From 9750e0309500259e9a56e267ce87984fb5bb5e53 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 26 Nov 2018 15:29:26 +0000
Subject: clean out; better response codes; prepare for batch

---
 batch.rb | 101 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 101 insertions(+)
 create mode 100644 batch.rb

(limited to 'batch.rb')

diff --git a/batch.rb b/batch.rb
new file mode 100644
index 0000000..2e72396
--- /dev/null
+++ b/batch.rb
@@ -0,0 +1,101 @@
+require 'csv'
+require 'tempfile'
+
+module OpenTox
+
+  class Batch
+
+    include OpenTox
+    include Mongoid::Document
+    include Mongoid::Timestamps
+    store_in collection: "batch"
+    field :name,  type: String
+    field :source,  type: String
+    field :identifiers, type: Array
+    field :ids, type: Array
+    field :compounds, type: Array
+    field :warnings, type: Array, default: []
+
+    def self.from_csv_file file
+      source = file
+      name = File.basename(file,".*")
+      batch = self.find_by(:source => source, :name => name)
+      if batch
+        $logger.debug "Skipping import of #{file}, it is already in the database (id: #{batch.id})."
+      else
+        $logger.debug "Parsing #{file}."
+        table = CSV.read file, :skip_blanks => true, :encoding => 'windows-1251:utf-8'
+        batch = self.new(:source => source, :name => name, :identifiers => [], :ids => [], :compounds => [])
+
+        # original IDs
+        if table[0][0] =~ /ID/i
+          @original_ids = table.collect{|row| row.shift}
+          @original_ids.shift
+        end
+        
+        # features
+        feature_names = table.shift.collect{|f| f.strip}
+        warnings << "Duplicated features in table header." unless feature_names.size == feature_names.uniq.size
+        compound_format = feature_names.shift.strip
+        bad_request_error "#{compound_format} is not a supported compound format. Accepted formats: SMILES, InChI." unless compound_format =~ /SMILES|InChI/i
+        numeric = []
+        features = []
+        # guess feature types
+        feature_names.each_with_index do |f,i|
+          metadata = {:name => f}
+          values = table.collect{|row| val=row[i+1].to_s.strip; val.blank? ? nil : val }.uniq.compact
+          types = values.collect{|v| v.numeric? ? true : false}.uniq
+          feature = nil
+          if values.size == 0 # empty feature
+          elsif  values.size > 5 and types.size == 1 and types.first == true # 5 max classes
+            numeric[i] = true
+            feature = NumericFeature.find_or_create_by(metadata)
+          else
+            metadata["accept_values"] = values
+            numeric[i] = false
+            feature = NominalFeature.find_or_create_by(metadata)
+          end
+          features << feature if feature
+        end
+        
+        table.each_with_index do |vals,i|
+          identifier = vals.shift.strip.gsub(/^'|'$/,"")
+          begin
+            case compound_format
+            when /SMILES/i
+              compound = OpenTox::Compound.from_smiles(identifier)
+            when /InChI/i
+              compound = OpenTox::Compound.from_inchi(identifier)
+            end
+          rescue 
+            compound = nil
+          end
+          # collect only for present compounds
+          unless compound.nil?
+            batch.identifiers << identifier
+            batch.compounds << compound.id
+            batch.ids << @original_ids[i] if @original_ids
+          else
+            batch.warnings << "Cannot parse #{compound_format} compound '#{identifier}' at line #{i+2} of #{source}."
+          end
+        end
+        batch.compounds.duplicates.each do |duplicate|
+          $logger.debug "Duplicates found in #{name}."
+          dup = Compound.find duplicate
+          positions = []
+          batch.compounds.each_with_index do |co,i|
+            c = Compound.find co
+            if !c.blank? and c.inchi and c.inchi == dup.inchi
+              positions << i+1
+            end
+          end
+          batch.warnings << "Duplicate compound at ID #{positions.join(' and ')}."
+        end
+        batch.save
+      end
+      batch
+    end
+
+  end
+
+end
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