bio-publisci 0.0.8 → 0.1.0

data/spec/resource/example.Rhistory

@@ -1,3 +1,3 @@
 library(qtl)
 data(listeria)
-mr = scanone(listeria,method='mr')
+mr = scanone(listeria,method='mr')

data/spec/turtle/bacon

@@ -1,13 +1,13 @@
-@base <http://www.rqtl.org/ns/dc/> .
-@prefix ns:    <http://www.rqtl.org/ns/dataset/bacon/> .
+@base <http://onto.strinz.me/dc/dataset/bacon/> .
+@prefix ns:    <http://onto.strinz.me/dc/dataset/bacon/> .
 @prefix qb:    <http://purl.org/linked-data/cube#> .
 @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix prop:  <http://www.rqtl.org/dc/properties/> .
+@prefix prop:  <http://onto.strinz.me/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://www.rqtl.org/dc/dataset/bacon/cs/> .
-@prefix code:  <http://www.rqtl.org/dc/dataset/bacon/code/> .
+@prefix cs:    <http://onto.strinz.me/dc/dataset/bacon/cs/> .
+@prefix code:  <http://onto.strinz.me/dc/dataset/bacon/code/> .
 @prefix owl:   <http://www.w3.org/2002/07/owl#> .
 @prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
 @prefix foaf:     <http://xmlns.com/foaf/0.1/> .
@@ -25,19 +25,19 @@ ns:dataset-bacon a qb:DataSet ;
   qb:structure ns:dsd-bacon .
 
 cs:producer a qb:ComponentSpecification ;
-  rdfs:label "producer Component" ;
+  rdfs:label "producer" ;
   qb:dimension prop:producer .
 
 cs:pricerange a qb:ComponentSpecification ;
-  rdfs:label "pricerange Component" ;
+  rdfs:label "pricerange" ;
   qb:dimension prop:pricerange .
 
 cs:chunkiness a qb:ComponentSpecification ;
-  rdfs:label "chunkiness Component" ;
+  rdfs:label "chunkiness" ;
   qb:measure prop:chunkiness .
 
 cs:deliciousness a qb:ComponentSpecification ;
-  rdfs:label "deliciousness Component" ;
+  rdfs:label "deliciousness" ;
   qb:measure prop:deliciousness .
 
 prop:producer a rdf:Property, qb:DimensionProperty ;

data/spec/turtle/reference

@@ -1,13 +1,13 @@
-@base <http://www.rqtl.org/ns/dc/> .
-@prefix ns:    <http://www.rqtl.org/ns/dataset/mr/> .
+@base <http://onto.strinz.me/dc/dataset/mr/> .
+@prefix ns:    <http://onto.strinz.me/dc/dataset/mr/> .
 @prefix qb:    <http://purl.org/linked-data/cube#> .
 @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix prop:  <http://www.rqtl.org/dc/properties/> .
+@prefix prop:  <http://onto.strinz.me/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://www.rqtl.org/dc/dataset/mr/cs/> .
-@prefix code:  <http://www.rqtl.org/dc/dataset/mr/code/> .
+@prefix cs:    <http://onto.strinz.me/dc/dataset/mr/cs/> .
+@prefix code:  <http://onto.strinz.me/dc/dataset/mr/code/> .
 @prefix owl:   <http://www.w3.org/2002/07/owl#> .
 @prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
 @prefix foaf:     <http://xmlns.com/foaf/0.1/> .
@@ -25,19 +25,19 @@ ns:dataset-mr a qb:DataSet ;
   qb:structure ns:dsd-mr .
 
 cs:refRow a qb:ComponentSpecification ;
-  rdfs:label "refRow Component" ;
+  rdfs:label "refRow" ;
   qb:dimension prop:refRow .
 
 cs:chr a qb:ComponentSpecification ;
-  rdfs:label "chr Component" ;
+  rdfs:label "chr" ;
   qb:measure prop:chr .
 
 cs:pos a qb:ComponentSpecification ;
-  rdfs:label "pos Component" ;
+  rdfs:label "pos" ;
   qb:measure prop:pos .
 
 cs:lod a qb:ComponentSpecification ;
-  rdfs:label "lod Component" ;
+  rdfs:label "lod" ;
   qb:measure prop:lod .
 
 prop:refRow a rdf:Property, qb:DimensionProperty ;
@@ -898,7 +898,7 @@ ns:obsD1M215 a qb:Observation ;
   prop:refRow <code/refrow/D1M215> ;
   prop:chr 1 ;
   prop:pos 40.41360872065924 ;
-  prop:lod 0.07012015768917834 ;
+  prop:lod 0.07012015768922852 ;
   .
 
 ns:obsD1M309 a qb:Observation ;
@@ -943,7 +943,7 @@ ns:obsD1M113 a qb:Observation ;
   prop:refRow <code/refrow/D1M113> ;
   prop:chr 1 ;
   prop:pos 80.62323562923214 ;
-  prop:lod 2.0726083948737966 ;
+  prop:lod 2.072608394873848 ;
   .
 
 ns:obsD1M355 a qb:Observation ;
@@ -970,7 +970,7 @@ ns:obsD1M209 a qb:Observation ;
   prop:refRow <code/refrow/D1M209> ;
   prop:chr 1 ;
   prop:pos 92.68393779641761 ;
-  prop:lod 1.0770292807569852 ;
+  prop:lod 1.077029280756939 ;
   .
 
 ns:obsD1M155 a qb:Observation ;
@@ -1042,7 +1042,7 @@ ns:obsD3M265 a qb:Observation ;
   prop:refRow <code/refrow/D3M265> ;
   prop:chr 3 ;
   prop:pos 0.0 ;
-  prop:lod 1.6120906204520224 ;
+  prop:lod 1.612090620452074 ;
   .
 
 ns:obsD3M51 a qb:Observation ;
@@ -1060,7 +1060,7 @@ ns:obsD3M106 a qb:Observation ;
   prop:refRow <code/refrow/D3M106> ;
   prop:chr 3 ;
   prop:pos 43.938030995679 ;
-  prop:lod 0.45374023883481307 ;
+  prop:lod 0.4537402388347749 ;
   .
 
 ns:obsD3M257 a qb:Observation ;
@@ -1087,7 +1087,7 @@ ns:obsD3M19 a qb:Observation ;
   prop:refRow <code/refrow/D3M19> ;
   prop:chr 3 ;
   prop:pos 70.83899918659391 ;
-  prop:lod 0.5681404735365145 ;
+  prop:lod 0.5681404735364763 ;
   .
 
 ns:obsD4M2 a qb:Observation ;
@@ -1096,7 +1096,7 @@ ns:obsD4M2 a qb:Observation ;
   prop:refRow <code/refrow/D4M2> ;
   prop:chr 4 ;
   prop:pos 0.0 ;
-  prop:lod 0.24331723281215023 ;
+  prop:lod 0.24331723281211204 ;
   .
 
 ns:obsD4M178 a qb:Observation ;
@@ -1114,7 +1114,7 @@ ns:obsD4M187 a qb:Observation ;
   prop:refRow <code/refrow/D4M187> ;
   prop:chr 4 ;
   prop:pos 35.32085637897066 ;
-  prop:lod 0.08949770136010748 ;
+  prop:lod 0.08949770136006929 ;
   .
 
 ns:obsD4M251 a qb:Observation ;
@@ -1123,7 +1123,7 @@ ns:obsD4M251 a qb:Observation ;
   prop:refRow <code/refrow/D4M251> ;
   prop:chr 4 ;
   prop:pos 68.10315769609147 ;
-  prop:lod 1.1744313367512351 ;
+  prop:lod 1.1744313367512866 ;
   .
 
 ns:obsD5M148 a qb:Observation ;
@@ -1186,7 +1186,7 @@ ns:obsD5M205 a qb:Observation ;
   prop:refRow <code/refrow/D5M205> ;
   prop:chr 5 ;
   prop:pos 30.896651923893483 ;
-  prop:lod 5.72843784026729 ;
+  prop:lod 5.72843784026734 ;
   .
 
 ns:obsD5M398 a qb:Observation ;
@@ -1195,7 +1195,7 @@ ns:obsD5M398 a qb:Observation ;
   prop:refRow <code/refrow/D5M398> ;
   prop:chr 5 ;
   prop:pos 30.897651923893616 ;
-  prop:lod 3.180821290624097 ;
+  prop:lod 3.1808212906241233 ;
   .
 
 ns:obsD5M91 a qb:Observation ;
@@ -1258,7 +1258,7 @@ ns:obsD6M188 a qb:Observation ;
   prop:refRow <code/refrow/D6M188> ;
   prop:chr 6 ;
   prop:pos 18.187535696625936 ;
-  prop:lod 1.296092065769776 ;
+  prop:lod 1.296092065769738 ;
   .
 
 ns:obsD6M284 a qb:Observation ;
@@ -1294,7 +1294,7 @@ ns:obsD6M194 a qb:Observation ;
   prop:refRow <code/refrow/D6M194> ;
   prop:chr 6 ;
   prop:pos 45.14579226981843 ;
-  prop:lod 1.4515021912783288 ;
+  prop:lod 1.4515021912782906 ;
   .
 
 ns:obsD6M290 a qb:Observation ;
@@ -1330,7 +1330,7 @@ ns:obsD6M59_ a qb:Observation ;
   prop:refRow <code/refrow/D6M59_> ;
   prop:chr 6 ;
   prop:pos 55.304776117994045 ;
-  prop:lod 2.9298420181331597 ;
+  prop:lod 2.9298420181331215 ;
   .
 
 ns:obsD6M201 a qb:Observation ;
@@ -1429,7 +1429,7 @@ ns:obsD8M339 a qb:Observation ;
   prop:refRow <code/refrow/D8M339> ;
   prop:chr 8 ;
   prop:pos 1.3398698853272393 ;
-  prop:lod 0.5508803120345327 ;
+  prop:lod 0.5508803120345833 ;
   .
 
 ns:obsD8M178 a qb:Observation ;
@@ -1447,7 +1447,7 @@ ns:obsD8M242 a qb:Observation ;
   prop:refRow <code/refrow/D8M242> ;
   prop:chr 8 ;
   prop:pos 27.140658391256373 ;
-  prop:lod 0.018444232219069434 ;
+  prop:lod 0.018444232219031242 ;
   .
 
 ns:obsD8M213 a qb:Observation ;
@@ -1465,7 +1465,7 @@ ns:obsD8M156 a qb:Observation ;
   prop:refRow <code/refrow/D8M156> ;
   prop:chr 8 ;
   prop:pos 50.8636380045854 ;
-  prop:lod 0.02846649364377729 ;
+  prop:lod 0.028466493643733326 ;
   .
 
 ns:obsD9M247 a qb:Observation ;
@@ -1501,7 +1501,7 @@ ns:obsD9M269 a qb:Observation ;
   prop:refRow <code/refrow/D9M269> ;
   prop:chr 9 ;
   prop:pos 27.324165906766122 ;
-  prop:lod 0.6881242583427829 ;
+  prop:lod 0.6881242583427478 ;
   .
 
 ns:obsD9M346 a qb:Observation ;
@@ -1510,7 +1510,7 @@ ns:obsD9M346 a qb:Observation ;
   prop:refRow <code/refrow/D9M346> ;
   prop:chr 9 ;
   prop:pos 32.95643946351727 ;
-  prop:lod 0.37223400725767464 ;
+  prop:lod 0.372234007257759 ;
   .
 
 ns:obsD9M55 a qb:Observation ;
@@ -1519,7 +1519,7 @@ ns:obsD9M55 a qb:Observation ;
   prop:refRow <code/refrow/D9M55> ;
   prop:chr 9 ;
   prop:pos 45.335668616330956 ;
-  prop:lod 0.48324303581163264 ;
+  prop:lod 0.48324303581159445 ;
   .
 
 ns:obsD9M18 a qb:Observation ;
@@ -1528,7 +1528,7 @@ ns:obsD9M18 a qb:Observation ;
   prop:refRow <code/refrow/D9M18> ;
   prop:chr 9 ;
   prop:pos 52.504037355687565 ;
-  prop:lod 0.2559094007707392 ;
+  prop:lod 0.255909400770701 ;
   .
 
 ns:obsD10M298 a qb:Observation ;
@@ -1546,7 +1546,7 @@ ns:obsD10M294 a qb:Observation ;
   prop:refRow <code/refrow/D10M294> ;
   prop:chr 10 ;
   prop:pos 24.747450377130114 ;
-  prop:lod 0.7596876212377977 ;
+  prop:lod 0.7596876212377595 ;
   .
 
 ns:obsD10M42_ a qb:Observation ;
@@ -1582,7 +1582,7 @@ ns:obsD11M78 a qb:Observation ;
   prop:refRow <code/refrow/D11M78> ;
   prop:chr 11 ;
   prop:pos 0.0 ;
-  prop:lod 0.18398849359838465 ;
+  prop:lod 0.18398849359834646 ;
   .
 
 ns:obsD11M20 a qb:Observation ;
@@ -1636,7 +1636,7 @@ ns:obsD12M105 a qb:Observation ;
   prop:refRow <code/refrow/D12M105> ;
   prop:chr 12 ;
   prop:pos 0.0 ;
-  prop:lod 0.6422735562058088 ;
+  prop:lod 0.6422735562057706 ;
   .
 
 ns:obsD12M46 a qb:Observation ;
@@ -1672,7 +1672,7 @@ ns:obsD12M99 a qb:Observation ;
   prop:refRow <code/refrow/D12M99> ;
   prop:chr 12 ;
   prop:pos 41.79568874486233 ;
-  prop:lod 1.1794642920048428 ;
+  prop:lod 1.1794642920048046 ;
   .
 
 ns:obsD12M150 a qb:Observation ;
@@ -1816,7 +1816,7 @@ ns:obsD14M265 a qb:Observation ;
   prop:refRow <code/refrow/D14M265> ;
   prop:chr 14 ;
   prop:pos 32.786788153054445 ;
-  prop:lod 0.05689288973059092 ;
+  prop:lod 0.05689288973064066 ;
   .
 
 ns:obsD14M266 a qb:Observation ;
@@ -1825,7 +1825,7 @@ ns:obsD14M266 a qb:Observation ;
   prop:refRow <code/refrow/D14M266> ;
   prop:chr 14 ;
   prop:pos 45.55021769882338 ;
-  prop:lod 0.07253305417930189 ;
+  prop:lod 0.0725330541792637 ;
   .
 
 ns:obsD15M226 a qb:Observation ;
@@ -1906,7 +1906,7 @@ ns:obsD16M154 a qb:Observation ;
   prop:refRow <code/refrow/D16M154> ;
   prop:chr 16 ;
   prop:pos 0.0 ;
-  prop:lod 0.540067799954115 ;
+  prop:lod 0.5400677999540768 ;
   .
 
 ns:obsD16M4 a qb:Observation ;
@@ -1933,7 +1933,7 @@ ns:obsD16M86 a qb:Observation ;
   prop:refRow <code/refrow/D16M86> ;
   prop:chr 16 ;
   prop:pos 41.79901031770399 ;
-  prop:lod 0.7981309541993991 ;
+  prop:lod 0.7981309541993609 ;
   .
 
 ns:obsD17M260 a qb:Observation ;
@@ -1942,7 +1942,7 @@ ns:obsD17M260 a qb:Observation ;
   prop:refRow <code/refrow/D17M260> ;
   prop:chr 17 ;
   prop:pos 0.0 ;
-  prop:lod 0.1818872799948723 ;
+  prop:lod 0.18188727999483412 ;
   .
 
 ns:obsD17M66 a qb:Observation ;
@@ -1951,7 +1951,7 @@ ns:obsD17M66 a qb:Observation ;
   prop:refRow <code/refrow/D17M66> ;
   prop:chr 17 ;
   prop:pos 11.728225830166531 ;
-  prop:lod 0.41891147924973726 ;
+  prop:lod 0.41891147924969907 ;
   .
 
 ns:obsD17M88 a qb:Observation ;
@@ -1978,7 +1978,7 @@ ns:obsD18M94 a qb:Observation ;
   prop:refRow <code/refrow/D18M94> ;
   prop:chr 18 ;
   prop:pos 0.0 ;
-  prop:lod 1.2303365279615814 ;
+  prop:lod 1.230336527961505 ;
   .
 
 ns:obsD18M58 a qb:Observation ;
@@ -2014,7 +2014,7 @@ ns:obsD19M68 a qb:Observation ;
   prop:refRow <code/refrow/D19M68> ;
   prop:chr 19 ;
   prop:pos 0.0 ;
-  prop:lod 0.3769326271704294 ;
+  prop:lod 0.37693262717035303 ;
   .
 
 ns:obsD19M117 a qb:Observation ;
@@ -2032,7 +2032,7 @@ ns:obsD19M65 a qb:Observation ;
   prop:refRow <code/refrow/D19M65> ;
   prop:chr 19 ;
   prop:pos 32.82934898998137 ;
-  prop:lod 0.0073635980130237755 ;
+  prop:lod 0.007363598013061079 ;
   .
 
 ns:obsD19M10 a qb:Observation ;

data/spec/turtle/weather

@@ -1,13 +1,13 @@
-@base <http://www.rqtl.org/ns/dc/> .
-@prefix ns:    <http://www.rqtl.org/ns/dataset/weather/> .
+@base <http://onto.strinz.me/dc/dataset/weather/> .
+@prefix ns:    <http://onto.strinz.me/dc/dataset/weather/> .
 @prefix qb:    <http://purl.org/linked-data/cube#> .
 @prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
 @prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
-@prefix prop:  <http://www.rqtl.org/dc/properties/> .
+@prefix prop:  <http://onto.strinz.me/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://www.rqtl.org/dc/dataset/weather/cs/> .
-@prefix code:  <http://www.rqtl.org/dc/dataset/weather/code/> .
+@prefix cs:    <http://onto.strinz.me/dc/dataset/weather/cs/> .
+@prefix code:  <http://onto.strinz.me/dc/dataset/weather/code/> .
 @prefix owl:   <http://www.w3.org/2002/07/owl#> .
 @prefix skos:  <http://www.w3.org/2004/02/skos/core#> .
 @prefix foaf:     <http://xmlns.com/foaf/0.1/> .
@@ -26,23 +26,23 @@ ns:dataset-weather a qb:DataSet ;
   qb:structure ns:dsd-weather .
 
 cs:outlook a qb:ComponentSpecification ;
-  rdfs:label "outlook Component" ;
+  rdfs:label "outlook" ;
   qb:dimension prop:outlook .
 
 cs:play a qb:ComponentSpecification ;
-  rdfs:label "play Component" ;
+  rdfs:label "play" ;
   qb:dimension prop:play .
 
 cs:windy a qb:ComponentSpecification ;
-  rdfs:label "windy Component" ;
+  rdfs:label "windy" ;
   qb:dimension prop:windy .
 
 cs:humidity a qb:ComponentSpecification ;
-  rdfs:label "humidity Component" ;
+  rdfs:label "humidity" ;
   qb:measure prop:humidity .
 
 cs:temperature a qb:ComponentSpecification ;
-  rdfs:label "temperature Component" ;
+  rdfs:label "temperature" ;
   qb:measure prop:temperature .
 
 prop:outlook a rdf:Property, qb:DimensionProperty ;

data/spec/writer_spec.rb

@@ -37,12 +37,26 @@ describe PubliSci::Writers do
     out.should == IO.read('resources/weather.numeric.arff').gsub(/%.*\n/,'')
   end
 
+  it "can output JSON from turtle string" do
+    writer = PubliSci::Writers::JSON.new
+    out = writer.from_turtle('spec/turtle/weather')
+    JSON.parse(out).size.should > 0
+  end
+
+  it "can output JSON from a store" do
+    writer = PubliSci::Writers::JSON.new
+    repo = RDF::Repository.load('spec/turtle/weather')
+    out = writer.from_store(repo)
+    # minor hack since metadata isn't the same
+    JSON.parse(out).size.should > 0
+  end
+
   context "can restrict to a particular dataset" do
     it "for arff" do
       writer = PubliSci::Writers::ARFF.new
       repo = RDF::Repository.load('spec/turtle/weather')
       repo.load('spec/turtle/bacon')
-      out = writer.from_store(repo, 'http://www.rqtl.org/ns/dataset/weather/dataset-weather','weather')
+      out = writer.from_store(repo, 'http://onto.strinz.me/dc/dataset/weather/dataset-weather','weather')
 
       out = out.gsub(/%.*\n/,'')
 
@@ -53,7 +67,7 @@ describe PubliSci::Writers do
       writer = PubliSci::Writers::CSV.new
       repo = RDF::Repository.load('spec/turtle/reference')
       repo.load('spec/turtle/bacon')
-      out = writer.from_store(repo,'http://www.rqtl.org/ns/dataset/bacon/dataset-bacon')
+      out = writer.from_store(repo,'http://onto.strinz.me/dc/dataset/bacon/dataset-bacon')
 
       out.should == IO.read('spec/csv/bacon.csv')
     end