Class: BEL::Extension::Format::FormatXBEL::EvidenceHandler

Inherits:
Object
  • Object
show all
Includes:
Model, REXML::StreamListener
Defined in:
lib/bel/extensions/xbel.rb

Constant Summary collapse

ANNOTATION = 
"annotation"
ANNOTATION_DEFINITION_GROUP = 
"annotationDefinitionGroup"
ANNOTATION_GROUP = 
"annotationGroup"
AUTHOR = 
"author"
AUTHOR_GROUP = 
"authorGroup"
CITATION = 
"citation"
COMMENT = 
"comment"
CONTACT_INFO = 
"contactInfo"
"copyright"
DATE = 
"date"
DESCRIPTION = 
"description"
DOCUMENT = 
"document"
EVIDENCE = 
"evidence"
EXTERNAL_ANNOTATION_DEFINITION = 
"externalAnnotationDefinition"
FUNCTION = 
"function"
HEADER = 
"header"
ID = 
"id"
INTERNAL_ANNOTATION_DEFINITION = 
"internalAnnotationDefinition"
LICENSE = 
"license"
LICENSE_GROUP = 
"licenseGroup"
LIST_ANNOTATION = 
"listAnnotation"
LIST_VALUE = 
"listValue"
NAME = 
"name"
NAMESPACE = 
"namespace"
NAMESPACE_GROUP = 
"namespaceGroup"
NS = 
"ns"
OBJECT = 
"object"
PARAMETER = 
"parameter"
PATTERN_ANNOTATION = 
"patternAnnotation"
PREFIX = 
"prefix"
REFERENCE = 
"reference"
REF_ID = 
"refID"
RELATIONSHIP = 
"relationship"
RESOURCE_LOCATION = 
"resourceLocation"
STATEMENT = 
"statement"
STATEMENT_GROUP = 
"statementGroup"
SUBJECT = 
"subject"
TERM = 
"term"
TYPE = 
"type"
URL = 
"url"
USAGE = 
"usage"
VERSION = 
"version"

Instance Method Summary collapse

Constructor Details

#initialize(callable) ⇒ EvidenceHandler

Returns a new instance of EvidenceHandler.



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# File 'lib/bel/extensions/xbel.rb', line 507

def initialize(callable)
  @callable          = callable
  @element_stack     = []
  @text              = nil
  @evidence          = Evidence.new
end

Instance Method Details

#end_annotation ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 838

def end_annotation
  if @element_stack[-3] == :statement
    ref_id = @annotation_id

    annotation  = @evidence.experiment_context.find { |annotation|
      annotation[:name] == ref_id
    }
    if annotation
      # create array for multiple values by refID
      annotation[:value] = [annotation[:value], @text].flatten
    else
      @evidence.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/extensions/xbel.rb', line 718

def end_annotation_definition_group
  @element_stack.pop
end

#end_annotation_group ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 834

def end_annotation_group
  @element_stack.pop
end

#end_author ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 893

def end_author
  if stack_top == :header
    @evidence.metadata.document_header['authors'] ||= []
    @evidence.metadata.document_header['authors'] <<  @text
  end

  if stack_top == :citation
    (@evidence.citation.authors ||= []) << @text
  end
end

#end_citation ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 867

def end_citation
  @element_stack.pop
end

#end_comment ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 904

def end_comment
  if stack_top == :citation
    @evidence.citation.comment = @text
  end
end

#end_contact_info ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 701

def end_contact_info
  if stack_top == :header
    @evidence.metadata.document_header['contactInfo'] = @text
  end
end

#end_copyright ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 695

def end_copyright
  if stack_top == :header
    @evidence.metadata.document_header['copyright'] = @text
  end
end

#end_date ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 887

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

#end_description ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 748

def end_description
  if stack_top == :header
    @evidence.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/extensions/xbel.rb', line 859

def end_evidence
  if @element_stack[-3] == :statement
    @evidence.summary_text.value = @text
  end

  @element_stack.pop
end

#end_external_annotation_definition ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 726

def end_external_annotation_definition
  @element_stack.pop
end

#end_header ⇒ Object

End element methods, dynamically invoked.



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# File 'lib/bel/extensions/xbel.rb', line 685

def end_header
  @element_stack.pop
end

#end_internal_annotation_definition ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 730

def end_internal_annotation_definition
  @element_stack.pop
end

#end_license ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 707

def end_license
  if stack_top == :header
    @evidence.metadata.document_header['licenses'] ||= []
    @evidence.metadata.document_header['licenses'] <<  @text
  end
end

#end_list_annotation ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 734

def end_list_annotation
  @element_stack.pop
end

#end_list_value ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 764

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/extensions/xbel.rb', line 877

def end_name
  if stack_top == :header
    @evidence.metadata.document_header['name'] = @text
  end

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

#end_namespace ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 722

def end_namespace
  @element_stack.pop
end

#end_namespace_group ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 714

def end_namespace_group
  @element_stack.pop
end

#end_object ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 811

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/extensions/xbel.rb', line 828

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/extensions/xbel.rb', line 738

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/extensions/xbel.rb', line 871

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

#end_statement ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 774

def end_statement
  @element_stack.pop

  stmt = @statement_stack.pop
  if @statement_stack.empty?
    # create new evidence from parsed data
    evidence_copy = Evidence.create({
      :bel_statement      => stmt,
      :citation           => @evidence.citation.to_h,
      :summary_text       => @evidence.summary_text.value,
      :experiment_context => @evidence.experiment_context.values.dup,
      :references         => @evidence.references.values.dup,
      :metadata           => @evidence.metadata.values.dup
    })

    # yield evidence
    @callable.call(evidence_copy)

    # clear evidence parser state
    # note:
    #   - preserve @evidence.references
    #   - preserve @evidence.metadata.document_header
    @evidence.bel_statement      = nil
    @evidence.citation           = nil
    @evidence.summary_text       = nil
    @evidence.experiment_context = nil
    @evidence.metadata.delete_if { |key|
      key != :document_header
    }
  end
end

#end_statement_group ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 770

def end_statement_group
  @element_stack.pop
end

#end_subject ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 806

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

#end_term ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 819

def end_term
  @element_stack.pop

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

#end_usage ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 758

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/extensions/xbel.rb', line 689

def end_version
  if stack_top == :header
    @evidence.metadata.document_header['version'] = @text
  end
end

#start_annotation(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 665

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/extensions/xbel.rb', line 557

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

#start_annotation_group(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 660

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

#start_citation(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 673

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

#start_evidence(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 679

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

#start_external_annotation_definition(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 570

def start_external_annotation_definition(attributes)
  if stack_top == :annotation_definition_group
    id                 = attr_value(attributes, ID)
    url                = attr_value(attributes, URL)
    @evidence.references.annotation_definitions[id] = {
      :type   => :url,
      :domain => url
    }
  end
  @element_stack << :external_annotation_definition
end

#start_header(attributes) ⇒ Object

Start element methods, dynamically invoked.



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# File 'lib/bel/extensions/xbel.rb', line 549

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

#start_internal_annotation_definition(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 582

def start_internal_annotation_definition(attributes)
  if stack_top == :annotation_definition_group
    id                 = attr_value(attributes, ID)
    @current_anno_def  = {}
    @evidence.references.annotation_definitions[id] = @current_anno_def
  end
  @element_stack << :internal_annotation_definition
end

#start_list_annotation(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 591

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/extensions/xbel.rb', line 561

def start_namespace(attributes)
  if stack_top == :namespace_group
    prefix             = attr_value(attributes, PREFIX)
    resource_location  = attr_value(attributes, RESOURCE_LOCATION)
    @evidence.references.namespace_definitions[prefix] = resource_location
  end
  @element_stack << :namespace
end

#start_namespace_group(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 553

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

#start_object(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 628

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

#start_parameter(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 646

def start_parameter(attributes)
  if stack_top == :term
    ns_id              = attr_value(attributes, NS)
    # XXX Hitting a SystemStackError on line 174 (inside call).
    # Example: large_corpus.xbel
    ns                 = {
      :prefix => ns_id,
      :url    => @evidence.references.namespace_definitions[ns_id]
    }
    @current_parameter = Parameter.new(ns, nil)
  end
  @element_stack << :parameter
end

#start_pattern_annotation(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 599

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

#start_statement(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 610

def start_statement(attributes)
  stmt = Statement.new
  stmt.relationship = attr_value(attributes, 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/extensions/xbel.rb', line 606

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

#start_subject(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 624

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

#start_term(attributes) ⇒ Object 



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# File 'lib/bel/extensions/xbel.rb', line 632

def start_term(attributes)
  term = Term.new(attr_value(attributes, 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

#tag_end(name) ⇒ Object

Called on element end by REXML.



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# File 'lib/bel/extensions/xbel.rb', line 527

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/extensions/xbel.rb', line 515

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/extensions/xbel.rb', line 539

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