Class: OpenTox::Import::Enanomapper

Inherits:
Object
  • Object
show all
Includes:
OpenTox
Defined in:
lib/enm-import.rb

Class Method Summary collapse

Class Method Details

.import ⇒ Object

Import from eNanoMapper



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# File 'lib/enm-import.rb', line 10

def self.import
  # time critical step: JSON parsing (>99%), Oj brings only minor speed gains (~1%)
  datasets = {}
  bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle', {}, {accept: :json}))["dataset"]
  bundles.each do |bundle|
    datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"].strip)
    $logger.debug bundle["title"].strip
    nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"], {}, {accept: :json}))["dataEntry"]
    nanoparticles.each_with_index do |np,n|
      core_id = nil
      coating_ids = []
      np["composition"].each do |c|
        uri = c["component"]["compound"]["URI"]
        data = JSON.parse(RestClientWrapper.get("https://data.enanomapper.net/query/compound/url/all?search=#{uri}", {}, {accept: :json}))
        source = data["dataEntry"][0]["compound"]["URI"]
        smiles = data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23SMILESDefault"]
        names = []
        names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
        names << data["dataEntry"][0]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23IUPACNameDefault"]
        if smiles
          compound = Compound.find_or_create_by(:smiles => smiles)
          compound.name = names.first
          compound.names = names.compact
        else
          compound = Compound.find_or_create_by(:name => names.first,:names => names.compact)
        end
        compound.source = source
        compound.save
        if c["relation"] == "HAS_CORE"
          core_id = compound.id.to_s
        elsif c["relation"] == "HAS_COATING"
          coating_ids << compound.id.to_s
        end
      end if np["composition"]
      nanoparticle = Nanoparticle.find_or_create_by(
        :name => np["values"]["https://data.enanomapper.net/identifier/name"],
        :source => np["compound"]["URI"],
        :core_id => core_id,
        :coating_ids => coating_ids
      )
      #np["bundles"].keys.each do |bundle_uri|
        #nanoparticle.dataset_ids << datasets[bundle_uri].id
      #end

      studies = JSON.parse(RestClientWrapper.get(File.join(np["compound"]["URI"],"study"), {}, {accept: :json}))["study"]
      studies.each do |study|
        dataset = datasets[np["bundles"].keys.first]
        proteomics_features = {}
        category = study["protocol"]["topcategory"]
        source = study["protocol"]["category"]["term"]
        study["effects"].each do |effect|

          effect["result"]["textValue"] ?  klass = NominalFeature : klass = NumericFeature
          effect["conditions"].delete_if { |k, v| v.nil? }

          if study["protocol"]["category"]["title"].match(/Proteomics/) and effect["result"]["textValue"] and effect["result"]["textValue"].length > 50 # parse proteomics data

            JSON.parse(effect["result"]["textValue"]).each do |identifier, value| # time critical step
              proteomics_features[identifier] ||= NumericFeature.find_or_create_by(:name => identifier, :category => "Proteomics", :unit => "Spectral counts", :source => source,:measured => true)
              nanoparticle.parse_ambit_value proteomics_features[identifier], value, dataset
            end
          else
            name = effect["endpoint"]
            unit = effect["result"]["unit"]
            warnings = []
            case name
            when "Log2 transformed" # use a sensible name
              name = "log2(Net cell association)"
              warnings = ["Original name was 'Log2 transformed'"]
              unit = "log2(mL/ug(Mg))"
            when "Total protein (BCA assay)"
              category = "P-CHEM"
              warnings = ["Category changed from TOX to P-CHEM"]
            end
            feature = klass.find_or_create_by(
              :name => name,
              :unit => unit,
              :category => category,
              :conditions => effect["conditions"],
              :source => study["protocol"]["category"]["term"],
              :measured => true,
              :warnings => warnings
            )
            nanoparticle.parse_ambit_value feature, effect["result"], dataset
          end
        end
      end
      nanoparticle.save
      print "#{n}, "
    end
    puts
  end
  datasets.each { |u,d| d.save }
end