mimic-hosp-csv-to-fhir-server.json

{
  "id" : "mimic-hosp-csv-to-fhir-server",
  "name" : "mimic-hosp-csv-to-fhir-server",
  "sourceSettings" : {
    "source" : {
      "jsonClass" : "FileSystemSourceSettings",
      "name" : "MIMIC-IV v2.0",
      "sourceUri" : "https://physionet.org/content/mimiciv/2.0",
      "dataFolderPath" : "hdfs://master:9000/mimic-iv-data",
      "asStream" : false
    }
  },
  "sinkSettings" : {
    "jsonClass" : "FileSystemSinkSettings",
    "path" : "hdfs://178.251.45.193:9000/fhir.ndjson",
    "numOfPartitions" : 1,
    "options" : { }
  },
  "terminologyServiceSettings" : {
    "jsonClass" : "LocalFhirTerminologyServiceSettings",
    "folderPath" : "/C:/Users/srdc/IdeaProjects/dt4h/mimic/terminology-systems/terminology",
    "conceptMapFiles" : [ {
      "id" : "labitems-to-loinc.csv",
      "name" : "labitems-to-loinc.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhirmimic-hosp-csv-to-fhir-server.json/ConceptMap/labitems-to-loinc",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/labitems",
      "targetValueSetUrl" : "http://loinc.org/vs"
    }, {
      "id" : "labitem-coded-values-to-loinc.csv",
      "name" : "labitem-coded-values-to-loinc.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/labitem-coded-values-to-other",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/labitem-coded-values",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/labitem-coded-values"
    }, {
      "id" : "admission-location-to-hl7.csv",
      "name" : "admission-location-to-hl7.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/admission-location-to-hl7",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/admission-locations",
      "targetValueSetUrl" : "http://hl7.org/fhir/ValueSet/encounter-admit-source"
    }, {
      "id" : "discharge-location-to-hl7.csv",
      "name" : "discharge-location-to-hl7.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/discharge-location-to-hl7",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/discharge-locations",
      "targetValueSetUrl" : "http://hl7.org/fhir/ValueSet/encounter-discharge-disposition"
    }, {
      "id" : "marital-status-to-hl7.csv",
      "name" : "marital-status-to-hl7.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/marital-status-to-hl7",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/marital-status",
      "targetValueSetUrl" : "http://hl7.org/fhir/ValueSet/marital-status"
    }, {
      "id" : "race-to-hl7.csv",
      "name" : "race-to-hl7.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/race-to-hl7",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/race",
      "targetValueSetUrl" : "http://terminology.hl7.org/ValueSet/v3-Race"
    }, {
      "id" : "medication-units-to-ucum-or-drugform.csv",
      "name" : "medication-units-to-ucum-or-drugform.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/medication-units-to-ucum-or-drugform",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/medication-form-units",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/medication-units"
    }, {
      "id" : "medication-dose-to-orderable-drug-form.csv",
      "name" : "medication-dose-to-orderable-drug-form.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/medication-dose-to-orderable-drug-form",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/medication-dose-units",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/medication-units"
    }, {
      "id" : "medication-route-codes-to-snomed.csv",
      "name" : "medication-route-codes-to-snomed.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/medication-route-codes-to-snomed",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/medication-route-codes",
      "targetValueSetUrl" : "http://hl7.org/fhir/ValueSet/route-codes"
    }, {
      "id" : "careunits-to-hl7.csv",
      "name" : "careunits-to-hl7.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/careunits-to-hl7",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/care-units",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/care-units"
    }, {
      "id" : "services-to-snomed.csv",
      "name" : "services-to-snomed.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/services-to-snomed",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/services",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/services"
    }, {
      "id" : "order-types-to-snomed.csv",
      "name" : "order-types-to-snomed.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/order-types-to-snomed",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/order-types",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/order-types"
    }, {
      "id" : "order-subtypes-to-snomed.csv",
      "name" : "order-subtypes-to-snomed.csv",
      "conceptMapUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ConceptMap/order-subtypes-to-snomed",
      "sourceValueSetUrl" : "https://mimic.mit.edu/fhir/ValueSet/order-subtypes",
      "targetValueSetUrl" : "https://github.com/srdc/mimic-iv-to-fhir/fhir/ValueSet/order-subtypes"
    } ],
    "codeSystemFiles" : [ {
      "id" : "labitems-code-system.csv",
      "name" : "labitems-code-system.csv",
      "codeSystem" : "https://mimic.mit.edu/fhir/CodeSystem/labitems"
    }, {
      "id" : "services.csv",
      "name" : "services.csv",
      "codeSystem" : "https://mimic.mit.edu/fhir/CodeSystem/services"
    } ]
  },
  "mappings" : [ {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/admissions",
    "sourceContext" : {
      "services" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/services.csv",
        "fileFormat" : "csv",
        "options" : { }
      },
      "diagnoses" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/diagnoses_icd.csv",
        "fileFormat" : "csv",
        "options" : { }
      },
      "procedures" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/procedures_icd.csv",
        "fileFormat" : "csv",
        "options" : { }
      },
      "transfers" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/transfers.csv",
        "fileFormat" : "csv",
        "options" : { }
      },
      "admissions" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/admissions.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/careunits",
    "sourceContext" : {
      "careunits" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/transfers.csv",
        "fileFormat" : "csv",
        "options" : { },
        "preprocessSql" : "SELECT DISTINCT CU.careunit FROM careunits CU WHERE CU.careunit IS NOT NULL"
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/diagnoses-icd",
    "sourceContext" : {
      "diagnoses" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/diagnoses_icd.csv",
        "fileFormat" : "csv",
        "options" : { }
      },
      "icdConceptMap" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/d_icd_diagnoses.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/labevents",
    "sourceContext" : {
      "source" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/labevents.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/medications",
    "sourceContext" : {
      "prescribed_meds" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/prescriptions.csv",
        "fileFormat" : "csv",
        "options" : { },
        "preprocessSql" : "SELECT P.drug,P.gsn,P.ndc,P.formulary_drug_cd,first(P.prod_strength) as prod_strength,first(P.form_unit_disp) as form_unit_disp FROM prescribed_meds P GROUP BY P.drug, P.gsn, P.ndc, P.formulary_drug_cd"
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/medications-without-rxn",
    "sourceContext" : {
      "prescribed_meds" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/prescriptions.csv",
        "fileFormat" : "csv",
        "options" : { },
        "preprocessSql" : "SELECT P.drug,P.gsn,P.ndc,P.formulary_drug_cd,first(P.prod_strength) as prod_strength,first(P.form_unit_disp) as form_unit_disp FROM prescribed_meds P GROUP BY P.drug, P.gsn, P.ndc, P.formulary_drug_cd"
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/microbiologyevents",
    "sourceContext" : {
      "microbiologyresults" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/microbiologyevents.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/omr",
    "sourceContext" : {
      "source" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/omr.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/patients",
    "sourceContext" : {
      "source" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/patients.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/poe",
    "sourceContext" : {
      "source" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/poe.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/prescriptions",
    "sourceContext" : {
      "source" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/prescriptions.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  }, {
    "mappingRef" : "https://mimic.mit.edu/fhir/mappings/procedures-icd",
    "sourceContext" : {
      "procedures" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/procedures_icd.csv",
        "fileFormat" : "csv",
        "options" : { }
      },
      "icdConceptMap" : {
        "jsonClass" : "FileSystemSource",
        "path" : "hosp/d_icd_procedures.csv",
        "fileFormat" : "csv",
        "options" : { }
      }
    }
  } ],
  "dataProcessingSettings" : {
    "saveErroneousRecords" : false,
    "archiveMode" : "off"
  },
  "useFhirSinkAsIdentityService" : false
}