Class: ImageMatrix

Inherits:
Object
  • Object
show all
Defined in:
lib/image_matrix.rb

Overview

Contains methods used to build an image_matrix table

localhost:3000/tasks/observation_matrices/image_matrix/0/key?otu_filter=30947|22978|23065

@proceps: TODO: remove all `@` when getting the value from @variable in methods. Only use `@` when setting the variable, like so:

attr_accessor :foo
@foo = 1
foo = 1 ? true : false

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(observation_matrix_id: nil, project_id: nil, language_id: nil, keyword_ids: nil, row_filter: nil, otu_filter: nil, identified_to_rank: nil) ⇒ ImageMatrix

Returns a new instance of ImageMatrix.



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# File 'lib/image_matrix.rb', line 138

def initialize(
  observation_matrix_id: nil,
  project_id: nil,
  language_id: nil,
  keyword_ids: nil,
  row_filter: nil,
  otu_filter: nil,
  identified_to_rank: nil)

  @observation_matrix_id = observation_matrix_id
  @project_id = project_id
  @observation_matrix = find_observation_matrix
  @observation_matrix_citation = @observation_matrix&.source
  @language_id = language_id
  @keyword_ids = keyword_ids
  @descriptor_available_keywords = descriptor_available_keywords
  @row_filter = row_filter
  @otu_filter = otu_filter
  @row_id_filter_array = row_filter_array
  @otu_id_filter_array = otu_filter_array
  @rows_with_filter = get_rows_with_filter
  @identified_to_rank = identified_to_rank
  @row_hash = row_hash_initiate
 
 
  @descriptors_with_filter = descriptors_with_keywords

  @descriptor_available_languages = descriptor_available_languages_list
  @language_to_use = language_to_use
  ###main_logic
  @list_of_image_ids = []
  @list_of_descriptors = build_list_of_descriptors
  @depiction_matrix = descriptors_hash_initiate
  @image_hash = build_image_hash
  ###delete temporary data
  @row_hash = nil
  @rows_with_filter = []
  @list_of_image_ids = nil

  @descriptors_with_filter = nil #!?@#
end

Instance Attribute Details

#depiction_matrix ⇒ Object

Returns the table of observations with images.



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# File 'lib/image_matrix.rb', line 116

def depiction_matrix
  @depiction_matrix
end

#descriptor_available_keywords ⇒ Object

Returns the list of all Tags used with the descriptors. Descriptors could be filtered by tag_id



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# File 'lib/image_matrix.rb', line 76

def descriptor_available_keywords
  @descriptor_available_keywords
end

#descriptor_available_languages ⇒ Object

Returns the list of available Languages used as translations for descriptors (in translations are available)



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# File 'lib/image_matrix.rb', line 91

def descriptor_available_languages
  @descriptor_available_languages
end

#descriptors ⇒ Object

Temporary attribute. Used for validation.



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# File 'lib/image_matrix.rb', line 71

def descriptors
  @descriptors
end

#descriptors_hash ⇒ Object

temporary hash of descriptors; used for calculation of useful and not useful descriptors and their states



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# File 'lib/image_matrix.rb', line 131

def descriptors_hash
  @descriptors_hash
end

#descriptors_with_filter ⇒ Object

Temporary attribute. Used for validation. List of descriptors reduced by keyword_ids



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# File 'lib/image_matrix.rb', line 86

def descriptors_with_filter
  @descriptors_with_filter
end

#eliminate_unknown ⇒ Object

Optional attribute to eliminate taxa with no scores on a used descriptor: 'false' - default or 'true' If true, the rows without scores will be eliminated



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# File 'lib/image_matrix.rb', line 49

def eliminate_unknown
  @eliminate_unknown
end

#identified_to_rank ⇒ Object

Optional attribute to limit identification to OTU or a particular nomenclatural rank. Valid values are 'otu', 'species', 'genus', etc.



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# File 'lib/image_matrix.rb', line 54

def identified_to_rank
  @identified_to_rank
end

#image_hash ⇒ Object

Returns the hash with image attributes



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# File 'lib/image_matrix.rb', line 121

def image_hash
  @image_hash
end

#keyword_ids ⇒ Object

Optional attribute to provide a list of tagIDs to limit the set of descriptors to those taged: “keyword_ids=1|5|15”



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# File 'lib/image_matrix.rb', line 33

def keyword_ids
  @keyword_ids
end

#language_id ⇒ Object

Optional attribute to display the descriptors and character_states in a particular language (when translations are available)



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# File 'lib/image_matrix.rb', line 28

def language_id
  @language_id
end

#language_to_use ⇒ Object

Returns Language as an object if the language_id was provided (used to display descriptors in a particular language)



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# File 'lib/image_matrix.rb', line 81

def language_to_use
  @language_to_use
end

#list_of_descriptors ⇒ Object

Return the list of descriptors and their states. Translated (if needed) and Sorted



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# File 'lib/image_matrix.rb', line 111

def list_of_descriptors
  @list_of_descriptors
end

#list_of_image_ids ⇒ Object

@! list_of_image_ids

@return [null]

temporary array of image.ids; used to build the @image_hash



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# File 'lib/image_matrix.rb', line 136

def list_of_image_ids
  @list_of_image_ids
end

#observation_matrix ⇒ Object

Returns observation_matrix as an object



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# File 'lib/image_matrix.rb', line 61

def observation_matrix
  @observation_matrix
end

#observation_matrix_citation ⇒ Object

Returns observation_matrix_citation as an object



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# File 'lib/image_matrix.rb', line 66

def observation_matrix_citation
  @observation_matrix_citation
end

#observation_matrix_id ⇒ Object

Required attribude to build the key



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# File 'lib/image_matrix.rb', line 18

def observation_matrix_id
  @observation_matrix_id
end

#otu_filter ⇒ Object

Optional attribute to provide a list of rowIDs to limit the set “otu_filter=1|5|10”



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# File 'lib/image_matrix.rb', line 43

def otu_filter
  @otu_filter
end

#otu_id_filter_array ⇒ Object

Array of otu_ids in the @otu_filter



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# File 'lib/image_matrix.rb', line 106

def otu_id_filter_array
  @otu_id_filter_array
end

#project_id ⇒ Object

Required attribute to build the key



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# File 'lib/image_matrix.rb', line 23

def project_id
  @project_id
end

#row_filter ⇒ Object

Optional attribute to provide a list of rowIDs to limit the set “row_filter=1|5|10”



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# File 'lib/image_matrix.rb', line 38

def row_filter
  @row_filter
end

#row_hash ⇒ Object

Temporary hash of rows; used for calculation of remaining and eliminated rows



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# File 'lib/image_matrix.rb', line 126

def row_hash
  @row_hash
end

#row_id_filter_array ⇒ Object

Array of row_ids in the @row_filter



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# File 'lib/image_matrix.rb', line 101

def row_id_filter_array
  @row_id_filter_array
end

#rows_with_filter ⇒ Object

Temporary attribute. Used for validation. list of rows to be included into the matrix



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# File 'lib/image_matrix.rb', line 96

def rows_with_filter
  @rows_with_filter
end

Instance Method Details

#build_image_hash ⇒ Object 



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# File 'lib/image_matrix.rb', line 363

def build_image_hash
  #    if !@otu_filter.blank? || !@row_filter.blank?
  #      img_ids = observation_depictions_from_otu_filter.pluck(:image_id).uniq
  #    else
  #      img_ids = @observation_matrix.observation_depictions.pluck(:image_id).uniq
  #    end
  h = {}
  #imgs = Image.where('id IN (?)', img_ids )
  imgs = Image.where('id IN (?)', @list_of_image_ids )
  imgs.each do |d|
    i = {}
    i[:global_id] = d.to_global_id.to_s
    i[:image_file_file_name] = d.image_file_file_name
    i[:image_file_file_size] = d.image_file_file_size
    i[:image_file_content_type] = d.image_file_content_type
    i[:user_file_name] = d.user_file_name
    i[:height] = d.height
    i[:width] = d.width
    i[:original_url] = d.image_file.url
    #i[:short_url] = short_url(d.image_file.url) #this does not work in a model
    i[:medium_url] = d.image_file.url(:medium)
    i[:thumb_url] = d.image_file.url(:thumb)
    i[:citations] = []
    h[d.id] = i
  end

  #cit = Citation.where(citation_object_type: 'Image').where('citation_object_id IN (?)', img_ids )
  cit = Citation.select('citations.*, sources.cached, sources.cached_author_string, sources.year')
          .joins(:source)
          .where(citation_object_type: 'Image')
          .where('citation_object_id IN (?)', @list_of_image_ids )
  cit.each do |c|
    i = {}
    i[:id] = c.id
    i[:source_id] = c.source_id
    i[:pages] = c.pages
    i[:is_original] = c.is_original
    i[:cached] = c.cached
    i[:cached_author_string] = c.cached_author_string
    i[:year] = c.year
    #i[:citation_object_id] = c.citation_object_id
    #i[:citation_object_type] = c.citation_object_type
    h[c.citation_object_id][:citations].push(i)
  end
  h
end

#build_list_of_descriptors ⇒ Object 



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# File 'lib/image_matrix.rb', line 345

def build_list_of_descriptors
  language = @language_id.blank? ? nil : @language_id.to_i
  n = 0
  h = {}
  @descriptors_with_filter.each do |d|
    descriptor = {}
    descriptor[:index] = n
    descriptor[:id] = d.id
    descriptor[:type] = d.type
    descriptor[:name] = d.target_name(:key, language)
    descriptor[:weight] = d.weight
    descriptor[:description] = d.description
    h[d.id] = descriptor
    n += 1
  end
  h
end

#descriptor_available_languages_list ⇒ Object 



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# File 'lib/image_matrix.rb', line 189

def descriptor_available_languages_list
  return nil if @descriptors_with_filter.nil?
  descriptor_ids = @descriptors_with_filter.collect{|i| i.id}
  languages = Language.joins(:alternate_value_translations)
    .where(alternate_values: {alternate_value_object_type: 'Descriptor', type: 'AlternateValue::Translation'})
    .where('alternate_values.alternate_value_object_id IN (?)', descriptor_ids ).order('languages.english_name').distinct.to_a
  unless languages.empty?
    languages = Language.where(english_name: 'English').to_a + languages
  end
  languages
end

#descriptors_hash_initiate ⇒ Object

descriptors_hash: {:descriptor, ### (descriptor)

:observations,         ### (array of observations for )
:state_ids,            ### {hash of state_ids used in the particular matrix
}}



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# File 'lib/image_matrix.rb', line 288

def descriptors_hash_initiate
  h = {}
  if @observation_matrix_id.to_i == 0 && !@otu_filter.blank?
    depictions = observation_depictions_from_otu_filter
  else
    depictions = @observation_matrix.observation_depictions
  end

  descriptors_count = @list_of_descriptors.count
  @row_hash.each do |r_key, r_value|
    if (@row_id_filter_array.nil? && @otu_id_filter_array.nil?) ||
        (@row_id_filter_array && @row_id_filter_array.include?(r_value[:object].id)) ||
        (@otu_id_filter_array && @otu_id_filter_array.include?(r_value[:otu_id]))
      h[r_key] = {object: r_value[:object_at_rank],
                  row_id: r_value[:object].id,
                  otu_id: r_value[:otu_id],
                  depictions: Array.new(descriptors_count) {Array.new},
      } if h[r_key].nil?
    end
  end

  depictions.each do |o|
    next if @otu_id_filter_array && !@otu_id_filter_array.include?(o.otu_id)
    otu_collection_object = o.otu_id.to_s + '|' + o.collection_object_id.to_s
    if h[otu_collection_object]
      descriptor_index = @list_of_descriptors[o.descriptor_id][:index]
      h[otu_collection_object][:depictions][descriptor_index] += [o]
      @list_of_image_ids.append(o.image_id)
    end
  end
  h
end

#descriptors_with_keywords ⇒ Object 



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# File 'lib/image_matrix.rb', line 216

def descriptors_with_keywords
  if @observation_matrix_id.to_i == 0 && !@otu_filter.blank?
    d = observation_depictions_from_otu_filter.pluck(:descriptor_id).uniq
    ds = Descriptor.where("descriptors.type = 'Descriptor::Media' AND descriptors.id IN (?)", d).not_weight_zero
  elsif @keyword_ids
    ds = descriptors.joins(:tags).where('tags.keyword_id IN (?)', @keyword_ids.to_s.split('|').map(&:to_i) )
  else
    ds = descriptors
  end
  return [] if ds.nil? || ds.empty?
  ds = ds.sort{|a,b| a.observation_matrix_columns.first.try(:position).to_i <=> b.observation_matrix_columns.first.try(:position).to_i}
  ds
end

#find_observation_matrix ⇒ Object 



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# File 'lib/image_matrix.rb', line 180

def find_observation_matrix
  ObservationMatrix.where(id: @observation_matrix_id.to_i, project_id: @project_id).first
end

#get_rows_with_filter ⇒ Object 



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# File 'lib/image_matrix.rb', line 238

def get_rows_with_filter
  return [] if @observation_matrix.nil?
  @observation_matrix.observation_matrix_rows.order(:position)
end

#observation_depictions_from_otu_filter ⇒ Object 



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# File 'lib/image_matrix.rb', line 321

def observation_depictions_from_otu_filter
  Depiction.select('depictions.*, observations.descriptor_id, observations.otu_id, observations.collection_object_id, 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("observations.type = 'Observation::Media' AND observations.otu_id IN (?)", @otu_id_filter_array)
    .where('observations.project_id = (?)', @project_id)
    .order('depictions.position')
end

#otu_filter_array ⇒ Object 



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# File 'lib/image_matrix.rb', line 234

def otu_filter_array
  @otu_filter.blank? ? nil : otu_filter.to_s.split('|').map(&:to_i)
end

#row_filter_array ⇒ Object 



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# File 'lib/image_matrix.rb', line 230

def row_filter_array
  @row_filter.blank? ? nil : row_filter.to_s.split('|').map(&:to_i)
end

#row_hash_initiate ⇒ Object 



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# File 'lib/image_matrix.rb', line 243

def row_hash_initiate
  h = {}
  if @observation_matrix_id.to_i == 0 && !@otu_filter.blank?
    o = observation_depictions_from_otu_filter.pluck(:otu_id).uniq
    @otu_id_filter_array = @otu_id_filter_array & o
    rows = Otu.where('otus.id IN (?)', @otu_id_filter_array)
  else
    rows = @rows_with_filter
  end
  rows.each do |r|
    case r.class.to_s
    when 'Otu'
      otu_collection_object = r.id.to_s + '|'
    when 'ObservationMatrixRow'
      otu_collection_object = r.otu_id.to_s + '|' + r.collection_object_id.to_s
    end
    h[otu_collection_object] = {}
    h[otu_collection_object][:object] = r

    if @identified_to_rank == 'otu'
      case r.class.to_s
      when 'Otu'
        h[otu_collection_object][:object_at_rank] = r
      when 'ObservationMatrixRow'
        h[otu_collection_object][:object_at_rank] = r.current_otu || r
      end
    elsif @identified_to_rank
      case r.class.to_s
      when 'Otu'
        h[otu_collection_object][:object_at_rank] = r&.taxon_name&.valid_taxon_name&.ancestor_at_rank(@identified_to_rank, inlude_self = true) || r
      when 'ObservationMatrixRow'
        h[otu_collection_object][:object_at_rank] = r&.current_taxon_name&.ancestor_at_rank(@identified_to_rank, inlude_self = true) || r
      end
    else
      h[otu_collection_object][:object_at_rank] = r
    end
    h[otu_collection_object][:otu_id] = r.class.to_s == 'Otu' ? r.id : r.otu_id
  end
  h
end

#selected_descriptors_hash_initiate ⇒ Object

returns ['1', '3'], 125: ['3', '5'], 135: ['2'], 136: ['true'], 140: ['5-10']



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# File 'lib/image_matrix.rb', line 333

def selected_descriptors_hash_initiate
  # "123:1|3||125:3|5||135:2"
  h = {}
  return h if @selected_descriptors.blank?
  a = @selected_descriptors.include?('||') ? @selected_descriptors.to_s.split('||') : [@selected_descriptors]
  a.each do |i|
    d = i.split(':')
    h[d[0].to_i] = d[1].include?('|') ? d[1].split('|') : [d[1]]
  end
  h
end