ro-bundle 0.1.0

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data/.gitignore

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+pkg/
+html/
+coverage/
+.buildpath
+.project
+.settings
+.idea
+.rvmrc
+example.zip
+.bundle
+Gemfile.lock

data/.ruby-env

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+RUBYLIB=./lib:../lib

data/.ruby-gemset

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+ro-bundle
+

data/.ruby-version

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+ruby-1.9.3
+

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.3
+  - 2.0.0
+  - 2.1.2
+  - ruby-head
+  - rbx-2
+matrix:
+  allow_failures:
+    - rvm: ruby-head
+    - rvm: rbx-2

data/Changes.rdoc

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+= Changes log for the RO Bundle Ruby Gem
+
+== Version 0.1.0
+
+* Use the ZipContainer::ZipError in examples and tests.
+* Use "self" for the File class methods and fix docs.
+* Read the id from the manifest.
+* Set .ro and .ro/manifest.json to be required entries.
+* Properly detect missing manifest during creation.
+* Simple validation of the manifest file.
+* Read createdOn and authoredOn info from the manifest.
+* Add a class to represent an Agent in an RO.
+* Read createdBy and authoredBy from the manifest.
+* Move the .ro directory code to a sub-directory.
+* Move the manifest class to its own file.
+* Document the RODir and Manifest classes.
+* Move operations on the manifest data into the manifest class.
+* Harden getting a missing time from the manifest.
+* Harden getting the id from the manifest.
+* Harden getting the creator and author list.
+* Get the list of history files from the manifest.
+* Ensure that an Agent always has a name.
+* Ensure lists are always returned when necessary.
+* Add separate tests for the Manifest class.
+* Add an exception for invalid aggregates.
+* Add a class to represent an aggregated resource.
+* Cache created_on and authored_on in the manifest.
+* Expose the aggregates method in the File class.
+* Ensure that Manifest#aggregates always returns a list.
+* Add a class to represent an annotation.
+* Add the #annotations method to the Manifest class.
+* Expose the annotations method in the File class.
+* Add Agent#to_json.
+* Refactor to use hashes for internal state storage.
+* Add a utility module for mixing in common functions.
+* Use the utility module to parse time values.
+* Use the utility module to parse URIs.
+* Use the utility module to clean JSON structures.
+* Fixup the to_json methods so that JSON#generate can use them.
+* Add a Util test case and test the parse_time method.
+* Add tests for the Util#parse_uri method.
+* Add tests for the Util#clean_json method.
+* Refactor the annotation tests to share setup.
+* Add json output for the Annotation class.
+* Return "/" by default for Manifest#id.
+* Refactor Manifest for easier serialization.
+* Improve Util#clean_json.
+* Add Manifest#to_json.
+* Add write support for Manifest#id.
+* Write support for Manifest#created_on and #authored_on.
+* Write support for Manifest#created_by.
+* Return duplicate lists from Manifest.
+* Add an edited flag to Manifest to detect changes.
+* Add Manifest write access methods to the File class.
+* Add File#add and File#add_aggregate.
+* Add File#add_history and support in the manifest.
+* Support for adding an author to the authoredBy list.
+* Override File#commit_required? to include the manifest.
+* Annotation: generate id on create, not on access.
+* Fix erroneous Annotation test data.
+* Allow annotation content to be set at creation time.
+* Edit annotation content.
+* Rename Annotation#about to Annotation#target.
+* Add access to the manifest @context element.
+* Create the .ro directory on init if needs be.
+* Write out the manifest when closing the bundle.
+* Don't create an empty Agent for Manifest#created_by.
+* Initialize default manifest @context if missing.
+* Initialize default manifest id if missing.
+* Allow Manifest#add_aggregate to be passed an Aggregate object.
+* Set aggregate mediatype on creation.
+* Add Util.is_absolute_uri? method.
+* Add File#aggregate? to test if an entry is aggregated.
+* Improve Util.is_absolute_uri?().
+* Mangle aggregate paths when building an Aggregate.
+* Enable adding URI aggregates.
+* Handle URIs in File#aggregate?().
+* Override File#find_entry() to cope with URIs.
+* Add URI aggregation tests.
+* Add File#annotation? to test registered annotations.
+* Add File#annotatable?().
+* Add support for adding annotations to the manifest.
+* Keep an internal manifest reference in RODir.
+* Add AnnotationsDir managed directory to RODir.
+* Add File#add_annotation.
+* Manifest#add_author now returns an Agent object.
+* Manifest#add_aggregate now returns an Aggregate object.
+* Manifest#add_annotation now returns an Annotation object.
+* Add tests for annotations with no targets.
+* Use released versions of ucf and zip-container gems.
+* Fix File#add_history documentation.
+* Make Manifest#created_by= more flexible.
+* Update the example manifest test fixture.
+* Add Manifest#remove_annotation.
+* Don't store an aggregate's uri as a URI object.
+* Add Manifest#remove_aggregate.
+* Don't store an agent's uri or orcid as URI objects.
+* Remove the Util.parse_uri() method.
+* Consolidate all require directives into one place.
+* Tests on an empty manifest ({}).
+* Tests on an invalid manifest.
+* Tests on a bundle with an invalid manifest.
+* Factor out the provenance information from the manifest.
+* Factor out the provenance information from aggregates.
+* Add provenance information to annotations.
+* Add Provenance#remove_author.
+* Refactor Manifest#remove_annotation.
+* Allow annotations to be removed by their content field.
+* Override File#remove to ensure manifest is kept up to date.
+* Cleanup annotation content stored in .ro/annotations.
+* Add Util.strip_leading_slash.
+* Add Aggregate#file_entry for convenience.
+* Add File#remove_aggregate.
+* Add a new example script "zip2ro".
+* Add a new example script "dir2ro".
+* Add example and limitations detail to the ReadMe.
+
+== Version 0.0.1
+
+* Very basic RO Bundle facilities complete (plus examples).
+* Very simple verification of RO Bundle files.
+* API documentation added.
+* Add tests.
+
+== About this Changes file
+
+This file is, at least in part, generated by the following command:
+
+ $ git log --pretty=format:"* %s" --reverse --no-merges <commit-hash>..

data/Gemfile

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+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+source 'https://rubygems.org'
+
+gemspec

data/Licence.rdoc

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+Copyright (c) 2014 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/Rakefile

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+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require "bundler/gem_tasks"
+require "rake/testtask"
+require "rdoc/task"
+
+task :default => [:test]
+
+Rake::TestTask.new do |t|
+  t.libs << "test"
+  t.test_files = FileList['test/ts_ro_bundle.rb']
+  t.verbose = true
+end
+
+RDoc::Task.new do |r|
+  r.main = "ReadMe.rdoc"
+  lib = Dir.glob("lib/**/*.rb")
+  r.rdoc_files.include("ReadMe.rdoc", "Licence.rdoc", "Changes.rdoc", lib)
+  r.options << "-t Research Object Bundle Ruby Library version " +
+    "#{ROBundle::VERSION}"
+  r.options << "-N"
+  r.options << "--tab-width=2"
+end

data/ReadMe.rdoc

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+= Research Object Bundle Ruby Library
+
+Authors::     Robert Haines
+Contact::     mailto:support@mygrid.org.uk
+Homepage::    http://mygrid.github.io/ruby-ro-bundle
+Source code:: https://github.com/myGrid/ruby-ro-bundle
+Licence::     BSD (See Licence file or http://www.opensource.org/licenses/bsd-license.php)
+Copyright::   (c) 2014 The University of Manchester, UK
+
+{<img src="https://codeclimate.com/github/myGrid/ruby-ro-bundle.png" />}[https://codeclimate.com/github/myGrid/ruby-ro-bundle]
+{<img src="https://travis-ci.org/myGrid/ruby-ro-bundle.svg?branch=master" alt="Build Status" />}[https://travis-ci.org/myGrid/ruby-ro-bundle]
+{<img src="https://coveralls.io/repos/myGrid/ruby-ro-bundle/badge.png?branch=master" alt="Coverage Status" />}[https://coveralls.io/r/myGrid/ruby-ro-bundle?branch=master]
+
+== Synopsis
+
+This is a Ruby library for working with Research Object Bundle files. See the
+{Research Object Bundle}[http://wf4ever.github.io/ro/bundle/] specification
+for more details.
+
+<b>This library is a work in progress!</b> Until we release version 1.0.0 you
+can expect the API to change in incompatible ways, although we will try to
+keep this to an absolute minimum. Once version 1.0.0 is released we will be
+following the principles of {Semantic Versioning}[http://semver.org/] for our
+version numbering scheme.
+
+== Usage
+
+Most of this library's API is provided by two underlying gems. Please consult
+their documentation in addition to this:
+
+* {zip-container gem}[https://rubygems.org/gems/zip-container]
+  {documentation}[http://mygrid.github.io/ruby-zip-container/]
+* {ucf gem}[https://rubygems.org/gems/ucf]
+  {documentation}[http://mygrid.github.io/ruby-ucf]
+
+There are some examples of how to use the library provided in the bin
+directory:
+
+* <tt>ro-bundle-info</tt>: Print out simple metrics about this RO Bundle. This
+  is analogous to the standard <tt>zipinfo</tt> command.
+* <tt>verify-ro-bundle</tt>: Verify that the specified RO Bundle is valid.
+* <tt>dir2ro</tt>: Recursively package up a directory into a RO Bundle. All
+  files in the directory are added as aggregates.
+* <tt>zip2ro</tt>: Copy all files from a normal zip file into a RO Bundle. All
+  files in the zip file are added as aggregates.
+
+See the contents of the tests directory for even more example usage.
+
+== What this library cannot do yet
+
+The {RO Bundle specification}[http://wf4ever.github.io/ro/bundle/] is largely
+implemented but there are notable gaps at present, including:
+
+* Aggregates do not support ORE proxies yet.
+* Extra provenance information cannot yet be added using the <tt>pav:</tt>
+  namespace.
+* The <tt>@graph</tt> member is not supported in the top-level manifest.

data/bin/dir2ro

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+#!/usr/bin/env ruby
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'rubygems'
+require 'ro-bundle'
+
+def usage
+  puts "Usage:\n  dir2ro <directory> <ro-bundle> [name]"
+  exit 1
+end
+
+usage unless ARGV.length >= 2
+
+dir_name = ARGV[0]
+bundle_file = ARGV[1]
+creator = ARGV[2]
+time_now = Time.now
+
+begin
+  ROBundle::File.create(bundle_file) do |bundle|
+    # Set provenance data.
+    bundle.created_by = creator unless creator.nil?
+    bundle.created_on = time_now
+
+    dir_path = Pathname(dir_name)
+    Dir[File.join(dir_name, "**", "**")].each do |entry|
+      relative_path = Pathname.new(entry).relative_path_from(dir_path).to_s
+
+      # If the current entry is a directory, create it;
+      # if it's a file, add it.
+      if ::File.directory?(entry)
+        bundle.mkdir(relative_path)
+      else
+        aggregate = bundle.add(relative_path, entry)
+        aggregate.created_on = time_now
+      end
+    end
+  end
+rescue Errno::ENOENT, Zip::Error => err
+  puts err.to_s
+  exit 1
+end

data/bin/ro-bundle-info

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+#!/usr/bin/env ruby
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'rubygems'
+require 'ro-bundle'
+
+def usage
+  puts "Usage:\n  ro-bundle-info <ro-bundle>"
+  exit 1
+end
+
+usage unless ARGV.length == 1
+
+bundle = ARGV[0]
+
+begin
+  ro = ROBundle::File.open(bundle)
+rescue ZipContainer::MalformedContainerError, ZipContainer::ZipError => err
+  puts err.to_s
+  exit 1
+end
+
+puts "Research Object Bundle: #{ro.to_s}"
+puts "Bundle file size: #{File.size(bundle)} bytes, number of entries: #{ro.size}"
+
+total_size = 0
+total_comp = 0
+
+ro.each do |entry|
+  total_size += entry.size
+  total_comp += entry.compressed_size
+  comp = entry.compression_method == 0 ? "stor" : "defN"
+  size = entry.size.to_s.rjust(8)
+  puts "#{size} #{comp} #{entry.time} #{entry.name}"
+end
+
+ratio = ((total_size - total_comp) / total_size.to_f) * 100
+puts "%d files, %d bytes uncompressed, %d bytes compressed: %.1f%%" %
+  [ro.size, total_size, total_comp, ratio]

data/bin/verify-ro-bundle

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+#!/usr/bin/env ruby
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'rubygems'
+require 'ro-bundle'
+
+def usage
+  puts "Usage:\n  verify-ro-bundle <ro-bundle-file>"
+  exit 1
+end
+
+usage unless ARGV.length == 1
+
+rofile = ARGV[0]
+
+begin
+  ROBundle::File.verify!(rofile)
+rescue ZipContainer::MalformedContainerError, ZipContainer::ZipError => err
+  puts err.to_s
+  exit 1
+end

data/bin/zip2ro

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+#!/usr/bin/env ruby
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'rubygems'
+require 'ro-bundle'
+
+def usage
+  puts "Usage:\n  zip2ro <zip-file> <ro-bundle> [name]"
+  exit 1
+end
+
+usage unless ARGV.length >= 2
+
+zip_file = ARGV[0]
+bundle_file = ARGV[1]
+creator = ARGV[2]
+time_now = Time.now
+
+begin
+  ROBundle::File.create(bundle_file) do |bundle|
+    # Set provenance data.
+    bundle.created_by = creator unless creator.nil?
+    bundle.created_on = time_now
+
+    Zip::File.open(zip_file) do |zip|
+      zip.each do |entry|
+
+        # If the current entry is a directory, create it;
+        # if it's a file, copy it.
+        if zip.file.directory?(entry.name)
+          bundle.mkdir entry.name
+        else
+          zip.file.open(entry.name, "r") do |z_file|
+
+            # Copy the contents of the entry.
+            bundle.file.open(entry.name, "w") do |b_file|
+              b_file.write z_file.read
+            end
+
+            # Register the new entry as an aggregate of the RO.
+            aggregate = bundle.add_aggregate entry.name
+            aggregate.created_on = time_now
+          end
+        end
+      end
+    end
+  end
+rescue Errno::ENOENT, Zip::Error => err
+  puts err.to_s
+  exit 1
+end