diff options
Diffstat (limited to 'lib/nanoparticle.rb')
| -rw-r--r-- | lib/nanoparticle.rb | 37 |
1 files changed, 21 insertions, 16 deletions
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb index 9bf419d..b79981d 100644 --- a/lib/nanoparticle.rb +++ b/lib/nanoparticle.rb @@ -9,10 +9,14 @@ module OpenTox field :proteomics, type: Hash, default: {} def nanoparticle_neighbors params - Dataset.find(params[:training_dataset_id]).nanoparticles.collect{|np| np["tanimoto"] = 1; np} + dataset = Dataset.find(params[:training_dataset_id]) + Dataset.find(params[:training_dataset_id]).nanoparticles.collect do |np| + np["tanimoto"] = 1 + np unless np.toxicities.empty? + end.compact end - def add_feature feature, value + def add_feature feature, value, dataset_id case feature.category when "P-CHEM" physchem_descriptors[feature.id.to_s] ||= [] @@ -23,51 +27,52 @@ module OpenTox proteomics[feature.id.to_s] << value proteomics[feature.id.to_s].uniq! when "TOX" - toxicities[feature.id.to_s] ||= [] + toxicities[feature.id.to_s] ||= {} + toxicities[feature.id.to_s][dataset_id.to_s] ||= [] # TODO generic way of parsing TOX values if feature.name == "7.99 Toxicity (other) ICP-AES" and feature.unit == "mL/ug(Mg)" - toxicities[feature.id.to_s] << -Math.log10(value) + toxicities[feature.id.to_s][dataset_id.to_s] << -Math.log10(value) else - toxicities[feature.id.to_s] << value + toxicities[feature.id.to_s][dataset_id.to_s] << value end - toxicities[feature.id.to_s].uniq! + toxicities[feature.id.to_s][dataset_id.to_s].uniq! else warn "Unknown feature type '#{feature.category}'. Value '#{value}' not inserted." end end - def parse_ambit_value feature, v + def parse_ambit_value feature, v, dataset_id v.delete "unit" # TODO: ppm instead of weights if v.keys == ["textValue"] - add_feature feature, v["textValue"] + add_feature feature, v["textValue"], dataset_id elsif v.keys == ["loValue"] - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id elsif v.keys.size == 2 and v["errorValue"] - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id warn "Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'." elsif v.keys.size == 2 and v["loQualifier"] == "mean" - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id warn "'#{feature.name}' is a mean value. Original data is not available." elsif v.keys.size == 2 and v["loQualifier"] #== ">=" warn "Only min value available for '#{feature.name}', entry ignored" elsif v.keys.size == 2 and v["upQualifier"] #== ">=" warn "Only max value available for '#{feature.name}', entry ignored" elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil? - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id warn "loQualifier and upQualifier are empty." elsif v.keys.size == 3 and v["loValue"] and v["loQualifier"] == "" and v["upQualifier"] == "" - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id warn "loQualifier and upQualifier are empty." elsif v.keys.size == 4 and v["loValue"] and v["loQualifier"].nil? and v["upQualifier"].nil? - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id warn "loQualifier and upQualifier are empty." elsif v.size == 4 and v["loQualifier"] and v["upQualifier"] and v["loValue"] and v["upValue"] - add_feature feature, [v["loValue"],v["upValue"]].mean + add_feature feature, [v["loValue"],v["upValue"]].mean, dataset_id warn "Using mean value of range #{v["loValue"]} - #{v["upValue"]} for '#{feature.name}'. Original data is not available." elsif v.size == 4 and v["loQualifier"] == "mean" and v["errorValue"] warn "'#{feature.name}' is a mean value. Original data is not available. Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'." - add_feature feature, v["loValue"] + add_feature feature, v["loValue"], dataset_id elsif v == {} # do nothing else warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'." |