bio-publisci 0.0.6 → 0.0.7

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

@@ -1,316 +1,5 @@
-class String
-  def unindent
-    gsub /^#{self[/\A\s*/]}/, ''
-  end
-end
-
-module R2RDF
-  module Metadata
-    include R2RDF::Parser
-
-    def defaults
-    {
-      encode_nulls: false,
-      base_url: "http://www.rqtl.org",
-    }
-    end
-
-    def basic(fields)
-      #TODO don't assume base dataset is "ns:dataset-var",
-      #make it just "var", and try to make that clear to calling classes
-
-      fields[:var] = sanitize([fields[:var]]).first
-
-      unless fields[:creator]
-        if ENV['USER']
-          fields[:creator] = ENV['USER']
-        elsif ENV['USERNAME']
-          fields[:creator] = ENV['USERNAME']
-        end
-      end
-
-      fields[:date] = Time.now.strftime("%Y-%m-%d") unless fields[:date]
-
-      #TODO some of these should probably be resources, eg dct:creator, or put under DC namespace
-      str = <<-EOF.unindent
-      ns:dataset-#{fields[:var]} rdfs:label "#{fields[:title]}";
-        dct:title "#{fields[:title]}";
-        dct:creator "#{fields[:creator]}";
-        rdfs:comment "#{fields[:description]}";
-        dct:description "#{fields[:description]}";
-        dct:issued "#{fields[:date]}"^^xsd:date;
-      EOF
-
-      end_str = ""
-
-      if fields[:subject] && fields[:subject].size > 0
-        str << "\tdct:subject \n"
-        fields[:subject].each{|subject| str << "\t\t" + subject + ",\n" }
-        str[-2] = ";"
-      end
-
-      if fields[:publishers]
-        fields[:publishers].map{|publisher|
-          raise "No URI for publisher #{publisher}" unless publisher[:uri]
-          raise "No label for publisher #{publisher}" unless publisher[:label]
-          str << "\tdct:publisher <#{publisher[:uri]}> ;\n"
-          end_str << "<#{publisher[:uri]}> a org:Organization, foaf:Agent;\n\trdfs:label \"#{publisher[:label]}\" .\n\n"
-        }
-        str[-2] = '.'
-      end
-
-      str + "\n" + end_str
-    end
-
-    def provenance(original, triplified, chain, options={})
-      #TODO: should either add a prefixes method or replace some with full URIs
-      raise "MissingOriginal: must specify a provenance source" unless original && original[:resource]
-
-      #TODO include file type etc, or create a separate method for it
-
-      str = <<-EOF.unindent
-        <#{original[:resource]}> a prov:Entity ;
-          prov:wasGeneratredBy ns:activity-1 .
-
-        ns:activity-1 a prov:Activity ;
-          prov:generated <#{original[:resource]}> .
-
-      EOF
-
-      if original[:software]
-        original_assoc_id = Time.now.nsec.to_s(32)
-
-
-        str << <<-EOF.unindent
-          <#{original[:software]}> a prov:Entity.
-
-          ns:activity-1 prov:qualifiedAssociation ns:assoc-1_#{original_assoc_id} .
-
-          ns:assoc-1_#{original_assoc_id} a prov:Assocation ;
-            prov:entity <#{original[:software]}> .
-
-        EOF
-
-        if original[:process]
-          original[:process] = IO.read(original[:process]) if File.exist? original[:process]
-
-          steps = '"' + original[:process].split("\n").join('" "') + '"'
-          str << <<-EOF.unindent
-            ns:assoc-1_#{original_assoc_id} prov:hadPlan ns:plan-1.
-
-            ns:plan-1 a prov:Plan ;
-              rdfs:comment (#{steps});
-
-          EOF
-        end
-      end
-
-      if original[:author]
-        str << "<#{original[:author]}> a prov:Agent, prov:Person .\n"
-        str << "ns:activity-1 prov:wasAssociatedWith <#{original[:author]}> .\n"
-
-        str << "<#{original[:author]}> foaf:givenName \"#{original[:author_name]}\" .\n" if original[:author_name]
-
-        if original[:organization]
-          str << "<#{original[:author]}> prov:actedOnBehalfOf <#{original[:organization]}> .\n\n"
-          str << "<#{original[:organization]}> a prov:Agent, prov:Organization.\n"
-          if original[:organization_name]
-            str << "<#{original[:organization]}> foaf:name \"#{original[:organization_name]}\" .\n\n"
-          else
-            str << "\n"
-          end
-        else
-          str << "\n"
-        end
-      end
-
-      if triplified
-        triples_assoc_id = Time.now.nsec.to_s(32)
-
-        str << <<-EOF.unindent
-          <#{triplified[:resource]}> a prov:Entity;
-            prov:wasGeneratredBy ns:activity-0 .
-
-          </ns/R2RDF> a prov:Agent, prov:SoftwareAgent ;
-            rdfs:label "Semantic Publishing Toolkit" .
-
-          ns:activity-0 a prov:Activity ;
-            prov:qualifiedAssociation ns:assoc-0_#{triples_assoc_id};
-            prov:generated <#{triplified[:resource]}> ;
-            prov:used <#{original[:resource]}> .
-
-          ns:assoc-0_#{triples_assoc_id} a prov:Assocation ;
-            prov:entity </ns/R2RDF>;
-            prov:hadPlan ns:plan-0.
-
-          ns:plan-0 a prov:Plan ;
-            rdfs:comment "generation of <#{triplified[:resource]}> by R2RDF gem" .
-
-        EOF
-
-        if triplified[:author]
-          str << "<#{triplified[:author]}> a prov:Agent, prov:Person .\n"
-
-          str << "<#{triplified[:author]}> foaf:givenName \"#{triplified[:author_name]}\" .\n" if triplified[:author_name]
-
-          if triplified[:organization]
-            str << "<#{triplified[:author]}> prov:actedOnBehalfOf <#{triplified[:organization]}> .\n\n"
-            str << "<#{triplified[:organization]}> a prov:Agent, prov:Organization.\n"
-            if triplified[:organization_name]
-              str << "<#{triplified[:organization]}> foaf:name \"#{triplified[:organization_name]}\" .\n\n"
-            else
-              str << "\n"
-            end
-          else
-            str << "\n"
-          end
-        end
-      end
-
-      if chain
-        str << "ns:activity-1 prov:used <#{chain.first[:resource]}> .\n"
-        str << "<#{original[:resource]}> prov:wasDerivedFrom <#{chain.first[:resource]}> .\n\n"
-        chain.each_with_index{ |src,i|
-          if i == chain.size-1
-            str << activity(src[:resource],nil,src)
-          else
-            str << activity(src[:resource],chain[i+1][:resource],src)
-          end
-        }
-      end
-
-      str
-    end
-
-    def activity(entity, used, options={})
-      assoc_id = Time.now.nsec.to_s(32)
-      activity_id = Time.now.nsec.to_s(32)
-      plan_id = Time.now.nsec.to_s(32)
-
-      raise "NoEntityGiven: activity generation requires a subject entity" unless entity
-
-      entity_str = <<-EOF.unindent
-        <#{entity}> a prov:Entity ;
-          prov:wasGeneratredBy ns:activity-a_#{activity_id} ;
-      EOF
-
-      activity_str = <<-EOF.unindent
-        ns:activity-a_#{activity_id} a prov:Activity ;
-          prov:generated <#{entity}> ;
-      EOF
-
-      if used
-        entity_str << "\tprov:wasDerivedFrom <#{used}> . \n\n"
-        activity_str << "\tprov:used <#{used}> . \n\n"
-      else
-        entity_str[-2] = ".\n"
-        activity_str[-2] = ".\n"
-      end
-
-      activity_str << <<-EOF.unindent
-        ns:activity-a_#{activity_id} prov:qualifiedAssociation ns:assoc-s_#{assoc_id} .
-
-        ns:assoc-s_#{assoc_id} a prov:Assocation .
-
-      EOF
-
-      if options[:software]
-
-        activity_str << <<-EOF.unindent
-          <#{options[:software]}> a prov:Entity .
-
-          ns:assoc-s_#{assoc_id} prov:agent <#{options[:software]}> .
-        EOF
-
-        if options[:process]
-          options[:process] = IO.read(options[:process]) if File.exist? options[:process]
-
-          steps = '"' + options[:process].split("\n").join('" "') + '"'
-          activity_str << <<-EOF.unindent
-            ns:assoc-s_#{assoc_id} prov:hadPlan ns:plan-p_#{plan_id}.
-
-            ns:plan-p_#{plan_id} a prov:Plan ;
-              rdfs:comment (#{steps});
-          EOF
-        end
-      end
-
-      if options[:author]
-        entity_str << "<#{options[:author]}> a prov:Agent, prov:Person .\n"
-        entity_str << "<#{options[:author]}> foaf:givenName \"#{options[:author_name]}\" .\n" if options[:author_name]
-
-        activity_str << "ns:activity-a_#{activity_id} prov:wasAssociatedWith <#{options[:author]}> .\n"
-        activity_str << "ns:assoc-s_#{assoc_id} prov:agent <#{options[:author]}> .\n"
-
-        if options[:organization]
-          entity_str << "<#{options[:organization]}> a prov:Agent, prov:Organization .\n"
-          activity_str << "<#{options[:author]}> prov:actedOnBehalfOf <#{options[:organization]}> .\n\n"
-          if options[:organization_name]
-            entity_str << "<#{options[:organization]}> foaf:name \"#{options[:organization_name]}\" .\n\n"
-          end
-        else
-          activity_str << "\n"
-          # entity_str << "\n"
-        end
-      end
-
-      entity_str + "\n" + activity_str
-    end
-
-    def process(id, step_string, software_resource, software_var, options={})
-      #TODO a better predicate for the steplist than rdfs:comment
-      # and make sure it looks good.
-      steps = '"' + step_string.split("\n").join('" "') + '"'
-      assoc_id = Time.now.nsec.to_s(32)
-      str = <<-EOF.unindent
-        ns:activity-#{id} a prov:Activity ;
-          prov:qualifiedAssociation ns:assoc-#{assoc_id} ;
-          prov:used </ns/dataset/#{software_var}#var>.
-
-        ns:assoc-#{id}_#{assoc_id} a prov:Assocation ;
-          prov:entity <#{software_resource}>;
-          prov:hadPlan ns:plan-#{id}.
-
-        ns:plan-#{id} a prov:Plan ;
-          rdfs:comment (#{steps});
-
-      EOF
-
-    end
-
-    def r2rdf_metadata
-      str <<-EOF.unindent
-      <#{options[:base_url]}/ns/R2RDF> a foaf:Agent;
-        foaf:name "R2RDF Semantic Web Toolkit";
-        org:memberOf <http://sciruby.com/>
-      EOF
-    end
-
-    def org_metadata
-      str <<-EOF.unindent
-        <http://sciruby.com/> a org:Organization, prov:Organization;
-          skos:prefLabel "SciRuby";
-          rdfs:description "A Project to Build and Improve Tools for Scientific Computing in Ruby".
-      EOF
-    end
-
-    def metadata_help(topic=nil)
-      if topic
-        puts "This should display help information for #{topic}, but there's none here yet :("
-      else
-        puts <<-EOF.unindent
-        Available metadata fields:
-        (Field)         (Ontology)                              (Description)
-
-        publishers      dct/foaf/org        The Organization/s responsible for publishing the dataset
-        subject         dct                 The subject of this dataset. Use resources when possible
-        var             dct                 The name of the datset resource (used internally)
-        creator         dct                 The person or process responsible for creating the dataset
-        description     dct/rdfs            A descriptions of the dataset
-        issued          dct                 The date of issuance for the dataset
-
-        EOF
-      end
-    end
+module PubliSci
+  class Metadata
+    extend PubliSci::Registry
   end
 end

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

@@ -1,5 +1,5 @@
 module PubliSci
-module Prov
+class Prov
   class Activity
     include Prov::Element
     class Associations < Array
@@ -26,6 +26,8 @@ module Prov
     def generated(entity=nil)
       if entity.is_a? Entity
         entity.generated_by self
+      elsif Prov.entities[entity]
+        Prov.entities[entity].generated_by self
       end
       basic_list(:generated,:entities,Generations,entity)
     end

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

@@ -1,5 +1,5 @@
 module PubliSci
-  module Prov
+  class Prov
     class Agent
       include Prov::Element
       attr_accessor :organization

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

@@ -1,5 +1,5 @@
 module PubliSci
-module Prov
+class Prov
   class Association
     include Prov::Element
 
@@ -95,7 +95,7 @@ module Prov
       str << "\tprov:agent <#{agent}> ;\n"
       str << "\tprov:hadPlan <#{plan}> ;\n" if plan
       str << "\tprov:hadRole <#{role}> ;\n" if role
-      str[-2] = ".\n"
+      str << "\trdfs:label \"#{__label}\".\n\n"
       str
     end
 

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

@@ -0,0 +1,34 @@
+module PubliSci
+  class Prov
+    class Configuration
+      def self.defaults
+        {
+          output: :generate_n3,
+          abbreviate: false,
+          repository: :in_memory,
+          repository_url: 'http://localhost:8080/'
+        }
+      end
+
+      defaults.keys.each{|k|
+        default = defaults[k]
+        define_method(k) do |input=nil|
+          var = instance_variable_get :"@#{k}"
+          if var
+            var
+          else
+            instance_variable_set :"@#{k}", default
+          end
+
+          if input
+            instance_variable_set :"@#{k}", input
+          end
+
+          instance_variable_get :"@#{k}"
+        end
+
+        attr_writer k
+      }
+    end
+  end
+end

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

@@ -1,9 +1,14 @@
 module PubliSci
-  module Prov
+  class Prov
     class Derivation
 
       include PubliSci::CustomPredicate
 
+    def __label
+      # raise "MissingInternalLabel: no __label for #{self.inspect}" unless @__label
+      @__label ||= Time.now.nsec.to_s(32)
+    end
+
       def subject(sub=nil)
         if sub
           @subject = sub
@@ -40,10 +45,10 @@ module PubliSci
         str = "<#{subject}> a prov:Derivation ;\n"
         str << "\tprov:entity <#{entity}> ;\n" if entity
         str << "\tprov:hadActivity <#{had_activity}> ;\n" if had_activity
+        str << "\trdfs:label \"#{__label}\".\n\n"
 
         add_custom(str)
 
-        str[-2] = ".\n"
         str
       end
 

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

@@ -1,5 +1,5 @@
 module PubliSci
-  module Prov
+  class Prov
     module Element
       include PubliSci::Vocabulary
       include PubliSci::CustomPredicate
@@ -103,7 +103,7 @@ module PubliSci
             instance_variable_set("@#{var}",collection_class.new)
           end
           instance_variable_get("@#{var}") << inst
-          Prov.register(type,inst)
+          Prov.register(inst.__label,inst)
         else
           if name
             unless instance_variable_get("@#{var}")

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

@@ -1,5 +1,5 @@
 module PubliSci
-  module Prov
+  class Prov
     class Entity
       include Prov::Element
 
@@ -28,31 +28,10 @@ module PubliSci
 
       def attributed_to(agent=nil)
         basic_keyword(:attributed_to,:agents,agent)
-        # if agent
-        #   @attributed_to = agent
-        # elsif @attributed_to.is_a? Symbol
-        #   raise "UnknownAgent: #{@attributed_to}" unless Prov.agents[@attributed_to]
-        #   @attributed_to = Prov.agents[@attributed_to]
-        # else
-        #   @attributed_to
-        # end
       end
 
       def derived_from(entity=nil,&block)
         block_list(:derived_from,:derivations,Derivation,Derivations,entity,&block)
-        # if block_given?
-        #   deriv = Derivation.new
-        #   deriv.instance_eval(&block)
-        #   (@derived_from ||= Derivations.new) << deriv
-        #   Prov.register(nil,deriv)
-        # else
-        #   if entity
-
-        #     (@derived_from ||= Derivations.new) << entity
-        #   else
-        #     @derived_from
-        #   end
-        # end
       end
 
       def to_n3