From f46ba3b7262f5b551c81fc9396c5b7f0cac7f030 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Fri, 27 May 2016 19:16:16 +0200
Subject: first correlation of nanoparticle predictions

---
 lib/import.rb | 57 ++++++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 42 insertions(+), 15 deletions(-)

(limited to 'lib/import.rb')

diff --git a/lib/import.rb b/lib/import.rb
index 2dcc361..80d4579 100644
--- a/lib/import.rb
+++ b/lib/import.rb
@@ -10,15 +10,15 @@ module OpenTox
         bundles = JSON.parse(RestClientWrapper.get('https://data.enanomapper.net/bundle?media=application%2Fjson'))["dataset"]
         File.open(File.join(dir,"bundles.json"),"w+"){|f| f.puts JSON.pretty_generate(bundles)}
         bundles.each do |bundle|
-          p bundle["title"]
+          $logger.debug bundle["title"]
           nanoparticles = JSON.parse(RestClientWrapper.get(bundle["dataset"]+"?media=application%2Fjson"))["dataEntry"]
-          p nanoparticles.size
+          $logger.debug nanoparticles.size
           nanoparticles.each do |nanoparticle|
             uuid = nanoparticle["values"]["https://data.enanomapper.net/identifier/uuid"]
             $logger.debug uuid
             File.open(File.join(dir,"nanoparticle-#{uuid}.json"),"w+"){|f| f.puts JSON.pretty_generate(nanoparticle)}
             studies = JSON.parse(RestClientWrapper.get(File.join(nanoparticle["compound"]["URI"],"study")))["study"]
-            p uuid if studies.size < 1 
+            $logger.debug uuid if studies.size < 1 
             studies.each do |study|
               File.open(File.join(dir,"study-#{study["uuid"]}.json"),"w+"){|f| f.puts JSON.pretty_generate(study)}
             end
@@ -27,35 +27,58 @@ module OpenTox
       end
 
       def self.import dir="."
+        start_time = Time.now
+        t1 = 0
+        t2 = 0
         datasets = {}
         JSON.parse(File.read(File.join(dir,"bundles.json"))).each do |bundle|
           datasets[bundle["URI"]] = Dataset.find_or_create_by(:source => bundle["URI"],:name => bundle["title"])
         end
         Dir[File.join(dir,"study*.json")].each do |s|
+          t = Time.now
           study = JSON.parse(File.read(s))
           np = JSON.parse(File.read(File.join(dir,"nanoparticle-#{study['owner']['substance']['uuid']}.json")))
+          core = {}
+          coating = []
+          np["composition"].each do |c|
+            if c["relation"] == "HAS_CORE"
+              core = {
+                :uri => c["component"]["compound"]["URI"],
+                :name => c["component"]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
+              }
+            elsif c["relation"] == "HAS_COATING"
+              coating << {
+                :uri => c["component"]["compound"]["URI"],
+                :name => c["component"]["values"]["https://data.enanomapper.net/feature/http%3A%2F%2Fwww.opentox.org%2Fapi%2F1.1%23ChemicalNameDefault"]
+              }
+            end
+          end if np["composition"]
           nanoparticle = Nanoparticle.find_or_create_by(
             :name => np["values"]["https://data.enanomapper.net/identifier/name"],
             :source => np["compound"]["URI"],
+            :core => core,
+            :coating => coating
           )
           np["bundles"].keys.each do |bundle_uri|
-            nanoparticle["dataset_ids"] << datasets[bundle_uri].id
+            nanoparticle.dataset_ids << datasets[bundle_uri].id
           end
-          bundle = datasets[np["bundles"].keys.first].id if np["bundles"].size == 1
+          dataset = datasets[np["bundles"].keys.first]
+          proteomics_features = {}
           study["effects"].each do |effect|
             effect["result"]["textValue"] ?  klass = NominalFeature : klass = NumericFeature
-            # TODO parse core/coating
-            #$logger.debug File.join(np["compound"]["URI"],"study")
             effect["conditions"].delete_if { |k, v| v.nil? }
-            # parse proteomics data
-            if study["protocol"]["category"]["title"].match(/Proteomics/) and effect["result"]["textValue"] and effect["result"]["textValue"].length > 50
+            if study["protocol"]["category"]["title"].match(/Proteomics/) and effect["result"]["textValue"] and effect["result"]["textValue"].length > 50 # parse proteomics data
+=begin
               JSON.parse(effect["result"]["textValue"]).each do |identifier, value|
-                feature = klass.find_or_create_by(
-                  :name => identifier,
-                  :category => "Proteomics",
-                )
-                nanoparticle.parse_ambit_value feature, value, bundle
+                # time critical step
+              t = Time.now
+                proteomics_features[identifier] ||= klass.find_or_create_by(:name => identifier, :category => "Proteomics")
+              t1 += Time.now - t
+              t = Time.now
+                nanoparticle.parse_ambit_value proteomics_features[identifier], value, dataset
+              t2 += Time.now - t
               end
+=end
             else
               feature = klass.find_or_create_by(
                 :name => effect["endpoint"],
@@ -63,10 +86,14 @@ module OpenTox
                 :category => study["protocol"]["topcategory"],
                 :conditions => effect["conditions"]
               )
-              nanoparticle.parse_ambit_value feature, effect["result"], bundle
+              nanoparticle.parse_ambit_value feature, effect["result"], dataset
             end
           end
           nanoparticle.save
+          #p "Total time: #{Time.now - start_time}"
+          #p "Proteomics features: #{t1}"
+          #p "Proteomics values: #{t2}"
+          #p "Time2: #{t2}"
         end
         datasets.each { |u,d| d.save }
       end
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