cirneco 0.3.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 91b2c099d3fade3b4caf760314e6c3b35fe09ec3
+  data.tar.gz: 940bf640c48072d50dcbd1f051f4ee42a54b8789
+SHA512:
+  metadata.gz: 84ebda4764d474fd4f090e45943c7e7e0d8a7992c5a540559362b1e922035c4fa27c2458ef1f2540055bb0e37f16b0e14044759fc63312be387217dde97b7c95
+  data.tar.gz: bfbf0bf90bbf230a18721c0ae1ca3b8129ce4afe68903c39564dba2e86d1807e030e01abb0a6a19be543ac4274f458f3204b11af95091e1d22c770f706d9d094

data/.gitignore

@@ -0,0 +1,57 @@
+*.gem
+*.rbc
+/.config
+/coverage/
+/InstalledFiles
+/pkg/
+/spec/reports/
+/spec/examples.txt
+/test/tmp/
+/test/version_tmp/
+/tmp/
+
+# Used by dotenv library to load environment variables.
+# .env
+
+## Specific to RubyMotion:
+.dat*
+.repl_history
+build/
+*.bridgesupport
+build-iPhoneOS/
+build-iPhoneSimulator/
+
+## Specific to RubyMotion (use of CocoaPods):
+#
+# We recommend against adding the Pods directory to your .gitignore. However
+# you should judge for yourself, the pros and cons are mentioned at:
+# https://guides.cocoapods.org/using/using-cocoapods.html#should-i-check-the-pods-directory-into-source-control
+#
+# vendor/Pods/
+
+## Documentation cache and generated files:
+/.yardoc/
+/_yardoc/
+/doc/
+/rdoc/
+
+## Environment normalization:
+/.bundle/
+/vendor/bundle
+/lib/bundler/man/
+
+# for a library or gem, you might want to ignore these files since the code is
+# intended to run in multiple environments; otherwise, check them in:
+# Gemfile.lock
+# .ruby-version
+# .ruby-gemset
+
+# unless supporting rvm < 1.11.0 or doing something fancy, ignore this:
+.rvmrc
+
+coverage/
+
+.env
+.env.*
+!.env.example
+!.env.travis

data/.travis.yml

@@ -0,0 +1,17 @@
+language: ruby
+rvm:
+- 2.3.1
+install:
+- travis_retry bundle install
+script: bundle exec rspec
+notifications:
+  slack: "$SLACK_TOKEN"
+  email: false
+deploy:
+  provider: rubygems
+  api_key:
+    secure: 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
+  gem: cirneco
+  on:
+    tags: true
+    repo: datacite/cirneco

data/Gemfile

@@ -0,0 +1,5 @@
+source 'https://rubygems.org'
+
+gemspec
+
+gem "base32-crockford", :git => "https://github.com/datacite/base32.git"

data/Gemfile.lock

@@ -0,0 +1,129 @@
+GIT
+  remote: https://github.com/datacite/base32.git
+  revision: 6e80183adae3f98018687e79164fa4970cf4ccbe
+  specs:
+    base32-crockford (0.2.0)
+
+PATH
+  remote: .
+  specs:
+    cirneco (0.3.1)
+      activesupport (~> 4.2, >= 4.2.5)
+      base32-crockford (~> 0.2.0)
+      builder (~> 3.2, >= 3.2.2)
+      dotenv (~> 2.1, >= 2.1.1)
+      maremma (~> 3.1)
+      namae (~> 0.10.1)
+      nokogiri (~> 1.6, >= 1.6.8)
+      sanitize (~> 4.0, >= 4.0.1)
+      thor (~> 0.19)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (4.2.7.1)
+      i18n (~> 0.7)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.3, >= 0.3.4)
+      tzinfo (~> 1.1)
+    addressable (2.5.0)
+      public_suffix (~> 2.0, >= 2.0.2)
+    builder (3.2.2)
+    codeclimate-test-reporter (1.0.3)
+      simplecov
+    crack (0.4.3)
+      safe_yaml (~> 1.0.0)
+    crass (1.0.2)
+    diff-lcs (1.2.5)
+    docile (1.1.5)
+    dotenv (2.1.1)
+    excon (0.45.4)
+    faraday (0.9.2)
+      multipart-post (>= 1.2, < 3)
+    faraday-encoding (0.0.4)
+      faraday
+    faraday_middleware (0.10.1)
+      faraday (>= 0.7.4, < 1.0)
+    hashdiff (0.3.1)
+    i18n (0.7.0)
+    json (1.8.3)
+    maremma (3.1)
+      activesupport (~> 4.2, >= 4.2.5)
+      builder (~> 3.2, >= 3.2.2)
+      excon (~> 0.45.0)
+      faraday (~> 0.9.2)
+      faraday-encoding (~> 0.0.1)
+      faraday_middleware (~> 0.10.0)
+      multi_json (~> 1.11.2)
+      nokogiri (~> 1.6.7)
+      oj (~> 2.13.1)
+    mini_portile2 (2.1.0)
+    minitest (5.10.1)
+    multi_json (1.11.3)
+    multipart-post (2.0.0)
+    namae (0.10.2)
+    nokogiri (1.6.8.1)
+      mini_portile2 (~> 2.1.0)
+    nokogumbo (1.4.10)
+      nokogiri
+    oj (2.13.1)
+    public_suffix (2.0.4)
+    rack (2.0.1)
+    rack-test (0.6.3)
+      rack (>= 1.0)
+    rake (12.0.0)
+    rspec (3.5.0)
+      rspec-core (~> 3.5.0)
+      rspec-expectations (~> 3.5.0)
+      rspec-mocks (~> 3.5.0)
+    rspec-core (3.5.4)
+      rspec-support (~> 3.5.0)
+    rspec-expectations (3.5.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.5.0)
+    rspec-mocks (3.5.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.5.0)
+    rspec-support (3.5.0)
+    rspec-xsd (0.1.0)
+      nokogiri (~> 1.6)
+      rspec (~> 3)
+    safe_yaml (1.0.4)
+    sanitize (4.4.0)
+      crass (~> 1.0.2)
+      nokogiri (>= 1.4.4)
+      nokogumbo (~> 1.4.1)
+    simplecov (0.12.0)
+      docile (~> 1.1.0)
+      json (>= 1.8, < 3)
+      simplecov-html (~> 0.10.0)
+    simplecov-html (0.10.0)
+    thor (0.19.4)
+    thread_safe (0.3.5)
+    tzinfo (1.2.2)
+      thread_safe (~> 0.1)
+    vcr (3.0.3)
+    webmock (1.24.6)
+      addressable (>= 2.3.6)
+      crack (>= 0.3.2)
+      hashdiff
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  base32-crockford!
+  bundler (~> 1.0)
+  cirneco!
+  codeclimate-test-reporter (~> 1.0, >= 1.0.0)
+  rack-test (~> 0)
+  rake (~> 12.0)
+  rspec (~> 3.4)
+  rspec-xsd (~> 0.1.0)
+  simplecov (~> 0.12.0)
+  vcr (~> 3.0, >= 3.0.3)
+  webmock (~> 1.22, >= 1.22.3)
+
+BUNDLED WITH
+   1.13.6

data/LICENSE.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2016 DataCite
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

data/README.md

@@ -0,0 +1,44 @@
+# Cirneco: command-line client for DataCite MDS
+
+[![Gem Version](https://badge.fury.io/rb/cirneco.svg)](https://badge.fury.io/rb/cirneco)
+[![Build Status](https://travis-ci.org/datacite/cirneco.svg?branch=master)](https://travis-ci.org/datacite/cirneco)
+[![Code Climate](https://codeclimate.com/github/datacite/cirneco/badges/gpa.svg)](https://codeclimate.com/github/datacite/cirneco)
+[![Test Coverage](https://codeclimate.com/github/datacite/cirneco/badges/coverage.svg)](https://codeclimate.com/github/datacite/cirneco/coverage)
+
+Cirneco is a command-line client for the DataCite Metadata Store (MDS), written as Ruby gem. Uses the MDS API, and includes several utlity functions.
+
+## Features
+
+The following functionality is supported:
+
+* the MDS API (DOI, Metadata and Media APIs) is fully supported
+* generates valid metadata, using Schema 4.0 (currently only partial support of available metadata fields)
+* generates a DOI name to be used for registration, using [Base32 Crockford encoded](https://github.com/levinalex/base32) sequential numbers that include a checksum
+
+## Requirements
+
+* valid username and password for DataCite MDS account (production and/or test system)
+
+## Installation
+
+The usual way with Bundler: add the following to your `Gemfile` to install the current version of the gem:
+
+```ruby
+gem 'cirneco'
+```
+
+Then run `bundle install` to install into your environment.
+
+You can also install the gem system-wide in the usual way:
+
+```bash
+gem install cirneco
+```
+
+## Use
+
+TBD.
+
+## License
+
+[MIT](license.md)

data/Rakefile

@@ -0,0 +1,5 @@
+#!/usr/bin/env rake
+
+# Get useful helper tasks from Bundler
+require "bundler/gem_tasks"
+

data/bin/cirneco.rb

@@ -0,0 +1,5 @@
+#!/usr/bin/env ruby
+
+require File.expand_path("../../lib/cirneco", __FILE__)
+
+Cirneco::CLI.start

data/cirneco.gemspec

@@ -0,0 +1,41 @@
+require "date"
+require File.expand_path("../lib/cirneco/version", __FILE__)
+
+Gem::Specification.new do |s|
+  s.authors       = "Martin Fenner"
+  s.email         = "mfenner@datacite.org"
+  s.name          = "cirneco"
+  s.homepage      = "https://github.com/datacite/cirneco"
+  s.summary       = "Ruby client library for the DataCite MDS"
+  s.date          = Date.today
+  s.description   = "Ruby client library for the DataCite Metadata Store (MDS) API."
+  s.require_paths = ["lib"]
+  s.version       = Cirneco::VERSION
+  s.extra_rdoc_files = ["README.md"]
+  s.license       = 'MIT'
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.require_paths = ["lib"]
+  s.executables   = ["cirneco.rb"]
+
+  # Declary dependencies here, rather than in the Gemfile
+  s.add_dependency 'maremma', '~> 3.1'
+  s.add_dependency 'nokogiri', '~> 1.6', '>= 1.6.8'
+  s.add_dependency 'builder', '~> 3.2', '>= 3.2.2'
+  s.add_dependency 'namae', '~> 0.10.1'
+  s.add_dependency 'activesupport', '~> 4.2', '>= 4.2.5'
+  s.add_dependency 'sanitize', '~> 4.0', '>= 4.0.1'
+  s.add_dependency 'dotenv', '~> 2.1', '>= 2.1.1'
+  s.add_dependency 'base32-crockford', '~> 0.2.0'
+  s.add_dependency 'thor', '~> 0.19'
+  s.add_development_dependency 'bundler', '~> 1.0'
+  s.add_development_dependency 'rspec', '~> 3.4'
+  s.add_development_dependency 'rspec-xsd', '~> 0.1.0'
+  s.add_development_dependency 'rake', '~> 12.0'
+  s.add_development_dependency 'rack-test', '~> 0'
+  s.add_development_dependency 'vcr', '~> 3.0', '>= 3.0.3'
+  s.add_development_dependency 'webmock', '~> 1.22', '>= 1.22.3'
+  s.add_development_dependency 'codeclimate-test-reporter', '~> 1.0', '>= 1.0.0'
+  s.add_development_dependency 'simplecov', '~> 0.12.0'
+end

data/lib/cirneco/api.rb

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+require "uri"
+
+module Cirneco
+  module Api
+    def post_metadata(data, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/metadata"
+      Maremma.post(url, content_type: 'application/xml;charset=UTF-8', data: data, username: options[:username], password: options[:password])
+    end
+
+    def get_metadata(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/metadata/#{doi}"
+      Maremma.get(url, accept: 'application/xml', username: options[:username], password: options[:password], raw: true)
+    end
+
+    def delete_metadata(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/metadata/#{doi}"
+      Maremma.delete(url, username: options[:username], password: options[:password])
+    end
+
+    def put_doi(doi, url, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      payload = "doi=#{doi}\nurl=#{url}"
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/doi/#{doi}"
+      Maremma.put(url, content_type: 'text/plain;charset=UTF-8', data: payload, username: options[:username], password: options[:password])
+    end
+
+    def get_doi(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/doi/#{doi}"
+      Maremma.get(url, username: options[:username], password: options[:password])
+    end
+
+    def get_dois(options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/doi"
+      response = Maremma.get(url, username: options[:username], password: options[:password])
+      response.body["data"] = response.body["data"].split("\n") if response.body["data"].present?
+      response
+    end
+
+    def post_media(doi, media, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      payload = media.map { |m| "#{m[:mime_type]}=#{m[:url]}" }.join("\n")
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/media/#{doi}"
+      Maremma.post(url, content_type: 'text/plain;charset=UTF-8', data: payload, username: options[:username], password: options[:password])
+    end
+
+    def get_media(doi, options={})
+      return OpenStruct.new(body: { "errors" => [{ "title" => "Username or password missing" }] }) unless options[:username].present? && options[:password].present?
+
+      mds_url = options[:sandbox] ? 'https://mds.test.datacite.org' : 'https://mds.datacite.org'
+
+      url = "#{mds_url}/media/#{doi}"
+      response = Maremma.get(url, accept: 'application/xml', username: options[:username], password: options[:password])
+      if response.body["data"].present?
+        response.body["data"] = response.body["data"].split("\n").map do |m|
+          mime_type, url = m.split('=', 2)
+          { mime_type: mime_type, url: url }
+        end
+      end
+      response
+    end
+  end
+end

data/lib/cirneco/base.rb

@@ -0,0 +1,21 @@
+module Cirneco
+  module Base
+    # load ENV variables from .env file if it exists
+    env_file = File.expand_path("../../../.env", __FILE__)
+    if File.exist?(env_file)
+      require 'dotenv'
+      Dotenv.load! env_file
+    end
+
+    # load ENV variables from container environment if json file exists
+    # see https://github.com/phusion/baseimage-docker#envvar_dumps
+    env_json_file = "/etc/container_environment.json"
+    if File.exist?(env_json_file)
+      env_vars = JSON.parse(File.read(env_json_file))
+      env_vars.each { |k, v| ENV[k] = v }
+    end
+
+    # default values for some ENV variables
+    ENV['MDS_URL'] ||= "https://mds.test.datacite.org"
+  end
+end

data/lib/cirneco/cli.rb

@@ -0,0 +1,28 @@
+# encoding: UTF-8
+
+require "thor"
+
+require_relative 'doi'
+require_relative 'media'
+require_relative 'metadata'
+
+module Cirneco
+  class CLI < Thor
+    include Cirneco::Base
+    include Cirneco::Api
+    include Cirneco::Utils
+
+    def self.exit_on_failure?
+      true
+    end
+
+    desc "hello NAME", "say hello to NAME"
+    def hello(name, from=nil)
+      puts "from: #{from}" if from
+      puts "Hello #{name}"
+    end
+
+    desc "parentcommand SUBCOMMAND", "Some Parent Command"
+    subcommand "doi", Cirneco::Doi
+  end
+end

data/lib/cirneco/data_center.rb

@@ -0,0 +1,23 @@
+require 'active_support/all'
+require 'nokogiri'
+require 'sanitize'
+
+require_relative 'api'
+require_relative 'utils'
+require_relative 'base'
+
+module Cirneco
+  class DataCenter
+    include Cirneco::Base
+    include Cirneco::Api
+    include Cirneco::Utils
+
+    attr_accessor :prefix, :username, :password
+
+    def initialize(prefix:, username:, password:, **options)
+      @prefix = prefix
+      @username = username
+      @password = password
+    end
+  end
+end

data/lib/cirneco/doi.rb

@@ -0,0 +1,33 @@
+require "thor"
+
+require_relative 'api'
+require_relative 'utils'
+require_relative 'base'
+
+module Cirneco
+  class Doi < Thor
+    include Cirneco::Base
+    include Cirneco::Api
+    include Cirneco::Utils
+
+    method_option :sandbox, :type => :boolean
+    method_option :prefix, :default => ENV['PREFIX']
+    method_option :username, :default => ENV['MDS_USERNAME']
+    method_option :password, :default => ENV['MDS_PASSWORD']
+
+    desc "get DOI", "get handle url for DOI"
+    def get(doi)
+      get_doi(doi)
+    end
+
+    desc "encode NUMBER", "say hello to NAME"
+    def encode(number)
+      puts encode_doi(prefix, number)
+    end
+
+    desc "command", "an example task"
+    def command
+      puts "I'm a thor task!"
+    end
+  end
+end

data/lib/cirneco/media.rb

@@ -0,0 +1,15 @@
+require "thor"
+require 'active_support/all'
+
+require_relative 'api'
+require_relative 'utils'
+require_relative 'base'
+
+module Cirneco
+  class Media < Thor
+    include Cirneco::Base
+    include Cirneco::Api
+    include Cirneco::Utils
+
+  end
+end

data/lib/cirneco/metadata.rb

@@ -0,0 +1,15 @@
+require "thor"
+require 'active_support/all'
+
+require_relative 'api'
+require_relative 'utils'
+require_relative 'base'
+
+module Cirneco
+  class Metadata < Thor
+    include Cirneco::Base
+    include Cirneco::Api
+    include Cirneco::Utils
+
+  end
+end

data/lib/cirneco/utils.rb

@@ -0,0 +1,28 @@
+require 'base32/crockford'
+require 'securerandom'
+
+module Cirneco
+  module Utils
+    # "ZZZZZZZ" decoded as number
+    UPPER_LIMIT = 34359738367
+
+    def get_dois_by_prefix(prefix, options={})
+      response = get_dois(options)
+
+      if response.body["data"].present?
+        response.body["data"] = response.body["data"].select { |doi| doi.start_with?(prefix) }
+      end
+      response
+    end
+
+    def decode_doi(doi)
+      prefix, string = doi.split('/', 2)
+      Base32::Crockford.decode(string, checksum: true).to_i
+    end
+
+    def encode_doi(prefix, options={})
+      number = options[:number] || SecureRandom.random_number(UPPER_LIMIT)
+      prefix + "/" + Base32::Crockford.encode(number, split: 4, length: 8, checksum: true)
+    end
+  end
+end

data/lib/cirneco/version.rb

@@ -0,0 +1,3 @@
+module Cirneco
+  VERSION = "0.3.1"
+end