Module: BEL

Extended by:
Translate::ClassMethods
Defined in:
lib/bel.rb,
lib/bel/dsl.rb,
lib/bel/gen.rb,
lib/bel/util.rb,
lib/bel/libbel.rb,
lib/bel/script.rb,
lib/bel/quoting.rb,
lib/bel/version.rb,
lib/bel/gen/term.rb,
lib/bel/language.rb,
lib/bel/resource.rb,
lib/bel/namespace.rb,
lib/bel/translate.rb,
lib/bel/annotation.rb,
lib/bel/completion.rb,
lib/bel/translator.rb,
lib/bel/gen/nanopub.rb,
lib/bel/gen/citation.rb,
lib/bel/nanopub/util.rb,
lib/bel/gen/namespace.rb,
lib/bel/gen/parameter.rb,
lib/bel/gen/statement.rb,
lib/bel/gen/annotation.rb,
lib/bel/rdf_repository.rb,
lib/bel/completion_rule.rb,
lib/bel/nanopub/nanopub.rb,
lib/bel/nanopub/support.rb,
lib/bel/resource/search.rb,
lib/bel/libbel/bel_token.rb,
lib/bel/libbel/node_test.rb,
lib/bel/nanopub/citation.rb,
lib/bel/nanopub/metadata.rb,
lib/bel/resource/concept.rb,
lib/bel/nanopub/references.rb,
lib/bel/resource/namespace.rb,
lib/bel/gen/document_header.rb,
lib/bel/resource/annotation.rb,
lib/bel/resource/namespaces.rb,
lib/bel/gen/sample_resources.rb,
lib/bel/resource/annotations.rb,
lib/bel/libbel/bel_token_list.rb,
lib/bel/libbel/node_traversal.rb,
lib/bel/libbel/bel_ast_structs.rb,
lib/bel/nanopub/map_references.rb,
lib/bel/libbel/library_resolver.rb,
lib/bel/resource/concept_scheme.rb,
lib/bel/resource/namespace_value.rb,
lib/bel/libbel/library_load_error.rb,
lib/bel/resource/annotation_value.rb,
lib/bel/libbel/node_transformation.rb,
lib/bel/nanopub/experiment_context.rb,
lib/bel/nanopub/hash_map_references.rb,
lib/bel/translator/plugins/rdf2/uuid.rb,
lib/bel/libbel/platform_support_error.rb,
lib/bel/resource/search/search_result.rb,
lib/bel/translator/plugins/rdf2/reader.rb,
lib/bel/nanopub/map_references_combiner.rb,
lib/bel/translator/plugins/rdf2/belv2_0.rb,
lib/bel/translator/plugins/rdf2/converter.rb,
lib/bel/nanopub/buffering_nanopub_combiner.rb,
lib/bel/nanopub/streaming_nanopub_combiner.rb,
lib/bel/translator/plugins/rdf2/rdf_writer.rb,
lib/bel/translator/plugins/rdf2/translator.rb,
lib/bel/translator/plugins/rdf2/rdf_converter.rb,
lib/bel/translator/plugins/rdf2/term_converter.rb,
lib/bel/translator/plugins/rdf2/nanopub_converter.rb,
lib/bel/translator/plugins/rdf2/namespace_converter.rb,
lib/bel/translator/plugins/rdf2/parameter_converter.rb,
lib/bel/translator/plugins/rdf2/statement_converter.rb,
lib/bel/translator/plugins/rdf2/relationship_converter.rb

Defined Under Namespace

Modules: Annotation, BELRDF, Completion, DSL, Gen, JSON, Language, LibBEL, Namespace, Nanopub, Quoting, RdfRepository, Resource, Script, Translate, Translator, Version

Constant Summary collapse

DEFAULT_RESOURCE_VALUE_DELIMITER =

The default delimiter to use when parsing values from BEL Resource files.

'|'

Class Method Summary collapse

Methods included from Translate::ClassMethods

nanopub, process_input, translate, translator

Class Method Details

.keys_to_symbols(obj) ⇒ Object 



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# File 'lib/bel/util.rb', line 84

def self.keys_to_symbols(obj)
  self.object_convert(:key, obj) { |key| key.to_sym }
end

.object_convert(type, source, &block) ⇒ Object 



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# File 'lib/bel/util.rb', line 88

def self.object_convert(type, source, &block)
  case source
  when Array
    source.inject([]) { |new, v|
      new << object_convert(type, v, &block)
      new
    }
  when Hash
    source.inject({}) { |new, (k,v)|
      if type == :key || k.is_a?(type)
        k = block.call(k)
      end

      new[k] = object_convert(type, v, &block)
      new
    }
  else
    if type != :key && source.is_a?(type)
      block.call(source)
    else
      source
    end
  end
end

.read_all(reference, options = {}) ⇒ Object 



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# File 'lib/bel/util.rb', line 51

def self.read_all(reference, options = {})
  return [] if reference.to_s.strip.empty?

  if cached? reference
    read_cached reference do |cf|
      return cf.read
    end
  end

  multi_open(reference, options) do |f|
    content = f.read
    write_cached reference, content
    return content
  end
end

.read_lines(reference, options = {}) ⇒ Object 



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# File 'lib/bel/util.rb', line 67

def self.read_lines(reference, options = {})
  return [] if reference.to_s.strip.empty?

  if cached? reference
    read_cached reference do |cf|
      return cf.readlines
    end
  end

  multi_open(reference, options) do |f|
    content = f.read
    write_cached reference, content
    f.rewind
    return f.readlines
  end
end

.read_resource(url) ⇒ Hash

Retrieves values from a BEL resource file (e.g. .belns, .belanno).

The file parser respects the DelimiterString value specified in the file but will default to #DEFAULT_RESOURCE_VALUE_DELIMITER if not present.

argument is the value encoding for a BEL namespace file (e.g. lung disease|O) and a database value identifier for a BEL annotation file (e.g. lung|UBERON_0002048).

Parameters:

  • url (String) —

    the resource file URL to fetch

Returns:

  • (Hash) —

    hash of value symbol to extra argument symbol; the extra



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# File 'lib/bel/util.rb', line 21

def self.read_resource(url)
  @@url_content_cache ||= {}
  @@url_content_cache.fetch(url) {
    resource_lines = BEL::read_lines(url)

    # Drop until the delimiter line and extract the delimiter, e.g.
    # DelimiterString=|
    delimiter_line = resource_lines.take(100).find { |l| l.start_with?("DelimiterString") }
    delimiter =
      if delimiter_line
        delimiter_line.strip.split('=')[1]
      else
        DEFAULT_RESOURCE_VALUE_DELIMITER
      end

    # Extract resource values based on the delimiter.
    resource_values = Hash[
      resource_lines.
      drop_while { |l| !l.start_with?("[Values]") }.
      drop(1).
      map { |s|
        val_enc = s.strip!.split(delimiter).map(&:to_sym)
        val_enc[0..1]
      }
    ]
    @@url_content_cache[url] = resource_values
    resource_values
  }
end