dbd 0.0.5 → 0.0.6
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- checksums.yaml +4 -4
- data/Guardfile +3 -2
- data/HISTORY.txt +5 -0
- data/dbd.gemspec +1 -1
- data/docs/stories/013_read_graph_from_CSV.txt +10 -0
- data/lib/dbd.rb +1 -1
- data/lib/dbd/fact.rb +23 -1
- data/lib/dbd/fact/id.rb +3 -3
- data/lib/dbd/fact/subject.rb +3 -3
- data/lib/dbd/graph.rb +25 -4
- data/lib/dbd/provenance_fact.rb +5 -8
- data/lib/dbd/provenance_resource.rb +21 -13
- data/lib/dbd/{rdf.rb → rdf_base.rb} +0 -0
- data/lib/dbd/resource.rb +25 -23
- data/lib/dbd/time_stamp.rb +13 -2
- data/lib/dbd/version.rb +1 -1
- data/spec/factories/fact.rb +23 -0
- data/spec/factories/fact/id.rb +14 -0
- data/spec/factories/fact/subject.rb +18 -0
- data/spec/factories/graph.rb +23 -0
- data/spec/factories/provenance_resource.rb +3 -3
- data/spec/factories/time_stamp.rb +12 -0
- data/spec/lib/dbd/fact/{collection_spec.rb → collection/collection_spec.rb} +0 -0
- data/spec/lib/dbd/fact/factory_spec.rb +82 -0
- data/spec/lib/dbd/fact/id/factory_spec.rb +20 -0
- data/spec/lib/dbd/fact/id/id_spec.rb +27 -0
- data/spec/lib/dbd/fact/methods_spec.rb +117 -0
- data/spec/lib/dbd/fact/new_spec.rb +91 -0
- data/spec/lib/dbd/fact/subject/factory_spec.rb +33 -0
- data/spec/lib/dbd/fact/subject/subject_spec.rb +27 -0
- data/spec/lib/dbd/graph/add_to_graph_spec.rb +139 -0
- data/spec/lib/dbd/graph/factory_spec.rb +33 -0
- data/spec/lib/dbd/graph/from_csv_spec.rb +29 -0
- data/spec/lib/dbd/{graph_spec.rb → graph/to_csv_spec.rb} +0 -120
- data/spec/lib/dbd/helpers/{ordered_set_collection_spec.rb → ordered_set_collection/ordered_set_collection_spec.rb} +0 -0
- data/spec/lib/dbd/helpers/{uuid_spec.rb → uuid/uuid_spec.rb} +0 -0
- data/spec/lib/dbd/performance_spec.rb +3 -1
- data/spec/lib/dbd/provenance_fact/factory_spec.rb +24 -0
- data/spec/lib/dbd/provenance_fact/methods_spec.rb +78 -0
- data/spec/lib/dbd/provenance_fact/new_spec.rb +51 -0
- data/spec/lib/dbd/{provenance_resource_spec.rb → provenance_resource/provenance_resource_spec.rb} +6 -10
- data/spec/lib/dbd/{rdf_base_spec.rb → rdf_base/rdf_base_spec.rb} +0 -0
- data/spec/lib/dbd/{resource_spec.rb → resource/collection_spec.rb} +8 -47
- data/spec/lib/dbd/resource/factory_spec.rb +14 -0
- data/spec/lib/dbd/resource/new_spec.rb +44 -0
- data/spec/lib/dbd/time_stamp/comparisons_spec.rb +64 -0
- data/spec/lib/dbd/time_stamp/factory_spec.rb +17 -0
- data/spec/lib/dbd/time_stamp/methods_spec.rb +37 -0
- data/spec/lib/dbd/time_stamp/new_spec.rb +38 -0
- metadata +66 -29
- data/spec/lib/dbd/fact/id_spec.rb +0 -19
- data/spec/lib/dbd/fact/subject_spec.rb +0 -19
- data/spec/lib/dbd/fact_spec.rb +0 -216
- data/spec/lib/dbd/provenance_fact_spec.rb +0 -120
- data/spec/lib/dbd/time_stamp_spec.rb +0 -115
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
|
|
1
1
|
---
|
2
2
|
SHA1:
|
3
|
-
metadata.gz:
|
4
|
-
data.tar.gz:
|
3
|
+
metadata.gz: cc144cf2ae12eb90508d2da68006a9cc5ac247dd
|
4
|
+
data.tar.gz: 7bac3b578951f4a3a610aa988d5f06c180095368
|
5
5
|
SHA512:
|
6
|
-
metadata.gz:
|
7
|
-
data.tar.gz:
|
6
|
+
metadata.gz: 0e0f6fa90ad08943e62780b350a058e4d27286eb0396e3524222cd4d488ca81ac3764b58076bdb5331a91cd851fa710440a3e1b7060e81d2734c2f069f56a8ed
|
7
|
+
data.tar.gz: fb95d9bb0d1ecb5f13d297fa69ab01d661e460653d80333967583c46e843412ea46324fa025330d59f1dfcbf19c4dd5fa53a51099fe39db9d972a0e5339b1595
|
data/Guardfile
CHANGED
@@ -1,8 +1,9 @@
|
|
1
1
|
guard 'rspec' do
|
2
2
|
watch(%r{^spec/.+_spec\.rb$})
|
3
3
|
watch(%r{^spec/factories}) { "spec" }
|
4
|
-
watch(%r{^lib/dbd/helpers})
|
5
|
-
watch(%r{^lib/(.+)\.rb$}) { |m| "spec/lib/#{m[1]}_spec.rb" }
|
4
|
+
watch(%r{^lib/dbd/helpers}) { "spec" }
|
5
|
+
# watch(%r{^lib/(.+)\.rb$}) { |m| "spec/lib/#{m[1]}_spec.rb" }
|
6
|
+
watch(%r{^lib/(.+)\.rb$}) { |m| "spec/lib/#{m[1]}/" }
|
6
7
|
watch('spec/spec_helper.rb') { "spec" }
|
7
8
|
watch('lib/dbd.rb') { "spec" }
|
8
9
|
end
|
data/HISTORY.txt
CHANGED
data/dbd.gemspec
CHANGED
@@ -26,5 +26,5 @@ Gem::Specification.new do |spec|
|
|
26
26
|
spec.add_development_dependency 'yard'
|
27
27
|
spec.add_runtime_dependency 'neography'
|
28
28
|
spec.add_runtime_dependency 'rdf', '~> 1.0.6'
|
29
|
-
spec.add_runtime_dependency 'ruby_peter_v', '>= 0.0.
|
29
|
+
spec.add_runtime_dependency 'ruby_peter_v', '>= 0.0.9'
|
30
30
|
end
|
data/lib/dbd.rb
CHANGED
data/lib/dbd/fact.rb
CHANGED
@@ -123,8 +123,11 @@ module Dbd
|
|
123
123
|
# @option options [#to_s] :object Required : the object for this Fact (required)
|
124
124
|
# @option options [Subject] :provenance_subject (nil) Optional: the subject of the provenance(resource|fact)
|
125
125
|
# @option options [Subject] :subject (nil) Optional: the subject for this Fact
|
126
|
+
# @option options [TimeStamp] :time_stamp (nil) Optional: the time_stamp for this Fact
|
127
|
+
# @option options [ID] :id Optional : set the id
|
126
128
|
def initialize(options)
|
127
|
-
@id = self.class.new_id
|
129
|
+
@id = options[:id] || self.class.new_id
|
130
|
+
@time_stamp = options[:time_stamp]
|
128
131
|
@provenance_subject = options[:provenance_subject]
|
129
132
|
@subject = options[:subject]
|
130
133
|
@predicate = options[:predicate]
|
@@ -139,6 +142,16 @@ module Dbd
|
|
139
142
|
self.class.attributes.map{ |attribute| self.send(attribute) }
|
140
143
|
end
|
141
144
|
|
145
|
+
##
|
146
|
+
# Constructs a Fact from a values array
|
147
|
+
# (e.g. pulled from a CSV row).
|
148
|
+
#
|
149
|
+
# @param [Array] values Required : the array with values, organized as in attributes
|
150
|
+
# @return [Fact] the constructed fact
|
151
|
+
def self.from_values(values)
|
152
|
+
new(Hash[[self.attributes, values].transpose])
|
153
|
+
end
|
154
|
+
|
142
155
|
##
|
143
156
|
# @return [String] a short string representation of a Fact
|
144
157
|
def short
|
@@ -190,6 +203,15 @@ module Dbd
|
|
190
203
|
"Provenance subject is missing" unless provenance_subject
|
191
204
|
end
|
192
205
|
|
206
|
+
##
|
207
|
+
# Confirms this is not a ProvenanceFact
|
208
|
+
#
|
209
|
+
# Needed for validations that depend on different behavior for
|
210
|
+
# a provenance_fact (mainly, no provenance_subject).
|
211
|
+
def provenance_fact?
|
212
|
+
false
|
213
|
+
end
|
214
|
+
|
193
215
|
private
|
194
216
|
|
195
217
|
def provenance_subject_short
|
data/lib/dbd/fact/id.rb
CHANGED
data/lib/dbd/fact/subject.rb
CHANGED
data/lib/dbd/graph.rb
CHANGED
@@ -5,19 +5,26 @@ module Dbd
|
|
5
5
|
##
|
6
6
|
# The Graph stores the Facts and ProvenanceFacts in an in-memory
|
7
7
|
# collection structure.
|
8
|
+
#
|
9
|
+
# On the other hand, it acts as an "interface" that can be
|
10
|
+
# re-implemented by other persistence mechanisms (duck typing).
|
8
11
|
class Graph
|
9
12
|
|
10
13
|
include Fact::Collection
|
11
14
|
|
12
15
|
##
|
13
|
-
# Add a Fact
|
16
|
+
# Add a Fact, Resource or other recursive collection of facts.
|
14
17
|
#
|
15
|
-
#
|
16
|
-
|
17
|
-
|
18
|
+
# Side effect: this will set the time_stamp of the facts.
|
19
|
+
#
|
20
|
+
# @param [#time_stamp, #time_stamp=, #each] fact_collection a recursive collection of facts
|
21
|
+
# @return [Graph] self
|
22
|
+
def <<(fact_collection)
|
23
|
+
fact_collection.each_recursively do |fact|
|
18
24
|
enforce_strictly_monotonic_time(fact)
|
19
25
|
super(fact)
|
20
26
|
end
|
27
|
+
self
|
21
28
|
end
|
22
29
|
|
23
30
|
##
|
@@ -32,6 +39,20 @@ module Dbd
|
|
32
39
|
end.encode("utf-8")
|
33
40
|
end
|
34
41
|
|
42
|
+
##
|
43
|
+
# Import a graph from a CSV string.
|
44
|
+
#
|
45
|
+
# @param [String] csv a string that contains the CSV serialization
|
46
|
+
# @return [Graph] the imported graph
|
47
|
+
def self.from_CSV(csv)
|
48
|
+
Graph.new.tap do |graph|
|
49
|
+
CSV.new(csv).each do |row|
|
50
|
+
# TODO validate the input formats (e.g. invalid uuid codes)
|
51
|
+
graph << Fact.from_values(row)
|
52
|
+
end
|
53
|
+
end
|
54
|
+
end
|
55
|
+
|
35
56
|
private
|
36
57
|
|
37
58
|
##
|
data/lib/dbd/provenance_fact.rb
CHANGED
@@ -53,15 +53,12 @@ module Dbd
|
|
53
53
|
end
|
54
54
|
|
55
55
|
##
|
56
|
-
#
|
56
|
+
# Confirms this is a ProvenanceFact
|
57
57
|
#
|
58
|
-
#
|
59
|
-
#
|
60
|
-
def
|
61
|
-
|
62
|
-
subject: subject_arg, # from arg
|
63
|
-
predicate: predicate,
|
64
|
-
object: object)
|
58
|
+
# Needed for validations that depend on different behavior for
|
59
|
+
# a provenance_fact (mainly, no provenance_subject).
|
60
|
+
def provenance_fact?
|
61
|
+
true
|
65
62
|
end
|
66
63
|
|
67
64
|
private
|
@@ -1,7 +1,9 @@
|
|
1
1
|
module Dbd
|
2
2
|
##
|
3
3
|
# A ProvenanceResource is derived from a Resource, specifically
|
4
|
-
# for a Provenance
|
4
|
+
# for a Provenance.
|
5
|
+
#
|
6
|
+
# The main difference is that it does not have a provenance_subject.
|
5
7
|
class ProvenanceResource < Resource
|
6
8
|
|
7
9
|
##
|
@@ -17,38 +19,44 @@ module Dbd
|
|
17
19
|
end
|
18
20
|
|
19
21
|
##
|
20
|
-
# Add a ProvenanceFact.
|
22
|
+
# Add a ProvenanceFact (strictly only a ProvenanceFact).
|
21
23
|
#
|
24
|
+
# Side effect on subject:
|
22
25
|
# * if it has no subject, the subject is set in a duplicate provenance_fact
|
23
26
|
# * if is has the same subject as the resource, added unchanged.
|
24
27
|
# * if it has a different subject, a SubjectError is raised.
|
25
28
|
def <<(provenance_fact)
|
26
|
-
# TODO: check the type of the provenance_fact (ProvenanceFact)
|
27
29
|
super
|
28
30
|
end
|
29
31
|
|
30
32
|
private
|
31
33
|
|
32
|
-
##
|
33
34
|
# Should not be called in ProvenanceResource subclass.
|
34
35
|
def provenance_subject
|
35
|
-
raise
|
36
|
+
raise NoMethodError, "provenance_subject should not be called in ProvenanceResource."
|
36
37
|
end
|
37
38
|
|
38
|
-
|
39
|
-
|
39
|
+
def set_provenance_subject(options)
|
40
|
+
raise ArgumentError, "provenance_subject must not be in the options" if options[:provenance_subject]
|
41
|
+
end
|
42
|
+
|
43
|
+
# Validate that provenance_subject is not present here.
|
44
|
+
# This should never raise as the setter was blocked above.
|
40
45
|
def validate_provenance_subject
|
41
46
|
raise ProvenanceError if @provenance_subject
|
42
47
|
end
|
43
48
|
|
44
49
|
##
|
45
|
-
#
|
50
|
+
# Assert _only_ ProvenanceFacts here
|
51
|
+
def assert_fact_provenance_fact(fact)
|
52
|
+
raise ArgumentError, "Trying to add a non-ProvenanceFact to a ProvenanceResource." unless fact.provenance_fact?
|
53
|
+
end
|
54
|
+
|
55
|
+
##
|
56
|
+
# A noop for ProvenanceResource.
|
46
57
|
# @param [ProvenanceFact] provenance_fact
|
47
|
-
def
|
48
|
-
|
49
|
-
raise ProvenanceError,
|
50
|
-
"trying to set provenance_subject to#{provenance_fact.provenance_subject}"
|
51
|
-
end
|
58
|
+
def set_fact_provenance!(provenance_fact)
|
59
|
+
# Do nothing
|
52
60
|
end
|
53
61
|
|
54
62
|
end
|
File without changes
|
data/lib/dbd/resource.rb
CHANGED
@@ -2,12 +2,12 @@ require 'dbd/helpers/ordered_set_collection'
|
|
2
2
|
|
3
3
|
module Dbd
|
4
4
|
##
|
5
|
-
# A Resource is a collection of
|
5
|
+
# A Resource is a collection of Facts that have the same subject.
|
6
6
|
#
|
7
7
|
# In the real-world this is a mainly an "instance" about which all
|
8
8
|
# facts are giving information (e.g. a conference, a person, a
|
9
9
|
# bicycle, ...). More generally this can also be used to describe
|
10
|
-
# classes and other concepts in the
|
10
|
+
# classes and other concepts in the system.
|
11
11
|
#
|
12
12
|
# A new (random) subject is generated for a resource. In Dbd,
|
13
13
|
# a subject is a random uuid (like a oid), not a meaningful URI
|
@@ -25,15 +25,7 @@ module Dbd
|
|
25
25
|
|
26
26
|
include Helpers::OrderedSetCollection
|
27
27
|
|
28
|
-
attr_reader :subject
|
29
|
-
|
30
|
-
##
|
31
|
-
# Getter for provenance_subject.
|
32
|
-
#
|
33
|
-
# Will be overridden in the ProvenanceResource subclass.
|
34
|
-
def provenance_subject
|
35
|
-
@provenance_subject
|
36
|
-
end
|
28
|
+
attr_reader :subject, :provenance_subject
|
37
29
|
|
38
30
|
##
|
39
31
|
# @return [Fact::Subject] a new (random) Resource subject
|
@@ -51,19 +43,20 @@ module Dbd
|
|
51
43
|
#
|
52
44
|
# The provenance_subject argument is required. This will typically be
|
53
45
|
# taken from an earlier created ProvenanceResource.
|
46
|
+
#
|
54
47
|
# @param [Hash{Symbol => Object}] options
|
55
48
|
# @option options [Fact::Subject] :provenance_subject (required) the subject of the provenance resource for this resource
|
56
49
|
# @option options [Fact::Subject] :subject (new_subject) Optional: the subject for the resource
|
57
50
|
def initialize(options)
|
58
|
-
|
59
|
-
|
60
|
-
validate_provenance_subject
|
51
|
+
set_subject(options)
|
52
|
+
set_provenance_subject(options)
|
61
53
|
super()
|
62
54
|
end
|
63
55
|
|
64
56
|
##
|
65
|
-
# Add a
|
57
|
+
# Add a Fact (strictly not a ProvenanceFact)
|
66
58
|
#
|
59
|
+
# Side effects on subject and provenance_subject:
|
67
60
|
# * if it has no subject, the subject is set (this modifies the fact !)
|
68
61
|
# * if is has the same subject as the resource, added unchanged.
|
69
62
|
# * if it has a different subject, a SubjectError is raised.
|
@@ -71,25 +64,34 @@ module Dbd
|
|
71
64
|
# * if is has the same provenance_subject as the resource, added unchanged.
|
72
65
|
# * if it has a different provenance_subject, a ProvenanceError is raised.
|
73
66
|
def <<(fact)
|
74
|
-
|
75
|
-
|
76
|
-
|
67
|
+
assert_fact_provenance_fact(fact)
|
68
|
+
set_fact_subject!(fact)
|
69
|
+
set_fact_provenance!(fact)
|
77
70
|
super(fact)
|
78
71
|
end
|
79
72
|
|
80
73
|
private
|
81
74
|
|
82
|
-
def set_subject
|
75
|
+
def set_subject(options)
|
76
|
+
@subject = options[:subject] || self.class.new_subject
|
77
|
+
end
|
78
|
+
|
79
|
+
def set_provenance_subject(options)
|
80
|
+
@provenance_subject = options[:provenance_subject]
|
81
|
+
raise ProvenanceError, "provenance_subject cannot be nil" if @provenance_subject.nil?
|
82
|
+
end
|
83
|
+
|
84
|
+
def set_fact_subject!(fact)
|
83
85
|
fact.subject = subject
|
84
86
|
end
|
85
87
|
|
86
|
-
|
87
|
-
def set_provenance!(fact)
|
88
|
+
def set_fact_provenance!(fact)
|
88
89
|
fact.provenance_subject = provenance_subject
|
89
90
|
end
|
90
91
|
|
91
|
-
|
92
|
-
|
92
|
+
# Assert _no_ ProvenanceFacts here
|
93
|
+
def assert_fact_provenance_fact(fact)
|
94
|
+
raise ArgumentError, "Trying to add a ProvenanceFact to a Resource." if fact.provenance_fact?
|
93
95
|
end
|
94
96
|
|
95
97
|
end
|
data/lib/dbd/time_stamp.rb
CHANGED
@@ -66,12 +66,23 @@ module Dbd
|
|
66
66
|
Rational("#{1+rand(999)}/1_000_000_000")
|
67
67
|
end
|
68
68
|
|
69
|
+
def self.time_format
|
70
|
+
'%F %T.%N %Z'
|
71
|
+
end
|
72
|
+
|
69
73
|
public
|
70
74
|
|
71
75
|
##
|
72
|
-
#
|
76
|
+
# with a nanosecond granularity and in UTC
|
73
77
|
def to_s
|
74
|
-
@time.strftime(
|
78
|
+
@time.strftime(self.class.time_format)
|
79
|
+
end
|
80
|
+
|
81
|
+
##
|
82
|
+
# with a nanosecond granularity and in UTC
|
83
|
+
def self.from_s(time_string)
|
84
|
+
date_time = DateTime.strptime(time_string, time_format)
|
85
|
+
TimeStamp.new(time: date_time.to_time.utc)
|
75
86
|
end
|
76
87
|
|
77
88
|
def >(other)
|
data/lib/dbd/version.rb
CHANGED
data/spec/factories/fact.rb
CHANGED
@@ -16,6 +16,20 @@ module Factories
|
|
16
16
|
object: "Gandhi")
|
17
17
|
end
|
18
18
|
|
19
|
+
def self.fact_with_forced_id(forced_id)
|
20
|
+
factory_for.new(
|
21
|
+
id: forced_id,
|
22
|
+
predicate: "http://example.org/test/name",
|
23
|
+
object: "Gandhi")
|
24
|
+
end
|
25
|
+
|
26
|
+
def self.fact_with_time_stamp(time_stamp)
|
27
|
+
factory_for.new(
|
28
|
+
time_stamp: time_stamp,
|
29
|
+
predicate: "http://example.org/test/name",
|
30
|
+
object: "Gandhi")
|
31
|
+
end
|
32
|
+
|
19
33
|
def self.fact_2_with_subject(provenance_subject = nil)
|
20
34
|
factory_for.new(
|
21
35
|
provenance_subject: provenance_subject,
|
@@ -56,6 +70,15 @@ module Factories
|
|
56
70
|
object: "A long story\nreally.")
|
57
71
|
end
|
58
72
|
|
73
|
+
def self.full_fact
|
74
|
+
fixed_id = Factories::Fact::ID.fixed_id
|
75
|
+
fact_with_forced_id(fixed_id).tap do |fact|
|
76
|
+
fact.time_stamp = Factories::TimeStamp.fixed_time_stamp
|
77
|
+
fact.subject = Factories::Fact::Subject.fixed_subject
|
78
|
+
fact.provenance_subject = Factories::Fact::Subject.fixed_provenance_subject
|
79
|
+
end
|
80
|
+
end
|
81
|
+
|
59
82
|
module Collection
|
60
83
|
|
61
84
|
def self.factory_for_instance
|