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Fix #276 - Prevent contained resources being encoded as duplicates

This commit is contained in:
James Agnew 2016-11-25 17:18:57 -05:00
parent 69871bb8c2
commit 81773de261
4 changed files with 100 additions and 69 deletions
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3
hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java
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@ -244,6 +244,9 @@ public abstract class BaseParser implements IParser {
continue;
}
theContained.addContained(resource);
if (resource.getIdElement().isLocal() && existingIdToContainedResource != null) {
existingIdToContainedResource.remove(resource.getIdElement().getValue());
}
} else {
continue;
}

13
hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java
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@ -11,14 +11,10 @@ import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.io.StringReader;
import java.io.*;
import java.nio.charset.Charset;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.nio.charset.StandardCharsets;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.hamcrest.core.IsNot;
@ -84,7 +80,7 @@ public class JsonParserTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserTest.class);
private void parseAndEncode(String name) throws IOException {
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream(name));
String msg = IOUtils.toString(XmlParser.class.getResourceAsStream(name), StandardCharsets.UTF_8);
// ourLog.info(msg);
msg = msg.replace("\"div\": \"<div>", "\"div\":\"<div xmlns=\\\"http://www.w3.org/1999/xhtml\\\">");
@ -107,6 +103,7 @@ public class JsonParserTest {
assertEquals(exp, act);
}
@Test
public void testDecimalPrecisionPreserved() {
String number = "52.3779939997090374535378485873776474764643249869328698436986235758587";

144
hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java
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@ -1,5 +1,6 @@
package ca.uhn.fhir.parser;
import static org.apache.commons.lang3.StringUtils.countMatches;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
@ -17,7 +18,9 @@ import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.math.BigDecimal;
import java.nio.charset.StandardCharsets;
import java.util.*;
@ -36,6 +39,7 @@ import org.hl7.fhir.dstu3.model.Enumeration;
import org.hl7.fhir.dstu3.model.Enumerations.AdministrativeGender;
import org.hl7.fhir.dstu3.model.Identifier.IdentifierUse;
import org.hl7.fhir.dstu3.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.utilities.xhtml.XhtmlNode;
import org.junit.*;
import org.mockito.ArgumentCaptor;
@ -66,6 +70,32 @@ public class JsonParserDstu3Test {
ourCtx.setNarrativeGenerator(null);
}
/**
* See #276
*/
@Test
public void testDoubleEncodingContainedResources() throws Exception {
Patient patient = new Patient();
patient.setId("#patient-1");
patient.setActive(true);
Coverage coverage = new Coverage();
coverage.setId("#coverage-1");
coverage.getBeneficiary().setResource(patient);
Claim resource = new Claim();
resource.getContained().add(patient);
resource.getContained().add(coverage);
resource.getPatient().setReference("#patient-1");
resource.addCoverage().getCoverage().setReference("#coverage-1");
IParser p = ourCtx.newJsonParser().setPrettyPrint(true);
String encoded = p.encodeResourceToString(resource);
ourLog.info(encoded);
assertEquals(3, countMatches(encoded, "resourceType"));
}
/**
* #480
*/
@ -77,15 +107,15 @@ public class JsonParserDstu3Test {
qr.getItemFirstRep().setLinkIdElement(new StringType());
qr.getItemFirstRep().addItem().setLinkIdElement(new StringType(""));
qr.getItemFirstRep().addItem().setLinkIdElement(new StringType("LINKID"));
String encoded = ourCtx.newJsonParser().encodeResourceToString(qr);
ourLog.info(encoded);
assertThat(encoded, stringContainsInOrder("123"));
assertThat(encoded, not(stringContainsInOrder("\"\"")));
assertThat(encoded, not(stringContainsInOrder("null")));
}
/**
* #480
*/
@ -93,7 +123,7 @@ public class JsonParserDstu3Test {
public void testParseEmptyValue() {
String input = "{\"resourceType\":\"QuestionnaireResponse\",\"id\":\"123\",\"authored\":\"\",\"item\":[{\"item\":[{\"linkId\":\"\"}]}]}";
QuestionnaireResponse qr = ourCtx.newJsonParser().parseResource(QuestionnaireResponse.class, input);
assertEquals("QuestionnaireResponse/123", qr.getIdElement().getValue());
assertEquals(null, qr.getAuthored());
assertEquals(null, qr.getAuthoredElement().getValue());
@ -108,7 +138,7 @@ public class JsonParserDstu3Test {
@Test
public void testUnexpectedElementsWithUnderscoreAtStartOfName() throws Exception {
String input = IOUtils.toString(JsonParserDstu3Test.class.getResourceAsStream("/bug477.json"), StandardCharsets.UTF_8);
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
// Do it once without the custom error handler just for the logging
@ -117,23 +147,22 @@ public class JsonParserDstu3Test {
p = ourCtx.newJsonParser();
p.setParserErrorHandler(errorHandler);
Patient parsed = p.parseResource(Patient.class, input);
assertEquals("1", parsed.getIdElement().getIdPart());
ArgumentCaptor<String> elementName = ArgumentCaptor.forClass(String.class);
ArgumentCaptor<ValueType> expected = ArgumentCaptor.forClass(ValueType.class);
ArgumentCaptor<ValueType> actual = ArgumentCaptor.forClass(ValueType.class);
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),elementName.capture(), expected.capture(), actual.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class),Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), elementName.capture(), expected.capture(), actual.capture());
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_id"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("__v"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
verify(errorHandler, atLeastOnce()).incorrectJsonType(Mockito.any(IParseLocation.class), Mockito.eq("_status"), Mockito.eq(ValueType.OBJECT), Mockito.eq(ValueType.SCALAR));
assertEquals("_id", elementName.getAllValues().get(0));
assertEquals(ValueType.OBJECT, expected.getAllValues().get(0));
assertEquals(ValueType.SCALAR, actual.getAllValues().get(0));
}
@Test
public void testEncodeAndParseExtensions() throws Exception {
@ -221,7 +250,6 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeAndParseMetaProfileAndTags() {
Patient p = new Patient();
@ -300,7 +328,6 @@ public class JsonParserDstu3Test {
assertEquals("sec_label2", tagList.get(1).getDisplay());
}
/**
* See #336
*/
@ -355,7 +382,6 @@ public class JsonParserDstu3Test {
}
@Test
public void testEncodeAndParseSecurityLabels() {
Patient p = new Patient();
@ -415,7 +441,7 @@ public class JsonParserDstu3Test {
assertEquals("DISPLAY2", label.getDisplay());
assertEquals("VERSION2", label.getVersion());
}
@Test
public void testEncodeBundleNewBundleNoText() {
@ -434,8 +460,6 @@ public class JsonParserDstu3Test {
}
/**
* See #326
*/
@ -481,7 +505,7 @@ public class JsonParserDstu3Test {
String actual = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(p);
assertThat(actual, not(containsString("78ef6f64c2f2")));
}
@Test
public void testEncodeEmptyBinary() {
String output = ourCtx.newJsonParser().encodeResourceToString(new Binary());
@ -503,8 +527,7 @@ public class JsonParserDstu3Test {
String encoded = ourCtx.newJsonParser().encodeResourceToString(p);
assertThat(encoded, not(containsString("tag")));
}
/**
* #158
*/
@ -697,14 +720,14 @@ public class JsonParserDstu3Test {
@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);
@ -714,15 +737,15 @@ public class JsonParserDstu3Test {
@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);
@ -732,30 +755,30 @@ public class JsonParserDstu3Test {
@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);
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);
parser.setDontStripVersionsFromReferencesAtPaths((List<String>) null);
enc = parser.setPrettyPrint(true).encodeResourceToString(auditEvent);
ourLog.info(enc);
assertThat(enc, containsString("\"reference\": \"http://foo.com/Organization/2\""));
@ -764,21 +787,21 @@ public class JsonParserDstu3Test {
@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);
@ -793,17 +816,17 @@ 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);
@ -815,17 +838,17 @@ public class JsonParserDstu3Test {
@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);
@ -1015,7 +1038,7 @@ public class JsonParserDstu3Test {
assertEquals("home", ref.getValue().toCode());
}
@Test
public void testEncodeWithDontEncodeElements() throws Exception {
Patient patient = new Patient();
@ -1645,7 +1668,7 @@ public class JsonParserDstu3Test {
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'extension'", e.getMessage());
}
}
/**
@ -1675,7 +1698,7 @@ public class JsonParserDstu3Test {
} catch (DataFormatException e) {
assertEquals("Resource is missing required element 'url' in parent element 'modifierExtension'", e.getMessage());
}
}
@Test
@ -1744,15 +1767,14 @@ public class JsonParserDstu3Test {
@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());
}
/**
@ -1763,7 +1785,7 @@ public class JsonParserDstu3Test {
String input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div/>\"}}";
Basic basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals(null, basic.getText().getDivAsString());
input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"div\":\"<div></div>\"}}";
basic = ourCtx.newJsonParser().parseResource(Basic.class, input);
assertEquals(null, basic.getText().getDivAsString());
@ -1938,7 +1960,7 @@ public class JsonParserDstu3Test {
@Test
public void testValidateCustomStructure() throws Exception {
FooMessageHeader.FooMessageSourceComponent source = new FooMessageHeader.FooMessageSourceComponent();
source.getMessageHeaderApplicationId().setValue("APPID");
source.setName("NAME");
@ -1952,9 +1974,9 @@ public class JsonParserDstu3Test {
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());
}

9
src/changes/changes.xml
View File

@ -46,6 +46,15 @@
or log a warning depending on the configured
error handler.
</action>
<action type="fix" issue="276">
Fix issue when serializing resources that have
contained resources which are referred to
from multiple places. Sometimes when serializing
these resources the contained resource section
would contain duplicates. Thanks to Hugo Soares
and Stefan Evinance for reporting and providing
a test case!
</action>
</release>
<release version="2.1" date="2016-11-11">
<action type="add">