bel 0.7.0 → 1.0.0

data/lib/bel/parser.rb

@@ -1,39 +0,0 @@
-require_relative 'libbel'
-
-module BEL
-  module Parser
-
-    # Parses BEL expressions to a {BEL::LibBEL::BelAst}.
-    #
-    # If +bel_expression+ is +nil+ then +nil+ is returned.
-    #
-    # @param bel_expression [responds to #to_s] the bel expression to parse
-    # @return [BEL::LibBEL::BelAst]
-    def self.parse(bel_expression, options = {})
-      if !bel_expression
-        return nil
-      end
-
-      LibBEL.parse_statement(
-        ensure_newline(bel_expression.to_s)
-      )
-    end
-
-    private
-
-    # Ensures a newline (e.g. +\n+) is the last character in +string+.
-    #
-    # +Pure function+ but returns the +string+ reference if it already ends
-    # with a newline.
-    #
-    # @param string [String] the string which must have a newline
-    # @return [String]
-    def self.ensure_newline(string)
-      if string[-1] != "\n"
-        string + "\n"
-      else
-        string
-      end
-    end
-  end
-end

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

@@ -1,36 +0,0 @@
-module BEL::Translator::Plugins
-
-  module BelScript
-
-    ID          = :bel
-    NAME        = 'BEL Script Translator'
-    DESCRIPTION = 'A translator that can read and write evidence to BEL Script (version 1.0).'
-    MEDIA_TYPES = %i(application/bel)
-    EXTENSIONS  = %i(bel)
-
-    def self.create_translator(options = {})
-      require_relative 'bel_script/translator'
-      BelScriptTranslator.new
-    end
-
-    def self.id
-      ID
-    end
-
-    def self.name
-      NAME
-    end
-
-    def self.description
-      DESCRIPTION
-    end
-
-    def self.media_types
-      MEDIA_TYPES
-    end
-
-    def self.file_extensions
-      EXTENSIONS
-    end
-  end
-end

data/lib/bel/translator/plugins/bel_script/bel_citation_serialization.rb

@@ -1,125 +0,0 @@
-require_relative 'evidence_serialization.rb'
-
-# BEL Script evidence serialization that groups evidence by citation scoped to
-# individual statement groups (i.e. BEL Script's +SET STATEMENT_GROUP+ and
-# +UNSET STATEMENT_GROUP+).
-#
-# @example Citation serialization for a group of evidence
-#   SET STATEMENT_GROUP = 12857727
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   complex(p(HGNC:USF1),g(HGNC:IGF2R))
-#
-#   complex(p(HGNC:USF2),g(HGNC:IGF2R))
-#
-#   tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
-#
-#   tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
-#
-#   SET Evidence = "c-Myc was present on the CDK4 promoter to the ..."
-#   complex(p(HGNC:MYC),g(HGNC:CDK4))
-#   UNSET STATEMENT_GROUP
-module BEL::Translator::Plugins::BelScript::BelCitationSerialization
-  include BEL::Translator::Plugins::BelScript::EvidenceSerialization
-
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
-  #
-  # Includes +SET AnnotationName+ and +UNSET AnnotationName+ where needed in
-  # order to remove duplicating annotations.
-  #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
-  # @return [String]               the BEL Script string
-  def to_bel(evidence)
-    bel = ''
-
-    citation     = citation_value(evidence)
-    summary_text = summary_text_value(evidence)
-    annotations  = annotation_values(evidence)
-
-    current_annotations            = {}.merge(annotations)
-    current_annotations[:Citation] = citation if citation
-    current_annotations[:Evidence] = summary_text if summary_text
-
-    if !evidence.citation.id || evidence.citation.id.empty?
-      citation_id = quote('')
-    else
-      citation_id = quote_if_needed(evidence.citation.id)
-    end
-
-    # Reset cumulative annotations if new citation.
-    if cumulative_citation == nil
-      bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
-      cumulative_annotations.clear
-    elsif evidence.citation != cumulative_citation
-      bel << %Q{UNSET STATEMENT_GROUP\n}
-      bel << "\n\n"
-      bel << %Q{SET STATEMENT_GROUP = #{citation_id}\n}
-      cumulative_annotations.clear
-    end
-
-    # Hang on to the last citation.
-    self.cumulative_citation = evidence.citation
-
-    # UNSET unused annotations from previous evidence.
-    (cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
-      bel << "UNSET #{unset_key}\n"
-      cumulative_annotations.delete(unset_key)
-    end
-
-    # Remove annotation if key/value was SET by a previous evidence.
-    Hash[
-      cumulative_annotations.to_a & current_annotations.to_a
-    ].each do |same_k, _|
-      current_annotations.delete(same_k)
-    end
-
-    # Retain the current evidence's annotation in cumulative set.
-    cumulative_annotations.merge!(current_annotations)
-
-    # SET Citation
-    citation = current_annotations.delete(:Citation)
-    if citation
-      bel << "SET Citation = {#{citation}}\n"
-    end
-
-    # SET Evidence
-    summary_text = current_annotations.delete(:Evidence)
-    if summary_text
-      bel << %Q{SET Evidence = "#{summary_text}"\n}
-    end
-
-    # SET new or modified annotations
-    current_annotations.sort.each do |(name, value)|
-      bel << "SET #{name} = #{value}\n"
-    end
-
-    # Assert BEL statement
-    bel << "#{evidence.bel_statement}\n"
-
-    # Separate evidence by new line.
-    bel << "\n"
-
-    bel
-  end
-
-  private
-
-  # The cumulative citation that is active for the current evidence. This is
-  # tracked in order to decide when to begin a new statement group.
-  attr_accessor :cumulative_citation
-
-  # Returns the cumulative +Hash+ of annotations. This *state* is used to keep
-  # track of the active, scoped annotations as evidence is serialized.
-  def cumulative_annotations
-    @cumulative_annotations ||= {}
-  end
-
-  # Return BEL Script syntax that should completes the BEL Script document.
-  # For Citation serialization we will always end with the unset of a
-  # statement group.
-  def epilogue
-    %Q{UNSET STATEMENT_GROUP\n}
-  end
-end

data/lib/bel/translator/plugins/bel_script/bel_discrete_serialization.rb

@@ -1,109 +0,0 @@
-require_relative 'evidence_serialization'
-
-# BEL Script evidence serialization that writes each evidence with their full
-# set of annotations (i.e. includes all `SET` and necessary `UNSET` records).
-# This style is more readable because it groups all set annotations near the
-# BEL statement.
-#
-# @example Discrete serialization for a group of evidence
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   complex(p(HGNC:USF1),g(HGNC:IGF2R))
-#
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   complex(p(HGNC:USF2),g(HGNC:IGF2R))
-#
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
-#
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
-#
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "c-Myc was present on the CDK4 promoter to the ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   complex(p(HGNC:MYC),g(HGNC:CDK4))
-#
-#   UNSET CellLine
-module BEL::Translator::Plugins::BelScript::BelDiscreteSerialization
-  include BEL::Translator::Plugins::BelScript::EvidenceSerialization
-
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
-  # Includes all necessary +SET AnnotationName+ and +UNSET AnnotationName+
-  # records around the BEL statement.
-  #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
-  # @return [String]               the BEL Script string
-  def to_bel(evidence)
-    bel = ''
-
-    citation     = citation_value(evidence)
-    summary_text = summary_text_value(evidence)
-    annotations  = annotation_values(evidence)
-
-    current_annotations            = {}.merge(annotations)
-    current_annotations[:Citation] = citation if citation
-    current_annotations[:Evidence] = summary_text if summary_text
-
-    # UNSET unused annotations from previous evidence.
-    (cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
-      bel << "UNSET #{unset_key}\n"
-      cumulative_annotations.delete(unset_key)
-    end
-
-    # Retain the current evidence's annotation in cumulative set.
-    cumulative_annotations.merge!(current_annotations)
-
-    # SET Citation
-    citation = current_annotations.delete(:Citation)
-    if citation
-      bel << "SET Citation = {#{citation}}\n"
-    end
-
-    # SET Evidence
-    summary_text = current_annotations.delete(:Evidence)
-    if summary_text
-      bel << %Q{SET Evidence = "#{summary_text}"\n}
-    end
-
-    # SET new or modified annotations
-    current_annotations.sort.each do |(name, value)|
-      bel << "SET #{name} = #{value}\n"
-    end
-
-    # Assert BEL statement
-    bel << "#{evidence.bel_statement}\n"
-
-    # Separate evidence by new line.
-    bel << "\n"
-
-    bel
-  end
-
-  private
-
-  # Returns the cumulative +Hash+ of annotations. This *state* is used to keep
-  # track of the active, scoped annotations as evidence is serialized.
-  def cumulative_annotations
-    @cumulative_annotations ||= {}
-  end
-
-  # Return BEL Script syntax that completes the BEL Script document.
-  # The empty string is returned since no ending syntax is necessary when
-  # serializing each evidence discretely.
-  def epilogue
-    ""
-  end
-end

data/lib/bel/translator/plugins/bel_script/bel_top_down_serialization.rb

@@ -1,100 +0,0 @@
-require_relative 'evidence_serialization.rb'
-
-# BEL Script evidence serialization that writes evidence sequentially while
-# including only the necessary unsetting of annotations (i.e. BEL Script's
-# +UNSET AnnotationName+ syntax).
-#
-# @example Top-down serialization for a group of evidence
-#   SET Citation = {"PubMed", "Journal...", "12857727", "2003-08-11", "", ""}
-#   SET Evidence = "USF1 and USF2 bound the IGF2R promoter in vitro, ..."
-#   SET CellLine = "MCF 10A"
-#   SET TextLocation = Abstract
-#   complex(p(HGNC:USF1),g(HGNC:IGF2R))
-#
-#   complex(p(HGNC:USF2),g(HGNC:IGF2R))
-#
-#   tscript(p(HGNC:USF2)) directlyIncreases r(HGNC:IGF2R)
-#
-#   tscript(p(HGNC:USF1)) causesNoChange r(HGNC:IGF2R)
-#
-#   SET Evidence = "c-Myc was present on the CDK4 promoter to the ..."
-#   complex(p(HGNC:MYC),g(HGNC:CDK4))
-#
-#   UNSET CellLine
-module BEL::Translator::Plugins::BelScript::BelTopDownSerialization
-  include BEL::Translator::Plugins::BelScript::EvidenceSerialization
-
-  # Serialize the {BEL::Model::Evidence evidence} to a BEL Script string.
-  # Includes all necessary +SET AnnotationName+ and +UNSET AnnotationName+
-  # records within the scope of a citation's statement group.
-  #
-  # @param  [BEL::Model::Evidence] evidence the evidence to serialize
-  # @return [String]               the BEL Script string
-  def to_bel(evidence)
-    bel = ''
-
-    citation     = citation_value(evidence)
-    summary_text = summary_text_value(evidence)
-    annotations  = annotation_values(evidence)
-
-    current_annotations            = {}.merge(annotations)
-    current_annotations[:Citation] = citation if citation
-    current_annotations[:Evidence] = summary_text if summary_text
-
-    # UNSET unused annotations from previous evidence.
-    (cumulative_annotations.keys - current_annotations.keys).each do |unset_key|
-      bel << "UNSET #{unset_key}\n"
-      cumulative_annotations.delete(unset_key)
-    end
-
-    # Remove annotation if key/value was SET by a previous evidence.
-    Hash[
-      cumulative_annotations.to_a & current_annotations.to_a
-    ].each do |same_k, _|
-      current_annotations.delete(same_k)
-    end
-
-    # Retain the current evidence's annotation in cumulative set.
-    cumulative_annotations.merge!(current_annotations)
-
-    # SET Citation
-    citation = current_annotations.delete(:Citation)
-    if citation
-      bel << "SET Citation = {#{citation}}\n"
-    end
-
-    # SET Evidence
-    summary_text = current_annotations.delete(:Evidence)
-    if summary_text
-      bel << %Q{SET Evidence = "#{summary_text}"\n}
-    end
-
-    # SET new or modified annotations
-    current_annotations.sort.each do |(name, value)|
-      bel << "SET #{name} = #{value}\n"
-    end
-
-    # Assert BEL statement
-    bel << "#{evidence.bel_statement}\n"
-
-    # Separate evidence by new line.
-    bel << "\n"
-
-    bel
-  end
-
-  private
-
-  # Returns the cumulative +Hash+ of annotations. This *state* is used to keep
-  # track of the active, scoped annotations as evidence is serialized.
-  def cumulative_annotations
-    @cumulative_annotations ||= {}
-  end
-
-  # Return BEL Script syntax that completes the BEL Script document.
-  # The empty string is returned since no ending syntax is necessary when
-  # serializing in a top-down manner.
-  def epilogue
-    ""
-  end
-end

data/lib/bel/translator/plugins/bel_script/bel_yielder.rb

@@ -1,180 +0,0 @@
-require_relative 'bel_citation_serialization'
-require_relative 'bel_discrete_serialization'
-require_relative 'bel_top_down_serialization'
-require 'bel'
-
-module BEL::Translator::Plugins
-
-  module BelScript
-
-    class BelYielder
-
-      # Create a {BelYielder} object that serializes {BEL::Model::Evidence} to
-      # BEL Script.
-      #
-      # @param [Enumerator<BEL::Model::Evidence>] data evidence data iterated
-      #        using +each+
-      # @option options [Boolean] :write_header +true+ to write the BEL Script
-      #         document header; +false+ to not write the BEL Script document
-      #         header
-      # @option options [Symbol,Module] :serialization the serialization
-      #         technique to use for evidence; a +Module+ type will be used as
-      #         is; a +Symbol+ type will be mapped as
-      #         +:discrete+ => {BelDiscreteSerialization},
-      #         +:topdown+ => {BelTopDownSerialization},
-      #         +:citation+ => {BelCitationSerialization}; otherwise the default
-      #         of {BelCitationSerialization} is used
-      def initialize(data, options = {})
-        @data                     = data
-        @streaming                = options.fetch(:streaming, false)
-        @write_header             = options.fetch(:write_header, true)
-        @annotation_reference_map = options.fetch(:annotation_reference_map, nil)
-        @namespace_reference_map  = options.fetch(:namespace_reference_map, nil)
-
-        # augment self with BEL serialization stategy.
-        serialization = options[:serialization]
-        serialization_module =
-          case serialization
-          when Module
-            serialization
-          when String, Symbol
-            serialization_refs = {
-              :discrete => BelDiscreteSerialization,
-              :topdown  => BelTopDownSerialization,
-              :citation => BelCitationSerialization,
-            }
-            serialization_module = serialization_refs[serialization.to_sym]
-            unless serialization_module
-                raise %Q{No BEL serialization strategy for "#{serialization}"}
-            end
-            serialization_module
-          else
-            # Default to citation serialization.
-            BelCitationSerialization
-          end
-
-        self_eigenclass = (class << self; self; end)
-        self_eigenclass.send(:include, serialization_module)
-      end
-
-      def each
-        if block_given?
-          combiner =
-            if @streaming
-              BEL::Model::StreamingEvidenceCombiner.new(@data)
-            elsif @annotation_reference_map && @namespace_reference_map
-              BEL::Model::MapReferencesCombiner.new(
-                @data,
-                BEL::Model::HashMapReferences.new(
-                  @annotation_reference_map,
-                  @namespace_reference_map
-                )
-              )
-            else
-              BEL::Model::BufferingEvidenceCombiner.new(@data)
-            end
-
-          header_flag = true
-          combiner.each { |evidence|
-
-            # serialize evidence
-            bel = to_bel(evidence)
-
-            if @write_header && header_flag
-              yield document_header(evidence.metadata.document_header)
-              yield namespaces(combiner.namespace_references)
-              yield annotations(combiner.annotation_references)
-
-              yield <<-COMMENT.gsub(/^\s+/, '')
-                ###############################################
-                # Statements Section
-              COMMENT
-              header_flag = false
-            end
-
-            yield bel
-          }
-
-          yield epilogue
-        else
-          to_enum(:each)
-        end
-      end
-
-      private
-
-      def document_header(header)
-        return "" unless header
-
-        bel = <<-COMMENT.gsub(/^\s+/, '')
-          ###############################################
-          # Document Properties Section
-        COMMENT
-
-        header.each { |name, value|
-          name_s  = name.to_s
-          value_s =
-            if value.respond_to?(:each)
-              value.join('|')
-            else
-              value.to_s
-            end
-
-          # handle casing for document properties (special case, contactinfo)
-          name_s = (name_s.downcase == 'contactinfo') ?
-            'ContactInfo' :
-            name_s.capitalize
-
-          bel << %Q{SET DOCUMENT #{name_s} = "#{value_s}"\n}
-        }
-
-        bel << "\n"
-        bel
-      end
-
-      def annotations(annotation_references)
-        bel = <<-COMMENT.gsub(/^\s+/, '')
-          ###############################################
-          # Annotation Definitions Section
-        COMMENT
-
-        return bel unless annotation_references
-
-        annotation_references.reduce(bel) { |bel, ref|
-          keyword, type, domain = ref.values_at(:keyword, :type, :domain)
-          bel << "DEFINE ANNOTATION #{keyword} AS "
-
-          case type.to_sym
-          when :uri
-            bel << %Q{URL "#{domain}"\n}
-          when :pattern
-            regex = domain.respond_to?(:source) ? domain.source : domain
-            bel << %Q{PATTERN "#{regex}"\n}
-          when :list
-            bel << %Q|LIST {#{domain.inspect[1...-1]}}\n|
-          end
-          bel
-        }
-        bel << "\n"
-        bel
-      end
-
-      def namespaces(namespace_references)
-        bel = <<-COMMENT.gsub(/^\s+/, '')
-          ###############################################
-          # Namespace Definitions Section
-        COMMENT
-
-        return bel unless namespace_references
-
-        namespace_references.reduce(bel) { |bel, ref|
-          keyword, url = ref.values_at(:keyword, :uri)
-          bel << %Q{DEFINE NAMESPACE #{keyword} AS URL "#{url}"\n}
-          bel
-        }
-        bel << "\n"
-        bel
-      end
-    end
-  end
-end