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 140

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 "      SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid\n        FROM concept_attribute ca\n      INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id\n        AND ca2.attribute_type_id = \#{ConceptAttributeType.nlims_code.concept_attribute_type_id}\n      INNER JOIN concept c ON c.concept_id = ca.concept_id\n      WHERE ca.attribute_type_id = \#{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}\n      AND ca.concept_id IN (\#{specimen_types.select(:concept_id).to_sql})\n      GROUP BY ca.concept_id\n    SQL\n  end\n\n  # Retrieve only those specimen types that belong to concept\n  # set of the selected test_type\n  test_types = ConceptSet.find_members_by_name(Lab::Metadata::TEST_TYPE_CONCEPT_NAME)\n                         .filter_members(name: test_type&.strip)\n                         .select(:concept_id)\n\n  concept_set = ConceptSet.where(\n    concept_id: specimen_types.select(:concept_id),\n    concept_set: test_types\n  )\n\n  return ActiveRecord::Base.connection.select_all <<~SQL\n    SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid\n      FROM concept_attribute ca\n    INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id\n      AND ca2.attribute_type_id = \#{ConceptAttributeType.nlims_code.concept_attribute_type_id}\n    INNER JOIN concept c ON c.concept_id = ca.concept_id\n    WHERE ca.attribute_type_id = \#{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}\n    AND ca.concept_id IN (\#{concept_set.pluck(:concept_id).push(0).join(',')})\n    GROUP BY ca.concept_id\n  SQL\nend\n"

.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 "    SELECT cn.name, cn.concept_id\n    FROM concept_set cs\n            INNER JOIN concept_name cn ON cn.concept_id = cs.concept_id\n            INNER JOIN concept_attribute ca ON ca.value_reference = \#{ActiveRecord::Base.connection.quote(nlims_code)}\n        AND ca.attribute_type_id = \#{ConceptAttributeType.nlims_code.concept_attribute_type_id}\n    WHERE cs.concept_id IN (SELECT concept_set.concept_id\n                            FROM concept_set\n                            WHERE concept_set.concept_set IN (SELECT concept_name.concept_id\n                                                              FROM concept_name\n                                                              WHERE concept_name.voided = 0\n                                                                AND concept_name.name = 'Recommended test method'))\n      AND cs.concept_set IN (SELECT concept_set.concept_id\n                                      FROM concept_set\n                                      WHERE concept_set.concept_set IN (SELECT concept_name.concept_id\n                                                                        FROM concept_name\n                                                                        WHERE concept_name.voided = 0\n                                                                          AND concept_name.name = 'Test type')\n                                        )\n    AND cs.concept_set = ca.concept_id\n    GROUP BY cn.concept_id\n  SQL\nend\n"

.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)
        # Get specimen types to exclude from results
  specimen_types = ConceptSet.find_members_by_name(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME)
                             .select(:concept_id)

  # Find concepts that are linked to the test type AND are measures (but NOT specimens)
  sets = ConceptSet.where(concept_set: test, concept_id: measures)
                   .where.not(concept_id: specimen_types)

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

.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 "      SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid\n        FROM concept_attribute ca\n      INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id\n        AND ca2.attribute_type_id = \#{ConceptAttributeType.nlims_code.concept_attribute_type_id}\n      INNER JOIN concept c ON c.concept_id = ca.concept_id\n      WHERE ca.attribute_type_id = \#{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}\n      AND ca.concept_id IN (\#{test_types.select(:concept_id).to_sql})\n      GROUP BY ca.concept_id\n    SQL\n  end\n\n  # Filter out only those test types that have the specified specimen\n  # type.\n  specimen_types = ConceptSet.find_members_by_name(Lab::Metadata::SPECIMEN_TYPE_CONCEPT_NAME)\n                             .filter_members(name: specimen_type)\n                             .select(:concept_id)\n\n  concept_set = ConceptSet.where(\n    concept_id: specimen_types,\n    concept_set: test_types.select(:concept_id)\n  )\n\n  return ActiveRecord::Base.connection.select_all <<~SQL\n    SELECT ca.concept_id, ca.value_reference as name, ca2.value_reference as nlims_code, c.uuid\n      FROM concept_attribute ca\n    INNER JOIN concept_attribute ca2 ON ca.concept_id = ca2.concept_id\n      AND ca2.attribute_type_id = \#{ConceptAttributeType.nlims_code.concept_attribute_type_id}\n    INNER JOIN concept c ON c.concept_id = ca.concept_id\n    WHERE ca.attribute_type_id = \#{ConceptAttributeType.test_catalogue_name.concept_attribute_type_id}\n    AND ca.concept_id IN (\#{concept_set.select(:concept_set).to_sql})\n    GROUP BY ca.concept_id\n  SQL\nend\n"