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json roundtrip cda title

This commit is contained in:
Oliver Egger 2020-05-14 13:38:54 +02:00
parent 5576a02378
commit d0ee44dfa8
2 changed files with 78 additions and 23 deletions
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2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
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@ -184,7 +184,7 @@ public class JsonParser extends ParserBase {
} }
public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) { public void parseChildItem(String path, JsonObject object, Element context, Set<String> processed, Property property) {
if (property.isChoice()) { if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) {
for (TypeRefComponent type : property.getDefinition().getType()) { for (TypeRefComponent type : property.getDefinition().getType()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode()); String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode());
if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) { if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {

99
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java
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@ -1,5 +1,7 @@
package org.hl7.fhir.r5.test; package org.hl7.fhir.r5.test;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.IOException; import java.io.IOException;
import org.hl7.fhir.r5.context.SimpleWorkerContext; import org.hl7.fhir.r5.context.SimpleWorkerContext;
@ -18,6 +20,29 @@ import org.junit.jupiter.api.Test;
public class CDARoundTripTests { public class CDARoundTripTests {
private static SimpleWorkerContext context;
private static FHIRPathEngine fp;
@BeforeAll
public static void setUp() throws Exception {
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1"));
fp = new FHIRPathEngine(context);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "st.xml"), "st.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cda.xml"), "cda.xml", null);
for (StructureDefinition sd : context.getStructures()) {
if (!sd.hasSnapshot()) {
System.out.println("generate snapshot for " + sd.getUrl());
context.generateSnapshot(sd, true);
}
}
}
// old-test // old-test
// @Test // @Test
@ -161,28 +186,58 @@ public class CDARoundTripTests {
// FhirFormat.TURTLE, OutputStyle.PRETTY, null); // FhirFormat.TURTLE, OutputStyle.PRETTY, null);
// } // }
@Test public void assertsExample(Element cdaExample) {
public void testSimple() throws IOException { Assertions.assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.templateId.root")));
FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION); Assertions.assertEquals("SoEN", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.displayName")));
SimpleWorkerContext context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1")); Assertions.assertEquals("SoEN2", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.sdtcDisplayName")));
FHIRPathEngine fp = new FHIRPathEngine(context); Assertions.assertEquals("c266", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.extension")));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "any.xml"), "any.xml", null); Assertions.assertEquals("2.16.840.1.113883.19.4", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.root")));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ii.xml"), "ii.xml", null); Assertions.assertEquals("X-34133-9", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.code")));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cd.xml"), "cd.xml", null); Assertions.assertEquals("2.16.840.1.113883.6.1", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystem")));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ce.xml"), "ce.xml", null); Assertions.assertEquals("LOINC", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystemName")));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "ed.xml"), "ed.xml", null); Assertions.assertEquals("Episode Note", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.title.dataString")));
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "st.xml"), "st.xml", null);
context.loadFromFile(TestingUtilities.loadTestResourceStream("validator", "cda", "cda.xml"), "cda.xml", null);
for (StructureDefinition sd : context.getStructures()) {
if (!sd.hasSnapshot()) {
System.out.println("generate snapshot for " + sd.getUrl());
context.generateSnapshot(sd, true);
}
}
Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"), FhirFormat.XML);
Assertions.assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.templateId.root")));
Assertions.assertEquals("SoEN", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.code.displayName")));
Assertions.assertEquals("SoEN2", fp.evaluateToString(null, cda, cda, cda, fp.parse("ClinicalDocument.code.sdtcDisplayName")));
} }
@Test
/**
* Deserializes a simplified CDA example into the logical model and checks that
* xml deserialization/serialization
*
* @throws IOException
*/
public void testClinicalDocumentXmlParser() throws IOException {
Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"),
FhirFormat.XML);
assertsExample(cda);
ByteArrayOutputStream baosXml = new ByteArrayOutputStream();
Manager.compose(context, cda, baosXml, FhirFormat.XML, OutputStyle.PRETTY, null);
Element cdaXmlRoundtrip = Manager.parse(context, new ByteArrayInputStream(baosXml.toString().getBytes()), FhirFormat.XML);
// assertsExample(cdaXmlRoundtrip);
}
@Test
/**
* Deserializes a simplified CDA example into the logical model and checks that
* json deserialization/serialization works
*
* @throws IOException
*/
public void testClinicalDocumentJsonParser() throws IOException {
Element cda = Manager.parse(context, TestingUtilities.loadTestResourceStream("validator", "cda", "example.xml"),
FhirFormat.XML);
assertsExample(cda);
ByteArrayOutputStream baosJson = new ByteArrayOutputStream();
Manager.compose(context, cda, baosJson, FhirFormat.JSON, OutputStyle.PRETTY, null);
Element cdaJsonRoundtrip = Manager.parse(context, new ByteArrayInputStream(baosJson.toString().getBytes()),
FhirFormat.JSON);
assertsExample(cdaJsonRoundtrip);
}
} }