stash-sword 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 3e0a9bb5934ab1313698dde7e68177a63ffb0597
+  data.tar.gz: 2ad46f630eb85d4349e24c8bf866607358c5ae4c
+SHA512:
+  metadata.gz: 66c005b599f1359ad1fe9884a065d4a96619af9764b791c034f8c5f197f413ef50a2d08c0f654ad662496aae6c387cee9f2d9ebed96ae9503a996930dfcebaae
+  data.tar.gz: 124321ab9db2a6d31f43f16fb717f595337f92778219f45521adccb74d63af3e8ee26d5afbe65c078164f9175374c4aaa1435522a9809e124934d995addadc57

data/.gitignore

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+# Ruby defaults
+
+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+*.bundle
+*.so
+*.o
+*.a
+mkmf.log
+
+# Database
+
+db/*.sqlite3
+
+# Logs
+
+/log/
+
+# IntellJ
+
+*.iml
+*.ipr
+*.iws
+*.ids
+.rakeTasks
+
+# Emacs
+
+*~
+\#*
+.#*
+
+# Mac OS
+
+.DS_Store

data/.rubocop.yml

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+# Ruby version
+AllCops:
+  TargetRubyVersion: 2.2
+  Exclude:
+  - 'old/**/*'
+
+# Disable line-length check; it's too easy for the cure to be worse than the disease
+Metrics/LineLength:
+  Enabled: False
+
+# Disable problematic module documentation check (see https://github.com/bbatsov/rubocop/issues/947)
+Style/Documentation:
+  Enabled: false
+
+# Allow one line around class body (Style/EmptyLines will still disallow two or more)
+Style/EmptyLinesAroundClassBody:
+  Enabled: false
+
+# Allow one line around module body (Style/EmptyLines will still disallow two or more)
+Style/EmptyLinesAroundModuleBody:
+  Enabled: false
+
+# Allow one line around block body (Style/EmptyLines will still disallow two or more)
+Style/EmptyLinesAroundBlockBody:
+  Enabled: false

data/.ruby-version

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+2.2.3

data/.travis.yml

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+language: ruby
+

data/.yardopts

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+--markup-provider=redcarpet
+--markup=markdown
+--default-return ''

data/Gemfile

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+source 'https://rubygems.org'
+
+gemspec
+
+# gem 'sword2ruby', git: 'https://github.com/dmolesUC3/sword2ruby.git'
+# gem 'multipart-post', git: 'https://github.com/dmolesUC3/multipart-post'

data/LICENSE.md

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+The MIT License (MIT)
+
+Copyright (c) 2016 The Regents of the University of California
+
+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

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+# stash-sword
+
+A minimal SWORD 2.0 connector providing those features needed for Stash.
+

data/Rakefile

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+# ------------------------------------------------------------
+# RSpec
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+
+namespace :spec do
+
+  desc 'Run all unit tests'
+  RSpec::Core::RakeTask.new(:unit) do |task|
+    task.rspec_opts = %w(--color --format documentation --order default)
+    task.pattern = 'unit/**/*_spec.rb'
+  end
+
+  task all: [:unit]
+end
+
+desc 'Run all tests'
+task spec: 'spec:all'
+
+# ------------------------------------------------------------
+# Coverage
+
+desc 'Run all unit tests with coverage'
+task :coverage do
+  ENV['COVERAGE'] = 'true'
+  Rake::Task['spec:unit'].execute
+end
+
+# ------------------------------------------------------------
+# RuboCop
+
+require 'rubocop/rake_task'
+RuboCop::RakeTask.new
+
+# ------------------------------------------------------------
+# TODOs
+
+desc 'List TODOs (from spec/todo.rb)'
+RSpec::Core::RakeTask.new(:todo) do |task|
+  task.rspec_opts = %w(--color --format documentation --order default)
+  task.pattern = 'todo.rb'
+end
+
+# ------------------------------------------------------------
+# Defaults
+
+desc 'Run unit tests, check test coverage, run acceptance tests, check code style'
+task default: [:coverage, :rubocop]

data/examples/example.rb

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+#! /usr/bin/env ruby
+
+require 'stash/sword'
+
+include Stash::Sword
+
+username, password, collection = ARGV
+
+client = Client.new(
+  username: username,
+  password: password,
+  collection_uri: URI("http://uc3-mrtsword-dev.cdlib.org:39001/mrtsword/collection/#{collection}")
+)
+
+doi = "doi:10.5072/FK#{Time.now.to_i}"
+zipfile = File.expand_path('../uploads/example.zip', __FILE__)
+
+receipt = client.create(doi: doi, zipfile: zipfile)
+em_iri = receipt.em_iri
+se_iri = receipt.se_iri
+
+puts "em_iri: #{em_iri}"
+puts "se_iri: #{se_iri}"
+
+code = client.update(se_iri: se_iri, zipfile: zipfile)
+puts "update response code: #{code}"

data/examples/uploads/example/lorem-ipsum.txt

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+Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do
+eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad
+minim veniam, quis nostrud exercitation ullamco laboris nisi ut
+aliquip ex ea commodo consequat. Duis aute irure dolor in
+reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla
+pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
+culpa qui officia deserunt mollit anim id est laborum.

data/examples/uploads/example/mrt-datacite.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<resource xmlns='http://datacite.org/schema/kernel-3' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:schemaLocation='http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd'>
+  <identifier identifierType='DOI'>10.5072/FK20160408dmoles</identifier>
+  <creators>
+    <creator>
+      <creatorName>Moles, David</creatorName>
+    </creator>
+  </creators>
+  <titles>
+    <title xml:lang='en'>Merrit SWORD upload test</title>
+  </titles>
+  <publisher>UC Office of the President</publisher>
+  <publicationYear>2016</publicationYear>
+  <subjects>
+    <subject xml:lang='en'>Data literacy</subject>
+  </subjects>
+  <language>en</language>
+  <resourceType resourceTypeGeneral='Dataset'>Text</resourceType>
+  <descriptions>
+    <description xml:lang='en' descriptionType='Abstract'>Lorem ipsum dolor sit amet.</description>
+  </descriptions>
+</resource>

data/examples/uploads/example/mrt-dc.xml

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+<?xml version="1.0"?>
+<qualifieddc xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xsi:noNamespaceSchemaLocation="http://dublincore.org/schemas/xmls/qdc/2008/02/11/qualifieddc.xsd">
+    <dc:creator>Moles, David</dc:creator>
+    <dc:title>Merrit SWORD upload test</dc:title>
+    <dc:publisher>UC Office of the President</dc:publisher>
+    <dc:date>2016</dc:date>
+    <dc:subject>Data literacy</dc:subject>
+    <dc:format>Collection</dc:format>
+    <dcterms:extent>446</dcterms:extent>
+    <dc:rights>Creative Commons Attribution 4.0 International (CC-BY 4.0)</dc:rights>
+    <dcterms:license xsi:type="dcterms:URI">https://creativecommons.org/licenses/by/4.0/</dcterms:license>
+    <dc:description>Lorem ipsum dolor sit amet.</dc:description>
+</qualifieddc>

data/examples/uploads/example/stash-wrapper.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<st:stash_wrapper xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                  xsi:schemaLocation="http://dash.cdlib.org/stash_wrapper/ http://dash.cdlib.org/stash_wrapper/stash_wrapper.xsd"
+                  xmlns:st="http://dash.cdlib.org/stash_wrapper/">
+  <st:identifier type="DOI">10.5072/FK20160408dmoles</st:identifier>
+  <st:stash_administrative>
+    <st:version>
+      <st:version_number>1</st:version_number>
+      <st:date>2016-04-08</st:date>
+    </st:version>
+    <st:license>
+      <st:name>Creative Commons Attribution 4.0 International (CC-BY)</st:name>
+      <st:uri>https://creativecommons.org/licenses/by/4.0/legalcode</st:uri>
+    </st:license>
+    <st:embargo>
+      <st:type>download</st:type>
+      <st:period>1 year</st:period>
+      <st:start>2015-04-08</st:start>
+      <st:end>2016-04-08</st:end>
+    </st:embargo>
+    <st:inventory num_files="1">
+      <st:file>
+        <st:pathname>lorem-ipsum.txt</st:pathname>
+        <st:size unit="B">446</st:size>
+        <st:mime_type>text/plain</st:mime_type>
+      </st:file>
+    </st:inventory>
+  </st:stash_administrative>
+  <st:stash_descriptive>
+    <dcs:resource xmlns:dcs="http://datacite.org/schema/kernel-3"
+                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+                  xsi:schemaLocation="http://datacite.org/schema/kernel-3
+                                http://schema.datacite.org/meta/kernel-3/metadata.xsd">
+      <dcs:identifier identifierType="DOI">doi:10.5072/FK20160408dmoles</dcs:identifier>
+      <dcs:creators>
+        <dcs:creator>
+          <dcs:creatorName>Moles, David</dcs:creatorName>
+        </dcs:creator>
+      </dcs:creators>
+      <dcs:titles>
+        <dcs:title>Merrit SWORD upload test</dcs:title>
+      </dcs:titles>
+      <dcs:publisher>UC Office of the President</dcs:publisher>
+      <dcs:publicationYear>2016</dcs:publicationYear>
+      <dcs:subjects>
+        <dcs:subject>Data literacy</dcs:subject>
+      </dcs:subjects>
+      <dcs:resourceType resourceTypeGeneral="Dataset">Text</dcs:resourceType>
+      <dcs:descriptions>
+        <dcs:description descriptionType="Abstract">
+          Lorem ipsum dolor sit amet.
+        </dcs:description>
+      </dcs:descriptions>
+    </dcs:resource>
+  </st:stash_descriptive>
+</st:stash_wrapper>

data/lib/stash/sword.rb

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+require 'uri'
+require 'logger'
+
+module Stash
+
+  # TODO: Make this configurable
+  LOG_LEVEL = case ENV['RAILS_ENV'].to_s.downcase
+              when 'test'
+                Logger::DEBUG
+              when 'development'
+                Logger::INFO
+              else
+                Logger::WARN
+              end
+
+  module Sword
+
+    Dir.glob(File.expand_path('../sword/*.rb', __FILE__)).sort.each(&method(:require))
+
+    def self.log
+      @log ||= new_logger(logdev: $stdout)
+    end
+
+    def self.log_device=(value)
+      @log = new_logger(logdev: value)
+    end
+
+    def self.new_logger(logdev:, level: Stash::LOG_LEVEL, shift_age: 10, shift_size: 1024 * 1024)
+      logger = Logger.new(logdev, shift_age, shift_size)
+      logger.level = level
+      logger.formatter = proc do |severity, datetime, progname, msg|
+        "#{datetime.to_time.utc} #{severity} -#{progname}- #{msg}\n"
+      end
+      logger
+    end
+
+    private_class_method :new_logger
+  end
+end

data/lib/stash/sword/client.rb

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+require 'digest'
+require 'uri'
+require 'stash/sword/header_utils'
+require 'stash/sword/log_utils'
+require 'stash/sword/http_helper'
+require 'stash/sword/sequence_io'
+
+module Stash
+  module Sword
+    class Client
+      include HeaderUtils, LogUtils
+
+      EOL = "\r\n".freeze
+
+      attr_reader :collection_uri
+      attr_reader :username
+      attr_reader :password
+      attr_reader :helper
+
+      # Creates a new {Client} for the specified collection URI, with the specified credentials.
+      #
+      # @param collection_uri [URI, String] The collection URI
+      # @param username [String] the username
+      # @param password [String] the password
+      # @param on_behalf_of [String, nil] the user for whom the original sword package was deposited on behalf of.
+      #   Defaults to `username`.
+      def initialize(collection_uri:, username:, password:, on_behalf_of: nil, helper: nil)
+        raise 'no collection URI provided' unless collection_uri
+        raise 'no username provided' unless username
+        raise 'no password provided' unless password
+        @collection_uri = to_uri(collection_uri)
+        @username     = username
+        @password     = password
+        @on_behalf_of = on_behalf_of || username
+        @helper       = helper || HTTPHelper.new(username: username, password: password, user_agent: "stash-sword #{VERSION}")
+      end
+
+      # Creates a new resource for the specified DOI with the specified zipfile
+      #
+      # @param doi [String] the DOI
+      # @param zipfile [String] the zipfile path
+      # @return [DepositReceipt] the deposit receipt
+      def create(doi:, zipfile:)
+        log.debug("Stash::Sword::Client.create(doi: #{doi}, zipfile: #{zipfile})")
+        uri = collection_uri.to_s
+        response = do_post(uri, zipfile, create_request_headers(zipfile, doi))
+        receipt_from(response)
+      rescue => e
+        log_error(e)
+        raise
+      end
+
+      # Updates a resource with a new zipfile
+      #
+      # @param edit_iri [URI, String] the Atom Edit-IRI
+      # @param zipfile [String] the zipfile path
+      def update(edit_iri:, zipfile:)
+        log.debug("Stash::Sword::Client.update(edit_iri: #{edit_iri}, zipfile: #{zipfile})")
+        uri = to_uri(edit_iri).to_s
+        response = maybe_redirect(do_put(uri, zipfile))
+        log.debug(response_to_log_msg(response))
+        response.code # TODO: what if anything should we return here?
+      rescue => e
+        log_error(e)
+        raise
+      end
+
+      private
+
+      def maybe_redirect(response)
+        return response unless [301, 302, 307].include?(response.code)
+        log.debug(response_to_log_msg(response))
+        log.debug("Response code #{response.code}; redirecting")
+        response.follow_get_redirection
+      end
+
+      def receipt_from(response)
+        log.debug(response_to_log_msg(response))
+
+        body = response.body.strip
+        return DepositReceipt.parse_xml(body) unless body.empty?
+
+        receipt_from_location(response)
+      end
+
+      def receipt_from_location(response)
+        log.debug('Desposit receipt not provided in SWORD response body')
+        edit_iri = response.headers[:location]
+        return nil unless edit_iri
+
+        log.debug("Retrieving deposit receipt from Location header Edit-IRI: #{edit_iri}")
+        body = helper.get(to_uri(edit_iri))
+        return nil unless body
+
+        DepositReceipt.parse_xml(body)
+      end
+
+      def do_post(uri, zipfile, headers)
+        File.open(zipfile, 'rb') do |file|
+          return helper.post(uri: uri, payload: file, headers: headers)
+        end
+      end
+
+      def do_put(uri, zipfile)
+        boundary        = "========#{Time.now.to_i}=="
+        stream          = stream_for(zipfile: File.open(zipfile, 'rb'), boundary: boundary)
+        begin
+          return helper.put(uri: uri, headers: update_request_headers(stream, boundary), payload: stream)
+        ensure
+          stream.close
+        end
+      end
+
+      def stream_for(zipfile:, boundary:)
+        content = []
+        # strictly speaking, do we need an Atom <entry/> first?
+        content << "--#{boundary}#{EOL}"
+        update_mime_headers(zipfile).each { |k, v| content << "#{k}: #{v}#{EOL}" }
+        content << EOL
+        content << zipfile
+        content << "--#{boundary}--#{EOL}"
+        SequenceIO.new(content).binmode
+      end
+
+      def to_uri(url)
+        ::XML::MappingExtensions.to_uri(url)
+      end
+      protected :to_uri
+
+    end
+  end
+end