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8763316ab6
Author | SHA1 | Date |
---|---|---|
jdar8 | 8763316ab6 | |
volodymyr-korzh | fb7571185a | |
Tadgh | 919e2d2405 | |
jdar | e148c76a09 | |
jdar | 9f4630db06 | |
jdar | f2150dd947 | |
jdar | c91bee21e9 | |
jdar | ebb256c5d2 |
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@ -0,0 +1,6 @@
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---
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type: add
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issue: 6210
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jira: SMILE-8428
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title: "The batch instance and chunk IDs have been added to the logging MDC so that the IDs can be automatically added to
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batch-related messages in the log."
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@ -0,0 +1,5 @@
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---
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type: change
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issue: 6261
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title: "Upgrading to Jakarta had caused a problem with the version of java-simple-mail that was in use. This has been updated to be conformant
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with the Jakarta Mail APIs. Thanks to Thomas Papke(@thopap) for the contribution!"
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@ -0,0 +1,7 @@
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---
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type: fix
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issue: 6317
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title: "Previously, defining a unique combo Search Parameter with the DateTime component and submitting multiple
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resources with the same dateTime element (e.g. Observation.effectiveDateTime) resulted in duplicate resource creation.
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This has been fixed."
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@ -70,3 +70,7 @@ If a Job Definition is set to having Gated Execution, then all work chunks for a
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### Job Instance Completion
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A Batch Job Maintenance Service runs every minute to monitor the status of all Job Instances and the Job Instance is transitioned to either `COMPLETED`, `ERRORED` or `FAILED` according to the status of all outstanding work chunks for that job instance. If the job instance is still `IN_PROGRESS` this maintenance service also estimates the time remaining to complete the job.
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## Logging
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The job instance ID and work chunk ID are both available through the logback MDC and can be accessed using the `%X` specifier in a `logback.xml` file. See [Logging](/docs/appendix/logging.html#logging) for more details about logging in HAPI.
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@ -1972,7 +1972,7 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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* The loop allows us to create multiple combo index joins if there
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* are multiple AND expressions for the related parameters.
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*/
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while (validateParamValuesAreValidForComboParam(theRequest, theParams, comboParamNames)) {
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while (validateParamValuesAreValidForComboParam(theRequest, theParams, comboParamNames, comboParam)) {
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applyComboSearchParam(theQueryStack, theParams, theRequest, comboParamNames, comboParam);
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}
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}
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@ -2068,7 +2068,10 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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* (e.g. <code>?date=gt2024-02-01</code>), etc.
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*/
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private boolean validateParamValuesAreValidForComboParam(
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RequestDetails theRequest, @Nonnull SearchParameterMap theParams, List<String> theComboParamNames) {
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RequestDetails theRequest,
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@Nonnull SearchParameterMap theParams,
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List<String> theComboParamNames,
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RuntimeSearchParam theComboParam) {
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boolean paramValuesAreValidForCombo = true;
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List<List<IQueryParameterType>> paramOrValues = new ArrayList<>(theComboParamNames.size());
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@ -2129,6 +2132,19 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
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break;
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}
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}
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// Date params are not eligible for using composite unique index
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// as index could contain date with different precision (e.g. DAY, SECOND)
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if (nextParamDef.getParamType() == RestSearchParameterTypeEnum.DATE
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&& theComboParam.getComboSearchParamType() == ComboSearchParamType.UNIQUE) {
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ourLog.debug(
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"Search with params {} is not a candidate for combo searching - "
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+ "Unique combo search parameter '{}' has DATE type",
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theComboParamNames,
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nextParamName);
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paramValuesAreValidForCombo = false;
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break;
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}
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}
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if (CartesianProductUtil.calculateCartesianProductSize(paramOrValues) > 500) {
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@ -566,7 +566,8 @@ public abstract class BaseSearchParamExtractor implements ISearchParamExtractor
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for (BaseResourceIndexedSearchParam nextParam : paramsListForCompositePart) {
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IQueryParameterType nextParamAsClientParam = nextParam.toQueryParameterType();
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if (nextParamAsClientParam instanceof DateParam) {
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if (theParam.getComboSearchParamType() == ComboSearchParamType.NON_UNIQUE
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&& nextParamAsClientParam instanceof DateParam) {
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DateParam date = (DateParam) nextParamAsClientParam;
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if (date.getPrecision() != TemporalPrecisionEnum.DAY) {
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continue;
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@ -135,10 +135,10 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
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addCreateDefaultPartition();
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addReadDefaultPartition(); // one for search param validation
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SearchParameter sp = new SearchParameter();
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sp.setId("SearchParameter/patient-birthdate");
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sp.setType(Enumerations.SearchParamType.DATE);
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sp.setCode("birthdate");
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sp.setExpression("Patient.birthDate");
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sp.setId("SearchParameter/patient-gender");
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sp.setType(Enumerations.SearchParamType.TOKEN);
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sp.setCode("gender");
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sp.setExpression("Patient.gender");
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sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
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sp.addBase("Patient");
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mySearchParameterDao.update(sp, mySrd);
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@ -156,13 +156,13 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
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addCreateDefaultPartition();
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sp = new SearchParameter();
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sp.setId("SearchParameter/patient-birthdate-unique");
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sp.setId("SearchParameter/patient-gender-family-unique");
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sp.setType(Enumerations.SearchParamType.COMPOSITE);
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sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
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sp.addBase("Patient");
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sp.addComponent()
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.setExpression("Patient")
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.setDefinition("SearchParameter/patient-birthdate");
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.setDefinition("SearchParameter/patient-gender");
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sp.addComponent()
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.setExpression("Patient")
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.setDefinition("SearchParameter/patient-family");
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@ -13,10 +13,10 @@ import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.jpa.searchparam.util.JpaParamUtil;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.param.DateAndListParam;
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import ca.uhn.fhir.rest.param.DateOrListParam;
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import ca.uhn.fhir.rest.param.DateParam;
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import ca.uhn.fhir.rest.param.ReferenceParam;
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import ca.uhn.fhir.rest.param.StringOrListParam;
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import ca.uhn.fhir.rest.param.StringParam;
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import ca.uhn.fhir.rest.param.TokenAndListParam;
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import ca.uhn.fhir.rest.param.TokenParam;
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import ca.uhn.fhir.rest.server.exceptions.ResourceVersionConflictException;
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@ -33,6 +33,7 @@ import org.hl7.fhir.r4.model.DateType;
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import org.hl7.fhir.r4.model.Encounter;
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import org.hl7.fhir.r4.model.Enumerations;
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import org.hl7.fhir.r4.model.Enumerations.PublicationStatus;
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import org.hl7.fhir.r4.model.HumanName;
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import org.hl7.fhir.r4.model.IdType;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Organization;
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@ -115,6 +116,46 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
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myMessages.clear();
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}
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private void createUniqueGenderFamilyComboSp() {
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SearchParameter sp = new SearchParameter();
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sp.setId("SearchParameter/patient-gender");
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sp.setType(Enumerations.SearchParamType.TOKEN);
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sp.setCode("gender");
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sp.setExpression("Patient.gender");
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sp.setStatus(PublicationStatus.ACTIVE);
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sp.addBase("Patient");
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mySearchParameterDao.update(sp, mySrd);
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sp = new SearchParameter();
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sp.setId("SearchParameter/patient-family");
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sp.setType(Enumerations.SearchParamType.STRING);
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sp.setCode("family");
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sp.setExpression("Patient.name.family");
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sp.setStatus(Enumerations.PublicationStatus.ACTIVE);
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sp.addBase("Patient");
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mySearchParameterDao.update(sp, mySrd);
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sp = new SearchParameter();
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sp.setId("SearchParameter/patient-gender-family");
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sp.setType(Enumerations.SearchParamType.COMPOSITE);
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sp.setStatus(PublicationStatus.ACTIVE);
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sp.addBase("Patient");
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sp.addComponent()
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.setExpression("Patient")
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.setDefinition("SearchParameter/patient-gender");
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sp.addComponent()
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.setExpression("Patient")
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.setDefinition("SearchParameter/patient-family");
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sp.addExtension()
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.setUrl(HapiExtensions.EXT_SP_UNIQUE)
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.setValue(new BooleanType(true));
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mySearchParameterDao.update(sp, mySrd);
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mySearchParamRegistry.forceRefresh();
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myMessages.clear();
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}
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private void createUniqueIndexCoverageBeneficiary() {
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SearchParameter sp = new SearchParameter();
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sp.setId("SearchParameter/coverage-beneficiary");
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@ -276,6 +317,45 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
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mySearchParamRegistry.forceRefresh();
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}
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private void createUniqueObservationDateCode() {
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SearchParameter sp = new SearchParameter();
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sp.setId("SearchParameter/obs-effective");
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sp.setType(Enumerations.SearchParamType.DATE);
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sp.setCode("date");
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sp.setExpression("Observation.effective");
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sp.setStatus(PublicationStatus.ACTIVE);
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sp.addBase("Observation");
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mySearchParameterDao.update(sp, mySrd);
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sp = new SearchParameter();
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sp.setId("SearchParameter/obs-code");
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sp.setType(Enumerations.SearchParamType.TOKEN);
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sp.setCode("code");
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sp.setExpression("Observation.code");
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sp.setStatus(PublicationStatus.ACTIVE);
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sp.addBase("Observation");
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mySearchParameterDao.update(sp, mySrd);
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sp = new SearchParameter();
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sp.setId("SearchParameter/observation-date-code");
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sp.setType(Enumerations.SearchParamType.COMPOSITE);
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sp.setStatus(PublicationStatus.ACTIVE);
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sp.addBase("Observation");
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sp.setExpression("Observation.code");
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sp.addComponent()
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.setExpression("Observation")
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.setDefinition("SearchParameter/obs-effective");
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sp.addComponent()
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.setExpression("Observation")
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.setDefinition("SearchParameter/obs-code");
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sp.addExtension()
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.setUrl(HapiExtensions.EXT_SP_UNIQUE)
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.setValue(new BooleanType(true));
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mySearchParameterDao.update(sp, mySrd);
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mySearchParamRegistry.forceRefresh();
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}
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private void createUniqueObservationSubjectDateCode() {
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SearchParameter sp = new SearchParameter();
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sp.setId("SearchParameter/obs-subject");
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@ -471,11 +551,11 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
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public void testDoubleMatchingOnAnd_Search_TwoAndOrValues() {
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myStorageSettings.setUniqueIndexesCheckedBeforeSave(false);
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createUniqueBirthdateAndGenderSps();
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createUniqueGenderFamilyComboSp();
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Patient pt1 = new Patient();
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pt1.setGender(Enumerations.AdministrativeGender.MALE);
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pt1.setBirthDateElement(new DateType("2011-01-01"));
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pt1.getName().add(new HumanName().setFamily("Family1"));
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String id1 = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
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// Two OR values on the same resource - Currently composite SPs don't work for this
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@ -484,17 +564,22 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
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sp.setLoadSynchronous(true);
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sp.add(Patient.SP_GENDER,
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new TokenAndListParam()
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.addAnd(new TokenParam("http://hl7.org/fhir/administrative-gender","male"), new TokenParam( "http://hl7.org/fhir/administrative-gender","female"))
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.addAnd(new TokenParam("http://hl7.org/fhir/administrative-gender","male"),
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new TokenParam( "http://hl7.org/fhir/administrative-gender","female"))
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);
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sp.add(Patient.SP_BIRTHDATE,
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new DateAndListParam()
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.addAnd(new DateParam("2011-01-01"), new DateParam( "2011-02-02"))
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sp.add(Patient.SP_FAMILY,
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new StringOrListParam()
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.addOr(new StringParam("Family1")).addOr(new StringParam("Family2"))
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);
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IBundleProvider outcome = myPatientDao.search(sp, mySrd);
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myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
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assertThat(toUnqualifiedVersionlessIdValues(outcome)).containsExactlyInAnyOrder(id1);
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String unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
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assertEquals("SELECT t0.RES_ID FROM HFJ_IDX_CMP_STRING_UNIQ t0 WHERE (t0.IDX_STRING IN ('Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cfemale','Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale','Patient?birthdate=2011-02-02&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cfemale','Patient?birthdate=2011-02-02&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale') )", unformattedSql);
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assertEquals("SELECT t0.RES_ID FROM HFJ_IDX_CMP_STRING_UNIQ t0 WHERE (t0.IDX_STRING IN (" +
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"'Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cfemale'," +
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"'Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale'," +
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"'Patient?family=Family2&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cfemale'," +
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"'Patient?family=Family2&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale') )", unformattedSql);
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}
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|
@ -1167,16 +1252,16 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
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@Test
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public void testOrQuery() {
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myStorageSettings.setAdvancedHSearchIndexing(false);
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createUniqueBirthdateAndGenderSps();
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createUniqueGenderFamilyComboSp();
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Patient pt1 = new Patient();
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pt1.setGender(Enumerations.AdministrativeGender.MALE);
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pt1.setBirthDateElement(new DateType("2011-01-01"));
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pt1.getName().add(new HumanName().setFamily("Family1"));
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IIdType id1 = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless();
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Patient pt2 = new Patient();
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pt2.setGender(Enumerations.AdministrativeGender.MALE);
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pt2.setBirthDateElement(new DateType("2011-01-02"));
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pt2.getName().add(new HumanName().setFamily("Family2"));
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IIdType id2 = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless();
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myCaptureQueriesListener.clear();
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|
@ -1184,16 +1269,21 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronousUpTo(100);
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params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
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params.add("birthdate", new DateOrListParam().addOr(new DateParam("2011-01-01")).addOr(new DateParam("2011-01-02")));
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params.add("family", new StringOrListParam()
|
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.addOr(new StringParam("Family1")).addOr(new StringParam("Family2")));
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myCaptureQueriesListener.clear();
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IBundleProvider results = myPatientDao.search(params, mySrd);
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myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
|
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assertThat(toUnqualifiedVersionlessIdValues(results)).containsExactlyInAnyOrder(id1.getValue(), id2.getValue());
|
||||
|
||||
assertThat(myCaptureQueriesListener.getSelectQueries().get(0).getSql(true, false))
|
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.contains("SELECT t0.RES_ID FROM HFJ_IDX_CMP_STRING_UNIQ t0 WHERE (t0.IDX_STRING IN ('Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale','Patient?birthdate=2011-01-02&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale') )");
|
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.contains("SELECT t0.RES_ID FROM HFJ_IDX_CMP_STRING_UNIQ t0 WHERE (t0.IDX_STRING IN " +
|
||||
"('Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale'," +
|
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"'Patient?family=Family2&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale') )");
|
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logCapturedMessages();
|
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assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: [Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale, Patient?birthdate=2011-01-02&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale]");
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: " +
|
||||
"[Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale, " +
|
||||
"Patient?family=Family2&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale]");
|
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myMessages.clear();
|
||||
|
||||
}
|
||||
|
@ -1201,16 +1291,16 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
@Test
|
||||
public void testSearchSynchronousUsingUniqueComposite() {
|
||||
myStorageSettings.setAdvancedHSearchIndexing(false);
|
||||
createUniqueBirthdateAndGenderSps();
|
||||
createUniqueGenderFamilyComboSp();
|
||||
|
||||
Patient pt1 = new Patient();
|
||||
pt1.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt1.setBirthDateElement(new DateType("2011-01-01"));
|
||||
pt1.getName().add(new HumanName().setFamily("Family1"));
|
||||
IIdType id1 = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
Patient pt2 = new Patient();
|
||||
pt2.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt2.setBirthDateElement(new DateType("2011-01-02"));
|
||||
pt2.getName().add(new HumanName().setFamily("Family2"));
|
||||
myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
myCaptureQueriesListener.clear();
|
||||
|
@ -1218,13 +1308,14 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.setLoadSynchronousUpTo(100);
|
||||
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
||||
params.add("birthdate", new DateParam("2011-01-01"));
|
||||
params.add("family", new StringParam("Family1"));
|
||||
IBundleProvider results = myPatientDao.search(params, mySrd);
|
||||
myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).containsExactlyInAnyOrder(id1.getValue());
|
||||
|
||||
logCapturedMessages();
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: " +
|
||||
"Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
myMessages.clear();
|
||||
|
||||
}
|
||||
|
@ -1232,33 +1323,34 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
|
||||
@Test
|
||||
public void testSearchUsingUniqueComposite() {
|
||||
createUniqueBirthdateAndGenderSps();
|
||||
createUniqueGenderFamilyComboSp();
|
||||
|
||||
Patient pt1 = new Patient();
|
||||
pt1.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt1.setBirthDateElement(new DateType("2011-01-01"));
|
||||
pt1.getName().add(new HumanName().setFamily("Family1"));
|
||||
String id1 = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
Patient pt2 = new Patient();
|
||||
pt2.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt2.setBirthDateElement(new DateType("2011-01-02"));
|
||||
pt2.getName().add(new HumanName().setFamily("Family2"));
|
||||
myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
myMessages.clear();
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
||||
params.add("birthdate", new DateParam("2011-01-01"));
|
||||
params.add("family", new StringParam("Family1"));
|
||||
IBundleProvider results = myPatientDao.search(params, mySrd);
|
||||
String searchId = results.getUuid();
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).containsExactlyInAnyOrder(id1);
|
||||
logCapturedMessages();
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: " +
|
||||
"Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
myMessages.clear();
|
||||
|
||||
// Other order
|
||||
myMessages.clear();
|
||||
params = new SearchParameterMap();
|
||||
params.add("birthdate", new DateParam("2011-01-01"));
|
||||
params.add("family", new StringParam("Family1"));
|
||||
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
||||
results = myPatientDao.search(params, mySrd);
|
||||
assertEquals(searchId, results.getUuid());
|
||||
|
@ -1272,16 +1364,17 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
myMessages.clear();
|
||||
params = new SearchParameterMap();
|
||||
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
||||
params.add("birthdate", new DateParam("2011-01-03"));
|
||||
params.add("family", new StringParam("Family3"));
|
||||
results = myPatientDao.search(params, mySrd);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).isEmpty();
|
||||
logCapturedMessages();
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: Patient?birthdate=2011-01-03&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: " +
|
||||
"Patient?family=Family3&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
myMessages.clear();
|
||||
|
||||
myMessages.clear();
|
||||
params = new SearchParameterMap();
|
||||
params.add("birthdate", new DateParam("2011-01-03"));
|
||||
params.add("family", new StringParam("Family3"));
|
||||
results = myPatientDao.search(params, mySrd);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).isEmpty();
|
||||
// STANDARD QUERY
|
||||
|
@ -1666,7 +1759,7 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testDuplicateUniqueValuesAreRejected() {
|
||||
public void testDuplicateUniqueValuesWithDateAreRejected() {
|
||||
createUniqueBirthdateAndGenderSps();
|
||||
|
||||
Patient pt1 = new Patient();
|
||||
|
@ -1699,13 +1792,75 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testReplaceOneWithAnother() {
|
||||
myStorageSettings.setAdvancedHSearchIndexing(false);
|
||||
public void testDuplicateUniqueValuesWithDateTimeAreRejected() {
|
||||
createUniqueObservationDateCode();
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.getCode().addCoding().setSystem("foo").setCode("bar");
|
||||
obs.setEffective(new DateTimeType("2017-10-10T00:00:00"));
|
||||
myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
try {
|
||||
myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless();
|
||||
fail();
|
||||
} catch (ResourceVersionConflictException e) {
|
||||
assertThat(e.getMessage())
|
||||
.contains("new unique index created by SearchParameter/observation-date-code");
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUniqueComboSearchWithDateNotUsingUniqueIndex() {
|
||||
createUniqueBirthdateAndGenderSps();
|
||||
|
||||
Patient pt1 = new Patient();
|
||||
pt1.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt1.setBirthDateElement(new DateType("2011-01-01"));
|
||||
String pId = myPatientDao.create(pt1, mySrd).getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
myCaptureQueriesListener.clear();
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.setLoadSynchronousUpTo(100);
|
||||
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
||||
params.add("birthdate", new DateParam("2011-01-01"));
|
||||
|
||||
IBundleProvider results = myPatientDao.search(params, mySrd);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).containsExactlyInAnyOrder(pId);
|
||||
myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
|
||||
String unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
|
||||
assertThat(unformattedSql).doesNotContain("HFJ_IDX_CMP_STRING_UNIQ");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testUniqueComboSearchWithDateTimeNotUsingUniqueIndex() {
|
||||
createUniqueObservationDateCode();
|
||||
|
||||
Observation obs = new Observation();
|
||||
obs.getCode().addCoding().setSystem("foo").setCode("bar");
|
||||
obs.setEffective(new DateTimeType("2017-10-10T00:00:00"));
|
||||
String obsId = myObservationDao.create(obs, mySrd).getId().toUnqualifiedVersionless().getValue();
|
||||
|
||||
myCaptureQueriesListener.clear();
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.setLoadSynchronousUpTo(100);
|
||||
params.add("code", new TokenParam("foo", "bar"));
|
||||
params.add("date", new DateParam("2017-10-10T00:00:00"));
|
||||
|
||||
IBundleProvider results = myObservationDao.search(params, mySrd);
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).containsExactlyInAnyOrder(obsId);
|
||||
myCaptureQueriesListener.logFirstSelectQueryForCurrentThread();
|
||||
String unformattedSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, false);
|
||||
assertThat(unformattedSql).doesNotContain("HFJ_IDX_CMP_STRING_UNIQ");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testReplaceOneWithAnother() {
|
||||
myStorageSettings.setAdvancedHSearchIndexing(false);
|
||||
createUniqueGenderFamilyComboSp();
|
||||
|
||||
Patient pt1 = new Patient();
|
||||
pt1.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt1.getName().add(new HumanName().setFamily("Family1"));
|
||||
IIdType id1 = myPatientDao.create(pt1, mySrd).getId().toUnqualified();
|
||||
assertNotNull(id1);
|
||||
|
||||
|
@ -1714,27 +1869,28 @@ public class FhirResourceDaoR4ComboUniqueParamTest extends BaseComboParamsR4Test
|
|||
pt1 = new Patient();
|
||||
pt1.setId(id1);
|
||||
pt1.setGender(Enumerations.AdministrativeGender.FEMALE);
|
||||
pt1.setBirthDateElement(new DateType("2011-01-01"));
|
||||
pt1.getName().add(new HumanName().setFamily("Family1"));
|
||||
id1 = myPatientDao.update(pt1, mySrd).getId().toUnqualified();
|
||||
assertNotNull(id1);
|
||||
assertEquals("2", id1.getVersionIdPart());
|
||||
|
||||
Patient pt2 = new Patient();
|
||||
pt2.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
pt2.setBirthDateElement(new DateType("2011-01-01"));
|
||||
pt2.getName().add(new HumanName().setFamily("Family1"));
|
||||
IIdType id2 = myPatientDao.create(pt2, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
myMessages.clear();
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.add("gender", new TokenParam("http://hl7.org/fhir/administrative-gender", "male"));
|
||||
params.add("birthdate", new DateParam("2011-01-01"));
|
||||
params.add("family", new StringParam("Family1"));
|
||||
IBundleProvider results = myPatientDao.search(params, mySrd);
|
||||
String searchId = results.getUuid();
|
||||
assertThat(searchId).isNotBlank();
|
||||
assertThat(toUnqualifiedVersionlessIdValues(results)).containsExactlyInAnyOrder(id2.getValue());
|
||||
|
||||
logCapturedMessages();
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: Patient?birthdate=2011-01-01&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
assertThat(myMessages.toString()).contains("Using UNIQUE index(es) for query for search: " +
|
||||
"Patient?family=Family1&gender=http%3A%2F%2Fhl7.org%2Ffhir%2Fadministrative-gender%7Cmale");
|
||||
myMessages.clear();
|
||||
|
||||
}
|
||||
|
|
|
@ -413,7 +413,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
p.getMeta().addTag("http://system", "code", "diisplay");
|
||||
p.addName().setFamily("FAM");
|
||||
p.addIdentifier().setSystem("system").setValue("value");
|
||||
p.setBirthDateElement(new DateType("2020-01-01"));
|
||||
p.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
p.getManagingOrganization().setReferenceElement(orgId);
|
||||
Long patientId = myPatientDao.create(p, mySrd).getId().getIdPartAsLong();
|
||||
|
||||
|
@ -502,7 +502,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
p.getMeta().addTag("http://system", "code", "diisplay");
|
||||
p.addName().setFamily("FAM");
|
||||
p.addIdentifier().setSystem("system").setValue("value");
|
||||
p.setBirthDate(new Date());
|
||||
p.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
p.getManagingOrganization().setReferenceElement(orgId);
|
||||
Long patientId = myPatientDao.create(p, mySrd).getId().getIdPartAsLong();
|
||||
|
||||
|
@ -679,7 +679,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
p.getMeta().addTag("http://system", "code", "display");
|
||||
p.addName().setFamily("FAM");
|
||||
p.addIdentifier().setSystem("system").setValue("value");
|
||||
p.setBirthDate(new Date());
|
||||
p.setGender(Enumerations.AdministrativeGender.MALE);
|
||||
p.getManagingOrganization().setReference(org.getId());
|
||||
input.addEntry()
|
||||
.setFullUrl(p.getId())
|
||||
|
@ -2541,14 +2541,14 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
public void testSearch_UniqueParam_SearchAllPartitions() {
|
||||
createUniqueComboSp();
|
||||
|
||||
IIdType id = createPatient(withPartition(1), withBirthdate("2020-01-01"), withFamily("FAM"));
|
||||
IIdType id = createPatient(withPartition(1), withGender("male"), withFamily("FAM"));
|
||||
|
||||
addReadAllPartitions();
|
||||
|
||||
myCaptureQueriesListener.clear();
|
||||
SearchParameterMap map = new SearchParameterMap();
|
||||
map.add(Patient.SP_FAMILY, new StringParam("FAM"));
|
||||
map.add(Patient.SP_BIRTHDATE, new DateParam("2020-01-01"));
|
||||
map.add(Patient.SP_GENDER, new TokenParam(null, "male"));
|
||||
map.setLoadSynchronous(true);
|
||||
IBundleProvider results = myPatientDao.search(map, mySrd);
|
||||
List<IIdType> ids = toUnqualifiedVersionlessIds(results);
|
||||
|
@ -2558,7 +2558,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
|
||||
ourLog.info("Search SQL:\n{}", searchSql);
|
||||
assertThat(searchSql).doesNotContain("PARTITION_ID");
|
||||
assertThat(searchSql).containsOnlyOnce("IDX_STRING = 'Patient?birthdate=2020-01-01&family=FAM'");
|
||||
assertThat(searchSql).containsOnlyOnce("IDX_STRING = 'Patient?family=FAM&gender=male'");
|
||||
}
|
||||
|
||||
|
||||
|
@ -2566,13 +2566,13 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
public void testSearch_UniqueParam_SearchOnePartition() {
|
||||
createUniqueComboSp();
|
||||
|
||||
IIdType id = createPatient(withPartition(1), withBirthdate("2020-01-01"), withFamily("FAM"));
|
||||
IIdType id = createPatient(withPartition(1), withGender("male"), withFamily("FAM"));
|
||||
|
||||
addReadPartition(1);
|
||||
myCaptureQueriesListener.clear();
|
||||
SearchParameterMap map = new SearchParameterMap();
|
||||
map.add(Patient.SP_FAMILY, new StringParam("FAM"));
|
||||
map.add(Patient.SP_BIRTHDATE, new DateParam("2020-01-01"));
|
||||
map.add(Patient.SP_GENDER, new TokenParam(null, "male"));
|
||||
map.setLoadSynchronous(true);
|
||||
IBundleProvider results = myPatientDao.search(map, mySrd);
|
||||
List<IIdType> ids = toUnqualifiedVersionlessIds(results);
|
||||
|
@ -2582,13 +2582,13 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
String searchSql = myCaptureQueriesListener.getSelectQueriesForCurrentThread().get(0).getSql(true, true);
|
||||
ourLog.info("Search SQL:\n{}", searchSql);
|
||||
assertThat(searchSql).containsOnlyOnce( "PARTITION_ID = '1'");
|
||||
assertThat(searchSql).containsOnlyOnce("IDX_STRING = 'Patient?birthdate=2020-01-01&family=FAM'");
|
||||
assertThat(searchSql).containsOnlyOnce("IDX_STRING = 'Patient?family=FAM&gender=male'");
|
||||
|
||||
// Same query, different partition
|
||||
addReadPartition(2);
|
||||
myCaptureQueriesListener.clear();
|
||||
map = new SearchParameterMap();
|
||||
map.add(Patient.SP_BIRTHDATE, new DateParam("2020-01-01"));
|
||||
map.add(Patient.SP_GENDER, new TokenParam(null, "male"));
|
||||
map.setLoadSynchronous(true);
|
||||
results = myPatientDao.search(map, mySrd);
|
||||
ids = toUnqualifiedVersionlessIds(results);
|
||||
|
@ -2661,7 +2661,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
public void testSearch_RefParam_TargetPid_SearchOnePartition() {
|
||||
createUniqueComboSp();
|
||||
|
||||
IIdType patientId = createPatient(withPartition(myPartitionId), withBirthdate("2020-01-01"));
|
||||
IIdType patientId = createPatient(withPartition(myPartitionId), withGender("male"));
|
||||
IIdType observationId = createObservation(withPartition(myPartitionId), withSubject(patientId));
|
||||
|
||||
addReadPartition(myPartitionId);
|
||||
|
@ -2698,7 +2698,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
public void testSearch_RefParam_TargetPid_SearchDefaultPartition() {
|
||||
createUniqueComboSp();
|
||||
|
||||
IIdType patientId = createPatient(withPartition(null), withBirthdate("2020-01-01"));
|
||||
IIdType patientId = createPatient(withPartition(null), withGender("male"));
|
||||
IIdType observationId = createObservation(withPartition(null), withSubject(patientId));
|
||||
|
||||
addReadDefaultPartition();
|
||||
|
@ -2735,7 +2735,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
public void testSearch_RefParam_TargetForcedId_SearchOnePartition() {
|
||||
createUniqueComboSp();
|
||||
|
||||
IIdType patientId = createPatient(withPartition(myPartitionId), withId("ONE"), withBirthdate("2020-01-01"));
|
||||
IIdType patientId = createPatient(withPartition(myPartitionId), withId("ONE"), withGender("male"));
|
||||
IIdType observationId = createObservation(withPartition(myPartitionId), withSubject(patientId));
|
||||
|
||||
addReadPartition(myPartitionId);
|
||||
|
@ -2805,7 +2805,7 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
public void testSearch_RefParam_TargetForcedId_SearchDefaultPartition() {
|
||||
createUniqueComboSp();
|
||||
|
||||
IIdType patientId = createPatient(withPartition(null), withId("ONE"), withBirthdate("2020-01-01"));
|
||||
IIdType patientId = createPatient(withPartition(null), withId("ONE"), withGender("male"));
|
||||
IIdType observationId = createObservation(withPartition(null), withSubject(patientId));
|
||||
|
||||
addReadDefaultPartition();
|
||||
|
|
|
@ -32,6 +32,7 @@ import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
|
|||
import ca.uhn.fhir.util.Logs;
|
||||
import jakarta.annotation.Nonnull;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.MDC;
|
||||
import org.springframework.messaging.Message;
|
||||
import org.springframework.messaging.MessageHandler;
|
||||
import org.springframework.messaging.MessagingException;
|
||||
|
@ -218,7 +219,10 @@ class WorkChannelMessageHandler implements MessageHandler {
|
|||
}
|
||||
|
||||
private void handleWorkChannelMessage(JobWorkNotificationJsonMessage theMessage) {
|
||||
try {
|
||||
JobWorkNotification workNotification = theMessage.getPayload();
|
||||
// Load the job instance and work chunk IDs into the logging MDC context
|
||||
BatchJobTracingContext.setBatchJobIds(workNotification.getInstanceId(), workNotification.getChunkId());
|
||||
ourLog.info("Received work notification for {}", workNotification);
|
||||
|
||||
// There are three paths through this code:
|
||||
|
@ -255,6 +259,9 @@ class WorkChannelMessageHandler implements MessageHandler {
|
|||
// discard the chunk
|
||||
ourLog.debug("Discarding chunk notification {}", workNotification);
|
||||
});
|
||||
} finally {
|
||||
BatchJobTracingContext.clearBatchJobsIds();
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
|
@ -279,4 +286,22 @@ class WorkChannelMessageHandler implements MessageHandler {
|
|||
return setupProcessing;
|
||||
});
|
||||
}
|
||||
|
||||
/**
|
||||
* Simple wrapper around the slf4j MDC threadlocal log context.
|
||||
*/
|
||||
public static class BatchJobTracingContext {
|
||||
static final String INSTANCE_ID = "instanceId";
|
||||
static final String CHUNK_ID = "chunkId";
|
||||
|
||||
public static void setBatchJobIds(String theInstanceId, String theChunkId) {
|
||||
MDC.put(INSTANCE_ID, theInstanceId);
|
||||
MDC.put(CHUNK_ID, theChunkId);
|
||||
}
|
||||
|
||||
public static void clearBatchJobsIds() {
|
||||
MDC.remove(INSTANCE_ID);
|
||||
MDC.remove(CHUNK_ID);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
@ -0,0 +1,87 @@
|
|||
package ca.uhn.fhir.batch2.coordinator;
|
||||
|
||||
import ca.uhn.fhir.batch2.api.IJobMaintenanceService;
|
||||
import ca.uhn.fhir.batch2.api.IJobPersistence;
|
||||
import ca.uhn.fhir.batch2.channel.BatchJobSender;
|
||||
|
||||
import static ca.uhn.fhir.batch2.coordinator.WorkChannelMessageHandler.*;
|
||||
|
||||
import ca.uhn.fhir.batch2.model.JobWorkNotification;
|
||||
import ca.uhn.fhir.batch2.model.JobWorkNotificationJsonMessage;
|
||||
import ca.uhn.fhir.jpa.dao.tx.IHapiTransactionService;
|
||||
import ca.uhn.fhir.jpa.dao.tx.NonTransactionalHapiTransactionService;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
|
||||
import ch.qos.logback.classic.spi.ILoggingEvent;
|
||||
import ch.qos.logback.core.Appender;
|
||||
import jakarta.annotation.Nonnull;
|
||||
|
||||
import java.util.Collection;
|
||||
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import ch.qos.logback.classic.Logger;
|
||||
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.mockito.ArgumentCaptor;
|
||||
import org.mockito.Captor;
|
||||
import org.mockito.Mock;
|
||||
|
||||
import static org.mockito.Mockito.atLeastOnce;
|
||||
import static org.mockito.Mockito.verify;
|
||||
|
||||
class WorkChannelMessageHandlerTest extends BaseBatch2Test {
|
||||
@Mock
|
||||
private BatchJobSender myBatchJobSender;
|
||||
@Mock
|
||||
private IJobPersistence myJobInstancePersister;
|
||||
@Mock
|
||||
private JobDefinitionRegistry myJobDefinitionRegistry;
|
||||
@Mock
|
||||
private IJobMaintenanceService myJobMaintenanceService;
|
||||
private final IHapiTransactionService myTransactionService = new NonTransactionalHapiTransactionService();
|
||||
private WorkChunkProcessor jobStepExecutorSvc;
|
||||
|
||||
@Mock
|
||||
private Appender<ILoggingEvent> myAppender;
|
||||
@Captor
|
||||
private ArgumentCaptor<ILoggingEvent> myLoggingEvent;
|
||||
|
||||
@BeforeEach
|
||||
public void beforeEach() {
|
||||
jobStepExecutorSvc = new WorkChunkProcessor(myJobInstancePersister, myBatchJobSender, new NonTransactionalHapiTransactionService());
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testWorkChannelMessageHandlerLogging_containsJobAndBatchIdInLoggingContext(){
|
||||
// Setup
|
||||
((Logger) Logs.getBatchTroubleshootingLog()).addAppender(myAppender);
|
||||
|
||||
// When
|
||||
WorkChannelMessageHandler handler = new WorkChannelMessageHandler(myJobInstancePersister, myJobDefinitionRegistry, myBatchJobSender, jobStepExecutorSvc, myJobMaintenanceService, myTransactionService);
|
||||
handler.handleMessage(new JobWorkNotificationJsonMessage(createWorkNotification(STEP_1)));
|
||||
|
||||
// Then
|
||||
verify(myAppender, atLeastOnce()).doAppend(myLoggingEvent.capture());
|
||||
myLoggingEvent.getAllValues()
|
||||
.forEach(event -> {
|
||||
Map<String, String> mdcPropertyMap = event.getMDCPropertyMap();
|
||||
assertThat(mdcPropertyMap).containsEntry(BatchJobTracingContext.CHUNK_ID, CHUNK_ID);
|
||||
assertThat(mdcPropertyMap).containsEntry(BatchJobTracingContext.INSTANCE_ID, INSTANCE_ID);
|
||||
});
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private JobWorkNotification createWorkNotification(String theStepId) {
|
||||
JobWorkNotification payload = new JobWorkNotification();
|
||||
payload.setJobDefinitionId(JOB_DEFINITION_ID);
|
||||
payload.setJobDefinitionVersion(1);
|
||||
payload.setInstanceId(INSTANCE_ID);
|
||||
payload.setChunkId(BaseBatch2Test.CHUNK_ID);
|
||||
payload.setTargetStepId(theStepId);
|
||||
return payload;
|
||||
}
|
||||
}
|
Loading…
Reference in New Issue