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hapi-fhir
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Fix an issue in the JPA server if a resource has been previously saved containing vocabulary that is no longer valid. This only really happened if you were using a non-final version of FHIR (e.g. using DSTU3 before it was finalized) but if you were in this situation, upgrading HAPI could cause you to have old codes that no longer exist in your database. This fix prevents these from blocking you from accesing those resources.

This commit is contained in:
James Agnew 2017-05-06 10:51:17 +02:00
parent e53d747f2b
commit ef772547c3
4 changed files with 53 additions and 4 deletions
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5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
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@ -102,8 +102,7 @@ import ca.uhn.fhir.model.primitive.InstantDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.XhtmlDt;
import ca.uhn.fhir.model.valueset.BundleEntryTransactionMethodEnum;
import ca.uhn.fhir.parser.DataFormatException;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.*;
import ca.uhn.fhir.rest.api.RestOperationTypeEnum;
import ca.uhn.fhir.rest.method.MethodUtil;
import ca.uhn.fhir.rest.method.QualifiedParamList;
@ -1222,6 +1221,8 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
}
IParser parser = theEntity.getEncoding().newParser(getContext(theEntity.getFhirVersion()));
parser.setParserErrorHandler(new LenientErrorHandler(false).setErrorOnInvalidValue(false));
R retVal;
try {
retVal = parser.parseResource(resourceType, resourceText);

7
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
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@ -288,6 +288,13 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
}
@Test
public void testExpandWithOpEquals() {
ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", "");
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
}
@Test
public void testExpandWithCodesAndDisplayFilterPartialOnFilter() {
CodeSystem codeSystem = createExternalCsDogs();

37
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
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@ -49,12 +49,14 @@ import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.mockito.ArgumentCaptor;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.*;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import ca.uhn.fhir.jpa.dao.*;
import ca.uhn.fhir.jpa.entity.ResourceIndexedSearchParamString;
import ca.uhn.fhir.jpa.entity.TagTypeEnum;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.model.api.Include;
import ca.uhn.fhir.model.api.ResourceMetadataKeyEnum;
import ca.uhn.fhir.model.dstu.valueset.QuantityCompararatorEnum;
@ -245,6 +247,37 @@ public class FhirResourceDaoDstu3Test extends BaseJpaDstu3Test {
}
}
/**
* Can we handle content that was previously saved containing vocabulary that
* is no longer valid
*/
@Test
public void testResourceInDatabaseContainsInvalidVocabulary() {
final Patient p = new Patient();
p.setGender(AdministrativeGender.MALE);
final IIdType id = myPatientDao.create(p).getId().toUnqualifiedVersionless();
TransactionTemplate tx = new TransactionTemplate(myTxManager);
tx.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tx.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theStatus) {
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
String newContent = myFhirCtx.newJsonParser().encodeResourceToString(p);
newContent = newContent.replace("male", "foo");
table.setResource(newContent.getBytes(Charsets.UTF_8));
table.setEncoding(ResourceEncodingEnum.JSON);
myResourceTableDao.save(table);
}
});
Patient read = myPatientDao.read(id);
String string = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(read);
ourLog.info(string);
assertThat(string, containsString("value=\"foo\""));
}
@Test
public void testChoiceParamDateEquals() {
Encounter enc = new Encounter();

8
src/changes/changes.xml
View File

@ -67,6 +67,14 @@
starting a context up on Android. Thanks to GitHub issue @Jaypeg85 for
the pull request!
</action>
<action type="fix">
Fix an issue in the JPA server if a resource has been previously
saved containing vocabulary that is no longer valid. This only really
happened if you were using a non-final version of FHIR (e.g. using DSTU3
before it was finalized) but if you were in this situation, upgrading HAPI
could cause you to have old codes that no longer exist in your database. This
fix prevents these from blocking you from accesing those resources.
</action>
</release>
<release version="2.4" date="2017-04-19">
<action type="add">