG_CHCK_DB
|
242
|
+
|
243
|
+
cursor.bind_param(':filesize', info[:size].to_i)
|
244
|
+
cursor.bind_param(':checksum', info[:md5].to_s)
|
245
|
+
|
246
|
+
cursor.exec
|
247
|
+
|
248
|
+
while (found = cursor.fetch_hash)
|
249
|
+
SQL_DATA.each {|x| info[x.to_sym] = found[x.upcase]}
|
250
|
+
logger.info " found match: #{info[:ie_id]}/#{info[:rep_id]}/#{info[:fl_id]}"
|
251
|
+
if info[:original_name] =~ Regexp.new(info[:file].split(/[ #._-]/).join('.*'))
|
252
|
+
logger.info " name matches: #{info[:original_name]}"
|
253
|
+
info[:name_match] = true
|
254
|
+
else
|
255
|
+
info[:name_match] = false
|
256
|
+
end
|
257
|
+
|
258
|
+
end
|
259
|
+
|
260
|
+
info[:found] = cursor.row_count
|
261
|
+
|
262
|
+
to_report(info)
|
263
|
+
|
264
|
+
end
|
265
|
+
|
266
|
+
def to_report(info = nil)
|
267
|
+
return unless @cfg.report
|
268
|
+
unless @report
|
269
|
+
@report ||= CSV.open(@cfg.report_file, 'wb')
|
270
|
+
@report << CSV_HEADER
|
271
|
+
end
|
272
|
+
@report << CSV_HEADER.map {|x| info[x.to_sym]} if info
|
273
|
+
end
|
274
|
+
|
275
|
+
end
|
276
|
+
end
|
277
|
+
end
|