Class: Tools::ImageMatrix

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

Overview

Contains methods used to build an image_matrix table

endpoint: localhost:3000/tasks/observation_matrices/image_matrix/36/key?observation_matrix_id=36&page=5 localhost:3000/tasks/observation_matrices/image_matrix/0/key?otu_filter=30947|22978|23065

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, per: nil, page: nil, pagination_page: nil, pagination_next_page: nil, pagination_previous_page: nil, pagination_per_page: nil, pagination_total: nil, pagination_total_pages: nil) ⇒ ImageMatrix

Returns a new instance of ImageMatrix.



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# File 'lib/tools/image_matrix.rb', line 170

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,
  per: nil,
  page: nil,
  pagination_page: nil,
  pagination_next_page: nil,
  pagination_previous_page: nil,
  pagination_per_page: nil,
  pagination_total: nil,
  pagination_total_pages: 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
  @per = per.blank? ? 250 : per
  @page = page.blank? ? 1 : page
  @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

  # Memoized now
  # @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 = []

  # Initiate on getter, memoized, only breaks then when requested
  # @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/tools/image_matrix.rb', line 118

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/tools/image_matrix.rb', line 78

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/tools/image_matrix.rb', line 93

def descriptor_available_languages
  @descriptor_available_languages
end

#descriptors ⇒ Object

Temporary attribute. Used for validation.



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# File 'lib/tools/image_matrix.rb', line 73

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/tools/image_matrix.rb', line 133

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/tools/image_matrix.rb', line 88

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/tools/image_matrix.rb', line 44

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/tools/image_matrix.rb', line 49

def identified_to_rank
  @identified_to_rank
end

#image_hash ⇒ Object

Returns the hash with image attributes



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# File 'lib/tools/image_matrix.rb', line 123

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/tools/image_matrix.rb', line 28

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/tools/image_matrix.rb', line 23

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/tools/image_matrix.rb', line 83

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/tools/image_matrix.rb', line 113

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/tools/image_matrix.rb', line 138

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/tools/image_matrix.rb', line 63

def observation_matrix
  @observation_matrix
end

#observation_matrix_citation ⇒ Object

Returns observation_matrix_citation as an object



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# File 'lib/tools/image_matrix.rb', line 68

def observation_matrix_citation
  @observation_matrix_citation
end

#observation_matrix_id ⇒ Object

Required attribude to build the key



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# File 'lib/tools/image_matrix.rb', line 13

def observation_matrix_id
  @observation_matrix_id
end

#otu_filter ⇒ Object

Optional attribute to provide a list of rowIDs to limit the set



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

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/tools/image_matrix.rb', line 108

def otu_id_filter_array
  @otu_id_filter_array
end

#pagination_next_page ⇒ Object

Returns the next page number



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# File 'lib/tools/image_matrix.rb', line 148

def pagination_next_page
  @pagination_next_page
end

#pagination_page ⇒ Object

Returns the page number



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# File 'lib/tools/image_matrix.rb', line 143

def pagination_page
  @pagination_page
end

#pagination_per_page ⇒ Object

Returns number of records per page



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# File 'lib/tools/image_matrix.rb', line 158

def pagination_per_page
  @pagination_per_page
end

#pagination_previous_page ⇒ Object

Returns the previous page number



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# File 'lib/tools/image_matrix.rb', line 153

def pagination_previous_page
  @pagination_previous_page
end

#pagination_total ⇒ Object

Returns total number of records



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# File 'lib/tools/image_matrix.rb', line 163

def pagination_total
  @pagination_total
end

#pagination_total_pages ⇒ Object

Returns total number of pages



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# File 'lib/tools/image_matrix.rb', line 168

def pagination_total_pages
  @pagination_total_pages
end

#per ⇒ Object

Optional attribute. Number of rows displayed per page



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

def per
  @per
end

#project_id ⇒ Object

Required attribute to build the key



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

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/tools/image_matrix.rb', line 33

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/tools/image_matrix.rb', line 128

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/tools/image_matrix.rb', line 103

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/tools/image_matrix.rb', line 98

def rows_with_filter
  @rows_with_filter
end

Instance Method Details

#build_image_hash ⇒ Object 



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# File 'lib/tools/image_matrix.rb', line 458

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 (?)', 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[: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[:global_id] = c.to_global_id.to_s
    #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

#descriptor_available_languages_list ⇒ Object 



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

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/tools/image_matrix.rb', line 368

def descriptors_hash_initiate
  h = {}

  # Depictions is depictions with other attributes added
  depictions = nil

  if observation_matrix_id.to_i == 0 && !otu_filter.blank?
    depictions = observation_depictions_from_otu_filter
  else
    return h if observation_matrix.nil?
    depictions = observation_matrix.observation_depictions
  end

  descriptors_count = list_of_descriptors.count

  otu_ids = {}
  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?
      otu_ids[r_value[:otu_id]] = true
    end
  end

  depictions.each do |o|
    if (o.observation_object_type == 'Otu' && otu_ids[o.observation_object_id].nil?) ||
      (otu_id_filter_array && (o.observation_object_type == 'Otu' && !otu_id_filter_array.include?(o.observation_object_id)))
      next
    end

    otu_collection_object = o.observation_object_type + o.observation_object_id.to_s # 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/tools/image_matrix.rb', line 265

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/tools/image_matrix.rb', line 229

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

#observation_depictions_from_otu_filter ⇒ Depiction scope

TODO: CHANGED FLAG REMOVE

Returns:



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# File 'lib/tools/image_matrix.rb', line 415

def observation_depictions_from_otu_filter
  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("observations.type = 'Observation::Media' AND observations.observation_object_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/tools/image_matrix.rb', line 283

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/tools/image_matrix.rb', line 279

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/tools/image_matrix.rb', line 302

def row_hash_initiate
  h = {}
  rows = nil # Of either Otu or ObservationMatrixRow of type Otu !! TODO:
  if observation_matrix_id.to_i == 0 && !otu_filter.blank?

    o = observation_depictions_from_otu_filter.where("observations.observation_object_type = 'Otu'").pluck(:observation_object_id).uniq

    @otu_id_filter_array = otu_id_filter_array & o

    rows = Otu.where(id: otu_id_filter_array)
  else
    rows = rows_with_filter
  end

  i = 0
  per = @per.to_i
  page = @page.to_i

  @pagination_page = page
  @pagination_total = rows.count
  @pagination_total_pages = (@pagination_total.to_f / per).ceil
  @pagination_next_page = @pagination_total_pages > @pagination_page ? @pagination_page + 1 : nil
  @pagination_previous_page = @pagination_page > 1 ? @pagination_page - 1 : nil
  @pagination_per_page = per
  rows.each do |r|
    i += 1
    next if i < per * (page - 1) + 1
    break if i > per * page

    case r.class.to_s
    when 'Otu'
      otu_collection_object = 'Otu' + r.id.to_s
      # otu_collection_object = r.id.to_s + '|'
    when 'ObservationMatrixRow'
      otu_collection_object = r.observation_object_type + r.observation_object_id.to_s # 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.observation_object_id # 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/tools/image_matrix.rb', line 427

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