Class: BatchLoad::Import::CollectionObjects

Inherits:
BatchLoad::Import show all
Defined in:
lib/batch_load/import/collection_objects.rb

Defined Under Namespace

Classes: BufferedInterpreter, CastorInterpreter

Instance Attribute Summary collapse

Attributes inherited from BatchLoad::Import

#create_attempted, #csv, #errors, #file, #file_errors, #import_level, #processed, #processed_rows, #project, #project_id, #successful_rows, #total_data_lines, #total_lines, #user, #user_header_map, #user_id

Instance Method Summary collapse

Methods inherited from BatchLoad::Import

#all_objects, #create, #create_attempted?, #import_level_ok?, #line_strict_level_ok?, #processed?, #ready_to_create?, #save_order, #sorted_processed_rows, #strict_level_ok?, #total_records_created, #user_map, #valid?, #valid_objects, #warn_level_ok?

Constructor Details

#initialize(**args) ⇒ CollectionObjects

Returns a new instance of CollectionObjects.

Parameters:

  • args (Hash) 


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# File 'lib/batch_load/import/collection_objects.rb', line 14

def initialize(**args)
  @collection_objects   = {}
  @collecting_events    = {}
  @taxon_determinations = {}
  @otus                 = {}
  super(**args)
end

Instance Attribute Details

#collecting_events ⇒ Object

Returns the value of attribute collecting_events.



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# File 'lib/batch_load/import/collection_objects.rb', line 7

def collecting_events
  @collecting_events
end

#collection_objects ⇒ Object

Returns the value of attribute collection_objects.



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# File 'lib/batch_load/import/collection_objects.rb', line 6

def collection_objects
  @collection_objects
end

#namespace ⇒ Object

Returns the value of attribute namespace.



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# File 'lib/batch_load/import/collection_objects.rb', line 11

def namespace
  @namespace
end

#otus ⇒ Object

Returns the value of attribute otus.



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# File 'lib/batch_load/import/collection_objects.rb', line 9

def otus
  @otus
end

#taxon_determinations ⇒ Object

Returns the value of attribute taxon_determinations.



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# File 'lib/batch_load/import/collection_objects.rb', line 8

def taxon_determinations
  @taxon_determinations
end

Instance Method Details

#build ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/batch_load/import/collection_objects.rb', line 293

def build
  if valid?
    build_collection_objects
    @processed = true
  end
end

#build_collection_objects ⇒ Integer

rubocop:disable Metrics/MethodLength

Returns:

  • (Integer) 


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# File 'lib/batch_load/import/collection_objects.rb', line 24

def build_collection_objects
  # test_build
  build_objects = {}
  i             = 1 # accounting for headers
  # identifier namespace
  header5       = csv.headers[5] # should be 'collecting_event_identifier_namespace_short_name'
  header6       = csv.headers[6] # should be 'collecting_event_identifier_identifier'
  header7       = csv.headers[7] # should be 'collecting_event_identifier_type'
  #
  # first pass for CollectingEvent with Georeference and Identifier
  csv.each do |row|
    parse_result = BatchLoad::RowParse.new
    # creation of the possible-objects list
    parse_result.objects.merge!(co: [], otu: [], td: [], ce: [])
    # attach the results to the row
    @processed_rows[i] = parse_result

    # hot-wire the project into the row
    temp_row               = row
    temp_row['project_id'] = @project_id.to_s if row['project_id'].blank?

    begin # processing the CollectionObject
      co_list = BatchLoad::ColumnResolver.collection_object_by_identifier(temp_row)
      if co_list.no_matches? # no namespace to search!
        parse_result.parse_errors.push(co_list.error_messages.first)
        i += 1 # can't skip the increment!
        next
      end
      co = co_list.item # there can be only one
      unless co.collecting_event.nil? # if it exists
        parse_result.parse_errors.push('The specified CollectionObject already has a CollectingEvent.')
        i += 1 # can't skip the increment!
        next
      end
      parse_result.objects[:co].push(co)
    end

    begin # processing the Otu
      otu            = nil
      otu_attributes = {name: row['otu_name']}
      otu_list       = BatchLoad::ColumnResolver.otu(temp_row)
      otu            = otu_list.item if otu_list.resolvable?
      otu_match      = Digest::SHA256.digest(otu_attributes.to_s)
      otu            = build_objects[otu_match] if otu.blank?
      otu            = Otu.new(otu_attributes) if otu.blank?
      build_objects[otu_match] = otu # .merge!(otu_match => otu)
      parse_result.objects[:otu].push(otu)
    end

    begin # processing the TaxonDetermination
      td_attributes = {otu:,
      taxon_determination_object: co}
      # td_match      = Digest::SHA256.digest(td_attributes.to_s)
      # td            = build_objects[td_match]
      # td            = TaxonDetermination.find_by(td_attributes) if td.nil?
      td            = TaxonDetermination.new(td_attributes)
      parse_result.objects[:td].push(td)
      # build_objects.merge!(td_match => td)
    end

    begin # processing the CollectingEvent
      id_ce    = row[header6]
      vert_loc = row['verbatim_location']
      long     = row['longitude'] # longitude
      lat      = row['latitude'] # latitude
      method   = row['method']
      error    = (row['error'].to_s + ' ' + row['georeference_error_units'].to_s).strip

      ce_namespace = row[header5]
      ns_ce        = Namespace.where(short_name: ce_namespace).first
      parse_result.parse_errors.push("No available namespace '#{ce_namespace}'.") if ns_ce.nil?

      # force a verbatim_locality, if none is provided.
      if vert_loc.blank?
        vert_loc = "#{ns_ce.short_name} #{id_ce}"
      end
      ce_attributes = {verbatim_locality:                vert_loc,
                       verbatim_geolocation_uncertainty: error.empty? ? nil : error,
                       start_date_day:                   row['start_date_day'],
                       start_date_month:                 row['start_date_month'],
                       start_date_year:                  row['start_date_year'],
                       end_date_day:                     row['end_date_day'],
                       end_date_month:                   row['end_date_month'],
                       end_date_year:                    row['end_date_year'],
                       verbatim_longitude:               long,
                       verbatim_latitude:                lat,
                       verbatim_method:                  method,
                       geographic_area_id:               nil,
                       minimum_elevation:                nil,
                       maximum_elevation:                nil,
                       elevation_precision:              nil,
                       field_notes:                      nil,
                       verbatim_elevation:               nil,
                       verbatim_habitat:                 nil,
                       verbatim_datum:                   nil,
                       time_start_hour:                  nil,
                       time_start_minute:                nil,
                       time_start_second:                nil,
                       time_end_hour:                    nil,
                       time_end_minute:                  nil,
                       time_end_second:                  nil,
                       verbatim_date:                    row['verbatim_date'],
                       verbatim_field_number:         nil,
                       verbatim_collectors:              nil,
                       verbatim_label:                   nil,
                       document_label:                   nil,
                       print_label:                      nil,
                       project_id:                       @project_id
      }

      ce_id_attributes = {identifiers_attributes: [{namespace:  ns_ce,
                                                    project_id: @project_id,
                                                    type:       'Identifier::' + row[header7],
                                                    identifier: id_ce}]}
      id_attributes    = ce_id_attributes[:identifiers_attributes][0]
      ce_key           = ce_attributes.merge(ce_id_attributes)
      # id_match         = Digest::SHA256.digest(ce_id_attributes.to_s)

      gr_attributes    = {}
      case method.downcase
        when 'geolocate'
          gr_attributes = {geo_locate_georeferences_attributes: [{iframe_response: "#{lat}|#{long}|#{Utilities::Geo.distance_in_meters(error).to_f}|Unavailable"}]}
        else
      end unless method.nil?

      case row[1]
        when '35397', '38866'
          ce_a1 = ce_attributes
          ce_m1 = Digest::SHA256.digest(ce_key.to_s)
        else
      end

      ce_match = Digest::SHA256.digest(ce_key.to_s)
      ce       = build_objects[ce_match]
      ce       = CollectingEvent.includes(:identifiers).find_by(ce_attributes, id_attributes) if ce.nil?
      # ce       = CollectingEvent.find_by(ce_attributes) if ce.nil?
      ce       = CollectingEvent.new(ce_key.merge(gr_attributes)) if ce.nil?

      if ce.valid? # various different possible errors.
        co.collecting_event = ce
        parse_result.objects[:ce].push(ce)
        build_objects.merge!(ce_match => ce)
      else
        err_list = 'Collecting event problems: '
        ce.errors.messages.each { |msg|
          msg.each { |key, value|
            err_list += "#{key}: #{value}"
          }
        }
        parse_result.parse_errors.push(err_list)
        # parse_result.parse_errors.push("Identifier '#{id_test.namespace} #{id_test.identifier}'
        # has been used for a different collecting event.")
      end
    end

    i += 1
  end
  @total_lines = i - 1

end

#build_collection_objects_ori ⇒ Integer

rubocop:disable Metrics/MethodLength process each row for information:

Returns:

  • (Integer) 


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# File 'lib/batch_load/import/collection_objects.rb', line 208

def build_collection_objects_ori
  ce_a1         = ''
  ce_m1         = ''
  ce1           = CollectingEvent.find(1)
  # here we store the attributes of stuff we want to find later
  build_objects = {}
  i             = 1 # accounting for headers
  # identifier namespace
  # header0 = csv.headers[0] # should be 'collection_object_identifier_namespace_short_name'
  # header1 = csv.headers[1] # should be 'collection_object_identifier_identifier'
  header5       = csv.headers[5] # should be 'collecting_event_identifier_namespace_short_name'
  header6       = csv.headers[6] # should be 'collecting_event_identifier_identifier'
  header7       = csv.headers[7] # should be 'collecting_event_identifier_type'
  csv.each do |row|
    parse_result                 = BatchLoad::RowParse.new
    # creation of the possible-objects list
    parse_result.objects[:otu]   = []
    parse_result.objects[:co]    = []
    parse_result.objects[:td]    = []
    parse_result.objects[:ce]    = []
    parse_result.objects[:gr]    = []
    parse_result.objects[:ce_id] = []
    # attach the results to the row
    @processed_rows.merge!(i => parse_result)

    # hot-wire the project into the row
    row['project_id'] = @project_id.to_s if row['project_id'].blank?

    co_list  = BatchLoad::ColumnResolver.collection_object_by_identifier(row)
    otu_list = BatchLoad::ColumnResolver.otu(row)
    if co_list.no_matches? # no namespace to search!
      parse_result.parse_errors.push('No CollectionObject found with the specified identifier.')
      next
    end
    co = co_list.item # there can be only one
    unless co.collecting_event.nil? # if it exists
      parse_result.parse_errors.push('The specified CollectionObject already has a CollectingEvent.')
      next
    end
    parse_result.objects[:co].push(co)
    otu = otu_list.item if otu_list.resolvable?
    otu = Otu.new(name: row['otu_name']) if otu.blank?
    parse_result.objects[:otu].push(otu)
    long         = row['longitude'] # longitude
    lat          = row['latitude'] # latitude
    method       = row['method']
    error        = (row['error'].to_s + ' ' + row['georeference_error_units'].to_s).strip
    ce_namespace = row[header5]
    ns_ce        = Namespace.where(short_name: ce_namespace).first
    parse_result.parse_errors.push["No available namespace '#{ce_namespace}'."] if ns_ce.nil?

    begin # processing the TaxonDetermination
      td_attributes = {
        otu:,
        taxon_determination_object: co}
      td_match      = Digest::SHA256.digest(td_attributes.to_s)
      td            = build_objects[td_match]
      td            = TaxonDetermination.find_by(td_attributes) if td.nil?
      td            = TaxonDetermination.new(td_attributes) if td.nil?
      parse_result.objects[:td].push(td)
      build_objects.merge!(td_match => td)
    end

    begin # processing Identifier
      ce_id_attributes = {namespace:              ns_ce,
                          identifier_object_type: 'CollectingEvent',
                          project_id:             @project_id,
                          type:                   'Identifier::' + row[header7],
                          identifier:             row[header6]}
      ce_id_match      = Digest::SHA256.digest(ce_id_attributes.to_s)
      ce_id            = build_objects[ce_id_match]
      ce_id            = Identifier.find_by(ce_id_attributes) if ce_id.nil?
      ce_id            = Identifier.new(ce_id_attributes) if ce_id.nil?
      parse_result.objects[:ce_id].push(ce_id)
      build_objects.merge!(ce_id_match => ce_id) # whichever way we came by it, save the item in our stash
    end

    co.collecting_event = ce
    i                   += 1
  end
  @total_lines = i - 1
end

#test_build ⇒ Object 



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# File 'lib/batch_load/import/collection_objects.rb', line 185

def test_build
  file_name = 'spec/files/batch/collection_object/CollectionObjectTest.tsvP'
  ns_1      = Namespace.find_by(short_name: 'PSUC')
  csv1      = CSV.read(file_name, {headers: true, header_converters: :downcase, col_sep: "\t", encoding: 'UTF-8'})

  csv1.each do |row|
    # the following invocation also creates a valid specimen as a collection_object
    # FactoryBot.create(:valid_identifier, namespace: ns_1, identifier: ident)
    co = CollectionObject.new(type: 'Specimen', total: 1, preparation_type_id: 5)
    id = Identifier.new(namespace:  ns_1,
                        type:       'Identifier::Local::CatalogNumber',
                        identifier: row[1])
    co.identifiers << id

    if co.valid?
      co.save
    end
  end
end