mirror of
https://github.com/hapifhir/hapi-fhir.git
synced 2025-02-20 20:09:51 +00:00
More cleanup in advance of DB Partitioning Mode (#6553)
* Work on next merge * Bring cleanup forward * Add error code * Address review comments * Build fix * Cleanup
This commit is contained in:
James Agnew
GitHub
parent
e174572a3b
commit
c3eba4681f
@ -2,12 +2,14 @@ package ca.uhn.fhir.cli;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.provider.BaseJpaSystemProvider;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.system.HapiSystemProperties;
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import ca.uhn.fhir.test.utilities.RestServerR4Helper;
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import ca.uhn.fhir.test.utilities.TlsAuthenticationTestHelper;
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import ca.uhn.fhir.util.ParametersUtil;
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import ca.uhn.test.util.LogbackTestExtension;
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import ca.uhn.test.util.LogbackTestExtensionAssert;
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import ch.qos.logback.classic.Level;
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import ch.qos.logback.classic.Logger;
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import org.hl7.fhir.instance.model.api.IBaseParameters;
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import org.junit.jupiter.api.BeforeEach;
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@ -40,9 +42,8 @@ class ReindexTerminologyCommandTest {
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public final RestServerR4Helper myRestServerR4Helper = RestServerR4Helper.newInitialized();
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@RegisterExtension
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public TlsAuthenticationTestHelper myTlsAuthenticationTestHelper = new TlsAuthenticationTestHelper();
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// Deliberately not registered - we manually run this later because App startup resets the logging.
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LogbackTestExtension myAppLogCapture;
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@RegisterExtension
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public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension(BaseApp.ourLog);
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static {
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HapiSystemProperties.enableTestMode();
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@ -69,7 +70,7 @@ class ReindexTerminologyCommandTest {
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);
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runAppWithStartupHook(args, getLoggingStartupHook());
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LogbackTestExtensionAssert.assertThat(myAppLogCapture).doesNotHaveMessage(FAILURE_MESSAGE);
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LogbackTestExtensionAssert.assertThat(myLogbackTestExtension).doesNotHaveMessage(FAILURE_MESSAGE);
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}
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@ParameterizedTest
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@ -131,7 +132,7 @@ class ReindexTerminologyCommandTest {
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);
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runAppWithStartupHook(args, getLoggingStartupHook());
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LogbackTestExtensionAssert.assertThat(myAppLogCapture)
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LogbackTestExtensionAssert.assertThat(myLogbackTestExtension)
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.hasMessage(FAILURE_MESSAGE)
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.hasMessage("Internal error. Command result unknown. Check system logs for details");
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}
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@ -156,7 +157,7 @@ class ReindexTerminologyCommandTest {
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);
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runAppWithStartupHook(args, getLoggingStartupHook());
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LogbackTestExtensionAssert.assertThat(myAppLogCapture)
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LogbackTestExtensionAssert.assertThat(myLogbackTestExtension)
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.hasMessage(FAILURE_MESSAGE)
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.hasMessage("Freetext service is not configured. Operation didn't run.");
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}
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@ -176,8 +177,11 @@ class ReindexTerminologyCommandTest {
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*/
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Consumer<BaseApp> getLoggingStartupHook() {
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return (unused) -> {
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myAppLogCapture = new LogbackTestExtension((Logger) BaseApp.ourLog);
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myAppLogCapture.setUp();
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try {
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myLogbackTestExtension.reRegister();
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} catch (Exception e) {
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throw new InternalErrorException(e);
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}
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};
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}
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}
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@ -130,17 +130,17 @@ public class RequestPartitionHelperSvc extends BaseRequestPartitionHelperSvc {
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}
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if (theRequestPartitionId.hasPartitionIds()) {
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Integer partitionId = theRequestPartitionId.getPartitionIds().get(i);
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if (partition == null) {
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Validate.isTrue(
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theRequestPartitionId.getPartitionIds().get(i) == null,
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partitionId == null || partitionId.equals(myPartitionSettings.getDefaultPartitionId()),
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"Partition %s must not have an ID",
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JpaConstants.DEFAULT_PARTITION_NAME);
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} else {
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Validate.isTrue(
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Objects.equals(
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theRequestPartitionId.getPartitionIds().get(i), partition.getId()),
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Objects.equals(partitionId, partition.getId()),
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"Partition ID %s does not match name %s",
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theRequestPartitionId.getPartitionIds().get(i),
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partitionId,
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theRequestPartitionId.getPartitionNames().get(i));
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}
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} else {
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@ -491,7 +491,7 @@ public class QueryStack {
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}
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private void addSortCustomJoin(
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DbColumn theFromDbColumn[],
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DbColumn[] theFromDbColumn,
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BaseJoiningPredicateBuilder theToJoiningPredicateBuilder,
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Condition theCondition) {
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@ -550,14 +550,14 @@ public class QueryStack {
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private Condition createPredicateComposite(
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@Nullable DbColumn[] theSourceJoinColumn,
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String theResourceName,
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String theSpnamePrefix,
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String theSPNamePrefix,
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RuntimeSearchParam theParamDef,
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List<? extends IQueryParameterType> theNextAnd,
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RequestPartitionId theRequestPartitionId) {
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return createPredicateComposite(
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theSourceJoinColumn,
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theResourceName,
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theSpnamePrefix,
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theSPNamePrefix,
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theParamDef,
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theNextAnd,
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theRequestPartitionId,
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@ -698,7 +698,7 @@ public class QueryStack {
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}
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// TODO - Change this when we have HFJ_SPIDX_MISSING table
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/**
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/*
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* How we search depends on if the
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* {@link JpaStorageSettings#getIndexMissingFields()} property
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* is Enabled or Disabled.
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@ -821,7 +821,6 @@ public class QueryStack {
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ICanMakeMissingParamPredicate innerQuery = PredicateBuilderFactory.createPredicateBuilderForParamType(
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theParams.getParamType(), theParams.getSqlBuilder(), this);
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return innerQuery.createPredicateParamMissingValue(new MissingQueryParameterPredicateParams(
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table, theParams.isMissing(), theParams.getParamName(), theParams.getRequestPartitionId()));
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}
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@ -943,16 +942,13 @@ public class QueryStack {
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QueryStack theQueryStack3,
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SearchFilterParser.BaseFilter theFilter,
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String theResourceName,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId) {
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if (theFilter instanceof SearchFilterParser.FilterParameter) {
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return createPredicateFilter(
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theRequest,
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theQueryStack3,
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(SearchFilterParser.FilterParameter) theFilter,
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theResourceName,
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theRequest,
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theRequestPartitionId);
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} else if (theFilter instanceof SearchFilterParser.FilterLogical) {
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// Left side
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@ -960,7 +956,6 @@ public class QueryStack {
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theQueryStack3,
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((SearchFilterParser.FilterLogical) theFilter).getFilter1(),
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theResourceName,
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theRequest,
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theRequestPartitionId);
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// Right side
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@ -968,7 +963,6 @@ public class QueryStack {
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theQueryStack3,
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((SearchFilterParser.FilterLogical) theFilter).getFilter2(),
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theResourceName,
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theRequest,
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theRequestPartitionId);
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if (((SearchFilterParser.FilterLogical) theFilter).getOperation()
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@ -987,17 +981,14 @@ public class QueryStack {
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theQueryStack3,
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((SearchFilterParser.FilterParameterGroup) theFilter).getContained(),
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theResourceName,
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theRequest,
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theRequestPartitionId);
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}
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}
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private Condition createPredicateFilter(
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RequestDetails theRequestDetails,
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QueryStack theQueryStack3,
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SearchFilterParser.FilterParameter theFilter,
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String theResourceName,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId) {
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String paramName = theFilter.getParamPath().getName();
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@ -1089,7 +1080,6 @@ public class QueryStack {
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new ArrayList<>(),
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Collections.singletonList(referenceParam),
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operation,
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theRequest,
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theRequestPartitionId);
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} else if (typeEnum == RestSearchParameterTypeEnum.QUANTITY) {
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return theQueryStack3.createPredicateQuantity(
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@ -1240,9 +1230,8 @@ public class QueryStack {
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Condition pathPredicate = toEqualToOrInPredicate(
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resourceLinkTableJoin.getColumnSourcePath(), mySqlBuilder.generatePlaceholders(paths));
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Condition linkedPredicate = searchForIdsWithAndOr(
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theRequest,
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with().setSourceJoinColumn(resourceLinkTableJoin.getJoinColumnsForSource())
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Condition linkedPredicate =
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searchForIdsWithAndOr(with().setSourceJoinColumn(resourceLinkTableJoin.getJoinColumnsForSource())
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.setResourceName(targetResourceType)
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.setParamName(parameterName)
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.setAndOrParams(Collections.singletonList(orValues))
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@ -1433,7 +1422,6 @@ public class QueryStack {
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List<String> theQualifiers,
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List<? extends IQueryParameterType> theList,
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SearchFilterParser.CompareOperation theOperation,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId) {
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return createPredicateReference(
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theSourceJoinColumn,
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@ -1442,7 +1430,6 @@ public class QueryStack {
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theQualifiers,
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theList,
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theOperation,
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theRequest,
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theRequestPartitionId,
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mySqlBuilder);
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}
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@ -1454,7 +1441,6 @@ public class QueryStack {
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List<String> theQualifiers,
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List<? extends IQueryParameterType> theList,
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SearchFilterParser.CompareOperation theOperation,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId,
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SearchQueryBuilder theSqlBuilder) {
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@ -1484,7 +1470,7 @@ public class QueryStack {
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() -> theSqlBuilder.addReferencePredicateBuilder(this, theSourceJoinColumn))
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.getResult();
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return predicateBuilder.createPredicate(
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theRequest,
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myRequestDetails,
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theResourceName,
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theParamName,
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theQualifiers,
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@ -1526,7 +1512,6 @@ public class QueryStack {
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RuntimeSearchParam theSearchParam,
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List<? extends IQueryParameterType> theList,
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SearchFilterParser.CompareOperation theOperation,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId,
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EmbeddedChainedSearchModeEnum theEmbeddedChainedSearchModeEnum) {
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@ -1553,14 +1538,11 @@ public class QueryStack {
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}
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UnionQuery union = null;
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List<Condition> predicates = null;
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if (wantChainedAndNormal) {
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union = new UnionQuery(SetOperationQuery.Type.UNION_ALL);
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} else {
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predicates = new ArrayList<>();
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}
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predicates = new ArrayList<>();
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List<Condition> predicates = new ArrayList<>();
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for (List<String> nextReferenceLink : referenceLinks.keySet()) {
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for (LeafNodeDefinition leafNodeDefinition : referenceLinks.get(nextReferenceLink)) {
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SearchQueryBuilder builder;
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@ -1593,7 +1575,6 @@ public class QueryStack {
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leafNodeDefinition.getOrValues(),
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theOperation,
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leafNodeDefinition.getQualifiers(),
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theRequest,
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theRequestPartitionId,
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builder);
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@ -1792,11 +1773,7 @@ public class QueryStack {
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Map<List<String>, Set<LeafNodeDefinition>> theReferenceLinksMap,
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ArrayList<String> thePath,
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Set<LeafNodeDefinition> theLeafNodesToAdd) {
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Set<LeafNodeDefinition> leafNodes = theReferenceLinksMap.get(thePath);
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if (leafNodes == null) {
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leafNodes = Sets.newHashSet();
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theReferenceLinksMap.put(thePath, leafNodes);
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}
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Set<LeafNodeDefinition> leafNodes = theReferenceLinksMap.computeIfAbsent(thePath, k -> Sets.newHashSet());
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leafNodes.addAll(theLeafNodesToAdd);
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}
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@ -1822,7 +1799,6 @@ public class QueryStack {
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ArrayList<IQueryParameterType> theOrValues,
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SearchFilterParser.CompareOperation theOperation,
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List<String> theQualifiers,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId,
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SearchQueryBuilder theSqlBuilder) {
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Condition containedCondition;
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@ -1912,7 +1888,6 @@ public class QueryStack {
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theQualifiers,
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theOrValues,
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theOperation,
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theRequest,
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theRequestPartitionId,
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theSqlBuilder);
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break;
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@ -2396,7 +2371,7 @@ public class QueryStack {
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}
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@Nullable
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public Condition searchForIdsWithAndOr(RequestDetails theRequestDetails, SearchForIdsParams theSearchForIdsParams) {
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public Condition searchForIdsWithAndOr(SearchForIdsParams theSearchForIdsParams) {
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if (theSearchForIdsParams.myAndOrParams.isEmpty()) {
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return null;
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@ -2432,7 +2407,6 @@ public class QueryStack {
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theSearchForIdsParams.myResourceName,
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theSearchForIdsParams.myParamName,
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theSearchForIdsParams.myAndOrParams,
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theSearchForIdsParams.myRequest,
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theSearchForIdsParams.myRequestPartitionId);
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} else {
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return createPredicateTag(
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@ -2460,7 +2434,6 @@ public class QueryStack {
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theSearchForIdsParams.myResourceName,
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theSearchForIdsParams.myParamName,
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theSearchForIdsParams.myAndOrParams,
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theSearchForIdsParams.myRequest,
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theSearchForIdsParams.myRequestPartitionId);
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}
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}
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@ -2520,7 +2493,6 @@ public class QueryStack {
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String theResourceName,
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String theParamName,
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List<List<IQueryParameterType>> theAndOrParams,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId) {
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List<Condition> andPredicates = new ArrayList<>();
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RuntimeSearchParam nextParamDef = mySearchParamRegistry.getActiveSearchParam(
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@ -2540,7 +2512,7 @@ public class QueryStack {
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// FT: 2021-01-18 use operation 'gt', 'ge', 'le' or 'lt'
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// to create the predicateDate instead of generic one with operation = null
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SearchFilterParser.CompareOperation operation = null;
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if (nextAnd.size() > 0) {
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if (!nextAnd.isEmpty()) {
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DateParam param = (DateParam) nextAnd.get(0);
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operation = toOperation(param.getPrefix());
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}
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@ -2557,7 +2529,7 @@ public class QueryStack {
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case QUANTITY:
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for (List<? extends IQueryParameterType> nextAnd : theAndOrParams) {
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SearchFilterParser.CompareOperation operation = null;
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if (nextAnd.size() > 0) {
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if (!nextAnd.isEmpty()) {
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QuantityParam param = (QuantityParam) nextAnd.get(0);
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operation = toOperation(param.getPrefix());
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}
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@ -2580,7 +2552,6 @@ public class QueryStack {
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theSourceJoinColumn,
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theResourceName,
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theParamName,
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theRequest,
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theRequestPartitionId,
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andPredicates,
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nextAnd)) {
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@ -2597,7 +2568,6 @@ public class QueryStack {
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new ArrayList<>(),
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nextAnd,
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null,
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theRequest,
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theRequestPartitionId));
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} else {
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andPredicates.add(createPredicateReferenceForEmbeddedChainedSearchResource(
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@ -2606,7 +2576,6 @@ public class QueryStack {
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nextParamDef,
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nextAnd,
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null,
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theRequest,
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theRequestPartitionId,
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embeddedChainedSearchModeEnum));
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}
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@ -2721,8 +2690,8 @@ public class QueryStack {
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+ " parameter is disabled on this server");
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}
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Condition predicate = createPredicateFilter(
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this, filter, theResourceName, theRequest, theRequestPartitionId);
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Condition predicate =
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createPredicateFilter(this, filter, theResourceName, theRequestPartitionId);
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if (predicate != null) {
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mySqlBuilder.addPredicate(predicate);
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}
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@ -2779,7 +2748,6 @@ public class QueryStack {
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@Nullable DbColumn[] theSourceJoinColumn,
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String theResourceName,
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String theParamName,
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RequestDetails theRequest,
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RequestPartitionId theRequestPartitionId,
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List<Condition> andPredicates,
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List<? extends IQueryParameterType> nextAnd) {
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@ -2795,7 +2763,7 @@ public class QueryStack {
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.collect(Collectors.toList());
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List<List<IQueryParameterType>> params = List.of(swappedParamTypes);
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Condition predicate = createPredicateSearchParameter(
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theSourceJoinColumn, theResourceName, fullName, params, theRequest, theRequestPartitionId);
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theSourceJoinColumn, theResourceName, fullName, params, theRequestPartitionId);
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andPredicates.add(predicate);
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return true;
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}
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@ -2955,7 +2923,7 @@ public class QueryStack {
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/**
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* @see #isEligibleForEmbeddedChainedResourceSearch(String, String, List) for an explanation of the values in this enum
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*/
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enum EmbeddedChainedSearchModeEnum {
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public enum EmbeddedChainedSearchModeEnum {
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UPLIFTED_ONLY(true),
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UPLIFTED_AND_REF_JOIN(true),
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REF_JOIN_ONLY(false);
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@ -3119,11 +3087,8 @@ public class QueryStack {
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orValues.add(qp);
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}
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Set<LeafNodeDefinition> leafNodes = myChains.get(theSearchParams);
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if (leafNodes == null) {
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leafNodes = Sets.newHashSet();
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myChains.put(theSearchParams, leafNodes);
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}
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Set<LeafNodeDefinition> leafNodes =
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myChains.computeIfAbsent(theSearchParams, k -> Sets.newHashSet());
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leafNodes.add(new LeafNodeDefinition(
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nextSearchParam, orValues, nextTarget, nextParamName, "", qualifiersBranch));
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} else {
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@ -3244,16 +3209,11 @@ public class QueryStack {
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List<List<IQueryParameterType>> myAndOrParams;
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RequestDetails myRequest;
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RequestPartitionId myRequestPartitionId;
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ResourceTablePredicateBuilder myResourceTablePredicateBuilder;
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public static SearchForIdsParams with() {
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return new SearchForIdsParams();
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}
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public DbColumn[] getSourceJoinColumn() {
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return mySourceJoinColumn;
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}
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public SearchForIdsParams setSourceJoinColumn(DbColumn[] theSourceJoinColumn) {
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mySourceJoinColumn = theSourceJoinColumn;
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return this;
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@ -3277,10 +3237,6 @@ public class QueryStack {
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return this;
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}
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public List<List<IQueryParameterType>> getAndOrParams() {
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return myAndOrParams;
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}
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public SearchForIdsParams setAndOrParams(List<List<IQueryParameterType>> theAndOrParams) {
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myAndOrParams = theAndOrParams;
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return this;
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@ -3303,15 +3259,5 @@ public class QueryStack {
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myRequestPartitionId = theRequestPartitionId;
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return this;
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||||
}
|
||||
|
||||
public ResourceTablePredicateBuilder getResourceTablePredicateBuilder() {
|
||||
return myResourceTablePredicateBuilder;
|
||||
}
|
||||
|
||||
public SearchForIdsParams setResourceTablePredicateBuilder(
|
||||
ResourceTablePredicateBuilder theResourceTablePredicateBuilder) {
|
||||
myResourceTablePredicateBuilder = theResourceTablePredicateBuilder;
|
||||
return this;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@ -340,13 +340,11 @@ public class SearchBuilder implements ISearchBuilder<JpaPid> {
|
||||
continue;
|
||||
}
|
||||
List<List<IQueryParameterType>> andOrParams = myParams.get(nextParamName);
|
||||
Condition predicate = theQueryStack.searchForIdsWithAndOr(
|
||||
theRequest,
|
||||
with().setResourceName(myResourceName)
|
||||
.setParamName(nextParamName)
|
||||
.setAndOrParams(andOrParams)
|
||||
.setRequest(theRequest)
|
||||
.setRequestPartitionId(myRequestPartitionId));
|
||||
Condition predicate = theQueryStack.searchForIdsWithAndOr(with().setResourceName(myResourceName)
|
||||
.setParamName(nextParamName)
|
||||
.setAndOrParams(andOrParams)
|
||||
.setRequest(theRequest)
|
||||
.setRequestPartitionId(myRequestPartitionId));
|
||||
if (predicate != null) {
|
||||
theSearchSqlBuilder.addPredicate(predicate);
|
||||
}
|
||||
|
||||
@ -36,8 +36,6 @@ import com.healthmarketscience.sqlbuilder.Condition;
|
||||
import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
|
||||
import jakarta.annotation.Nullable;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import java.util.HashSet;
|
||||
@ -50,7 +48,6 @@ import static org.apache.commons.lang3.ObjectUtils.defaultIfNull;
|
||||
import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
||||
|
||||
public class ResourceIdPredicateBuilder extends BasePredicateBuilder {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(ResourceIdPredicateBuilder.class);
|
||||
|
||||
@Autowired
|
||||
private IIdHelperService<JpaPid> myIdHelperService;
|
||||
|
||||
@ -549,9 +549,8 @@ public class ResourceLinkPredicateBuilder extends BaseJoiningPredicateBuilder im
|
||||
List<Condition> andPredicates = new ArrayList<>();
|
||||
|
||||
List<List<IQueryParameterType>> chainParamValues = Collections.singletonList(orValues);
|
||||
andPredicates.add(childQueryFactory.searchForIdsWithAndOr(
|
||||
theRequest,
|
||||
with().setSourceJoinColumn(getJoinColumnsForTarget())
|
||||
andPredicates.add(
|
||||
childQueryFactory.searchForIdsWithAndOr(with().setSourceJoinColumn(getJoinColumnsForTarget())
|
||||
.setResourceName(subResourceName)
|
||||
.setParamName(chain)
|
||||
.setAndOrParams(chainParamValues)
|
||||
|
||||
@ -19,6 +19,7 @@
|
||||
*/
|
||||
package ca.uhn.fhir.jpa.search.builder.sql;
|
||||
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.search.builder.QueryStack;
|
||||
import ca.uhn.fhir.jpa.search.builder.predicate.CoordsPredicateBuilder;
|
||||
import ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder;
|
||||
@ -30,13 +31,12 @@ import ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder;
|
||||
import ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder;
|
||||
import ca.uhn.fhir.jpa.search.builder.predicate.UriPredicateBuilder;
|
||||
import ca.uhn.fhir.rest.api.RestSearchParameterTypeEnum;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import jakarta.annotation.Nonnull;
|
||||
|
||||
public class PredicateBuilderFactory {
|
||||
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(PredicateBuilderFactory.class);
|
||||
|
||||
@Nonnull
|
||||
public static ICanMakeMissingParamPredicate createPredicateBuilderForParamType(
|
||||
RestSearchParameterTypeEnum theParamType, SearchQueryBuilder theBuilder, QueryStack theQueryStack) {
|
||||
switch (theParamType) {
|
||||
@ -59,51 +59,40 @@ public class PredicateBuilderFactory {
|
||||
return createCoordsPredicateBuilder(theBuilder);
|
||||
case COMPOSITE:
|
||||
default:
|
||||
// we don't expect to see this
|
||||
ourLog.error("Invalid param type " + theParamType.name());
|
||||
return null;
|
||||
throw new InternalErrorException(Msg.code(2593) + "Invalid param type " + theParamType.name());
|
||||
}
|
||||
}
|
||||
|
||||
private static StringPredicateBuilder createStringPredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
StringPredicateBuilder sp = theBuilder.getSqlBuilderFactory().stringIndexTable(theBuilder);
|
||||
return sp;
|
||||
return theBuilder.getSqlBuilderFactory().stringIndexTable(theBuilder);
|
||||
}
|
||||
|
||||
private static NumberPredicateBuilder createNumberPredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
NumberPredicateBuilder np = theBuilder.getSqlBuilderFactory().numberIndexTable(theBuilder);
|
||||
return np;
|
||||
return theBuilder.getSqlBuilderFactory().numberIndexTable(theBuilder);
|
||||
}
|
||||
|
||||
private static QuantityPredicateBuilder createQuantityPredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
QuantityPredicateBuilder qp = theBuilder.getSqlBuilderFactory().quantityIndexTable(theBuilder);
|
||||
return qp;
|
||||
return theBuilder.getSqlBuilderFactory().quantityIndexTable(theBuilder);
|
||||
}
|
||||
|
||||
private static CoordsPredicateBuilder createCoordsPredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
CoordsPredicateBuilder cp = theBuilder.getSqlBuilderFactory().coordsPredicateBuilder(theBuilder);
|
||||
return cp;
|
||||
return theBuilder.getSqlBuilderFactory().coordsPredicateBuilder(theBuilder);
|
||||
}
|
||||
|
||||
private static TokenPredicateBuilder createTokenPredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
TokenPredicateBuilder tp = theBuilder.getSqlBuilderFactory().tokenIndexTable(theBuilder);
|
||||
return tp;
|
||||
return theBuilder.getSqlBuilderFactory().tokenIndexTable(theBuilder);
|
||||
}
|
||||
|
||||
private static DatePredicateBuilder createDatePredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
DatePredicateBuilder dp = theBuilder.getSqlBuilderFactory().dateIndexTable(theBuilder);
|
||||
return dp;
|
||||
return theBuilder.getSqlBuilderFactory().dateIndexTable(theBuilder);
|
||||
}
|
||||
|
||||
private static UriPredicateBuilder createUriPredicateBuilder(SearchQueryBuilder theBuilder) {
|
||||
UriPredicateBuilder up = theBuilder.getSqlBuilderFactory().uriIndexTable(theBuilder);
|
||||
return up;
|
||||
return theBuilder.getSqlBuilderFactory().uriIndexTable(theBuilder);
|
||||
}
|
||||
|
||||
private static ResourceLinkPredicateBuilder createReferencePredicateBuilder(
|
||||
QueryStack theQueryStack, SearchQueryBuilder theBuilder) {
|
||||
ResourceLinkPredicateBuilder retVal =
|
||||
theBuilder.getSqlBuilderFactory().referenceIndexTable(theQueryStack, theBuilder, false);
|
||||
return retVal;
|
||||
return theBuilder.getSqlBuilderFactory().referenceIndexTable(theQueryStack, theBuilder, false);
|
||||
}
|
||||
}
|
||||
|
||||
@ -177,7 +177,7 @@ public class InstanceReindexServiceImpl implements IInstanceReindexService {
|
||||
|
||||
List<String> messages = new ArrayList<>();
|
||||
|
||||
JpaPid pid = entity.getPersistentId();
|
||||
JpaPid pid = entity.getId();
|
||||
ReindexOutcome outcome = dao.reindex(pid, new ReindexParameters(), theRequestDetails, new TransactionDetails());
|
||||
messages.add("Reindex completed in " + sw);
|
||||
|
||||
|
||||
@ -3,6 +3,7 @@ package ca.uhn.fhir.jpa.search.builder;
|
||||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
|
||||
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
|
||||
import ca.uhn.fhir.jpa.model.dao.JpaPid;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.server.util.FhirContextSearchParamRegistry;
|
||||
import ca.uhn.fhir.rest.server.util.ISearchParamRegistry;
|
||||
@ -14,9 +15,12 @@ import org.mockito.Mock;
|
||||
import org.mockito.Spy;
|
||||
import org.mockito.junit.jupiter.MockitoExtension;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
import static org.junit.jupiter.api.Assertions.assertSame;
|
||||
import static org.mockito.Mockito.when;
|
||||
|
||||
@ExtendWith(MockitoExtension.class)
|
||||
@ -68,4 +72,58 @@ class SearchBuilderTest {
|
||||
assertThat(types).hasSize(146);
|
||||
}
|
||||
|
||||
@Test
|
||||
void testPartitionBySizeAndPartitionId_ReuseIfSmallEnoughAndAllSamePartition() {
|
||||
List<JpaPid> input = List.of(
|
||||
JpaPid.fromId(100L, 1),
|
||||
JpaPid.fromId(101L, 1)
|
||||
);
|
||||
Iterable<Collection<JpaPid>> actual = SearchBuilder.partitionBySizeAndPartitionId(input, 3);
|
||||
assertSame(input, actual.iterator().next());
|
||||
}
|
||||
|
||||
@Test
|
||||
void testPartitionBySizeAndPartitionId_Partitioned() {
|
||||
List<JpaPid> input = List.of(
|
||||
JpaPid.fromId(0L),
|
||||
JpaPid.fromId(1L),
|
||||
JpaPid.fromId(2L),
|
||||
JpaPid.fromId(3L),
|
||||
JpaPid.fromId(100L, 1),
|
||||
JpaPid.fromId(101L, 1),
|
||||
JpaPid.fromId(102L, 1),
|
||||
JpaPid.fromId(103L, 1),
|
||||
JpaPid.fromId(200L, 2),
|
||||
JpaPid.fromId(201L, 2),
|
||||
JpaPid.fromId(202L, 2),
|
||||
JpaPid.fromId(203L, 2)
|
||||
);
|
||||
|
||||
// Test
|
||||
Iterable<Collection<JpaPid>> actual = SearchBuilder.partitionBySizeAndPartitionId(input, 3);
|
||||
|
||||
// Verify
|
||||
assertThat(actual).asList().containsExactlyInAnyOrder(
|
||||
List.of(
|
||||
JpaPid.fromId(0L),
|
||||
JpaPid.fromId(1L),
|
||||
JpaPid.fromId(2L)),
|
||||
List.of(
|
||||
JpaPid.fromId(3L)),
|
||||
List.of(
|
||||
JpaPid.fromId(100L, 1),
|
||||
JpaPid.fromId(101L, 1),
|
||||
JpaPid.fromId(102L, 1)),
|
||||
List.of(
|
||||
JpaPid.fromId(103L, 1)),
|
||||
List.of(
|
||||
JpaPid.fromId(200L, 2),
|
||||
JpaPid.fromId(201L, 2),
|
||||
JpaPid.fromId(202L, 2)),
|
||||
List.of(
|
||||
JpaPid.fromId(203L, 2)
|
||||
)
|
||||
);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -8,6 +8,7 @@ import ca.uhn.fhir.jpa.fql.executor.IHfqlExecutor;
|
||||
import ca.uhn.fhir.jpa.fql.parser.HfqlStatement;
|
||||
import ca.uhn.fhir.jpa.fql.provider.HfqlRestProvider;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.test.utilities.LoggingExtension;
|
||||
import ca.uhn.fhir.test.utilities.server.RestfulServerExtension;
|
||||
import com.google.common.collect.Lists;
|
||||
import org.apache.commons.dbcp2.BasicDataSource;
|
||||
@ -68,6 +69,8 @@ public class JdbcDriverTest {
|
||||
public RestfulServerExtension myServer = new RestfulServerExtension(ourCtx)
|
||||
.registerProvider(myProvider)
|
||||
.registerInterceptor(ourHeaderCaptureInterceptor);
|
||||
@RegisterExtension
|
||||
public LoggingExtension myLoggingExtension = new LoggingExtension();
|
||||
|
||||
private BasicDataSource myDs;
|
||||
|
||||
|
||||
@ -180,8 +180,8 @@ public class MdmLinkUpdaterSvcImpl implements IMdmLinkUpdaterSvc {
|
||||
// with the link broken, the golden resource has delta info from a resource
|
||||
// that is no longer matched to it; we need to remove this delta. But it's
|
||||
// easier to just rebuild the resource from scratch using survivorship rules/current links
|
||||
goldenResource =
|
||||
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(goldenResource, mdmContext);
|
||||
goldenResource = myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(
|
||||
theParams.getRequestDetails(), goldenResource, mdmContext);
|
||||
}
|
||||
|
||||
if (myInterceptorBroadcaster.hasHooks(Pointcut.MDM_POST_UPDATE_LINK)) {
|
||||
|
||||
@ -72,7 +72,7 @@ public class FindCandidateByEidSvc extends BaseCandidateFinder {
|
||||
if (isNoMatch(foundGoldenResource, theIncomingResource)) {
|
||||
continue;
|
||||
}
|
||||
IResourcePersistentId pidOrNull =
|
||||
IResourcePersistentId<?> pidOrNull =
|
||||
myIdHelperService.getPidOrNull(RequestPartitionId.allPartitions(), foundGoldenResource);
|
||||
MatchedGoldenResourceCandidate mpc =
|
||||
new MatchedGoldenResourceCandidate(pidOrNull, MdmMatchOutcome.EID_MATCH);
|
||||
|
||||
@ -59,7 +59,6 @@ import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
import java.util.function.Function;
|
||||
import java.util.function.Supplier;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.slf4j.LoggerFactory.getLogger;
|
||||
|
||||
@ -10,7 +10,6 @@ import ca.uhn.fhir.mdm.api.MdmMatchResultEnum;
|
||||
import ca.uhn.fhir.model.primitive.IdDt;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import ca.uhn.fhir.test.utilities.RangeTestHelper;
|
||||
import ca.uhn.fhir.util.ParametersUtil;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
@ -82,7 +82,7 @@ class MdmSurvivorshipSvcImplIT extends BaseMdmR4Test {
|
||||
myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, frankPatient1, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
|
||||
myMdmLinkDaoSvc.createOrUpdateLinkEntity(goldenPatient, frankPatient2, MdmMatchOutcome.NEW_GOLDEN_RESOURCE_MATCH, MdmLinkSourceEnum.MANUAL, createContextForCreate("Patient"));
|
||||
|
||||
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(goldenPatient, new MdmTransactionContext(MdmTransactionContext.OperationType.UPDATE_LINK));
|
||||
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(mySrd, goldenPatient, new MdmTransactionContext(MdmTransactionContext.OperationType.UPDATE_LINK));
|
||||
}
|
||||
|
||||
@Test
|
||||
@ -169,7 +169,7 @@ class MdmSurvivorshipSvcImplIT extends BaseMdmR4Test {
|
||||
}
|
||||
|
||||
// test
|
||||
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(goldenPatient, transactionContext);
|
||||
myMdmSurvivorshipService.rebuildGoldenResourceWithSurvivorshipRules(mySrd, goldenPatient, transactionContext);
|
||||
|
||||
IBundleProvider provider = myPatientDao.search(new SearchParameterMap().setLoadSynchronous(true),
|
||||
new SystemRequestDetails().setRequestPartitionId(RequestPartitionId.allPartitions()));
|
||||
|
||||
@ -25,6 +25,7 @@ import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
|
||||
import ca.uhn.fhir.mdm.util.MdmPartitionHelper;
|
||||
import ca.uhn.fhir.mdm.util.MdmResourceUtil;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.Patient;
|
||||
@ -184,6 +185,7 @@ public class MdmSurvivorshipSvcImplTest {
|
||||
|
||||
// test
|
||||
Patient goldenPatientRebuilt = mySvc.rebuildGoldenResourceWithSurvivorshipRules(
|
||||
new SystemRequestDetails(),
|
||||
goldenPatient,
|
||||
createTransactionContext()
|
||||
);
|
||||
|
||||
@ -157,6 +157,8 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
|
||||
Parameters parameters = (Parameters) result.toParameters(myFhirContext, null);
|
||||
|
||||
ourLog.debug(myFhirContext.newXmlParser().setPrettyPrint(true).encodeResourceToString(parameters));
|
||||
logAllConcepts();
|
||||
logAllConceptProperties();
|
||||
|
||||
Optional<Coding> propertyValue = findProperty(parameters, "SCALE_TYP");
|
||||
assertThat(propertyValue).isPresent();
|
||||
|
||||
@ -184,6 +184,8 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
|
||||
mySearchParameterDao.update(sp, mySrd);
|
||||
|
||||
mySearchParamRegistry.forceRefresh();
|
||||
|
||||
assertNoRemainingPartitionIds();
|
||||
}
|
||||
|
||||
protected void createNonUniqueComboSp() {
|
||||
@ -288,6 +290,18 @@ public abstract class BasePartitioningR4Test extends BaseJpaR4SystemTest {
|
||||
};
|
||||
}
|
||||
|
||||
protected ICreationArgument withReadWritePartitions(Integer thePartitionId) {
|
||||
return t -> {
|
||||
if (thePartitionId != null) {
|
||||
addReadPartition(thePartitionId);
|
||||
addCreatePartition(thePartitionId, null);
|
||||
} else {
|
||||
addReadDefaultPartition();
|
||||
addCreateDefaultPartition();
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
@Interceptor
|
||||
public static class MyReadWriteInterceptor extends MyWriteInterceptor {
|
||||
|
||||
|
||||
@ -687,6 +687,9 @@ public class FhirResourceDaoCreatePlaceholdersR4Test extends BaseJpaR4Test {
|
||||
patient.setActive(true);
|
||||
myPatientDao.update(patient);
|
||||
|
||||
logAllResources();
|
||||
logAllResourceVersions();
|
||||
|
||||
// observation (with version 2)
|
||||
Observation obs = new Observation();
|
||||
obs.setId("Observation/DEF");
|
||||
|
||||
@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.model.util.SearchParamHash;
|
||||
import ca.uhn.fhir.jpa.model.util.UcumServiceUtil;
|
||||
import ca.uhn.fhir.jpa.reindex.ReindexStepV1Test;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.jpa.searchparam.submit.interceptor.SearchParamValidatingInterceptor;
|
||||
import ca.uhn.fhir.jpa.test.BaseJpaR4Test;
|
||||
import ca.uhn.fhir.rest.param.BaseParam;
|
||||
import ca.uhn.fhir.rest.param.DateParam;
|
||||
@ -79,6 +80,16 @@ public class FhirResourceDaoR4IndexStorageOptimizedTest extends BaseJpaR4Test {
|
||||
@Autowired
|
||||
private SearchConfig mySearchConfig;
|
||||
|
||||
@Override
|
||||
@BeforeEach
|
||||
public void before() throws Exception {
|
||||
super.before();
|
||||
|
||||
// We rely on this interceptor being in place, and it should be unless some cheeky other test
|
||||
// has removed it
|
||||
assertEquals(1, myInterceptorRegistry.getAllRegisteredInterceptors().stream().filter(t -> t instanceof SearchParamValidatingInterceptor).count());
|
||||
}
|
||||
|
||||
@AfterEach
|
||||
void cleanUp() {
|
||||
myPartitionSettings.setIncludePartitionInSearchHashes(false);
|
||||
|
||||
@ -1492,6 +1492,10 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
|
||||
return (OperationOutcome) e.getOperationOutcome();
|
||||
}
|
||||
break;
|
||||
case RDF:
|
||||
break;
|
||||
case NDJSON:
|
||||
break;
|
||||
}
|
||||
|
||||
throw new IllegalStateException(); // shouldn't get here
|
||||
@ -1502,8 +1506,6 @@ public class FhirResourceDaoR4ValidateTest extends BaseJpaR4Test {
|
||||
// setup
|
||||
IParser parser = myFhirContext.newJsonParser();
|
||||
|
||||
myLogbackTestExtension.setUp(Level.WARN);
|
||||
|
||||
String obsStr ="""
|
||||
{
|
||||
"resourceType": "Observation",
|
||||
|
||||
@ -4,6 +4,7 @@ import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import ca.uhn.fhir.jpa.model.config.PartitionSettings;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.jpa.searchparam.submit.interceptor.SearchParamValidatingInterceptor;
|
||||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
|
||||
import org.hl7.fhir.r4.model.Enumerations;
|
||||
@ -32,6 +33,10 @@ public class PartitioningNonNullDefaultPartitionR4Test extends BasePartitioningR
|
||||
super.before();
|
||||
|
||||
myPartitionSettings.setDefaultPartitionId(1);
|
||||
|
||||
// This test relies on this interceptor already being in place, which it should be unless
|
||||
// another test misbehaved
|
||||
assertEquals(1, myInterceptorRegistry.getAllRegisteredInterceptors().stream().filter(t->t instanceof SearchParamValidatingInterceptor).count());
|
||||
}
|
||||
|
||||
@AfterEach
|
||||
|
||||
@ -47,7 +47,7 @@ public class DeleteConflictServiceR4Test extends BaseJpaR4Test {
|
||||
|
||||
@AfterEach
|
||||
public void afterUnregisterInterceptor() {
|
||||
myInterceptorRegistry.unregisterAllInterceptors();
|
||||
myInterceptorRegistry.unregisterInterceptor(myDeleteInterceptor);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
||||
@ -6,7 +6,6 @@ import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.interceptor.api.Hook;
|
||||
import ca.uhn.fhir.interceptor.api.Pointcut;
|
||||
import ca.uhn.fhir.jpa.api.config.JpaStorageSettings;
|
||||
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
|
||||
import ca.uhn.fhir.jpa.entity.Search;
|
||||
import ca.uhn.fhir.jpa.model.entity.EntityIndexStatusEnum;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamString;
|
||||
@ -45,7 +44,6 @@ import org.hl7.fhir.r4.model.Reference;
|
||||
import org.hl7.fhir.r4.model.SearchParameter;
|
||||
import org.hl7.fhir.r4.model.SearchParameter.XPathUsageType;
|
||||
import org.hl7.fhir.r4.model.StringType;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.springframework.transaction.TransactionStatus;
|
||||
@ -70,15 +68,6 @@ public class ResourceProviderCustomSearchParamR4Test extends BaseResourceProvide
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderCustomSearchParamR4Test.class);
|
||||
|
||||
|
||||
@Override
|
||||
@AfterEach
|
||||
public void after() throws Exception {
|
||||
super.after();
|
||||
myStorageSettings.setDefaultSearchParamsCanBeOverridden(new JpaStorageSettings().isDefaultSearchParamsCanBeOverridden());
|
||||
myStorageSettings.setAllowContainsSearches(new JpaStorageSettings().isAllowContainsSearches());
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
@Override
|
||||
public void before() throws Exception {
|
||||
|
||||
@ -1441,6 +1441,7 @@ public class ResourceProviderR4EverythingTest extends BaseResourceProviderR4Test
|
||||
}
|
||||
|
||||
private List<IIdType> validateAndGetIdListFromBundle(Bundle theBundle, int theSize) {
|
||||
ourLog.info("Resource IDs: {}", theBundle.getEntry().stream().map(t->t.getResource().getIdElement().toUnqualifiedVersionless().getValue()).toList());
|
||||
assertEquals(Bundle.BundleType.SEARCHSET, theBundle.getType());
|
||||
assertThat(theBundle.getEntry()).hasSize(theSize);
|
||||
return toUnqualifiedVersionlessIds(theBundle);
|
||||
|
||||
@ -30,8 +30,6 @@ import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.junit.jupiter.api.extension.RegisterExtension;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.boot.test.mock.mockito.SpyBean;
|
||||
import org.springframework.context.annotation.Bean;
|
||||
@ -48,10 +46,9 @@ import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
|
||||
@ContextConfiguration(classes = {AsyncSubscriptionMessageSubmissionIT.SpringConfig.class})
|
||||
public class AsyncSubscriptionMessageSubmissionIT extends BaseSubscriptionsR4Test {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(AsyncSubscriptionMessageSubmissionIT.class);
|
||||
|
||||
@RegisterExtension
|
||||
public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension(AsyncResourceModifiedSubmitterSvc.class);
|
||||
public LogbackTestExtension myLogbackTestExtension = new LogbackTestExtension(AsyncResourceModifiedSubmitterSvc.class.getName(), Level.DEBUG);
|
||||
|
||||
@SpyBean
|
||||
IResourceModifiedConsumer myResourceModifiedConsumer;
|
||||
@ -98,8 +95,6 @@ public class AsyncSubscriptionMessageSubmissionIT extends BaseSubscriptionsR4Tes
|
||||
@Test
|
||||
public void runDeliveryPass_withManyResources_isBatchedAndKeepsResourceUsageDown() throws JsonProcessingException, InterruptedException {
|
||||
// setup
|
||||
myLogbackTestExtension.setUp(Level.DEBUG);
|
||||
|
||||
String resourceType = "Patient";
|
||||
int factor = 5;
|
||||
int numberOfResourcesToCreate = factor * AsyncResourceModifiedSubmitterSvc.MAX_LIMIT;
|
||||
|
||||
@ -1,16 +1,17 @@
|
||||
package ca.uhn.fhir.batch2.jobs.models;
|
||||
|
||||
import ca.uhn.fhir.batch2.jobs.chunk.TypedPidJson;
|
||||
import ca.uhn.fhir.util.JsonUtil;
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
class BatchResourceIdTest {
|
||||
class TypedPidJsonTest {
|
||||
|
||||
@Test
|
||||
public void testEstimateSize() {
|
||||
BatchResourceId id = new BatchResourceId();
|
||||
id.setId("12345");
|
||||
TypedPidJson id = new TypedPidJson();
|
||||
id.setPid("12345");
|
||||
id.setResourceType("Patient");
|
||||
String serialized = JsonUtil.serialize(id, false);
|
||||
assertEquals(serialized.length(), id.estimateSerializedSize(), serialized);
|
||||
|
||||
@ -7,6 +7,7 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.param.StringParam;
|
||||
import ca.uhn.fhir.util.HapiExtensions;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.instance.model.api.IPrimitiveType;
|
||||
import org.hl7.fhir.r5.model.BooleanType;
|
||||
@ -22,6 +23,7 @@ import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import jakarta.annotation.Nonnull;
|
||||
import java.util.List;
|
||||
import java.util.Objects;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
@ -344,7 +346,8 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private static List<Parameters.ParametersParameterComponent> findIndexes(Parameters theResponse, String theParamName, int theExpectedSize, String theSectionName) {
|
||||
private static List<Parameters.ParametersParameterComponent> findIndexes(Parameters theResponse, @Nonnull String theParamName, int theExpectedSize, String theSectionName) {
|
||||
Validate.notBlank(theParamName, "theParamName must not be blank");
|
||||
List<Parameters.ParametersParameterComponent> indexes = theResponse.getParameters(theSectionName);
|
||||
assertThat(indexes).hasSize(1);
|
||||
|
||||
@ -352,7 +355,7 @@ public class InstanceReindexServiceImplR5Test extends BaseJpaR5Test {
|
||||
.get(0)
|
||||
.getPart()
|
||||
.stream()
|
||||
.filter(t -> t.getName().equals(theParamName))
|
||||
.filter(t -> Objects.equals(theParamName, t.getName()))
|
||||
.toList();
|
||||
|
||||
assertThat(indexInstances).hasSize(theExpectedSize);
|
||||
|
||||
@ -20,6 +20,7 @@
|
||||
package ca.uhn.fhir.jpa.embedded;
|
||||
|
||||
import ca.uhn.fhir.jpa.migrate.DriverTypeEnum;
|
||||
import ca.uhn.fhir.jpa.migrate.util.SqlUtil;
|
||||
import jakarta.annotation.PreDestroy;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.slf4j.Logger;
|
||||
@ -29,10 +30,8 @@ import org.springframework.jdbc.core.JdbcTemplate;
|
||||
import java.sql.Connection;
|
||||
import java.sql.SQLException;
|
||||
import java.sql.Statement;
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.Map;
|
||||
import java.util.stream.Collectors;
|
||||
import javax.sql.DataSource;
|
||||
|
||||
/**
|
||||
@ -108,7 +107,7 @@ public abstract class JpaEmbeddedDatabase {
|
||||
}
|
||||
|
||||
public void executeSqlAsBatch(String theSql) {
|
||||
List<String> statements = Arrays.stream(theSql.split(";")).collect(Collectors.toList());
|
||||
List<String> statements = SqlUtil.splitSqlFileIntoStatements(theSql);
|
||||
executeSqlAsBatch(statements);
|
||||
}
|
||||
|
||||
|
||||
@ -419,6 +419,7 @@ public abstract class BaseJpaTest extends BaseTest {
|
||||
JpaStorageSettings defaultConfig = new JpaStorageSettings();
|
||||
myStorageSettings.setAccessMetaSourceInformationFromProvenanceTable(defaultConfig.isAccessMetaSourceInformationFromProvenanceTable());
|
||||
myStorageSettings.setAllowContainsSearches(defaultConfig.isAllowContainsSearches());
|
||||
myStorageSettings.setDefaultSearchParamsCanBeOverridden(defaultConfig.isDefaultSearchParamsCanBeOverridden());
|
||||
myStorageSettings.setDeleteEnabled(defaultConfig.isDeleteEnabled());
|
||||
myStorageSettings.setHibernateSearchIndexSearchParams(defaultConfig.isHibernateSearchIndexSearchParams());
|
||||
myStorageSettings.setHibernateSearchIndexFullText(defaultConfig.isHibernateSearchIndexFullText());
|
||||
@ -428,6 +429,7 @@ public abstract class BaseJpaTest extends BaseTest {
|
||||
myStorageSettings.setPreExpandValueSets(defaultConfig.isPreExpandValueSets());
|
||||
myStorageSettings.getTreatBaseUrlsAsLocal().clear();
|
||||
|
||||
|
||||
ParserOptions defaultParserOptions = new ParserOptions();
|
||||
myFhirContext.getParserOptions().setStripVersionsFromReferences(defaultParserOptions.isStripVersionsFromReferences());
|
||||
|
||||
|
||||
@ -75,15 +75,6 @@ public class HapiFhirJpaMigrationTasksTest {
|
||||
// Create migrator and initialize schema using a static version
|
||||
// of the schema from the 7.2.0 release
|
||||
HapiFhirJpaMigrationTasks tasks = new HapiFhirJpaMigrationTasks(Set.of());
|
||||
|
||||
// This is just logging to try and track down an intermittent failure
|
||||
for (VersionEnum next : VersionEnum.values()) {
|
||||
int size = tasks.getAllTasks(next).size();
|
||||
if (size > 0) {
|
||||
ourLog.info("Version {} has {} tasks", next, size);
|
||||
}
|
||||
}
|
||||
|
||||
HapiMigrator migrator = new HapiMigrator(MIGRATION_TABLE_NAME, myDataSource, DriverTypeEnum.H2_EMBEDDED);
|
||||
migrator.addTask(new InitializeSchemaTask("7.2.0", "20180115.0",
|
||||
new SchemaInitializationProvider(
|
||||
@ -142,30 +133,30 @@ public class HapiFhirJpaMigrationTasksTest {
|
||||
"""
|
||||
insert into
|
||||
HFJ_RESOURCE (
|
||||
RES_DELETED_AT,
|
||||
RES_VERSION,
|
||||
FHIR_ID,
|
||||
HAS_TAGS,
|
||||
RES_PUBLISHED,
|
||||
RES_UPDATED,
|
||||
SP_HAS_LINKS,
|
||||
HASH_SHA256,
|
||||
SP_INDEX_STATUS,
|
||||
RES_LANGUAGE,
|
||||
SP_CMPSTR_UNIQ_PRESENT,
|
||||
SP_COORDS_PRESENT,
|
||||
SP_DATE_PRESENT,
|
||||
SP_NUMBER_PRESENT,
|
||||
SP_QUANTITY_PRESENT,
|
||||
SP_STRING_PRESENT,
|
||||
SP_TOKEN_PRESENT,
|
||||
SP_URI_PRESENT,
|
||||
SP_QUANTITY_NRML_PRESENT,
|
||||
RES_TYPE,
|
||||
RES_VER,
|
||||
RES_ID)
|
||||
values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
|
||||
""",
|
||||
RES_DELETED_AT,
|
||||
RES_VERSION,
|
||||
FHIR_ID,
|
||||
HAS_TAGS,
|
||||
RES_PUBLISHED,
|
||||
RES_UPDATED,
|
||||
SP_HAS_LINKS,
|
||||
HASH_SHA256,
|
||||
SP_INDEX_STATUS,
|
||||
RES_LANGUAGE,
|
||||
SP_CMPSTR_UNIQ_PRESENT,
|
||||
SP_COORDS_PRESENT,
|
||||
SP_DATE_PRESENT,
|
||||
SP_NUMBER_PRESENT,
|
||||
SP_QUANTITY_PRESENT,
|
||||
SP_STRING_PRESENT,
|
||||
SP_TOKEN_PRESENT,
|
||||
SP_URI_PRESENT,
|
||||
SP_QUANTITY_NRML_PRESENT,
|
||||
RES_TYPE,
|
||||
RES_VER,
|
||||
RES_ID)
|
||||
values (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
|
||||
""",
|
||||
new AbstractLobCreatingPreparedStatementCallback(new DefaultLobHandler()) {
|
||||
@Override
|
||||
protected void setValues(@Nonnull PreparedStatement thePs, @Nonnull LobCreator theLobCreator) throws SQLException {
|
||||
|
||||
@ -24,7 +24,7 @@ import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
|
||||
|
||||
import java.util.Date;
|
||||
|
||||
public interface IMdmLink<T extends IResourcePersistentId> {
|
||||
public interface IMdmLink<T extends IResourcePersistentId<?>> {
|
||||
T getId();
|
||||
|
||||
IMdmLink<T> setId(T theId);
|
||||
|
||||
@ -20,6 +20,7 @@
|
||||
package ca.uhn.fhir.mdm.api;
|
||||
|
||||
import ca.uhn.fhir.mdm.model.MdmTransactionContext;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import org.hl7.fhir.instance.model.api.IBase;
|
||||
|
||||
/**
|
||||
@ -78,5 +79,5 @@ public interface IMdmSurvivorshipService {
|
||||
* @param <T> - Resource type to apply the survivorship rules to
|
||||
*/
|
||||
<T extends IBase> T rebuildGoldenResourceWithSurvivorshipRules(
|
||||
T theGoldenResource, MdmTransactionContext theMdmTransactionContext);
|
||||
RequestDetails theRequestDetails, T theGoldenResource, MdmTransactionContext theMdmTransactionContext);
|
||||
}
|
||||
|
||||
@ -41,7 +41,7 @@ import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
public interface IMdmLinkDao<P extends IResourcePersistentId, M extends IMdmLink<P>> {
|
||||
public interface IMdmLinkDao<P extends IResourcePersistentId<?>, M extends IMdmLink<P>> {
|
||||
int deleteWithAnyReferenceToPid(P thePid);
|
||||
|
||||
int deleteWithAnyReferenceToPidAndMatchResultNot(P thePid, MdmMatchResultEnum theMatchResult);
|
||||
|
||||
@ -36,6 +36,7 @@ import ca.uhn.fhir.mdm.model.MdmTransactionContext;
|
||||
import ca.uhn.fhir.mdm.model.mdmevents.MdmLinkJson;
|
||||
import ca.uhn.fhir.mdm.util.GoldenResourceHelper;
|
||||
import ca.uhn.fhir.rest.api.Constants;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.SystemRequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
|
||||
import ca.uhn.fhir.util.TerserUtil;
|
||||
@ -108,13 +109,13 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
|
||||
@SuppressWarnings({"rawtypes", "unchecked"})
|
||||
@Override
|
||||
public <T extends IBase> T rebuildGoldenResourceWithSurvivorshipRules(
|
||||
T theGoldenResourceBase, MdmTransactionContext theMdmTransactionContext) {
|
||||
RequestDetails theRequestDetails, T theGoldenResourceBase, MdmTransactionContext theMdmTransactionContext) {
|
||||
IBaseResource goldenResource = (IBaseResource) theGoldenResourceBase;
|
||||
|
||||
// we want a list of source ids linked to this
|
||||
// golden resource id; sorted and filtered for only MATCH results
|
||||
Stream<IBaseResource> sourceResources =
|
||||
getMatchedSourceIdsByLinkUpdateDate(goldenResource, theMdmTransactionContext);
|
||||
getMatchedSourceIdsByLinkUpdateDate(theRequestDetails, goldenResource, theMdmTransactionContext);
|
||||
|
||||
IBaseResource toSave = myGoldenResourceHelper.createGoldenResourceFromMdmSourceResource(
|
||||
(IAnyResource) goldenResource,
|
||||
@ -145,7 +146,9 @@ public class MdmSurvivorshipSvcImpl implements IMdmSurvivorshipService {
|
||||
|
||||
@SuppressWarnings("rawtypes")
|
||||
private Stream<IBaseResource> getMatchedSourceIdsByLinkUpdateDate(
|
||||
IBaseResource theGoldenResource, MdmTransactionContext theMdmTransactionContext) {
|
||||
RequestDetails theRequestDetails,
|
||||
IBaseResource theGoldenResource,
|
||||
MdmTransactionContext theMdmTransactionContext) {
|
||||
String resourceType = theGoldenResource.fhirType();
|
||||
IFhirResourceDao<?> dao = myDaoRegistry.getResourceDao(resourceType);
|
||||
|
||||
|
||||
@ -255,6 +255,8 @@ public class HapiMigrator {
|
||||
}
|
||||
|
||||
public void addTask(BaseTask theTask) {
|
||||
// Don't add a check for unit test mode here - We call this from
|
||||
// tests which expect tasks to always be added
|
||||
myTaskList.add(theTask);
|
||||
}
|
||||
|
||||
|
||||
@ -0,0 +1,49 @@
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR Server - SQL Migration
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2024 Smile CDR, Inc.
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
package ca.uhn.fhir.jpa.migrate.util;
|
||||
|
||||
import jakarta.annotation.Nonnull;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
|
||||
import java.util.Arrays;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
public class SqlUtil {
|
||||
|
||||
/**
|
||||
* Non instantiable
|
||||
*/
|
||||
private SqlUtil() {
|
||||
// nothing
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
public static List<String> splitSqlFileIntoStatements(String theSql) {
|
||||
String sqlWithoutComments = Arrays.stream(theSql.split("\n"))
|
||||
.filter(t -> !t.trim().startsWith("--"))
|
||||
.collect(Collectors.joining("\n"));
|
||||
|
||||
return Arrays.stream(sqlWithoutComments.split(";"))
|
||||
.filter(StringUtils::isNotBlank)
|
||||
.map(StringUtils::trim)
|
||||
.collect(Collectors.toList());
|
||||
}
|
||||
}
|
||||
@ -0,0 +1,31 @@
|
||||
package ca.uhn.fhir.jpa.migrate.util;
|
||||
|
||||
import org.junit.jupiter.api.Test;
|
||||
|
||||
import java.util.List;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.*;
|
||||
|
||||
class SqlUtilTest {
|
||||
|
||||
@Test
|
||||
public void testSplit() {
|
||||
String input = """
|
||||
select
|
||||
*
|
||||
-- COMMENT
|
||||
FROM FOO;
|
||||
|
||||
-- Also a comment
|
||||
|
||||
;
|
||||
select BLAH
|
||||
""";
|
||||
List<String> statements = SqlUtil.splitSqlFileIntoStatements(input);
|
||||
assertEquals(2, statements.size());
|
||||
assertEquals("select * FROM FOO", statements.get(0).replace("\n ", " "));
|
||||
assertEquals("select BLAH", statements.get(1).replace("\n ", " "));
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
@ -128,6 +128,13 @@ public class BulkDataExportProvider {
|
||||
@Autowired
|
||||
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
public BulkDataExportProvider() {
|
||||
super();
|
||||
}
|
||||
|
||||
/**
|
||||
* $export
|
||||
*/
|
||||
|
||||
@ -49,9 +49,7 @@ public class DeleteCodeSystemVersionStep
|
||||
throws JobExecutionFailedException {
|
||||
CodeSystemVersionPIDResult versionPidResult = theStepExecutionDetails.getData();
|
||||
|
||||
long versionId = versionPidResult.getCodeSystemVersionPID();
|
||||
|
||||
myITermCodeSystemSvc.deleteCodeSystemVersion(versionId);
|
||||
myITermCodeSystemSvc.deleteCodeSystemVersion(versionPidResult.getCodeSystemVersionPID());
|
||||
|
||||
theDataSink.accept(versionPidResult);
|
||||
return RunOutcome.SUCCESS;
|
||||
|
||||
@ -29,6 +29,7 @@ import ca.uhn.fhir.batch2.progress.InstanceProgress;
|
||||
import ca.uhn.fhir.batch2.progress.JobInstanceProgressCalculator;
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.model.api.IModelJson;
|
||||
import ca.uhn.fhir.model.primitive.InstantDt;
|
||||
import ca.uhn.fhir.util.JsonUtil;
|
||||
import ca.uhn.fhir.util.Logs;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
@ -66,9 +67,10 @@ public class ReductionStepDataSink<PT extends IModelJson, IT extends IModelJson,
|
||||
boolean changed = myJobPersistence.updateInstance(instanceId, instance -> {
|
||||
Validate.validState(
|
||||
StatusEnum.FINALIZE.equals(instance.getStatus()),
|
||||
"Job %s must be in FINALIZE state. In %s",
|
||||
"Job %s must be in FINALIZE state. In %s with update time %s",
|
||||
instanceId,
|
||||
instance.getStatus());
|
||||
instance.getStatus(),
|
||||
new InstantDt(instance.getUpdateTime()));
|
||||
|
||||
if (instance.getReport() != null) {
|
||||
// last in wins - so we won't throw
|
||||
|
||||
@ -482,7 +482,7 @@ public class JobMaintenanceServiceImplTest extends BaseBatch2Test {
|
||||
JobInstance instance = createInstance();
|
||||
instance.setCurrentGatedStepId(STEP_2);
|
||||
|
||||
myLogCapture.setUp(Level.ERROR);
|
||||
myLogCapture.setLoggerLevel(Level.ERROR);
|
||||
|
||||
// when
|
||||
doAnswer(args -> {
|
||||
|
||||
@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.api.model.ExpungeOutcome;
|
||||
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
|
||||
import ca.uhn.fhir.rest.api.server.storage.IResourceVersionPersistentId;
|
||||
import com.google.common.annotations.VisibleForTesting;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
@ -38,19 +39,20 @@ import java.util.concurrent.atomic.AtomicInteger;
|
||||
|
||||
@Component
|
||||
@Scope("prototype")
|
||||
public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(ExpungeService.class);
|
||||
public class ExpungeOperation<T extends IResourcePersistentId<?>, V extends IResourceVersionPersistentId>
|
||||
implements Callable<ExpungeOutcome> {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(ExpungeOperation.class);
|
||||
public static final String PROCESS_NAME = "Expunging";
|
||||
public static final String THREAD_PREFIX = "expunge";
|
||||
|
||||
@Autowired
|
||||
private IResourceExpungeService myResourceExpungeService;
|
||||
private IResourceExpungeService<T, V> myResourceExpungeService;
|
||||
|
||||
@Autowired
|
||||
private JpaStorageSettings myStorageSettings;
|
||||
|
||||
private final String myResourceName;
|
||||
private final IResourcePersistentId myResourceId;
|
||||
private final T myResourceId;
|
||||
private final ExpungeOptions myExpungeOptions;
|
||||
private final RequestDetails myRequestDetails;
|
||||
private final AtomicInteger myRemainingCount;
|
||||
@ -60,7 +62,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
|
||||
public ExpungeOperation(
|
||||
String theResourceName,
|
||||
IResourcePersistentId theResourceId,
|
||||
T theResourceId,
|
||||
ExpungeOptions theExpungeOptions,
|
||||
RequestDetails theRequestDetails) {
|
||||
myResourceName = theResourceName;
|
||||
@ -91,7 +93,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
}
|
||||
|
||||
private void expungeDeletedResources() {
|
||||
List<IResourcePersistentId> resourceIds = findHistoricalVersionsOfDeletedResources();
|
||||
List<T> resourceIds = findHistoricalVersionsOfDeletedResources();
|
||||
|
||||
deleteHistoricalVersions(resourceIds);
|
||||
if (expungeLimitReached()) {
|
||||
@ -101,8 +103,8 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
deleteCurrentVersionsOfDeletedResources(resourceIds);
|
||||
}
|
||||
|
||||
private List<IResourcePersistentId> findHistoricalVersionsOfDeletedResources() {
|
||||
List<IResourcePersistentId> retVal = getPartitionAwareSupplier()
|
||||
private List<T> findHistoricalVersionsOfDeletedResources() {
|
||||
List<T> retVal = getPartitionAwareSupplier()
|
||||
.supplyInPartitionedContext(() -> myResourceExpungeService.findHistoricalVersionsOfDeletedResources(
|
||||
myResourceName, myResourceId, myRemainingCount.get()));
|
||||
|
||||
@ -119,7 +121,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
}
|
||||
|
||||
private void expungeOldVersions() {
|
||||
List<IResourcePersistentId> historicalIds = getPartitionAwareSupplier()
|
||||
List<V> historicalIds = getPartitionAwareSupplier()
|
||||
.supplyInPartitionedContext(() -> myResourceExpungeService.findHistoricalVersionsOfNonDeletedResources(
|
||||
myResourceName, myResourceId, myRemainingCount.get()));
|
||||
|
||||
@ -144,7 +146,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
myRequestDetails);
|
||||
}
|
||||
|
||||
private void deleteCurrentVersionsOfDeletedResources(List<IResourcePersistentId> theResourceIds) {
|
||||
private void deleteCurrentVersionsOfDeletedResources(List<T> theResourceIds) {
|
||||
getPartitionRunner()
|
||||
.runInPartitionedThreads(
|
||||
theResourceIds,
|
||||
@ -152,7 +154,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
myRequestDetails, partition, myRemainingCount));
|
||||
}
|
||||
|
||||
private void deleteHistoricalVersions(List<IResourcePersistentId> theResourceIds) {
|
||||
private void deleteHistoricalVersions(List<T> theResourceIds) {
|
||||
getPartitionRunner()
|
||||
.runInPartitionedThreads(
|
||||
theResourceIds,
|
||||
@ -174,6 +176,7 @@ public class ExpungeOperation implements Callable<ExpungeOutcome> {
|
||||
myStorageSettings = theStorageSettings;
|
||||
}
|
||||
|
||||
@SuppressWarnings({"unchecked", "rawtypes"})
|
||||
@VisibleForTesting
|
||||
public void setExpungeDaoServiceForTesting(IResourceExpungeService theIResourceExpungeService) {
|
||||
myResourceExpungeService = theIResourceExpungeService;
|
||||
|
||||
@ -22,6 +22,7 @@ package ca.uhn.fhir.jpa.dao.expunge;
|
||||
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import jakarta.annotation.Nonnull;
|
||||
import org.apache.commons.lang3.Validate;
|
||||
|
||||
import java.util.function.Supplier;
|
||||
|
||||
@ -33,7 +34,6 @@ public class PartitionAwareSupplier {
|
||||
private final HapiTransactionService myTransactionService;
|
||||
private final RequestDetails myRequestDetails;
|
||||
|
||||
@Nonnull
|
||||
public PartitionAwareSupplier(HapiTransactionService theTxService, RequestDetails theRequestDetails) {
|
||||
myTransactionService = theTxService;
|
||||
myRequestDetails = theRequestDetails;
|
||||
@ -41,6 +41,9 @@ public class PartitionAwareSupplier {
|
||||
|
||||
@Nonnull
|
||||
public <T> T supplyInPartitionedContext(Supplier<T> theResourcePersistentIdSupplier) {
|
||||
return myTransactionService.withRequest(myRequestDetails).execute(tx -> theResourcePersistentIdSupplier.get());
|
||||
T retVal =
|
||||
myTransactionService.withRequest(myRequestDetails).execute(tx -> theResourcePersistentIdSupplier.get());
|
||||
Validate.notNull(retVal, "No resource persistent id supplied by supplier %s", theResourcePersistentIdSupplier);
|
||||
return retVal;
|
||||
}
|
||||
}
|
||||
|
||||
@ -22,7 +22,6 @@ package ca.uhn.fhir.jpa.dao.expunge;
|
||||
import ca.uhn.fhir.i18n.Msg;
|
||||
import ca.uhn.fhir.jpa.dao.tx.HapiTransactionService;
|
||||
import ca.uhn.fhir.rest.api.server.RequestDetails;
|
||||
import ca.uhn.fhir.rest.api.server.storage.IResourcePersistentId;
|
||||
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
|
||||
import ca.uhn.fhir.rest.server.exceptions.PreconditionFailedException;
|
||||
import ca.uhn.fhir.util.StopWatch;
|
||||
@ -83,8 +82,7 @@ public class PartitionRunner {
|
||||
myRequestDetails = theRequestDetails;
|
||||
}
|
||||
|
||||
public void runInPartitionedThreads(
|
||||
List<IResourcePersistentId> theResourceIds, Consumer<List<IResourcePersistentId>> partitionConsumer) {
|
||||
public <T> void runInPartitionedThreads(List<T> theResourceIds, Consumer<List<T>> partitionConsumer) {
|
||||
|
||||
List<Callable<Void>> runnableTasks = buildCallableTasks(theResourceIds, partitionConsumer);
|
||||
if (runnableTasks.size() == 0) {
|
||||
@ -134,8 +132,7 @@ public class PartitionRunner {
|
||||
}
|
||||
}
|
||||
|
||||
private List<Callable<Void>> buildCallableTasks(
|
||||
List<IResourcePersistentId> theResourceIds, Consumer<List<IResourcePersistentId>> partitionConsumer) {
|
||||
private <T> List<Callable<Void>> buildCallableTasks(List<T> theResourceIds, Consumer<List<T>> partitionConsumer) {
|
||||
List<Callable<Void>> retval = new ArrayList<>();
|
||||
|
||||
if (myBatchSize > theResourceIds.size()) {
|
||||
@ -143,10 +140,10 @@ public class PartitionRunner {
|
||||
} else {
|
||||
ourLog.info("Creating batch job of {} entries", theResourceIds.size());
|
||||
}
|
||||
List<List<IResourcePersistentId>> partitions = Lists.partition(theResourceIds, myBatchSize);
|
||||
List<List<T>> partitions = Lists.partition(theResourceIds, myBatchSize);
|
||||
|
||||
for (List<IResourcePersistentId> nextPartition : partitions) {
|
||||
if (nextPartition.size() > 0) {
|
||||
for (List<T> nextPartition : partitions) {
|
||||
if (!nextPartition.isEmpty()) {
|
||||
Callable<Void> callableTask = () -> {
|
||||
ourLog.info(myProcessName + " {} resources", nextPartition.size());
|
||||
partitionConsumer.accept(nextPartition);
|
||||
|
||||
@ -41,6 +41,7 @@ import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Arrays;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
@ -58,7 +59,7 @@ public abstract class BaseRequestPartitionHelperSvc implements IRequestPartition
|
||||
private IInterceptorBroadcaster myInterceptorBroadcaster;
|
||||
|
||||
@Autowired
|
||||
private PartitionSettings myPartitionSettings;
|
||||
PartitionSettings myPartitionSettings;
|
||||
|
||||
public BaseRequestPartitionHelperSvc() {
|
||||
myNonPartitionableResourceNames = new HashSet<>();
|
||||
@ -322,6 +323,19 @@ public abstract class BaseRequestPartitionHelperSvc implements IRequestPartition
|
||||
validateHasPartitionPermissions(theRequest, theResourceType, retVal);
|
||||
}
|
||||
|
||||
// Replace null partition ID with non-null default partition ID if one is being used
|
||||
if (myPartitionSettings.getDefaultPartitionId() != null
|
||||
&& retVal.hasPartitionIds()
|
||||
&& retVal.hasDefaultPartitionId()) {
|
||||
List<Integer> partitionIds = new ArrayList<>(retVal.getPartitionIds());
|
||||
for (int i = 0; i < partitionIds.size(); i++) {
|
||||
if (partitionIds.get(i) == null) {
|
||||
partitionIds.set(i, myPartitionSettings.getDefaultPartitionId());
|
||||
}
|
||||
}
|
||||
retVal = RequestPartitionId.fromPartitionIds(partitionIds);
|
||||
}
|
||||
|
||||
return retVal;
|
||||
}
|
||||
|
||||
|
||||
@ -187,7 +187,6 @@
|
||||
<plugin>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-tinder-plugin</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<executions>
|
||||
<execution>
|
||||
<id>generate</id>
|
||||
|
||||
@ -77,6 +77,13 @@ public class LogbackTestExtension implements BeforeEachCallback, AfterEachCallba
|
||||
this((Logger) theLogger);
|
||||
}
|
||||
|
||||
/**
|
||||
* Sets the root logger to the given level
|
||||
*/
|
||||
public LogbackTestExtension(Level theLevel) {
|
||||
this(org.slf4j.Logger.ROOT_LOGGER_NAME, theLevel);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns a copy to avoid concurrent modification errors.
|
||||
* @return A copy of the log events so far.
|
||||
@ -95,28 +102,49 @@ public class LogbackTestExtension implements BeforeEachCallback, AfterEachCallba
|
||||
|
||||
@Override
|
||||
public void beforeEach(ExtensionContext context) throws Exception {
|
||||
setUp();
|
||||
}
|
||||
|
||||
public void setUp() {
|
||||
setUp(myLevel);
|
||||
}
|
||||
|
||||
public void setUp(Level theLevel) {
|
||||
assert myListAppender == null;
|
||||
myListAppender = new ListAppender<>();
|
||||
myListAppender.start();
|
||||
myLogger.addAppender(myListAppender);
|
||||
|
||||
mySavedLevel = myLogger.getLevel();
|
||||
setLoggerLevel(myLevel);
|
||||
}
|
||||
|
||||
/**
|
||||
* Temporarily set the logger level - It will be reset after the current test method is done
|
||||
*/
|
||||
public void setLoggerLevel(Level theLevel) {
|
||||
if (theLevel != null) {
|
||||
mySavedLevel = myLogger.getLevel();
|
||||
myLogger.setLevel(theLevel);
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated Use {@link #setLoggerLevel(Level)} instead
|
||||
*/
|
||||
@Deprecated
|
||||
public void setUp(Level theLevel) {
|
||||
setLoggerLevel(theLevel);
|
||||
}
|
||||
|
||||
/**
|
||||
* @deprecated This class should be registered as a junit5 extension, and will be set
|
||||
* up automatically.
|
||||
*/
|
||||
@Deprecated
|
||||
public void setUp() {
|
||||
// nothing
|
||||
}
|
||||
|
||||
@Override
|
||||
public void afterEach(ExtensionContext context) throws Exception {
|
||||
myLogger.detachAppender(myListAppender);
|
||||
myListAppender.stop();
|
||||
if (myLevel != null) {
|
||||
if (myListAppender != null) {
|
||||
myLogger.detachAppender(myListAppender);
|
||||
myListAppender.stop();
|
||||
myListAppender = null;
|
||||
}
|
||||
if (mySavedLevel != null) {
|
||||
myLogger.setLevel(mySavedLevel);
|
||||
}
|
||||
}
|
||||
@ -130,4 +158,16 @@ public class LogbackTestExtension implements BeforeEachCallback, AfterEachCallba
|
||||
return getLogEvents().stream().map(ILoggingEvent::getMessage).toList();
|
||||
}
|
||||
|
||||
public void reRegister() throws Exception {
|
||||
afterEach(null);
|
||||
beforeEach(null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Predicate for passing to {@link #getLogEvents(Predicate)}
|
||||
*/
|
||||
public static Predicate<ILoggingEvent> atLeastLevel(Level theLevel) {
|
||||
return e -> e.getLevel().isGreaterOrEqual(theLevel);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -33,22 +33,20 @@ import org.junit.jupiter.api.extension.ExtensionContext;
|
||||
public class StaticLogbackTestExtension implements BeforeAllCallback, AfterAllCallback {
|
||||
private final LogbackTestExtension myLogbackTestExtension;
|
||||
|
||||
public StaticLogbackTestExtension(LogbackTestExtension theLogbackTestExtension) {
|
||||
myLogbackTestExtension = theLogbackTestExtension;
|
||||
}
|
||||
|
||||
public StaticLogbackTestExtension() {
|
||||
myLogbackTestExtension = new LogbackTestExtension();
|
||||
}
|
||||
|
||||
public static StaticLogbackTestExtension withThreshold(Level theLevel) {
|
||||
LogbackTestExtension logbackTestExtension = new LogbackTestExtension();
|
||||
logbackTestExtension.setUp(theLevel);
|
||||
ThresholdFilter thresholdFilter = new ThresholdFilter();
|
||||
thresholdFilter.setLevel(theLevel.levelStr);
|
||||
logbackTestExtension.getAppender().addFilter(thresholdFilter);
|
||||
public StaticLogbackTestExtension(String theLoggerName, Level theLevel) {
|
||||
myLogbackTestExtension = new LogbackTestExtension(theLoggerName, theLevel);
|
||||
}
|
||||
|
||||
return new StaticLogbackTestExtension(logbackTestExtension);
|
||||
public StaticLogbackTestExtension(Level theLevel) {
|
||||
myLogbackTestExtension = new LogbackTestExtension(theLevel);
|
||||
}
|
||||
|
||||
private StaticLogbackTestExtension(LogbackTestExtension theLogbackTestExtension) {
|
||||
myLogbackTestExtension = theLogbackTestExtension;
|
||||
}
|
||||
|
||||
@Override
|
||||
@ -65,4 +63,8 @@ public class StaticLogbackTestExtension implements BeforeAllCallback, AfterAllCa
|
||||
return myLogbackTestExtension;
|
||||
}
|
||||
|
||||
public static StaticLogbackTestExtension withThreshold(Level theLevel) {
|
||||
return new StaticLogbackTestExtension(theLevel);
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@ -130,7 +130,7 @@ public class TinderJpaRestServerMojo extends AbstractMojo {
|
||||
baseResourceNames.removeAll(excludeResourceNames);
|
||||
}
|
||||
|
||||
ourLog.info("Including the following resources: {}", baseResourceNames);
|
||||
ourLog.debug("Including the following resources: {}", baseResourceNames);
|
||||
|
||||
File configPackageDirectoryBase =
|
||||
new File(targetDirectory, configPackageBase.replace(".", File.separatorChar + ""));
|
||||
|
||||
@ -601,7 +601,7 @@ public abstract class BaseStructureParser {
|
||||
}
|
||||
|
||||
if (!actuallyWrite) {
|
||||
ourLog.info("Skipping writing already up-to-date file: {}", theFile.getAbsolutePath());
|
||||
ourLog.debug("Skipping writing already up-to-date file: {}", theFile.getAbsolutePath());
|
||||
return;
|
||||
}
|
||||
|
||||
|
||||
@ -98,7 +98,6 @@
|
||||
<plugin>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-tinder-plugin</artifactId>
|
||||
<version>${project.version}</version>
|
||||
<dependencies>
|
||||
<dependency>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
|
||||
@ -6,7 +6,7 @@ import org.junit.jupiter.api.Test;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
|
||||
public class TestParticulars {
|
||||
public class ParticularsTest {
|
||||
|
||||
@Test
|
||||
public void testElementsWithSpecialNames() {
|
||||
5
pom.xml
5
pom.xml
@ -2398,6 +2398,11 @@
|
||||
<build>
|
||||
<pluginManagement>
|
||||
<plugins>
|
||||
<plugin>
|
||||
<groupId>ca.uhn.hapi.fhir</groupId>
|
||||
<artifactId>hapi-tinder-plugin</artifactId>
|
||||
<version>${project.version}</version>
|
||||
</plugin>
|
||||
<plugin>
|
||||
<groupId>com.diffplug.spotless</groupId>
|
||||
<artifactId>spotless-maven-plugin</artifactId>
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user