Module: ObservationMatrices::Export::NexmlHelper

Defined in:
app/helpers/observation_matrices/export/nexml_helper.rb

Instance Method Summary collapse

Instance Method Details

#include_collection_objects(options = {}) ⇒ Object



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 187

def include_collection_objects(options = {})
  opt = {target: ''}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])
  otu = opt[:otu] 

  # otu.collection_objects.with_identifiers.each do |s|
  otu.current_collection_objects.each do |s|
    xml.meta('xsi:type' => 'ResourceMeta', 'rel' => 'dwc:individualID') do
      if a = s.preferred_catalog_number
        xml.meta(a.namespace.name, 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:collectionID') 
        xml.meta(a.identifier, 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:catalogNumber') 
      else
        xml.meta('UNDEFINED', 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:collectionID') 
        xml.meta(s.id, 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:catalogNumber') 
      end
    end
  end # end specimens

  return opt[:target]
end

#include_continuous_matrix(options = {}) ⇒ Object



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 134

def include_continuous_matrix(options = {})
  opt = {target:  '', descriptors: []}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])
  m = opt[:observation_matrix]

  # the matrix 
  cells = m.observations_in_grid({})[:grid]

  z = m.observation_matrix_rows.map.collect{|i| i.row_object.to_global_id}

  xml.matrix do |mx|
    m.observation_matrix_rows.each do |o|
      xml.row(id: "continuous_row#{o.id}", otu: "row_#{o.id}") do |r| # use Otu#id to uniquely id the row

        # cell representation
        opt[:descriptors].each do |c|

          x = m.descriptors.index(c)
          y = z.index(o.row_object.to_global_id)

          observations = cells[ x ][ y ]
          if observations.size > 0  && !observations.first.continuous_value.nil?
            xml.cell(char: "c#{c.id}", state: observations.first.continuous_value)
          end
        end
      end # end the row
    end # end OTUs
  end # end matrix
  return opt[:target]
end

#include_multistate_matrix(options = {}) ⇒ Object



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 77

def include_multistate_matrix(options = {})
  opt = {target: '', descriptors: []}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])

  m = opt[:observation_matrix]

  # the matrix
  cells = m.observations_in_grid({})[:grid]

  p = m.observation_matrix_columns.order('observation_matrix_columns.position').map(&:descriptor_id)
  q = m.observation_matrix_rows.order('observation_matrix_rows.position').collect{|i| i.row_object.to_global_id }

  xml.matrix do
    m.observation_matrix_rows.each do |r|
      xml.row(id: "multistate_row#{r.id}", otu: "row_#{r.id}") do |row| # use row_id to uniquel identify the row ##  Otu#id to uniquely id the row

        # cell representation
        opt[:descriptors].each do |d|

          #  byebug if d.id == 37
          x = p.index(d.id) # opt[:descriptors].index(d)  #   .index(d)
          y = q.index(r.row_object.to_global_id)

          observations = cells[ x  ][ y ]

          case observations.size
          when 0 
            state = "missing#{d.id}"
          when 1
            o = observations.first
            if d.qualitative? 
              state = "cs#{o.character_state_id}"
            elsif d.presence_absence?
              # WRONG
              state = "cs_#{o.descriptor_id}_#{o.presence ? '1' : '0'}"
            else
              state = "ERROR"
            end
          else # > 1 
            if d.qualitative?
              state = "cs#{d.id}unc_#{observations.collect{|i| i.character_state_id}.sort.join}" # should just unify identifiers with above.
            elsif d.presence_absence?
              state = "cs_#{o.descriptor_id}_unc_#{ observations.collect{|i| i.character_state_id}.sort.join}"
            end
          end

          #byebug if state == 'cs' # d.id == 37 

          xml.cell(char: "c#{d.id}", state: state)
        end
      end # end the row
    end # end OTUs
  end # end matrix

  opt[:target]
end

#nexml_descriptors(options = {}) ⇒ Object



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 3

def nexml_descriptors(options = {})
  opt = {target: ''}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])
  m = opt[:observation_matrix]

  # Multistate characters
  xml.characters(
    id: "multistate_character_block_#{m.id}",
    otus: "otu_block_#{m.id}",
    'xsi:type' => 'nex:StandardCells',
    label:  "Multistate characters for matrix #{m.name}"
  ) do

    descriptors = m.symbol_descriptors.load
    xml.format do

      descriptors.each do |c|
        xml.states(id: "states_for_chr_#{c.id}") do
          if c.qualitative?

            c.character_states.each_with_index do |cs,i|
              xml.state(id: "cs#{cs.id}", label: cs.name, symbol: "#{i}")
            end

            # Add a missing state for each character regardless of whether we use it or not
            xml.state(id: "missing#{c.id}", symbol: c.character_states.size, label: "?")

            # Poll the matrix for polymorphic/uncertain states
            uncertain = m.polymorphic_cells_for_descriptor(descriptor_id: c.id, symbol_start: c.character_states.size + 1)
            uncertain.keys.each do |pc|
              xml.uncertain_state_set(id: "cs#{c.id}unc_#{uncertain[pc].sort.join}", symbol: pc) do
                uncertain[pc].collect{|m| xml.member(state: "cs#{m}") }
              end
            end

          elsif c.presence_absence?
            # like "cs_4_0'
            xml.state(id: "cs_#{c.id}_0", label: 'absent', symbol: "0")
            xml.state(id: "cs_#{c.id}_1", label: 'present', symbol: "1")

            xml.state(id: "missing#{c.id}", symbol: '2', label: "?")

            uncertain = m.polymorphic_cells_for_descriptor(descriptor_id: c.id, symbol_start: 2)
            uncertain.keys.each do |pc|
              xml.uncertain_state_set(id: "cs#{c.id}unc_#{uncertain[pc].sort.join}", symbol: pc) do
                uncertain[pc].collect{|m| xml.member(state: "cs_#{m}") } # m is built in pcfd
              end
            end
          end # end states block

        end
      end  # end character loop for multistate states

      descriptors.collect{|c| xml.char(id: "c#{c.id}", states: "states_for_chr_#{c.id}", label: c.name)}
    end # end format
    include_multistate_matrix(opt.merge(descriptors: descriptors)) if opt[:include_matrix]
  end # end characters

  d = m.continuous_descriptors.order('observation_matrix_columns.position').load
  # continuous characters
  xml.characters(
    id: "continuous_character_block_#{m.id}",
    otus: "otu_block_#{m.id}",
    'xsi:type' => 'nex:ContinuousCells',
    label: "Continuous characters for matrix #{m.name}") do
      xml.format do
        d.collect{|c| xml.char(id: "c#{c.id}", label: c.name)}
      end # end format

      include_continuous_matrix(opt.merge(descriptors: d)) if opt[:include_matrix]
    end # end multistate characters
    opt[:target]
end

#nexml_otus(options = {}) ⇒ Object



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 165

def nexml_otus(options = {})
  opt = {target: ''}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])
  m = opt[:observation_matrix]

  xml.otus(
    id: "otu_block_#{m.id}",
    label: "Otus for matrix #{m.name}"
  ) do
    m.observation_matrix_rows.each do |r|
      xml.otu(
        id: "row_#{r.id}",
        about: "#row_#{r.id}", # technically only need this for proper RDFa extraction  !!! Might need this to be different, is it about row, or row object!
        label: observation_matrix_row_label(r)
      ) do
        include_collection_objects(opt.merge(otu: r.row_object)) if opt[:include_collection_objects]
      end
    end
  end
  return opt[:target]
end