Implement :below qualifier for tag parameters (#3613)
* Initial implementation * Implement job cancellation * Implement :below qualifier for tag parameters * Add changelog * Add tests Co-authored-by: juan.marchionatto <juan.marchionatto@smilecdr.com>
This commit is contained in:
jmarchionatto
GitHub
parent
544ef3de1b
commit
231c2659b8
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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: 2078
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* Last code value: 2079
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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: fix
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issue: 3612
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jira: SMILE-4112
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title: "Search with tag parameters using `:below` qualifier was not working. This is now fixed."
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@ -31,11 +31,12 @@ import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
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import ca.uhn.fhir.jpa.entity.Batch2WorkChunkEntity;
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import org.apache.commons.lang3.Validate;
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import org.springframework.data.domain.PageRequest;
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import org.springframework.data.domain.Sort;
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import javax.annotation.Nonnull;
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import javax.transaction.Transactional;
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import java.util.Collection;
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import java.util.Date;
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import java.util.EnumSet;
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import java.util.List;
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import java.util.Optional;
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import java.util.UUID;
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@ -113,7 +114,15 @@ public class JpaJobPersistenceImpl implements IJobPersistence {
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@Override
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public List<JobInstance> fetchInstances(int thePageSize, int thePageIndex) {
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return myJobInstanceRepository.fetchAll(PageRequest.of(thePageIndex, thePageSize)).stream().map(t -> toInstance(t)).collect(Collectors.toList());
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// default sort is myCreateTime Asc
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PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.ASC, "myCreateTime");
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return myJobInstanceRepository.findAll(pageRequest).stream().map(t -> toInstance(t)).collect(Collectors.toList());
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}
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@Override
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public Collection<JobInstance> fetchRecentInstances(int thePageSize, int thePageIndex) {
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PageRequest pageRequest = PageRequest.of(thePageIndex, thePageSize, Sort.Direction.DESC, "myCreateTime");
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return myJobInstanceRepository.findAll(pageRequest).stream().map(this::toInstance).collect(Collectors.toList());
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}
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private WorkChunk toChunk(Batch2WorkChunkEntity theEntity, boolean theIncludeData) {
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@ -22,23 +22,17 @@ package ca.uhn.fhir.jpa.dao.data;
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import ca.uhn.fhir.batch2.model.StatusEnum;
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import ca.uhn.fhir.jpa.entity.Batch2JobInstanceEntity;
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import org.springframework.data.domain.Pageable;
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import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Modifying;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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import java.util.List;
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public interface IBatch2JobInstanceRepository extends JpaRepository<Batch2JobInstanceEntity, String>, IHapiFhirJpaRepository {
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@Modifying
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@Query("UPDATE Batch2JobInstanceEntity e SET e.myStatus = :status WHERE e.myId = :id")
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void updateInstanceStatus(@Param("id") String theInstanceId, @Param("status") StatusEnum theInProgress);
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@Query("SELECT e FROM Batch2JobInstanceEntity e ORDER BY e.myCreateTime ASC")
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List<Batch2JobInstanceEntity> fetchAll(Pageable thePageRequest);
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@Modifying
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@Query("UPDATE Batch2JobInstanceEntity e SET e.myCancelled = :cancelled WHERE e.myId = :id")
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void updateInstanceCancelled(@Param("id") String theInstanceId, @Param("cancelled") boolean theCancelled);
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@ -101,7 +101,7 @@ import org.apache.commons.collections4.bidimap.UnmodifiableBidiMap;
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import org.apache.commons.lang3.StringUtils;
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import org.apache.commons.lang3.builder.EqualsBuilder;
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import org.apache.commons.lang3.builder.HashCodeBuilder;
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import org.apache.commons.lang3.tuple.Pair;
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import org.apache.commons.lang3.tuple.Triple;
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import org.hl7.fhir.instance.model.api.IAnyResource;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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@ -1221,52 +1221,11 @@ public class QueryStack {
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List<Condition> andPredicates = new ArrayList<>();
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for (List<? extends IQueryParameterType> nextAndParams : theList) {
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boolean haveTags = false;
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for (IQueryParameterType nextParamUncasted : nextAndParams) {
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if (nextParamUncasted instanceof TokenParam) {
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TokenParam nextParam = (TokenParam) nextParamUncasted;
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if (isNotBlank(nextParam.getValue())) {
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haveTags = true;
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} else if (isNotBlank(nextParam.getSystem())) {
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throw new InvalidRequestException(Msg.code(1218) + "Invalid " + theParamName + " parameter (must supply a value/code and not just a system): " + nextParam.getValueAsQueryToken(myFhirContext));
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}
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} else {
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UriParam nextParam = (UriParam) nextParamUncasted;
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if (isNotBlank(nextParam.getValue())) {
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haveTags = true;
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}
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}
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}
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if (!haveTags) {
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continue;
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}
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if ( ! checkHaveTags(nextAndParams, theParamName)) { continue; }
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boolean paramInverted = false;
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List<Pair<String, String>> tokens = Lists.newArrayList();
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for (IQueryParameterType nextOrParams : nextAndParams) {
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String code;
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String system;
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if (nextOrParams instanceof TokenParam) {
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TokenParam nextParam = (TokenParam) nextOrParams;
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code = nextParam.getValue();
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system = nextParam.getSystem();
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if (nextParam.getModifier() == TokenParamModifier.NOT) {
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paramInverted = true;
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}
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} else {
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UriParam nextParam = (UriParam) nextOrParams;
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code = nextParam.getValue();
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system = null;
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}
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if (isNotBlank(code)) {
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tokens.add(Pair.of(system, code));
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}
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}
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if (tokens.isEmpty()) {
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continue;
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}
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List<Triple<String, String, String>> tokens = Lists.newArrayList();
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boolean paramInverted = populateTokens(tokens, nextAndParams);
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if (tokens.isEmpty()) { continue; }
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Condition tagPredicate;
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BaseJoiningPredicateBuilder join;
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@ -1296,6 +1255,50 @@ public class QueryStack {
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return toAndPredicate(andPredicates);
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}
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private boolean populateTokens(List<Triple<String, String, String>> theTokens, List<? extends IQueryParameterType> theAndParams) {
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boolean paramInverted = false;
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for (IQueryParameterType nextOrParam : theAndParams) {
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String code;
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String system;
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if (nextOrParam instanceof TokenParam) {
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TokenParam nextParam = (TokenParam) nextOrParam;
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code = nextParam.getValue();
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system = nextParam.getSystem();
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if (nextParam.getModifier() == TokenParamModifier.NOT) {
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paramInverted = true;
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}
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} else {
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UriParam nextParam = (UriParam) nextOrParam;
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code = nextParam.getValue();
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system = null;
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}
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if (isNotBlank(code)) {
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theTokens.add(Triple.of(system, nextOrParam.getQueryParameterQualifier(), code));
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}
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}
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return paramInverted;
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}
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private boolean checkHaveTags(List<? extends IQueryParameterType> theParams, String theParamName) {
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for (IQueryParameterType nextParamUncasted : theParams) {
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if (nextParamUncasted instanceof TokenParam) {
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TokenParam nextParam = (TokenParam) nextParamUncasted;
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if (isNotBlank(nextParam.getValue())) { return true; }
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if (isNotBlank(nextParam.getSystem())) {
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throw new InvalidRequestException(Msg.code(1218) + "Invalid " + theParamName +
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" parameter (must supply a value/code and not just a system): " + nextParam.getValueAsQueryToken(myFhirContext));
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}
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}
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UriParam nextParam = (UriParam) nextParamUncasted;
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if (isNotBlank(nextParam.getValue())) { return true; }
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}
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return false;
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}
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public Condition createPredicateToken(@Nullable DbColumn theSourceJoinColumn, String theResourceName,
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String theSpnamePrefix, RuntimeSearchParam theSearchParam, List<? extends IQueryParameterType> theList,
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SearchFilterParser.CompareOperation theOperation, RequestPartitionId theRequestPartitionId) {
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@ -24,17 +24,19 @@ import ca.uhn.fhir.interceptor.model.RequestPartitionId;
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import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
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import ca.uhn.fhir.jpa.model.entity.TagTypeEnum;
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import ca.uhn.fhir.jpa.search.builder.sql.SearchQueryBuilder;
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import ca.uhn.fhir.rest.param.UriParamQualifierEnum;
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import com.google.common.collect.Lists;
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import com.healthmarketscience.sqlbuilder.BinaryCondition;
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import com.healthmarketscience.sqlbuilder.ComboCondition;
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import com.healthmarketscience.sqlbuilder.Condition;
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import com.healthmarketscience.sqlbuilder.UnaryCondition;
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import com.healthmarketscience.sqlbuilder.dbspec.basic.DbColumn;
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import com.healthmarketscience.sqlbuilder.dbspec.basic.DbTable;
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import org.apache.commons.lang3.tuple.Pair;
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import org.apache.commons.lang3.tuple.Triple;
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import java.util.List;
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import java.util.Objects;
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import static ca.uhn.fhir.jpa.search.builder.predicate.StringPredicateBuilder.createLeftMatchLikeExpression;
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import static org.apache.commons.lang3.StringUtils.isNotBlank;
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public class TagPredicateBuilder extends BaseJoiningPredicateBuilder {
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@ -61,24 +63,28 @@ public class TagPredicateBuilder extends BaseJoiningPredicateBuilder {
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}
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public Condition createPredicateTag(TagTypeEnum theTagType, List<Pair<String, String>> theTokens, String theParamName, RequestPartitionId theRequestPartitionId) {
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public Condition createPredicateTag(TagTypeEnum theTagType, List<Triple<String, String, String>> theTokens, String theParamName, RequestPartitionId theRequestPartitionId) {
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addJoin(getTable(), myTagDefinitionTable, myColumnTagId, myTagDefinitionColumnTagId);
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return createPredicateTagList(theTagType, theTokens);
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}
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private Condition createPredicateTagList(TagTypeEnum theTagType, List<Pair<String, String>> theTokens) {
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private Condition createPredicateTagList(TagTypeEnum theTagType, List<Triple<String, String, String>> theTokens) {
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Condition typePredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagType, generatePlaceholder(theTagType.ordinal()));
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List<Condition> orPredicates = Lists.newArrayList();
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for (Pair<String, String> next : theTokens) {
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for (Triple<String, String, String> next : theTokens) {
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String system = next.getLeft();
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String code = next.getRight();
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String qualifier = next.getMiddle();
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if (theTagType == TagTypeEnum.PROFILE) {
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system = BaseHapiFhirDao.NS_JPA_PROFILE;
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}
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Condition codePredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagCode, generatePlaceholder(code));
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Condition codePredicate = Objects.equals(qualifier, UriParamQualifierEnum.BELOW.getValue())
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? BinaryCondition.like(myTagDefinitionColumnTagCode, generatePlaceholder(createLeftMatchLikeExpression(code)))
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: BinaryCondition.equalTo(myTagDefinitionColumnTagCode, generatePlaceholder(code));
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if (isNotBlank(system)) {
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Condition systemPredicate = BinaryCondition.equalTo(myTagDefinitionColumnTagSystem, generatePlaceholder(system));
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orPredicates.add(ComboCondition.and(typePredicate, systemPredicate, codePredicate));
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@ -101,6 +101,7 @@ import org.hl7.fhir.r4.model.Location;
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import org.hl7.fhir.r4.model.Medication;
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import org.hl7.fhir.r4.model.MedicationAdministration;
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import org.hl7.fhir.r4.model.MedicationRequest;
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import org.hl7.fhir.r4.model.Meta;
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import org.hl7.fhir.r4.model.MolecularSequence;
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import org.hl7.fhir.r4.model.Observation;
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import org.hl7.fhir.r4.model.Observation.ObservationStatus;
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@ -132,6 +133,7 @@ import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.BeforeEach;
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import org.junit.jupiter.api.Disabled;
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import org.junit.jupiter.api.DisplayName;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.ArgumentCaptor;
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@ -157,6 +159,9 @@ import java.util.Set;
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import java.util.TreeSet;
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import java.util.stream.Collectors;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_PROFILE;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_SECURITY;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_TAG;
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import static ca.uhn.fhir.rest.api.Constants.PARAM_TYPE;
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import static org.apache.commons.lang3.StringUtils.countMatches;
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import static org.apache.commons.lang3.StringUtils.leftPad;
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@ -5641,6 +5646,96 @@ public class FhirResourceDaoR4SearchNoFtTest extends BaseJpaR4Test {
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}
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}
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@Nested
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public class TagBelowTests {
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@Test
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public void testTagProfile() {
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Patient p1 = new Patient();
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p1.setActive(true);
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p1.setMeta(new Meta().addProfile("http://acme.com/some-profile|1.0"));
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IIdType p1Id = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
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Patient p2 = new Patient();
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p2.setActive(true);
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p2.setMeta(new Meta().addProfile("http://acme.com/some-profile|1.1"));
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IIdType p2Id = myPatientDao.create(p2).getId().toUnqualifiedVersionless();
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Patient p3 = new Patient();
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p3.setActive(true);
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p3.setMeta(new Meta().addProfile("http://acme.com/some-profile|2.0"));
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IIdType p3Id = myPatientDao.create(p3).getId().toUnqualifiedVersionless();
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronous(true);
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params.add(PARAM_PROFILE, new UriParam(
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"http://acme.com/some-profile|1").setQualifier(UriParamQualifierEnum.BELOW));
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IBundleProvider results = myPatientDao.search(params);
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List<String> values = toUnqualifiedVersionlessIdValues(results);
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assertThat(values.toString(), values, containsInAnyOrder(p1Id.getValue(), p2Id.getValue()));
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}
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@Test
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public void testTagTag() {
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Patient p1 = new Patient();
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p1.setActive(true);
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p1.setMeta(new Meta().addTag("http://acme.com", "some-code", "some-display"));
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IIdType p1Id = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
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Patient p2 = new Patient();
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p2.setActive(true);
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p2.setMeta(new Meta().addTag("http://acme.com", "some-code-2", "some-display-2"));
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IIdType p2Id = myPatientDao.create(p2).getId().toUnqualifiedVersionless();
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Patient p3 = new Patient();
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p3.setActive(true);
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p3.setMeta(new Meta().addTag("http://acme.com", "another-code", "another-display"));
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IIdType p3Id = myPatientDao.create(p3).getId().toUnqualifiedVersionless();
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronous(true);
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params.add(PARAM_TAG, new TokenParam("http://acme.com", "some").setModifier(TokenParamModifier.BELOW));
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IBundleProvider results = myPatientDao.search(params);
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List<String> values = toUnqualifiedVersionlessIdValues(results);
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assertThat(values.toString(), values, containsInAnyOrder(p1Id.getValue(), p2Id.getValue()));
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}
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@Test
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public void testSecurityLabelTag() {
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Patient p1 = new Patient();
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p1.setActive(true);
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p1.setMeta(new Meta().addSecurity(
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"http://terminology.hl7.org/CodeSystem/v3-Confidentiality", "DELAU", "delete after use"));
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IIdType p1Id = myPatientDao.create(p1).getId().toUnqualifiedVersionless();
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Patient p2 = new Patient();
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p2.setActive(true);
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p2.setMeta(new Meta().addSecurity(
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"http://terminology.hl7.org/CodeSystem/v3-Confidentiality", "DELBU", "delete before use"));
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IIdType p2Id = myPatientDao.create(p2).getId().toUnqualifiedVersionless();
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Patient p3 = new Patient();
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p3.setActive(true);
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p3.setMeta(new Meta().addSecurity(
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"http://terminology.hl7.org/CodeSystem/v3-Confidentiality", "R", "restricted"));
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IIdType p3Id = myPatientDao.create(p3).getId().toUnqualifiedVersionless();
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SearchParameterMap params = new SearchParameterMap();
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params.setLoadSynchronous(true);
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params.add(PARAM_SECURITY, new TokenParam(
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"http://terminology.hl7.org/CodeSystem/v3-Confidentiality", "DEL").setModifier(TokenParamModifier.BELOW));
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IBundleProvider results = myPatientDao.search(params);
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List<String> values = toUnqualifiedVersionlessIdValues(results);
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assertThat(values.toString(), values, containsInAnyOrder(p1Id.getValue(), p2Id.getValue()));
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}
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}
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private String toStringMultiline(List<?> theResults) {
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StringBuilder b = new StringBuilder();
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for (Object next : theResults) {
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@ -52,6 +52,8 @@ public interface IJobCoordinator {
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*/
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List<JobInstance> getInstances(int thePageSize, int thePageIndex);
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List<JobInstance> getRecentInstances(int thePageSize, int thePageIndex);
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void cancelInstance(String theInstanceId) throws ResourceNotFoundException;
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}
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@ -24,6 +24,7 @@ import ca.uhn.fhir.batch2.impl.BatchWorkChunk;
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import ca.uhn.fhir.batch2.model.JobInstance;
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import ca.uhn.fhir.batch2.model.WorkChunk;
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import java.util.Collection;
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import java.util.List;
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import java.util.Optional;
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@ -68,6 +69,11 @@ public interface IJobPersistence {
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*/
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List<JobInstance> fetchInstances(int thePageSize, int thePageIndex);
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/**
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* Fetch instance in 'myCreateTime' descending order
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*/
|
||||
Collection<JobInstance> fetchRecentInstances(int thePageSize, int thePageIndex);
|
||||
|
||||
/**
|
||||
* Fetch a given instance and update the stored status
|
||||
* * to {@link ca.uhn.fhir.batch2.model.StatusEnum#IN_PROGRESS}
|
||||
|
|
|
|||
|
|
@ -161,6 +161,12 @@ public class JobCoordinatorImpl extends BaseJobService implements IJobCoordinato
|
|||
return myJobPersistence.fetchInstances(thePageSize, thePageIndex).stream().map(t -> massageInstanceForUserAccess(t)).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public List<JobInstance> getRecentInstances(int thePageSize, int thePageIndex) {
|
||||
return myJobPersistence.fetchRecentInstances(thePageSize, thePageIndex).stream()
|
||||
.map(this::massageInstanceForUserAccess).collect(Collectors.toList());
|
||||
}
|
||||
|
||||
@Override
|
||||
public void cancelInstance(String theInstanceId) throws ResourceNotFoundException {
|
||||
myJobPersistence.cancelInstance(theInstanceId);
|
||||
|
|
|
|||
|
|
@ -22,10 +22,9 @@ package ca.uhn.fhir.batch2.impl;
|
|||
|
||||
import ca.uhn.fhir.batch2.api.IJobPersistence;
|
||||
import ca.uhn.fhir.batch2.model.JobInstance;
|
||||
import ca.uhn.fhir.batch2.model.StatusEnum;
|
||||
import ca.uhn.fhir.batch2.model.WorkChunk;
|
||||
|
||||
import java.util.EnumSet;
|
||||
import java.util.Collection;
|
||||
import java.util.List;
|
||||
import java.util.Optional;
|
||||
|
||||
|
|
@ -65,6 +64,11 @@ public class SynchronizedJobPersistenceWrapper implements IJobPersistence {
|
|||
return myWrap.fetchInstances(thePageSize, thePageIndex);
|
||||
}
|
||||
|
||||
@Override
|
||||
public Collection<JobInstance> fetchRecentInstances(int thePageSize, int thePageIndex) {
|
||||
return myWrap.fetchRecentInstances(thePageSize, thePageIndex);
|
||||
}
|
||||
|
||||
@Override
|
||||
public synchronized Optional<JobInstance> fetchInstanceAndMarkInProgress(String theInstanceId) {
|
||||
return myWrap.fetchInstanceAndMarkInProgress(theInstanceId);
|
||||
|
|
|
|||
Loading…
Reference in New Issue