dataframe.rb in bio-publisci-0.0.7

- old
+ new

@@ -1,6 +1,6 @@
-module R2RDF
+module PubliSci
   module Writer
     module Dataframe
 
     def framestring(name,vectors)
       framestr = "#{name} = data.frame("
@@ -37,11 +37,11 @@
     end
 
   end
 
   class Builder
-    include R2RDF::Writer::Dataframe
+    include PubliSci::Writer::Dataframe
 
 
     def from_turtle(turtle_file, connection, variable_in=nil, variable_out=nil, verbose=true, save=true)
       unless variable_in && variable_out
         puts "no variable specified. Simple inference coming soon" if verbose
@@ -49,11 +49,11 @@
       end
       puts "loading #{turtle_file}" if verbose
       repo = RDF::Repository.load(turtle_file)
       puts "loaded #{repo.size} statements into temporary repo" if verbose
       # connection = Rserve::Connection.new
-      query = R2RDF::QueryHelper.new
+      query = PubliSci::QueryHelper.new
       rows = get_rownames(variable_in, query, repo)
       puts "frame has #{rows.size} rows" if verbose
 
       vectors = get_vectors(variable_in, query, repo)
       puts "got vectors of size #{vectors.first.last.size}" if verbose && vectors.first
@@ -67,11 +67,11 @@
         puts "no variable specified. Simple inference coming soon" if verbose
         return
       end
       puts "connecting to endpoint at #{endpoint_url}" if verbose
       sparql = SPARQL::Client.new(endpoint_url)
-      # client = R2RDF::Client.new
-      query = R2RDF::QueryHelper.new
+      # client = PubliSci::Client.new
+      query = PubliSci::QueryHelper.new
 
       rows = query.get_ary(sparql.query(query.row_names(variable_in))).flatten
 
     end
 
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