remove R4B CDA tests
This commit is contained in:
Grahame Grieve
parent
9d742dcd24
commit
d6ef09dd77
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@ -1,275 +0,0 @@
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package org.hl7.fhir.r4b.test;
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import java.io.ByteArrayInputStream;
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import java.io.ByteArrayOutputStream;
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import java.io.IOException;
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import java.util.List;
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import org.hl7.fhir.r4b.context.SimpleWorkerContext;
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import org.hl7.fhir.r4b.elementmodel.Element;
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import org.hl7.fhir.r4b.elementmodel.Manager;
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import org.hl7.fhir.r4b.elementmodel.Manager.FhirFormat;
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import org.hl7.fhir.r4b.formats.IParser.OutputStyle;
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import org.hl7.fhir.r4b.model.StructureDefinition;
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import org.hl7.fhir.r4b.test.utils.TestingUtilities;
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import org.hl7.fhir.r4b.utils.FHIRPathEngine;
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import org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager;
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import org.hl7.fhir.utilities.npm.ToolsVersion;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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public class CDARoundTripTests {
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private static SimpleWorkerContext context;
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private static FHIRPathEngine fp;
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@BeforeAll
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public static void setUp() throws Exception {
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FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(
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org.hl7.fhir.utilities.npm.FilesystemPackageCacheManager.FilesystemPackageCacheMode.USER);
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context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
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fp = new FHIRPathEngine(context);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "st.xml"), "st.xml", null);
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context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cda.xml"), "cda.xml", null);
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for (StructureDefinition sd : context.getStructures()) {
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if (!sd.hasSnapshot()) {
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// System.out.println("generate snapshot for " + sd.getUrl());
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context.generateSnapshot(sd, true);
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}
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}
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}
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// old-test
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// @Test
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// public void testCDA() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
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// try {
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//
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// InputStream fileSource = TestingUtilities.loadTestResourceStream("cda", "cda-original.xml");
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// String roundTrip = TestingUtilities.tempFile("cda", "cda-roundtrip.xml");
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// String jsonRoundTrip = TestingUtilities.tempFile("cda", "cda-roundtrip.json");
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//
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// Element e = Manager.parse(context, fileSource, FhirFormat.XML);
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//
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// Manager.compose(context, e, new FileOutputStream(roundTrip), FhirFormat.XML, OutputStyle.PRETTY, null);
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// Manager.compose(context, e, new FileOutputStream(jsonRoundTrip), FhirFormat.JSON, OutputStyle.PRETTY, null);
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//
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//// <typeId root="2.16.840.1.113883.1.3" extension="POCD_HD000040"/>
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//// assertEquals("POCD_HD000040", fp.evaluateToString(e, "typeId.extension"));
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//// assertEquals("2.16.840.1.113883.1.3", fp.evaluateToString(e, "typeId.root"));
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//// <templateId root="2.16.840.1.113883.3.27.1776"/>
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//// assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(e, "templateId.root"));
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//// <id extension="c266" root="2.16.840.1.113883.19.4"/>
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// assertEquals("2.16.840.1.113883.19.4", fp.evaluateToString(e, "id.root"));
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// assertEquals("c266", fp.evaluateToString(e, "id.extension"));
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//
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//// <title>Good Health Clinic Consultation Note</title>
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// assertEquals("Good Health Clinic Consultation Note", fp.evaluateToString(e, "title.dataString"));
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//// <effectiveTime value="20000407"/>
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// assertEquals("2000-04-07", fp.evaluateToString(e, "effectiveTime.value"));
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//// <confidentialityCode code="N" codeSystem="2.16.840.1.113883.5.25"/>
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// assertEquals("N", fp.evaluateToString(e, "confidentialityCode.code"));
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// assertEquals("2.16.840.1.113883.5.25", fp.evaluateToString(e, "confidentialityCode.codeSystem"));
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//// <languageCode code="en-US"/>
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// assertEquals("en-US", fp.evaluateToString(e, "languageCode.code"));
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//// <setId extension="BB35" root="2.16.840.1.113883.19.7"/>
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// assertEquals("BB35", fp.evaluateToString(e, "setId.extension"));
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// assertEquals("2.16.840.1.113883.19.7", fp.evaluateToString(e, "setId.root"));
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//// <versionNumber value="2"/>
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// assertEquals("2", fp.evaluateToString(e, "versionNumber.value"));
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//// <recordTarget>
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//// <patientRole>
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//// <id extension="12345" root="2.16.840.1.113883.19.5"/>
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// assertEquals("12345", fp.evaluateToString(e, "recordTarget.patientRole.id.extension"));
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// assertEquals("2.16.840.1.113883.19.5", fp.evaluateToString(e, "recordTarget.patientRole.id.root"));
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//// <patient>
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//// <name>
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//// <family>Levin</family>
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// assertEquals("Levin", fp.evaluateToString(e, "recordTarget.patientRole.patient.name.family.dataString"));
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//// <given>Henry</given>
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// assertEquals("Henry", fp.evaluateToString(e, "recordTarget.patientRole.patient.name.given.dataString"));
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//// <suffix>the 7th</suffix>
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//// </name>
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//// <administrativeGenderCode code="M" codeSystem="2.16.840.1.113883.5.1"/>
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//// <birthTime value="19320924"/>
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//// </patient>
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//// <providerOrganization>
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//// <id root="2.16.840.1.113883.19.5"/>
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//// </providerOrganization>
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//// </patientRole>
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//// </recordTarget>
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//
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//// <component>
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//// <structuredBody>
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//// <component>
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//// <section>
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//
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//// <component>
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//// <section>
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//// <code code="8709-8" codeSystem="2.16.840.1.113883.6.1" codeSystemName="LOINC"/>
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//// <title>Skin Exam</title>
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//// <text>Erythematous rash, palmar surface, left index finger.
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//// <renderMultiMedia referencedObject="MM1"/>
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//// </text>
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//
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// assertEquals("Skin Exam", fp.evaluateToString(e, "component.structuredBody.component.section.component.section.where(code.code='8709-8' and code.codeSystem='2.16.840.1.113883.6.1').title.dataString"));
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// // <div>Erythematous rash, palmar surface, left index finger.
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// // <img src="MM1"/></div>
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// String text = fp.evaluateToString(e, "component.structuredBody.component.section.component.section.where(code.code='8709-8' and code.codeSystem='2.16.840.1.113883.6.1').text");
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// assertTrue(text.contains("<img src=\"MM1\"/>"));
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// } catch (Exception e) {
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// System.out.println(e.getMessage());
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// e.printStackTrace();
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// throw e;
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// }
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// }
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//
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// @Ignore
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// public void testDCI() throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
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// try {
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// Element e = Manager.parse(context,
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// new FileInputStream("C:\\work\\org.hl7.fhir.us\\ccda-to-fhir-maps\\cda\\IAT2-Discharge_Summary-DCI.xml"),
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// FhirFormat.XML);
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//
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// Manager.compose(context, e, new FileOutputStream(Utilities.path("[tmp]", "ccda.xml"), FhirFormat.XML, OutputStyle.PRETTY, null);
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//// Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge_Summary-DCI.out.json"), FhirFormat.JSON, OutputStyle.PRETTY, null);
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//// Manager.compose(context, e, new FileOutputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge_Summary-DCI.out.ttl"), FhirFormat.TURTLE, OutputStyle.PRETTY, null);
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// } catch (Exception e) {
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// System.out.println(e.getMessage());
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// e.printStackTrace();
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// throw e;
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// }
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// }
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//
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// @Ignore
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// public void testEpic()
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// throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
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// Element e = Manager.parse(context,
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// new FileInputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.xml"),
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// FhirFormat.XML);
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// Manager.compose(context, e,
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// new FileOutputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.xml"),
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// FhirFormat.XML, OutputStyle.PRETTY, null);
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// Manager.compose(context, e,
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// new FileOutputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.json"),
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// FhirFormat.JSON, OutputStyle.PRETTY, null);
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// Manager.compose(context, e,
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// new FileOutputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-Discharge-Homework-Epic.out.ttl"),
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// FhirFormat.TURTLE, OutputStyle.PRETTY, null);
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// }
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//
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// @Ignore
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// public void testDHIT()
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// throws FHIRFormatError, DefinitionException, FileNotFoundException, IOException, FHIRException {
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// Element e = Manager.parse(context,
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// new FileInputStream("C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.xml"),
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// FhirFormat.XML);
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// Manager.compose(context, e,
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// new FileOutputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.xml"),
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// FhirFormat.XML, OutputStyle.PRETTY, null);
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// Manager.compose(context, e,
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// new FileOutputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.json"),
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// FhirFormat.JSON, OutputStyle.PRETTY, null);
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// Manager.compose(context, e,
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// new FileOutputStream(
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// "C:\\work\\org.hl7.fhir.test\\ccda-to-fhir-maps\\testdocuments\\IAT2-DS-Homework-DHIT.out.ttl"),
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// FhirFormat.TURTLE, OutputStyle.PRETTY, null);
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// }
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public void assertsExample(Element cdaExample) {
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Assertions.assertEquals("2.16.840.1.113883.3.27.1776",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.templateId.root")));
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Assertions.assertEquals("SoEN",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.displayName")));
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Assertions.assertEquals("SoEN2", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample,
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fp.parse("ClinicalDocument.code.sdtcDisplayName")));
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Assertions.assertEquals("c266",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.extension")));
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Assertions.assertEquals("2.16.840.1.113883.19.4",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.root")));
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Assertions.assertEquals("X-34133-9",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.code")));
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Assertions.assertEquals("2.16.840.1.113883.6.1",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystem")));
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Assertions.assertEquals("LOINC", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample,
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fp.parse("ClinicalDocument.code.codeSystemName")));
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Assertions.assertEquals("Episode Note",
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fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.title.dataString")));
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}
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@Test
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/**
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* Deserializes a simplified CDA example into the logical model and checks that
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* xml deserialization/serialization
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*
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* @throws IOException
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*/
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public void testClinicalDocumentXmlParser() throws IOException {
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Element cda = Manager.parseSingle(context,
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TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"), FhirFormat.XML);
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assertsExample(cda);
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ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
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Manager.compose(context, cda, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
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Element cdaXmlRoundtrip = Manager.parseSingle(context, new ByteArrayInputStream(baosXml.toString().getBytes()),
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FhirFormat.XML);
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assertsExample(cdaXmlRoundtrip);
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}
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@Test
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/**
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* Deserializes a simplified CDA example into the logical model and checks that
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* json deserialization/serialization works
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*
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* @throws IOException
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*/
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public void testClinicalDocumentJsonParser() throws IOException {
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Element cda = Manager.parseSingle(context,
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TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"), FhirFormat.XML);
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assertsExample(cda);
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ByteArrayOutputStream baosJson = new ByteArrayOutputStream();
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Manager.compose(context, cda, baosJson, FhirFormat.JSON, OutputStyle.PRETTY, null);
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Element cdaJsonRoundtrip = Manager.parseSingle(context, new ByteArrayInputStream(baosJson.toString().getBytes()),
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FhirFormat.JSON);
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assertsExample(cdaJsonRoundtrip);
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}
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@Test
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/**
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* verify that umlaut like äö etc are not encoded in UTF-8 in attributes
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*/
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public void testSerializeUmlaut() throws IOException {
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Element xml = Manager.parseSingle(context,
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TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"), FhirFormat.XML);
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List<Element> title = xml.getChildrenByName("title");
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Assertions.assertTrue(title != null && title.size() == 1);
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Element value = title.get(0).getChildren().get(0);
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Assertions.assertEquals("Episode Note", value.getValue());
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value.setValue("öé");
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ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
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Manager.compose(TestingUtilities.context(), xml, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
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String cdaSerialised = baosXml.toString("UTF-8");
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Assertions.assertTrue(cdaSerialised.indexOf("öé") > 0);
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}
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}
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