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Merge remote-tracking branch 'remotes/origin/master' into ks-flyway

This commit is contained in:
Ken Stevens 2019-10-29 21:27:47 -04:00
parent 7bd29d69fd 84803a02ef
commit 0501f13e66
14 changed files with 66 additions and 45 deletions
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11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
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@ -131,13 +131,16 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
CodeSystem csDstu3 = (CodeSystem) theResource;
CodeSystem csDstu3 = (CodeSystem) theResource;
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
org.hl7.fhir.r4.model.CodeSystem cs = VersionConvertor_30_40.convertCodeSystem(csDstu3);
addPidToResource(theEntity, cs);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
}
return retVal;
}

20
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoConceptMapDstu3.java
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@ -160,16 +160,18 @@ public class FhirResourceDaoConceptMapDstu3 extends FhirResourceDaoDstu3<Concept
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
try {
ConceptMap conceptMap = (ConceptMap) theResource;
org.hl7.fhir.r4.model.ConceptMap converted = VersionConvertor_30_40.convertConceptMap(conceptMap);
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, converted);
} catch (FHIRException fe) {
throw new InternalErrorException(fe);
}
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
return retVal;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -410,7 +410,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSets()) {
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
try {
ValueSet valueSet = (ValueSet) theResource;

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -135,10 +135,12 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
if (!retVal.isUnchangedInCurrentOperation()) {
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(cs, theEntity);
}
return retVal;
}

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoConceptMapR4.java
View File

@ -160,11 +160,13 @@ public class FhirResourceDaoConceptMapR4 extends FhirResourceDaoR4<ConceptMap> i
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, conceptMap);
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
}
return retVal;

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoValueSetR4.java
View File

@ -391,7 +391,7 @@ public class FhirResourceDaoValueSetR4 extends FhirResourceDaoR4<ValueSet> imple
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSets()) {
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, valueSet);

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoCodeSystemR5.java
View File

@ -134,11 +134,13 @@ public class FhirResourceDaoCodeSystemR5 extends FhirResourceDaoR5<CodeSystem> i
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
CodeSystem cs = (CodeSystem) theResource;
addPidToResource(theEntity, theResource);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
myTerminologyCodeSystemStorageSvc.storeNewCodeSystemVersionIfNeeded(org.hl7.fhir.convertors.conv40_50.CodeSystem.convertCodeSystem(cs), theEntity);
}
return retVal;
}

14
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoConceptMapR5.java
View File

@ -160,14 +160,16 @@ public class FhirResourceDaoConceptMapR5 extends FhirResourceDaoR5<ConceptMap> i
public ResourceTable updateEntity(RequestDetails theRequestDetails, IBaseResource theResource, ResourceTable theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
if (retVal.getDeleted() == null) {
ConceptMap conceptMap = (ConceptMap) theResource;
myHapiTerminologySvc.storeTermConceptMapAndChildren(retVal, org.hl7.fhir.convertors.conv40_50.ConceptMap.convertConceptMap(conceptMap));
} else {
myHapiTerminologySvc.deleteConceptMapAndChildren(retVal);
}
}
return retVal;
}
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoValueSetR5.java
View File

@ -403,7 +403,7 @@ public class FhirResourceDaoValueSetR5 extends FhirResourceDaoR5<ValueSet> imple
boolean theUpdateVersion, Date theUpdateTime, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequestDetails, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theUpdateTime, theForceUpdate, theCreateNewHistoryEntry);
if (myDaoConfig.isPreExpandValueSets()) {
if (myDaoConfig.isPreExpandValueSets() && !retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
ValueSet valueSet = (ValueSet) theResource;
myHapiTerminologySvc.storeTermValueSet(retVal, org.hl7.fhir.convertors.conv40_50.ValueSet.convertValueSet(valueSet));

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3Test.java
View File

@ -4080,22 +4080,16 @@ public class ResourceProviderDstu3Test extends BaseResourceProviderDstu3Test {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDateElement(new DateType("2011-02-02"));
patient.addContact().setGender(AdministrativeGender.MALE);
String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
post.setEntity(new StringEntity(inputStr, ContentType.create(Constants.CT_FHIR_XML, "UTF-8")));
CloseableHttpResponse response = ourHttpClient.execute(post);
try {
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(412, response.getStatusLine().getStatusCode());
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, containsString("<issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization [name.exists() or telecom.exists() or address.exists() or organization.exists()]\"/><location value=\"Patient.contact[0]\"/><location value=\"Line 0, Col 0\"/></issue>"));
} finally {
IOUtils.closeQuietly(response.getEntity().getContent());
response.close();
}
}

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4Test.java
View File

@ -5308,7 +5308,6 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
Patient patient = new Patient();
patient.addName().addGiven("James");
patient.setBirthDateElement(new DateType("2011-02-02"));
patient.addContact().setGender(AdministrativeGender.MALE);
String inputStr = myFhirCtx.newXmlParser().encodeResourceToString(patient);
HttpPost post = new HttpPost(ourServerBase + "/Patient/$validate");
@ -5317,9 +5316,8 @@ public class ResourceProviderR4Test extends BaseResourceProviderR4Test {
try (CloseableHttpResponse response = ourHttpClient.execute(post)) {
String resp = IOUtils.toString(response.getEntity().getContent(), StandardCharsets.UTF_8);
ourLog.info(resp);
assertEquals(412, response.getStatusLine().getStatusCode());
assertEquals(200, response.getStatusLine().getStatusCode());
assertThat(resp, not(containsString("Resource has no id")));
assertThat(resp, containsString("<issue><severity value=\"error\"/><code value=\"processing\"/><diagnostics value=\"SHALL at least contain a contact's details or a reference to an organization [name.exists() or telecom.exists() or address.exists() or organization.exists()]\"/><location value=\"Patient.contact[0]\"/><location value=\"Line 0, Col 0\"/></issue>"));
}
}

6
hapi-fhir-validation/src/main/java/org/hl7/fhir/common/hapi/validation/ValidatorWrapper.java
View File

@ -111,7 +111,11 @@ public class ValidatorWrapper {
profileSet.getCanonical().add(new ValidationProfileSet.ProfileRegistration(nextProfile, true));
}
v.validate(null, messages, document, profileSet);
String resourceAsString = theValidationContext.getResourceAsString();
InputStream inputStream = new ReaderInputStream(new StringReader(resourceAsString), Charsets.UTF_8);
Manager.FhirFormat format = Manager.FhirFormat.XML;
v.validate(null, messages, inputStream, format, profileSet);
} else if (encoding == EncodingEnum.JSON) {

2
hapi-fhir-validation/src/test/java/org/hl7/fhir/r4/validation/FhirInstanceValidatorR4Test.java
View File

@ -799,6 +799,8 @@ public class FhirInstanceValidatorR4Test extends BaseTest {
ourLog.info(output.getMessages().get(0).getMessage());
assertEquals("/f:Patient", output.getMessages().get(0).getLocationString());
assertEquals("Undefined element 'foo'", output.getMessages().get(0).getMessage());
assertEquals(28, output.getMessages().get(0).getLocationCol().intValue());
assertEquals(4, output.getMessages().get(0).getLocationLine().intValue());
}
@Test

10
src/site/xdoc/download.xml.vm
View File

@ -262,6 +262,16 @@
<td style="background: #CEC;">4.0.0</td>
<td style="background: #EEB;">4.1.0-e0e3caf9ba</td>
</tr>
<tr>
<td>HAPI FHIR 4.1.0</td>
<td>JDK8</td>
<td style="background: #DDD;"></td>
<td style="background: #CEC;">1.0.2</td>
<td style="background: #EEB;">1.4.0</td>
<td style="background: #CEC;">3.0.1</td>
<td style="background: #CEC;">4.0.0</td>
<td style="background: #EEB;">4.1.0-1a7623d866</td>
</tr>
</tbody>
</table>