linked_research_metadata 0.1.1 → 0.2.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -4,9 +4,14 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## Unreleased
 
+## 0.2.0 - 2017-07-28
+### Added
+- Granularity control for associated resource URIs.
+- Identifiers available as a hash of sets.
+
 ## 0.1.1 - 2017-07-03
 ### Fixed
-- Strings become URIs for rdf::type.
+- Strings become URIs for rdf:type.
 
 ## 0.1.0 - 2017-06-30
 ### Added

data/MODEL.md

@@ -1,18 +1,18 @@
 # Data Model
-Version 0.1.0
+Version 0.2.0
 
 ## Prefixes
 Prefix | URI
 --- | ---
-dcterms | http://purl.org/dc/terms/
-foaf | http://xmlns.com/foaf/0.1/
-mads | http://www.loc.gov/mads/rdf/v1#
-owl | http://www.w3.org/2002/07/owl#
-premis | http://www.loc.gov/premis/rdf/v1#
-rdf | http://www.w3.org/1999/02/22-rdf-syntax-ns#
-swpo | http://sw-portal.deri.org/ontologies/swportal#
-vivo | http://vivoweb.org/ontology/core#
-xsd | http://www.w3.org/2001/XMLSchema#
+dcterms: | http://purl.org/dc/terms/
+foaf: | http://xmlns.com/foaf/0.1/
+mads: | http://www.loc.gov/mads/rdf/v1#
+owl: | http://www.w3.org/2002/07/owl#
+premis: | http://www.loc.gov/premis/rdf/v1#
+rdf: | http://www.w3.org/1999/02/22-rdf-syntax-ns#
+swpo: | http://sw-portal.deri.org/ontologies/swportal#
+vivo: | http://vivoweb.org/ontology/core#
+xsd: | http://www.w3.org/2001/XMLSchema#
 
 ## Resources
 
@@ -21,12 +21,12 @@ Property | Value | Cardinality
 --- | --- | ---
 dcterms:available | xsd:date | 1
 dcterms:created | xsd:date | 1
-dcterms:creator | URI | 1..n
-dcterms:contributor | URI | 0..n
+dcterms:creator | Person URI | 1..n
+dcterms:contributor | Person URI | 0..n
 dcterms:description | Literal (String) | 0..1
-dcterms:hasPart | URI | 0..n
-dcterms:identifier | URI. DOI. | 0..1
-dcterms:relation | URI | 0..n
+dcterms:hasPart | File URI | 0..n
+dcterms:identifier | DOI URI | 0..1
+dcterms:relation | Dataset, Publication URI | 0..n
 dcterms:spatial | Literal (String) | 0..n
 dcterms:subject | Literal (String) | 0..n
 dcterms:temporal | Literal (String). RKMS‐ISO8601 form. | 0..1
@@ -52,7 +52,7 @@ rdf:type | foaf:Organization | 1
 Property | Value | Cardinality
 --- | --- | ---
 foaf:name | Literal (String) | 1
-mads:hasAffiliation | URI | 0..n
+mads:hasAffiliation | Organisation URI | 0..n
 rdf:type | foaf:Person | 1
 vivo:OrcidId | URI | 0..1
 
@@ -60,7 +60,10 @@ vivo:OrcidId | URI | 0..1
 Property | Value | Cardinality
 --- | --- | ---
 dcterms:title | Literal (String) | 1
+foaf:homepage | URI | 0..1
 rdf:type | vivo:Project | 1
+vivo:PrincipalInvestigatorRole | Literal (String) | 0..1
+vivo:CoPrincipalInvestigatorRole | Literal (String) | 0..n
 
 ### Publication
 Property | Value | Cardinality

data/README.md

@@ -34,7 +34,8 @@ config = {
   url:      ENV['PURE_URL'],
   username: ENV['PURE_USERNAME'],
   password: ENV['PURE_PASSWORD'],
-  minting_uri: 'http://data.example.com'
+  minting_uri: 'http://data.example.com',
+  granularity: 1
 }
 ```
 
@@ -42,10 +43,32 @@ config = {
 # Pure host without authentication.
 config = {
   url: ENV['PURE_URL'],
-  minting_uri: 'http://data.example.com'
+  minting_uri: 'http://data.example.com',
+  granularity: 2
 }
 ```
 
+#### Parameters
+
+**minting_uri**
+
+Prefix for URIs minted e.g.
+
+```
+http://data.example.com/datasets/c11d50c1-ade2-493a-ab42-ca54ef233b78
+```
+
+UUIDs used are system identifiers wherever possible.
+
+
+**granularity**
+
+Control how much metadata is put into the graph for associated resources.
+
++ 0 - gives resource URI only. Omitting the parameter has the same effect.
++ 1 - gives resource URI plus type and title/name from the model metadata.
++ 2 - gives resource URI plus all the model metadata for a resource.
+
 ### Transformation
 
 Create a metadata transformer for a Pure dataset.
@@ -61,3 +84,23 @@ graph = transformer.transform uuid: 'xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx'
 ```
 
 ...and get an RDF graph.
+
+### Some possible publishing strategies
+
+Associated identifiers (UUIDs) are available after transformation in a hash of
+sets for :dataset, :organisation, :person, :project, and :publication.
+Organisation is only available if the granularity parameter is set to 2.
+
++ Transform a single resource, setting granularity to 0, 1 or 2.
+
++ Transform a single dataset resource, setting granularity to 0. Transform
+other resources using UUIDs from the identifiers hash later, setting
+granularity to 2.
+
++ Transform a single dataset resource, setting granularity to 0. Repeat,
+combining statements together from subsequent graphs and merging subsequent sets
+of identifiers. Transform other resources using UUIDs from the identifiers hash
+later, setting granularity to 2.
+
++ Transform a single dataset resource, setting granularity to 2.
+Repeat, combining statements from subsequent graphs into a larger graph.

data/lib/linked_research_metadata.rb

@@ -1,7 +1,11 @@
 require 'puree'
 require 'linkeddata'
+require 'linked_research_metadata/transformer/shared'
 require 'linked_research_metadata/transformer/base'
 require 'linked_research_metadata/transformer/dataset'
+require 'linked_research_metadata/transformer/organisation'
+require 'linked_research_metadata/transformer/person'
+require 'linked_research_metadata/transformer/project'
 require 'linked_research_metadata/version'
 
 # Metadata extraction from the Pure Research Information System and

data/lib/linked_research_metadata/transformer/base.rb

@@ -10,14 +10,60 @@ module LinkedResearchMetadata
       # @option config [String] :username The username of the Pure host account.
       # @option config [String] :password The password of the Pure host account.
       # @option config [String] :minting_uri The URI at which to mint a resource.
+      # @option config [Fixnum] :granularity Expand associated resource URIs with varying amounts of metadata.
+
       def initialize(config)
         @config = config
+        @config[:granularity] = 0 if !@config[:granularity]
         raise 'Minting URI missing' if @config[:minting_uri].empty?
         @graph = RDF::Graph.new
+        @identifiers = {
+            dataset: Set.new,
+            organisation: Set.new,
+            person: Set.new,
+            project: Set.new,
+            publication: Set.new
+        }
+      end
+
+      # Pure UUIDs available after transformation for :dataset, :organisation,
+      # :person, :project, :publication.
+      #
+      # @return [Hash{Symbol => Set<String>}]
+      def identifiers
+        @identifiers
       end
 
       private
 
+      def make_transformer(resource)
+        resource_class = "LinkedResearchMetadata::Transformer::#{resource.to_s.capitalize}"
+        Object.const_get(resource_class).new @config
+      end
+
+      # @param uuid [String]
+      # @param resource [Symbol]
+      # @return [RDF::Graph]
+      def transform(uuid:, resource:)
+        resource_class = "Puree::Extractor::#{resource.to_s.capitalize}"
+        resource_extractor = Object.const_get(resource_class).new @config
+        @resource = resource_extractor.find uuid: uuid
+        if @resource
+          resource_uri = mint_uri uuid, resource
+          @resource_uri = RDF::URI.new(resource_uri)
+          build_graph
+        end
+        @graph
+      end
+
+      def merge_graph(graph)
+        graph.each { |i| @graph << i }
+      end
+
+      def merge_identifiers(identifiers)
+        @identifiers.each { |k,v| v.merge identifiers[k] }
+      end
+
       def add_triple(subject, predicate, object)
         @graph << [ subject, predicate, object ]
       end
@@ -43,6 +89,18 @@ module LinkedResearchMetadata
         File.join @config[:minting_uri], uri_resource_map[resource], uuid
       end
 
+      def identifiers_to_graph(resource)
+        graph = RDF::Graph.new
+        @identifiers[resource].each do |i|
+          identifiers_graph = RDF::Graph.new
+          transformer = make_transformer resource
+          graph = transformer.transform uuid: i
+          identifiers_graph.each { |i| graph << i }
+        end
+        graph
+      end
+
+
     end
   end
 end

data/lib/linked_research_metadata/transformer/dataset.rb

@@ -4,12 +4,14 @@ module LinkedResearchMetadata
     # Dataset transformer
     #
     class Dataset < Base
+      include LinkedResearchMetadata::Transformer::Shared
 
       # @param config [Hash]
       # @option config [String] :url The URL of the Pure host.
       # @option config [String] :username The username of the Pure host account.
       # @option config [String] :password The password of the Pure host account.
       # @option config [String] :minting_uri The URI at which to mint a resource.
+      # @option config [Fixnum] :granularity Expand associated resource URIs with varying amounts of metadata.
       def initialize(config)
         super
       end
@@ -19,21 +21,11 @@ module LinkedResearchMetadata
       # @param uuid [String]
       # @return [RDF::Graph]
       def transform(uuid:)
-        dataset_extractor = Puree::Extractor::Dataset.new @config
-        @resource = dataset_extractor.find uuid: uuid
-        raise 'No metadata for ' + uuid if !@resource
-        dataset_uri = mint_uri uuid, :dataset
-        @resource_uri = RDF::URI.new(dataset_uri)
-        build_graph
-        @graph
+        super uuid: uuid, resource: :dataset
       end
 
       private
 
-      def meta
-        add_triple @resource_uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Dataset")
-      end
-
       def available
         object = @resource.available
         if object
@@ -72,24 +64,24 @@ module LinkedResearchMetadata
 
           add_triple @resource_uri, RDF::Vocab::DC.hasPart, file_uri
 
-          # license
-          if i.license && i.license.url
+          minimal_file file_uri, i if @config[:granularity] > 0
+
+          if @config[:granularity] > 1
+
+            # license
+            if i.license && i.license.url
               uri = RDF::URI.new(i.license.url)
               add_triple file_uri, RDF::Vocab::DC.license, uri
-          end
-
-          # mime
-          add_triple file_uri, RDF::Vocab::DC.format, i.mime
+            end
 
-          # size
-          size_predicate = RDF::Vocab::DC.extent
-          add_triple file_uri, size_predicate, i.size
+            # mime
+            add_triple file_uri, RDF::Vocab::DC.format, i.mime
 
-          #name
-          add_triple file_uri, RDF::Vocab::DC.title, i.name
+            # size
+            size_predicate = RDF::Vocab::DC.extent
+            add_triple file_uri, size_predicate, i.size
+          end
 
-          #type
-          add_triple file_uri, RDF.type, RDF::Vocab::PREMIS.File
         end
       end
 
@@ -99,46 +91,31 @@ module LinkedResearchMetadata
         end
       end
 
-      def person(person_uri, uuid, name)
-        add_triple person_uri, RDF.type, RDF::Vocab::FOAF.Person
-        add_triple person_uri, RDF::Vocab::FOAF.name, name
-        person_extractor = Puree::Extractor::Person.new @config
-        person = person_extractor.find uuid: uuid
-        if person
-          person.affiliations.each do |i|
-            organisation_uri = RDF::URI.new(mint_uri(i.uuid, :organisation))
-            add_triple person_uri, RDF::Vocab::MADS.hasAffiliation, organisation_uri
-            add_triple organisation_uri, RDF::Vocab::DC.title, i.name
-            add_triple organisation_uri, RDF.type, RDF::Vocab::FOAF.Organization
-          end
-          if person.orcid
-            orcid_uri = RDF::URI.new("http://orcid.org/#{person.orcid}")
-            orcid_predicate_uri = RDF::URI.new("#{vocab(:vivo)}OrcidId")
-            add_triple person_uri, orcid_predicate_uri, orcid_uri
-          end
-        end
-      end
-
       def projects
         @resource.projects.each do |i|
+          @identifiers[:project] << i.uuid
           project_uri = RDF::URI.new(mint_uri(i.uuid, :project))
           add_triple @resource_uri, RDF::Vocab::DC.relation, project_uri
-          add_triple project_uri, RDF::Vocab::DC.title, i.title
-          add_triple project_uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Project")
+          minimal_project project_uri, i  if @config[:granularity] > 0
+          if @config[:granularity] > 1
+            transformer = make_transformer :project
+            graph = transformer.transform uuid: i.uuid
+            merge_graph graph if graph
+          end
         end
       end
 
       def publications
         @resource.publications.each do |i|
           if i.type == 'Dataset'
+            @identifiers[:dataset] << i.uuid
             publication_uri = RDF::URI.new(mint_uri(i.uuid, :dataset))
-            add_triple publication_uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Dataset")
           else
+            @identifiers[:publication] << i.uuid
             publication_uri = RDF::URI.new(mint_uri(i.uuid, :publication))
-            add_triple publication_uri, RDF.type, RDF::URI.new("#{vocab(:swpo)}Publication")
           end
           add_triple @resource_uri, RDF::Vocab::DC.relation, publication_uri
-          add_triple publication_uri, RDF::Vocab::DC.title, i.title
+          minimal_publication publication_uri, i if @config[:granularity] > 0
         end
       end
 
@@ -153,24 +130,30 @@ module LinkedResearchMetadata
         all_persons << @resource.persons_other
         all_persons.each do |person_type|
           person_type.each do |i|
-            name = i.name.first_last
             if i.uuid
               uuid = i.uuid
+              @identifiers[:person] << i.uuid
             else
               uuid = SecureRandom.uuid
             end
-            person_uri = RDF::URI.new(mint_uri(uuid, :person))
-            if i.role == 'Creator'
-              add_triple @resource_uri, RDF::Vocab::DC.creator, person_uri
-              person person_uri, uuid, name
-            end
-            if i.role == 'Contributor'
-              add_triple @resource_uri, RDF::Vocab::DC.contributor, person_uri
-              person person_uri, uuid, name
+            if i.name
+              person_uri = RDF::URI.new(mint_uri(uuid, :person))
+              if i.role == 'Creator'
+                add_triple @resource_uri, RDF::Vocab::DC.creator, person_uri
+              end
+              if i.role == 'Contributor'
+                add_triple @resource_uri, RDF::Vocab::DC.contributor, person_uri
+              end
+              minimal_person(person_uri, i) if @config[:granularity] > 0
+              if i.uuid && @config[:granularity] > 1
+                transformer = make_transformer :person
+                graph = transformer.transform uuid: uuid
+                merge_graph graph if graph
+                merge_identifiers transformer.identifiers
+              end
             end
           end
         end
-
       end
 
       def spatial
@@ -202,8 +185,11 @@ module LinkedResearchMetadata
         end
       end
 
+      def type
+        add_triple @resource_uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Dataset")
+      end
+
       def build_graph
-        meta
         available
         created
         description
@@ -217,6 +203,7 @@ module LinkedResearchMetadata
         spatial
         temporal
         title
+        type
       end
 
     end

data/lib/linked_research_metadata/transformer/organisation.rb

@@ -0,0 +1,43 @@
+module LinkedResearchMetadata
+  module Transformer
+
+    # Organisation transformer
+    #
+    class Organisation < Base
+
+      # @param config [Hash]
+      # @option config [String] :url The URL of the Pure host.
+      # @option config [String] :username The username of the Pure host account.
+      # @option config [String] :password The password of the Pure host account.
+      # @option config [String] :minting_uri The URI at which to mint a resource.
+      # @option config [Fixnum] :granularity Expand associated resource URIs with varying amounts of metadata.
+      def initialize(config)
+        super
+      end
+
+      # Organisation transformation
+      #
+      # @param uuid [String]
+      # @return [RDF::Graph]
+      def transform(uuid:)
+        super uuid: uuid, resource: :organisation
+      end
+
+      private
+
+      def name
+        add_triple @resource_uri, RDF::Vocab::DC.title, @resource.name
+      end
+
+      def type
+        add_triple @resource_uri, RDF.type, RDF::Vocab::FOAF.Organization
+      end
+
+      def build_graph
+        name
+        type
+      end
+
+    end
+  end
+end

data/lib/linked_research_metadata/transformer/person.rb

@@ -0,0 +1,68 @@
+module LinkedResearchMetadata
+  module Transformer
+
+    # Person transformer
+    #
+    class Person < Base
+      include LinkedResearchMetadata::Transformer::Shared
+
+      # @param config [Hash]
+      # @option config [String] :url The URL of the Pure host.
+      # @option config [String] :username The username of the Pure host account.
+      # @option config [String] :password The password of the Pure host account.
+      # @option config [String] :minting_uri The URI at which to mint a resource.
+      # @option config [Fixnum] :granularity Expand associated resource URIs with varying amounts of metadata.
+      def initialize(config)
+        super
+      end
+
+      # Person transformation
+      #
+      # @param uuid [String]
+      # @return [RDF::Graph]
+      def transform(uuid:)
+        super uuid: uuid, resource: :person
+      end
+
+      private
+
+      def affiliations
+        @resource.affiliations.each do |i|
+          @identifiers[:organisation] << i.uuid
+          organisation_uri = RDF::URI.new(mint_uri(i.uuid, :organisation))
+          add_triple @resource_uri, RDF::Vocab::MADS.hasAffiliation, organisation_uri
+          minimal_organisation organisation_uri, i if @config[:granularity] > 0
+          if @config[:granularity] > 1
+            transformer = make_transformer :organisation
+            graph = transformer.transform uuid: i.uuid
+            merge_graph graph if graph
+          end
+        end
+      end
+
+      def name
+        add_triple @resource_uri, RDF::Vocab::FOAF.name, @resource.name.first_last
+      end
+
+      def orcid
+        if @resource.orcid
+          orcid_uri = RDF::URI.new("http://orcid.org/#{@resource.orcid}")
+          orcid_predicate_uri = RDF::URI.new("#{vocab(:vivo)}OrcidId")
+          add_triple @resource_uri, orcid_predicate_uri, orcid_uri
+        end
+      end
+
+      def type
+        add_triple @resource_uri, RDF.type, RDF::Vocab::FOAF.Person
+      end
+
+      def build_graph
+        affiliations
+        name
+        orcid
+        type
+      end
+
+    end
+  end
+end

data/lib/linked_research_metadata/transformer/project.rb

@@ -0,0 +1,90 @@
+module LinkedResearchMetadata
+  module Transformer
+
+    # Project transformer
+    #
+    class Project < Base
+      include LinkedResearchMetadata::Transformer::Shared
+
+      # @param config [Hash]
+      # @option config [String] :url The URL of the Pure host.
+      # @option config [String] :username The username of the Pure host account.
+      # @option config [String] :password The password of the Pure host account.
+      # @option config [String] :minting_uri The URI at which to mint a resource.
+      # @option config [Fixnum] :granularity Expand associated resource URIs with varying amounts of metadata.
+      def initialize(config)
+        super
+      end
+
+      # Project transformation
+      #
+      # @param uuid [String]
+      # @return [RDF::Graph]
+      def transform(uuid:)
+        super uuid: uuid, resource: :project
+      end
+
+      private
+
+      def roles
+        all_persons = []
+        all_persons << @resource.persons_internal
+        all_persons << @resource.persons_external
+        all_persons << @resource.persons_other
+        all_persons.each do |person_type|
+          person_type.each do |i|
+            name = i.name.first_last if i.name
+            if i.uuid
+              uuid = i.uuid
+            else
+              uuid = SecureRandom.uuid
+            end
+            if name
+              person_uri = RDF::URI.new(mint_uri(uuid, :person))
+              if i.role == 'Principal Investigator'
+                role_uri = RDF::URI.new("#{vocab(:vivo)}PrincipalInvestigatorRole")
+                add_triple @resource_uri, role_uri, person_uri
+              end
+              if i.role == 'Co-investigator'
+                role_uri = RDF::URI.new("#{vocab(:vivo)}CoPrincipalInvestigatorRole")
+                add_triple @resource_uri, role_uri, person_uri
+              end
+              minimal_person(person_uri, i) if @config[:granularity] > 0
+            end
+            # Phd Student
+            # RA
+            # Researcher
+            # Research Associate
+            # Team Member
+          end
+        end
+      end
+
+      def title
+        object = @resource.title
+        if object
+          add_triple @resource_uri, RDF::Vocab::DC.title, object
+        end
+      end
+
+      def type
+        add_triple @resource_uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Project")
+      end
+
+      def url
+        object = @resource.url
+        if object
+          add_triple @resource_uri, RDF::Vocab::FOAF.homepage, RDF::URI.new(object)
+        end
+      end
+
+      def build_graph
+        roles
+        title
+        type
+        url
+      end
+
+    end
+  end
+end

data/lib/linked_research_metadata/transformer/shared.rb

@@ -0,0 +1,45 @@
+module LinkedResearchMetadata
+  module Transformer
+
+    # Shared
+    #
+    module Shared
+
+      private
+
+      def minimal_file(uri, file)
+        #name
+        add_triple uri, RDF::Vocab::DC.title, file.name
+
+        #type
+        add_triple uri, RDF.type, RDF::Vocab::PREMIS.File
+      end
+
+      def minimal_organisation(uri, organisation_header)
+        add_triple uri, RDF.type, RDF::Vocab::FOAF.Organization
+        add_triple uri, RDF::Vocab::DC.title, organisation_header.name
+      end
+
+      def minimal_person(uri, person)
+        add_triple uri, RDF.type, RDF::Vocab::FOAF.Person
+        add_triple uri, RDF::Vocab::FOAF.name, person.name.first_last
+      end
+
+      def minimal_project(uri, related_content_header)
+        add_triple uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Project")
+        add_triple uri, RDF::Vocab::DC.title, related_content_header.title
+      end
+
+      def minimal_publication(uri, related_content_header)
+        if related_content_header.type == 'Dataset'
+          add_triple uri, RDF.type, RDF::URI.new("#{vocab(:vivo)}Dataset")
+        else
+          add_triple uri, RDF.type, RDF::URI.new("#{vocab(:swpo)}Publication")
+        end
+        add_triple uri, RDF::Vocab::DC.title, related_content_header.title
+      end
+
+    end
+
+  end
+end

data/lib/linked_research_metadata/version.rb

@@ -1,5 +1,5 @@
 module LinkedResearchMetadata
   # Semantic version number
   #
-  VERSION = "0.1.1"
+  VERSION = "0.2.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: linked_research_metadata
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.2.0
 platform: ruby
 authors:
 - Adrian Albin-Clark
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2017-07-03 00:00:00.000000000 Z
+date: 2017-07-28 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: puree
@@ -68,6 +68,10 @@ files:
 - lib/linked_research_metadata.rb
 - lib/linked_research_metadata/transformer/base.rb
 - lib/linked_research_metadata/transformer/dataset.rb
+- lib/linked_research_metadata/transformer/organisation.rb
+- lib/linked_research_metadata/transformer/person.rb
+- lib/linked_research_metadata/transformer/project.rb
+- lib/linked_research_metadata/transformer/shared.rb
 - lib/linked_research_metadata/transformer/transformer.rb
 - lib/linked_research_metadata/version.rb
 - linked_research_metadata.gemspec