bio-publisci 0.0.5 → 0.0.6

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 017f15f45cc8f40401aebe96aaf5dd886ba602e7
-  data.tar.gz: f59abde75019333ff918968a8717f51f419946ee
+  metadata.gz: 89e183556979b5f6ddcdd98d3a88c990d352eaea
+  data.tar.gz: c4497bc982cb6452d648066dc1bb642bdd6ab315
 SHA512:
-  metadata.gz: 7c80715a4e5354b330c93591b812f5a6c5105fbf6be2fe3d3028721796246e8a13cd1410af29411ba46d396cb82e494319f7137cd1aa2985e0e5d6cf08ce2422
-  data.tar.gz: 96dd7d0f7fb252837524640f21ec6513197366c2455ce3691b8c2a36ba9dd7acfa438eb87cb2b0c3b6560a54fc87e3ab972fd7ae9e5ebec515f74869ac87334c
+  metadata.gz: 10abfdbb88cf57d251f784e4106ea9f42b1fbe56fd75fcddc02dd329a32e0b1b3ac130f152aaf4d8d7d3e3f7a98a56236d27a5f444f695401a6281c8d9ecc488
+  data.tar.gz: f1c4888880e431f668f47e80786855953acb1edd61395f3c32135a063ed583ef5dde9002433fe338462034af17863bf58377da5aba8fe99f74e5ae83d55bf56b

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 = "0.0.5"
+  gem.version = "0.0.6"
 
   # dependencies defined in Gemfile
 end

data/examples/no_magic.rb

@@ -0,0 +1,58 @@
+# Example using as little generation "magic" as possible, for execution
+# as plain Ruby script.
+#
+# Run using "ruby no_magic.prov"
+
+require 'bio-publisci'
+include PubliSci::Prov::DSL
+
+
+# Subject and type for most elements can be set manually
+agent :publisci, subject: 'http://gsocsemantic.wordpress.com/publisci', type: "software"
+agent :R, subject: "http://r-project.org"
+agent :sciruby, subject: "http://sciruby.com", type: "organization"
+
+plan :R_steps, subject: "http://example.org/plan/R_steps", steps: "spec/resource/example.Rhistory"
+
+agent :Will do
+  # subject can be called within a block as well
+  subject "http://gsocsemantic.wordpress.com/me"
+  type "person"
+  name "Will Strinz"
+  on_behalf_of "http://sciruby.com"
+end
+
+# The wasGeneratedBy relationship is usually created automatically when an activitiy
+#   is associated with an entity, but it can be specified manually
+entity :triplified_example, subject: "http://example.org/dataset/ex", generated_by: :triplify
+
+entity :original do
+  generated_by :use_R
+  subject "http://example.org/R/ex"
+  source "./example.RData"
+
+  # Custom predicates and objects can be used for flexibility and extensibility
+  has "http://purl.org/dc/terms/title", "original data object"
+end
+
+activity :triplify do
+  # Most methods will take either Symbols or Strings, and correctly handle
+  #   resources vs literals
+  subject "http://example.org/activity/triplify"
+  generated "http://example.org/dataset/ex"
+  associated_with :publisci
+  used :original
+end
+
+activity :use_R do
+  subject "http://example.org/activity/use_R"
+  generated "http://example.org/R/ex"
+
+  associated_with :R
+  associated_with :Will
+end
+
+# Running a prov script using the gem executable will print the result, but
+#   if you use the DSL you'll have to do it manually. You also read out to a file
+#   or other method/object of course (eg "open('out.ttl','w'){|file| file.write generate_n3}")
+puts generate_n3

data/examples/orm.prov

@@ -0,0 +1,48 @@
+agent :R, subject: "http://r-project.org"
+agent :publisci, type: "software"
+plan :R_steps, steps: "spec/resource/example.Rhistory"
+organization :sciruby, subject: "http://sciruby.com"
+
+foaf = vocabulary "http://xmlns.com/foaf/0.1/"
+
+agent :Will do
+  type "person"
+  name "Will Strinz"
+  on_behalf_of :sciruby
+
+  has foaf.mailbox, "wstrinz@gmail.com"
+  has "http://xmlns.com/foaf/0.1/", "http://gsocsemantic.wordpress.com/"
+end
+
+data :field_work
+
+data :original do
+  attributed_to :R
+  derived_from :field_work
+end
+
+data :triplified_example do
+  attributed_to :Will
+  derived_from do
+    entity :original
+    activity :triplify
+  end
+end
+
+activity :triplify do
+  generated :triplified_example
+  associated_with :publisci
+  used :original
+end
+
+
+activity :use_R do
+  generated :original
+  associated_with do
+    agent :R
+    plan :R_steps
+  end
+  associated_with :Will
+end
+
+to_repository

data/examples/primer-full.prov

@@ -0,0 +1,120 @@
+###
+#
+# Complete PROV-O primer example,
+#   as shown in http://www.w3.org/TR/prov-primer/images/everything.png
+#   (some prefixes are different)
+#
+# See Section 3.10 of http://www.w3.org/TR/prov-primer/
+#
+
+base_url "http://example.org"
+
+dct = vocabulary "http://purl.org/dc/terms/"
+prov = vocabulary "http://www.w3.org/ns/prov#"
+
+###
+# Entities
+###
+
+entity :dataSet1
+entity :regionList
+entity :composition1
+
+entity :chart1 do
+  attributed_to :derek
+  has prov.generatedAtTime, "2012-03-02T10:30:00"
+end
+
+entity :dataSet2 do
+  has prov.wasRevisionOf, :dataSet1
+end
+
+entity :chart2 do
+  derived_from :dataSet2
+  has prov.wasRevisionOf, :chart1
+end
+
+entity :article do
+  has dct.title, "Crime rises in cities"
+end
+
+entity :articleV1 do
+  has prov.specializationOf, :article
+end
+
+entity :articleV2 do
+  has prov.specializationOf, :article
+  has prov.alternateOf, :articleV1
+end
+
+entity :quoteInBlogEntry20130326 do
+  subject "http://example.com/blog_entry"
+  has prov.wasQuotedFrom, :article
+end
+
+###
+# Agents
+###
+
+agent :edith, type: "person"
+
+organization :chartgen, name: "Chart Generators Inc"
+
+agent :derek do
+  name "Derek"
+  on_behalf_of :chartgen
+end
+
+###
+# Activities
+###
+
+activity :illustrate1 do
+  generated :chart1
+  associated_with :derek
+  used :composition1
+end
+
+activity :compose1 do
+  generated :composition1
+
+  associated_with do
+    agent :derek
+    role :analyst
+  end
+
+  used do
+    entity :regionList
+    role :regionsToAggregateBy
+  end
+
+  used do
+    entity :dataSet1
+    role :dataToCompose
+  end
+end
+
+activity :correct1 do
+  generated :dataSet2
+  used :dataSet1
+
+  associated_with do
+    agent :edith
+    plan :instructions
+  end
+
+  has prov.startedAtTime, "2012-03-31T09:21:00"
+  has prov.endedAtTime, "2012-04-01T15:21:00"
+end
+
+activity :compile1 do
+  generated :chart1
+  used :dataSet1
+end
+
+activity :compile2 do
+  generated :chart2
+  used :dataSet2
+end
+
+generate_n3 true

data/examples/prov_dsl.prov

@@ -63,10 +63,12 @@ end
 activity :triplify do
   generated :triplified_example
   associated_with :publisci
-  used :original
+  used do
+    entity :original
+    role :generation_input, comment: "source data for triplification"
+  end
 end
 
-
 activity :use_R do
   generated :original
 

data/features/prov_dsl.feature

@@ -4,7 +4,7 @@ Feature: Receive metadata as user input or extract from data sources
   I want to use a DSL for the PROV ontology
 
   Scenario: Generate based on example for w3.org
-    Given the prov DSL string from file examples/primer.prov
+    Given the prov DSL string from file examples/primer-full.prov
     When I call Prov.run on it
     Then I should receive a provenance string
 

data/lib/bio-publisci.rb

@@ -34,6 +34,7 @@ load File.dirname(__FILE__) + '/bio-publisci/metadata/prov/element.rb'
 
 load_folder('bio-publisci/metadata')
 load_folder('bio-publisci/metadata/prov')
+load_folder('bio-publisci/metadata/prov/model')
 load_folder('bio-publisci/readers')
 load_folder('bio-publisci/writers')
 load_folder('bio-publisci/dataset/ORM')

data/lib/bio-publisci/dataset/ORM/data_cube_orm.rb

@@ -34,7 +34,7 @@ module R2RDF
       def self.load(graph,options={},verbose=false)
 
 
-        graph = create_graph(graph) unless graph =~ /^http/
+        graph = load_string(graph) unless graph =~ /^http/
 
         # puts get_hashes(execute_from_file('dimension_ranges.rq',graph))
         dimensions = Hash[get_hashes(execute_from_file('dimension_ranges.rq',graph),"to_s").map{|solution|

data/lib/bio-publisci/metadata/prov/activity.rb

@@ -3,59 +3,39 @@ module Prov
   class Activity
     include Prov::Element
     class Associations < Array
-      def [](index)
-        if self.fetch(index).is_a? Symbol
-            Prov.agents[self.fetch(index)]
-        else
-          self.fetch(index)
-        end
+      include PubliSci::Prov::Dereferencable
+      def method
+        :agents
       end
     end
 
-    def generated(entity=nil)
-      if entity
-        # if entity.is_a? Symbol
-        #   entity = Prov.entities[entity.to_sym]
-        # end
-
-        if entity.is_a? Entity
-          entity.generated_by self
-        end
+    class Generations < Array
+      include PubliSci::Prov::Dereferencable
+      def method
+        :entities
+      end
+    end
 
-        (@generated ||= []) << entity
-      elsif @generated.is_a? Symbol
-        @generated = Prov.entities[@generated]
-      else
-        @generated
+    class Usages < Array
+      include PubliSci::Prov::Dereferencable
+      def method
+        :entities
       end
     end
 
-    def generated=(gen)
-      @generated = gen
+    def generated(entity=nil)
+      if entity.is_a? Entity
+        entity.generated_by self
+      end
+      basic_list(:generated,:entities,Generations,entity)
     end
 
     def associated_with(agent=nil, &block)
-      if agent
-        (@associated ||= Associations.new) << agent
-        # Prov.register(nil,assoc)
-      elsif block_given?
-        assoc = Association.new
-        assoc.instance_eval(&block)
-        (@associated ||= Associations.new) << assoc
-        Prov.register(nil,assoc)
-      else
-        @associated
-      end
+      block_list(:associated,:associations,Association,Associations,agent,&block)
     end
 
-    def used(entity=nil)
-      if entity
-        (@used ||= []) << entity
-      elsif @used
-        @used.map{|u| u.is_a?(Symbol) ? Prov.entities[u] : u}
-      else
-        @used
-      end
+    def used(entity=nil, &block)
+      block_list(:use,:usages,Usage,Usages,entity, &block)
     end
 
     def to_n3
@@ -63,8 +43,7 @@ module Prov
 
       if generated
         str << "\tprov:generated "
-        generated.map{|src|
-          src = Prov.entities[src] if src.is_a?(Symbol) && Prov.entities[src]
+        generated.dereference.map{|src|
           str << "<#{src}>, "
         }
         str[-2]=" "
@@ -72,18 +51,18 @@ module Prov
       end
 
       if used
-        str << "\tprov:used "
-        used.map{|used|
-          str << "<#{used}>, "
+        used.dereference.map{|u|
+          if u.is_a? Usage
+            str << "\tprov:used <#{u.entity}> ;\n"
+            str << "\tprov:qualifiedUsage <#{u}> ;\n"
+          else
+            str << "\tprov:used <#{u}> ;\n"
+          end
         }
-        str[-2]=";"
-        str[-1]="\n"
       end
 
       if associated_with
-        associated_with.map{|assoc|
-          assoc = Prov.agents[assoc] if assoc.is_a?(Symbol) && Prov.agents[assoc]
-
+        associated_with.dereference.map{|assoc|
           if assoc.is_a? Association
             str << "\tprov:wasAssociatedWith <#{assoc.agent}> ;\n"
             str << "\tprov:qualifiedAssociation <#{assoc}> ;\n"

data/lib/bio-publisci/metadata/prov/agent.rb

@@ -1,95 +1,100 @@
 module PubliSci
-module Prov
-  class Agent
-    include Prov::Element
+  module Prov
+    class Agent
+      include Prov::Element
+      attr_accessor :organization
+      attr_accessor :behalf_of
 
-    def type(t=nil)
-      if t
+      def type(t=nil)
+        if t
+          @type = t.to_sym
+        else
+          @type
+        end
+      end
+
+      def type=(t)
         @type = t.to_sym
-      else
-        @type
       end
-    end
 
-    def type=(t)
-      @type = t.to_sym
-    end
+      def name(name=nil)
+        if name
+          @name = name
+        else
+          @name
+        end
+      end
 
-    def name(name=nil)
-      if name
+      def name=(name)
         @name = name
-      else
-        @name
       end
-    end
 
-    def name=(name)
-      @name = name
-    end
-
-    def organization(organization=nil)
-      if organization
-        @organization = organization
-      elsif @organization.is_a? Symbol
-        @organization = Prov.agents[@organization]
-      else
-        @organization
+      def organization(organization=nil)
+        basic_keyword(:organization,:agents,organization)
+        # if organization
+        #   @organization = organization
+        # elsif @organization.is_a? Symbol
+        #   raise "UnknownAgent: #{@organization}" unless Prov.agents[@organization]
+        #   @organization = Prov.agents[@organization]
+        # else
+        #   @organization
+        # end
       end
-    end
 
-    def organization=(organization)
-      @organization = organization
-    end
-
-    def on_behalf_of(other_agent=nil)
-      if other_agent
-        @on_behalf_of = other_agent
-      elsif @on_behalf_of.is_a? Symbol
-        raise "UnknownAgent: #{@on_behalf_of}" unless Prov.agents.has_key?(@on_behalf_of)
-        @on_behalf_of = Prov.agents[@on_behalf_of]
-      else
-        @on_behalf_of
-      end
+      # def organization=(organization)
+      #   @organization = organization
+      # end
 
-      @on_behalf_of
-    end
-    alias_method :worked_for, :on_behalf_of
+      def on_behalf_of(other_agent=nil)
+        basic_keyword(:behalf_of,:agents,other_agent)
+        # if other_agent
+        #   @behalf_of = other_agent
+        # elsif @on_behalf_of.is_a? Symbol
+        #   raise "UnknownAgent: #{@on_behalf_of}" unless Prov.agents.has_key?(@on_behalf_of)
+        #   @behalf_of = Prov.agents[@on_behalf_of]
+        # else
+        #   @behalf_of
+        # end
 
-    def to_n3
-      str = "<#{subject}> a prov:Agent"
-      if type
-        case type.to_sym
-        when :software
-          str << ", prov:SoftwareAgent ;\n"
-        when :person
-          str << ", prov:Person ;\n"
-        when :organization
-          str << ", prov:Organization ;\n"
-        end
-      else
-        str << " ;\n"
+        # @behalf_of
       end
+      alias_method :worked_for, :on_behalf_of
 
-      if name
-        if type && type.to_sym == :person
-          str << "\tfoaf:givenName \"#{name}\" ;\n"
+      def to_n3
+        str = "<#{subject}> a"
+        if type
+          case type.to_sym
+          when :software
+            str << " prov:SoftwareAgent ;\n"
+          when :person
+            str << " prov:Person ;\n"
+          when :organization
+            str << " prov:Organization ;\n"
+          end
         else
-          str << "\tfoaf:name \"#{name}\" ;\n"
+          str << " prov:Agent ;\n"
         end
-      end
 
-      if on_behalf_of
-        str << "\tprov:actedOnBehalfOf <#{on_behalf_of}> ;\n"
-      end
+        if name
+          if type && type.to_sym == :person
+            str << "\tfoaf:givenName \"#{name}\" ;\n"
+          else
+            str << "\tfoaf:name \"#{name}\" ;\n"
+          end
+        end
 
-      add_custom(str)
+        if on_behalf_of
+          str << "\tprov:actedOnBehalfOf <#{on_behalf_of}> ;\n"
+        end
 
-      str << "\trdfs:label \"#{__label}\" .\n\n"
-    end
+        add_custom(str)
 
-    def to_s
-      subject
+        str << "\trdfs:label \"#{__label}\" .\n\n"
+      end
+
+      def to_s
+        subject
+      end
     end
   end
-end
 end