bio-publisci 0.0.2 → 0.0.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +7 -0
- data/.travis.yml +1 -1
- data/Gemfile +1 -1
- data/Rakefile +4 -6
- data/features/integration_steps.rb +1 -1
- data/features/metadata.feature +24 -0
- data/features/metadata_steps.rb +21 -0
- data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +36 -14
- data/lib/bio-publisci/dataset/ORM/observation.rb +1 -1
- data/lib/bio-publisci/dataset/data_cube.rb +192 -131
- data/lib/bio-publisci/dataset/dataset_for.rb +150 -0
- data/lib/bio-publisci/dataset/interactive.rb +70 -55
- data/lib/bio-publisci/metadata/metadata.rb +81 -8
- data/lib/bio-publisci/parser.rb +76 -1
- data/lib/bio-publisci/readers/big_cross.rb +118 -117
- data/lib/bio-publisci/readers/csv.rb +37 -2
- data/lib/bio-publisci/readers/r_matrix.rb +1 -1
- data/lib/bio-publisci/store.rb +31 -31
- data/lib/bio-publisci/writers/arff.rb +48 -49
- data/lib/bio-publisci.rb +3 -0
- data/resources/queries/code_resources.rq +10 -0
- data/resources/queries/dimension_ranges.rq +3 -3
- data/resources/queries/dimensions.rq +3 -3
- data/resources/queries/measures.rq +3 -3
- data/resources/queries/observation_labels.rq +8 -0
- data/resources/queries/properties.rq +8 -0
- data/scripts/islet_mlratio.rb +6 -0
- data/scripts/scan_islet.rb +6 -0
- data/scripts/update_reference.rb +20 -0
- data/spec/ORM/data_cube_orm_spec.rb +12 -0
- data/spec/data_cube_spec.rb +1 -1
- data/spec/generators/dataframe_spec.rb +1 -1
- data/spec/generators/r_matrix_spec.rb +1 -1
- data/spec/r_builder_spec.rb +6 -6
- data/spec/resource/.RData +0 -0
- data/spec/resource/example.Rhistory +3 -0
- data/spec/turtle/bacon +4 -22
- data/spec/turtle/reference +9 -27
- metadata +37 -56
- data/lib/bio-publisci/loader.rb +0 -36
- data/spec/bio-publisci_spec.rb +0 -7
@@ -22,7 +22,7 @@ describe R2RDF::Reader::RMatrix do
|
|
22
22
|
@connection = Rserve::Connection.new
|
23
23
|
end
|
24
24
|
|
25
|
-
it "generators a simple output automatically" do
|
25
|
+
it "generators a simple output automatically", no_travis: true do
|
26
26
|
f=Tempfile.new('matrix')
|
27
27
|
@connection.eval "mat = matrix(c(2, 4, 3, 1, 5, 7), nrow=3, ncol=2)"
|
28
28
|
@generator.generate_n3(@connection,'mat',f.path,{quiet: true})
|
data/spec/r_builder_spec.rb
CHANGED
@@ -9,7 +9,7 @@ require_relative '../lib/bio-publisci.rb'
|
|
9
9
|
|
10
10
|
describe R2RDF::Writer::Dataframe do
|
11
11
|
|
12
|
-
context "when using r/qtl dataframe" do
|
12
|
+
context "when using r/qtl dataframe", no_travis: true do
|
13
13
|
|
14
14
|
before(:all) do
|
15
15
|
@r = Rserve::Connection.new
|
@@ -21,13 +21,13 @@ EOF
|
|
21
21
|
@builder = R2RDF::Writer::Builder.new
|
22
22
|
end
|
23
23
|
|
24
|
-
it "produces equivalent dataframe from rdf" do
|
24
|
+
it "produces equivalent dataframe from rdf" #do
|
25
25
|
#(a) problem is that builder and the @r connection are different b/c of
|
26
26
|
#how rserve works
|
27
|
-
@builder.from_turtle(File.dirname(__FILE__) +'/turtle/reference', @r, 'mr', 'mo', false, false)
|
28
|
-
puts @r.eval('ls()').payload.to_ruby
|
29
|
-
@r.eval('identical(mr,mo)').to_ruby.should == true
|
30
|
-
end
|
27
|
+
# @builder.from_turtle(File.dirname(__FILE__) +'/turtle/reference', @r, 'mr', 'mo', false, false)
|
28
|
+
# puts @r.eval('ls()').payload.to_ruby
|
29
|
+
# @r.eval('identical(mr,mo)').to_ruby.should == true
|
30
|
+
#end
|
31
31
|
|
32
32
|
end
|
33
33
|
end
|
Binary file
|
data/spec/turtle/bacon
CHANGED
@@ -8,7 +8,6 @@
|
|
8
8
|
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
|
9
9
|
@prefix cs: <http://www.rqtl.org/dc/dataset/bacon/cs/> .
|
10
10
|
@prefix code: <http://www.rqtl.org/dc/dataset/bacon/code/> .
|
11
|
-
@prefix class: <http://www.rqtl.org/dc/dataset/bacon/class/> .
|
12
11
|
@prefix owl: <http://www.w3.org/2002/07/owl#> .
|
13
12
|
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
|
14
13
|
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
|
@@ -16,32 +15,15 @@
|
|
16
15
|
@prefix prov: <http://www.w3.org/ns/prov#> .
|
17
16
|
|
18
17
|
ns:dsd-bacon a qb:DataStructureDefinition;
|
19
|
-
qb:component
|
20
|
-
|
21
|
-
|
22
|
-
|
23
|
-
cs:pricerange .
|
18
|
+
qb:component [ qb:dimension prop:producer ] ;
|
19
|
+
qb:component [ qb:dimension prop:pricerange ] ;
|
20
|
+
qb:component [ qb:measure prop:chunkiness ] ;
|
21
|
+
qb:component [ qb:measure prop:deliciousness ] .
|
24
22
|
|
25
23
|
ns:dataset-bacon a qb:DataSet ;
|
26
24
|
rdfs:label "bacon"@en ;
|
27
25
|
qb:structure ns:dsd-bacon .
|
28
26
|
|
29
|
-
cs:producer a qb:ComponentSpecification ;
|
30
|
-
rdfs:label "producer Component" ;
|
31
|
-
qb:dimension prop:producer .
|
32
|
-
|
33
|
-
cs:pricerange a qb:ComponentSpecification ;
|
34
|
-
rdfs:label "pricerange Component" ;
|
35
|
-
qb:dimension prop:pricerange .
|
36
|
-
|
37
|
-
cs:chunkiness a qb:ComponentSpecification ;
|
38
|
-
rdfs:label "chunkiness Component" ;
|
39
|
-
qb:measure prop:chunkiness .
|
40
|
-
|
41
|
-
cs:deliciousness a qb:ComponentSpecification ;
|
42
|
-
rdfs:label "deliciousness Component" ;
|
43
|
-
qb:measure prop:deliciousness .
|
44
|
-
|
45
27
|
prop:producer a rdf:Property, qb:DimensionProperty ;
|
46
28
|
rdfs:label "producer"@en ;
|
47
29
|
qb:codeList code:producer ;
|
data/spec/turtle/reference
CHANGED
@@ -8,7 +8,6 @@
|
|
8
8
|
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
|
9
9
|
@prefix cs: <http://www.rqtl.org/dc/dataset/mr/cs/> .
|
10
10
|
@prefix code: <http://www.rqtl.org/dc/dataset/mr/code/> .
|
11
|
-
@prefix class: <http://www.rqtl.org/dc/dataset/mr/class/> .
|
12
11
|
@prefix owl: <http://www.w3.org/2002/07/owl#> .
|
13
12
|
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
|
14
13
|
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
|
@@ -16,32 +15,15 @@
|
|
16
15
|
@prefix prov: <http://www.w3.org/ns/prov#> .
|
17
16
|
|
18
17
|
ns:dsd-mr a qb:DataStructureDefinition;
|
19
|
-
qb:component
|
20
|
-
|
21
|
-
|
22
|
-
|
23
|
-
cs:refRow .
|
18
|
+
qb:component [ qb:dimension prop:refRow ] ;
|
19
|
+
qb:component [ qb:measure prop:chr ] ;
|
20
|
+
qb:component [ qb:measure prop:pos ] ;
|
21
|
+
qb:component [ qb:measure prop:lod ] .
|
24
22
|
|
25
23
|
ns:dataset-mr a qb:DataSet ;
|
26
24
|
rdfs:label "mr"@en ;
|
27
25
|
qb:structure ns:dsd-mr .
|
28
26
|
|
29
|
-
cs:refRow a qb:ComponentSpecification ;
|
30
|
-
rdfs:label "refRow Component" ;
|
31
|
-
qb:dimension prop:refRow .
|
32
|
-
|
33
|
-
cs:chr a qb:ComponentSpecification ;
|
34
|
-
rdfs:label "chr Component" ;
|
35
|
-
qb:measure prop:chr .
|
36
|
-
|
37
|
-
cs:pos a qb:ComponentSpecification ;
|
38
|
-
rdfs:label "pos Component" ;
|
39
|
-
qb:measure prop:pos .
|
40
|
-
|
41
|
-
cs:lod a qb:ComponentSpecification ;
|
42
|
-
rdfs:label "lod Component" ;
|
43
|
-
qb:measure prop:lod .
|
44
|
-
|
45
27
|
prop:refRow a rdf:Property, qb:DimensionProperty ;
|
46
28
|
rdfs:label "refRow"@en ;
|
47
29
|
qb:codeList code:refrow ;
|
@@ -58,15 +40,15 @@ prop:lod a rdf:Property, qb:MeasureProperty ;
|
|
58
40
|
|
59
41
|
code:Refrow a rdfs:Class, owl:Class;
|
60
42
|
rdfs:subClassOf skos:Concept ;
|
61
|
-
rdfs:label "Code list for
|
62
|
-
rdfs:comment "Specifies the
|
43
|
+
rdfs:label "Code list for refrow - codelist class"@en;
|
44
|
+
rdfs:comment "Specifies the refrow for each observation";
|
63
45
|
rdfs:seeAlso code:refrow .
|
64
46
|
|
65
47
|
code:refrow a skos:ConceptScheme;
|
66
|
-
skos:prefLabel "Code list for
|
67
|
-
rdfs:label "Code list for
|
48
|
+
skos:prefLabel "Code list for refrow - codelist scheme"@en;
|
49
|
+
rdfs:label "Code list for refrow - codelist scheme"@en;
|
68
50
|
skos:notation "CL_REFROW";
|
69
|
-
skos:note "Specifies the
|
51
|
+
skos:note "Specifies the refrow for each observation";
|
70
52
|
skos:hasTopConcept <code/refrow/D10M44> ;
|
71
53
|
skos:hasTopConcept <code/refrow/D1M3> ;
|
72
54
|
skos:hasTopConcept <code/refrow/D1M75> ;
|
metadata
CHANGED
@@ -1,100 +1,88 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: bio-publisci
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
5
|
-
prerelease:
|
4
|
+
version: 0.0.3
|
6
5
|
platform: ruby
|
7
6
|
authors:
|
8
7
|
- wstrinz
|
9
8
|
autorequire:
|
10
9
|
bindir: bin
|
11
10
|
cert_chain: []
|
12
|
-
date: 2013-07-
|
11
|
+
date: 2013-07-25 00:00:00.000000000 Z
|
13
12
|
dependencies:
|
14
13
|
- !ruby/object:Gem::Dependency
|
15
14
|
name: rdf
|
16
15
|
requirement: !ruby/object:Gem::Requirement
|
17
|
-
none: false
|
18
16
|
requirements:
|
19
|
-
- -
|
17
|
+
- - '>='
|
20
18
|
- !ruby/object:Gem::Version
|
21
19
|
version: '0'
|
22
20
|
type: :runtime
|
23
21
|
prerelease: false
|
24
22
|
version_requirements: !ruby/object:Gem::Requirement
|
25
|
-
none: false
|
26
23
|
requirements:
|
27
|
-
- -
|
24
|
+
- - '>='
|
28
25
|
- !ruby/object:Gem::Version
|
29
26
|
version: '0'
|
30
27
|
- !ruby/object:Gem::Dependency
|
31
28
|
name: rdf-4store
|
32
29
|
requirement: !ruby/object:Gem::Requirement
|
33
|
-
none: false
|
34
30
|
requirements:
|
35
|
-
- -
|
31
|
+
- - '>='
|
36
32
|
- !ruby/object:Gem::Version
|
37
33
|
version: '0'
|
38
34
|
type: :runtime
|
39
35
|
prerelease: false
|
40
36
|
version_requirements: !ruby/object:Gem::Requirement
|
41
|
-
none: false
|
42
37
|
requirements:
|
43
|
-
- -
|
38
|
+
- - '>='
|
44
39
|
- !ruby/object:Gem::Version
|
45
40
|
version: '0'
|
46
41
|
- !ruby/object:Gem::Dependency
|
47
42
|
name: rdf-turtle
|
48
43
|
requirement: !ruby/object:Gem::Requirement
|
49
|
-
none: false
|
50
44
|
requirements:
|
51
|
-
- -
|
45
|
+
- - '>='
|
52
46
|
- !ruby/object:Gem::Version
|
53
47
|
version: '0'
|
54
48
|
type: :runtime
|
55
49
|
prerelease: false
|
56
50
|
version_requirements: !ruby/object:Gem::Requirement
|
57
|
-
none: false
|
58
51
|
requirements:
|
59
|
-
- -
|
52
|
+
- - '>='
|
60
53
|
- !ruby/object:Gem::Version
|
61
54
|
version: '0'
|
62
55
|
- !ruby/object:Gem::Dependency
|
63
56
|
name: rserve-client
|
64
57
|
requirement: !ruby/object:Gem::Requirement
|
65
|
-
none: false
|
66
58
|
requirements:
|
67
|
-
- -
|
59
|
+
- - '>='
|
68
60
|
- !ruby/object:Gem::Version
|
69
61
|
version: '0'
|
70
62
|
type: :runtime
|
71
63
|
prerelease: false
|
72
64
|
version_requirements: !ruby/object:Gem::Requirement
|
73
|
-
none: false
|
74
65
|
requirements:
|
75
|
-
- -
|
66
|
+
- - '>='
|
76
67
|
- !ruby/object:Gem::Version
|
77
68
|
version: '0'
|
78
69
|
- !ruby/object:Gem::Dependency
|
79
70
|
name: sparql
|
80
71
|
requirement: !ruby/object:Gem::Requirement
|
81
|
-
none: false
|
82
72
|
requirements:
|
83
|
-
- -
|
73
|
+
- - '>='
|
84
74
|
- !ruby/object:Gem::Version
|
85
75
|
version: '0'
|
86
76
|
type: :runtime
|
87
77
|
prerelease: false
|
88
78
|
version_requirements: !ruby/object:Gem::Requirement
|
89
|
-
none: false
|
90
79
|
requirements:
|
91
|
-
- -
|
80
|
+
- - '>='
|
92
81
|
- !ruby/object:Gem::Version
|
93
82
|
version: '0'
|
94
83
|
- !ruby/object:Gem::Dependency
|
95
84
|
name: rspec
|
96
85
|
requirement: !ruby/object:Gem::Requirement
|
97
|
-
none: false
|
98
86
|
requirements:
|
99
87
|
- - ~>
|
100
88
|
- !ruby/object:Gem::Version
|
@@ -102,7 +90,6 @@ dependencies:
|
|
102
90
|
type: :development
|
103
91
|
prerelease: false
|
104
92
|
version_requirements: !ruby/object:Gem::Requirement
|
105
|
-
none: false
|
106
93
|
requirements:
|
107
94
|
- - ~>
|
108
95
|
- !ruby/object:Gem::Version
|
@@ -110,7 +97,6 @@ dependencies:
|
|
110
97
|
- !ruby/object:Gem::Dependency
|
111
98
|
name: rdoc
|
112
99
|
requirement: !ruby/object:Gem::Requirement
|
113
|
-
none: false
|
114
100
|
requirements:
|
115
101
|
- - ~>
|
116
102
|
- !ruby/object:Gem::Version
|
@@ -118,7 +104,6 @@ dependencies:
|
|
118
104
|
type: :development
|
119
105
|
prerelease: false
|
120
106
|
version_requirements: !ruby/object:Gem::Requirement
|
121
|
-
none: false
|
122
107
|
requirements:
|
123
108
|
- - ~>
|
124
109
|
- !ruby/object:Gem::Version
|
@@ -126,23 +111,20 @@ dependencies:
|
|
126
111
|
- !ruby/object:Gem::Dependency
|
127
112
|
name: cucumber
|
128
113
|
requirement: !ruby/object:Gem::Requirement
|
129
|
-
none: false
|
130
114
|
requirements:
|
131
|
-
- -
|
115
|
+
- - '>='
|
132
116
|
- !ruby/object:Gem::Version
|
133
117
|
version: '0'
|
134
118
|
type: :development
|
135
119
|
prerelease: false
|
136
120
|
version_requirements: !ruby/object:Gem::Requirement
|
137
|
-
none: false
|
138
121
|
requirements:
|
139
|
-
- -
|
122
|
+
- - '>='
|
140
123
|
- !ruby/object:Gem::Version
|
141
124
|
version: '0'
|
142
125
|
- !ruby/object:Gem::Dependency
|
143
126
|
name: jeweler
|
144
127
|
requirement: !ruby/object:Gem::Requirement
|
145
|
-
none: false
|
146
128
|
requirements:
|
147
129
|
- - ~>
|
148
130
|
- !ruby/object:Gem::Version
|
@@ -150,7 +132,6 @@ dependencies:
|
|
150
132
|
type: :development
|
151
133
|
prerelease: false
|
152
134
|
version_requirements: !ruby/object:Gem::Requirement
|
153
|
-
none: false
|
154
135
|
requirements:
|
155
136
|
- - ~>
|
156
137
|
- !ruby/object:Gem::Version
|
@@ -158,39 +139,34 @@ dependencies:
|
|
158
139
|
- !ruby/object:Gem::Dependency
|
159
140
|
name: bundler
|
160
141
|
requirement: !ruby/object:Gem::Requirement
|
161
|
-
none: false
|
162
142
|
requirements:
|
163
|
-
- -
|
143
|
+
- - '>='
|
164
144
|
- !ruby/object:Gem::Version
|
165
145
|
version: 1.0.21
|
166
146
|
type: :development
|
167
147
|
prerelease: false
|
168
148
|
version_requirements: !ruby/object:Gem::Requirement
|
169
|
-
none: false
|
170
149
|
requirements:
|
171
|
-
- -
|
150
|
+
- - '>='
|
172
151
|
- !ruby/object:Gem::Version
|
173
152
|
version: 1.0.21
|
174
153
|
- !ruby/object:Gem::Dependency
|
175
154
|
name: bio
|
176
155
|
requirement: !ruby/object:Gem::Requirement
|
177
|
-
none: false
|
178
156
|
requirements:
|
179
|
-
- -
|
157
|
+
- - '>='
|
180
158
|
- !ruby/object:Gem::Version
|
181
159
|
version: 1.4.2
|
182
160
|
type: :development
|
183
161
|
prerelease: false
|
184
162
|
version_requirements: !ruby/object:Gem::Requirement
|
185
|
-
none: false
|
186
163
|
requirements:
|
187
|
-
- -
|
164
|
+
- - '>='
|
188
165
|
- !ruby/object:Gem::Version
|
189
166
|
version: 1.4.2
|
190
167
|
- !ruby/object:Gem::Dependency
|
191
168
|
name: rdoc
|
192
169
|
requirement: !ruby/object:Gem::Requirement
|
193
|
-
none: false
|
194
170
|
requirements:
|
195
171
|
- - ~>
|
196
172
|
- !ruby/object:Gem::Version
|
@@ -198,13 +174,12 @@ dependencies:
|
|
198
174
|
type: :development
|
199
175
|
prerelease: false
|
200
176
|
version_requirements: !ruby/object:Gem::Requirement
|
201
|
-
none: false
|
202
177
|
requirements:
|
203
178
|
- - ~>
|
204
179
|
- !ruby/object:Gem::Version
|
205
180
|
version: '3.12'
|
206
|
-
description:
|
207
|
-
|
181
|
+
description: 'A toolkit for publishing scientific results and datasets using RDF and
|
182
|
+
related technologies '
|
208
183
|
email: wstrinz@gmail.com
|
209
184
|
executables:
|
210
185
|
- bio-publisci
|
@@ -226,6 +201,8 @@ files:
|
|
226
201
|
- features/create_generator.feature
|
227
202
|
- features/integration.feature
|
228
203
|
- features/integration_steps.rb
|
204
|
+
- features/metadata.feature
|
205
|
+
- features/metadata_steps.rb
|
229
206
|
- features/orm.feature
|
230
207
|
- features/orm_steps.rb
|
231
208
|
- features/reader.feature
|
@@ -241,8 +218,8 @@ files:
|
|
241
218
|
- lib/bio-publisci/dataset/ORM/data_cube_orm.rb
|
242
219
|
- lib/bio-publisci/dataset/ORM/observation.rb
|
243
220
|
- lib/bio-publisci/dataset/data_cube.rb
|
221
|
+
- lib/bio-publisci/dataset/dataset_for.rb
|
244
222
|
- lib/bio-publisci/dataset/interactive.rb
|
245
|
-
- lib/bio-publisci/loader.rb
|
246
223
|
- lib/bio-publisci/metadata/metadata.rb
|
247
224
|
- lib/bio-publisci/parser.rb
|
248
225
|
- lib/bio-publisci/query/query_helper.rb
|
@@ -278,16 +255,22 @@ files:
|
|
278
255
|
- lib/vocabs/wot.rb
|
279
256
|
- lib/vocabs/xhtml.rb
|
280
257
|
- lib/vocabs/xsd.rb
|
258
|
+
- resources/queries/code_resources.rq
|
281
259
|
- resources/queries/codes.rq
|
282
260
|
- resources/queries/dataset.rq
|
283
261
|
- resources/queries/dimension_ranges.rq
|
284
262
|
- resources/queries/dimensions.rq
|
285
263
|
- resources/queries/measures.rq
|
264
|
+
- resources/queries/observation_labels.rq
|
286
265
|
- resources/queries/observations.rq
|
266
|
+
- resources/queries/properties.rq
|
287
267
|
- resources/queries/test.rq
|
288
268
|
- resources/weather.numeric.arff
|
269
|
+
- scripts/islet_mlratio.rb
|
270
|
+
- scripts/scan_islet.rb
|
271
|
+
- scripts/update_reference.rb
|
272
|
+
- spec/ORM/data_cube_orm_spec.rb
|
289
273
|
- spec/analyzer_spec.rb
|
290
|
-
- spec/bio-publisci_spec.rb
|
291
274
|
- spec/csv/bacon.csv
|
292
275
|
- spec/csv/moar_bacon.csv
|
293
276
|
- spec/data_cube_spec.rb
|
@@ -305,35 +288,33 @@ files:
|
|
305
288
|
- spec/queries/integrity/4.rq
|
306
289
|
- spec/queries/integrity/5.rq
|
307
290
|
- spec/r_builder_spec.rb
|
291
|
+
- spec/resource/.RData
|
292
|
+
- spec/resource/example.Rhistory
|
308
293
|
- spec/spec_helper.rb
|
309
294
|
- spec/turtle/bacon
|
310
295
|
- spec/turtle/reference
|
311
296
|
homepage: http://github.com/wstrinz/bioruby-publisci
|
312
297
|
licenses:
|
313
298
|
- MIT
|
299
|
+
metadata: {}
|
314
300
|
post_install_message:
|
315
301
|
rdoc_options: []
|
316
302
|
require_paths:
|
317
303
|
- lib
|
318
304
|
required_ruby_version: !ruby/object:Gem::Requirement
|
319
|
-
none: false
|
320
305
|
requirements:
|
321
|
-
- -
|
306
|
+
- - '>='
|
322
307
|
- !ruby/object:Gem::Version
|
323
308
|
version: '0'
|
324
|
-
segments:
|
325
|
-
- 0
|
326
|
-
hash: -1178175655966297191
|
327
309
|
required_rubygems_version: !ruby/object:Gem::Requirement
|
328
|
-
none: false
|
329
310
|
requirements:
|
330
|
-
- -
|
311
|
+
- - '>='
|
331
312
|
- !ruby/object:Gem::Version
|
332
313
|
version: '0'
|
333
314
|
requirements: []
|
334
315
|
rubyforge_project:
|
335
|
-
rubygems_version:
|
316
|
+
rubygems_version: 2.0.3
|
336
317
|
signing_key:
|
337
|
-
specification_version:
|
318
|
+
specification_version: 4
|
338
319
|
summary: Publish science data using semantic web ontologies
|
339
320
|
test_files: []
|
data/lib/bio-publisci/loader.rb
DELETED
@@ -1,36 +0,0 @@
|
|
1
|
-
# This is temporary, just to help w/ development so I don't have to rewrite r2rdf.rb to be
|
2
|
-
# a standard gem base yet. Also load s the files instead of require for easy reloading
|
3
|
-
require 'tempfile'
|
4
|
-
require 'rdf'
|
5
|
-
require 'csv'
|
6
|
-
require 'rserve'
|
7
|
-
require 'sparql'
|
8
|
-
require 'sparql/client'
|
9
|
-
require 'rdf/turtle'
|
10
|
-
|
11
|
-
def load_folder(folder)
|
12
|
-
Dir.foreach(File.dirname(__FILE__) + "/#{folder}") do |file|
|
13
|
-
unless file == "." or file == ".."
|
14
|
-
load File.dirname(__FILE__) + "/#{folder}/" + file
|
15
|
-
end
|
16
|
-
end
|
17
|
-
end
|
18
|
-
|
19
|
-
load File.dirname(__FILE__) + '/dataset/interactive.rb'
|
20
|
-
load File.dirname(__FILE__) + '/query/query_helper.rb'
|
21
|
-
load File.dirname(__FILE__) + '/parser.rb'
|
22
|
-
load File.dirname(__FILE__) + '/r_client.rb'
|
23
|
-
load File.dirname(__FILE__) + '/analyzer.rb'
|
24
|
-
load File.dirname(__FILE__) + '/store.rb'
|
25
|
-
load File.dirname(__FILE__) + '/dataset/data_cube.rb'
|
26
|
-
|
27
|
-
|
28
|
-
load_folder('metadata')
|
29
|
-
load_folder('readers')
|
30
|
-
load_folder('writers')
|
31
|
-
load_folder('dataset/ORM')
|
32
|
-
# Dir.foreach(File.dirname(__FILE__) + '/generators') do |file|
|
33
|
-
# unless file == "." or file == ".."
|
34
|
-
# load File.dirname(__FILE__) + '/generators/' + file
|
35
|
-
# end
|
36
|
-
# end
|