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hapi-fhir
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Lots of addition of loinc

This commit is contained in:
James Agnew 2018-03-07 13:33:49 -03:00
parent e31aa760dd
commit 611ee457cb
45 changed files with 1989 additions and 884 deletions
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4
LOINC_NOTES.txt Normal file
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@ -0,0 +1,4 @@
Database migration:
update table TRM_CODESYSTEM_VER drop column RES_VERSION_ID;

17
hapi-fhir-base/src/main/java/ca/uhn/fhir/context/support/IContextValidationSupport.java
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@ -9,9 +9,9 @@ package ca.uhn.fhir.context.support;
* 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.
@ -25,6 +25,17 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import java.util.List;
/**
* This interface is a version-independent representation of the
* various functions that can be provided by validation and terminology
* services.
* <p>
* Implementations are not required to implement all of the functions
* in this interface; in fact it is expected that most won't. Any
* methods which are not implemented may simply return <code>null</code>
* and calling code is expected to be able to handle this.
* </p>
*/
public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST> {
/**
@ -91,7 +102,7 @@ public interface IContextValidationSupport<EVS_IN, EVS_OUT, SDT, CST, CDCT, IST>
*/
CodeValidationResult<CDCT, IST> validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay);
public class CodeValidationResult<CDCT, IST> {
class CodeValidationResult<CDCT, IST> {
private CDCT definition;
private String message;
private IST severity;

6
hapi-fhir-base/src/main/resources/ca/uhn/fhir/i18n/hapi-messages.properties
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@ -91,7 +91,7 @@ ca.uhn.fhir.jpa.dao.SearchBuilder.invalidNumberPrefix=Unable to handle number pr
ca.uhn.fhir.jpa.provider.BaseJpaProvider.cantCombintAtAndSince=Unable to combine _at and _since parameters for history operation
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl.cannotCreateDuplicateCodeSystemUri=Can not create multiple code systems with URI "{0}", already have one with resource ID: {1}
ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!
ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl.expansionTooLarge=Expansion of ValueSet produced too many codes (maximum {0}) - Operation aborted!

12
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
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@ -10,10 +10,7 @@ import ca.uhn.fhir.jpa.dao.ISearchParamRegistry;
import ca.uhn.fhir.jpa.dao.dstu3.SearchParamExtractorDstu3;
import ca.uhn.fhir.jpa.dao.dstu3.SearchParamRegistryDstu3;
import ca.uhn.fhir.jpa.provider.dstu3.TerminologyUploaderProviderDstu3;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.*;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
import ca.uhn.fhir.validation.IValidatorModule;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
@ -113,7 +110,12 @@ public class BaseDstu3Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcDstu3 terminologyService() {
public IHapiTerminologySvc terminologyService() {
return new HapiTerminologySvcImpl();
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcDstu3 terminologyServiceDstu3() {
return new HapiTerminologySvcDstu3();
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/r4/BaseR4Config.java
View File

@ -122,7 +122,7 @@ public class BaseR4Config extends BaseConfig {
}
@Bean(autowire = Autowire.BY_TYPE)
public IHapiTerminologySvcR4 terminologyService() {
public IHapiTerminologySvcR4 terminologyServiceR4() {
return new HapiTerminologySvcR4();
}

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoCodeSystemDstu3.java
View File

@ -232,7 +232,6 @@ public class FhirResourceDaoCodeSystemDstu3 extends FhirResourceDaoDstu3<CodeSys
persCs = new TermCodeSystemVersion();
persCs.setResource(retVal);
persCs.setResourceVersionId(retVal.getVersion());
persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, persCs);

5
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoCodeSystemR4.java
View File

@ -95,7 +95,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
public List<IIdType> findCodeSystemIdsContainingSystemAndCode(String theCode, String theSystem) {
List<IIdType> valueSetIds;
Set<Long> ids = searchForIds(new SearchParameterMap(CodeSystem.SP_CODE, new TokenParam(theSystem, theCode)));
valueSetIds = new ArrayList<IIdType>();
valueSetIds = new ArrayList<>();
for (Long next : ids) {
valueSetIds.add(new IdType("CodeSystem", next));
}
@ -190,7 +190,7 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
}
private List<TermConcept> toPersistedConcepts(List<ConceptDefinitionComponent> theConcept, TermCodeSystemVersion theCodeSystemVersion) {
ArrayList<TermConcept> retVal = new ArrayList<TermConcept>();
ArrayList<TermConcept> retVal = new ArrayList<>();
for (ConceptDefinitionComponent next : theConcept) {
if (isNotBlank(next.getCode())) {
@ -226,7 +226,6 @@ public class FhirResourceDaoCodeSystemR4 extends FhirResourceDaoR4<CodeSystem> i
persCs = new TermCodeSystemVersion();
persCs.setResource(retVal);
persCs.setResourceVersionId(retVal.getVersion());
persCs.getConcepts().addAll(toPersistedConcepts(cs.getConcept(), persCs));
ourLog.info("Code system has {} concepts", persCs.getConcepts().size());
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, codeSystemUrl, persCs);

22
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermCodeSystemVersion.java
View File

@ -62,8 +62,8 @@ public class TermCodeSystemVersion implements Serializable {
@JoinColumn(name = "RES_ID", referencedColumnName = "RES_ID", nullable = false, updatable = false, foreignKey=@ForeignKey(name="FK_CODESYSVER_RES_ID"))
private ResourceTable myResource;
@Column(name = "RES_VERSION_ID", nullable = false, updatable = false)
private Long myResourceVersionId;
@Column(name = "CS_VERSION_ID", nullable = true, updatable = false)
private String myCodeSystemVersionId;
/**
* Constructor
@ -74,7 +74,7 @@ public class TermCodeSystemVersion implements Serializable {
public Collection<TermConcept> getConcepts() {
if (myConcepts == null) {
myConcepts = new ArrayList<TermConcept>();
myConcepts = new ArrayList<>();
}
return myConcepts;
}
@ -88,7 +88,7 @@ public class TermCodeSystemVersion implements Serializable {
final int prime = 31;
int result = 1;
result = prime * result + ((myResource.getId() == null) ? 0 : myResource.getId().hashCode());
result = prime * result + ((myResourceVersionId == null) ? 0 : myResourceVersionId.hashCode());
result = prime * result + ((myCodeSystemVersionId == null) ? 0 : myCodeSystemVersionId.hashCode());
return result;
}
@ -111,11 +111,11 @@ public class TermCodeSystemVersion implements Serializable {
return false;
}
if (myResourceVersionId == null) {
if (other.myResourceVersionId != null) {
if (myCodeSystemVersionId == null) {
if (other.myCodeSystemVersionId != null) {
return false;
}
} else if (!myResourceVersionId.equals(other.myResourceVersionId)) {
} else if (!myCodeSystemVersionId.equals(other.myCodeSystemVersionId)) {
return false;
}
return true;
@ -125,16 +125,16 @@ public class TermCodeSystemVersion implements Serializable {
return myResource;
}
public Long getResourceVersionId() {
return myResourceVersionId;
public String getCodeSystemVersionId() {
return myCodeSystemVersionId;
}
public void setResource(ResourceTable theResource) {
myResource = theResource;
}
public void setResourceVersionId(Long theResourceVersionId) {
myResourceVersionId = theResourceVersionId;
public void setCodeSystemVersionId(String theCodeSystemVersionId) {
myCodeSystemVersionId = theCodeSystemVersionId;
}
}

190
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
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@ -1,5 +1,20 @@
package ca.uhn.fhir.jpa.entity;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.annotations.*;
import javax.annotation.Nonnull;
import javax.persistence.*;
import javax.persistence.Index;
import java.io.Serializable;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -11,9 +26,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* 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.
@ -22,52 +37,12 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.persistence.Column;
import javax.persistence.Entity;
import javax.persistence.FetchType;
import javax.persistence.ForeignKey;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
import javax.persistence.Index;
import javax.persistence.JoinColumn;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.PrePersist;
import javax.persistence.PreUpdate;
import javax.persistence.SequenceGenerator;
import javax.persistence.Table;
import javax.persistence.Transient;
import javax.persistence.UniqueConstraint;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.builder.EqualsBuilder;
import org.apache.commons.lang3.builder.HashCodeBuilder;
import org.apache.commons.lang3.builder.ToStringBuilder;
import org.apache.commons.lang3.builder.ToStringStyle;
import org.hibernate.search.annotations.Analyze;
import org.hibernate.search.annotations.Analyzer;
import org.hibernate.search.annotations.Field;
import org.hibernate.search.annotations.Fields;
import org.hibernate.search.annotations.Indexed;
import org.hibernate.search.annotations.Store;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
@Entity
@Indexed(interceptor=DeferConceptIndexingInterceptor.class)
@Table(name="TRM_CONCEPT", uniqueConstraints= {
@UniqueConstraint(name="IDX_CONCEPT_CS_CODE", columnNames= {"CODESYSTEM_PID", "CODE"})
}, indexes= {
@Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList="INDEX_STATUS")
@Indexed(interceptor = DeferConceptIndexingInterceptor.class)
@Table(name = "TRM_CONCEPT", uniqueConstraints = {
@UniqueConstraint(name = "IDX_CONCEPT_CS_CODE", columnNames = {"CODESYSTEM_PID", "CODE"})
}, indexes = {
@Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList = "INDEX_STATUS")
})
public class TermConcept implements Serializable {
private static final int MAX_DESC_LENGTH = 400;
@ -75,11 +50,11 @@ public class TermConcept implements Serializable {
private static final long serialVersionUID = 1L;
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade= {})
@OneToMany(fetch = FetchType.LAZY, mappedBy = "myParent", cascade = {})
private Collection<TermConceptParentChildLink> myChildren;
@Column(name = "CODE", length = 100, nullable = false)
@Fields({ @Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")), })
@Fields({@Field(name = "myCode", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "exactAnalyzer")),})
private String myCode;
@ManyToOne()
@ -87,10 +62,10 @@ public class TermConcept implements Serializable {
private TermCodeSystemVersion myCodeSystem;
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@Fields({ @Field(name = "myCodeSystemVersionPid") })
@Fields({@Field(name = "myCodeSystemVersionPid")})
private long myCodeSystemVersionPid;
@Column(name="DISPLAY", length=MAX_DESC_LENGTH, nullable=true)
@Column(name = "DISPLAY", length = MAX_DESC_LENGTH, nullable = true)
@Fields({
@Field(name = "myDisplay", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
@Field(name = "myDisplayEdgeNGram", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompleteEdgeAnalyzer")),
@ -99,24 +74,25 @@ public class TermConcept implements Serializable {
})
private String myDisplay;
@OneToMany(mappedBy="myConcept")
@OneToMany(mappedBy = "myConcept")
@Field
@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
private Collection<TermConceptProperty> myProperties;
@Id()
@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PID")
@Column(name = "PID")
private Long myId;
@Column(name = "INDEX_STATUS", nullable = true)
private Long myIndexStatus;
@Transient
@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.YES, analyze = Analyze.YES, analyzer = @Analyzer(definition = "conceptParentPidsAnalyzer"))
private String myParentPids;
@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myChild")
private Collection<TermConceptParentChildLink> myParents;
@Column(name = "CODE_SEQUENCE", nullable = true)
private Integer mySequence;
public TermConcept() {
super();
@ -145,6 +121,16 @@ public class TermConcept implements Serializable {
}
}
public void addProperty(@Nonnull String thePropertyName, @Nonnull String thePropertyValue) {
Validate.notBlank(thePropertyName);
TermConceptProperty property = new TermConceptProperty();
property.setConcept(this);
property.setKey(thePropertyName);
property.setValue(thePropertyValue);
getProperties().add(property);
}
@Override
public boolean equals(Object theObj) {
if (!(theObj instanceof TermConcept)) {
@ -164,7 +150,7 @@ public class TermConcept implements Serializable {
public Collection<TermConceptParentChildLink> getChildren() {
if (myChildren == null) {
myChildren = new ArrayList<TermConceptParentChildLink>();
myChildren = new ArrayList<>();
}
return myChildren;
}
@ -173,14 +159,37 @@ public class TermConcept implements Serializable {
return myCode;
}
public Integer getSequence() {
return mySequence;
}
public void setCode(String theCode) {
myCode = theCode;
}
public TermCodeSystemVersion getCodeSystem() {
return myCodeSystem;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
if (theCodeSystem.getPid() != null) {
myCodeSystemVersionPid = theCodeSystem.getPid();
}
}
public String getDisplay() {
return myDisplay;
}
public TermConcept setDisplay(String theDisplay) {
myDisplay = theDisplay;
if (isNotBlank(theDisplay) && theDisplay.length() > MAX_DESC_LENGTH) {
myDisplay = myDisplay.substring(0, MAX_DESC_LENGTH);
}
return this;
}
public Long getId() {
return myId;
}
@ -189,17 +198,37 @@ public class TermConcept implements Serializable {
return myIndexStatus;
}
public void setIndexStatus(Long theIndexStatus) {
myIndexStatus = theIndexStatus;
}
public String getParentPidsAsString() {
return myParentPids;
}
public Collection<TermConceptParentChildLink> getParents() {
if (myParents == null) {
myParents = new ArrayList<TermConceptParentChildLink>();
myParents = new ArrayList<>();
}
return myParents;
}
public Collection<TermConceptProperty> getProperties() {
if (myProperties == null) {
myProperties = new ArrayList<>();
}
return myProperties;
}
public String getProperty(String thePropertyName) {
for (TermConceptProperty next : getProperties()) {
if (thePropertyName.equals(next.getKey())) {
return next.getValue();
}
}
return null;
}
@Override
public int hashCode() {
HashCodeBuilder b = new HashCodeBuilder();
@ -211,51 +240,31 @@ public class TermConcept implements Serializable {
private void parentPids(TermConcept theNextConcept, Set<Long> theParentPids) {
for (TermConceptParentChildLink nextParentLink : theNextConcept.getParents()) {
TermConcept parent = nextParentLink.getParent();
Long parentConceptId = parent.getId();
Validate.notNull(parentConceptId);
if (parent != null && theParentPids.add(parentConceptId)) {
parentPids(parent, theParentPids);
if (parent != null) {
Long parentConceptId = parent.getId();
Validate.notNull(parentConceptId);
if (theParentPids.add(parentConceptId)) {
parentPids(parent, theParentPids);
}
}
}
}
@SuppressWarnings("unused")
@PreUpdate
@PrePersist
public void prePersist() {
if (myParentPids == null) {
Set<Long> parentPids = new HashSet<Long>();
Set<Long> parentPids = new HashSet<>();
TermConcept entity = this;
parentPids(entity, parentPids);
entity.setParentPids(parentPids);
ourLog.trace("Code {}/{} has parents {}", entity.getId(), entity.getCode(), entity.getParentPidsAsString());
}
}
public void setCode(String theCode) {
myCode = theCode;
}
public void setCodeSystem(TermCodeSystemVersion theCodeSystem) {
myCodeSystem = theCodeSystem;
if (theCodeSystem.getPid() != null) {
myCodeSystemVersionPid = theCodeSystem.getPid();
}
}
public TermConcept setDisplay(String theDisplay) {
myDisplay = theDisplay;
if (isNotBlank(theDisplay) && theDisplay.length() > MAX_DESC_LENGTH) {
myDisplay = myDisplay.substring(0, MAX_DESC_LENGTH);
}
return this;
}
public void setIndexStatus(Long theIndexStatus) {
myIndexStatus = theIndexStatus;
}
public void setParentPids(Set<Long> theParentPids) {
private void setParentPids(Set<Long> theParentPids) {
StringBuilder b = new StringBuilder();
for (Long next : theParentPids) {
if (b.length() > 0) {
@ -275,8 +284,13 @@ public class TermConcept implements Serializable {
myParentPids = theParentPids;
}
public void setSequence(Integer theSequence) {
mySequence = theSequence;
}
@Override
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();
}
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptProperty.java
View File

@ -20,9 +20,11 @@ package ca.uhn.fhir.jpa.entity;
* #L%
*/
import java.io.Serializable;
import org.hibernate.search.annotations.Field;
import org.hibernate.validator.constraints.NotBlank;
import javax.persistence.*;
import java.io.Serializable;
@Entity
@Table(name = "TRM_CONCEPT_PROPERTY", uniqueConstraints = {
@ -43,8 +45,9 @@ public class TermConceptProperty implements Serializable {
private Long myId;
@Column(name="PROP_KEY", length=200, nullable=false)
@NotBlank
private String myKey;
@Column(name="PROP_VAL", length=200, nullable=true)
private String myValue;

39
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptPropertyFieldBridge.java Normal file
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@ -0,0 +1,39 @@
package ca.uhn.fhir.jpa.entity;
import org.apache.lucene.document.Document;
import org.hibernate.search.bridge.FieldBridge;
import org.hibernate.search.bridge.LuceneOptions;
import org.hibernate.search.bridge.StringBridge;
import java.util.Collection;
/**
* Allows hibernate search to index individual concepts' properties
*/
public class TermConceptPropertyFieldBridge implements FieldBridge, StringBridge {
public static final String PROP_PREFIX = "PROP__";
/**
* Constructor
*/
public TermConceptPropertyFieldBridge() {
super();
}
@Override
public String objectToString(Object theObject) {
return theObject.toString();
}
@Override
public void set(String theName, Object theValue, Document theDocument, LuceneOptions theLuceneOptions) {
Collection<TermConceptProperty> properties = (Collection<TermConceptProperty>) theValue;
if (properties != null) {
for (TermConceptProperty next : properties) {
String propValue = next.getKey() + "=" + next.getValue();
theLuceneOptions.addFieldToDocument(theName, propValue, theDocument);
}
}
}
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu2.java
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@ -20,14 +20,12 @@ package ca.uhn.fhir.jpa.term;
* #L%
*/
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.instance.hapi.validation.IValidationSupport;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.List;
public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvc {
public class HapiTerminologySvcDstu2 extends HapiTerminologySvcImpl {
@Autowired
private IValidationSupport myValidationSupport;
@ -39,10 +37,6 @@ public class HapiTerminologySvcDstu2 extends BaseHapiTerminologySvc {
}
@Override
public void storeNewCodeSystemVersion(String theSystem, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails) {
// nothing yet
}
}

239
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -3,36 +3,39 @@ package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.lucene.search.Query;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.dstu3.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.convertors.VersionConvertor_30_40;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.dstu3.model.CodeableConcept;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.StructureDefinition;
import org.hl7.fhir.dstu3.model.ValueSet.*;
import org.hl7.fhir.dstu3.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -47,9 +50,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* 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.
@ -58,14 +61,50 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements IValidationSupport, IHapiTerminologySvcDstu3 {
public class HapiTerminologySvcDstu3 implements IValidationSupport, IHapiTerminologySvcDstu3 {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiTerminologySvcDstu3.class);
private final VersionConvertor_30_40 myConverter;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
protected FhirContext myContext;
@Autowired
protected ITermCodeSystemDao myCodeSystemDao;
@Autowired
private IFhirResourceDaoCodeSystem<CodeSystem, Coding, CodeableConcept> myCodeSystemResourceDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private IHapiTerminologySvc myTerminologySvc;
/**
* Constructor
*/
public HapiTerminologySvcDstu3() {
myConverter = new VersionConvertor_30_40();
}
@Override
public List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
if (system != null) {
findCodesBelow(system, theSystem, theCode, retVal);
}
return retVal;
}
private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
if (isNotBlank(theCode.getCode())) {
theListToPopulate.add(new VersionIndependentConcept(theSystemString, theCode.getCode()));
}
for (ConceptDefinitionComponent nextChild : theCode.getConcept()) {
addAllChildren(theSystemString, nextChild, theListToPopulate);
}
}
private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
if (addedCodes.add(nextConcept.getCode())) {
@ -76,36 +115,20 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
}
@Override
protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
if (system != null) {
findCodesBelow(system, theSystem, theCode, retVal);
}
return retVal;
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}
private void findCodesBelow(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
}
private void findCodesBelow(String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate, List<ConceptDefinitionComponent> conceptList) {
for (ConceptDefinitionComponent next : conceptList) {
if (theCode.equals(next.getCode())) {
addAllChildren(theSystemString, next, theListToPopulate);
} else {
findCodesBelow(theSystemString, theCode, theListToPopulate, next.getConcept());
}
}
}
private void findCodesAbove(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
for (ConceptDefinitionComponent next : conceptList) {
addTreeIfItContainsCode(theSystemString, next, theCode, theListToPopulate);
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
Query textQuery = qb
.phrase()
.withSlop(2)
.onField("myDisplay").boostedTo(4.0f)
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
// .andField("myDisplayNGram").boostedTo(1.0f)
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
}
private boolean addTreeIfItContainsCode(String theSystemString, ConceptDefinitionComponent theNext, String theCode, List<VersionIndependentConcept> theListToPopulate) {
@ -122,18 +145,9 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
return false;
}
private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
if (isNotBlank(theCode.getCode())) {
theListToPopulate.add(new VersionIndependentConcept(theSystemString, theCode.getCode()));
}
for (ConceptDefinitionComponent nextChild : theCode.getConcept()) {
addAllChildren(theSystemString, nextChild, theListToPopulate);
}
}
@Override
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
public List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
if (system != null) {
findCodesAbove(system, theSystem, theCode, retVal);
@ -141,22 +155,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
return retVal;
}
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ConceptSetFilterComponent nextFilter) {
Query textQuery = qb
.phrase()
.withSlop(2)
.onField("myDisplay").boostedTo(4.0f)
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
// .andField("myDisplayNGram").boostedTo(1.0f)
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
}
@Override
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
String system = theInclude.getSystem();
@ -166,7 +164,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
TermCodeSystemVersion csv = cs.getCurrentVersion();
ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
Set<String> addedCodes = new HashSet<String>();
Set<String> addedCodes = new HashSet<>();
boolean haveIncludeCriteria = false;
/*
@ -176,7 +174,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
String nextCode = next.getCode();
if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
haveIncludeCriteria = true;
TermConcept code = super.findCode(system, nextCode);
TermConcept code = myTerminologySvc.findCode(system, nextCode);
if (code != null) {
addedCodes.add(nextCode);
ValueSetExpansionContainsComponent contains = retVal.addContains();
@ -208,8 +206,8 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
}
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
addDisplayFilterExact(qb, bool, nextFilter);
} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == FilterOperator.EQUAL) {
@ -219,7 +217,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
addDisplayFilterInexact(qb, bool, nextFilter);
}
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
TermConcept code = super.findCode(system, nextFilter.getValue());
TermConcept code = myTerminologySvc.findCode(system, nextFilter.getValue());
if (code == null) {
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
}
@ -236,12 +234,12 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
jpaQuery.setMaxResults(1000);
StopWatch sw = new StopWatch();
@SuppressWarnings("unchecked")
List<TermConcept> result = jpaQuery.getResultList();
ourLog.info("Expansion completed in {}ms", sw.getMillis());
for (TermConcept nextConcept : result) {
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
}
@ -250,7 +248,7 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
if (!haveIncludeCriteria) {
List<TermConcept> allCodes = super.findCodes(system);
List<TermConcept> allCodes = myTerminologySvc.findCodes(system);
for (TermConcept nextConcept : allCodes) {
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
}
@ -264,29 +262,6 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
return null;
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet source = new ValueSet();
source.getCompose().addInclude().addValueSet(theValueSet);
try {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
ValueSetExpansionOutcome outcome = worker.expand(source, null);
for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
}
return retVal;
} catch (BaseServerResponseException e) {
throw e;
} catch (Exception e) {
throw new InternalErrorException(e);
}
}
@Override
public List<StructureDefinition> fetchAllStructureDefinitions(FhirContext theContext) {
return Collections.emptyList();
@ -303,25 +278,70 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
return null;
}
// @Override
// public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
// ValueSet source = new ValueSet();
// source.getCompose().addInclude().addValueSet(theValueSet);
// try {
// ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
//
// HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
// ValueSetExpansionOutcome outcome = worker.expand(source, null);
// for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
// retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
// }
//
// return retVal;
//
// } catch (BaseServerResponseException e) {
// throw e;
// } catch (Exception e) {
// throw new InternalErrorException(e);
// }
//
// }
@CoverageIgnore
@Override
public StructureDefinition fetchStructureDefinition(FhirContext theCtx, String theUrl) {
return null;
}
@Override
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return super.supportsSystem(theSystem);
private void findCodesAbove(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
for (ConceptDefinitionComponent next : conceptList) {
addTreeIfItContainsCode(theSystemString, next, theCode, theListToPopulate);
}
}
private void findCodesBelow(CodeSystem theSystem, String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate) {
List<ConceptDefinitionComponent> conceptList = theSystem.getConcept();
findCodesBelow(theSystemString, theCode, theListToPopulate, conceptList);
}
private void findCodesBelow(String theSystemString, String theCode, List<VersionIndependentConcept> theListToPopulate, List<ConceptDefinitionComponent> conceptList) {
for (ConceptDefinitionComponent next : conceptList) {
if (theCode.equals(next.getCode())) {
addAllChildren(theSystemString, next, theListToPopulate);
} else {
findCodesBelow(theSystemString, theCode, theListToPopulate, next.getConcept());
}
}
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(String theSystem, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails) {
CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
cs.setUrl(theSystem);
cs.setContent(CodeSystemContentMode.NOTPRESENT);
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return myTerminologySvc.supportsSystem(theSystem);
}
DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escapeUrlParam(theSystem), theRequestDetails);
@Override
@org.springframework.transaction.annotation.Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(org.hl7.fhir.r4.model.CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets) {
CodeSystem cs = new org.hl7.fhir.dstu3.model.CodeSystem();
cs.setUrl(theCodeSystemResource.getUrl());
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl()), theRequestDetails);
IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
if (createOutcome.getCreated() != Boolean.TRUE) {
CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
@ -336,15 +356,14 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
theCodeSystemVersion.setResource(resource);
theCodeSystemVersion.setResourceVersionId(resource.getVersion());
super.storeNewCodeSystemVersion(codeSystemResourcePid, theSystem, theCodeSystemVersion);
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemVersion);
}
@CoverageIgnore
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
TermConcept code = super.findCode(theCodeSystem, theCode);
TermConcept code = myTerminologySvc.findCode(theCodeSystem, theCode);
if (code != null) {
ConceptDefinitionComponent def = new ConceptDefinitionComponent();
def.setCode(code.getCode());

320
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java → hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcImpl.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* 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.
@ -19,13 +19,32 @@ package ca.uhn.fhir.jpa.term;
* limitations under the License.
* #L%
*/
import java.util.*;
import java.util.concurrent.TimeUnit;
import javax.persistence.*;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemVersionDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptParentChildLinkDao;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.ValidateUtil;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Stopwatch;
import com.google.common.collect.ArrayListMultimap;
import org.apache.commons.lang3.Validate;
import org.apache.commons.lang3.time.DateUtils;
import org.apache.lucene.search.Query;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
@ -37,71 +56,91 @@ import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Stopwatch;
import com.google.common.collect.ArrayListMultimap;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.util.*;
import java.util.concurrent.TimeUnit;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.BaseHapiFhirDao;
import ca.uhn.fhir.jpa.dao.DaoConfig;
import ca.uhn.fhir.jpa.dao.data.*;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ObjectUtil;
import ca.uhn.fhir.util.ValidateUtil;
import static org.apache.commons.lang3.StringUtils.isBlank;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
private static boolean ourForceSaveDeferredAlwaysForUnitTest;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(BaseHapiTerminologySvc.class);
public class HapiTerminologySvcImpl implements IHapiTerminologySvc {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiTerminologySvcImpl.class);
private static final Object PLACEHOLDER_OBJECT = new Object();
private ArrayListMultimap<Long, Long> myChildToParentPidCache;
private static boolean ourForceSaveDeferredAlwaysForUnitTest;
@Autowired
protected ITermCodeSystemDao myCodeSystemDao;
@Autowired
private ITermCodeSystemVersionDao myCodeSystemVersionDao;
@Autowired
protected ITermConceptDao myConceptDao;
private List<TermConceptParentChildLink> myConceptLinksToSaveLater = new ArrayList<TermConceptParentChildLink>();
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
private List<TermConcept> myConceptsToSaveLater = new ArrayList<TermConcept>();
@Autowired
protected FhirContext myContext;
@Autowired
private DaoConfig myDaoConfig;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
private ArrayListMultimap<Long, Long> myChildToParentPidCache;
@Autowired
private ITermCodeSystemVersionDao myCodeSystemVersionDao;
private List<TermConceptParentChildLink> myConceptLinksToSaveLater = new ArrayList<>();
@Autowired
private ITermConceptParentChildLinkDao myConceptParentChildLinkDao;
private List<TermConcept> myConceptsToSaveLater = new ArrayList<>();
@Autowired
private DaoConfig myDaoConfig;
private long myNextReindexPass;
private boolean myProcessDeferred = true;
@Autowired
private PlatformTransactionManager myTransactionMgr;
@Autowired
private IVersionSpecificValidationSupport myVersionSpecificValidationSupport;
private void addCodeIfNotAlreadyAdded(String system, ValueSet.ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
if (addedCodes.add(nextConcept.getCode())) {
ValueSet.ValueSetExpansionContainsComponent contains = retVal.addContains();
contains.setCode(nextConcept.getCode());
contains.setSystem(system);
contains.setDisplay(nextConcept.getDisplay());
}
}
private void addDisplayFilterExact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}
private void addDisplayFilterInexact(QueryBuilder qb, BooleanJunction<?> bool, ValueSet.ConceptSetFilterComponent nextFilter) {
Query textQuery = qb
.phrase()
.withSlop(2)
.onField("myDisplay").boostedTo(4.0f)
.andField("myDisplayEdgeNGram").boostedTo(2.0f)
// .andField("myDisplayNGram").boostedTo(1.0f)
// .andField("myDisplayPhonetic").boostedTo(0.5f)
.sentence(nextFilter.getValue().toLowerCase()).createQuery();
bool.must(textQuery);
}
private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
boolean retVal = theSetToPopulate.add(theConcept);
if (retVal) {
if (theSetToPopulate.size() >= myDaoConfig.getMaximumExpansionSize()) {
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvc.class, "expansionTooLarge", myDaoConfig.getMaximumExpansionSize());
String msg = myContext.getLocalizer().getMessage(HapiTerminologySvcImpl.class, "expansionTooLarge", myDaoConfig.getMaximumExpansionSize());
throw new InvalidRequestException(msg);
}
}
return retVal;
}
@Override
public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
for (TermCodeSystemVersion next : myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystem.getPid())) {
myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
myConceptDao.deleteByCodeSystemVersion(next.getPid());
}
myCodeSystemDao.delete(theCodeSystem.getPid());
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
@ -121,6 +160,127 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return retVal;
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public ValueSet expandValueSet(ValueSet theValueSetToExpand) {
ValueSet.ConceptSetComponent include = theValueSetToExpand.getCompose().getIncludeFirstRep();
String system = include.getSystem();
ourLog.info("Starting expansion around code system: {}", system);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
if (cs == null) {
throw new InvalidRequestException("Unknown code system: " + system);
}
TermCodeSystemVersion csv = cs.getCurrentVersion();
ValueSet.ValueSetExpansionComponent expansionComponent = new ValueSet.ValueSetExpansionComponent();
Set<String> addedCodes = new HashSet<>();
boolean haveIncludeCriteria = false;
/*
* Include Concepts
*/
for (ValueSet.ConceptReferenceComponent next : include.getConcept()) {
String nextCode = next.getCode();
if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
haveIncludeCriteria = true;
TermConcept code = findCode(system, nextCode);
if (code != null) {
addedCodes.add(nextCode);
ValueSet.ValueSetExpansionContainsComponent contains = expansionComponent.addContains();
contains.setCode(nextCode);
contains.setSystem(system);
contains.setDisplay(code.getDisplay());
}
}
}
/*
* Filters
*/
if (include.getFilter().size() > 0) {
haveIncludeCriteria = true;
FullTextEntityManager em = org.hibernate.search.jpa.Search.getFullTextEntityManager(myEntityManager);
QueryBuilder qb = em.getSearchFactory().buildQueryBuilder().forEntity(TermConcept.class).get();
BooleanJunction<?> bool = qb.bool();
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
for (ValueSet.ConceptSetFilterComponent nextFilter : include.getFilter()) {
if (isBlank(nextFilter.getValue()) && nextFilter.getOp() == null && isBlank(nextFilter.getProperty())) {
continue;
}
if (isBlank(nextFilter.getValue()) || nextFilter.getOp() == null || isBlank(nextFilter.getProperty())) {
throw new InvalidRequestException("Invalid filter, must have fields populated: property op value");
}
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
addDisplayFilterExact(qb, bool, nextFilter);
} else if ("display".equals(nextFilter.getProperty()) && nextFilter.getOp() == ValueSet.FilterOperator.EQUAL) {
if (nextFilter.getValue().trim().contains(" ")) {
addDisplayFilterExact(qb, bool, nextFilter);
} else {
addDisplayFilterInexact(qb, bool, nextFilter);
}
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == ValueSet.FilterOperator.ISA) {
TermConcept code = findCode(system, nextFilter.getValue());
if (code == null) {
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
}
ourLog.info(" * Filtering on codes with a parent of {}/{}/{}", code.getId(), code.getCode(), code.getDisplay());
bool.must(qb.keyword().onField("myParentPids").matching("" + code.getId()).createQuery());
} else {
// bool.must(qb.keyword().onField("myProperties").matching(nextFilter.getProperty()+"="+nextFilter.getValue()).createQuery());
bool.must(qb.phrase().onField("myProperties").sentence(nextFilter.getProperty()+"="+nextFilter.getValue()).createQuery());
}
}
Query luceneQuery = bool.createQuery();
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
jpaQuery.setMaxResults(1000);
StopWatch sw = new StopWatch();
@SuppressWarnings("unchecked")
List<TermConcept> result = jpaQuery.getResultList();
ourLog.info("Expansion completed in {}ms", sw.getMillis());
for (TermConcept nextConcept : result) {
addCodeIfNotAlreadyAdded(system, expansionComponent, addedCodes, nextConcept);
}
expansionComponent.setTotal(jpaQuery.getResultSize());
}
if (!haveIncludeCriteria) {
List<TermConcept> allCodes = findCodes(system);
for (TermConcept nextConcept : allCodes) {
addCodeIfNotAlreadyAdded(system, expansionComponent, addedCodes, nextConcept);
}
}
ValueSet valueSet = new ValueSet();
valueSet.setExpansion(expansionComponent);
return valueSet;
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
throw new UnsupportedOperationException(); // FIXME implement
}
private void fetchChildren(TermConcept theConcept, Set<TermConcept> theSetToPopulate) {
for (TermConceptParentChildLink nextChildLink : theConcept.getChildren()) {
TermConcept nextChild = nextChildLink.getChild();
@ -145,6 +305,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
}
}
@Override
public TermConcept findCode(String theCodeSystem, String theCode) {
TermCodeSystemVersion csv = findCurrentCodeSystemVersionForSystem(theCodeSystem);
@ -159,19 +320,19 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
@Transactional(propagation = Propagation.REQUIRED)
@Override
public Set<TermConcept> findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
Stopwatch stopwatch = Stopwatch.createStarted();
StopWatch stopwatch = new StopWatch();
TermConcept concept = fetchLoadedCode(theCodeSystemResourcePid, theCodeSystemVersionPid, theCode);
if (concept == null) {
return Collections.emptySet();
}
Set<TermConcept> retVal = new HashSet<TermConcept>();
Set<TermConcept> retVal = new HashSet<>();
retVal.add(concept);
fetchParents(concept, retVal);
ourLog.info("Fetched {} codes above code {} in {}ms", new Object[] { retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS) });
ourLog.info("Fetched {} codes above code {} in {}ms", new Object[] {retVal.size(), theCode, stopwatch.getMillis()});
return retVal;
}
@ -179,27 +340,15 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
public List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode) {
TermCodeSystem cs = getCodeSystem(theSystem);
if (cs == null) {
return findCodesAboveUsingBuiltInSystems(theSystem, theCode);
return myVersionSpecificValidationSupport.findCodesAboveUsingBuiltInSystems(theSystem, theCode);
}
TermCodeSystemVersion csv = cs.getCurrentVersion();
Set<TermConcept> codes = findCodesAbove(cs.getResource().getId(), csv.getResourceVersionId(), theCode);
Set<TermConcept> codes = findCodesAbove(cs.getResource().getId(), csv.getPid(), theCode);
ArrayList<VersionIndependentConcept> retVal = toVersionIndependentConcepts(theSystem, codes);
return retVal;
}
/**
* Subclasses may override
*
* @param theSystem
* The code system
* @param theCode
* The code
*/
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
public Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemVersionPid, String theCode) {
@ -210,12 +359,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return Collections.emptySet();
}
Set<TermConcept> retVal = new HashSet<TermConcept>();
Set<TermConcept> retVal = new HashSet<>();
retVal.add(concept);
fetchChildren(concept, retVal);
ourLog.info("Fetched {} codes below code {} in {}ms", new Object[] { retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS) });
ourLog.info("Fetched {} codes below code {} in {}ms", new Object[] {retVal.size(), theCode, stopwatch.elapsed(TimeUnit.MILLISECONDS)});
return retVal;
}
@ -223,25 +372,12 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
public List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode) {
TermCodeSystem cs = getCodeSystem(theSystem);
if (cs == null) {
return findCodesBelowUsingBuiltInSystems(theSystem, theCode);
return myVersionSpecificValidationSupport.findCodesBelowUsingBuiltInSystems(theSystem, theCode);
}
TermCodeSystemVersion csv = cs.getCurrentVersion();
Set<TermConcept> codes = findCodesBelow(cs.getResource().getId(), csv.getResourceVersionId(), theCode);
ArrayList<VersionIndependentConcept> retVal = toVersionIndependentConcepts(theSystem, codes);
return retVal;
}
/**
* Subclasses may override
*
* @param theSystem
* The code system
* @param theCode
* The code
*/
protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
return Collections.emptyList();
Set<TermConcept> codes = findCodesBelow(cs.getResource().getId(), csv.getPid(), theCode);
return toVersionIndependentConcepts(theSystem, codes);
}
private TermCodeSystemVersion findCurrentCodeSystemVersionForSystem(String theCodeSystem) {
@ -249,13 +385,11 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
if (cs == null || cs.getCurrentVersion() == null) {
return null;
}
TermCodeSystemVersion csv = cs.getCurrentVersion();
return csv;
return cs.getCurrentVersion();
}
private TermCodeSystem getCodeSystem(String theSystem) {
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(theSystem);
return cs;
return myCodeSystemDao.findByCodeSystemUri(theSystem);
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
@ -314,7 +448,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
if (codeCount > 0) {
ourLog.info("Saved {} deferred concepts ({} codes remain and {} relationships remain) in {}ms ({}ms / code)",
new Object[] { codeCount, myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount) });
new Object[] {codeCount, myConceptsToSaveLater.size(), myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
}
if (codeCount == 0) {
@ -335,7 +469,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
if (relCount > 0) {
ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / code)",
new Object[] { relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount) });
new Object[] {relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
}
if ((myConceptsToSaveLater.size() + myConceptLinksToSaveLater.size()) == 0) {
@ -413,7 +547,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] {count, concepts.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count)});
}
});
@ -517,8 +651,8 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
myCodeSystemDao.save(codeSystem);
} else {
if (!ObjectUtil.equals(codeSystem.getResource().getId(), theCodeSystemVersion.getResource().getId())) {
String msg = myContext.getLocalizer().getMessage(BaseHapiTerminologySvc.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
String msg = myContext.getLocalizer().getMessage(HapiTerminologySvcImpl.class, "cannotCreateDuplicateCodeSystemUri", theSystemUri,
codeSystem.getResource().getIdDt().toUnqualifiedVersionless().getValue());
throw new UnprocessableEntityException(msg);
}
}
@ -582,7 +716,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
}
private int validateConceptForStorage(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, ArrayList<String> theConceptsStack,
IdentityHashMap<TermConcept, Object> theAllConcepts) {
IdentityHashMap<TermConcept, Object> theAllConcepts) {
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystem() != null, "CodesystemValue is null");
ValidateUtil.isTrueOrThrowInvalidRequest(theConcept.getCodeSystem() == theCodeSystem, "CodeSystems are not equal");
ValidateUtil.isNotBlankOrThrowInvalidRequest(theConcept.getCode(), "Codesystem contains a code with no code value");
@ -618,15 +752,5 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourForceSaveDeferredAlwaysForUnitTest = theForceSaveDeferredAlwaysForUnitTest;
}
@Override
public void deleteCodeSystem(TermCodeSystem theCodeSystem) {
ourLog.info(" * Deleting code system {}", theCodeSystem.getPid());
for (TermCodeSystemVersion next : myCodeSystemVersionDao.findByCodeSystemResource(theCodeSystem.getPid())) {
myConceptParentChildLinkDao.deleteByCodeSystemVersion(next.getPid());
myConceptDao.deleteByCodeSystemVersion(next.getPid());
}
myCodeSystemDao.delete(theCodeSystem.getPid());
}
}

111
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcR4.java
View File

@ -1,19 +1,18 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.dao.DaoMethodOutcome;
import ca.uhn.fhir.jpa.dao.IFhirResourceDao;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.BaseServerResponseException;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.CoverageIgnore;
import ca.uhn.fhir.util.StopWatch;
import ca.uhn.fhir.util.UrlUtil;
import org.apache.commons.lang3.Validate;
import org.apache.lucene.search.Query;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
@ -21,21 +20,21 @@ import org.hibernate.search.query.dsl.BooleanJunction;
import org.hibernate.search.query.dsl.QueryBuilder;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.r4.hapi.ctx.HapiWorkerContext;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.r4.model.StructureDefinition;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.r4.model.ValueSet.*;
import org.hl7.fhir.r4.terminologies.ValueSetExpander.ValueSetExpansionOutcome;
import org.hl7.fhir.utilities.validation.ValidationMessage.IssueSeverity;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import java.util.*;
import static org.apache.commons.lang3.StringUtils.isBlank;
@ -50,9 +49,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* 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.
@ -61,15 +60,21 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* #L%
*/
public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IValidationSupport, IHapiTerminologySvcR4 {
public class HapiTerminologySvcR4 implements IHapiTerminologySvcR4 {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(HapiTerminologySvcR4.class);
@Autowired
protected ITermCodeSystemDao myCodeSystemDao;
@PersistenceContext(type = PersistenceContextType.TRANSACTION)
protected EntityManager myEntityManager;
@Autowired
@Qualifier("myCodeSystemDaoR4")
private IFhirResourceDao<CodeSystem> myCodeSystemResourceDao;
@Autowired
private IValidationSupport myValidationSupport;
@Autowired
private IHapiTerminologySvc myTerminologySvc;
@Autowired
private FhirContext myContext;
private void addAllChildren(String theSystemString, ConceptDefinitionComponent theCode, List<VersionIndependentConcept> theListToPopulate) {
if (isNotBlank(theCode.getCode())) {
@ -128,7 +133,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
TermCodeSystemVersion csv = cs.getCurrentVersion();
ValueSetExpansionComponent retVal = new ValueSetExpansionComponent();
Set<String> addedCodes = new HashSet<String>();
Set<String> addedCodes = new HashSet<>();
boolean haveIncludeCriteria = false;
/*
@ -138,7 +143,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
String nextCode = next.getCode();
if (isNotBlank(nextCode) && !addedCodes.contains(nextCode)) {
haveIncludeCriteria = true;
TermConcept code = super.findCode(system, nextCode);
TermConcept code = myTerminologySvc.findCode(system, nextCode);
if (code != null) {
addedCodes.add(nextCode);
ValueSetExpansionContainsComponent contains = retVal.addContains();
@ -181,7 +186,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
addDisplayFilterInexact(qb, bool, nextFilter);
}
} else if ((nextFilter.getProperty().equals("concept") || nextFilter.getProperty().equals("code")) && nextFilter.getOp() == FilterOperator.ISA) {
TermConcept code = super.findCode(system, nextFilter.getValue());
TermConcept code = myTerminologySvc.findCode(system, nextFilter.getValue());
if (code == null) {
throw new InvalidRequestException("Invalid filter criteria - code does not exist: {" + system + "}" + nextFilter.getValue());
}
@ -212,7 +217,7 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
}
if (!haveIncludeCriteria) {
List<TermConcept> allCodes = super.findCodes(system);
List<TermConcept> allCodes = myTerminologySvc.findCodes(system);
for (TermConcept nextConcept : allCodes) {
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
}
@ -221,28 +226,28 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
return retVal;
}
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet source = new ValueSet();
source.getCompose().addInclude().addValueSet(theValueSet);
try {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
ValueSetExpansionOutcome outcome = worker.expand(source, null);
for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
}
return retVal;
} catch (BaseServerResponseException e) {
throw e;
} catch (Exception e) {
throw new InternalErrorException(e);
}
}
// @Override
// public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
// ValueSet source = new ValueSet();
// source.getCompose().addInclude().addValueSet(theValueSet);
// try {
// ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
//
// HapiWorkerContext worker = new HapiWorkerContext(myContext, myValidationSupport);
// ValueSetExpansionOutcome outcome = worker.expand(source, null);
// for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
// retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
// }
//
// return retVal;
//
// } catch (BaseServerResponseException e) {
// throw e;
// } catch (Exception e) {
// throw new InternalErrorException(e);
// }
//
// }
@Override
public List<IBaseResource> fetchAllConformanceResources(FhirContext theContext) {
@ -279,8 +284,8 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
}
@Override
protected List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
public List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
if (system != null) {
findCodesAbove(system, theSystem, theCode, retVal);
@ -304,8 +309,8 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
}
@Override
protected List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
public List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode) {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<>();
CodeSystem system = myValidationSupport.fetchCodeSystem(myContext, theSystem);
if (system != null) {
findCodesBelow(system, theSystem, theCode, retVal);
@ -315,24 +320,15 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
@Override
public boolean isCodeSystemSupported(FhirContext theContext, String theSystem) {
return super.supportsSystem(theSystem);
return myTerminologySvc.supportsSystem(theSystem);
}
@Override
@Transactional(propagation = Propagation.REQUIRED)
public void storeNewCodeSystemVersion(String theSystem, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails) {
CodeSystem cs = new org.hl7.fhir.r4.model.CodeSystem();
cs.setUrl(theSystem);
cs.setContent(CodeSystemContentMode.NOTPRESENT);
public void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets) {
Validate.notBlank(theCodeSystemResource.getUrl(), "theCodeSystemResource must have a URL");
DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escapeUrlParam(theSystem), theRequestDetails);
IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
if (createOutcome.getCreated() != Boolean.TRUE) {
CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
csId = myCodeSystemResourceDao.update(existing, null, false, true, theRequestDetails).getId();
ourLog.info("Created new version of CodeSystem, got ID: {}", csId.toUnqualified().getValue());
}
IIdType csId = myCodeSystemResourceDao.update(theCodeSystemResource, "CodeSystem?url=" + UrlUtil.escapeUrlParam(theCodeSystemResource.getUrl()), theRequestDetails).getId();
ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
Long codeSystemResourcePid = resource.getId();
@ -340,15 +336,14 @@ public class HapiTerminologySvcR4 extends BaseHapiTerminologySvc implements IVal
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
theCodeSystemVersion.setResource(resource);
theCodeSystemVersion.setResourceVersionId(resource.getVersion());
super.storeNewCodeSystemVersion(codeSystemResourcePid, theSystem, theCodeSystemVersion);
myTerminologySvc.storeNewCodeSystemVersion(codeSystemResourcePid, theCodeSystemResource.getUrl(), theCodeSystemVersion);
}
@CoverageIgnore
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {
TermConcept code = super.findCode(theCodeSystem, theCode);
TermConcept code = myTerminologySvc.findCode(theCodeSystem, theCode);
if (code != null) {
ConceptDefinitionComponent def = new ConceptDefinitionComponent();
def.setCode(code.getCode());

43
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvc.java
View File

@ -1,6 +1,12 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.List;
import java.util.Set;
/*
* #%L
@ -11,9 +17,9 @@ import java.util.List;
* 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.
@ -22,35 +28,26 @@ import java.util.List;
* #L%
*/
import java.util.Set;
import ca.uhn.fhir.jpa.entity.TermCodeSystem;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
public interface IHapiTerminologySvc {
void deleteCodeSystem(TermCodeSystem thePersCs);
ValueSet expandValueSet(ValueSet theValueSetToExpand);
List<VersionIndependentConcept> expandValueSet(String theValueSet);
TermConcept findCode(String theCodeSystem, String theCode);
List<TermConcept> findCodes(String theSystem);
Set<TermConcept> findCodesAbove(Long theCodeSystemResourcePid, Long theCodeSystemResourceVersionPid, String theCode);
List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode);
Set<TermConcept> findCodesBelow(Long theCodeSystemResourcePid, Long theCodeSystemResourceVersionPid, String theCode);
List<VersionIndependentConcept> findCodesBelow(String theSystem, String theCode);
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, TermCodeSystemVersion theCodeSytemVersion);
public boolean supportsSystem(String theCodeSystem);
List<VersionIndependentConcept> expandValueSet(String theValueSet);
List<VersionIndependentConcept> findCodesAbove(String theSystem, String theCode);
void storeNewCodeSystemVersion(String theSystem, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails);
List<TermConcept> findCodes(String theSystem);
void saveDeferred();
/**
@ -59,4 +56,8 @@ public interface IHapiTerminologySvc {
*/
void setProcessDeferred(boolean theProcessDeferred);
void storeNewCodeSystemVersion(Long theCodeSystemResourcePid, String theSystemUri, TermCodeSystemVersion theCodeSytemVersion);
boolean supportsSystem(String theCodeSystem);
}

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvcDstu3.java
View File

@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
import org.hl7.fhir.dstu3.hapi.ctx.IValidationSupport;
public interface IHapiTerminologySvcDstu3 extends IHapiTerminologySvc, IValidationSupport {
// nothing
public interface IHapiTerminologySvcDstu3 extends IValidationSupport, IVersionSpecificValidationSupport {
}

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IHapiTerminologySvcR4.java
View File

@ -9,9 +9,9 @@ package ca.uhn.fhir.jpa.term;
* 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.
@ -22,6 +22,6 @@ package ca.uhn.fhir.jpa.term;
import org.hl7.fhir.r4.hapi.ctx.IValidationSupport;
public interface IHapiTerminologySvcR4 extends IHapiTerminologySvc, IValidationSupport {
// nothing
public interface IHapiTerminologySvcR4 extends IValidationSupport {
}

7
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IRecordHandler.java Normal file
View File

@ -0,0 +1,7 @@
package ca.uhn.fhir.jpa.term;
import org.apache.commons.csv.CSVRecord;
public interface IRecordHandler {
void accept(CSVRecord theRecord);
}

18
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/IVersionSpecificValidationSupport.java Normal file
View File

@ -0,0 +1,18 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.List;
public interface IVersionSpecificValidationSupport {
List<VersionIndependentConcept> findCodesAboveUsingBuiltInSystems(String theSystem, String theCode);
List<VersionIndependentConcept> findCodesBelowUsingBuiltInSystems(String theSystem, String theCode);
void storeNewCodeSystemVersion(CodeSystem theCodeSystemResource, TermCodeSystemVersion theCodeSystemVersion, RequestDetails theRequestDetails, List<ValueSet> theValueSets);
}

461
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvc.java
View File

@ -1,5 +1,40 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.loinc.LoincAnswerListHandler;
import ca.uhn.fhir.jpa.term.loinc.LoincHandler;
import ca.uhn.fhir.jpa.term.loinc.LoincHierarchyHandler;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerConcept;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerDescription;
import ca.uhn.fhir.jpa.term.snomedct.SctHandlerRelationship;
import ca.uhn.fhir.jpa.util.Counter;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVParser;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.csv.QuoteMode;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.apache.commons.lang3.ObjectUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import org.springframework.beans.factory.annotation.Autowired;
import java.io.*;
import java.util.*;
import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
/*
@ -11,9 +46,9 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* 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.
@ -21,47 +56,29 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
* limitations under the License.
* #L%
*/
import java.io.*;
import java.util.*;
import java.util.Map.Entry;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.apache.commons.csv.*;
import org.apache.commons.io.IOUtils;
import org.apache.commons.io.input.BOMInputStream;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
import org.springframework.beans.factory.annotation.Autowired;
import com.google.common.annotations.VisibleForTesting;
import com.google.common.base.Charsets;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.util.Counter;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
private static final int LOG_INCREMENT = 100000;
public static final String LOINC_FILE = "loinc.csv";
public static final String LOINC_HIERARCHY_FILE = "MULTI-AXIAL_HIERARCHY.CSV";
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvc.class);
public static final String LOINC_ANSWERLIST_FILE = "AnswerList_Beta_1.csv";
public static final String LOINC_ANSWERLIST_LINK_FILE = "LoincAnswerListLink_Beta_1.csv";
public static final String SCT_FILE_CONCEPT = "Terminology/sct2_Concept_Full_";
public static final String SCT_FILE_DESCRIPTION = "Terminology/sct2_Description_Full-en";
public static final String SCT_FILE_RELATIONSHIP = "Terminology/sct2_Relationship_Full";
private static final int LOG_INCREMENT = 100000;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvc.class);
@Autowired
private IHapiTerminologySvc myTermSvc;
@Autowired(required = false)
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Autowired(required = false)
private IHapiTerminologySvcR4 myTermSvcR4;
private void dropCircularRefs(TermConcept theConcept, ArrayList<String> theChain, Map<String, TermConcept> theCode2concept, Counter theCircularCounter) {
theChain.add(theConcept.getCode());
for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext();) {
for (Iterator<TermConceptParentChildLink> childIter = theConcept.getChildren().iterator(); childIter.hasNext(); ) {
TermConceptParentChildLink next = childIter.next();
TermConcept nextChild = next.getChild();
if (theChain.contains(nextChild.getCode())) {
@ -82,7 +99,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
ourLog.info(b.toString(), theConcept.getCode());
childIter.remove();
nextChild.getParents().remove(next);
} else {
dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
}
@ -91,71 +108,21 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
}
private void extractFiles(List<byte[]> theZipBytes, List<String> theExpectedFilenameFragments) {
Set<String> foundFragments = new HashSet<String>();
for (byte[] nextZipBytes : theZipBytes) {
ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new ByteArrayInputStream(nextZipBytes)));
try {
for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null;) {
for (String next : theExpectedFilenameFragments) {
if (nextEntry.getName().contains(next)) {
foundFragments.add(next);
}
}
}
} catch (IOException e) {
throw new InternalErrorException(e);
} finally {
IOUtils.closeQuietly(zis);
}
}
for (String next : theExpectedFilenameFragments) {
if (!foundFragments.contains(next)) {
throw new InvalidRequestException("Invalid input zip file, expected zip to contain the following name fragments: " + theExpectedFilenameFragments + " but found: " + foundFragments);
}
}
}
public String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
private TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystem(codeSystemVersion);
}
return concept;
}
private void iterateOverZipFile(List<byte[]> theZipBytes, String fileNamePart, IRecordHandler handler, char theDelimiter, QuoteMode theQuoteMode) {
boolean found = false;
for (byte[] nextZipBytes : theZipBytes) {
ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new ByteArrayInputStream(nextZipBytes)));
try {
for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null;) {
ZippedFileInputStream inputStream = new ZippedFileInputStream(zis);
for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null; ) {
String nextFilename = nextEntry.getName();
if (nextFilename.contains(fileNamePart)) {
ourLog.info("Processing file {}", nextFilename);
found = true;
Reader reader = null;
CSVParser parsed = null;
Reader reader;
CSVParser parsed;
try {
reader = new InputStreamReader(new BOMInputStream(zis), Charsets.UTF_8);
CSVFormat format = CSVFormat.newFormat(theDelimiter).withFirstRecordAsHeader();
@ -197,9 +164,11 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
@Override
public UploadStatistics loadLoinc(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
List<String> expectedFilenameFragments = Arrays.asList(LOINC_FILE, LOINC_HIERARCHY_FILE);
List<String> expectedFilenameFragments = Arrays.asList(
LOINC_FILE,
LOINC_HIERARCHY_FILE);
extractFiles(theZipBytes, expectedFilenameFragments);
verifyMandatoryFilesExist(theZipBytes, expectedFilenameFragments);
ourLog.info("Beginning LOINC processing");
@ -210,7 +179,7 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
public UploadStatistics loadSnomedCt(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
List<String> expectedFilenameFragments = Arrays.asList(SCT_FILE_DESCRIPTION, SCT_FILE_RELATIONSHIP, SCT_FILE_CONCEPT);
extractFiles(theZipBytes, expectedFilenameFragments);
verifyMandatoryFilesExist(theZipBytes, expectedFilenameFragments);
ourLog.info("Beginning SNOMED CT processing");
@ -219,23 +188,41 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
UploadStatistics processLoincFiles(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> code2concept = new HashMap<String, TermConcept>();
final Map<String, TermConcept> code2concept = new HashMap<>();
final List<ValueSet> valueSets = new ArrayList<>();
IRecordHandler handler = new LoincHandler(codeSystemVersion, code2concept);
CodeSystem loincCs;
try {
String loincCsString = IOUtils.toString(HapiTerminologySvcImpl.class.getResourceAsStream("/ca/uhn/fhir/jpa/term/loinc/loinc.xml"), Charsets.UTF_8);
loincCs = FhirContext.forR4().newXmlParser().parseResource(CodeSystem.class, loincCsString);
} catch (IOException e) {
throw new InternalErrorException("Failed to load loinc.xml", e);
}
Set<String> propertyNames = new HashSet<>();
for (CodeSystem.PropertyComponent nextProperty : loincCs.getProperty()) {
if (isNotBlank(nextProperty.getCode())) {
propertyNames.add(nextProperty.getCode());
}
}
IRecordHandler handler;
// Loinc Codes
handler = new LoincHandler(codeSystemVersion, code2concept, propertyNames);
iterateOverZipFile(theZipBytes, LOINC_FILE, handler, ',', QuoteMode.NON_NUMERIC);
// Loinc Hierarchy
handler = new LoincHierarchyHandler(codeSystemVersion, code2concept);
iterateOverZipFile(theZipBytes, LOINC_HIERARCHY_FILE, handler, ',', QuoteMode.NON_NUMERIC);
// Answer lists (ValueSets of potential answers/values for loinc "questions")
handler = new LoincAnswerListHandler(codeSystemVersion, code2concept, propertyNames, valueSets);
iterateOverZipFile(theZipBytes, LOINC_ANSWERLIST_FILE, handler, ',', QuoteMode.NON_NUMERIC);
theZipBytes.clear();
for (Iterator<Entry<String, TermConcept>> iter = code2concept.entrySet().iterator(); iter.hasNext();) {
Entry<String, TermConcept> next = iter.next();
// if (isBlank(next.getKey())) {
// ourLog.info("Removing concept with blankc code[{}] and display [{}", next.getValue().getCode(), next.getValue().getDisplay());
// iter.remove();
// continue;
// }
for (Entry<String, TermConcept> next : code2concept.entrySet()) {
TermConcept nextConcept = next.getValue();
if (nextConcept.getParents().isEmpty()) {
codeSystemVersion.getConcepts().add(nextConcept);
@ -244,18 +231,11 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
ourLog.info("Have {} total concepts, {} root concepts", code2concept.size(), codeSystemVersion.getConcepts().size());
String url = LOINC_URL;
storeCodeSystem(theRequestDetails, codeSystemVersion, url);
storeCodeSystem(theRequestDetails, codeSystemVersion, loincCs, valueSets);
return new UploadStatistics(code2concept.size());
}
private void storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion codeSystemVersion, String url) {
myTermSvc.setProcessDeferred(false);
myTermSvc.storeNewCodeSystemVersion(url, codeSystemVersion, theRequestDetails);
myTermSvc.setProcessDeferred(true);
}
UploadStatistics processSnomedCtFiles(List<byte[]> theZipBytes, RequestDetails theRequestDetails) {
final TermCodeSystemVersion codeSystemVersion = new TermCodeSystemVersion();
final Map<String, TermConcept> id2concept = new HashMap<String, TermConcept>();
@ -284,244 +264,99 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
iter.remove();
}
}
ourLog.info("Done loading SNOMED CT files - {} root codes, {} total codes", rootConcepts.size(), code2concept.size());
Counter circularCounter = new Counter();
for (TermConcept next : rootConcepts.values()) {
long count = circularCounter.getThenAdd();
float pct = ((float)count / rootConcepts.size()) * 100.0f;
float pct = ((float) count / rootConcepts.size()) * 100.0f;
ourLog.info(" * Scanning for circular refs - have scanned {} / {} codes ({}%)", count, rootConcepts.size(), pct);
dropCircularRefs(next, new ArrayList<String>(), code2concept, circularCounter);
}
codeSystemVersion.getConcepts().addAll(rootConcepts.values());
String url = SCT_URL;
storeCodeSystem(theRequestDetails, codeSystemVersion, url);
CodeSystem cs = new org.hl7.fhir.r4.model.CodeSystem();
cs.setUrl(SCT_URL);
cs.setContent(CodeSystem.CodeSystemContentMode.NOTPRESENT);
storeCodeSystem(theRequestDetails, codeSystemVersion, cs, null);
return new UploadStatistics(code2concept.size());
}
@VisibleForTesting
void setTermSvcDstu3ForUnitTest(IHapiTerminologySvcDstu3 theTermSvcDstu3) {
myTermSvcDstu3 = theTermSvcDstu3;
}
@VisibleForTesting
void setTermSvcForUnitTests(IHapiTerminologySvc theTermSvc) {
myTermSvc = theTermSvc;
}
private interface IRecordHandler {
void accept(CSVRecord theRecord);
private void storeCodeSystem(RequestDetails theRequestDetails, final TermCodeSystemVersion theCodeSystemVersion, CodeSystem theCodeSystem, List<ValueSet> theValueSets) {
Validate.isTrue(theCodeSystem.getContent() == CodeSystem.CodeSystemContentMode.NOTPRESENT);
List<ValueSet> valueSets = ObjectUtils.defaultIfNull(theValueSets, Collections.<ValueSet>emptyList());
myTermSvc.setProcessDeferred(false);
if (myTermSvcDstu3 != null) {
myTermSvcDstu3.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets);
} else {
myTermSvcR4.storeNewCodeSystemVersion(theCodeSystem, theCodeSystemVersion, theRequestDetails, valueSets);
}
myTermSvc.setProcessDeferred(true);
}
public class LoincHandler implements IRecordHandler {
private void verifyMandatoryFilesExist(List<byte[]> theZipBytes, List<String> theExpectedFilenameFragments) {
Set<String> foundFragments = new HashSet<>();
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
public LoincHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {
myCodeSystemVersion = theCodeSystemVersion;
myCode2Concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String code = theRecord.get("LOINC_NUM");
if (isNotBlank(code)) {
String longCommonName = theRecord.get("LONG_COMMON_NAME");
String shortName = theRecord.get("SHORTNAME");
String consumerName = theRecord.get("CONSUMER_NAME");
String display = firstNonBlank(longCommonName, shortName, consumerName);
TermConcept concept = new TermConcept(myCodeSystemVersion, code);
concept.setDisplay(display);
Validate.isTrue(!myCode2Concept.containsKey(code));
myCode2Concept.put(code, concept);
}
}
}
public class LoincHierarchyHandler implements IRecordHandler {
private Map<String, TermConcept> myCode2Concept;
private TermCodeSystemVersion myCodeSystemVersion;
public LoincHierarchyHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {
myCodeSystemVersion = theCodeSystemVersion;
myCode2Concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String parentCode = theRecord.get("IMMEDIATE_PARENT");
String childCode = theRecord.get("CODE");
String childCodeText = theRecord.get("CODE_TEXT");
if (isNotBlank(parentCode) && isNotBlank(childCode)) {
TermConcept parent = getOrCreate(parentCode, "(unknown)");
TermConcept child = getOrCreate(childCode, childCodeText);
parent.addChild(child, RelationshipTypeEnum.ISA);
}
}
private TermConcept getOrCreate(String theCode, String theDisplay) {
TermConcept retVal = myCode2Concept.get(theCode);
if (retVal == null) {
retVal = new TermConcept();
retVal.setCodeSystem(myCodeSystemVersion);
retVal.setCode(theCode);
retVal.setDisplay(theDisplay);
myCode2Concept.put(theCode, retVal);
}
return retVal;
}
}
private final class SctHandlerConcept implements IRecordHandler {
private Set<String> myValidConceptIds;
private Map<String, String> myConceptIdToMostRecentDate = new HashMap<String, String>();
public SctHandlerConcept(Set<String> theValidConceptIds) {
myValidConceptIds = theValidConceptIds;
}
@Override
public void accept(CSVRecord theRecord) {
String id = theRecord.get("id");
String date = theRecord.get("effectiveTime");
if (!myConceptIdToMostRecentDate.containsKey(id) || myConceptIdToMostRecentDate.get(id).compareTo(date) < 0) {
boolean active = "1".equals(theRecord.get("active"));
if (active) {
myValidConceptIds.add(id);
} else {
myValidConceptIds.remove(id);
}
myConceptIdToMostRecentDate.put(id, date);
}
}
}
private final class SctHandlerDescription implements IRecordHandler {
private final Map<String, TermConcept> myCode2concept;
private final TermCodeSystemVersion myCodeSystemVersion;
private final Map<String, TermConcept> myId2concept;
private Set<String> myValidConceptIds;
private SctHandlerDescription(Set<String> theValidConceptIds, Map<String, TermConcept> theCode2concept, Map<String, TermConcept> theId2concept, TermCodeSystemVersion theCodeSystemVersion) {
myCode2concept = theCode2concept;
myId2concept = theId2concept;
myCodeSystemVersion = theCodeSystemVersion;
myValidConceptIds = theValidConceptIds;
}
@Override
public void accept(CSVRecord theRecord) {
String id = theRecord.get("id");
boolean active = "1".equals(theRecord.get("active"));
if (!active) {
return;
}
String conceptId = theRecord.get("conceptId");
if (!myValidConceptIds.contains(conceptId)) {
return;
}
String term = theRecord.get("term");
TermConcept concept = getOrCreateConcept(myCodeSystemVersion, myId2concept, id);
concept.setCode(conceptId);
concept.setDisplay(term);
myCode2concept.put(conceptId, concept);
}
}
private final class SctHandlerRelationship implements IRecordHandler {
private final Map<String, TermConcept> myCode2concept;
private final TermCodeSystemVersion myCodeSystemVersion;
private final Map<String, TermConcept> myRootConcepts;
private SctHandlerRelationship(TermCodeSystemVersion theCodeSystemVersion, HashMap<String, TermConcept> theRootConcepts, Map<String, TermConcept> theCode2concept) {
myCodeSystemVersion = theCodeSystemVersion;
myRootConcepts = theRootConcepts;
myCode2concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
Set<String> ignoredTypes = new HashSet<String>();
ignoredTypes.add("Method (attribute)");
ignoredTypes.add("Direct device (attribute)");
ignoredTypes.add("Has focus (attribute)");
ignoredTypes.add("Access instrument");
ignoredTypes.add("Procedure site (attribute)");
ignoredTypes.add("Causative agent (attribute)");
ignoredTypes.add("Course (attribute)");
ignoredTypes.add("Finding site (attribute)");
ignoredTypes.add("Has definitional manifestation (attribute)");
String sourceId = theRecord.get("sourceId");
String destinationId = theRecord.get("destinationId");
String typeId = theRecord.get("typeId");
boolean active = "1".equals(theRecord.get("active"));
TermConcept typeConcept = myCode2concept.get(typeId);
TermConcept sourceConcept = myCode2concept.get(sourceId);
TermConcept targetConcept = myCode2concept.get(destinationId);
if (sourceConcept != null && targetConcept != null && typeConcept != null) {
if (typeConcept.getDisplay().equals("Is a (attribute)")) {
RelationshipTypeEnum relationshipType = RelationshipTypeEnum.ISA;
if (!sourceId.equals(destinationId)) {
if (active) {
TermConceptParentChildLink link = new TermConceptParentChildLink();
link.setChild(sourceConcept);
link.setParent(targetConcept);
link.setRelationshipType(relationshipType);
link.setCodeSystem(myCodeSystemVersion);
targetConcept.addChild(sourceConcept, relationshipType);
} else {
// not active, so we're removing any existing links
for (TermConceptParentChildLink next : new ArrayList<TermConceptParentChildLink>(targetConcept.getChildren())) {
if (next.getRelationshipType() == relationshipType) {
if (next.getChild().getCode().equals(sourceConcept.getCode())) {
next.getParent().getChildren().remove(next);
next.getChild().getParents().remove(next);
}
}
}
for (byte[] nextZipBytes : theZipBytes) {
ZipInputStream zis = new ZipInputStream(new BufferedInputStream(new ByteArrayInputStream(nextZipBytes)));
try {
for (ZipEntry nextEntry; (nextEntry = zis.getNextEntry()) != null; ) {
for (String next : theExpectedFilenameFragments) {
if (nextEntry.getName().contains(next)) {
foundFragments.add(next);
}
}
} else if (ignoredTypes.contains(typeConcept.getDisplay())) {
// ignore
} else {
// ourLog.warn("Unknown relationship type: {}/{}", typeId, typeConcept.getDisplay());
}
} catch (IOException e) {
throw new InternalErrorException(e);
} finally {
IOUtils.closeQuietly(zis);
}
}
for (String next : theExpectedFilenameFragments) {
if (!foundFragments.contains(next)) {
throw new InvalidRequestException("Invalid input zip file, expected zip to contain the following name fragments: " + theExpectedFilenameFragments + " but found: " + foundFragments);
}
}
}
private static class ZippedFileInputStream extends InputStream {
private ZipInputStream is;
public ZippedFileInputStream(ZipInputStream is) {
this.is = is;
}
@Override
public void close() throws IOException {
is.closeEntry();
}
@Override
public int read() throws IOException {
return is.read();
public static String firstNonBlank(String... theStrings) {
String retVal = "";
for (String nextString : theStrings) {
if (isNotBlank(nextString)) {
retVal = nextString;
break;
}
}
return retVal;
}
public static TermConcept getOrCreateConcept(TermCodeSystemVersion codeSystemVersion, Map<String, TermConcept> id2concept, String id) {
TermConcept concept = id2concept.get(id);
if (concept == null) {
concept = new TermConcept();
id2concept.put(id, concept);
concept.setCodeSystem(codeSystemVersion);
}
return concept;
}
}

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hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincAnswerListHandler.java Normal file
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package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IHapiTerminologyLoaderSvc;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import org.hl7.fhir.r4.model.Enumerations;
import org.hl7.fhir.r4.model.ValueSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincAnswerListHandler implements IRecordHandler {
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
private final Set<String> myPropertyNames;
private final List<ValueSet> myValueSets;
private final Map<String, ValueSet> myIdToValueSet = new HashMap<>();
public LoincAnswerListHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept, Set<String> thePropertyNames, List<ValueSet> theValueSets) {
myCodeSystemVersion = theCodeSystemVersion;
myCode2Concept = theCode2concept;
myPropertyNames = thePropertyNames;
myValueSets = theValueSets;
}
@Override
public void accept(CSVRecord theRecord) {
// this is the code for the list (will repeat)
String answerListId = trim(theRecord.get("AnswerListId"));
String answerListName = trim(theRecord.get("AnswerListName"));
String answerListOid = trim(theRecord.get("AnswerListOID"));
String externallyDefined = trim(theRecord.get("ExtDefinedYN"));
String extenrallyDefinedCs = trim(theRecord.get("ExtDefinedAnswerListCodeSystem"));
String externallyDefinedLink = trim(theRecord.get("ExtDefinedAnswerListLink"));
// this is the code for the actual answer (will not repeat)
String answerString = trim(theRecord.get("AnswerStringId"));
String sequenceNumber = trim(theRecord.get("SequenceNumber"));
String displayText = trim(theRecord.get("DisplayText"));
String extCodeId = trim(theRecord.get("ExtCodeId"));
String extCodeDisplayName = trim(theRecord.get("ExtCodeDisplayName"));
String extCodeSystem = trim(theRecord.get("ExtCodeSystem"));
String extCodeSystemVersion = trim(theRecord.get("ExtCodeSystemVersion"));
// Answer list code
if (!myCode2Concept.containsKey(answerListId)) {
TermConcept concept = new TermConcept(myCodeSystemVersion, answerListId);
concept.setDisplay(answerListName);
myCode2Concept.put(answerListId, concept);
}
// Answer code
if (!myCode2Concept.containsKey(answerString)) {
TermConcept concept = new TermConcept(myCodeSystemVersion, answerString);
concept.setDisplay(displayText);
if (isNotBlank(sequenceNumber) && sequenceNumber.matches("^[0-9]$")) {
concept.setSequence(Integer.parseInt(sequenceNumber));
}
myCode2Concept.put(answerString, concept);
}
// Answer list ValueSet
ValueSet vs;
if (!myIdToValueSet.containsKey(answerListId)) {
vs = new ValueSet();
vs.setUrl("urn:oid:" + answerListOid);
vs.addIdentifier()
.setSystem(IHapiTerminologyLoaderSvc.LOINC_URL)
.setValue(answerListId);
vs.setId(answerListId);
vs.setName(answerListName);
vs.setStatus(Enumerations.PublicationStatus.ACTIVE);
myIdToValueSet.put(answerListId, vs);
myValueSets.add(vs);
} else {
vs = myIdToValueSet.get(answerListId);
}
vs
.getCompose()
.getIncludeFirstRep()
.setSystem(IHapiTerminologyLoaderSvc.LOINC_URL)
.addConcept()
.setCode(answerString)
.setDisplay(displayText);
}
}

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hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHandler.java Normal file
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package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvc;
import org.apache.commons.csv.CSVRecord;
import org.apache.commons.lang3.Validate;
import java.util.Map;
import java.util.Set;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincHandler implements IRecordHandler {
private final Map<String, TermConcept> myCode2Concept;
private final TermCodeSystemVersion myCodeSystemVersion;
private final Set<String> myPropertyNames;
public LoincHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept, Set<String> thePropertyNames) {
myCodeSystemVersion = theCodeSystemVersion;
myCode2Concept = theCode2concept;
myPropertyNames = thePropertyNames;
}
@Override
public void accept(CSVRecord theRecord) {
String code = trim(theRecord.get("LOINC_NUM"));
if (isNotBlank(code)) {
String longCommonName = trim(theRecord.get("LONG_COMMON_NAME"));
String shortName = trim(theRecord.get("SHORTNAME"));
String consumerName = trim(theRecord.get("CONSUMER_NAME"));
String display = TerminologyLoaderSvc.firstNonBlank(longCommonName, shortName, consumerName);
TermConcept concept = new TermConcept(myCodeSystemVersion, code);
concept.setDisplay(display);
for (String nextPropertyName : myPropertyNames) {
if (!theRecord.toMap().containsKey(nextPropertyName)) {
continue;
}
String nextPropertyValue = theRecord.get(nextPropertyName);
if (isNotBlank(nextPropertyValue)) {
concept.addProperty(nextPropertyName, nextPropertyValue);
}
}
Validate.isTrue(!myCode2Concept.containsKey(code));
myCode2Concept.put(code, concept);
}
}
}

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hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/loinc/LoincHierarchyHandler.java Normal file
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package ca.uhn.fhir.jpa.term.loinc;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import java.util.Map;
import static org.apache.commons.lang3.StringUtils.isNotBlank;
import static org.apache.commons.lang3.StringUtils.trim;
public class LoincHierarchyHandler implements IRecordHandler {
private Map<String, TermConcept> myCode2Concept;
private TermCodeSystemVersion myCodeSystemVersion;
public LoincHierarchyHandler(TermCodeSystemVersion theCodeSystemVersion, Map<String, TermConcept> theCode2concept) {
myCodeSystemVersion = theCodeSystemVersion;
myCode2Concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
String parentCode = trim(theRecord.get("IMMEDIATE_PARENT"));
String childCode = trim(theRecord.get("CODE"));
String childCodeText = trim(theRecord.get("CODE_TEXT"));
if (isNotBlank(parentCode) && isNotBlank(childCode)) {
TermConcept parent = getOrCreate(parentCode, "(unknown)");
TermConcept child = getOrCreate(childCode, childCodeText);
parent.addChild(child, TermConceptParentChildLink.RelationshipTypeEnum.ISA);
}
}
private TermConcept getOrCreate(String theCode, String theDisplay) {
TermConcept retVal = myCode2Concept.get(theCode);
if (retVal == null) {
retVal = new TermConcept();
retVal.setCodeSystem(myCodeSystemVersion);
retVal.setCode(theCode);
retVal.setDisplay(theDisplay);
myCode2Concept.put(theCode, retVal);
}
return retVal;
}
}

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hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/snomedct/SctHandlerConcept.java Normal file
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package ca.uhn.fhir.jpa.term.snomedct;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
public final class SctHandlerConcept implements IRecordHandler {
private Set<String> myValidConceptIds;
private Map<String, String> myConceptIdToMostRecentDate = new HashMap<String, String>();
public SctHandlerConcept(Set<String> theValidConceptIds) {
myValidConceptIds = theValidConceptIds;
}
@Override
public void accept(CSVRecord theRecord) {
String id = theRecord.get("id");
String date = theRecord.get("effectiveTime");
if (!myConceptIdToMostRecentDate.containsKey(id) || myConceptIdToMostRecentDate.get(id).compareTo(date) < 0) {
boolean active = "1".equals(theRecord.get("active"));
if (active) {
myValidConceptIds.add(id);
} else {
myValidConceptIds.remove(id);
}
myConceptIdToMostRecentDate.put(id, date);
}
}
}

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package ca.uhn.fhir.jpa.term.snomedct;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import ca.uhn.fhir.jpa.term.TerminologyLoaderSvc;
import org.apache.commons.csv.CSVRecord;
import java.util.Map;
import java.util.Set;
public final class SctHandlerDescription implements IRecordHandler {
private final Map<String, TermConcept> myCode2concept;
private final TermCodeSystemVersion myCodeSystemVersion;
private final Map<String, TermConcept> myId2concept;
private Set<String> myValidConceptIds;
public SctHandlerDescription(Set<String> theValidConceptIds, Map<String, TermConcept> theCode2concept, Map<String, TermConcept> theId2concept, TermCodeSystemVersion theCodeSystemVersion) {
myCode2concept = theCode2concept;
myId2concept = theId2concept;
myCodeSystemVersion = theCodeSystemVersion;
myValidConceptIds = theValidConceptIds;
}
@Override
public void accept(CSVRecord theRecord) {
String id = theRecord.get("id");
boolean active = "1".equals(theRecord.get("active"));
if (!active) {
return;
}
String conceptId = theRecord.get("conceptId");
if (!myValidConceptIds.contains(conceptId)) {
return;
}
String term = theRecord.get("term");
TermConcept concept = TerminologyLoaderSvc.getOrCreateConcept(myCodeSystemVersion, myId2concept, id);
concept.setCode(conceptId);
concept.setDisplay(term);
myCode2concept.put(conceptId, concept);
}
}

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package ca.uhn.fhir.jpa.term.snomedct;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.term.IRecordHandler;
import org.apache.commons.csv.CSVRecord;
import java.util.*;
public final class SctHandlerRelationship implements IRecordHandler {
private final Map<String, TermConcept> myCode2concept;
private final TermCodeSystemVersion myCodeSystemVersion;
private final Map<String, TermConcept> myRootConcepts;
public SctHandlerRelationship(TermCodeSystemVersion theCodeSystemVersion, HashMap<String, TermConcept> theRootConcepts, Map<String, TermConcept> theCode2concept) {
myCodeSystemVersion = theCodeSystemVersion;
myRootConcepts = theRootConcepts;
myCode2concept = theCode2concept;
}
@Override
public void accept(CSVRecord theRecord) {
Set<String> ignoredTypes = new HashSet<String>();
ignoredTypes.add("Method (attribute)");
ignoredTypes.add("Direct device (attribute)");
ignoredTypes.add("Has focus (attribute)");
ignoredTypes.add("Access instrument");
ignoredTypes.add("Procedure site (attribute)");
ignoredTypes.add("Causative agent (attribute)");
ignoredTypes.add("Course (attribute)");
ignoredTypes.add("Finding site (attribute)");
ignoredTypes.add("Has definitional manifestation (attribute)");
String sourceId = theRecord.get("sourceId");
String destinationId = theRecord.get("destinationId");
String typeId = theRecord.get("typeId");
boolean active = "1".equals(theRecord.get("active"));
TermConcept typeConcept = myCode2concept.get(typeId);
TermConcept sourceConcept = myCode2concept.get(sourceId);
TermConcept targetConcept = myCode2concept.get(destinationId);
if (sourceConcept != null && targetConcept != null && typeConcept != null) {
if (typeConcept.getDisplay().equals("Is a (attribute)")) {
TermConceptParentChildLink.RelationshipTypeEnum relationshipType = TermConceptParentChildLink.RelationshipTypeEnum.ISA;
if (!sourceId.equals(destinationId)) {
if (active) {
TermConceptParentChildLink link = new TermConceptParentChildLink();
link.setChild(sourceConcept);
link.setParent(targetConcept);
link.setRelationshipType(relationshipType);
link.setCodeSystem(myCodeSystemVersion);
targetConcept.addChild(sourceConcept, relationshipType);
} else {
// not active, so we're removing any existing links
for (TermConceptParentChildLink next : new ArrayList<TermConceptParentChildLink>(targetConcept.getChildren())) {
if (next.getRelationshipType() == relationshipType) {
if (next.getChild().getCode().equals(sourceConcept.getCode())) {
next.getParent().getChildren().remove(next);
next.getChild().getParents().remove(next);
}
}
}
}
}
} else if (ignoredTypes.contains(typeConcept.getDisplay())) {
// ignore
} else {
// ourLog.warn("Unknown relationship type: {}/{}", typeId, typeConcept.getDisplay());
}
}
}
}

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<!--
LOINC is a well maintained, version independent code system
This CodeSystem resource describes 'LOINC' independent of
any particular version. There are notes about changes for
version specific LOINC code system resources.
Note that the following set of codes constitute the
LOINC code systems:
- the main LOINC codes
- the LOINC answer codes (LA-) and the LOINC answer list codes (LL-)
- the Part codes in the Multiaxial Hierarchy
- the Part codes for the properties.
Note: there are license restrictions on the use of LOINC Part codes
Servers may generate variants of this for the LOINC version(s) and features they support.
-->
<!--
Version History of this specification
0.1 | published 2016 11 18
0.2 | published 2017 03 10 (fixed rad properties, removed list-specific LA properties, typos)
0.3 | published 2017 05 09 (removed CHNGE_TYP based on LOINC Committee recommendation, change filter types from code vs coding -> which allows use of the LP codes or the Part names)
0.4 | published 2018 02 09 (fixed multiaxial hierarchy relationship, added clarifying statement about English as the language for filters)
-->
<CodeSystem xmlns="http://hl7.org/fhir">
<id value="loinc"/>
<!-- This url is unchanged for all versions of LOINC. There
can only be one correct Code System resource for each value of the
version attribute (at least, only one per server) -->
<url value="http://loinc.org"/>
<!-- the HL7 v3 OID assigned to LOINC -->
<identifier>
<system value="urn:ietf:rfc:3986"/>
<value value="urn:oid:2.16.840.1.113883.6.1"/>
</identifier>
<!--
// if a version is specified:
<version value="2.59"/>
-->
<!-- if a specific version is specified, the name should carry this information should be in the name (e.g. LOINC_259) and title -->
<name value="LOINC"/>
<title value="LOINC Code System"/>
<status value="active"/>
<experimental value="false"/>
<publisher value="Regenstrief Institute, Inc."/>
<contact>
<telecom>
<value value="http://loinc.org"/>
</telecom>
</contact>
<!--
<date value=[date for this version]"/>
-->
<description value="LOINC is a freely available international standard for tests, measurements, and observations"/>
<copyright value="This content from LOINC® is copyright © 1995 Regenstrief Institute, Inc. and the LOINC Committee, and available at no cost under the license at http://loinc.org/terms-of-use"/>
<caseSensitive value="false"/>
<valueSet value=" http://loinc.org/vs"/>
<!--
for a version specific reference:
<valueSet value="http://loinc.org/2.56/vs"/>
-->
<!--
It's at the discretion of servers whether to present fragments of LOINC heirarchically or not, when
using the code system resource. But, if they are heirarchical, the Hierarchy SHALL be based on the is-a relationship that is derived from the LOINC Multiaxial Hierarchy.
-->
<HierarchyMeaning value="is-a"/>
<compositional value="false"/> <!-- no compositional grammar in LOINC -->
<versionNeeded value="false"/>
<!-- this canonical definition of LOINC does not include the content.
Servers may choose to include fragments (but not, due to size constraints, all of LOINC) -->
<content value="not-present"/>
<!-- <count value="65000"/>... if working with a specific version, you could nominate a count of the total number of concepts (including the answers, Hierarchy, etc.) -->
<!--
Generally defined filters for specifying value sets
In LOINC, all the properties can be used as filters too, but they are not defined explicitly as filters as well.
Note that parent/child/ancestor/descendant are defined by FHIR, but repeated here to document them clearly.
For illustration purposes, consider this slice of the LOINC Multiaxial Hierarchy when reading the descriptions:
Microbiology [LP31755-9]
Microorganism [LP14559-6]
Virus [LP14855-8]
Zika virus [LP200137-0]
Zika virus RNA | XXX [LP203413-2]
Zika virus RNA [Presence] in Unspecified specimen by Probe and target amplification method [79190-5]
Language Note: The filters defined here are specified using the default LOINC language - English (US). Requests are meant to be specified and interpreted on the English version. The return can be in a specified language (if supported by the server). But note that not all filters/properties have language translations available.
-->
<filter>
<code value="parent"/>
<description value="Allows for the selection of a set of codes based on their appearance in the LOINC Multiaxial Hierarchy. parent selects immediate children only. For example, the code '79190-5' has the parent 'LP203413-2'"/>
<operator value="="/>
<value value="A Part code"/>
</filter>
<filter>
<code value="child"/>
<description value="Allows for the selection of a set of codes based on their appearance in the LOINC Multiaxial Hierarchy. child selects immediate children only. For example, the code 'LP203413-2' has the child '79190-5'"/>
<operator value="in"/>
<value value="A comma separated list of Part codes"/>
</filter>
<filter>
<code value="ancestor"/>
<description value="Allows for the selection of a set of codes based on their appearance in the LOINC Multiaxial Hierarchy. ancestor includes parents transitively, e.g. 'LP203413-2' eventually has an ancestor 'LP14559-6', so the code '79190-5' is in the set of codes that have ancestor=LP14559-6"/>
<operator value="="/>
<value value="A Part code"/>
</filter>
<filter>
<code value="descendant"/>
<description value="Allows for the selection of a set of codes based on their appearance in the LOINC Multiaxial Hierarchy. descendant includes children transitively, e.g. 'LP14559-6' eventually has a descendant 'LP203413-2', so the code '79190-5' is in the set of codes that have descendant=LP14559-6"/>
<operator value="in"/>
<value value="A comma separated list of Part codes"/>
</filter>
<filter>
<code value="copyright"/>
<description value="Allows for the inclusion or exclusion of LOINC codes that include 3rd party copyright notices. LOINC = only codes with a sole copyright by Regenstrief. 3rdParty = only codes with a 3rd party copyright in addition to the one from Regenstrief"/>
<operator value="="/>
<value value="LOINC | 3rdParty"/>
</filter>
<!-- properties. There are 3 kinds of properties:
fhir: display, designation; these are not described here since they are inherent in the specification
infrastructural: defined by FHIR, but documented here for LOINC
LOINC properties: defined by the main LOINC table
concept model: defined by the LOINC Multiaxial Hierarchy
-->
<!-- first, the infrastructural properties - inherited from FHIR, but documented here -->
<property>
<code value="parent"/>
<uri value="http://hl7.org/fhir/concept-properties#parent"/>
<description value="A parent code in the Multiaxial Hierarchy"/>
<type value=""/>
</property>
<property>
<code value="child"/>
<uri value="http://hl7.org/fhir/concept-properties#child"/>
<description value="A child code in the Multiaxial Hierarchy"/>
<type value=""/>
</property>
<!--
LOINC properties.
These apply to the main LOINC codes, but not the Multiaxial Hierarchy, the answer lists, or the part codes.
Notes:
SHORTNAME = display & LONG_COMMON_NAME = definition
Properties are specified as type "code", which are LOINC Part codes (LP-).
It is anticipated that the LOINC Part codes to be used in these properties will be published in the June 2017 LOINC release.
-->
<property>
<code value="STATUS"/>
<uri value="http://loinc.org/property/STATUS"/>
<description value="Status of the term. Within LOINC, codes with STATUS=DEPRECATED are considered inactive. Current values: ACTIVE, TRIAL, DISCOURAGED, and DEPRECATED"/>
<!-- DV NOTE: changed this from boolean to string -->
<type value="string"/>
</property>
<property>
<code value="COMPONENT"/>
<uri value="http://loinc.org/property/COMPONENT"/>
<description value="First major axis-component or analyte: Analyte Name, Analyte sub-class, Challenge"/>
<type value="Coding"/>
</property>
<property>
<code value="PROPERTY"/>
<uri value="http://loinc.org/property/PROPERTY"/>
<description value="Second major axis-property observed: Kind of Property (also called kind of quantity)"/>
<type value="Coding"/>
</property>
<property>
<code value="TIME_ASPCT"/>
<uri value="http://loinc.org/property/TIME_ASPCT"/>
<description value="Third major axis-timing of the measurement: Time Aspect (Point or moment in time vs. time interval)"/>
<type value="Coding"/>
</property>
<property>
<code value="SYSTEM"/>
<uri value="http://loinc.org/property/SYSTEM"/>
<description value="Fourth major axis-type of specimen or system: System (Sample) Type"/>
<type value="Coding"/>
</property>
<property>
<code value="SCALE_TYP"/>
<uri value="http://loinc.org/property/SCALE_TYP"/>
<description value="Fifth major axis-scale of measurement: Type of Scale"/>
<type value="Coding"/>
</property>
<property>
<code value="METHOD_TYP"/>
<uri value="http://loinc.org/property/METHOD_TYP"/>
<description value="Sixth major axis-method of measurement: Type of Method"/>
<type value="Coding"/>
</property>
<property>
<code value="CLASS"/>
<uri value="http://loinc.org/property/CLASS"/>
<description value="An arbitrary classification of the terms for grouping related observations together"/>
<type value="string"/>
</property>
<!-- Note: removed in 0.3
<property>
<code value="CHNG_TYPE"/>
<uri value="http://loinc.org/property/CHNG_TYPE"/>
<description value="A classification of the type of change made to a LOINC term, e.g. DEL=deprecated, ADD=add"/>
<type value="string"/>
</property>
-->
<property>
<code value="VersionLastChanged"/>
<uri value="http://loinc.org/property/VersionLastChanged"/>
<description value="The LOINC version number in which the record has last changed. For new records, this field contains the same value as the FirstPublishedRelease property."/>
<type value="string"/>
</property>
<property>
<code value="CONSUMER_NAME"/>
<uri value="http://loinc.org/property/CONSUMER_NAME"/>
<description value="An experimental (beta) consumer friendly name for this item. The intent is to provide a test name that health care consumers will recognize; it will be similar to the names that might appear on a lab report"/>
<type value="string"/>
</property>
<property>
<code value="CLASSTYPE"/>
<uri value="http://loinc.org/property/CLASSTYPE"/>
<description value="1=Laboratory class; 2=Clinical class; 3=Claims attachments; 4=Surveys"/>
<type value="string"/>
</property>
<property>
<code value="ORDER_OBS"/>
<uri value="http://loinc.org/property/ORDER_OBS"/>
<description value="Provides users with an idea of the intended use of the term by categorizing it as an order only, observation only, or both"/>
<type value="string"/>
</property>
<property>
<code value="HL7_ATTACHMENT_STRUCTURE"/>
<uri value="http://loinc.org/property/HL7_ATTACHMENT_STRUCTURE"/>
<description value="This property is populated in collaboration with the HL7 Attachments Work Group as described in the HL7 Attachment Specification: Supplement to Consolidated CDA Templated Guide."/>
<type value="string"/>
</property>
<property>
<code value="VersionFirstReleased"/>
<uri value="http://loinc.org/property/VersionFirstReleased"/>
<description value="This is the LOINC version number in which this LOINC term was first published."/>
<type value="string"/>
</property>
<property>
<code value="PanelType"/>
<uri value="http://loinc.org/property/PanelType"/>
<description value="For LOINC terms that are panels, this attribute classifies them as a 'Convenience group', 'Organizer', or 'Panel'"/>
<type value="string"/>
</property>
<property>
<code value="ValidHL7AttachmentRequest"/>
<uri value="http://loinc.org/property/ValidHL7AttachmentRequest"/>
<description value="A value of Y in this field indicates that this LOINC code can be sent by a payer as part of an HL7 Attachment request for additional information."/>
<type value="string"/>
</property>
<!-- LOINC/RSNA Radiology Playbook properties. These apply only to terms in the LOINC/RSNA Radiology Playbook File.
Notes:
Properties are specified as type "code", which are LOINC Part codes (LP-)
Converted the attribute names from LOINC style to FHIR style b/c they contained periods
Maneuver sub-attributes are being released in 2016 12.
-->
<property>
<code value="rad-modality-modality-type"/>
<uri value="http://loinc.org/property/rad-modality-type"/>
<description value="Modality is used to represent the device used to acquire imaging information."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-modality-modality-subtype"/>
<uri value="http://loinc.org/property/rad-modality-subtype"/>
<description value="Modality subtype may be optionally included to signify a particularly common or evocative configuration of the modality."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-anatomic-location-region-imaged"/>
<uri value="http://loinc.org/property/rad-anatomic-location-region-imaged"/>
<description value="The Anatomic Location Region Imaged attribute is used in two ways: as a coarse-grained descriptor of the area imaged and a grouper for finding related imaging exams; or, it is used just as a grouper."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-anatomic-location-imaging-focus"/>
<uri value="http://loinc.org/property/rad-anatomic-location-imaging-focus"/>
<description value="The Anatomic Location Imaging Focus is a more fine-grained descriptor of the specific target structure of an imaging exam. In many areas, the focus should be a specific organ."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-anatomic-location-laterality-presence"/>
<uri value="http://loinc.org/property/rad-anatomic-location-laterality-presence"/>
<description value="Radiology Exams that require laterality to be specified in order to be performed are signified with an Anatomic Location Laterality Presence attribute set to 'True'"/>
<type value="Coding"/>
</property>
<property>
<code value="rad-anatomic-location-laterality"/>
<uri value="http://loinc.org/property/rad-anatomic-location-laterality"/>
<description value="Radiology exam Laterality is specified as one of: Left, Right, Bilateral, Unilateral, Unspecified"/>
<type value="Coding"/>
</property>
<property>
<code value="rad-view-view-aggregation"/>
<uri value="http://loinc.org/property/rad-view-aggregation"/>
<description value="Aggregation describes the extent of the imaging performed, whether in quantitative terms (e.g., '3 or more views') or subjective terms (e.g., 'complete')."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-view-view-type"/>
<uri value="http://loinc.org/property/rad-view-view-type"/>
<description value="View type names specific views, such as 'lateral' or 'AP'."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-maneuver-maneuver-type"/>
<uri value="http://loinc.org/property/rad-maneuver-maneuver-type"/>
<description value="Maneuver type indicates an action taken with the goal of elucidating or testing a dynamic aspect of the anatomy."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-timing"/>
<uri value="http://loinc.org/property/rad-timing"/>
<description value="The Timing/Existence property used in conjunction with pharmaceutical and manueuver properties. It specifies whether or not the imaging occurs in the presence of the administered pharmaceutical or a manuever designed to test some dynamic aspect of anatomy or physiology ."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-pharmaceutical-substance-given"/>
<uri value="http://loinc.org/property/rad-pharmaceutical-substance-given"/>
<description value="The Pharmaceutical Substance Given specifies administered contrast agents, radiopharmaceuticals, medications, or other clinically important agents and challenges during the imaging procedure."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-pharmaceutical-route"/>
<uri value="http://loinc.org/property/rad-pharmaceutical-route"/>
<description value="Route specifies the route of administration of the pharmeceutical."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-reason-for-exam"/>
<uri value="http://loinc.org/property/rad-reason-for-exam"/>
<description value="Reason for exam is used to describe a clinical indication or a purpose for the study."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-guidance-for-presence"/>
<uri value="http://loinc.org/property/rad-guidance-for-presence"/>
<description value="Guidance for.Presence indicates when a procedure is guided by imaging."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-guidance-for-approach"/>
<uri value="http://loinc.org/property/rad-guidance-for-approach"/>
<description value="Guidance for.Approach refers to the primary route of access used, such as percutaneous, transcatheter, or transhepatic."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-guidance-for-action"/>
<uri value="http://loinc.org/property/rad-guidance-for-action"/>
<description value="Guidance for.Action indicates the intervention performed, such as biopsy, aspiration, or ablation."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-guidance-for-object"/>
<uri value="http://loinc.org/property/rad-guidance-for-object"/>
<description value="Guidance for.Object specifies the target of the action, such as mass, abscess or cyst."/>
<type value="Coding"/>
</property>
<property>
<code value="rad-subject"/>
<uri value="http://loinc.org/property/rad-subject"/>
<description value="Subject is intended for use when there is a need to distinguish between the patient associated with an imaging study, and the target of the study."/>
<type value="Coding"/>
</property>
<!-- Document Ontology properties. These apply only to terms in the LOINC Document Ontology File
Notes:
Properties are specified as type "code", which are LOINC Part codes (LP-)
Converted the attribute names from LOINC style to FHIR style b/c they contained periods
-->
<property>
<code value="document-kind"/>
<uri value="http://loinc.org/property/document-kind"/>
<description value="Characterizes the general structure of the document at a macro level."/>
<type value="Coding"/>
</property>
<property>
<code value="document-role"/>
<uri value="http://loinc.org/property/document-role"/>
<description value="Characterizes the training or professional level of the author of the document, but does not break down to specialty or subspecialty.."/>
<type value="Coding"/>
</property>
<property>
<code value="document-setting"/>
<uri value="http://loinc.org/property/document-setting"/>
<description value="Setting is a modest extension of CMS’s coarse definition of care settings, such as outpatient, hospital, etc. Setting is not equivalent to location, which typically has more locally defined meanings."/>
<type value="Coding"/>
</property>
<property>
<code value="document-subject-matter-domain"/>
<uri value="http://loinc.org/property/document-subject-matter-domain"/>
<description value="Characterizes the clinical domain that is the subject of the document. For example, Internal Medicine, Neurology, Physical Therapy, etc."/>
<type value="Coding"/>
</property>
<property>
<code value="document-type-of-service"/>
<uri value="http://loinc.org/property/document-type-of-service"/>
<description value="Characterizes the kind of service or activity provided to/for the patient (or other subject of the service) that is described in the document."/>
<type value="Coding"/>
</property>
<!-- Answer list related properties -->
<property>
<code value="answer-list"/>
<uri value="http://loinc.org/property/answer-list"/>
<description value="An answer list associated with this LOINC code (if there are matching answer lists defined). Only on normal LOINC Codes"/>
<type value="Coding"/>
</property>
<!-- Note: We expect to add an AnswerListType property when LOINC publishes new answer list file format in June 2017 -->
<property>
<code value="answers-for"/>
<uri value="http://loinc.org/property/answers-for"/>
<description value="A LOINC Code for which this answer list is used. Only on normal LL- Codes"/>
<type value="Coding"/>
</property>
<!-- Note for future consideration. These are properties of LA codes in the context of a particular list. Not global properties
<property>
<code value="sequence"/>
<uri value="http://loinc.org/property/sequence"/>
<description value="Sequence Number of a answer in a set of answers (LA- codes only)"/>
<type value="integer"/>
</property>
<property>
<code value="score"/>
<uri value="http://loinc.org/property/score"/>
<description value="Score assigned to an answer (LA- codes only)"/>
<type value="integer"/>
</property>
-->
</CodeSystem>

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/BaseJpaDstu3Test.java
View File

@ -13,6 +13,7 @@ import ca.uhn.fhir.jpa.search.ISearchCoordinatorSvc;
import ca.uhn.fhir.jpa.search.IStaleSearchDeletingSvc;
import ca.uhn.fhir.jpa.sp.ISearchParamPresenceSvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvcDstu3;
import ca.uhn.fhir.jpa.validation.JpaValidationSupportChainDstu3;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.parser.StrictErrorHandler;

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3CodeSystemTest.java
View File

@ -4,12 +4,12 @@ import static org.junit.Assert.assertNotEquals;
import java.nio.charset.StandardCharsets;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
import org.apache.commons.io.IOUtils;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
@ -18,13 +18,13 @@ public class FhirResourceDaoDstu3CodeSystemTest extends BaseJpaDstu3Test {
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Test
public void testIndexContained() throws Exception {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/dstu3_codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3SearchNoFtTest.java
View File

@ -11,10 +11,8 @@ import java.util.*;
import javax.servlet.http.HttpServletRequest;
import ca.uhn.fhir.jpa.search.StaleSearchDeletingSvcImpl;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.time.DateUtils;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.Bundle.*;
import org.hl7.fhir.dstu3.model.ContactPoint.ContactPointSystem;

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

@ -9,6 +9,7 @@ import static org.junit.Assert.fail;
import java.util.*;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
import org.hl7.fhir.dstu3.model.*;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.dstu3.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
@ -24,7 +25,6 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
@ -48,7 +48,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
public void after() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Before
@ -67,7 +67,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
@ -111,7 +110,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
cs.getConcepts().add(parentA);
@ -149,7 +147,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept hello = new TermConcept(cs, "hello").setDisplay("Hello");
cs.getConcepts().add(hello);
@ -486,7 +483,7 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
@Test
public void testExpandWithIsAInExternalValueSetReindex() {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
createExternalCsAndLocalVs();
@ -714,7 +711,6 @@ public class FhirResourceDaoDstu3TerminologyTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", cs);

2
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3Test.java
View File

@ -23,12 +23,10 @@ import org.hl7.fhir.dstu3.model.Quantity.QuantityComparator;
import org.hl7.fhir.instance.model.api.*;
import org.junit.*;
import org.mockito.ArgumentCaptor;
import org.springframework.transaction.TransactionDefinition;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.base.Charsets;
import com.google.common.collect.Lists;
import ca.uhn.fhir.jpa.dao.*;

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4CodeSystemTest.java
View File

@ -9,7 +9,7 @@ import org.hl7.fhir.r4.model.CodeSystem;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
@ -18,13 +18,13 @@ public class FhirResourceDaoR4CodeSystemTest extends BaseJpaR4Test {
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Test
public void testIndexContained() throws Exception {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
String input = IOUtils.toString(getClass().getResource("/r4/codesystem_complete.json"), StandardCharsets.UTF_8);
CodeSystem cs = myFhirCtx.newJsonParser().parseResource(CodeSystem.class, input);

10
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4TerminologyTest.java
View File

@ -9,6 +9,7 @@ import static org.junit.Assert.fail;
import java.util.*;
import ca.uhn.fhir.jpa.term.HapiTerminologySvcImpl;
import org.hl7.fhir.r4.model.*;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCategory;
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
@ -24,7 +25,6 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.SearchParameterMap;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvc;
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
import ca.uhn.fhir.parser.IParser;
import ca.uhn.fhir.rest.param.TokenParam;
@ -48,7 +48,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
public void after() {
myDaoConfig.setDeferIndexingForCodesystemsOfSize(new DaoConfig().getDeferIndexingForCodesystemsOfSize());
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(false);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(false);
}
@Before
@ -67,7 +67,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
@ -111,7 +110,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
cs.getConcepts().add(parentA);
@ -149,7 +147,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept hello = new TermConcept(cs, "hello").setDisplay("Hello");
cs.getConcepts().add(hello);
@ -486,7 +483,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
@Test
public void testExpandWithIsAInExternalValueSetReindex() {
BaseHapiTerminologySvc.setForceSaveDeferredAlwaysForUnitTest(true);
HapiTerminologySvcImpl.setForceSaveDeferredAlwaysForUnitTest(true);
createExternalCsAndLocalVs();
@ -714,7 +711,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", cs);

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3CodeSystemTest.java
View File

@ -1,6 +1,5 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -551,7 +551,6 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);

1
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/ResourceProviderR4ValueSetTest.java
View File

@ -492,7 +492,6 @@ public class ResourceProviderR4ValueSetTest extends BaseResourceProviderR4Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);

146
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcLoincTest.java Normal file
View File

@ -0,0 +1,146 @@
package ca.uhn.fhir.jpa.term;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.runners.MockitoJUnitRunner;
import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyListOf;
import static org.mockito.Mockito.times;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcLoincTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcLoincTest.class);
private TerminologyLoaderSvc mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
@Captor
private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
private ArrayList<byte[]> myFiles;
@Captor
private ArgumentCaptor<CodeSystem> mySystemCaptor;
@Mock
private RequestDetails details;
@Captor
private ArgumentCaptor<List<ValueSet>> myValueSetsCaptor;
private void addFile(String theClasspathPrefix, String theClasspathFileName, String theOutputFilename) throws IOException {
ByteArrayOutputStream bos;
bos = new ByteArrayOutputStream();
ZipOutputStream zos = new ZipOutputStream(bos);
ourLog.info("Adding {} to test zip", theClasspathFileName);
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + theOutputFilename));
String classpathName = theClasspathPrefix + theClasspathFileName;
InputStream stream = getClass().getResourceAsStream(classpathName);
Validate.notNull(stream, "Couldn't load " + classpathName);
byte[] byteArray = IOUtils.toByteArray(stream);
Validate.notNull(byteArray);
zos.write(byteArray);
zos.closeEntry();
zos.close();
ourLog.info("ZIP file has {} bytes", bos.toByteArray().length);
myFiles.add(bos.toByteArray());
}
@Before
public void before() {
mySvc = new TerminologyLoaderSvc();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
myFiles = new ArrayList<>();
}
@Test
public void testLoadLoinc() throws Exception {
addFile("/loinc/", "loinc.csv", TerminologyLoaderSvc.LOINC_FILE);
addFile("/loinc/", "hierarchy.csv", TerminologyLoaderSvc.LOINC_HIERARCHY_FILE);
addFile("/loinc/", "AnswerList_Beta_1.csv", TerminologyLoaderSvc.LOINC_ANSWERLIST_FILE);
// Actually do the load
mySvc.loadLoinc(myFiles, details);
verify(myTermSvcDstu3, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class), myValueSetsCaptor.capture());
TermCodeSystemVersion ver = myCsvCaptor.getValue();
Map<String, TermConcept> concepts = new HashMap<>();
for (TermConcept next : ver.getConcepts()) {
concepts.put(next.getCode(), next);
}
// Normal loinc code
TermConcept code = concepts.get("10013-1");
assertEquals("10013-1", code.getCode());
assertEquals("Elpot", code.getProperty("PROPERTY"));
assertEquals("Pt", code.getProperty("TIME_ASPCT"));
assertEquals("R' wave amplitude in lead I", code.getDisplay());
// Answer list
code = concepts.get("LL1001-8");
assertEquals("LL1001-8", code.getCode());
assertEquals("PhenX05_14_30D freq amts", code.getDisplay());
// Answer list code
code = concepts.get("LA13834-9");
assertEquals("LA13834-9", code.getCode());
assertEquals("1-2 times per week", code.getDisplay());
assertEquals(3, code.getSequence().intValue());
// AnswerList valueSet
Map<String, ValueSet> valueSets = new HashMap<>();
for (ValueSet next : myValueSetsCaptor.getValue()) {
valueSets.put(next.getId(), next);
}
ValueSet vs = valueSets.get("LL1001-8");
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URL, vs.getIdentifier().get(0).getSystem());
assertEquals("LL1001-8", vs.getIdentifier().get(0).getValue());
assertEquals("PhenX05_14_30D freq amts", vs.getName());
assertEquals("urn:oid:1.3.6.1.4.1.12009.10.1.166", vs.getUrl());
assertEquals(1, vs.getCompose().getInclude().size());
assertEquals(6, vs.getCompose().getInclude().get(0).getConcept().size());
assertEquals(IHapiTerminologyLoaderSvc.LOINC_URL, vs.getCompose().getInclude().get(0).getSystem());
assertEquals("LA6270-8", vs.getCompose().getInclude().get(0).getConcept().get(0).getCode());
assertEquals("Never", vs.getCompose().getInclude().get(0).getConcept().get(0).getDisplay());
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

166
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcTest.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcSnomedCtTest.java
View File

@ -1,92 +1,71 @@
package ca.uhn.fhir.jpa.term;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.*;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.hl7.fhir.r4.model.CodeSystem;
import org.hl7.fhir.r4.model.ValueSet;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Ignore;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.ArgumentCaptor;
import org.mockito.Captor;
import org.mockito.Mock;
import org.mockito.runners.MockitoJUnitRunner;
import java.io.*;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.*;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
import org.junit.*;
import org.junit.runner.RunWith;
import org.mockito.*;
import org.mockito.runners.MockitoJUnitRunner;
import ca.uhn.fhir.jpa.entity.*;
import ca.uhn.fhir.rest.api.server.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.TestUtil;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
import static org.mockito.Matchers.any;
import static org.mockito.Matchers.anyListOf;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
@RunWith(MockitoJUnitRunner.class)
public class TerminologyLoaderSvcTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcTest.class);
public class TerminologyLoaderSvcSnomedCtTest {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TerminologyLoaderSvcSnomedCtTest.class);
private TerminologyLoaderSvc mySvc;
@Mock
private IHapiTerminologySvc myTermSvc;
@Captor
private ArgumentCaptor<TermCodeSystemVersion> myCsvCaptor;
@Mock
private IHapiTerminologySvcDstu3 myTermSvcDstu3;
private void addEntry(ZipOutputStream zos, String theClasspathPrefix, String theFileName) throws IOException {
ourLog.info("Adding {} to test zip", theFileName);
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + theFileName));
byte[] byteArray = IOUtils.toByteArray(getClass().getResourceAsStream(theClasspathPrefix + theFileName));
Validate.notNull(byteArray);
zos.write(byteArray);
zos.closeEntry();
}
@Before
public void before() {
mySvc = new TerminologyLoaderSvc();
mySvc.setTermSvcForUnitTests(myTermSvc);
mySvc.setTermSvcDstu3ForUnitTest(myTermSvcDstu3);
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
private List<byte[]> list(byte[]... theByteArray) {
return new ArrayList<>(Arrays.asList(theByteArray));
}
@Test
public void testLoadLoinc() throws Exception {
ByteArrayOutputStream bos1 = new ByteArrayOutputStream();
ZipOutputStream zos1 = new ZipOutputStream(bos1);
addEntry(zos1, "/loinc/", "loinc.csv");
zos1.close();
ourLog.info("ZIP file has {} bytes", bos1.toByteArray().length);
ByteArrayOutputStream bos2 = new ByteArrayOutputStream();
ZipOutputStream zos2 = new ZipOutputStream(bos2);
addEntry(zos2, "/loinc/", "LOINC_2.54_MULTI-AXIAL_HIERARCHY.CSV");
zos2.close();
ourLog.info("ZIP file has {} bytes", bos2.toByteArray().length);
RequestDetails details = mock(RequestDetails.class);
mySvc.loadLoinc(list(bos1.toByteArray(), bos2.toByteArray()), details);
verify(myTermSvc, times(1)).storeNewCodeSystemVersion(mySystemCaptor.capture(), myCsvCaptor.capture(), any(RequestDetails.class));
TermCodeSystemVersion ver = myCsvCaptor.getValue();
TermConcept code = ver.getConcepts().iterator().next();
assertEquals("10013-1", code.getCode());
}
@Captor
private ArgumentCaptor<String> mySystemCaptor;
/**
* This is just for trying stuff, it won't run without
* local files external to the git repo
*/
@Ignore
@Test
public void testLoadSnomedCtAgainstRealFile() throws Exception {
byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(list(bytes), details);
}
@Test
public void testLoadSnomedCt() throws Exception {
ByteArrayOutputStream bos = new ByteArrayOutputStream();
@ -105,7 +84,7 @@ public class TerminologyLoaderSvcTest {
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(list(bos.toByteArray()), details);
verify(myTermSvc).storeNewCodeSystemVersion(any(String.class), myCsvCaptor.capture(), any(RequestDetails.class));
verify(myTermSvcDstu3).storeNewCodeSystemVersion(any(CodeSystem.class), myCsvCaptor.capture(), any(RequestDetails.class), anyListOf(ValueSet.class));
TermCodeSystemVersion csv = myCsvCaptor.getValue();
TreeSet<String> allCodes = toCodes(csv, true);
@ -119,25 +98,17 @@ public class TerminologyLoaderSvcTest {
assertThat(allCodes, hasItem("126816002"));
}
private List<byte[]> list(byte[]... theByteArray) {
return new ArrayList<byte[]>(Arrays.asList(theByteArray));
}
/**
* This is just for trying stuff, it won't run without
* local files external to the git repo
*/
@Ignore
@Test
public void testLoadSnomedCtAgainstRealFile() throws Exception {
byte[] bytes = IOUtils.toByteArray(new FileInputStream("/Users/james/Downloads/SnomedCT_Release_INT_20160131_Full.zip"));
private TreeSet<String> toCodes(TermCodeSystemVersion theCsv, boolean theAddChildren) {
TreeSet<String> retVal = new TreeSet<String>();
for (TermConcept next : theCsv.getConcepts()) {
toCodes(retVal, next, theAddChildren);
}
return retVal;
}
private void toCodes(TreeSet<String> theCodes, TermConcept theConcept, boolean theAddChildren) {
theCodes.add(theConcept.getCode());
if (theAddChildren) {
for (TermConceptParentChildLink next : theConcept.getChildren()) {
toCodes(theCodes, next.getChild(), theAddChildren);
}
}
RequestDetails details = mock(RequestDetails.class);
mySvc.loadSnomedCt(list(bytes), details);
}
@Test
@ -158,13 +129,26 @@ public class TerminologyLoaderSvcTest {
}
}
private void addEntry(ZipOutputStream zos, String theClasspathPrefix, String theFileName) throws IOException {
ourLog.info("Adding {} to test zip", theFileName);
zos.putNextEntry(new ZipEntry("SnomedCT_Release_INT_20160131_Full/Terminology/" + theFileName));
byte[] byteArray = IOUtils.toByteArray(getClass().getResourceAsStream(theClasspathPrefix + theFileName));
Validate.notNull(byteArray);
zos.write(byteArray);
zos.closeEntry();
private TreeSet<String> toCodes(TermCodeSystemVersion theCsv, boolean theAddChildren) {
TreeSet<String> retVal = new TreeSet<>();
for (TermConcept next : theCsv.getConcepts()) {
toCodes(retVal, next, theAddChildren);
}
return retVal;
}
private void toCodes(TreeSet<String> theCodes, TermConcept theConcept, boolean theAddChildren) {
theCodes.add(theConcept.getCode());
if (theAddChildren) {
for (TermConceptParentChildLink next : theConcept.getChildren()) {
toCodes(theCodes, next.getChild(), theAddChildren);
}
}
}
@AfterClass
public static void afterClassClearContext() {
TestUtil.clearAllStaticFieldsForUnitTest();
}
}

149
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplTest.java → hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologySvcImplDstu3Test.java
View File

@ -1,22 +1,6 @@
package ca.uhn.fhir.jpa.term;
import static org.hamcrest.Matchers.containsInAnyOrder;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.empty;
import static org.hamcrest.Matchers.greaterThan;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import java.util.List;
import java.util.Set;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Test;
import ca.uhn.fhir.jpa.dao.data.ITermCodeSystemDao;
import ca.uhn.fhir.jpa.dao.dstu3.BaseJpaDstu3Test;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
@ -25,10 +9,25 @@ import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.TestUtil;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.r4.model.ValueSet;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Test;
import org.springframework.beans.factory.annotation.Autowired;
public class TerminologySvcImplTest extends BaseJpaDstu3Test {
import java.util.ArrayList;
import java.util.List;
import java.util.Set;
import static org.hamcrest.Matchers.*;
import static org.junit.Assert.*;
public class TerminologySvcImplDstu3Test extends BaseJpaDstu3Test {
private static final String CS_URL = "http://example.com/my_code_system";
private static final String CS_URL_2 = "http://example.com/my_code_system2";
@AfterClass
@ -48,7 +47,6 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parent = new TermConcept();
parent.setCodeSystem(cs);
@ -159,6 +157,10 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
assertThat(mySystemDao.performReindexingPass(100), greaterThan(0));
}
@Autowired
private ITermCodeSystemDao myTermCodeSystemDao;
private IIdType createCodeSystem() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL);
@ -169,7 +171,6 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA");
cs.getConcepts().add(parentA);
@ -178,9 +179,13 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
parentA.addChild(childAA, RelationshipTypeEnum.ISA);
TermConcept childAAA = new TermConcept(cs, "childAAA");
childAAA.addProperty("propA", "valueAAA");
childAAA.addProperty("propB", "foo");
childAA.addChild(childAAA, RelationshipTypeEnum.ISA);
TermConcept childAAB = new TermConcept(cs, "childAAB");
childAAB.addProperty("propA", "valueAAB");
childAAB.addProperty("propB", "foo");
childAA.addChild(childAAB, RelationshipTypeEnum.ISA);
TermConcept childAB = new TermConcept(cs, "childAB");
@ -189,10 +194,30 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
TermConcept parentB = new TermConcept(cs, "ParentB");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://foo", cs);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
return id;
}
private IIdType createCodeSystem2() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(CS_URL_2);
codeSystem.setContent(CodeSystemContentMode.NOTPRESENT);
IIdType id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
ResourceTable table = myResourceTableDao.findOne(id.getIdPartAsLong());
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
TermConcept parentA = new TermConcept(cs, "CS2");
cs.getConcepts().add(parentA);
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL_2, cs);
return id;
}
@Test
public void testFindCodesAbove() {
IIdType id = createCodeSystem();
@ -214,7 +239,82 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
assertThat(codes, empty());
}
@Test
public void testExpandValueSetPropertySearch() {
createCodeSystem();
createCodeSystem2();
List<String> codes;
ValueSet vs;
ValueSet outcome;
ValueSet.ConceptSetComponent include;
// Property matches one code
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("propA")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("valueAAA");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA"));
// Property matches several codes
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
include
.addFilter()
.setProperty("propB")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("foo");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("childAAA", "childAAB"));
// Property matches no codes
vs = new ValueSet();
include = vs.getCompose().addInclude();
include.setSystem(CS_URL_2);
include
.addFilter()
.setProperty("propA")
.setOp(ValueSet.FilterOperator.EQUAL)
.setValue("valueAAA");
outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, empty());
}
@Test
public void testExpandValueSetWholeSystem() {
createCodeSystem();
List<String> codes;
ValueSet vs = new ValueSet();
ValueSet.ConceptSetComponent include = vs.getCompose().addInclude();
include.setSystem(CS_URL);
ValueSet outcome = myTermSvc.expandValueSet(vs);
codes = toCodesContains(outcome.getExpansion().getContains());
assertThat(codes, containsInAnyOrder("ParentA", "childAAA", "childAAB", "childAA", "childAB", "ParentB"));
}
private List<String> toCodesContains(List<ValueSet.ValueSetExpansionContainsComponent> theContains) {
List<String> retVal = new ArrayList<>();
for (ValueSet.ValueSetExpansionContainsComponent next : theContains) {
retVal.add(next.getCode());
}
return retVal;
}
@Test
public void testCreateDuplicateCodeSystemUri() {
CodeSystem codeSystem = new CodeSystem();
@ -226,7 +326,6 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
TermCodeSystemVersion cs = new TermCodeSystemVersion();
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
@ -237,7 +336,6 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
id = myCodeSystemDao.update(codeSystem, null, true, true, mySrd).getId().toUnqualified();
table = myResourceTableDao.findOne(id.getIdPartAsLong());
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
// Try to update to a different resource
@ -247,7 +345,6 @@ public class TerminologySvcImplTest extends BaseJpaDstu3Test {
id = myCodeSystemDao.create(codeSystem, mySrd).getId().toUnqualified();
table = myResourceTableDao.findOne(id.getIdPartAsLong());
cs.setResource(table);
cs.setResourceVersionId(table.getVersion());
try {
myTermSvc.storeNewCodeSystemVersion(table.getId(), CS_URL, cs);
fail();

10
hapi-fhir-jpaserver-base/src/test/resources/loinc/AnswerList_Beta_1.csv Normal file
View File

@ -0,0 +1,10 @@
"AnswerListId","AnswerListName" ,"AnswerListOID" ,"ExtDefinedYN","ExtDefinedAnswerListCodeSystem","ExtDefinedAnswerListLink","AnswerStringId","LocalAnswerCode","LocalAnswerCodeSystem","SequenceNumber","DisplayText" ,"ExtCodeId","ExtCodeDisplayName","ExtCodeSystem","ExtCodeSystemVersion","ExtCodeSystemCopyrightNotice","SubsequentTextPrompt","Description","Score"
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13825-7" ,"1" , ,1 ,"1 slice or 1 dinner roll" , , , , , , , ,
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13838-0" ,"2" , ,2 ,"2 slices or 2 dinner rolls" , , , , , , , ,
"LL1000-0" ,"PhenX05_13_30D bread amt","1.3.6.1.4.1.12009.10.1.165","N" , , ,"LA13892-7" ,"3" , ,3 ,"More than 2 slices or 2 dinner rolls", , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA6270-8" ,"00" , ,1 ,"Never" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13836-4" ,"01" , ,2 ,"1-3 times per month" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13834-9" ,"02" , ,3 ,"1-2 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13853-9" ,"03" , ,4 ,"3-4 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13860-4" ,"04" , ,5 ,"5-6 times per week" , , , , , , , ,
"LL1001-8" ,"PhenX05_14_30D freq amts","1.3.6.1.4.1.12009.10.1.166","N" , , ,"LA13827-3" ,"05" , ,6 ,"1 time per day" , , , , , , , ,
Can't render this file because it contains an unexpected character in line 1 and column 31.

11
hapi-fhir-jpaserver-base/src/test/resources/loinc/LoincAnswerListLink_Beta_1.csv Normal file
View File

@ -0,0 +1,11 @@
"LoincNumber","LongCommonName" ,"AnswerListId","AnswerListName" ,"AnswerListLinkType","ApplicableContext"
"10061-0" ,"S' wave amplitude in lead I" ,"LL1311-1" ,"PhenX12_44" ,"EXAMPLE" ,
"10331-7" ,"Rh [Type] in Blood" ,"LL360-9" ,"Pos|Neg" ,"EXAMPLE" ,
"10389-5" ,"Blood product.other [Type]" ,"LL2413-4" ,"Othr bld prod" ,"EXAMPLE" ,
"10390-3" ,"Blood product special preparation [Type]" ,"LL2422-5" ,"Blood prod treatment" ,"EXAMPLE" ,
"10393-7" ,"Factor IX given [Type]" ,"LL2420-9" ,"Human/Recomb" ,"EXAMPLE" ,
"10395-2" ,"Factor VIII given [Type]" ,"LL2420-9" ,"Human/Recomb" ,"EXAMPLE" ,
"10401-8" ,"Immune serum globulin given [Type]" ,"LL2421-7" ,"IM/IV" ,"EXAMPLE" ,
"10410-9" ,"Plasma given [Type]" ,"LL2417-5" ,"Plasma type" ,"EXAMPLE" ,
"10568-4" ,"Clarity of Semen" ,"LL2427-4" ,"Clear/Opales/Milky" ,"EXAMPLE" ,
"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]","LL1000-0" ,"PhenX05_13_30D bread amt","NORMATIVE" ,
Can't render this file because it contains an unexpected character in line 1 and column 30.

10
hapi-fhir-jpaserver-base/src/test/resources/loinc/hierarchy.csv Normal file
View File

@ -0,0 +1,10 @@
PATH_TO_ROOT,SEQUENCE,IMMEDIATE_PARENT,CODE,CODE_TEXT
,1,,LP31755-9,Microbiology
LP31755-9,1,LP31755-9,LP14559-6,Microorganism
LP31755-9.LP14559-6,1,LP14559-6,LP98185-9,Bacteria
LP31755-9.LP14559-6.LP98185-9,1,LP98185-9,LP14082-9,Bacteria
LP31755-9.LP14559-6.LP98185-9.LP14082-9,1,LP14082-9,LP52258-8,Bacteria | Body Fluid
LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52258-8,1,LP52258-8,41599-2,Bacteria Fld Ql Micro
LP31755-9.LP14559-6.LP98185-9.LP14082-9,2,LP14082-9,LP52260-4,Bacteria | Cerebral spinal fluid
LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52260-4,1,LP52260-4,41602-4,Bacteria CSF Ql Micro
LP31755-9.LP14559-6.LP98185-9.LP14082-9,3,LP14082-9,LP52960-9,Bacteria | Cervix
1 PATH_TO_ROOT SEQUENCE IMMEDIATE_PARENT CODE CODE_TEXT
2 1 LP31755-9 Microbiology
3 LP31755-9 1 LP31755-9 LP14559-6 Microorganism
4 LP31755-9.LP14559-6 1 LP14559-6 LP98185-9 Bacteria
5 LP31755-9.LP14559-6.LP98185-9 1 LP98185-9 LP14082-9 Bacteria
6 LP31755-9.LP14559-6.LP98185-9.LP14082-9 1 LP14082-9 LP52258-8 Bacteria | Body Fluid
7 LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52258-8 1 LP52258-8 41599-2 Bacteria Fld Ql Micro
8 LP31755-9.LP14559-6.LP98185-9.LP14082-9 2 LP14082-9 LP52260-4 Bacteria | Cerebral spinal fluid
9 LP31755-9.LP14559-6.LP98185-9.LP14082-9.LP52260-4 1 LP52260-4 41602-4 Bacteria CSF Ql Micro
10 LP31755-9.LP14559-6.LP98185-9.LP14082-9 3 LP14082-9 LP52960-9 Bacteria | Cervix

21
hapi-fhir-jpaserver-base/src/test/resources/loinc/loinc.csv
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@ -1,10 +1,11 @@
"LOINC_NUM","COMPONENT","PROPERTY","TIME_ASPCT","SYSTEM","SCALE_TYP","METHOD_TYP","CLASS","SOURCE","VersionLastChanged","CHNG_TYPE","DefinitionDescription","STATUS","CONSUMER_NAME","CLASSTYPE","FORMULA","SPECIES","EXMPL_ANSWERS","SURVEY_QUEST_TEXT","SURVEY_QUEST_SRC","UNITSREQUIRED","SUBMITTED_UNITS","RELATEDNAMES2","SHORTNAME","ORDER_OBS","CDISC_COMMON_TESTS","HL7_FIELD_SUBFIELD_ID","EXTERNAL_COPYRIGHT_NOTICE","EXAMPLE_UNITS","LONG_COMMON_NAME","UnitsAndRange","DOCUMENT_SECTION","EXAMPLE_UCUM_UNITS","EXAMPLE_SI_UCUM_UNITS","STATUS_REASON","STATUS_TEXT","CHANGE_REASON_PUBLIC","COMMON_TEST_RANK","COMMON_ORDER_RANK","COMMON_SI_TEST_RANK","HL7_ATTACHMENT_STRUCTURE","EXTERNAL_COPYRIGHT_LINK","PanelType","AskAtOrderEntry","AssociatedObservations"
"10013-1","R' wave amplitude.lead I","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-I; R wave Amp L-I; Random; Right; Voltage","R' wave Amp L-I","Observation",,,,"mV","R' wave amplitude in lead I",,,"mV",,,,,0,0,0,,,,,
"10014-9","R' wave amplitude.lead II","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"2; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-II; R wave Amp L-II; Random; Right; Voltage","R' wave Amp L-II","Observation",,,,"mV","R' wave amplitude in lead II",,,"mV",,,,,0,0,0,,,,,
"10015-6","R' wave amplitude.lead III","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"3; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-III; R wave Amp L-III; Random; Right; Voltage","R' wave Amp L-III","Observation",,,,"mV","R' wave amplitude in lead III",,,"mV",,,,,0,0,0,,,,,
"10016-4","R' wave amplitude.lead V1","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V1; R wave Amp L-V1; Random; Right; Voltage","R' wave Amp L-V1","Observation",,,,"mV","R' wave amplitude in lead V1",,,"mV",,,,,0,0,0,,,,,
"1001-7","DBG Ab","Pr","Pt","Ser/Plas^donor","Ord",,"BLDBK","FS","2.44","MIN",,"ACTIVE",,1,,,,,,,,"ABS; Aby; Antby; Anti; Antibodies; Antibody; Autoantibodies; Autoantibody; BLOOD BANK; Donna Bennett-Goodspeed; Donr; Ordinal; Pl; Plasma; Plsm; Point in time; QL; Qual; Qualitative; Random; Screen; SerP; SerPl; SerPl^donor; SerPlas; Serum; Serum or plasma; SR","DBG Ab SerPl Donr Ql","Observation",,,,,"DBG Ab [Presence] in Serum or Plasma from donor",,,,,,,"The Property has been changed from ACnc to Pr (Presence) to reflect the new model for ordinal terms where results are based on presence or absence.",0,0,0,,,,,
"10017-2","R' wave amplitude.lead V2","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V2; R wave Amp L-V2; Random; Right; Voltage","R' wave Amp L-V2","Observation",,,,"mV","R' wave amplitude in lead V2",,,"mV",,,,,0,0,0,,,,,
"10018-0","R' wave amplitude.lead V3","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V3; R wave Amp L-V3; Random; Right; Voltage","R' wave Amp L-V3","Observation",,,,"mV","R' wave amplitude in lead V3",,,"mV",,,,,0,0,0,,,,,
"10019-8","R' wave amplitude.lead V4","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V4; R wave Amp L-V4; Random; Right; Voltage","R' wave Amp L-V4","Observation",,,,"mV","R' wave amplitude in lead V4",,,"mV",,,,,0,0,0,,,,,
"10020-6","R' wave amplitude.lead V5","Elpot","Pt","Heart","Qn","EKG","EKG.MEAS","CH","2.48","MIN",,"ACTIVE",,2,,,,,,"Y",,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V5; R wave Amp L-V5; Random; Right; Voltage","R' wave Amp L-V5","Observation",,,,"mV","R' wave amplitude in lead V5",,,"mV",,,,,0,0,0,,,,,
"LOINC_NUM","COMPONENT" ,"PROPERTY","TIME_ASPCT","SYSTEM" ,"SCALE_TYP","METHOD_TYP","CLASS" ,"SOURCE","VersionLastChanged","CHNG_TYPE","DefinitionDescription","STATUS","CONSUMER_NAME","CLASSTYPE","FORMULA","SPECIES","EXMPL_ANSWERS","SURVEY_QUEST_TEXT" ,"SURVEY_QUEST_SRC" ,"UNITSREQUIRED","SUBMITTED_UNITS","RELATEDNAMES2" ,"SHORTNAME" ,"ORDER_OBS" ,"CDISC_COMMON_TESTS","HL7_FIELD_SUBFIELD_ID","EXTERNAL_COPYRIGHT_NOTICE","EXAMPLE_UNITS","LONG_COMMON_NAME" ,"UnitsAndRange","DOCUMENT_SECTION","EXAMPLE_UCUM_UNITS","EXAMPLE_SI_UCUM_UNITS","STATUS_REASON","STATUS_TEXT","CHANGE_REASON_PUBLIC" ,"COMMON_TEST_RANK","COMMON_ORDER_RANK","COMMON_SI_TEST_RANK","HL7_ATTACHMENT_STRUCTURE","EXTERNAL_COPYRIGHT_LINK","PanelType","AskAtOrderEntry","AssociatedObservations"
"10013-1" ,"R' wave amplitude.lead I" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-I; R wave Amp L-I; Random; Right; Voltage" ,"R' wave Amp L-I" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead I" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"10014-9" ,"R' wave amplitude.lead II" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"2; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-II; R wave Amp L-II; Random; Right; Voltage" ,"R' wave Amp L-II" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead II" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"10015-6" ,"R' wave amplitude.lead III" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"3; Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-III; R wave Amp L-III; Random; Right; Voltage" ,"R' wave Amp L-III" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead III" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"10016-4" ,"R' wave amplitude.lead V1" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V1; R wave Amp L-V1; Random; Right; Voltage" ,"R' wave Amp L-V1" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V1" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"1001-7" ,"DBG Ab" ,"Pr" ,"Pt" ,"Ser/Plas^donor","Ord" , ,"BLDBK" ,"FS" ,"2.44" ,"MIN" , ,"ACTIVE", ,1 , , , , , , , ,"ABS; Aby; Antby; Anti; Antibodies; Antibody; Autoantibodies; Autoantibody; BLOOD BANK; Donna Bennett-Goodspeed; Donr; Ordinal; Pl; Plasma; Plsm; Point in time; QL; Qual; Qualitative; Random; Screen; SerP; SerPl; SerPl^donor; SerPlas; Serum; Serum or plasma; SR","DBG Ab SerPl Donr Ql" ,"Observation", , , , ,"DBG Ab [Presence] in Serum or Plasma from donor" , , , , , , ,"The Property has been changed from ACnc to Pr (Presence) to reflect the new model for ordinal terms where results are based on presence or absence.",0 ,0 ,0 , , , , ,
"10017-2" ,"R' wave amplitude.lead V2" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V2; R wave Amp L-V2; Random; Right; Voltage" ,"R' wave Amp L-V2" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V2" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"10018-0" ,"R' wave amplitude.lead V3" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V3; R wave Amp L-V3; Random; Right; Voltage" ,"R' wave Amp L-V3" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V3" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"10019-8" ,"R' wave amplitude.lead V4" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V4; R wave Amp L-V4; Random; Right; Voltage" ,"R' wave Amp L-V4" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V4" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"10020-6" ,"R' wave amplitude.lead V5" ,"Elpot" ,"Pt" ,"Heart" ,"Qn" ,"EKG" ,"EKG.MEAS","CH" ,"2.48" ,"MIN" , ,"ACTIVE", ,2 , , , , , ,"Y" , ,"Cardiac; ECG; EKG.MEASUREMENTS; Electrical potential; Electrocardiogram; Electrocardiograph; Hrt; Painter's colic; PB; Plumbism; Point in time; QNT; Quan; Quant; Quantitative; R prime; R' wave Amp L-V5; R wave Amp L-V5; Random; Right; Voltage" ,"R' wave Amp L-V5" ,"Observation", , , ,"mV" ,"R' wave amplitude in lead V5" , , ,"mV" , , , , ,0 ,0 ,0 , , , , ,
"61438-8" ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30D","Find" ,"Pt" ,"^Patient" ,"Ord" ,"PhenX" ,"PHENX" ,"PhenX" ,"2.44" ,"MIN" , ,"TRIAL" , ,2 , , , ,"Each time you eat bread, toast or dinner rolls, how much do you usually eat?","PhenX.050201100100","N" , ,"Finding; Findings; How much bread in 30D; Last; Ordinal; Point in time; QL; Qual; Qualitative; Random; Screen" ,"How much bread in 30D PhenX", , , , , ,"Each time you ate bread, toast or dinner rolls, how much did you usually eat in the past 30 days [PhenX]", , , , , , , ,0 ,0 ,0 , , , , ,

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