Module: Lab::ConceptsService

Defined in:
app/services/lab/concepts_service.rb

Overview

A read-only repository of sort for all lab-centric concepts.

Class Method Summary collapse

Class Method Details

.reasons_for_test ⇒ Object 



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# File 'app/services/lab/concepts_service.rb', line 135

def self.reasons_for_test
  ConceptSet.find_members_by_name(Lab::Metadata::REASON_FOR_TEST_CONCEPT_NAME)
            .joins('INNER JOIN concept_name ON concept_name.concept_id = concept_set.concept_id')
            .select('concept_name.concept_id, concept_name.name, concept_name.uuid')
            .map { |concept| { name: concept.name, concept_id: concept.concept_id, uuid: concept.uuid } }
end

.specimen_types(name: nil, test_type: nil) ⇒ Object 



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# File 'app/services/lab/concepts_service.rb', line 71

def self.specimen_types(name: nil, test_type: nil)
  specimen_types = ConceptSet.find_members_by_name(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME)
  specimen_types = specimen_types.filter_members(name: name) if name

  unless test_type
    return ActiveRecord::Base.connection.select_all <<~SQL
      SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
        FROM concept_attribute ca
      INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
        AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
      INNER JOIN concept c ON c.concept_id = ca.concept_id
      WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
      AND ca.concept_id IN (#{specimen_types.select(:concept_id).to_sql})
      GROUP BY ca.concept_id
    SQL
  end

  # Retrieve only those specimen types that belong to concept
  # set of the selected test_type
  test_types = ConceptSet.find_members_by_name(Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
                         .filter_members(name: test_type&.strip)
                         .select(:concept_id)

  concept_set = ConceptSet.where(
    concept_id: specimen_types.select(:concept_id),
    concept_set: test_types
  )

  return ActiveRecord::Base.connection.select_all <<~SQL
    SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
      FROM concept_attribute ca
    INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
      AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
    INNER JOIN concept c ON c.concept_id = ca.concept_id
    WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
    AND ca.concept_id IN (#{concept_set.pluck(:concept_id).push(0).join(',')})
    GROUP BY ca.concept_id
  SQL
end

.test_methods(nlims_code) ⇒ Object 



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# File 'app/services/lab/concepts_service.rb', line 6

def self.test_methods(nlims_code)
  return ActiveRecord::Base.connection.select_all <<~SQL
    SELECT cn.name, cn.concept_id
    FROM concept_set cs
            INNER JOIN concept_name cn ON cn.concept_id = cs.concept_id
            INNER JOIN concept_attribute ca ON ca.value_reference = #{ActiveRecord::Base.connection.quote(nlims_code)}
        AND ca.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
    WHERE cs.concept_id IN (SELECT concept_set.concept_id
                            FROM concept_set
                            WHERE concept_set.concept_set IN (SELECT concept_name.concept_id
                                                              FROM concept_name
                                                              WHERE concept_name.voided = 0
                                                                AND concept_name.name = 'Recommended test method'))
      AND cs.concept_set IN (SELECT concept_set.concept_id
                                      FROM concept_set
                                      WHERE concept_set.concept_set IN (SELECT concept_name.concept_id
                                                                        FROM concept_name
                                                                        WHERE concept_name.voided = 0
                                                                          AND concept_name.name = 'Test type')
                                        )
    AND cs.concept_set = ca.concept_id
    GROUP BY cn.concept_id
  SQL
end

.test_result_indicators(test_type_id) ⇒ Object 



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# File 'app/services/lab/concepts_service.rb', line 111

def self.test_result_indicators(test_type_id)
  # Verify that the specified test_type is indeed a test_type
  test = ConceptSet.find_members_by_name(Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
                   .where(concept_id: Concept.find(test_type_id)&.id)
                   .select(:concept_id)

  # From the members above, filter out only those concepts that are result indicators
  measures = ConceptSet.find_members_by_name(Lab::Metadata::TEST_RESULT_INDICATOR_CONCEPT_NAME)
                       .select(:concept_id)

  sets = ConceptSet.where(concept_set: test, concept_id: measures)

  return ActiveRecord::Base.connection.select_all <<~SQL
    SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
      FROM concept_attribute ca
      INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
        AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
      INNER JOIN concept c ON c.concept_id = ca.concept_id
      WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
      AND ca.concept_id IN (#{sets.pluck(:concept_id).push(0).join(',')})
      GROUP BY ca.concept_id
  SQL
end

.test_types(name: nil, specimen_type: nil) ⇒ Object 



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# File 'app/services/lab/concepts_service.rb', line 31

def self.test_types(name: nil, specimen_type: nil)
  test_types = ConceptSet.find_members_by_name(Lab::Metadata::TEST_TYPE_CONCEPT_NAME)
  test_types = test_types.filter_members(name:) if name

  unless specimen_type
    return ActiveRecord::Base.connection.select_all <<~SQL
      SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
        FROM concept_attribute ca
      INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
        AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
      INNER JOIN concept c ON c.concept_id = ca.concept_id
      WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
      AND ca.concept_id IN (#{test_types.select(:concept_id).to_sql})
      GROUP BY ca.concept_id
    SQL
  end

  # Filter out only those test types that have the specified specimen
  # type.
  specimen_types = ConceptSet.find_members_by_name(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME)
                             .filter_members(name: specimen_type)
                             .select(:concept_id)

  concept_set = ConceptSet.where(
    concept_id: specimen_types,
    concept_set: test_types.select(:concept_id)
  )

  return ActiveRecord::Base.connection.select_all <<~SQL
    SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid
      FROM concept_attribute ca
    INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id
      AND ca2.attribute_type_id = #{ConceptAttributeType.nlims_code.concept_attribute_type_id}
    INNER JOIN concept c ON c.concept_id = ca.concept_id
    WHERE ca.attribute_type_id = #{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}
    AND ca.concept_id IN (#{concept_set.select(:concept_set).to_sql})
    GROUP BY ca.concept_id
  SQL
end