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ValidatorTest.java
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ValidatorTest.java
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package tr.com.srdc.cda2fhir;
/*
* #%L
* CDA to FHIR Transformer Library
* %%
* Copyright (C) 2016 SRDC Yazilim Arastirma ve Gelistirme ve Danismanlik Tic. A.S.
* %%
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
* #L%
*/
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import org.hl7.fhir.r4.model.Bundle;
import org.hl7.fhir.r4.model.Bundle.BundleType;
import org.hl7.fhir.r4.model.Identifier;
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Ignore;
import org.junit.Test;
import org.openhealthtools.mdht.uml.cda.consol.ConsolPackage;
import org.openhealthtools.mdht.uml.cda.consol.ContinuityOfCareDocument;
import org.openhealthtools.mdht.uml.cda.util.CDAUtil;
import tr.com.srdc.cda2fhir.conf.Config;
import tr.com.srdc.cda2fhir.transform.CCDTransformerImpl;
import tr.com.srdc.cda2fhir.transform.ICDATransformer;
import tr.com.srdc.cda2fhir.util.FHIRUtil;
import tr.com.srdc.cda2fhir.util.IdGeneratorEnum;
import tr.com.srdc.cda2fhir.validation.IValidator;
import tr.com.srdc.cda2fhir.validation.ValidatorImpl;
public class ValidatorTest {
@BeforeClass
public static void init() {
// Load MDHT CDA packages. Otherwise ContinuityOfCareDocument and similar
// documents will not be recognised.
// This has to be called before loading the document; otherwise will have no
// effect.
CDAUtil.loadPackages();
}
// 170.315_b1_toc_gold_sample2_v1.xml without profile
@Test
public void testGoldSampleBundleWithoutProfile() throws Exception {
String cdaResourcePath = "src/test/resources/170.315_b1_toc_gold_sample2_v1.xml";
String targetPathForFHIRResource = "src/test/resources/output/170.315_b1_toc_gold_sample2_v1-wo-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-wo-profile-for-170.315_b1_toc_gold_sample2_v1.html";
boolean generateDAFProfileMetadata = false;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, true);
}
// 170.315_b1_toc_gold_sample2_v1.xml with profile
@Test
public void testGoldSampleBundleWithProfile() throws Exception {
String cdaResourcePath = "src/test/resources/170.315_b1_toc_gold_sample2_v1.xml";
String targetPathForFHIRResource = "src/test/resources/output/170.315_b1_toc_gold_sample2_v1-w-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-w-profile-for-170.315_b1_toc_gold_sample2_v1.html";
boolean generateDAFProfileMetadata = true;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// 170.315_b1_toc_inp_ccd_r21_sample1_v5.xml without profile
@Test
public void testInpSampleBundleWithoutProfile() throws Exception {
String cdaResourcePath = "src/test/resources/170.315_b1_toc_inp_ccd_r21_sample1_v5.xml";
String targetPathForFHIRResource = "src/test/resources/output/170.315_b1_toc_inp_ccd_r21_sample1_v5-wo-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-wo-profile-for-170.315_b1_toc_inp_ccd_r21_sample1_v5.html";
boolean generateDAFProfileMetadata = false;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// 170.315_b1_toc_inp_ccd_r21_sample1_v5.xml without profile
@Test
public void testInpSampleBundleWithProfile() throws Exception {
String cdaResourcePath = "src/test/resources/170.315_b1_toc_inp_ccd_r21_sample1_v5.xml";
String targetPathForFHIRResource = "src/test/resources/output/170.315_b1_toc_inp_ccd_r21_sample1_v5-w-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-w-profile-for-170.315_b1_toc_inp_ccd_r21_sample1_v5.html";
boolean generateDAFProfileMetadata = true;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// C-CDA_R2-1_CCD.xml without DAF profile
@Test
public void testReferenceCCDBundleWithoutProfile() throws Exception {
String cdaResourcePath = "src/test/resources/C-CDA_R2-1_CCD.xml";
String targetPathForFHIRResource = "src/test/resources/output/C-CDA_R2-1_CCD-wo-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-wo-profile-for-C-CDA_R2-1_CCD.html";
boolean generateDAFProfileMetadata = false;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// C-CDA_R2-1_CCD.xml with provenance
@Test
public void testReferenceCCDBundleWithProvenance() throws Exception {
String cdaResourcePath = "src/test/resources/C-CDA_R2-1_CCD.xml";
String targetPathForFHIRResource = "src/test/resources/output/C-CDA_R2-1_CCD-w-provenance.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-w-provenance-for-C-CDA_R2-1_CCD.html";
boolean generateDAFProfileMetadata = false;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, true);
}
// C-CDA_R2-1_CCD.xml with DAF profile
@Test
public void testReferenceCCDBundleWithProfile() throws Exception {
String cdaResourcePath = "src/test/resources/C-CDA_R2-1_CCD.xml";
String targetPathForFHIRResource = "src/test/resources/output/C-CDA_R2-1_CCD-w-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-w-profile-for-C-CDA_R2-1_CCD.html";
boolean generateDAFProfileMetadata = false;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// Vitera_CCDA_SMART_Sample.xml without profile
@Test
public void testViteraBundleWithoutProfile() throws Exception {
String cdaResourcePath = "src/test/resources/Vitera_CCDA_SMART_Sample.xml";
String targetPathForFHIRResource = "src/test/resources/output/Vitera_CCDA_SMART_Sample-wo-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-wo-profile-for-Vitera_CCDA_SMART_Sample.html";
boolean generateDAFProfileMetadata = false;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// Vitera_CCDA_SMART_Sample.xml with profile
@Test
public void testViteraBundleWithProfile() throws Exception {
String cdaResourcePath = "src/test/resources/Vitera_CCDA_SMART_Sample.xml";
String targetPathForFHIRResource = "src/test/resources/output/Vitera_CCDA_SMART_Sample-w-profile-validation.xml";
String targetPathForResultFile = "src/test/resources/output/validation-result-w-profile-for-Vitera_CCDA_SMART_Sample.html";
boolean generateDAFProfileMetadata = true;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// HannahBanana_EpicCCD.xml
@Ignore
public void testHannahBanana() throws Exception {
String cdaResourcePath = "src/test/resources/Epic/HannahBanana_EpicCCD-pretty.xml";
String targetPathForFHIRResource = "src/test/resources/output/Epic/HannahBanana_EpicCCD-pretty.fhir.xml";
String targetPathForResultFile = "src/test/resources/output/Epic/HannahBanana_EpicCCD-pretty.validation-result.html";
boolean generateDAFProfileMetadata = true;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// robust CCD.XML
@Ignore
public void testRobust() throws Exception {
String cdaResourcePath = "src/test/resources/Epic/robust CCD.XML";
String targetPathForFHIRResource = "src/test/resources/output/Epic/robust CCD.fhir.xml";
String targetPathForResultFile = "src/test/resources/output/Epic/robust CCD.validation-result.html";
boolean generateDAFProfileMetadata = true;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
// Person-RAKIA_TEST_DOC0001 (1).xml
@Ignore
public void testRakia() throws Exception {
String cdaResourcePath = "src/test/resources/Cerner/Person-RAKIA_TEST_DOC00001 (1).xml";
String targetPathForFHIRResource = "src/test/resources/output/Cerner/Person-RAKIA_TEST_DOC00001 (1).fhir.xml";
String targetPathForResultFile = "src/test/resources/output/Cerner/Person-RAKIA_TEST_DOC00001 (1).validation-result.html";
boolean generateDAFProfileMetadata = true;
transformAndValidate(cdaResourcePath, targetPathForFHIRResource, targetPathForResultFile,
generateDAFProfileMetadata, false);
}
/**
* Transforms a CDA resource to a FHIR resource, validates the FHIR resource and
* prints the validation result to the target path.
*
* @param cdaResourcePath A file path of the CDA resource that is to
* be transformed
* @param targetPathForFHIRResource A file path where the FHIR resource is to
* be created
* @param targetPathForResultFile A file path where the validation result
* file is to be created
* @param generateDAFProfileMetadata A boolean indicating whether the generated
* resources will include DAF profile
* declarations in meta.profile
* @throws Exception
*/
private void transformAndValidate(String cdaResourcePath, String targetPathForFHIRResource,
String targetPathForResultFile, boolean generateDAFProfileMetadata, boolean generateProvenance)
throws Exception {
IValidator validator = new ValidatorImpl();
ByteArrayOutputStream os = null;
// file to be transformed
FileInputStream fis = new FileInputStream(cdaResourcePath);
ContinuityOfCareDocument cda = (ContinuityOfCareDocument) CDAUtil.loadAs(fis,
ConsolPackage.eINSTANCE.getContinuityOfCareDocument());
ICDATransformer ccdTransformer = new CCDTransformerImpl(IdGeneratorEnum.COUNTER);
// set whether DAF Profile URLs will be created in meta.profile of relevant
// resources
Config.setGenerateDafProfileMetadata(generateDAFProfileMetadata);
Config.setAddedZerosToDateTime(true);
Bundle bundle = null;
if (generateProvenance) {
// CDAUtil closes the stream, re-open it.
FileInputStream fisStream = new FileInputStream(cdaResourcePath);
byte[] buffer = new byte[10];
StringBuilder sb = new StringBuilder();
while (fisStream.read(buffer) != -1) {
sb.append(new String(buffer));
buffer = new byte[10];
}
fisStream.close();
String content = sb.toString();
Identifier assemblerDevice = new Identifier();
assemblerDevice.setValue("Higgs");
assemblerDevice.setSystem("http://www.amida.com");
bundle = ccdTransformer.transformDocument(cda, BundleType.TRANSACTION, null, content, assemblerDevice);
} else {
bundle = ccdTransformer.transformDocument(cda, null, null);
}
Config.setAddedZerosToDateTime(false);
Assert.assertNotNull(bundle);
// print the bundle for checking against validation results
// printed as XML, because HL7 FHIR Validator works with XML encoded resources
FHIRUtil.printXML(bundle, targetPathForFHIRResource);
os = (ByteArrayOutputStream) validator.validateBundle(bundle);
// ValidationResult fileResult =
// validator.validateFile(targetPathForFHIRResource);
// Assert.assertNotNull(fileResult);
// Assert.assertTrue(fileResult.isSuccessful()); TODO: Investigate and fix why
// this is failing
if (os != null) {
File validationFile = new File(targetPathForResultFile);
validationFile.getParentFile().mkdirs();
FileOutputStream fos = new FileOutputStream(validationFile);
os.writeTo(fos);
os.close();
fos.close();
}
}
}