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Forward port #695 

Merge branch 'master' into hapi3_refactor
This commit is contained in:
James 2017-08-13 10:52:59 -04:00
parent 7c39a47852 dedd3d635b
commit 1f534985e8
12 changed files with 850 additions and 346 deletions
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2
hapi-fhir-base/src/main/java/ca/uhn/fhir/model/primitive/IdDt.java
View File

@ -386,7 +386,7 @@ public class IdDt extends UriDt implements /*IPrimitiveDatatype<String>, */IIdTy
@Override
public boolean isEmpty() {
return isBlank(getValue());
return super.isBaseEmpty() && isBlank(getValue());
}
@Override

81
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -47,6 +47,8 @@ import ca.uhn.fhir.parser.json.JsonLikeValue.ScalarType;
import ca.uhn.fhir.parser.json.JsonLikeValue.ValueType;
import ca.uhn.fhir.rest.api.EncodingEnum;
import ca.uhn.fhir.util.ElementUtil;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.ID_DATATYPE;
import static ca.uhn.fhir.context.BaseRuntimeElementDefinition.ChildTypeEnum.PRIMITIVE_DATATYPE;
/**
* This class is the FHIR JSON parser/encoder. Users should not interact with this class directly, but should use
@ -612,9 +614,23 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
write(theEventWriter, "resourceType", resDef.getName());
if (theResourceId != null && theResourceId.hasIdPart()) {
write(theEventWriter, "id", theResourceId.getIdPart());
if (theResourceId.hasFormatComment()) {
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theResourceId, extensions, modifierExtensions, null, null);
boolean haveExtension = false;
if (!extensions.isEmpty()) {
haveExtension = true;
}
if (theResourceId.hasFormatComment() || haveExtension) {
beginObject(theEventWriter, "_id");
if (theResourceId.hasFormatComment()) {
writeCommentsPreAndPost(theResourceId, theEventWriter);
}
if (haveExtension) {
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
}
theEventWriter.endObject();
}
}
@ -1014,6 +1030,9 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
}
private void parseExtension(ParserState<?> theState, JsonLikeArray theValues, boolean theIsModifier) {
int allUnderscoreNames = 0;
int handledUnderscoreNames = 0;
for (int i = 0; i < theValues.size(); i++) {
JsonLikeObject nextExtObj = JsonLikeValue.asObject(theValues.get(i));
JsonLikeValue jsonElement = nextExtObj.get("url");
@ -1040,9 +1059,43 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
} else if ("modifierExtension".equals(next)) {
JsonLikeArray jsonVal = JsonLikeValue.asArray(nextExtObj.get(next));
parseExtension(theState, jsonVal, true);
} else if (next.charAt(0) == '_') {
allUnderscoreNames++;
continue;
} else {
JsonLikeValue jsonVal = nextExtObj.get(next);
parseChildren(theState, next, jsonVal, null, null, false);
String alternateName = '_' + next;
JsonLikeValue alternateVal = nextExtObj.get(alternateName);
if (alternateVal != null) {
handledUnderscoreNames++;
}
parseChildren(theState, next, jsonVal, alternateVal, alternateName, false);
}
}
/*
* This happens if an element has an extension but no actual value. I.e.
* if a resource has a "_status" element but no corresponding "status"
* element. This could be used to handle a null value with an extension
* for example.
*/
if (allUnderscoreNames > handledUnderscoreNames) {
for (String alternateName : nextExtObj.keySet()) {
if (alternateName.startsWith("_") && alternateName.length() > 1) {
JsonLikeValue nextValue = nextExtObj.get(alternateName);
if (nextValue != null) {
if (nextValue.isObject()) {
String nextName = alternateName.substring(1);
if (nextExtObj.get(nextName) == null) {
theState.enteringNewElement(null, nextName);
parseAlternates(nextValue, theState, alternateName, alternateName);
theState.endingElement();
}
} else {
getErrorHandler().incorrectJsonType(null, alternateName, ValueType.OBJECT, null, nextValue.getJsonType(), null);
}
}
}
}
}
theState.endingElement();
@ -1314,6 +1367,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
} else {
String childName = myDef.getChildNameByDatatype(myValue.getClass());
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, myValue, def, childName, false, myParent, false);
managePrimitiveExtension(myValue, theResDef, theResource, theEventWriter, def, childName);
}
theEventWriter.endObject();
@ -1368,6 +1422,7 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
throw new ConfigurationException("Unable to encode extension, unregognized child element type: " + value.getClass().getCanonicalName());
}
encodeChildElementToStreamWriter(theResDef, theResource, theEventWriter, value, childDef, childName, true, myParent, false);
managePrimitiveExtension(value, theResDef, theResource, theEventWriter, childDef, childName);
}
// theEventWriter.name(myUndeclaredExtension.get);
@ -1375,6 +1430,26 @@ public class JsonParser extends BaseParser implements IJsonLikeParser {
theEventWriter.endObject();
}
private void managePrimitiveExtension(final IBase theValue, final RuntimeResourceDefinition theResDef, final IBaseResource theResource, final JsonLikeWriter theEventWriter, final BaseRuntimeElementDefinition<?> def, final String childName) throws IOException {
if (def.getChildType().equals(ID_DATATYPE) || def.getChildType().equals(PRIMITIVE_DATATYPE)) {
final List<HeldExtension> extensions = new ArrayList<HeldExtension>(0);
final List<HeldExtension> modifierExtensions = new ArrayList<HeldExtension>(0);
// Undeclared extensions
extractUndeclaredExtensions(theValue, extensions, modifierExtensions, myParent, null);
// Declared extensions
if (def != null) {
extractDeclaredExtensions(theValue, def, extensions, modifierExtensions, myParent);
}
boolean haveContent = false;
if (!extensions.isEmpty() || !modifierExtensions.isEmpty()) {
haveContent = true;
}
if (haveContent) {
beginObject(theEventWriter, '_' + childName);
writeExtensionsAsDirectChild(theResource, theEventWriter, theResDef, extensions, modifierExtensions);
theEventWriter.endObject();
}
}
}
}
}

9
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/ParserState.java
View File

@ -422,6 +422,7 @@ class ParserState<T> {
push(newState);
return;
}
case ID_DATATYPE:
case PRIMITIVE_DATATYPE: {
RuntimePrimitiveDatatypeDefinition primitiveTarget = (RuntimePrimitiveDatatypeDefinition) target;
IPrimitiveType<?> newChildInstance = primitiveTarget.newInstance(myDefinition.getInstanceConstructorArguments());
@ -1158,10 +1159,16 @@ class ParserState<T> {
// if (isNotBlank(entryBaseUrl)) {
// nextResource.setId(new IdDt(entryBaseUrl, resourceName, bundleIdPart, version));
// } else {
IdDt previousId = nextResource.getId();
nextResource.setId(new IdDt(null, resourceName, bundleIdPart, version));
// Copy extensions
if (!previousId.getAllUndeclaredExtensions().isEmpty()) {
for (final ExtensionDt ext : previousId.getAllUndeclaredExtensions()) {
nextResource.getId().addUndeclaredExtension(ext);
}
}
// }
}
}
}

32
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/XmlParser.java
View File

@ -184,9 +184,9 @@ public class XmlParser extends BaseParser /* implements IParser */ {
heldComments.clear();
}
parserState.endingElement();
// if (parserState.isComplete()) {
// return parserState.getObject();
// }
// if (parserState.isComplete()) {
// return parserState.getObject();
// }
break;
}
case XMLStreamConstants.CHARACTERS: {
@ -229,10 +229,14 @@ public class XmlParser extends BaseParser /* implements IParser */ {
case ID_DATATYPE: {
IIdType value = IIdType.class.cast(theElement);
String encodedValue = "id".equals(childName) ? value.getIdPart() : value.getValue();
if (StringUtils.isNotBlank(encodedValue) || super.hasExtensions(value)) {
theEventWriter.writeStartElement(childName);
if (StringUtils.isNotBlank(encodedValue)) {
theEventWriter.writeAttribute("value", encodedValue);
}
encodeExtensionsIfPresent(theResource, theEventWriter, theElement, theIncludedResource);
theEventWriter.writeEndElement();
}
break;
}
case PRIMITIVE_DATATYPE: {
@ -354,8 +358,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
}
if (nextChild instanceof RuntimeChildContainedResources) {
encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theContainedResource,
nextChildElem);
encodeChildElementToStreamWriter(theResource, theEventWriter, null, nextChild.getChildNameByDatatype(null), nextChild.getChildElementDefinitionByDatatype(null), null, theContainedResource, nextChildElem);
} else {
List<? extends IBase> values = nextChild.getAccessor().getValues(theElement);
@ -398,8 +401,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
}
}
private void encodeExtension(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement nextChildElem, BaseRuntimeChildDefinition nextChild,
IBase nextValue, String childName, String extensionUrl, BaseRuntimeElementDefinition<?> childDef)
private void encodeExtension(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theContainedResource, CompositeChildElement nextChildElem, BaseRuntimeChildDefinition nextChild, IBase nextValue, String childName, String extensionUrl, BaseRuntimeElementDefinition<?> childDef)
throws XMLStreamException {
BaseRuntimeDeclaredChildDefinition extDef = (BaseRuntimeDeclaredChildDefinition) nextChild;
if (extDef.isModifier()) {
@ -434,8 +436,7 @@ public class XmlParser extends BaseParser /* implements IParser */ {
}
}
private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, boolean theSubResource)
throws XMLStreamException, DataFormatException {
private void encodeResourceToXmlStreamWriter(IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource, boolean theSubResource) throws XMLStreamException, DataFormatException {
IIdType resourceId = null;
if (StringUtils.isNotBlank(theResource.getIdElement().getIdPart())) {
@ -470,11 +471,13 @@ public class XmlParser extends BaseParser /* implements IParser */ {
theEventWriter.writeDefaultNamespace(FHIR_NS);
if (theResource instanceof IAnyResource) {
// HL7.org Structures
if (theResourceId != null) {
writeCommentsPre(theEventWriter, theResourceId);
writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
theEventWriter.writeStartElement("id");
theEventWriter.writeAttribute("value", theResourceId.getIdPart());
encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false);
theEventWriter.writeEndElement();
writeCommentsPost(theEventWriter, theResourceId);
}
@ -486,8 +489,13 @@ public class XmlParser extends BaseParser /* implements IParser */ {
IResource resource = (IResource) theResource;
if (theResourceId != null) {
writeCommentsPre(theEventWriter, theResourceId);
/* writeCommentsPre(theEventWriter, theResourceId);
writeOptionalTagWithValue(theEventWriter, "id", theResourceId.getIdPart());
writeCommentsPost(theEventWriter, theResourceId);*/
theEventWriter.writeStartElement("id");
theEventWriter.writeAttribute("value", theResourceId.getIdPart());
encodeExtensionsIfPresent(theResource, theEventWriter, theResourceId, false);
theEventWriter.writeEndElement();
writeCommentsPost(theEventWriter, theResourceId);
}

121
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/ElementWithExtensionDstu2Test.java
View File

@ -1,14 +1,15 @@
package ca.uhn.fhir.parser;
import static org.junit.Assert.assertEquals;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.ExtensionDt;
import ca.uhn.fhir.model.dstu2.composite.HumanNameDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.util.TestUtil;
import org.junit.AfterClass;
import org.junit.Test;
import static org.junit.Assert.assertEquals;
/**
* Created by Sébastien Rivière 12/04/2017
@ -16,7 +17,7 @@ import ca.uhn.fhir.util.TestUtil;
public class ElementWithExtensionDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ca.uhn.fhir.parser.ElementWithExtensionDstu2Test.class);
private static FhirContext ctx = FhirContext.forDstu2();
private final FhirContext ctx = FhirContext.forDstu2();
@AfterClass
public static void afterClassClearContext() {
@ -24,13 +25,42 @@ public class ElementWithExtensionDstu2Test {
}
@Test
@Ignore
public void testExtensionOnPrimitiveExtensionJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final HumanNameDt name = patient.getNameFirstRep();
name.addFamily(new StringDt("family"));
name.getFamilyFirstRep().addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
final StringDt stringExt = new StringDt();
stringExt.setValue("myStringExt");
stringExt.addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
final ExtensionDt ext = new ExtensionDt();
ext.setValue(stringExt);
ext.setUrl("/myExt");
patient.addUndeclaredExtension(ext);
patient.setPetName(new StringDt("myPet"));
patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getName().get(0).getFamilyFirstRep().getUndeclaredExtensions().size());
assertEquals(1, ((StringDt) patient.getUndeclaredExtensionsByUrl("/myExt").get(0).getValue()).getUndeclaredExtensions().size());
assertEquals(1, patient.getPetName().getUndeclaredExtensions().size());
}
@Test
public void testExtensionOnPrimitiveExtensionWithNullValueJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
parser.setServerBaseUrl("http://foo");
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
@ -39,13 +69,44 @@ public class ElementWithExtensionDstu2Test {
assertEquals(1, patient.getPetName().getUndeclaredExtensions().size());
}
@Test
public void testExtensionOnPrimitiveExtensionXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final HumanNameDt name = patient.getNameFirstRep();
name.addFamily(new StringDt("family"));
name.getFamilyFirstRep().addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
final StringDt stringExt = new StringDt();
stringExt.setValue("myStringExt");
stringExt.addUndeclaredExtension(new ExtensionDt(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK")));
final ExtensionDt ext = new ExtensionDt();
ext.setValue(stringExt);
ext.setUrl("/myExt");
patient.addUndeclaredExtension(ext);
patient.setPetName(new StringDt("myPet"));
patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getName().get(0).getFamilyFirstRep().getUndeclaredExtensions().size());
assertEquals(1, ((StringDt) patient.getUndeclaredExtensionsByUrl("/myExt").get(0).getValue()).getUndeclaredExtensions().size());
assertEquals(1, patient.getPetName().getUndeclaredExtensions().size());
}
@Test
public void testExtensionOnPrimitiveExtensionWithNullValueXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getPetName().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
parser.setServerBaseUrl("http://foo");
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
@ -55,13 +116,11 @@ public class ElementWithExtensionDstu2Test {
}
@Test
@Ignore
public void testExtensionOnIDDatatypeJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
parser.setServerBaseUrl("http://foo");
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
@ -70,14 +129,14 @@ public class ElementWithExtensionDstu2Test {
assertEquals(1, patient.getId().getUndeclaredExtensions().size());
}
@Test
@Ignore
public void testExtensionOnIDDatatypeXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
parser.setServerBaseUrl("http://foo");
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
@ -87,13 +146,26 @@ public class ElementWithExtensionDstu2Test {
}
@Test
@Ignore
public void testExtensionOnIDDatatypeExtensionJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.setCustomId(new IdDt("3"));
patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getCustomId().getUndeclaredExtensions().size());
}
@Test
public void testExtensionOnIDDatatypeExtensionNullValueJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
parser.setServerBaseUrl("http://foo");
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
@ -103,13 +175,26 @@ public class ElementWithExtensionDstu2Test {
}
@Test
@Ignore
public void testExtensionOnIDDatatypeExtensionXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.setCustomId(new IdDt("4"));
patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getCustomId().getUndeclaredExtensions().size());
}
@Test
public void testExtensionOnIDDatatypeExtensionNullValueXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getCustomId().addUndeclaredExtension(false, "http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringDt("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
parser.setServerBaseUrl("http://foo");
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);

2
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/model/IdType.java
View File

@ -436,7 +436,7 @@ public final class IdType extends UriType implements IPrimitiveType<String>, IId
@Override
public boolean isEmpty() {
return isBlank(getValue());
return super.isEmpty() && isBlank(getValue());
}
@Override

60
hapi-fhir-structures-dstu3/src/test/java/MinimizeResources.java
View File

@ -1,60 +0,0 @@
import java.io.File;
import java.io.FileNotFoundException;
import java.io.FileReader;
import java.io.FileWriter;
import java.io.IOException;
import java.util.Collection;
import org.apache.commons.io.FileUtils;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.Bundle;
import org.hl7.fhir.dstu3.model.Bundle.BundleEntryComponent;
import org.hl7.fhir.dstu3.model.DomainResource;
import org.hl7.fhir.dstu3.model.Narrative;
import org.hl7.fhir.dstu3.model.Resource;
import org.junit.AfterClass;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.TestUtil;
public class MinimizeResources {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(MinimizeResources.class);
private static FhirContext ourCtx = FhirContext.forDstu3();
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
public static void main(String[] args) throws Exception {
Collection<File> xml = FileUtils.listFiles(new File("../hapi-fhir-validation-resources-dstu3/src/main/resources/org/hl7/fhir/dstu3/model/profile"), new String[] {"xml"}, false);
for (File next : xml) {
ourLog.info("Checking: {}", next.getAbsoluteFile());
String inputFile = IOUtils.toString(new FileReader(next));
Bundle bundle = (Bundle) ourCtx.newXmlParser().parseResource(inputFile);
for (BundleEntryComponent nextEntry : bundle.getEntry()) {
Resource resource;
resource = nextEntry.getResource();
if (resource instanceof DomainResource) {
((DomainResource) resource).setText(new Narrative());
}
}
String output = ourCtx.newXmlParser().setPrettyPrint(false).encodeResourceToString(bundle);
if (!output.equals(inputFile)) {
ourLog.info("Rewriting {}", next.getAbsolutePath());
FileWriter writer = new FileWriter(next, false);
writer.append(output);
writer.close();
}
}
}
}

139
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/ElementWithExtensionDstu3Test.java
View File

@ -1,14 +1,14 @@
package ca.uhn.fhir.parser;
import static org.junit.Assert.assertEquals;
import org.hl7.fhir.dstu3.model.StringType;
import org.junit.AfterClass;
import org.junit.Ignore;
import org.junit.Test;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.*;
import org.junit.AfterClass;
import org.junit.Test;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
/**
* Created by Sébastien Rivière 12/04/2017
@ -16,7 +16,7 @@ import ca.uhn.fhir.util.TestUtil;
public class ElementWithExtensionDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ca.uhn.fhir.parser.ElementWithExtensionDstu3Test.class);
private static final FhirContext ctx = FhirContext.forDstu3();
private final FhirContext ctx = FhirContext.forDstu3();
@AfterClass
public static void afterClassClearContext() {
@ -24,11 +24,43 @@ public class ElementWithExtensionDstu3Test {
}
@Test
@Ignore
public void testNullFlavorPrimitiveExtensionJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final HumanName name = patient.getNameFirstRep();
name.setFamily("family");
name.getFamilyElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
patient.setPetName(new StringType("myPet"));
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final StringType stringExt = new StringType();
stringExt.setValue("myStringExt");
stringExt.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final Extension ext = new Extension();
ext.setValue(stringExt);
ext.setUrl("/myExt");
patient.addExtension(ext);
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getName().get(0).getFamilyElement().getExtension().size());
assertEquals(1, patient.getExtensionsByUrl("/myExt").get(0).getValue().getExtension().size());
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
public void testNullFlavorPrimitiveExtensionNullValueJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
@ -39,11 +71,45 @@ public class ElementWithExtensionDstu3Test {
}
@Test
@Ignore
public void testNullFlavorPrimitiveExtensionXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final HumanName name = patient.getNameFirstRep();
name.setFamily("family");
name.getFamilyElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
patient.setPetName(new StringType("myPet"));
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final StringType stringExt = new StringType();
stringExt.setValue("myStringExt");
stringExt.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final Extension ext = new Extension();
ext.setValue(stringExt);
ext.setUrl("/myExt");
patient.addExtension(ext);
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getName().get(0).getFamilyElement().getExtension().size());
assertEquals(1, patient.getExtensionsByUrl("/myExt").get(0).getValue().getExtension().size());
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
public void testNullFlavorPrimitiveExtensionNullValueXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
@ -53,8 +119,8 @@ public class ElementWithExtensionDstu3Test {
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
@Ignore
public void testNullFlavorIDDatatypeJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
@ -69,7 +135,6 @@ public class ElementWithExtensionDstu3Test {
}
@Test
@Ignore
public void testNullFlavorIDDatatypeXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
@ -84,10 +149,10 @@ public class ElementWithExtensionDstu3Test {
}
@Test
@Ignore
public void testNullFlavorExtensionIDDatatypeJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.setCustomId(new IdType(("4")));
patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ctx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
@ -99,12 +164,13 @@ public class ElementWithExtensionDstu3Test {
}
@Test
@Ignore
public void testNullFlavorExtensionIDDatatypeXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ctx.newXmlParser().setPrettyPrint(true);
patient.setCustomId(new IdType(("4")));
patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
@ -112,5 +178,48 @@ public class ElementWithExtensionDstu3Test {
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getCustomId().getExtension().size());
}
@Test
public void testExtensionOnResourceIdXml(){
Patient p = new Patient();
p.setActive(true);
p.getIdElement().setValue("123");
p.getIdElement().addExtension().setUrl("http://foo").setValue(new StringType("FOO"));
IParser parser = ctx.newXmlParser();
String encoded = parser.encodeResourceToString(p);
assertThat(encoded, containsString("http://foo"));
assertThat(encoded, containsString("FOO"));
p = (Patient) parser.parseResource(encoded);
assertEquals("Patient/123", p.getId());
Extension ex = p.getIdElement().getExtension().get(0);
assertEquals("http://foo", ex.getUrl());
assertEquals("FOO", ex.getValueAsPrimitive().getValueAsString());
}
@Test
public void testExtensionOnResourceIdJson(){
Patient p = new Patient();
p.setActive(true);
p.getIdElement().setValue("123");
p.getIdElement().addExtension().setUrl("http://foo").setValue(new StringType("FOO"));
IParser parser = ctx.newJsonParser();
String encoded = parser.encodeResourceToString(p);
assertThat(encoded, containsString("http://foo"));
assertThat(encoded, containsString("FOO"));
p = (Patient) parser.parseResource(encoded);
assertEquals("Patient/123", p.getId());
Extension ex = p.getIdElement().getExtension().get(0);
assertEquals("http://foo", ex.getUrl());
assertEquals("FOO", ex.getValueAsPrimitive().getValueAsString());
}
}

2
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/MyPatientWithCustomUrlExtension.java
View File

@ -36,7 +36,7 @@ public class MyPatientWithCustomUrlExtension extends Patient {
@Override
public boolean isEmpty() {
return super.isEmpty() && myPetName.isEmpty();
return super.isEmpty() && getCustomId().isEmpty() && getPetName().isEmpty();
}
public IdType getCustomId() {

224
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/ElementWithExtensionR4Test.java Normal file
View File

@ -0,0 +1,224 @@
package ca.uhn.fhir.parser;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.r4.model.*;
import org.junit.AfterClass;
import org.junit.Test;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.*;
/**
* Created by Sébastien Rivière 12/04/2017
*/
public class ElementWithExtensionR4Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ElementWithExtensionR4Test.class);
private static FhirContext ourCtx = FhirContext.forR4();
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
@Test
public void testNullFlavorPrimitiveExtensionJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final HumanName name = patient.getNameFirstRep();
name.setFamily("family");
name.getFamilyElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
patient.setPetName(new StringType("myPet"));
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final StringType stringExt = new StringType();
stringExt.setValue("myStringExt");
stringExt.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final Extension ext = new Extension();
ext.setValue(stringExt);
ext.setUrl("/myExt");
patient.addExtension(ext);
final IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getName().get(0).getFamilyElement().getExtension().size());
assertEquals(1, patient.getExtensionsByUrl("/myExt").get(0).getValue().getExtension().size());
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
public void testNullFlavorPrimitiveExtensionNullValueJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
public void testNullFlavorPrimitiveExtensionXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final HumanName name = patient.getNameFirstRep();
name.setFamily("family");
name.getFamilyElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
patient.setPetName(new StringType("myPet"));
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final StringType stringExt = new StringType();
stringExt.setValue("myStringExt");
stringExt.addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final Extension ext = new Extension();
ext.setValue(stringExt);
ext.setUrl("/myExt");
patient.addExtension(ext);
final IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getName().get(0).getFamilyElement().getExtension().size());
assertEquals(1, patient.getExtensionsByUrl("/myExt").get(0).getValue().getExtension().size());
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
public void testNullFlavorPrimitiveExtensionNullValueXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getExtensionsByUrl("/petname");
patient.getPetName().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getPetName().getExtension().size());
}
@Test
public void testNullFlavorIDDatatypeJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getIdElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getIdElement().getExtension().size());
}
@Test
public void testNullFlavorIDDatatypeXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.getIdElement().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getIdElement().getExtension().size());
}
@Test
public void testNullFlavorExtensionIDDatatypeJson() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
patient.setCustomId(new IdType(("4")));
patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final IParser parser = ourCtx.newJsonParser().setPrettyPrint(true);
final String json = parser.encodeResourceToString(patient);
ourLog.info(json);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, json);
assertEquals(1, patient.getCustomId().getExtension().size());
}
@Test
public void testNullFlavorExtensionIDDatatypeXml() throws Exception {
MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setId("1");
final IParser parser = ourCtx.newXmlParser().setPrettyPrint(true);
patient.setCustomId(new IdType(("4")));
patient.getCustomId().addExtension("http://hl7.org/fhir/StructureDefinition/iso21090-nullFlavor", new StringType("UNK"));
final String xml = parser.encodeResourceToString(patient);
ourLog.info(xml);
patient = parser.parseResource(MyPatientWithCustomUrlExtension.class, xml);
assertEquals(1, patient.getCustomId().getExtension().size());
}
@Test
public void testExtensionOnResourceIdXml(){
Patient p = new Patient();
p.setActive(true);
p.getIdElement().setValue("123");
p.getIdElement().addExtension().setUrl("http://foo").setValue(new StringType("FOO"));
IParser parser = ourCtx.newXmlParser();
String encoded = parser.encodeResourceToString(p);
assertThat(encoded, containsString("http://foo"));
assertThat(encoded, containsString("FOO"));
p = (Patient) parser.parseResource(encoded);
assertEquals("Patient/123", p.getId());
Extension ex = p.getIdElement().getExtension().get(0);
assertEquals("http://foo", ex.getUrl());
assertEquals("FOO", ex.getValueAsPrimitive().getValueAsString());
}
@Test
public void testExtensionOnResourceIdJson(){
Patient p = new Patient();
p.setActive(true);
p.getIdElement().setValue("123");
p.getIdElement().addExtension().setUrl("http://foo").setValue(new StringType("FOO"));
IParser parser = ourCtx.newJsonParser();
String encoded = parser.encodeResourceToString(p);
assertThat(encoded, containsString("http://foo"));
assertThat(encoded, containsString("FOO"));
p = (Patient) parser.parseResource(encoded);
assertEquals("Patient/123", p.getId());
Extension ex = p.getIdElement().getExtension().get(0);
assertEquals("http://foo", ex.getUrl());
assertEquals("FOO", ex.getValueAsPrimitive().getValueAsString());
}
}

52
hapi-fhir-structures-r4/src/test/java/ca/uhn/fhir/parser/MyPatientWithCustomUrlExtension.java Normal file
View File

@ -0,0 +1,52 @@
package ca.uhn.fhir.parser;
import ca.uhn.fhir.model.api.annotation.Child;
import ca.uhn.fhir.model.api.annotation.Description;
import ca.uhn.fhir.model.api.annotation.Extension;
import ca.uhn.fhir.model.api.annotation.ResourceDef;
import org.hl7.fhir.r4.model.IdType;
import org.hl7.fhir.r4.model.Patient;
import org.hl7.fhir.r4.model.StringType;
@ResourceDef()
public class MyPatientWithCustomUrlExtension extends Patient {
private static final long serialVersionUID = 1L;
@Child(name = "petName")
@Extension(url = "/petname", definedLocally = false, isModifier = false)
@Description(shortDefinition = "The name of the patient's favourite pet")
private StringType myPetName;
@Child(name = "customid")
@Extension(url = "/customid", definedLocally = false, isModifier = false)
@Description(shortDefinition = "The customid of the patient's ")
private IdType myCustomId;
public StringType getPetName() {
if (myPetName == null) {
myPetName = new StringType();
}
return myPetName;
}
public void setPetName(final StringType thePetName) {
myPetName = thePetName;
}
@Override
public boolean isEmpty() {
return super.isEmpty() && getCustomId().isEmpty() && getPetName().isEmpty();
}
public IdType getCustomId() {
if (myCustomId == null) {
myCustomId = new IdType();
}
return myCustomId;
}
public void setCustomId(final IdType myCustomId) {
this.myCustomId = myCustomId;
}
}

4
src/changes/changes.xml
View File

@ -279,6 +279,10 @@
Previously my.org was treated as the resource type and Foo was treated as the ID. Thanks
to GitHub user @CarthageKing for the pull request!
</action>
<action type="fix" issue="695">
Extensions on ID datatypes were not parsed or serialized correctly. Thanks to
Stephen Rivière for the pull request!
</action>
</release>
<release version="2.5" date="2017-06-08">
<action type="fix">