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

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id: Data_Source_SQL_Adapter
adapter: care.smith.top.top_phenotypic_query.adapter.sql.SQLAdapter
connection:
  url: jdbc:h2:mem:data_source_db?allowMultiQueries=true'
  user: user
  password: password
subjectQuery:
  baseQuery: "SELECT encounter_id, birth_date, sex FROM subject s, encounter e\nWHERE s.subject_id = e.subject_id\nAND s.data_source_id = e.data_source_id\nAND s.data_source_id = '{data_source}'"
  sexListPart: "\nAND sex IN ({values})"
  birthdateIntervalPart: "\nAND birth_date {operator} {value}"
  output:
    id: encounter_id
    sex: sex
    birthdate: birth_date
phenotypeQueries:
  default:
    baseQuery: "SELECT encounter_id, date_time, start_date_time, end_date_time, unit, number_value, text_value, date_time_value, boolean_value FROM subject_resource\nWHERE code_system || '|' || code IN ({codes})\nAND data_source_id = '{data_source}'\nAND (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 date_time {operator} {value}"
    output:
      subject: encounter_id
      numberValue: number_value
      textValue: text_value
      dateTimeValue: date_time_value
      booleanValue: boolean_value
      dateTime: date_time
      startDateTime: start_date_time
      endDateTime: end_date_time
  encounter:
    baseQuery: "SELECT encounter_id, type, start_date_time, end_date_time FROM encounter\nWHERE data_source_id = '{data_source}'"
    textValueListPart: "\nAND type IN ({values})"
    dateTimeIntervalPart: "\nAND start_date_time {operator} {value}"
    output:
      subject: encounter_id
      textValue: type
      startDateTime: start_date_time
      endDateTime: end_date_time