Module: Hookkaido

Extended by:
Configuration
Defined in:
lib/hookkaido.rb,
lib/hookkaido/error.rb,
lib/hookkaido/request.rb,
lib/hookkaido/version.rb,
lib/hookkaido/sources/ols.rb

Defined Under Namespace

Modules: Sources Classes: BadGateway, BadRequest, Error, GatewayTimeout, InternalServerError, NotFound, Request, ServiceUnavailable

Constant Summary collapse

VERSION = 
"0.1.1"

Class Method Summary collapse

Methods included from Configuration

configuration, define_setting

Class Method Details

.ontologies(verbose: false) ⇒ Object

List available ontology IDs (lowercased)



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# File 'lib/hookkaido.rb', line 16

def self.ontologies(verbose: false)
  Sources::OLS.ontologies(verbose: verbose, timeout: timeout)
end

.search(term, ontologies: [], per: 25, page: 1, verbose: false) ⇒ Object

Search OLS for terms in specific ontologies matching a user-provided term. Return: { results:, page:, per:, total: }

Raises:

  • (ArgumentError) 


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# File 'lib/hookkaido.rb', line 25

def self.search(term, ontologies: [], per: 25, page: 1, verbose: false)
  raise ArgumentError, 'term cannot be blank' if term.to_s.strip.empty?

  requested = Array(ontologies).flat_map { |t| t.is_a?(String) && t.include?(',') ? t.split(',') : [t] }
  requested = requested.map { |t| t.to_s.strip.downcase }.reject(&:empty?)
  requested = ['uberon'] if requested.empty?
  requested = requested.uniq.first(3)
  # Uberon is a union of many other ontologies, so can return a lot of results
  # - put other results first.
  requested.push('uberon') if requested.delete('uberon')

  # Validate against OLS catalog
  #available = ontologies(verbose: verbose)
  #targets = (requested & available)
  #targets = ['uberon'] if targets.empty?
  targets = requested

  per_page = per.to_i
  start    = [(page.to_i - 1), 0].max * per_page

  payload = Sources::OLS.search(
    term,
    ontologies: targets,
    rows: per_page,
    start: start,
    verbose: verbose,
    timeout: timeout
  )

  results = payload[:results] || []
  total   = payload[:total].to_i

  # De-duplicate by IRI
  uniq = {}
  results.each { |r| uniq[r[:iri]] ||= r if r[:iri] }

  {
    results: uniq.values,
    page: page.to_i,
    per: per_page,
    total: total
  }
end