/// <summary>
/// Gets back a resource from a xml sample file.
/// </summary>
/// <param name="fileName">The XML filename, omit the extension</param>
public static Resource GetXmlSample(string fileName)
{
var fhirSource = GetXml(fileName);
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
return(parser.Parse <Resource>(fhirSource));
}
public PatientFixture()
{
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
var tpXml = TestData.ReadTextFile("fp-test-patient.xml");
var patient = parser.Parse <Patient>(tpXml);
TestInput = new PocoNavigator(patient);
tpXml = TestData.ReadTextFile("questionnaire-example.xml");
var quest = parser.Parse <Questionnaire>(tpXml);
Questionnaire = new PocoNavigator(quest);
tpXml = TestData.ReadTextFile("uuid.profile.xml");
var uuid = parser.Parse <StructureDefinition>(tpXml);
UuidProfile = new PocoNavigator(uuid);
Xdoc = new XDocument(new XElement("group", new XAttribute("name", "CSharpTests")));
}
protected void ParseResponseBody()
{
var tpXml = this.Body;
Patient Patient = null;
if (this.Format == FhirApi.FhirFormat.Xml)
{
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
Patient = parser.Parse <Patient>(tpXml);
}
else
{
var parser = new Hl7.Fhir.Serialization.FhirJsonParser();
Patient = parser.Parse <Patient>(tpXml);
}
IElementNavigator PocoPatient = new PocoNavigator(Patient);
this.ApiPatient = new ApiPatient(PocoPatient);
}
protected void ParseResponseBody()
{
var tpXml = this.Body;
Bundle Bundle = null;
if (this.Format == FhirApi.FhirFormat.Xml)
{
var parser = new Hl7.Fhir.Serialization.FhirXmlParser();
Bundle = parser.Parse <Bundle>(tpXml);
}
else
{
var parser = new Hl7.Fhir.Serialization.FhirJsonParser();
Bundle = parser.Parse <Bundle>(tpXml);
}
IElementNavigator PocoBundel = new PocoNavigator(Bundle);
foreach (var RelatedPerson in PocoBundel.Select(@"Bundle.entry.select(resource as RelatedPerson)"))
{
ApiRelatedPerson ApiRelatedPerson = new ApiRelatedPerson(RelatedPerson);
ApiRelatedPersonList.Add(ApiRelatedPerson);
}
}
private Resource DeSerializeFromXml(System.Xml.XmlReader XmlReader)
{
Hl7.Fhir.Serialization.FhirXmlParser FhirXmlParser = new Hl7.Fhir.Serialization.FhirXmlParser();
return(FhirXmlParser.Parse <Resource>(XmlReader));
}
/// <summary>
/// Process the specified excel file into a dataset file
/// </summary>
private static void Main(string[] args)
{
try
{
Console.WriteLine("SanteDB Vocabulary Importer v{0} ({1})", Assembly.GetEntryAssembly().GetName().Version, Assembly.GetEntryAssembly().GetCustomAttribute <AssemblyInformationalVersionAttribute>().InformationalVersion);
Console.WriteLine("Copyright (C) 2015-2022 See NOTICE for contributors");
var parms = new ParameterParser <ConsoleParameters>().Parse(args);
Dataset retVal = new Dataset()
{
Id = parms.Name ?? "Imported Dataset",
Action = new List <DataInstallAction>()
};
// Process a FHIR
if (parms.Fhir || parms.Csv)
{
if (!File.Exists(parms.SourceFile))
{
throw new FileNotFoundException($"{parms.SourceFile} not found");
}
if (parms.Fhir)
{
using (var fhirFileStream = File.OpenRead(parms.SourceFile))
{
using (var xreader = XmlReader.Create(fhirFileStream))
{
var fsz = new Hl7.Fhir.Serialization.FhirXmlParser();
var cs = fsz.Parse <Hl7.Fhir.Model.CodeSystem>(xreader);
retVal.Id = $"Import FHIR Code System {cs.Id}";
var csId = Guid.NewGuid();
retVal.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = new CodeSystem()
{
Key = csId,
Authority = CamelCase(cs.Name),
Url = cs.Url,
Oid = cs.Identifier.First(i => i.System == "urn:ietf:rfc:3986").Value,
VersionText = cs.Version,
Name = cs.Title
}
});
if (parms.CreateConcept)
{
var setId = Guid.NewGuid();
retVal.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
Key = setId,
Name = cs.Name,
Mnemonic = CamelCase(cs.Name),
Url = cs.Url,
Oid = cs.Identifier.First(i => i.System == "urn:ietf:rfc:3986").Value
}
});
retVal.Action.AddRange(cs.Concept.SelectMany(o => ConvertToReferenceTerm(o, csId, setId, cs.Name)));
}
else
{
retVal.Action.AddRange(cs.Concept.SelectMany(o => ConvertToReferenceTerm(o, csId, null, null)));
}
}
}
}
else if (parms.Csv)
{
// Open excel file stream
using (var excelFileStream = File.OpenRead(parms.SourceFile))
{
using (var importWkb = new XLWorkbook(excelFileStream, new LoadOptions()
{
RecalculateAllFormulas = false
}))
{
retVal.Action = importWkb.Worksheets.SelectMany(o => o.Rows()).SelectMany(o => CreateReferenceTermInstruction(o, parms)).ToList();
}
}
}
if (parms.CreateConcept)
{
retVal.Action.Add(new DataUpdate()
{
InsertIfNotExists = true,
Element = new ConceptSet()
{
ConceptsXml = retVal.Action.Where(o => o.Element is Concept).Select(o => o.Element.Key.Value).ToList(),
Mnemonic = parms.Prefix,
Name = "A new Code System",
Oid = ""
}
});
}
if (parms.OutputFile == "-")
{
new XmlSerializer(typeof(Dataset)).Serialize(Console.Out, retVal);
}
else
{
using (var fs = File.Create(parms.OutputFile))
{
new XmlSerializer(typeof(Dataset)).Serialize(fs, retVal);
}
}
}
else
{
new ParameterParser <ConsoleParameters>().WriteHelp(Console.Out);
}
}
catch (Exception e)
{
Console.Error.WriteLine("Error processing file: {0}", e);
}
}