Merge branch 'next'

* next: (125 commits)
  Add example and limitations detail to the ReadMe.
  Add "internal use only" warnings to the documentation.
  Add a new example script "dir2ro".
  Add a new example script "zip2ro".
  Add File#remove_aggregate.
  Add Aggregate#file_entry for convenience.
  Add Util.strip_leading_slash.
  Cleanup annotation content stored in .ro/annotations.
  Override File#remove to ensure manifest is kept up to date.
  Allow annotations to be removed by their content field.
  Refactor Manifest#remove_annotation.
  Add Provenance#remove_author.
  Add provenance information to annotations.
  Factor out the provenance information from aggregates.
  Factor out the provenance information from the manifest.
  Tests on a bundle with an invalid manifest.
  Tests on an invalid manifest.
  Tests on an empty manifest ({}).
  Generalize the fake manifest test class.
  Consolidate all require directives into one place.
  ...

Author: hainesr

.ruby-env

@@ -0,0 +1 @@
+RUBYLIB=./lib:../lib

.travis.yml

@@ -3,3 +3,9 @@ rvm:
   - 1.9.3
   - 2.0.0
   - 2.1.2
+  - ruby-head
+  - rbx-2
+matrix:
+  allow_failures:
+    - rvm: ruby-head
+    - rvm: rbx-2

Gemfile

@@ -1,3 +1,11 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
 source 'https://rubygems.org'
 
 gemspec

Rakefile

@@ -20,9 +20,7 @@ end
 
 RDoc::Task.new do |r|
   r.main = "ReadMe.rdoc"
-  lib = Dir.glob("lib/**/*.rb").delete_if do |item|
-    item.include?("ro-dir.rb")
-  end
+  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}"

ReadMe.rdoc

@@ -34,4 +34,24 @@ their documentation in addition to this:
   {documentation}[http://mygrid.github.io/ruby-ucf]
 
 There are some examples of how to use the library provided in the bin
-directory. See the contents of the tests directory for even more.
+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.

bin/dir2ro

@@ -0,0 +1,48 @@
+#!/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

bin/ro-bundle-info

@@ -7,7 +7,6 @@
 # Author: Robert Haines
 #------------------------------------------------------------------------------
 
-
 require 'rubygems'
 require 'ro-bundle'
 
@@ -22,7 +21,7 @@ bundle = ARGV[0]
 
 begin
   ro = ROBundle::File.open(bundle)
-rescue ZipContainer::MalformedContainerError, Zip::ZipError => err
+rescue ZipContainer::MalformedContainerError, ZipContainer::ZipError => err
   puts err.to_s
   exit 1
 end

bin/verify-ro-bundle

@@ -1,35 +1,11 @@
 #!/usr/bin/env ruby
-# Copyright (c) 2013 The University of Manchester, UK.
+#------------------------------------------------------------------------------
+# 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.
+# BSD Licenced. See LICENCE.rdoc for details.
 #
 # Author: Robert Haines
+#------------------------------------------------------------------------------
 
 require 'rubygems'
 require 'ro-bundle'
@@ -45,7 +21,7 @@ rofile = ARGV[0]
 
 begin
   ROBundle::File.verify!(rofile)
-rescue ZipContainer::MalformedContainerError, Zip::ZipError => err
+rescue ZipContainer::MalformedContainerError, ZipContainer::ZipError => err
   puts err.to_s
   exit 1
 end

bin/zip2ro

@@ -0,0 +1,57 @@
+#!/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

lib/ro-bundle.rb

@@ -7,11 +7,22 @@
 #------------------------------------------------------------------------------
 
 require "bundler/setup"
+require "forwardable"
 require "json"
+require "time"
 require "ucf"
+require "uri"
+require "uuid"
 
 require "ro-bundle/version"
-require "ro-bundle/ro-dir"
+require "ro-bundle/util"
+require "ro-bundle/exceptions"
+require "ro-bundle/ro/agent"
+require "ro-bundle/ro/provenance"
+require "ro-bundle/ro/annotation"
+require "ro-bundle/ro/aggregate"
+require "ro-bundle/ro/manifest"
+require "ro-bundle/ro/directory"
 require "ro-bundle/file"
 
 # This is a ruby library to read and write Research Object Bundle files in PK