publisci 0.1.2

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

@@ -0,0 +1,64 @@
+module PubliSci
+  class Prov
+    class Entity
+      include Prov::Element
+
+      attr_accessor :derived_from
+      attr_accessor :attributed_to
+
+      class Derivations < Array
+        include PubliSci::Prov::Dereferencable
+        def method
+          :entities
+        end
+      end
+
+
+      def source(s=nil)
+        if s
+          (@sources ||= []) << s
+        else
+          @sources
+        end
+      end
+
+      def generated_by(activity=nil)
+        basic_keyword(:generated_by,:activities,activity)
+      end
+
+      def attributed_to(agent=nil)
+        basic_keyword(:attributed_to,:agents,agent)
+      end
+
+      def derived_from(entity=nil,&block)
+        block_list(:derived_from,:derivations,Derivation,Derivations,entity,&block)
+      end
+
+      def to_n3
+        str = "<#{subject}> a prov:Entity ;\n"
+        str << "\tprov:wasGeneratedBy <#{generated_by}> ;\n" if generated_by
+        str << "\tprov:wasAttributedTo <#{attributed_to}> ;\n" if attributed_to
+        if derived_from
+          derived_from.size.times.each{|k|
+            der = derived_from[k] # if der.is_a?(Symbol) && Prov.entities[der]
+
+            if der.is_a? Derivation
+              str << "\tprov:wasDerivedFrom <#{der.entity}> ;\n"
+              str << "\tprov:qualifiedDerivation <#{der.subject}> ;\n"
+            else
+              str << "\tprov:wasDerivedFrom <#{der}> ;\n"
+            end
+          }
+        end
+
+        add_custom(str)
+
+        str << %Q(\trdfs:label "#{__label}" .\n\n)
+      end
+
+      def to_s
+        subject
+      end
+    end
+  end
+end

data/lib/bio-publisci/metadata/prov/model/prov_models.rb

@@ -0,0 +1,109 @@
+require 'rdf/4store'
+
+begin
+  require 'spira'
+
+module PubliSci
+  class Prov
+    module Model
+      PROV ||= RDF::Vocabulary.new(RDF::URI.new('http://www.w3.org/ns/prov#'))
+
+      class Entity < Spira::Base
+        type PROV.Entity
+        property :label, predicate: RDF::RDFS.label
+        property :wasGeneratedBy, predicate: PROV.wasGeneratedBy
+        has_many :wasAttributedTo, predicate: PROV.wasAttributedTo
+        has_many :wasDerivedFrom, predicate: PROV.wasDerivedFrom
+        has_many :qualifiedAssociation, predicate: PROV.qualifiedAssociation
+
+        def organization
+          wasAttributedTo.map{|src|
+            if Agent.for(src).actedOnBehalfOf
+              Agent.for(Agent.for(src).actedOnBehalfOf).label
+            end
+          }
+        end
+
+        def all_types
+          me = self.subject
+          type_query = RDF::Query.new do
+            pattern [me, RDF.type, :type]
+          end
+
+          type_query.execute(self.class.repository).map{|t| t[:type]}
+        end
+
+        def has_data?
+          all_types.include?('http://purl.org/linked-data/cube#DataSet')
+        end
+
+      end
+
+      class Agent < Spira::Base
+        type PROV.Agent
+        type PROV.Organization
+        type PROV.SoftwareAgent
+        type PROV.Person
+        property :label, predicate: RDF::RDFS.label
+        property :foaf_name, predicate: RDF::FOAF.name
+        property :foaf_given, predicate: RDF::FOAF.givenName
+        property :actedOnBehalfOf, predicate: PROV.actedOnBehalfOf
+
+
+        def name
+          foaf_given || foaf_name
+        end
+
+        def name=(name)
+          foaf_given = name
+          foaf_name = name
+
+        end
+
+        def activities
+          #should do this in a SPARQL query instead
+          Activity.enum_for.map{|act|
+            subj = subject()
+            act if act.wasAssociatedWith.any?{|assoc| assoc == subj}
+          }.reject{|x| x==nil}
+        end
+      end
+
+      class Activity < Spira::Base
+        type PROV.Activity
+        property :label, predicate: RDF::RDFS.label
+        has_many :generated, predicate: PROV.generated
+        has_many :used, predicate: PROV.used
+        has_many :wasAssociatedWith, predicate: PROV.wasAssociatedWith
+        has_many :qualifiedAssociation, predicate: PROV.qualifiedAssociation
+      end
+
+      class Association < Spira::Base
+        type PROV.Association
+        property :label, predicate: RDF::RDFS.label
+        property :agent, predicate: PROV.agent
+        property :hadPlan, predicate: PROV.hadPlan
+
+        def activity
+          Activity.each.to_a.select{|act| act.qualifiedAssociation.include? self}
+        end
+      end
+
+      class Derivation < Spira::Base
+        type PROV.Derivation
+        property :label, predicate: RDF::RDFS.label
+        property :agent, predicate: PROV.agent
+        property :hadPlan, predicate: PROV.hadPlan
+      end
+
+      class Plan < Spira::Base
+        type PROV.Plan
+        property :label, predicate: RDF::RDFS.label
+        property :comment, predicate: RDF::RDFS.comment
+      end
+    end
+  end
+end
+rescue LoadError
+  # puts "spira not installed, ORM unavailable"
+end

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

@@ -0,0 +1,32 @@
+module PubliSci
+class Prov
+  class Plan
+    include Prov::Element
+
+    def steps(steps=nil)
+      if steps
+        if File.exist? steps
+          steps = Array[IO.read(steps).split("\n")]
+        end
+        @steps = Array[steps]
+      else
+        @steps
+      end
+    end
+
+    def to_n3
+      str = "<#{subject}> a prov:Plan ;\n"
+      if steps
+        str << "\trdfs:comment (\"#{steps.join('" "')}\") ;\n"
+      end
+      add_custom(str)
+
+      str << "\trdfs:label \"#{__label}\" .\n\n"
+    end
+
+    def to_s
+      subject
+    end
+  end
+end
+end

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

@@ -0,0 +1,78 @@
+module PubliSci
+  class Prov
+    extend PubliSci::Registry
+
+    def self.configuration
+      @config ||= Configuration.new
+    end
+
+    def self.symbol_for(object)
+      if object.is_a? Agent
+        :agents
+      elsif object.is_a? Entity
+        :entities
+      elsif object.is_a? Activity
+        :activities
+      elsif object.is_a? Association
+        :associations
+      elsif object.is_a? Plan
+        :plans
+      else
+        false
+      end
+    end
+
+
+    def self.run(string)
+      sing =DSL::Instance.new
+      if File.exists? string
+        sing.instance_eval(IO.read(string),string)
+      else
+        sing.instance_eval(string)
+      end
+      sing.output
+    end
+
+    def self.reset_settings
+      Configuration.defaults.map{|k,v| configuration.send("#{k}=",v)}
+      @base_url=nil
+    end
+
+    def self.agents
+      registry[:agents] ||= {}
+    end
+
+    def self.entities
+      registry[:entities] ||= {}
+    end
+
+    def self.activities
+      registry[:activities] ||= {}
+    end
+
+    def self.associations
+      registry[:associations] ||= {}
+    end
+
+    def self.plans
+      registry[:plans] ||= {}
+    end
+
+    def self.base_url
+      @base_url ||= "http://rqtl.org/ns"
+    end
+
+    def self.base_url=(url)
+      @base_url = url
+    end
+
+    def self.prefixes
+      <<-EOF
+@prefix prov: <http://www.w3.org/ns/prov#> .
+@prefix rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+@prefix foaf: <http://xmlns.com/foaf/0.1/> .
+      EOF
+    end
+  end
+end

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

@@ -0,0 +1,40 @@
+module PubliSci
+  class Prov
+    class Role
+      # attr_writer :comment
+
+      include Prov::Element
+
+      def comment(str=nil)
+        if str
+          @comment = str
+        else
+          @comment
+        end
+      end
+
+      # def steps(steps=nil)
+      #   if steps
+      #     if File.exist? steps
+      #       steps = Array[IO.read(steps).split("\n")]
+      #     end
+      #     @steps = Array[steps]
+      #   else
+      #     @steps
+      #   end
+      # end
+
+      def to_n3
+        str = "<#{subject}> a prov:Role ;\n"
+        str << "\trdfs:comment \"#{comment}\" ;\n" if comment
+        add_custom(str)
+
+        str << "\trdfs:label \"#{__label}\" .\n\n"
+      end
+
+      def to_s
+        subject
+      end
+    end
+  end
+end

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

@@ -0,0 +1,64 @@
+module PubliSci
+  class Prov
+    class Usage
+      include Prov::Element
+
+      def __label
+        @__label ||= Time.now.nsec.to_s(32)
+      end
+
+      def entity(entity=nil)
+        basic_keyword(:entity,:entities,entity)
+      end
+
+      def had_role(*args, &block)
+        if block_given?
+          p = Prov::Role.new
+          p.instance_eval(&block)
+          p.__label=args[0]
+          @role = p
+          # puts p.class
+          Prov.register(args[0], p)
+        elsif args.size == 0
+          if @role.is_a? Symbol
+            raise "UnknownRole: #{@role}" unless (Prov.registry[:role]||={})[@role]
+            @role = Prov.registry[:role][@role]
+          end
+          @role
+        elsif args.size == 1
+          unless (Prov.registry[:role]||={})[args[0]]
+            p = Prov::Role.new
+            p.__label=args[0]
+            @role = p
+            Prov.register(args[0], p)
+          end
+        else
+          name = args.shift
+          args = Hash[*args]
+          p = Prov::Role.new
+
+          p.__label=name
+          p.subject args[:subject]
+          (args.keys - [:subject]).map{|k|
+            raise "Unkown Role setting #{k}" unless try_auto_set(p,k,args[k])
+          }
+          @role = p
+          Prov.register(name, p)
+        end
+      end
+      alias_method :role, :had_role
+
+      def to_n3
+        str = "<#{subject}> a prov:Usage ;\n"
+        str << "\tprov:entity <#{entity}> ;\n"
+        str << "\tprov:hadRole <#{had_role}> ;\n" if had_role
+        str[-2] = ".\n"
+        str
+      end
+
+      def to_s
+        subject
+      end
+    end
+  end
+end

data/lib/bio-publisci/metadata/publisher.rb

@@ -0,0 +1,25 @@
+module PubliSci
+  class Metadata
+    class Publisher
+
+      def uri(uri=nil)
+        if uri
+          @uri = uri
+        else
+          @uri
+        end
+      end
+      alias_method :url, :uri
+
+      def label(label=nil)
+        if label
+          @label = label
+        else
+          @label
+        end
+      end
+      alias_method :name, :label
+
+    end
+  end
+end

data/lib/bio-publisci/mixins/custom_predicate.rb

@@ -0,0 +1,38 @@
+module PubliSci
+  module CustomPredicate
+    def has(predicate, object)
+      if object.is_a? Symbol
+        obj = object
+      else
+        predicate = RDF::Resource(predicate) if RDF::Resource(predicate).valid?
+        obj = RDF::Resource(object)
+        obj = RDF::Literal(object) unless obj.valid?
+      end
+        ((@custom ||= {})[predicate] ||= []) << obj
+    end
+    alias_method :set, :has
+
+    def custom
+      @custom
+    end
+
+    def add_custom(str)
+      if custom
+        custom.map{|k,v|
+          pk = k.respond_to?(:to_base) ? k.to_base : k
+          v.map{|vv|
+            if vv.is_a? Symbol
+
+              deref = Prov.registry.values.map{|h|
+                h[vv] if vv
+              }.reject{|x| x==nil}
+              raise "Unknown Element #{vv}" unless deref.size > 0
+              vv = RDF::Resource(deref.first)
+            end
+            str << "\t#{pk} #{vv.to_base} ;\n"
+          }
+        }
+      end
+    end
+  end
+end