/// <summary>
/// Parse Dataset
/// </summary>
/// <param name="prop"></param>
/// <param name="dataset"></param>
public void Parse(FHIRMapping prop, CSVDataset dataset)
{
foreach (var row in dataset.Rows)
{
var rowId = GetBaseResourceId(prop.BaseResourceId, row);
foreach (var mapping in prop.PropertyMapping)
{
Parse(rowId, prop.BaseReferenceUrl, mapping, row);
}
}
}
private static void Main(string[] args)
{
if (args.Length != 3)
{
Console.WriteLine("============================");
Console.WriteLine("FHIR Converter Tool usage");
Console.WriteLine("FHIRConverter.exe [CSV Flat File] [Mapping json] [Output Json]");
}
var mapping = FHIRMapping.FromJson(args[1]);
var store = new SimpleFHIRStore();
var parser = new FHIRParser(store);
var dataset = CSVLoader.LoadCSV(args[0], true, ',');
parser.Parse(mapping, dataset);
parser.Flush();
store.SaveJson(args[1]);
}
private FHIRMapping CreateTestMapping()
{
var mappings = new List <FHIRPropertyMapping>()
{
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 0,
ColumnName = "PersonID",
ResourceId = "0000001001",
ResourcePath = "ResearchSubject/Id",
ResourceBaseType = "ResearchSubject",
ResourcePathTypes = "ResearchSubject/String",
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 0,
ColumnName = "PersonID",
ResourceId = "0000001001",
ResourcePath = "ResearchSubject/Study/Reference",
ResourceBaseType = "ResearchSubject",
ResourcePathTypes = "ResearchSubject/ResourceReference/String",
ValueTemplate = "http://www.silicofcm.com/fhir/researchStudy/study1",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "ResearchSubject/Study/Type",
ResourcePathTypes = "ResearchSubject/ResourceReference/String",
Value = "ResearchStudy"
}
}
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 2,
ColumnName = "Age",
ResourceId = "{RowNumber}002002",
ResourcePath = "Observation/Value/Value",
ResourceBaseType = "Observation",
ResourcePathTypes = "Observation/SimpleQuantity/Double",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "Observation/Code/Text",
ResourcePathTypes = "Observation/CodeableConcept/String",
Value = "Age"
}
}
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 0,
ColumnName = "PersonID",
ResourceId = "{RowNumber}002002",
ResourcePath = "Observation/Subject/Reference",
ResourceBaseType = "Observation",
ResourcePathTypes = "Observation/ResourceReference/String",
ValueTemplate = "http://www.silicofcm.com/fhir/researchSubject/{value}",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "Observation/Subject/Type",
ResourcePathTypes = "Observation/ResourceReference/String",
Value = "ResearchSubject"
}
}
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 4,
ResourceId = "{RowNumber}002003",
ColumnName = "BP_Diastolic",
ResourceBaseType = "Observation",
ResourcePath = "Observation/Value/Value",
ResourcePathTypes = "Observation/SimpleQuantity/Double",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "Observation/Code/Text",
ResourcePathTypes = "Observation/CodeableConcept/String",
Value = "Diastolic Blood Pressure"
}
}
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 0,
ColumnName = "PersonID",
ResourceId = "{RowNumber}002003",
ResourcePath = "Observation/Subject/Reference",
ResourceBaseType = "Observation",
ResourcePathTypes = "Observation/ResourceReference/String",
ValueTemplate = "http://www.silicofcm.com/fhir/researchSubject/{value}",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "Observation/Subject/Type",
ResourcePathTypes = "Observation/ResourceReference/String",
Value = "ResearchSubject"
}
}
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 1,
ResourceId = "{RowNumber}002003",
ColumnName = "Encounter_Date",
ResourceBaseType = "Observation",
ResourcePath = "Observation/Issued",
ResourcePathTypes = "Observation/DateTimeOffset",
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 1,
ResourceId = "{RowNumber}002002",
ColumnName = "Encounter_Date",
ResourceBaseType = "Observation",
ResourcePath = "Observation/Issued",
ResourcePathTypes = "Observation/DateTimeOffset",
}
};
var mapping = new FHIRMapping();
mapping.BaseReferenceUrl = "http://www.silicofcm.com/fhir";
mapping.BaseResourceId = "001{PersonID}";
mapping.PropertyMapping = mappings;
return(mapping);
}
public static async Task <object> Run([HttpTrigger("post")] HttpRequestMessage req, TraceWriter log)
{
log.Info($"{nameof(PatientAdmissionFunc)} triggered on {DateTime.UtcNow}");
using (var patientTelemetry =
new PatientTelemetry(Environment.GetEnvironmentVariable(CommonConstants.InstumentationKey,
EnvironmentVariableTarget.Process),
nameof(PatientAdmissionFunc)))
{
try
{
var userIdentity = req.GetRequestContext().Principal.Identity as ClaimsIdentity;
var authorization = new ADAuthorization(userIdentity);
patientTelemetry.Caller(authorization.GetCallerName());
if (false == await authorization.Authorize(CommonConstants.CareLineManagerRole))
{
patientTelemetry.Unauthorized();
return(req.CreateResponse(HttpStatusCode.Unauthorized, new
{
result = $"Unauthorized {HttpStatusCode.Unauthorized}"
}));
}
// Get request data
dynamic data = await req.Content.ReadAsAsync <object>();
if (data == null)
{
return(req.CreateResponse(HttpStatusCode.BadRequest, new
{
result = "bad request"
}));
}
// convert the input to the corresponding objects
InPatient inPatient = data.patient.ToObject <InPatient>();
Encounter encounter = data.encounter.ToObject <Encounter>();
List <Observation> observations = data.observations.ToObject <List <Observation> >();
List <Condition> conditions = data.conditions.ToObject <List <Condition> >();
//get resource from key vault
var appResources = await Settings.GetAppResources();
new SqlEncryptionHelper();
//get patient data from FHIR data
var patient = FHIRMapping.PopulatePatientData(inPatient, encounter, observations, conditions);
try
{
var predictLengthOfStayService =
new PredictLengthOfStayService(appResources.PredictLengthOfStayServiceEndpoint,
appResources.PredictLengthOfStayServiceApiKey);
patientTelemetry.DependencyStarted();
patient.PredictedLengthOfStay = await predictLengthOfStayService.PredictLengthOfStay(patient);
patientTelemetry.DependencyCompleted(nameof(PredictLengthOfStayService),
"PredictLengthOfStay", true);
}
catch (PredictLengthOfStayServiceException ex)
{
patientTelemetry.DependencyCompleted(nameof(PredictLengthOfStayService),
"PredictLengthOfStay", false);
patientTelemetry.Error(ex);
}
var hospital = new Hospital(appResources.PatientDbConnectionString);
var id = await hospital.AdmitPatient(patient);
if (id == -1)
{
return(req.CreateResponse(HttpStatusCode.OK, new
{
result = "invalid encounter id"
}));
}
var existingPatient = await hospital.GetPatient(id);
patientTelemetry.Success();
return(req.CreateResponse(HttpStatusCode.OK, new
{
encounterId = existingPatient.Eid,
name = $"{existingPatient.FirstName} {existingPatient.MiddleName} {existingPatient.LastName}",
gender = existingPatient.Gender,
admittedOn = existingPatient.Vdate
}));
}
catch (AuthorizationException ex)
{
patientTelemetry.Error(ex);
return(req.CreateResponse(HttpStatusCode.ExpectationFailed, new
{
error = ex.Message
}));
}
catch (Exception ex)
{
patientTelemetry.Error(ex);
return(req.CreateResponse(HttpStatusCode.InternalServerError, new
{
result = "failed"
}));
}
}
}
public void CreateParserJson()
{
FHIRMapping parser = new FHIRMapping();
parser.PropertyMapping = new List <FHIRPropertyMapping>()
{
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 1,
ColumnName = "Age",
ResourceId = "001001",
ResourcePath = "Observation/Value/Value",
ResourceBaseType = "Observation",
ResourcePathTypes = "Observation/SimpleQuantity/Decimal",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "Observation/Code/Text",
ResourcePathTypes = "Observation/CodeableConcept/String",
Value = "Age"
},
new FHIRProperty()
{
ResourcePath = "Observation/Issued",
ResourcePathTypes = "Observation/DateTimeOffset",
Value = "GETDATE"
}
}
},
new FHIRPropertyMapping()
{
ColumnType = "string",
ColumnIndex = 2,
ResourceId = "001002",
ColumnName = "BMI",
ResourceBaseType = "Observation",
ResourcePath = "Observation/Value/Value",
ResourcePathTypes = "Observation/SimpleQuantity/Decimal",
FixedProperties = new List <FHIRProperty>()
{
new FHIRProperty()
{
ResourcePath = "Observation/Code/Text",
ResourcePathTypes = "Observation/CodeableConcept/String",
Value = "BMI"
},
new FHIRProperty()
{
ResourcePath = "Observation/Issued",
ResourcePathTypes = "Observation/DateTimeOffset",
Value = "GETDATE"
}
}
}
};
parser.ToJson("parser.json");
}
