Class: Queries::Extract::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Citations, Concerns::Confidences, Concerns::Containable, Concerns::DataAttributes, Concerns::DateRanges, Concerns::Protocols, Concerns::Tags, Helpers
Defined in:
lib/queries/extract/filter.rb

Constant Summary collapse

PARAMS = 
[
  :collection_object_id,
  :descendants,
  :exact_verbatim_anatomical_origin,
  :extract_end_date_range,
  :extract_id,
  :extract_origin,
  :extract_start_date_range,
  :otu_id,
  :protocol_id,
  :repository_id,
  :sequences,
  :taxon_name_id,
  :verbatim_anatomical_origin,
  collection_object_id: [],
  extract_id: [],
  otu_id: [],
  repository_id: [],
  taxon_name_id: [],
].freeze

Constants inherited from Query::Filter

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

Instance Attribute Summary collapse

Attributes inherited from Query::Filter

#anatomical_part_query, #api, #asserted_distribution_query, #biological_association_query, #biological_associations_graph_query, #collecting_event_query, #collection_object_query, #content_query, #controlled_vocabulary_term_query, #conveyance_query, #data_attribute_query, #depiction_query, #descriptor_query, #document_query, #dwc_occurrence_query, #extract_query, #field_occurrence_query, #image_query, #loan_query, #object_global_id, #observation_query, #order_by, #otu_query, #page, #paginate, #params, #per, #person_query, #project_id, #recent, #recent_target, #roll_call, #sound_query, #taxon_name_query, #taxon_name_relationship_query, #venn, #venn_ignore_pagination, #venn_mode

Attributes inherited from Query

#query_string, #terms

Instance Method Summary collapse

Methods included from Helpers

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

Methods inherited from Query::Filter

#all, #all_and_clauses, #all_merge_clauses, #annotator_and_clauses, #annotator_merge_clauses, annotator_params, api_except_params, api_excluded_params, #apply_venn, #attribute_exact_facet, base_filter, base_query_name, base_query_to_h, #deep_permit, #disable_paging, included_annotator_facets, instantiated_base_filter, inverted_subqueries, #model_id_facet, #object_global_id_facet, #only_project?, #only_project_or_less?, #paging_state, params, #permitted_params, #process_url_into_params, #project_id_facet, query_name, #set_nested_queries, #set_paging, set_paging, #shared_and_clauses, #subquery_vector, #target_and_clauses, #venn_query

Methods inherited from Query

#alphabetic_strings, #alphanumeric_strings, base_name, #base_name, #base_query, #build_terms, #cached_facet, #end_wildcard, #levenshtein_distance, #match_ordered_wildcard_pieces_in_cached, #no_terms?, referenced_klass, #referenced_klass, #referenced_klass_except, #referenced_klass_intersection, #referenced_klass_union, #start_and_end_wildcard, #start_wildcard, #table, #wildcard_pieces

Constructor Details

#initialize(query_params) ⇒ Filter

Returns a new instance of Filter.

Parameters:

  • args (Hash) —

    are permitted params



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# File 'lib/queries/extract/filter.rb', line 84

def initialize(query_params)
  super

  @collection_object_id = params[:collection_object_id]
  @descendants = boolean_param(params, :descendants)
  @exact_verbatim_anatomical_origin = params[:exact_verbatim_anatomical_origin]
  @extract_end_date_range = params[:extract_end_date_range]
  @extract_origin = params[:extract_origin]
  @extact_id = params[:extract_id]
  @extract_start_date_range = params[:extract_start_date_range]
  @otu_id = params[:otu_id]
  @repository_id = params[:repository_id]
  @sequences = boolean_param(params, :sequences)
  @taxon_name_id = params[:taxon_name_id]
  @verbatim_anatomical_origin = params[:verbatim_anatomical_origin]

  set_confidences_params(params)
  set_containable_params(params)
  set_citations_params(params)
  set_data_attributes_params(params)
  set_date_params(params)
  set_tags_params(params)
  set_protocols_params(params)
end

Instance Attribute Details

#collection_object_id ⇒ Array of Repository#id

Returns:



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# File 'lib/queries/extract/filter.rb', line 42

def collection_object_id
  @collection_object_id
end

#descendants ⇒ Object

Returns the value of attribute descendants.



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# File 'lib/queries/extract/filter.rb', line 48

def descendants
  @descendants
end

#exact_verbatim_anatomical_origin ⇒ Boolean?

Parameters:

  • extract_anatomical_origin (String) —

    'true', 'false', nil

Returns:

  • (Boolean, nil) 


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

def exact_verbatim_anatomical_origin
  @exact_verbatim_anatomical_origin
end

#extract_end_date_range ⇒ Date? (private)

Parameters:

  • extract_end_date_range (String) —

    yyyy-mm-dd

Returns:

  • (Date, nil) 


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

def extract_end_date_range
  @extract_end_date_range
end

#extract_id ⇒ Object

Returns Array.

Parameters:

  • extract_id (Numeric, String, Array) —

    a set of extract#id

Returns:

  • Array



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# File 'lib/queries/extract/filter.rb', line 81

def extract_id
  @extract_id
end

#extract_origin ⇒ String?

Parameters:

  • see (String) —

    originates_from in app/models/extract.rb for legal values

Returns:

  • (String, nil) 


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# File 'lib/queries/extract/filter.rb', line 67

def extract_origin
  @extract_origin
end

#extract_start_date_range ⇒ Date? (private)

Parameters:

  • extract_start_date_range (String) —

    yyyy-mm-dd

Returns:

  • (Date, nil) 


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# File 'lib/queries/extract/filter.rb', line 53

def extract_start_date_range
  @extract_start_date_range
end

#otu_id ⇒ Array of Repository#id

Returns:



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# File 'lib/queries/extract/filter.rb', line 39

def otu_id
  @otu_id
end

#repository_id ⇒ Array of Repository#id

Returns:



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# File 'lib/queries/extract/filter.rb', line 36

def repository_id
  @repository_id
end

#sequences ⇒ Boolean

Parameters:

  • (String, Boolean, nil)

Returns:

  • (Boolean) 


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# File 'lib/queries/extract/filter.rb', line 62

def sequences
  @sequences
end

#taxon_name_id ⇒ Protonym.id?

Return all extracts linked to OTUs AND CollectionObject that is self or descendant linked to this TaxonName

Returns:

  • (Protonym.id, nil) —

    return all extracts linked to OTUs AND CollectionObject that is self or descendant linked to this TaxonName



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# File 'lib/queries/extract/filter.rb', line 47

def taxon_name_id
  @taxon_name_id
end

#verbatim_anatomical_origin ⇒ String?

Parameters:

  • anatomical_origin (String)

Returns:

  • (String, nil) 


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# File 'lib/queries/extract/filter.rb', line 71

def verbatim_anatomical_origin
  @verbatim_anatomical_origin
end

Instance Method Details

#anatomical_part_query_facet ⇒ Object 



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# File 'lib/queries/extract/filter.rb', line 266

def anatomical_part_query_facet
  return nil if anatomical_part_query.nil?

  ::Extract
    .joins(:related_origin_relationships)
    .where("origin_relationships.old_object_id IN (#{ anatomical_part_query.all.select(:id).to_sql })")
end

#and_clauses ⇒ Array

Returns:

  • (Array) 


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

def and_clauses
  [
    extract_id_facet,
    attribute_exact_facet(:verbatim_anatomical_origin),
    date_made_facet,
    repository_id_facet,
  ]
end

#collection_object_id_facet ⇒ Object 



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

def collection_object_id_facet
  return nil if collection_object_id.empty?
  ::Extract.joins(:origin_collection_objects).where(collection_objects: {id: collection_object_id})
end

#collection_object_query_facet ⇒ Object 



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# File 'lib/queries/extract/filter.rb', line 243

def collection_object_query_facet
  return nil if collection_object_query.nil?
  s = 'WITH query_co_exs AS (' + collection_object_query.all.to_sql + ') ' +
    ::Extract
    .joins(:origin_collection_objects)
    .joins('JOIN query_co_exs as query_co_exs1 on collection_objects.id = query_co_exs1.id')
    .to_sql

  ::Extract.from('(' + s + ') as extracts')
end

#date_made_facet ⇒ Object

TODO: Abstract to single date store range helper



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# File 'lib/queries/extract/filter.rb', line 163

def date_made_facet
  return nil if extract_start_date_range.nil?
  a = extract_start_date_range
  sy,sm,sd = a.year, a.month, a.day
  b = extract_end_date_range
  ey,em,ed = b.year, b.month, b.day

  # 5 possible ranges to consider

  ranges = []

  if sy < ey
    # b/w years
    ranges.push table[:year_made].gt(sy).and(table[:year_made].lt(ey))

    # b/w months start
    ranges.push table[:year_made].eq(sy).and(table[:month_made].gt(sm))

    # b/w months end
    ranges.push table[:year_made].eq(ey).and(table[:month_made].lt(em))
  end

  # days in start month
  ranges.push table[:year_made].eq(sy).and(table[:month_made].eq(sm)).and(table[:day_made].gteq(sd)).and(table[:day_made].lteq(ed))

  # days in end month
  ranges.push table[:year_made].eq(ey).and(table[:month_made].eq(em)).and(table[:day_made].lteq(ed))

  a = ranges.shift
  ranges.each do |r|
    a = a.or(r)
  end
  a
end

#extract_id_facet ⇒ Object 



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

def extract_id_facet
  return nil if extract_id.empty?
  table[:id].in(extract_id)
end

#extract_origin_facet ⇒ Object 



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

def extract_origin_facet
  return nil if extract_origin.nil?
  ::Extract.joins(:related_origin_relationships).where(origin_relationships: {old_object_type: extract_origin})
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/extract/filter.rb', line 284

def merge_clauses
  [
    anatomical_part_query_facet,
    observation_query_facet,
    collection_object_query_facet,
    otu_query_facet,

    collection_object_id_facet,
    extract_origin_facet,
    otu_id_facet,
    sequences_facet,
    taxon_name_id_facet,
  ]
end

#observation_query_facet ⇒ Object 



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# File 'lib/queries/extract/filter.rb', line 255

def observation_query_facet
  return nil if observation_query.nil?
  s = 'WITH query_obs_extracts AS (' + observation_query.all.to_sql + ') ' +
      ::Extract
        .joins(:observations)
        .joins('JOIN query_obs_extracts as query_obs_extracts1 on observations.id = query_obs_extracts1.id')
        .to_sql

  ::Extract.from('(' + s + ') as extracts').distinct
end

#otu_id_facet ⇒ Object 



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

def otu_id_facet
  return nil if otu_id.empty?
  a = ::Extract.joins(:origin_otus).where(otus: {id: otu_id})
  b = ::Extract.joins(origin_collection_objects: [:otus]).where(otus: {id: otu_id})

  ::Extract.from("((#{a.to_sql}) UNION (#{b.to_sql})) as extracts")
end

#otu_query_facet ⇒ Object

!! Targets origins of both Otu, and Determined specimens



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# File 'lib/queries/extract/filter.rb', line 223

def otu_query_facet
  return nil if otu_query.nil?
  w = 'WITH query_otu_exs_a AS (' + otu_query.all.to_sql + ') '

  u1 = ::Extract
    .joins(:origin_otus)
    .joins('JOIN query_otu_exs_a as query_otu_exs_a1 on otus.id = query_otu_exs_a1.id')
    .to_sql

  u2 = ::Extract
    .joins(origin_collection_objects: [:taxon_determinations])
    .joins('JOIN query_otu_exs_a as query_otu_exs_a2 on taxon_determinations.otu_id = query_otu_exs_a2.id')
    .where('taxon_determinations.position = 1')
    .to_sql

  s = w + ::Extract.from("((#{u1}) UNION (#{u2})) as extracts").to_sql

  ::Extract.from('(' + s + ') as extracts')
end

#repository_id_facet ⇒ Object 



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# File 'lib/queries/extract/filter.rb', line 134

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

#sequences_facet ⇒ Object 



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# File 'lib/queries/extract/filter.rb', line 152

def sequences_facet
  return nil if sequences.nil?

  subquery = ::OriginRelationship.where(
    ::OriginRelationship.arel_table[:old_object_id].eq(table[:id])
    .and(::OriginRelationship.arel_table[:new_object_type].eq('Sequence')))
    .arel.exists
  ::Extract.where(sequences ? subquery : subquery.not)
end

#taxon_name_id_facet ⇒ Object

TODO: with() TODO: this is not a join, but an IN x2 UNION, i.e. there is likely room for optimization via a join.



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# File 'lib/queries/extract/filter.rb', line 206

def taxon_name_id_facet
  return nil if taxon_name_id.empty?

  o = nil
  if descendants
    o = ::Otu.descendant_of_taxon_name(taxon_name_id)
  else
    o = ::Otu.where(taxon_name_id:)
  end

  a = ::Extract.joins(:origin_otus).where(otus: o)
  b = ::Extract.joins(:origin_collection_objects).where(collection_objects: ::CollectionObject.joins(:otus).where(otus: o))

  ::Extract.from("((#{a.to_sql}) UNION (#{b.to_sql})) as extracts")
end