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Support lastupdate filtering and sorting on JPA everything operation

This commit is contained in:
James Agnew 2015-09-29 13:24:33 -04:00
parent 1cc6a05273
commit ca8c257833
9 changed files with 220 additions and 69 deletions
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35
hapi-fhir-base/src/main/java/ca/uhn/fhir/rest/method/OperationParameter.java
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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)) {
@ -153,13 +162,25 @@ 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)) {
for (String nextValue : paramValues) {
FhirContext ctx = theRequest.getServer().getFhirContext();
RuntimePrimitiveDatatypeDefinition def = (RuntimePrimitiveDatatypeDefinition) ctx.getElementDefinition((Class<? extends IBase>) myParameterType);
IPrimitiveType<?> instance = def.newInstance();
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
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);
IPrimitiveType<?> instance = def.newInstance();
instance.setValueAsString(nextValue);
matchingParamValues.add(instance);
}
}
} else {
HapiLocalizer localizer = theRequest.getServer().getFhirContext().getLocalizer();

102
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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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>();
}
@ -2020,6 +2020,14 @@ 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)) {
@ -2051,52 +2059,15 @@ 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.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
if (theParams.isEverythingMode()) {
revIncludedPids.addAll(loadReverseIncludes(pids, theParams.getIncludes(), false));
if (theParams.isEverythingMode() == false) {
if (theParams.getRevIncludes() != null && theParams.getRevIncludes().isEmpty() == false) {
revIncludedPids = loadReverseIncludes(pids, theParams.getRevIncludes(), true);
} else {
revIncludedPids = new HashSet<Long>();
}
} else {
revIncludedPids = new HashSet<Long>();
@ -2152,6 +2123,49 @@ 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));

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoPatientDstu2.java
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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;

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoPatient.java
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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);
}

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/JpaValidationSupportDstu2.java
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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;
}

19
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderPatientDstu2.java
View File

@ -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);
}

90
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2Test.java
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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
*/

10
hapi-fhir-structures-hl7org-dstu2/src/test/java/ca/uhn/fhir/validation/FhirInstanceValidatorTest.java
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@ -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;
@ -116,7 +118,7 @@ public class FhirInstanceValidatorTest {
@Override
public ValueSet answer(InvocationOnMock theInvocation) throws Throwable {
ValueSet retVal = myDefaultValidationSupport.fetchCodeSystem((FhirContext) theInvocation.getArguments()[0],(String) theInvocation.getArguments()[1]);
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[0], retVal });
ourLog.info("fetchCodeSystem({}) : {}", new Object[] { (String) theInvocation.getArguments()[1], retVal });
return retVal;
}
});
@ -378,7 +380,9 @@ 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

4
src/changes/changes.xml
View File

@ -91,6 +91,10 @@
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">