Parameterize term valueset concept view dao (#2477)
* Generic the list type to accomidate different substring queries * special subquery for Oracle * change the conceptview dao depending on dialect * address review comments * remove generics * no longer inherits * copy paste from non Oracle version * dang copy pasters * changelog Co-authored-by: Mike G <michel.gleeson@gmail.com>
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michelgleeson
GitHub
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0a6c61372c
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---
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type: fix
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issue: 1644
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title: "support Oracle specific syntax when using a TermValueSetConceptView"
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@ -0,0 +1,17 @@
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package ca.uhn.fhir.jpa.dao.data;
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import ca.uhn.fhir.jpa.entity.TermValueSetConceptViewOracle;
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import org.springframework.data.jpa.repository.JpaRepository;
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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.io.Serializable;
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import java.util.List;
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public interface ITermValueSetConceptViewOracleDao extends JpaRepository<TermValueSetConceptViewOracle, Long> {
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@Query("SELECT v FROM TermValueSetConceptView v WHERE v.myConceptValueSetPid = :pid AND v.myConceptOrder >= :from AND v.myConceptOrder < :to ORDER BY v.myConceptOrder")
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List<TermValueSetConceptViewOracle> findByTermValueSetId(@Param("from") int theFrom, @Param("to") int theTo, @Param("pid") Long theValueSetId);
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@Query("SELECT v FROM TermValueSetConceptView v WHERE v.myConceptValueSetPid = :pid AND LOWER(v.myConceptDisplay) LIKE :display ORDER BY v.myConceptOrder")
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List<TermValueSetConceptViewOracle> findByTermValueSetId(@Param("pid") Long theValueSetId, @Param("display") String theDisplay);
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}
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@ -0,0 +1,142 @@
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package ca.uhn.fhir.jpa.entity;
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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 - 2021 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 org.hibernate.annotations.Immutable;
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import org.hibernate.annotations.Subselect;
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import javax.persistence.Column;
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import javax.persistence.DiscriminatorValue;
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import javax.persistence.EmbeddedId;
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import javax.persistence.Entity;
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import javax.persistence.GeneratedValue;
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import javax.persistence.GenerationType;
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import javax.persistence.Id;
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import javax.persistence.Table;
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import java.io.Serializable;
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@Entity
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@Immutable
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@Subselect(
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/*
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* Note about the CONCAT function below- We need a primary key (an @Id) column
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* because hibernate won't allow the view the function without it, but
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*/
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"SELECT CONCAT(vsc.PID, CONCAT(' ', vscd.PID)) AS PID, " +
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" vsc.PID AS CONCEPT_PID, " +
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" vsc.VALUESET_PID AS CONCEPT_VALUESET_PID, " +
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" vsc.VALUESET_ORDER AS CONCEPT_VALUESET_ORDER, " +
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" vsc.SYSTEM_URL AS CONCEPT_SYSTEM_URL, " +
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" vsc.CODEVAL AS CONCEPT_CODEVAL, " +
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" vsc.DISPLAY AS CONCEPT_DISPLAY, " +
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" vscd.PID AS DESIGNATION_PID, " +
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" vscd.LANG AS DESIGNATION_LANG, " +
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" vscd.USE_SYSTEM AS DESIGNATION_USE_SYSTEM, " +
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" vscd.USE_CODE AS DESIGNATION_USE_CODE, " +
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" vscd.USE_DISPLAY AS DESIGNATION_USE_DISPLAY, " +
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" vscd.VAL AS DESIGNATION_VAL " +
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"FROM TRM_VALUESET_CONCEPT vsc " +
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"LEFT OUTER JOIN TRM_VALUESET_C_DESIGNATION vscd ON vsc.PID = vscd.VALUESET_CONCEPT_PID"
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)
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public class TermValueSetConceptViewOracle implements Serializable {
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private static final long serialVersionUID = 1L;
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@Id
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@Column(name="PID", length = 1000 /* length only needed to satisfy JpaEntityTest, it's not used*/)
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private String id; // still set automatically
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@Column(name = "CONCEPT_PID")
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private Long myConceptPid;
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@Column(name = "CONCEPT_VALUESET_PID")
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private Long myConceptValueSetPid;
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@Column(name = "CONCEPT_VALUESET_ORDER")
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private int myConceptOrder;
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@Column(name = "CONCEPT_SYSTEM_URL", length = TermCodeSystem.MAX_URL_LENGTH)
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private String myConceptSystemUrl;
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@Column(name = "CONCEPT_CODEVAL", length = TermConcept.MAX_CODE_LENGTH)
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private String myConceptCode;
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@Column(name = "CONCEPT_DISPLAY", length = TermConcept.MAX_DESC_LENGTH)
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private String myConceptDisplay;
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@Column(name = "DESIGNATION_PID")
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private Long myDesignationPid;
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@Column(name = "DESIGNATION_LANG", length = TermConceptDesignation.MAX_LENGTH)
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private String myDesignationLang;
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@Column(name = "DESIGNATION_USE_SYSTEM", length = TermConceptDesignation.MAX_LENGTH)
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private String myDesignationUseSystem;
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@Column(name = "DESIGNATION_USE_CODE", length = TermConceptDesignation.MAX_LENGTH)
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private String myDesignationUseCode;
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@Column(name = "DESIGNATION_USE_DISPLAY", length = TermConceptDesignation.MAX_LENGTH)
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private String myDesignationUseDisplay;
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@Column(name = "DESIGNATION_VAL", length = TermConceptDesignation.MAX_VAL_LENGTH)
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private String myDesignationVal;
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public Long getConceptPid() {
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return myConceptPid;
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}
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public String getConceptSystemUrl() {
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return myConceptSystemUrl;
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}
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public String getConceptCode() {
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return myConceptCode;
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}
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public String getConceptDisplay() {
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return myConceptDisplay;
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}
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public Long getDesignationPid() {
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return myDesignationPid;
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}
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public String getDesignationLang() {
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return myDesignationLang;
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}
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public String getDesignationUseSystem() {
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return myDesignationUseSystem;
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}
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public String getDesignationUseCode() {
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return myDesignationUseCode;
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}
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public String getDesignationUseDisplay() {
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return myDesignationUseDisplay;
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}
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public String getDesignationVal() {
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return myDesignationVal;
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}
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}
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@ -45,6 +45,7 @@ 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.ITermValueSetConceptDesignationDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetConceptViewOracleDao;
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import ca.uhn.fhir.jpa.dao.data.ITermValueSetDao;
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import ca.uhn.fhir.jpa.entity.TermCodeSystem;
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import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
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@ -62,6 +63,7 @@ import ca.uhn.fhir.jpa.entity.TermConceptPropertyTypeEnum;
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import ca.uhn.fhir.jpa.entity.TermValueSet;
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import ca.uhn.fhir.jpa.entity.TermValueSetConcept;
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import ca.uhn.fhir.jpa.entity.TermValueSetConceptView;
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import ca.uhn.fhir.jpa.entity.TermValueSetConceptViewOracle;
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import ca.uhn.fhir.jpa.entity.TermValueSetPreExpansionStatusEnum;
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import ca.uhn.fhir.jpa.model.entity.ResourceTable;
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import ca.uhn.fhir.jpa.model.sched.HapiJob;
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@ -246,6 +248,8 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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@Autowired
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private ITermValueSetConceptViewDao myTermValueSetConceptViewDao;
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@Autowired
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private ITermValueSetConceptViewOracleDao myTermValueSetConceptViewOracleDao;
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@Autowired
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private ISchedulerService mySchedulerService;
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@Autowired(required = false)
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private ITermDeferredStorageSvc myDeferredStorageSvc;
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@ -527,11 +531,126 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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*/
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String msg = myContext.getLocalizer().getMessage(BaseTermReadSvcImpl.class, "valueSetExpandedUsingPreExpansion");
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theAccumulator.addMessage(msg);
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expandConcepts(theAccumulator, termValueSet, theFilter, theAdd);
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if (isOracleDialect()) {
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expandConceptsOracle(theAccumulator, termValueSet, theFilter, theAdd);
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}
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else {
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expandConcepts(theAccumulator, termValueSet, theFilter, theAdd);
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}
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}
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private boolean isOracleDialect(){
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return myHibernatePropertiesProvider.getDialect() instanceof org.hibernate.dialect.Oracle12cDialect;
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}
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private void expandConceptsOracle(IValueSetConceptAccumulator theAccumulator, TermValueSet theTermValueSet, ExpansionFilter theFilter, boolean theAdd) {
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// Literal copy paste from expandConcepts but tailored for Oracle since we can't reliably extend the DAO and hibernate classes
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Integer offset = theAccumulator.getSkipCountRemaining();
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offset = ObjectUtils.defaultIfNull(offset, 0);
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offset = Math.min(offset, theTermValueSet.getTotalConcepts().intValue());
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Integer count = theAccumulator.getCapacityRemaining();
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count = defaultIfNull(count, myDaoConfig.getMaximumExpansionSize());
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int conceptsExpanded = 0;
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int designationsExpanded = 0;
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int toIndex = offset + count;
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Collection<TermValueSetConceptViewOracle> conceptViews;
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boolean wasFilteredResult = false;
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String filterDisplayValue = null;
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if (!theFilter.getFilters().isEmpty() && JpaConstants.VALUESET_FILTER_DISPLAY.equals(theFilter.getFilters().get(0).getProperty()) && theFilter.getFilters().get(0).getOp() == ValueSet.FilterOperator.EQUAL) {
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filterDisplayValue = lowerCase(theFilter.getFilters().get(0).getValue().replace("%", "[%]"));
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String displayValue = "%" + lowerCase(filterDisplayValue) + "%";
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conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(theTermValueSet.getId(), displayValue);
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wasFilteredResult = true;
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} else {
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// TODO JA HS: I'm pretty sure we are overfetching here. test says offset 3, count 4, but we are fetching index 3 -> 10 here, grabbing 7 concepts.
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//Specifically this test testExpandInline_IncludePreExpandedValueSetByUri_FilterOnDisplay_LeftMatch_SelectRange
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conceptViews = myTermValueSetConceptViewOracleDao.findByTermValueSetId(offset, toIndex, theTermValueSet.getId());
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theAccumulator.consumeSkipCount(offset);
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if (theAdd) {
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theAccumulator.incrementOrDecrementTotalConcepts(true, theTermValueSet.getTotalConcepts().intValue());
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}
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}
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if (conceptViews.isEmpty()) {
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logConceptsExpanded("No concepts to expand. ", theTermValueSet, conceptsExpanded);
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return;
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}
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Map<Long, FhirVersionIndependentConcept> pidToConcept = new LinkedHashMap<>();
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ArrayListMultimap<Long, TermConceptDesignation> pidToDesignations = ArrayListMultimap.create();
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for (TermValueSetConceptViewOracle conceptView : conceptViews) {
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String system = conceptView.getConceptSystemUrl();
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String code = conceptView.getConceptCode();
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String display = conceptView.getConceptDisplay();
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//-- this is quick solution, may need to revisit
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if (!applyFilter(display, filterDisplayValue))
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continue;
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Long conceptPid = conceptView.getConceptPid();
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if (!pidToConcept.containsKey(conceptPid)) {
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FhirVersionIndependentConcept concept = new FhirVersionIndependentConcept(system, code, display);
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pidToConcept.put(conceptPid, concept);
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}
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// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to designations optional.
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if (conceptView.getDesignationPid() != null) {
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TermConceptDesignation designation = new TermConceptDesignation();
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designation.setUseSystem(conceptView.getDesignationUseSystem());
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designation.setUseCode(conceptView.getDesignationUseCode());
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designation.setUseDisplay(conceptView.getDesignationUseDisplay());
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designation.setValue(conceptView.getDesignationVal());
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designation.setLanguage(conceptView.getDesignationLang());
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pidToDesignations.put(conceptPid, designation);
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if (++designationsExpanded % 250 == 0) {
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logDesignationsExpanded("Expansion of designations in progress. ", theTermValueSet, designationsExpanded);
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}
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}
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if (++conceptsExpanded % 250 == 0) {
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logConceptsExpanded("Expansion of concepts in progress. ", theTermValueSet, conceptsExpanded);
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}
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}
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for (Long nextPid : pidToConcept.keySet()) {
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FhirVersionIndependentConcept concept = pidToConcept.get(nextPid);
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List<TermConceptDesignation> designations = pidToDesignations.get(nextPid);
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String system = concept.getSystem();
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String code = concept.getCode();
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String display = concept.getDisplay();
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if (theAdd) {
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if (theAccumulator.getCapacityRemaining() != null) {
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if (theAccumulator.getCapacityRemaining() == 0) {
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break;
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}
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}
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theAccumulator.includeConceptWithDesignations(system, code, display, designations);
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} else {
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boolean removed = theAccumulator.excludeConcept(system, code);
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if (removed) {
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theAccumulator.incrementOrDecrementTotalConcepts(false, 1);
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}
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}
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}
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if (wasFilteredResult && theAdd) {
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theAccumulator.incrementOrDecrementTotalConcepts(true, pidToConcept.size());
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}
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logDesignationsExpanded("Finished expanding designations. ", theTermValueSet, designationsExpanded);
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logConceptsExpanded("Finished expanding concepts. ", theTermValueSet, conceptsExpanded);
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}
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private void expandConcepts(IValueSetConceptAccumulator theAccumulator, TermValueSet theTermValueSet, ExpansionFilter theFilter, boolean theAdd) {
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// NOTE: if you modifiy the logic here, look to `expandConceptsOracle` and see if your new code applies to its copy pasted sibling
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Integer offset = theAccumulator.getSkipCountRemaining();
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offset = ObjectUtils.defaultIfNull(offset, 0);
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offset = Math.min(offset, theTermValueSet.getTotalConcepts().intValue());
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@ -544,6 +663,7 @@ public abstract class BaseTermReadSvcImpl implements ITermReadSvc {
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int toIndex = offset + count;
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Collection<TermValueSetConceptView> conceptViews;
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Collection<TermValueSetConceptViewOracle> conceptViewsOracle;
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boolean wasFilteredResult = false;
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String filterDisplayValue = null;
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if (!theFilter.getFilters().isEmpty() && JpaConstants.VALUESET_FILTER_DISPLAY.equals(theFilter.getFilters().get(0).getProperty()) && theFilter.getFilters().get(0).getOp() == ValueSet.FilterOperator.EQUAL) {
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