publisci 0.1.2 → 0.1.3

checksums.yaml

@@ -1,7 +1,7 @@
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-  data.tar.gz: 289f4d7eda9047fcf18b626a9d66def6d033f3f7
+  metadata.gz: 992e9282183a5b68f85d5835b91c761a53dd53f2
+  data.tar.gz: 5764fee6d82a2a8fc6b8835cc3fc0383ab2ad6eb
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+  data.tar.gz: 341714efc592cbd634f2b427f37a72e6151902184e455028217d3c04d1cf3ee1b589cebb1da9cfde0055f612eb42743a7718f16e09a2d556feef430700fe1e1f

data/Gemfile

@@ -14,9 +14,9 @@ group :development do
   gem "bio", ">= 1.4.2"
   gem "rdoc", "~> 3.12"
   gem "spoon"
-  gem "spira", git: "https://github.com/ruby-rdf/spira.git"
 end
 
+gem 'rest-client'
 
 gem 'rdf'
 gem 'rdf-4store', :git => "https://github.com/fumi/rdf-4store.git"
@@ -26,11 +26,4 @@ gem 'json-ld'
 gem 'rserve-client'
 gem 'sparql'
 
-gem 'slop'
-
-gem 'sinatra'
-gem 'sinatra-contrib'
-gem 'sinatra-linkeddata'
-gem 'sinatra-cross_origin'
-gem 'rack-flash3'
-gem 'rest-client'
+gem "spira", git: "https://github.com/ruby-rdf/spira.git"

data/README.md

@@ -1,6 +1,6 @@
 # PubliSci
 
-[![Build Status](https://secure.travis-ci.org/wstrinz/bioruby-publisci.png)](http://travis-ci.org/wstrinz/bioruby-publisci)
+[![Build Status](https://travis-ci.org/wstrinz/publisci.png?branch=master)](https://travis-ci.org/wstrinz/publisci)
 
 Full description goes here
 
@@ -9,15 +9,50 @@ Note: this software is under active development!
 ## Installation
 
 ```sh
-gem install bio-publisci
+gem install publisci
 ```
 
 ## Usage
 
 ```ruby
-require 'bio-publisci'
+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)                                     
 ```
 
+
+
 The API doc is online. For more code examples see the test files in
 the source tree.
 
@@ -26,7 +61,7 @@ the source tree.
 Information on the source tree, documentation, examples, issues and
 how to contribute, see
 
-  http://github.com/wstrinz/bioruby-publisci
+  http://github.com/wstrinz/publisci
 
 The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 
@@ -43,7 +78,7 @@ and one of
 
 ## Biogems.info
 
-This Biogem is published at (http://biogems.info/index.html#bio-publisci)
+This Biogem is published at (http://biogems.info/index.html#publisci)
 
 ## Copyright
 

data/README.rdoc

@@ -1,8 +1,8 @@
-= bio-publisci
+= publisci
 
 {<img
-src="https://secure.travis-ci.org/wstrinz/bioruby-publisci.png"
-/>}[http://travis-ci.org/#!/wstrinz/bioruby-publisci]
+src="https://secure.travis-ci.org/wstrinz/publisci.png"
+/>}[http://travis-ci.org/#!/wstrinz/publisci]
 
 Full description goes here
 
@@ -10,7 +10,7 @@ Note: this software is under active development!
 
 == Installation
 
-        gem install bio-publisci
+        gem install publisci
 
 == Usage
 
@@ -18,7 +18,7 @@ Note: this software is under active development!
 
 To use the library 
 
-        require 'bio-publisci'
+        require 'publisci'
 
 The API doc is online. For more code examples see also the test files in
 the source tree.
@@ -27,7 +27,7 @@ the source tree.
 
 Information on the source tree, documentation, issues and how to contribute, see
 
-  http://github.com/wstrinz/bioruby-publisci
+  http://github.com/wstrinz/publisci
 
 The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 
@@ -40,7 +40,7 @@ The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
 
 == Biogems.info
 
-This Biogem is published at http://biogems.info/index.html#bio-publisci
+This Biogem is published at http://biogems.info/index.html#publisci
 
 == Copyright
 

data/Rakefile

@@ -15,13 +15,13 @@ require 'jeweler'
 Jeweler::Tasks.new do |gem|
   # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
   gem.name = "publisci"
-  gem.homepage = "http://github.com/wstrinz/bioruby-publisci"
+  gem.homepage = "http://github.com/wstrinz/publisci"
   gem.license = "MIT"
   gem.summary = %Q{Publish scientific results to the semantic web}
   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 = "0.1.2"
+  gem.version = "0.1.3"
 
   # dependencies defined in Gemfile
 end

data/bin/{bio-publisci → publisci}

@@ -1,23 +1,23 @@
 #!/usr/bin/env ruby
 #
-# BioRuby bio-publisci Plugin BioPublisci
+# BioRuby publisci Plugin BioPublisci
 # Author:: wstrinz
 # Copyright:: 2013
 
 version = "0.0.4" #File.new(VERSION_FILENAME).read.chomp
 
 USAGE = <<-EOF
-  bio-publisci #{version} by Will Strinz 2013
+  publisci #{version} by Will Strinz 2013
 
   Usage:
 
-  bio-publisci file
+  publisci file
   (execute PROV dsl file)
 EOF
 
 gempath = File.dirname(File.dirname(__FILE__))
 $: << File.join(gempath,'lib')
-require 'bio-publisci'
+require 'publisci'
 
 #VERSION_FILENAME=File.join(gempath,'VERSION')
 
@@ -42,7 +42,7 @@ else
   end
 end
 
-require 'bio-publisci'
+require 'publisci'
 require 'optparse'
 
 # Uncomment when using the bio-logger
@@ -97,7 +97,7 @@ begin
   opts.parse!(ARGV)
 
   # Uncomment the following when using the bio-logger
-  # Bio::Log::CLI.configure('bio-publisci')
+  # Bio::Log::CLI.configure('publisci')
 
   # TODO: your code here
   # use options for your logic

data/examples/bio-band_integration.rb

@@ -1,5 +1,5 @@
 require 'bio-band'
-require 'bio-publisci'
+require 'publisci'
 
 f = open(File.dirname(__FILE__) + '/../resources/weather.numeric.arff')
 clustering = Weka::Clusterer::SimpleKMeans::Base

data/examples/no_magic.prov

@@ -3,7 +3,7 @@
 #
 # Run using "ruby no_magic.prov"
 
-require 'bio-publisci'
+require 'publisci'
 include PubliSci::Prov::DSL
 
 

data/examples/no_magic.rb

@@ -3,7 +3,7 @@
 #
 # Run using "ruby no_magic.prov"
 
-require 'bio-publisci'
+require 'publisci'
 include PubliSci::Prov::DSL
 
 

data/examples/safe_gen.rb

@@ -1,4 +1,4 @@
-require 'bio-publisci'
+require 'publisci'
 
 str = IO.read(ARGV[0])
 str.untaint

data/examples/visualization/prov_viz.rb

@@ -1,4 +1,4 @@
-require 'bio-publisci'
+require 'publisci'
 require 'graphviz'
 
 def entity_node(label)

data/features/orm_steps.rb

@@ -1,4 +1,4 @@
-require_relative '../lib/bio-publisci.rb'
+require_relative '../lib/publisci.rb'
 
 Given /^an ORM::DataCube entitled "(.*?)"$/ do |name|
 	@cube = PubliSci::DataSet::ORM::DataCube.new(name: name)

data/features/reader_steps.rb

@@ -1,4 +1,4 @@
-require_relative '../lib/bio-publisci.rb'
+require_relative '../lib/publisci.rb'
 
 Given /^a (.*) generator$/ do |generator|
 	@generator = PubliSci::Readers.const_get(generator).new

data/features/store_steps.rb

@@ -1,4 +1,4 @@
-require_relative '../lib/bio-publisci.rb'
+require_relative '../lib/publisci.rb'
 
 Given /a store of type (.*?)$/ do |type|
 	@store = PubliSci::Store.new(type: :"#{type}")

data/features/support/env.rb

@@ -8,6 +8,6 @@ rescue Bundler::BundlerError => e
 end
 
 $LOAD_PATH.unshift(File.dirname(__FILE__) + '/../../lib')
-require 'bio-publisci'
+require 'publisci'
 
 require 'rspec/expectations'

data/lib/publisci.rb

@@ -0,0 +1,58 @@
+# This is temporary, just to help w/ development so I don't have to rewrite r2rdf.rb to be
+# a standard gem base yet. Also load s the files instead of require for easy reloading
+require 'tempfile'
+require 'fileutils'
+require 'csv'
+
+require 'rdf'
+require 'sparql'
+require 'sparql/client'
+require 'rdf/turtle'
+require 'rdf/rdfxml'
+require 'json/ld'
+
+require 'rserve'
+require 'rest-client'
+
+begin
+	require 'spira'
+rescue LoadError
+	puts "can't load spira; orm unavailable"
+end
+
+def load_folder(folder)
+	Dir.foreach(File.dirname(__FILE__) + "/#{folder}") do |file|
+		unless file == "." or file == ".."
+			f = File.dirname(__FILE__) + "/#{folder}/" + file
+      load f unless File.directory?(f)
+		end
+  end
+end
+
+load_folder('publisci/mixins')
+
+load File.dirname(__FILE__) + '/publisci/dataset/interactive.rb'
+load File.dirname(__FILE__) + '/publisci/query/query_helper.rb'
+load File.dirname(__FILE__) + '/publisci/parser.rb'
+load File.dirname(__FILE__) + '/publisci/post_processor.rb'
+load File.dirname(__FILE__) + '/publisci/analyzer.rb'
+load File.dirname(__FILE__) + '/publisci/store.rb'
+load File.dirname(__FILE__) + '/publisci/dataset/data_cube.rb'
+load File.dirname(__FILE__) + '/publisci/dataset/dataset_for.rb'
+load File.dirname(__FILE__) + '/publisci/dataset/configuration.rb'
+load File.dirname(__FILE__) + '/publisci/dataset/dataset.rb'
+load File.dirname(__FILE__) + '/publisci/datacube_model.rb'
+load File.dirname(__FILE__) + '/publisci/output.rb'
+load File.dirname(__FILE__) + '/publisci/metadata/prov/element.rb'
+load File.dirname(__FILE__) + '/publisci/metadata/prov/prov.rb'
+load File.dirname(__FILE__) + '/publisci/writers/base.rb'
+load File.dirname(__FILE__) + '/publisci/readers/base.rb'
+
+
+load_folder('publisci/dsl')
+load_folder('publisci/metadata')
+load_folder('publisci/metadata/prov')
+load_folder('publisci/metadata/prov/model')
+load_folder('publisci/readers')
+load_folder('publisci/writers')
+load_folder('publisci/dataset/ORM')

data/lib/{bio-publisci → publisci}/datacube_model.rb

@@ -3,11 +3,6 @@ begin
   require 'spira'
   module PubliSci
     module ORM
-      # class Observation < Spira::Base
-      #   type RDF::URI.new('http://purl.org/linked-data/cube#Observation')
-      #   property :label, predicate: RDFS.label
-
-      # end
       QB ||= RDF::Vocabulary.new(RDF::URI.new('http://purl.org/linked-data/cube#'))
 
       class Component < Spira::Base
@@ -45,22 +40,6 @@ begin
         Spira.add_repository :default, repo
       end
 
-      # def observation
-      #   unless PubliSci::ORM.const_defined?("Observation")
-      #     obs = Class.new(Spira::Base) do
-      #       type RDF::URI.new('http://purl.org/linked-data/cube#Observation')
-
-      #       property :structure, predicate: QB.dataSet
-
-      #       ((Dimension.each.to_a | Measure.each.to_a) || []).each{|component|
-      #         property strip_uri(component.subject.to_s), predicate: component.subject
-      #       }
-      #     end
-      #     PubliSci::ORM.const_set("Observation",obs)
-      #   end
-      #   Observation
-      # end
-
       class Observation < Spira::Base
         type QB.Observation
         property :label, predicate: RDFS.label
@@ -76,22 +55,12 @@ begin
           }
         end
 
-        # for testing; DRY up eventually
         def strip_uri(uri)
           uri = uri.to_s.dup
           uri[-1] = '' if uri[-1] == '>'
           uri.to_s.split('/').last.split('#').last
         end
-
-        # def method_missing(meth, *args, &block)
-        #         if meth.to_s =~ /^find_by_(.+)$/
-        #           run_find_by_method($1, *args, &block)
-        #         else
-        #           super # You *must* call super if you don't handle the
-        #                 # method, otherwise you'll mess up Ruby's method
-        #                 # lookup.
-        #         end
-        #       end
+        
       end
 
       def reload_observation

data/lib/{bio-publisci → publisci}/dataset/ORM/observation.rb

@@ -6,14 +6,6 @@ module PubliSci
           def initialize(data={})
             @data = data
           end
-
-          def method_missing(name, args)
-            #get entry of data hash
-          end
-
-          def respond_to_missing?(method, *)
-
-          end
         end
     end
   end

data/lib/{bio-publisci → publisci}/dsl/dataset_dsl.rb

@@ -18,6 +18,7 @@ module PubliSci
         add_or_get('object',file)
       end
       alias_method :source, :object
+      alias_method :input, :object
 
       def dimension(*args)
         if args.size == 0
@@ -55,7 +56,7 @@ module PubliSci
       def generate_n3
         opts = {}
         %w{dimension measure}.each{|field|
-          opts[field.to_sym] = send(field.to_sym) if send(field.to_sym)
+          opts["#{field}s".to_sym] = send(field.to_sym) if send(field.to_sym)
         }
         interact = settings.interactive
         if options