Class: OpenBEL::Routes::Nanopubs

Inherits:
Base
  • Object
show all
Includes:
BELParser::Parsers, Helpers, Nanopub::FacetFilter, OpenBEL::Resource::Nanopub
Defined in:
app/openbel/api/routes/nanopubs.rb

Constant Summary

Constants included from Helpers

Helpers::DEFAULT_CONTENT_TYPE, Helpers::DEFAULT_CONTENT_TYPE_ID

Constants included from Nanopub::FacetFilter

Nanopub::FacetFilter::EMPTY, Nanopub::FacetFilter::NANOPUB_PARTS

Constants inherited from Base

Base::DEFAULT_CONTENT_TYPE, Base::DEFAULT_CONTENT_TYPE_ID, Base::RESOURCE_SERIALIZERS, Base::SCHEMA_BASE_URL, Base::SPOKEN_CONTENT_TYPES

Constants included from Schemas

Schemas::COMPILED_SCHEMAS, Schemas::SCHEMA_DIR, Schemas::SUFFIX

Constants included from OpenBEL::Resource::Namespaces

OpenBEL::Resource::Namespaces::VOCABULARY_RDF

Constants included from OpenBEL::Resource::Annotations

OpenBEL::Resource::Annotations::VOCABULARY_RDF

Instance Method Summary collapse

Methods included from Helpers

#incomplete_filters, #invalid_fts_filters, #parse_filters, #render_nanopub_collection, #validate_experiment_context, #validate_filters!, #validate_nanopub!, #validate_statement, #wants_default?

Methods included from Nanopub::FacetFilter

#make_filter, #map_citation_facets, #map_experiment_context_facets, #map_metadata_facets, #map_nanopub_facets

Methods included from Schemas

#validate

Constructor Details

#initialize(app) ⇒ Nanopubs

Returns a new instance of Nanopubs.



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# File 'app/openbel/api/routes/nanopubs.rb', line 20

def initialize(app)
  super

  bel_version = OpenBEL::Settings[:bel][:version]
  @spec       = BELParser::Language.specification(bel_version)

  mongo = OpenBEL::Settings[:nanopub_store][:mongo]
  @api  = OpenBEL::Nanopub::Nanopub.new(mongo)

  # RdfRepository using Jena.
  tdb = OpenBEL::Settings[:resource_rdf][:jena][:tdb_directory]
  @rr = BEL::RdfRepository.plugins[:jena].create_repository(:tdb_directory => tdb)

  # Annotations and Namespaces using RdfRepository
  @annotations                   = BEL::Resource::Annotations.new(@rr)
  @namespaces                    = BEL::Resource::Namespaces.new(@rr)
  @annotation_transform          = AnnotationTransform.new(@annotations)
  @annotation_grouping_transform = AnnotationGroupingTransform.new
  @default_references            = {
    :annotations => @annotations.each.map { |an|
      prefix = an.prefix.first.capitalize

      {
        :keyword => prefix,
        :type    => :uri,
        :domain  => an.uri.to_s
      }
    },
    :namespaces  => @namespaces.each.map  { |ns|
      prefix = ns.prefix.first.upcase

      {
        :keyword => prefix,
        :type    => :uri,
        :domain  => ns.uri.to_s
      }
    }
  }

  @supported_namespaces = Hash[
    @namespaces.each.map { |ns|
      prefix = ns.prefix.first.upcase

      [
        prefix,
        BELParser::Expression::Model::Namespace.new(
          prefix,
          ns.uri
        )
      ]
    }
  ]
end