diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java index 34781546014..91898e2df9f 100644 --- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java +++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/parser/BaseParser.java @@ -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; } diff --git a/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java b/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java index 4f9219b4e35..14adfbe9bc6 100644 --- a/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java +++ b/hapi-fhir-structures-dstu/src/test/java/ca/uhn/fhir/parser/JsonParserTest.java @@ -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\":\"
"); @@ -107,6 +103,7 @@ public class JsonParserTest { assertEquals(exp, act); } + @Test public void testDecimalPrecisionPreserved() { String number = "52.3779939997090374535378485873776474764643249869328698436986235758587"; diff --git a/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java b/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java index e67c190e0df..b70bcf2ce9e 100644 --- a/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java +++ b/hapi-fhir-structures-dstu3/src/test/java/ca/uhn/fhir/parser/JsonParserDstu3Test.java @@ -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 elementName = ArgumentCaptor.forClass(String.class); ArgumentCaptor expected = ArgumentCaptor.forClass(ValueType.class); ArgumentCaptor 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()); 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)null); + parser.setDontStripVersionsFromReferencesAtPaths((List) 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\":\"
\"}}"; Basic basic = ourCtx.newJsonParser().parseResource(Basic.class, input); assertEquals(null, basic.getText().getDivAsString()); - + input = "{\"resourceType\":\"Basic\",\"id\":\"1\",\"text\":{\"status\":\"generated\",\"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()); } diff --git a/src/changes/changes.xml b/src/changes/changes.xml index 2675db22047..62d245082c2 100644 --- a/src/changes/changes.xml +++ b/src/changes/changes.xml @@ -46,6 +46,15 @@ or log a warning depending on the configured error handler. + + 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! +