Class: Queries::BiologicalAssociation::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, 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,
  :geographic_area_id,
  :geographic_area_mode,
  :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,

  any_global_id: [],
  biological_association_id: [],
  biological_associations_graph_id: [],
  biological_relationship_id: [],
  collecting_event_id: [],
  collection_object_id: [],
  geographic_area_id: [],
  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: [],
].freeze
API_PARAM_EXCLUSIONS = 
[
  :any_global_id
]

Constants inherited from Query::Filter

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

Instance Attribute Summary collapse

Attributes inherited from Query::Filter

#api, #asserted_distribution_query, #biological_association_query, #biological_associations_graph_query, #collecting_event_query, #collection_object_query, #content_query, #descriptor_query, #extract_query, #image_query, #loan_query, #object_global_id, #observation_query, #otu_query, #params, #person_query, #project_id, #recent, #taxon_name_query

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods inherited from Query::Filter

#all, #all_and_clauses, #all_merge_clauses, #annotator_and_clauses, #annotator_merge_clauses, annotator_params, api_except_params, api_excluded_params, #attribute_exact_facet, #deep_permit, included_annotator_facets, inverted_subqueries, #model_id_facet, #object_global_id_facet, params, #permitted_params, #project_id_facet, #set_nested_queries, #shared_and_clauses, #subquery_vector

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_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 153

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]
  @geographic_area_id = params[:geographic_area_id]
  @geographic_area_mode = boolean_param(params, :geographic_area_mode)
  @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]

  set_notes_params(params)
  set_tags_params(params)
  set_citations_params(params)
  set_depiction_params(params)
end

Instance Attribute Details

#any_global_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/biological_association/filter.rb', line 136

def any_global_id
  @any_global_id
end

#biological_association_id ⇒ Array

Returns one or more BiologicalAssociation#id.

Parameters:

  • biological_association_id (Array, Integer)

Returns:

  • (Array) —

    one or more BiologicalAssociation#id



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

def biological_association_id
  @biological_association_id
end

#biological_associations_graph_id ⇒ Array

Returns a biological relationship graph ID.

Parameters:

  • biological_associations_graph_id (Array, Integer)

Returns:

  • (Array) —

    a biological relationship graph ID



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# File 'lib/queries/biological_association/filter.rb', line 103

def biological_associations_graph_id
  @biological_associations_graph_id
end

#biological_relationship_id ⇒ Array

See also exclude_taxon_name_relationship

Parameters:

  • biological_relationship_id (Array, Integer)

Returns:

  • (Array) —

    one or more biological relationship ID



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# File 'lib/queries/biological_association/filter.rb', line 122

def biological_relationship_id
  @biological_relationship_id
end

#collecting_event_id ⇒ Object

linked to one or more CollectingEvent

Parameters:

  • collecting_event_id

Returns:

  • Integer All BiologicalAssociations with CollectionObjects



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# File 'lib/queries/biological_association/filter.rb', line 64

def collecting_event_id
  @collecting_event_id
end

#collection_object_id ⇒ Array

matching subject OR object

Parameters:

  • collection_object_id

Returns:

  • (Array) —

    All biological relationships with CollectionObject (only)



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# File 'lib/queries/biological_association/filter.rb', line 76

def collection_object_id
  @collection_object_id
end

#descendants ⇒ Object

Returns the value of attribute descendants.



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# File 'lib/queries/biological_association/filter.rb', line 99

def descendants
  @descendants
end

#exclude_taxon_name_relationship ⇒ Object

those listed in biological_relationship_id

Returns:

  • Boolean, nil if true then return relationships excluding



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# File 'lib/queries/biological_association/filter.rb', line 58

def exclude_taxon_name_relationship
  @exclude_taxon_name_relationship
end

#geo_json ⇒ Object

Returns the value of attribute geo_json.



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# File 'lib/queries/biological_association/filter.rb', line 140

def geo_json
  @geo_json
end

#geographic_area_id ⇒ Object

Returns the value of attribute geographic_area_id.



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# File 'lib/queries/biological_association/filter.rb', line 141

def geographic_area_id
  @geographic_area_id
end

#geographic_area_mode ⇒ Object

Returns the value of attribute geographic_area_mode.



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

def geographic_area_mode
  @geographic_area_mode
end

#object_biological_property_id ⇒ Array

Returns All BiologicalAssociations with object having this property.

Returns:

  • (Array) —

    All BiologicalAssociations with object having this property



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# File 'lib/queries/biological_association/filter.rb', line 111

def object_biological_property_id
  @object_biological_property_id
end

#object_object_global_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/biological_association/filter.rb', line 133

def object_object_global_id
  @object_object_global_id
end

#object_taxon_name_id ⇒ Object

its children !! TaxonName must be valid!

Parameters:

  • object_taxon_name_id —

    All BiologicalAssociations matching this name or



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# File 'lib/queries/biological_association/filter.rb', line 88

def object_taxon_name_id
  @object_taxon_name_id
end

#object_type ⇒ nil, ...

Returns limit object to a type.

Returns:



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# File 'lib/queries/biological_association/filter.rb', line 151

def object_type
  @object_type
end

#otu_id ⇒ Array

matching subject OR object

Parameters:

  • otu_id

Returns:

  • (Array) —

    All BiologicalAssociations with OTU (only)



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# File 'lib/queries/biological_association/filter.rb', line 70

def otu_id
  @otu_id
end

#subject_biological_property_id ⇒ Array

Returns All BiologicalAssociations with subject having this property.

Returns:

  • (Array) —

    All BiologicalAssociations with subject having this property



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# File 'lib/queries/biological_association/filter.rb', line 107

def subject_biological_property_id
  @subject_biological_property_id
end

#subject_object_global_id ⇒ Array

Returns:

  • (Array) 


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# File 'lib/queries/biological_association/filter.rb', line 130

def subject_object_global_id
  @subject_object_global_id
end

#subject_taxon_name_id ⇒ Object

its children. !! TaxonName must be valid!

Parameters:

  • subject_taxon_name_id —

    All BiologicalAssociations matching this name or



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# File 'lib/queries/biological_association/filter.rb', line 82

def subject_taxon_name_id
  @subject_taxon_name_id
end

#subject_type ⇒ nil, ...

Returns limit subject to a type.

Returns:



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# File 'lib/queries/biological_association/filter.rb', line 147

def subject_type
  @subject_type
end

#taxon_name_id ⇒ Array

their children

Parameters:

  • taxon_name_id

Returns:

  • (Array) —

    All BiologicalAssociations matching these names or



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# File 'lib/queries/biological_association/filter.rb', line 94

def taxon_name_id
  @taxon_name_id
end

#taxon_name_id_mode ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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

def taxon_name_id_mode
  @taxon_name_id_mode
end

#wkt ⇒ Object

See lib/queries/otu/filter.rb



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# File 'lib/queries/biological_association/filter.rb', line 139

def wkt
  @wkt
end

Instance Method Details

#and_clauses ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 662

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,
  ]
end

#any_global_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 533

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

#asserted_distribution_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 600

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

#base_collection_object_query(opts) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 325

def base_collection_object_query(opts)
  q = ::Queries::CollectionObject::Filter.new(opts)
  q.project_id = nil # reset at use
  q
end

#base_otu_query(opts) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 319

def base_otu_query(opts)
  q = ::Queries::Otu::Filter.new(opts)
  q.project_id = nil # reset at use
  q
end

#biological_association_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 553

def biological_association_id_facet
  return nil if biological_association_id.empty?
  table[:id].eq_any(biological_association_id)
end

#biological_associations_graph_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 270

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

#biological_relationship_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 544

def biological_relationship_id_facet
  return nil if biological_relationship_id.empty?
  if exclude_taxon_name_relationship
    table[:biological_relationship_id].not_eq_any(biological_relationship_id)
  else
    table[:biological_relationship_id].eq_any(biological_relationship_id)
  end
end

#collecting_event_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 568

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

#collection_object_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 391

def collection_object_facet
  subject_object_scope(subject_collection_object_query, object_collection_object_query, 'CollectionObject' )
end

#collection_object_params ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 275

def collection_object_params
  h = {}
  [
    :collecting_event_id,
    :collection_object_id,
    :geo_json,
    :geographic_area_id,
    :geographic_area_mode,
    :wkt,
  ].each
    .each do |p|
      v = send(p)
      h[p] = v if v.present?
    end
  h
end

#collection_object_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 614

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

#matching_global_id(target = :subject, global_id = []) ⇒ Object (private) 



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

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

#merge_clauses ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 674

def merge_clauses
  [
    asserted_distribution_query_facet,
    collecting_event_query_facet,
    collection_object_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, # This handles all Otu/CollectionObject attributes
  ]
end

#object_biological_property_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 258

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

#object_collection_object_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 345

def object_collection_object_query
  p = collection_object_params
  s = object_taxon_name_ids

  if p.blank? && s.empty? # .nil?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  q = base_collection_object_query(p)
end

#object_for(global_id) ⇒ Object (private) 



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# File 'lib/queries/biological_association/filter.rb', line 691

def object_for(global_id)
  if o = GlobalID::Locator.locate(global_id)
    o
  else
    nil
  end
end

#object_matches(object) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 252

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

#object_object_global_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 528

def object_object_global_id_facet
  return nil if object_object_global_id.empty?
  matching_global_id(:object, object_object_global_id)
end

#object_otu_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 373

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

#object_scope ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 399

def object_scope
  target_scope('object')
end

#object_taxon_name_ids ⇒ Object (private)

!! Plural is correct



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# File 'lib/queries/biological_association/filter.rb', line 711

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

#object_type_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 558

def object_type_facet
  return nil if object_type.nil?
  table[:biological_association_object_type].eq(object_type)
end

#otu_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 387

def otu_facet
  subject_object_scope(subject_otu_query, object_otu_query, 'Otu' )
end

#otu_params ⇒ Object 



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

def otu_params
  h = {}
  [
    :geo_json,
    :geographic_area_id,
    :geographic_area_mode,
    :otu_id,
    :wkt,
  ].each do |p|
    v = send(p)
    h[p] = v if v.present?
  end
  h
end

#otu_query_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 586

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

#subject_biological_property_id_facet ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 264

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

#subject_collection_object_query ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 331

def subject_collection_object_query
  p = collection_object_params
  s = subject_taxon_name_ids

  if p.blank? && s.empty? #.nil?
    return nil
  elsif s.present?
    p[:taxon_name_id] = s
    p[:descendants] = descendants
  end

  q = base_collection_object_query(p)
end

#subject_matches(object) ⇒ Object 



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# File 'lib/queries/biological_association/filter.rb', line 246

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 444

def subject_object_facet
  a = subject_scope
  b = object_scope

  return nil if a.nil? && b.nil?

  case taxon_name_id_mode
  when true # and
    ::BiologicalAssociation.from(
      '(' + [a,b].compact.collect{|q| '(' + q.to_sql + ')'}.join(' INTERSECT ') + ') as biological_associations'
    )
  when false, nil # or
    ::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 523

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 464

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?

  # Setup for "WITH" use
  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(', ')

  # subject/object queries reference different params
  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

    # subject/object queries reference same params
  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

    # subject only
  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

    # object_only
  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 359

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 395

def subject_scope
  target_scope('subject')
end

#subject_taxon_name_ids ⇒ Object (private)

!! Plural is correct



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# File 'lib/queries/biological_association/filter.rb', line 718

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 563

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 403

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?

  # Setup for "WITH" use
  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

Brute-force style



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# File 'lib/queries/biological_association/filter.rb', line 630

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.biological_collection_object_id = collection_objects.id')
    .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.biological_collection_object_id = collection_objects.id')
    .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