publisci 0.1.3 → 0.1.4

data/spec/ORM/data_cube_orm_spec.rb

@@ -19,7 +19,7 @@ describe PubliSci::ORM do
 
       to_repository
     end
-    Spira.add_repository :default, r
+    Spira.repository = r
 
     PubliSci::ORM::Observation.count.should > 0
 

data/spec/ORM/prov_model_spec.rb

@@ -13,7 +13,7 @@ describe PubliSci::Prov::Model do
       to_repository
     end
 
-    Spira.add_repository :default, r
+    Spira.repository = r
     PubliSci::Prov::Model::Entity.first.should_not be nil
   end
 
@@ -40,7 +40,7 @@ describe PubliSci::Prov::Model do
       #   generate_n3
       # end
 
-      Spira.add_repository :default, r
+      Spira.repository = r
       model_agent = PubliSci::Prov::Model::Agent.first
       ag.subject.should == model_agent.subject
       acts =  model_agent.activities
@@ -64,7 +64,7 @@ describe PubliSci::Prov::Model do
         to_repository
       end
 
-      Spira.add_repository :default, r
+      Spira.repository = r
       PubliSci::Prov::Model::Entity.first.all_types.should == %w{http://www.w3.org/ns/prov#Entity http://purl.org/linked-data/cube#DataSet}
       PubliSci::Prov::Model::Entity.first.has_data?.should == true
     end

data/spec/dataset_for_spec.rb

@@ -29,7 +29,7 @@ describe PubliSci::Dataset do
       PubliSci::Dataset.register_reader('.maf',PubliSci::Readers::MAF)
       file = PubliSci::Dataset.for('resources/maf_example.maf')
       str = IO.read(file)
-      File.delete(file.path)
+      File.delete(file)
       str.size.should > 0
       (str =~ /qb:Observation/).should_not be nil
     end

data/spec/generators/maf_spec.rb

@@ -7,12 +7,13 @@ require 'tempfile'
 
 describe PubliSci::Readers::MAF do
   before(:each) do
-    @generator = PubliSci::Readers::MAF.new
+    @generator = PubliSci::Readers::MAF
     @in_file = 'resources/maf_example.maf'
   end
 
   describe ".generate_n3" do
     def is_cube(str)
+
       str[/a qb:Observation/].should_not be nil
       str[/a rdf:Property, qb:DimensionProperty/].should_not be nil
       str[/a rdf:Property, qb:MeasureProperty/].should_not be nil

data/spec/maf_query_spec.rb

@@ -45,7 +45,7 @@ class MafQuery
     end
 
     def generate_data
-    	generator = PubliSci::Readers::MAF.new
+    	generator = PubliSci::Readers::MAF
     	in_file = 'resources/maf_example.maf'
     	f = Tempfile.new('graph')
     	f.close

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: publisci
 version: !ruby/object:Gem::Version
-  version: 0.1.3
+  version: 0.1.4
 platform: ruby
 authors:
 - Will Strinz
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-10 00:00:00.000000000 Z
+date: 2013-11-09 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rest-client
@@ -150,20 +150,6 @@ dependencies:
     - - ~>
       - !ruby/object:Gem::Version
         version: 2.8.0
-- !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
-  type: :development
-  prerelease: false
-  version_requirements: !ruby/object:Gem::Requirement
-    requirements:
-    - - ~>
-      - !ruby/object:Gem::Version
-        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: cucumber
   requirement: !ruby/object:Gem::Requirement
@@ -224,16 +210,30 @@ dependencies:
   name: rdoc
   requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '0'
   type: :development
   prerelease: false
   version_requirements: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: pry
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 - !ruby/object:Gem::Dependency
   name: spoon
   requirement: !ruby/object:Gem::Requirement
@@ -311,6 +311,8 @@ files:
 - lib/publisci/dsl/dsl.rb
 - lib/publisci/dsl/metadata_dsl.rb
 - lib/publisci/dsl/prov_dsl.rb
+- lib/publisci/generators/base.rb
+- lib/publisci/generators/maf.rb
 - lib/publisci/metadata/generator.rb
 - lib/publisci/metadata/metadata.rb
 - lib/publisci/metadata/metadata_model.rb
@@ -333,6 +335,8 @@ files:
 - lib/publisci/mixins/vocabulary.rb
 - lib/publisci/output.rb
 - lib/publisci/parser.rb
+- lib/publisci/parsers/base.rb
+- lib/publisci/parsers/maf.rb
 - lib/publisci/post_processor.rb
 - lib/publisci/query/query_helper.rb
 - lib/publisci/readers/arff.rb
@@ -347,8 +351,6 @@ files:
 - lib/publisci/writers/base.rb
 - lib/publisci/writers/csv.rb
 - lib/publisci/writers/dataframe.rb
-- lib/r2rdf.rb
-- lib/template_bak.rb
 - lib/template_bak/publisci.rb
 - lib/vocabs/cc.rb
 - lib/vocabs/cert.rb
@@ -438,7 +440,7 @@ files:
 - spec/writer_spec.rb
 homepage: http://github.com/wstrinz/publisci
 licenses:
-- MIT
+- BSD 2-Clause
 metadata: {}
 post_install_message: 
 rdoc_options: []

data/lib/r2rdf.rb

@@ -1,226 +0,0 @@
-require 'rserve'
-require 'rdf/4store'
-Dir[File.dirname(__FILE__) + '/vocabs/*.rb'].each {|file| require file }
-
-class QTL2RDF
-
-  attr_accessor :port_4s
-
-  def initialize(dir='.')
-    @dir = File.absolute_path(dir)
-    @R = Rserve::Connection.new()
-    if File.exist?(dir + "/.RData")
-      # puts "loading workspace #{dir}/.RData"
-      @R.eval("load('#{dir}/.RData')")
-    end
-
-    if File.exist?(dir + "/.Rhistory")
-      # puts "loading history #{dir}/.Rhistory"
-      @R.eval("loadhistory('#{dir}/.Rhistory')")
-    end
-
-    @port_4s = 8080
-  end
-
-  def load_workspace(dir=@dir,file='.RData')
-    path = File.join(File.absolute_path(dir),file)
-      if File.exist?(path)
-        # puts "loading workspace #{dir}/.RData"
-        @R.eval("load('#{path}')")
-      else
-        puts "Couldn't find #{path}"
-      end
-  end
-
-  def load_history(dir=@dir,file='.Rhistory')
-    path = File.join(File.absolute_path(dir),file)
-    if File.exist?(path)
-      # puts "loading history #{dir}/.Rhistory"
-      @R.eval("loadhistory('#{path}')")
-    else
-      puts "Couldn't find #{path}"
-    end
-  end
-
-  def dump_dataframe(var)
-    h = {}
-    h[var] = {"attr" => {}, "rows"=>{}}
-
-    x = @R.eval(var)
-
-    x.attr.payload.keys.map{ |a|
-      h[var]["attr"][a] = x.attr.payload[a].to_ruby
-    }
-
-    rownames = x.attr.payload["row.names"].to_ruby
-    colnames = x.payload.keys
-    rownames.each_with_index.map{ |row,i|
-      rh = {}
-      colnames.map{ |col|
-        rh[col] = x.payload[col].to_a[i].to_f
-      }
-      h[var]["rows"][row] = rh
-    }
-
-    h
-  end
-
-  def dump(var)
-    x = @R.eval(var)
-    if x.attr
-      # if x.attr.payload["class"].to_a.include? 'data.frame'
-        dump_dataframe var
-      # end
-    else
-      if x.list?
-        type = x.payload.class.to_s.split("::").last # seems hacky, but probably only temporary
-        value = x.payload.map(&:payload).flatten
-      elsif x.payload.size == 1
-        type = x.class.to_s.split("::").last 
-        value = x.payload.first
-      else
-        type = x.class.to_s.split("::").last 
-        value = x.payload
-      end
-      {var => {"attr"=>{"class" => type}, :value => value}}
-    end
-  end
-
-  def triples_for(h)
-    statements = []
-    base_n = RDF::Node.new
-    attr_n = RDF::Node.new
-    vocab = RDF::Vocabulary.new('http://www.placeholder.com/rqtl#')
-    base_uri = RDF::URI.new('http://www.placeholder.com/')
-    var = h.keys.first
-
-    statements << RDF::Statement.new(base_n, RDF::DC.title, RDF::Literal.new(var))
-
-    if h[var].is_a? Hash
-      if(h[var]["attr"])
-        statements << RDF::Statement.new(base_n, vocab.attributes, attr_n)
-        h[var]["attr"].map{ |k,v| statements << RDF::Statement.new(attr_n, vocab[k], RDF::Literal.new(v)) }
-      end
-
-      if h[var]["rows"]
-        h[var]["rows"].map{ |k,v|
-          row_uri = base_uri.join("row#{k}")
-          statements << RDF::Statement.new(row_uri, vocab.row_of, base_n)
-          statements << RDF::Statement.new(row_uri, RDF::DC.title, k)
-          num = 1 # maybe container support exists in RDF.rb?
-          v.map { |j,u|
-            n = RDF::Node.new
-            statements << RDF::Statement.new(n, vocab.entry_of, row_uri)
-            statements << RDF::Statement.new(n, RDF::DC.title, j)
-            statements << RDF::Statement.new(n, RDF::DC.title, j)
-            statements << RDF::Statement.new(n, vocab["_#{num}"], RDF::Literal.new(u))
-            num += 1
-          }
-        }
-      end
-
-      if h[var].has_key? :value        
-        statements << RDF::Statement.new(base_n, vocab.has_value, RDF::Literal.new(h[var][:value]))
-      end
-    else
-      statements << RDF::Statement.new(base_n, vocab.has_value, RDF::Literal.new(h[var]))
-    end
-    statements
-  end
-
-  #get n3 for a dataframe using datacube vocabulary
-  #still needs range for measures and dimensions, sdmx-dimension equivalent for rows
-  def n3_for(h)
-    str = <<-EOF
-@prefix : <http://www.rqtl.org/ns/#> .
-@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 cs: <http://www.rqtl.org/dc/cs/> .
-
-    EOF
-    #@prefix sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#>
-    var = h.keys.first
-    names = h[var]["attr"]["names"]
-
-    #generate data structure definition
-    str << ":dsd-#{var} a qb:DataStructureDefinition ;\n"
-    str << "\tqb:component cs:refRow ,\n"
-    names.map{ |n|
-      str << "\t\tcs:#{n} ,\n\n"
-    }
-    str[-3]="."
-
-    #generate component specifications
-    str << "cs:refRow a qb:ComponentSpecification ;\n\trdfs:label \"Component Specification for Row\" ;\n\tqb:dimension prop:refRow .\n\n"
-    names.map{ |n|
-      str << "cs:#{n} a qb:ComponentSpecification ;\n\trdfs:label \"Component Specification for #{n}\" ;\n\tqb:measure prop:#{n} .\n\n"
-    }
-
-    #generate dataset definition
-    str << ":dataset-#{var} a qb:DataSet ;\n\trdfs:label \"#{var}\"@en ;\n\tqb:structure :dsd-#{var} .\n\n"
-
-    #add DimensionProperty for row
-    str << <<-EOF
-:refRow a rdf:Property, qb:DimensionProperty ;
-\trdfs:label "Row"@en .
-
-    EOF
-
-    #generate MeasureProperties
-    names.map{ |n|
-      str << ":#{n} a rdf:Property, qb:MeasureProperty ;\n\trdfs:label \"#{n}\"@en .\n\n"
-    }
-
-    #add observations
-    h[var]["rows"].map{|k,v|
-      str << ":obs#{k} a qb:Observation ;\n\tqb:dataSet :dataset-#{var} ;\n\tprop:refRow :#{k} ;\n"
-      v.map{|l,w|
-        str << "\tprop:#{l} #{w} ;\n"
-      }
-      str << "\t.\n\n"
-    }
-
-    #add row property definitions
-    h[var]["rows"].map{|k,v|
-      str << ":#{k} a prop:refRow ;\n\trdfs:label \"#{k}\" .\n\n"
-    }
-
-    str
-  end
-
-  def statements_for(string,type=:turtle)
-    statements = []
-    RDF::Reader.for(:turtle).new(string) do |reader|
-      reader.each_statement do |statement|
-        # puts statement.inspect
-        statements << statement
-      end
-    end
-    statements
-  end
-
-  def turtletype_for(value)
-    #use for providing ranges to better define data (later)
-  end
-
-  def load_statements(statements)
-    #maybe a better way than inserting statements one at a time?
-    repo = RDF::FourStore::Repository.new("http://localhost:#{@port_4s}")
-    statements.each{|s| repo.insert(s)}
-  end
-
-  def to_store(var, parse_type=:turtle)
-    load_statements(triples_for(dump(var))) if parse_type==:ntriples
-    
-    #TODO: this doesn't work (needs to be converted to statments or 
-    # a way of inserting raw strings needs to be figured out.
-    load_statements(n3_for(dump(var))) if parse_type==:turtle
-  end
-
-  def vars
-    @R.eval("ls()").payload
-  end
-
-end

data/lib/template_bak.rb

@@ -1,12 +0,0 @@
-# Please require your code below, respecting the naming conventions in the
-# bioruby directory tree.
-#
-# For example, say you have a plugin named bio-plugin, the only uncommented
-# line in this file would be 
-#
-#   require 'bio/bio-plugin/plugin'
-#
-# In this file only require other files. Avoid other source code.
-
-require 'publisci/publisci.rb'
-