ro-bundle 0.1.0 → 0.2.0

data/test/tc_provenance.rb

@@ -31,6 +31,7 @@ class TestProvenance < Test::Unit::TestCase
     now = Time.now.to_s
     @prov.created_on = now
 
+    assert @prov.created_on.instance_of?(Time)
     assert_equal now, @prov.created_on.to_s
     assert_not_equal old.to_s, @prov.created_on.to_s
     assert @prov.edited?
@@ -55,6 +56,7 @@ class TestProvenance < Test::Unit::TestCase
     agent = "Stian Soiland-Reyes"
     @prov.created_by = agent
 
+    assert @prov.created_by.instance_of?(ROBundle::Agent)
     assert_not_same old, @prov.created_by
     assert @prov.edited?
   end
@@ -68,6 +70,7 @@ class TestProvenance < Test::Unit::TestCase
     now = Time.now.to_s
     @prov.authored_on = now
 
+    assert @prov.authored_on.instance_of?(Time)
     assert_equal now, @prov.authored_on.to_s
     assert_not_equal old.to_s, @prov.authored_on.to_s
     assert @prov.edited?
@@ -118,4 +121,76 @@ class TestProvenance < Test::Unit::TestCase
     refute name_in_agent_list(name, @prov.authored_by)
   end
 
+  def test_retrieved_by
+    retrievor = @prov.retrieved_by
+    assert retrievor.instance_of?(ROBundle::Agent)
+    assert_equal retrievor.name, "Robert Haines"
+  end
+
+  def test_change_retrieved_by
+    agent = ROBundle::Agent.new("Matt Gamble")
+    @prov.retrieved_by = agent
+
+    assert_same agent, @prov.retrieved_by
+    assert @prov.edited?
+  end
+
+  def test_retrieved_by_string_agent
+    old = @prov.retrieved_by
+    agent = "Stian Soiland-Reyes"
+    @prov.retrieved_by = agent
+
+    assert @prov.retrieved_by.instance_of?(ROBundle::Agent)
+    assert_not_same old, @prov.retrieved_by
+    assert @prov.edited?
+  end
+
+  def test_retrieved_from
+    assert @prov.retrieved_from.instance_of?(String)
+  end
+
+  def test_change_retrieved_from
+    old = @prov.retrieved_from
+    uri = "http://example.com:8080"
+    @prov.retrieved_from = uri
+
+    assert @prov.retrieved_from.instance_of?(String)
+    assert_not_equal old, @prov.retrieved_from
+    assert @prov.edited?
+  end
+
+  def test_change_retrieved_from_uri_object
+    old = @prov.retrieved_from
+    uri = URI.parse("http://example.com:8080")
+    @prov.retrieved_from = uri
+
+    assert @prov.retrieved_from.instance_of?(String)
+    assert_not_equal old, @prov.retrieved_from
+    assert @prov.edited?
+  end
+
+  def test_change_retrieved_from_fail
+    old = @prov.retrieved_from
+    uri = "www.example.com"
+    @prov.retrieved_from = uri
+
+    assert_equal old, @prov.retrieved_from
+    refute @prov.edited?
+  end
+
+  def test_retrieved_on
+    assert @prov.retrieved_on.instance_of?(Time)
+  end
+
+  def test_change_retrieved_on
+    old = @prov.retrieved_on
+    now = Time.now.to_s
+    @prov.retrieved_on = now
+
+    assert @prov.retrieved_on.instance_of?(Time)
+    assert_equal now, @prov.retrieved_on.to_s
+    assert_not_equal old.to_s, @prov.retrieved_on.to_s
+    assert @prov.edited?
+  end
+
 end

data/test/tc_proxy.rb

@@ -0,0 +1,56 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014, 2015 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'test/unit'
+require "ro-bundle"
+require "helpers/fake_manifest"
+
+class TestProxy < Test::Unit::TestCase
+
+  def setup
+    @manifest = FakeManifest.new($man_ex3)
+
+    @folder = "folder"
+    @file = "file.txt"
+    @proxy = ROBundle::Proxy.new(@folder, @file)
+  end
+
+  def test_read_no_proxy
+    assert_nil @manifest.aggregates[2].proxy
+  end
+
+  def test_new_empty_proxy
+    proxy = ROBundle::Proxy.new
+    assert ROBundle::Util.is_absolute_uri?(proxy.uri)
+    assert_equal "/", proxy.folder
+    assert_nil proxy.filename
+  end
+
+  def test_new_proxy
+    assert ROBundle::Util.is_absolute_uri?(@proxy.uri)
+    assert_equal "/#{@folder}/", @proxy.folder
+    assert_equal @file, @proxy.filename
+  end
+
+  def test_read_proxy
+    proxy = @manifest.aggregates[3].proxy
+
+    assert_not_nil proxy
+    assert_equal "/folder/", proxy.folder
+    assert_equal "external.txt", proxy.filename
+  end
+
+  def test_json_output
+    proxy = @manifest.aggregates[3].proxy
+    json = JSON.parse(JSON.generate(proxy))
+
+    assert_equal "/folder/", json["folder"]
+    assert_equal "external.txt", json["filename"]
+  end
+
+end

data/test/tc_read.rb

@@ -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.
 #
@@ -12,11 +12,11 @@ require "ro-bundle"
 class TestRead < Test::Unit::TestCase
 
   def test_verify_valid
-    assert_nothing_raised(ZipContainer::MalformedContainerError, ZipContainer::ZipError) do
+    assert_nothing_raised(ZipContainer::MalformedContainerError, ZipContainer::Error) do
       ROBundle::File.verify!($hello)
     end
 
-    assert(ROBundle::File.verify($hello))
+    assert ROBundle::File.verify?($hello)
   end
 
   def test_verify_invalid
@@ -24,7 +24,7 @@ class TestRead < Test::Unit::TestCase
       ROBundle::File.verify!($invalid)
     end
 
-    refute ROBundle::File.verify($invalid)
+    refute ROBundle::File.verify?($invalid)
   end
 
   def test_manifest

data/test/tc_remove.rb

@@ -19,7 +19,7 @@ class TestRemove < Test::Unit::TestCase
 
       rm_file = "workflow.wfbundle"
 
-      ROBundle::File.open(filename) do |b|
+      bundle = ROBundle::File.open(filename) do |b|
         assert b.aggregate?(rm_file)
         assert_not_nil b.find_entry(rm_file)
         num_agg = b.aggregates.length
@@ -31,8 +31,11 @@ class TestRemove < Test::Unit::TestCase
         assert_nil b.find_entry(rm_file)
         assert_equal num_agg - 1, b.aggregates.length
         assert_equal num_ann - 4, b.annotations.length
+        assert b.commit_required?
       end
 
+      refute bundle.commit_required?
+
       removed_annotations = [
         ".ro/annotations/workflow.wfdesc.ttl",
         ".ro/annotations/d2757512-7149-4ff7-b7f8-78de3e3a2bd5.ttl"
@@ -77,14 +80,14 @@ class TestRemove < Test::Unit::TestCase
 
       ROBundle::File.open(filename) do |b|
         rm_file = b.aggregates[0]
-        assert b.aggregate?(rm_file.file)
+        assert b.aggregate?(rm_file.uri)
         assert_not_nil b.find_entry(rm_file.file_entry)
         num_agg = b.aggregates.length
         num_ann = b.annotations.length
 
         b.remove_aggregate(rm_file)
 
-        refute b.aggregate?(rm_file.file)
+        refute b.aggregate?(rm_file.uri)
         assert_nil b.find_entry(rm_file.file_entry)
         assert_equal num_agg - 1, b.aggregates.length
         assert_equal num_ann - 4, b.annotations.length
@@ -122,14 +125,14 @@ class TestRemove < Test::Unit::TestCase
 
       ROBundle::File.open(filename) do |b|
         rm_file = b.aggregates[0]
-        assert b.aggregate?(rm_file.file)
+        assert b.aggregate?(rm_file.uri)
         assert_not_nil b.find_entry(rm_file.file_entry)
         num_agg = b.aggregates.length
         num_ann = b.annotations.length
 
         b.remove_aggregate(rm_file, :keep_file => true)
 
-        refute b.aggregate?(rm_file.file)
+        refute b.aggregate?(rm_file.uri)
         assert_not_nil b.find_entry(rm_file.file_entry)
         assert_equal num_agg - 1, b.aggregates.length
         assert_equal num_ann - 4, b.annotations.length

data/test/tc_util.rb

@@ -18,7 +18,8 @@ class TestUtil < Test::Unit::TestCase
     json_mix = json_ok.merge(json_nil).merge(json_empty)
     empty = {}
 
-    assert_same json_ok, ROBundle::Util.clean_json(json_ok)
+    assert_not_same json_ok, ROBundle::Util.clean_json(json_ok)
+    assert_equal json_ok, ROBundle::Util.clean_json(json_ok)
     assert_equal empty, ROBundle::Util.clean_json(json_nil)
     assert_equal empty, ROBundle::Util.clean_json(json_empty)
     assert_equal json_ok, ROBundle::Util.clean_json(json_mix)

data/test/ts_ro_bundle.rb

@@ -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.
 #
@@ -13,6 +13,7 @@ Coveralls.wear!
 $hello = "test/data/HelloAnyone.robundle"
 $invalid = "test/data/invalid-manifest.robundle"
 $man_ex3 = "test/data/example3-manifest.json"
+$man_ex6 = "test/data/example6-manifest.json"
 $man_empty = "test/data/empty-manifest.json"
 $man_invalid = "test/data/invalid-manifest.json"
 
@@ -20,6 +21,7 @@ require "tc_util"
 require "tc_agent"
 require "tc_provenance"
 require "tc_annotation"
+require "tc_proxy"
 require "tc_aggregate"
 require "tc_manifest"
 require "tc_read"

metadata

@@ -1,115 +1,129 @@
 --- !ruby/object:Gem::Specification
 name: ro-bundle
 version: !ruby/object:Gem::Version
-  version: 0.1.0
+  version: 0.2.0
 platform: ruby
 authors:
 - Robert Haines
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-22 00:00:00.000000000 Z
+date: 2015-06-04 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.5'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.5'
 - !ruby/object:Gem::Dependency
   name: rake
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '10.1'
 - !ruby/object:Gem::Dependency
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4.1'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '4.1'
+- !ruby/object:Gem::Dependency
+  name: test-unit
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
 - !ruby/object:Gem::Dependency
   name: coveralls
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
   name: ucf
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '2.0'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '1.0'
+        version: '2.0'
 - !ruby/object:Gem::Dependency
   name: json
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '1.8'
 - !ruby/object:Gem::Dependency
   name: uuid
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.3'
   type: :runtime
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '2.3'
 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.
+  The RO bundle specification can be found at https://w3id.org/bundle/.
 email:
 - support@mygrid.org.uk
 executables:
@@ -123,11 +137,11 @@ extra_rdoc_files:
 - Licence.rdoc
 - ReadMe.rdoc
 files:
-- .gitignore
-- .ruby-env
-- .ruby-gemset
-- .ruby-version
-- .travis.yml
+- ".gitignore"
+- ".ruby-env"
+- ".ruby-gemset"
+- ".ruby-version"
+- ".travis.yml"
 - Changes.rdoc
 - Gemfile
 - Licence.rdoc
@@ -144,14 +158,17 @@ files:
 - lib/ro-bundle/ro/aggregate.rb
 - lib/ro-bundle/ro/annotation.rb
 - lib/ro-bundle/ro/directory.rb
+- lib/ro-bundle/ro/manifest-entry.rb
 - lib/ro-bundle/ro/manifest.rb
 - lib/ro-bundle/ro/provenance.rb
+- lib/ro-bundle/ro/proxy.rb
 - lib/ro-bundle/util.rb
 - lib/ro-bundle/version.rb
 - ro-bundle.gemspec
 - test/data/HelloAnyone.robundle
 - test/data/empty-manifest.json
 - test/data/example3-manifest.json
+- test/data/example6-manifest.json
 - test/data/invalid-manifest.json
 - test/data/invalid-manifest.robundle
 - test/helpers/fake_manifest.rb
@@ -164,34 +181,35 @@ files:
 - test/tc_create.rb
 - test/tc_manifest.rb
 - test/tc_provenance.rb
+- test/tc_proxy.rb
 - test/tc_read.rb
 - test/tc_remove.rb
 - test/tc_util.rb
 - test/ts_ro_bundle.rb
-homepage: http://www.taverna.org.uk
+homepage: http://www.researchobject.org/
 licenses:
 - BSD
 metadata: {}
 post_install_message: 
 rdoc_options:
-- -N
-- --tab-width=2
-- --main=ReadMe.rdoc
+- "-N"
+- "--tab-width=2"
+- "--main=ReadMe.rdoc"
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: 1.9.3
 required_rubygems_version: !ruby/object:Gem::Requirement
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.2.2
+rubygems_version: 2.4.6
 signing_key: 
 specification_version: 4
 summary: This library provides an API for manipulating Research Object (RO) bundles.
@@ -199,6 +217,7 @@ test_files:
 - test/data/HelloAnyone.robundle
 - test/data/empty-manifest.json
 - test/data/example3-manifest.json
+- test/data/example6-manifest.json
 - test/data/invalid-manifest.json
 - test/data/invalid-manifest.robundle
 - test/helpers/fake_manifest.rb
@@ -211,6 +230,7 @@ test_files:
 - test/tc_create.rb
 - test/tc_manifest.rb
 - test/tc_provenance.rb
+- test/tc_proxy.rb
 - test/tc_read.rb
 - test/tc_remove.rb
 - test/tc_util.rb