Class: Queries::Observation::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, Concerns::Confidences, Concerns::DataAttributes, Concerns::Depictions, Concerns::Geo, Concerns::Notes, Concerns::Protocols, Concerns::Tags
Defined in:
lib/queries/observation/filter.rb

Overview

!! TODO: needs tests

Constant Summary collapse

PARAMS = 
[
  :character_state_id,
  :collection_object_id,
  :descendants,
  :descriptor_id,
  :descriptor_id,
  :geo_json,
  :geo_mode,
  :geo_shape_id,
  :geo_shape_type,
  :observation_id,
  :observation_matrix_id,
  :observation_object_global_id,
  :observation_object_id,
  :observation_object_type,
  :observation_type,
  :otu_id,
  :radius,
  :sound_id,
  :taxon_name_id,
  :wkt,

  charater_state_id: [],
  collection_object_id: [],
  descriptor_id: [],
  geo_shape_id: [],
  geo_shape_type: [],
  observation_id: [],
  observation_matrix_id: [],
  observation_object_type: [],
  observation_object_id: [],
  observation_type: [],
  otu_id: [],
  sound_id: [],
  taxon_name_id: [],
].freeze

Constants inherited from Query::Filter

Query::Filter::FILTER_QUERIES, Query::Filter::SUBQUERIES

Instance Attribute Summary collapse

Attributes inherited from Query::Filter

#api, #asserted_distribution_query, #biological_association_query, #biological_associations_graph_query, #collecting_event_query, #collection_object_query, #content_query, #controlled_vocabulary_term_query, #conveyance_query, #data_attribute_query, #depiction_query, #descriptor_query, #document_query, #dwc_occurrence_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #order_by, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #recent_target, #roll_call, #sound_query, #taxon_name_query, #taxon_name_relationship_query, #venn, #venn_ignore_pagination, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods inherited from Query::Filter

#all, #all_and_clauses, #all_merge_clauses, #annotator_and_clauses, #annotator_merge_clauses, annotator_params, api_except_params, api_excluded_params, #apply_venn, #attribute_exact_facet, base_filter, base_query_name, base_query_to_h, #deep_permit, #disable_paging, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #model_id_facet, #object_global_id_facet, #only_project?, #paging_state, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #set_nested_queries, #set_paging, set_paging, #shared_and_clauses, #subquery_vector, #target_and_clauses, #venn_query

Methods inherited from Query

#alphabetic_strings, #alphanumeric_strings, base_name, #base_name, #base_query, #build_terms, #cached_facet, #end_wildcard, #levenshtein_distance, #match_ordered_wildcard_pieces_in_cached, #no_terms?, referenced_klass, #referenced_klass, #referenced_klass_except, #referenced_klass_intersection, #referenced_klass_union, #start_and_end_wildcard, #start_wildcard, #table, #wildcard_pieces

Constructor Details

#initialize(query_params) ⇒ Filter

Returns a new instance of Filter.



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# File 'lib/queries/observation/filter.rb', line 105

def initialize(query_params)
  super

  @observation_id = params[:observation_id]
  @otu_id = params[:otu_id]
  @sound_id = params[:sound_id]
  @collection_object_id = params[:collection_object_id]
  @observation_object_global_id = params[:observation_object_global_id]
  @descriptor_id = params[:descriptor_id]
  @observation_type = params[:observation_type]
  @character_state_id = params[:character_state_id]
  @observation_matrix_id = params[:observation_matrix_id]
  @observation_object_id = params[:observation_object_id]
  @observation_object_type = params[:observation_object_type]

  @taxon_name_id = params[:taxon_name_id]
  @descendants = boolean_param(params, :descendants)

  set_confidences_params(params)
  set_data_attributes_params(params)
  set_protocols_params(params)
  set_citations_params(params)
  set_depiction_params(params)
  set_tags_params(params)
  set_notes_params(params)
  set_geo_params(params)
end

Instance Attribute Details

#character_state_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 57

def character_state_id
  @character_state_id
end

#collection_object_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 60

def collection_object_id
  @collection_object_id
end

#descendants ⇒ Object

Returns Boolean.

Returns:

  • Boolean



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# File 'lib/queries/observation/filter.rb', line 63

def descendants
  @descendants
end

#descriptor_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 66

def descriptor_id
  @descriptor_id
end

#geo_json ⇒ Object

Returns the value of attribute geo_json.



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# File 'lib/queries/observation/filter.rb', line 68

def geo_json
  @geo_json
end

#observation_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 54

def observation_id
  @observation_id
end

#observation_matrix_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/observation/filter.rb', line 71

def observation_matrix_id
  @observation_matrix_id
end

#observation_object_global_id ⇒ Object

Returns String, nil.

Returns:

  • String, nil



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# File 'lib/queries/observation/filter.rb', line 74

def observation_object_global_id
  @observation_object_global_id
end

#observation_object_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 80

def observation_object_id
  @observation_object_id
end

#observation_object_type ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 83

def observation_object_type
  @observation_object_type
end

#observation_type ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 77

def observation_type
  @observation_type
end

#otu_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 86

def otu_id
  @otu_id
end

#radius ⇒ Object

Integer in Meters

!! defaults to 100m



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# File 'lib/queries/observation/filter.rb', line 90

def radius
  @radius
end

#sound_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 93

def sound_id
  @sound_id
end

#taxon_name_id ⇒ Object

Returns Array.

Returns:

  • Array



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# File 'lib/queries/observation/filter.rb', line 96

def taxon_name_id
  @taxon_name_id
end

#wkt ⇒ Object

Returns String.

Returns:

  • String



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# File 'lib/queries/observation/filter.rb', line 99

def wkt
  @wkt
end

Instance Method Details

#and_clauses ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 393

def and_clauses
  [
    character_state_id_facet,
    collection_object_id_facet,
    descriptor_id_facet,
    observation_object_global_id_facet,
    observation_object_id_facet,
    observation_object_type_facet,
    observation_type_facet,
    otu_id_facet,
    sound_id_facet
  ]
end

#asserted_distribution_query_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 370

def asserted_distribution_query_facet
  return nil if asserted_distribution_query.nil?
  ::Observation
    .with(ad: asserted_distribution_query.all)
    .joins("JOIN ad ON observations.id = ad.asserted_distribution_object_id AND ad.asserted_distribution_object_type = 'Observation' AND observations.observation_object_type = 'Otu'")
    .distinct
end

#biological_association_geo_facet_by_type(shape_string, shape_ids) ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 233

def biological_association_geo_facet_by_type(shape_string, shape_ids)
  case geo_mode
  when nil, false # exact, descendants
    ::Observation
      .joins("JOIN asserted_distributions ON asserted_distributions.asserted_distribution_object_id = observations.id AND asserted_distributions.asserted_distribution_object_type = 'Observation' AND observations.observation_object_type = 'Otu'")
      .where(asserted_distributions: {
        asserted_distribution_shape: shape_ids
     })
  when true # spatial
    m = shape_string.tableize
    b = ::GeographicItem.joins(m.to_sym).where(m => shape_ids)
  end
end

#character_state_id_facet ⇒ Arel::Node?

Returns:

  • (Arel::Node, nil) 


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# File 'lib/queries/observation/filter.rb', line 308

def character_state_id_facet
  return nil if character_state_id.empty?
  table[:character_state_id].in(character_state_id)
end

#collection_object_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 296

def collection_object_id_facet
  return nil if collection_object_id.empty?
  table[:observation_object_id].eq(collection_object_id).and(table[:observation_object_type].eq('CollectionObject'))
end

#descriptor_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 333

def descriptor_id_facet
  return nil if descriptor_id.empty?
  table[:descriptor_id].in(descriptor_id)
end

#descriptor_query_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 338

def descriptor_query_facet
  return nil if descriptor_query.nil?

  s = 'WITH query_desc_obs AS (' + descriptor_query.all.to_sql + ') ' +
    ::Observation
    .joins('JOIN query_desc_obs as query_desc_obs1 on observations.descriptor_id = query_desc_obs1.id')
    .to_sql

  ::Observation.from('(' + s + ') as observations')
end

#from_wkt(wkt_shape) ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 182

def from_wkt(wkt_shape)
  a = ::Queries::AssertedDistribution::Filter.new(
    wkt: wkt_shape, project_id:,
    asserted_distribution_object_type: 'Observation'
  )

  ::Observation
    .with(ad: a.all)
    .joins("JOIN ad ON ad.asserted_distribution_object_id = observations.id AND observations.observation_object_type = 'Otu'")
end

#geo_json_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 193

def geo_json_facet
  return nil if geo_json.blank?
  return ::Observation.none if roll_call

  a = ::Queries::AssertedDistribution::Filter.new(
    geo_json:, project_id:, radius:,
    asserted_distribution_object_type: 'Observation'
  )

  ::Observation
    .with(ad: a.all)
    .joins("JOIN ad ON ad.asserted_distribution_object_id = observations.id AND observations.observation_object_type = 'Otu'")
end

#matching_character_state_id ⇒ Arel::Node?

Returns:

  • (Arel::Node, nil) 


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# File 'lib/queries/observation/filter.rb', line 292

def matching_character_state_id
  character_state_id.blank? ? nil : table[:character_state_id].eq(character_state_id)
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 407

def merge_clauses
  [
    *OBSERVABLE_TYPES.collect{ |t| observable_facet(t.underscore) },
    descriptor_query_facet,
    observation_matrix_id_facet,

    taxon_name_query_facet,
    asserted_distribution_query_facet,
    taxon_name_id_facet,
    wkt_facet,
    geo_json_facet,
    observation_geo_facet,
  ]
end

#observable_facet(name) ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 378

def observable_facet(name)
  return nil if name.nil?

  q = send((name + '_query').to_sym)

  return nil if q.nil?

  s = ::Observation
    .with(query_obs: q.all)
    .joins("JOIN query_obs ON observations.observation_object_id = query_obs.id AND observations.observation_object_type = '#{name.camelize}'")
    .to_sql

  ::Observation.from('(' + s + ') as observations')
end

#observation_geo_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 207

def observation_geo_facet
  return nil if geo_shape_id.empty? || geo_shape_type.empty? ||
    # TODO: this should raise an error(?)
    geo_shape_id.length != geo_shape_type.length
  return ::Observation.none if roll_call

  geographic_area_shapes, gazetteer_shapes = shapes_for_geo_mode

  a = biological_association_geo_facet_by_type(
    'GeographicArea', geographic_area_shapes
  )

  b = biological_association_geo_facet_by_type(
    'Gazetteer', gazetteer_shapes
  )

  if geo_mode == true # spatial
    i = ::Queries.union(::GeographicItem, [a,b])
    u = ::Queries::GeographicItem.st_union_text(i).to_a.first

    return from_wkt(u['st_astext'])
  end

  referenced_klass_union([a,b])
end

#observation_matrix_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 273

def observation_matrix_id_facet
  return nil if observation_matrix_id.empty?
  ::Observation.in_observation_matrix(observation_matrix_id)
end

#observation_object_global_id_facet ⇒ Arel::Node?

Returns:

  • (Arel::Node, nil) 


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# File 'lib/queries/observation/filter.rb', line 279

def observation_object_global_id_facet
  return nil if observation_object_global_id.blank?

  # TODO - make a hash method to parameterize these values
  o = GlobalID::Locator.locate(observation_object_global_id)

  a = o.id
  b = o.class.base_class.name

  table[:observation_object_id].eq(a).and(table[:observation_object_type].eq(b))
end

#observation_object_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 323

def observation_object_id_facet
  return nil if observation_object_id.empty?
  table[:observation_object_id].in(observation_object_id)
end

#observation_object_type_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 328

def observation_object_type_facet
  return nil if observation_object_type.empty?
  table[:observation_object_type].in(observation_object_type)
end

#observation_type_facet ⇒ Arel::Node?

Returns:

  • (Arel::Node, nil) 


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# File 'lib/queries/observation/filter.rb', line 302

def observation_type_facet
  return nil if observation_type.empty?
  table[:type].in(observation_type)
end

#otu_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 313

def otu_id_facet
  return nil if otu_id.empty?
  table[:observation_object_id].in(otu_id).and(table[:observation_object_type].eq('Otu'))
end

#sound_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 318

def sound_id_facet
  return nil if sound_id.empty?
  table[:observation_object_id].in(sound_id).and(table[:observation_object_type].eq('Sound'))
end

#taxon_name_id_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 247

def taxon_name_id_facet
  return nil if taxon_name_id.empty?

  if descendants
    t = ::TaxonName.descendants_of(taxon_name_id)
  else
    t = ::TaxonName.where(id: taxon_name_id)
  end

  a = ::Observation.joins("JOIN otus ON observations.observation_object_id = otus.id AND observations.observation_object_type = 'Otu'")
    .where(otus: {taxon_name_id: t})

  b = ::Observation.joins("JOIN collection_objects ON observations.observation_object_id = collection_objects.id AND observations.observation_object_type = 'CollectionObject'")
    .joins("JOIN taxon_determinations ON taxon_determinations.taxon_determination_object_id = collection_objects.id AND taxon_determinations.taxon_determination_object_type = 'CollectionObject'")
    .joins('JOIN otus ON taxon_determinations.otu_id = otus.id')
    .joins('JOIN taxon_names ON taxon_names.id = otus.id')
    .where(taxon_names: {id:  t})

  e = ::Queries::Extract::Filter.new(taxon_name_id:, descendants:, project_id:).all

  c = ::Observation.joins("JOIN extracts ON observations.observation_object_id = extracts.id AND observations.observation_object_type = 'Extract'")
    .where(extracts: {id: e})

  ::Observation.from( '(' + [a,b,c].collect{|q| "(#{q.to_sql})" }.join(' UNION ') + ') as observations' )
end

#taxon_name_query_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 349

def taxon_name_query_facet
  return nil if taxon_name_query.nil?
  s = 'WITH query_tn_obs AS (' + taxon_name_query.all.to_sql + ') '

  a = ::Observation
    .joins("JOIN collection_objects on observations.observation_object_id = collection_objects.id and observations.observation_object_type = 'CollectionObject'")
    .joins("JOIN taxon_determinations on collection_objects.id = taxon_determinations.taxon_determination_object_id AND taxon_determinations.taxon_determination_objec_type = 'CollectionObject'")
    .joins('JOIN otus on taxon_determinations.otu_id = otus.id')
    .joins('JOIN query_tn_obs as query_tn_obs1 on otus.taxon_name_id = query_tn_obs1.id')
    .to_sql

  b = ::Observation
    .joins("JOIN otus on observations.observation_object_id = otus.id and observations.observation_object_type = 'Otu'")
    .joins('JOIN query_tn_obs as query_tn_obs2 on otus.taxon_name_id = query_tn_obs2.id')
    .to_sql

  s << ::Observation.from("((#{a}) UNION (#{b})) as observations").to_sql

  ::Observation.from('(' + s + ') as observations')
end

#wkt_facet ⇒ Object 



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# File 'lib/queries/observation/filter.rb', line 177

def wkt_facet
  return nil if wkt.nil?
  from_wkt(wkt)
end