bel 0.7.0 → 1.0.0

data/lib/bel/translator/plugins/rdfa.rb

@@ -4,7 +4,7 @@ module BEL::Translator::Plugins
 
     ID          = :rdfa
     NAME        = 'RDFa RDF Translator'
-    DESCRIPTION = 'A translator that can read and write RDFa (https://rdfa.info/) for BEL evidence.'
+    DESCRIPTION = 'A translator that can read/write BEL nanopubs to RDFa (https://rdfa.info/).'
     MEDIA_TYPES = %i(application/xml)
     EXTENSIONS  = %i(rdfa)
 

data/lib/bel/translator/plugins/rdfxml.rb

@@ -4,7 +4,7 @@ module BEL::Translator::Plugins
 
     ID          = :rdfxml
     NAME        = 'RDF/XML RDF Translator'
-    DESCRIPTION = 'A translator that can read and write RDF/XML for BEL evidence.'
+    DESCRIPTION = 'A translator that can read/write BEL nanopubs to RDF/XML.'
     MEDIA_TYPES = %i(application/rdf+xml)
     EXTENSIONS  = %i(rdf)
 

data/lib/bel/translator/plugins/rj.rb

@@ -4,7 +4,7 @@ module BEL::Translator::Plugins
 
     ID          = :rj
     NAME        = 'RDF/JSON RDF Translator'
-    DESCRIPTION = 'A translator that can read and write RDF/JSON (https://dvcs.w3.org/hg/rdf/raw-file/default/rdf-json/index.html) for BEL evidence.'
+    DESCRIPTION = 'A translator that can read/write BEL nanopubs to RDF/JSON (https://dvcs.w3.org/hg/rdf/raw-file/default/rdf-json/index.html).'
     MEDIA_TYPES = %i(application/rdf+json)
     EXTENSIONS  = %i(rj)
 

data/lib/bel/translator/plugins/trig.rb

@@ -4,7 +4,7 @@ module BEL::Translator::Plugins
 
     ID          = :trig
     NAME        = 'TriG RDF Translator'
-    DESCRIPTION = 'A translator that can read and write TriG (https://www.w3.org/TR/trig/) for BEL evidence.'
+    DESCRIPTION = 'A translator that can read/write BEL nanopubs to TriG.'
     MEDIA_TYPES = %i(application/trig)
     EXTENSIONS  = %i(trig)
 

data/lib/bel/translator/plugins/trix.rb

@@ -4,7 +4,7 @@ module BEL::Translator::Plugins
 
     ID          = :trix
     NAME        = 'TriX RDF Translator'
-    DESCRIPTION = 'A translator that can read and write TriX (https://en.wikipedia.org/wiki/TriX_(syntax)) for BEL evidence.'
+    DESCRIPTION = 'A translator that can read/write BEL nanopubs to TriX.'
     MEDIA_TYPES = %i(application/trix)
     EXTENSIONS  = %i(trix)
 

data/lib/bel/translator/plugins/turtle.rb

@@ -4,18 +4,15 @@ module BEL::Translator::Plugins
 
     ID          = :turtle
     NAME        = 'Turtle RDF Translator'
-    DESCRIPTION = 'A translator that can read and write turtle for BEL evidence.'
+    DESCRIPTION = 'A translator that can read/write BEL nanopubs to RDF Turtle.'
     MEDIA_TYPES = %i(application/turtle application/x-turtle)
     EXTENSIONS  = %i(ttl)
 
     def self.create_translator(options = {})
       require 'rdf'
       require 'rdf/turtle'
-      require_relative 'rdf/translator'
-      BELRDF::Translator.new(
-        ID,
-        options[:write_schema]
-      )
+      require_relative 'rdf2/translator'
+      BEL::BELRDF::Translator.new(ID, options[:write_schema])
     end
 
     def self.id

data/lib/bel/translator/plugins/xbel.rb

@@ -1,12 +1,11 @@
 module BEL::Translator::Plugins
-
   module Xbel
-
     ID          = :xbel
-    NAME        = 'XBEL Translator'
-    DESCRIPTION = 'A translator that can read and write evidence to XBEL (version 1.0). XBEL is an XML dialect. XML Schema for version 1.0 is published here (http://resource.belframework.org/belframework/1.0/schema/xbel.xsd).'
-    MEDIA_TYPES = %i(application/xml)
-    EXTENSIONS  = %i(xml xbel)
+    NAME        = 'XBEL Translator'.freeze
+    DESCRIPTION =
+      'A translator that can read/write BEL nanopubs to XBEL.'.freeze
+    MEDIA_TYPES = %i(application/xml).freeze
+    EXTENSIONS  = %i(xml xbel).freeze
 
     def self.create_translator(options = {})
       require_relative 'xbel/translator'

data/lib/bel/translator/plugins/xbel/nanopub_handler.rb

@@ -0,0 +1,625 @@
+require 'rexml/streamlistener'
+
+module BEL::Translator::Plugins
+  module Xbel
+    class NanopubHandler
+      include REXML::StreamListener
+      include ::BEL::Nanopub
+
+      ANNOTATION                     = 'annotation'.freeze
+      ANNOTATION_DEFINITION_GROUP    = 'annotationDefinitionGroup'.freeze
+      ANNOTATION_GROUP               = 'annotationGroup'.freeze
+      AUTHOR                         = 'author'.freeze
+      AUTHOR_GROUP                   = 'authorGroup'.freeze
+      BEL_VERSION                    = 'belVersion'.freeze
+      CITATION                       = 'citation'.freeze
+      COMMENT                        = 'comment'.freeze
+      CONTACT_INFO                   = 'contactInfo'.freeze
+      COPYRIGHT                      = 'copyright'.freeze
+      DATE                           = 'date'.freeze
+      DEFAULT_NAMESPACE              = 'defaultNamespace'.freeze
+      DESCRIPTION                    = 'description'.freeze
+      DOCUMENT                       = 'document'.freeze
+      EVIDENCE                       = 'evidence'.freeze
+      EXTERNAL_ANNOTATION_DEFINITION = 'externalAnnotationDefinition'.freeze
+      FUNCTION                       = 'function'.freeze
+      HEADER                         = 'header'.freeze
+      ID                             = 'id'.freeze
+      INTERNAL_ANNOTATION_DEFINITION = 'internalAnnotationDefinition'.freeze
+      LICENSE                        = 'license'.freeze
+      LICENSE_GROUP                  = 'licenseGroup'.freeze
+      LIST_ANNOTATION                = 'listAnnotation'.freeze
+      LIST_VALUE                     = 'listValue'.freeze
+      NAME                           = 'name'.freeze
+      NAMESPACE                      = 'namespace'.freeze
+      NAMESPACE_GROUP                = 'namespaceGroup'.freeze
+      NANOPUB                        = 'nanopub'.freeze
+      NS                             = 'ns'.freeze
+      OBJECT                         = 'object'.freeze
+      PARAMETER                      = 'parameter'.freeze
+      PATTERN_ANNOTATION             = 'patternAnnotation'.freeze
+      PREFIX                         = 'prefix'.freeze
+      RESOURCE                       = 'resource'.freeze
+      REFERENCE                      = 'reference'.freeze
+      REF_ID                         = 'refID'.freeze
+      RELATIONSHIP                   = 'relationship'.freeze
+      RESOURCE_LOCATION              = 'resourceLocation'.freeze
+      STATEMENT                      = 'statement'.freeze
+      STATEMENT_GROUP                = 'statementGroup'.freeze
+      SUBJECT                        = 'subject'.freeze
+      SUPPORT                        = 'support'.freeze
+      TERM                           = 'term'.freeze
+      TYPE                           = 'type'.freeze
+      URI                            = 'uri'.freeze
+      URL                            = 'url'.freeze
+      USAGE                          = 'usage'.freeze
+      VERSION                        = 'version'.freeze
+      Model                          = BELParser::Expression::Model
+
+      def initialize(callable)
+        @callable      = callable
+        @element_stack = []
+        @text          = nil
+        @nanopub       = Nanopub.new
+        @annotations   = {}
+        @namespaces    = {}
+        @spec          = BELParser::Language.latest_supported_specification
+
+        @last_prefix   = nil
+        @last_keyword  = nil
+        # default BEL version to 1 for backwards compatibility
+        @bel_version   = 1
+        @nanopub.metadata.bel_version = "1.0"
+      end
+
+      # Called on element start by REXML.
+      def tag_start(name, attributes)
+        name.
+          sub!(/^bel:/, '').
+          gsub!(/([A-Z])/) { |match| "_#{match.downcase}" }
+
+        start_method = "start_#{name}"
+        if self.respond_to? start_method
+          self.send(start_method, attributes)
+        end
+      end
+
+      # Called on element end by REXML.
+      def tag_end(name)
+        name.
+          sub!(/^bel:/, '').
+          gsub!(/([A-Z])/) { |match| "_#{match.downcase}" }
+
+        end_method = "end_#{name}"
+        if self.respond_to? end_method
+          self.send end_method
+        end
+      end
+
+      # Called on text node by REXML.
+      def text(*args)
+        if args.size.zero?
+          @text = ''
+        else
+          @text = args.first
+        end
+      end
+
+      # Start element methods, dynamically invoked.
+
+      def start_header(attributes)
+        @element_stack << :header
+      end
+
+      def start_namespace_group(attributes)
+        @element_stack << :namespace_group
+      end
+
+      def start_annotation_definition_group(attributes)
+        @element_stack << :annotation_definition_group
+      end
+
+      def start_namespace(attributes)
+        if stack_top == :namespace_group
+          prefix = attr_value(attributes, PREFIX)
+          @last_prefix = prefix
+          if @bel_version == 1
+            resource_location   = attr_value(attributes, RESOURCE_LOCATION)
+            @namespaces[prefix] = {keyword: prefix, uri: resource_location}
+          end
+        end
+        @element_stack << :namespace
+      end
+
+      def start_external_annotation_definition(attributes)
+        if stack_top == :annotation_definition_group
+          keyword               = attr_value(attributes, ID)
+          @last_keyword         = keyword
+          if @bel_version == 1
+            uri                   = attr_value(attributes, URL)
+            @annotations[keyword] =
+              {keyword: keyword, type: :uri, domain: uri}
+          end
+        end
+        @element_stack << :external_annotation_definition
+      end
+
+      def start_internal_annotation_definition(attributes)
+        if stack_top == :annotation_definition_group
+          @current_anno_def = {
+            :keyword => attr_value(attributes, ID)
+          }
+        end
+        @element_stack << :internal_annotation_definition
+      end
+
+      def start_list_annotation(attributes)
+        if stack_top == :internal_annotation_definition
+          @current_anno_def[:type]   = :list
+          @current_anno_def[:domain] = []
+        end
+        @element_stack << :list_annotation
+      end
+
+      def start_pattern_annotation(attributes)
+        if stack_top == :internal_annotation_definition
+          @current_anno_def[:type] = :pattern
+        end
+        @element_stack << :pattern_annotation
+      end
+
+      def start_statement_group(attributes)
+        @element_stack << :statement_group
+      end
+
+      def start_statement(attributes)
+        relationship = attr_value(attributes, RELATIONSHIP)
+        stmt = {
+          relationship: convert_relationship(relationship)
+        }
+        if stack_top == :statement_group
+          @statement_stack = []
+          @statement_stack << stmt
+        elsif stack_top == :object
+          #@statement_stack.last[:object] = stmt
+          @statement_stack << stmt
+        end
+
+        @element_stack << :statement
+      end
+
+      def start_subject(attributes)
+        @element_stack << :subject
+      end
+
+      def start_object(attributes)
+        @element_stack << :object
+      end
+
+      def start_term(attributes)
+        function = @spec.function(attr_value(attributes, FUNCTION).to_sym)
+        term = BELParser::Expression::Model::Term.new(function, [])
+        if stack_top == :subject || stack_top == :object
+          # outer term
+          @term_stack = []
+        elsif stack_top == :term
+          # nested term
+          @term_stack.last.arguments << term
+        end
+
+        @term_stack    << term
+        @element_stack << :term
+      end
+
+      def start_parameter(attributes)
+        if stack_top == :term
+          ns =
+            if has_attr?(attributes, NS)
+              ns_id = attr_value(attributes, NS)
+              namespace_reference(ns_id, @nanopub)
+            else
+              nil
+            end
+          @current_parameter = Model::Parameter.new(ns, ns_id)
+        end
+        @element_stack << :parameter
+      end
+
+      def start_annotation_group(attributes)
+        @annotation_id = nil
+        @element_stack << :annotation_group
+      end
+
+      def start_annotation(attributes)
+        if @element_stack[-2] == :statement
+          ref_id = attr_value(attributes, REF_ID)
+          @annotation_id = ref_id
+          @element_stack << :annotation
+        end
+      end
+
+      def start_evidence(attributes)
+        @element_stack << :evidence
+      end
+
+      def start_support(attributes)
+        @element_stack << :support
+      end
+
+      def start_citation(attributes)
+        type = attr_value(attributes, TYPE)
+        @nanopub.citation.type = type
+        @element_stack << :citation
+      end
+
+      def start_nanopub(attributes)
+        @element_stack << :nanopub
+      end
+
+      def start_default_namespace(attributes)
+        if stack_top == :namespace_group
+          prefix              = attr_value(attributes, PREFIX)
+          @namespaces[prefix] = {keyword: prefix}
+          @last_prefix        = prefix
+        end
+        @element_stack << :default_namespace
+      end
+
+      def end_default_namespace
+        @element_stack.pop
+        @last_prefix = nil
+      end
+
+      def start_resource(attributes)
+        @element_stack << :resource
+      end
+
+      def end_resource
+        @element_stack.pop
+      end
+
+      def start_uri(attributes)
+        @element_stack << :uri
+      end
+
+      def end_uri
+        # context is namespace or annotation
+        context = peek(-2)
+        if context == :namespace || context == :default_namespace
+          @namespaces[@last_prefix][:uri] = @text
+        elsif context == :external_annotation_definition
+          annotation = @annotations[@last_keyword]
+          annotation[:type] = :uri
+          annotation[:domain] = @text
+        end
+        @element_stack.pop
+      end
+
+      def start_url(attributes)
+        @element_stack << :url
+      end
+
+      def end_url
+        # context is namespace or annotation
+        context = peek(-2)
+        if context == :namespace || context == :default_namespace
+          @namespaces[@last_prefix][:url] = @text
+        elsif context == :external_annotation_definition
+          annotation = @annotations[@last_keyword]
+          annotation[:type] = :url
+          annotation[:domain] = @text
+        end
+        @element_stack.pop
+      end
+
+      # End element methods, dynamically invoked.
+
+      def end_header
+        @element_stack.pop
+      end
+
+      def end_version
+        if stack_top == :header
+          @nanopub.metadata.document_header[:Version] = @text
+        end
+      end
+
+      def end_copyright
+        if stack_top == :header
+          @nanopub.metadata.document_header[:Copyright] = @text
+        end
+      end
+
+      def end_contact_info
+        if stack_top == :header
+          @nanopub.metadata.document_header[:ContactInfo] = @text
+        end
+      end
+
+      def end_license
+        if stack_top == :header
+          @nanopub.metadata.document_header[:Licenses] ||= []
+          @nanopub.metadata.document_header[:Licenses]  << @text
+        end
+      end
+
+      def end_bel_version
+        if stack_top == :header
+          @nanopub.metadata.document_header[:BELVersion] ||= []
+          version = @text
+          @nanopub.metadata.document_header[:BELVersion]  << version
+          @bel_version = version
+          @nanopub.metadata.bel_version = @bel_version
+        end
+      end
+
+      def end_namespace_group
+        @element_stack.pop
+      end
+
+      def end_annotation_definition_group
+        @element_stack.pop
+      end
+
+      def end_namespace
+        @element_stack.pop
+        @last_prefix = nil
+      end
+
+      def end_external_annotation_definition
+        @element_stack.pop
+        @last_keyword = nil
+      end
+
+      def end_internal_annotation_definition
+        @element_stack.pop
+        keyword, type, domain =
+          @current_anno_def.values_at(:keyword, :type, :domain)
+        @annotations[keyword] =
+          {keyword: keyword, type: type, domain: domain}
+      end
+
+      def end_list_annotation
+        @element_stack.pop
+      end
+
+      def end_pattern_annotation
+        begin
+          @current_anno_def[:domain] = Regexp.new(@text)
+        rescue RegexpError
+          @text = Regexp.escape(@text)
+          retry
+        end
+        @element_stack.pop
+      end
+
+      def end_description
+        if stack_top == :header
+          @nanopub.metadata.document_header[:Description] = @text
+        end
+
+        if stack_top == :internal_annotation_definition
+          @current_anno_def[:description] = @text
+        end
+      end
+
+      def end_usage
+        if stack_top == :internal_annotation_definition
+          @current_anno_def[:usage] = @text
+        end
+      end
+
+      def end_list_value
+        if stack_top == :list_annotation
+          @current_anno_def[:domain] << @text
+        end
+      end
+
+      def end_statement_group
+        @element_stack.pop
+      end
+
+      def end_statement
+        @element_stack.pop
+        stmt = @statement_stack.pop
+
+        if stack_top == :object
+          @statement_stack.last[:object] =
+            BELParser::Expression::Model::Statement.new(
+              stmt[:subject],
+              stmt[:relationship],
+              stmt[:object],
+              stmt[:comment]
+            )
+        elsif @statement_stack.empty?
+          # create new nanopub from parsed data
+          nanopub_copy = Nanopub.create({
+            :bel_statement      =>
+              BELParser::Expression::Model::Statement.new(
+                stmt[:subject],
+                stmt[:relationship],
+                stmt[:object],
+                stmt[:comment]
+              ),
+            :citation           => @nanopub.citation.to_h,
+            :support            => @nanopub.support.value,
+            :experiment_context => @nanopub.experiment_context.values.dup,
+            :references         => {
+              :annotations => @annotations.values,
+              :namespaces => @namespaces.values
+            },
+            :metadata           => @nanopub.metadata.values.dup
+          })
+
+          # yield nanopub
+          @callable.call(nanopub_copy)
+
+          # clear nanopub parser state
+          # note:
+          #   - preserve @nanopub.references
+          #   - preserve @nanopub.metadata.document_header
+          @nanopub.bel_statement      = nil
+          @nanopub.citation           = nil
+          @nanopub.support            = nil
+          @nanopub.experiment_context = nil
+          @nanopub.metadata.delete_if { |key|
+            key != :document_header
+          }
+        end
+      end
+
+      def end_subject
+        @statement_stack.last[:subject] = @term_stack.last
+        @element_stack.pop
+      end
+
+      def end_object
+        if @statement_stack.last[:object] == nil
+          # sets object if it wasn't already set by OBJECT STATEMENT
+          @statement_stack.last[:object] = @term_stack.last
+        end
+        @element_stack.pop
+      end
+
+      def end_term
+        @element_stack.pop
+
+        if @term_stack.size > 1
+          @term_stack.pop
+          @current_term = @term_stack.last
+        end
+      end
+
+      def end_parameter
+        @current_parameter.value    = @text
+        @term_stack.last.arguments << @current_parameter
+        @element_stack.pop
+      end
+
+      def end_annotation_group
+        @element_stack.pop
+      end
+
+      def end_evidence
+        @nanopub.support.value = @text
+        @element_stack.pop
+      end
+
+      def end_support
+        @nanopub.support.value = @text
+        @element_stack.pop
+      end
+
+      def end_annotation
+        if @element_stack[-3] == :statement
+          ref_id = @annotation_id
+
+          annotation  = @nanopub.experiment_context.find { |annotation|
+            annotation[:name] == ref_id
+          }
+          if annotation
+            # create array for multiple values by refID
+            annotation[:value] = [annotation[:value], @text].flatten
+          else
+            @nanopub.experiment_context << {
+              :name  => ref_id,
+              :value => @text
+            }
+          end
+        end
+
+        @element_stack.pop
+      end
+
+      def end_nanopub
+        if @element_stack[-3] == :statement
+          @nanopub.support.value = @text
+        end
+
+        @element_stack.pop
+      end
+
+      def end_citation
+        @element_stack.pop
+      end
+
+      def end_reference
+        if stack_top == :citation
+          @nanopub.citation.id   = @text
+        end
+      end
+
+      def end_name
+        if stack_top == :header
+          @nanopub.metadata.document_header[:Name] = @text
+        end
+
+        if stack_top == :citation
+          @nanopub.citation.name = @text
+        end
+      end
+
+      def end_date
+        if stack_top == :citation
+          @nanopub.citation.date = @text
+        end
+      end
+
+      def end_author
+        if stack_top == :header
+          @nanopub.metadata.document_header[:Authors] ||= []
+          @nanopub.metadata.document_header[:Authors] <<  @text
+        end
+
+        if stack_top == :citation
+          @nanopub.citation.authors ||= []
+          @nanopub.citation.authors  << @text
+        end
+      end
+
+      def end_comment
+        if stack_top == :citation
+          @nanopub.citation.comment = @text
+        elsif stack_top == :statement
+          @statement_stack.last[:comment] = @text
+        end
+      end
+
+      private
+
+      def stack_top
+        @element_stack.last
+      end
+
+      def peek(index)
+        @element_stack[index]
+      end
+
+      def attr_value(attributes, attr_name)
+        attributes["bel:#{attr_name}"]
+      end
+
+      def has_attr?(attributes, attr_name)
+        attributes.has_key?("bel:#{attr_name}")
+      end
+
+      def namespace_reference(ns_id, nanopub)
+        namespace_reference = @namespaces[ns_id]
+        if namespace_reference
+          keyword, uri = namespace_reference.values_at(:keyword, :uri)
+          BELParser::Expression::Model::Namespace.new(keyword, uri)
+        else
+          nil
+        end
+      end
+
+      def convert_relationship(relationship)
+        if relationship
+          @spec.relationship(relationship.to_sym)
+        else
+          nil
+        end
+      end
+    end
+  end
+end