1 files changed, 73 insertions, 0 deletions
diff --git a/lib/import.rb b/lib/import.rb
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index 0000000..9091207
--- /dev/null
+++ b/lib/import.rb
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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
+
+      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
+