public void Write(PathologyReportContainer PathologyReports, string OutputFilePath)
{
string jsonString = JsonConvert.SerializeObject(PathologyReports, Formatting.Indented, new JsonSerializerSettings
{
NullValueHandling = NullValueHandling.Include,
});
File.WriteAllText(OutputFilePath, jsonString);
}
public void Process()
{
this.Options.Validate();
DirectoryInfo RootOutputDirectoryInfo = new DirectoryInfo(this.Options.OutputDirectory);
DirectoryInfo RootHl7v2OutputDirectory = new DirectoryInfo(Path.Combine(RootOutputDirectoryInfo.FullName, "HL7v2 Messages"));
DirectoryInfo RootPdfDirectory = new DirectoryInfo(Options.PdfAttachmentInputDirectory);
DirectoryInfo RootReportDataDirectory = new DirectoryInfo(Options.LogicalModelInputDirectory);
DirectoryInfo RootFhirOutputDirectory = new DirectoryInfo(Path.Combine(RootOutputDirectoryInfo.FullName, "FHIR Bundles (experimental)"));
DirectoryInfo RootCdaPackagesOutputDirectory = new DirectoryInfo(Path.Combine(RootOutputDirectoryInfo.FullName, "CDA Packages"));
DirectoryInfo RootCdaDocumentOutputDirectory = new DirectoryInfo(Path.Combine(RootOutputDirectoryInfo.FullName, "CDA Documents"));
DirectoryInfo TempWorkingCDADocumentDirectoryInfo = new System.IO.DirectoryInfo(System.IO.Path.Combine(Environment.GetFolderPath(Environment.SpecialFolder.ApplicationData), "CdaGeneratorWorkingDirectory\\CDADocuments"));
List <PathologyReportContainer> PathologyReportContainerList = new List <PathologyReportContainer>();
//If below is true we generate the Pathology Data json files from the hard coded source.
if (this.Options.GenerateLogicalModels)
{
WriteLine("----------------------------------------------------------------------");
WriteLine($"The option {nameof(this.Options.GenerateLogicalModels)} is set to True.");
WriteLine("Generate Pathology Report Data files");
//Validate that the folder where we will output the generated LogicalModle files to is empty, as we do not want to overwrite files they may have created.
RootReportDataDirectory.CreateDirectoryIfNoExist();
RootReportDataDirectory = new DirectoryInfo(Options.LogicalModelInputDirectory);
if (RootReportDataDirectory.GetFiles("*.json", SearchOption.TopDirectoryOnly).Count() > 0)
{
throw new ApplicationException($"The {RootReportDataDirectory.FullName} directory must empty when {nameof(this.Options.GenerateLogicalModels)} is set to true.");
}
//Validate that the folder where we will output the PDF files to is empty, as we do not want to overwrite files they may have created.
RootPdfDirectory.CreateDirectoryIfNoExist();
RootPdfDirectory = new DirectoryInfo(Options.PdfAttachmentInputDirectory);
if (RootPdfDirectory.GetFiles("*.pdf", SearchOption.TopDirectoryOnly).Count() > 0)
{
throw new ApplicationException($"The {RootPdfDirectory.FullName} directory must empty when {nameof(this.Options.GenerateLogicalModels)} is set to true.");
}
DirectoryInfo StaticApplicationPdfDiectory = GetApplicationPdfDirectory();
foreach (FileInfo PdfFileInfo in StaticApplicationPdfDiectory.GetFiles("*.pdf", SearchOption.TopDirectoryOnly))
{
PdfFileInfo.CopyTo(Path.Combine(RootPdfDirectory.FullName, PdfFileInfo.Name));
}
var SpiaPathologyReportFactory = new Spia.PathologyReportModel.Factory.SpiaPathologyReportFactory();
PathologyReportContainerList = SpiaPathologyReportFactory.GetAll();
foreach (var PathologyReportContainer in PathologyReportContainerList)
{
FileInfo JsonFilePath = new FileInfo($@"{RootReportDataDirectory.FullName}\{PathologyReportContainer.PathologyReport.PdfFileName.Replace(".pdf", ".json")}");
WriteLine(JsonFilePath.Name);
var Writer = new Spia.PathologyReportModel.JsonFileGenerator();
Writer.Write(PathologyReportContainer, JsonFilePath.FullName);
//Test we can read it back it without error
var Reader = new Spia.PathologyReportModel.JsonFileReader();
var PathologyReportsRead = Reader.ReadPathologyReports(JsonFilePath.FullName);
}
PathologyReportContainerList.Clear();
}
//Read in all Pathology Data json files found in the directory
WriteLine("----------------------------------------------------------------------");
WriteLine("Reading in Pathology Report Logical Model files");
WriteLine($"Input Directory: {RootReportDataDirectory.FullName}");
if (!RootReportDataDirectory.Exists)
{
throw new ApplicationException($"The Pathology Report Logical Model folder does not exist at :{RootReportDataDirectory.FullName}");
}
FileInfo[] ReportDataFileInfoArray = RootReportDataDirectory.GetFiles("*.json", SearchOption.TopDirectoryOnly);
if (ReportDataFileInfoArray.Count() == 0)
{
throw new ApplicationException($"The Pathology Report Logical Model folder contains no Logical Model .json files.");
}
foreach (FileInfo ReportDataFileInfo in RootReportDataDirectory.GetFiles("*.json", SearchOption.TopDirectoryOnly))
{
var Reader = new Spia.PathologyReportModel.JsonFileReader();
try
{
WriteLine(ReportDataFileInfo.Name);
var PathologyReportsRead = Reader.ReadPathologyReports(ReportDataFileInfo.FullName);
PathologyReportContainerList.Add(PathologyReportsRead);
}
catch (Exception Exec)
{
WriteLine($"The Pathology Report Logical Model for file name {ReportDataFileInfo.Name} had the following issue:");
throw Exec;
}
}
if (Options.GenerateHL7Version2Messages)
{
//Validation for HL7 v2
foreach (PathologyReportContainer PathologyReportContainer in PathologyReportContainerList)
{
var ErrorMessageList = new List <string>();
if (!PathologyReportContainer.IsValid(PathologyReportContainer, PathologyReportModel.CustomAttribute.ScopeType.Hl7v2, ErrorMessageList))
{
StringBuilder sb = new StringBuilder("HL7 v2 validation errors where detected:\n");
ErrorMessageList.ForEach(x => sb.Append(x + "\n"));
throw new ApplicationException(sb.ToString());;
}
}
RootHl7v2OutputDirectory.CreateDirectoryIfNoExist();
RootHl7v2OutputDirectory.DeleteAllFileAndDirectories();
//Generate HL7 v2 Messages for each Pathology Data json file
WriteLine("----------------------------------------------------------------------");
WriteLine("Generate HL7 v2 Messages");
WriteLine($"Output Directory: {RootHl7v2OutputDirectory.FullName}");
foreach (PathologyReportContainer PathologyReportContainer in PathologyReportContainerList)
{
string HL7Message = MessageFactory.GetMessage(PathologyReportContainer.PathologyReport, RootPdfDirectory.FullName);
FileInfo HL7MessageFileInfo = new FileInfo($@"{RootHl7v2OutputDirectory}\{PathologyReportContainer.PathologyReport.PdfFileName.Replace(".pdf", ".hl7")}");
File.WriteAllText(HL7MessageFileInfo.FullName, HL7Message);
WriteLine(HL7MessageFileInfo.Name);
}
}
if (Options.GenerateFhirBundles)
{
//Generate FHIR Bundles
WriteLine("----------------------------------------------------------------------");
WriteLine("Generate FHIR Bundles");
WriteLine($"Output Directory: {RootFhirOutputDirectory.FullName}");
RootFhirOutputDirectory.CreateDirectoryIfNoExist();
RootFhirOutputDirectory.DeleteAllFileAndDirectories();
FhirPathologyFactory PathologyFactory = new FhirPathologyFactory();
foreach (PathologyReportContainer PathologyReportContainer in PathologyReportContainerList)
{
string PdfFileName = PathologyReportContainer.PathologyReport.PdfFileName;
FileInfo FhirBundleFilkeInfo = new FileInfo(Path.Combine(RootFhirOutputDirectory.FullName, PdfFileName.Replace(".pdf", ".json")));
string Resource = PathologyFactory.CreateJson(PathologyReportContainer, RootPdfDirectory.FullName);
File.WriteAllText(FhirBundleFilkeInfo.FullName, Resource);
WriteLine($"{FhirBundleFilkeInfo.Name}");
}
}
DirectoryInfo CurrentCDADocuementDirectoryInfo = null;
byte[] Logo = null;
//Generate CDA Documents
if (Options.GenerateCdaDocuments || Options.GenerateCdaPackages)
{
//Get the Logo and convert to Byte array
ImageConverter converter = new ImageConverter();
Logo = (byte[])converter.ConvertTo(Resource.RCPA_PITUS_Logo, typeof(byte[]));
if (!Options.GenerateCdaDocuments)
{
CurrentCDADocuementDirectoryInfo = TempWorkingCDADocumentDirectoryInfo;
}
else
{
CurrentCDADocuementDirectoryInfo = RootCdaDocumentOutputDirectory;
}
CurrentCDADocuementDirectoryInfo.CreateDirectoryIfNoExist();
CurrentCDADocuementDirectoryInfo.DeleteAllFileAndDirectories();
//Generate HL7 v2 Messages for each Pathology Data json file
if (Options.GenerateCdaDocuments)
{
WriteLine("----------------------------------------------------------------------");
WriteLine($"Generate CDA Documents");
WriteLine($"Output Directory: {CurrentCDADocuementDirectoryInfo.FullName}");
}
else
{
WriteLine("----------------------------------------------------------------------");
WriteLine($"Temporarily generate CDA Documents for CDA Packaging");
}
//Validation for CDA
foreach (PathologyReportContainer PathologyReportContainer in PathologyReportContainerList)
{
var ErrorMessageList = new List <string>();
if (!PathologyReportContainer.IsValid(PathologyReportContainer, PathologyReportModel.CustomAttribute.ScopeType.Cda, ErrorMessageList))
{
StringBuilder sb = new StringBuilder("CDA validation errors where detected:\n");
ErrorMessageList.ForEach(x => sb.Append(x + "\n"));
throw new ApplicationException(sb.ToString());;
}
}
foreach (PathologyReportContainer PathologyReportContainer in PathologyReportContainerList)
{
var FileName = PathologyReportContainer.PathologyReport.PdfFileName;
AdhaCdaFileGenerator CdaDocument = new AdhaCdaFileGenerator();
CdaDocument.LogEventMessageDelegate = SpiaFileGenerator.WriteLine;
CdaDocument.Process(PathologyReportContainer, RootPdfDirectory.FullName, CurrentCDADocuementDirectoryInfo.FullName, Logo);
}
}
//Generate CDA Package
if (Options.GenerateCdaPackages)
{
WriteLine("----------------------------------------------------------------------");
WriteLine($"Generate CDA Packages");
WriteLine($"Output Directory: {RootCdaPackagesOutputDirectory.FullName}");
AdhaCdaPackageFileGenerator CdaPackager = new AdhaCdaPackageFileGenerator(Options.NashCertificateSerial);
RootCdaPackagesOutputDirectory.CreateDirectoryIfNoExist();
RootCdaPackagesOutputDirectory.DeleteAllFiles(".zip");
CdaPackager.LogEventMessageDelegate = SpiaFileGenerator.WriteLine;
CdaPackager.Process(Options.CdaPackagerApproverPerson, RootPdfDirectory.FullName, CurrentCDADocuementDirectoryInfo.FullName, RootCdaPackagesOutputDirectory.FullName, Logo);
if (!Options.GenerateCdaDocuments)
{
CurrentCDADocuementDirectoryInfo.DeleteAllFiles(".xml");
}
}
}