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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.substance_ids << nanoparticle.id
dataset.substance_ids.uniq!
studies = JSON.parse(RestClientWrapper.get(File.join(np["compound"]["URI"],"study")))["study"]
studies.each do |study|
study["effects"].each do |effect|
effect["result"]["textValue"] ? klass = NominalFeature : klass = NumericFeature
# TODO parse core/coating
# TODO parse proteomics, they come as a large textValue
$logger.debug File.join(np["compound"]["URI"],"study")
effect["conditions"].delete_if { |k, v| v.nil? }
feature = klass.find_or_create_by(
#:source => File.join(np["compound"]["URI"],"study"),
:name => "#{study["protocol"]["category"]["title"]} #{study["protocol"]["endpoint"]}",
:unit => effect["result"]["unit"],
:category => study["protocol"]["topcategory"],
:conditions => effect["conditions"]
)
nanoparticle.parse_ambit_value feature, effect["result"]
dataset.feature_ids << feature.id
dataset.feature_ids.uniq!
end
end
end
dataset.save
datasets << dataset
end
datasets.collect{|d| d.id}
end
=begin
def self.import_ld # defunct, AMBIT JSON_LD does not have substance entries
#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"]
study = JSON.parse(`curl -H 'Accept:application/ld+json' '#{uri}/substance'`)
study["@graph"].each do |i|
puts i.to_yaml if i.keys.include? "sio:has-value"
end
end
datasets.collect{|d| d.id}
end
=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
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