Class: ObservationMatrix

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

Overview

A view to a set of Observations.

Constant Summary collapse

ALTERNATE_VALUES_FOR = 
[:name].freeze

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Shared::IsData

#errors_excepting, #full_error_messages_excepting, #identical, #is_community?, #is_destroyable?, #is_editable?, #is_in_use?, #is_in_users_projects?, #metamorphosize, #similar

Methods included from Shared::AlternateValues

#all_values_for, #alternate_valued?

Methods included from Shared::DataAttributes

#import_attributes, #internal_attributes, #keyword_value_hash, #reject_data_attributes

Methods included from Shared::Notes

#concatenated_notes_string, #reject_notes

Methods included from Shared::Tags

#reject_tags, #tag_with, #tagged?, #tagged_with?

Methods included from Shared::Identifiers

#dwc_occurrence_id, #identified?, #next_by_identifier, #previous_by_identifier, #reject_identifiers, #uri, #uuid

Methods included from Shared::Documentation

#document_array=, #documented?, #reject_documentation, #reject_documents

Methods included from Shared::Citations

#cited?, #mark_citations_for_destruction, #nomenclature_date, #origin_citation_source_id, #reject_citations, #requires_citation?, #sources_by_topic_id

Methods included from Housekeeping

#has_polymorphic_relationship?

Methods inherited from ApplicationRecord

transaction_with_retry

Class Method Details

.batch_add(params) ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 321

def self.batch_add(params)
  return false if params[:observation_matrix_id].blank?
  o = ObservationMatrix.find_by(project_id: params[:project_id], id: params[:observation_matrix_id])
  o.batch_populate(params)
end

.batch_create(params) ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 327

def self.batch_create(params)
  o = ObservationMatrix.create(params.require(:observation_matrix).permit(:name))
  if o.persisted?
    o.batch_populate(params)
  else
    o.errors.full_messages
  end
end

Instance Method Details

#batch_populate(params) ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 271

def batch_populate(params)
  queries = params.keys.select{|a| a =~ /_query/ }
  return false if queries.size != 1

  result = {
    rows: 0,
    columns: 0,
    observation_matrix_id: id,
    observation_matrix_name: name
  }

  otus = []
  descriptors = []
  collection_objects = []
  extracts = []

  case queries[0]

  when 'otu_query'
    otus = ::Queries::Otu::Filter.new(params[:otu_query]).all
  when 'descriptor_query'
    descriptors = ::Queries::Descriptor::Filter.new(params[:descriptor_query]).all
  when 'observation_query'

    otus = ::Queries::Otu::Filter.new(observation_query: params[:observation_query]).all
    descriptors = ::Queries::Descriptor::Filter.new(observation_query: params[:observation_query]).all
    collection_objects = ::Queries::CollectionObject::Filter.new(observation_query: params[:observation_query]).all
    extracts = ::Queries::Extract::Filter.new(observation_query: params[:observation_query]).all
  when 'collection_object_query'
    collection_objects = ::Queries::CollectionObject::Filter.new(params[:collection_object_query]).all
  when 'extract_query'
    extracts = ::Queries::Extract::Filter.new(params[:extract_query]).all
  end

  [otus, collection_objects, extracts].each do |t|
    t.each do |i|
      # Fail silently
      j = ObservationMatrixRowItem::Single.create(observation_matrix: self, observation_object: i)
      result[:rows] += 1 if j.persisted?
    end
  end

  descriptors.each do |d|
    j = ObservationMatrixColumnItem::Single::Descriptor.create(observation_matrix: self, descriptor: d)
    result[:columns] += 1 if j.persisted?
  end

  result
end

#cell_count ⇒ Object

TODO: helper method



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# File 'app/models/observation_matrix.rb', line 76

def cell_count
  observation_matrix_rows.count * observation_matrix_columns.count
end

#character_states ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 71

def character_states
  CharacterState.joins(descriptor: [:observation_matrices]).merge(descriptors)
end

#continuous_descriptors ⇒ Object 



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

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

#empty_grid(opts) ⇒ Array

Returns:

  • (Array) 


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# File 'app/models/observation_matrix.rb', line 214

def empty_grid(opts)
  re = if opts[:row_end] == 'all'
         observation_matrix_rows.count + 1
       else
         opts[:row_end]
       end

  ce = if opts[:col_end] == 'all'
         observation_matrix_columns.count + 1
       else
         opts[:col_end]
       end

  Array.new(ce - opts[:col_start]){Array.new(re - opts[:row_start]){Array.new}}
end

#gene_descriptors ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 57

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

#is_media_matrix? ⇒ Boolean

Returns True if every descriptor is a media descriptor.

Returns:

  • (Boolean) —

    True if every descriptor is a media descriptor



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# File 'app/models/observation_matrix.rb', line 81

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

#media_descriptors ⇒ Object 



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

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

#media_observations ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 133

def media_observations
  Observation::Media.in_observation_matrix(id)
end

#observation_depictions ⇒ Object

TODO: Railsify



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# File 'app/models/observation_matrix.rb', line 138

def observation_depictions
  Depiction.select('depictions.*, observations.descriptor_id, observations.observation_object_id, observations.observation_object_type, sources.id AS source_id, sources.cached_author_string, sources.year, sources.cached AS source_cached')
    .joins('INNER JOIN observations ON observations.id = depictions.depiction_object_id')
    .joins('INNER JOIN images ON depictions.image_id = images.id')
    .joins("LEFT OUTER JOIN citations ON citations.citation_object_id = images.id AND citations.citation_object_type = 'Image' AND citations.is_original IS TRUE")
    .joins('LEFT OUTER JOIN sources ON citations.source_id = sources.id')
    .where(depiction_object: media_observations).order('depictions.position')
end

#observations ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 129

def observations
  Observation.in_observation_matrix(id)
end

#observations_hash ⇒ Hash

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

descriptor_id1 =>{ "Otu1" => [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 =>{ "Otu1" => [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”



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# File 'app/models/observation_matrix.rb', line 264

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_type + o.observation_object_id.to_s].push(o) }
  #observations.each {|o| h[o.descriptor_id][o.observation_object_global_id].push(o) } ### potentially useful but extra compute slower
  h
end

#observations_in_grid(options = {}) ⇒ Hash

Note: old mx version had additional, at present not needed, they can be added via the row/column_index to get:

rows: [Otu1, Otu2... CollectonObject1]  (was a global ID in mx)
columns: [descriptor.id, desriptor.id]

!! :position attribute starts at 1 !! Grid starts at 0 !!

Returns:

  • (Hash) —

    grid: [columns][observations]



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# File 'app/models/observation_matrix.rb', line 156

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

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

  grid = empty_grid(opts)

  reindex_row_order if observation_matrix_rows.first.position != 1 || (observation_matrix_rows.last.position != observation_matrix_rows.size)
  reindex_column_order if observation_matrix_columns.first.position != 1 || (observation_matrix_columns.last.position != observation_matrix_columns.size)

  # Dump the observations into bins
  obs = Observation.by_matrix_and_position(self.id, opts)
    .select('omc.position as column_index, omr.position as row_index, observations.*')

  rows, cols = [], []

  obs.each do |o|
    grid[o.column_index - 1][o.row_index - 1].push(o)

    # These might not ever be needed, they were used in MX
    if opts[:row_index]
      rows[o.row_index - 1] = o.observation_object_type + o.observation_object_id.to_s if rows[o.row_index - 1].nil?
    end

    if opts[:column_index]
      cols[o.column_index - 1] = o.descriptor_id if cols[o.column_index - 1].nil?
    end
  end

  {grid:, rows:, 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) (defaults to: 0) —

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

Returns:

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



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# File 'app/models/observation_matrix.rb', line 236

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:).each do |o|
    g = "#{o.observation_object_type}|#{o.observation_object_id}"
    cells[g].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_descriptors ⇒ Object 



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

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

#qualitative_descriptors ⇒ Object 



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

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

#reindex_column_order ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 204

def reindex_column_order
  i = 1
  observation_matrix_columns.order(:position).find_each do |o|
    o.update_column(:position, i)
    i += 1
  end
  true
end

#reindex_row_order ⇒ Object 



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# File 'app/models/observation_matrix.rb', line 195

def reindex_row_order
  i = 1
  observation_matrix_rows.order(:position).find_each do |o|
    o.update_column(:position, i)
    i += 1
  end
  true
end

#reorder_columns(by = 'reindex') ⇒ Object 



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

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') ⇒ Boolean

Returns reorders all rows and returns true or false.

Returns:

  • (Boolean) —

    reorders all rows and returns true or false



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# File 'app/models/observation_matrix.rb', line 90

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'
    objects = []
    observation_matrix_rows.each do |r|
      t = r.current_taxon_name # not all rows have reference to a taxon name
      objects.push [r, (t ? TaxonName.self_and_ancestors_of(t).order('taxon_name_hierarchies.generations DESC').pluck(:name).to_s : '')]
    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_descriptors ⇒ Object 



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

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

#symbol_descriptors ⇒ Object

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



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# File 'app/models/observation_matrix.rb', line 67

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

#working_descriptors ⇒ Object 



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

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