Search Narrowing by Code Tweaks (#3453)
* Search narrowing tweaks * Search narrowing tweaks * Test * Test fixes * Try to fix LGTM * Add license headers * Test fixes * Test fixes
This commit is contained in:
James Agnew
GitHub
parent
0e9372775b
commit
ac80c7ffaa
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@ -25,7 +25,7 @@ public final class Msg {
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/**
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* IMPORTANT: Please update the following comment after you add a new code
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* Last code value: 2070
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* Last code value: 2071
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*/
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private Msg() {}
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@ -0,0 +1,5 @@
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---
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type: add
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issue: 3452
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title: "The JPA server terminology service can now process IS-A filters in ValueSet expansion on servers with
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Hibernate Search disabled."
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@ -1,5 +1,25 @@
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package ca.uhn.fhir.jpa.bulk.export.svc;
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/*-
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2022 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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@ -250,15 +250,15 @@ public class TermValueSet implements Serializable {
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@Override
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public String toString() {
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return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
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.append("myId", myId)
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.append("myUrl", myUrl)
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.append(myResource != null ? ("myResource=" + myResource.toString()) : ("myResource=(null)"))
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.append("myResourcePid", myResourcePid)
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.append("myName", myName)
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.append(myConcepts != null ? ("myConcepts - size=" + myConcepts.size()) : ("myConcepts=(null)"))
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.append("myTotalConcepts", myTotalConcepts)
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.append("myTotalConceptDesignations", myTotalConceptDesignations)
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.append("myExpansionStatus", myExpansionStatus)
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.append("id", myId)
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.append("url", myUrl)
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.append(myResource != null ? ("resource=" + myResource.toString()) : ("resource=(null)"))
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.append("resourcePid", myResourcePid)
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.append("name", myName)
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.append(myConcepts != null ? ("concepts - size=" + myConcepts.size()) : ("concepts=(null)"))
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.append("totalConcepts", myTotalConcepts)
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.append("totalConceptDesignations", myTotalConceptDesignations)
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.append("expansionStatus", myExpansionStatus)
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.toString();
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}
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}
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@ -1,5 +1,25 @@
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package ca.uhn.fhir.jpa.search.autocomplete;
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/*-
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2022 Smile CDR, Inc.
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import com.google.gson.JsonObject;
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import org.apache.commons.lang3.Validate;
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@ -132,7 +132,6 @@ import org.hl7.fhir.r4.model.IntegerType;
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import org.hl7.fhir.r4.model.StringType;
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import org.hl7.fhir.r4.model.ValueSet;
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import org.hl7.fhir.r4.model.codesystems.ConceptSubsumptionOutcome;
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import org.jetbrains.annotations.NotNull;
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import org.quartz.JobExecutionContext;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.context.ApplicationContext;
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@ -305,26 +304,32 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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}
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private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, boolean theAdd, String theCodeSystem, String theCodeSystemVersion, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids, Collection<TermConceptDesignation> theDesignations) {
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private boolean addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, boolean theAdd, String theCodeSystem, String theCodeSystemVersion, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids, Collection<TermConceptDesignation> theDesignations) {
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if (StringUtils.isNotEmpty(theCodeSystemVersion)) {
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if (isNoneBlank(theCodeSystem, theCode)) {
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if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
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theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem + "|" + theCodeSystemVersion, theCode, theDisplay, theDesignations, theSourceConceptPid, theSourceConceptDirectParentPids, theCodeSystemVersion);
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return true;
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}
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if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode)) {
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theValueSetCodeAccumulator.excludeConcept(theCodeSystem + "|" + theCodeSystemVersion, theCode);
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return true;
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}
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}
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} else {
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if (theAdd && theAddedCodes.add(theCodeSystem + "|" + theCode)) {
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theValueSetCodeAccumulator.includeConceptWithDesignations(theCodeSystem, theCode, theDisplay, theDesignations, theSourceConceptPid, theSourceConceptDirectParentPids, theCodeSystemVersion);
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return true;
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}
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if (!theAdd && theAddedCodes.remove(theCodeSystem + "|" + theCode)) {
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theValueSetCodeAccumulator.excludeConcept(theCodeSystem, theCode);
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return true;
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}
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}
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return false;
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}
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private boolean addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, Collection<TermConceptDesignation> theDesignations, boolean theAdd, String theCodeSystem, String theCode, String theDisplay, Long theSourceConceptPid, String theSourceConceptDirectParentPids, String theSystemVersion) {
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@ -1302,18 +1307,27 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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private void handleFilterConceptAndCode(String theSystem, SearchPredicateFactory f, BooleanPredicateClausesStep<?> b, ValueSet.ConceptSetFilterComponent theFilter) {
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TermConcept code = findCode(theSystem, theFilter.getValue())
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.orElseThrow(() -> new InvalidRequestException("Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
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TermConcept code = findCodeForFilterCriteria(theSystem, theFilter);
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if (theFilter.getOp() == ValueSet.FilterOperator.ISA) {
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ourLog.debug(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
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b.must(f.match().field("myParentPids").matching("" + code.getId()));
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} else {
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throw new InvalidRequestException(Msg.code(894) + "Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty());
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throwInvalidFilter(theFilter, "");
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}
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}
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@Nonnull
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private TermConcept findCodeForFilterCriteria(String theSystem, ValueSet.ConceptSetFilterComponent theFilter) {
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return findCode(theSystem, theFilter.getValue())
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.orElseThrow(() -> new InvalidRequestException(Msg.code(2071) + "Invalid filter criteria - code does not exist: {" + Constants.codeSystemWithDefaultDescription(theSystem) + "}" + theFilter.getValue()));
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}
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private void throwInvalidFilter(ValueSet.ConceptSetFilterComponent theFilter, String theErrorSuffix) {
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throw new InvalidRequestException(Msg.code(894) + "Don't know how to handle op=" + theFilter.getOp() + " on property " + theFilter.getProperty() + theErrorSuffix);
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}
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private void isCodeSystemLoincOrThrowInvalidRequestException(String theSystemIdentifier, String theProperty) {
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String systemUrl = getUrlFromIdentifier(theSystemIdentifier);
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if (!isCodeSystemLoinc(systemUrl)) {
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@ -1499,9 +1513,27 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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Validate.isTrue(((ValueSetExpansionComponentWithConceptAccumulator) theValueSetCodeAccumulator).getParameter().isEmpty(), "Can not expand ValueSet with parameters - Hibernate Search is not enabled on this server.");
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}
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Validate.isTrue(theInclude.getFilter().isEmpty(), "Can not expand ValueSet with filters - Hibernate Search is not enabled on this server.");
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Validate.isTrue(isNotBlank(theSystem), "Can not expand ValueSet without explicit system - Hibernate Search is not enabled on this server.");
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for (ValueSet.ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
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boolean handled = false;
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switch (nextFilter.getProperty()) {
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case "concept":
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case "code":
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if (nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
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theValueSetCodeAccumulator.addMessage("Processing IS-A filter in database - Note that Hibernate Search is not enabled on this server, so this operation can be inefficient.");
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TermConcept code = findCodeForFilterCriteria(theSystem, nextFilter);
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addConceptAndChildren(theValueSetCodeAccumulator, theAddedCodes, theInclude, theSystem, theAdd, code);
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handled = true;
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}
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break;
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}
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if (!handled) {
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throwInvalidFilter(nextFilter, " - Note that Hibernate Search is disabled on this server so not all ValueSet expansion funtionality is available.");
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}
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}
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if (theInclude.getConcept().isEmpty()) {
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Collection<TermConcept> concepts = myConceptDao.fetchConceptsAndDesignationsByVersionPid(theVersion.getPid());
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@ -1531,6 +1563,15 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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}
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private void addConceptAndChildren(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, ValueSet.ConceptSetComponent theInclude, String theSystem, boolean theAdd, TermConcept theConcept) {
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for (TermConcept nextChild : theConcept.getChildCodes()) {
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boolean added = addCodeIfNotAlreadyAdded(theValueSetCodeAccumulator, theAddedCodes, theAdd, theSystem, theInclude.getVersion(), nextChild.getCode(), nextChild.getDisplay(), nextChild.getId(), nextChild.getParentPidsAsString(), nextChild.getDesignations());
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if (added) {
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addConceptAndChildren(theValueSetCodeAccumulator, theAddedCodes, theInclude, theSystem, theAdd, nextChild);
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}
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}
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}
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@Override
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@Transactional
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public String invalidatePreCalculatedExpansion(IIdType theValueSetId, RequestDetails theRequestDetails) {
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@ -1925,21 +1966,21 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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expandValueSet(options, valueSet, accumulator);
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// We are done with this ValueSet.
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txTemplate.execute(t -> {
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txTemplate.executeWithoutResult(t -> {
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valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.EXPANDED);
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valueSetToExpand.setExpansionTimestamp(new Date());
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myTermValueSetDao.saveAndFlush(valueSetToExpand);
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return null;
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});
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ourLog.info("Pre-expanded ValueSet[{}] with URL[{}] - Saved {} concepts in {}", valueSet.getId(), valueSet.getUrl(), accumulator.getConceptsSaved(), sw);
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} catch (Exception e) {
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ourLog.error("Failed to pre-expand ValueSet: " + e.getMessage(), e);
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txTemplate.execute(t -> {
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txTemplate.executeWithoutResult(t -> {
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valueSetToExpand.setExpansionStatus(TermValueSetPreExpansionStatusEnum.FAILED_TO_EXPAND);
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myTermValueSetDao.saveAndFlush(valueSetToExpand);
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return null;
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});
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}
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}
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@ -2181,7 +2222,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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return result;
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} else {
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return null;
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return new LookupCodeResult()
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.setFound(false);
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}
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});
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}
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@ -189,17 +189,25 @@ public class ValueSetExpansionComponentWithConceptAccumulator extends ValueSet.V
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Integer capacityRemaining = getCapacityRemaining();
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if (capacityRemaining == 0) {
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String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionTooLarge", myMaxCapacity);
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msg = appendAccumulatorMessages(msg);
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throw new ExpansionTooCostlyException(Msg.code(831) + msg);
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}
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if (myHardExpansionMaximumSize > 0 && myAddedConcepts > myHardExpansionMaximumSize) {
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String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "expansionTooLarge", myHardExpansionMaximumSize);
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msg = appendAccumulatorMessages(msg);
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throw new ExpansionTooCostlyException(Msg.code(832) + msg);
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}
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myAddedConcepts++;
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}
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@Nonnull
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private String appendAccumulatorMessages(String msg) {
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msg += getMessages().stream().map(t->" - " + t).collect(Collectors.joining());
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return msg;
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}
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public Integer getTotalConcepts() {
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return myTotalConcepts;
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}
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@ -62,8 +62,8 @@ public class CustomTerminologySet {
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myRootConcepts = theRootConcepts;
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}
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public void addRootConcept(String theCode) {
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addRootConcept(theCode, null);
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public TermConcept addRootConcept(String theCode) {
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return addRootConcept(theCode, null);
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}
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public TermConcept addRootConcept(String theCode, String theDisplay) {
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@ -25,6 +25,7 @@ import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptDesignationDao;
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import ca.uhn.fhir.jpa.dao.data.ITermConceptPropertyDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptDesignation;
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import ca.uhn.fhir.jpa.entity.TermConceptProperty;
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@ -187,6 +188,8 @@ public abstract class BaseJpaTest extends BaseTest {
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@Autowired
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protected ITermValueSetConceptDao myTermValueSetConceptDao;
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@Autowired
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protected ITermValueSetDao myTermValueSetDao;
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@Autowired
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protected ITermConceptDesignationDao myTermConceptDesignationDao;
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@Autowired
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protected ITermConceptPropertyDao myTermConceptPropertyDao;
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@ -355,6 +358,14 @@ public abstract class BaseJpaTest extends BaseTest {
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});
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}
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protected int logAllValueSets() {
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return runInTransaction(() -> {
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List<TermValueSet> valueSets = myTermValueSetDao.findAll();
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ourLog.info("ValueSets:\n * {}", valueSets.stream().map(t -> t.toString()).collect(Collectors.joining("\n * ")));
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return valueSets.size();
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});
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}
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protected int logAllForcedIds() {
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return runInTransaction(() -> {
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List<ForcedId> forcedIds = myForcedIdDao.findAll();
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@ -49,6 +49,7 @@ import java.util.Set;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.containsStringIgnoringCase;
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import static org.hamcrest.Matchers.empty;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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@ -729,7 +730,8 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
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myObservationDao.search(params).size();
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fail();
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} catch (InternalErrorException e) {
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assertEquals(Msg.code(885) + "Expansion of ValueSet produced too many codes (maximum 1) - Operation aborted!", e.getMessage());
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assertThat(e.getMessage(), containsString(Msg.code(885) + "Expansion of ValueSet produced too many codes (maximum 1) - Operation aborted!"));
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}
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}
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@ -49,6 +49,7 @@ import java.util.stream.Collectors;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.containsInAnyOrder;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.containsStringIgnoringCase;
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import static org.hamcrest.Matchers.empty;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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@ -873,7 +874,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
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myObservationDao.search(params).size();
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fail();
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} catch (InternalErrorException e) {
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assertEquals(Msg.code(885) + "Expansion of ValueSet produced too many codes (maximum 1) - Operation aborted!", e.getMessage());
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assertThat(e.getMessage(), containsString(Msg.code(885) + "Expansion of ValueSet produced too many codes (maximum 1) - Operation aborted!"));
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}
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}
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@ -6,6 +6,9 @@ import ca.uhn.fhir.context.support.ValidationSupportContext;
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import ca.uhn.fhir.context.support.ValueSetExpansionOptions;
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import ca.uhn.fhir.i18n.Msg;
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import ca.uhn.fhir.jpa.api.config.DaoConfig;
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import ca.uhn.fhir.jpa.entity.TermConcept;
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import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
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import ca.uhn.fhir.jpa.term.BaseTermReadSvcImpl;
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import ca.uhn.fhir.jpa.term.custom.CustomTerminologySet;
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import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
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import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
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@ -29,9 +32,11 @@ import java.io.IOException;
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import static org.hamcrest.MatcherAssert.assertThat;
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import static org.hamcrest.Matchers.containsString;
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import static org.hamcrest.Matchers.startsWith;
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import static org.hamcrest.Matchers.stringContainsInOrder;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertFalse;
|
||||
import static org.junit.jupiter.api.Assertions.assertNotNull;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
|
||||
|
|
@ -43,6 +48,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
|
|||
|
||||
@AfterEach
|
||||
public void after() {
|
||||
BaseTermReadSvcImpl.setForceDisableHibernateSearchForUnitTest(false);
|
||||
myDaoConfig.setPreExpandValueSets(new DaoConfig().isPreExpandValueSets());
|
||||
myDaoConfig.setMaximumExpansionSize(new DaoConfig().getMaximumExpansionSize());
|
||||
}
|
||||
|
|
@ -91,6 +97,210 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
|
|||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testValidateCodeInValueSet_HierarchicalAndEnumeratedValueset() {
|
||||
myValueSetDao.delete(myExtensionalVsId);
|
||||
|
||||
ourLog.info("Creating CodeSystem");
|
||||
CodeSystem cs = new CodeSystem();
|
||||
cs.setId("CodeSystem/cs");
|
||||
cs.setUrl("http://cs");
|
||||
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
myCodeSystemDao.update(cs);
|
||||
|
||||
ourLog.info("Adding codes to codesystem");
|
||||
CustomTerminologySet delta = new CustomTerminologySet();
|
||||
TermConcept parent = delta.addRootConcept("parent");
|
||||
for (int j = 0; j < 1200; j++) {
|
||||
parent
|
||||
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA)
|
||||
.setCode("child" + j);
|
||||
}
|
||||
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://cs", delta);
|
||||
|
||||
ourLog.info("Creating ValueSet");
|
||||
ValueSet vs = new ValueSet();
|
||||
vs.setId("ValueSet/vs");
|
||||
vs.setUrl("http://vs");
|
||||
vs.getCompose()
|
||||
.addInclude()
|
||||
.setSystem("http://cs")
|
||||
.addFilter()
|
||||
.setProperty("concept")
|
||||
.setOp(ValueSet.FilterOperator.ISA)
|
||||
.setValue("parent");
|
||||
vs.getCompose()
|
||||
.addInclude()
|
||||
.setSystem("http://cs-np")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code0")))
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code1")));
|
||||
myValueSetDao.update(vs);
|
||||
|
||||
IValidationSupport.CodeValidationResult outcome;
|
||||
ValidationSupportContext ctx = new ValidationSupportContext(myValidationSupport);
|
||||
ConceptValidationOptions options = new ConceptValidationOptions();
|
||||
|
||||
// In memory - Hierarchy in existing CS
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "child10", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertEquals("Code was validated against in-memory expansion of ValueSet: http://vs", outcome.getMessage());
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "childX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertEquals("Unknown code 'http://cs#childX' for in-memory expansion of ValueSet 'http://vs'", outcome.getMessage());
|
||||
|
||||
// In memory - Enumerated in non-present CS
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "code1", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertEquals("Code was validated against in-memory expansion of ValueSet: http://vs", outcome.getMessage());
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "codeX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertEquals("Unknown code 'http://cs-np#codeX' for in-memory expansion of ValueSet 'http://vs'", outcome.getMessage());
|
||||
|
||||
// Precalculated
|
||||
|
||||
myTerminologyDeferredStorageSvc.saveAllDeferred();
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
logAllValueSets();
|
||||
myCachingValidationSupport.invalidateCaches();
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "child10", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), startsWith("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "childX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), containsString("Unknown code http://cs#childX"));
|
||||
assertThat(outcome.getMessage(), containsString("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
// Precalculated - Enumerated in non-present CS
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "code1", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), startsWith("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "codeX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), containsString("Unknown code http://cs-np#codeX"));
|
||||
assertThat(outcome.getMessage(), containsString("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeInValueSet_HierarchicalAndEnumeratedValueset_HibernateSearchDisabled() {
|
||||
BaseTermReadSvcImpl.setForceDisableHibernateSearchForUnitTest(true);
|
||||
|
||||
myValueSetDao.delete(myExtensionalVsId);
|
||||
|
||||
ourLog.info("Creating CodeSystem");
|
||||
CodeSystem cs = new CodeSystem();
|
||||
cs.setId("CodeSystem/cs");
|
||||
cs.setUrl("http://cs");
|
||||
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
|
||||
cs.setStatus(Enumerations.PublicationStatus.ACTIVE);
|
||||
myCodeSystemDao.update(cs);
|
||||
|
||||
ourLog.info("Adding codes to codesystem");
|
||||
CustomTerminologySet delta = new CustomTerminologySet();
|
||||
TermConcept parent = delta.addRootConcept("parent");
|
||||
for (int j = 0; j < 1200; j++) {
|
||||
parent
|
||||
.addChild(TermConceptParentChildLink.RelationshipTypeEnum.ISA)
|
||||
.setCode("child" + j);
|
||||
}
|
||||
myTermCodeSystemStorageSvc.applyDeltaCodeSystemsAdd("http://cs", delta);
|
||||
|
||||
ourLog.info("Creating ValueSet");
|
||||
ValueSet vs = new ValueSet();
|
||||
vs.setId("ValueSet/vs");
|
||||
vs.setUrl("http://vs");
|
||||
vs.getCompose()
|
||||
.addInclude()
|
||||
.setSystem("http://cs")
|
||||
.addFilter()
|
||||
.setProperty("concept")
|
||||
.setOp(ValueSet.FilterOperator.ISA)
|
||||
.setValue("parent");
|
||||
vs.getCompose()
|
||||
.addInclude()
|
||||
.setSystem("http://cs-np")
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code0")))
|
||||
.addConcept(new ValueSet.ConceptReferenceComponent(new CodeType("code1")));
|
||||
myValueSetDao.update(vs);
|
||||
|
||||
IValidationSupport.CodeValidationResult outcome;
|
||||
ValidationSupportContext ctx = new ValidationSupportContext(myValidationSupport);
|
||||
ConceptValidationOptions options = new ConceptValidationOptions();
|
||||
|
||||
// In memory - Hierarchy in existing CS
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "child10", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertEquals("Code was validated against in-memory expansion of ValueSet: http://vs", outcome.getMessage());
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "childX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertEquals("Unknown code 'http://cs#childX' for in-memory expansion of ValueSet 'http://vs'", outcome.getMessage());
|
||||
|
||||
// In memory - Enumerated in non-present CS
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "code1", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertEquals("Code was validated against in-memory expansion of ValueSet: http://vs", outcome.getMessage());
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "codeX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertEquals("Unknown code 'http://cs-np#codeX' for in-memory expansion of ValueSet 'http://vs'", outcome.getMessage());
|
||||
|
||||
// Precalculated
|
||||
|
||||
myTerminologyDeferredStorageSvc.saveAllDeferred();
|
||||
myTermSvc.preExpandDeferredValueSetsToTerminologyTables();
|
||||
logAllValueSets();
|
||||
myCachingValidationSupport.invalidateCaches();
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "child10", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), startsWith("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs", "childX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), containsString("Unknown code http://cs#childX"));
|
||||
assertThat(outcome.getMessage(), containsString("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
// Precalculated - Enumerated in non-present CS
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "code1", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertTrue(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), startsWith("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
outcome = myValidationSupport.validateCode(ctx, options, "http://cs-np", "codeX", null, "http://vs");
|
||||
assertNotNull(outcome);
|
||||
assertFalse(outcome.isOk());
|
||||
assertThat(outcome.getMessage(), containsString("Unknown code http://cs-np#codeX"));
|
||||
assertThat(outcome.getMessage(), containsString("Code validation occurred using a ValueSet expansion that was pre-calculated at "));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testValidateCodeOperationNoValueSet() {
|
||||
UriType valueSetIdentifier = null;
|
||||
|
|
@ -288,7 +498,8 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
|
|||
myValueSetDao.expand(vs, null);
|
||||
fail();
|
||||
} catch (InternalErrorException e) {
|
||||
assertEquals(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!", e.getMessage());
|
||||
assertThat(e.getMessage(), containsString(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!"));
|
||||
assertThat(e.getMessage(), containsString("Performing in-memory expansion"));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -340,7 +551,7 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
|
|||
"28571000087109",
|
||||
"MODERNA COVID-19 mRNA-1273",
|
||||
vs
|
||||
);
|
||||
);
|
||||
assertTrue(outcome.isOk());
|
||||
|
||||
ValueSet expansion = myValueSetDao.expand(new IdType("ValueSet/vaccinecode"), new ValueSetExpansionOptions(), mySrd);
|
||||
|
|
@ -349,7 +560,6 @@ public class FhirResourceDaoR4ValueSetTest extends BaseJpaR4Test {
|
|||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -258,7 +258,7 @@ public class FhirResourceDaoR5ValueSetTest extends BaseJpaR5Test {
|
|||
myValueSetDao.expand(vs, null);
|
||||
fail();
|
||||
} catch (InternalErrorException e) {
|
||||
assertEquals(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!", e.getMessage());
|
||||
assertThat(e.getMessage(), containsString(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!"));
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -686,23 +686,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandLocalVsWithUnknownCode() {
|
||||
createExternalCsAndLocalVsWithUnknownCode();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
try {
|
||||
ourClient
|
||||
.operation()
|
||||
.onInstance(myLocalValueSetId)
|
||||
.named("expand")
|
||||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
/**
|
||||
* #516
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -749,7 +749,7 @@ public class ResourceProviderR4ValueSetNoVerCSNoVerTest extends BaseResourceProv
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
assertEquals("HTTP 400 Bad Request: HAPI-2071: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -661,7 +661,7 @@ public class ResourceProviderR4ValueSetVerCSNoVerTest extends BaseResourceProvid
|
|||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
assertEquals("HTTP 400 Bad Request: HAPI-2071: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -946,23 +946,6 @@ public class ResourceProviderR5ValueSetTest extends BaseResourceProviderR5Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandLocalVsWithUnknownCode() {
|
||||
createExternalCsAndLocalVsWithUnknownCode();
|
||||
assertNotNull(myLocalValueSetId);
|
||||
|
||||
try {
|
||||
myClient
|
||||
.operation()
|
||||
.onInstance(myLocalValueSetId)
|
||||
.named("expand")
|
||||
.withNoParameters(Parameters.class)
|
||||
.execute();
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandValueSetBasedOnCodeSystemWithChangedUrl() {
|
||||
|
||||
|
|
|
|||
|
|
@ -68,6 +68,7 @@ import static ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc.MAKE_LOADING_VE
|
|||
import static ca.uhn.fhir.jpa.term.api.ITermLoaderSvc.LOINC_URI;
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.containsInAnyOrder;
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.hl7.fhir.common.hapi.validation.support.ValidationConstants.LOINC_LOW;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
|
@ -1432,7 +1433,7 @@ public abstract class AbstractValueSetFreeTextExpansionR4Test extends BaseJpaTes
|
|||
myTermSvc.expandValueSet(null, vs);
|
||||
fail();
|
||||
} catch (InternalErrorException e) {
|
||||
assertEquals(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!", e.getMessage());
|
||||
assertThat(e.getMessage(), containsString(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!"));
|
||||
}
|
||||
|
||||
// Increase the max so it won't exceed
|
||||
|
|
|
|||
|
|
@ -246,7 +246,7 @@ public class TerminologyLoaderSvcIntegrationDstu3Test extends BaseJpaDstu3Test {
|
|||
|
||||
IValidationSupport.CodeValidationResult result = myValueSetDao.validateCode(new UriType("http://loinc.org/vs"), null, new StringType("10013-1-9999999999"), new StringType(ITermLoaderSvc.LOINC_URI), null, null, null, mySrd);
|
||||
assertFalse(result.isOk());
|
||||
assertEquals("Failed to expand ValueSet 'http://loinc.org/vs' (in-memory). Could not validate code http://loinc.org#10013-1-9999999999. Error was: " + Msg.code(702) + "null", result.getMessage());
|
||||
assertEquals("Unknown code 'http://loinc.org#10013-1-9999999999' for in-memory expansion of ValueSet 'http://loinc.org/vs'", result.getMessage());
|
||||
}
|
||||
|
||||
private Set<String> toExpandedCodes(ValueSet theExpanded) {
|
||||
|
|
|
|||
|
|
@ -45,6 +45,8 @@ import org.springframework.test.context.junit.jupiter.SpringExtension;
|
|||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
|
||||
import static ca.uhn.fhir.jpa.term.api.ITermCodeSystemStorageSvc.MAKE_LOADING_VERSION_CURRENT;
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.containsString;
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.fail;
|
||||
import static org.mockito.ArgumentMatchers.anyCollection;
|
||||
|
|
@ -185,7 +187,7 @@ public class ValueSetExpansionR4ElasticsearchIT extends BaseJpaTest {
|
|||
myTermSvc.expandValueSet(null, vs);
|
||||
fail();
|
||||
} catch (InternalErrorException e) {
|
||||
assertEquals(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!", e.getMessage());
|
||||
assertThat(e.getMessage(), containsString(Msg.code(832) + "Expansion of ValueSet produced too many codes (maximum 50) - Operation aborted!"));
|
||||
}
|
||||
|
||||
// Increase the max so it won't exceed
|
||||
|
|
|
|||
|
|
@ -174,15 +174,16 @@ class SearchParameterAndValueSetRuleImpl extends RuleImplOp {
|
|||
if (validateCodeResult != null) {
|
||||
if (validateCodeResult.isOk()) {
|
||||
codeMatchCount.addMatchingCode();
|
||||
theTroubleshootingLog.debug("Code {}:{} was found in VS", system, code);
|
||||
theTroubleshootingLog.debug("Code {}#{} was found in ValueSet[{}] - {}", system, code, theValueSetUrl, validateCodeResult.getMessage());
|
||||
if (theReturnOnFirstMatch) {
|
||||
return codeMatchCount;
|
||||
}
|
||||
} else {
|
||||
codeMatchCount.addNonMatchingCode();
|
||||
theTroubleshootingLog.debug("Code {}:{} was not found in VS: {}", system, code, validateCodeResult.getMessage());
|
||||
theTroubleshootingLog.debug("Code {}#{} was not found in ValueSet[{}]: {}", system, code, theValueSetUrl, validateCodeResult.getMessage());
|
||||
}
|
||||
} else {
|
||||
theTroubleshootingLog.debug("Terminology service was unable to validate code {}#{} in ValueSet[{}] - No service was able to handle this request", system, code, theValueSetUrl);
|
||||
codeMatchCount.addUnableToValidate();
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,25 @@
|
|||
package ca.uhn.fhir.jpa.bulk.export.api;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR Storage api
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2022 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%
|
||||
*/
|
||||
|
||||
import javax.transaction.Transactional;
|
||||
|
||||
public interface IBulkDataExportJobSchedulingHelper {
|
||||
|
|
|
|||
4
lgtm.yml
4
lgtm.yml
|
|
@ -2,7 +2,9 @@
|
|||
extraction:
|
||||
java:
|
||||
index:
|
||||
java_version: 17
|
||||
java_version: 11
|
||||
maven:
|
||||
version: 3.8.4
|
||||
build_command:
|
||||
- mvn -Dmaven.test.skip install
|
||||
|
||||
|
|
|
|||
18
pom.xml
18
pom.xml
|
|
@ -2058,8 +2058,6 @@
|
|||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<version>3.8.1</version>
|
||||
<configuration>
|
||||
<source>1.8</source>
|
||||
<target>1.8</target>
|
||||
<forceJavacCompilerUse>true</forceJavacCompilerUse>
|
||||
<encoding>UTF-8</encoding>
|
||||
<fork>true</fork>
|
||||
|
|
@ -2989,6 +2987,12 @@
|
|||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
|
||||
<!--
|
||||
This profile is basically here to work around an IJ bug where the
|
||||
<testSource> tag is ignored in IJ's compiler. See:
|
||||
https://youtrack.jetbrains.com/issue/IDEA-85478
|
||||
-->
|
||||
<profile>
|
||||
<id>ide</id>
|
||||
<activation>
|
||||
|
|
@ -3002,16 +3006,16 @@
|
|||
<plugin>
|
||||
<groupId>org.apache.maven.plugins</groupId>
|
||||
<artifactId>maven-compiler-plugin</artifactId>
|
||||
<version>3.8.1</version>
|
||||
<configuration>
|
||||
<source>16</source>
|
||||
<target>16</target>
|
||||
<testSource>16</testSource>
|
||||
<testTarget>16</testTarget>
|
||||
<source>17</source>
|
||||
<target>17</target>
|
||||
<testSource>17</testSource>
|
||||
<testTarget>17</testTarget>
|
||||
</configuration>
|
||||
</plugin>
|
||||
</plugins>
|
||||
</build>
|
||||
</profile>
|
||||
|
||||
</profiles>
|
||||
</project>
|
||||
|
|
|
|||
Loading…
Reference in New Issue