top-phenotypic-query/src/test/resources/config/Generic_SQL_Adapter_Test.yml at main · Onto-Med/top-phenotypic-query · GitHub

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id: Generic_SQL_Adapter
adapter: care.smith.top.top_phenotypic_query.adapter.sql.SQLAdapter
connection:
  url: jdbc:h2:mem:generic_db;INIT=RUNSCRIPT FROM 'classpath:generic_schema.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:
  default:
    baseQuery: "SELECT subject_id, created_at, unit, number_value, text_value, date_time_value, boolean_value FROM weight\nWHERE code_system || '|' || code IN ({codes}) AND (number_value IS NOT NULL OR text_value IS NOT NULL OR date_time_value IS NOT NULL OR boolean_value IS NOT NULL)"
    numberValueIntervalPart: "\nAND number_value {operator} {value}"
    numberValueListPart: "\nAND number_value IN ({values})"
    dateTimeValueIntervalPart: "\nAND date_time_value {operator} {value}"
    dateTimeValueListPart: "\nAND date_time_value IN ({values})"
    textValueListPart: "\nAND text_value IN ({values})"
    booleanValueListPart: "\nAND boolean_value IN ({values})"
    dateTimeIntervalPart: "\nAND created_at {operator} {value}"
    subjectsPart: "\nAND subject_id IN ({values})"
    output:
      subject: subject_id
      numberValue: number_value
      textValue: text_value
      dateTimeValue: date_time_value
      booleanValue: boolean_value
      dateTime: created_at
  observation:
    baseQuery: "SELECT subject_id, created_at, unit, number_value, text_value, date_time_value, boolean_value FROM height\nWHERE code_system || '|' || code IN ({codes}) AND (number_value IS NOT NULL OR text_value IS NOT NULL OR date_time_value IS NOT NULL OR boolean_value IS NOT NULL)"
    numberValueIntervalPart: "\nAND number_value {operator} {value}"
    numberValueListPart: "\nAND number_value IN ({values})"
    dateTimeValueIntervalPart: "\nAND date_time_value {operator} {value}"
    dateTimeValueListPart: "\nAND date_time_value IN ({values})"
    textValueListPart: "\nAND text_value IN ({values})"
    booleanValueListPart: "\nAND boolean_value IN ({values})"
    dateTimeIntervalPart: "\nAND created_at {operator} {value}"
    subjectsPart: "\nAND subject_id IN ({values})"
    output:
      subject: subject_id
      numberValue: number_value
      textValue: text_value
      dateTimeValue: date_time_value
      booleanValue: boolean_value
      dateTime: created_at
birthdateMapping:
  code: http://loinc.org|21112-8
ageMapping:
  code: http://loinc.org|30525-0
sexMapping:
  code: http://loinc.org|46098-0
  restrictionMappings:
    - model: [ http://hl7.org/fhir/administrative-gender|female, http://hl7.org/fhir/administrative-gender|male ]
      source: [ female, male ]
    - 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
    unit: cm