Module: Otus::GisHelper

Defined in:
app/helpers/otus/gis_helper.rb

Instance Method Summary collapse

Instance Method Details

#add_aggregate_geo_json(otu, target) ⇒ Object 



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# File 'app/helpers/otus/gis_helper.rb', line 192

def add_aggregate_geo_json(otu, target)
  h = target

  if g = aggregate_geo_json(otu, h)
    g['properties'] = {'aggregate': true}
    g['properties']['target'] = geojson_target_for_otu(otu)

    h['features'].push g
  end

  h
end

#add_distribution_geo_json(otu, target, seen_shapes = nil) ⇒ Object 



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# File 'app/helpers/otus/gis_helper.rb', line 254

def add_distribution_geo_json(otu, target, seen_shapes = nil)
  h = target
  o = otu

  # internal target
  t = geojson_target_for_otu(otu)

  o.current_field_occurrences.where(is_absent: [nil, false]).each do |f|
    shape_key = seen_shapes && f.collecting_event&.geo_json_shape_key
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:field_occurrences), shape_key) do |skip_geometry|
      field_occurrence_to_geo_json_feature(f, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  o.current_collection_objects.each do |c|
    shape_key = seen_shapes && c.collecting_event&.geo_json_shape_key
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:collection_objects), shape_key) do |skip_geometry|
      collection_object_to_geo_json_feature(c, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  o.asserted_distributions.without_is_absent.each do |a|
    shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
      asserted_distribution_to_geo_json_feature(a, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  ba_ids = ::Queries::BiologicalAssociation::Filter.new(otu_query: { otu_id: [o.id] }).all.pluck(:id)
  unless ba_ids.empty?
    ::AssertedDistribution
      .where(
        asserted_distribution_object_type: 'BiologicalAssociation',
        asserted_distribution_object_id: ba_ids
      )
      .without_is_absent
      .each do |a|
        shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
        g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
          asserted_distribution_to_geo_json_feature(a, skip_geometry:)
        end
        next unless g
        g['properties']['target'] = t
        h['features'].push g
      end

    bag_ids = ::BiologicalAssociationsGraph
      .joins(:biological_associations_biological_associations_graphs)
      .where(biological_associations_biological_associations_graphs: { biological_association_id: ba_ids })
      .select(:id)

    unless bag_ids.empty?
      ::AssertedDistribution
        .where(
          asserted_distribution_object_type: 'BiologicalAssociationsGraph',
          asserted_distribution_object_id: bag_ids
        )
        .without_is_absent
        .each do |a|
          shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
          g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
            asserted_distribution_to_geo_json_feature(a, skip_geometry:)
          end
          next unless g
          g['properties']['target'] = t
          h['features'].push g
        end
    end
  end

  [
    [o.depictions, 'Depiction', :depiction_object_id],
    [o.conveyances, 'Conveyance', :conveyance_object_id],
    [o.observations, 'Observation', :observation_object_id],
  ].each do |related_records, object_type, _id_method|
    related_ids = related_records.map(&:id)
    next if related_ids.empty?

    ::AssertedDistribution
      .where(
        asserted_distribution_object_type: object_type,
        asserted_distribution_object_id: related_ids
      )
      .without_is_absent
      .each do |a|
        shape_key = seen_shapes && [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
        g = build_geo_json_feature_deduped(seen_shapes&.fetch(:asserted_distributions), shape_key) do |skip_geometry|
          asserted_distribution_to_geo_json_feature(a, skip_geometry:)
        end
        next unless g
        g['properties']['target'] = t
        h['features'].push g
      end
  end

  o.type_materials.includes(:protonym).each do |e|
    next unless type_material_is_primary_type(e) && o.taxon_name.cached_is_valid

    shape_key = seen_shapes && e.collection_object&.collecting_event&.geo_json_shape_key
    g = build_geo_json_feature_deduped(seen_shapes&.fetch(:type_materials), shape_key) do |skip_geometry|
      type_material_to_geo_json_feature(e, skip_geometry:)
    end
    next unless g
    g['properties']['target'] = t
    h['features'].push g
  end

  h
end

#aggregate_geo_json(otu, target, cached_map_type = 'CachedMapItem::WebLevel1') ⇒ Object

TODO: cleanup



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# File 'app/helpers/otus/gis_helper.rb', line 221

def aggregate_geo_json(otu, target, cached_map_type = 'CachedMapItem::WebLevel1')
  h = target

  if gj = otu.cached_map_geo_json(cached_map_type)

    i =
      {
        **gj,
        # 'type' => gj['type'],  # 'Feature',

        'properties' => {
          'base' => geojson_target_for_otu(otu),
          #     'shape' => {
          #       'type' => cached_map_type,
          #       'id' => 99999 }, # was nil
          'updated_at' => 'foo' # last updated at on CachedMapItem scope, possibly
        }
      }

    if gj.keys.include?('coordinates')
      i['coordinates'] = gj['coordinates'] # was 'coordinates' TODO: might not work
    elsif gj.keys.include?('geometries')
      i['geometries'] = gj['geometries'] # was 'coordinates' TODO: might not work
    end

    i

  else
    nil
  end

end

#build_geo_json_feature_deduped(seen, shape_key) ⇒ Object (private)

Yields once with skip_geometry true or false depending on whether shape_key [shape_type, shape_id] has already been recorded in seen.

First occurrence of a shape: yields skip_geometry=false (full geometry fetched). The shape is recorded in seen only if the block returns a non-nil feature, so shapes that produce no feature (e.g. no geographic item) are never marked seen. Subsequent occurrences: yields skip_geometry=true (geometry skipped, nil in feature).

When seen or shape_key is nil (deduplication disabled or no shape available), yields skip_geometry=false unconditionally.



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# File 'app/helpers/otus/gis_helper.rb', line 385

def build_geo_json_feature_deduped(seen, shape_key)
  if seen.nil? || shape_key.nil? || shape_key.first.nil?
    return yield(false)
  end

  key = "#{shape_key[0]}_#{shape_key[1]}"
  if seen.key?(key)
    yield(true)
  else
    g = yield(false)
    seen[key] = true if g
    g
  end
end

#geojson_feature_collection ⇒ Object 



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# File 'app/helpers/otus/gis_helper.rb', line 167

def geojson_feature_collection
  {
    'type' => 'FeatureCollection',
    'features' => []
  }
end

#geojson_for_otu(otu) ⇒ Object 



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# File 'app/helpers/otus/gis_helper.rb', line 174

def geojson_for_otu(otu)
  {
    'type' => 'FeatureCollection',
    'features' => [],
    'properties' => {
      'target' => geojson_target_for_otu(otu)
    }
  }
end

#geojson_target_for_otu(otu) ⇒ Object 



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# File 'app/helpers/otus/gis_helper.rb', line 184

def geojson_target_for_otu(otu)
  {
    'id' => otu.id,
    'label' => label_for_otu(otu),
    'type' => 'Otu'
  }
end

#otu_cached_map(otu, target, cached_map_type = 'CachedMapItem::WebLevel1', cache = true, force = false) ⇒ Object

NOT USED Caching the cached map



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# File 'app/helpers/otus/gis_helper.rb', line 207

def otu_cached_map(otu, target, cached_map_type = 'CachedMapItem::WebLevel1', cache = true, force = false)
  r = nil
  if force
    r = aggregate_geo_json(otu, target, cached_map_type)
  else
    # Check for map

    # TODO: extend with synced check
    if a = CachedMap.where(project_id: sessions_current_project_id).where(otu_id: otu.id, cached_map_type:  )
    end
  end
end

#otu_distribution(otu, children = true, cutoff = 200) ⇒ Object

TODO:

  • make properties universal type: 'Model', id: id, label:
  • merge origin_otu_id: id to reference coordinate OTUs

target:

type: Otu
label:
id

base: # one level above target (or one level below shape?!) type:

id:

shape: # Either GeographicArea or Georeference type id

Returns:

  • Hash A GeoJSON collection of distribution data in x parts need a to_geo_json for each object

    :asserted_distributions
  with shape
  without shapes
:collection_objects
    with georeferences
    with GeographicAreas
:type material
    with georeferences
    with GeographicAreas


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# File 'app/helpers/otus/gis_helper.rb', line 37

def otu_distribution(otu, children = true, cutoff = 200)
  return {} if otu.nil?
  otus = if children
    otu.coordinate_otus_with_children
  else
    Otu.coordinate_otus(otu.id)
  end

  h = geojson_for_otu(otu)

  if otu.taxon_name && otu.taxon_name.is_protonym? && !otu.taxon_name.is_species_rank?
    add_aggregate_geo_json(otu, h)
  else
    otus = if children
            otu.coordinate_otus_with_children
          else
            Otu.coordinate_otus(otu.id)
          end

    otus_distribution_geo_json(otus, target: h)
  end

  h
end

#otu_distribution_is_absent(otu, descendants: false) ⇒ Hash

Returns GeoJSON FeatureCollection of absent FieldOccurrences and AssertedDistributions for the OTU, its coordinate OTUs, and ancestor taxon names (traversed via TaxonNameHierarchies).

Parameters:

  • descendants (Boolean) (defaults to: false) —

    when true, also include direct absents from descendant OTUs. Off by default: a descendant's absence does not propagate up to the OTU, and a sibling descendant's presence in the same region may contradict it. Use only when the caller wants a clade-wide visualization.

Returns:

  • (Hash) —

    GeoJSON FeatureCollection of absent FieldOccurrences and AssertedDistributions for the OTU, its coordinate OTUs, and ancestor taxon names (traversed via TaxonNameHierarchies).



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# File 'app/helpers/otus/gis_helper.rb', line 112

def otu_distribution_is_absent(otu, descendants: false)
  return {} if otu.nil?

  otus = descendants ? otu.coordinate_otus_with_children : Otu.coordinate_otus(otu.id)

  otus_distribution_is_absent_geo_json(otus, target: geojson_for_otu(otu))
end

#otus_distribution_geo_json(otus, target: geojson_feature_collection) ⇒ Hash

Returns GeoJSON FeatureCollection of present distribution data for exactly otus (coordinate OTUs are not added).

Parameters:

  • otus (ActiveRecord::Relation) —

    of Otu

  • target (Hash) (defaults to: geojson_feature_collection) —

    the FeatureCollection features are added to

Returns:

  • (Hash) —

    GeoJSON FeatureCollection of present distribution data for exactly otus (coordinate OTUs are not added).



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# File 'app/helpers/otus/gis_helper.rb', line 67

def otus_distribution_geo_json(otus, target: geojson_feature_collection)
  h = target

  # Batch-load everything the downstream helpers touch.
  otus = otus.includes(
    :taxon_name,
    current_field_occurrences: [
      :identifiers,
      { collecting_event: [ :georeferences, :geographic_area, :geographic_items ] }
    ],
    current_collection_objects: [
      :identifiers,
      { collecting_event: [ :georeferences, :geographic_area, :geographic_items ] }
    ],
    asserted_distributions: { asserted_distribution_shape: :geographic_items },
    type_materials: [
      { collection_object: [
          :identifiers,
          { collecting_event: [ :georeferences, :geographic_area, :geographic_items ] }
        ] }
    ]
  )

  seen_shapes = {
    field_occurrences: {},
    collection_objects: {},
    asserted_distributions: {},
    type_materials: {}
  }

  otus.each do |o|
    add_distribution_geo_json(o, h, seen_shapes)
  end

  h
end

#otus_distribution_is_absent_geo_json(otus, only_requested: false, target: geojson_feature_collection) ⇒ Hash

Returns GeoJSON FeatureCollection of absent FieldOccurrences and AssertedDistributions for exactly otus (coordinate OTUs are not added) and their ancestor taxon names.

Parameters:

  • otus (ActiveRecord::Relation) —

    of Otu

  • only_requested (Boolean) (defaults to: false) —

    when true, absences of coordinate OTUs not in otus are excluded

  • target (Hash) (defaults to: geojson_feature_collection) —

    the FeatureCollection features are added to

Returns:

  • (Hash) —

    GeoJSON FeatureCollection of absent FieldOccurrences and AssertedDistributions for exactly otus (coordinate OTUs are not added) and their ancestor taxon names.



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# File 'app/helpers/otus/gis_helper.rb', line 126

def otus_distribution_is_absent_geo_json(otus, only_requested: false, target: geojson_feature_collection)
  h = target
  otu_ids = otus.pluck(:id) if only_requested

  seen_shapes = {
    field_occurrences: {},
    asserted_distributions: {}
  }

  otus.each do |o|
    t = geojson_target_for_otu(o)
    excluded_otu_ids = only_requested ? Otu.coordinate_otus(o.id).where.not(id: otu_ids).pluck(:id) : []

    o.absent_and_ancestor_absent_field_occurrences
      .where.not(taxon_determinations: { otu_id: excluded_otu_ids })
      .each do |f|
      shape_key = f.collecting_event&.geo_json_shape_key
      g = build_geo_json_feature_deduped(seen_shapes[:field_occurrences], shape_key) do |skip_geometry|
        field_occurrence_to_geo_json_feature(f, skip_geometry:)
      end
      next unless g
      g['properties']['target'] = t
      h['features'].push g
    end

    o.absent_and_ancestor_absent_asserted_distributions
      .where.not(asserted_distribution_object_id: excluded_otu_ids)
      .each do |a|
      shape_key = [a.asserted_distribution_shape_type, a.asserted_distribution_shape_id]
      g = build_geo_json_feature_deduped(seen_shapes[:asserted_distributions], shape_key) do |skip_geometry|
        asserted_distribution_to_geo_json_feature(a, skip_geometry:)
      end
      next unless g
      g['properties']['target'] = t
      h['features'].push g
    end
  end

  h
end