public t(
FhirDateTime endDate,
Func <FhirDateTime, PositiveInt> numberDaysAfterStartDate,
FhirDateTime startDate)
{
this.Log = LogManager.GetLogger(System.Reflection.MethodBase.GetCurrentMethod().DeclaringType);
this.EndDate = endDate;
this.NumberDaysAfterStartDate = numberDaysAfterStartDate;
this.StartDate = startDate;
ImmutableList <FhirDateTime> .Builder builder = ImmutableList.CreateBuilder <FhirDateTime>();
for (DateTime i = startDate.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date; i <= endDate.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date; i = i.AddDays(1))
{
builder.Add(
new FhirDateTime(
new DateTimeOffset(
i)));
}
this.Value = builder.ToImmutableList();
}
private static Patient GetSomePatientWithProfile(string patientId, string profile)
{
var date = new FhirDateTime(new DateTimeOffset(DateTime.Now));
return(new Patient
{
Meta = new Meta {
LastUpdated = date.ToDateTimeOffset(new TimeSpan()), Profile = new List <string> {
profile
}
},
Id = patientId,
Active = true,
Name =
new List <HumanName>
{
new HumanName {
Family = "Normann", Given = new List <string> {
"Ola"
}
}
},
Telecom =
new List <ContactPoint>
{
new ContactPoint {
System = ContactPoint.ContactPointSystem.Phone, Value = "123467890"
}
},
Gender = AdministrativeGender.Male,
BirthDate = "2000-01-01"
});
}
private static Base MockPatient()
{
var date = new FhirDateTime(DateTime.Now);
return(new Patient
{
Meta = new Meta {
LastUpdated = date.ToDateTimeOffset(), Profile = new List <string> {
"http://helse-nord.no/FHIR/profiles/Identification.Patient/Patient"
}
},
Id = "12345678901",
Active = true,
Name =
new List <HumanName>
{
new HumanName {
Family = "Normann", Given = new List <string> {
"Ola"
}
}
},
Telecom =
new List <ContactPoint>
{
new ContactPoint {
System = ContactPoint.ContactPointSystem.Phone, Value = "123467890"
}
},
Gender = AdministrativeGender.Male,
BirthDate = "2000-01-01"
});
}
public static Period ToPeriod(this FhirDateTime fdt)
{
var result = new Period();
var dtoStart = fdt.ToDateTimeOffset();
result.StartElement = new FhirDateTime(dtoStart);
var dtoEnd = dtoStart;
switch (fdt.Precision())
{
case FhirDateTimePrecision.Year: dtoEnd = dtoStart.AddYears(1); break;
case FhirDateTimePrecision.Month: dtoEnd = dtoStart.AddMonths(1); break;
case FhirDateTimePrecision.Day: dtoEnd = dtoStart.AddDays(1); break;
case FhirDateTimePrecision.Minute: dtoEnd = dtoStart.AddMinutes(1); break;
case FhirDateTimePrecision.Second: dtoEnd = dtoStart.AddSeconds(1); break;
default: dtoEnd = dtoStart; break;
}
result.EndElement = new FhirDateTime(dtoEnd);
return(result);
}
private static Base MockPatient()
{
var date = new FhirDateTime(new DateTimeOffset(DateTime.Now));
return(new Patient
{
Meta = new Meta {
LastUpdated = date.ToDateTimeOffset(new TimeSpan()), Profile = new List <string> {
"http://helse-nord.no/fhir/StructureDefinition/Clinical.Patient/Patient_HN"
}
},
Id = "12345678901",
Active = true,
Name =
new List <HumanName>
{
new HumanName {
Family = "Normann", Given = new List <string> {
"Ola"
}
}
},
Gender = AdministrativeGender.Male,
BirthDate = "2000-01-01"
});
}
private static Base MockPatient()
{
var date = new FhirDateTime(System.DateTime.Now);
return(new Patient
{
Meta = new Meta {
LastUpdated = date.ToDateTimeOffset()
},
Id = "12345678901",
Active = true,
Name =
new List <HumanName>
{
new HumanName {
Family = new List <string> {
"Normann"
}, Given = new List <string> {
"Ola"
}
}
},
Telecom =
new List <ContactPoint>
{
new ContactPoint {
System = ContactPoint.ContactPointSystem.Phone, Value = "123467890"
}
},
Gender = AdministrativeGender.Male,
BirthDate = "2000-01-01"
});
}
public DateTimeValue(string datetime)
{
if (!FhirDateTime.IsValidValue(datetime))
{
throw Error.Argument("datetime", "The string [" + datetime + "] cannot be translated to a DateTimeValue");
}
var fdt = new FhirDateTime(datetime);
Value = fdt.ToDateTimeOffset(TimeSpan.Zero);
}
private OperatorType ProcessLastUpdatedParameter(Tuple <string, string> enumerable, out string dateStr, out DateTimeOffset dateTimeOffset)
{
var dateOperator = GetOperatorForDateOrNumber(enumerable);
dateStr = RemovePrefix(enumerable.Item2, dateOperator);
var dateTime = new FhirDateTime(dateStr);
dateTimeOffset = dateTime.ToDateTimeOffset();
return(dateOperator);
}
public static bool IsValidFhirDateTime(string dateTime)
{
try
{
FhirDateTime dt = new FhirDateTime(dateTime);
DateTimeOffset offset = dt.ToDateTimeOffset(TimeSpan.Zero);
}
catch
{
return(false);
}
return(true);
}
private static ApproximateDateTime processDate(FhirDateTime fhirDateTime)
{
var dt = fhirDateTime.ToDateTimeOffset();
switch (FhirDateTimeExtensions.Precision(fhirDateTime))
{
case FhirDateTimeExtensions.FhirDateTimePrecision.Year:
return(new ItemTypes.ApproximateDateTime()
{
ApproximateDate = new ItemTypes.ApproximateDate(dt.Year)
});
case FhirDateTimeExtensions.FhirDateTimePrecision.Month:
return(new ItemTypes.ApproximateDateTime()
{
ApproximateDate = new ItemTypes.ApproximateDate(dt.Year, dt.Month)
});
case FhirDateTimeExtensions.FhirDateTimePrecision.Day:
return(new ItemTypes.ApproximateDateTime()
{
ApproximateDate = new ItemTypes.ApproximateDate(dt.Year, dt.Month, dt.Day)
});
case FhirDateTimeExtensions.FhirDateTimePrecision.Minute:
return(new ItemTypes.ApproximateDateTime()
{
ApproximateDate = new ItemTypes.ApproximateDate(dt.Year, dt.Month, dt.Day),
ApproximateTime = new ItemTypes.ApproximateTime(dt.Hour, dt.Minute)
});
case FhirDateTimeExtensions.FhirDateTimePrecision.Second:
return(new ItemTypes.ApproximateDateTime()
{
ApproximateDate = new ItemTypes.ApproximateDate(dt.Year, dt.Month, dt.Day),
ApproximateTime = new ItemTypes.ApproximateTime(dt.Hour, dt.Minute, dt.Second)
});
default:
return(new ItemTypes.ApproximateDateTime()
{
ApproximateDate = new ItemTypes.ApproximateDate(dt.Year, dt.Month, dt.Day),
ApproximateTime = new ItemTypes.ApproximateTime(dt.Hour, dt.Minute, dt.Second, dt.Millisecond)
});
}
}
public IDayCumulativeProbableCases_ResultElement Calculate(
FhirDateTime t_IndexElement,
It t,
IDayProbableCases dayProbableCases)
{
return(new C19M.M.C.A.Safi2010.Classes.ResultElements.DayCumulativeProbableCases.DayCumulativeProbableCases_ResultElement(
t_IndexElement,
new FhirDecimal(
t.Value
.Where(w => w.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date >= t.StartDate.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date&& w.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date <= t_IndexElement.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date)
.Select(w => dayProbableCases.GetElementAtAsdecimal(w))
.Max())));
}
public decimal GetElementAtAsdecimal(
FhirDateTime t_IndexElement)
{
return(this.Value
.Where(x => x.t_IndexElement.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date == t_IndexElement.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date)
.Select(x => x.Value.Value.Value)
.SingleOrDefault());
}
private static IMongoQuery DateQuery(String parameterName, Operator optor, String modifier, ValueExpression operand)
{
if (optor == Operator.IN)
{
IEnumerable <ValueExpression> opMultiple = ((ChoiceValue)operand).Choices;
return(M.Query.Or(opMultiple.Select(choice => DateQuery(parameterName, Operator.EQ, modifier, choice))));
}
string start = parameterName + ".start";
string end = parameterName + ".end";
var typedOperand = ((UntypedValue)operand).AsDateValue();
// var value = GroomDate(typedOperand.Value);
var fdtValue = new FhirDateTime(typedOperand.Value);
var value = BsonDateTime.Create(fdtValue.ToDateTimeOffset());
switch (optor)
{
case Operator.EQ:
return
(M.Query.And(
M.Query.Or(M.Query.Exists(start), M.Query.Exists(end)),
M.Query.Or(M.Query.LTE(start, value), M.Query.NotExists(start)),
M.Query.Or(M.Query.GT(end, value), M.Query.NotExists(end))
));
case Operator.GT:
return
(M.Query.Or(
M.Query.GT(parameterName, value),
M.Query.GT(start, value)
));
case Operator.GTE:
return
(M.Query.Or(
M.Query.GTE(parameterName, value),
M.Query.GTE(start, value)
));
case Operator.LT:
return
(M.Query.Or(
M.Query.LT(parameterName, value),
M.Query.LT(end, value)
));
case Operator.LTE:
return
(M.Query.Or(
M.Query.LTE(parameterName, value),
M.Query.LTE(end, value)
));
case Operator.ISNULL:
return(M.Query.EQ(parameterName, null)); //We don't use M.Query.NotExists, because that would exclude resources that have this field with an explicit null in it.
case Operator.NOTNULL:
return(M.Query.NE(parameterName, null)); //We don't use M.Query.Exists, because that would include resources that have this field with an explicit null in it.
default:
throw new ArgumentException(String.Format("Invalid operator {0} on date parameter {1}", optor.ToString(), parameterName));
}
}
public Figure6_DiseaseTransmission()
{
C19M.D.Gumel2006.Interfaces.IFigure6 Figure6 = new C19M.D.Gumel2006.Classes.Figure6();
// Use StartDate, EndDate,and NumberDaysAfterStartDate from Gumel et al. (2004)
FhirDateTime startDate = new FhirDateTime(new DateTimeOffset(new DateTime(2003, 2, 23)));
FhirDateTime endDate = new FhirDateTime(new DateTimeOffset(new DateTime(2003, 2, 23).AddDays(1200)));
Func <FhirDateTime, PositiveInt> numberDaysAfterStartDate =
(x) =>
{
if (x.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date >= startDate.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date)
{
return(new PositiveInt((int)Math.Abs(Math.Round((x.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date - startDate.ToDateTimeOffset(TimeSpan.Zero).UtcDateTime.Date).TotalDays))));
}
else
{
return(new PositiveInt(0));
}
};
// Context
C19M.M.C.A.Gumel2006.Interfaces.Contexts.IGumel2006_Context context = new C19M.M.C.A.Gumel2006.Classes.Contexts.Gumel2006_Context(
endDate,
numberDaysAfterStartDate,
startDate,
Figure6.DiseaseInducedMortalityRate,
new Hl7.Fhir.Model.FhirDecimal(0), // TODO: Change
new Hl7.Fhir.Model.FhirDecimal(10), // TODO: Change
new Hl7.Fhir.Model.FhirDecimal(0), // TODO: Change
new Hl7.Fhir.Model.FhirDecimal(4000000), // TODO: Change
new Hl7.Fhir.Model.FhirDecimal(0), // TODO: Change
Figure6.DevelopmentClinicalSymptomsRate,
Figure6.EffectiveContactRate,
Figure6.RecoveryRate,
Figure6.NaturalMortalityRate,
Figure6.VaccinationCoverageRate,
Figure6.RecruitmentRateSusceptibleHumans,
Figure6.VaccineEfficacy);
// Export
C19M.M.C.A.Gumel2006.Interfaces.Exports.IDiseaseTransmission_Export export = new C19M.M.C.A.Gumel2006.Classes.Exports.DiseaseTransmission_Export(
context);
export.Solve();
this.DayCumulativeDiseaseInducedDeaths = export.DayCumulativeDiseaseInducedDeaths;
this.DayCumulativeProbableCases = export.DayCumulativeProbableCases;
this.DayDiseaseInducedDeaths = export.DayDiseaseInducedDeaths;
this.DayProbableCases = export.DayProbableCases;
this.DayLatentIndividuals = export.DayLatentIndividuals;
this.DayInfectedIndividuals = export.DayInfectedIndividuals;
this.DayTreatedIndividuals = export.DayTreatedIndividuals;
this.DaySusceptibleIndividuals = export.DaySusceptibleIndividuals;
this.DayVaccinatedIndividuals = export.DayVaccinatedIndividuals;
}
public static DateTimeOffset LowerBound(this FhirDateTime fdt)
{
return(fdt.ToDateTimeOffset());
}
public static ThingBase ToHealthVault(this MedicationRequest medicationRequest)
{
var fhirMedication = MedicationRequestHelper.ExtractEmbeddedMedication(medicationRequest);
if (fhirMedication == null)
{
return(null);
}
var hvMedication = fhirMedication.ToHealthVault() as HVMedication;
var practitioner = ExtractEmbeddedPractitioner(medicationRequest);
if (practitioner == null)
{
throw new NotSupportedException($"{nameof(MedicationRequest)} needs to have an embedded Requester Agent");
}
var prescription = new Prescription(practitioner.ToHealthVault());
if (medicationRequest.AuthoredOnElement != null)
{
var dt = medicationRequest.AuthoredOnElement.ToDateTimeOffset();
prescription.DatePrescribed = new ApproximateDateTime(
new ApproximateDate(dt.Year, dt.Month, dt.Day),
new ApproximateTime(dt.Hour, dt.Minute, dt.Second, dt.Millisecond));
}
MedicationRequest.DispenseRequestComponent dispenseRequest = medicationRequest.DispenseRequest;
if (dispenseRequest != null)
{
var numerator = dispenseRequest.Quantity;
if (numerator != null)
{
var structuredMeasurement = new StructuredMeasurement
{
Value = (double)numerator.Value,
Units = CodeToHealthVaultHelper.CreateCodableValueFromQuantityValues(numerator.System,
numerator.Code, numerator.Unit)
};
prescription.AmountPrescribed = new GeneralMeasurement();
prescription.AmountPrescribed.Structured.Add(structuredMeasurement);
}
prescription.Refills = dispenseRequest.NumberOfRepeatsAllowed;
prescription.DaysSupply = GetDaysFromDuration(dispenseRequest.ExpectedSupplyDuration);
FhirDateTime end = dispenseRequest.ValidityPeriod?.EndElement;
if (end != null)
{
var endDate = end.ToDateTimeOffset();
prescription.PrescriptionExpiration = new HealthServiceDate(endDate.Year
, endDate.Month, endDate.Day);
}
}
if (medicationRequest.DosageInstruction.Any())
{
var dosageInstruction = medicationRequest.DosageInstruction
.FirstOrDefault(dosage => dosage.AdditionalInstruction.Any());
if (dosageInstruction != null)
{
var instruction = dosageInstruction.AdditionalInstruction.First();
prescription.Instructions = instruction.ToCodableValue();
}
}
if (medicationRequest.Substitution != null)
{
prescription.Substitution = GetSubstitutionCode(medicationRequest, prescription);
}
hvMedication.Prescription = prescription;
return(hvMedication);
}
(FhirDateTimePrecision)Math.Min(fdt.Value.Length, 18); //Ignore timezone for stating precision.
public static DateTimeOffset LowerBound(this FhirDateTime fdt) => fdt.ToDateTimeOffset(TimeSpan.Zero);
