ro-bundle 0.1.0 → 0.2.0

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

@@ -0,0 +1,80 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+#
+module ROBundle
+
+  # A class to represent an ORE Proxy for an Aggregate as per the specification
+  #of the
+  # {JSON structure}[https://researchobject.github.io/specifications/bundle/#json-structure]
+  # of the manifest.
+  class Proxy < ManifestEntry
+
+    # :call-seq:
+    #   new
+    #   new(folder)
+    #   new(folder, filename)
+    #
+    # Create a new ORE Proxy. If +folder+ is not supplied then "/" is assumed.
+    def initialize(object = "", filename = nil)
+      super()
+
+      if object.instance_of?(Hash)
+        @structure = object
+        init_provenance_defaults(@structure)
+      else
+        @structure = {}
+        @structure[:uri] = UUID.generate(:urn)
+        @structure[:folder] = folder_slashes(object)
+        @structure[:filename] = filename
+      end
+    end
+
+    # :call-seq:
+    #   folder
+    #
+    # Return the folder field of this Proxy.
+    def folder
+      @structure[:folder]
+    end
+
+    # :call-seq:
+    #   filename
+    #
+    # Return the filename field of this Proxy.
+    def filename
+      @structure[:filename]
+    end
+
+    # :call-seq:
+    #   uri -> String in the form of a urn:uuid URI.
+    #
+    # Return the annotation id of this Annotation.
+    def uri
+      @structure[:uri]
+    end
+
+    # :call-seq:
+    #   to_json(options = nil) -> String
+    #
+    # Write this Proxy out as a json string. Takes the same options as
+    # JSON#generate.
+    def to_json(*a)
+      JSON.generate(Util.clean_json(@structure),*a)
+    end
+
+    private
+
+    def folder_slashes(folder)
+      folder = "/#{folder}" unless folder.start_with?('/')
+      folder = "#{folder}/" unless folder.end_with?('/')
+      folder
+    end
+
+  end
+end

data/lib/ro-bundle/util.rb

@@ -17,7 +17,7 @@ module ROBundle
     #
     # Remove empty strings and nils from a json hash structure.
     def self.clean_json(structure)
-      structure.delete_if do |_, v|
+      structure.dup.delete_if do |_, v|
         v.nil? || (v.respond_to?(:empty?) && v.empty?)
       end
     end

data/lib/ro-bundle/version.rb

@@ -9,5 +9,5 @@
 #
 module ROBundle
   # The version number of this library as a String.
-  VERSION = "0.1.0"
+  VERSION = "0.2.0"
 end

data/ro-bundle.gemspec

@@ -1,5 +1,5 @@
 #------------------------------------------------------------------------------
-# Copyright (c) 2014 The University of Manchester, UK.
+# Copyright (c) 2014, 2015 The University of Manchester, UK.
 #
 # BSD Licenced. See LICENCE.rdoc for details.
 #
@@ -19,8 +19,8 @@ Gem::Specification.new do |spec|
     "Research Object (RO) bundles."
   spec.description   = "This library provides an API for manipulating "\
     "Research Object (RO) bundles. The RO bundle specification can be found "\
-    "at http://purl.org/wf4ever/ro-bundle."
-  spec.homepage      = "http://www.taverna.org.uk"
+    "at https://w3id.org/bundle/."
+  spec.homepage      = "http://www.researchobject.org/"
   spec.license       = "BSD"
 
   spec.files         = `git ls-files`.split($/)
@@ -35,9 +35,10 @@ Gem::Specification.new do |spec|
   spec.required_ruby_version = ">= 1.9.3"
   spec.add_development_dependency "bundler", "~> 1.5"
   spec.add_development_dependency "rake", "~> 10.1"
-  spec.add_development_dependency("rdoc", "~> 4.1")
+  spec.add_development_dependency "rdoc", "~> 4.1"
+  spec.add_development_dependency "test-unit", "~> 3.0"
   spec.add_development_dependency "coveralls"
-  spec.add_runtime_dependency "ucf", "~> 1.0"
+  spec.add_runtime_dependency "ucf", "~> 2.0"
   spec.add_runtime_dependency "json", "~> 1.8"
   spec.add_runtime_dependency "uuid", "~> 2.3"
 end

data/test/data/example3-manifest.json

@@ -11,9 +11,9 @@
         "name":    "Alice W. Land" },
     "history":   "evolution.ttl",
     "aggregates": [
-       { "file":  "/folder/soup.jpeg" },
-       { "uri": "http://example.com/blog/" },
-       { "file":      "/README.txt",
+       { "uri":  "/folder/soup.jpeg" },
+       { "uri":  "http://example.com/blog/" },
+       { "uri":  "/README.txt",
          "mediatype": "text/plain",
          "createdBy": {
              "uri":     "http://example.com/foaf#bob",
@@ -21,15 +21,15 @@
          "createdOn": "2013-02-12T19:37:32.939Z" },
        { "uri":    "http://example.com/comments.txt",
          "bundledAs": {
-            "uri":    "urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644",
+            "uri":      "urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644",
             "folder":   "/folder/",
             "filename": "external.txt" }
        }
     ],
     "annotations": [
-      { "annotation": "urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf",
-        "about":      "/folder/soup.jpeg",
-        "content":    "annotations/soup-properties.ttl" },
+      { "uri":     "urn:uuid:d67466b4-3aeb-4855-8203-90febe71abdf",
+        "about":   "/folder/soup.jpeg",
+        "content": "annotations/soup-properties.ttl" },
 
       { "about":   "urn:uuid:a0cf8616-bee4-4a71-b21e-c60e6499a644",
         "content": "http://example.com/blog/they-aggregated-our-file" },

data/test/data/example6-manifest.json

@@ -0,0 +1,17 @@
+{
+    "@context":  [
+        "https://w3id.org/bundle/context"
+    ],
+    "id": "/",
+    "manifest": "manifest.json",
+    "aggregates": [
+       { "uri": "http://example.com/blog/2012" },
+       { "uri": "http://example.com/blog/2013" }
+    ],
+    "@graph": [
+      { "@id": "http://example.com/blog/2013",
+        "dct:replaces": "http://example.com/blog/2012" },
+      { "@id": "http://example.com/blog/2012",
+        "dct:isReplacedBy": "http://example.com/blog/2013" }
+    ]
+}

data/test/helpers/fake_provenance.rb

@@ -25,7 +25,10 @@ class FakeProvenance
     @structure ||= init_provenance_defaults(
       {
         :createdBy => { :name => "Robert Haines" },
-        :createdOn => "2014-08-20T11:30:00+01:00"
+        :createdOn => "2014-08-20T11:30:00+01:00",
+        :retrievedBy => { :name => "Robert Haines" },
+        :retrievedFrom => "http://example.org/thing",
+        :retrievedOn => "2014-11-10T18:30:00Z"
       }
     )
   end

data/test/tc_add_annotation.rb

@@ -22,7 +22,7 @@ class TestAddAnnotation < Test::Unit::TestCase
       annotation2 = ROBundle::Annotation.new(entry, uri)
       annotation3 = ROBundle::Annotation.new(annotation1)
 
-      ROBundle::File.create(filename) do |b|
+      bundle = ROBundle::File.create(filename) do |b|
         b.add_aggregate(entry, $man_ex3)
 
         ann = b.add_annotation(annotation1)
@@ -33,17 +33,20 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         assert_same annotation1, ann1
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert_same annotation2, ann2
         assert_equal uri, ann2.content
 
-        assert b.annotation?(ann3.annotation_id)
+        assert b.annotation?(ann3.uri)
         assert_same annotation3, ann3
+        assert b.commit_required?
       end
 
+      refute bundle.commit_required?
+
       ROBundle::File.open(filename) do |b|
         refute b.aggregates.empty?
         refute b.annotations.empty?
@@ -51,14 +54,14 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         assert_not_same annotation1, ann1
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert_not_same annotation2, ann2
         assert_equal uri, ann2.content
 
-        assert b.annotation?(ann3.annotation_id)
+        assert b.annotation?(ann3.uri)
         assert_not_same annotation3, ann3
       end
     end
@@ -124,10 +127,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -141,10 +144,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -174,10 +177,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -191,10 +194,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -223,11 +226,11 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
         assert_equal content, b.file.read(".ro/#{ann1.content}")
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
         assert_equal content, b.file.read(ann2.content)
 
@@ -243,11 +246,11 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
         assert_equal content, b.file.read(".ro/#{ann1.content}")
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
         assert_equal content, b.file.read(ann2.content)
 
@@ -280,10 +283,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         refute b.aggregate?(uri1)
         assert b.aggregate?(ann2.content)
 
@@ -298,10 +301,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         refute b.aggregate?(uri1)
         assert b.aggregate?(ann2.content)
 
@@ -333,10 +336,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         refute b.aggregate?(uri1)
         assert b.aggregate?(ann2.content)
 
@@ -351,10 +354,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         refute b.aggregate?(uri1)
         assert b.aggregate?(ann2.content)
 
@@ -383,11 +386,11 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
         assert_equal content, b.file.read(".ro/#{ann1.content}")
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
         assert_equal content, b.file.read(ann2.content)
 
@@ -403,11 +406,11 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
         assert_equal content, b.file.read(".ro/#{ann1.content}")
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
         assert_equal content, b.file.read(ann2.content)
 
@@ -433,7 +436,7 @@ class TestAddAnnotation < Test::Unit::TestCase
         b.add_annotation(annotation1)
         b.add_annotation(annotation2)
 
-        ann = b.add_annotation(annotation1.annotation_id, $man_ex3)
+        ann = b.add_annotation(annotation1.uri, $man_ex3)
         b.add_annotation(annotation1, $man_ex3, :aggregate => true)
         b.add_annotation(annotation2, entry)
 
@@ -441,10 +444,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         _, _, ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -458,10 +461,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         _, _, ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -493,10 +496,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         _, ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -510,10 +513,10 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         _, ann1, ann2, ann3 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
 
         assert b.annotation?(ann3)
@@ -541,11 +544,11 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         _, ann1, ann2 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
         assert_equal content, b.file.read(".ro/#{ann1.content}")
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
         assert_equal content, b.file.read(ann2.content)
       end
@@ -557,11 +560,11 @@ class TestAddAnnotation < Test::Unit::TestCase
 
         _, ann1, ann2 = b.annotations
 
-        assert b.annotation?(ann1.annotation_id)
+        assert b.annotation?(ann1.uri)
         refute b.aggregate?(ann1.content)
         assert_equal content, b.file.read(".ro/#{ann1.content}")
 
-        assert b.annotation?(ann2.annotation_id)
+        assert b.annotation?(ann2.uri)
         assert b.aggregate?(ann2.content)
         assert_equal content, b.file.read(ann2.content)
       end