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hapi-fhir
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Work on JPA

This commit is contained in:
James Agnew 2017-02-02 06:23:28 -05:00
parent b4a362b8ee
commit 3191c907a3
7 changed files with 155 additions and 33 deletions
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23
hapi-fhir-android-realm/.project Normal file
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@ -0,0 +1,23 @@
<?xml version="1.0" encoding="UTF-8"?>
<projectDescription>
<name>hapi-fhir-android-realm</name>
<comment></comment>
<projects>
</projects>
<buildSpec>
<buildCommand>
<name>org.eclipse.jdt.core.javabuilder</name>
<arguments>
</arguments>
</buildCommand>
<buildCommand>
<name>org.eclipse.m2e.core.maven2Builder</name>
<arguments>
</arguments>
</buildCommand>
</buildSpec>
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
</natures>
</projectDescription>

3
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
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@ -43,11 +43,9 @@ ca.uhn.fhir.rest.param.ResourceParameter.noContentTypeInRequest=No Content-Type
ca.uhn.fhir.rest.param.ResourceParameter.failedToParseRequest=Failed to parse request body as {0} resource. Error was: {1}
ca.uhn.fhir.parser.ParserState.wrongResourceTypeFound=Incorrect resource type found, expected "{0}" but found "{1}"
ca.uhn.fhir.rest.server.RestfulServer.getPagesNonHttpGet=Requests for _getpages must use HTTP GET
ca.uhn.fhir.rest.server.RestfulServer.unknownMethod=Invalid request: The FHIR endpoint on this server does not know how to handle {0} operation[{1}] with parameters [{2}]
ca.uhn.fhir.rest.server.RestfulServer.rootRequest=This is the base URL of FHIR server. Unable to handle this request, as it does not contain a resource type or operation name.
ca.uhn.fhir.validation.ValidationContext.unableToDetermineEncoding=Unable to determine encoding (e.g. XML / JSON) on validation input. Is this a valid FHIR resource body?
ca.uhn.fhir.validation.FhirValidator.noPhlocWarningOnStartup=Phloc-schematron library not found on classpath, will not attempt to perform schematron validation
ca.uhn.fhir.validation.FhirValidator.noPhlocError=Phloc-schematron library not found on classpath, can not enable perform schematron validation
@ -81,6 +79,7 @@ ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.unableToDeleteNotFound=Unable to fin
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulCreate=Successfully created resource "{0}" in {1}ms
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulUpdate=Successfully updated resource "{0}" in {1}ms
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.successfulDeletes=Successfully deleted {0} resource(s) in {1}ms
ca.uhn.fhir.jpa.dao.BaseHapiFhirResourceDao.invalidSearchParameter=Unknown search parameter "{0}". Value search parameters for this search are: {1}
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidQuantityPrefix=Unable to handle quantity prefix "{0}" for value: {1}
ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number prefix "{0}" for value: {1}

73
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDao.java
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@ -57,6 +57,8 @@ import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.method.RestSearchParameterTypeEnum;
import ca.uhn.fhir.rest.method.SearchMethodBinding;
import ca.uhn.fhir.rest.method.SearchMethodBinding.QualifierDetails;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.*;
import ca.uhn.fhir.rest.server.interceptor.IServerInterceptor;
@ -73,6 +75,7 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Autowired
private DaoConfig myDaoConfig;
@Autowired
protected PlatformTransactionManager myPlatformTransactionManager;
@Autowired
@ -86,6 +89,8 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
@Autowired()
protected ISearchResultDao mySearchResultDao;
private String mySecondaryPrimaryKeyParamName;
@Autowired
private ISearchParamRegistry mySerarchParamRegistry;
@Autowired()
protected IHapiTerminologySvc myTerminologySvc;
@ -662,6 +667,30 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal;
}
@Override
public DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails) {
ResourceTable entityToUpdate = readEntityLatestVersion(theId);
if (theId.hasVersionIdPart()) {
if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) {
throw new ResourceVersionConflictException("Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch");
}
}
validateResourceType(entityToUpdate);
IBaseResource resourceToUpdate = toResource(entityToUpdate, false);
IBaseResource destination;
if (thePatchType == PatchTypeEnum.JSON_PATCH) {
destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
} else {
destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
}
@SuppressWarnings("unchecked")
T destinationCasted = (T) destination;
return update(destinationCasted, null, true, theRequestDetails);
}
@PostConstruct
public void postConstruct() {
RuntimeResourceDefinition def = getContext().getResourceDefinition(myResourceType);
@ -863,9 +892,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return search(map);
}
@Autowired
private ISearchParamRegistry mySerarchParamRegistry;
@Override
public IBundleProvider search(final SearchParameterMap theParams) {
// Notify interceptors
@ -988,6 +1014,23 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
return retVal;
}
@Override
public void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget) {
Map<String, RuntimeSearchParam> searchParams = mySerarchParamRegistry.getActiveSearchParams(getResourceName());
Set<String> paramNames = theSource.keySet();
for (String nextParamName : paramNames) {
QualifierDetails qualifiedParamName = SearchMethodBinding.extractQualifiersFromParameterName(nextParamName);
RuntimeSearchParam param = searchParams.get(qualifiedParamName.getParamName());
if (param == null) {
String msg = getContext().getLocalizer().getMessage(BaseHapiFhirResourceDao.class, "invalidSearchParameter", qualifiedParamName.getParamName(), new TreeSet<String>(searchParams.keySet()));
throw new InvalidRequestException(msg);
}
aaaa
}
}
@Override
public DaoMethodOutcome update(T theResource) {
return update(theResource, null, null);
@ -1078,30 +1121,6 @@ public abstract class BaseHapiFhirResourceDao<T extends IBaseResource> extends B
ourLog.info(msg);
return outcome;
}
@Override
public DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails) {
ResourceTable entityToUpdate = readEntityLatestVersion(theId);
if (theId.hasVersionIdPart()) {
if (theId.getVersionIdPartAsLong() != entityToUpdate.getVersion()) {
throw new ResourceVersionConflictException("Version " + theId.getVersionIdPart() + " is not the most recent version of this resource, unable to apply patch");
}
}
validateResourceType(entityToUpdate);
IBaseResource resourceToUpdate = toResource(entityToUpdate, false);
IBaseResource destination;
if (thePatchType == PatchTypeEnum.JSON_PATCH) {
destination = JsonPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
} else {
destination = XmlPatchUtils.apply(getContext(), resourceToUpdate, thePatchBody);
}
@SuppressWarnings("unchecked")
T destinationCasted = (T) destination;
return update(destinationCasted, null, true, theRequestDetails);
}
@Override

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDao.java
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@ -39,8 +39,10 @@ import ca.uhn.fhir.rest.api.MethodOutcome;
import ca.uhn.fhir.rest.api.PatchTypeEnum;
import ca.uhn.fhir.rest.api.ValidationModeEnum;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.param.StringParam;
import ca.uhn.fhir.rest.server.EncodingEnum;
import ca.uhn.fhir.rest.server.IBundleProvider;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
@ -134,6 +136,8 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
*/
<MT extends IBaseMetaType> MT metaGetOperation(Class<MT> theType, RequestDetails theRequestDetails);
DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails);
Set<Long> processMatchUrl(String theMatchUrl);
/**
@ -181,6 +185,15 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
Set<Long> searchForIdsWithAndOr(SearchParameterMap theParams);
/**
* Takes a map of incoming raw search parameters and translates/parses them into
* appropriate {@link IQueryParameterType} instances of the appropriate type
* for the given param
*
* @throws InvalidRequestException If any of the parameters are not known
*/
void translateRawParameters(Map<String, List<String>> theSource, SearchParameterMap theTarget);
/**
* Update a resource - Note that this variant of the method does not take in a {@link RequestDetails} and
* therefore can not fire any interceptors. Use only for internal system calls
@ -211,8 +224,6 @@ public interface IFhirResourceDao<T extends IBaseResource> extends IDao {
*/
MethodOutcome validate(T theResource, IIdType theId, String theRawResource, EncodingEnum theEncoding, ValidationModeEnum theMode, String theProfile, RequestDetails theRequestDetails);
DaoMethodOutcome patch(IIdType theId, PatchTypeEnum thePatchType, String thePatchBody, RequestDetails theRequestDetails);
// /**
// * Invoke the everything operation
// */

15
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoSearchParameterDstu3.java
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@ -29,17 +29,28 @@ import org.springframework.scheduling.annotation.Scheduled;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoSearchParameter;
import ca.uhn.fhir.jpa.dao.IFhirSystemDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class FhirResourceDaoSearchParameterDstu3 extends FhirResourceDaoDstu3<SearchParameter>implements IFhirResourceDaoSearchParameter<SearchParameter> {
@Autowired
private IFhirSystemDao<Bundle, Meta> mySystemDao;
@Override
protected void validateResourceForStorage(SearchParameter theResource, ResourceTable theEntityToSave) {
super.validateResourceForStorage(theResource, theEntityToSave);
if (theResource.getStatus() == null) {
throw new InvalidRequestException("Resource.status is missing or invalid: " + theResource.getStatusElement().getValueAsString());
}
}
/**
* This method is called once per minute to perform any required re-indexing. During most passes this will
* just check and find that there are no resources requiring re-indexing. In that case the method just returns
* immediately. If the search finds that some resources require reindexing, the system will do a bunch of
* reindexing and then return.
* immediately. If the search finds that some resources require reindexing, the system will do multiple
* reindexing passes and then return.
*/
@Override
@Scheduled(fixedDelay=DateUtils.MILLIS_PER_MINUTE)

56
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderCustomSearchParamDstu3Test.java Normal file
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@ -0,0 +1,56 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.fail;
import java.io.IOException;
import org.hl7.fhir.dstu3.model.SearchParameter;
import org.hl7.fhir.dstu3.model.SearchParameter.XPathUsageType;
import org.junit.After;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
public class ResourceProviderCustomSearchParamDstu3Test extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderCustomSearchParamDstu3Test.class);
@Override
@After
public void after() throws Exception {
super.after();
myDaoConfig.setDefaultSearchParamsCanBeOverridden(new DaoConfig().isDefaultSearchParamsCanBeOverridden());
}
@Override
public void before() throws Exception {
super.before();
}
@Test
public void saveCreateSearchParamInvalidWithMissingStatus() throws IOException {
SearchParameter sp = new SearchParameter();
sp.setCode("foo");
sp.setXpath("Patient.gender");
sp.setXpathUsage(XPathUsageType.NORMAL);
sp.setTitle("Foo Param");
try {
ourClient.create().resource(sp).execute();
fail();
} catch (InvalidRequestException e) {
assertEquals("", e.getMessage());
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

3
hapi-tinder-plugin/src/main/resources/vm/jpa_resource_provider.vm
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@ -99,6 +99,9 @@ public class ${className}ResourceProvider extends
#end
#end
@RawParam
Map<String, List<String>> theAdditionalRawParams,
#if ( $version != 'dstu' )
@IncludeParam(reverse=true)
Set<Include> theRevIncludes,