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



220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 220

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



144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
# 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.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



90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 90

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|

          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

          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.



281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 281

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



3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
# 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' => short_url(d.image.image_file.url(:original)) # root_url + d.image.image_file.url(:original)[1..-1]
                    )
                  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



245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 245

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 =  ImageMatrix.new(
    project_id: m.project_id,
    otu_filter: m.otus.pluck(:id).join('|'))
  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][:name],
            'label' => depiction[:figure_label],
            'citation' => depiction[:source_cached]
          )
        end
      end
    end
  end
  return opt[:target]
end

#nexml_otus(options = {}) ⇒ Object



177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
# File 'app/helpers/observation_matrices/export/nexml_helper.rb', line 177

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
        include_collection_objects(opt.merge(otu: r.row_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
        Observation::Media.where(otu_id: r.otu_id).each do |o|
          o.depictions.each do |d|

            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' => o.descriptor.name, #  descriptors[index][:name],
              'label' => d.figure_label, # epiction[:figure_label],
              'citation' =>  d.image.source&.cached # depiction[:source_cached]
            )

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