sample-template-generator 0.3.0

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+ ---
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+ SHA1:
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+ metadata.gz: c39abfbf9dcfd2fef15473ddd25d989918c1f7f3
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+ ---
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+ engines:
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+ duplication:
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+ enabled: true
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+ config:
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+ languages:
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+ - ruby
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+ - javascript
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+ - python
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+ - php
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+ fixme:
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+ enabled: true
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+ rubocop:
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+ enabled: true
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+ ratings:
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+ paths:
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+ - "**.inc"
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+ - "**.js"
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+ - "**.jsx"
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+ - "**.module"
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+ - "**.php"
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+ - "**.py"
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+ - "**.rb"
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+ exclude_paths:
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+ - test/
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+ /.bundle/
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+ /.yardoc
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+ /Gemfile.lock
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+ /_yardoc/
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+ /coverage/
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+ /doc/
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+ /pkg/
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+ /spec/reports/
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+ /tmp/
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+ .idea/
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+ *~
File without changes
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+ sample-template-generator
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+ ruby-2.1.9
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+ sudo: false
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+ language: ruby
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+ rvm:
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+ - 2.1.9
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+ - 2.2.5
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+ - 2.3.1
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+
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+ cache: bundler
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+
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+ before_install: gem install bundler -v 1.12.5
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+ # Contributor Code of Conduct
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+
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+ As contributors and maintainers of this project, and in the interest of
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+ fostering an open and welcoming community, we pledge to respect all people who
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+ contribute through reporting issues, posting feature requests, updating
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+ documentation, submitting pull requests or patches, and other activities.
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+
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+ We are committed to making participation in this project a harassment-free
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+ experience for everyone, regardless of level of experience, gender, gender
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+ identity and expression, sexual orientation, disability, personal appearance,
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+ body size, race, ethnicity, age, religion, or nationality.
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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
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+ * Personal attacks
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+ * Trolling or insulting/derogatory comments
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+ * Public or private harassment
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+ * Publishing other's private information, such as physical or electronic
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+ addresses, without explicit permission
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+ * Other unethical or unprofessional conduct
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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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+ By adopting this Code of Conduct, project maintainers commit themselves to
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+ fairly and consistently applying these principles to every aspect of managing
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+ this project. Project maintainers who do not follow or enforce the Code of
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+ Conduct may be permanently removed from the project team.
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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.
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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 a project maintainer at stuart.owen@manchester.ac.uk. 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. Maintainers are
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+ obligated to maintain confidentiality with regard to the reporter of an
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+ incident.
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+
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+ This Code of Conduct is adapted from the [Contributor Covenant][homepage],
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+ version 1.3.0, available at
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+ [http://contributor-covenant.org/version/1/3/0/][version]
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+
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+ [homepage]: http://contributor-covenant.org
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+ [version]: http://contributor-covenant.org/version/1/3/0/
data/Gemfile ADDED
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+ source 'https://rubygems.org'
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+
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+ # Specify your gem's dependencies in sample-template-generator-gem.gemspec
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+ gemspec
data/LICENSE ADDED
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+ Copyright (c) 2010-2016, The University of Manchester, UK.
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+
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+ All rights reserved.
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+
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+ Redistribution and use in source and binary forms, with or without
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+ modification, are permitted provided that the following conditions are met:
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+
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+ * Redistributions of source code must retain the above copyright notice,
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+ this list of conditions and the following disclaimer.
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+
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+ * Redistributions in binary form must reproduce the above copyright notice,
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+ this list of conditions and the following disclaimer in the documentation
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+ and/or other materials provided with the distribution.
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+
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+ * Neither the names of The University of Manchester nor the names of its
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+ contributors may be used to endorse or promote products derived from this
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+ software without specific prior written permission.
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+
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+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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+ AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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+ IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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+ ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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+ LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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+ CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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+ SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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+ INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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+ CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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+ ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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+ POSSIBILITY OF SUCH DAMAGE.
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+ # Sample Template Generator
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+
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+ [![Code Climate](https://codeclimate.com/github/seek4science/sample-template-generator-gem/badges/gpa.svg)](https://codeclimate.com/github/seek4science/sample-template-generator-gem) [![Build Status](https://travis-ci.org/seek4science/sample-template-generator-gem.svg?branch=master)](https://travis-ci.org/seek4science/sample-template-generator-gem)
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+
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+
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+ A very simple prototype of generating an Excel Template based upon Sample Type information in [SEEK](http://seekscience.org)
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+
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+ This is currently very basic and scruffy prototyping work.
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+
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+ SEEK is developed as part of [FAIRDOM](http://fair-dom.org)
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+
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+ SEEK github repository can be found at https://github.com/seek4science/seek
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+
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+ FAIRDOM runs the [FAIRDOMHub](https://fairdomhub.org) which is a public instance of SEEK for scientific research
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+ require "bundler/gem_tasks"
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+ require "rake/testtask"
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+
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+ Rake::TestTask.new(:test) do |t|
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+ t.libs << "test"
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+ t.libs << "lib"
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+ t.test_files = FileList['test/**/*_test.rb']
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+ end
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+
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+ task :default => :test
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+ #!/usr/bin/env ruby
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+
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+ require "bundler/setup"
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+ require "seek/sample_template_generator"
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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
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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
Binary file
Binary file
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+ require 'seek/sample_templates/column'
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+ require 'seek/sample_templates/generator'
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+
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+ module Seek
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+ # Main entry point for generating templates
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+ module SampleTemplates
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+ # generates a template at the specific path
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+ def self.generate(sheet_name, sheet_index, columns, path)
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+ Seek::SampleTemplates::Generator.new(
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+ path, create_json(columns, sheet_index, sheet_name)
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+ ).generate
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+ end
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+
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+ def self.create_json(columns, sheet_index, sheet_name)
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+ { sheet_name: sheet_name,
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+ sheet_index: sheet_index,
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+ columns: columns.collect(&:as_json) }.to_json
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+ end
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+
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+ private_class_method :create_json
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+ end
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+ end
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+ module Seek
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+ module SampleTemplates
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+ # Describes a column in the template.
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+ # The name is the text put in the top row,
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+ # and contents will create a dropdown in the row below unless empty
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+ class Column
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+ attr_reader :name, :contents
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+
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+ def initialize(name, contents = [])
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+ @name = name
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+ @contents = contents
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+ end
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+
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+ def as_json
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+ { @name => @contents }
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+ end
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+ end
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+ end
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+ end
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+ require 'cocaine'
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+
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+ module Seek
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+ module SampleTemplates
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+ # Generator class for creating templates.
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+ # Generally this shouldn't be used directly, but instead should be used
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+ # through Seek::SampleTemplates.generate(..)
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+ class Generator
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+ JAR_VERSION = '0.3'.freeze
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+ JAR_PATH = File.dirname(__FILE__) +
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+ "/../../../jars/sample-template-generator-#{JAR_VERSION}.jar"
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+ DEFAULT_MEMORY_ALLOCATION = '512M'.freeze
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+ BUFFER_SIZE = 250_000 # 1/4 a megabyte
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+
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+ attr_reader :json, :path, :memory_allocation
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+
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+ def initialize(path, json, memory_allocation = DEFAULT_MEMORY_ALLOCATION)
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+ @path = path
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+ @json = json
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+ @memory_allocation = memory_allocation
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+ end
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+
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+ def generate
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+ run_with_cocaine
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+ end
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+
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+ private
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+
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+ def command
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+ command = "java -Xmx#{@memory_allocation} -jar #{JAR_PATH}"
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+ command += " -f '#{path}'"
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+ command += " -j '#{json}'"
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+ command
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+ end
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+
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+ def run_with_cocaine
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+ output = Cocaine::CommandLine.new(command).run
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+ output.strip
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+ rescue Cocaine::ExitStatusError => exception
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+ raise exception.message
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+ end
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+ end
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+ end
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+ end
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+ module Seek
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+ module SampleTemplates
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+ VERSION = '0.3.0'.freeze
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+ end
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+ end
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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 'seek/sample_templates/version'
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+
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+ Gem::Specification.new do |spec|
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+ spec.name = 'sample-template-generator'
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+ spec.version = Seek::SampleTemplates::VERSION
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+ spec.authors = ['Stuart Owen']
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+ spec.email = ['stuart.owen@manchester.ac.uk']
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+
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+ spec.summary = 'Bespoke tool for generating spreadsheet templates from Sample Types for use with SEEK.'
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+ spec.homepage = 'http://seek4science.org'
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+ spec.license = 'BSD-3-Clause'
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+
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+ spec.files = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
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+ spec.bindir = 'exe'
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+ spec.executables = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
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+ spec.require_paths = ['lib']
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+
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+ spec.add_dependency('rdoc', ['>= 0'])
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+ spec.add_dependency('cocaine', ['>= 0'])
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+
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+ spec.add_development_dependency('rubocop', ['>= 0'])
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+ spec.add_development_dependency('rubycritic', ['>= 0'])
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+ spec.add_development_dependency 'bundler', '~> 1.12'
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+ spec.add_development_dependency 'rake', '~> 10.0'
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+ spec.add_development_dependency 'minitest', '~> 5.0'
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+ spec.add_development_dependency('activesupport', ">= 3.0.0", "< 5.0")
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: sample-template-generator
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+ version: !ruby/object:Gem::Version
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+ version: 0.3.0
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+ platform: ruby
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+ authors:
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+ - Stuart Owen
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+ autorequire:
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+ bindir: exe
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+ cert_chain: []
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+ date: 2016-09-20 00:00:00.000000000 Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: cocaine
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :runtime
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: rubocop
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: rubycritic
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '1.12'
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+ - !ruby/object:Gem::Dependency
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+ name: rake
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '10.0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: !ruby/object:Gem::Requirement
93
+ requirements:
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+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '10.0'
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+ - !ruby/object:Gem::Dependency
98
+ name: minitest
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
101
+ - - "~>"
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+ - !ruby/object:Gem::Version
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+ version: '5.0'
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+ type: :development
105
+ prerelease: false
106
+ version_requirements: !ruby/object:Gem::Requirement
107
+ requirements:
108
+ - - "~>"
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+ - !ruby/object:Gem::Version
110
+ version: '5.0'
111
+ - !ruby/object:Gem::Dependency
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+ name: activesupport
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+ requirement: !ruby/object:Gem::Requirement
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+ requirements:
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+ - - ">="
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+ - !ruby/object:Gem::Version
117
+ version: 3.0.0
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+ - - "<"
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+ - !ruby/object:Gem::Version
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+ version: '5.0'
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+ type: :development
122
+ prerelease: false
123
+ version_requirements: !ruby/object:Gem::Requirement
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+ requirements:
125
+ - - ">="
126
+ - !ruby/object:Gem::Version
127
+ version: 3.0.0
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+ - - "<"
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+ - !ruby/object:Gem::Version
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+ version: '5.0'
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+ description:
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+ email:
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+ - stuart.owen@manchester.ac.uk
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+ executables: []
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+ extensions: []
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+ extra_rdoc_files: []
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+ files:
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+ - ".codeclimate.yml"
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+ - ".gitignore"
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+ - ".rubocop.yml"
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+ - ".ruby-gemset"
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+ - ".ruby-version"
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+ - ".travis.yml"
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+ - CODE_OF_CONDUCT.md
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+ - Gemfile
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+ - LICENSE
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+ - README.md
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+ - Rakefile
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+ - bin/console
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+ - bin/setup
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+ - jars/lib/commons-codec-1.10.jar
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+ - jars/lib/curvesapi-1.03.jar
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+ - jars/lib/json-simple-1.1.1.jar
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+ - jars/lib/junit-4.8.2.jar
155
+ - jars/lib/poi-3.14.jar
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+ - jars/lib/poi-ooxml-3.14.jar
157
+ - jars/lib/poi-ooxml-schemas-3.14.jar
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+ - jars/lib/stax-api-1.0.1.jar
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+ - jars/lib/xmlbeans-2.6.0.jar
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+ - jars/sample-template-generator-0.3.jar
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+ - lib/seek/sample_templates.rb
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+ - lib/seek/sample_templates/column.rb
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+ - lib/seek/sample_templates/generator.rb
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+ - lib/seek/sample_templates/version.rb
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+ - sample-template-generator-gem.gemspec
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+ homepage: http://seek4science.org
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+ licenses:
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+ - BSD-3-Clause
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+ metadata: {}
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
175
+ requirements:
176
+ - - ">="
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+ - !ruby/object:Gem::Version
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+ version: '0'
179
+ required_rubygems_version: !ruby/object:Gem::Requirement
180
+ requirements:
181
+ - - ">="
182
+ - !ruby/object:Gem::Version
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+ version: '0'
184
+ requirements: []
185
+ rubyforge_project:
186
+ rubygems_version: 2.4.8
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+ signing_key:
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+ specification_version: 4
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+ summary: Bespoke tool for generating spreadsheet templates from Sample Types for use
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+ with SEEK.
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+ test_files: []