initial ambit import

7 files changed, 87 insertions, 2 deletions

diff --git a/data/enm-dump.rb b/data/enm-dump.rb
new file mode 100644
index 0000000..c1c25e7
--- /dev/null
+++ b/data/enm-dump.rb
@@ -0,0 +1,16 @@
+require 'json'
+
+#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
diff --git a/data/enm-import.rb b/data/enm-import.rb
new file mode 100644
index 0000000..65fd3c7
--- /dev/null
+++ b/data/enm-import.rb
@@ -0,0 +1,50 @@
+require_relative '../lib/lazar.rb'
+include OpenTox
+
+
+#get list of bundle URIs
+bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
+bundles.each do |bundle|
+  uri = bundle["URI"]
+  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"],
+      )
+      np["composition"].each do |comp|
+        case comp["relation"]
+        when "HAS_CORE"
+          nanoparticle[:core] = comp["component"]["compound"]["URI"]
+        when "HAS_COATING"
+          nanoparticle[:coating] ||= []
+          nanoparticle[:coating] << comp["component"]["compound"]["URI"]
+        end
+      end if np["composition"]
+      np["values"].each do |u,v|
+        if u.match(/property/)
+          name, unit = nil
+          features.each do |uri,feat|
+            if u.match(/#{uri}/)
+              name = feat["title"]
+              unit = feat["units"]
+            end
+          end
+          feature = Feature.find_or_create_by(
+            :name => name,
+            :unit => unit,
+            #:source => uri
+          )
+          nanoparticle[:features] ||= {}
+          if v.size == 1 and v.first.keys == ["loValue"]
+            nanoparticle[:features][feature.id] = v.first["loValue"]
+          else
+            #TODO
+          end
+        end
+      end
+      p nanoparticle
+      nanoparticle.save
+  end
+end
diff --git a/lib/dataset.rb b/lib/dataset.rb
index 5d8aeaf..2e48626 100644
--- a/lib/dataset.rb
+++ b/lib/dataset.rb
@@ -9,7 +9,6 @@ module OpenTox
     field :feature_ids, type: Array, default: []
     field :compound_ids, type: Array, default: []
     field :data_entries, type: Array, default: []
-    field :source, type: String
 
     # Readers
 
diff --git a/lib/feature.rb b/lib/feature.rb
index b58946b..f13a3fb 100644
--- a/lib/feature.rb
+++ b/lib/feature.rb
@@ -6,6 +6,7 @@ module OpenTox
     field :numeric, type: Boolean
     field :measured, type: Boolean
     field :calculated, type: Boolean
+    field :unit, type: String
   end
 
   # Feature for categorical variables
diff --git a/lib/lazar.rb b/lib/lazar.rb
index a28ba3a..39dd8fa 100644
--- a/lib/lazar.rb
+++ b/lib/lazar.rb
@@ -61,7 +61,7 @@ suppressPackageStartupMessages({
 "
 
 # OpenTox classes and includes
-CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment"]# Algorithm and Models are modules
+CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveOneOutValidation","RepeatedCrossValidation","Experiment","Nanoparticle"]# Algorithm and Models are modules
 
 [ # be aware of the require sequence as it affects class/method overwrites
   "overwrite.rb",
@@ -71,6 +71,7 @@ CLASSES = ["Feature","Compound","Dataset","Validation","CrossValidation","LeaveO
   "feature.rb",
   "physchem.rb",
   "compound.rb",
+  "nanoparticle.rb",
   "dataset.rb",
   "algorithm.rb",
   "model.rb",
diff --git a/lib/nanoparticle.rb b/lib/nanoparticle.rb
new file mode 100644
index 0000000..3783ece
--- /dev/null
+++ b/lib/nanoparticle.rb
@@ -0,0 +1,17 @@
+module OpenTox
+
+  class Nanoparticle
+    include OpenTox
+
+    field :particle_id, type: String
+    field :core, type: String
+    field :coatings, type: Array
+
+    #field :physchem_descriptors, type: Hash, default: {}
+    #field :toxicities, type: Hash, default: {}
+    field :features, type: Hash, default: {}
+
+  end
+end
+
+
diff --git a/lib/opentox.rb b/lib/opentox.rb
index 186c87a..cc18cc6 100644
--- a/lib/opentox.rb
+++ b/lib/opentox.rb
@@ -13,6 +13,7 @@ module OpenTox
       include Mongoid::Timestamps
       store_in collection: klass.downcase.pluralize
       field :name,  type: String
+      field :source,  type: String
       field :warnings, type: Array, default: []
     end
     OpenTox.const_set klass,c