sample-template-generator 0.3.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: c39abfbf9dcfd2fef15473ddd25d989918c1f7f3
+  data.tar.gz: b4fe52ccf5ba84fff6f0e5af834ffc9fd9ff23a9
+SHA512:
+  metadata.gz: b8d5ce348811e40411fa455b17b70e1ad3124083c86bf3722371d5a0965d2335543fae0929e7f78d99845b2df2f78153e197d89f8057ec0b2327bcee2cb148d3
+  data.tar.gz: a4f1a410c476b8b2bfb5b8e32423a6f5c81edd180d9a6341e597a676bd78ff24fa12362abe7414610e39a72e719687696725b34449ab015bf70ffbc2121b0a8e

data/.codeclimate.yml

@@ -0,0 +1,25 @@
+---
+engines:
+  duplication:
+    enabled: true
+    config:
+      languages:
+      - ruby
+      - javascript
+      - python
+      - php
+  fixme:
+    enabled: true
+  rubocop:
+    enabled: true
+ratings:
+  paths:
+  - "**.inc"
+  - "**.js"
+  - "**.jsx"
+  - "**.module"
+  - "**.php"
+  - "**.py"
+  - "**.rb"
+exclude_paths:
+- test/

data/.gitignore

@@ -0,0 +1,11 @@
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+.idea/
+*~

data/.ruby-gemset

@@ -0,0 +1 @@
+sample-template-generator

data/.ruby-version

@@ -0,0 +1 @@
+ruby-2.1.9

data/.travis.yml

@@ -0,0 +1,10 @@
+sudo: false
+language: ruby
+rvm:
+  - 2.1.9
+  - 2.2.5
+  - 2.3.1
+
+cache: bundler
+
+before_install: gem install bundler -v 1.12.5

data/CODE_OF_CONDUCT.md

@@ -0,0 +1,49 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of
+fostering an open and welcoming community, we pledge to respect all people who
+contribute through reporting issues, posting feature requests, updating
+documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, ethnicity, age, religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic
+  addresses, without explicit permission
+* Other unethical or unprofessional conduct
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project maintainers commit themselves to
+fairly and consistently applying these principles to every aspect of managing
+this project. Project maintainers who do not follow or enforce the Code of
+Conduct may be permanently removed from the project team.
+
+This code of conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting a project maintainer at stuart.owen@manchester.ac.uk. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. Maintainers are
+obligated to maintain confidentiality with regard to the reporter of an
+incident.
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.3.0, available at
+[http://contributor-covenant.org/version/1/3/0/][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/3/0/

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in sample-template-generator-gem.gemspec
+gemspec

data/LICENSE

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+Copyright (c) 2010-2016, The University of Manchester, UK.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+
+ * Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+ * Neither the names of The University of Manchester nor the names of its
+   contributors may be used to endorse or promote products derived from this
+   software without specific prior written permission. 
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGE.

data/README.md

@@ -0,0 +1,14 @@
+# Sample Template Generator
+
+[![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)
+
+
+A very simple prototype of generating an Excel Template based upon Sample Type information in [SEEK](http://seekscience.org)
+
+This is currently very basic and scruffy prototyping work.
+
+SEEK is developed as part of [FAIRDOM](http://fair-dom.org)
+
+SEEK github repository can be found at https://github.com/seek4science/seek
+
+FAIRDOM runs the [FAIRDOMHub](https://fairdomhub.org) which is a public instance of SEEK for scientific research

data/Rakefile

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+require "bundler/gem_tasks"
+require "rake/testtask"
+
+Rake::TestTask.new(:test) do |t|
+  t.libs << "test"
+  t.libs << "lib"
+  t.test_files = FileList['test/**/*_test.rb']
+end
+
+task :default => :test

data/bin/console

@@ -0,0 +1,14 @@
+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "seek/sample_template_generator"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start

data/bin/setup

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/seek/sample_templates.rb

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+require 'seek/sample_templates/column'
+require 'seek/sample_templates/generator'
+
+module Seek
+  # Main entry point for generating templates
+  module SampleTemplates
+    # generates a template at the specific path
+    def self.generate(sheet_name, sheet_index, columns, path)
+      Seek::SampleTemplates::Generator.new(
+        path, create_json(columns, sheet_index, sheet_name)
+      ).generate
+    end
+
+    def self.create_json(columns, sheet_index, sheet_name)
+      { sheet_name: sheet_name,
+        sheet_index: sheet_index,
+        columns: columns.collect(&:as_json) }.to_json
+    end
+
+    private_class_method :create_json
+  end
+end

data/lib/seek/sample_templates/column.rb

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+module Seek
+  module SampleTemplates
+    # Describes a column in the template.
+    # The name is the text put in the top row,
+    # and contents will create a dropdown in the row below unless empty
+    class Column
+      attr_reader :name, :contents
+
+      def initialize(name, contents = [])
+        @name = name
+        @contents = contents
+      end
+
+      def as_json
+        { @name => @contents }
+      end
+    end
+  end
+end

data/lib/seek/sample_templates/generator.rb

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+require 'cocaine'
+
+module Seek
+  module SampleTemplates
+    # Generator class for creating templates.
+    # Generally this shouldn't be used directly, but instead should be used
+    # through Seek::SampleTemplates.generate(..)
+    class Generator
+      JAR_VERSION = '0.3'.freeze
+      JAR_PATH = File.dirname(__FILE__) +
+                 "/../../../jars/sample-template-generator-#{JAR_VERSION}.jar"
+      DEFAULT_MEMORY_ALLOCATION = '512M'.freeze
+      BUFFER_SIZE = 250_000 # 1/4 a megabyte
+
+      attr_reader :json, :path, :memory_allocation
+
+      def initialize(path, json, memory_allocation = DEFAULT_MEMORY_ALLOCATION)
+        @path = path
+        @json = json
+        @memory_allocation = memory_allocation
+      end
+
+      def generate
+        run_with_cocaine
+      end
+
+      private
+
+      def command
+        command = "java -Xmx#{@memory_allocation} -jar #{JAR_PATH}"
+        command += " -f '#{path}'"
+        command += " -j '#{json}'"
+        command
+      end
+
+      def run_with_cocaine
+        output = Cocaine::CommandLine.new(command).run
+        output.strip
+      rescue Cocaine::ExitStatusError => exception
+        raise exception.message
+      end
+    end
+  end
+end

data/lib/seek/sample_templates/version.rb

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+module Seek
+  module SampleTemplates
+    VERSION = '0.3.0'.freeze
+  end
+end

data/sample-template-generator-gem.gemspec

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+# coding: utf-8
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'seek/sample_templates/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'sample-template-generator'
+  spec.version       = Seek::SampleTemplates::VERSION
+  spec.authors       = ['Stuart Owen']
+  spec.email         = ['stuart.owen@manchester.ac.uk']
+
+  spec.summary       = 'Bespoke tool for generating spreadsheet templates from Sample Types for use with SEEK.'
+  spec.homepage      = 'http://seek4science.org'
+  spec.license       = 'BSD-3-Clause'
+
+  spec.files         = `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  spec.bindir        = 'exe'
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+
+  spec.add_dependency('rdoc', ['>= 0'])
+  spec.add_dependency('cocaine', ['>= 0'])
+
+  spec.add_development_dependency('rubocop', ['>= 0'])
+  spec.add_development_dependency('rubycritic', ['>= 0'])
+  spec.add_development_dependency 'bundler', '~> 1.12'
+  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'minitest', '~> 5.0'
+  spec.add_development_dependency('activesupport', ">= 3.0.0", "< 5.0")
+end

metadata

@@ -0,0 +1,191 @@
+--- !ruby/object:Gem::Specification
+name: sample-template-generator
+version: !ruby/object:Gem::Version
+  version: 0.3.0
+platform: ruby
+authors:
+- Stuart Owen
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2016-09-20 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: cocaine
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubocop
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: rubycritic
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.12'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+- !ruby/object:Gem::Dependency
+  name: activesupport
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.0.0
+    - - "<"
+      - !ruby/object:Gem::Version
+        version: '5.0'
+description: 
+email:
+- stuart.owen@manchester.ac.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".codeclimate.yml"
+- ".gitignore"
+- ".rubocop.yml"
+- ".ruby-gemset"
+- ".ruby-version"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- jars/lib/commons-codec-1.10.jar
+- jars/lib/curvesapi-1.03.jar
+- jars/lib/json-simple-1.1.1.jar
+- jars/lib/junit-4.8.2.jar
+- jars/lib/poi-3.14.jar
+- jars/lib/poi-ooxml-3.14.jar
+- jars/lib/poi-ooxml-schemas-3.14.jar
+- jars/lib/stax-api-1.0.1.jar
+- jars/lib/xmlbeans-2.6.0.jar
+- jars/sample-template-generator-0.3.jar
+- lib/seek/sample_templates.rb
+- lib/seek/sample_templates/column.rb
+- lib/seek/sample_templates/generator.rb
+- lib/seek/sample_templates/version.rb
+- sample-template-generator-gem.gemspec
+homepage: http://seek4science.org
+licenses:
+- BSD-3-Clause
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.8
+signing_key: 
+specification_version: 4
+summary: Bespoke tool for generating spreadsheet templates from Sample Types for use
+  with SEEK.
+test_files: []