Class: BEL::Translator::Plugins::Xbel::NanopubHandler

Inherits:
Object
  • Object
show all
Includes:
Nanopub, REXML::StreamListener
Defined in:
lib/bel/translator/plugins/xbel/nanopub_handler.rb

Constant Summary collapse

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'.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

Instance Method Summary collapse

Methods included from Nanopub

union_annotation_references, union_by_keyword, union_namespace_references

Constructor Details

#initialize(callable) ⇒ NanopubHandler

Returns a new instance of NanopubHandler.



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 59

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

Instance Method Details

#end_annotation ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 513

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

#end_annotation_definition_group ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 360

def end_annotation_definition_group
  @element_stack.pop
end

#end_annotation_group ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 499

def end_annotation_group
  @element_stack.pop
end

#end_author ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 568

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

#end_bel_version ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 346

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

#end_citation ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 542

def end_citation
  @element_stack.pop
end

#end_comment ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 580

def end_comment
  if stack_top == :citation
    @nanopub.citation.comment = @text
  elsif stack_top == :statement
    @statement_stack.last[:comment] = @text
  end
end

#end_contact_info ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 333

def end_contact_info
  if stack_top == :header
    @nanopub.metadata.document_header[:ContactInfo] = @text
  end
end

#end_copyright ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 327

def end_copyright
  if stack_top == :header
    @nanopub.metadata.document_header[:Copyright] = @text
  end
end

#end_date ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 562

def end_date
  if stack_top == :citation
    @nanopub.citation.date = @text
  end
end

#end_default_namespace ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 268

def end_default_namespace
  @element_stack.pop
  @last_prefix = nil
end

#end_description ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 396

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

#end_evidence ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 503

def end_evidence
  @nanopub.support.value = @text
  @element_stack.pop
end

#end_external_annotation_definition ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 369

def end_external_annotation_definition
  @element_stack.pop
  @last_keyword = nil
end

#end_header ⇒ Object

End element methods, dynamically invoked.



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 317

def end_header
  @element_stack.pop
end

#end_internal_annotation_definition ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 374

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

#end_license ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 339

def end_license
  if stack_top == :header
    @nanopub.metadata.document_header[:Licenses] ||= []
    @nanopub.metadata.document_header[:Licenses]  << @text
  end
end

#end_list_annotation ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 382

def end_list_annotation
  @element_stack.pop
end

#end_list_value ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 412

def end_list_value
  if stack_top == :list_annotation
    @current_anno_def[:domain] << @text
  end
end

#end_name ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 552

def end_name
  if stack_top == :header
    @nanopub.metadata.document_header[:Name] = @text
  end

  if stack_top == :citation
    @nanopub.citation.name = @text
  end
end

#end_namespace ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 364

def end_namespace
  @element_stack.pop
  @last_prefix = nil
end

#end_namespace_group ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 356

def end_namespace_group
  @element_stack.pop
end

#end_nanopub ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 534

def end_nanopub
  if @element_stack[-3] == :statement
    @nanopub.support.value = @text
  end

  @element_stack.pop
end

#end_object ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 476

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

#end_parameter ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 493

def end_parameter
  @current_parameter.value    = @text
  @term_stack.last.arguments << @current_parameter
  @element_stack.pop
end

#end_pattern_annotation ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 386

def end_pattern_annotation
  begin
    @current_anno_def[:domain] = Regexp.new(@text)
  rescue RegexpError
    @text = Regexp.escape(@text)
    retry
  end
  @element_stack.pop
end

#end_reference ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 546

def end_reference
  if stack_top == :citation
    @nanopub.citation.id   = @text
  end
end

#end_resource ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 277

def end_resource
  @element_stack.pop
end

#end_statement ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 422

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

#end_statement_group ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 418

def end_statement_group
  @element_stack.pop
end

#end_subject ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 471

def end_subject
  @statement_stack.last[:subject] = @term_stack.last
  @element_stack.pop
end

#end_support ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 508

def end_support
  @nanopub.support.value = @text
  @element_stack.pop
end

#end_term ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 484

def end_term
  @element_stack.pop

  if @term_stack.size > 1
    @term_stack.pop
    @current_term = @term_stack.last
  end
end

#end_uri ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 285

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

#end_url ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 302

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_usage ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 406

def end_usage
  if stack_top == :internal_annotation_definition
    @current_anno_def[:usage] = @text
  end
end

#end_version ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 321

def end_version
  if stack_top == :header
    @nanopub.metadata.document_header[:Version] = @text
  end
end

#start_annotation(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 233

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

#start_annotation_definition_group(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 118

def start_annotation_definition_group(attributes)
  @element_stack << :annotation_definition_group
end

#start_annotation_group(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 228

def start_annotation_group(attributes)
  @annotation_id = nil
  @element_stack << :annotation_group
end

#start_citation(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 249

def start_citation(attributes)
  type = attr_value(attributes, TYPE)
  @nanopub.citation.type = type
  @element_stack << :citation
end

#start_default_namespace(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 259

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

#start_evidence(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 241

def start_evidence(attributes)
  @element_stack << :evidence
end

#start_external_annotation_definition(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 134

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

#start_header(attributes) ⇒ Object

Start element methods, dynamically invoked.



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 110

def start_header(attributes)
  @element_stack << :header
end

#start_internal_annotation_definition(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 147

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

#start_list_annotation(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 156

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

#start_namespace(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 122

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

#start_namespace_group(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 114

def start_namespace_group(attributes)
  @element_stack << :namespace_group
end

#start_nanopub(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 255

def start_nanopub(attributes)
  @element_stack << :nanopub
end

#start_object(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 195

def start_object(attributes)
  @element_stack << :object
end

#start_parameter(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 214

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

#start_pattern_annotation(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 164

def start_pattern_annotation(attributes)
  if stack_top == :internal_annotation_definition
    @current_anno_def[:type] = :pattern
  end
  @element_stack << :pattern_annotation
end

#start_resource(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 273

def start_resource(attributes)
  @element_stack << :resource
end

#start_statement(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 175

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

#start_statement_group(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 171

def start_statement_group(attributes)
  @element_stack << :statement_group
end

#start_subject(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 191

def start_subject(attributes)
  @element_stack << :subject
end

#start_support(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 245

def start_support(attributes)
  @element_stack << :support
end

#start_term(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 199

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

#start_uri(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 281

def start_uri(attributes)
  @element_stack << :uri
end

#start_url(attributes) ⇒ Object 



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 298

def start_url(attributes)
  @element_stack << :url
end

#tag_end(name) ⇒ Object

Called on element end by REXML.



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 88

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

#tag_start(name, attributes) ⇒ Object

Called on element start by REXML.



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 76

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

#text(*args) ⇒ Object

Called on text node by REXML.



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# File 'lib/bel/translator/plugins/xbel/nanopub_handler.rb', line 100

def text(*args)
  if args.size.zero?
    @text = ''
  else
    @text = args.first
  end
end