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Add credit for #798 and fix broken test

This commit is contained in:
jamesagnew 2018-03-15 07:30:32 -04:00
parent 84e606cfe8
commit 83b1cf5b9f
4 changed files with 133 additions and 332 deletions
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2
hapi-fhir-jpaserver-elasticsearch/pom.xml
View File

@ -4,7 +4,7 @@
<parent> <parent>
<groupId>ca.uhn.hapi.fhir</groupId> <groupId>ca.uhn.hapi.fhir</groupId>
<artifactId>hapi-deployable-pom</artifactId> <artifactId>hapi-deployable-pom</artifactId>
<version>3.2.0-SNAPSHOT</version> <version>3.3.0-SNAPSHOT</version>
<relativePath>../hapi-deployable-pom/pom.xml</relativePath> <relativePath>../hapi-deployable-pom/pom.xml</relativePath>
</parent> </parent>

3
hapi-fhir-jpaserver-example/src/main/java/ca/uhn/fhir/jpa/demo/elasticsearch/FhirServerConfig.java
View File

@ -12,6 +12,7 @@ import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor; import ca.uhn.fhir.rest.server.interceptor.ResponseHighlighterInterceptor;
import org.apache.commons.dbcp2.BasicDataSource; import org.apache.commons.dbcp2.BasicDataSource;
import org.hibernate.jpa.HibernatePersistenceProvider; import org.hibernate.jpa.HibernatePersistenceProvider;
import org.hibernate.search.elasticsearch.cfg.ElasticsearchEnvironment;
import org.springframework.beans.factory.annotation.Autowire; import org.springframework.beans.factory.annotation.Autowire;
import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration; import org.springframework.context.annotation.Configuration;
@ -76,7 +77,7 @@ public class FhirServerConfig extends BaseJavaConfigDstu3 {
extraProperties.put("hibernate.cache.use_minimal_puts", "false"); extraProperties.put("hibernate.cache.use_minimal_puts", "false");
// the belowing properties are used for ElasticSearch integration // the belowing properties are used for ElasticSearch integration
extraProperties.put("hibernate.search.elasticsearch.analyzer_definition_provider", ElasticsearchMappingProvider.class.getName()); extraProperties.put(ElasticsearchEnvironment.ANALYZER_DEFINITION_PROVIDER, ElasticsearchMappingProvider.class.getName());
extraProperties.put("hibernate.search.default.indexmanager", "elasticsearch"); extraProperties.put("hibernate.search.default.indexmanager", "elasticsearch");
extraProperties.put("hibernate.search.default.elasticsearch.host", "http://127.0.0.1:9200"); extraProperties.put("hibernate.search.default.elasticsearch.host", "http://127.0.0.1:9200");
extraProperties.put("hibernate.search.default.elasticsearch.index_schema_management_strategy", "CREATE"); extraProperties.put("hibernate.search.default.elasticsearch.index_schema_management_strategy", "CREATE");

454
hapi-fhir-structures-dstu2/src/test/java/ca/uhn/fhir/parser/JsonParserDstu2Test.java
View File

@ -1,40 +1,5 @@
package ca.uhn.fhir.parser; package ca.uhn.fhir.parser;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.hamcrest.core.IsInstanceOf.instanceOf;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import java.io.IOException;
import java.io.StringReader;
import java.util.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.hamcrest.Matchers;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Assert;
import org.junit.Test;
import org.mockito.ArgumentCaptor;
import org.mockito.Mockito;
import org.mockito.internal.stubbing.answers.ThrowsException;
import org.slf4j.LoggerFactory;
import com.google.common.collect.Sets;
import ca.uhn.fhir.context.FhirContext; import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.model.api.*; import ca.uhn.fhir.model.api.*;
import ca.uhn.fhir.model.base.composite.BaseCodingDt; import ca.uhn.fhir.model.base.composite.BaseCodingDt;
@ -66,12 +31,13 @@ import org.mockito.Mockito;
import org.mockito.internal.stubbing.answers.ThrowsException; import org.mockito.internal.stubbing.answers.ThrowsException;
import org.slf4j.LoggerFactory; import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.io.StringReader; import java.io.StringReader;
import java.util.*; import java.util.*;
import static org.hamcrest.CoreMatchers.equalTo;
import static org.hamcrest.Matchers.contains; import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.*; import static org.hamcrest.Matchers.*;
import static org.hamcrest.core.IsInstanceOf.instanceOf;
import static org.junit.Assert.*; import static org.junit.Assert.*;
import static org.mockito.Mockito.*; import static org.mockito.Mockito.*;
@ -79,6 +45,33 @@ public class JsonParserDstu2Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class); private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(JsonParserDstu2Test.class);
private static FhirContext ourCtx = FhirContext.forDstu2(); private static FhirContext ourCtx = FhirContext.forDstu2();
private void assertExtensionMetadata(
BaseResource resource,
String url,
boolean isModifier,
Class<?> expectedType,
String expectedValue) {
ExtensionDt extension = (ExtensionDt) resource.getResourceMetadata().get(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(url));
assertThat(extension.getValue(), instanceOf(expectedType));
assertThat(extension.isModifier(), equalTo(isModifier));
assertThat(extension.getValueAsPrimitive().getValueAsString(), equalTo(expectedValue));
}
private void assertParsedResourcesExtensionMetadata(ProcedureRequest resource) {
ExtensionDt payment = (ExtensionDt) resource.getResourceMetadata().get(
new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://fhir.sjanic.com/procedureRequest/requiresPatientPayment"));
assertThat(payment.isModifier(), equalTo(true));
assertThat(((BooleanDt) payment.getValue()).getValue(), equalTo(true));
TimestampFields timestampFields = new TimestampFields(resource);
assertThat(timestampFields.user.getReference().getIdPart(), equalTo("sjanic"));
assertThat(timestampFields.instance.getValue(), equalTo(new InstantDt("2012-01-01T13:00:00Z").getValue()));
assertThat(timestampFields.organization.getReference().getIdPart(), equalTo("sjanic_org"));
assertThat(timestampFields.role.getCodingFirstRep().getSystem(), equalTo("sjanic"));
assertThat(timestampFields.role.getCodingFirstRep().getCode(), equalTo("Doctor"));
}
@Test @Test
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() { public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar"; String refVal = "http://my.org/FooBar";
@ -103,7 +96,7 @@ public class JsonParserDstu2Test {
* See #544 * See #544
*/ */
@Test @Test
public void testBundleStitchReferencesByUuid() throws Exception { public void testBundleStitchReferencesByUuid() {
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle(); ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
DocumentManifest dm = new DocumentManifest(); DocumentManifest dm = new DocumentManifest();
@ -180,6 +173,7 @@ public class JsonParserDstu2Test {
assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue()); assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
} }
@Test @Test
public void testCustomUrlExtensioninBundle() { public void testCustomUrlExtensioninBundle() {
final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}"; final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
@ -252,7 +246,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testEncodeAndParseExtensions() throws Exception { public void testEncodeAndParseExtensions() {
Patient patient = new Patient(); Patient patient = new Patient();
patient.addIdentifier().setUse(IdentifierUseEnum.OFFICIAL).setSystem("urn:example").setValue("7000135"); patient.addIdentifier().setUse(IdentifierUseEnum.OFFICIAL).setSystem("urn:example").setValue("7000135");
@ -398,9 +392,9 @@ public class JsonParserDstu2Test {
assertEquals(2, gotLabels.size()); assertEquals(2, gotLabels.size());
IdDt label = (IdDt) gotLabels.get(0); IdDt label = gotLabels.get(0);
assertEquals("http://foo/Profile1", label.getValue()); assertEquals("http://foo/Profile1", label.getValue());
label = (IdDt) gotLabels.get(1); label = gotLabels.get(1);
assertEquals("http://foo/Profile2", label.getValue()); assertEquals("http://foo/Profile2", label.getValue());
tagList = ResourceMetadataKeyEnum.TAG_LIST.get(parsed); tagList = ResourceMetadataKeyEnum.TAG_LIST.get(parsed);
@ -421,7 +415,7 @@ public class JsonParserDstu2Test {
HumanNameDt name = p.addName(); HumanNameDt name = p.addName();
name.addFamily().setValue(null).addUndeclaredExtension(new ExtensionDt(false, "http://foo", new StringDt("FOOEXT0"))); name.addFamily().setValue(null).addUndeclaredExtension(new ExtensionDt(false, "http://foo", new StringDt("FOOEXT0")));
name.getFamily().get(0).setElementSpecificId("f0"); name.getFamily().get(0).setElementSpecificId("f0");
name.addFamily().setValue("V1").addUndeclaredExtension((ExtensionDt) new ExtensionDt(false, "http://foo", new StringDt("FOOEXT1"))); name.addFamily().setValue("V1").addUndeclaredExtension(new ExtensionDt(false, "http://foo", new StringDt("FOOEXT1")));
name.getFamily().get(1).setElementSpecificId("f1"); name.getFamily().get(1).setElementSpecificId("f1");
name.getFamily().get(1).getUndeclaredExtensions().get(0).setElementSpecificId("ext1id"); name.getFamily().get(1).getUndeclaredExtensions().get(0).setElementSpecificId("ext1id");
name.addFamily(); // this one shouldn't get encoded name.addFamily(); // this one shouldn't get encoded
@ -548,7 +542,6 @@ public class JsonParserDstu2Test {
ca.uhn.fhir.model.dstu2.resource.Bundle b = new ca.uhn.fhir.model.dstu2.resource.Bundle(); ca.uhn.fhir.model.dstu2.resource.Bundle b = new ca.uhn.fhir.model.dstu2.resource.Bundle();
b.getText().setDiv(""); b.getText().setDiv("");
b.getText().getStatus().setValueAsString(""); b.getText().getStatus().setValueAsString("");
;
Entry e = b.addEntry(); Entry e = b.addEntry();
e.setResource(new Patient()); e.setResource(new Patient());
@ -651,7 +644,6 @@ public class JsonParserDstu2Test {
c = new Conformance(); c = new Conformance();
c.getAcceptUnknownElement().setValueAsEnum(UnknownContentCodeEnum.UNKNOWN_ELEMENTS); c.getAcceptUnknownElement().setValueAsEnum(UnknownContentCodeEnum.UNKNOWN_ELEMENTS);
;
c.getAcceptUnknownElement().addUndeclaredExtension(false, "http://foo", new StringDt("AAA")); c.getAcceptUnknownElement().addUndeclaredExtension(false, "http://foo", new StringDt("AAA"));
encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c); encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(c);
@ -805,7 +797,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testEncodeNarrativeSuppressed() throws Exception { public void testEncodeNarrativeSuppressed() {
Patient patient = new Patient(); Patient patient = new Patient();
patient.setId("Patient/1/_history/1"); patient.setId("Patient/1/_history/1");
patient.getText().setDiv("<div>THE DIV</div>"); patient.getText().setDiv("<div>THE DIV</div>");
@ -823,6 +815,7 @@ public class JsonParserDstu2Test {
assertThat(encoded, containsString("maritalStatus")); assertThat(encoded, containsString("maritalStatus"));
} }
/** /**
* See #537 * See #537
*/ */
@ -850,6 +843,69 @@ public class JsonParserDstu2Test {
assertThat(encoded, stringContainsInOrder("LEVEL02", "LEVEL03", "LEVEL04", "LEVEL01")); assertThat(encoded, stringContainsInOrder("LEVEL02", "LEVEL03", "LEVEL04", "LEVEL01"));
} }
@Test
public void testEncodeResourceWithExtensionMetadata() {
ProcedureRequest procedureRequest = new ProcedureRequest();
procedureRequest.setStatus(ProcedureRequestStatusEnum.ACCEPTED);
ExtensionDt timestamp = new ExtensionDt(false, "http://fhir.sjanic.com/timestamp");
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/user", new ResourceReferenceDt("sjanic"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/instance", new InstantDt("2012-01-01T13:00:00Z"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/organization", new ResourceReferenceDt("sjanic_org"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/role", new CodeableConceptDt().addCoding(new CodingDt("sjanic", "Doctor").setDisplay("Doctorin")));
ExtensionDt payment = new ExtensionDt(true, "http://fhir.sjanic.com/procedureRequest/requiresPatientPayment", new BooleanDt(true));
procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(timestamp.getUrl()), timestamp);
procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(payment.getUrl()), payment);
String json = ourCtx.newJsonParser().encodeResourceToString(procedureRequest);
// @formatter:off
assertThat(json, stringContainsInOrder(
"\"meta\":{" +
"\"extension\":[" +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp\"," +
"\"extension\":[" +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/user\"," +
"\"valueReference\":{" +
"\"reference\":\"sjanic\"" +
"}" +
"}," +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/instance\"," +
"\"valueInstant\":\"2012-01-01T13:00:00Z\"" +
"}," +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/organization\"," +
"\"valueReference\":{" +
"\"reference\":\"sjanic_org\"" +
"}" +
"}," +
"{" +
"\"url\":\"http://fhir.sjanic.com/timestamp/role\"," +
"\"valueCodeableConcept\":{" +
"\"coding\":[" +
"{" +
"\"system\":\"sjanic\"," +
"\"code\":\"Doctor\"," +
"\"display\":\"Doctorin\"" +
"}" +
"]" +
"}" +
"}" +
"]" +
"}" +
"]," +
"\"modifierExtension\":[" +
"{" +
"\"url\":\"http://fhir.sjanic.com/procedureRequest/requiresPatientPayment\"," +
"\"valueBoolean\":true" +
"}" +
"]" +
"},"));
// @formatter:on
}
@Test @Test
public void testEncodeSummary() { public void testEncodeSummary() {
Patient patient = new Patient(); Patient patient = new Patient();
@ -916,7 +972,7 @@ public class JsonParserDstu2Test {
// see #241 // see #241
@Test @Test
public void testEncodeThenParseShouldNotAddSpuriousId() throws Exception { public void testEncodeThenParseShouldNotAddSpuriousId() {
Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatusEnum.CONFIRMED); Condition condition = new Condition().setVerificationStatus(ConditionVerificationStatusEnum.CONFIRMED);
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle(); ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
ca.uhn.fhir.model.dstu2.resource.Bundle.Entry entry = new ca.uhn.fhir.model.dstu2.resource.Bundle.Entry(); ca.uhn.fhir.model.dstu2.resource.Bundle.Entry entry = new ca.uhn.fhir.model.dstu2.resource.Bundle.Entry();
@ -931,7 +987,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testEncodeWithDontEncodeElements() throws Exception { public void testEncodeWithDontEncodeElements() {
Patient patient = new Patient(); Patient patient = new Patient();
patient.setId("123"); patient.setId("123");
@ -1072,6 +1128,7 @@ public class JsonParserDstu2Test {
assertEquals("2011-01-01", condition.getDateRecordedElement().getValueAsString()); assertEquals("2011-01-01", condition.getDateRecordedElement().getValueAsString());
} }
/** /**
* #65 * #65
*/ */
@ -1089,7 +1146,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testNamespacePreservationEncode() throws Exception { public void testNamespacePreservationEncode() {
//@formatter:off //@formatter:off
String input = "<Patient xmlns=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\">" + String input = "<Patient xmlns=\"http://hl7.org/fhir\" xmlns:xhtml=\"http://www.w3.org/1999/xhtml\">" +
"<text>" + "<text>" +
@ -1111,7 +1168,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testNamespacePreservationParse() throws Exception { public void testNamespacePreservationParse() {
String input = "{\"resourceType\":\"Patient\",\"text\":{\"div\":\"<xhtml:div xmlns:xhtml=\\\"http://www.w3.org/1999/xhtml\\\"><xhtml:img src=\\\"foo\\\"/>@fhirabend</xhtml:div>\"}}"; String input = "{\"resourceType\":\"Patient\",\"text\":{\"div\":\"<xhtml:div xmlns:xhtml=\\\"http://www.w3.org/1999/xhtml\\\"><xhtml:img src=\\\"foo\\\"/>@fhirabend</xhtml:div>\"}}";
Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, input); Patient parsed = ourCtx.newJsonParser().parseResource(Patient.class, input);
@ -1428,7 +1485,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testParseAndEncodeComments() throws IOException { public void testParseAndEncodeComments() {
//@formatter:off //@formatter:off
String input = "{\n" + String input = "{\n" +
" \"resourceType\": \"Patient\",\n" + " \"resourceType\": \"Patient\",\n" +
@ -1661,7 +1718,7 @@ public class JsonParserDstu2Test {
} }
@Test @Test
public void testParseMetadata() throws Exception { public void testParseMetadata() {
//@formatter:off //@formatter:off
String bundle = "{\n" + String bundle = "{\n" +
" \"resourceType\" : \"Bundle\",\n" + " \"resourceType\" : \"Bundle\",\n" +
@ -1874,6 +1931,20 @@ public class JsonParserDstu2Test {
assertEquals("Patient", reincarnatedPatient.getId().getResourceType()); assertEquals("Patient", reincarnatedPatient.getId().getResourceType());
} }
@Test
public void testParseResourceWithExtensionMetadata() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/procedure-request.json"));
IParser parser = ourCtx.newJsonParser();
IParserErrorHandler peh = mock(IParserErrorHandler.class);
parser.setParserErrorHandler(peh);
ProcedureRequest p = parser.parseResource(ProcedureRequest.class, input);
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(peh, Mockito.never()).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
assertParsedResourcesExtensionMetadata(p);
}
/** /**
* See #207 * See #207
*/ */
@ -1908,18 +1979,8 @@ public class JsonParserDstu2Test {
Patient p = parser.parseResource(Patient.class, input); Patient p = parser.parseResource(Patient.class, input);
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class); ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(peh, times(4)).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture()); verify(peh, times(0)).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
//@formatter:off
List<String> strings = capt.getAllValues();
assertThat(strings, contains(
"extension",
"extension",
"modifierExtension",
"modifierExtension"
));
//@formatter:off
assertEquals("Smith", p.getName().get(0).getGiven().get(0).getValue()); assertEquals("Smith", p.getName().get(0).getGiven().get(0).getValue());
assertExtensionMetadata(p, "fhir-request-method", false, StringDt.class, "POST"); assertExtensionMetadata(p, "fhir-request-method", false, StringDt.class, "POST");
assertExtensionMetadata(p, "fhir-request-uri", false, UriDt.class, "Patient"); assertExtensionMetadata(p, "fhir-request-uri", false, UriDt.class, "Patient");
@ -1927,109 +1988,6 @@ public class JsonParserDstu2Test {
assertExtensionMetadata(p, "modified-fhir-request-uri", true, UriDt.class, "Patient"); assertExtensionMetadata(p, "modified-fhir-request-uri", true, UriDt.class, "Patient");
} }
private void assertExtensionMetadata(
BaseResource resource,
String url,
boolean isModifier,
Class<?> expectedType,
String expectedValue) {
ExtensionDt extension = (ExtensionDt) resource.getResourceMetadata().get(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(url));
assertThat(extension.getValue(), instanceOf(expectedType));
assertThat(extension.isModifier(), equalTo(isModifier));
assertThat(extension.getValueAsPrimitive().getValueAsString(), equalTo(expectedValue));
}
@Test
public void testEncodeResourceWithExtensionMetadata() throws Exception {
ProcedureRequest procedureRequest = new ProcedureRequest();
procedureRequest.setStatus(ProcedureRequestStatusEnum.ACCEPTED);
ExtensionDt timestamp = new ExtensionDt(false, "http://fhir.sjanic.com/timestamp");
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/user", new ResourceReferenceDt("sjanic"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/instance", new InstantDt("2012-01-01T13:00:00Z"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/organization", new ResourceReferenceDt("sjanic_org"));
timestamp.addUndeclaredExtension(false, "http://fhir.sjanic.com/timestamp/role", new CodeableConceptDt().addCoding(new CodingDt("sjanic", "Doctor").setDisplay("Doctorin")));
ExtensionDt payment = new ExtensionDt(true, "http://fhir.sjanic.com/procedureRequest/requiresPatientPayment", new BooleanDt(true));
procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(timestamp.getUrl()), timestamp);
procedureRequest.getResourceMetadata().put(new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey(payment.getUrl()), payment);
String json = ourCtx.newJsonParser().encodeResourceToString(procedureRequest);
// @formatter:off
assertThat(json, stringContainsInOrder(
"\"meta\":{"+
"\"extension\":["+
"{"+
"\"url\":\"http://fhir.sjanic.com/timestamp\","+
"\"extension\":["+
"{"+
"\"url\":\"http://fhir.sjanic.com/timestamp/user\","+
"\"valueReference\":{"+
"\"reference\":\"sjanic\""+
"}"+
"},"+
"{"+
"\"url\":\"http://fhir.sjanic.com/timestamp/instance\","+
"\"valueInstant\":\"2012-01-01T13:00:00Z\""+
"},"+
"{"+
"\"url\":\"http://fhir.sjanic.com/timestamp/organization\","+
"\"valueReference\":{"+
"\"reference\":\"sjanic_org\""+
"}"+
"},"+
"{"+
"\"url\":\"http://fhir.sjanic.com/timestamp/role\","+
"\"valueCodeableConcept\":{"+
"\"coding\":["+
"{"+
"\"system\":\"sjanic\","+
"\"code\":\"Doctor\","+
"\"display\":\"Doctorin\""+
"}"+
"]"+
"}"+
"}"+
"]"+
"}"+
"],"+
"\"modifierExtension\":["+
"{"+
"\"url\":\"http://fhir.sjanic.com/procedureRequest/requiresPatientPayment\","+
"\"valueBoolean\":true"+
"}"+
"]"+
"},"));
// @formatter:on
}
@Test
public void testParseResourceWithExtensionMetadata() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/procedure-request.json"));
IParser parser = ourCtx.newJsonParser();
IParserErrorHandler peh = mock(IParserErrorHandler.class);
parser.setParserErrorHandler(peh);
ProcedureRequest p = parser.parseResource(ProcedureRequest.class, input);
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(peh, Mockito.never()).unknownElement(Mockito.isNull(IParseLocation.class), capt.capture());
assertParsedResourcesExtensionMetadata(p);
}
private void assertParsedResourcesExtensionMetadata(ProcedureRequest resource) throws Exception {
ExtensionDt payment = (ExtensionDt) resource.getResourceMetadata().get(
new ResourceMetadataKeyEnum.ExtensionResourceMetadataKey("http://fhir.sjanic.com/procedureRequest/requiresPatientPayment"));
assertThat(payment.isModifier(), equalTo(true));
assertThat(((BooleanDt)payment.getValue()).getValue(), equalTo(true));
TimestampFields timestampFields = new TimestampFields(resource);
assertThat(timestampFields.user.getReference().getIdPart(), equalTo("sjanic"));
assertThat(timestampFields.instance.getValue(), equalTo(new InstantDt("2012-01-01T13:00:00Z").getValue()));
assertThat(timestampFields.organization.getReference().getIdPart(), equalTo("sjanic_org"));
assertThat(timestampFields.role.getCodingFirstRep().getSystem(), equalTo("sjanic"));
assertThat(timestampFields.role.getCodingFirstRep().getCode(), equalTo("Doctor"));
}
@Test @Test
public void testParseWithWrongTypeObjectShouldBeArray() throws Exception { public void testParseWithWrongTypeObjectShouldBeArray() throws Exception {
String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json")); String input = IOUtils.toString(getClass().getResourceAsStream("/invalid_metadata.json"));
@ -2131,170 +2089,6 @@ public class JsonParserDstu2Test {
public static void afterClassClearContext() { public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest(); TestUtil.clearAllStaticFieldsForUnitTest();
} }
/**
* See #537
*/
@Test
public void testEncodeNestedContained() {
Organization org04 = new Organization();
org04.setName("LEVEL04");
Organization org03 = new Organization();
org03.setName("LEVEL03");
org03.getPartOf().setResource(org04);
Organization org02 = new Organization();
org02.setName("LEVEL02");
org02.getPartOf().setResource(org03);
Organization org01 = new Organization();
org01.setName("LEVEL01");
org01.getPartOf().setResource(org02);
String encoded = ourCtx.newJsonParser().setPrettyPrint(true).encodeResourceToString(org01);
ourLog.info(encoded);
assertThat(encoded, stringContainsInOrder("LEVEL02","LEVEL03","LEVEL04","LEVEL01" ));
}
/**
* See #505
*/
@Test
public void testIncludeResourceWhenEncoding() {
Condition condition = new Condition();
condition.setDateRecorded(new DateDt("2011-01-01"));
Goal goal = new Goal();
goal.setId("Goal1");
ResourceReferenceDt resourceReferenceDt = new ResourceReferenceDt(condition);
goal.setAddresses(Collections.singletonList(resourceReferenceDt));
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
Entry entry = bundle.addEntry();
entry.setResource(goal);
IParser parser = ourCtx.newJsonParser();
String resourceToString = parser.setPrettyPrint(true).encodeResourceToString(bundle);
ourLog.info(resourceToString);
assertThat(resourceToString, containsString("2011-01-01"));
bundle = parser.parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, resourceToString);
assertEquals(1, bundle.getEntry().size());
goal = (Goal) bundle.getEntry().get(0).getResource();
condition = (Condition) goal.getAddresses().get(0).getResource();
assertEquals("2011-01-01", condition.getDateRecordedElement().getValueAsString());
}
/**
* Test for the url generated based on the server config
*/
@Test
public void testGeneratedUrls() {
final IParser jsonParser = ourCtx.newJsonParser().setPrettyPrint(true);
jsonParser.setServerBaseUrl("http://myserver.com");
final CustomPatientDstu2 patient = new CustomPatientDstu2();
patient.setHomeless(new BooleanDt(true));
final String parsedPatient = jsonParser.encodeResourceToString(patient);
assertTrue(parsedPatient.contains("http://myserver.com/StructureDefinition/Patient"));
assertTrue(parsedPatient.contains("http://myserver.com/StructureDefinition/homeless"));
}
/**
* Test for the url generated based on the server config
*/
@Test
public void testCustomUrlExtension() {
final String expected = "{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}";
final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setPetName(new StringDt("myName"));
final IParser jsonParser = ourCtx.newJsonParser();
jsonParser.setServerBaseUrl("http://www.example.com");
final String parsedPatient = jsonParser.encodeResourceToString(patient);
System.out.println(parsedPatient);
assertEquals(expected, parsedPatient);
// Parse with string
MyPatientWithCustomUrlExtension newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, parsedPatient);
assertEquals("myName", newPatient.getPetName().getValue());
// Parse with stream
newPatient = jsonParser.parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
assertEquals("myName", newPatient.getPetName().getValue());
//Check no NPE if base server not configure
newPatient = ourCtx.newJsonParser().parseResource(MyPatientWithCustomUrlExtension.class, new StringReader(parsedPatient));
assertNull("myName", newPatient.getPetName().getValue());
assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
}
@Test
public void testCustomUrlExtensioninBundle() {
final String expected = "{\"resourceType\":\"Bundle\",\"entry\":[{\"resource\":{\"resourceType\":\"Patient\",\"extension\":[{\"url\":\"http://www.example.com/petname\",\"valueString\":\"myName\"}]}}]}";
final MyPatientWithCustomUrlExtension patient = new MyPatientWithCustomUrlExtension();
patient.setPetName(new StringDt("myName"));
final Bundle bundle = new Bundle();
final Entry entry = new Entry();
entry.setResource(patient);
bundle.addEntry(entry);
final IParser jsonParser = ourCtx.newJsonParser();
jsonParser.setServerBaseUrl("http://www.example.com");
final String parsedBundle = jsonParser.encodeResourceToString(bundle);
System.out.println(parsedBundle);
assertEquals(expected, parsedBundle);
// Parse with string
Bundle newBundle = jsonParser.parseResource(Bundle.class, parsedBundle);
assertNotNull(newBundle);
assertEquals(1, newBundle.getEntry().size());
Patient newPatient = (Patient) newBundle.getEntry().get(0).getResource();
assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
// Parse with stream
newBundle = jsonParser.parseResource(Bundle.class, new StringReader(parsedBundle));
assertNotNull(newBundle);
assertEquals(1, newBundle.getEntry().size());
newPatient = (Patient) newBundle.getEntry().get(0).getResource();
assertEquals("myName", ((StringDt) newPatient.getUndeclaredExtensionsByUrl("http://www.example.com/petname").get(0).getValue()).getValue());
}
@Test
public void testBaseUrlFooResourceCorrectlySerializedInExtensionValueReference() {
String refVal = "http://my.org/FooBar";
Patient fhirPat = new Patient();
fhirPat.addUndeclaredExtension(false, "x1").setValue(new ResourceReferenceDt(refVal));
IParser parser = ourCtx.newJsonParser();
String output = parser.encodeResourceToString(fhirPat);
System.out.println("output: " + output);
// Deserialize then check that valueReference value is still correct
fhirPat = parser.parseResource(Patient.class, output);
List<ExtensionDt> extlst = fhirPat.getUndeclaredExtensionsByUrl("x1");
Assert.assertEquals(1, extlst.size());
Assert.assertEquals(refVal, ((ResourceReferenceDt) extlst.get(0).getValue()).getReference().getValue());
}
private static final class TimestampFields { private static final class TimestampFields {
ResourceReferenceDt user; ResourceReferenceDt user;
@ -2310,7 +2104,7 @@ public class JsonParserDstu2Test {
for (ExtensionDt extensionDt : timestamp.getExtension()) { for (ExtensionDt extensionDt : timestamp.getExtension()) {
timestampFields.put(extensionDt.getUrl(), extensionDt); timestampFields.put(extensionDt.getUrl(), extensionDt);
} }
user = ((ResourceReferenceDt)timestampFields.get("http://fhir.sjanic.com/timestamp/user").getValue()); user = ((ResourceReferenceDt) timestampFields.get("http://fhir.sjanic.com/timestamp/user").getValue());
instance = (InstantDt) timestampFields.get("http://fhir.sjanic.com/timestamp/instance").getValue(); instance = (InstantDt) timestampFields.get("http://fhir.sjanic.com/timestamp/instance").getValue();
organization = (ResourceReferenceDt) timestampFields.get("http://fhir.sjanic.com/timestamp/organization").getValue(); organization = (ResourceReferenceDt) timestampFields.get("http://fhir.sjanic.com/timestamp/organization").getValue();
role = (CodeableConceptDt) timestampFields.get("http://fhir.sjanic.com/timestamp/role").getValue(); role = (CodeableConceptDt) timestampFields.get("http://fhir.sjanic.com/timestamp/role").getValue();

6
src/changes/changes.xml
View File

@ -218,6 +218,12 @@
framework in a server with HAPI FHIR JPA. Thanks to Chris Schuler framework in a server with HAPI FHIR JPA. Thanks to Chris Schuler
for the pull request! for the pull request!
</action> </action>
<action type="add" issue="798">
A new module has been contributed called hapi-fhir-jpaserver-elasticsearch
which adds support for Elasticsearch instead of raw Lucene for fulltext
indexing. Testing help on this would be appreciated! Thanks to
Jiajing Liang for the pull request!
</action>
</release> </release>
<release version="3.2.0" date="2018-01-13"> <release version="3.2.0" date="2018-01-13">
<action type="add"> <action type="add">