Class: ObservationMatrix
- Inherits:
-
ApplicationRecord
- Object
- ActiveRecord::Base
- ApplicationRecord
- ObservationMatrix
- Includes:
- Housekeeping, Shared::AlternateValues, Shared::Attributions, 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.
TODO: soft validate that this OTU actually makes sense given the content of the key
Constant Summary collapse
- ALTERNATE_VALUES_FOR =
[:name].freeze
Class Method Summary collapse
Instance Method Summary collapse
- #batch_populate(params) ⇒ Object
-
#cell_count ⇒ Object
TODO: helper method.
- #character_states ⇒ Object
- #continuous_descriptors ⇒ Object
- #empty_grid(opts) ⇒ Array
- #gene_descriptors ⇒ Object
-
#is_media_matrix? ⇒ Boolean
True if every descriptor is a media descriptor.
- #media_descriptors ⇒ Object
- #media_observations ⇒ Object
-
#observation_depictions ⇒ Object
TODO: Railsify.
- #observations ⇒ Object
-
#observations_hash ⇒ Hash
A hash of hashes of arrays with the coding objects nicely organized descriptor_id1 =>{ “Otu1” => [observation1, observation2], descriptor_id: nil}.
-
#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].
-
#polymorphic_cells_for_descriptor(symbol_start: 0, descriptor_id:) ⇒ Object
Used soley as a indexing method for nexml output Original code in mx.
- #presence_absence_descriptors ⇒ Object
- #qualitative_descriptors ⇒ Object
- #reindex_column_order ⇒ Object
- #reindex_row_order ⇒ Object
- #reorder_columns(by = 'reindex') ⇒ Object
-
#reorder_rows(by = 'reindex') ⇒ Boolean
Reorders all rows and returns true or false.
- #sample_descriptors ⇒ Object
-
#symbol_descriptors ⇒ Object
As handled in export/parsing by external tools !! Note order() is applied !!.
- #working_descriptors ⇒ Object
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::Attributions
#attributed?, #reject_attribution
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
Class Method Details
.batch_add(params) ⇒ Object
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# File 'app/models/observation_matrix.rb', line 334 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 340 def self.batch_create(params) o = ObservationMatrix.create(params.require(:observation_matrix).permit(:name)) if o.persisted? o.batch_populate(params) else o.errors. end end |
Instance Method Details
#batch_populate(params) ⇒ Object
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# File 'app/models/observation_matrix.rb', line 284 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 89 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 84 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 58 def continuous_descriptors descriptors.where(type: 'Descriptor::Continuous').order('observation_matrix_columns.position') end |
#empty_grid(opts) ⇒ Array
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# File 'app/models/observation_matrix.rb', line 227 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 70 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.
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# File 'app/models/observation_matrix.rb', line 94 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 66 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 146 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 151 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 142 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”.
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# File 'app/models/observation_matrix.rb', line 277 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 !!
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# File 'app/models/observation_matrix.rb', line 169 def observations_in_grid( = {}) opts = { row_start: 1, row_end: 'all', col_start: 1, col_end: 'all', row_index: false, column_index: false, }.merge!(.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
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# File 'app/models/observation_matrix.rb', line 249 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 54 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 50 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 217 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 208 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 126 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.
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# File 'app/models/observation_matrix.rb', line 103 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 62 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 80 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 74 def working_descriptors descriptors.where(type: 'Descriptor::Working').order('observation_matrix_columns.position') end |