bio-publisci 0.0.6 → 0.0.7

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 89e183556979b5f6ddcdd98d3a88c990d352eaea
-  data.tar.gz: c4497bc982cb6452d648066dc1bb642bdd6ab315
+  metadata.gz: 84c3e7a1f4ffe93284a75856a424d4f86624032f
+  data.tar.gz: 834eb95f1ef0e2353d3aab93bcf4d9c35f34a1d4
 SHA512:
-  metadata.gz: 10abfdbb88cf57d251f784e4106ea9f42b1fbe56fd75fcddc02dd329a32e0b1b3ac130f152aaf4d8d7d3e3f7a98a56236d27a5f444f695401a6281c8d9ecc488
-  data.tar.gz: f1c4888880e431f668f47e80786855953acb1edd61395f3c32135a063ed583ef5dde9002433fe338462034af17863bf58377da5aba8fe99f74e5ae83d55bf56b
+  metadata.gz: b1c7a7e6f43f26f089a871fffafc10b0f6eb35b6367dde310e1e2df09c9ab40d725048d6291c5e67c12d32454d36a5539342f71130a90121bd4dd19946050f2b
+  data.tar.gz: 91a1bf68f52d3477d5fa5a89762619cdf7b038d3af49042cf34ce1b6f90e833324cea537bc60e9c6afc23c86163f44855f739e1838266cf0b905f5c20b2a9679

data/Gemfile

@@ -14,6 +14,7 @@ group :development do
   gem "bio", ">= 1.4.2"
   gem "rdoc", "~> 3.12"
   gem "spoon"
+  gem "spira"
 end
 
 

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 = "0.0.6"
+  gem.version = "0.0.7"
 
   # dependencies defined in Gemfile
 end

data/examples/prov_dsl.prov

@@ -81,4 +81,5 @@ activity :use_R do
   associated_with :Will
 end
 
-generate_n3 true
+generate_n3
+# generate_n3 true

data/examples/safe_gen.rb

@@ -0,0 +1,7 @@
+require 'bio-publisci'
+
+str = IO.read(ARGV[0])
+str.untaint
+$SAFE=4
+runner = PubliSci::Prov::DSL::Instance.new
+puts runner.instance_eval(str,ARGV[0])

data/examples/visualization/primer.prov

@@ -0,0 +1,66 @@
+# Provenance generation code for primer example at
+#  http://www.w3.org/TR/prov-primer/images/agents.png
+
+# Set the base url
+base_url "http://example.org"
+
+# Elements can be created with an options hash
+entity :chart1, attributed_to: :derek
+
+# entity => http://www.w3.org/TR/prov-o/#Entity
+entity :composition1
+entity :regionList1
+
+# Elements can also be defined using a block
+#
+# agent => http://www.w3.org/TR/prov-o/#Agent
+agent :derek do
+
+  # name => foaf:name
+  name "Derek"
+
+  # on_behalf_of => http://www.w3.org/TR/prov-o/#actedOnBehalfOf
+  on_behalf_of :chartgen
+end
+
+# Some methods are just wrappers with argument generation
+#  "organization" is short for agent :chartgen, type: "organization"
+#
+# organization => http://www.w3.org/TR/prov-o/#Organization
+organization :chartgen
+
+
+# An element of the correct type will be looked up for any
+#  method whose argument is a symbol
+activity :illustrate do
+
+  # generated => http://www.w3.org/TR/prov-o/#generated
+  generated :chart1
+
+  # associated_with => http://www.w3.org/TR/prov-o/#wasAssociatedWith
+  associated_with :derek
+
+  # used => http://www.w3.org/TR/prov-o/#used
+  used :composition1
+
+end
+
+activity :compose1 do
+  generated :composition1
+  associated_with :derek
+  used :regionList1
+
+  # Since symbols are lazy loaded (only when looked up by generate_n3)
+  #  you can call used here before declaring dataSet1
+  used :dataSet1
+end
+
+# data is aliased to entity
+data :dataSet1
+
+# Returns the turtle form of each element
+generate_n3
+
+# Can return abbreviated form by passing true
+#  (easier to read, some prefixes not yet included so may not work w/ triple stores)
+#  generate_n3(true)

data/examples/visualization/prov_viz.rb

@@ -0,0 +1,140 @@
+require 'bio-publisci'
+require 'graphviz'
+
+def entity_node(label)
+  ent = @g.add_nodes(label)
+  ent.color = "#F3F781"
+  ent.style = "filled"
+  ent
+end
+
+def agent_node(label)
+  ag = @g.add_nodes(label)
+  ag.color = "#FE9A2E"
+  ag.style = "filled"
+	ag.shape = "box"
+	ag
+end
+
+def activity_node(label)
+	act = @g.add_nodes(label)
+	act.color = "#5858FA"
+	act.style = "filled"
+	act.shape = "box"
+	act
+end
+
+def generic_node(label)
+  act = @g.add_nodes(label)
+  # act.color = "#5858FA"
+  # act.style = "filled"
+  act.shape = "box"
+  act
+end
+
+def make_edges(from_obj,to_class,predicate)
+  # from_class.enum_for.to_a.map{|from_obj|
+    raise "Unknown From Node: #{from_obj.subject}" unless @nodemap[from_obj.subject]
+    relation = from_obj.send(predicate)
+    if relation
+      if relation.is_a? Array
+        relation.map{|r|
+        other = to_class.for(r)
+        raise "Unknown To Node: #{other.subject}" unless @nodemap[other.subject]
+          @g.add_edges(@nodemap[from_obj.subject],@nodemap[other.subject]).label=predicate.to_s
+        }
+      else
+        other = to_class.for(relation)
+        raise "Unknown To Node: #{other.subject}" unless @nodemap[other.subject]
+        @g.add_edges(@nodemap[from_obj.subject],@nodemap[other.subject]).label=predicate.to_s
+      end
+    end
+  # }
+end
+
+@nodemap={}
+@g = GraphViz.new(:G, type: :digraph)
+infile = ARGV[0] || 'primer.prov'
+runner = PubliSci::Prov::DSL::Instance.new
+runner.instance_eval(IO.read(infile),infile)
+repo = runner.to_repository
+Spira.add_repository :default, repo
+
+include PubliSci::Prov::Model
+
+Entity.enum_for.to_a.map{|e|
+  @nodemap[e.subject]=entity_node(e.label)
+}
+
+Agent.enum_for.to_a.map{|agent|
+  @nodemap[agent.subject]=agent_node(agent.label)
+}
+
+Activity.enum_for.to_a.map{|act|
+  @nodemap[act.subject]=activity_node(act.label)
+}
+
+Association.enum_for.to_a.map{|association|
+  @nodemap[association.subject]=generic_node(association.label)
+}
+
+Plan.enum_for.to_a.map{|plan|
+  @nodemap[plan.subject]=generic_node(plan.label)
+}
+
+
+# Derivation.enum_for.to_a.map{|deriv|
+#   @nodemap[deriv.subject]=generic_node(deriv.label)
+# }
+
+Entity.enum_for.to_a.map{|e|
+  attribs ={
+    "wasAttributedTo" => Agent,
+    "wasGeneratedBy" => Activity,
+    "wasDerivedFrom" => Entity,
+  }
+  attribs.each{|predicate,range| make_edges(e,range,predicate)}
+}
+
+Activity.enum_for.to_a.map{|act|
+  attribs ={
+    "generated" => Entity,
+    "used" => Entity,
+    "wasAssociatedWith" => Agent,
+    "qualifiedAssociation" => Agent,
+  }
+  attribs.each{|predicate,range| make_edges(act,range,predicate)}
+}
+
+Agent.enum_for.to_a.map{|agent|
+  attribs = {
+    "actedOnBehalfOf" => Agent
+  }
+  attribs.each{|predicate,range| make_edges(agent,range,predicate)}
+}
+
+Association.enum_for.to_a.map{|assoc|
+  attribs ={
+    "agent" => Agent,
+    "hadPlan" => Plan
+  }
+  attribs.each{|predicate,range| make_edges(assoc,range,predicate)}
+}
+
+# Association.enum_for.to_a.map{|assoc|
+#   attribs ={
+#     "agent" => Agent
+#     "hadPlan" => Plan
+#   }
+#   attribs.each{|predicate,range| make_edges(assoc,range,predicate)}
+# }
+
+# Derivation.enum_for.to_a.map{|assoc|
+#   attribs ={
+#     "agent" => Entity
+#   }
+#   attribs.each{|predicate,range| make_edges(assoc,range,predicate)}
+# }
+
+@g.output(png: "out.png")
+begin `eog out.png` rescue nil end

data/examples/visualization/viz.rb

@@ -0,0 +1,35 @@
+require 'graphviz'
+
+def entity_node(label)
+  ent = @g.add_nodes(label)
+  ent.color = "#F3F781"
+  ent.style = "filled"
+  ent
+end
+
+def agent_node(label)
+  ag = @g.add_nodes(label)
+  ag.color = "#FE9A2E"
+  ag.style = "filled"
+	ag.shape = "box"
+	ag
+end
+
+def activity_node(label)
+  act = @g.add_nodes(label)
+  act.color = "#5858FA"
+  act.style = "filled"
+  act.shape = "box"
+  act
+end
+
+@g = GraphViz.new(:G, type: :digraph)
+g = @g
+
+ent_n = entity_node("entity") #g.add_nodes("entity")
+ag_n = activity_node("activity")
+
+g.add_edges(ent_n,ag_n).label="attributed"
+
+g.output(png: "out.png")
+`eog out.png`

data/features/metadata_steps.rb

@@ -1,8 +1,6 @@
 Given(/^a class which includes the Metadata module$/) do
-  class Meta
-    include R2RDF::Metadata
-  end
-  @klass = Meta
+
+  @klass = Class.new {include PubliSci::Metadata::Generator}
 end
 
 Given(/^the source object (\{.+\})$/) do |fields|

data/features/orm_steps.rb

@@ -1,7 +1,7 @@
 require_relative '../lib/bio-publisci.rb'
 
 Given /^an ORM::DataCube entitled "(.*?)"$/ do |name|
-	@cube = R2RDF::ORM::DataCube.new(name: name)
+	@cube = PubliSci::ORM::DataCube.new(name: name)
 end
 
 Given /^an ORM::DataCube entitled "(.*?)" with the following options:$/ do |name, opts|
@@ -18,7 +18,7 @@ Given /^an ORM::DataCube entitled "(.*?)" with the following options:$/ do |name
 
 		options_hash[k] = v
 	}
-	@cube = R2RDF::ORM::DataCube.new(options_hash)
+	@cube = PubliSci::ORM::DataCube.new(options_hash)
 end
 
 Given(/^a turtle string from file (.*)$/) do |file|
@@ -30,7 +30,7 @@ Given(/^the URI string "(.*?)"$/) do |uri|
 end
 
 When(/^I call the ORM::DataCube class method load on it$/) do
-  @cube = R2RDF::ORM::DataCube.load(@string)
+  @cube = PubliSci::ORM::DataCube.load(@string)
 end
 
 When /^I add a "(.*?)" dimension$/ do |dim|
@@ -70,5 +70,5 @@ Then /^the to_n3 method should return a string with a "(.*?)"$/ do |search|
 end
 
 Then(/^I should receive an ORM::DataCube object$/) do
-  @cube.is_a?(R2RDF::ORM::DataCube).should == true
+  @cube.is_a?(PubliSci::ORM::DataCube).should == true
 end

data/features/reader_steps.rb

@@ -1,7 +1,7 @@
 require_relative '../lib/bio-publisci.rb'
 
 Given /^a (.*) generator$/ do |generator|
-	@generator = R2RDF::Reader.const_get(generator).new
+	@generator = PubliSci::Reader.const_get(generator).new
 end
 
 When /^I ask for its methods$/ do

data/features/store_steps.rb

@@ -1,7 +1,7 @@
 require_relative '../lib/bio-publisci.rb'
 
 Given /a store of type (.*?)$/ do |type|
-	@store = R2RDF::Store.new(type: :"#{type}")
+	@store = PubliSci::Store.new(type: :"#{type}")
 end
 
 When /^I call the stores add method with the turtle file (.*?) and an RDF::(.*?)$/ do |file,graph|

data/features/writer.feature

@@ -1,7 +1,7 @@
 Feature: export to various formats using writers
 
 	In order to use RDF encoded data in other applications
-	I want to export domain objects using an R2RDF::Writer object
+	I want to export domain objects using an PubliSci::Writer object
 
 	Scenario: write to ARFF format
 		Given a ARFF writer

data/features/writer_steps.rb

@@ -1,5 +1,5 @@
 Given(/^a (.*) writer$/) do |type|
-  @writer = R2RDF::Writer.const_get(type).new
+  @writer = PubliSci::Writer.const_get(type).new
 end
 
 When(/^I call its from_turtle method on the file (.*)$/) do |file|

data/lib/bio-publisci.rb

@@ -7,6 +7,11 @@ require 'rserve'
 require 'sparql'
 require 'sparql/client'
 require 'rdf/turtle'
+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|
@@ -27,11 +32,14 @@ load File.dirname(__FILE__) + '/bio-publisci/analyzer.rb'
 load File.dirname(__FILE__) + '/bio-publisci/store.rb'
 load File.dirname(__FILE__) + '/bio-publisci/dataset/data_cube.rb'
 load File.dirname(__FILE__) + '/bio-publisci/dataset/dataset_for.rb'
+load File.dirname(__FILE__) + '/bio-publisci/dataset/configuration.rb'
+load File.dirname(__FILE__) + '/bio-publisci/dataset/dataset.rb'
 load File.dirname(__FILE__) + '/bio-publisci/output.rb'
-load File.dirname(__FILE__) + '/bio-publisci/metadata/prov/prov.rb'
 load File.dirname(__FILE__) + '/bio-publisci/metadata/prov/element.rb'
+load File.dirname(__FILE__) + '/bio-publisci/metadata/prov/prov.rb'
 
 
+load_folder('bio-publisci/dsl')
 load_folder('bio-publisci/metadata')
 load_folder('bio-publisci/metadata/prov')
 load_folder('bio-publisci/metadata/prov/model')
@@ -42,4 +50,4 @@ load_folder('bio-publisci/dataset/ORM')
 # 	unless file == "." or file == ".."
 # 		load File.dirname(__FILE__) + '/generators/' + file
 # 	end
-# end
+# end

data/lib/bio-publisci/analyzer.rb

@@ -1,5 +1,5 @@
-module R2RDF
-  
+module PubliSci
+
   #handles analysis of R expression to extract properties and recognize potential
   #ambiguity
   module Analyzer
@@ -13,10 +13,10 @@ module R2RDF
   			data.map{|datum|
   				return true if dirty?(datum)
   			}
-  		else 
+  		else
   			dirty_characters = [".",' ']
   			if data.to_s.scan(/./) & dirty_characters
-  				true 
+  				true
   			else
   				false
   			end

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

@@ -1,7 +1,6 @@
 require 'rdf/4store'
-require 'spira'
 
-module R2RDF
+module PubliSci
   module ORM
 
     # class Person < Spira::Base
@@ -53,7 +52,7 @@ module R2RDF
     end
 
     def observation
-      unless R2RDF::ORM.const_defined?("Observation")
+      unless PubliSci::ORM.const_defined?("Observation")
         obs = Class.new(Spira::Base) do
           type RDF::URI.new('http://purl.org/linked-data/cube#Observation')
 
@@ -63,13 +62,13 @@ module R2RDF
             property strip_uri(component.subject.to_s), predicate: component.subject
           }
         end
-        R2RDF::ORM.const_set("Observation",obs)
+        PubliSci::ORM.const_set("Observation",obs)
       end
       Observation
     end
 
     def reload_observation
-      R2RDF::ORM.send(:remove_const, "Observation")
+      PubliSci::ORM.send(:remove_const, "Observation")
       observation
     end