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Fix #327 - Correctly serialize JSON extension with a reference to a 

contained resource
This commit is contained in:
James Agnew 2016-10-14 16:36:29 -04:00
parent e56c75e80c
commit f80bf98dcd
3 changed files with 426 additions and 415 deletions
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9
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/JsonParser.java
View File

@ -1605,6 +1605,15 @@ public class JsonParser extends BaseParser implements IParser {
JsonParser.write(theEventWriter, "url", myDef.getExtensionUrl()); JsonParser.write(theEventWriter, "url", myDef.getExtensionUrl());
/*
* This makes sure that even if the extension contains a reference to a contained
* resource which has a HAPI-assigned ID we'll still encode that ID.
*
* See #327
*/
List<? extends IBase> preProcessedValue = preProcessValues(myDef, theResource, Collections.singletonList(myValue), myChildElem);
myValue = preProcessedValue.get(0);
BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass()); BaseRuntimeElementDefinition<?> def = myDef.getChildElementDefinitionByDatatype(myValue.getClass());
if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) { if (def.getChildType() == ChildTypeEnum.RESOURCE_BLOCK) {
extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem); extractAndWriteExtensionsAsDirectChild(myValue, theEventWriter, def, theResDef, theResource, myChildElem);

826
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
View File

@ -59,224 +59,6 @@ public class JsonParserDstu3Test {
} }
/**
* See #414
*/
@Test
public void testParseJsonModifierExtensionWithoutUrl() {
//@formatter:off
String input =
"{\"resourceType\":\"Patient\"," +
"\"modifierExtension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
//@formatter:on
IParser parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getModifierExtension().size());
assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getMessage());
}
}
/**
* See #327
*/
@Test
public void testEncodeExtensionWithContainedResource() {
TestPatientFor327 patient = new TestPatientFor327();
patient.setBirthDateElement(new DateType("2016-04-14"));
List<Reference> conditions = new ArrayList<Reference>();
Condition condition = new Condition();
condition.addBodySite().setText("BODY SITE");
conditions.add(new Reference(condition));
patient.setCondition(conditions);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
ourLog.info(encoded);
//@formatter:off
assertThat(encoded, stringContainsInOrder(
"<Patient xmlns=\"http://hl7.org/fhir\">",
"<contained>",
"<Condition xmlns=\"http://hl7.org/fhir\">",
"<id value=\"1\"/>",
"<bodySite>",
"<text value=\"BODY SITE\"/>",
"</bodySite>",
"</Condition>",
"</contained>",
"<extension url=\"testCondition\">",
"<valueReference>",
"<reference value=\"#1\"/>",
"</valueReference>",
"</extension>",
"<birthDate value=\"2016-04-14\"/>",
"</Patient>"
));
//@formatter:on
}
@Test
public void testParseMissingArray() throws IOException {
// RelatedPerson.name is 0..* but this file has it as a 0..1 (no array around the object)
// We're lenient so we accept it. Maybe this could change, or be a warning in future though
String input = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/missing_array.json"), StandardCharsets.UTF_8);
RelatedPerson rp = ourCtx.newJsonParser().parseResource(RelatedPerson.class, input);
assertEquals(1, rp.getName().size());
assertEquals("Doe", rp.getName().get(0).getFamilyAsSingleString());
}
@Test
public void testEncodeNarrativeShouldIncludeNamespace() {
Patient p = new Patient();
p.getText().setDivAsString("<div>VALUE</div>");
String output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(output);
assertThat(output, containsString("\"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">VALUE</div>\""));
}
@Test
public void testEncodeNarrativeShouldIncludeNamespaceWithProcessingInstruction() {
Patient p = new Patient();
p.getText().setDivAsString("<?xml version=\"1.0\" encoding=\"UTF-8\"?><div>VALUE</div>");
String output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(output);
assertThat(output, containsString("\"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">VALUE</div>\""));
}
@Test
public void testValidateCustomStructure() throws Exception {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
source.setName("NAME");
source.setEndpoint("http://foo");
FooMessageHeader header = new FooMessageHeader();
header.setTimestamp(new Date());
header.getEvent().setSystem("http://system").setCode("value");
header.setSource(source);
FhirValidator val = ourCtx.newValidator();
val.setValidateAgainstStandardSchema(true);
val.setValidateAgainstStandardSchematron(true);
ValidationResult result = val.validateWithResult(header);
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
assertTrue(result.isSuccessful());
}
@Test
public void testEncodeUndeclaredBlock() throws Exception {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
source.setName("NAME");
FooMessageHeader header = new FooMessageHeader();
header.setSource(source);
Bundle bundle = new Bundle();
bundle.addEntry().setResource(header);
IParser p = ourCtx.newJsonParser();
p.setPrettyPrint(true);
String encode = p.encodeResourceToString(bundle);
ourLog.info(encode);
assertThat(encode, containsString("\"value\": \"APPID\""));
}
/**
* See #414
*/
@Test
public void testParseJsonExtensionWithoutUrl() {
//@formatter:off
String input =
"{\"resourceType\":\"Patient\"," +
"\"extension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
//@formatter:on
IParser parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getExtension().size());
assertEquals(null, parsed.getExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getMessage());
}
}
/**
* See #344
*/
@Test
public void testParserIsCaseSensitive() {
Observation obs = new Observation();
SampledData data = new SampledData();
data.setData("1 2 3");
data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
data.setPeriod(1000L);
obs.setValue(data);
IParser p = ourCtx.newJsonParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
String encoded = p.encodeResourceToString(obs);
ourLog.info(encoded);
p.parseResource(encoded);
try {
p.parseResource(encoded.replace("Observation", "observation"));
fail();
} catch (DataFormatException e) {
assertEquals("Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'", e.getMessage());
}
try {
p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
fail();
} catch (DataFormatException e) {
assertEquals("Unknown element 'valueSampleddata' found during parse", e.getMessage());
}
}
@Test @Test
public void testEncodeAndParseExtensions() throws Exception { public void testEncodeAndParseExtensions() throws Exception {
@ -363,6 +145,7 @@ public class JsonParserDstu3Test {
} }
@Test @Test
public void testEncodeAndParseMetaProfileAndTags() { public void testEncodeAndParseMetaProfileAndTags() {
Patient p = new Patient(); Patient p = new Patient();
@ -441,6 +224,7 @@ public class JsonParserDstu3Test {
assertEquals("sec_label2", tagList.get(1).getDisplay()); assertEquals("sec_label2", tagList.get(1).getDisplay());
} }
/** /**
* See #336 * See #336
*/ */
@ -494,7 +278,7 @@ public class JsonParserDstu3Test {
assertEquals(null, name.getFamily().get(2).getExtension().get(0).getId()); assertEquals(null, name.getFamily().get(2).getExtension().get(0).getId());
} }
@Test @Test
public void testEncodeAndParseSecurityLabels() { public void testEncodeAndParseSecurityLabels() {
Patient p = new Patient(); Patient p = new Patient();
@ -555,6 +339,8 @@ public class JsonParserDstu3Test {
assertEquals("VERSION2", label.getVersion()); assertEquals("VERSION2", label.getVersion());
} }
@Test @Test
public void testEncodeBundleNewBundleNoText() { public void testEncodeBundleNewBundleNoText() {
@ -608,7 +394,7 @@ public class JsonParserDstu3Test {
)); ));
//@formatter:on //@formatter:on
} }
@Test @Test
public void testEncodeDoesntIncludeUuidId() { public void testEncodeDoesntIncludeUuidId() {
Patient p = new Patient(); Patient p = new Patient();
@ -624,7 +410,8 @@ public class JsonParserDstu3Test {
String output = ourCtx.newJsonParser().encodeResourceToString(new Binary()); String output = ourCtx.newJsonParser().encodeResourceToString(new Binary());
assertEquals("{\"resourceType\":\"Binary\"}", output); assertEquals("{\"resourceType\":\"Binary\"}", output);
} }
/** /**
* #158 * #158
*/ */
@ -659,6 +446,31 @@ public class JsonParserDstu3Test {
assertThat(encoded, not(containsString("Label"))); assertThat(encoded, not(containsString("Label")));
} }
@Test
public void testEncodeExtendedInfrastructureComponent() {
IParser parser = ourCtx.newJsonParser();
PatientWithExtendedContactDstu3 patient = new PatientWithExtendedContactDstu3();
patient.setId("123");
CustomContactComponent customContactComponent = new CustomContactComponent();
customContactComponent.getEyeColour().setValue("EYE");
customContactComponent.getName().addFamily("FAMILY");
patient.getCustomContact().add(customContactComponent);
String val = parser.encodeResourceToString(patient);
ourLog.info(val);
assertEquals(
"{\"resourceType\":\"Patient\",\"id\":\"123\",\"contact\":[{\"extension\":[{\"url\":\"http://foo.com/contact-eyecolour\",\"valueIdentifier\":{\"value\":\"EYE\"}}],\"name\":{\"family\":[\"FAMILY\"]}}]}",
val);
FhirContext newCtx = FhirContext.forDstu3();
PatientWithExtendedContactDstu3 actual = newCtx.newJsonParser().parseResource(PatientWithExtendedContactDstu3.class, val);
assertEquals("EYE", actual.getCustomContact().get(0).getEyeColour().getValue());
}
@Test @Test
public void testEncodeExtensionInPrimitiveElement() { public void testEncodeExtensionInPrimitiveElement() {
@ -769,6 +581,209 @@ public class JsonParserDstu3Test {
assertEquals("sub_ext_value", ((StringType) obs.getExtension().get(0).getExtension().get(0).getValue()).getValue()); assertEquals("sub_ext_value", ((StringType) obs.getExtension().get(0).getExtension().get(0).getValue()).getValue());
} }
/**
* See #327
*/
@Test
public void testEncodeExtensionWithContainedResource() {
TestPatientFor327 patient = new TestPatientFor327();
patient.setBirthDateElement(new DateType("2016-04-14"));
List<Reference> conditions = new ArrayList<Reference>();
Condition condition = new Condition();
condition.addBodySite().setText("BODY SITE");
conditions.add(new Reference(condition));
patient.setCondition(conditions);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(patient);
ourLog.info(encoded);
//@formatter:off
assertThat(encoded, stringContainsInOrder(
"\"resourceType\": \"Patient\"",
"\"contained\": [",
"\"resourceType\": \"Condition\"",
"\"id\": \"1\"",
"\"bodySite\": [",
"\"text\": \"BODY SITE\"",
"\"extension\": [",
"\"url\": \"testCondition\",",
"\"valueReference\": {",
"\"reference\": \"#1\"",
"\"birthDate\": \"2016-04-14\"",
"}"
));
//@formatter:on
}
@Test
public void testEncodeHistoryEncodeVersionsAtPath1() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
parser.setDontStripVersionsFromReferencesAtPaths("Patient.managingOrganization");
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
}
@Test
public void testEncodeHistoryEncodeVersionsAtPath2() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
assertTrue(ourCtx.getParserOptions().isStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
}
@Test
public void testEncodeHistoryEncodeVersionsAtPath3() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
AuditEvent auditEvent = new AuditEvent();
auditEvent.addEntity().setReference(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
String enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setDontStripVersionsFromReferencesAtPaths((String[])null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setDontStripVersionsFromReferencesAtPaths((List<String>)null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
}
@Test
public void testEncodeHistoryEncodeVersionsAtPathUsingOptions() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
assertTrue(ourCtx.getParserOptions().isStripVersionsFromReferences());
assertThat(ourCtx.getParserOptions().getDontStripVersionsFromReferencesAtPaths(), empty());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("Patient.managingOrganization");
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(Arrays.asList("Patient.managingOrganization"));
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(new HashSet<String>(Arrays.asList("Patient.managingOrganization")));
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
}
@Test
public void testEncodeHistoryStripVersionsFromReferences() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setStripVersionsFromReferences(false);
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx = FhirContext.forDstu3();
}
@Test
public void testEncodeHistoryStripVersionsFromReferencesFromContext() {
ourCtx = FhirContext.forDstu3();
assertTrue(ourCtx.getParserOptions().isStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
ourCtx.getParserOptions().setStripVersionsFromReferences(false);
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
parser.setStripVersionsFromReferences(true);
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
ourCtx = FhirContext.forDstu3();
}
@Test
public void testEncodeNarrativeShouldIncludeNamespace() {
Patient p = new Patient();
p.getText().setDivAsString("<div>VALUE</div>");
String output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(output);
assertThat(output, containsString("\"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">VALUE</div>\""));
}
@Test
public void testEncodeNarrativeShouldIncludeNamespaceWithProcessingInstruction() {
Patient p = new Patient();
p.getText().setDivAsString("<?xml version=\"1.0\" encoding=\"UTF-8\"?><div>VALUE</div>");
String output = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(output);
assertThat(output, containsString("\"div\": \"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">VALUE</div>\""));
}
@Test @Test
public void testEncodeNarrativeSuppressed() throws Exception { public void testEncodeNarrativeSuppressed() throws Exception {
Patient patient = new Patient(); Patient patient = new Patient();
@ -882,6 +897,27 @@ public class JsonParserDstu3Test {
assertEquals(null, condition.getId()); assertEquals(null, condition.getId());
} }
@Test
public void testEncodeUndeclaredBlock() throws Exception {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
source.setName("NAME");
FooMessageHeader header = new FooMessageHeader();
header.setSource(source);
Bundle bundle = new Bundle();
bundle.addEntry().setResource(header);
IParser p = ourCtx.newJsonParser();
p.setPrettyPrint(true);
String encode = p.encodeResourceToString(bundle);
ourLog.info(encode);
assertThat(encode, containsString("\"value\": \"APPID\""));
}
@Test @Test
public void testEncodeUndeclaredExtensionWithEnumerationContent() { public void testEncodeUndeclaredExtensionWithEnumerationContent() {
IParser parser = ourCtx.newJsonParser(); IParser parser = ourCtx.newJsonParser();
@ -903,176 +939,6 @@ public class JsonParserDstu3Test {
} }
@Test
public void testEncodeHistoryStripVersionsFromReferences() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setStripVersionsFromReferences(false);
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx = FhirContext.forDstu3();
}
@Test
public void testEncodeHistoryStripVersionsFromReferencesFromContext() {
ourCtx = FhirContext.forDstu3();
assertTrue(ourCtx.getParserOptions().isStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
ourCtx.getParserOptions().setStripVersionsFromReferences(false);
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
parser.setStripVersionsFromReferences(true);
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
ourCtx = FhirContext.forDstu3();
}
@Test
public void testEncodeHistoryEncodeVersionsAtPath1() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
parser.setDontStripVersionsFromReferencesAtPaths("Patient.managingOrganization");
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
}
@Test
public void testEncodeHistoryEncodeVersionsAtPath2() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
assertTrue(ourCtx.getParserOptions().isStripVersionsFromReferences());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
}
@Test
public void testEncodeHistoryEncodeVersionsAtPathUsingOptions() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
assertTrue(ourCtx.getParserOptions().isStripVersionsFromReferences());
assertThat(ourCtx.getParserOptions().getDontStripVersionsFromReferencesAtPaths(), empty());
Patient p = new Patient();
p.setManagingOrganization(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths("Patient.managingOrganization");
String enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(Arrays.asList("Patient.managingOrganization"));
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
ourCtx.getParserOptions().setDontStripVersionsFromReferencesAtPaths(new HashSet<String>(Arrays.asList("Patient.managingOrganization")));
enc = parser.setPrettyPrint(true).encodeResourceToString(p);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
}
@Test
public void testEncodeHistoryEncodeVersionsAtPath3() {
ourCtx = FhirContext.forDstu3();
assertNull(ourCtx.newJsonParser().getStripVersionsFromReferences());
AuditEvent auditEvent = new AuditEvent();
auditEvent.addEntity().setReference(new Reference("http://foo.com/Organization/2/_history/1"));
IParser parser = ourCtx.newJsonParser();
parser.setDontStripVersionsFromReferencesAtPaths("AuditEvent.entity.reference");
String enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2/_history/1\""));
parser.setDontStripVersionsFromReferencesAtPaths(new ArrayList<String>());
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setDontStripVersionsFromReferencesAtPaths((String[])null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
parser.setDontStripVersionsFromReferencesAtPaths((List<String>)null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
}
@Test
public void testEncodeExtendedInfrastructureComponent() {
IParser parser = ourCtx.newJsonParser();
PatientWithExtendedContactDstu3 patient = new PatientWithExtendedContactDstu3();
patient.setId("123");
CustomContactComponent customContactComponent = new CustomContactComponent();
customContactComponent.getEyeColour().setValue("EYE");
customContactComponent.getName().addFamily("FAMILY");
patient.getCustomContact().add(customContactComponent);
String val = parser.encodeResourceToString(patient);
ourLog.info(val);
assertEquals(
"{\"resourceType\":\"Patient\",\"id\":\"123\",\"contact\":[{\"extension\":[{\"url\":\"http://foo.com/contact-eyecolour\",\"valueIdentifier\":{\"value\":\"EYE\"}}],\"name\":{\"family\":[\"FAMILY\"]}}]}",
val);
FhirContext newCtx = FhirContext.forDstu3();
PatientWithExtendedContactDstu3 actual = newCtx.newJsonParser().parseResource(PatientWithExtendedContactDstu3.class, val);
assertEquals("EYE", actual.getCustomContact().get(0).getEyeColour().getValue());
}
@Test @Test
public void testEncodeWithDontEncodeElements() throws Exception { public void testEncodeWithDontEncodeElements() throws Exception {
Patient patient = new Patient(); Patient patient = new Patient();
@ -1504,20 +1370,6 @@ public class JsonParserDstu3Test {
assertThat(encoded, not(containsString("\"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\""))); assertThat(encoded, not(containsString("\"id\":\"180f219f-97a8-486d-99d9-ed631fe4fc57\"")));
} }
/**
* See #399
*/
@Test
public void testParseCommunicationWithThreeTypes() throws IOException {
String content = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/tara-test.json"));
Communication comm = ourCtx.newJsonParser().parseResource(Communication.class, content);
assertEquals(3, comm.getPayload().size());
assertEquals(Attachment.class, comm.getPayload().get(0).getContent().getClass());
assertEquals(Reference.class, comm.getPayload().get(1).getContent().getClass());
assertEquals(StringType.class, comm.getPayload().get(2).getContent().getClass());
}
@Test @Test
public void testParseAndEncodeComments() throws IOException { public void testParseAndEncodeComments() throws IOException {
//@formatter:off //@formatter:off
@ -1602,6 +1454,20 @@ public class JsonParserDstu3Test {
assertEquals(expected, val); assertEquals(expected, val);
} }
/**
* See #399
*/
@Test
public void testParseCommunicationWithThreeTypes() throws IOException {
String content = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/tara-test.json"));
Communication comm = ourCtx.newJsonParser().parseResource(Communication.class, content);
assertEquals(3, comm.getPayload().size());
assertEquals(Attachment.class, comm.getPayload().get(0).getContent().getClass());
assertEquals(Reference.class, comm.getPayload().get(1).getContent().getClass());
assertEquals(StringType.class, comm.getPayload().get(2).getContent().getClass());
}
/** /**
* see #144 and #146 * see #144 and #146
*/ */
@ -1675,6 +1541,66 @@ public class JsonParserDstu3Test {
} }
/**
* See #414
*/
@Test
public void testParseJsonExtensionWithoutUrl() {
//@formatter:off
String input =
"{\"resourceType\":\"Patient\"," +
"\"extension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
//@formatter:on
IParser parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getExtension().size());
assertEquals(null, parsed.getExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getMessage());
}
}
/**
* See #414
*/
@Test
public void testParseJsonModifierExtensionWithoutUrl() {
//@formatter:off
String input =
"{\"resourceType\":\"Patient\"," +
"\"modifierExtension\":[ {\"valueDateTime\":\"2011-01-02T11:13:15\"} ]" +
"}";
//@formatter:on
IParser parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new LenientErrorHandler());
Patient parsed = (Patient) parser.parseResource(input);
assertEquals(1, parsed.getModifierExtension().size());
assertEquals(null, parsed.getModifierExtension().get(0).getUrl());
assertEquals("2011-01-02T11:13:15", parsed.getModifierExtension().get(0).getValueAsPrimitive().getValueAsString());
try {
parser = ourCtx.newJsonParser();
parser.setParserErrorHandler(new StrictErrorHandler());
parser.parseResource(input);
fail();
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getMessage());
}
}
@Test @Test
public void testParseMetadata() throws Exception { public void testParseMetadata() throws Exception {
//@formatter:off //@formatter:off
@ -1738,16 +1664,18 @@ public class JsonParserDstu3Test {
} }
@Test(expected = DataFormatException.class) @Test
public void testParseWithTrailingContent() throws Exception { public void testParseMissingArray() throws IOException {
//@formatter:off // RelatedPerson.name is 0..* but this file has it as a 0..1 (no array around the object)
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" + // We're lenient so we accept it. Maybe this could change, or be a warning in future though
" \"total\" : 1\n" +
"}}"; String input = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/missing_array.json"), StandardCharsets.UTF_8);
//@formatter:on RelatedPerson rp = ourCtx.newJsonParser().parseResource(RelatedPerson.class, input);
assertEquals(1, rp.getName().size());
Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, bundle); assertEquals("Doe", rp.getName().get(0).getFamilyAsSingleString());
} }
/** /**
@ -1796,6 +1724,39 @@ public class JsonParserDstu3Test {
} }
} }
/**
* See #344
*/
@Test
public void testParserIsCaseSensitive() {
Observation obs = new Observation();
SampledData data = new SampledData();
data.setData("1 2 3");
data.setOrigin((SimpleQuantity) new SimpleQuantity().setValue(0L));
data.setPeriod(1000L);
obs.setValue(data);
IParser p = ourCtx.newJsonParser().setPrettyPrint(true).setParserErrorHandler(new StrictErrorHandler());
String encoded = p.encodeResourceToString(obs);
ourLog.info(encoded);
p.parseResource(encoded);
try {
p.parseResource(encoded.replace("Observation", "observation"));
fail();
} catch (DataFormatException e) {
assertEquals("Unknown resource type 'observation': Resource names are case sensitive, found similar name: 'Observation'", e.getMessage());
}
try {
p.parseResource(encoded.replace("valueSampledData", "valueSampleddata"));
fail();
} catch (DataFormatException e) {
assertEquals("Unknown element 'valueSampleddata' found during parse", e.getMessage());
}
}
@Test @Test
public void testParseWithPrecision() { public void testParseWithPrecision() {
String input = "{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}"; String input = "{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}";
@ -1809,6 +1770,18 @@ public class JsonParserDstu3Test {
assertEquals("{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}", str); assertEquals("{\"resourceType\":\"Observation\",\"valueQuantity\":{\"value\":0.000000000000000100}}", str);
} }
@Test(expected = DataFormatException.class)
public void testParseWithTrailingContent() throws Exception {
//@formatter:off
String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" +
" \"total\" : 1\n" +
"}}";
//@formatter:on
Bundle b = ourCtx.newJsonParser().parseResource(Bundle.class, bundle);
}
@Test @Test
@Ignore @Ignore
public void testParseWithWrongTypeObjectShouldBeArray() throws Exception { public void testParseWithWrongTypeObjectShouldBeArray() throws Exception {
@ -1867,6 +1840,29 @@ public class JsonParserDstu3Test {
Assert.assertThat(message, containsString("contained")); Assert.assertThat(message, containsString("contained"));
} }
@Test
public void testValidateCustomStructure() throws Exception {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
source.setName("NAME");
source.setEndpoint("http://foo");
FooMessageHeader header = new FooMessageHeader();
header.setTimestamp(new Date());
header.getEvent().setSystem("http://system").setCode("value");
header.setSource(source);
FhirValidator val = ourCtx.newValidator();
val.setValidateAgainstStandardSchema(true);
val.setValidateAgainstStandardSchematron(true);
ValidationResult result = val.validateWithResult(header);
ourLog.info(ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result.toOperationOutcome()));
assertTrue(result.isSuccessful());
}
@AfterClass @AfterClass
public static void afterClassClearContext() { public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest(); TestUtil.clearAllStaticFieldsForUnitTest();

6
src/changes/changes.xml
View File

@ -195,6 +195,12 @@
pass in a number of IDs by a collection of Strings. Thanks to pass in a number of IDs by a collection of Strings. Thanks to
Thomas Andersen for the pul request! Thomas Andersen for the pul request!
</action> </action>
<action type="fix" issue="327">
When encoding a resource in JSON where the resource has
an extension with a value where the value is a reference to a
contained resource, the reference value (e.g. "#1") did not
get serialized. Thanks to GitHub user @fw060 for reporting!
</action>
</release> </release>
<release version="2.0" date="2016-08-30"> <release version="2.0" date="2016-08-30">
<action type="fix"> <action type="fix">