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 255

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 144

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.collect{|i| i.observation_index }

  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.observation_index )

          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 89

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.observation_index } # could pluck this string concat from the db

  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 uniquely identify the row, Otu#id to uniquely id the row Otu

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

          x = p.index(d.id) # opt[:descriptors].index(d)  #   .index(d)
          y = q.index( r.observation_index)

          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

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

  opt[:target]
end

#nexml_depictions(options = {}) ⇒ Object

TODO: if semantics change we can add them as block later. This is just character state depictions for now.



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 314

def nexml_depictions(options = {})
  opt = {target: '', descriptors: []}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])
  m = opt[:observation_matrix]
  xml.depictions do
    if true # character state options

      xml.character_state_depictions(
        id: "character_state_depiction_block_#{m.id}",
        otus: "otu_block_#{m.id}",
        #   'xsi:type' => 'nex:StandardCells',
        label:  "Character state depictions for matrix #{m.name}"
      ) do
        ::Depiction.joins(image: [:character_states]).merge(m.character_states).each do |d|
          xml.meta(
            'xsi:type' => 'ResourceMeta',
            'rel' => 'foaf:depiction',
            'about' => "cs#{d.depiction_object_id}",
            'href' => short_url(d.image.image_file.url(:original)) # root_url + d.image.image_file.url(:original)[1..-1]
          )
        end
      end
    end
    opt[:target]
  end
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|
              if cs.depictions.load.any?
                xml.state(id: "cs#{cs.id}", label: cs.target_name(:key, nil), symbol: "#{i}") do
                  cs.depictions.each do |d|
                    xml.meta(
                      'xsi:type' => 'ResourceMeta',
                      'rel' => 'foaf:depiction',
                      'href' => image_short_url(d.image), # see app/helpers/images_helper.rb
                      'label' => c.target_name(:description, nil) + ' ' + cs.target_name(:description, nil)
                    )
                  end
                end
              else
                xml.state(id: "cs#{cs.id}", label: cs.target_name(:key, nil), symbol: "#{i}")
              end
            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.target_name(:key, nil))}
    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.target_name(:key, nil))}
      end # end format

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

#nexml_otu_depictions(options = {}) ⇒ Object

NOT USED - current using inline approach to handle depictions



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 277

def nexml_otu_depictions(options = {})
  opt = {target:  '', descriptors: []}.merge!(options)
  xml = Builder::XmlMarkup.new(target: opt[:target])
  m = opt[:observation_matrix]
  otus = m.otus
  im = Tools::ImageMatrix.new(
    project_id: m.project_id,
    otu_filter: m.otus.pluck(:id).join('|'),
    per: 1000000)
  descriptors = im.list_of_descriptors.values
  row_hash = m.observation_matrix_rows.map{|i| [i.otu_id, i.id]}.to_h

  xml.otu_depictions do |d|
    im.depiction_matrix.each do |object|
      object[1][:depictions].each_with_index do |depictions, index|
        depictions.each do |depiction|

          xml.meta(
            'xsi:type' => 'ResourceMeta',
            'rel' => 'foaf:depiction',
            'about' => "row_#{row_hash[object[1][:otu_id].to_i].to_s}",
            'href' => root_url + im.image_hash[depiction[:image_id]][:original_url],
            'object' => object[1][:object].otu_name,
            'description' => descriptors[index][:caption],
            'label' => depiction[:figure_label],
            'citation' => depiction[:source_cached]
          )
        end
      end
    end
  end
  return opt[:target]
end

#nexml_otus(options = {}) ⇒ Object 



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# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 175

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_nexml(r)
      ) do
        # TODO: should otu: be more generic
        include_collection_objects(opt.merge(otu: r.observation_object)) if opt[:include_collection_objects]

        # This is experimental only. Issues:
        # * It draws images and data from all matrices, # not just this one
        # * Depictions are on Observation::Media, not OTU, i.e. we could be more granular throughout
        # * Citations are on Image, not Depiction
        im = Tools::ImageMatrix.new(project_id: r.project_id, otu_filter: r.otu_id.to_s)
        descriptors = im.list_of_descriptors.values
        if !im.blank? && !im.depiction_matrix.empty?
          object = im.depiction_matrix.first

          object[1][:depictions].each_with_index do |depictions, index|
            depictions.each do |depiction|
              lbl = []
              cit = im.image_hash[depiction[:image_id]][:citations].collect{|i| i[:cached]}.join('')
              #lbl.push('<b>Taxon name:</b> ' + object[1][:object].otu_name) unless object[1][:object].otu_name.blank?
              lbl.push(descriptors[index][:name]) unless descriptors[index][:name].blank?
              lbl.push(depiction[:caption]) unless depiction[:caption].blank?
              #lbl.push('<b>Citation:</b> ' + cit) unless cit.blank?
              img_attr = Image.find(depiction[:image_id]).attribution
              #lbl.push(attribution_tag(img_attr).gsub('&#169;', '')) unless img_attr.nil?
              lbl.push(attribution_nexml_label(img_attr)) unless img_attr.nil?
              lbl = lbl.compact.join('; ')

              xml.meta(
                'xsi:type' => 'ResourceMeta',
                'rel' => 'foaf:depiction',
                'about' => "row_#{r.id}",
                'href' => image_short_url( im.image_hash[depiction[:image_id]][:original_url] ),
                'label' => lbl
                #'object' => object[1][:object].otu_name,
                #'label' => descriptors[index][:name], ###
                #'caption' => depiction[:caption],
                #'citation' => im.image_hash[depiction[:image_id]][:citations].collect{|i| i[:cached]}.join('')
              )
            end
          end
        end

=begin
        Observation::Media.where(otu_id: r.otu_id).each do |o|
          o.depictions.each do |d|
            lbl = d.figure_label.blank? ? o.descriptor.name : d.figure_label
            dscr = d.figure_label.blank? ? '' : o.descriptor.name
              xml.meta(
              'xsi:type' => 'ResourceMeta',
              'rel' => 'foaf:depiction',
              'about' => "row_#{r.id}",
              'href' => short_url(d.image.image_file.url),  #  root_url + im.image_hash[depiction[:image_id]][:original_url],
              # 'object' => observation_matrix_row_label_nexml(r), # label_for_otu(o) #  o.otu.otu_name, #  object[1][:object].otu_name,  -- redundant with label=""
              'description' => dscr, #  descriptors[index][:name],
              'label' => lbl, # epiction[:figure_label],
              'citation' =>  d.image.source&.cached # depiction[:source_cached]
            )

          end
        end
=end
      end
    end
  end
  return opt[:target]
end