Class: Queries::Otu::Filter
- Inherits:
-
Query::Filter
show all
- Includes:
- Concerns::Citations, Concerns::DataAttributes, Concerns::Depictions, Concerns::Notes, Concerns::Tags, Helpers
- Defined in:
- lib/queries/otu/filter.rb
Constant Summary
collapse
- PARAMS =
[
:ancestrify,
:asserted_distributions,
:biological_association_id,
:biological_associations,
:collecting_event_id,
:collection_objects,
:contents,
:coordinatify,
:descendants,
:descriptor_id,
:geo_json,
:geographic_area_id,
:geographic_area_mode,
:name,
:name_exact,
:observations,
:otu_id,
:radius,
:taxon_name,
:taxon_name_id,
:with_name,
:wkt,
collecting_event_id: [],
descriptor_id: [],
geographic_area_id: [],
name: [],
otu_id: [],
taxon_name_id: [],
].freeze
Query::Filter::FILTER_QUERIES, Query::Filter::SUBQUERIES
Instance Attribute Summary collapse
#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, #descriptor_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #taxon_name_query, #venn, #venn_mode
Attributes inherited from Query
#query_string, #terms
Instance Method Summary
collapse
Methods included from Helpers
#boolean_param
#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, #deep_permit, included_annotator_facets, inverted_subqueries, #model_id_facet, #object_global_id_facet, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #query_name, #set_nested_queries, #shared_and_clauses, #subquery_vector, #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/otu/filter.rb', line 177
def initialize(query_params)
super
@ancestrify = boolean_param(params, :ancestrify)
@asserted_distributions = boolean_param(params, :asserted_distributions)
@biological_association_id = params[:biological_association_id]
@biological_associations = boolean_param(params, :biological_associations)
@collecting_event_id = params[:collecting_event_id]
@collection_objects = boolean_param(params, :collection_objects)
@contents = boolean_param(params, :contents)
@coordinatify = boolean_param(params, :coordinatify)
@descendants = boolean_param(params, :descendants)
@descriptor_id = params[:descriptor_id]
@geo_json = params[:geo_json]
@geographic_area_id = params[:geographic_area_id]
@geographic_area_mode = boolean_param(params, :geographic_area_mode)
@historical_determinations = boolean_param(params, :historical_determinations)
@name = params[:name]
@name_exact = boolean_param(params, :name_exact)
@observations = boolean_param(params, :observations)
@otu_id = params[:otu_id]
@radius = params[:radius].presence || 100.0
@taxon_name = boolean_param(params, :taxon_name)
@taxon_name_id = params[:taxon_name_id]
@with_name = boolean_param(params, :with_name)
@wkt = params[:wkt]
set_notes_params(params)
set_citations_params(params)
set_depiction_params(params)
set_data_attributes_params(params)
set_tags_params(params)
end
|
Instance Attribute Details
#ancestrify ⇒ Object
!! This param is not like the others. !! See parallel in TaxonName filter ‘ancestrify’.
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# File 'lib/queries/otu/filter.rb', line 49
def ancestrify
@ancestrify
end
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#asserted_distributions ⇒ True, ...
Returns true - Otu has AssertedDistribution false - Otu without AssertedDistribution nil - not applied.
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# File 'lib/queries/otu/filter.rb', line 147
def asserted_distributions
@asserted_distributions
end
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#biological_association_id ⇒ Object
Finds all OTUs that are the current determination of a CollectionObject that is in the BiologicalAssociation or are part of the Biological association itself. Altered by historical_determinations.
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# File 'lib/queries/otu/filter.rb', line 112
def biological_association_id
@biological_association_id
end
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#biological_associations ⇒ True, ...
Returns true - Otu has BiologicalAssocation (subject or object) false - Otu without BiologicalAssociation nil - not applied.
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# File 'lib/queries/otu/filter.rb', line 165
def biological_associations
@biological_associations
end
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#collecting_event_id ⇒ Object
Finds all OTUs that are the current determination of a CollectionObject that was collecting in these Collecting events. Altered by historical_determinations.
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# File 'lib/queries/otu/filter.rb', line 94
def collecting_event_id
@collecting_event_id
end
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#collection_objects ⇒ True, ...
Returns true - Otu has CollectionObjects false - Otu without CollectionObjects nil - not applied.
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# File 'lib/queries/otu/filter.rb', line 159
def collection_objects
@collection_objects
end
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#contents ⇒ True, ...
Returns true - Otu has Conten false - Otu without Conten nil - not applied.
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# File 'lib/queries/otu/filter.rb', line 153
def contents
@contents
end
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#coordinatify ⇒ Object
See ‘coordinatify_result` for more.
!! This param is not like the others. !! See parallel in TaxonName filter ‘validify’.
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# File 'lib/queries/otu/filter.rb', line 57
def coordinatify
@coordinatify
end
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#descendants ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 85
def descendants
@descendants
end
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#descriptor_id ⇒ Array
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# File 'lib/queries/otu/filter.rb', line 141
def descriptor_id
@descriptor_id
end
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#geo_json ⇒ Hash?
Returns in geo_json format (no Feature …) ?!.
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# File 'lib/queries/otu/filter.rb', line 120
def geo_json
@geo_json
end
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#geographic_area_id ⇒ Array
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# File 'lib/queries/otu/filter.rb', line 124
def geographic_area_id
@geographic_area_id
end
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#geographic_area_mode ⇒ Boolean?
Returns How to treat GeographicAreas
nil - non-spatial match by only those records matching the geographic_area_id exactly
true - spatial match
false - non-spatial match (exact and descendants).
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# File 'lib/queries/otu/filter.rb', line 131
def geographic_area_mode
@geographic_area_mode
end
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#historical_determinations ⇒ Boolean?
Where applicable:
true - include only historical determinations (ignores only determinations)
false - include both current and historical
nil - include only current determinations
Impacts all TaxonDetermination referencing queries
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# File 'lib/queries/otu/filter.rb', line 103
def historical_determinations
@historical_determinations
end
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#name ⇒ Object
Returns Array literal match against one or more Otu#name.
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# File 'lib/queries/otu/filter.rb', line 62
def name
@name
end
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#name_exact ⇒ Object
Returns Boolean if true then match on ‘name` exactly.
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# File 'lib/queries/otu/filter.rb', line 66
def name_exact
@name_exact
end
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#observations ⇒ True, ...
Returns true - Otu has observations false - Otu without observations nil - not applied.
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# File 'lib/queries/otu/filter.rb', line 171
def observations
@observations
end
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#otu_id ⇒ Object
Returns Array one or more Otu ids.
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# File 'lib/queries/otu/filter.rb', line 77
def otu_id
@otu_id
end
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#radius ⇒ Object
Integer in Meters
!! defaults to 100m
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# File 'lib/queries/otu/filter.rb', line 175
def radius
@radius
end
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#taxon_name ⇒ True, ...
Returns true - Otu has taxon name false - Otu without taxon name nil - not applied.
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# File 'lib/queries/otu/filter.rb', line 137
def taxon_name
@taxon_name
end
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#taxon_name_id ⇒ Object
Returns Array one or more Otu taxon_name_id.
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# File 'lib/queries/otu/filter.rb', line 82
def taxon_name_id
@taxon_name_id
end
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#with_name ⇒ Object
Returns Boolean true - has name false - has no name nil - both.
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# File 'lib/queries/otu/filter.rb', line 72
def with_name
@with_name
end
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#wkt ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 116
def wkt
@wkt
end
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Instance Method Details
#all(nil_empty = false) ⇒ ActiveRecord::Relation
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# File 'lib/queries/otu/filter.rb', line 636
def all(nil_empty = false)
q = super
q = ancestrify_result(q) if ancestrify
q = coordinatify_result(q) if coordinatify
q
end
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#ancestrify_result(q) ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 585
def ancestrify_result(q)
a = q
s = 'WITH otu_base AS (' + a.all.to_sql + ') ' +
::Otu
.joins('JOIN taxon_name_hierarchies tnh on tnh.ancestor_id = otus.taxon_name_id')
.joins('JOIN otu_base as otu_base1 on otu_base1.taxon_name_id = tnh.descendant_id')
.to_sql
b = ::Otu.from('(' + s + ') as otus')
referenced_klass_union([a, b])
end
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#and_clauses ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 599
def and_clauses
[
name_facet,
taxon_name_facet,
]
end
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#asserted_distribution_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 436
def asserted_distribution_query_facet
return nil if asserted_distribution_query.nil?
s = 'WITH query_ad_otus AS (' + asserted_distribution_query.all.to_sql + ') ' +
::Otu
.joins('JOIN query_ad_otus as query_ad_otus1 on otus.id = query_ad_otus1.otu_id')
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#asserted_distributions_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 292
def asserted_distributions_facet
return nil if asserted_distributions.nil?
if asserted_distributions
::Otu.joins(:asserted_distributions)
else
::Otu.where.missing(:asserted_distributions)
end
end
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#biological_association_id_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 379
def biological_association_id_facet
return nil if biological_association_id.empty?
q1 = ::Otu.joins(:biological_associations).where(biological_associations: { id: biological_association_id, biological_association_subject_type: 'Otu' })
q2 = ::Otu.joins(:related_biological_associations).where(related_biological_associations: { id: biological_association_id, biological_association_object_type: 'Otu' })
q3 = ::Otu.joins(collection_objects: [:biological_associations]).where(biological_associations: { id: biological_association_id, biological_association_subject_type: 'CollectionObject' })
q4 = ::Otu.joins(collection_objects: [:related_biological_associations]).where(related_biological_associations: { id: biological_association_id, biological_association_object_type: 'CollectionObject' })
if historical_determinations.nil?
q3 = q3.where(taxon_determinations: { position: 1 })
q4 = q4.where(taxon_determinations: { position: 1 })
elsif historical_determinations
q3 = q3.where.not(taxon_determinations: { position: 1 })
q4 = q4.where.not(taxon_determinations: { position: 1 })
end
query = referenced_klass_union([q1, q2, q3, q4])
::Otu.from("(#{query.to_sql}) as otus").distinct
end
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#biological_association_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 456
def biological_association_query_facet
return nil if biological_association_query.nil?
s = 'WITH query_ba_otu AS (' + biological_association_query.all.to_sql + ') '
a = ::Otu
.joins("JOIN query_ba_otu as query_ba_otu1 on otus.id = query_ba_otu1.biological_association_subject_id AND query_ba_otu1.biological_association_subject_type = 'Otu'")
b = ::Otu
.joins("JOIN query_ba_otu as query_ba_otu2 on otus.id = query_ba_otu2.biological_association_object_id AND query_ba_otu2.biological_association_object_type = 'Otu'")
s << referenced_klass_union([a, b]).to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#biological_associations_facet ⇒ Object
UNION, NOT EXISTS example
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# File 'lib/queries/otu/filter.rb', line 320
def biological_associations_facet
return nil if biological_associations.nil?
a = ::Otu.joins(:biological_associations)
b = ::Otu.joins(:related_biological_associations)
c = ::Otu.from("((#{a.to_sql}) UNION (#{b.to_sql})) as otus")
if biological_associations
::Otu.from("((#{a.to_sql}) UNION (#{b.to_sql})) as otus")
else
::Otu.where('NOT EXISTS (' + ::Otu.select('1').from( ::Otu.from(
"((#{a.to_sql}) UNION (#{b.to_sql})) as ba_otus_join"
).where('otus.id = ba_otus_join.id')
).to_sql + ')') end
end
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#biological_associations_table ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 211
def biological_associations_table
::BiologicalAssociation.arel_table
end
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#collecting_event_id_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 368
def collecting_event_id_facet
return nil if collecting_event_id.empty?
if historical_determinations.nil?
::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: }, taxon_determinations: { position: 1 })
elsif historical_determinations
::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: }).where.not(taxon_determinations: { position: 1 })
else
::Otu.joins(:collection_objects).where(collection_objects: { collecting_event_id: })
end
end
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#collecting_event_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 482
def collecting_event_query_facet
return nil if collecting_event_query.nil?
s = 'WITH query_ce_otus AS (' + collecting_event_query.all.to_sql + ') ' +
::Otu
.joins(:collecting_events)
.joins('JOIN query_ce_otus as query_ce_otus1 on collecting_events.id = query_ce_otus1.id')
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#collection_object_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 471
def collection_object_query_facet
return nil if collection_object_query.nil?
s = 'WITH query_co_otus AS (' + collection_object_query.all.to_sql + ') ' +
::Otu
.joins(:collection_objects)
.joins('JOIN query_co_otus as query_co_otus1 on collection_objects.id = query_co_otus1.id')
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#collection_objects_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 339
def collection_objects_facet
return nil if collection_objects.nil?
if collection_objects
::Otu.joins(:collection_objects)
else
::Otu.where.missing(:collection_objects)
end
end
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#content_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 446
def content_query_facet
return nil if content_query.nil?
s = 'WITH query_con_otus AS (' + content_query.all.to_sql + ') ' +
::Otu
.joins('JOIN query_con_otus as query_con_otus1 on otus.id = query_con_otus1.otu_id')
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#contents_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 310
def contents_facet
return nil if contents.nil?
if contents
::Otu.joins(:contents)
else
::Otu.where.missing(:contents)
end
end
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#coordinatify_result(q) ⇒ Object
Expands result of OTU filter query in 2 ways:
1 - to include all valid OTUs by (proxy of TaxonName) if OTU is by proxy invalid
2 - to include all invalid OTUS (by proxy of TaxonName) if OTU is by proxy valid
In essence this creates full sets of TaxonConcepts from partial results. The result can be used to, for example, get a comprehensive list of Sources for the concept, or a comprehensive historical list of Specimens, etc.
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# File 'lib/queries/otu/filter.rb', line 559
def coordinatify_result(q)
i = q.joins(:taxon_name).where('taxon_names.id != taxon_names.cached_valid_taxon_name_id').where(project_id:)
v = q.joins(:taxon_name).where('taxon_names.id = taxon_names.cached_valid_taxon_name_id').where(project_id:)
s = 'WITH invalid_otu_result AS (' + i.to_sql + ') ' +
::Otu
.joins('JOIN taxon_names tn1 on otus.taxon_name_id = tn1.cached_valid_taxon_name_id')
.joins('JOIN invalid_otu_result AS invalid_otu_result1 ON invalid_otu_result1.taxon_name_id = tn1.id') .to_sql
a = ::Otu.from('(' + s + ') as otus')
t = 'WITH valid_otu_result AS (' + v.to_sql + ') ' +
::Otu
.joins('JOIN taxon_names tn2 on otus.taxon_name_id = tn2.id')
.joins('JOIN valid_otu_result AS valid_otu_result1 ON valid_otu_result1.taxon_name_id = tn2.cached_valid_taxon_name_id') .to_sql
b = ::Otu.from('(' + t + ') as otus')
referenced_klass_union([a, b, q]).distinct end
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#descriptor_id_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 427
def descriptor_id_facet
return nil if descriptor_id.empty?
q1 = ::Otu.joins(:descriptors).where(descriptors: { id: descriptor_id })
q2 = ::Otu.joins(collection_objects: [:descriptors]).where(descriptors: { id: descriptor_id })
referenced_klass_union([q1, q2]).distinct
end
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#descriptor_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 515
def descriptor_query_facet
return nil if descriptor_query.nil?
s = 'WITH query_de_otus AS (' + descriptor_query.all.to_sql + ') ' +
::Otu
.joins(:observations)
.joins('JOIN query_de_otus as query_de_otus1 on observations.descriptor_id = query_de_otus1.id')
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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# File 'lib/queries/otu/filter.rb', line 493
def
return nil if .nil?
s = 'WITH query_ex_otus AS (' + .all.to_sql + ') ' +
::Otu
.joins(:origin_relationships)
.joins("JOIN query_ex_otus as query_ex_otus1 on origin_relationships.new_object_id = query_ex_otus1.id and origin_relationships.new_object_type = 'Extract'")
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#from_wkt(wkt_shape) ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 270
def from_wkt(wkt_shape)
c = ::Queries::CollectingEvent::Filter.new(wkt: wkt_shape, project_id:)
a = ::Queries::AssertedDistribution::Filter.new(wkt: wkt_shape, project_id:)
q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all, project_id:)
q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all, project_id:)
referenced_klass_union([q1, q2]).distinct
end
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#geo_json_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 280
def geo_json_facet
return nil if geo_json.blank?
c = ::Queries::CollectingEvent::Filter.new(geo_json:, project_id:, radius:)
a = ::Queries::AssertedDistribution::Filter.new(geo_json:, project_id:, radius:)
q1 = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: c.all, project_id:)
q2 = ::Otu.joins(:asserted_distributions).where(asserted_distributions: a.all, project_id:)
referenced_klass_union([q1, q2]).distinct
end
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#geographic_area_id_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 400
def geographic_area_id_facet
return nil if geographic_area_id.empty?
a = nil
case geographic_area_mode
when nil, true a = ::GeographicArea.where(id: geographic_area_id)
when false a = ::GeographicArea.descendants_of_any(geographic_area_id)
end
b = nil c = nil
case geographic_area_mode
when nil, false b = ::Otu.joins(:asserted_distributions).where(asserted_distributions: { geographic_area: a })
c = ::Otu.joins(collection_objects: [:collecting_event]).where(collecting_events: { geographic_area: a })
when true i = ::GeographicItem.joins(:geographic_areas).where(geographic_areas: a) wkt_shape = ::GeographicItem.st_union(i).to_a.first['collection'].to_s return from_wkt(wkt_shape)
end
referenced_klass_union([b, c])
end
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#loan_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 526
def loan_query_facet
return nil if loan_query.nil?
s = 'WITH query_loan_otus AS (' + loan_query.all.to_sql + ') '
a = ::Otu.joins(:loan_items)
.joins('JOIN query_loan_otus as query_loan_otus1 on loan_items.loan_id = query_loan_otus1.id')
b = ::Otu.joins(collection_objects: [:loan_items])
.joins('JOIN query_loan_otus as query_loan_otus1 on loan_items.loan_id = query_loan_otus1.id')
s << referenced_klass_union([a, b]).to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#merge_clauses ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 606
def merge_clauses
[
asserted_distribution_query_facet,
asserted_distributions_facet,
biological_association_query_facet,
collecting_event_query_facet,
collection_object_query_facet,
content_query_facet,
descriptor_query_facet,
,
loan_query_facet,
observation_query_facet,
taxon_name_query_facet,
biological_association_id_facet,
biological_associations_facet,
collecting_event_id_facet,
collection_objects_facet,
contents_facet,
descriptor_id_facet,
geo_json_facet,
geographic_area_id_facet,
observations_facet,
taxon_name_id_facet,
with_name_facet,
wkt_facet,
].compact
end
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#name_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 243
def name_facet
return nil if name.empty?
if name_exact
table[:name].in(name)
else
table[:name].matches_any(name.collect { |n| '%' + n.gsub(/\s+/, '%') + '%' })
end
end
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#observation_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 541
def observation_query_facet
return nil if observation_query.nil?
s = 'WITH query_obs_otus AS (' + observation_query.all.to_sql + ') ' +
::Otu
.joins(:observations)
.joins('JOIN query_obs_otus as query_obs_otus1 on observations.id = query_obs_otus1.id')
.to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#observations_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 358
def observations_facet
return nil if observations.nil?
if observations
::Otu.joins(:observations)
else
::Otu.where.missing(:observations)
end
end
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#taxon_name_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 348
def taxon_name_facet
return nil if taxon_name.nil?
if taxon_name
table[:taxon_name_id].not_eq(nil)
else
table[:taxon_name_id].eq(nil)
end
end
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#taxon_name_id_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 252
def taxon_name_id_facet
return nil if taxon_name_id.empty?
if descendants
h = Arel::Table.new(:taxon_name_hierarchies)
j = table.join(h, Arel::Nodes::InnerJoin).on(table[:taxon_name_id].eq(h[:descendant_id]))
z = h[:ancestor_id].in(taxon_name_id)
::Otu.joins(j.join_sources).where(z)
else
::Otu.where(taxon_name_id:)
end
end
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#taxon_name_query_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 504
def taxon_name_query_facet
return nil if taxon_name_query.nil?
s = 'WITH query_taxon_names AS (' + taxon_name_query.all.to_sql + ') ' +
::Otu
.joins('JOIN query_taxon_names as query_taxon_names1 on otus.taxon_name_id = query_taxon_names1.id')
.where.not(taxon_name_id: nil) .to_sql
::Otu.from('(' + s + ') as otus').distinct
end
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#with_name_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 301
def with_name_facet
return nil if with_name.nil?
if with_name
::Otu.where.not(name: nil)
else
::Otu.where(name: nil)
end
end
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#wkt_facet ⇒ Object
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# File 'lib/queries/otu/filter.rb', line 265
def wkt_facet
return nil if wkt.nil?
from_wkt(wkt)
end
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