dbd 0.0.9 → 0.0.10

data/lib/dbd/graph.rb

@@ -52,13 +52,11 @@ module Dbd
     #
     # @param [IO Stream] csv an IO Stream that contains the CSV serialization
     # @return [Graph] the imported graph
-    def self.from_CSV(csv)
-      new.tap do |graph|
-        CSV.new(csv).each do |row|
-          # TODO validate the input formats (e.g. invalid uuid codes)
-          graph << Fact.from_string_values(row)
-        end
+    def from_CSV(csv)
+      CSV.new(csv).each do |row|
+        self << Fact.factory.from_string_values(row, validate: true)
       end
+      self
     end
 
   private

data/lib/dbd/helpers/uuid.rb

@@ -10,8 +10,8 @@ module Dbd
       ##
       # A regexp that can be used in tests.
       # @return [Regexp]
-      def self.regexp
-        /[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}/
+      def self.valid_regexp
+        /\A[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}\Z/
       end
 
       ##

data/lib/dbd/resource.rb

@@ -30,7 +30,7 @@ module Dbd
     ##
     # @return [Fact::Subject] a new (random) Resource subject
     def self.new_subject
-      Fact.new_subject
+      Fact.factory.new_subject
     end
 
     ##

data/lib/dbd/time_stamp.rb

@@ -53,8 +53,8 @@ module Dbd
     # regexp for the nanosecond granularity and in UTC
     #
     # Can be used to validate input strings or in tests.
-    def self.to_s_regexp
-      /\d{4}-\d\d-\d\d \d\d:\d\d:\d\d\.\d{9} UTC/
+    def self.valid_regexp
+      /\A\d{4}-\d\d-\d\d \d\d:\d\d:\d\d\.\d{9} UTC\Z/
     end
 
   private
@@ -63,15 +63,24 @@ module Dbd
       [Time.now.utc, (larger_than && larger_than.time)].compact.max + random_offset
     end
 
+    # Minimum offset between consecutive times.
+    # For jruby, a 1 ns offset was not enough
+    # (some collisions, see https://github.com/jruby/jruby/issues/843)
+    # With 2 ns, the problem disappears (probably a "1 off" rounding error
+    # that cannot occur with a minimum distance of 2?).
+    def minimum_time_offset
+      Rational('2/1_000_000_000')
+    end
+
+    # Random offset, between minimum_time_offset and 1 us (1 micro second)
     def random_offset
-      Rational("#{1+rand(999)}/1_000_000_000")
+      minimum_time_offset + Rational("#{rand(990)}/1_000_000_000")
     end
 
     def time_format
       '%F %T.%N %Z'
     end
 
-    ##
     # with a nanosecond granularity and in UTC
     def time_from_s(time_string)
       # For ns precision in JRuby this extended process is required
@@ -83,7 +92,7 @@ module Dbd
                time_hash[:hour],
                time_hash[:min],
                time_hash[:sec],
-               time_hash[:sec_fraction] * 1_000_000)
+               time_hash[:sec_fraction] * 1_000_000 + Rational('3/10_000_000_000'))
     end
 
     def validate_time_zone(time_hash)
@@ -100,8 +109,8 @@ module Dbd
       @time.strftime(time_format)
     end
 
-    # Max drift in time_stamp
-    MAX_DRIFT = Rational("1/1_000_000")
+    # Max drift in time_stamp for near?
+    MAX_DRIFT = Rational("1/1_000_000").freeze
 
     ##
     # determines if 2 time_stamps are "near".

data/lib/dbd/version.rb

@@ -1,3 +1,3 @@
 module Dbd
-  VERSION = "0.0.9"
+  VERSION = "0.0.10"
 end

data/spec/lib/dbd/fact/collection/collection_spec.rb

@@ -4,19 +4,19 @@ module Dbd
   class Fact
     describe Collection do
 
-      let(:provenance_subject_1) { ProvenanceFact.new_subject }
-      let(:provenance_subject_2) { ProvenanceFact.new_subject }
+      let(:provenance_subject_1) { Fact.factory.new_subject }
+      let(:provenance_subject_2) { Fact.factory.new_subject }
 
-      let(:provenance_fact_context) { Factories::ProvenanceFact.context(provenance_subject_1) }
-      let(:provenance_fact_created_by) { Factories::ProvenanceFact.created_by(provenance_subject_1) }
-      let(:provenance_fact_original_source) { Factories::ProvenanceFact.original_source(provenance_subject_2) }
+      let(:provenance_fact_context) { TestFactories::ProvenanceFact.context(provenance_subject_1) }
+      let(:provenance_fact_created_by) { TestFactories::ProvenanceFact.created_by(provenance_subject_1) }
+      let(:provenance_fact_original_source) { TestFactories::ProvenanceFact.original_source(provenance_subject_2) }
 
-      let(:fact_1) { Factories::Fact.fact_1(provenance_subject_1) }
-      let(:fact_2_with_subject) { Factories::Fact.fact_2_with_subject(provenance_subject_1) }
-      let(:fact_3_with_subject) { Factories::Fact.fact_3_with_subject(provenance_subject_1) }
+      let(:fact_1) { TestFactories::Fact.fact_1(provenance_subject_1) }
+      let(:fact_2_with_subject) { TestFactories::Fact.fact_2_with_subject(provenance_subject_1) }
+      let(:fact_3_with_subject) { TestFactories::Fact.fact_3_with_subject(provenance_subject_1) }
 
-      let(:fact_2_3) { Factories::Fact::Collection.fact_2_3(provenance_subject_1) }
-      let(:provenance_facts) { Factories::Fact::Collection.provenance_facts(provenance_subject_1) }
+      let(:fact_2_3) { TestFactories::Fact::Collection.fact_2_3(provenance_subject_1) }
+      let(:provenance_facts) { TestFactories::Fact::Collection.provenance_facts(provenance_subject_1) }
 
       let(:subject) do
         Object.new.tap do |object_with_Fact_Collection|
@@ -25,52 +25,52 @@ module Dbd
         end
       end
 
-      describe ".new : " do
-        it "the collection is not an array" do
+      describe '.new : ' do
+        it 'the collection is not an array' do
           subject.should_not be_a(Array)
         end
 
-        it "the collection has Enumerable methods" do
+        it 'the collection has Enumerable methods' do
           subject.map #should_not raise_exception
         end
       end
 
-      describe ".methods : " do
+      describe '.methods : ' do
 
-        describe "#<< : " do
-          it "adding a fact works" do
+        describe '#<< : ' do
+          it 'adding a fact works' do
             subject << fact_2_with_subject
             subject.size.should == 1
           end
 
-          it "adding a provenance_fact works" do
+          it 'adding a provenance_fact works' do
             subject << provenance_fact_context
             subject.size.should == 1
           end
 
-          it "returns self to allow chaining" do
+          it 'returns self to allow chaining' do
             (subject << provenance_fact_context).should == subject
           end
         end
 
-        it "#first should be a Fact" do
+        it '#first should be a Fact' do
           subject << fact_2_with_subject
           subject.first.should be_a(Fact)
         end
 
-        it "other functions (e.g. []) do not work" do
+        it 'other functions (e.g. []) do not work' do
           subject << fact_2_with_subject
           lambda { subject[0] } . should raise_exception NoMethodError
         end
 
-        it "#<< returns self, so chaining is possible" do
+        it '#<< returns self, so chaining is possible' do
           (subject << fact_2_with_subject).should == subject
         end
       end
 
-      describe "adding a fact with a ref to a provenance_fact" do
+      describe 'adding a fact with a ref to a provenance_fact' do
 
-        it "fact_2_with_subject has a provenance_subject that refers to context and created_by" do
+        it 'fact_2_with_subject has a provenance_subject that refers to context and created_by' do
           subject << provenance_fact_context
           subject << provenance_fact_created_by
           subject << fact_2_with_subject
@@ -79,65 +79,65 @@ module Dbd
         end
       end
 
-      describe "newest_time_stamp" do
-        it "returns nil for empty collection" do
+      describe 'newest_time_stamp' do
+        it 'returns nil for empty collection' do
           subject.newest_time_stamp.should be_nil
         end
 
-        it "returns a time_stamp" do
+        it 'returns a time_stamp' do
           subject << fact_2_with_subject
           subject.newest_time_stamp.should be_a(fact_2_with_subject.time_stamp.class)
         end
 
-        it "returns the newest time_stamp" do
+        it 'returns the newest time_stamp' do
           subject << fact_2_with_subject
           subject << fact_3_with_subject
           subject.newest_time_stamp.should == fact_3_with_subject.time_stamp
         end
       end
 
-      describe "validate that only 'newer' elements are added" do
+      describe 'validate that only "newer" elements are added' do
         before(:each) do
           fact_2_with_subject.stub(:time_stamp).and_return(TimeStamp.new(time: Time.utc(2013,05,9,12,0,0)))
           fact_3_with_subject.stub(:time_stamp).and_return(TimeStamp.new(time: Time.utc(2013,05,9,12,0,1)))
         end
 
-        it "adding an element with a newer time_stamp succeeds" do
+        it 'adding an element with a newer time_stamp succeeds' do
           subject << fact_2_with_subject
           subject << fact_3_with_subject
         end
 
-        it "adding an element with an older time_stamp fails" do
+        it 'adding an element with an older time_stamp fails' do
           fact_2_with_subject # will be older then fact_3_with_subject
           subject << fact_3_with_subject
           lambda { subject << fact_2_with_subject } . should raise_error OutOfOrderError
         end
 
-        it "adding an element with an equal time_stamp fails" do
+        it 'adding an element with an equal time_stamp fails' do
           subject << fact_2_with_subject
           lambda { subject << fact_2_with_subject } . should raise_error OutOfOrderError
         end
       end
 
-      describe "oldest_time_stamp" do
-        it "returns nil for empty collection" do
+      describe 'oldest_time_stamp' do
+        it 'returns nil for empty collection' do
           subject.oldest_time_stamp.should be_nil
         end
 
-        it "returns a time_stamp" do
+        it 'returns a time_stamp' do
           subject << fact_2_with_subject
           subject.oldest_time_stamp.should be_a(fact_2_with_subject.time_stamp.class)
         end
 
-        it "returns the oldest time_stamp" do
+        it 'returns the oldest time_stamp' do
           subject << fact_2_with_subject
           subject << fact_3_with_subject
           subject.oldest_time_stamp.should == fact_2_with_subject.time_stamp
         end
       end
 
-      describe "provenance_facts must all come before first use by a fact" do
-        it "adding a provenance_fact, depending fact, another provenance_fact with same subject fail" do
+      describe 'provenance_facts must all come before first use by a fact' do
+        it 'adding a provenance_fact, depending fact, another provenance_fact with same subject fail' do
           subject << provenance_fact_context
           subject << fact_2_with_subject
           lambda { subject << provenance_fact_created_by } . should raise_error OutOfOrderError
@@ -147,23 +147,23 @@ module Dbd
         # A hash with all the provenance_subjects that are used by at least one fact.
         # Needed for the validation that no provenance_fact may be added that is
         # referred from a fact that is already in the fact stream.
-        describe "used_provenance_subjects" do
+        describe 'used_provenance_subjects' do
           # testing an internal variable ...
 
           let(:used_provenance_subjects) do
             subject.instance_variable_get(:@used_provenance_subjects)
           end
 
-          it "is empty initially" do
+          it 'is empty initially' do
             used_provenance_subjects.should be_empty
           end
 
-          it "adding a provenance_fact alone does not create an entry" do
+          it 'adding a provenance_fact alone does not create an entry' do
             subject << provenance_fact_context
             used_provenance_subjects.should be_empty
           end
 
-          it "adding a provenance_fact and a depending fact create an entry" do
+          it 'adding a provenance_fact and a depending fact create an entry' do
             subject << provenance_fact_context
             subject << fact_2_with_subject
             used_provenance_subjects[provenance_subject_1].should == true
@@ -171,21 +171,21 @@ module Dbd
         end
       end
 
-      describe "validate that facts do not have errors when loading in the Fact::Collection" do
-        it "succeeds with a fact from factory" do
+      describe 'validate that facts do not have errors when loading in the Fact::Collection' do
+        it 'succeeds with a fact from factory' do
            subject << fact_2_with_subject # should_not raise_error
         end
 
-        it "raises FactError with message when fact.errors has errors" do
-           provenance_fact_context.stub(:errors).and_return(["Error 1", "Error 2"])
+        it 'raises FactError with message when fact.errors has errors' do
+           provenance_fact_context.stub(:errors).and_return(['Error 1', 'Error 2'])
            lambda { subject << provenance_fact_context } . should raise_error(
              FactError,
-             "Error 1, Error 2.")
+             'Error 1, Error 2.')
         end
       end
 
-      describe "by_subject : " do
-        it "finds entries for a given subject" do
+      describe 'by_subject : ' do
+        it 'finds entries for a given subject' do
           subject << provenance_fact_context
           subject << provenance_fact_created_by
           subject << provenance_fact_original_source
@@ -198,35 +198,35 @@ module Dbd
         end
       end
 
-      describe "Factories::Fact::Collection" do
-        describe ".fact_2_3" do
-          it "has the given provenance_subject with explicit subject arg" do
+      describe 'TestFactories::Fact::Collection' do
+        describe '.fact_2_3' do
+          it 'has the given provenance_subject with explicit subject arg' do
             fact_2_3.each do |fact|
               fact.provenance_subject.should == provenance_subject_1
             end
           end
         end
 
-        describe ".provenance_facts" do
-          it "has a context" do
+        describe '.provenance_facts' do
+          it 'has a context' do
             provenance_facts.select do |provenance_fact|
-              provenance_fact.predicate == "https://data.vandenabeele.com/ontologies/provenance#context"
+              provenance_fact.predicate == 'https://data.vandenabeele.com/ontologies/provenance#context'
             end.size.should == 1
           end
 
-          it "has a created_by" do
+          it 'has a created_by' do
             provenance_facts.select do |provenance_fact|
-              provenance_fact.predicate == "https://data.vandenabeele.com/ontologies/provenance#created_by"
+              provenance_fact.predicate == 'https://data.vandenabeele.com/ontologies/provenance#created_by'
             end.size.should == 1
           end
 
-          it "has an original_source" do
+          it 'has an original_source' do
             provenance_facts.select do |provenance_fact|
-              provenance_fact.predicate == "https://data.vandenabeele.com/ontologies/provenance#original_source"
+              provenance_fact.predicate == 'https://data.vandenabeele.com/ontologies/provenance#original_source'
             end.size.should == 1
           end
 
-          it "has the given subjects with explicit subject arg" do
+          it 'has the given subjects with explicit subject arg' do
             provenance_facts.each do |provenance_fact|
               provenance_fact.subject.should == provenance_subject_1
             end

data/spec/lib/dbd/fact/factory/factory_spec.rb

@@ -0,0 +1,109 @@
+require 'spec_helper'
+
+module Dbd
+  class Fact
+    describe Factory do
+
+      let(:top_class) { described_class.top_class }
+      let(:string_values) { TestFactories::Fact.string_values }
+      let(:id_valid_regexp) { top_class::ID.valid_regexp }
+      let(:subject_valid_regexp) { top_class::Subject.valid_regexp }
+
+      describe '.new_subject' do
+        it 'creates a new (random) subject' do
+          described_class.new_subject.should match(subject_valid_regexp)
+        end
+
+        it 'creating a second one is different' do
+          subject_1 = described_class.new_subject
+          subject_2 = described_class.new_subject
+          subject_1.should_not == subject_2
+        end
+      end
+
+      describe '.new_id' do
+        it 'creates a new (random) id' do
+          described_class.new_id.should match(id_valid_regexp)
+        end
+
+        it 'creating a second one is different' do
+          id_1 = described_class.new_id
+          id_2 = described_class.new_id
+          id_1.should_not == id_2
+        end
+      end
+
+      describe '.from_string_values' do
+        it 'reads the values correctly (round trip test)' do
+          fact = described_class.from_string_values(string_values)
+          fact.string_values.should == string_values
+        end
+
+        it 'calls validate_string_hash if options[:validate]' do
+          described_class.should_receive(:validate_string_hash)
+          described_class.from_string_values(string_values, validate: true)
+        end
+
+        it 'does not call validate_string_hash if not options[:validate]' do
+          described_class.should_not_receive(:validate_string_hash)
+          described_class.from_string_values(string_values)
+        end
+      end
+
+      describe 'validation of the string_hash' do
+
+        def with_validation(string_values)
+          described_class.from_string_values(string_values, :validate => true)
+        end
+
+        describe 'does not raise exception' do
+          it 'for unmodified string_values' do
+            with_validation(string_values)
+          end
+
+          it 'for a nil provenance_subject (for provenance_facts)' do
+            string_values[2] = nil
+            with_validation(string_values)
+          end
+
+          it 'for an empty provenance_subject (for provenance_facts)' do
+            string_values[2] = ''
+            with_validation(string_values)
+          end
+        end
+
+        describe 'does raise exception' do
+          it 'for invalid id' do
+            string_values[0] = 'foo'
+            lambda{ with_validation(string_values) }.should raise_error(FactError)
+          end
+
+          it 'for invalid time_stamp' do
+            string_values[1] = 'foo'
+            lambda{ with_validation(string_values) }.should raise_error(FactError)
+          end
+
+          it 'for invalid provenance_subject' do
+            string_values[2] = 'foo'
+            lambda{ with_validation(string_values) }.should raise_error(FactError)
+          end
+
+          it 'for invalid subject' do
+            string_values[3] = 'foo'
+            lambda{ with_validation(string_values) }.should raise_error(FactError)
+          end
+
+          it 'for invalid predicate' do
+            string_values[4] = ''
+            lambda{ with_validation(string_values) }.should raise_error(FactError)
+          end
+
+          it 'for invalid object' do
+            string_values[5] = ''
+            lambda{ with_validation(string_values) }.should raise_error(FactError)
+          end
+        end
+      end
+    end
+  end
+end