module OpenTox

  module Import

    class Enanomapper
      include OpenTox

      def self.import
        #get list of bundle URIs
        bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
        datasets = []
        bundles.each do |bundle|
          uri = bundle["URI"]
          dataset = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"])
          nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"]
          features = JSON.parse(RestClientWrapper.get(bundle["property"]+"?media=application%2Fjson"))["feature"]
          nanoparticles.each do |np|
            nanoparticle = Nanoparticle.find_or_create_by(
              :name => np["values"]["https://data.enanomapper.net/identifier/name"],
              :source => np["compound"]["URI"],
            )
            dataset.data_entries[nanoparticle.id.to_s] ||= {}
            nanoparticle.bundles << uri
            nanoparticle.dataset_ids << dataset.id
            np["composition"].each do |comp|
              case comp["relation"]
              when "HAS_CORE"
                nanoparticle.core = comp["component"]["compound"]["URI"]
              when "HAS_COATING"
                nanoparticle.coating << comp["component"]["compound"]["URI"]
              end
            end if np["composition"]
            np["values"].each do |u,v|
              if u.match(/property/)
                name, unit, source = nil
                features.each do |uri,feat|
                  if u.match(/#{uri}/)
                    name = feat["title"]
                    unit = feat["units"]
                    source = uri
                  end
                end
                feature = Feature.find_or_create_by(
                  :name => name,
                  :unit => unit,
                  :source => source
                )
              end
              v.each{|value| nanoparticle.parse_ambit_value feature, value} if v.is_a? Array
            end
            nanoparticle.bundles.uniq!
            nanoparticle.physchem_descriptors.each{|f,v| v.uniq!}
            #nanoparticle.toxicities.each{|f,v| v.uniq!}
            nanoparticle.toxicities.each do |f,v|
              dataset.data_entries[nanoparticle.id.to_s][f.to_s] ||= []
              dataset.data_entries[nanoparticle.id.to_s][f.to_s] += v
            end
            nanoparticle.save
          end
          dataset.save
          datasets << dataset
        end
        datasets.collect{|d| d.id}
      end

      def self.dump
        #get list of bundle URIs
        `wget 'https://data.enanomapper.net/bundle?media=application%2Fjson' -O bundles.json`
        json = JSON.parse File.read('./bundles.json')
        json["dataset"].each do |dataset|
          uri = dataset["URI"]
          id = uri.split("/").last
          `wget --header='accept:application/json' '#{uri}' -O 'bundle#{id}'`
          `wget --header='accept:application/json' '#{dataset["summary"]}' -O 'summary#{id}.json'`
          `wget --header='accept:application/json' '#{dataset["compound"]}' -O 'compound#{id}.json'`
          `wget --header='accept:application/json' '#{dataset["substance"]}' -O 'substance#{id}.json'`
          `wget --header='accept:application/json' '#{dataset["property"]}' -O 'property#{id}.json'`
          `wget --header='accept:application/json' '#{dataset["dataset"]}' -O 'dataset#{id}.json'`
          `wget --header='accept:application/json' '#{dataset["matrix"]}' -O 'matrix#{id}.json'`
        end
      end

    end

  end

end