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Fix teerm sevice indexing

This commit is contained in:
jamesagnew 2016-06-26 23:10:02 -04:00
parent fae4344c36
commit e9cb518012
26 changed files with 1123 additions and 570 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/config/dstu3/BaseDstu3Config.java
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@ -101,6 +101,7 @@ public class BaseDstu3Config extends BaseConfig {
@Bean(name = "mySystemProviderDstu3")
public ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 systemProviderDstu3() {
ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3 retVal = new ca.uhn.fhir.jpa.provider.dstu3.JpaSystemProviderDstu3();
retVal.setContext(defaultFhirContext());
retVal.setDao(systemDaoDstu3());
return retVal;
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirDao.java
View File

@ -1174,7 +1174,7 @@ public abstract class BaseHapiFhirDao<T extends IBaseResource> implements IDao {
coordsParams = extractSearchParamCoords(theEntity, theResource);
// ourLog.info("Indexing resource: {}", entity.getId());
ourLog.info("Storing date indexes: {}", dateParams);
ourLog.trace("Storing date indexes: {}", dateParams);
tokenParams = new HashSet<ResourceIndexedSearchParamToken>();
for (BaseResourceIndexedSearchParam next : extractSearchParamTokens(theEntity, theResource)) {

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirSystemDao.java
View File

@ -37,8 +37,6 @@ import javax.persistence.criteria.Root;
import org.hl7.fhir.instance.model.api.IBaseResource;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Propagation;
@ -50,7 +48,6 @@ import ca.uhn.fhir.jpa.dao.data.IForcedIdDao;
import ca.uhn.fhir.jpa.dao.data.ITermConceptDao;
import ca.uhn.fhir.jpa.entity.ForcedId;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.util.ReindexFailureException;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.model.api.TagList;
@ -89,7 +86,6 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
TransactionTemplate txTemplate = new TransactionTemplate(myTxManager);
txTemplate.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRED);
int retVal = doPerformReindexingPassForResources(theCount, txTemplate);
retVal += doPerformReindexingPassForConcepts(txTemplate);
return retVal;
}
@ -152,37 +148,6 @@ public abstract class BaseHapiFhirSystemDao<T, MT> extends BaseHapiFhirDao<IBase
});
}
private int doPerformReindexingPassForConcepts(TransactionTemplate txTemplate) {
return txTemplate.execute(new TransactionCallback<Integer>() {
@Override
public Integer doInTransaction(TransactionStatus theStatus) {
int maxResult = 10000;
Page<TermConcept> resources = myTermConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (resources.hasContent() == false) {
return 0;
}
ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
int count = 0;
long start = System.currentTimeMillis();
for (TermConcept resourceTable : resources) {
resourceTable.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
myTermConceptDao.save(resourceTable);
count++;
}
long delay = System.currentTimeMillis() - start;
long avg = (delay / resources.getContent().size());
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), delay, avg });
return resources.getContent().size();
}
});
}
@Override
public TagList getAllTags(RequestDetails theRequestDetails) {
// Notify interceptors

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/FhirResourceDaoValueSetDstu2.java
View File

@ -78,7 +78,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
}
@Override
public ValueSet expand(IIdType theId, String theFilter) {
public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
ValueSet source = loadValueSetForExpansion(theId);
return expand(source, theFilter);
@ -179,7 +179,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
}
@Override
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept) {
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CodingDt theCoding, CodeableConceptDt theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds;
boolean haveCodeableConcept = theCodeableConcept != null && theCodeableConcept.getCoding().size() > 0;
@ -212,7 +212,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
}
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null);
ValueSet expansion = expand(nextId, null, theRequestDetails);
List<ExpansionContains> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {
@ -314,7 +314,7 @@ public class FhirResourceDaoValueSetDstu2 extends FhirResourceDaoDstu2<ValueSet>
List<IIdType> valueSetIds = findCodeSystemIdsContainingSystemAndCode(code, system);
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null);
ValueSet expansion = expand(nextId, null, theRequestDetails);
List<ExpansionContains> contains = expansion.getExpansion().getContains();
LookupCodeResult result = lookup(contains, system, code);
if (result != null) {

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/IFhirResourceDaoValueSet.java
View File

@ -24,9 +24,11 @@ import org.hl7.fhir.instance.model.api.IBaseResource;
import org.hl7.fhir.instance.model.api.IIdType;
import org.hl7.fhir.instance.model.api.IPrimitiveType;
import ca.uhn.fhir.rest.method.RequestDetails;
public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> extends IFhirResourceDao<T> {
T expand(IIdType theId, String theFilter);
T expand(IIdType theId, String theFilter, RequestDetails theRequestDetails);
T expand(T theSource, String theFilter);
@ -34,7 +36,7 @@ public interface IFhirResourceDaoValueSet<T extends IBaseResource, CD, CC> exten
void purgeCaches();
ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept);
ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode, IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, CD theCoding, CC theCodeableConcept, RequestDetails theRequestDetails);
public class ValidateCodeResult {
private String myDisplay;

13
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoValueSetDstu3.java
View File

@ -26,6 +26,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.nio.file.FileVisitOption;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Date;
import java.util.Iterator;
import java.util.List;
import java.util.Set;
@ -56,6 +57,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoCodeSystem.LookupCodeResult;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.util.LogicUtil;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.util.ElementUtil;
@ -70,8 +72,8 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
private IFhirResourceDaoCodeSystem<CodeSystem, CodeableConcept, Coding> myCodeSystemDao;
@Override
public ValueSet expand(IIdType theId, String theFilter) {
ValueSet source = myValidationSupport.fetchResource(getContext(), ValueSet.class, theId.getValue());
public ValueSet expand(IIdType theId, String theFilter, RequestDetails theRequestDetails) {
ValueSet source = read(theId, theRequestDetails);
return expand(source, theFilter);
}
@ -86,6 +88,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
ValueSetExpansionComponent expansion = outcome.getValueset().getExpansion();
ValueSet retVal = new ValueSet();
retVal.getMeta().setLastUpdated(new Date());
retVal.setExpansion(expansion);
return retVal;
}
@ -166,7 +169,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
@Override
public ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult validateCode(IPrimitiveType<String> theValueSetIdentifier, IIdType theId, IPrimitiveType<String> theCode,
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept) {
IPrimitiveType<String> theSystem, IPrimitiveType<String> theDisplay, Coding theCoding, CodeableConcept theCodeableConcept, RequestDetails theRequestDetails) {
List<IIdType> valueSetIds = Collections.emptyList();
List<IIdType> codeSystemIds = Collections.emptyList();
@ -205,7 +208,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
for (IIdType nextId : valueSetIds) {
ValueSet expansion = expand(nextId, null);
ValueSet expansion = expand(nextId, null, theRequestDetails);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {
@ -219,7 +222,7 @@ public class FhirResourceDaoValueSetDstu3 extends FhirResourceDaoDstu3<ValueSet>
}
for (IIdType nextId : codeSystemIds) {
ValueSet expansion = expand(nextId, null);
ValueSet expansion = expand(nextId, null, theRequestDetails);
List<ValueSetExpansionContainsComponent> contains = expansion.getExpansion().getContains();
ValidateCodeResult result = validateCodeIsInContains(contains, toStringOrNull(theSystem), toStringOrNull(theCode), theCoding, theCodeableConcept);
if (result != null) {

79
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConcept.java
View File

@ -25,6 +25,7 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@ -39,6 +40,8 @@ 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;
@ -49,45 +52,54 @@ 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.apache.lucene.analysis.core.WhitespaceTokenizerFactory;
import org.hibernate.search.annotations.Analyze;
import org.hibernate.search.annotations.Analyzer;
import org.hibernate.search.annotations.AnalyzerDef;
import org.hibernate.search.annotations.AnalyzerDefs;
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 org.hibernate.search.annotations.TokenizerDef;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.search.DeferConceptIndexingInterceptor;
//@formatter:off
@Entity
@Indexed()
@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")
})
@AnalyzerDefs({
@AnalyzerDef(name = "conceptParentPidsAnalyzer",
tokenizer = @TokenizerDef(factory = WhitespaceTokenizerFactory.class),
filters = {
})
})
//@formatter:on
public class TermConcept implements Serializable {
private static final int MAX_DESC_LENGTH = 400;
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(TermConcept.class);
private static final long serialVersionUID = 1L;
@OneToMany(fetch=FetchType.LAZY, mappedBy="myParent")
@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")),
})
@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")), })
private String myCode;
@ManyToOne()
@JoinColumn(name="CODESYSTEM_PID", referencedColumnName="PID", foreignKey=@ForeignKey(name="FK_CONCEPT_PID_CS_PID"))
@JoinColumn(name = "CODESYSTEM_PID", referencedColumnName = "PID", foreignKey = @ForeignKey(name = "FK_CONCEPT_PID_CS_PID"))
private TermCodeSystemVersion myCodeSystem;
@Column(name="CODESYSTEM_PID", insertable=false, updatable=false)
@Fields({
@Field(name="myCodeSystemVersionPid")
})
@Column(name = "CODESYSTEM_PID", insertable = false, updatable = false)
@Fields({ @Field(name = "myCodeSystemVersionPid") })
private long myCodeSystemVersionPid;
//@formatter:off
@ -102,21 +114,19 @@ public class TermConcept implements Serializable {
//@formatter:on
@Id()
@SequenceGenerator(name="SEQ_CONCEPT_PID", sequenceName="SEQ_CONCEPT_PID")
@GeneratedValue(strategy=GenerationType.AUTO, generator="SEQ_CONCEPT_PID")
@Column(name="PID")
@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
@Fields({
@Field(name = "myParentPids", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "standardAnalyzer")),
})
@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")
@OneToMany(cascade = {}, fetch = FetchType.LAZY, mappedBy = "myChild")
private Collection<TermConceptParentChildLink> myParents;
public TermConcept() {
@ -155,7 +165,7 @@ public class TermConcept implements Serializable {
return true;
}
TermConcept obj = (TermConcept)theObj;
TermConcept obj = (TermConcept) theObj;
EqualsBuilder b = new EqualsBuilder();
b.append(myCodeSystem, obj.myCodeSystem);
@ -190,6 +200,10 @@ public class TermConcept implements Serializable {
return myIndexStatus;
}
public String getParentPidsAsString() {
return myParentPids;
}
public Collection<TermConceptParentChildLink> getParents() {
if (myParents == null) {
myParents = new ArrayList<TermConceptParentChildLink>();
@ -205,6 +219,28 @@ public class TermConcept implements Serializable {
return b.toHashCode();
}
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);
}
}
}
@PreUpdate
@PrePersist
public void prePersist() {
Set<Long> parentPids = new HashSet<Long>();
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;
}
@ -237,6 +273,10 @@ public class TermConcept implements Serializable {
b.append(next);
}
if (b.length() == 0) {
b.append("NONE");
}
myParentPids = b.toString();
}
@ -244,5 +284,4 @@ public class TermConcept implements Serializable {
public String toString() {
return new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE).append("code", myCode).append("display", myDisplay).build();
}
}

48
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/entity/TermConceptParentChildLink.java
View File

@ -96,7 +96,55 @@ public class TermConceptParentChildLink implements Serializable {
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((myChild == null) ? 0 : myChild.hashCode());
result = prime * result + ((myCodeSystem == null) ? 0 : myCodeSystem.hashCode());
result = prime * result + ((myParent == null) ? 0 : myParent.hashCode());
result = prime * result + ((myRelationshipType == null) ? 0 : myRelationshipType.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
TermConceptParentChildLink other = (TermConceptParentChildLink) obj;
if (myChild == null) {
if (other.myChild != null)
return false;
} else if (!myChild.equals(other.myChild))
return false;
if (myCodeSystem == null) {
if (other.myCodeSystem != null)
return false;
} else if (!myCodeSystem.equals(other.myCodeSystem))
return false;
if (myParent == null) {
if (other.myParent != null)
return false;
} else if (!myParent.equals(other.myParent))
return false;
if (myRelationshipType != other.myRelationshipType)
return false;
return true;
}
public enum RelationshipTypeEnum{
// ********************************************
// IF YOU ADD HERE MAKE SURE ORDER IS PRESERVED
ISA
}
public Long getId() {
return myPid;
}
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/BaseJpaResourceProviderValueSetDstu2.java
View File

@ -53,7 +53,8 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
@IdParam(optional=true) IdDt theId,
@OperationParam(name="valueSet", min=0, max=1) ValueSet theValueSet,
@OperationParam(name="identifier", min=0, max=1) UriDt theIdentifier,
@OperationParam(name = "filter", min=0, max=1) StringDt theFilter) {
@OperationParam(name = "filter", min=0, max=1) StringDt theFilter,
RequestDetails theRequestDetails) {
//@formatter:on
boolean haveId = theId != null && theId.hasIdPart();
@ -72,7 +73,7 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
try {
IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>) getDao();
if (haveId) {
return dao.expand(theId, toFilterString(theFilter));
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theIdentifier.getValue(), toFilterString(theFilter));
} else {
@ -155,14 +156,15 @@ public class BaseJpaResourceProviderValueSetDstu2 extends JpaResourceProviderDst
@OperationParam(name="system", min=0, max=1) UriDt theSystem,
@OperationParam(name="display", min=0, max=1) StringDt theDisplay,
@OperationParam(name="coding", min=0, max=1) CodingDt theCoding,
@OperationParam(name="codeableConcept", min=0, max=1) CodeableConceptDt theCodeableConcept
@OperationParam(name="codeableConcept", min=0, max=1) CodeableConceptDt theCodeableConcept,
RequestDetails theRequestDetails
) {
//@formatter:on
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt> dao = (IFhirResourceDaoValueSet<ValueSet, CodingDt, CodeableConceptDt>) getDao();
ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept);
ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
Parameters retVal = new Parameters();
retVal.addParameter().setName("result").setValue(new BooleanDt(result.isResult()));
if (isNotBlank(result.getMessage())) {

11
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/provider/dstu3/BaseJpaResourceProviderValueSetDstu3.java
View File

@ -39,6 +39,7 @@ import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.rest.annotation.IdParam;
import ca.uhn.fhir.rest.annotation.Operation;
import ca.uhn.fhir.rest.annotation.OperationParam;
import ca.uhn.fhir.rest.method.RequestDetails;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDstu3<ValueSet> {
@ -50,7 +51,8 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
@IdParam(optional=true) IdType theId,
@OperationParam(name="valueSet", min=0, max=1) ValueSet theValueSet,
@OperationParam(name="identifier", min=0, max=1) UriType theIdentifier,
@OperationParam(name = "filter", min=0, max=1) StringType theFilter) {
@OperationParam(name = "filter", min=0, max=1) StringType theFilter,
RequestDetails theRequestDetails) {
//@formatter:on
boolean haveId = theId != null && theId.hasIdPart();
@ -69,7 +71,7 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
if (haveId) {
return dao.expand(theId, toFilterString(theFilter));
return dao.expand(theId, toFilterString(theFilter), theRequestDetails);
} else if (haveIdentifier) {
return dao.expandByIdentifier(theIdentifier.getValue(), toFilterString(theFilter));
} else {
@ -118,14 +120,15 @@ public class BaseJpaResourceProviderValueSetDstu3 extends JpaResourceProviderDst
@OperationParam(name="system", min=0, max=1) UriType theSystem,
@OperationParam(name="display", min=0, max=1) StringType theDisplay,
@OperationParam(name="coding", min=0, max=1) Coding theCoding,
@OperationParam(name="codeableConcept", min=0, max=1) CodeableConcept theCodeableConcept
@OperationParam(name="codeableConcept", min=0, max=1) CodeableConcept theCodeableConcept,
RequestDetails theRequestDetails
) {
//@formatter:on
startRequest(theServletRequest);
try {
IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept> dao = (IFhirResourceDaoValueSet<ValueSet, Coding, CodeableConcept>) getDao();
ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept);
ValidateCodeResult result = dao.validateCode(theValueSetIdentifier, theId, theCode, theSystem, theDisplay, theCoding, theCodeableConcept, theRequestDetails);
Parameters retVal = new Parameters();
retVal.addParameter().setName("result").setValue(new BooleanType(result.isResult()));
if (isNotBlank(result.getMessage())) {

35
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/DeferConceptIndexingInterceptor.java Normal file
View File

@ -0,0 +1,35 @@
package ca.uhn.fhir.jpa.search;
import org.hibernate.search.indexes.interceptor.EntityIndexingInterceptor;
import org.hibernate.search.indexes.interceptor.IndexingOverride;
import ca.uhn.fhir.jpa.entity.TermConcept;
public class DeferConceptIndexingInterceptor implements EntityIndexingInterceptor<TermConcept> {
@Override
public IndexingOverride onAdd(TermConcept theEntity) {
if (theEntity.getIndexStatus() == null) {
return IndexingOverride.SKIP;
}
return IndexingOverride.APPLY_DEFAULT;
}
@Override
public IndexingOverride onCollectionUpdate(TermConcept theEntity) {
return IndexingOverride.APPLY_DEFAULT;
}
@Override
public IndexingOverride onDelete(TermConcept theEntity) {
return IndexingOverride.APPLY_DEFAULT;
}
@Override
public IndexingOverride onUpdate(TermConcept theEntity) {
return onAdd(theEntity);
}
}

122
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/BaseHapiTerminologySvc.java
View File

@ -21,6 +21,7 @@ package ca.uhn.fhir.jpa.term;
*/
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.IdentityHashMap;
@ -32,10 +33,17 @@ import javax.persistence.EntityManager;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceContextType;
import org.apache.commons.lang3.time.DateUtils;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.PageRequest;
import org.springframework.scheduling.annotation.Scheduled;
import org.springframework.transaction.PlatformTransactionManager;
import org.springframework.transaction.TransactionStatus;
import org.springframework.transaction.annotation.Propagation;
import org.springframework.transaction.annotation.Transactional;
import org.springframework.transaction.support.TransactionCallbackWithoutResult;
import org.springframework.transaction.support.TransactionTemplate;
import com.google.common.base.Stopwatch;
@ -50,6 +58,8 @@ 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.jpa.entity.TermConceptParentChildLink;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.jpa.util.StopWatch;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
import ca.uhn.fhir.util.ObjectUtil;
@ -85,6 +95,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
protected EntityManager myEntityManager;
private boolean myProcessDeferred = true;
private long myNextReindexPass;
private boolean addToSet(Set<TermConcept> theSetToPopulate, TermConcept theConcept) {
boolean retVal = theSetToPopulate.add(theConcept);
@ -209,15 +220,6 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
return cs;
}
private void parentPids(TermConcept theNextConcept, Set<Long> theParentPids) {
for (TermConceptParentChildLink nextParentLink : theNextConcept.getParents()){
TermConcept parent = nextParentLink.getParent();
if (parent != null && theParentPids.add(parent.getId())) {
parentPids(parent, theParentPids);
}
}
}
private void persistChildren(TermConcept theConcept, TermCodeSystemVersion theCodeSystem, IdentityHashMap<TermConcept, Object> theConceptsStack, int theTotalConcepts) {
if (theConceptsStack.put(theConcept, PLACEHOLDER_OBJECT) != null) {
return;
@ -231,12 +233,8 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
theConcept.setCodeSystem(theCodeSystem);
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
Set<Long> parentPids = new HashSet<Long>();
parentPids(theConcept, parentPids);
theConcept.setParentPids(parentPids);
if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
myConceptDao.save(theConcept);
saveConcept(theConcept);
} else {
myConceptsToSaveLater.add(theConcept);
}
@ -247,7 +245,7 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
for (TermConceptParentChildLink next : theConcept.getChildren()) {
if (theConceptsStack.size() <= myDaoConfig.getDeferIndexingForCodesystemsOfSize()) {
myConceptParentChildLinkDao.save(next);
saveConceptLink(next);
} else {
myConceptLinksToSaveLater.add(next);
}
@ -255,6 +253,44 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
}
private void saveConceptLink(TermConceptParentChildLink next) {
if (next.getId() == null) {
myConceptParentChildLinkDao.save(next);
}
}
private int saveConcept(TermConcept theConcept) {
int retVal = 0;
retVal += ensureParentsSaved(theConcept.getParents());
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
retVal++;
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
myConceptDao.saveAndFlush(theConcept);
}
ourLog.trace("Saved {} and got PID {}", theConcept.getCode(), theConcept.getId());
return retVal;
}
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
ourLog.trace("Checking {} parents", theParents.size());
int retVal = 0;
for (TermConceptParentChildLink nextLink : theParents) {
if (nextLink.getRelationshipType() == RelationshipTypeEnum.ISA) {
TermConcept nextParent = nextLink.getParent();
retVal += ensureParentsSaved(nextParent.getParents());
if (nextParent.getId() == null) {
myConceptDao.saveAndFlush(nextParent);
retVal++;
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
}
}
}
return retVal;
}
private void populateVersion(TermConcept theNext, TermCodeSystemVersion theCodeSystemVersion) {
if (theNext.getCodeSystem() != null) {
return;
@ -270,17 +306,21 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
@Override
public synchronized void saveDeferred() {
if (!myProcessDeferred || ((myConceptsToSaveLater.isEmpty() && myConceptLinksToSaveLater.isEmpty()))) {
return;
processReindexing();
}
int codeCount = 0, relCount = 0;
StopWatch stopwatch = new StopWatch();
int count = Math.min(myDaoConfig.getDeferIndexingForCodesystemsOfSize(), myConceptsToSaveLater.size());
ourLog.info("Saving {} deferred concepts...", count);
while (codeCount < count && myConceptsToSaveLater.size() > 0) {
TermConcept next = myConceptsToSaveLater.remove(0);
myConceptDao.save(next);
codeCount++;
codeCount += saveConcept(next);
}
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)});
}
if (codeCount == 0) {
@ -288,12 +328,54 @@ public abstract class BaseHapiTerminologySvc implements IHapiTerminologySvc {
ourLog.info("Saving {} deferred concept relationships...", count);
while (relCount < count && myConceptLinksToSaveLater.size() > 0) {
TermConceptParentChildLink next = myConceptLinksToSaveLater.remove(0);
myConceptParentChildLinkDao.save(next);
saveConceptLink(next);
relCount++;
}
}
ourLog.info("Saved {} deferred concepts ({} remain) and {} deferred relationships ({} remain)", new Object[] {codeCount, myConceptsToSaveLater.size(), relCount, myConceptLinksToSaveLater.size()});
if (relCount > 0) {
ourLog.info("Saved {} deferred relationships ({} remain) in {}ms ({}ms / code)", new Object[] {relCount, myConceptLinksToSaveLater.size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(codeCount)});
}
if ((myConceptsToSaveLater.size() + myConceptLinksToSaveLater.size()) == 0) {
ourLog.info("All deferred concepts and relationships have now been synchronized to the database");
}
}
@Autowired
private PlatformTransactionManager myTransactionMgr;
private void processReindexing() {
if (System.currentTimeMillis() < myNextReindexPass) {
return;
}
TransactionTemplate tt = new TransactionTemplate(myTransactionMgr);
tt.setPropagationBehavior(TransactionTemplate.PROPAGATION_REQUIRES_NEW);
tt.execute(new TransactionCallbackWithoutResult() {
@Override
protected void doInTransactionWithoutResult(TransactionStatus theArg0) {
int maxResult = 1000;
Page<TermConcept> resources = myConceptDao.findResourcesRequiringReindexing(new PageRequest(0, maxResult));
if (resources.hasContent() == false) {
myNextReindexPass = System.currentTimeMillis() + DateUtils.MILLIS_PER_MINUTE;
return;
}
ourLog.info("Indexing {} / {} concepts", resources.getContent().size(), resources.getTotalElements());
int count = 0;
StopWatch stopwatch = new StopWatch();
for (TermConcept resourceTable : resources) {
saveConcept(resourceTable);
count++;
}
ourLog.info("Indexed {} / {} concepts in {}ms - Avg {}ms / resource", new Object[] { count, resources.getContent().size(), stopwatch.getMillis(), stopwatch.getMillisPerOperation(count) });
}
});
}
@Override

145
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/HapiTerminologySvcDstu3.java
View File

@ -29,6 +29,7 @@ import java.util.List;
import java.util.Set;
import org.apache.lucene.search.Query;
import org.apache.lucene.search.QueryWrapperFilter;
import org.hibernate.search.jpa.FullTextEntityManager;
import org.hibernate.search.jpa.FullTextQuery;
import org.hibernate.search.query.dsl.BooleanJunction;
@ -78,56 +79,38 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
@Autowired
private ValueSetExpander myValueSetExpander;
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet source = new ValueSet();
source.getCompose().addImport(theValueSet);
try {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
ValueSetExpansionOutcome outcome = myValueSetExpander.expand(source);
for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
}
return retVal;
} catch (Exception e) {
throw new InternalErrorException(e);
private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
if (addedCodes.add(nextConcept.getCode())) {
ValueSetExpansionContainsComponent contains = retVal.addContains();
contains.setCode(nextConcept.getCode());
contains.setSystem(system);
contains.setDisplay(nextConcept.getDisplay());
}
}
@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);
DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escape(theSystem), theRequestDetails);
IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
if (createOutcome.getCreated() != Boolean.TRUE) {
CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
csId = myCodeSystemResourceDao.update(existing, theRequestDetails).getId();
ourLog.info("Created new version of CodeSystem, got ID: {}", csId.toUnqualified().getValue());
}
ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
Long codeSystemResourcePid = resource.getId();
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
theCodeSystemVersion.setResource(resource);
theCodeSystemVersion.setResourceVersionId(resource.getVersion());
super.storeNewCodeSystemVersion(codeSystemResourcePid, theSystem, theCodeSystemVersion);
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) {
//@formatter:off
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);
//@formatter:on
}
@Override
public ValueSetExpansionComponent expandValueSet(FhirContext theContext, ConceptSetComponent theInclude) {
String system = theInclude.getSystem();
ourLog.info("Starting expansion around code system: {}", system);
TermCodeSystem cs = myCodeSystemDao.findByCodeSystemUri(system);
TermCodeSystemVersion csv = cs.getCurrentVersion();
@ -167,27 +150,40 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
bool.must(qb.keyword().onField("myCodeSystemVersionPid").matching(csv.getPid()).createQuery());
for (ConceptSetFilterComponent nextFilter : theInclude.getFilter()) {
if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == FilterOperator.EQUAL) {
if (isNotBlank(nextFilter.getValue())) {
bool.must(qb.phrase().onField("myDisplay").sentence(nextFilter.getValue()).createQuery());
}
} else if (nextFilter.getOp() == FilterOperator.ISA) {
if (isNotBlank(nextFilter.getValue())) {
if (isNotBlank(nextFilter.getValue())) {
if (nextFilter.getProperty().equals("display:exact") && nextFilter.getOp() == FilterOperator.EQUAL) {
addDisplayFilterExact(qb, bool, nextFilter);
} else if (nextFilter.getProperty().equals("display") && nextFilter.getOp() == 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() == FilterOperator.ISA) {
TermConcept code = super.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 {
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
}
} else {
throw new InvalidRequestException("Unknown filter property[" + nextFilter + "] + op[" + nextFilter.getOpElement().getValueAsString() + "]");
}
}
Query luceneQuery = bool.createQuery();
FullTextQuery jpaQuery = em.createFullTextQuery(luceneQuery, TermConcept.class);
jpaQuery.setMaxResults(1000);
@SuppressWarnings("unchecked")
List<TermConcept> result = jpaQuery.getResultList();
for (TermConcept nextConcept : result) {
addCodeIfNotAlreadyAdded(system, retVal, addedCodes, nextConcept);
}
retVal.setTotal(jpaQuery.getResultSize());
}
if (!haveIncludeCriteria) {
@ -197,18 +193,28 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
}
}
retVal.setTotal(retVal.getContains().size());
return retVal;
}
private void addCodeIfNotAlreadyAdded(String system, ValueSetExpansionComponent retVal, Set<String> addedCodes, TermConcept nextConcept) {
if (addedCodes.add(nextConcept.getCode())) {
ValueSetExpansionContainsComponent contains = retVal.addContains();
contains.setCode(nextConcept.getCode());
contains.setSystem(system);
contains.setDisplay(nextConcept.getDisplay());
@Override
public List<VersionIndependentConcept> expandValueSet(String theValueSet) {
ValueSet source = new ValueSet();
source.getCompose().addImport(theValueSet);
try {
ArrayList<VersionIndependentConcept> retVal = new ArrayList<VersionIndependentConcept>();
ValueSetExpansionOutcome outcome = myValueSetExpander.expand(source);
for (ValueSetExpansionContainsComponent next : outcome.getValueset().getExpansion().getContains()) {
retVal.add(new VersionIndependentConcept(next.getSystem(), next.getCode()));
}
return retVal;
} catch (Exception e) {
throw new InternalErrorException(e);
}
}
@Override
@ -238,6 +244,33 @@ public class HapiTerminologySvcDstu3 extends BaseHapiTerminologySvc implements I
return super.supportsSystem(theSystem);
}
@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);
DaoMethodOutcome createOutcome = myCodeSystemResourceDao.create(cs, "CodeSystem?url=" + UrlUtil.escape(theSystem), theRequestDetails);
IIdType csId = createOutcome.getId().toUnqualifiedVersionless();
if (createOutcome.getCreated() != Boolean.TRUE) {
CodeSystem existing = myCodeSystemResourceDao.read(csId, theRequestDetails);
csId = myCodeSystemResourceDao.update(existing, theRequestDetails).getId();
ourLog.info("Created new version of CodeSystem, got ID: {}", csId.toUnqualified().getValue());
}
ResourceTable resource = (ResourceTable) myCodeSystemResourceDao.readEntity(csId);
Long codeSystemResourcePid = resource.getId();
ourLog.info("CodeSystem resource has ID: {}", csId.getValue());
theCodeSystemVersion.setResource(resource);
theCodeSystemVersion.setResourceVersionId(resource.getVersion());
super.storeNewCodeSystemVersion(codeSystemResourcePid, theSystem, theCodeSystemVersion);
}
@CoverageIgnore
@Override
public CodeValidationResult validateCode(FhirContext theContext, String theCodeSystem, String theCode, String theDisplay) {

6
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvc.java
View File

@ -24,15 +24,12 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
import java.io.BufferedInputStream;
import java.io.ByteArrayInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.OutputStream;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
@ -47,7 +44,6 @@ 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.FileUtils;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.lang3.Validate;
@ -102,6 +98,8 @@ public class TerminologyLoaderSvc implements IHapiTerminologyLoaderSvc {
}
ourLog.info(b.toString(), theConcept.getCode());
childIter.remove();
nextChild.getParents().remove(next);
} else {
dropCircularRefs(nextChild, theChain, theCode2concept, theCircularCounter);
}

10
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/util/StopWatch.java
View File

@ -32,4 +32,14 @@ public class StopWatch {
return retVal;
}
public long getMillis() {
long now = System.currentTimeMillis();
long retVal = now - myStarted;
return retVal;
}
public double getMillisPerOperation(int theNumOperations) {
return ((double)getMillis()) / Math.max(1.0, theNumOperations);
}
}

22
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu2/FhirResourceDaoValueSetDstu2Test.java
View File

@ -16,7 +16,6 @@ import org.junit.Before;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.model.dstu2.composite.CodeableConceptDt;
import ca.uhn.fhir.model.dstu2.composite.CodingDt;
@ -25,7 +24,6 @@ import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.IdDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
@ -58,7 +56,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
}
@ -71,7 +69,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure--expiration", result.getDisplay());
}
@ -85,7 +83,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -99,7 +97,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = new StringDt("Systolic blood pressure at First encounterXXXX");
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -113,7 +111,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = new StringDt("Systolic blood pressure at First encounter");
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -127,7 +125,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = new CodeableConceptDt("http://loinc.org", "11378-7");
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -141,7 +139,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
StringDt display = null;
CodingDt coding = null;
CodeableConceptDt codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -150,7 +148,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
public void testExpandById() throws IOException {
String resp;
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null);
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
// @formatter:off
@ -175,7 +173,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
* Filter with display name
*/
expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"));
expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off
@ -188,7 +186,7 @@ public class FhirResourceDaoValueSetDstu2Test extends BaseJpaDstu2Test {
* Filter with code
*/
expanded = myValueSetDao.expand(myExtensionalVsId, ("11378"));
expanded = myValueSetDao.expand(myExtensionalVsId, ("11378"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off

990
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3TerminologyTest.java
View File

File diff suppressed because it is too large Load Diff

19
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoDstu3ValueSetTest.java
View File

@ -26,7 +26,6 @@ import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.dao.IFhirResourceDaoValueSet.ValidateCodeResult;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
@ -62,7 +61,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
}
@ -75,7 +74,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure--expiration", result.getDisplay());
}
@ -89,7 +88,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -103,7 +102,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = new StringType("Systolic blood pressure at First encounterXXXX");
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertFalse(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -117,7 +116,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = new StringType("Systolic blood pressure at First encounter");
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -132,7 +131,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
Coding coding = null;
CodeableConcept codeableConcept = new CodeableConcept();
codeableConcept.addCoding().setSystem("http://acme.org").setCode("11378-7");
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -146,7 +145,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
StringType display = null;
Coding coding = null;
CodeableConcept codeableConcept = null;
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept);
ValidateCodeResult result = myValueSetDao.validateCode(valueSetIdentifier, id, code, system, display, coding, codeableConcept, mySrd);
assertTrue(result.isResult());
assertEquals("Systolic blood pressure at First encounter", result.getDisplay());
}
@ -155,7 +154,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
public void testExpandById() throws IOException {
String resp;
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null);
ValueSet expanded = myValueSetDao.expand(myExtensionalVsId, null, mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsString("<ValueSet xmlns=\"http://hl7.org/fhir\">"));
@ -176,7 +175,7 @@ public class FhirResourceDaoDstu3ValueSetTest extends BaseJpaDstu3Test {
* Filter with display name
*/
expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"));
expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off

3
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/ResourceProviderDstu2ValueSetTest.java
View File

@ -24,7 +24,6 @@ import ca.uhn.fhir.model.primitive.CodeDt;
import ca.uhn.fhir.model.primitive.StringDt;
import ca.uhn.fhir.model.primitive.UriDt;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.servlet.ServletRequestDetails;
import ca.uhn.fhir.util.TestUtil;
public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2Test {
@ -251,7 +250,7 @@ public class ResourceProviderDstu2ValueSetTest extends BaseResourceProviderDstu2
expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"));
expanded = myValueSetDao.expand(myExtensionalVsId, ("systolic"), mySrd);
resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
//@formatter:off

247
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/ResourceProviderDstu3ValueSetTest.java
View File

@ -1,9 +1,12 @@
package ca.uhn.fhir.jpa.provider.dstu3;
import static ca.uhn.fhir.jpa.dao.dstu3.FhirResourceDaoDstu3TerminologyTest.*;
import static org.hamcrest.Matchers.containsString;
import static org.hamcrest.Matchers.containsStringIgnoringCase;
import static org.hamcrest.Matchers.not;
import static org.hamcrest.Matchers.stringContainsInOrder;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
@ -12,25 +15,33 @@ import java.io.IOException;
import org.hl7.fhir.dstu3.model.BooleanType;
import org.hl7.fhir.dstu3.model.CodeSystem;
import org.hl7.fhir.dstu3.model.CodeType;
import org.hl7.fhir.dstu3.model.Coding;
import org.hl7.fhir.dstu3.model.Parameters;
import org.hl7.fhir.dstu3.model.StringType;
import org.hl7.fhir.dstu3.model.UriType;
import org.hl7.fhir.dstu3.model.ValueSet;
import org.hl7.fhir.dstu3.model.ValueSet.ConceptSetComponent;
import org.hl7.fhir.dstu3.model.ValueSet.FilterOperator;
import org.hl7.fhir.dstu3.model.CodeSystem.CodeSystemContentMode;
import org.hl7.fhir.dstu3.model.CodeSystem.ConceptDefinitionComponent;
import org.hl7.fhir.instance.model.api.IIdType;
import org.junit.AfterClass;
import org.junit.Before;
import org.junit.Test;
import org.springframework.transaction.annotation.Transactional;
import ca.uhn.fhir.jpa.entity.ResourceTable;
import ca.uhn.fhir.jpa.entity.TermCodeSystemVersion;
import ca.uhn.fhir.jpa.entity.TermConcept;
import ca.uhn.fhir.jpa.entity.TermConceptParentChildLink.RelationshipTypeEnum;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import ca.uhn.fhir.rest.server.exceptions.ResourceNotFoundException;
import ca.uhn.fhir.util.TestUtil;
public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3Test {
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(ResourceProviderDstu3ValueSetTest.class);
private IIdType myExtensionalVsId;
private IIdType myLocalValueSetId;
private ValueSet myLocalVs;
@AfterClass
public static void afterClassClearContext() {
@ -78,6 +89,140 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
}
@Test
public void testExpandLocalVsAgainstExternalCs() throws IOException {
createExternalCsAndLocalVs();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onInstance(myLocalValueSetId)
.named("expand")
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsStringIgnoringCase("<code value=\"childAAA\"/>"));
assertThat(resp, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
assertThat(resp, not(containsStringIgnoringCase("<code value=\"ParentA\"/>")));
}
@Test
public void testExpandLocalVsWithUnknownCode() throws IOException {
createExternalCsAndLocalVsWithUnknownCode();
assertNotNull(myLocalValueSetId);
//@formatter:off
try {
ourClient
.operation()
.onInstance(myLocalValueSetId)
.named("expand")
.withNoParameters(Parameters.class)
.execute();
} catch (InvalidRequestException e) {
assertEquals("HTTP 400 Bad Request: Invalid filter criteria - code does not exist: {http://example.com/my_code_system}childFOOOOOOO", e.getMessage());
}
//@formatter:on
}
@Test
public void testExpandInlineVsAgainstBuiltInCs() throws IOException {
createLocalVsPointingAtBuiltInCodeSystem();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "valueSet", myLocalVs)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsStringIgnoringCase("<code value=\"M\"/>"));
}
@Test
public void testExpandLocalVsAgainstBuiltInCs() throws IOException {
createLocalVsPointingAtBuiltInCodeSystem();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onInstance(myLocalValueSetId)
.named("expand")
.withNoParameters(Parameters.class)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsStringIgnoringCase("<code value=\"M\"/>"));
}
@Test
public void testExpandLocalVsCanonicalAgainstExternalCs() throws IOException {
createExternalCsAndLocalVs();
assertNotNull(myLocalValueSetId);
//@formatter:off
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "identifier", new UriType(URL_MY_VALUE_SET))
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsStringIgnoringCase("<code value=\"childAAA\"/>"));
assertThat(resp, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
assertThat(resp, not(containsStringIgnoringCase("<code value=\"ParentA\"/>")));
}
@Test
public void testExpandInlineVsAgainstExternalCs() throws IOException {
createExternalCsAndLocalVs();
assertNotNull(myLocalVs);
myLocalVs.setId("");
//@formatter:off
Parameters respParam = ourClient
.operation()
.onType(ValueSet.class)
.named("expand")
.withParameter(Parameters.class, "valueSet", myLocalVs)
.execute();
ValueSet expanded = (ValueSet) respParam.getParameter().get(0).getResource();
//@formatter:on
String resp = myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(expanded);
ourLog.info(resp);
assertThat(resp, containsStringIgnoringCase("<code value=\"childAAA\"/>"));
assertThat(resp, containsStringIgnoringCase("<code value=\"childAAB\"/>"));
assertThat(resp, not(containsStringIgnoringCase("<code value=\"ParentA\"/>")));
}
@Test
public void testExpandByIdWithFilter() throws IOException {
@ -231,4 +376,102 @@ public class ResourceProviderDstu3ValueSetTest extends BaseResourceProviderDstu3
assertEquals(true, ((BooleanType)respParam.getParameter().get(0).getValue()).booleanValue());
}
private CodeSystem createExternalCs() {
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
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);
cs.setResourceVersionId(table.getVersion());
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
cs.getConcepts().add(parentA);
TermConcept childAA = new TermConcept(cs, "childAA").setDisplay("Child AA");
parentA.addChild(childAA, RelationshipTypeEnum.ISA);
TermConcept childAAA = new TermConcept(cs, "childAAA").setDisplay("Child AAA");
childAA.addChild(childAAA, RelationshipTypeEnum.ISA);
TermConcept childAAB = new TermConcept(cs, "childAAB").setDisplay("Child AAB");
childAA.addChild(childAAB, RelationshipTypeEnum.ISA);
TermConcept childAB = new TermConcept(cs, "childAB").setDisplay("Child AB");
parentA.addChild(childAB, RelationshipTypeEnum.ISA);
TermConcept parentB = new TermConcept(cs, "ParentB").setDisplay("Parent B");
cs.getConcepts().add(parentB);
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, cs);
return codeSystem;
}
private void createExternalCsAndLocalVs() {
CodeSystem codeSystem = createExternalCs();
createLocalVs(codeSystem);
}
private void createExternalCsAndLocalVsWithUnknownCode() {
CodeSystem codeSystem = createExternalCs();
createLocalVsWithUnknownCode(codeSystem);
}
private void createLocalCsAndVs() {
//@formatter:off
CodeSystem codeSystem = new CodeSystem();
codeSystem.setUrl(URL_MY_CODE_SYSTEM);
codeSystem.setContent(CodeSystemContentMode.COMPLETE);
codeSystem
.addConcept().setCode("A").setDisplay("Code A")
.addConcept(new ConceptDefinitionComponent().setCode("AA").setDisplay("Code AA")
.addConcept(new ConceptDefinitionComponent().setCode("AAA").setDisplay("Code AAA"))
)
.addConcept(new ConceptDefinitionComponent().setCode("AB").setDisplay("Code AB"));
codeSystem
.addConcept().setCode("B").setDisplay("Code B")
.addConcept(new ConceptDefinitionComponent().setCode("BA").setDisplay("Code BA"))
.addConcept(new ConceptDefinitionComponent().setCode("BB").setDisplay("Code BB"));
//@formatter:on
myCodeSystemDao.create(codeSystem, mySrd);
createLocalVs(codeSystem);
}
private void createLocalVs(CodeSystem codeSystem) {
myLocalVs = new ValueSet();
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(codeSystem.getUrl());
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childAA");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
private void createLocalVsWithUnknownCode(CodeSystem codeSystem) {
myLocalVs = new ValueSet();
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem(codeSystem.getUrl());
include.addFilter().setProperty("concept").setOp(FilterOperator.ISA).setValue("childFOOOOOOO");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
private void createLocalVsPointingAtBuiltInCodeSystem() {
myLocalVs = new ValueSet();
myLocalVs.setUrl(URL_MY_VALUE_SET);
ConceptSetComponent include = myLocalVs.getCompose().addInclude();
include.setSystem("http://hl7.org/fhir/v3/MaritalStatus");
myLocalValueSetId = myValueSetDao.create(myLocalVs, mySrd).getId().toUnqualifiedVersionless();
}
}

13
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/dstu3/SystemProviderDstu3Test.java
View File

@ -367,6 +367,19 @@ public class SystemProviderDstu3Test extends BaseJpaDstu3Test {
}
}
@Test
public void testMarkResourcesForReindexing() throws Exception {
HttpGet get = new HttpGet(ourServerBase + "/$mark-all-resources-for-reindexing");
CloseableHttpResponse http = ourHttpClient.execute(get);
try {
String output = IOUtils.toString(http.getEntity().getContent());
ourLog.info(output);
assertEquals(200, http.getStatusLine().getStatusCode());
} finally {
IOUtils.closeQuietly(http);;
}
}
@Transactional(propagation = Propagation.NEVER)
@Test
public void testSuggestKeywords() throws Exception {

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

@ -30,10 +30,6 @@ public class TerminologyLoaderSvcIntegrationTest extends BaseJpaDstu3Test {
@Test
@Ignore
public void testLoadAndStoreSnomedCt() {
Map<String, File> files = new HashMap<String, File>();
files.put(TerminologyLoaderSvc.SCT_FILE_CONCEPT, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Concept_Full_INT_20160131.txt"));
files.put(TerminologyLoaderSvc.SCT_FILE_DESCRIPTION, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Description_Full-en_INT_20160131.txt"));
files.put(TerminologyLoaderSvc.SCT_FILE_RELATIONSHIP, new File("/Users/james/tmp/sct/SnomedCT_Release_INT_20160131_Full/Terminology/sct2_Relationship_Full_INT_20160131.txt"));
// myLoader.processSnomedCtFiles(files, mySrd);
}

20
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/term/TerminologyLoaderSvcTest.java
View File

@ -1,17 +1,17 @@
package ca.uhn.fhir.jpa.term;
import static org.hamcrest.Matchers.contains;
import static org.hamcrest.Matchers.containsInRelativeOrder;
import static org.hamcrest.Matchers.hasItem;
import static org.hamcrest.Matchers.not;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertThat;
import static org.junit.Assert.fail;
import static org.mockito.Mockito.any;
import static org.mockito.Matchers.any;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.verify;
import java.io.ByteArrayOutputStream;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
@ -25,6 +25,7 @@ import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.Validate;
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;
@ -79,6 +80,21 @@ public class TerminologyLoaderSvcTest {
mySvc.loadLoinc(list(bos1.toByteArray(), bos2.toByteArray()), details);
}
/**
* 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();

1
hapi-fhir-jpaserver-base/src/test/resources/sct/sct2_Concept_Full_INT_20160131.txt
View File

@ -17,3 +17,4 @@ id effectiveTime active moduleId definitionStatusId
207527008 20020131 1 900000000000207008 900000000000074008
207527008 20040731 1 900000000000207008 900000000000073002
207527008 20090731 0 900000000000207008 900000000000074008
404684003 20040131 1 900000000000207008 900000000000074008

6
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/hapi/validation/HapiWorkerContext.java
View File

@ -67,6 +67,8 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
ValueSetExpansionOutcome vso;
try {
vso = getExpander().expand(theSource);
} catch (InvalidRequestException e) {
throw e;
} catch (Exception e) {
throw new InternalErrorException(e);
}
@ -125,7 +127,9 @@ public final class HapiWorkerContext implements IWorkerContext, ValueSetExpander
@Override
public ValueSetExpander getExpander() {
return new ValueSetExpanderSimple(this, this);
ValueSetExpanderSimple retVal = new ValueSetExpanderSimple(this, this);
retVal.setMaxExpansionSize(Integer.MAX_VALUE);
return retVal;
}
@Override

15
hapi-fhir-structures-dstu3/src/main/java/org/hl7/fhir/dstu3/terminologies/ValueSetExpanderSimple.java
View File

@ -70,8 +70,10 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
private Set<String> excludeKeys = new HashSet<String>();
private ValueSetExpanderFactory factory;
private ValueSet focus;
private int maxExpansionSize = 500;
private Map<String, ValueSetExpansionContainsComponent> map = new HashMap<String, ValueSet.ValueSetExpansionContainsComponent>();
private int total;
public ValueSetExpanderSimple(IWorkerContext context, ValueSetExpanderFactory factory) {
super();
@ -79,6 +81,10 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
this.factory = factory;
}
public void setMaxExpansionSize(int theMaxExpansionSize) {
maxExpansionSize = theMaxExpansionSize;
}
private void addCode(String system, String code, String display) {
ValueSetExpansionContainsComponent n = new ValueSet.ValueSetExpansionContainsComponent();
n.setSystem(system);
@ -101,7 +107,7 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
}
private void addCodes(ValueSetExpansionComponent expand, List<ValueSetExpansionParameterComponent> params) throws ETooCostly {
if (expand.getContains().size() > 500)
if (expand.getContains().size() > maxExpansionSize)
throw new ETooCostly("Too many codes to display (>" + Integer.toString(expand.getContains().size()) + ")");
for (ValueSetExpansionParameterComponent p : expand.getParameter()) {
if (!existsInParams(params, p.getName(), p.getValue()))
@ -111,6 +117,8 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
for (ValueSetExpansionContainsComponent c : expand.getContains()) {
addCode(c.getSystem(), c.getCode(), c.getDisplay());
}
total = expand.getTotal();
}
private void excludeCode(String theSystem, String theCode) {
@ -171,6 +179,11 @@ public class ValueSetExpanderSimple implements ValueSetExpander {
focus.getExpansion().getContains().add(c);
}
}
if (total > 0) {
focus.getExpansion().setTotal(total);
}
return new ValueSetExpansionOutcome(focus, null);
} catch (RuntimeException e) {
// TODO: we should put something more specific instead of just Exception below, since