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.
Files changed (41) hide show
  1. checksums.yaml +7 -0
  2. data/.travis.yml +1 -1
  3. data/Gemfile +1 -1
  4. data/Rakefile +4 -6
  5. data/features/integration_steps.rb +1 -1
  6. data/features/metadata.feature +24 -0
  7. data/features/metadata_steps.rb +21 -0
  8. data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb +36 -14
  9. data/lib/bio-publisci/dataset/ORM/observation.rb +1 -1
  10. data/lib/bio-publisci/dataset/data_cube.rb +192 -131
  11. data/lib/bio-publisci/dataset/dataset_for.rb +150 -0
  12. data/lib/bio-publisci/dataset/interactive.rb +70 -55
  13. data/lib/bio-publisci/metadata/metadata.rb +81 -8
  14. data/lib/bio-publisci/parser.rb +76 -1
  15. data/lib/bio-publisci/readers/big_cross.rb +118 -117
  16. data/lib/bio-publisci/readers/csv.rb +37 -2
  17. data/lib/bio-publisci/readers/r_matrix.rb +1 -1
  18. data/lib/bio-publisci/store.rb +31 -31
  19. data/lib/bio-publisci/writers/arff.rb +48 -49
  20. data/lib/bio-publisci.rb +3 -0
  21. data/resources/queries/code_resources.rq +10 -0
  22. data/resources/queries/dimension_ranges.rq +3 -3
  23. data/resources/queries/dimensions.rq +3 -3
  24. data/resources/queries/measures.rq +3 -3
  25. data/resources/queries/observation_labels.rq +8 -0
  26. data/resources/queries/properties.rq +8 -0
  27. data/scripts/islet_mlratio.rb +6 -0
  28. data/scripts/scan_islet.rb +6 -0
  29. data/scripts/update_reference.rb +20 -0
  30. data/spec/ORM/data_cube_orm_spec.rb +12 -0
  31. data/spec/data_cube_spec.rb +1 -1
  32. data/spec/generators/dataframe_spec.rb +1 -1
  33. data/spec/generators/r_matrix_spec.rb +1 -1
  34. data/spec/r_builder_spec.rb +6 -6
  35. data/spec/resource/.RData +0 -0
  36. data/spec/resource/example.Rhistory +3 -0
  37. data/spec/turtle/bacon +4 -22
  38. data/spec/turtle/reference +9 -27
  39. metadata +37 -56
  40. data/lib/bio-publisci/loader.rb +0 -36
  41. data/spec/bio-publisci_spec.rb +0 -7
@@ -11,7 +11,7 @@ describe R2RDF::Reader::Dataframe do
11
11
  graph
12
12
  end
13
13
 
14
- context "with r/qtl dataframe" do
14
+ context "with r/qtl dataframe", no_travis: true do
15
15
  before(:all) do
16
16
  @r = Rserve::Connection.new
17
17
  @generator = R2RDF::Reader::Dataframe.new
@@ -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})
@@ -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
@@ -0,0 +1,3 @@
1
+ library(qtl)
2
+ data(listeria)
3
+ mr = scanone(listeria,method='mr')
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
- cs:chunkiness ,
21
- cs:deliciousness ,
22
- cs:producer ,
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 ;
@@ -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
- cs:chr ,
21
- cs:pos ,
22
- cs:lod ,
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 refRow - codelist class"@en;
62
- rdfs:comment "Specifies the refRow for each observation";
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 refRow - codelist scheme"@en;
67
- rdfs:label "Code list for refRow - codelist scheme"@en;
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 refRow for each observation";
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: 0.0.2
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: 2013-07-20 00:00:00.000000000 Z
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: ! 'A toolkit for publishing scientific results and datasets using RDF
207
- and related technologies '
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: 1.8.25
316
+ rubygems_version: 2.0.3
336
317
  signing_key:
337
- specification_version: 3
318
+ specification_version: 4
338
319
  summary: Publish science data using semantic web ontologies
339
320
  test_files: []
@@ -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
@@ -1,7 +0,0 @@
1
- require File.expand_path(File.dirname(__FILE__) + '/spec_helper')
2
-
3
- describe "BioPublisci" do
4
- it "fails" do
5
- fail "hey buddy, you should probably rename this file and start specing for real"
6
- end
7
- end