require 'csv'
require 'tempfile'

module OpenTox

  class Dataset
    include Mongoid::Document

    field :feature_ids, type: Array, default: []
    field :compound_ids, type: Array, default: []
    field :source, type: String
    field :warnings, type: Array, default: []

    # Readers

    def compounds
      self.compound_ids.collect{|id| OpenTox::Compound.find id}
    end

    def features
      self.feature_ids.collect{|id| OpenTox::Feature.find(id)}
    end

    # Writers

    def compounds=(compounds)
      self.compound_ids = compounds.collect{|c| c.id}
    end

    def add_compound compound
        self.compound_ids << compound.id
    end

    def features=(features)
      self.feature_ids = features.collect{|f| f.id}
    end

    def add_feature feature
      self.feature_ids << feature.id
    end

    def self.create compounds, features, warnings=[], source=nil
      dataset = Dataset.new(:warnings => warnings)
      dataset.compounds = compounds
      dataset.features = features
      dataset
    end

    # for prediction result datasets
    # assumes that there are feature_ids with title prediction and confidence
    # @return [Array] of Hashes with keys { :compound, :value ,:confidence } (compound value is object not uri)
    # TODO
    #def predictions
    #end

    # Serialisation
    
    # converts dataset to csv format including compound smiles as first column, other column headers are feature titles
    # @return [String]
    def to_csv(inchi=false)
      CSV.generate() do |csv| #{:force_quotes=>true}
        csv << [inchi ? "InChI" : "SMILES"] + features.collect{|f| f.title}
        compounds.each_with_index do |c,i|
          csv << [inchi ? c.inchi : c.smiles] + data_entries[i]
        end
      end
    end

    # Methods for for validation service

    # create a new dataset with the specified compounds and features
    # @param compound_indices [Array] compound indices (integers)
    # @param feats [Array] features objects
    # @param metadata [Hash]
    # @return [OpenTox::Dataset]
    # TODO
    def split( compound_indices, feats, metadata)

      bad_request_error "Dataset.split : Please give compounds as indices" if compound_indices.size==0 or !compound_indices[0].is_a?(Fixnum)
      bad_request_error "Dataset.split : Please give features as feature objects (given: #{feats})" if feats!=nil and feats.size>0 and !feats[0].is_a?(OpenTox::Feature)
      dataset = OpenTox::Dataset.new
      dataset.metadata = metadata
      dataset.features = (feats ? feats : self.features)
      compound_indices.each do |c_idx|
        d = [ self.compounds[c_idx] ]
        dataset.features.each_with_index.each do |f,f_idx|
          d << (self.data_entries[c_idx] ? self.data_entries[c_idx][f_idx] : nil)
        end
        dataset << d
      end
      dataset.put
      dataset
    end


    # maps a compound-index from another dataset to a compound-index from this dataset
    # mapping works as follows:
    # (compound c is the compound identified by the compound-index of the other dataset)
    # * c occurs only once in this dataset? map compound-index of other dataset to index in this dataset
    # * c occurs >1 in this dataset?
    # ** number of occurences is equal in both datasets? assume order is preserved(!) and map accordingly
    # ** number of occurences is not equal in both datasets? cannot map, raise error
    # @param dataset [OpenTox::Dataset] dataset that should be mapped to this dataset (fully loaded)
    # @param compound_index [Fixnum], corresponding to dataset
    # TODO
    def compound_index( dataset, compound_index )
      compound_inchi = dataset.compounds[compound_index].inchi
      self_indices = compound_indices(compound_inchi)
      if self_indices==nil
        nil
      else
        dataset_indices = dataset.compound_indices(compound_inchi)
        if self_indices.size==1
          self_indices.first
        elsif self_indices.size==dataset_indices.size
          # we do assume that the order is preseverd (i.e., the nth occurences in both datasets are mapped to each other)!
          self_indices[dataset_indices.index(compound_index)]
        else
          raise "cannot map compound #{compound_inchi} from dataset #{dataset.id} to dataset #{self.id}, "+
            "compound occurs #{dataset_indices.size} times and #{self_indices.size} times"
        end
      end
    end

    # returns the inidices of the compound in the dataset
    # @param compound_inchi [String]
    # @return [Array] compound index (position) of the compound in the dataset, array-size is 1 unless multiple occurences
    # TODO
    def compound_indices( compound_inchi )
      unless defined?(@cmp_indices) and @cmp_indices.has_key?(compound_inchi)
        @cmp_indices = {}
        compounds().size.times do |i|
          c = self.compounds[i].inchi
          if @cmp_indices[c]==nil
            @cmp_indices[c] = [i]
          else
            @cmp_indices[c] = @cmp_indices[c]+[i]
          end
        end
      end
      @cmp_indices[compound_inchi]
    end

    # Adding data methods
    # (Alternatively, you can directly change @data["feature_ids"] and @data["compounds"])

    # Create a dataset from file (csv,sdf,...)
    # @param filename [String]
    # @return [String] dataset uri
    # TODO
    #def self.from_sdf_file
    #end

    def self.from_csv_file file, source=nil, bioassay=true
      source ||= file
      table = CSV.read file, :skip_blanks => true
      from_table table, source, bioassay
    end

    # parse data in tabular format (e.g. from csv)
    # does a lot of guesswork in order to determine feature types
    def self.from_table table, source, bioassay=true

      time = Time.now

      # features
      feature_names = table.shift.collect{|f| f.strip}
      dataset = Dataset.new(:source => source)
      dataset.warnings << "Duplicate 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 = []
      # guess feature types
      feature_names.each_with_index do |f,i|
        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
        metadata = {"name" => f, "source" => source}
        if values.size == 0 # empty feature
        elsif  values.size > 5 and types.size == 1 and types.first == true # 5 max classes
          metadata["numeric"] = true
          numeric[i] = true
        else
          metadata["nominal"] = true
          metadata["accept_values"] = values
          numeric[i] = false
        end
        if bioassay
          if metadata["numeric"]
            feature = NumericBioAssay.find_or_create_by(metadata)
          elsif metadata["nominal"]
            feature = NominalBioAssay.find_or_create_by(metadata)
          end
        else
          metadata.merge({:measured => false, :calculated => true})
          if metadata["numeric"]
            feature = NumericFeature.find_or_create_by(metadata)
          elsif metadata["nominal"]
            feature = NominalFeature.find_or_create_by(metadata)
          end
        end
        dataset.feature_ids << OpenTox::Feature.find_or_create_by(metadata).id
      end
      feature_ids = dataset.features.collect{|f| f.id.to_s}
      
      $logger.debug "Feature values: #{Time.now-time}"
      time = Time.now

      # compounds and values
      r = -1
      csv = ["compound_id,feature_id,value"]

      compound_time = 0
      value_time = 0

      table.each_with_index do |vals,j|
        ct = Time.now
        identifier = vals.shift
        begin
          case compound_format
          when /SMILES/i
            compound = OpenTox::Compound.from_smiles(identifier)
            if compound.inchi.empty?
              dataset.warnings << "Cannot parse #{compound_format} compound '#{compound.strip}' at position #{j+2}, all entries are ignored."
              next
            end
          when /InChI/i
            compound = OpenTox::Compound.from_inchi(identifier)
          end
        rescue
          dataset.warnings << "Cannot parse #{compound_format} compound '#{compound}' at position #{j+2}, all entries are ignored."
          next
        end
        compound_time += Time.now-ct
        dataset.compound_ids << compound.id
          
        r += 1
        unless vals.size == feature_ids.size # way cheaper than accessing dataset.features
          dataset.warnings << "Number of values at position #{j+2} is different than header size (#{vals.size} vs. #{features.size}), all entries are ignored."
          next
        end

        cid = compound.id.to_s
        vals.each_with_index do |v,i|
          if v.blank?
            dataset.warnings << "Empty value for compound '#{identifier}' (row #{r+2}) and feature '#{feature_names[i]}' (column #{i+2})."
            next
          elsif numeric[i]
            csv << "#{cid},#{feature_ids[i]},#{v.to_f}" # retrieving ids from dataset.{compounds|features} kills performance
          else
            csv << "#{cid},#{feature_ids[i]},#{v.strip}" # retrieving ids from dataset.{compounds|features} kills performance
          end
        end
      end
      dataset.compounds.duplicates.each do |duplicates|
        # TODO fix and check
        positions = []
        compounds.each_with_index{|c,i| positions << i+1 if !c.blank? and c == compound}
        dataset.warnings << "Duplicate compound #{compound.inchi} at rows #{positions.join(', ')}. Entries are accepted, assuming that measurements come from independent experiments." 
      end
      
      $logger.debug "Value parsing: #{Time.now-time} (Compound creation: #{compound_time})"
      time = Time.now

      # Workaround for mongo bulk insertions (insertion of single data_entries is far too slow)
      # Skip ruby JSON serialisation:
      #   - to_json is too slow to write to file
      #   - json (or bson) serialisation is probably causing very long parse times of Mongo::BulkWrite, or any other ruby insert operation
      f = Tempfile.new("#{dataset.id.to_s}.csv","/tmp")
      f.puts csv.join("\n")
      f.close
      $logger.debug "Write file: #{Time.now-time}"
      time = Time.now
      # TODO DB name from config
      `mongoimport --db opentox --collection data_entries --type csv --headerline --file #{f.path}`
      $logger.debug "Bulk insert: #{Time.now-time}"
      time = Time.now
      
      dataset
    end
  end
end