Class: ObservationMatrix

Inherits:
ApplicationRecord show all
Includes:
Housekeeping, Shared::Citations, Shared::DataAttributes, Shared::Identifiers, Shared::IsData, Shared::Notes, Shared::Tags
Defined in:
app/models/observation_matrix.rb

Overview

A view to a set of observations.

Instance Method Summary collapse

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Instance Method Details

#cell_countObject



63
64
65
# File 'app/models/observation_matrix.rb', line 63

def cell_count
  observation_matrix_rows.count * observation_matrix_columns.count 
end

#continuous_descriptorsObject



37
38
39
# File 'app/models/observation_matrix.rb', line 37

def continuous_descriptors
  descriptors.where(type: 'Descriptor::Continuous')
end

#gene_descriptorsObject



49
50
51
# File 'app/models/observation_matrix.rb', line 49

def gene_descriptors
  descriptors.where(type: 'Descriptor::Gene')
end

#is_media_matrix?Boolean

Returns:

  • (Boolean)


67
68
69
70
71
72
# File 'app/models/observation_matrix.rb', line 67

def is_media_matrix?
  observation_matrix_columns.each do |c|
    return false unless c.descriptor.type == 'Descriptor::Media'
  end
  true
end

#media_descriptorsObject



45
46
47
# File 'app/models/observation_matrix.rb', line 45

def media_descriptors
  descriptors.where(type: 'Descriptor::Media')
end

#observationsObject



113
114
115
# File 'app/models/observation_matrix.rb', line 113

def observations
  Observation.in_observation_matrix(id)
end

#observations_hashHash

Returns a hash of hashes of arrays with the coding objects nicely organized

descriptor_id1 =>{row_object_global_id => [observation1, observation2], descriptor_id: nil}

was `codings_mx` in mx where this: “likely should add scope and merge with above, though this seems to be slower”

Returns:

  • (Hash)

    a hash of hashes of arrays with the coding objects nicely organized

    descriptor_id1 =>{row_object_global_id => [observation1, observation2], descriptor_id: nil}
    

    was `codings_mx` in mx where this: “likely should add scope and merge with above, though this seems to be slower”



205
206
207
208
209
# File 'app/models/observation_matrix.rb', line 205

def observations_hash
  h = Hash.new{|hash, key| hash[key] = Hash.new{|hash2, key2| hash2[key2] = Array.new}} 
  observations.each {|o| h[o.descriptor_id][o.observation_object_global_id].push(o) }
  h
end

#observations_in_grid(options = {}) ⇒ Hash

Derived from mx code. TODO: optimize by returning only observations with Otu range, not just Chr range (? still relevant ?)

:position attribute starts at 1

Grid starts at 0!!

Returns:

  • (Hash)

    grid: [columns][observations] rows: [row_object.GlobalId, row_object.GlobalId] (Klass) columns: [descriptor.id, desriptor.id]



124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
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
# File 'app/models/observation_matrix.rb', line 124

def observations_in_grid(options = {})
  opts = {
    row_start:  1,
    row_end: 'all',
    col_start: 1,
    col_end: 'all'
  }.merge!(options.symbolize_keys)

  return false if (opts[:row_start] == 0) || (opts[:col_start] == 0) # catch problems with forgetting index starts at 1

  rows = []  # y axis
  cols = []  # x axis
  r = []
  if opts[:row_end] == 'all'
    r = observation_matrix_rows.order('observation_matrix_rows.position')
  else
    r = observation_matrix_rows.where("observation_matrix_rows.position >= ? and observation_matrix_rows.position <= ?", opts[:row_start], opts[:row_end]).order('observation_matrix_rows.position')
  end
  
  return false if r.size == 0

  rows = r.collect{|i| i.row_object.to_global_id}

  if opts[:col_end] == 'all'
    cols = descriptors.order('observation_matrix_columns.position').pluck(:id) # all descriptors
  else
    cols = observation_matrix_rows.
      where("observation_matrix_columns.position >= ? and observation_matrix_columns.position <= ?", opts[:col_start], opts[:col_end]).
      order('observation_matrix_columns.position').
      pluck(:descriptor_id)  # self.chrs.within_mx_range(opts[:chr_start], opts[:chr_end])
  end

  return false if cols.size == 0

  grid = Array.new(cols.size){Array.new(rows.size){Array.new}}

  # Dump the observations into bins
  Observation.by_descriptors_and_rows(cols, rows).each do |o|
    i = o.observation_object.to_global_id
    if rows.index(i)
      grid[cols.index(o.descriptor_id)][rows.index(i)].push(o) 
    end
  end
  
  {grid: grid, rows: rows, cols: cols }
end

#polymorphic_cells_for_descriptor(symbol_start: 0, descriptor_id:) ⇒ Object

Used soley as a indexing method for nexml output Original code in mx

Parameters:

  • descriptor_id (Descriptor)
  • symbol_start (Integer)

    # takes :chr => Chr, :symbol_start => Int

Returns:

  • Hash 1 => [character_state.id, charater_state.id]



177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
# File 'app/models/observation_matrix.rb', line 177

def polymorphic_cells_for_descriptor(symbol_start: 0, descriptor_id:)
  symbol_start ||= 0
  cells = Hash.new{|hash, key| hash[key] = Array.new}

  observations.where(descriptor_id: descriptor_id).each do |o|
    cells[o.observation_object_global_id].push(
      o.qualitative? ? o.character_state_id : "#{o.descriptor_id}_#{o.presence_absence? ? '1' : '0'}"
    )
  end

  r = Hash.new{|hash, key| hash[key] = Array.new}
  i = 0
  cells.keys.each do |k|
    if r # must be some other idiom
      if cells[k].size > 1
        r[symbol_start + i] = cells[k].sort 
        i += 1
      end
    end
  end
  r 
end

#presence_absence_descriptorsObject



33
34
35
# File 'app/models/observation_matrix.rb', line 33

def presence_absence_descriptors
  descriptors.where(type: 'Descriptor::PresenceAbsence')
end

#qualitative_descriptorsObject



29
30
31
# File 'app/models/observation_matrix.rb', line 29

def qualitative_descriptors
  descriptors.where(type: 'Descriptor::Qualitative')
end

#reorder_columns(by = 'reindex') ⇒ Object



97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
# File 'app/models/observation_matrix.rb', line 97

def reorder_columns(by = 'reindex')
  case by
  when 'reindex'
    observation_matrix_columns.order('observation_matrix_columns.position').each.with_index do |c,i|
      c.update_column(:position, i)
    end
  when 'name'
    observation_matrix_columns.order('descriptors.name').each.with_index do |c,i|
      c.update_column(:position, i)
    end
  else
    return false
  end
  true
end

#reorder_rows(by = 'reindex') ⇒ Object



74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
# File 'app/models/observation_matrix.rb', line 74

def reorder_rows(by = 'reindex')
  case by
  when 'reindex'
    observation_matrix_rows.order('observation_matrix_rows.position').each.with_index do |r,i|
      r.update_column(:position, i)
    end
  when 'nomenclature'
    # TODO: probably not correct, a quick and dirty attempt
    objects = []
    observation_matrix_rows.each do |r|
      objects.push [r, r.current_taxon_name.ancestor_ids]
    end

    objects.sort!{|a, b| a[1] <=> b[1]} # add internal loop on name
    objects.each_with_index do |r,i|
      r[0].update_column(:position, i)
    end
  else
    return false
  end
  true
end

#sample_descriptorsObject



41
42
43
# File 'app/models/observation_matrix.rb', line 41

def sample_descriptors
  descriptors.where(type: 'Descriptor::Sample')
end

#symbol_descriptorsObject

As handled in export/parsing by external tools !! Note order() is applied !!



59
60
61
# File 'app/models/observation_matrix.rb', line 59

def symbol_descriptors
  descriptors.where(type: ['Descriptor::PresenceAbsence', 'Descriptor::Qualitative']).order('observation_matrix_columns.position')
end

#working_descriptorsObject



53
54
55
# File 'app/models/observation_matrix.rb', line 53

def working_descriptors
  descriptors.where(type: 'Descriptor::Working')
end