publisci 0.1.5 → 0.1.6

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -8,7 +8,7 @@ source "http://rubygems.org"
 group :development do
   gem "rspec", "~> 2.8.0"
   gem "cucumber", ">= 0"
-  gem "jeweler", "~> 1.8.4", :git => "https://github.com/technicalpickles/jeweler.git"
+  gem "jeweler"
   gem "bundler", ">= 1.0.21"
   gem "bio", ">= 1.4.2"
   gem "rdoc"
@@ -26,4 +26,4 @@ gem 'json-ld'
 gem 'rserve-client'
 gem 'sparql'
 
-gem "spira", git: "https://github.com/ruby-rdf/spira.git"
+gem "spira", git: "https://github.com/ruby-rdf/spira.git"

data/README.md

@@ -2,8 +2,6 @@
 
 [![Build Status](https://travis-ci.org/wstrinz/publisci.png?branch=master)](https://travis-ci.org/wstrinz/publisci)
 
-Note: this software is under active development! Until it hits v 1.0.0, the overall API and usage pattern is subject to change.
-
 ## Installation
 
 ```sh

data/README.rdoc

@@ -12,6 +12,43 @@ Note: this software is under active development!
 
 == Usage
 
+Most of the gem's functions can be accessed through its DSL
+
+        require 'publisci'
+        include PubliSci::DSL
+        
+        # Specify input data
+        data do
+          # use local or remote paths
+          source 'https://github.com/wstrinz/publisci/raw/master/spec/csv/bacon.csv'
+        
+          # specify datacube properties
+          dimension 'producer', 'pricerange'
+          measure 'chunkiness'
+        
+          # set parser specific options
+          option 'label_column', 'producer'
+        end
+        
+        # Describe dataset
+        metadata do
+          dataset 'bacon'
+          title 'Bacon dataset'
+          creator 'Will Strinz'
+          description 'some data about bacon'
+          date '1-10-2010'
+        end
+        
+        # Send output to an RDF::Repository
+        #  can also use 'generate_n3' to output a turtle string
+        repo = to_repository
+        
+        # run SPARQL queries on the dataset
+        PubliSci::QueryHelper.execute('select * where {?s ?p ?o} limit 5', repo)
+        
+        # export in other formats
+        PubliSci::Writers::ARFF.new.from_store(repo)
+
 == Developers
 
 To use the library

data/Rakefile

@@ -21,7 +21,7 @@ Jeweler::Tasks.new do |gem|
   gem.description = %Q{A toolkit for publishing scientific results and datasets using RDF, OWL, and related technologies }
   gem.email = "wstrinz@gmail.com"
   gem.authors = ["Will Strinz"]
-  gem.version = "0.1.5"
+  gem.version = "0.1.6"
 
 end
 Jeweler::RubygemsDotOrgTasks.new

data/examples/dsl.rb

@@ -0,0 +1,43 @@
+require 'publisci'
+include PubliSci::DSL
+
+# Specify input data
+# Not that every statement in the datablock is essentially declarative;
+#  since the generator won't be run until the end of the block, you can
+#  specify input parameters in any order.
+
+data do
+  # use local or remote paths
+  # The gem will determine which transformer to use for your input data based
+  # on the file's extension
+  source 'https://github.com/wstrinz/publisci/raw/master/spec/csv/bacon.csv'
+
+  # specify datacube properties
+  # see http://www.w3.org/TR/vocab-data-cube/#cubes-model
+  dimension 'producer', 'pricerange'
+  measure 'chunkiness'
+
+  # set transformer options
+  # These will generally be parameters relevant only to a certain input type
+  # In this case, we're using the "producer" column to label each operation.
+  option 'label_column', 'producer'
+end
+
+# Describe dataset
+metadata do
+  dataset 'bacon'
+  title 'Bacon dataset'
+  creator 'Will Strinz'
+  description 'some data about bacon'
+  date '1-10-2010'
+end
+
+# Send output to an RDF::Repository
+#  can also use 'generate_n3' to output a turtle string
+repo = to_repository
+
+# run SPARQL queries on the dataset
+PubliSci::QueryHelper.execute('select * where {?s ?p ?o} limit 5', repo)
+
+# export in other formats
+PubliSci::Writers::ARFF.new.from_store(repo)

data/lib/publisci/datacube_model.rb

@@ -46,8 +46,8 @@ begin
         property :dataset, predicate: QB.dataSet
 
         def load_properties
-          comps = dataset.as(DataSet).structure.as(DataStructureDefinition).component.map{|comp| comp.as(Component)}
-          props = comps.map{|comp| comp.dimension ? comp.dimension.as(Dimension) : comp.measure.as(Measure) }
+          comps = RDF::URI(RDF::URI(dataset).as(DataSet).structure).as(DataStructureDefinition).component.map{|comp| RDF::URI(comp).as(Component)}
+          props = comps.map{|comp| comp.dimension ? RDF::URI(comp.dimension).as(Dimension) : RDF::URI(comp.measure).as(Measure) }
           props.each{|prop|
             ss =  strip_uri(prop.subject.to_s)
 

data/lib/publisci/dataset/data_cube.rb

@@ -13,7 +13,7 @@ module PubliSci
       {
         type: :dataframe,
         encode_nulls: false,
-        base_url: "http://onto.strinz.me",
+        base_url: "http://example.org",
       }
       end
 

data/lib/publisci/metadata/prov/model/prov_models.rb

@@ -62,9 +62,10 @@ module PubliSci
 
         def activities
           #should do this in a SPARQL query instead
+          #
           Activity.enum_for.map{|act|
             subj = subject()
-            act if act.wasAssociatedWith.any?{|assoc| assoc == subj}
+            act if act.wasAssociatedWith.any?{|assoc| RDF::URI(assoc) == subj}
           }.reject{|x| x==nil}
         end
       end
@@ -106,4 +107,4 @@ module PubliSci
 end
 rescue LoadError
   # puts "spira not installed, ORM unavailable"
-end
+end

data/lib/publisci/readers/csv.rb

@@ -1,6 +1,6 @@
 module PubliSci
-	module Readers
-		class CSV
+  module Readers
+    class CSV
       include Base
       def automatic(file=nil,dataset_name=nil,options={},interactive=true)
         #to do
@@ -39,51 +39,51 @@ module PubliSci
         generate_n3(file,dataset_name,options)
       end
 
-			def generate_n3(file, dataset_name, options={})
-				@data = ::CSV.read(file)
-				@options = options
-				generate(measures, dimensions, codes, observation_data, observation_labels, dataset_name, options)
-			end
-
-			def dimensions
-				@options[:dimensions] || [@data[0][0]]
-			end
-
-			def codes
-				@options[:codes] || dimensions()
-			end
-
-			def measures
-				@options[:measures] || @data[0] - dimensions()
-			end
-
-			def observation_labels
-				if @options[:label_column]
-					tmp = @data.dup
-					tmp.shift
-					tmp.map{|row|
-						row[@options[:label_column]]
-					}
-				else
-					(1..@data.size - 1).to_a
-				end
-			end
-
-			def observation_data
-				obs = {}
-				@data[0].map{|label|
-					obs[label] = []
-				}
-				tmp = @data.dup
-				tmp.shift
-
-				tmp.map{|row|
-					row.each_with_index{|entry,i|
-						obs[@data[0][i]] << entry
-					}
-				}
-				obs
-			end
-		end
-	end
-end
+      def generate_n3(file, dataset_name, options={})
+        @data = ::CSV.read(file)
+        @options = options
+        generate(measures, dimensions, codes, observation_data, observation_labels, dataset_name, options)
+      end
+
+      def dimensions
+        @options[:dimensions] || [@data[0][0]]
+      end
+
+      def codes
+        @options[:codes] || dimensions()
+      end
+
+      def measures
+        @options[:measures] || @data[0] - dimensions()
+      end
+
+      def observation_labels
+        if @options[:label_column]
+          tmp = @data.dup
+          tmp.shift
+          tmp.map{|row|
+            row[@options[:label_column]]
+          }
+        else
+          (1..@data.size - 1).to_a
+        end
+      end
+
+      def observation_data
+        obs = {}
+        @data[0].map{|label|
+          obs[label] = []
+        }
+        tmp = @data.dup
+        tmp.shift
+
+        tmp.map{|row|
+          row.each_with_index{|entry,i|
+            obs[@data[0][i]] << entry
+          }
+        }
+        obs
+      end
+    end
+  end
+end

data/resources/maf_rdf.ttl

@@ -1,20 +1,20 @@
-@base <http://onto.strinz.me/dc/dataset/MAF_ah1iit/> .
-@prefix ns:    <http://onto.strinz.me/dc/dataset/MAF_ah1iit/> .
+@base <http://example.org/dc/dataset/MAF_h94778/> .
+@prefix ns:    <http://example.org/dc/dataset/MAF_h94778/> .
 @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://onto.strinz.me/properties/> .
+@prefix prop:  <http://example.org/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://onto.strinz.me/dc/dataset/MAF_ah1iit/cs/> .
-@prefix code:  <http://onto.strinz.me/dc/dataset/MAF_ah1iit/code/> .
+@prefix cs:    <http://example.org/dc/dataset/MAF_h94778/cs/> .
+@prefix code:  <http://example.org/dc/dataset/MAF_h94778/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/> .
 @prefix org:      <http://www.w3.org/ns/org#> .
 @prefix prov:     <http://www.w3.org/ns/prov#> .
 
-ns:dsd-MAF_ah1iit a qb:DataStructureDefinition;
+ns:dsd-MAF_h94778 a qb:DataStructureDefinition;
   qb:component cs:Variant_Classification ;
   qb:component cs:Variant_Type ;
   qb:component cs:dbSNP_Val_Status ;
@@ -52,9 +52,9 @@ ns:dsd-MAF_ah1iit a qb:DataStructureDefinition;
   qb:component cs:patient_id ;
   qb:component cs:sample_id .
 
-ns:dataset-MAF_ah1iit a qb:DataSet ;
-  rdfs:label "MAF_ah1iit"@en ;
-  qb:structure ns:dsd-MAF_ah1iit .
+ns:dataset-MAF_h94778 a qb:DataSet ;
+  rdfs:label "MAF_h94778"@en ;
+  qb:structure ns:dsd-MAF_h94778 .
 
 cs:Variant_Classification a qb:ComponentSpecification ;
   rdfs:label "Variant_Classification" ;
@@ -951,7 +951,7 @@ code:sequencer a skos:ConceptScheme;
   skos:inScheme code:sequencer .
 
 ns:obs2 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
@@ -986,7 +986,7 @@ ns:obs2 a qb:Observation ;
   .
 
 ns:obs3 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/byFrequency> ;
@@ -1021,7 +1021,7 @@ ns:obs3 a qb:Observation ;
   .
 
 ns:obs4 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
@@ -1057,7 +1057,7 @@ ns:obs4 a qb:Observation ;
   .
 
 ns:obs5 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Silent> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
@@ -1093,7 +1093,7 @@ ns:obs5 a qb:Observation ;
   .
 
 ns:obs6 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Silent> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
@@ -1128,7 +1128,7 @@ ns:obs6 a qb:Observation ;
   .
 
 ns:obs7 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Missense_Mutation> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
@@ -1168,7 +1168,7 @@ ns:obs7 a qb:Observation ;
   .
 
 ns:obs8 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Silent> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;
@@ -1208,7 +1208,7 @@ ns:obs8 a qb:Observation ;
   .
 
 ns:obs9 a qb:Observation ;
-  qb:dataSet ns:dataset-MAF_ah1iit ;
+  qb:dataSet ns:dataset-MAF_h94778 ;
   prop:Variant_Classification <code/variant_classification/Nonsense_Mutation> ;
   prop:Variant_Type <code/variant_type/SNP> ;
   prop:dbSNP_Val_Status <code/dbsnp_val_status/> ;

data/resources/queries/gene.rq

@@ -8,9 +8,9 @@ SELECT DISTINCT ?gene WHERE {
 
   ?patient_obs a qb:Observation;
     ?barcode_measure ?barcode;
-    <http://onto.strinz.me/properties/patient_id> "%{patient}";
-    <http://onto.strinz.me/properties/Hugo_Symbol> ?gene.
+    <http://example.org/properties/patient_id> "%{patient}";
+    <http://example.org/properties/Hugo_Symbol> ?gene.
 
 
   #  ?node <http://semanticscience.org/resource/SIO_000300> ?gene ;  
-}
+}

data/spec/ORM/prov_model_spec.rb

@@ -69,4 +69,4 @@ describe PubliSci::Prov::Model do
       PubliSci::Prov::Model::Entity.first.has_data?.should == true
     end
   end
-end
+end

data/spec/dsl_spec.rb

@@ -36,7 +36,7 @@ describe PubliSci::DSL do
         qry = <<-EOF
         SELECT ?observation where {
           ?observation a <http://purl.org/linked-data/cube#Observation>;
-            <http://onto.strinz.me/properties/Hugo_Symbol> ?node.
+            <http://example.org/properties/Hugo_Symbol> ?node.
 
         }
 
@@ -141,4 +141,4 @@ describe PubliSci::DSL do
     repo.is_a?(RDF::FourStore::Repository).should be true
     repo.size.should > old_size
   end
-end
+end

data/spec/generators/csv_spec.rb

@@ -35,10 +35,10 @@ describe PubliSci::Readers::CSV do
 
 		dims = RDF::Query.execute(graph){ pattern [:dataset, qb.dimension, :dimension] }
 		dims.size.should == 1
-		dims.first[:dimension].to_s.should == "http://onto.strinz.me/properties/producer"
+		dims.first[:dimension].to_s.should == "http://example.org/properties/producer"
 
 		measures = RDF::Query.execute(graph){ pattern [:dataset, qb.measure, :measure] }
 		measures.map{|s| s[:measure].to_s.split('/').last}.should == ["pricerange", "chunkiness", "deliciousness"]
 	end
 
-end
+end

data/spec/maf_query_spec.rb

@@ -4,9 +4,9 @@ require_relative '../lib/publisci.rb'
 
 class MafQuery
   RESTRICTIONS = {
-    patient: '<http://onto.strinz.me/properties/patient_id>',
-    sample: '<http://onto.strinz.me/properties/sample_id>',
-    gene: '<http://onto.strinz.me/properties/Hugo_Symbol>',
+    patient: '<http://example.org/properties/patient_id>',
+    sample: '<http://example.org/properties/sample_id>',
+    gene: '<http://example.org/properties/Hugo_Symbol>',
   }
 
     def to_por(solution)
@@ -78,7 +78,7 @@ class MafQuery
       property = Array(property)
       selects = property
       property = property.map{|prop|
-        RESTRICTIONS[prop.to_sym] || "<http://onto.strinz.me/properties/#{prop}>"
+        RESTRICTIONS[prop.to_sym] || "<http://example.org/properties/#{prop}>"
       }
 
       targets = ""
@@ -88,7 +88,7 @@ class MafQuery
 
       str = ""
       restrictions.each{|restrict,value|
-        prop = RESTRICTIONS[restrict.to_sym] || "<http://onto.strinz.me/properties/#{restrict}>"
+        prop = RESTRICTIONS[restrict.to_sym] || "<http://example.org/properties/#{restrict}>"
         if value.is_a? String
           if RDF::Resource(value).valid?
             if(value[/http:\/\//])
@@ -191,10 +191,6 @@ class MafQuery
       end
     end
 
-    def derive_gene_lengths
-
-    end
-
     def patient_info(id,repo)
       symbols = Array(to_por(select_property(repo,"Hugo_Symbol",patient: id)))
       # patient_id = select_property(repo,"patient_id",patient: id).to_s
@@ -337,7 +333,10 @@ describe QueryScript do
       it { @ev.instance_eval("select 'patient_count', patient: 'BH-A0HP'").should > 0 }
       it { @ev.instance_eval("select 'Hugo_Symbol', patient: 'BH-A0HP'").should == 'http://identifiers.org/hgnc.symbol/A1CF' }
       it { @ev.instance_eval("select 'Chromosome', patient: 'BH-A0HP'").is_a?(Fixnum).should be true }
-      it { @ev.instance_eval("report_for 'patient', 'BH-A0HP'").is_a?(Hash).should be true }
+      it { 
+        pending("bio2rdf vocabulary changed")
+        #@ev.instance_eval("report_for 'patient', 'BH-A0HP'").is_a?(Hash).should be true 
+      }
     end
   end
-end
+end

data/spec/turtle/bacon

@@ -1,13 +1,13 @@
-@base <http://onto.strinz.me/dc/dataset/bacon/> .
-@prefix ns:    <http://onto.strinz.me/dc/dataset/bacon/> .
+@base <http://example.org/dc/dataset/bacon/> .
+@prefix ns:    <http://example.org/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://onto.strinz.me/properties/> .
+@prefix prop:  <http://example.org/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://onto.strinz.me/dc/dataset/bacon/cs/> .
-@prefix code:  <http://onto.strinz.me/dc/dataset/bacon/code/> .
+@prefix cs:    <http://example.org/dc/dataset/bacon/cs/> .
+@prefix code:  <http://example.org/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/> .

data/spec/turtle/reference

@@ -1,13 +1,13 @@
-@base <http://onto.strinz.me/dc/dataset/mr/> .
-@prefix ns:    <http://onto.strinz.me/dc/dataset/mr/> .
+@base <http://example.org/dc/dataset/mr/> .
+@prefix ns:    <http://example.org/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://onto.strinz.me/properties/> .
+@prefix prop:  <http://example.org/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://onto.strinz.me/dc/dataset/mr/cs/> .
-@prefix code:  <http://onto.strinz.me/dc/dataset/mr/code/> .
+@prefix cs:    <http://example.org/dc/dataset/mr/cs/> .
+@prefix code:  <http://example.org/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/> .
@@ -898,7 +898,7 @@ ns:obsD1M215 a qb:Observation ;
   prop:refRow <code/refrow/D1M215> ;
   prop:chr 1 ;
   prop:pos 40.41360872065924 ;
-  prop:lod 0.07012015768922852 ;
+  prop:lod 0.07012015768917834 ;
   .
 
 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 2.072608394873848 ;
+  prop:lod 2.0726083948737966 ;
   .
 
 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 1.077029280756939 ;
+  prop:lod 1.0770292807569852 ;
   .
 
 ns:obsD1M155 a qb:Observation ;
@@ -979,7 +979,7 @@ ns:obsD1M155 a qb:Observation ;
   prop:refRow <code/refrow/D1M155> ;
   prop:chr 1 ;
   prop:pos 93.64343584009433 ;
-  prop:lod 1.1873613330194863 ;
+  prop:lod 1.187361333019437 ;
   .
 
 ns:obsD2M365 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 0.4537402388347749 ;
+  prop:lod 0.45374023883481307 ;
   .
 
 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 0.5681404735364763 ;
+  prop:lod 0.5681404735365145 ;
   .
 
 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 0.24331723281211204 ;
+  prop:lod 0.24331723281215023 ;
   .
 
 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 0.08949770136006929 ;
+  prop:lod 0.08949770136010748 ;
   .
 
 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 1.1744313367512866 ;
+  prop:lod 1.1744313367512351 ;
   .
 
 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 5.72843784026734 ;
+  prop:lod 5.72843784026729 ;
   .
 
 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 3.1808212906241233 ;
+  prop:lod 3.180821290624097 ;
   .
 
 ns:obsD5M91 a qb:Observation ;
@@ -1222,7 +1222,7 @@ ns:obsD5M188 a qb:Observation ;
   prop:refRow <code/refrow/D5M188> ;
   prop:chr 5 ;
   prop:pos 44.02376273652883 ;
-  prop:lod 3.249708646147218 ;
+  prop:lod 3.249708646147167 ;
   .
 
 ns:obsD5M29 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 1.296092065769738 ;
+  prop:lod 1.296092065769776 ;
   .
 
 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 1.4515021912782906 ;
+  prop:lod 1.4515021912783288 ;
   .
 
 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 2.9298420181331215 ;
+  prop:lod 2.9298420181331597 ;
   .
 
 ns:obsD6M201 a qb:Observation ;
@@ -1411,7 +1411,7 @@ ns:obsD7M259 a qb:Observation ;
   prop:refRow <code/refrow/D7M259> ;
   prop:chr 7 ;
   prop:pos 72.084242243197 ;
-  prop:lod 0.10483451594920368 ;
+  prop:lod 0.10483451594923476 ;
   .
 
 ns:obsD8M94 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 0.5508803120345833 ;
+  prop:lod 0.5508803120345327 ;
   .
 
 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 0.018444232219031242 ;
+  prop:lod 0.018444232219069434 ;
   .
 
 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 0.028466493643733326 ;
+  prop:lod 0.02846649364377729 ;
   .
 
 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 0.6881242583427478 ;
+  prop:lod 0.6881242583427829 ;
   .
 
 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 0.372234007257759 ;
+  prop:lod 0.3722340072577168 ;
   .
 
 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 0.48324303581159445 ;
+  prop:lod 0.48324303581163264 ;
   .
 
 ns:obsD9M18 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 0.7596876212377595 ;
+  prop:lod 0.7596876212377977 ;
   .
 
 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 0.18398849359834646 ;
+  prop:lod 0.18398849359838465 ;
   .
 
 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 0.6422735562057706 ;
+  prop:lod 0.6422735562058088 ;
   .
 
 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 1.1794642920048046 ;
+  prop:lod 1.1794642920048428 ;
   .
 
 ns:obsD12M150 a qb:Observation ;
@@ -1708,7 +1708,7 @@ ns:obsD13M21 a qb:Observation ;
   prop:refRow <code/refrow/D13M21> ;
   prop:chr 13 ;
   prop:pos 10.365882919967524 ;
-  prop:lod 2.8121111806924652 ;
+  prop:lod 2.812111180692509 ;
   .
 
 ns:obsD13M39 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 0.0725330541792637 ;
+  prop:lod 0.07253305417930189 ;
   .
 
 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 0.5400677999540768 ;
+  prop:lod 0.540067799954115 ;
   .
 
 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 0.7981309541993609 ;
+  prop:lod 0.7981309541993991 ;
   .
 
 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 0.18188727999483412 ;
+  prop:lod 0.1818872799948723 ;
   .
 
 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 0.41891147924969907 ;
+  prop:lod 0.41891147924973726 ;
   .
 
 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 1.230336527961505 ;
+  prop:lod 1.2303365279615814 ;
   .
 
 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 0.37693262717035303 ;
+  prop:lod 0.3769326271704294 ;
   .
 
 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 0.007363598013061079 ;
+  prop:lod 0.0073635980130237755 ;
   .
 
 ns:obsD19M10 a qb:Observation ;

data/spec/turtle/weather

@@ -1,13 +1,13 @@
-@base <http://onto.strinz.me/dc/dataset/weather/> .
-@prefix ns:    <http://onto.strinz.me/dc/dataset/weather/> .
+@base <http://example.org/dc/dataset/weather/> .
+@prefix ns:    <http://example.org/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://onto.strinz.me/properties/> .
+@prefix prop:  <http://example.org/properties/> .
 @prefix dct:   <http://purl.org/dc/terms/> .
 @prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
-@prefix cs:    <http://onto.strinz.me/dc/dataset/weather/cs/> .
-@prefix code:  <http://onto.strinz.me/dc/dataset/weather/code/> .
+@prefix cs:    <http://example.org/dc/dataset/weather/cs/> .
+@prefix code:  <http://example.org/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/> .

data/spec/writer_spec.rb

@@ -58,7 +58,7 @@ describe PubliSci::Writers do
       writer = PubliSci::Writers::ARFF.new
       repo = RDF::Repository.load('spec/turtle/weather')
       repo.load('spec/turtle/bacon')
-      out = writer.from_store(repo, 'http://onto.strinz.me/dc/dataset/weather/dataset-weather','weather')
+      out = writer.from_store(repo, 'http://example.org/dc/dataset/weather/dataset-weather','weather')
 
       out = out.gsub(/%.*\n/,'')
 
@@ -69,9 +69,9 @@ 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://onto.strinz.me/dc/dataset/bacon/dataset-bacon')
+      out = writer.from_store(repo,'http://example.org/dc/dataset/bacon/dataset-bacon')
 
       out.should == IO.read('spec/csv/bacon.csv')
     end
   end
-end
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: publisci
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.1.6
 platform: ruby
 authors:
 - Will Strinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-11-09 00:00:00.000000000 Z
+date: 2014-06-10 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -168,16 +168,16 @@ dependencies:
   name: jeweler
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: 1.8.4
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: bundler
   requirement: !ruby/object:Gem::Requirement
@@ -269,6 +269,7 @@ files:
 - Rakefile
 - bin/publisci
 - examples/bio-band_integration.rb
+- examples/dsl.rb
 - examples/no_magic.prov
 - examples/no_magic.rb
 - examples/orm.prov
@@ -458,7 +459,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.0.3
+rubygems_version: 2.2.2
 signing_key: 
 specification_version: 4
 summary: Publish scientific results to the semantic web