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module OpenTox
class Nanoparticle < Substance
include OpenTox
field :core, type: Hash, default: {}
field :coating, type: Array, default: []
def add_feature feature, value, dataset
unless feature.name == "ATOMIC COMPOSITION" or feature.name == "FUNCTIONAL GROUP" # redundand
case feature.category
when "P-CHEM"
properties[feature.id.to_s] ||= []
properties[feature.id.to_s] << value
properties[feature.id.to_s].uniq!
when "Proteomics"
properties[feature.id.to_s] ||= []
properties[feature.id.to_s] << value
properties[feature.id.to_s].uniq!
when "TOX"
dataset.add self, feature, value
else
warn "Unknown feature type '#{feature.category}'. Value '#{value}' not inserted."
end
dataset_ids << dataset.id
dataset_ids.uniq!
end
end
def parse_ambit_value feature, v, dataset
# TODO add study id to warnings
v.delete "unit"
# TODO: ppm instead of weights
if v.keys == ["textValue"]
add_feature feature, v["textValue"], dataset
elsif v.keys == ["loValue"]
add_feature feature, v["loValue"], dataset
elsif v.keys.size == 2 and v["errorValue"]
add_feature feature, v["loValue"], dataset
warn "Ignoring errorValue '#{v["errorValue"]}' for '#{feature.name}'."
elsif v.keys.size == 2 and v["loQualifier"] == "mean"
add_feature feature, v["loValue"], dataset
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"], dataset
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"], dataset
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"], dataset
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, dataset
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"], dataset
elsif v == {} # do nothing
else
warn "Cannot parse Ambit eNanoMapper value '#{v}' for feature '#{feature.name}'."
end
end
end
end
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