From d0ee44dfa80f3d65368238c9ba198a7f82aa1e36 Mon Sep 17 00:00:00 2001 From: Oliver Egger Date: Thu, 14 May 2020 13:38:54 +0200 Subject: [PATCH] json roundtrip cda title --- .../hl7/fhir/r5/elementmodel/JsonParser.java | 2 +- .../hl7/fhir/r5/test/CDARoundTripTests.java | 99 ++++++++++++++----- 2 files changed, 78 insertions(+), 23 deletions(-) diff --git a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java index e98f50711..82701ee7f 100644 --- a/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java +++ b/org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java @@ -184,7 +184,7 @@ public class JsonParser extends ParserBase { } public void parseChildItem(String path, JsonObject object, Element context, Set processed, Property property) { - if (property.isChoice()) { + if (property.isChoice() || property.getDefinition().getPath().endsWith("data[x]")) { for (TypeRefComponent type : property.getDefinition().getType()) { String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode()); if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) { diff --git a/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java b/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java index 1ff468574..f9fd0efe2 100644 --- a/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java +++ b/org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java @@ -1,5 +1,7 @@ package org.hl7.fhir.r5.test; +import java.io.ByteArrayInputStream; +import java.io.ByteArrayOutputStream; import java.io.IOException; import org.hl7.fhir.r5.context.SimpleWorkerContext; @@ -18,6 +20,29 @@ import org.junit.jupiter.api.Test; 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 // @Test @@ -161,28 +186,58 @@ public class CDARoundTripTests { // FhirFormat.TURTLE, OutputStyle.PRETTY, null); // } - @Test - public void testSimple() throws IOException { - FilesystemPackageCacheManager pcm = new FilesystemPackageCacheManager(true, ToolsVersion.TOOLS_VERSION); - SimpleWorkerContext context = SimpleWorkerContext.fromPackage(pcm.loadPackage("hl7.fhir.r4.core", "4.0.1")); - FHIRPathEngine 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); - } - } - 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"))); + public void assertsExample(Element cdaExample) { + Assertions.assertEquals("2.16.840.1.113883.3.27.1776", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.templateId.root"))); + Assertions.assertEquals("SoEN", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.displayName"))); + Assertions.assertEquals("SoEN2", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.sdtcDisplayName"))); + Assertions.assertEquals("c266", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.extension"))); + Assertions.assertEquals("2.16.840.1.113883.19.4", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.id.root"))); + Assertions.assertEquals("X-34133-9", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.code"))); + Assertions.assertEquals("2.16.840.1.113883.6.1", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystem"))); + Assertions.assertEquals("LOINC", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.code.codeSystemName"))); + Assertions.assertEquals("Episode Note", fp.evaluateToString(null, cdaExample, cdaExample, cdaExample, fp.parse("ClinicalDocument.title.dataString"))); } + @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); + + } + } \ No newline at end of file