Merge branch 'master' of github.com:jamesagnew/hapi-fhir

This commit is contained in:
jamesagnew 2015-09-29 17:55:59 -04:00
commit 04764ed07e
21 changed files with 681 additions and 389 deletions

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@ -24,6 +24,7 @@ import java.lang.reflect.Method;
import java.lang.reflect.Modifier;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.List;
import java.util.Map;
@ -47,6 +48,7 @@ import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.api.RequestTypeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.param.CollectionBinder;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.ResourceParameter;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
@ -66,6 +68,7 @@ public class OperationParameter implements IParameter {
private Class<?> myParameterType;
private String myParamType;
private FhirContext myContext;
private boolean myAllowGet;
public OperationParameter(FhirContext theCtx, String theOperationName, OperationParam theOperationParam) {
this(theCtx, theOperationName, theOperationParam.name(), theOperationParam.min(), theOperationParam.max());
@ -107,6 +110,8 @@ public class OperationParameter implements IParameter {
myMax = 1;
}
myAllowGet = IPrimitiveType.class.isAssignableFrom(myParameterType);
/*
* The parameter can be of type string for validation methods - This is a bit
* weird. See ValidateDstu2Test. We should probably clean this up..
@ -114,6 +119,10 @@ public class OperationParameter implements IParameter {
if (!myParameterType.equals(IBase.class) && !myParameterType.equals(String.class)) {
if (IBaseResource.class.isAssignableFrom(myParameterType) && myParameterType.isInterface()) {
myParamType = "Resource";
} else if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
myParamType = "date";
myMax = 2;
myAllowGet = true;
} else if (!IBase.class.isAssignableFrom(myParameterType) || myParameterType.isInterface() || Modifier.isAbstract(myParameterType.getModifiers())) {
throw new ConfigurationException("Invalid type for @OperationParam: " + myParameterType.getName());
} else if (myParameterType.equals(ValidationModeEnum.class)) {
@ -153,7 +162,18 @@ public class OperationParameter implements IParameter {
if (theRequest.getRequestType() == RequestTypeEnum.GET) {
String[] paramValues = theRequest.getParameters().get(myName);
if (paramValues != null && paramValues.length > 0) {
if (IPrimitiveType.class.isAssignableFrom(myParameterType)) {
if (myAllowGet) {
if (DateRangeParam.class.isAssignableFrom(myParameterType)) {
List<QualifiedParamList> parameters = new ArrayList<QualifiedParamList>();
parameters.add(QualifiedParamList.singleton(paramValues[0]));
if (paramValues.length > 1) {
parameters.add(QualifiedParamList.singleton(paramValues[1]));
}
DateRangeParam dateRangeParam = new DateRangeParam();
dateRangeParam.setValuesAsQueryTokens(parameters);
matchingParamValues.add(dateRangeParam);
} else {
for (String nextValue : paramValues) {
FhirContext ctx = theRequest.getServer().getFhirContext();
RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
@ -161,6 +181,7 @@ public class OperationParameter implements IParameter {
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
}
}
} else {
HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();
String msg = localizer.getMessage(OperationParameter.class, "urlParamNotPrimitive", myOperationName, myName);

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@ -11,7 +11,14 @@ a browser.
<!--*/-->
<div>
<th:block th:switch="${fhirVersion}">
<th:block th:case="'DSTU1'">
<div class="hapiHeaderText" th:if="${not resource.nameElement.empty}" th:narrative="${resource.name}"></div>
</th:block>
<th:block th:case="*">
<div class="hapiHeaderText" th:if="${not resource.code.empty}" th:narrative="${resource.code}"></div>
</th:block>
</th:block>
</div>
<!--/*-->

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@ -1615,7 +1615,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
/**
* THIS SHOULD RETURN HASHSET and not jsut Set because we add to it later (so it can't be Collections.emptySet())
*/
private HashSet<Long> loadReverseIncludes(List<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
private HashSet<Long> loadReverseIncludes(Collection<Long> theMatches, Set<Include> theRevIncludes, boolean theReverseMode) {
if (theMatches.size() == 0) {
return new HashSet<Long>();
}
@ -2023,6 +2023,14 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
}
}
// Load _include and _revinclude before filter and sort in everything mode
if (theParams.isEverythingMode() == true) {
if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
loadPids.addAll(loadReverseIncludes(loadPids, theParams.getRevIncludes(), true));
loadPids.addAll(loadReverseIncludes(loadPids, theParams.getIncludes(), false));
}
}
// Handle _lastUpdated
DateRangeParam lu = theParams.getLastUpdated();
if (lu != null && (lu.getLowerBoundAsInstant() != null || lu.getUpperBoundAsInstant() != null)) {
@ -2054,52 +2062,15 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
}
// Handle sorting if any was provided
final List<Long> pids;
if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
List<Order> orders = new ArrayList<Order>();
List<Predicate> predicates = new ArrayList<Predicate>();
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<ResourceTable> from = cq.from(ResourceTable.class);
predicates.add(from.get("myId").in(loadPids));
createSort(builder, from, theParams.getSort(), orders, predicates);
if (orders.size() > 0) {
Set<Long> originalPids = loadPids;
loadPids = new LinkedHashSet<Long>();
cq.multiselect(from.get("myId").as(Long.class));
cq.where(predicates.toArray(new Predicate[0]));
cq.orderBy(orders);
TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
for (Tuple next : query.getResultList()) {
loadPids.add(next.get(0, Long.class));
}
ourLog.debug("Sort PID order is now: {}", loadPids);
pids = new ArrayList<Long>(loadPids);
// Any ressources which weren't matched by the sort get added to the bottom
for (Long next : originalPids) {
if (loadPids.contains(next) == false) {
pids.add(next);
}
}
} else {
pids = new ArrayList<Long>(loadPids);
}
} else {
pids = new ArrayList<Long>(loadPids);
}
final List<Long> pids = processSort(theParams, loadPids);
// Load _revinclude resources
final Set<Long> revIncludedPids;
if (theParams.isEverythingMode() == false) {
if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
if (theParams.isEverythingMode()) {
revIncludedPids.addAll(loadReverseIncludes(pids, theParams.getIncludes(), false));
} else {
revIncludedPids = new HashSet<Long>();
}
} else {
revIncludedPids = new HashSet<Long>();
@ -2155,6 +2126,49 @@ public abstract class BaseHapiFhirResourceDao<T extends IResource> extends BaseH
return retVal;
}
private List<Long> processSort(final SearchParameterMap theParams, Set<Long> loadPids) {
final List<Long> pids;
if (theParams.getSort() != null && isNotBlank(theParams.getSort().getParamName())) {
List<Order> orders = new ArrayList<Order>();
List<Predicate> predicates = new ArrayList<Predicate>();
CriteriaBuilder builder = myEntityManager.getCriteriaBuilder();
CriteriaQuery<Tuple> cq = builder.createTupleQuery();
Root<ResourceTable> from = cq.from(ResourceTable.class);
predicates.add(from.get("myId").in(loadPids));
createSort(builder, from, theParams.getSort(), orders, predicates);
if (orders.size() > 0) {
Set<Long> originalPids = loadPids;
loadPids = new LinkedHashSet<Long>();
cq.multiselect(from.get("myId").as(Long.class));
cq.where(predicates.toArray(new Predicate[0]));
cq.orderBy(orders);
TypedQuery<Tuple> query = myEntityManager.createQuery(cq);
for (Tuple next : query.getResultList()) {
loadPids.add(next.get(0, Long.class));
}
ourLog.debug("Sort PID order is now: {}", loadPids);
pids = new ArrayList<Long>(loadPids);
// Any ressources which weren't matched by the sort get added to the bottom
for (Long next : originalPids) {
if (loadPids.contains(next) == false) {
pids.add(next);
}
}
} else {
pids = new ArrayList<Long>(loadPids);
}
} else {
pids = new ArrayList<Long>(loadPids);
}
return pids;
}
@Override
public IBundleProvider search(String theParameterName, IQueryParameterType theValue) {
return search(Collections.singletonMap(theParameterName, theValue));

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@ -8,13 +8,15 @@ import ca.uhn.fhir.model.api.IResource;
import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.UnsignedIntDt;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>implements IFhirResourceDaoPatient<Patient> {
@Override
public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount) {
public IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdated, SortSpec theSort) {
SearchParameterMap paramMap = new SearchParameterMap();
if (theCount != null) {
paramMap.setCount(theCount.getValue());
@ -23,6 +25,8 @@ public class FhirResourceDaoPatientDstu2 extends FhirResourceDaoDstu2<Patient>im
paramMap.setRevIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
paramMap.setIncludes(Collections.singleton(IResource.INCLUDE_ALL.asRecursive()));
paramMap.setEverythingMode(true);
paramMap.setSort(theSort);
paramMap.setLastUpdated(theLastUpdated);
paramMap.add("_id", new StringParam(theId.getIdPart()));
ca.uhn.fhir.rest.server.IBundleProvider retVal = search(paramMap);
return retVal;

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@ -26,10 +26,12 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.UnsignedIntDt;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.IBundleProvider;
public interface IFhirResourceDaoPatient<T extends IBaseResource> extends IFhirResourceDao<T> {
IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount);
IBundleProvider everything(HttpServletRequest theServletRequest, IdDt theId, UnsignedIntDt theCount, DateRangeParam theLastUpdate, SortSpec theSort);
}

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@ -51,12 +51,12 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
private FhirContext myDstu2Ctx;
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
return null;
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
return null;
}
@ -85,20 +85,19 @@ public class JpaValidationSupportDstu2 implements IValidationSupport {
/*
* Validator wants RI structures and not HAPI ones, so convert
*
* TODO: we really need a more efficient way of converting.. Or maybe this will
* just go away when we move to RI structures
* TODO: we really need a more efficient way of converting.. Or maybe this will just go away when we move to RI structures
*/
String encoded = myDstu2Ctx.newJsonParser().encodeResourceToString(res);
return myRiCtx.newJsonParser().parseResource(theClass, encoded);
}
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
return false;
}
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
return null;
}

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@ -6,6 +6,10 @@ import ca.uhn.fhir.model.dstu2.resource.Patient;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.annotation.Sort;
import ca.uhn.fhir.rest.api.SortSpec;
import ca.uhn.fhir.rest.param.DateRangeParam;
import ca.uhn.fhir.rest.server.Constants;
public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu2<Patient> {
@ -18,12 +22,21 @@ public class BaseJpaResourceProviderPatientDstu2 extends JpaResourceProviderDstu
ca.uhn.fhir.model.primitive.IdDt theId,
@Description(formalDefinition="Results from this method are returned across multiple pages. This parameter controls the size of those pages.")
@OperationParam(name = "_count")
ca.uhn.fhir.model.primitive.UnsignedIntDt theCount) {
@OperationParam(name = Constants.PARAM_COUNT)
ca.uhn.fhir.model.primitive.UnsignedIntDt theCount,
@Description(shortDefinition="Only return resources which were last updated as specified by the given range")
@OperationParam(name = Constants.PARAM_LASTUPDATED, min=0, max=1)
DateRangeParam theLastUpdated,
// @OperationParam(name = Constants.PARAM_SORT, min=0, max=1)
@Sort
SortSpec theSortSpec
) {
startRequest(theServletRequest);
try {
return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount);
return ((IFhirResourceDaoPatient<Patient>)getDao()).everything(theServletRequest, theId, theCount, theLastUpdated, theSortSpec);
} finally {
endRequest(theServletRequest);
}

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@ -13,7 +13,7 @@
<context:annotation-config />
<websocket:handlers>
<websocket:mapping path="/baseDstu2/websocket" handler="mySubscriptionWebsocketHandler" />
<websocket:mapping path="/websocket/dstu2" handler="mySubscriptionWebsocketHandler" />
</websocket:handlers>
<!--

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@ -602,6 +602,96 @@ public class ResourceProviderDstu2Test extends BaseResourceProviderDstu2Test {
}
}
@Test
public void testEverythingWithLastUpdatedAndSort() throws Exception {
String methodName = "testEverythingWithLastUpdatedAndSort";
long time0 = System.currentTimeMillis();
Thread.sleep(10);
Organization org = new Organization();
org.setName(methodName);
IIdType oId = ourClient.create().resource(org).execute().getId().toUnqualifiedVersionless();
long time1 = System.currentTimeMillis();
Thread.sleep(10);
Patient p = new Patient();
p.addName().addFamily(methodName);
p.getManagingOrganization().setReference(oId);
IIdType pId = ourClient.create().resource(p).execute().getId().toUnqualifiedVersionless();
long time2 = System.currentTimeMillis();
Thread.sleep(10);
Condition c = new Condition();
c.getCode().setText(methodName);
c.getPatient().setReference(pId);
IIdType cId = ourClient.create().resource(c).execute().getId().toUnqualifiedVersionless();
Thread.sleep(10);
long time3 = System.currentTimeMillis();
// %3E=> %3C=<
HttpGet get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString());
CloseableHttpResponse response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(pId, cId));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time2)).getValueAsString() + "&_lastUpdated=%3C" + new InstantDt(new Date(time3)).getValueAsString());
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, containsInAnyOrder(cId));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_lastUpdated=%3E" + new InstantDt(new Date(time1)).getValueAsString() + "&_sort=_lastUpdated");
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, contains(pId, cId));
} finally {
response.close();
}
get = new HttpGet(ourServerBase + "/Patient/" + pId.getIdPart() + "/$everything?_sort:desc=_lastUpdated");
response = ourHttpClient.execute(get);
try {
assertEquals(200, response.getStatusLine().getStatusCode());
String output = IOUtils.toString(response.getEntity().getContent());
IOUtils.closeQuietly(response.getEntity().getContent());
ourLog.info(output);
List<IdDt> ids = toIdListUnqualifiedVersionless(myFhirCtx.newXmlParser().parseBundle(output));
ourLog.info(ids.toString());
assertThat(ids, contains(cId, pId, oId));
} finally {
response.close();
}
}
/**
* See #148
*/

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@ -324,7 +324,7 @@ public class SubscriptionsDstu2Test extends BaseResourceProviderDstu2Test {
SimpleEchoSocket socket = new SimpleEchoSocket(subsId);
try {
client.start();
URI echoUri = new URI("ws://localhost:" + ourPort + "/baseDstu2/websocket");
URI echoUri = new URI("ws://localhost:" + ourPort + "/websocket/dstu2");
ClientUpgradeRequest request = new ClientUpgradeRequest();
client.connect(socket, echoUri, request);
ourLog.info("Connecting to : {}", echoUri);

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@ -1,5 +1,9 @@
package ca.uhn.fhirtest;
import java.io.IOException;
import java.io.PrintWriter;
import java.io.Writer;
import org.apache.derby.drda.NetworkServerControl;
import org.springframework.beans.factory.DisposableBean;
import org.springframework.beans.factory.InitializingBean;
@ -22,7 +26,30 @@ public class DerbyNetworkServer implements InitializingBean, DisposableBean {
@Override
public void afterPropertiesSet() throws Exception {
server = new NetworkServerControl();
server.start (null);
Writer w = new Writer() {
@Override
public void write(char[] theCbuf, int theOff, int theLen) throws IOException {
ourLog.info("[DERBY] " + new String(theCbuf, theOff, theLen));
}
@Override
public void flush() throws IOException {
// nothing
}
@Override
public void close() throws IOException {
// nothing
}};
server.start (new PrintWriter(w));
}
public static void main(String[] args) throws Exception {
DerbyNetworkServer s = new DerbyNetworkServer();
s.afterPropertiesSet();
s.destroy();
}
}

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@ -8,6 +8,7 @@ import javax.servlet.ServletException;
import javax.servlet.http.HttpServletRequest;
import org.apache.commons.lang3.StringUtils;
import org.springframework.context.ApplicationContext;
import org.springframework.context.support.ClassPathXmlApplicationContext;
import org.springframework.web.context.ContextLoaderListener;
import org.springframework.web.context.WebApplicationContext;
@ -35,7 +36,7 @@ public class TestRestfulServer extends RestfulServer {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TestRestfulServer.class);
private ClassPathXmlApplicationContext myAppCtx;
private ApplicationContext myAppCtx;
@SuppressWarnings("unchecked")
@Override
@ -44,6 +45,7 @@ public class TestRestfulServer extends RestfulServer {
// Get the spring context from the web container (it's declared in web.xml)
WebApplicationContext parentAppCtx = ContextLoaderListener.getCurrentWebApplicationContext();
myAppCtx = (parentAppCtx);
// These two parmeters are also declared in web.xml
String implDesc = getInitParameter("ImplementationDescription");
@ -64,9 +66,6 @@ public class TestRestfulServer extends RestfulServer {
String baseUrlProperty;
switch (fhirVersionParam.trim().toUpperCase()) {
case "DSTU1": {
myAppCtx = new ClassPathXmlApplicationContext(new String[] {
"hapi-fhir-server-database-config-dstu1.xml",
"hapi-fhir-server-resourceproviders-dstu1.xml"}, parentAppCtx);
setFhirContext(FhirContext.forDstu1());
beans = myAppCtx.getBean("myResourceProvidersDstu1", List.class);
systemProviderDstu1 = myAppCtx.getBean("mySystemProviderDstu1", JpaSystemProviderDstu1.class);
@ -79,11 +78,6 @@ public class TestRestfulServer extends RestfulServer {
break;
}
case "DSTU2": {
myAppCtx = new ClassPathXmlApplicationContext(new String[] {
"hapi-fhir-server-database-config-dstu2.xml",
"hapi-fhir-server-resourceproviders-dstu2.xml",
"fhir-spring-subscription-config-dstu2.xml"
}, parentAppCtx);
setFhirContext(FhirContext.forDstu2());
beans = myAppCtx.getBean("myResourceProvidersDstu2", List.class);
systemProviderDstu2 = myAppCtx.getBean("mySystemProviderDstu2", JpaSystemProviderDstu2.class);

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@ -12,6 +12,11 @@
/WEB-INF/hapi-fhir-server-config.xml
/WEB-INF/hapi-fhir-tester-application-context.xml
/WEB-INF/hapi-fhir-tester-config.xml
classpath:/hapi-fhir-server-database-config-dstu1.xml
classpath:/hapi-fhir-server-database-config-dstu2.xml
classpath:hapi-fhir-server-resourceproviders-dstu1.xml
classpath:hapi-fhir-server-resourceproviders-dstu2.xml
classpath:fhir-spring-subscription-config-dstu2.xml
</param-value>
</context-param>
@ -25,6 +30,7 @@
<param-value>
/WEB-INF/hapi-fhir-tester-application-context.xml
/WEB-INF/hapi-fhir-tester-config.xml
classpath:fhir-spring-subscription-config-dstu2.xml
</param-value>
</init-param>
<load-on-startup>2</load-on-startup>

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@ -1,5 +1,6 @@
package ca.uhn.fhir.narrative;
import static org.hamcrest.Matchers.containsString;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.assertTrue;
@ -92,7 +93,6 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
}
@Test
public void testGenerateDiagnosticReport() throws DataFormatException {
DiagnosticReport value = new DiagnosticReport();
@ -216,4 +216,20 @@ public class DefaultThymeleafNarrativeGeneratorTestDstu2 {
}
@Test
public void testGenerateMedication() {
Medication med = new Medication();
med.getCode().setText("ciproflaxin");
NarrativeDt narrative = new NarrativeDt();
myGen.generateNarrative(med, narrative);
String string = narrative.getDiv().toString();
assertThat(string, containsString("ciproflaxin"));
String title = myGen.generateTitle(med);
assertEquals("ciproflaxin", title);
}
}

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@ -92,63 +92,6 @@ public class XmlParserDstu2Test {
private static final FhirContext ourCtx = FhirContext.forDstu2();
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(XmlParserDstu2Test.class);
@Test
public void testParseBundleWithResourceId() {
//@formatter:off
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "</Bundle>\n";
//@formatter:on
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
}
@Test
public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
Patient patient = new Patient();
patient.setId("phitcc_pat_normal");
patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
patient.setGender(AdministrativeGenderEnum.FEMALE);
patient.setBirthDate(new DateDt("2001-10-13"));
DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
Observation obsParent = new Observation();
obsParent.setId("phitcc_obs_bp_parent");
obsParent.getSubject().setResource(patient);
obsParent.setStatus(ObservationStatusEnum.FINAL);
obsParent.setEffective(obsEffectiveTime);
Observation obsSystolic = new Observation();
obsSystolic.setId("phitcc_obs_bp_dia");
obsSystolic.getSubject().setResource(patient);
obsSystolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
Observation obsDiastolic = new Observation();
obsDiastolic.setId("phitcc_obs_bp_dia");
obsDiastolic.getSubject().setResource(patient);
obsDiastolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
ourLog.info(str);
assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
}
@Test
public void testBundleWithBinary() {
//@formatter:off
@ -231,86 +174,6 @@ public class XmlParserDstu2Test {
assertTrue(parsed.getEntries().get(0).getResource().getId().isEmpty());
}
/**
* See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
*/
@Test
public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
IParser xmlParser = ourCtx.newXmlParser();
String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
assertEquals("1", q.getValueElement().getValueAsString());
String output = xmlParser.encodeResourceToString(ms);
assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
}
/**
* See #216
*/
@Test
public void testEncodeAndParseIdentifierDstu2() {
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
Patient patient = new Patient();
patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
String out = xmlParser.encodeResourceToString(patient);
ourLog.info(out);
//@formatter:off
assertThat(out, stringContainsInOrder("<identifier>",
"<type>",
"<coding>",
"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
"<code value=\"MR\"/>",
"</coding>",
"</type>",
"<system value=\"SYS\"/>",
"<value value=\"VAL\"/>",
"</identifier>"));
//@formatter:on
patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
}
/**
* See #216
*/
@Test
public void testParseMalformedIdentifierDstu2() {
// This was changed from 0.5 to 1.0.0
//@formatter:off
String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <identifier>\n" +
" <type value=\"MRN\"/>\n" +
" <system value=\"SYS\"/>\n" +
" <value value=\"VAL\"/>\n" +
" </identifier>\n" +
"</Patient>";
//@formatter:on
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
IParser p = ourCtx.newXmlParser();
p.setParserErrorHandler(errorHandler);
Patient patient = p.parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
assertEquals("value", capt.getValue());
}
@Test
public void testEncodeAndParseContained() {
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
@ -448,9 +311,11 @@ public class XmlParserDstu2Test {
String enc = ourCtx.newXmlParser().encodeResourceToString(patient);
assertThat(enc, containsString("<Patient xmlns=\"http://hl7.org/fhir\"><extension url=\"http://example.com/extensions#someext\"><valueDateTime value=\"2011-01-02T11:13:15\"/></extension>"));
assertThat(enc, containsString("<modifierExtension url=\"http://example.com/extensions#modext\"><valueDate value=\"1995-01-02\"/></modifierExtension>"));
assertThat(enc, containsString("<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
assertThat(enc, containsString(
"<extension url=\"http://example.com#parent\"><extension url=\"http://example.com#child\"><valueString value=\"value1\"/></extension><extension url=\"http://example.com#child\"><valueString value=\"value2\"/></extension></extension>"));
assertThat(enc, containsString("<given value=\"Joe\"><extension url=\"http://examples.com#givenext\"><valueString value=\"given\"/></extension></given>"));
assertThat(enc, containsString("<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
assertThat(enc, containsString(
"<given value=\"Shmoe\"><extension url=\"http://examples.com#givenext_parent\"><extension url=\"http://examples.com#givenext_child\"><valueString value=\"CHILD\"/></extension></extension></given>"));
/*
* Now parse this back
@ -490,6 +355,38 @@ public class XmlParserDstu2Test {
}
/**
* See #216
*/
@Test
public void testEncodeAndParseIdentifierDstu2() {
IParser xmlParser = ourCtx.newXmlParser().setPrettyPrint(true);
Patient patient = new Patient();
patient.addIdentifier().setSystem("SYS").setValue("VAL").setType(IdentifierTypeCodesEnum.MR);
String out = xmlParser.encodeResourceToString(patient);
ourLog.info(out);
//@formatter:off
assertThat(out, stringContainsInOrder("<identifier>",
"<type>",
"<coding>",
"<system value=\"http://hl7.org/fhir/v2/0203\"/>",
"<code value=\"MR\"/>",
"</coding>",
"</type>",
"<system value=\"SYS\"/>",
"<value value=\"VAL\"/>",
"</identifier>"));
//@formatter:on
patient = ourCtx.newXmlParser().parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), contains(IdentifierTypeCodesEnum.MR));
assertEquals("http://hl7.org/fhir/v2/0203", patient.getIdentifier().get(0).getType().getCoding().get(0).getSystem());
assertEquals("MR", patient.getIdentifier().get(0).getType().getCoding().get(0).getCode());
}
@Test
public void testEncodeAndParseMetaProfileAndTags() {
Patient p = new Patient();
@ -595,6 +492,38 @@ public class XmlParserDstu2Test {
assertEquals(new Tag("scheme2", "term2", "label2"), tagList.get(1));
}
/**
* Test for #233
*/
@Test
public void testEncodeAndParseProfiledDatatype() {
MedicationOrder mo = new MedicationOrder();
mo.addDosageInstruction().getTiming().getRepeat().setBounds(new DurationDt().setCode("code"));
String out = ourCtx.newXmlParser().encodeResourceToString(mo);
ourLog.info(out);
assertThat(out, containsString("</boundsQuantity>"));
mo = ourCtx.newXmlParser().parseResource(MedicationOrder.class, out);
DurationDt duration = (DurationDt) mo.getDosageInstruction().get(0).getTiming().getRepeat().getBounds();
assertEquals("code", duration.getCode());
}
/**
* See #216 - Profiled datatypes should use their unprofiled parent type as the choice[x] name
*/
@Test
public void testEncodeAndParseProfiledDatatypeChoice() throws Exception {
IParser xmlParser = ourCtx.newXmlParser();
String input = IOUtils.toString(XmlParser.class.getResourceAsStream("/medicationstatement_invalidelement.xml"));
MedicationStatement ms = xmlParser.parseResource(MedicationStatement.class, input);
SimpleQuantityDt q = (SimpleQuantityDt) ms.getDosage().get(0).getQuantity();
assertEquals("1", q.getValueElement().getValueAsString());
String output = xmlParser.encodeResourceToString(ms);
assertThat(output, containsString("<quantityQuantity><value value=\"1\"/></quantityQuantity>"));
}
@Test
public void testEncodeAndParseSecurityLabels() {
Patient p = new Patient();
@ -791,8 +720,10 @@ public class XmlParserDstu2Test {
ourLog.info(encoded);
// @formatter:on
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
assertThat(encoded,
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
//@formatter:off
}
@ -824,12 +755,13 @@ public class XmlParserDstu2Test {
ourLog.info(encoded);
//@formatter:on
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
assertThat(encoded,
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"1\"/>", "<code>", "<coding>",
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#1\"/>",
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
//@formatter:off
}
/**
* See #113
*/
@ -861,8 +793,10 @@ public class XmlParserDstu2Test {
ourLog.info(encoded);
//@formatter:on
assertThat(encoded, stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>", "<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>",
"</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>", "<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
assertThat(encoded,
stringContainsInOrder("<MedicationOrder xmlns=\"http://hl7.org/fhir\">", "<contained>", "<Medication xmlns=\"http://hl7.org/fhir\">", "<id value=\"123\"/>", "<code>", "<coding>",
"<system value=\"urn:sys\"/>", "<code value=\"code1\"/>", "</coding>", "</code>", "</Medication>", "</contained>", "<medicationReference>", "<reference value=\"#123\"/>",
"<display value=\"MedRef\"/>", "</medicationReference>", "</MedicationOrder>"));
//@formatter:off
}
@ -894,7 +828,6 @@ public class XmlParserDstu2Test {
}
/**
* #158
*/
@ -911,6 +844,7 @@ public class XmlParserDstu2Test {
assertThat(encoded, not(containsString("tag")));
}
/**
* #158
*/
@ -929,7 +863,6 @@ public class XmlParserDstu2Test {
assertThat(encoded, not(containsString("Label")));
}
@Test
public void testEncodeExtensionWithResourceContent() {
IParser parser = ourCtx.newXmlParser();
@ -951,6 +884,7 @@ public class XmlParserDstu2Test {
}
@Test
public void testEncodeNarrativeSuppressed() {
Patient patient = new Patient();
@ -1011,6 +945,43 @@ public class XmlParserDstu2Test {
}
@Test
public void testEncodeReferenceUsingUnqualifiedResourceWorksCorrectly() {
Patient patient = new Patient();
patient.setId("phitcc_pat_normal");
patient.addName().addGiven("Patty").setUse(NameUseEnum.NICKNAME);
patient.addTelecom().setSystem(ContactPointSystemEnum.EMAIL).setValue("patpain@ehealthinnovation.org");
patient.setGender(AdministrativeGenderEnum.FEMALE);
patient.setBirthDate(new DateDt("2001-10-13"));
DateTimeDt obsEffectiveTime = new DateTimeDt("2015-04-11T12:22:01-04:00");
Observation obsParent = new Observation();
obsParent.setId("phitcc_obs_bp_parent");
obsParent.getSubject().setResource(patient);
obsParent.setStatus(ObservationStatusEnum.FINAL);
obsParent.setEffective(obsEffectiveTime);
Observation obsSystolic = new Observation();
obsSystolic.setId("phitcc_obs_bp_dia");
obsSystolic.getSubject().setResource(patient);
obsSystolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsSystolic));
Observation obsDiastolic = new Observation();
obsDiastolic.setId("phitcc_obs_bp_dia");
obsDiastolic.getSubject().setResource(patient);
obsDiastolic.setEffective(obsEffectiveTime);
obsParent.addRelated().setType(ObservationRelationshipTypeEnum.HAS_MEMBER).setTarget(new ResourceReferenceDt(obsDiastolic));
String str = ourCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(obsParent);
ourLog.info(str);
assertThat(str, containsString("<reference value=\"Patient/phitcc_pat_normal\"/>"));
assertThat(str, containsString("<reference value=\"Observation/phitcc_obs_bp_dia\"/>"));
}
@Test
public void testEncodeSummary() {
Patient patient = new Patient();
@ -1052,6 +1023,57 @@ public class XmlParserDstu2Test {
assertThat(encoded, not(containsString("maritalStatus")));
}
@Test
public void testEncodeWithEncodeElements() throws Exception {
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
Patient patient = new Patient();
patient.addName().addFamily("FAMILY");
patient.addAddress().addLine("LINE1");
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
bundle.setTotal(100);
bundle.addEntry().setResource(patient);
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, not(containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, (containsString("address")));
}
}
@Test
public void testMoreExtensions() throws Exception {
@ -1117,57 +1139,6 @@ public class XmlParserDstu2Test {
assertThat(ourCtx.newXmlParser().setOmitResourceId(true).encodeResourceToString(p), not(containsString("123")));
}
@Test
public void testEncodeWithEncodeElements() throws Exception {
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
Patient patient = new Patient();
patient.addName().addFamily("FAMILY");
patient.addAddress().addLine("LINE1");
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = new ca.uhn.fhir.model.dstu2.resource.Bundle();
bundle.setTotal(100);
bundle.addEntry().setResource(patient);
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name", "Bundle.entry")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, not(containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient.name")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, not(containsString("address")));
}
{
IParser p = ourCtx.newXmlParser();
p.setEncodeElements(new HashSet<String>(Arrays.asList("Patient")));
p.setEncodeElementsAppliesToResourceTypes(new HashSet<String>(Arrays.asList("Patient")));
p.setPrettyPrint(true);
String out = p.encodeResourceToString(bundle);
ourLog.info(out);
assertThat(out, (containsString("total")));
assertThat(out, (containsString("Patient")));
assertThat(out, (containsString("name")));
assertThat(out, (containsString("address")));
}
}
@Test
public void testParseAndEncodeBundle() throws Exception {
String content = IOUtils.toString(XmlParserDstu2Test.class.getResourceAsStream("/bundle-example.xml"));
@ -1240,6 +1211,7 @@ public class XmlParserDstu2Test {
}
@Test
public void testParseAndEncodeExtensionOnResourceReference() {
//@formatter:off
@ -1642,6 +1614,22 @@ public class XmlParserDstu2Test {
assertEquals("Observation", link.getUrl());
}
@Test
public void testParseBundleWithResourceId() {
//@formatter:off
String input = "<Bundle xmlns=\"http://hl7.org/fhir\">"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"3\"/><lastUpdated value=\"2015-09-11T23:35:43.273-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"2\"/><lastUpdated value=\"2015-09-11T23:35:42.849-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "<entry><fullUrl value=\"http://localhost:58402/fhir/context/Patient/1\"/><resource><Patient xmlns=\"http://hl7.org/fhir\"><id value=\"1\"/><meta><versionId value=\"1\"/><lastUpdated value=\"2015-09-11T23:35:42.295-04:00\"/></meta><name><family value=\"testHistoryWithDeletedResource\"/></name></Patient></resource></entry>"
+ "</Bundle>\n";
//@formatter:on
ca.uhn.fhir.model.dstu2.resource.Bundle bundle = ourCtx.newXmlParser().parseResource(ca.uhn.fhir.model.dstu2.resource.Bundle.class, input);
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/3", bundle.getEntry().get(0).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/2", bundle.getEntry().get(1).getResource().getId().getValue());
assertEquals("http://localhost:58402/fhir/context/Patient/1/_history/1", bundle.getEntry().get(2).getResource().getId().getValue());
}
/**
* see #144 and #146
*/
@ -1710,6 +1698,38 @@ public class XmlParserDstu2Test {
}
/**
* See #216
*/
@Test
public void testParseMalformedIdentifierDstu2() {
// This was changed from 0.5 to 1.0.0
//@formatter:off
String out = "<Patient xmlns=\"http://hl7.org/fhir\">\n" +
" <identifier>\n" +
" <type value=\"MRN\"/>\n" +
" <system value=\"SYS\"/>\n" +
" <value value=\"VAL\"/>\n" +
" </identifier>\n" +
"</Patient>";
//@formatter:on
IParserErrorHandler errorHandler = mock(IParserErrorHandler.class);
IParser p = ourCtx.newXmlParser();
p.setParserErrorHandler(errorHandler);
Patient patient = p.parseResource(Patient.class, out);
assertThat(patient.getIdentifier().get(0).getType().getValueAsEnum(), IsEmptyCollection.empty());
ArgumentCaptor<String> capt = ArgumentCaptor.forClass(String.class);
verify(errorHandler, times(1)).unknownAttribute(any(IParseLocation.class), capt.capture());
assertEquals("value", capt.getValue());
}
@Test
public void testParseMetadata() throws Exception {
//@formatter:off

View File

@ -1,5 +1,7 @@
package ca.uhn.fhir.validation;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.UnsupportedEncodingException;
@ -21,9 +23,10 @@ import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
public class DefaultProfileValidationSupport implements IValidationSupport {
private Map<String, ValueSet> myDefaultValueSets;
private Map<String, ValueSet> myCodeSystems;
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return false;
}
@ -70,17 +73,51 @@ public class DefaultProfileValidationSupport implements IValidationSupport {
}
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
return new CodeValidationResult(IssueSeverity.INFORMATION, "Unknown code: " + theCodeSystem + " / " + theCode);
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
return null;
public ValueSet fetchCodeSystem(FhirContext theContext, String theSystem) {
Map<String, ValueSet> codeSystems = myCodeSystems;
if (codeSystems == null) {
codeSystems = new HashMap<String, ValueSet>();
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/valuesets.xml");
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v2-tables.xml");
loadCodeSystems(theContext, codeSystems, "/org/hl7/fhir/instance/model/valueset/v3-codesystems.xml");
myCodeSystems = codeSystems;
}
return codeSystems.get(theSystem);
}
private void loadCodeSystems(FhirContext theContext, Map<String, ValueSet> codeSystems, String file) {
InputStream valuesetText = DefaultProfileValidationSupport.class.getResourceAsStream(file);
if (valuesetText != null) {
InputStreamReader reader;
try {
reader = new InputStreamReader(valuesetText, "UTF-8");
} catch (UnsupportedEncodingException e) {
// Shouldn't happen!
throw new InternalErrorException("UTF-8 encoding not supported on this platform", e);
}
FhirContext ctx = FhirInstanceValidator.getHl7OrgDstu2Ctx(theContext);
Bundle bundle = ctx.newXmlParser().parseResource(Bundle.class, reader);
for (BundleEntryComponent next : bundle.getEntry()) {
ValueSet nextValueSet = (ValueSet) next.getResource();
String system = nextValueSet.getCodeSystem().getSystem();
if (isNotBlank(system)) {
codeSystems.put(system, nextValueSet);
}
}
}
}
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
return null;
}

View File

@ -269,7 +269,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
@Override
public ValueSetExpansionComponent expandVS(ConceptSetComponent theInc) {
return myValidationSupport.expandValueSet(theInc);
return myValidationSupport.expandValueSet(myCtx, theInc);
}
@Override
@ -282,7 +282,7 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
if (myValidationSupport == null) {
return null;
} else {
return myValidationSupport.fetchCodeSystem(theSystem);
return myValidationSupport.fetchCodeSystem(myCtx, theSystem);
}
}
@ -335,13 +335,13 @@ public class FhirInstanceValidator extends BaseValidatorBridge implements IValid
if (myValidationSupport == null) {
return false;
} else {
return myValidationSupport.isCodeSystemSupported(theSystem);
return myValidationSupport.isCodeSystemSupported(myCtx, theSystem);
}
}
@Override
public ValidationResult validateCode(String theSystem, String theCode, String theDisplay) {
CodeValidationResult result = myValidationSupport.validateCode(theSystem, theCode, theDisplay);
CodeValidationResult result = myValidationSupport.validateCode(myCtx, theSystem, theCode, theDisplay);
if (result == null) {
return null;
}

View File

@ -18,7 +18,7 @@ public interface IValidationSupport {
* The portion to include
* @return The expansion
*/
ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude);
ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude);
/**
* Fetch a code system by ID
@ -27,7 +27,7 @@ public interface IValidationSupport {
* The code system
* @return The valueset (must not be null, but can be an empty ValueSet)
*/
ValueSet fetchCodeSystem(String theSystem);
ValueSet fetchCodeSystem(FhirContext theContext, String theSystem);
/**
* Loads a resource needed by the validation (a StructureDefinition, or a
@ -53,7 +53,7 @@ public interface IValidationSupport {
* @return Returns <code>true</code> if codes in the given code system can be
* validated
*/
boolean isCodeSystemSupported(String theSystem);
boolean isCodeSystemSupported(FhirContext theContext, String theSystem);
/**
* Validates that the given code exists and if possible returns a display
@ -68,7 +68,7 @@ public interface IValidationSupport {
* The display name, if it should also be validated
* @return Returns a validation result object
*/
CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay);
CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
public class CodeValidationResult {
private ConceptDefinitionComponent definition;

View File

@ -24,19 +24,19 @@ public class ValidationSupportChain implements IValidationSupport {
}
@Override
public ValueSetExpansionComponent expandValueSet(ConceptSetComponent theInclude) {
public ValueSetExpansionComponent expandValueSet(FhirContext theCtx, ConceptSetComponent theInclude) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theInclude.getSystem())) {
return next.expandValueSet(theInclude);
if (next.isCodeSystemSupported(theCtx, theInclude.getSystem())) {
return next.expandValueSet(theCtx, theInclude);
}
}
return myChain.get(0).expandValueSet(theInclude);
return myChain.get(0).expandValueSet(theCtx, theInclude);
}
@Override
public ValueSet fetchCodeSystem(String theSystem) {
public ValueSet fetchCodeSystem(FhirContext theCtx, String theSystem) {
for (IValidationSupport next : myChain) {
ValueSet retVal = next.fetchCodeSystem(theSystem);
ValueSet retVal = next.fetchCodeSystem(theCtx, theSystem);
if (retVal != null) {
return retVal;
}
@ -56,9 +56,9 @@ public class ValidationSupportChain implements IValidationSupport {
}
@Override
public boolean isCodeSystemSupported(String theSystem) {
public boolean isCodeSystemSupported(FhirContext theCtx, String theSystem) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theSystem)) {
if (next.isCodeSystemSupported(theCtx, theSystem)) {
return true;
}
}
@ -66,13 +66,13 @@ public class ValidationSupportChain implements IValidationSupport {
}
@Override
public CodeValidationResult validateCode(String theCodeSystem, String theCode, String theDisplay) {
public CodeValidationResult validateCode(FhirContext theCtx, String theCodeSystem, String theCode, String theDisplay) {
for (IValidationSupport next : myChain) {
if (next.isCodeSystemSupported(theCodeSystem)) {
return next.validateCode(theCodeSystem, theCode, theDisplay);
if (next.isCodeSystemSupported(theCtx, theCodeSystem)) {
return next.validateCode(theCtx, theCodeSystem, theCode, theDisplay);
}
}
return myChain.get(0).validateCode(theCodeSystem, theCode, theDisplay);
return myChain.get(0).validateCode(theCtx, theCodeSystem, theCode, theDisplay);
}
}

View File

@ -2,7 +2,9 @@ package ca.uhn.fhir.validation;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
@ -16,6 +18,7 @@ import org.apache.commons.io.IOUtils;
import org.hl7.fhir.instance.model.CodeType;
import org.hl7.fhir.instance.model.Observation;
import org.hl7.fhir.instance.model.Observation.ObservationStatus;
import org.hl7.fhir.instance.model.Patient;
import org.hl7.fhir.instance.model.StringType;
import org.hl7.fhir.instance.model.ValueSet;
import org.hl7.fhir.instance.model.ValueSet.ConceptDefinitionComponent;
@ -61,19 +64,19 @@ public class FhirInstanceValidatorTest {
myValidConcepts = new ArrayList<String>();
myMockSupport = mock(IValidationSupport.class);
when(myMockSupport.expandValueSet(any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
when(myMockSupport.expandValueSet(any(FhirContext.class), any(ConceptSetComponent.class))).thenAnswer(new Answer<ValueSetExpansionComponent>() {
@Override
public ValueSetExpansionComponent answer(InvocationOnMock theInvocation) throws Throwable {
ConceptSetComponent arg = (ConceptSetComponent)theInvocation.getArguments()[0];
ValueSetExpansionComponent retVal = mySupportedCodeSystemsForExpansion.get(arg.getSystem());
if (retVal == null) {
retVal = myDefaultValidationSupport.expandValueSet(arg);
retVal = myDefaultValidationSupport.expandValueSet(any(FhirContext.class), arg);
}
ourLog.info("expandValueSet({}) : {}", new Object[] { theInvocation.getArguments()[0], retVal });
return retVal;
}
});
when(myMockSupport.isCodeSystemSupported(any(String.class))).thenAnswer(new Answer<Boolean>() {
when(myMockSupport.isCodeSystemSupported(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<Boolean>() {
@Override
public Boolean answer(InvocationOnMock theInvocation) throws Throwable {
boolean retVal = mySupportedCodeSystemsForExpansion.containsKey(theInvocation.getArguments()[0]);
@ -93,28 +96,29 @@ public class FhirInstanceValidatorTest {
return retVal;
}
});
when(myMockSupport.validateCode(any(String.class), any(String.class), any(String.class)))
when(myMockSupport.validateCode(any(FhirContext.class), any(String.class), any(String.class), any(String.class)))
.thenAnswer(new Answer<CodeValidationResult>() {
@Override
public CodeValidationResult answer(InvocationOnMock theInvocation) throws Throwable {
String system = (String) theInvocation.getArguments()[0];
String code = (String) theInvocation.getArguments()[1];
FhirContext ctx = (FhirContext) theInvocation.getArguments()[0];
String system = (String) theInvocation.getArguments()[1];
String code = (String) theInvocation.getArguments()[2];
CodeValidationResult retVal;
if (myValidConcepts.contains(system + "___" + code)) {
retVal = new CodeValidationResult(new ConceptDefinitionComponent(new CodeType(code)));
} else {
retVal = myDefaultValidationSupport.validateCode(system, code, (String) theInvocation.getArguments()[2]);
retVal = myDefaultValidationSupport.validateCode(ctx, system, code, (String) theInvocation.getArguments()[2]);
}
ourLog.info("validateCode({}, {}, {}) : {}",
new Object[] { system, code, (String) theInvocation.getArguments()[2], retVal });
return retVal;
}
});
when(myMockSupport.fetchCodeSystem(any(String.class))).thenAnswer(new Answer<ValueSet>() {
when(myMockSupport.fetchCodeSystem(any(FhirContext.class), any(String.class))).thenAnswer(new Answer<ValueSet>() {
@Override
public ValueSet answer(InvocationOnMock theInvocation) throws Throwable {
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((String) theInvocation.getArguments()[0]);
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[0], retVal });
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0],(String) theInvocation.getArguments()[1]);
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
return retVal;
}
});
@ -306,6 +310,29 @@ public class FhirInstanceValidatorTest {
output.getMessages().get(0).getMessage());
}
@Test
public void testValidateResourceWithValuesetExpansion() {
Patient patient = new Patient();
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("foo").setCode("bar");
ValidationResult output = myVal.validateWithResult(patient);
List<SingleValidationMessage> all = logResultsAndReturnAll(output);
assertEquals(1, all.size());
assertEquals("/f:Patient/f:identifier/f:type", all.get(0).getLocationString());
assertEquals("None of the codes are in the expected value set http://hl7.org/fhir/ValueSet/identifier-type (http://hl7.org/fhir/ValueSet/identifier-type)", all.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, all.get(0).getSeverity());
patient = new Patient();
patient.addIdentifier().setSystem("http://system").setValue("12345").getType().addCoding().setSystem("http://hl7.org/fhir/v2/0203").setCode("MR");
output = myVal.validateWithResult(patient);
all = logResultsAndReturnAll(output);
assertEquals(0, all.size());
}
@Test
public void testValidateResourceWithExampleBindingCodeValidationFailing() {
Observation input = new Observation();
@ -353,7 +380,11 @@ public class FhirInstanceValidatorTest {
ValidationResult output = myVal.validateWithResult(input);
List<SingleValidationMessage> errors = logResultsAndReturnNonInformationalOnes(output);
assertEquals(errors.toString(), 0, errors.size());
assertEquals(errors.toString(), 1, errors.size());
assertEquals("Unable to validate code \"1234\" in code system \"http://loinc.org\"", errors.get(0).getMessage());
assertEquals(ResultSeverityEnum.WARNING, errors.get(0).getSeverity());
}
@Test

View File

@ -84,6 +84,17 @@
a more appropriate 400/404 in the JPA server (vread on invalid version,
delete with no ID, etc.)
</action>
<action type="fix">
Fix narrative generation for DSTU2 Medication resource
</action>
<action type="fix">
Profile validator now works for valuesets which use
v2 tables
</action>
<action type="add">
JPA server Patient/[id]/$everything operation now supports
_lastUpdated filtering and _sort'ing of results.
</action>
</release>
<release version="1.2" date="2015-09-18">
<action type="add">