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Merge pull request #197 from ahdis/oliveregger_cdatitle 

Deserializing CDA ST and ED elements from JSON fix
This commit is contained in:
Grahame Grieve 2020-06-10 08:47:13 +10:00 committed by GitHub
parent 4d9ace1619 473a9aab0a
commit b01c64dc2c
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GPG Key ID: 4AEE18F83AFDEB23
4 changed files with 142 additions and 76 deletions
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2
org.hl7.fhir.r4/src/main/java/org/hl7/fhir/r4/elementmodel/JsonParser.java
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@ -183,7 +183,7 @@ public class JsonParser extends ParserBase {
}
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()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode());
if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {

2
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/JsonParser.java
View File

@ -184,7 +184,7 @@ public class JsonParser extends ParserBase {
}
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()) {
String eName = property.getName().substring(0, property.getName().length()-3) + Utilities.capitalize(type.getWorkingCode());
if (!isPrimitive(type.getWorkingCode()) && object.has(eName)) {

104
org.hl7.fhir.r5/src/main/java/org/hl7/fhir/r5/elementmodel/XmlParser.java
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@ -1,33 +1,33 @@
package org.hl7.fhir.r5.elementmodel;
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
/*
Copyright (c) 2011+, HL7, Inc.
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of HL7 nor the names of its contributors may be used to
endorse or promote products derived from this software without specific
prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED.
IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT
NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
POSSIBILITY OF SUCH DAMAGE.
*/
import java.io.IOException;
@ -210,6 +210,10 @@ public class XmlParser extends ParserBase {
return "h:";
if (ns.equals("urn:hl7-org:v3"))
return "v3:";
if (ns.equals("urn:hl7-org:sdtc"))
return "sdtc:";
if (ns.equals("urn:ihe:pharm"))
return "pharm:";
return "?:";
}
@ -538,11 +542,31 @@ public class XmlParser extends ParserBase {
xml.setDefaultNamespace(e.getProperty().getXmlNamespace());
if (hasTypeAttr(e))
xml.namespace("http://www.w3.org/2001/XMLSchema-instance", "xsi");
addNamespaces(xml, e);
composeElement(xml, e, e.getType(), true);
xml.end();
}
private void addNamespaces(IXMLWriter xml, Element e) throws IOException {
String ns = e.getProperty().getXmlNamespace();
if (ns!=null && !xml.getDefaultNamespace().equals(ns)){
if (!xml.namespaceDefined(ns)) {
String prefix = pathPrefix(ns);
if (prefix.endsWith(":")) {
prefix = prefix.substring(0, prefix.length()-1);
}
if ("?".equals(prefix)) {
xml.namespace(ns);
} else {
xml.namespace(ns, prefix);
}
}
}
for (Element c : e.getChildren()) {
addNamespaces(xml, c);
}
}
private boolean hasTypeAttr(Element e) {
if (isTypeAttr(e.getProperty()))
return true;
@ -584,9 +608,9 @@ public class XmlParser extends ParserBase {
if (isText(element.getProperty())) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.enter(elementName);
xml.enter(element.getProperty().getXmlNamespace(),elementName);
xml.text(element.getValue());
xml.exit(elementName);
xml.exit(element.getProperty().getXmlNamespace(),elementName);
} else if (!element.hasChildren() && !element.hasValue()) {
if (element.getExplicitType() != null)
xml.attribute("xsi:type", element.getExplicitType());
@ -614,10 +638,10 @@ public class XmlParser extends ParserBase {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
if (element.hasChildren()) {
xml.enter(elementName);
for (Element child : element.getChildren())
xml.enter(element.getProperty().getXmlNamespace(), elementName);
for (Element child : element.getChildren())
composeElement(xml, child, child.getName(), false);
xml.exit(elementName);
xml.exit(element.getProperty().getXmlNamespace(),elementName);
} else
xml.element(elementName);
}
@ -630,16 +654,16 @@ public class XmlParser extends ParserBase {
String av = child.getValue();
if (ToolingExtensions.hasExtension(child.getProperty().getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"))
av = convertForDateFormatToExternal(ToolingExtensions.readStringExtension(child.getProperty().getDefinition(), "http://www.healthintersections.com.au/fhir/StructureDefinition/elementdefinition-dateformat"), av);
xml.attribute(child.getName(), av);
}
xml.attribute(child.getProperty().getXmlNamespace(),child.getProperty().getXmlName(), av);
}
}
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.enter(elementName);
xml.enter(element.getProperty().getXmlNamespace(),elementName);
if (!root && element.getSpecial() != null) {
if (linkResolver != null)
xml.link(linkResolver.resolveProperty(element.getProperty()));
xml.enter(element.getType());
xml.enter(element.getProperty().getXmlNamespace(),element.getType());
}
for (Element child : element.getChildren()) {
if (isText(child.getProperty())) {
@ -650,8 +674,8 @@ public class XmlParser extends ParserBase {
composeElement(xml, child, child.getName(), false);
}
if (!root && element.getSpecial() != null)
xml.exit(element.getType());
xml.exit(elementName);
xml.exit(element.getProperty().getXmlNamespace(),element.getType());
xml.exit(element.getProperty().getXmlNamespace(),elementName);
}
}

110
org.hl7.fhir.r5/src/test/java/org/hl7/fhir/r5/test/CDARoundTripTests.java
View File

@ -1,11 +1,14 @@
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;
import org.hl7.fhir.r5.elementmodel.Element;
import org.hl7.fhir.r5.elementmodel.Manager;
import org.hl7.fhir.r5.elementmodel.Manager.FhirFormat;
import org.hl7.fhir.r5.formats.IParser.OutputStyle;
import org.hl7.fhir.r5.model.StructureDefinition;
import org.hl7.fhir.r5.test.utils.TestingUtilities;
import org.hl7.fhir.r5.utils.FHIRPathEngine;
@ -13,22 +16,33 @@ import org.hl7.fhir.utilities.cache.FilesystemPackageCacheManager;
import org.hl7.fhir.utilities.cache.ToolsVersion;
import org.junit.jupiter.api.Assertions;
import org.junit.jupiter.api.BeforeAll;
import org.junit.jupiter.api.Disabled;
import org.junit.jupiter.api.Test;
public class CDARoundTripTests {
// private SimpleWorkerContext context;
// old-test private FHIRPathEngine fp;
private static SimpleWorkerContext context;
private static FHIRPathEngine fp;
@BeforeAll
public static void setUp() throws Exception {
// old-test context = new SimpleWorkerContext();
// old-test PackageCacheManager pcm = new PackageCacheManager(true, ToolsVersion.TOOLS_VERSION);
// old-test context.loadFromPackage(pcm.loadPackage("hl7.fhir.core", "dev"), null, "StructureDefinition");
// old-test context.loadFromPackage(pcm.loadPackage("hl7.fhir.cda", "dev"), null, "StructureDefinition");
// old-test fp = new FHIRPathEngine(context);
}
@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
@ -172,29 +186,57 @@ 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"));
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);
FHIRPathEngine fp = new FHIRPathEngine(context);
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);
}
}