Class: Queries::CollectionObject::Filter

Inherits:
Query::Filter show all
Includes:
Queries::Concerns::Citations, Queries::Concerns::Confidences, Queries::Concerns::Containable, Queries::Concerns::Conveyances, Queries::Concerns::DataAttributes, Queries::Concerns::Depictions, Queries::Concerns::Notes, Queries::Concerns::Protocols, Queries::Concerns::Tags, Helpers
Defined in:
lib/queries/collection_object/filter.rb

Constant Summary collapse

PARAMS = 
[
  *::Queries::CollectingEvent::Filter::BASE_PARAMS,
  *Queries::Concerns::DateRanges.params, # Fead to CE query. Revisit possibly.

  :biological_association_id,
  :biological_associations,
  :biological_relationship_id,
  :buffered_collecting_event,
  :buffered_determinations,
  :buffered_other_labels,
  :collecting_event,
  :collection_object_id,
  :collection_object_type,
  :collectors,
  :containerized,
  :current_determinations,
  :current_repository,
  :current_repository_id,
  :dates,
  :deaccessioned,
  :descendants,
  :determiner_id_all,
  :determiner_id,
  :determiner_name_regex,
  :determiners,
  :dwc_indexed,
  :exact_buffered_collecting_event,
  :exact_buffered_determinations,
  :exact_buffered_other_labels,
  :extract_id,
  :georeferences,
  :import_dataset_id,
  :loaned,
  :never_loaned,
  :on_loan,
  :preparation_type,
  :preparation_type_id,
  :repository,
  :repository_id,
  :sled_image_id,
  :spatial_geographic_areas,
  :taxon_determination_id, # not used?!
  :taxon_determinations,
  :taxon_name_id,
  :taxon_name_current_determination,
  :type_material,
  :type_specimen_taxon_name_id,
  :validity,
  :with_buffered_collecting_event,
  :with_buffered_determinations,
  :with_buffered_other_labels,
  biocuration_class_id: [],
  biological_association_id: [],
  biological_relationship_id: [],
  collecting_event_id: [],
  collection_object_id: [],
  determiner_id: [],
  extract_id: [],
  geographic_area_id: [],
  import_dataset_id: [],
  is_type: [],
  loan_id: [],
  otu_id: [],
  preparation_type_id: [],
  taxon_name_id: [],
].inject([{}]) { |ary, k| k.is_a?(Hash) ? ary.last.merge!(k) : ary.unshift(k); ary }.freeze

Constants inherited from Query::Filter

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

Instance Attribute Summary collapse

Attributes inherited from Query::Filter

#anatomical_part_query, #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 included from Helpers

#boolean_param, #integer_param, #split_pairs, #split_repeated_pairs, #tri_value_array

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?, #only_project_or_less?, #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

rubocop:disable Metric/MethodLength



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# File 'lib/queries/collection_object/filter.rb', line 335

def initialize(query_params)
  super

  # Only CollectingEvent fields are permitted, for advanced nesting (e.g. tags on CEs), use collecting_event_query
  collecting_event_params = ::Queries::CollectingEvent::Filter.base_params + Queries::Concerns::DateRanges.params

  # project_id is handled during use
  @base_collecting_event_query = ::Queries::CollectingEvent::Filter.new(
    params.select{ |a, b| collecting_event_params.include?(a) } # maintain this to avoid sub query initialization for now
  )

  @biological_association_id = params[:biological_association_id]
  @biocuration_class_id = params[:biocuration_class_id]
  @biological_relationship_id = params[:biological_relationship_id] # TODO: no reference?
  @buffered_collecting_event = params[:buffered_collecting_event]
  @buffered_determinations = params[:buffered_determinations]
  @buffered_other_labels = params[:buffered_other_labels]
  @biological_associations = boolean_param(params, :biological_associations)
  @collecting_event = boolean_param(params, :collecting_event)
  @collectors = boolean_param(params, :collectors)
  @collecting_event_id = params[:collecting_event_id]
  @collection_object_id = params[:collection_object_id]
  @collection_object_type = params[:collection_object_type].presence
  @containerized = boolean_param(params, :containerized)
  @current_determinations = boolean_param(params, :current_determinations)
  @taxon_name_current_determination = boolean_param(params, :taxon_name_current_determination)
  @current_repository = boolean_param(params, :current_repository)
  @current_repository_id = params[:current_repository_id].presence
  @dates = boolean_param(params, :dates)
  @descendants = boolean_param(params, :descendants)
  @deaccessioned = boolean_param(params, :deaccessioned)
  @determiners = boolean_param(params, :determiners)
  @determiner_id = params[:determiner_id]
  @determiner_id_all = boolean_param(params, :determiner_id_all)
  @determiner_name_regex = params[:determiner_name_regex]
  @dwc_indexed = boolean_param(params, :dwc_indexed)
  @exact_buffered_collecting_event = boolean_param(params, :exact_buffered_collecting_event)
  @exact_buffered_determinations = boolean_param(params, :exact_buffered_determinations)
  @exact_buffered_other_labels = boolean_param(params, :exact_buffered_other_labels)
  @extract_id = params[:extract_id]
  @geographic_area = boolean_param(params, :geographic_area)
  @georeferences = boolean_param(params, :georeferences)
  @import_dataset_id = params[:import_dataset_id]
  @is_type = params[:is_type] || []
  @loan_id = params[:loan_id]
  @loaned = boolean_param(params, :loaned)
  @never_loaned = boolean_param(params, :never_loaned)
  @on_loan = boolean_param(params, :on_loan)
  @otu_descendants = boolean_param(params, :otu_descendants)
  @otu_id = params[:otu_id]
  @preparation_type = boolean_param(params, :preparation_type)
  @preparation_type_id = params[:preparation_type_id]
  @repository = boolean_param(params, :repository)
  @repository_id = params[:repository_id]
  @sled_image_id = (params[:sled_image_id].presence)
  @taxon_determinations = boolean_param(params, :taxon_determinations)
  @taxon_name_id = params[:taxon_name_id]
  @type_material = boolean_param(params, :type_material)
  @type_specimen_taxon_name_id = (params[:type_specimen_taxon_name_id].presence)
  @validity = boolean_param(params, :validity)
  @with_buffered_collecting_event = boolean_param(params, :with_buffered_collecting_event)
  @with_buffered_determinations = boolean_param(params, :with_buffered_determinations)
  @with_buffered_other_labels = boolean_param(params, :with_buffered_other_labels)

  set_confidences_params(params)
  set_citations_params(params)
  set_containable_params(params)
  set_conveyance_params(params)
  set_data_attributes_params(params)
  set_depiction_params(params)
  set_notes_params(params)
  set_protocols_params(params)
  set_tags_params(params)
end

Instance Attribute Details

#base_collecting_event_query ⇒ Object

All params managed by CollectingEvent filter are available here as well



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# File 'lib/queries/collection_object/filter.rb', line 119

def base_collecting_event_query
  @base_collecting_event_query
end

#biocuration_class_id ⇒ Array

Returns of biocuration_class ids.

Returns:

  • (Array) —

    of biocuration_class ids



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# File 'lib/queries/collection_object/filter.rb', line 188

def biocuration_class_id
  @biocuration_class_id
end

#biological_association_id ⇒ Object

Returns Array Matching records in this BiologicalAssociation.

Returns:

  • Array Matching records in this BiologicalAssociation



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# File 'lib/queries/collection_object/filter.rb', line 97

def biological_association_id
  @biological_association_id
end

#biological_associations ⇒ True, ...

Returns true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied.

Returns:

  • (True, False, nil) —

    true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied



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

def biological_associations
  @biological_associations
end

#biological_relationship_id ⇒ Array

Returns of biological_relationship#id.

Returns:

  • (Array) —

    of biological_relationship#id



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# File 'lib/queries/collection_object/filter.rb', line 192

def biological_relationship_id
  @biological_relationship_id
end

#buffered_collecting_event ⇒ String?

Returns:

  • (String, nil) 


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# File 'lib/queries/collection_object/filter.rb', line 289

def buffered_collecting_event
  @buffered_collecting_event
end

#buffered_determinations ⇒ String?

Returns:

  • (String, nil) 


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# File 'lib/queries/collection_object/filter.rb', line 281

def buffered_determinations
  @buffered_determinations
end

#buffered_other_labels ⇒ String?

Returns:

  • (String, nil) 


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# File 'lib/queries/collection_object/filter.rb', line 298

def buffered_other_labels
  @buffered_other_labels
end

#collecting_event ⇒ True, ...

Parameters:

  • collecting_event ('true', 'false') —

    true - has collecting_event_id false - does not have collecting_event_id nil - not applied

Returns:

  • (True, False, nil) 


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# File 'lib/queries/collection_object/filter.rb', line 261

def collecting_event
  @collecting_event
end

#collecting_event_id ⇒ Object

Array

only return objects with these collecting event ID



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# File 'lib/queries/collection_object/filter.rb', line 109

def collecting_event_id
  @collecting_event_id
end

#collection_object_id ⇒ Object

Parameters:

  • Array (String, nil) —

    or Integer of CollectionObject ids



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# File 'lib/queries/collection_object/filter.rb', line 101

def collection_object_id
  @collection_object_id
end

#collection_object_type ⇒ Object

Parameters:

  • one (String, nil) —

    of ‘Specimen’, ‘Lot’, or ‘RangedLot’



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

def collection_object_type
  @collection_object_type
end

#collectors ⇒ Boolean?

Returns true - A collector role exists false - A collector role exists nil - not applied.

Returns:

  • (Boolean, nil) —

    true - A collector role exists false - A collector role exists nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 168

def collectors
  @collectors
end

#containerized ⇒ Object

Parameters:

  • true (True, False, nil) —

    • the collection object is in a container

    false - the collection object is not in a container nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 116

def containerized
  @containerized
end

#current_determinations ⇒ Boolean?

Returns nil = TaxonDeterminations match regardless of current or historical true = TaxonDetermination must be .current false = TaxonDetermination must be .historical.

Returns:

  • (Boolean, nil) —

    nil = TaxonDeterminations match regardless of current or historical true = TaxonDetermination must be .current false = TaxonDetermination must be .historical



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# File 'lib/queries/collection_object/filter.rb', line 149

def current_determinations
  @current_determinations
end

#current_repository ⇒ True, ...

Returns true - has current_repository_id false - does not have current_repository_id nil - not applied.

Returns:

  • (True, False, nil) —

    true - has current_repository_id false - does not have current_repository_id nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 245

def current_repository
  @current_repository
end

#current_repository_id ⇒ CurrentRepository#id?

Returns:

  • (CurrentRepository#id, nil) 


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

def current_repository_id
  @current_repository_id
end

#dates ⇒ Object

Returns Boolean true - any of start/end date or verbatim date are populated false - none of start/end date or verbatim date are populated nil - ignored.

Returns:

  • Boolean true - any of start/end date or verbatim date are populated false - none of start/end date or verbatim date are populated nil - ignored



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# File 'lib/queries/collection_object/filter.rb', line 332

def dates
  @dates
end

#deaccessioned ⇒ Boolean?

Returns nil = Ignored true = CollectionObject with deaccessioned_at OR deaccessioned_reason populated or deaccession_recipient.present? false = without true.

Returns:

  • (Boolean, nil) —

    nil = Ignored true = CollectionObject with deaccessioned_at OR deaccessioned_reason populated or deaccession_recipient.present? false = without true



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# File 'lib/queries/collection_object/filter.rb', line 137

def deaccessioned
  @deaccessioned
end

#descendants ⇒ Object

Returns the value of attribute descendants.



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# File 'lib/queries/collection_object/filter.rb', line 131

def descendants
  @descendants
end

#determiner_id ⇒ Array

Parameters:

  • determiner (Array or Person#id) —

    one ore more people id

Returns:

  • (Array) 


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# File 'lib/queries/collection_object/filter.rb', line 272

def determiner_id
  @determiner_id
end

#determiner_id_all ⇒ Boolean

Parameters:

  • determiner_id_all (String, nil) —

    ‘false`, nil - treat the ids in determiner_id as “or” ’true’ - treat the ids in determiner_id as “and” (only collection objects with all and only all will match)

Returns:

  • (Boolean) 


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# File 'lib/queries/collection_object/filter.rb', line 278

def determiner_id_all
  @determiner_id_all
end

#determiner_name_regex ⇒ Object

A PostgreSQL valid regular expression. Note that simple strings evaluate as wildcard matches. !! Probably shouldn’t expose to external API.

Returns:

  • String



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# File 'lib/queries/collection_object/filter.rb', line 322

def determiner_name_regex
  @determiner_name_regex
end

#determiners ⇒ Boolean?

Returns true - A determiner role exists false - No determiner role exists nil - not applied.

Returns:

  • (Boolean, nil) —

    true - A determiner role exists false - No determiner role exists nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 162

def determiners
  @determiners
end

#dwc_indexed ⇒ True, ...

Returns true - index is built false - index is not built nil - not applied.

Returns:

  • (True, False, nil) —

    true - index is built false - index is not built nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 198

def dwc_indexed
  @dwc_indexed
end

#exact_buffered_collecting_event ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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

def exact_buffered_collecting_event
  @exact_buffered_collecting_event
end

#exact_buffered_determinations ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/collection_object/filter.rb', line 286

def exact_buffered_determinations
  @exact_buffered_determinations
end

#exact_buffered_other_labels ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/collection_object/filter.rb', line 295

def exact_buffered_other_labels
  @exact_buffered_other_labels
end

#extract_id ⇒ Object

Returns Array match all CollectionObjects that are the origin of these Extracts.

Returns:

  • Array match all CollectionObjects that are the origin of these Extracts



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# File 'lib/queries/collection_object/filter.rb', line 326

def extract_id
  @extract_id
end

#geographic_area ⇒ True, ...

Returns true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied.

Returns:

  • (True, False, nil) —

    true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 267

def geographic_area
  @geographic_area
end

#georeferences ⇒ True, ...

Returns true - has one ore more georeferences false - does not have any georeferences nil - not applied.

Returns:

  • (True, False, nil) —

    true - has one ore more georeferences false - does not have any georeferences nil - not applied



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

def georeferences
  @georeferences
end

#import_dataset_id ⇒ Array

Returns of ImportDataset ids.

Returns:

  • (Array) —

    of ImportDataset ids



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# File 'lib/queries/collection_object/filter.rb', line 87

def import_dataset_id
  @import_dataset_id
end

#is_type ⇒ Array?

Returns one of ‘holotype`, `lectotype` etc.

nil - not applied.

Returns:

  • (Array, nil) —

    one of ‘holotype`, `lectotype` etc.

    nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 212

def is_type
  @is_type
end

#loan_id ⇒ Array

Returns a list of loan#id, all collection objects inside them will be included.

Returns:

  • (Array) —

    a list of loan#id, all collection objects inside them will be included



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# File 'lib/queries/collection_object/filter.rb', line 184

def loan_id
  @loan_id
end

#loaned ⇒ Object

Parameters:

  • loaned (True) —

    true - the CollectionObject has been loaned at least once



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# File 'lib/queries/collection_object/filter.rb', line 176

def loaned
  @loaned
end

#never_loaned ⇒ Object

Parameters:

  • never_loaned (True) —

    true - the CollectionObject has never been loaned



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# File 'lib/queries/collection_object/filter.rb', line 180

def never_loaned
  @never_loaned
end

#on_loan ⇒ Object

Parameters:

  • on_loan (True) —

    true - the CollectionObject currently on loan



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# File 'lib/queries/collection_object/filter.rb', line 172

def on_loan
  @on_loan
end

#otu_id ⇒ Array?

Returns Otu ids, matches on the TaxonDetermination, see also current_determinations.

Parameters:

  • (Array)

Returns:

  • (Array, nil) —

    Otu ids, matches on the TaxonDetermination, see also current_determinations



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# File 'lib/queries/collection_object/filter.rb', line 124

def otu_id
  @otu_id
end

#preparation_type ⇒ True, ...

Returns true - has preparation_type false - does not have preparation_type nil - not applied.

Returns:

  • (True, False, nil) —

    true - has preparation_type false - does not have preparation_type nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 251

def preparation_type
  @preparation_type
end

#preparation_type_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/collection_object/filter.rb', line 254

def preparation_type_id
  @preparation_type_id
end

#repository ⇒ True, ...

Returns true - has repository_id false - does not have repository_id nil - not applied.

Returns:

  • (True, False, nil) —

    true - has repository_id false - does not have repository_id nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 239

def repository
  @repository
end

#repository_id ⇒ Repository#id?

Returns:



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# File 'lib/queries/collection_object/filter.rb', line 204

def repository_id
  @repository_id
end

#sled_image_id ⇒ SledImage#id?

Returns:



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# File 'lib/queries/collection_object/filter.rb', line 215

def sled_image_id
  @sled_image_id
end

#taxon_determinations ⇒ True, ...

Returns true - has one ore more taxon_determinations false - does not have any taxon_determinations nil - not applied.

Returns:

  • (True, False, nil) —

    true - has one ore more taxon_determinations false - does not have any taxon_determinations nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 221

def taxon_determinations
  @taxon_determinations
end

#taxon_name ⇒ True, ...

Returns true - Otu has taxon name false - Otu without taxon name nil - not applied.

Returns:

  • (True, False, nil) —

    true - Otu has taxon name false - Otu without taxon name nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 227

def taxon_name
  @taxon_name
end

#taxon_name_current_determination ⇒ Boolean?

Returns nil = TaxonDeterminations match regardless of current or historical true = TaxonDetermination must be .current false = TaxonDetermination must be .historical Used for taxon_name_id facets.

Returns:

  • (Boolean, nil) —

    nil = TaxonDeterminations match regardless of current or historical true = TaxonDetermination must be .current false = TaxonDetermination must be .historical Used for taxon_name_id facets



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# File 'lib/queries/collection_object/filter.rb', line 156

def taxon_name_current_determination
  @taxon_name_current_determination
end

#taxon_name_id ⇒ Array of Protonym.id?

Return all collection objects determined as an Otu that is self or descendant linked to this TaxonName

Returns:

  • (Array of Protonym.id, nil) —

    return all collection objects determined as an Otu that is self or descendant linked to this TaxonName



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# File 'lib/queries/collection_object/filter.rb', line 129

def taxon_name_id
  @taxon_name_id
end

#type_material ⇒ True, ...

Returns true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied.

Returns:

  • (True, False, nil) —

    true - has collecting event that has geographic_area false - does not have collecting event that has geographic area nil - not applied



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# File 'lib/queries/collection_object/filter.rb', line 304

def type_material
  @type_material
end

#type_specimen_taxon_name_id ⇒ Protonym#id?

Returns:



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# File 'lib/queries/collection_object/filter.rb', line 201

def type_specimen_taxon_name_id
  @type_specimen_taxon_name_id
end

#validity ⇒ Boolean?

Returns nil = Match against all ancestors, valid or invalid true = Match against only valid ancestors false = Match against only invalid ancestors.

Returns:

  • (Boolean, nil) —

    nil = Match against all ancestors, valid or invalid true = Match against only valid ancestors false = Match against only invalid ancestors



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# File 'lib/queries/collection_object/filter.rb', line 143

def validity
  @validity
end

#with_buffered_collecting_event ⇒ Object

See with_buffered_determinations



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

def with_buffered_collecting_event
  @with_buffered_collecting_event
end

#with_buffered_determinations ⇒ Boolean?

Returns Boolean, nil.

Parameters:

  • with_buffered_determinations (String, nil) —

    ‘false`, nil - without buffered determination field value ’true’ - with buffered_determinations field value

Returns:

  • (Boolean, nil) —

    Boolean, nil



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# File 'lib/queries/collection_object/filter.rb', line 310

def with_buffered_determinations
  @with_buffered_determinations
end

#with_buffered_other_labels ⇒ Object

See with_buffered_determinations



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# File 'lib/queries/collection_object/filter.rb', line 316

def with_buffered_other_labels
  @with_buffered_other_labels
end

Instance Method Details

#anatomical_part_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 935

def anatomical_part_query_facet
  return nil if anatomical_part_query.nil?

  ::CollectionObject
    .joins(:origin_relationships)
    .where("origin_relationships.new_object_id IN (#{ anatomical_part_query.all.select(:id).to_sql })")
end

#and_clauses ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 1030

def and_clauses
  [
    attribute_exact_facet(:buffered_collecting_event),
    attribute_exact_facet(:buffered_determinations),
    attribute_exact_facet(:buffered_other_labels),
    collecting_event_id_facet,
    current_repository_id_facet,
    preparation_type_id_facet,
    repository_id_facet,
    type_facet,
  ]
end

#base_collecting_event_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 911

def base_collecting_event_query_facet
  return nil if
    base_collecting_event_query.only_project?

  s = 'WITH query_ce_base_co AS (' + base_collecting_event_query.all.select(:id).to_sql + ') ' +
    ::CollectionObject
    .joins('JOIN query_ce_base_co as query_ce_base_co1 on query_ce_base_co1.id = collection_objects.collecting_event_id')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#biocuration_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 657

def biocuration_facet
  return nil if biocuration_class_id.empty?
  ::CollectionObject::BiologicalCollectionObject.joins(:biocuration_classifications)
    .where(biocuration_classifications: { biocuration_class_id: })
end

#biological_association_id_facet ⇒ Object

TODO: turn into UNION!



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# File 'lib/queries/collection_object/filter.rb', line 964

def biological_association_id_facet
  return nil if biological_association_id.empty?
  b = ::BiologicalAssociation.where(id: biological_association_id)
  s = 'WITH query_ba_id_co AS (' + b.all.to_sql + ') ' +
    ::CollectionObject
    .joins("LEFT JOIN query_ba_id_co as query_ba_id_co1 on collection_objects.id = query_ba_id_co1.biological_association_subject_id AND query_ba_id_co1.biological_association_subject_type = 'CollectionObject'")
    .joins("LEFT JOIN query_ba_id_co as query_ba_id_co2 on collection_objects.id = query_ba_id_co2.biological_association_object_id AND query_ba_id_co2.biological_association_object_type = 'CollectionObject'")
    .where('(query_ba_id_co1.id) IS NOT NULL OR (query_ba_id_co2.id IS NOT NULL)')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#biological_association_query_facet ⇒ Object

TODO: turn into UNION!



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# File 'lib/queries/collection_object/filter.rb', line 978

def biological_association_query_facet
  return nil if biological_association_query.nil?
  s = 'WITH query_ba_co AS (' + biological_association_query.all.to_sql + ') ' +
    ::CollectionObject
    .joins("LEFT JOIN query_ba_co as query_ba_co1 on collection_objects.id = query_ba_co1.biological_association_subject_id AND query_ba_co1.biological_association_subject_type = 'CollectionObject'")
    .joins("LEFT JOIN query_ba_co as query_ba_co2 on collection_objects.id = query_ba_co2.biological_association_object_id AND query_ba_co2.biological_association_object_type = 'CollectionObject'")
    .where('(query_ba_co1.id) IS NOT NULL OR (query_ba_co2.id IS NOT NULL)')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#biological_associations_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 955

def biological_associations_facet
  return nil if biological_associations.nil?
  a = ::CollectionObject.joins(:biological_associations)
  b = ::CollectionObject.joins(:related_biological_associations)

  referenced_klass_union([a, b])
end

#biological_relationship_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 678

def biological_relationship_id_facet
  return nil if biological_relationship_id.empty?
  ::CollectionObject.with_biological_relationship_id(biological_relationship_id)
end

#collecting_event_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 608

def collecting_event_facet
  return nil if collecting_event.nil?
  if collecting_event
    ::CollectionObject.where.not(collecting_event_id: nil)
  else
    ::CollectionObject.where(collecting_event_id: nil)
  end
end

#collecting_event_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 716

def collecting_event_id_facet
  return nil if collecting_event_id.empty?
  table[:collecting_event_id].in(collecting_event_id)
end

#collecting_event_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 891

def collecting_event_query_facet
  return nil if collecting_event_query.nil?
  s = 'WITH query_ce_co AS (' + collecting_event_query.all.select(:id).to_sql + ') ' +
    ::CollectionObject
    .joins('JOIN query_ce_co as query_ce_co1 on query_ce_co1.id = collection_objects.collecting_event_id')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#collecting_event_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/collection_object/filter.rb', line 411

def collecting_event_table
  ::CollectingEvent.arel_table
end

#collectors_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 556

def collectors_facet
  return nil if collectors.nil?
  if collectors
    ::CollectionObject.joins(:collectors)
  else
    ::CollectionObject.where.missing(:collectors)
  end
end

#containerized_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 699

def containerized_facet
  return nil if containerized.nil?

  if containerized
    ::CollectionObject.joins(:container_item).distinct
  else
    ::CollectionObject.left_outer_joins(:container_item).where(container_item: { id: nil }).distinct
  end
end

#current_repository_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 590

def current_repository_facet
  return nil if current_repository.nil?
  if current_repository
    ::CollectionObject.where.not(current_repository_id: nil)
  else
    ::CollectionObject.where(current_repository_id: nil)
  end
end

#current_repository_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 731

def current_repository_id_facet
  return nil if current_repository_id.blank?
  table[:current_repository_id].eq(current_repository_id)
end

#dates_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 836

def dates_facet
  return nil if dates.nil?
  if dates
    ::CollectionObject.left_joins(:collecting_event).where(
      'start_date_year IS NOT NULL OR ' \
      'start_date_month IS NOT NULL OR ' \
      'start_date_day IS NOT NULL OR ' \
      'end_date_year IS NOT NULL OR ' \
      'end_date_month IS NOT NULL OR ' \
      'end_date_day IS NOT NULL OR ' \
      'verbatim_date IS NOT NULL'
    )
  else
    ::CollectionObject.left_joins(:collecting_event).where(
      collecting_event: {
        start_date_year: nil,
        start_date_month: nil,
        start_date_day: nil,
        end_date_year: nil,
        end_date_month: nil,
        end_date_day: nil,
        verbatim_date: nil,
      },
    )
  end
end

#deaccessioned_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 863

def deaccessioned_facet
  return nil if deaccessioned.nil?
  a = ::CollectionObject.where('(deaccession_reason IS NOT NULL) OR (deaccessioned_at IS NOT NULL)')
  b = ::CollectionObject.joins(:deaccession_recipient)

  c = referenced_klass_union([a, b])
  if deaccessioned
    c
  else
    s = 'WITH query_deac AS (' + c.all.unscope(:select).select(:id).to_sql + ') ' +
      ::CollectionObject
      .joins('LEFT JOIN query_deac as query_deac1 on query_deac1.id = collection_objects.id')
      .where('query_deac1.id IS NULL').to_sql
    ::CollectionObject.from('(' + s + ') as collection_objects').distinct
  end
end

#determiner_facet ⇒ Object

TODO: DRY with Source (author), TaxonName, etc. See Queries::ColletingEvent::Filter for other use



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# File 'lib/queries/collection_object/filter.rb', line 512

def determiner_facet
  return nil if determiner_id.empty?
  tt = table

  o = ::TaxonDetermination.arel_table
  r = ::Role.arel_table

  a = o.alias('a_det__')
  b = o.project(a[Arel.star]).from(a)

  c = r.alias('det_r1')

  b = b.join(c, Arel::Nodes::OuterJoin)
    .on(
      a[:id].eq(c[:role_object_id])
    .and(c[:role_object_type].eq('TaxonDetermination'))
    .and(c[:type].eq('Determiner'))
    )

  e = c[:id].not_eq(nil)
  f = c[:person_id].in(determiner_id)

  b = b.where(e.and(f))
  b = b.group(a['id'])
  b = b.having(a['id'].count.eq(determiner_id.length)) if determiner_id_all

  b = b.as('det_z1_')

  ::CollectionObject.joins(Arel::Nodes::InnerJoin.new(
    b,
    Arel::Nodes::On.new(
      b['taxon_determination_object_id'].eq(tt['id']).and( b['taxon_determination_object_type'].eq('CollectionObject'))
    )))
end

#determiner_name_regex_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 565

def determiner_name_regex_facet
  return nil if determiner_name_regex.nil?
  ::CollectionObject.joins(:determiners).where('people.cached ~* ?', determiner_name_regex)
end

#determiners_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 547

def determiners_facet
  return nil if determiners.nil?
  if determiners
    ::CollectionObject.joins(:determiners)
  else
    ::CollectionObject.where.missing(:determiners)
  end
end

#dwc_indexed_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 709

def dwc_indexed_facet
  return nil if dwc_indexed.nil?
  dwc_indexed ?
    ::CollectionObject.dwc_indexed :
    ::CollectionObject.dwc_not_indexed
end

#dwc_occurrence_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 943

def dwc_occurrence_query_facet
  return nil if dwc_occurrence_query.nil?

  s = ::CollectionObject
    .with(query_dwc_co: dwc_occurrence_query.all.select(:dwc_occurrence_object_id, :dwc_occurrence_object_type, :id))
    .joins(:dwc_occurrence)
    .joins('JOIN query_dwc_co as query_dwc_co1 on query_dwc_co1.id = dwc_occurrences.id')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#extract_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 493

def extract_id_facet
  return nil if extract_id.empty?
  ::CollectionObject
    .joins(:origin_relationships)
    .where(origin_relationships: { new_object_id: extract_id, new_object_type: 'Extract' })
end

#extract_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 990

def extract_query_facet
  return nil if extract_query.nil?

  s = 'WITH query_extract_co AS (' + extract_query.all.to_sql + ') ' +
    ::CollectionObject
    .joins(:origin_relationships)
    .joins("JOIN query_extract_co as query_extract_co1 on origin_relationships.new_object_id = query_extract_co1.id and origin_relationships.new_object_type = 'Extract'")
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#geographic_area_facet ⇒ Object

This is not spatial



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# File 'lib/queries/collection_object/filter.rb', line 645

def geographic_area_facet
  return nil if geographic_area.nil?

  if geographic_area
    ::CollectionObject.joins(:collecting_event).where.not(collecting_events: { geographic_area_id: nil }).distinct
  else
    ::CollectionObject.left_outer_joins(:collecting_event)
      .where(collecting_events: { geographic_area_id: nil })
      .distinct
  end
end

#georeferences_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 570

def georeferences_facet
  return nil if georeferences.nil?
  if georeferences
    ::CollectionObject.joins(:georeferences).distinct
  else
    ::CollectionObject.left_outer_joins(:georeferences)
      .where(georeferences: { id: nil })
      .distinct
  end
end

#housekeeping_extensions ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 1014

def housekeeping_extensions
  [
    housekeeping_extension_query(target: ::CollectingEvent, joins: [:collecting_event]),
    housekeeping_extension_query(target: ::TaxonDetermination, joins: [:taxon_determinations]),
    housekeeping_extension_query(target: ::DataAttribute, joins: [:data_attributes]),
    housekeeping_extension_query(target: ::Georeference, joins: [:georeferences]),
    housekeeping_extension_query(target: ::DataAttribute, joins: {collecting_event: [:data_attributes]}),
    housekeeping_extension_query(target: ::DataAttribute, joins: {collecting_event: [:data_attributes]}),
    housekeeping_extension_query(target: ::Note, joins: {collecting_event: [:notes]}),
    housekeeping_extension_query(target: ::Note, joins: [:notes]),
    housekeeping_extension_query(target: ::Role, joins: [:roles]),
    housekeeping_extension_query(target: ::Role, joins: {collecting_event: [:roles]}),
    housekeeping_extension_query(target: ::Role, joins: { taxon_determinations: [:determiner_roles]}),
  ]
end

#import_dataset_id_facet ⇒ Object

def collection_object_id_facet

  return nil if collection_object_id.empty?
  table[:id].in(collection_object_id)
end



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# File 'lib/queries/collection_object/filter.rb', line 487

def import_dataset_id_facet
  return nil if import_dataset_id.blank?
  ::CollectionObject.joins(:related_origin_relationships)
    .where(origin_relationships: {old_object_id: import_dataset_id, old_object_type: 'ImportDataset'})
end

#loan_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 663

def loan_facet
  return nil if loan_id.empty?
  ::CollectionObject::BiologicalCollectionObject.joins(:loans).where(loans: { id: loan_id })
end

#loan_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 901

def loan_query_facet
  return nil if loan_query.nil?
  s = 'WITH query_loan_co AS (' + loan_query.all.to_sql + ') ' +
    ::CollectionObject.joins(:loan_items)
    .joins('JOIN query_loan_co as query_loan_co1 on query_loan_co1.id = loan_items.loan_id')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#loaned_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 683

def loaned_facet
  return nil unless loaned
  ::CollectionObject.loaned
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 1043

def merge_clauses
  [
    import_dataset_id_facet,
    biological_association_id_facet,
    anatomical_part_query_facet,
    base_collecting_event_query_facet,
    biological_association_query_facet,
    dwc_occurrence_query_facet,
    collecting_event_query_facet,
    extract_query_facet,
    loan_query_facet,
    observation_query_facet,
    otu_query_facet,
    taxon_name_query_facet,

    biocuration_facet,
    biological_associations_facet,
    biological_relationship_id_facet,
    collecting_event_facet,
    collectors_facet,
    containerized_facet,
    current_repository_facet,
    dates_facet,
    deaccessioned_facet,
    determiner_facet,
    determiner_name_regex_facet,
    determiners_facet,
    dwc_indexed_facet,
    extract_id_facet,
    geographic_area_facet,
    georeferences_facet,
    loan_facet,
    loaned_facet,
    never_loaned_facet,
    on_loan_facet,
    otu_id_facet,
    preparation_type_facet,
    repository_facet,
    sled_image_facet,
    taxon_determinations_facet,
    taxon_name_id_facet,
    type_by_taxon_name_facet,
    type_material_facet,
    type_material_type_facet,
    with_buffered_collecting_event_facet,
    with_buffered_determinations_facet,
    with_buffered_other_labels_facet,
  ]
end

#never_loaned_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 688

def never_loaned_facet
  return nil unless never_loaned
  ::CollectionObject.never_loaned
end

#observation_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 1002

def observation_query_facet
  return nil if observation_query.nil?

  s = 'WITH query_obs_co AS (' + observation_query.all.to_sql + ') ' +
    ::CollectionObject
    .joins(:observations)
    .joins('JOIN query_obs_co as query_obs_co1 on observations.id = query_obs_co1.id')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#on_loan_facet ⇒ Object

TODO: change to not/on



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# File 'lib/queries/collection_object/filter.rb', line 694

def on_loan_facet
  return nil unless on_loan
  ::CollectionObject.on_loan
end

#otu_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 769

def otu_id_facet
  return nil if otu_id.empty?

  w = taxon_determination_table[:taxon_determination_object_id].eq(table[:id])
    .and(taxon_determination_table[:otu_id].in(otu_id))
    .and(taxon_determination_table[:taxon_determination_object_type].eq('CollectionObject'))

  if current_determinations
    w = w.and(taxon_determination_table[:position].eq(1))
  elsif current_determinations == false
    w = w.and(taxon_determination_table[:position].gt(1))
  end

  ::CollectionObject.where(
    ::TaxonDetermination.where(w).arel.exists
  )
end

#otu_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 923

def otu_query_facet
  return nil if otu_query.nil?
  s = 'WITH query_otu_co AS (' + otu_query.all.select(:id).to_sql + ') ' +
    ::CollectionObject
    .joins(:taxon_determinations)
    .joins('JOIN query_otu_co as query_otu_co1 on query_otu_co1.id = taxon_determinations.otu_id')
    .where(taxon_determinations: { position: 1 })
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#otu_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/collection_object/filter.rb', line 416

def otu_table
  ::Otu.arel_table
end

#preparation_type_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 599

def preparation_type_facet
  return nil if preparation_type.nil?
  if preparation_type
    ::CollectionObject.where.not(preparation_type_id: nil)
  else
    ::CollectionObject.where(preparation_type_id: nil)
  end
end

#preparation_type_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 721

def preparation_type_id_facet
  return nil if preparation_type_id.empty?
  table[:preparation_type_id].in(preparation_type_id)
end

#repository_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 581

def repository_facet
  return nil if repository.nil?
  if repository
    ::CollectionObject.where.not(repository_id: nil)
  else
    ::CollectionObject.where(repository_id: nil)
  end
end

#repository_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 726

def repository_id_facet
  return nil if repository_id.blank?
  table[:repository_id].in(repository_id)
end

#sled_image_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 673

def sled_image_facet
  return nil if sled_image_id.nil?
  ::CollectionObject::BiologicalCollectionObject.joins(:depictions).where('depictions.sled_image_id = ?', sled_image_id)
end

#taxon_determination_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/collection_object/filter.rb', line 426

def taxon_determination_table
  ::TaxonDetermination.arel_table
end

#taxon_determinations_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 500

def taxon_determinations_facet
  return nil if taxon_determinations.nil?

  if taxon_determinations
    ::CollectionObject.joins(:taxon_determinations).distinct
  else
    ::CollectionObject.where.missing(:taxon_determinations)
  end
end

#taxon_name_id_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 787

def taxon_name_id_facet
  return nil if taxon_name_id.empty?

  q = nil
  z = nil

  if descendants
    h = Arel::Table.new(:taxon_name_hierarchies)
    t = ::TaxonName.arel_table

    q = table.join(taxon_determination_table, Arel::Nodes::InnerJoin).on(
      table[:id].eq(taxon_determination_table[:taxon_determination_object_id])
      .and(taxon_determination_table[:taxon_determination_object_type]).eq('CollectionObject')
    ).join(otu_table, Arel::Nodes::InnerJoin).on(
      taxon_determination_table[:otu_id].eq(otu_table[:id])
    ).join(t, Arel::Nodes::InnerJoin).on(
      otu_table[:taxon_name_id].eq(t[:id])
    ).join(h, Arel::Nodes::InnerJoin).on(
      t[:id].eq(h[:descendant_id])
    )
    z = h[:ancestor_id].in(taxon_name_id)

    if validity == true
      z = z.and(t[:cached_valid_taxon_name_id].eq(t[:id]))
    elsif validity == false
      z = z.and(t[:cached_valid_taxon_name_id].not_eq(t[:id]))
    end

    if taxon_name_current_determination == true
      z = z.and(taxon_determination_table[:position].eq(1))
    elsif taxon_name_current_determination == false
      z = z.and(taxon_determination_table[:position].gt(1))
    end
  else
    q = ::CollectionObject.joins(taxon_determinations: [:otu])
      .where(otus: { taxon_name_id: })

    if taxon_name_current_determination == true
      q = q.where(taxon_determinations: { position: 1 })
    elsif taxon_name_current_determination == false
      q = q.where.not(taxon_determinations: {position: 1})
    end

    return q
  end

  ::CollectionObject.joins(q.join_sources).where(z).distinct
end

#taxon_name_query_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 880

def taxon_name_query_facet
  return nil if taxon_name_query.nil?
  s = 'WITH query_tn_co AS (' + taxon_name_query.all.unscope(:select).select(:id).to_sql + ') ' +
    ::CollectionObject
    .joins(:taxon_names)
    .joins('JOIN query_tn_co as query_tn_co1 on query_tn_co1.id = taxon_names.id')
    .to_sql

  ::CollectionObject.from('(' + s + ') as collection_objects').distinct
end

#type_by_taxon_name_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 736

def type_by_taxon_name_facet
  return nil if type_specimen_taxon_name_id.nil?

  w = type_materials_table[:collection_object_id].eq(table[:id])
    .and(type_materials_table[:protonym_id].eq(type_specimen_taxon_name_id))

  ::CollectionObject.where(
    ::TypeMaterial.where(w).arel.exists
  )
end

#type_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 668

def type_facet
  return nil if collection_object_type.nil?
  table[:type].eq(collection_object_type)
end

#type_material_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 758

def type_material_facet
  return nil if type_material.nil?
  if type_material
    ::CollectionObject.joins(:type_materials).distinct
  else
    ::CollectionObject.left_outer_joins(:type_materials)
      .where(type_materials: { id: nil })
      .distinct
  end
end

#type_material_type_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 747

def type_material_type_facet
  return nil if is_type.empty?

  w = type_materials_table[:collection_object_id].eq(table[:id])
    .and(type_materials_table[:type_type].in(is_type))

  ::CollectionObject.where(
    ::TypeMaterial.where(w).arel.exists
  )
end

#type_materials_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/collection_object/filter.rb', line 421

def type_materials_table
  ::TypeMaterial.arel_table
end

#with_buffered_collecting_event_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 617

def with_buffered_collecting_event_facet
  return nil if with_buffered_collecting_event.nil?
  if with_buffered_collecting_event
    ::CollectionObject.where.not(buffered_collecting_event: nil)
  else
    ::CollectionObject.where(buffered_collecting_event: nil)
  end
end

#with_buffered_determinations_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 635

def with_buffered_determinations_facet
  return nil if with_buffered_determinations.nil?
  if with_buffered_determinations
    ::CollectionObject.where.not(buffered_determinations: nil)
  else
    ::CollectionObject.where(buffered_determinations: nil)
  end
end

#with_buffered_other_labels_facet ⇒ Object 



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# File 'lib/queries/collection_object/filter.rb', line 626

def with_buffered_other_labels_facet
  return nil if with_buffered_other_labels.nil?
  if with_buffered_other_labels
    ::CollectionObject.where.not(buffered_other_labels: nil)
  else
    ::CollectionObject.where(buffered_other_labels: nil)
  end
end