/// <summary>
/// Deserialize JSON into a FHIR MeasureReport
/// </summary>
public static void DeserializeJson(this MeasureReport current, ref Utf8JsonReader reader, JsonSerializerOptions options)
{
string propertyName;
while (reader.Read())
{
if (reader.TokenType == JsonTokenType.EndObject)
{
return;
}
if (reader.TokenType == JsonTokenType.PropertyName)
{
propertyName = reader.GetString();
if (Hl7.Fhir.Serialization.FhirSerializerOptions.Debug)
{
Console.WriteLine($"MeasureReport >>> MeasureReport.{propertyName}, depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
reader.Read();
current.DeserializeJsonProperty(ref reader, options, propertyName);
}
}
throw new JsonException($"MeasureReport: invalid state! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
/// <summary>Adds a report.</summary>
/// <exception cref="ArgumentNullException">Thrown when one or more required arguments are null.</exception>
/// <exception cref="ArgumentException"> Thrown when one or more arguments have unsupported or
/// illegal values.</exception>
/// <param name="report">The report.</param>
public void AddReport(MeasureReport report)
{
if (report == null)
{
throw new ArgumentNullException(nameof(report));
}
if (report.Reporter.Reference != _orgRef)
{
throw new ArgumentException($"Invalid Reporter: {report.Reporter} != collection org: {_orgRef}");
}
if (_reportById.ContainsKey(report.Id))
{
return;
}
if (!_periods.Contains(report.Period.End))
{
_periods.Add(report.Period.End);
}
_reportById.Add(report.Id, report);
_reportByKey.Add(GetKey(report), report);
}
/// <summary>Adds a group to report to 'reportGroup'.</summary>
/// <param name="report"> The report.</param>
/// <param name="reportGroup">Group the report belongs to.</param>
private static void AddGroupToReport(
MeasureReport report,
MeasureReport.GroupComponent reportGroup)
{
if (reportGroup.Population.Count == 0)
{
reportGroup.Population = null;
}
if (reportGroup.Stratifier.Count == 0)
{
reportGroup.Stratifier = null;
}
report.Group.Add(reportGroup);
}
/// <summary>Reports for cdc grouped measure.</summary>
/// <param name="id"> [out] The identifier.</param>
/// <param name="measure">The measure.</param>
/// <param name="data"> The data.</param>
/// <returns>A MeasureReport.</returns>
private static MeasureReport ReportForMeasure(
out string id,
Measure measure,
ReportData data)
{
id = FhirIds.NextId;
MeasureReport report = new MeasureReport()
{
Meta = new Meta()
{
Profile = new string[]
{
FhirSystems.MeasureReport,
},
Security = FhirTriplet.SecurityTest.GetCodingList(),
},
Id = id,
Status = MeasureReport.MeasureReportStatus.Complete,
Type = MeasureReport.MeasureReportType.Summary,
Date = new FhirDateTime(new DateTimeOffset(DateTime.Now)).ToString(),
Period = data.FhirPeriod(),
Measure = measure.Url,
Group = new List <MeasureReport.GroupComponent>(),
};
if (data.ReportDate != null)
{
report.Date = new FhirDateTime(new DateTimeOffset((DateTime)data.ReportDate !)).ToString();
}
if (data.CoveredLocation != null)
{
report.Subject = new ResourceReference(
$"Location/{data.CoveredLocation.Id}",
data.CoveredLocation.Name);
if (data.CoveredOrganization != null)
{
report.Subject.AddExtension(
"http://build.fhir.org/ig/AudaciousInquiry/saner-ig/connectathon/locations",
new FhirString(data.CoveredOrganization.Id));
}
#if false // 2020.05.05 - figure out if we still want contained
data.CoveredLocation.ToFhir(
out ResourceReference resourceReference,
out Resource contained);
report.Subject = resourceReference;
if (contained != null)
{
if (report.Contained == null)
{
report.Contained = new List <Resource>();
}
report.Contained.Add(contained);
}
#endif
}
if (data.Reporter != null)
{
report.Reporter = new ResourceReference(
$"Organization/{data.Reporter.Id}",
data.Reporter.Name);
#if false // 2020.05.05 - figure out if we still want contained
data.Reporter.ToFhir(
out ResourceReference resourceReference,
out Resource contained);
report.Reporter = resourceReference;
if (contained != null)
{
if (report.Contained == null)
{
report.Contained = new List <Resource>();
}
report.Contained.Add(contained);
}
#endif
}
if ((data.Reporter == null) && (data.CoveredOrganization != null))
{
report.Reporter = new ResourceReference(
$"Organization/{data.CoveredOrganization.Id}",
data.CoveredOrganization.Name);
#if false // 2020.05.05 - figure out if we still want contained
data.CoveredOrganization.ToFhir(
out ResourceReference resourceReference,
out Resource contained);
report.Reporter = resourceReference;
if (contained != null)
{
if (report.Contained == null)
{
report.Contained = new List <Resource>();
}
report.Contained.Add(contained);
}
#endif
}
foreach (Measure.GroupComponent measureGroup in measure.Group)
{
if ((measureGroup.Code == null) ||
(measureGroup.Code.Coding == null) ||
(measureGroup.Code.Coding.Count == 0))
{
continue;
}
string groupName = measureGroup.Code.Coding[0].Code;
MeasureReport.GroupComponent reportGroup = new MeasureReport.GroupComponent()
{
Code = measureGroup.Code,
Population = new List <MeasureReport.PopulationComponent>(),
Stratifier = new List <MeasureReport.StratifierComponent>(),
};
if (data.Values.ContainsKey(groupName))
{
if (data.Values[groupName].Score != null)
{
reportGroup.MeasureScore = new Quantity()
{
Value = data.Values[groupName].Score,
};
}
}
if ((measureGroup.Population == null) || (measureGroup.Population.Count == 0))
{
if (data.Values.ContainsKey(groupName))
{
reportGroup.MeasureScore = new Quantity()
{
Value = data.Values[groupName].Score,
};
}
AddGroupToReport(report, reportGroup);
continue;
}
foreach (Measure.PopulationComponent population in measureGroup.Population)
{
if ((population.Code == null) ||
(population.Code.Coding == null) ||
(population.Code.Coding.Count == 0))
{
continue;
}
string populationSystem = null;
string populationName = null;
string populationCode = null;
foreach (Coding popCoding in population.Code.Coding)
{
if ((popCoding.System == FhirSystems.MeasurePopulation) ||
(popCoding.System == FhirSystems.SanerAggregateBool) ||
(popCoding.System == FhirSystems.SanerAggregateChoice))
{
populationSystem = popCoding.System;
populationCode = popCoding.Code;
}
if (data.Values.ContainsKey(popCoding.Code))
{
populationName = popCoding.Code;
}
}
if (populationSystem == FhirSystems.SanerAggregateBool)
{
if (populationCode == "true")
{
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = (data.Values[groupName].BoolValue == true) ? 1 : 0,
});
}
else
{
{
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = (data.Values[groupName].BoolValue == false) ? 1 : 0,
});
}
}
continue;
}
if (!string.IsNullOrEmpty(populationName))
{
switch (populationCode)
{
case "initial-population":
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = (int)data.Values[populationName].Score,
});
break;
case "measure-population":
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = (int)data.Values[populationName].Score,
});
break;
case "measure-observation":
// ignore
break;
case "numerator":
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = data.Values[populationName].Numerator ?? (int)data.Values[populationName].Score,
});
break;
case "denominator":
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = data.Values[populationName].Denominator ?? (int?)data.Values[populationName].Score ?? 1,
});
break;
default:
if (data.Values.ContainsKey(populationName))
{
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
Count = (int)data.Values[populationName].Score,
});
}
else
{
reportGroup.Population.Add(new MeasureReport.PopulationComponent()
{
Code = population.Code,
});
}
break;
}
}
}
AddGroupToReport(report, reportGroup);
}
return(report);
}
/// <summary>
/// Serialize a FHIR MeasureReport into JSON
/// </summary>
public static void SerializeJson(this MeasureReport current, Utf8JsonWriter writer, JsonSerializerOptions options, bool includeStartObject = true)
{
if (includeStartObject)
{
writer.WriteStartObject();
}
writer.WriteString("resourceType", "MeasureReport");
// Complex: MeasureReport, Export: MeasureReport, Base: DomainResource (DomainResource)
((Hl7.Fhir.Model.DomainResource)current).SerializeJson(writer, options, false);
if ((current.Identifier != null) && (current.Identifier.Count != 0))
{
writer.WritePropertyName("identifier");
writer.WriteStartArray();
foreach (Identifier val in current.Identifier)
{
val.SerializeJson(writer, options, true);
}
writer.WriteEndArray();
}
writer.WriteString("status", Hl7.Fhir.Utility.EnumUtility.GetLiteral(current.StatusElement.Value));
writer.WriteString("type", Hl7.Fhir.Utility.EnumUtility.GetLiteral(current.TypeElement.Value));
writer.WriteString("measure", current.MeasureElement.Value);
if (current.Subject != null)
{
writer.WritePropertyName("subject");
current.Subject.SerializeJson(writer, options);
}
if (current.DateElement != null)
{
if (!string.IsNullOrEmpty(current.DateElement.Value))
{
writer.WriteString("date", current.DateElement.Value);
}
if (current.DateElement.HasExtensions() || (!string.IsNullOrEmpty(current.DateElement.ElementId)))
{
JsonStreamUtilities.SerializeExtensionList(writer, options, "_date", false, current.DateElement.Extension, current.DateElement.ElementId);
}
}
if (current.Reporter != null)
{
writer.WritePropertyName("reporter");
current.Reporter.SerializeJson(writer, options);
}
writer.WritePropertyName("period");
current.Period.SerializeJson(writer, options);
if (current.ImprovementNotation != null)
{
writer.WritePropertyName("improvementNotation");
current.ImprovementNotation.SerializeJson(writer, options);
}
if ((current.Group != null) && (current.Group.Count != 0))
{
writer.WritePropertyName("group");
writer.WriteStartArray();
foreach (MeasureReport.GroupComponent val in current.Group)
{
val.SerializeJson(writer, options, true);
}
writer.WriteEndArray();
}
if ((current.EvaluatedResource != null) && (current.EvaluatedResource.Count != 0))
{
writer.WritePropertyName("evaluatedResource");
writer.WriteStartArray();
foreach (ResourceReference val in current.EvaluatedResource)
{
val.SerializeJson(writer, options, true);
}
writer.WriteEndArray();
}
if (includeStartObject)
{
writer.WriteEndObject();
}
}
/// <summary>
/// Deserialize JSON into a FHIR MeasureReport
/// </summary>
public static void DeserializeJsonProperty(this MeasureReport current, ref Utf8JsonReader reader, JsonSerializerOptions options, string propertyName)
{
switch (propertyName)
{
case "identifier":
if ((reader.TokenType != JsonTokenType.StartArray) || (!reader.Read()))
{
throw new JsonException($"MeasureReport error reading 'identifier' expected StartArray, found {reader.TokenType}! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
current.Identifier = new List <Identifier>();
while (reader.TokenType != JsonTokenType.EndArray)
{
Hl7.Fhir.Model.Identifier v_Identifier = new Hl7.Fhir.Model.Identifier();
v_Identifier.DeserializeJson(ref reader, options);
current.Identifier.Add(v_Identifier);
if (!reader.Read())
{
throw new JsonException($"MeasureReport error reading 'identifier' array, read failed! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
if (reader.TokenType == JsonTokenType.EndObject)
{
reader.Read();
}
}
if (current.Identifier.Count == 0)
{
current.Identifier = null;
}
break;
case "status":
if (reader.TokenType == JsonTokenType.Null)
{
current.StatusElement = new Code <Hl7.Fhir.Model.MeasureReport.MeasureReportStatus>();
reader.Skip();
}
else
{
current.StatusElement = new Code <Hl7.Fhir.Model.MeasureReport.MeasureReportStatus>(Hl7.Fhir.Utility.EnumUtility.ParseLiteral <Hl7.Fhir.Model.MeasureReport.MeasureReportStatus>(reader.GetString()));
}
break;
case "_status":
if (current.StatusElement == null)
{
current.StatusElement = new Code <Hl7.Fhir.Model.MeasureReport.MeasureReportStatus>();
}
((Hl7.Fhir.Model.Element)current.StatusElement).DeserializeJson(ref reader, options);
break;
case "type":
if (reader.TokenType == JsonTokenType.Null)
{
current.TypeElement = new Code <Hl7.Fhir.Model.MeasureReport.MeasureReportType>();
reader.Skip();
}
else
{
current.TypeElement = new Code <Hl7.Fhir.Model.MeasureReport.MeasureReportType>(Hl7.Fhir.Utility.EnumUtility.ParseLiteral <Hl7.Fhir.Model.MeasureReport.MeasureReportType>(reader.GetString()));
}
break;
case "_type":
if (current.TypeElement == null)
{
current.TypeElement = new Code <Hl7.Fhir.Model.MeasureReport.MeasureReportType>();
}
((Hl7.Fhir.Model.Element)current.TypeElement).DeserializeJson(ref reader, options);
break;
case "measure":
if (reader.TokenType == JsonTokenType.Null)
{
current.MeasureElement = new Canonical();
reader.Skip();
}
else
{
current.MeasureElement = new Canonical(reader.GetString());
}
break;
case "_measure":
if (current.MeasureElement == null)
{
current.MeasureElement = new Canonical();
}
((Hl7.Fhir.Model.Element)current.MeasureElement).DeserializeJson(ref reader, options);
break;
case "subject":
current.Subject = new Hl7.Fhir.Model.ResourceReference();
((Hl7.Fhir.Model.ResourceReference)current.Subject).DeserializeJson(ref reader, options);
break;
case "date":
if (reader.TokenType == JsonTokenType.Null)
{
current.DateElement = new FhirDateTime();
reader.Skip();
}
else
{
current.DateElement = new FhirDateTime(reader.GetString());
}
break;
case "_date":
if (current.DateElement == null)
{
current.DateElement = new FhirDateTime();
}
((Hl7.Fhir.Model.Element)current.DateElement).DeserializeJson(ref reader, options);
break;
case "reporter":
current.Reporter = new Hl7.Fhir.Model.ResourceReference();
((Hl7.Fhir.Model.ResourceReference)current.Reporter).DeserializeJson(ref reader, options);
break;
case "period":
current.Period = new Hl7.Fhir.Model.Period();
((Hl7.Fhir.Model.Period)current.Period).DeserializeJson(ref reader, options);
break;
case "improvementNotation":
current.ImprovementNotation = new Hl7.Fhir.Model.CodeableConcept();
((Hl7.Fhir.Model.CodeableConcept)current.ImprovementNotation).DeserializeJson(ref reader, options);
break;
case "group":
if ((reader.TokenType != JsonTokenType.StartArray) || (!reader.Read()))
{
throw new JsonException($"MeasureReport error reading 'group' expected StartArray, found {reader.TokenType}! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
current.Group = new List <MeasureReport.GroupComponent>();
while (reader.TokenType != JsonTokenType.EndArray)
{
Hl7.Fhir.Model.MeasureReport.GroupComponent v_Group = new Hl7.Fhir.Model.MeasureReport.GroupComponent();
v_Group.DeserializeJson(ref reader, options);
current.Group.Add(v_Group);
if (!reader.Read())
{
throw new JsonException($"MeasureReport error reading 'group' array, read failed! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
if (reader.TokenType == JsonTokenType.EndObject)
{
reader.Read();
}
}
if (current.Group.Count == 0)
{
current.Group = null;
}
break;
case "evaluatedResource":
if ((reader.TokenType != JsonTokenType.StartArray) || (!reader.Read()))
{
throw new JsonException($"MeasureReport error reading 'evaluatedResource' expected StartArray, found {reader.TokenType}! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
current.EvaluatedResource = new List <ResourceReference>();
while (reader.TokenType != JsonTokenType.EndArray)
{
Hl7.Fhir.Model.ResourceReference v_EvaluatedResource = new Hl7.Fhir.Model.ResourceReference();
v_EvaluatedResource.DeserializeJson(ref reader, options);
current.EvaluatedResource.Add(v_EvaluatedResource);
if (!reader.Read())
{
throw new JsonException($"MeasureReport error reading 'evaluatedResource' array, read failed! depth: {reader.CurrentDepth}, pos: {reader.BytesConsumed}");
}
if (reader.TokenType == JsonTokenType.EndObject)
{
reader.Read();
}
}
if (current.EvaluatedResource.Count == 0)
{
current.EvaluatedResource = null;
}
break;
// Complex: MeasureReport, Export: MeasureReport, Base: DomainResource
default:
((Hl7.Fhir.Model.DomainResource)current).DeserializeJsonProperty(ref reader, options, propertyName);
break;
}
}
/// <summary>Loads from directory.</summary>
/// <exception cref="DirectoryNotFoundException">Thrown when the requested directory is not
/// present.</exception>
/// <param name="dir"> The dir.</param>
private static void LoadFromDirectory(string dir)
{
if (!Directory.Exists(dir))
{
throw new DirectoryNotFoundException($"input directory: {dir} not found!");
}
string[] files = Directory.GetFiles(dir, "*.json", SearchOption.AllDirectories);
foreach (string filename in files)
{
Bundle bundle = _fhirJsonParser.Parse <Bundle>(File.ReadAllText(filename));
if ((bundle.Entry == null) || (bundle.Entry.Count == 0))
{
continue;
}
// traverse the bundle entries
foreach (Bundle.EntryComponent entry in bundle.Entry)
{
if ((entry == null) || (entry.Resource == null))
{
continue;
}
switch (entry.Resource.TypeName)
{
case "Organization":
string orgRef = $"Organization/{entry.Resource.Id}";
if (!_orgsByRef.ContainsKey(orgRef))
{
_orgsByRef.Add(orgRef, (Organization)entry.Resource);
}
break;
case "Location":
// only load site locations
Location loc = (Location)entry.Resource;
if ((loc.PhysicalType != null) &&
(loc.PhysicalType.Coding != null) &&
(loc.PhysicalType.Coding.Count != 0) &&
(loc.PhysicalType.Coding[0].Code == "si"))
{
string locRef = $"Location/{entry.Resource.Id}";
if (!_locationsByRef.ContainsKey(locRef))
{
_locationsByRef.Add(locRef, loc);
}
}
break;
case "Measure":
Measure measure = (Measure)entry.Resource;
if (!_measuresByUrl.ContainsKey(measure.Url))
{
_measuresByUrl.Add(measure.Url, measure);
}
break;
case "MeasureReport":
MeasureReport report = (MeasureReport)entry.Resource;
if (!_reportsByOrgRef.ContainsKey(report.Reporter.Reference))
{
_reportsByOrgRef.Add(
report.Reporter.Reference,
new ReportCollection(report.Reporter.Reference));
}
_reportsByOrgRef[report.Reporter.Reference].AddReport(report);
break;
}
}
}
}
/// <summary>Gets a key.</summary>
/// <param name="report">The report.</param>
/// <returns>The key.</returns>
private static string GetKey(MeasureReport report)
{
return($"{report.Period.End}{report.Measure}");
}