Class: Queries::Source::Filter

Inherits:
Query::Filter show all
Includes:
Concerns::Attributes, Concerns::DataAttributes, Concerns::Empty, Concerns::Notes, Concerns::Tags
Defined in:
lib/queries/source/filter.rb

Constant Summary collapse

ATTRIBUTES = 
(::Source.core_attributes - %w{bibtex_type title author serial_id}).map(&:to_sym).freeze
PARAMS = 
[
  *ATTRIBUTES,
  :source_id,
  :taxon_name_id,
  :descendants,
  :author,
  :author_id_or,
  :bibtex_type,
  :citations,
  :citations_on_otus,
  :documents,
  :exact_author,
  :exact_title,
  :in_project,
  :nomenclature,
  :query_term,
  :roles,
  :serial,
  :source_type,
  :title,
  :with_doi,
  :with_title,
  :year_end,
  :year_start,
  author_id: [],
  bibtex_type: [],
  citation_object_type: [],
  empty: [],
  not_empty: [],
  serial_id: [],
  source_id: [],
  taxon_name_id: [],
  topic_id: [],
].freeze

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, #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 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, #deep_permit, included_annotator_facets, inverted_subqueries, #model_id_facet, #object_global_id_facet, params, #permitted_params, #process_url_into_params, 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.

Parameters:

  • params (Hash) 


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# File 'lib/queries/source/filter.rb', line 156

def initialize(query_params)
  super

  @author = params[:author]
  @author_id = params[:author_id]
  @author_id_or =  boolean_param(params,:author_id_or)
  @bibtex_type = params[:bibtex_type]
  @citation_object_type = params[:citation_object_type]
  @citations = boolean_param(params,:citations) # TODO: rename coming to reflect conflict with Citations concern
  @citations_on_otus = boolean_param(params,:citations_on_otus)
  @descendants = boolean_param(params, :descendants)
  @documents = boolean_param(params,:documents)
  @exact_author = boolean_param(params,:exact_author)
  @exact_title = boolean_param(params,:exact_title)
  @in_project = boolean_param(params,:in_project)
  @nomenclature = boolean_param(params,:nomenclature)
  @query_string = params[:query_term]&.delete("\u0000") # TODO: likely remove with current permit() paradigm
  @roles = boolean_param(params,:roles)
  @serial = boolean_param(params,:serial)
  @serial_id = params[:serial_id]
  @source_id = params[:source_id]
  @source_type = params[:source_type]
  @taxon_name_id = params[:taxon_name_id]
  @title = params[:title]
  @topic_id = params[:topic_id]
  @with_doi = boolean_param(params, :with_doi)
  @with_title = boolean_param(params, :with_title)
  @year_end = params[:year_end]
  @year_start = params[:year_start]

  build_terms

  set_data_attributes_params(params)
  set_attributes_params(params)
  set_empty_params(params)
  set_tags_params(params)
  set_user_dates(params)
end

Instance Attribute Details

#author ⇒ Object

Returns the value of attribute author.



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

def author
  @author
end

#author_id ⇒ Object

Returns the value of attribute author_id.



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# File 'lib/queries/source/filter.rb', line 69

def author_id
  @author_id
end

#author_id_or ⇒ Object

Returns the value of attribute author_id_or.



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# File 'lib/queries/source/filter.rb', line 74

def author_id_or
  @author_id_or
end

#bibtex_type ⇒ Array, ...

one of the allowed BibTeX types

Returns:

  • (Array, String, nil) 


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# File 'lib/queries/source/filter.rb', line 153

def bibtex_type
  @bibtex_type
end

#citation_object_type ⇒ Array?

TODO: move tc citations concern

Returns:

  • (Array, nil) 


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

def citation_object_type
  @citation_object_type
end

#citations ⇒ Boolean?

!! TODO - conflicts with citations? !! - yes, this is *used in citations*

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/source/filter.rb', line 95

def citations
  @citations
end

#citations_on_otus ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/queries/source/filter.rb', line 137

def citations_on_otus
  @citations_on_otus
end

#descendants ⇒ Object

Returns the value of attribute descendants.



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# File 'lib/queries/source/filter.rb', line 132

def descendants
  @descendants
end

#documents ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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

def documents
  @documents
end

#exact_author ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/source/filter.rb', line 66

def exact_author
  @exact_author
end

#exact_title ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/source/filter.rb', line 90

def exact_title
  @exact_title
end

#in_project ⇒ Boolean?

! requires ‘project_id`

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/source/filter.rb', line 55

def in_project
  @in_project
end

#nomenclature ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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

def nomenclature
  @nomenclature
end

#roles ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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

def roles
  @roles
end

#serial ⇒ Boolean?

true - with serial_id false - without_serial_id nil - both

Returns:

  • (Boolean, nil) 


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

def serial
  @serial
end

#serial_id ⇒ Object

Returns the value of attribute serial_id.



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# File 'lib/queries/source/filter.rb', line 126

def serial_id
  @serial_id
end

#source_id ⇒ Object

TODO: Change to source_id



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

def source_id
  @source_id
end

#source_type ⇒ String?

Returns:

  • (String, nil) 


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# File 'lib/queries/source/filter.rb', line 123

def source_type
  @source_type
end

#taxon_name_id ⇒ Protonym.id?

Return all sources in Citations linked to this name (or descendants option) to this TaxonName

Returns:

  • (Protonym.id, nil) —

    return all sources in Citations linked to this name (or descendants option) to this TaxonName



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# File 'lib/queries/source/filter.rb', line 131

def taxon_name_id
  @taxon_name_id
end

#title ⇒ Object

Returns the value of attribute title.



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# File 'lib/queries/source/filter.rb', line 86

def title
  @title
end

#topic_id ⇒ Object

Returns the value of attribute topic_id.



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# File 'lib/queries/source/filter.rb', line 77

def topic_id
  @topic_id
end

#with_doi ⇒ Boolean?

Returns:

  • (Boolean, nil) 


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

def with_doi
  @with_doi
end

#with_title ⇒ Boolean?

true - with a title false - without a title nil - both

Returns:

  • (Boolean, nil) 


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# File 'lib/queries/source/filter.rb', line 149

def with_title
  @with_title
end

#year_end ⇒ Object

Returns the value of attribute year_end.



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# File 'lib/queries/source/filter.rb', line 83

def year_end
  @year_end
end

#year_start ⇒ Object

Returns the value of attribute year_start.



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# File 'lib/queries/source/filter.rb', line 80

def year_start
  @year_start
end

Instance Method Details

#ancestor_otus_join ⇒ Object (private) 



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# File 'lib/queries/source/filter.rb', line 468

def ancestor_otus_join
  h = Arel::Table.new(:taxon_name_hierarchies)
  c = ::Citation.arel_table
  o = ::Otu.arel_table

  c.join(o, Arel::Nodes::InnerJoin).on(
    o[:id].eq(c[:citation_object_id]).and(c[:citation_object_type].eq('Otu'))
  ).join(h, Arel::Nodes::InnerJoin).on(
    o[:taxon_name_id].eq(h[:descendant_id]).and(h[:ancestor_id].in(taxon_name_id))
  )
end

#ancestor_taxon_name_classifications_join ⇒ Object (private) 



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# File 'lib/queries/source/filter.rb', line 492

def ancestor_taxon_name_classifications_join
  return nil if taxon_name_id.nil?

  h = Arel::Table.new(:taxon_name_hierarchies)
  c = ::Citation.arel_table
  t = ::TaxonNameClassification.arel_table

  c.join(t, Arel::Nodes::InnerJoin).on(
    t[:id].eq(c[:citation_object_id]).and(c[:citation_object_type].eq('TaxonNameClassification'))
  ).join(h, Arel::Nodes::InnerJoin).on(
    t[:taxon_name_id].eq(h[:descendant_id]).and(h[:ancestor_id].in(taxon_name_id))
  )
end

#ancestor_taxon_name_relationship_join(join_on = :subject_taxon_name_id) ⇒ Object (private) 



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# File 'lib/queries/source/filter.rb', line 506

def ancestor_taxon_name_relationship_join(join_on = :subject_taxon_name_id)
  return nil if taxon_name_id.nil?

  h = Arel::Table.new(:taxon_name_hierarchies)
  c = ::Citation.arel_table
  t = ::TaxonNameRelationship.arel_table

  c.join(t, Arel::Nodes::InnerJoin).on(
    t[:id].eq(c[:citation_object_id]).and(c[:citation_object_type].eq('TaxonNameRelationship'))
  ).join(h, Arel::Nodes::InnerJoin).on(
    t[join_on].eq(h[:descendant_id]).and(h[:ancestor_id].in(taxon_name_id))
  )
end

#ancestor_taxon_names_join ⇒ Object (private) 



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# File 'lib/queries/source/filter.rb', line 480

def ancestor_taxon_names_join
  h = Arel::Table.new(:taxon_name_hierarchies)
  c = ::Citation.arel_table
  t = ::TaxonName.arel_table

  c.join(t, Arel::Nodes::InnerJoin).on(
    t[:id].eq(c[:citation_object_id]).and(c[:citation_object_type].eq('TaxonName'))
  ).join(h, Arel::Nodes::InnerJoin).on(
    t[:id].eq(h[:descendant_id]).and(h[:ancestor_id].in(taxon_name_id))
  )
end

#and_clauses ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 452

def and_clauses
  [
    attribute_exact_facet(:author),
    attribute_exact_facet(:title),
    bibtex_type_facet,
    cached_facet,
    serial_facet,
    serial_id_facet,
    source_type_facet,
    with_title_facet,
    year_facet,
  ]
end

#author_id_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 271

def author_id_facet
  return nil if author_id.empty?
  o = table
  r = ::Role.arel_table

  a = o.alias('a_')
  b = o.project(a[Arel.star]).from(a)

  c = r.alias('r1')

  b = b.join(c, Arel::Nodes::OuterJoin)
    .on(
      a[:id].eq(c[:role_object_id])
    .and(c[:role_object_type].eq('Source'))
    .and(c[:type].eq('SourceAuthor'))
    )

  e = c[:id].not_eq(nil)
  f = c[:person_id].in(author_id)

  b = b.where(e.and(f))
  b = b.group(a['id'])
  b = b.having(a['id'].count.eq(author_id.length)) unless author_id_or
  b = b.as('aut_z1_')

  ::Source.joins(Arel::Nodes::InnerJoin.new(b, Arel::Nodes::On.new(b['id'].eq(o['id'])))).distinct
end

#bibtex_type_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 224

def bibtex_type_facet
  return nil if bibtex_type.empty?
  table[:type].eq('Source::Bibtex').and(table[:bibtex_type].in(bibtex_type))
end

#citation_object_type_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 381

def citation_object_type_facet
  return nil if citation_object_type.empty?
  ::Source.joins(:citations)
    .where(citations: {citation_object_type:}).distinct
end

#citations_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 401

def citations_facet
  return nil if citations.nil?
  if citations
    ::Source.joins(:citations).distinct
  else
    ::Source.where.missing(:citations).distinct
  end
end

#document_facet ⇒ Object

TODO: move to a concern



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# File 'lib/queries/source/filter.rb', line 358

def document_facet
  return nil if documents.nil?

  if documents
    ::Source.joins(:documents, :project_sources).where(project_sources: {project_id:}).distinct
  else
    a = ::Source.where.missing(:documents).distinct
    b = ::Source.joins(:project_sources).where(project_sources: {project_id: }).where.missing(:documentation).distinct

    ::Source.from("((#{a.to_sql}) UNION (#{b.to_sql})) as sources")
  end
end

#identifier_type_facet ⇒ Object

Over-rides Query::Filter identifier_type_facet to handle with_doi exception



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# File 'lib/queries/source/filter.rb', line 318

def identifier_type_facet
  return nil if identifier_type.empty? || with_doi
  q = referenced_klass.joins(:identifiers)
  w = identifier_table[:type].in(identifier_type)
  q.where(w).distinct
end

#in_project_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 304

def in_project_facet
  return nil if project_id.empty? || in_project.nil?

  if in_project
    ::Source.joins(:project_sources)
      .where(project_sources: {project_id:})
  else
    ::Source.left_outer_joins(:project_sources)
      .where('project_sources.project_id != ? OR project_sources.id IS NULL', project_id) # TODO: probably project_id
      .distinct
  end
end

#merge_clauses ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 433

def merge_clauses
  s = ::Queries::Query::Filter::SUBQUERIES.select{|k,v| v.include?(:source)}.keys.map(&:to_s)
  [
    *s.collect{|m| query_facets_facet(m)}, # Reference all the Source referencing SUBQUERIES
    author_id_facet,
    citation_object_type_facet,
    citations_facet,
    document_facet,
    empty_fields_facet, # See Queries::Concerns::Empty
    in_project_facet,
    nomenclature_facet,
    not_empty_fields_facet,
    role_facet,
    taxon_name_id_facet,
    topic_id_facet,
    with_doi_facet,
  ]
end

#nomenclature_facet ⇒ Object 



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

def nomenclature_facet
  return nil if nomenclature.nil?

  if nomenclature
    ::Source.joins(:citations)
      .where(citations: {citation_object_type: ['TaxonName', 'TaxonNameRelationship', 'TaxonNameClassification', 'TypeMaterial']})
      .distinct
  else
    ::Source.left_outer_joins(:citations)
      .where("(citations.citation_object_type NOT IN ('TaxonName','TaxonNameRelationship','TaxonNameClassification','TypeMaterial')) OR (citations.id is null)")
      .distinct
  end
end

#project_id_facet ⇒ Object

Over-ride the inclusion of this facet at the Filter level.



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# File 'lib/queries/source/filter.rb', line 411

def project_id_facet
  nil
end

#project_sources_table ⇒ Arel::Table

Returns:

  • (Arel::Table) 


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# File 'lib/queries/source/filter.rb', line 216

def project_sources_table
  ::ProjectSource.arel_table
end

#query_facets_facet(name = nil) ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 415

def query_facets_facet(name = nil)
  return nil if name.nil?

  q = send((name + '_query').to_sym)

  return nil if q.nil?

  n = "query_#{name}_src"

  s = "WITH #{n} AS (" + q.all.to_sql + ') ' +
    ::Source
    .joins(:citations)
    .joins("JOIN #{n} as #{n}1 on citations.citation_object_id = #{n}1.id AND citations.citation_object_type = '#{name.treetop_camelize}'")
    .to_sql

  ::Source.from('(' + s + ') as sources').distinct
end

#role_facet ⇒ Object

TODO: move to a concern



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# File 'lib/queries/source/filter.rb', line 346

def role_facet
  return nil if roles.nil?

  if roles
    ::Source.joins(:roles).distinct
  else
    ::Source.left_outer_joins(:roles)
      .where(roles: {id: nil}).distinct
  end
end

#serial_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 371

def serial_facet
  return nil if serial.nil?

  if serial
    table[:serial_id].not_eq(nil)
  else
    table[:serial_id].eq(nil)
  end
end

#serial_id_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 267

def serial_id_facet
  serial_id.empty? ? nil : table[:serial_id].in(serial_id)
end

#source_type_facet ⇒ Object 



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

def source_type_facet
  return nil if source_type.blank?
  table[:type].eq(source_type)
end

#taxon_name_id_facet ⇒ Object

Return all citations on Taxon names and descendants, and optionally OTUs.



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# File 'lib/queries/source/filter.rb', line 235

def taxon_name_id_facet
  return nil if taxon_name_id.empty?

  joins = [
    ancestor_taxon_names_join,
    ancestor_taxon_name_classifications_join,
    ancestor_taxon_name_relationship_join(:subject_taxon_name_id),
    ancestor_taxon_name_relationship_join(:object_taxon_name_id)
  ]

  joins.push ancestor_otus_join if citations_on_otus

  union = joins.collect{|j| '(' + ::Source.joins(:citations).joins( j.join_sources).to_sql + ')'}.join(' UNION ')

  ::Source.from("( #{union} ) as sources").distinct
end

#topic_id_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 299

def topic_id_facet
  return nil if topic_id.empty?
  ::Source.joins(:citation_topics).where(citation_topics: { topic_id:}).distinct
end

#with_doi_facet ⇒ Object

TODO: move to generalized code in Identifiers concern



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# File 'lib/queries/source/filter.rb', line 326

def with_doi_facet
  return nil if with_doi.nil?
  if with_doi
    ::Source.joins(:identifiers).where(identifiers: {type: 'Identifier::Global::Doi'}).distinct
  else
    ::Source.left_outer_joins(:identifiers).where("(identifiers.type != 'Identifier::Global::Doi') OR (identifiers.identifier_object_id is null)").distinct
  end
end

#with_title_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 335

def with_title_facet
  return nil if with_title.nil?

  if with_title
    table[:title].not_eq(nil)
  else
    table[:title].eq(nil)
  end
end

#year_facet ⇒ Object 



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# File 'lib/queries/source/filter.rb', line 257

def year_facet
  return nil if year_start.blank?
  if year_start && year_end.present?
    table[:year].gteq(year_start)
      .and(table[:year].lteq(year_end))
  else # only start
    table[:year].eq(year_start)
  end
end