Hello @Pranouti mam,
below is our file of prescription sample for which we are facing null pointer issue in validate function .
package com.dpdocter.security;
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.List;
import java.util.Scanner;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.filefilter.WildcardFileFilter;
import org.apache.log4j.Logger;
import org.hl7.fhir.common.hapi.validation.support.CommonCodeSystemsTerminologyService;
import org.hl7.fhir.common.hapi.validation.support.InMemoryTerminologyServerValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.PrePopulatedValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.SnapshotGeneratingValidationSupport;
import org.hl7.fhir.common.hapi.validation.support.ValidationSupportChain;
import org.hl7.fhir.common.hapi.validation.validator.FhirInstanceValidator;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.hl7.fhir.r4.model.Composition;
import org.hl7.fhir.r4.model.Composition.CompositionStatus;
import org.hl7.fhir.r4.model.Composition.SectionComponent;
import org.hl7.fhir.r4.model.DateTimeType;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.InstantType;
import org.hl7.fhir.r4.model.Meta;
import org.hl7.fhir.r4.model.Narrative;
import org.hl7.fhir.r4.model.Narrative.NarrativeStatus;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.FileSystemResource;
import org.hl7.fhir.r4.model.Reference;
import org.hl7.fhir.r4.model.StructureDefinition;
import com.amazonaws.auth.BasicAWSCredentials;
import com.amazonaws.services.s3.AmazonS3;
import com.amazonaws.services.s3.AmazonS3Client;
import com.amazonaws.services.s3.model.ObjectMetadata;
import com.amazonaws.services.s3.model.PutObjectRequest;
import com.dpdocter.collections.PatientCollection;
import com.dpdocter.collections.PrescriptionCollection;
import com.dpdocter.exceptions.BusinessException;
import com.dpdocter.exceptions.ServiceError;
import com.dpdocter.response.JasperReportResponse;
import com.dpdocter.services.impl.JasperReportServiceImpl;
import com.jaspersoft.mongodb.connection.MongoDbConnection;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.context.support.DefaultProfileValidationSupport;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.validation.FhirValidator;
import ca.uhn.fhir.validation.SingleValidationMessage;
import ca.uhn.fhir.validation.ValidationResult;
import common.util.web.DPDoctorUtils;
import net.sf.jasperreports.engine.JREmptyDataSource;
import net.sf.jasperreports.engine.JRException;
import net.sf.jasperreports.engine.JasperCompileManager;
import net.sf.jasperreports.engine.JasperExportManager;
import net.sf.jasperreports.engine.JasperFillManager;
import net.sf.jasperreports.engine.JasperPrint;
import net.sf.jasperreports.engine.JasperReport;
import net.sf.jasperreports.engine.design.JasperDesign;
/**
-
The PrescriptionSample class populates, validates, parse and serializes Clinical Artifact - Prescription
*/
public class PrescriptionSample {
private static Logger logger = Logger.getLogger(PrescriptionSample.class.getName());
@Value(value = “${bucket.name}”)
private String bucketName;
@Value(value = “${mail.aws.key.id}”)
private String AWS_KEY;
@Value(value = “${mail.aws.secret.key}”)
private String AWS_SECRET_KEY;
// The FHIR context is the central starting point for the use of the HAPI FHIR API
// It should be created once, and then used as a factory for various other types of objects (parsers, clients, etc.)
static FhirContext ctx = FhirContext.forR4();
static FhirInstanceValidator instanceValidator;
static FhirValidator validator;
public static String prescriptionConvert(PrescriptionCollection prescriptionCollection,PatientCollection patientCollection) throws DataFormatException, IOException
{
String serializeBundle=null;
try {
//Initialize validation support and loads all required profiles
init();
// Populate the resource
Bundle prescriptionBundle = populatePrescriptionBundle(prescriptionCollection,patientCollection);
// Validate it. Validate method return result of validation in boolean
// If validation result is true then parse, serialize operations are performed
if(validate(prescriptionBundle))
{
System.out.println("Validated populated Prescripton bundle successfully");
// Instantiate a new parser
IParser parser= ctx.newJsonParser();
// Enter file path (Eg: C://generatedexamples//bundle-prescriptionrecord.json)
// Depending on file type xml/json instantiate the parser
// File file;
// Scanner scanner = new Scanner(System.in);
// System.out.println("\nEnter file path to write bundle");
// String filePath = scanner.nextLine();
// if(FilenameUtils.getExtension(filePath).equals(“json”))
// {
// parser = ctx.newJsonParser();
// }
// else if(FilenameUtils.getExtension(filePath).equals(“xml”))
// {
// parser = ctx.newXmlParser();
// }
// else
// {
// System.out.println(“Invalid file extention!”);
// scanner.close();
// return null;
// }
// Indent the output
parser.setPrettyPrint(true);
// Serialize populated bundle
serializeBundle = parser.encodeResourceToString(prescriptionBundle);
System.out.println("out"+serializeBundle);
// Write serialized bundle in xml/json file
// file = new File(filePath);
// file.createNewFile();
// FileWriter writer = new FileWriter(file);
// writer.write(serializeBundle);
// writer.flush();
// writer.close();
// scanner.close();
// Parse the xml/json file
//IBaseResource resource = parser.parseResource(new FileReader(new File(filePath)));
IBaseResource resource = parser.parseResource(serializeBundle);
// Validate Parsed file
if(validate(resource)){
System.out.println("Validated parsed file successfully");
}
else{
throw new BusinessException(ServiceError.Unknown, "Failed to validate parsed file");
}
}
else
{
throw new BusinessException(ServiceError.Unknown, "Failed to validate populate Prescription bundle : ");
}
}
catch (BusinessException e) {
e.printStackTrace();
logger.error("Error : " + e.getMessage());
throw new BusinessException(ServiceError.Unknown, "Error : " + e.getMessage());
}
return serializeBundle;
}
// Populate Composition for Prescription
static Composition populatePrescriptionCompositionResource()
{
Composition composition = new Composition();
// Set logical id of this artifact
composition.setId("Composition-01");
// Set metadata about the resource - Version Id, Lastupdated Date, Profile
Meta meta = composition.getMeta();
meta.setVersionId("1");
meta.setLastUpdatedElement(new InstantType("2020-07-09T15:32:26.605+05:30"));
meta.addProfile("https://nrces.in/ndhm/fhir/r4/StructureDefinition/PrescriptionRecord");
// Set language of the resource content
composition.setLanguage("en-IN");
// Plain text representation of the concept
Narrative text= composition.getText();
text.setStatus((NarrativeStatus.GENERATED));
text.setDivAsString("<div xmlns=\"http://www.w3.org/1999/xhtml\">Prescription report</div>");
// Set version-independent identifier for the Composition
Identifier identifier = composition.getIdentifier();
identifier.setSystem("https://ndhm.in/phr");
identifier.setValue("645bb0c3-ff7e-4123-bef5-3852a4784813");
// Status can be preliminary | final | amended | entered-in-error
composition.setStatus(CompositionStatus.FINAL);
// Kind of composition ("Prescription record ")
composition.setType(new CodeableConcept(new Coding("http://snomed.info/sct", "440545006", "Prescription record")));
// Set subject - Who and/or what the composition/Prescription record is about
composition.setSubject(new Reference().setReference("Patient/Patient-01"));
// Set Timestamp
composition.setDateElement(new DateTimeType("2017-05-27T11:46:09+05:30"));
// Set author - Who and/or what authored the composition/Presciption record
composition.addAuthor(new Reference().setReference("Practitioner/Practitioner-01"));
// Set a Human Readable name/title
composition.setTitle("Prescription record");
// Composition is broken into sections / Prescription record contains single section to define the relevant medication requests
// Entry is a reference to data that supports this section
Reference reference1 = new Reference();
reference1.setReference("MedicationRequest/MedicationRequest-01");
reference1.setType("MedicationRequest");
Reference reference2 = new Reference();
reference2.setReference("MedicationRequest/MedicationRequest-02");
reference2.setType("MedicationRequest");
Reference reference3 = new Reference();
reference3.setReference("Binary/Binary-01");
reference3.setType("Binary");
SectionComponent section = new SectionComponent();
section.setTitle("Prescription record");
section.setCode(new CodeableConcept(new Coding("http://snomed.info/sct", "440545006", "Prescription record"))).
addEntry(reference1).
addEntry(reference2).
addEntry(reference3);
composition.addSection(section);
return composition;
}
// Populate Prescription Bundle
public static Bundle populatePrescriptionBundle(PrescriptionCollection prescriptionCollection, PatientCollection patientCollection)
{
Bundle prescriptionBundle = new Bundle();
// Set logical id of this artifact
prescriptionBundle.setId("prescription-bundle-01");
// Set metadata about the resource
Meta meta = prescriptionBundle.getMeta();
meta.setVersionId("1");
meta.setLastUpdatedElement(new InstantType("2020-07-09T15:32:26.605+05:30"));
meta.addProfile("https://nrces.in/ndhm/fhir/r4/StructureDefinition/DocumentBundle");
// Set Confidentiality as defined by affinity domain
meta.addSecurity(new Coding("http://terminology.hl7.org/CodeSystem/v3-Confidentiality", "V", "very restricted"));
// Set version-independent identifier for the Bundle
Identifier identifier = prescriptionBundle.getIdentifier();
identifier.setValue("bc3c6c57-2053-4d0e-ac40-139ccccff645");
identifier.setSystem("http://hip.in");
// Set Bundle Type
prescriptionBundle.setType(BundleType.DOCUMENT);
// Set Timestamp
prescriptionBundle.setTimestampElement(new InstantType("2020-07-09T15:32:26.605+05:30"));
// Add resources entries for bundle with Full URL
List<BundleEntryComponent> listBundleEntries = prescriptionBundle.getEntry();
BundleEntryComponent bundleEntry1 = new BundleEntryComponent();
bundleEntry1.setFullUrl("Composition/Composition-01");
bundleEntry1.setResource(populatePrescriptionCompositionResource());
BundleEntryComponent bundleEntry2 = new BundleEntryComponent();
bundleEntry2.setFullUrl("Patient/Patient-01");
bundleEntry2.setResource(ResourcePopulator.populatePatientResource(patientCollection));
BundleEntryComponent bundleEntry3 = new BundleEntryComponent();
bundleEntry3.setFullUrl("Practitioner/Practitioner-01");
bundleEntry3.setResource(ResourcePopulator.populatePractitionerResource());
BundleEntryComponent bundleEntry4 = new BundleEntryComponent();
bundleEntry4.setFullUrl("MedicationRequest/MedicationRequest-01");
bundleEntry4.setResource(ResourcePopulator.populateMedicationRequestResource());
BundleEntryComponent bundleEntry5 = new BundleEntryComponent();
bundleEntry5.setFullUrl("MedicationRequest/MedicationRequest-02");
bundleEntry5.setResource(ResourcePopulator.populateSecondMedicationRequestResource());
BundleEntryComponent bundleEntry6 = new BundleEntryComponent();
bundleEntry6.setFullUrl("Condition/Condition-01");
bundleEntry6.setResource(ResourcePopulator.populateConditionResource());
BundleEntryComponent bundleEntry7 = new BundleEntryComponent();
bundleEntry7.setFullUrl("Binary/Binary-01");
bundleEntry7.setResource(ResourcePopulator.populateBinaryResource());
listBundleEntries.add(bundleEntry1);
listBundleEntries.add(bundleEntry2);
listBundleEntries.add(bundleEntry3);
listBundleEntries.add(bundleEntry4);
listBundleEntries.add(bundleEntry5);
listBundleEntries.add(bundleEntry6);
listBundleEntries.add(bundleEntry7);
return prescriptionBundle;
}
/**
* This method initiates loading of FHIR default profiles and NDHM profiles for validation
*/
static void init() throws DataFormatException, FileNotFoundException
{
// Create xml parser object for reading profiles
IParser parser = ctx.newJsonParser();
// Create a chain that will hold our modules
ValidationSupportChain supportChain = new ValidationSupportChain();
// Add Default Profile Support
// DefaultProfileValidationSupport supplies base FHIR definitions. This is generally required
// even if you are using custom profiles, since those profiles will derive from the base
// definitions.
DefaultProfileValidationSupport defaultSupport = new DefaultProfileValidationSupport(ctx);
// Create a PrePopulatedValidationSupport which can be used to load custom definitions.
// In this example we're loading all the custom Profile Structure Definitions, in other scenario we might
// load many StructureDefinitions, ValueSets, CodeSystems, etc.
PrePopulatedValidationSupport prePopulatedSupport = new PrePopulatedValidationSupport(ctx);
StructureDefinition sd ;
/** LOADING PROFILES **/
// Read all Profile Structure Definitions
String[] fileList = new File("/home/ubuntu/Ndhm Sample/").list(new WildcardFileFilter("*.json"));
for(String file:fileList)
{
//Parse All Profiles and add to prepopulated support
sd = parser.parseResource(StructureDefinition.class, new FileReader("/home/ubuntu/Ndhm Sample/"+file));
prePopulatedSupport.addStructureDefinition(sd);
}
//Add Snapshot Generation Support
SnapshotGeneratingValidationSupport snapshotGenerator = new SnapshotGeneratingValidationSupport(ctx);
//Add prepopulated support consisting all structure definitions and Terminology support
supportChain.addValidationSupport(defaultSupport);
supportChain.addValidationSupport(prePopulatedSupport);
supportChain.addValidationSupport(snapshotGenerator);
supportChain.addValidationSupport(new InMemoryTerminologyServerValidationSupport(ctx));
supportChain.addValidationSupport(new CommonCodeSystemsTerminologyService(ctx));
// Create a validator using the FhirInstanceValidator module and register.
instanceValidator = new FhirInstanceValidator(supportChain);
validator = ctx.newValidator().registerValidatorModule(instanceValidator);
}
/**
* This method validates the FHIR resources
*/
static boolean validate(IBaseResource resource)
{
// Validate
ValidationResult result = validator.validateWithResult(resource);
// The result object now contains the validation results
for (SingleValidationMessage next : result.getMessages()) {
System.out.println(next.getSeverity().name() + " : " + next.getLocationString() + " " + next.getMessage());
}
return result.isSuccessful();
}
}
