honeymoose
/
hapi-fhir
mirror of https://github.com/hapifhir/hapi-fhir.git
1
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity

Finally this is fast!

This commit is contained in:
James Agnew 2019-09-06 16:29:09 -04:00
parent 0cabc0392f
commit 6ec991cd39
6 changed files with 255 additions and 58 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/ITermValueSetConceptViewDao.java Normal file
View File

@ -0,0 +1,38 @@
package ca.uhn.fhir.jpa.dao.data;
import ca.uhn.fhir.jpa.entity.ResourceSearchView;
import ca.uhn.fhir.jpa.entity.TermValueSetConceptView;
import org.springframework.data.domain.Pageable;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.data.jpa.repository.Query;
import org.springframework.data.repository.query.Param;
import java.util.Collection;
import java.util.List;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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%
*/
public interface ITermValueSetConceptViewDao extends JpaRepository<TermValueSetConceptView, Long> {
@Query("SELECT v FROM TermValueSetConceptView v WHERE v.myConceptValueSetPid = :pid AND v.myConceptOrder >= :from AND v.myConceptOrder < :to ORDER BY v.myConceptOrder")
List<TermValueSetConceptView> findConceptsByValueSetPid(@Param("from") int theOffset, @Param("to") int theToIndex, @Param("pid") Long thePid);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSet.java
View File

@ -196,9 +196,7 @@ public class TermValueSet implements Serializable {
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getUrl())
.toHashCode();
return getUrl().hashCode();
}
@Override

30
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConcept.java
View File

@ -53,7 +53,7 @@ public class TermValueSetConcept implements Serializable {
@Column(name = "PID")
private Long myId;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_PID"))
private TermValueSet myValueSet;
@ -78,9 +78,12 @@ public class TermValueSetConcept implements Serializable {
@Column(name = "DISPLAY", nullable = true, length = TermConcept.MAX_DESC_LENGTH)
private String myDisplay;
@OneToMany(mappedBy = "myConcept")
@OneToMany(mappedBy = "myConcept", fetch = FetchType.LAZY)
private List<TermValueSetConceptDesignation> myDesignations;
@Transient
private transient Integer myHashCode;
public Long getId() {
return myId;
}
@ -169,7 +172,7 @@ public class TermValueSetConcept implements Serializable {
TermValueSetConcept that = (TermValueSetConcept) theO;
return new EqualsBuilder()
.append(getValueSetUrl(), that.getValueSetUrl())
.append(myValueSetPid, that.myValueSetPid)
.append(getSystem(), that.getSystem())
.append(getCode(), that.getCode())
.isEquals();
@ -177,26 +180,29 @@ public class TermValueSetConcept implements Serializable {
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getValueSetUrl())
.append(getSystem())
.append(getCode())
.toHashCode();
if (myHashCode == null) {
myHashCode = new HashCodeBuilder(17, 37)
.append(myValueSetPid)
.append(getSystem())
.append(getCode())
.toHashCode();
}
return myHashCode;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
// .append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
.append("myValueSetPid", myValueSetPid)
.append("myOrder", myOrder)
.append("myValueSetUrl", this.getValueSetUrl())
.append("myValueSetName", this.getValueSetName())
// .append("myValueSetUrl", this.getValueSetUrl())
// .append("myValueSetName", this.getValueSetName())
.append("mySystem", mySystem)
.append("myCode", myCode)
.append("myDisplay", myDisplay)
.append(myDesignations != null ? ("myDesignations - size=" + myDesignations.size()) : ("myDesignations=(null)"))
// .append(myDesignations != null ? ("myDesignations - size=" + myDesignations.size()) : ("myDesignations=(null)"))
.toString();
}
}

32
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptDesignation.java
View File

@ -48,14 +48,14 @@ public class TermValueSetConceptDesignation implements Serializable {
@Column(name = "PID")
private Long myId;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "VALUESET_CONCEPT_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VALUESET_CONCEPT_PID"))
private TermValueSetConcept myConcept;
@Column(name = "VALUESET_CONCEPT_PID", insertable = false, updatable = false, nullable = false)
private Long myConceptPid;
@ManyToOne()
@ManyToOne(fetch = FetchType.LAZY)
@JoinColumn(name = "VALUESET_PID", referencedColumnName = "PID", nullable = false, foreignKey = @ForeignKey(name = "FK_TRM_VSCD_VS_PID"))
private TermValueSet myValueSet;
@ -83,6 +83,9 @@ public class TermValueSetConceptDesignation implements Serializable {
@Column(name = "VAL", nullable = false, length = MAX_LENGTH)
private String myValue;
@Transient
private transient Integer myHashCode;
public Long getId() {
return myId;
}
@ -194,25 +197,28 @@ public class TermValueSetConceptDesignation implements Serializable {
@Override
public int hashCode() {
return new HashCodeBuilder(17, 37)
.append(getLanguage())
.append(getUseSystem())
.append(getUseCode())
.append(getUseDisplay())
.append(getValue())
.toHashCode();
if (myHashCode == null) {
myHashCode = new HashCodeBuilder(17, 37)
.append(getLanguage())
.append(getUseSystem())
.append(getUseCode())
.append(getUseDisplay())
.append(getValue())
.toHashCode();
}
return myHashCode;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE)
.append("myId", myId)
.append(myConcept != null ? ("myConcept - id=" + myConcept.getId()) : ("myConcept=(null)"))
// .append(myConcept != null ? ("myConcept - id=" + myConcept.getId()) : ("myConcept=(null)"))
.append("myConceptPid", myConceptPid)
.append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
// .append(myValueSet != null ? ("myValueSet - id=" + myValueSet.getId()) : ("myValueSet=(null)"))
.append("myValueSetPid", myValueSetPid)
.append("myValueSetUrl", this.getValueSetUrl())
.append("myValueSetName", this.getValueSetName())
// .append("myValueSetUrl", this.getValueSetUrl())
// .append("myValueSetName", this.getValueSetName())
.append("myLanguage", myLanguage)
.append("myUseSystem", myUseSystem)
.append("myUseCode", myUseCode)

133
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermValueSetConceptView.java Normal file
View File

@ -0,0 +1,133 @@
package ca.uhn.fhir.jpa.entity;
/*
* #%L
* HAPI FHIR JPA Server
* %%
* Copyright (C) 2014 - 2019 University Health Network
* %%
* 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 org.hibernate.annotations.Immutable;
import org.hibernate.annotations.Subselect;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.Id;
import java.io.Serializable;
@Entity
@Immutable
@Subselect("select " +
" CONCAT(vsc.PID, ' ', cd.PID) as PID," +
" vsc.PID as CONCEPT_PID, " +
" cd.PID as DESIG_PID, " +
" vsc.CODEVAL as CONCEPT_CODE, " +
" vsc.DISPLAY as CONCEPT_DISPLAY, " +
" vsc.VALUESET_ORDER as CONCEPT_ORDER, " +
" vsc.SYSTEM_URL as CONCEPT_SYSTEM_URL, " +
" vsc.VALUESET_PID as CONCEPT_VS_PID, " +
// " cd.VALUESET_CONCEPT_PID as VALUESET2_35_1_, " +
" cd.LANG as DESIG_LANG, " +
" cd.USE_CODE as DESIG_USE_CODE, " +
" cd.USE_DISPLAY as DESIG_USE_DISPLAY, " +
" cd.USE_SYSTEM as DESIG_USE_SYSTEM, " +
" cd.VAL as DESIG_VAL " +
" from TRM_VALUESET_CONCEPT vsc " +
" left outer join TRM_VALUESET_C_DESIGNATION cd on vsc.PID=cd.VALUESET_CONCEPT_PID "
// +
// " order by vsc.VALUESET_ORDER"
)
public class TermValueSetConceptView implements Serializable {
private static final long serialVersionUID = 1L;
@Id
@Column(name="PID")
private String myPid;
@Column(name = "CONCEPT_PID")
private Long myConceptPid;
@Column(name = "DESIG_PID")
private Long myDesigPid;
@Column(name = "CONCEPT_CODE")
private String myConceptCode;
@Column(name = "CONCEPT_DISPLAY")
private String myConceptDisplay;
@Column(name = "CONCEPT_ORDER")
private int myConceptOrder;
@Column(name = "CONCEPT_SYSTEM_URL")
private String myConceptSystemUrl;
@Column(name = "CONCEPT_VS_PID")
private Long myConceptValueSetPid;
@Column(name = "DESIG_LANG")
private String myDesigLang;
@Column(name = "DESIG_USE_CODE")
private String myDesigUseCode;
@Column(name = "DESIG_USE_DISPLAY")
private String myDesigUseDisplay;
@Column(name = "DESIG_USE_SYSTEM")
private String myDesigUseSystem;
@Column(name = "DESIG_VAL")
private String myDesigVal;
public Long getConceptPid() {
return myConceptPid;
}
public Long getDesigPid() {
return myDesigPid;
}
public String getConceptCode() {
return myConceptCode;
}
public String getConceptDisplay() {
return myConceptDisplay;
}
public int getConceptOrder() {
return myConceptOrder;
}
public String getConceptSystemUrl() {
return myConceptSystemUrl;
}
public Long getConceptValueSetPid() {
return myConceptValueSetPid;
}
public String getDesigLang() {
return myDesigLang;
}
public String getDesigUseCode() {
return myDesigUseCode;
}
public String getDesigUseDisplay() {
return myDesigUseDisplay;
}
public String getDesigUseSystem() {
return myDesigUseSystem;
}
public String getDesigVal() {
return myDesigVal;
}
}

76
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvcImpl.java
View File

@ -68,6 +68,7 @@ import org.springframework.context.ApplicationContext;
import org.springframework.context.ApplicationContextAware;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.data.domain.Pageable;
import org.springframework.data.domain.Slice;
import org.springframework.data.jpa.repository.JpaRepository;
import org.springframework.scheduling.annotation.Scheduled;
@ -159,6 +160,8 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private IFulltextSearchSvc myFulltextSearchSvc;
@Autowired
private PlatformTransactionManager myTxManager;
@Autowired
private ITermValueSetConceptViewDao myTermValueSetConceptViewDao;
private void addCodeIfNotAlreadyAdded(IValueSetConceptAccumulator theValueSetCodeAccumulator, Set<String> theAddedCodes, TermConcept theConcept, boolean theAdd, AtomicInteger theCodeCounter) {
String codeSystem = theConcept.getCodeSystemVersion().getCodeSystem().getCodeSystemUri();
@ -528,21 +531,53 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
private void expandConcepts(ValueSet.ValueSetExpansionComponent theExpansionComponent, TermValueSet theTermValueSet, int theOffset, int theCount) {
int conceptsExpanded = 0;
int toIndex = theOffset + theCount;
Slice<TermValueSetConcept> slice = myValueSetConceptDao.findByTermValueSetIdAndPreFetchDesignations(SearchCoordinatorSvcImpl.toPage(theOffset, toIndex), theTermValueSet.getId());
if (!slice.hasContent()) {
// Slice<TermValueSetConcept> slice = myValueSetConceptDao.findByTermValueSetIdAndPreFetchDesignations(SearchCoordinatorSvcImpl.toPage(theOffset, toIndex), theTermValueSet.getId());
Pageable page = SearchCoordinatorSvcImpl.toPage(theOffset, toIndex);
Collection<TermValueSetConceptView> slice = myTermValueSetConceptViewDao.findConceptsByValueSetPid(theOffset, toIndex, theTermValueSet.getId());
if (slice.isEmpty()) {
logConceptsExpanded(theTermValueSet, conceptsExpanded);
return;
}
for (TermValueSetConcept concept : slice.getContent()) {
ValueSet.ValueSetExpansionContainsComponent containsComponent = theExpansionComponent.addContains();
containsComponent.setSystem(concept.getSystem());
containsComponent.setCode(concept.getCode());
containsComponent.setDisplay(concept.getDisplay());
Map<Long, ValueSet.ValueSetExpansionContainsComponent> pidToConcept = new HashMap<>();
int designationsExpanded = 0;
for (TermValueSetConceptView concept : slice) {
Long conceptPid = concept.getConceptPid();
ValueSet.ValueSetExpansionContainsComponent containsComponent;
if (!pidToConcept.containsKey(conceptPid)) {
containsComponent = theExpansionComponent.addContains();
containsComponent.setSystem(concept.getConceptSystemUrl());
containsComponent.setCode(concept.getConceptCode());
containsComponent.setDisplay(concept.getConceptDisplay());
pidToConcept.put(conceptPid, containsComponent);
} else {
containsComponent = pidToConcept.get(conceptPid);
}
if (concept.getDesigPid() != null) {
ValueSet.ConceptReferenceDesignationComponent designationComponent = containsComponent.addDesignation();
designationComponent.setLanguage(concept.getDesigLang());
designationComponent.setUse(new Coding(
concept.getDesigUseSystem(),
concept.getDesigUseCode(),
concept.getDesigUseDisplay()));
designationComponent.setValue(concept.getDesigVal());
if (++designationsExpanded % 250 == 0) {
logDesignationsExpanded(theTermValueSet, designationsExpanded);
}
logDesignationsExpanded(theTermValueSet, designationsExpanded);
}
// TODO: DM 2019-08-17 - Implement includeDesignations parameter for $expand operation to make this optional.
// FIXME: DM 2019-09-05 - Let's try removing the pre-fetch and the code in BaseHapiTerminologySvcImpl that handles designations so we can compare the processing time. 2/2
expandDesignations(theTermValueSet, concept, containsComponent);
// expandDesignations(theTermValueSet, concept, containsComponent);
if (++conceptsExpanded % 250 == 0) {
logConceptsExpanded(theTermValueSet, conceptsExpanded);
@ -559,30 +594,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
}
}
private void expandDesignations(TermValueSet theValueSet, TermValueSetConcept theConcept, ValueSet.ValueSetExpansionContainsComponent theContainsComponent) {
int designationsExpanded = 0;
for (TermValueSetConceptDesignation designation : theConcept.getDesignations()) {
ValueSet.ConceptReferenceDesignationComponent designationComponent = theContainsComponent.addDesignation();
designationComponent.setLanguage(designation.getLanguage());
designationComponent.setUse(new Coding(
designation.getUseSystem(),
designation.getUseCode(),
designation.getUseDisplay()));
designationComponent.setValue(designation.getValue());
if (++designationsExpanded % 250 == 0) {
logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
}
}
logDesignationsExpanded(theValueSet, theConcept, designationsExpanded);
}
private void logDesignationsExpanded(TermValueSet theValueSet, TermValueSetConcept theConcept, int theDesignationsExpanded) {
private void logDesignationsExpanded(TermValueSet theValueSet, int theDesignationsExpanded) {
if (theDesignationsExpanded > 0) {
// FIXME: DM 2019-09-05 - Account for in progress vs. total.
// FIXME: DM 2019-09-06 - Change to debug.
ourLog.info("Have expanded {} designations for Concept[{}|{}] in ValueSet[{}]", theDesignationsExpanded, theConcept.getSystem(), theConcept.getCode(), theValueSet.getUrl());
ourLog.info("Have expanded {} designations in ValueSet[{}]", theDesignationsExpanded, theValueSet.getUrl());
}
}
@ -972,7 +988,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
if (theCoding.hasSystem() && theCoding.hasCode()) {
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, theCoding.getSystem(), theCoding.getCode()));
}
} else if (theCodeableConcept != null){
} else if (theCodeableConcept != null) {
for (Coding coding : theCodeableConcept.getCoding()) {
if (coding.hasSystem() && coding.hasCode()) {
concepts.addAll(findByValueSetResourcePidSystemAndCode(valueSetResourcePid, coding.getSystem(), coding.getCode()));