Class: Queries::BiologicalAssociation::Filter
- Inherits:
-
Query::Filter
show all
- Includes:
- Concerns::Citations, Concerns::Confidences, Concerns::Depictions, Concerns::Notes, Concerns::Tags
- Defined in:
- lib/queries/biological_association/filter.rb
Constant Summary
collapse
- PARAMS =
[
:biological_association_id,
:biological_associations_graph_id,
:biological_relationship_id,
:collecting_event_id,
:collection_object_id,
:descendants,
:exclude_taxon_name_relationship,
:geo_json,
:geo_mode,
:geo_shape_id,
:geo_shape_type,
:object_biological_property_id,
:object_object_global_id,
:object_taxon_name_id,
:object_type,
:otu_id,
:subject_biological_property_id,
:subject_object_global_id,
:subject_taxon_name_id,
:subject_type,
:taxon_name_id,
:taxon_name_id_mode,
:wkt,
:biological_association_object_id,
:biological_association_object_type,
:biological_association_subject_id,
:biological_association_subject_type,
any_global_id: [],
biological_association_id: [],
biological_associations_graph_id: [],
biological_relationship_id: [],
collecting_event_id: [],
collection_object_id: [],
geo_shape_id: [],
geo_shape_type: [],
object_biological_property_id: [],
object_object_global_id: [],
object_taxon_name_id: [],
otu_id: [],
subject_biological_property_id: [],
subject_object_global_id: [],
subject_taxon_name_id: [],
taxon_name_id: [],
biological_association_object_id: [],
biological_association_object_type: [],
biological_association_subject_id: [],
biological_association_subject_type: []
].freeze
- API_PARAM_EXCLUSIONS =
[
:any_global_id
]
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, #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, #sound_query, #taxon_name_query, #venn, #venn_mode
Attributes inherited from Query
#query_string, #terms
Instance Method Summary
collapse
#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, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #model_id_facet, #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/biological_association/filter.rb', line 172
def initialize(query_params)
super
@any_global_id = params[:any_global_id]
@biological_association_id = params[:biological_association_id]
@biological_associations_graph_id = params[:biological_associations_graph_id]
@biological_relationship_id = params[:biological_relationship_id]
@collecting_event_id = params[:collecting_event_id]
@collection_object_id = params[:collection_object_id]
@descendants = boolean_param(params, :descendants)
@exclude_taxon_name_relationship = boolean_param(params, :exclude_taxon_name_relationship)
@geo_json = params[:geo_json]
@geo_mode = params[:geo_mode]
@geo_shape_id = params[:geo_shape_id]
@geo_shape_type = params[:geo_shape_type]
@object_biological_property_id = params[:object_biological_property_id]
@object_object_global_id = params[:object_object_global_id]
@object_taxon_name_id = params[:object_taxon_name_id]
@object_type = params[:object_type]
@otu_id = params[:otu_id]
@subject_biological_property_id = params[:subject_biological_property_id]
@subject_object_global_id = params[:subject_object_global_id]
@subject_taxon_name_id = params[:subject_taxon_name_id]
@subject_type = params[:subject_type]
@taxon_name_id = params[:taxon_name_id]
@taxon_name_id_mode = boolean_param(params, :taxon_name_id_mode)
@wkt = params[:wkt]
@biological_association_object_id = params[:biological_association_object_id]
@biological_association_object_type = params[:biological_association_object_type]
@biological_association_subject_id = params[:biological_association_subject_id]
@biological_association_subject_type = params[:biological_association_subject_type]
set_confidences_params(params)
set_notes_params(params)
set_tags_params(params)
set_citations_params(params)
set_depiction_params(params)
end
|
Instance Attribute Details
#any_global_id ⇒ Array
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# File 'lib/queries/biological_association/filter.rb', line 147
def any_global_id
@any_global_id
end
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#biological_association_id ⇒ Array
Returns one or more BiologicalAssociation#id.
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# File 'lib/queries/biological_association/filter.rb', line 127
def biological_association_id
@biological_association_id
end
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#biological_association_object_id ⇒ Object
Returns the value of attribute biological_association_object_id.
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# File 'lib/queries/biological_association/filter.rb', line 164
def biological_association_object_id
@biological_association_object_id
end
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#biological_association_object_type ⇒ Object
Returns the value of attribute biological_association_object_type.
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# File 'lib/queries/biological_association/filter.rb', line 166
def biological_association_object_type
@biological_association_object_type
end
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#biological_association_subject_id ⇒ Object
Returns the value of attribute biological_association_subject_id.
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# File 'lib/queries/biological_association/filter.rb', line 168
def biological_association_subject_id
@biological_association_subject_id
end
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#biological_association_subject_type ⇒ Object
Returns the value of attribute biological_association_subject_type.
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# File 'lib/queries/biological_association/filter.rb', line 170
def biological_association_subject_type
@biological_association_subject_type
end
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#biological_associations_graph_id ⇒ Array
Returns a biological relationship graph ID.
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# File 'lib/queries/biological_association/filter.rb', line 114
def biological_associations_graph_id
@biological_associations_graph_id
end
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#biological_relationship_id ⇒ Array
See also exclude_taxon_name_relationship
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# File 'lib/queries/biological_association/filter.rb', line 133
def biological_relationship_id
@biological_relationship_id
end
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#collecting_event_id ⇒ Object
linked to one or more CollectingEvent
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# File 'lib/queries/biological_association/filter.rb', line 75
def collecting_event_id
@collecting_event_id
end
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#collection_object_id ⇒ Array
matching subject OR object
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# File 'lib/queries/biological_association/filter.rb', line 87
def collection_object_id
@collection_object_id
end
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#descendants ⇒ Object
Returns the value of attribute descendants.
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# File 'lib/queries/biological_association/filter.rb', line 110
def descendants
@descendants
end
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#exclude_taxon_name_relationship ⇒ Object
those listed in biological_relationship_id
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# File 'lib/queries/biological_association/filter.rb', line 69
def exclude_taxon_name_relationship
@exclude_taxon_name_relationship
end
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#geo_json ⇒ Object
Returns the value of attribute geo_json.
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# File 'lib/queries/biological_association/filter.rb', line 151
def geo_json
@geo_json
end
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#geo_mode ⇒ Object
Returns the value of attribute geo_mode.
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# File 'lib/queries/biological_association/filter.rb', line 152
def geo_mode
@geo_mode
end
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#geo_shape_id ⇒ Object
Returns the value of attribute geo_shape_id.
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# File 'lib/queries/biological_association/filter.rb', line 153
def geo_shape_id
@geo_shape_id
end
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#geo_shape_type ⇒ Object
Returns the value of attribute geo_shape_type.
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# File 'lib/queries/biological_association/filter.rb', line 154
def geo_shape_type
@geo_shape_type
end
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#object_biological_property_id ⇒ Array
Returns All BiologicalAssociations with object having this property.
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# File 'lib/queries/biological_association/filter.rb', line 122
def object_biological_property_id
@object_biological_property_id
end
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#object_object_global_id ⇒ Array
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# File 'lib/queries/biological_association/filter.rb', line 144
def object_object_global_id
@object_object_global_id
end
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#object_taxon_name_id ⇒ Object
its children !! TaxonName must be valid!
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# File 'lib/queries/biological_association/filter.rb', line 99
def object_taxon_name_id
@object_taxon_name_id
end
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#object_type ⇒ nil, ...
Returns limit object to a type.
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# File 'lib/queries/biological_association/filter.rb', line 162
def object_type
@object_type
end
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#otu_id ⇒ Array
matching subject OR object
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# File 'lib/queries/biological_association/filter.rb', line 81
def otu_id
@otu_id
end
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#subject_biological_property_id ⇒ Array
Returns All BiologicalAssociations with subject having this property.
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# File 'lib/queries/biological_association/filter.rb', line 118
def subject_biological_property_id
@subject_biological_property_id
end
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#subject_object_global_id ⇒ Array
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# File 'lib/queries/biological_association/filter.rb', line 141
def subject_object_global_id
@subject_object_global_id
end
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#subject_taxon_name_id ⇒ Object
its children. !! TaxonName must be valid!
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# File 'lib/queries/biological_association/filter.rb', line 93
def subject_taxon_name_id
@subject_taxon_name_id
end
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#subject_type ⇒ nil, ...
Returns limit subject to a type.
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# File 'lib/queries/biological_association/filter.rb', line 158
def subject_type
@subject_type
end
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#taxon_name_id ⇒ Array
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# File 'lib/queries/biological_association/filter.rb', line 105
def taxon_name_id
@taxon_name_id
end
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#taxon_name_id_mode ⇒ Boolean?
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# File 'lib/queries/biological_association/filter.rb', line 108
def taxon_name_id_mode
@taxon_name_id_mode
end
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#wkt ⇒ Object
See lib/queries/otu/filter.rb
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# File 'lib/queries/biological_association/filter.rb', line 150
def wkt
@wkt
end
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Instance Method Details
#and_clauses ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 734
def and_clauses
[
any_global_id_facet,
biological_association_id_facet,
biological_relationship_id_facet,
object_object_global_id_facet,
object_type_facet,
subject_object_global_id_facet,
subject_type_facet,
biological_association_object_id_facet,
biological_association_object_type_facet,
biological_association_subject_id_facet,
biological_association_subject_id_facet
]
end
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#any_global_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 590
def any_global_id_facet
return nil if any_global_id.empty?
a = matching_global_id(:subject, any_global_id)
b = matching_global_id(:object, any_global_id)
if a && b
return a.or(b)
else
return a ? a : b
end
end
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#asserted_distribution_query_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 657
def asserted_distribution_query_facet
return nil if asserted_distribution_query.nil?
s = 'WITH query_ad_ba AS (' + asserted_distribution_query.all.to_sql + ') '
a = ::BiologicalAssociation
.joins("JOIN query_ad_ba as query_ad_ba1 on biological_associations.biological_association_subject_id = query_ad_ba1.otu_id AND biological_associations.biological_association_subject_type = 'Otu'")
b = ::BiologicalAssociation
.joins("JOIN query_ad_ba as query_ad_ba2 on biological_associations.biological_association_object_id = query_ad_ba2.otu_id AND biological_associations.biological_association_object_type = 'Otu'")
s << referenced_klass_union([a,b]).to_sql
::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
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#base_collection_object_query(opts) ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 384
def base_collection_object_query(opts)
q = ::Queries::CollectionObject::Filter.new(opts)
q.project_id = nil q
end
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#base_otu_query(opts) ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 378
def base_otu_query(opts)
q = ::Queries::Otu::Filter.new(opts)
q.project_id = nil q
end
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#biological_association_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 610
def biological_association_id_facet
return nil if biological_association_id.empty?
table[:id].in(biological_association_id)
end
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#biological_association_object_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 300
def biological_association_object_id_facet
return nil if biological_association_object_id.empty?
table[:biological_association_object_id].in(biological_association_object_id)
end
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#biological_association_object_type_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 295
def biological_association_object_type_facet
return nil if biological_association_object_type.empty?
table[:biological_association_object_type].in(biological_association_object_type)
end
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#biological_association_subject_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 310
def biological_association_subject_id_facet
return nil if biological_association_subject_id.empty?
table[:biological_association_subject_id].in(biological_association_subject_id)
end
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#biological_association_subject_type_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 305
def biological_association_subject_type_facet
return nil if biological_association_subject_type.empty?
table[:biological_association_subject_type].in(biological_association_subject_type)
end
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#biological_associations_graph_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 327
def biological_associations_graph_id_facet
return nil if biological_associations_graph_id.empty?
::BiologicalAssociation.joins(:biological_associations_graphs).where(biological_associations_graphs: {id: biological_associations_graph_id})
end
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#biological_relationship_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 601
def biological_relationship_id_facet
return nil if biological_relationship_id.empty?
if exclude_taxon_name_relationship
table[:biological_relationship_id].not_in(biological_relationship_id)
else
table[:biological_relationship_id].in(biological_relationship_id)
end
end
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#collecting_event_query_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 625
def collecting_event_query_facet
return nil if collecting_event_query.nil?
s = 'WITH query_ce_ba AS (' + collecting_event_query.all.to_sql + ') '
a = ::BiologicalAssociation
.joins("JOIN collection_objects co1 on co1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = 'CollectionObject'")
.joins('JOIN query_ce_ba as query_ce_ba1 on co1.collecting_event_id = query_ce_ba1.id')
b = ::BiologicalAssociation
.joins("JOIN collection_objects co2 on co2.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = 'CollectionObject'")
.joins('JOIN query_ce_ba as query_ce_ba2 on co2.collecting_event_id = query_ce_ba2.id')
s << referenced_klass_union([a,b]).to_sql
::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
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#collection_object_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 450
def collection_object_facet
subject_object_scope(subject_collection_object_query, object_collection_object_query, 'CollectionObject' )
end
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#collection_object_params ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 332
def collection_object_params
h = {}
[
:collecting_event_id,
:collection_object_id,
:geo_json,
:geo_mode,
:geo_shape_id,
:geo_shape_type,
:wkt,
].each
.each do |p|
v = send(p)
h[p] = v if v.present?
end
h
end
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#collection_object_query_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 671
def collection_object_query_facet
return nil if collection_object_query.nil?
s = 'WITH query_co_ba AS (' + collection_object_query.all.to_sql + ') '
a = ::BiologicalAssociation
.joins("JOIN query_co_ba as query_co_ba1 on biological_associations.biological_association_subject_id = query_co_ba1.id AND biological_associations.biological_association_subject_type = 'CollectionObject'")
b = ::BiologicalAssociation
.joins("JOIN query_co_ba as query_co_ba2 on biological_associations.biological_association_object_id = query_co_ba2.id AND biological_associations.biological_association_object_type = 'CollectionObject'")
s << referenced_klass_union([a,b]).to_sql
::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
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#field_occurrence_query_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 686
def field_occurrence_query_facet
return nil if field_occurrence_query.nil?
s = 'WITH query_fo_ba AS (' + field_occurrence_query.all.to_sql + ') '
a = ::BiologicalAssociation
.joins("JOIN query_fo_ba as query_fo_ba1 on biological_associations.biological_association_subject_id = query_fo_ba1.id AND biological_associations.biological_association_subject_type = 'FieldOccurrence'")
b = ::BiologicalAssociation
.joins("JOIN query_fo_ba as query_fo_ba2 on biological_associations.biological_association_object_id = query_fo_ba2.id AND biological_associations.biological_association_object_type = 'FieldOccurrence'")
s << referenced_klass_union([a,b]).to_sql
::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
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#matching_global_id(target = :subject, global_id = []) ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 776
def matching_global_id(target = :subject, global_id = [])
a = global_id
b = "#{target}_matches".to_sym
q = send(b, object_for(a[0]))
a[1..a.length].each do |i|
q = q.or( send(b, object_for(i) ))
end
q
end
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#merge_clauses ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 750
def merge_clauses
[
asserted_distribution_query_facet,
collecting_event_query_facet,
collection_object_query_facet,
field_occurrence_query_facet,
otu_query_facet,
taxon_name_query_facet,
biological_associations_graph_id_facet,
object_biological_property_id_facet,
subject_biological_property_id_facet,
subject_object_facet, ]
end
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#object_biological_property_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 315
def object_biological_property_id_facet
return nil if object_biological_property_id.empty?
::BiologicalAssociation.joins(:object_biological_relationship_types)
.where(biological_relationship_types: {biological_property_id: object_biological_property_id })
end
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#object_collection_object_query ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 404
def object_collection_object_query
p = collection_object_params
s = object_taxon_name_ids
if p.blank? && s.empty? return nil
elsif s.present?
p[:taxon_name_id] = s
p[:descendants] = descendants
end
q = base_collection_object_query(p)
end
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#object_for(global_id) ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 768
def object_for(global_id)
if o = GlobalID::Locator.locate(global_id)
o
else
nil
end
end
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#object_matches(object) ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 289
def object_matches(object)
table['biological_association_object_id'].eq(object.id).and(
table['biological_association_object_type'].eq(object.class.base_class.name)
)
end
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#object_object_global_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 585
def object_object_global_id_facet
return nil if object_object_global_id.empty?
matching_global_id(:object, object_object_global_id)
end
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#object_otu_query ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 432
def object_otu_query
p = otu_params
s = object_taxon_name_ids
if p.blank? && s.nil?
return nil
elsif s.present?
p[:taxon_name_id] = s
p[:descendants] = descendants
end
base_otu_query(p)
end
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#object_scope ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 458
def object_scope
target_scope('object')
end
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#object_taxon_name_ids ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 788
def object_taxon_name_ids
return taxon_name_id if taxon_name_id.present?
return object_taxon_name_id if object_taxon_name_id.present?
return nil
end
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#object_type_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 615
def object_type_facet
return nil if object_type.nil?
table[:biological_association_object_type].eq(object_type)
end
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#otu_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 446
def otu_facet
subject_object_scope(subject_otu_query, object_otu_query, 'Otu' )
end
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#otu_params ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 350
def otu_params
h = {}
[
:geo_json,
:geo_mode,
:geo_shape_id,
:geo_shape_type,
:otu_id,
:wkt,
].each do |p|
v = send(p)
h[p] = v if v.present?
end
h
end
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#otu_query_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 643
def otu_query_facet
return nil if otu_query.nil?
s = 'WITH query_otu_ba AS (' + otu_query.all.to_sql + ') '
a = ::BiologicalAssociation
.joins("JOIN query_otu_ba as query_otu_ba1 on biological_associations.biological_association_subject_id = query_otu_ba1.id AND biological_associations.biological_association_subject_type = 'Otu'")
b = ::BiologicalAssociation
.joins("JOIN query_otu_ba as query_otu_ba2 on biological_associations.biological_association_object_id = query_otu_ba2.id AND biological_associations.biological_association_object_type = 'Otu'")
s << referenced_klass_union([a,b]).to_sql
::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
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#subject_biological_property_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 321
def subject_biological_property_id_facet
return nil if subject_biological_property_id.empty?
::BiologicalAssociation.joins(:subject_biological_relationship_types)
.where(biological_relationship_types: {biological_property_id: subject_biological_property_id })
end
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#subject_collection_object_query ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 390
def subject_collection_object_query
p = collection_object_params
s = subject_taxon_name_ids
if p.blank? && s.empty? return nil
elsif s.present?
p[:taxon_name_id] = s
p[:descendants] = descendants
end
q = base_collection_object_query(p)
end
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#subject_matches(object) ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 283
def subject_matches(object)
table['biological_association_subject_id'].eq(object.id).and(
table['biological_association_subject_type'].eq(object.class.base_class.name)
)
end
|
#subject_object_facet ⇒ Object
Merges results from Otu and CollectionObject filters as the basis for the query
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# File 'lib/queries/biological_association/filter.rb', line 503
def subject_object_facet
a = subject_scope
b = object_scope
return nil if a.nil? && b.nil?
case taxon_name_id_mode
when true ::BiologicalAssociation.from(
'(' + [a,b].compact.collect{|q| '(' + q.to_sql + ')'}.join(' INTERSECT ') + ') as biological_associations'
)
when false, nil ::BiologicalAssociation.from(
'(' + [a,b].compact.collect{|q| '(' + q.to_sql + ')'}.join(' UNION ') + ') as biological_associations'
)
end
end
|
#subject_object_global_id_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 580
def subject_object_global_id_facet
return nil if subject_object_global_id.empty?
matching_global_id(:subject, subject_object_global_id)
end
|
#subject_object_scope(subject_query, object_query, target = 'Otu') ⇒ Object
rubocop:disable Metrics/MethodLength This is “or”
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# File 'lib/queries/biological_association/filter.rb', line 523
def subject_object_scope(subject_query, object_query, target = 'Otu')
a = subject_query
b = object_query
a_sql, b_sql = nil, nil
if !a&.all(true).nil?
a.project_id = project_id
a_sql = a.all.to_sql
end
if !b&.all(true).nil?
b.project_id = project_id
b_sql = b.all.to_sql
end
return nil if a_sql.nil? and b_sql.nil?
t = []
t.push 'a_objects AS (' + a_sql + ')' if a_sql
t.push 'b_objects AS (' + b_sql + ')' if b_sql && (b_sql != a_sql)
s = 'WITH ' + t.join(', ')
if a_sql && b_sql && (a_sql != b_sql)
s << ' ' + ::BiologicalAssociation
.joins("LEFT JOIN a_objects as a_objects1 on a_objects1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = '" + target + "'")
.joins("LEFT JOIN b_objects as b_objects1 on b_objects1.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = '" + target + "'")
.where('a_objects1.id is not null').or('b_objects1.id is not null')
.to_sql
elsif a_sql && b_sql
s << ' ' + ::BiologicalAssociation
.joins("LEFT JOIN a_objects as a_objects1 on a_objects1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = '" + target + "'")
.joins("LEFT JOIN a_objects as a_objects2 on a_objects2.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = '" + target + "'")
.where('a_objects1.id is not null').or('a_objects2.id is not null')
.to_sql
elsif a_sql
s << ' ' + ::BiologicalAssociation
.joins("JOIN a_objects as a_objects1 on a_objects1.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = '" + target + "'")
.to_sql
else
s << ' ' + ::BiologicalAssociation
.joins("JOIN b_objects as b_objects1 on b_objects1.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = '" + target + "'")
.to_sql
end
return ::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
|
#subject_otu_query ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 418
def subject_otu_query
p = otu_params
s = subject_taxon_name_ids
if p.blank? && s.nil?
return nil
elsif s.present?
p[:taxon_name_id] = s
p[:descendants] = descendants
end
base_otu_query(p)
end
|
#subject_scope ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 454
def subject_scope
target_scope('subject')
end
|
#subject_taxon_name_ids ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 795
def subject_taxon_name_ids
return taxon_name_id if taxon_name_id.present?
return subject_taxon_name_id if subject_taxon_name_id.present?
return nil
end
|
#subject_type_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 620
def subject_type_facet
return nil if subject_type.nil?
table[:biological_association_subject_type].eq(subject_type)
end
|
#target_scope(target = 'subject') ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 462
def target_scope(target = 'subject')
a = send((target + '_otu_query').to_sym)
b = send((target + '_collection_object_query').to_sym)
a_sql, b_sql = nil, nil
if !a&.all(true).nil?
a.project_id = project_id
a_sql = a.all.to_sql
end
if !b&.all(true).nil?
b.project_id = project_id
b_sql = b.all.to_sql
end
return nil if a_sql.nil? and b_sql.nil?
a_with = "WITH a_#{target}_objects AS (" + a_sql + ') ' if a_sql
b_with = "WITH b_#{target}_objects AS (" + b_sql + ') ' if b_sql
d, e = nil, nil
if a_with
d = a_with + ::BiologicalAssociation
.joins("JOIN a_#{target}_objects as a_#{target}_objects1 on a_#{target}_objects1.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'Otu'").to_sql
end
if b_with
e = b_with + ::BiologicalAssociation
.joins("JOIN b_#{target}_objects as b_#{target}_objects1 on b_#{target}_objects1.id = biological_associations.biological_association_#{target}_id AND biological_associations.biological_association_#{target}_type = 'CollectionObject'").to_sql
end
::BiologicalAssociation.from(
'(' + [d,e].compact.collect{|q| '(' + q + ')'}.join(' UNION ') + ') as biological_associations'
)
end
|
#taxon_name_query_facet ⇒ Object
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# File 'lib/queries/biological_association/filter.rb', line 702
def taxon_name_query_facet
return nil if taxon_name_query.nil?
s = 'WITH query_tn_ba AS (' + taxon_name_query.all.to_sql + ') '
a = ::BiologicalAssociation
.joins("JOIN otus on otus.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = 'Otu'")
.joins('JOIN query_tn_ba as query_tn_ba1 on otus.taxon_name_id = query_tn_ba1.id')
b = ::BiologicalAssociation
.joins("JOIN otus on otus.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = 'Otu'")
.joins('JOIN query_tn_ba as query_tn_ba2 on otus.taxon_name_id = query_tn_ba2.id')
c = ::BiologicalAssociation
.joins("JOIN collection_objects on collection_objects.id = biological_associations.biological_association_subject_id AND biological_associations.biological_association_subject_type = 'CollectionObject'")
.joins("JOIN taxon_determinations on taxon_determinations.taxon_determination_object_id = collection_objects.id AND taxon_determinations.taxon_determination_object_type = 'CollectionObject'")
.joins('JOIN otus on otus.id = taxon_determinations.otu_id')
.joins('JOIN query_tn_ba as query_tn_ba3 on otus.taxon_name_id = query_tn_ba3.id')
.where('taxon_determinations.position = 1')
d = ::BiologicalAssociation
.joins("JOIN collection_objects on collection_objects.id = biological_associations.biological_association_object_id AND biological_associations.biological_association_object_type = 'CollectionObject'")
.joins("JOIN taxon_determinations on taxon_determinations.taxon_determination_object_id = collection_objects.id AND taxon_determinations.taxon_determination_object_type = 'CollectionObject'")
.joins('JOIN otus on otus.id = taxon_determinations.otu_id')
.joins('JOIN query_tn_ba as query_tn_ba4 on otus.taxon_name_id = query_tn_ba4.id')
.where('taxon_determinations.position = 1')
s << referenced_klass_union([a,b,c,d]).to_sql
::BiologicalAssociation.from('(' + s + ') as biological_associations')
end
|