ro-bundle 0.1.0 → 0.2.0

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data/.ruby-gemset

@@ -1,2 +1 @@
 ro-bundle
-

data/.ruby-version

@@ -1,2 +1 @@
-ruby-1.9.3
-
+ruby-2.2.1

data/.travis.yml

@@ -1,11 +1,19 @@
 language: ruby
+
 rvm:
   - 1.9.3
   - 2.0.0
-  - 2.1.2
+  - 2.1.6
+  - 2.2.1
   - ruby-head
   - rbx-2
+
+sudo: false
+
+cache: bundler
+
 matrix:
   allow_failures:
+    - rvm: 1.9.3
     - rvm: ruby-head
     - rvm: rbx-2

data/Licence.rdoc

@@ -1,4 +1,4 @@
-Copyright (c) 2014 The University of Manchester, UK.
+Copyright (c) 2014, 2015 The University of Manchester, UK.
 
 All rights reserved.
 

data/ReadMe.rdoc

@@ -5,16 +5,17 @@ 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
+Copyright::   (c) 2014, 2015 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://badge.fury.io/rb/ro-bundle.svg" alt="Gem Version" />}[http://badge.fury.io/rb/ro-bundle]
+{<img src="https://codeclimate.com/github/myGrid/ruby-ro-bundle.svg" />}[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]
+{<img src="https://coveralls.io/repos/myGrid/ruby-ro-bundle/badge.svg?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
+{Research Object Bundle}[https://w3id.org/bundle/] specification
 for more details.
 
 <b>This library is a work in progress!</b> Until we release version 1.0.0 you
@@ -48,10 +49,10 @@ 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
+The {RO Bundle specification}[https://w3id.org/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.
+* The <tt>@graph</tt> member is not supported in the top-level manifest
+  (although if it is present it will be preserved).

data/bin/dir2ro

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 #------------------------------------------------------------------------------
-# Copyright (c) 2014 The University of Manchester, UK.
+# Copyright (c) 2014, 2015 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -9,6 +9,7 @@
 
 require 'rubygems'
 require 'ro-bundle'
+require 'pathname'
 
 def usage
   puts "Usage:\n  dir2ro <directory> <ro-bundle> [name]"
@@ -42,7 +43,7 @@ begin
       end
     end
   end
-rescue Errno::ENOENT, Zip::Error => err
+rescue Errno::ENOENT, ZipContainer::Error => err
   puts err.to_s
   exit 1
 end

data/bin/ro-bundle-info

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 #------------------------------------------------------------------------------
-# Copyright (c) 2014 The University of Manchester, UK.
+# Copyright (c) 2014, 2015 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -21,7 +21,7 @@ bundle = ARGV[0]
 
 begin
   ro = ROBundle::File.open(bundle)
-rescue ZipContainer::MalformedContainerError, ZipContainer::ZipError => err
+rescue ZipContainer::MalformedContainerError, ZipContainer::Error => err
   puts err.to_s
   exit 1
 end

data/bin/verify-ro-bundle

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 #------------------------------------------------------------------------------
-# Copyright (c) 2014 The University of Manchester, UK.
+# Copyright (c) 2014, 2015 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -21,7 +21,7 @@ rofile = ARGV[0]
 
 begin
   ROBundle::File.verify!(rofile)
-rescue ZipContainer::MalformedContainerError, ZipContainer::ZipError => err
+rescue ZipContainer::MalformedContainerError, ZipContainer::Error => err
   puts err.to_s
   exit 1
 end

data/bin/zip2ro

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 #------------------------------------------------------------------------------
-# Copyright (c) 2014 The University of Manchester, UK.
+# Copyright (c) 2014, 2015 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -51,7 +51,7 @@ begin
       end
     end
   end
-rescue Errno::ENOENT, Zip::Error => err
+rescue Errno::ENOENT, ZipContainer::Error => err
   puts err.to_s
   exit 1
 end

data/lib/ro-bundle.rb

@@ -19,6 +19,8 @@ require "ro-bundle/util"
 require "ro-bundle/exceptions"
 require "ro-bundle/ro/agent"
 require "ro-bundle/ro/provenance"
+require "ro-bundle/ro/manifest-entry"
+require "ro-bundle/ro/proxy"
 require "ro-bundle/ro/annotation"
 require "ro-bundle/ro/aggregate"
 require "ro-bundle/ro/manifest"
@@ -29,8 +31,7 @@ require "ro-bundle/file"
 # Zip format. See the ROBundle::File class for more information.
 #
 # See
-# {the RO Bundle specification}[http://wf4ever.github.io/ro/bundle/]
-# for more details.
+# {the RO Bundle specification}[https://w3id.org/bundle/] for more details.
 #
 # Most of this library's API is provided by two underlying gems. Please
 # consult their documentation in addition to this:

data/lib/ro-bundle/exceptions.rb

@@ -13,18 +13,4 @@ module ROBundle
   class ROError < RuntimeError
   end
 
-  # This exception is raised when an invalid aggregate is detected.
-  class InvalidAggregateError < ROError
-
-    # :call-seq:
-    #   new(name)
-    #
-    # Create a new InvalidAggregateError with the invalid object (file or
-    # URI) supplied.
-    def initialize(object)
-      super("'#{object}' is not an absolute filename or a URI.")
-    end
-
-  end
-
 end

data/lib/ro-bundle/file.rb

@@ -10,8 +10,7 @@
 module ROBundle
 
   # This class represents a Research Object Bundle file. See the
-  # {RO Bundle specification}[http://wf4ever.github.io/ro/bundle/]
-  # for more details.
+  # {RO Bundle specification}[https://w3id.org/bundle/] for more details.
   #
   # Many of the methods that this class provides are actually implemented in
   # the Manifest class, so please see its documentation for details.
@@ -35,12 +34,6 @@ module ROBundle
       @manifest = Manifest.new
       @ro_dir = RODir.new(@manifest)
       initialize_managed_entries(@ro_dir)
-
-      # Create the .ro directory if it does not already exist.
-      if find_entry(@ro_dir.full_name).nil?
-        mkdir(@ro_dir.full_name)
-        commit
-      end
     end
     # :startdoc:
 
@@ -59,7 +52,20 @@ module ROBundle
     # for much more information and a list of all the other methods available
     # in this class. RDoc does not list inherited methods, unfortunately.
     def self.create(filename, mimetype = MIMETYPE, &block)
-      super(filename, mimetype, &block)
+      # Wow. I have to specifically send nil as the block to stop super from
+      # sending the other block up automatically. Is this a bug in Ruby?
+      ro = super(filename, mimetype, &nil)
+      ro.init_metadata
+
+      if block_given?
+        begin
+          yield ro
+        ensure
+          ro.close
+        end
+      end
+
+      ro
     end
 
     # :call-seq:
@@ -189,9 +195,7 @@ module ROBundle
       end
 
       aggregates.each do |agg|
-        return true if agg.uri == entry ||
-          agg.file == entry ||
-          agg.file_entry == entry
+        return true if agg.uri == entry || agg.file_entry == entry
       end
 
       false
@@ -213,10 +217,10 @@ module ROBundle
     #
     # Is the supplied id or annotation registered in this Research Object?
     def annotation?(id)
-      id = id.annotation_id if id.instance_of?(Annotation)
+      id = id.uri if id.instance_of?(Annotation)
 
       annotations.each do |ann|
-        return true if ann.annotation_id == id
+        return true if ann.uri == id
       end
 
       false
@@ -231,12 +235,8 @@ module ROBundle
     # otherwise.
     def commit
       if @manifest.edited?
-        name = @manifest.full_name
-        remove(name, true) unless find_entry(name).nil?
-
-        file.open(name, "w") do |m|
-          m.puts JSON.pretty_generate(@manifest)
-        end
+        # This will overwrite the old version.
+        @manifest.write
 
         @ro_dir.cleanup_annotation_data
       end
@@ -319,5 +319,13 @@ module ROBundle
       @manifest.remove_aggregate(object)
     end
 
+    # :stopdoc:
+    def init_metadata
+      mkdir(@ro_dir.full_name)
+      @manifest.init
+      commit
+    end
+    # :startdoc:
+
   end
 end

data/lib/ro-bundle/ro/agent.rb

@@ -65,7 +65,7 @@ module ROBundle
     # Write this Agent out as a json string. Takes the same options as
     # JSON#generate.
     def to_json(*a)
-      Util.clean_json(@structure).to_json(*a)
+      JSON.generate(Util.clean_json(@structure),*a)
     end
 
   end

data/lib/ro-bundle/ro/aggregate.rb

@@ -11,35 +11,40 @@ module ROBundle
 
   # A class to represent an aggregated resource in a Research Object. It holds
   # standard meta-data for either file or URI resources. An aggregate can only
-  # represent a file OR a URI resource, not both at once.
-  class Aggregate
-    include Provenance
+  # represent a file path OR a URI resource, not both at once.
+  #
+  # If a file path is passed, it will be correctly encoded into a valid absolute URI. If an absolute URI is passed, it is
+  # assumed to already have been encoded.
+  class Aggregate < ManifestEntry
 
     # :call-seq:
-    #   new(filename, mediatype = nil)
-    #   new(URI)
+    #   new(uri, mediatype)
+    #   new(uri)
+    #   new(filepath)
+    #   new(filepath, mediatype)
     #
     # Create a new file or URI aggregate.
-    def initialize(object, second = nil)
-      @structure = {}
+    def initialize(object, mediatype = nil)
+      super()
 
       if object.instance_of?(Hash)
         init_json(object)
       else
-        init_file_or_uri(object)
-
-        if @structure[:file]
-          @structure[:mediatype] = second
-        end
+        @structure[:uri] = if Util.is_absolute_uri?(object)
+                             object.to_s
+                           else
+                             URI.encode(object.start_with?("/") ? object : "/#{object}")
+                           end
+        @structure[:mediatype] = mediatype
       end
     end
 
     # :call-seq:
-    #   file
+    #   edited? -> true or false
     #
-    # The path of this aggregate. It should start with '/'.
-    def file
-      @structure[:file]
+    # Has this aggregate been altered in any way?
+    def edited?
+      @edited || (proxy.nil? ? false : proxy.edited?)
     end
 
     # :call-seq:
@@ -47,7 +52,7 @@ module ROBundle
     #
     # The path of this aggregate in "rubyzip" format, i.e. no leading '/'.
     def file_entry
-      Util.strip_leading_slash(file)
+      URI.decode(Util.strip_leading_slash(uri)) unless Util.is_absolute_uri?(uri)
     end
 
     # :call-seq:
@@ -61,44 +66,47 @@ module ROBundle
     # :call-seq:
     #   mediatype
     #
-    # For a file aggregate, its
+    # This aggregate's
     # {IANA media type}[http://www.iana.org/assignments/media-types].
     def mediatype
       @structure[:mediatype]
     end
 
+    # :call-seq:
+    #   proxy -> Proxy
+    #
+    # Return this aggregate's ORE proxy as per the specification of the
+    # {JSON structure}[https://researchobject.github.io/specifications/bundle/#json-structure]
+    # of the manifest.
+    def proxy
+      @structure[:bundledAs]
+    end
+
     # :call-seq:
     #   to_json(options = nil) -> String
     #
     # Write this Aggregate out as a json string. Takes the same options as
     # JSON#generate.
     def to_json(*a)
-      Util.clean_json(@structure).to_json(*a)
+      JSON.generate(Util.clean_json(@structure),*a)
     end
 
-    private
-
-    def structure
-      @structure
+    # :stopdoc:
+    # For internal use only!
+    def stored
+      super
+      proxy.stored unless proxy.nil?
     end
+    # :startdoc:
+
+    private
 
     def init_json(object)
-      init_file_or_uri(object[:file] || object[:uri])
       @structure = init_provenance_defaults(object)
-
-      if @structure[:file]
-        @structure[:mediatype] = object[:mediatype]
-      end
-    end
-
-    def init_file_or_uri(object)
-      if object.is_a?(String) && !Util.is_absolute_uri?(object)
-        name = object.start_with?("/") ? object : "/#{object}"
-        @structure[:file] = name
-      elsif Util.is_absolute_uri?(object)
-        @structure[:uri] = object.to_s
-      else
-        raise InvalidAggregateError.new(object)
+      @structure[:uri] = object[:uri]
+      @structure[:mediatype] = object[:mediatype]
+      unless object[:bundledAs].nil?
+        @structure[:bundledAs] = Proxy.new(object[:bundledAs])
       end
     end