Class: Queries::TaxonName::Filter
- Inherits:
-
Query::Filter
- Object
- Query
- Query::Filter
- Queries::TaxonName::Filter
- Includes:
- Concerns::Citations, Concerns::Confidences, Concerns::DataAttributes, Concerns::Depictions, Concerns::Notes, Concerns::Tags, Helpers
- Defined in:
- lib/queries/taxon_name/filter.rb
Constant Summary collapse
- PARAMS =
[ :ancestors, :ancestrify, :author, :author_exact, :authors, :collecting_event_id, :collection_object_id, :combinations, :combinationify, :descendants, :descendants_max_depth, :epithet_only, :etymology, :latinized, :leaves, :name, :name_exact, :nomenclature_code, :nomenclature_date, :nomenclature_group, # !! different than autocomplete :not_specified, :original_combination, :otu_id, :otus, :rank, :relation_to_relationship, :sort, :synonymify, :taxon_name_author_id_or, :taxon_name_id, :taxon_name_type, :type_metadata, :validify, :validity, :verbatim_name, :year, :year_end, :year_start, collection_object_id: [], collecting_event_id: [], combination_taxon_name_id: [], name: [], otu_id: [], parent_id: [], rank: [], taxon_name_author_id: [], taxon_name_classification: [], taxon_name_id: [], taxon_name_relationship: [ :subject_taxon_name_id, :object_taxon_name_id, :type, ], taxon_name_relationship_type_subject: [], taxon_name_relationship_type_object: [], taxon_name_relationship_type_either: [], type: [], ].freeze
Constants inherited from Query::Filter
Query::Filter::FILTER_QUERIES, Query::Filter::SUBQUERIES
Instance Attribute Summary collapse
-
#ancestors ⇒ Object
Boolean Ignored when taxon_name_id[].empty? Works as AND clause with descendants :(.
-
#ancestrify ⇒ Object
!! This parameter is not like the others, it is applied POST result, see also synonymify and validify, etc.
- #author ⇒ Object
-
#author_exact ⇒ Object
Boolean.
-
#authors ⇒ Object
- ‘true’ or ‘false’
-
on initialize whether the name has an author string, from any source, provided.
-
#collecting_event_id ⇒ Object
Array.
-
#collection_object_id ⇒ Object
Array.
-
#combination_taxon_name_id ⇒ Array
Taxon_name_ids for which all Combinations will be returned.
-
#combinationify ⇒ Object
!! This parameter is not like the others, it is applied POST result, see also synonymify and validify.
-
#combinations ⇒ Object
This parameter should be used along side species or genus group limits.
-
#descendants ⇒ Boolean
True - only descendants NOT SELF false - self AND descendants nil - ignored Ignored when taxon_name_id[].empty?.
-
#descendants_max_depth ⇒ Integer?
A positive integer indicating how many levels deep of descendants to retrieve.
- #epithet_only ⇒ Object
-
#etymology ⇒ Object
- ‘true’ or ‘false’
-
on initialize whether the name has etymology.
-
#geo_json ⇒ Object
Returns the value of attribute geo_json.
-
#latinized ⇒ Boolean?
&latinized=<“true”|“false”> if ‘true’ then return only genus group names with gender and species group names with part of speech if ‘false’ then return only genus group names without gender and species group names without part of speech if nil, ignore.
-
#leaves ⇒ Boolean?
TODO: inverse is duplicated in autocomplete.
-
#name ⇒ Array
Matches against cached.
-
#name_exact ⇒ Object
Boolean.
-
#nomenclature_code ⇒ String?
Accessor for attr :nomenclature_code, wrap with needed wildcards.
-
#nomenclature_date ⇒ Object
Boolean with/out cached nomenclature date set.
-
#nomenclature_group ⇒ String?
Accessor for attr :nomenclature_group, wrap with needed wildcards.
-
#not_specified ⇒ Object
Returns the value of attribute not_specified.
-
#original_combination ⇒ Boolean?
True - name has at least one element of original combination false - name has no element of original combination nil - ignored.
-
#otu_id ⇒ Array?
One or more OTU ids.
-
#otus ⇒ Object
- ‘true’ or ‘false’
-
on initialize whether the name has an Otu.
-
#parent_id ⇒ Object
Return the taxon names with this/these parent_ids.
- #rank ⇒ Array
-
#relation_to_relationship ⇒ String?
&relation_to_relationship=<subject|object|either> All names that are subject|object|either of any relationship.
- #sort ⇒ String?
-
#synonymify ⇒ Object
!! This parameter is not like the others, it is applied POST result, see also combinationify and validify.
- #taxon_name_author_id ⇒ Array
- #taxon_name_author_id_or ⇒ Boolean
- #taxon_name_classification ⇒ Object
-
#taxon_name_id ⇒ Object
Return the taxon name(s) with this/these ids.
-
#taxon_name_relationship ⇒ Object
Each entry must have a ‘type’ Each entry must have one (and only one) of ‘subject_taxon_name_id’ or ‘object_taxon_name_id’.
- #taxon_name_relationship_type_either ⇒ Object
- #taxon_name_relationship_type_object ⇒ Object
- #taxon_name_relationship_type_subject ⇒ Object
-
#taxon_name_type ⇒ String?
&taxon_name_type=<Protonym|Combination|Hybrid>.
-
#type_metadata ⇒ Object
- ‘true’ or ‘false’
-
on initialize whether the name has TypeMaterial.
-
#validify ⇒ Object
name is returned !! This param is not like the others.
-
#validity ⇒ Object
- ‘true’ or ‘false’
-
on initialize true if only valid, false if only invalid, nil if both.
-
#verbatim_name ⇒ Object
Boolean if true then ‘verbatim_name` is populated.
-
#year ⇒ Object
Matches against cached_author_year.
-
#year_end ⇒ Object
Matches against cached_nomenclature_date.
-
#year_start ⇒ Object
Matches against cached_nomenclature_date.
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, #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, #taxon_name_query, #venn, #venn_mode
Attributes inherited from Query
Instance Method Summary collapse
- #all(nil_empty = false) ⇒ ActiveRecord::Relation
-
#ancestor_facet ⇒ Object
A merge facet.
- #ancestrify_result(q) ⇒ Object
- #and_clauses ⇒ ActiveRecord::Relation
- #asserted_distribution_query_facet ⇒ Object
- #author_facet ⇒ Object
-
#authors_facet ⇒ Object
This is not true! It includes records that are year only.
- #biological_association_query_facet ⇒ Object
- #collecting_event_id_facet ⇒ Object
- #collecting_event_query_facet ⇒ Object
- #collection_object_id_facet ⇒ Object
- #collection_object_query_facet ⇒ Object
- #combination_taxon_name_id_facet ⇒ Object
- #combinationify_result(q) ⇒ Object
- #combinations_facet ⇒ Object
-
#descendant_facet ⇒ Object
Scope match only names that are a descendant of some taxon_name_id.
- #geo_json_facet ⇒ Object
-
#initialize(query_params) ⇒ Filter
constructor
A new instance of Filter.
-
#latinized_facet ⇒ Object
Scope.
-
#leaves_facet ⇒ Object
Scope.
- #merge_clauses ⇒ Object
-
#model_id_facet ⇒ Object
Overrides base class.
- #name_facet ⇒ Object
- #nomenclature_date_facet ⇒ Object
- #not_specified_facet ⇒ Object
- #order_clause(query) ⇒ Object
- #original_combination_facet ⇒ Object
- #otu_id_facet ⇒ Object
- #otu_query_facet ⇒ Object
-
#otus_facet ⇒ Object
Scope.
- #parent_id_facet ⇒ Object
- #rank_facet ⇒ Arel::Nodes::Grouping?
-
#relation_to_relationship_facet ⇒ Object
Scope.
- #synonimify_result(q) ⇒ Object
- #taxon_name_author_id_facet ⇒ Object
-
#taxon_name_classification_facet ⇒ Object
Scope.
-
#taxon_name_relationship_facet(hsh) ⇒ Object
Scope wrapped in descendant_facet!.
-
#taxon_name_relationship_type_facet ⇒ Object
Scope.
- #taxon_name_type_facet ⇒ Object
-
#type_metadata_facet ⇒ Object
Scope.
- #validify_result(q) ⇒ Object
- #validity_facet ⇒ Object
- #verbatim_name_facet ⇒ Object
-
#with_etymology_facet ⇒ Object
Scope.
- #with_nomenclature_code ⇒ Arel::Nodes::Grouping?
- #with_nomenclature_group ⇒ Arel::Nodes::Grouping?
- #year_facet ⇒ Object
- #year_range_facet ⇒ Object
Methods included from Helpers
#boolean_param, #integer_param
Methods inherited from Query::Filter
#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, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #object_global_id_facet, #only_project?, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #query_name, #set_nested_queries, #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/taxon_name/filter.rb', line 328 def initialize(query_params) super @ancestors = boolean_param(params, :ancestors) @ancestrify = boolean_param(params, :ancestrify) @author = params[:author] @author_exact = boolean_param(params, :author_exact) @authors = boolean_param(params, :authors) @collecting_event_id = params[:collecting_event_id] @collection_object_id = params[:collection_object_id] @combination_taxon_name_id = params[:combination_taxon_name_id] @combinations = boolean_param(params, :combinations) @combinationify = boolean_param(params, :combinationify) @descendants = boolean_param(params, :descendants) @descendants_max_depth = params[:descendants_max_depth] @etymology = boolean_param(params, :etymology) @epithet_only = params[:epithet_only] @latinized = boolean_param(params, :latinized) @geo_json = params[:geo_json] @leaves = boolean_param(params, :leaves) @name = params[:name] @name_exact = boolean_param(params, :name_exact) @nomenclature_date = boolean_param(params, :nomenclature_date) @nomenclature_code = params[:nomenclature_code] if params[:nomenclature_code].present? @nomenclature_group = params[:nomenclature_group] if params[:nomenclature_group].present? @not_specified = boolean_param(params, :not_specified) @otu_id = params[:otu_id] @otus = boolean_param(params, :otus) @original_combination = boolean_param(params, :original_combination) @parent_id = params[:parent_id] @rank = params[:rank] @relation_to_relationship = params[:relation_to_relationship] @sort = params[:sort] @synonymify = boolean_param(params, :synonymify) @taxon_name_author_id = params[:taxon_name_author_id] @taxon_name_author_id_or = boolean_param(params, :taxon_name_author_id_or) @taxon_name_classification = params[:taxon_name_classification] || [] @taxon_name_id = params[:taxon_name_id] @taxon_name_relationship = params[:taxon_name_relationship] || [] @taxon_name_relationship_type_subject = params[:taxon_name_relationship_type_subject] || [] @taxon_name_relationship_type_object = params[:taxon_name_relationship_type_object] || [] @taxon_name_relationship_type_either = params[:taxon_name_relationship_type_either] || [] @taxon_name_type = params[:taxon_name_type] @type_metadata = boolean_param(params, :type_metadata) @validify = boolean_param(params, :validify) @validity = boolean_param(params, :validity) @verbatim_name = boolean_param(params, :verbatim_name) @year = params[:year] @year_end = params[:year_end] @year_start = params[:year_start] set_confidences_params(params) set_citations_params(params) set_depiction_params(params) set_notes_params(params) set_data_attributes_params(params) (params) end |
Instance Attribute Details
#ancestors ⇒ Object
Returns Boolean Ignored when taxon_name_id[].empty? Works as AND clause with descendants :(.
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# File 'lib/queries/taxon_name/filter.rb', line 77 def ancestors @ancestors end |
#ancestrify ⇒ Object
!! This parameter is not like the others, it is applied POST result, see also synonymify and validify, etc.
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# File 'lib/queries/taxon_name/filter.rb', line 83 def ancestrify @ancestrify end |
#author ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 125 def @author end |
#author_exact ⇒ Object
Returns Boolean.
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# File 'lib/queries/taxon_name/filter.rb', line 128 def @author_exact end |
#authors ⇒ Object
- ‘true’ or ‘false’
-
on initialize
whether the name has an author string, from any source, provided
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# File 'lib/queries/taxon_name/filter.rb', line 256 def @authors end |
#collecting_event_id ⇒ Object
Returns Array.
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# File 'lib/queries/taxon_name/filter.rb', line 113 def collecting_event_id @collecting_event_id end |
#collection_object_id ⇒ Object
Returns Array.
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# File 'lib/queries/taxon_name/filter.rb', line 92 def collection_object_id @collection_object_id end |
#combination_taxon_name_id ⇒ Array
Returns taxon_name_ids for which all Combinations will be returned.
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# File 'lib/queries/taxon_name/filter.rb', line 315 def combination_taxon_name_id @combination_taxon_name_id end |
#combinationify ⇒ Object
!! This parameter is not like the others, it is applied POST result, see also synonymify and validify
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# File 'lib/queries/taxon_name/filter.rb', line 105 def combinationify @combinationify end |
#combinations ⇒ Object
This parameter should be used along side species or genus group limits.
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# File 'lib/queries/taxon_name/filter.rb', line 99 def combinations @combinations end |
#descendants ⇒ Boolean
Returns true - only descendants NOT SELF false - self AND descendants nil - ignored Ignored when taxon_name_id[].empty?.
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# File 'lib/queries/taxon_name/filter.rb', line 186 def descendants @descendants end |
#descendants_max_depth ⇒ Integer?
A positive integer indicating how many levels deep of descendants to retrieve.
Ignored when descentants is false/unspecified.
Defaults to nil
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# File 'lib/queries/taxon_name/filter.rb', line 193 def descendants_max_depth @descendants_max_depth end |
#epithet_only ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 88 def epithet_only @epithet_only end |
#etymology ⇒ Object
- ‘true’ or ‘false’
-
on initialize
whether the name has etymology
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# File 'lib/queries/taxon_name/filter.rb', line 251 def etymology @etymology end |
#geo_json ⇒ Object
Returns the value of attribute geo_json.
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# File 'lib/queries/taxon_name/filter.rb', line 324 def geo_json @geo_json end |
#latinized ⇒ Boolean?
Returns &latinized=<“true”|“false”> if ‘true’ then return only genus group names with gender and species
group names with part of speech
if ‘false’ then return only genus group names without gender and
species group names without part of speech
if nil, ignore.
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# File 'lib/queries/taxon_name/filter.rb', line 293 def latinized @latinized end |
#leaves ⇒ Boolean?
TODO: inverse is duplicated in autocomplete
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# File 'lib/queries/taxon_name/filter.rb', line 284 def leaves @leaves end |
#name ⇒ Array
Returns Matches against cached. See also name_exact.
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# File 'lib/queries/taxon_name/filter.rb', line 118 def name @name end |
#name_exact ⇒ Object
Returns Boolean.
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# File 'lib/queries/taxon_name/filter.rb', line 121 def name_exact @name_exact end |
#nomenclature_code ⇒ String?
Returns accessor for attr :nomenclature_code, wrap with needed wildcards.
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# File 'lib/queries/taxon_name/filter.rb', line 277 def nomenclature_code @nomenclature_code end |
#nomenclature_date ⇒ Object
Returns Boolean with/out cached nomenclature date set.
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# File 'lib/queries/taxon_name/filter.rb', line 138 def nomenclature_date @nomenclature_date end |
#nomenclature_group ⇒ String?
Returns accessor for attr :nomenclature_group, wrap with needed wildcards.
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# File 'lib/queries/taxon_name/filter.rb', line 273 def nomenclature_group @nomenclature_group end |
#not_specified ⇒ Object
Returns the value of attribute not_specified.
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# File 'lib/queries/taxon_name/filter.rb', line 268 def not_specified @not_specified end |
#original_combination ⇒ Boolean?
Returns true - name has at least one element of original combination false - name has no element of original combination nil - ignored.
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# File 'lib/queries/taxon_name/filter.rb', line 236 def original_combination @original_combination end |
#otu_id ⇒ Array?
Returns one or more OTU ids.
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# File 'lib/queries/taxon_name/filter.rb', line 241 def otu_id @otu_id end |
#otus ⇒ Object
- ‘true’ or ‘false’
-
on initialize
whether the name has an Otu
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# File 'lib/queries/taxon_name/filter.rb', line 246 def otus @otus end |
#parent_id ⇒ Object
Return the taxon names with this/these parent_ids
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# File 'lib/queries/taxon_name/filter.rb', line 177 def parent_id @parent_id end |
#rank ⇒ Array
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# File 'lib/queries/taxon_name/filter.rb', line 322 def rank @rank end |
#relation_to_relationship ⇒ String?
Returns &relation_to_relationship=<subject|object|either> All names that are subject|object|either of any relationship.
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# File 'lib/queries/taxon_name/filter.rb', line 225 def relation_to_relationship @relation_to_relationship end |
#sort ⇒ String?
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# File 'lib/queries/taxon_name/filter.rb', line 311 def sort @sort end |
#synonymify ⇒ Object
!! This parameter is not like the others, it is applied POST result, see also combinationify and validify
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# File 'lib/queries/taxon_name/filter.rb', line 199 def synonymify @synonymify end |
#taxon_name_author_id ⇒ Array
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# File 'lib/queries/taxon_name/filter.rb', line 300 def @taxon_name_author_id end |
#taxon_name_author_id_or ⇒ Boolean
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# File 'lib/queries/taxon_name/filter.rb', line 306 def @taxon_name_author_id_or end |
#taxon_name_classification ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 229 def taxon_name_classification @taxon_name_classification end |
#taxon_name_id ⇒ Object
Return the taxon name(s) with this/these ids
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# File 'lib/queries/taxon_name/filter.rb', line 171 def taxon_name_id @taxon_name_id end |
#taxon_name_relationship ⇒ Object
Each entry must have a ‘type’ Each entry must have one (and only one) of ‘subject_taxon_name_id’ or ‘object_taxon_name_id’
Return all taxon names in a relationship of a given type and in relation to a another name. For example, return all synonyms of Aus bus.
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# File 'lib/queries/taxon_name/filter.rb', line 207 def taxon_name_relationship @taxon_name_relationship end |
#taxon_name_relationship_type_either ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 220 def taxon_name_relationship_type_either @taxon_name_relationship_type_either end |
#taxon_name_relationship_type_object ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 215 def taxon_name_relationship_type_object @taxon_name_relationship_type_object end |
#taxon_name_relationship_type_subject ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 211 def taxon_name_relationship_type_subject @taxon_name_relationship_type_subject end |
#taxon_name_type ⇒ String?
Returns &taxon_name_type=<Protonym|Combination|Hybrid>.
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# File 'lib/queries/taxon_name/filter.rb', line 297 def taxon_name_type @taxon_name_type end |
#type_metadata ⇒ Object
- ‘true’ or ‘false’
-
on initialize
whether the name has TypeMaterial
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# File 'lib/queries/taxon_name/filter.rb', line 261 def @type_metadata end |
#validify ⇒ Object
name is returned !! This param is not like the others. !!
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# File 'lib/queries/taxon_name/filter.rb', line 160 def validify @validify end |
#validity ⇒ Object
- ‘true’ or ‘false’
-
on initialize
true if only valid, false if only invalid, nil if both
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# File 'lib/queries/taxon_name/filter.rb', line 153 def validity @validity end |
#verbatim_name ⇒ Object
Returns Boolean if true then ‘verbatim_name` is populated.
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# File 'lib/queries/taxon_name/filter.rb', line 165 def verbatim_name @verbatim_name end |
#year ⇒ Object
Matches against cached_author_year.
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# File 'lib/queries/taxon_name/filter.rb', line 133 def year @year end |
#year_end ⇒ Object
Matches against cached_nomenclature_date
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# File 'lib/queries/taxon_name/filter.rb', line 148 def year_end @year_end end |
#year_start ⇒ Object
Matches against cached_nomenclature_date
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# File 'lib/queries/taxon_name/filter.rb', line 143 def year_start @year_start end |
Instance Method Details
#all(nil_empty = false) ⇒ ActiveRecord::Relation
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# File 'lib/queries/taxon_name/filter.rb', line 1050 def all(nil_empty = false) q = super # Order matters, use this first to go up q = ancestrify_result(q) if ancestrify # Then out in various ways q = validify_result(q) if validify q = combinationify_result(q) if combinationify q = synonimify_result(q) if synonymify # Then sort q = order_clause(q) if sort q end |
#ancestor_facet ⇒ Object
A merge facet.
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# File 'lib/queries/taxon_name/filter.rb', line 543 def ancestor_facet return nil if taxon_name_id.empty? || !(ancestors == true) ancestors_subquery = ::TaxonNameHierarchy.where( ::TaxonNameHierarchy.arel_table[:ancestor_id].eq(::TaxonName.arel_table[:id]).and( ::TaxonNameHierarchy.arel_table[:descendant_id].in(taxon_name_id) ) ) ::TaxonName.where(ancestors_subquery.arel.exists) end |
#ancestrify_result(q) ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 1019 def ancestrify_result(q) s = 'WITH tn_result_query_anc AS (' + q.to_sql + ') ' + ::TaxonName .joins('JOIN taxon_name_hierarchies tnh on tnh.ancestor_id = taxon_names.id') .joins('JOIN tn_result_query_anc as tn_result_query_anc1 on tn_result_query_anc1.id = tnh.descendant_id') .distinct .to_sql # !! Do not use .distinct here ::TaxonName.from('(' + s + ') as taxon_names') end |
#and_clauses ⇒ ActiveRecord::Relation
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# File 'lib/queries/taxon_name/filter.rb', line 928 def and_clauses [ nomenclature_date_facet, , name_facet, parent_id_facet, rank_facet, taxon_name_type_facet, validity_facet, verbatim_name_facet, with_nomenclature_code, with_nomenclature_group, year_facet, ] end |
#asserted_distribution_query_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 877 def asserted_distribution_query_facet return nil if asserted_distribution_query.nil? s = 'WITH query_ad_tn AS (' + asserted_distribution_query.all.to_sql + ') ' + ::TaxonName .joins(otus: [:asserted_distributions]) .joins('JOIN query_ad_tn as query_ad_tn1 on query_ad_tn1.otu_id = asserted_distributions.otu_id') .to_sql ::TaxonName.from('(' + s + ') as taxon_names').distinct end |
#author_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 797 def return nil if .blank? if table[:cached_author_year].eq(.strip) else table[:cached_author_year].matches('%' + .strip.gsub(/\s/, '%') + '%') end end |
#authors_facet ⇒ Object
This is not true! It includes records that are year only.
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# File 'lib/queries/taxon_name/filter.rb', line 573 def return nil if .nil? ? ::TaxonName.where.not(cached_author_year: nil) : ::TaxonName.where(cached_author_year: nil) end |
#biological_association_query_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 910 def biological_association_query_facet return nil if biological_association_query.nil? s = 'WITH query_tn_ba AS (' + biological_association_query.all.to_sql + ') ' a = ::TaxonName .joins(:otus) .joins("JOIN query_tn_ba as query_tn_ba1 on query_tn_ba1.biological_association_subject_id = otus.id AND query_tn_ba1.biological_association_subject_type = 'Otu'").to_sql b = ::TaxonName .joins(:otus) .joins("JOIN query_tn_ba as query_tn_ba2 on query_tn_ba2.biological_association_object_id = otus.id AND query_tn_ba2.biological_association_object_type = 'Otu'").to_sql s << ::TaxonName.from("((#{a}) UNION (#{b})) as taxon_names").to_sql ::TaxonName.from('(' + s + ') as taxon_names') end |
#collecting_event_id_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 849 def collecting_event_id_facet return nil if collecting_event_id.empty? ::TaxonName .joins(:collection_objects) .where(collection_objects: { collecting_event_id: }) end |
#collecting_event_query_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 899 def collecting_event_query_facet return nil if collecting_event_query.nil? s = 'WITH query_ce_tns AS (' + collecting_event_query.all.to_sql + ') ' + ::TaxonName .joins(:collection_objects) .joins('JOIN query_ce_tns as query_ce_tns1 on collection_objects.collecting_event_id = query_ce_tns1.id') .to_sql ::TaxonName.from('(' + s + ') as taxon_names').distinct end |
#collection_object_id_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 555 def collection_object_id_facet return nil if collection_object_id.empty? ::TaxonName.joins(:collection_objects).where(collection_objects: { id: collection_object_id }) end |
#collection_object_query_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 888 def collection_object_query_facet return nil if collection_object_query.nil? s = 'WITH query_collection_objects AS (' + collection_object_query.all.to_sql + ') ' + ::TaxonName .joins(:collection_objects) .joins('JOIN query_collection_objects as query_collection_objects1 on collection_objects.id = query_collection_objects1.id') .to_sql ::TaxonName.from('(' + s + ') as taxon_names').distinct end |
#combination_taxon_name_id_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 838 def combination_taxon_name_id_facet return nil if combination_taxon_name_id.empty? ::Combination.joins(:related_taxon_name_relationships) .where( taxon_name_relationships: { type: ::TAXON_NAME_RELATIONSHIP_COMBINATION_TYPES.values, subject_taxon_name_id: combination_taxon_name_id, }, ).distinct end |
#combinationify_result(q) ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 1007 def combinationify_result(q) s = 'WITH tn_result_query AS (' + q.to_sql + ') ' + ::TaxonName .joins('JOIN tn_result_query as tn_result_query3 on tn_result_query3.id = taxon_names.cached_valid_taxon_name_id') .where("taxon_names.type = 'Combination'") .to_sql a = ::TaxonName.from('(' + s + ') as taxon_names').distinct referenced_klass_union([q, a]) end |
#combinations_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 856 def combinations_facet return nil if combinations.nil? a = ::Protonym.joins(:combination_relationships) if combinations a else referenced_klass_except(a) end end |
#descendant_facet ⇒ Object
Returns Scope match only names that are a descendant of some taxon_name_id.
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# File 'lib/queries/taxon_name/filter.rb', line 513 def descendant_facet return nil if taxon_name_id.empty? || descendants.nil? h = ::TaxonNameHierarchy.arel_table if descendants descendants_subquery = ::TaxonNameHierarchy.where( h[:descendant_id].eq(::TaxonName.arel_table[:id]).and( h[:ancestor_id].in(taxon_name_id) ) ).where(h[:ancestor_id].not_eq(h[:descendant_id])) if descendants_max_depth.present? descendants_subquery = descendants_subquery.where(::TaxonNameHierarchy.arel_table[:generations].lteq(descendants_max_depth.to_i)) end ::TaxonName.where(descendants_subquery.arel.exists) else q = ::TaxonName.joins('JOIN taxon_name_hierarchies ON taxon_name_hierarchies.descendant_id = taxon_names.id') .where(taxon_name_hierarchies: {ancestor_id: taxon_name_id}) if descendants_max_depth.present? q = q.where(::TaxonNameHierarchy.arel_table[:generations].lteq(descendants_max_depth.to_i)) end q end end |
#geo_json_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 469 def geo_json_facet return nil if geo_json.nil? otus = ::Queries::Otu::Filter.new(geo_json:).all collection_objects = ::Queries::CollectionObject::Filter.new(geo_json:).all a = ::TaxonName.joins(:taxon_taxon_determinations).where(taxon_determinations: { taxon_determination_object: collection_objects }) b = ::TaxonName.joins(:otus).where(otus:) ::TaxonName.from("((#{a.to_sql}) UNION (#{b.to_sql})) as taxon_names") end |
#latinized_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 628 def latinized_facet return nil if latinized.nil? tnc = ::TaxonNameClassification.arel_table if latinized == true # Note the query here does not restrict to genus/species groups - a # genus whose rank is changed to subfamily can retain its gender, # e.g., and we want to include those here. ::TaxonName.where( ::TaxonNameClassification.where( tnc[:taxon_name_id].eq(table[:id]).and( tnc[:type].in(LATINIZED_TAXON_NAME_CLASSIFICATION_NAMES) ) ).arel.exists ) else ::TaxonName .where( table[:rank_class].in(GENUS_AND_SPECIES_RANK_NAMES) ) .where.not( ::TaxonNameClassification.where( tnc[:taxon_name_id].eq(table[:id]).and( tnc[:type].in(LATINIZED_TAXON_NAME_CLASSIFICATION_NAMES) ) ).arel.exists ) end end |
#leaves_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 622 def leaves_facet return nil if leaves.nil? leaves ? ::TaxonName.leaves : ::TaxonName.not_leaves end |
#merge_clauses ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 944 def merge_clauses clauses = [ asserted_distribution_query_facet, biological_association_query_facet, collecting_event_query_facet, collection_object_query_facet, otu_query_facet, ancestor_facet, , collecting_event_id_facet, collection_object_id_facet, combination_taxon_name_id_facet, combinations_facet, descendant_facet, latinized_facet, leaves_facet, not_specified_facet, original_combination_facet, otu_id_facet, otus_facet, relation_to_relationship_facet, , taxon_name_classification_facet, taxon_name_relationship_type_facet, , with_etymology_facet, year_range_facet, ] taxon_name_relationship.each do |hsh| clauses << taxon_name_relationship_facet(hsh) end clauses.compact end |
#model_id_facet ⇒ Object
Overrides base class
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# File 'lib/queries/taxon_name/filter.rb', line 982 def model_id_facet return nil if taxon_name_id.empty? || !descendants.nil? || ancestors table[:id].in(taxon_name_id) end |
#name_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 774 def name_facet return nil if name.empty? if name_exact if (epithet_only) table[:name].in(name) else table[:cached].in(name).or(table[:cached_original_combination].in(name)) end # table[:cached].eq(name.strip).or(table[:cached_original_combination].eq(name.strip)) else if (epithet_only) table[:name].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' }) else table[:cached].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' }).or(table[:cached_original_combination].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' })) end end end |
#nomenclature_date_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 502 def nomenclature_date_facet return nil if nomenclature_date.nil? if nomenclature_date table[:cached_nomenclature_date].not_eq(nil) else table[:cached_nomenclature_date].eq(nil) end end |
#not_specified_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 480 def not_specified_facet return nil if not_specified.nil? if not_specified ::TaxonName.where(table[:cached].matches('%NOT SPECIFIED%').or( table[:cached_original_combination].matches('%NOT SPECIFIED%') )) else ::TaxonName.where(table[:cached].does_not_match('%NOT SPECIFIED%').and( table[:cached_original_combination].does_not_match('%NOT SPECIFIED%') )) end end |
#order_clause(query) ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 1031 def order_clause(query) case sort when 'alphabetical' ::TaxonName.select('*').from( query.order('taxon_names.cached'), :inner_query ) when 'classification' ::TaxonName.select('*').from( query .joins('INNER JOIN taxon_name_hierarchies ON taxon_names.id = taxon_name_hierarchies.descendant_id') .order('taxon_name_hierarchies.generations, taxon_name_hierarchies.ancestor_id, taxon_names.cached'), :inner_query ) else query end end |
#original_combination_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 493 def original_combination_facet return nil if original_combination.nil? if original_combination ::Protonym.joins(:original_combination_relationships).distinct else ::Protonym.left_joins(:original_combination_relationships).where(taxon_name_relationships: {id: nil}) end end |
#otu_id_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 560 def otu_id_facet return nil if otu_id.empty? ::TaxonName.joins(:otus).where(otus: { id: otu_id }) end |
#otu_query_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 866 def otu_query_facet return nil if otu_query.nil? s = 'WITH query_otu_tn AS (' + otu_query.all.to_sql + ') ' + ::TaxonName .joins(:otus) .joins('JOIN query_otu_tn as query_otu_tn1 on otus.id = query_otu_tn1.id') # Don't change, see `validify` .to_sql ::TaxonName.from('(' + s + ') as taxon_names').distinct end |
#otus_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 743 def otus_facet return nil if otus.nil? subquery = ::Otu.where(::Otu.arel_table[:taxon_name_id].eq(::TaxonName.arel_table[:id])).arel.exists ::TaxonName.where(otus ? subquery : subquery.not) end |
#parent_id_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 792 def parent_id_facet return nil if parent_id.empty? table[:parent_id].in(parent_id) end |
#rank_facet ⇒ Arel::Nodes::Grouping?
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# File 'lib/queries/taxon_name/filter.rb', line 756 def rank_facet return nil if rank.blank? # We don't wildcard end so that we can isolate to specific ranks and below r = rank.collect { |i| "%#{i}" } table[:rank_class].matches_any(r) end |
#relation_to_relationship_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 677 def relation_to_relationship_facet return nil if relation_to_relationship.nil? if relation_to_relationship == 'subject' ::TaxonName.with_taxon_name_relationships_as_subject.distinct elsif relation_to_relationship == 'object' ::TaxonName.with_taxon_name_relationships_as_object.distinct else # 3-4x more time-performant than using # :with_taxon_name_relationships.distinct ::TaxonName.joins('join taxon_name_relationships ON ' \ 'taxon_names.id = taxon_name_relationships.subject_taxon_name_id OR ' \ 'taxon_names.id = taxon_name_relationships.object_taxon_name_id' ).distinct end end |
#synonimify_result(q) ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 996 def synonimify_result(q) s = 'WITH tn_result_query AS (' + q.to_sql + ') ' + ::TaxonName .joins('JOIN tn_result_query as tn_result_query2 on tn_result_query2.id = taxon_names.cached_valid_taxon_name_id') .to_sql a = ::TaxonName.from('(' + s + ') as taxon_names').distinct referenced_klass_union([q, a]) end |
#taxon_name_author_id_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 707 def return nil if .empty? o = table r = ::Role.arel_table a = o.alias('a_') b = o.project(a[Arel.star]).from(a) c = r.alias('r1') b = b.join(c, Arel::Nodes::OuterJoin) .on( a[:id].eq(c[:role_object_id]) .and(c[:role_object_type].eq('TaxonName')) .and(c[:type].eq('TaxonNameAuthor')) ) e = c[:id].not_eq(nil) f = c[:person_id].in() b = b.where(e.and(f)) b = b.group(a['id']) b = b.having(a['id'].count.eq(.length)) unless b = b.as('tn_z1_') ::TaxonName.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(o['id'])))) end |
#taxon_name_classification_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 695 def taxon_name_classification_facet return nil if taxon_name_classification.empty? ::TaxonName.where( ::TaxonNameClassification.where( ::TaxonNameClassification.arel_table[:taxon_name_id].eq(::TaxonName.arel_table[:id]).and( ::TaxonNameClassification.arel_table[:type].in(taxon_name_classification) ) ).arel.exists ) end |
#taxon_name_relationship_facet(hsh) ⇒ Object
Returns Scope wrapped in descendant_facet!.
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# File 'lib/queries/taxon_name/filter.rb', line 660 def taxon_name_relationship_facet(hsh) hsh = hsh.symbolize_keys param_key = hsh[:subject_taxon_name_id] ? :subject_taxon_name_id : :object_taxon_name_id join_key = hsh[:subject_taxon_name_id] ? :object_taxon_name_id : :subject_taxon_name_id ::TaxonName.where( ::TaxonNameRelationship.where( ::TaxonNameRelationship.arel_table[join_key].eq(::TaxonName.arel_table[:id]).and( ::TaxonNameRelationship.arel_table[param_key].eq(hsh[param_key]) ).and( ::TaxonNameRelationship.arel_table[:type].eq(hsh[:type]) ) ).arel.exists ) end |
#taxon_name_relationship_type_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 589 def taxon_name_relationship_type_facet if taxon_name_relationship_type_subject.empty? && taxon_name_relationship_type_object.empty? && taxon_name_relationship_type_either.empty? return nil end s = nil o = nil e = nil if taxon_name_relationship_type_subject.present? s = ::TaxonName.as_subject_with_taxon_name_relationship( taxon_name_relationship_type_subject ).distinct end if taxon_name_relationship_type_object.present? o = ::TaxonName.as_object_with_taxon_name_relationship( taxon_name_relationship_type_object ).distinct end if taxon_name_relationship_type_either.present? e = ::TaxonName.with_taxon_name_relationship( taxon_name_relationship_type_either ) end referenced_klass_union([s, o, e]) end |
#taxon_name_type_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 769 def taxon_name_type_facet return nil if taxon_name_type.blank? table[:type].eq(taxon_name_type) end |
#type_metadata_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 736 def return nil if .nil? subquery = ::TypeMaterial.where(::TypeMaterial.arel_table[:protonym_id].eq(::TaxonName.arel_table[:id])).arel.exists ::TaxonName.where( ? subquery : subquery.not) end |
#validify_result(q) ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 987 def validify_result(q) s = 'WITH tn_result_query AS (' + q.to_sql + ') ' + ::TaxonName .joins('JOIN tn_result_query as tn_result_query1 on tn_result_query1.cached_valid_taxon_name_id = taxon_names.id') .to_sql ::TaxonName.from('(' + s + ') as taxon_names').distinct end |
#validity_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 820 def validity_facet return nil if validity.nil? if validity table[:cached_is_valid].eq(true) else table[:cached_is_valid].eq(false) end end |
#verbatim_name_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 829 def verbatim_name_facet return nil if verbatim_name.nil? if verbatim_name table[:verbatim_name].not_eq(nil) else table[:verbatim_name].eq(nil) end end |
#with_etymology_facet ⇒ Object
Returns Scope.
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# File 'lib/queries/taxon_name/filter.rb', line 581 def with_etymology_facet return nil if etymology.nil? etymology ? ::TaxonName.where.not(etymology: nil) : ::TaxonName.where(etymology: nil) end |
#with_nomenclature_code ⇒ Arel::Nodes::Grouping?
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# File 'lib/queries/taxon_name/filter.rb', line 764 def with_nomenclature_code return nil if nomenclature_code.nil? table[:rank_class].matches(nomenclature_code) end |
#with_nomenclature_group ⇒ Arel::Nodes::Grouping?
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# File 'lib/queries/taxon_name/filter.rb', line 750 def with_nomenclature_group return nil if nomenclature_group.blank? table[:rank_class].matches(nomenclature_group) end |
#year_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 806 def year_facet return nil if year.blank? s = Date.new(@year.to_i) e = Date.new(@year.to_i, 12, 31) table[:cached_nomenclature_date].between(s..e) end |
#year_range_facet ⇒ Object
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# File 'lib/queries/taxon_name/filter.rb', line 814 def year_range_facet return nil if year_end.nil? && year_start.nil? s, e = [year_start, year_end].compact ::TaxonName.where(cached_nomenclature_date: (s..e)) end |