ro-bundle 0.1.0

data/test/tc_provenance.rb

@@ -0,0 +1,121 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'test/unit'
+require "ro-bundle"
+require "helpers/fake_provenance"
+
+class TestProvenance < Test::Unit::TestCase
+
+  def setup
+    @prov = FakeProvenance.new
+
+    @agent = ROBundle::Agent.new(
+      "Robert Haines",
+      "https://github.com/hainesr",
+      "http://orcid.org/0000-0002-9538-7919"
+    )
+  end
+
+  def test_created_on
+    assert @prov.created_on.instance_of?(Time)
+  end
+
+  def test_change_created_on
+    old = @prov.created_on
+    now = Time.now.to_s
+    @prov.created_on = now
+
+    assert_equal now, @prov.created_on.to_s
+    assert_not_equal old.to_s, @prov.created_on.to_s
+    assert @prov.edited?
+  end
+
+  def test_created_by
+    creator = @prov.created_by
+    assert creator.instance_of?(ROBundle::Agent)
+    assert_equal creator.name, "Robert Haines"
+  end
+
+  def test_change_created_by
+    agent = ROBundle::Agent.new("Matt Gamble")
+    @prov.created_by = agent
+
+    assert_same agent, @prov.created_by
+    assert @prov.edited?
+  end
+
+  def test_created_by_string_agent
+    old = @prov.created_by
+    agent = "Stian Soiland-Reyes"
+    @prov.created_by = agent
+
+    assert_not_same old, @prov.created_by
+    assert @prov.edited?
+  end
+
+  def test_authored_on
+    assert_nil @prov.authored_on
+  end
+
+  def test_change_authored_on
+    old = @prov.authored_on
+    now = Time.now.to_s
+    @prov.authored_on = now
+
+    assert_equal now, @prov.authored_on.to_s
+    assert_not_equal old.to_s, @prov.authored_on.to_s
+    assert @prov.edited?
+  end
+
+  def test_authored_by
+    assert @prov.authored_by.instance_of?(Array)
+  end
+
+  def test_add_author
+    name = "Mr. Bigglesworth"
+
+    assert @prov.authored_by.empty?
+
+    author = @prov.add_author(@agent)
+    assert @prov.authored_by.include?(@agent)
+    assert_same @agent, author
+    assert @prov.edited?
+
+    author = @prov.add_author(name)
+    assert name_in_agent_list(name, @prov.authored_by)
+    assert author.instance_of?(ROBundle::Agent)
+    assert @prov.edited?
+  end
+
+  def test_remove_author_by_object
+    name = "Mr. Bigglesworth"
+
+    author = @prov.add_author(name)
+    refute @prov.authored_by.empty?
+    assert name_in_agent_list(name, @prov.authored_by)
+
+    @prov.remove_author(author)
+    assert @prov.authored_by.empty?
+    refute name_in_agent_list(name, @prov.authored_by)
+  end
+
+  def test_remove_authors_by_name
+    name = "Robert Haines"
+    @prov.add_author(@agent)
+    @prov.add_author(name)
+
+    assert_equal 2, @prov.authored_by.length
+    assert name_in_agent_list(name, @prov.authored_by)
+
+    @prov.remove_author(name)
+    assert @prov.authored_by.empty?
+    refute name_in_agent_list(name, @prov.authored_by)
+  end
+
+end

data/test/tc_read.rb

@@ -0,0 +1,66 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'test/unit'
+require "ro-bundle"
+
+class TestRead < Test::Unit::TestCase
+
+  def test_verify_valid
+    assert_nothing_raised(ZipContainer::MalformedContainerError, ZipContainer::ZipError) do
+      ROBundle::File.verify!($hello)
+    end
+
+    assert(ROBundle::File.verify($hello))
+  end
+
+  def test_verify_invalid
+    assert_raises(ZipContainer::MalformedContainerError) do
+      ROBundle::File.verify!($invalid)
+    end
+
+    refute ROBundle::File.verify($invalid)
+  end
+
+  def test_manifest
+    ROBundle::File.open($hello) do |b|
+      assert_equal("/", b.id)
+
+      assert b.created_on.instance_of?(Time)
+      assert_nil b.authored_on
+
+      creator = b.created_by
+      assert creator.instance_of?(ROBundle::Agent)
+
+      author = b.authored_by
+      assert author.instance_of?(Array)
+
+      history = b.history
+      assert history.instance_of?(Array)
+
+      aggregates = b.aggregates
+      assert aggregates.instance_of?(Array)
+
+      annotations = b.annotations
+      assert annotations.instance_of?(Array)
+
+      refute b.commit_required?
+    end
+  end
+
+  def test_aggregates
+    ROBundle::File.open($hello) do |b|
+      assert b.aggregate?(b.id)
+      assert b.aggregate?("/")
+
+      assert b.aggregate?("/inputs/name.txt")
+      assert b.aggregate?("inputs/name.txt")
+    end
+  end
+
+end

data/test/tc_remove.rb

@@ -0,0 +1,140 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'test/unit'
+require "fileutils"
+require "ro-bundle"
+
+class TestRemove < Test::Unit::TestCase
+
+  def test_remove_entry
+    Dir.mktmpdir do |dir|
+      filename = File.join(dir, "test.bundle")
+      FileUtils.cp $hello, filename
+
+      rm_file = "workflow.wfbundle"
+
+      ROBundle::File.open(filename) do |b|
+        assert b.aggregate?(rm_file)
+        assert_not_nil b.find_entry(rm_file)
+        num_agg = b.aggregates.length
+        num_ann = b.annotations.length
+
+        b.remove(rm_file)
+
+        refute b.aggregate?(rm_file)
+        assert_nil b.find_entry(rm_file)
+        assert_equal num_agg - 1, b.aggregates.length
+        assert_equal num_ann - 4, b.annotations.length
+      end
+
+      removed_annotations = [
+        ".ro/annotations/workflow.wfdesc.ttl",
+        ".ro/annotations/d2757512-7149-4ff7-b7f8-78de3e3a2bd5.ttl"
+      ]
+
+      ROBundle::File.open(filename) do |b|
+        assert_nil b.find_entry(rm_file)
+        removed_annotations.each do |ann|
+          assert_nil b.find_entry(ann, :include_hidden => true)
+        end
+      end
+    end
+  end
+
+  def test_remove_aggregate_by_filename
+    Dir.mktmpdir do |dir|
+      filename = File.join(dir, "test.bundle")
+      FileUtils.cp $hello, filename
+
+      rm_file = "workflow.wfbundle"
+
+      ROBundle::File.open(filename) do |b|
+        assert b.aggregate?(rm_file)
+        assert_not_nil b.find_entry(rm_file)
+        num_agg = b.aggregates.length
+        num_ann = b.annotations.length
+
+        b.remove_aggregate(rm_file)
+
+        refute b.aggregate?(rm_file)
+        assert_nil b.find_entry(rm_file)
+        assert_equal num_agg - 1, b.aggregates.length
+        assert_equal num_ann - 4, b.annotations.length
+      end
+    end
+  end
+
+  def test_remove_aggregate_by_object
+    Dir.mktmpdir do |dir|
+      filename = File.join(dir, "test.bundle")
+      FileUtils.cp $hello, filename
+
+      ROBundle::File.open(filename) do |b|
+        rm_file = b.aggregates[0]
+        assert b.aggregate?(rm_file.file)
+        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)
+        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
+      end
+    end
+  end
+
+  def test_remove_aggregate_by_filename_keep_file
+    Dir.mktmpdir do |dir|
+      filename = File.join(dir, "test.bundle")
+      FileUtils.cp $hello, filename
+
+      rm_file = "workflow.wfbundle"
+
+      ROBundle::File.open(filename) do |b|
+        assert b.aggregate?(rm_file)
+        assert_not_nil b.find_entry(rm_file)
+        num_agg = b.aggregates.length
+        num_ann = b.annotations.length
+
+        b.remove_aggregate(rm_file, :keep_file => true)
+
+        refute b.aggregate?(rm_file)
+        assert_not_nil b.find_entry(rm_file)
+        assert_equal num_agg - 1, b.aggregates.length
+        assert_equal num_ann - 4, b.annotations.length
+      end
+    end
+  end
+
+  def test_remove_aggregate_by_object_keep_file
+    Dir.mktmpdir do |dir|
+      filename = File.join(dir, "test.bundle")
+      FileUtils.cp $hello, filename
+
+      ROBundle::File.open(filename) do |b|
+        rm_file = b.aggregates[0]
+        assert b.aggregate?(rm_file.file)
+        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)
+        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
+      end
+    end
+  end
+
+end

data/test/tc_util.rb

@@ -0,0 +1,64 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'test/unit'
+require "ro-bundle"
+
+class TestUtil < Test::Unit::TestCase
+
+  def test_clean_json
+    json_ok = { :one => "one", :uri => URI.parse("/file.txt") }
+    json_nil = { :nil => nil }
+    json_empty = { :empty1 => "", :empty2 => [], :empty3 => {} }
+    json_mix = json_ok.merge(json_nil).merge(json_empty)
+    empty = {}
+
+    assert_same 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)
+  end
+
+  def test_parse_time
+    now = Time.now
+    iso = now.iso8601
+
+    assert ROBundle::Util.parse_time(iso).instance_of?(Time)
+    assert_nil ROBundle::Util.parse_time(nil)
+  end
+
+  def test_absolute_uri
+    assert ROBundle::Util.is_absolute_uri?("http://example.com/test.txt")
+    assert ROBundle::Util.is_absolute_uri?("urn:uuid:and-so-on")
+    assert ROBundle::Util.is_absolute_uri?(URI.parse("http://example.com/test.txt"))
+    assert ROBundle::Util.is_absolute_uri?(URI.parse("urn:uuid:and-so-on"))
+    refute ROBundle::Util.is_absolute_uri?("/file.txt")
+    refute ROBundle::Util.is_absolute_uri?("file.txt")
+    refute ROBundle::Util.is_absolute_uri?(URI.parse("/file.txt"))
+    refute ROBundle::Util.is_absolute_uri?(URI.parse("file.txt"))
+    refute ROBundle::Util.is_absolute_uri?(":file.txt")
+    refute ROBundle::Util.is_absolute_uri?("")
+    refute ROBundle::Util.is_absolute_uri?(nil)
+  end
+
+  def test_strip_slash
+    str1 = ""
+    str2 = "/"
+    str3 = "test"
+    str4 = "test/path"
+    str5 = "test/path/trailing/"
+
+    assert_nil ROBundle::Util.strip_leading_slash(nil)
+    assert_equal str1, ROBundle::Util.strip_leading_slash(str1)
+    assert_equal str1, ROBundle::Util.strip_leading_slash(str2)
+    assert_equal str3, ROBundle::Util.strip_leading_slash("/#{str3}")
+    assert_equal str4, ROBundle::Util.strip_leading_slash("/#{str4}")
+    assert_equal str5, ROBundle::Util.strip_leading_slash("/#{str5}")
+  end
+
+end

data/test/ts_ro_bundle.rb

@@ -0,0 +1,28 @@
+#------------------------------------------------------------------------------
+# Copyright (c) 2014 The University of Manchester, UK.
+#
+# BSD Licenced. See LICENCE.rdoc for details.
+#
+# Author: Robert Haines
+#------------------------------------------------------------------------------
+
+require 'coveralls'
+Coveralls.wear!
+
+# Example data files
+$hello = "test/data/HelloAnyone.robundle"
+$invalid = "test/data/invalid-manifest.robundle"
+$man_ex3 = "test/data/example3-manifest.json"
+$man_empty = "test/data/empty-manifest.json"
+$man_invalid = "test/data/invalid-manifest.json"
+
+require "tc_util"
+require "tc_agent"
+require "tc_provenance"
+require "tc_annotation"
+require "tc_aggregate"
+require "tc_manifest"
+require "tc_read"
+require "tc_create"
+require "tc_add_annotation"
+require "tc_remove"

metadata

@@ -0,0 +1,217 @@
+--- !ruby/object:Gem::Specification
+name: ro-bundle
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- Robert Haines
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-08-22 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: 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'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '1.0'
+- !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.
+email:
+- support@mygrid.org.uk
+executables:
+- dir2ro
+- ro-bundle-info
+- verify-ro-bundle
+- zip2ro
+extensions: []
+extra_rdoc_files:
+- Changes.rdoc
+- Licence.rdoc
+- ReadMe.rdoc
+files:
+- .gitignore
+- .ruby-env
+- .ruby-gemset
+- .ruby-version
+- .travis.yml
+- Changes.rdoc
+- Gemfile
+- Licence.rdoc
+- Rakefile
+- ReadMe.rdoc
+- bin/dir2ro
+- bin/ro-bundle-info
+- bin/verify-ro-bundle
+- bin/zip2ro
+- lib/ro-bundle.rb
+- lib/ro-bundle/exceptions.rb
+- lib/ro-bundle/file.rb
+- lib/ro-bundle/ro/agent.rb
+- lib/ro-bundle/ro/aggregate.rb
+- lib/ro-bundle/ro/annotation.rb
+- lib/ro-bundle/ro/directory.rb
+- lib/ro-bundle/ro/manifest.rb
+- lib/ro-bundle/ro/provenance.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/invalid-manifest.json
+- test/data/invalid-manifest.robundle
+- test/helpers/fake_manifest.rb
+- test/helpers/fake_provenance.rb
+- test/helpers/list_tests.rb
+- test/tc_add_annotation.rb
+- test/tc_agent.rb
+- test/tc_aggregate.rb
+- test/tc_annotation.rb
+- test/tc_create.rb
+- test/tc_manifest.rb
+- test/tc_provenance.rb
+- test/tc_read.rb
+- test/tc_remove.rb
+- test/tc_util.rb
+- test/ts_ro_bundle.rb
+homepage: http://www.taverna.org.uk
+licenses:
+- BSD
+metadata: {}
+post_install_message: 
+rdoc_options:
+- -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
+signing_key: 
+specification_version: 4
+summary: This library provides an API for manipulating Research Object (RO) bundles.
+test_files:
+- test/data/HelloAnyone.robundle
+- test/data/empty-manifest.json
+- test/data/example3-manifest.json
+- test/data/invalid-manifest.json
+- test/data/invalid-manifest.robundle
+- test/helpers/fake_manifest.rb
+- test/helpers/fake_provenance.rb
+- test/helpers/list_tests.rb
+- test/tc_add_annotation.rb
+- test/tc_agent.rb
+- test/tc_aggregate.rb
+- test/tc_annotation.rb
+- test/tc_create.rb
+- test/tc_manifest.rb
+- test/tc_provenance.rb
+- test/tc_read.rb
+- test/tc_remove.rb
+- test/tc_util.rb
+- test/ts_ro_bundle.rb