SQL_Adapter_QuantifierTest.yml

id: Simple_SQL_Adapter
adapter: care.smith.top.top_phenotypic_query.adapter.sql.SQLAdapter
connection:
  url: jdbc:h2:mem:QuantifierTest;INIT=RUNSCRIPT FROM 'classpath:schemaQuantifierTest.sql'
  user: user
  password: password
subjectQuery:
  baseQuery: "SELECT subject_id, birth_date, sex FROM subject\nWHERE TRUE"
  sexListPart: "\nAND sex IN ({values})"
  birthdateIntervalPart: "\nAND birth_date {operator} {value}"
  output:
    id: subject_id
    sex: sex
    birthdate: birth_date
phenotypeQueries:
  Assessment1:
    baseQuery: "SELECT subject_id, created_at, {phenotype} FROM assessment1\nWHERE {phenotype} IS NOT NULL"
    valueIntervalPart: "\nAND {phenotype} {operator} {value}"
    valueListPart: "\nAND {phenotype} IN ({values})"
    dateTimeIntervalPart: "\nAND created_at {operator} {value}"
    subjectsPart: "\nAND subject_id IN ({values})"
    output:
      subject: subject_id
      value: "{phenotype}"
      dateTime: created_at
birthdateMapping:
  code: http://loinc.org|21112-8
ageMapping:
  code: http://loinc.org|30525-0
  restrictionMappings:
    - model: [ ">=", 18, "<", 34 ]
      source: [ ">=", 19, "<", 34 ]
sexMapping:
  code: http://loinc.org|46098-0
  restrictionMappings:
    - model: [ http://hl7.org/fhir/administrative-gender|male ]
      source: [ male ]
    - model: [ http://hl7.org/fhir/administrative-gender|female ]
      source: [ female ]
    - model: [ http://hl7.org/fhir/administrative-gender|other ]
      source: [ other ]
    - model: [ http://hl7.org/fhir/administrative-gender|unknown ]
      source: [ unknown ]
codeMappings:
  - code: http://loinc.org|3137-7
    type: Assessment1
    unit: cm
    phenotypeMappings:
      phenotype: height
  - code: http://loinc.org|3141-9
    type: Assessment1
    phenotypeMappings:
      phenotype: weight