Module: ObservationMatrices::Export::NexmlHelper
- Defined in:
- app/helpers/observation_matrices/export/nexml_helper.rb
Instance Method Summary collapse
- #include_collection_objects(options = {}) ⇒ Object
- #include_continuous_matrix(options = {}) ⇒ Object
- #include_multistate_matrix(options = {}) ⇒ Object
- #nexml_descriptors(options = {}) ⇒ Object
- #nexml_otus(options = {}) ⇒ Object
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( = {}) opt = {target: ''}.merge!() 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.('xsi:type' => 'ResourceMeta', 'rel' => 'dwc:individualID') do if a = s.preferred_catalog_number xml.(a.namespace.name, 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:collectionID') xml.(a.identifier, 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:catalogNumber') else xml.('UNDEFINED', 'xsi:type' => 'LiteralMeta', 'property' => 'dwc:collectionID') xml.(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( = {}) opt = {target: '', descriptors: []}.merge!() 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( = {}) opt = {target: '', descriptors: []}.merge!() 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( = {}) opt = {target: ''}.merge!() 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( = {}) opt = {target: ''}.merge!() 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 include_collection_objects(opt.merge(otu: r.row_object)) if opt[:include_collection_objects] end end end return opt[:target] end |