Clean up concept reindexing
This commit is contained in:
jamesagnew
parent
116b9e335d
commit
401a4cd738
|
|
@ -10,6 +10,7 @@ import org.springframework.data.jpa.repository.Modifying;
|
|||
import org.springframework.data.jpa.repository.Query;
|
||||
import org.springframework.data.repository.query.Param;
|
||||
|
||||
import java.util.Date;
|
||||
import java.util.List;
|
||||
|
||||
/*
|
||||
|
|
@ -34,21 +35,42 @@ import java.util.List;
|
|||
|
||||
public interface ITermConceptDao extends JpaRepository<TermConcept, Long> {
|
||||
|
||||
@Query("SELECT COUNT(t) FROM TermConcept t WHERE t.myCodeSystem.myId = :cs_pid")
|
||||
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);
|
||||
|
||||
/**
|
||||
* Used in Smile CDR - Do not delete
|
||||
*/
|
||||
@SuppressWarnings("unused")
|
||||
@Query("SELECT COUNT(*) FROM TermConcept t WHERE t.myUpdated > :cutoff")
|
||||
long countUpdatedAfter(@Param("cutoff") Date theFullTextIndexedUntil);
|
||||
|
||||
/**
|
||||
* Used in Smile CDR - Do not delete
|
||||
*/
|
||||
@SuppressWarnings("unused")
|
||||
@Query("SELECT t FROM TermConcept t ORDER BY t.myUpdated ASC")
|
||||
Slice<TermConcept> findAllOrderedByLastUpdated(Pageable thePage);
|
||||
|
||||
@Query("SELECT c FROM TermConcept c WHERE c.myCodeSystem = :code_system AND c.myCode = :code")
|
||||
TermConcept findByCodeSystemAndCode(@Param("code_system") TermCodeSystemVersion theCodeSystem, @Param("code") String theCode);
|
||||
|
||||
@Query("SELECT c FROM TermConcept c WHERE c.myCodeSystem = :code_system")
|
||||
List<TermConcept> findByCodeSystemVersion(@Param("code_system") TermCodeSystemVersion theCodeSystem);
|
||||
|
||||
@Query("SELECT t FROM TermConcept t WHERE t.myCodeSystem.myId = :cs_pid")
|
||||
Slice<TermConcept> findByCodeSystemVersion(Pageable thePage, @Param("cs_pid") Long thePid);
|
||||
|
||||
@Query("SELECT COUNT(t) FROM TermConcept t WHERE t.myCodeSystem.myId = :cs_pid")
|
||||
Integer countByCodeSystemVersion(@Param("cs_pid") Long thePid);
|
||||
@Query("SELECT c FROM TermConcept c WHERE c.myCodeSystem = :code_system")
|
||||
List<TermConcept> findByCodeSystemVersion(@Param("code_system") TermCodeSystemVersion theCodeSystem);
|
||||
|
||||
@Query("SELECT t FROM TermConcept t WHERE t.myIndexStatus = null")
|
||||
Page<TermConcept> findResourcesRequiringReindexing(Pageable thePageRequest);
|
||||
|
||||
/**
|
||||
* Used in Smile CDR - Do not delete
|
||||
*/
|
||||
@SuppressWarnings("unused")
|
||||
@Query("SELECT t FROM TermConcept t WHERE t.myUpdated > :cutoff ORDER BY t.myUpdated ASC")
|
||||
Slice<TermConcept> findUpdatedAfterOrderedByLastUpdated(Pageable thePage, @Param("cutoff") Date theFullTextIndexedUntil);
|
||||
|
||||
@Query("UPDATE TermConcept t SET t.myIndexStatus = null")
|
||||
@Modifying
|
||||
int markAllForReindexing();
|
||||
|
|
|
|||
|
|
@ -45,7 +45,8 @@ import static org.apache.commons.lang3.StringUtils.isNotBlank;
|
|||
@Table(name = "TRM_CONCEPT", uniqueConstraints = {
|
||||
@UniqueConstraint(name = "IDX_CONCEPT_CS_CODE", columnNames = {"CODESYSTEM_PID", "CODE"})
|
||||
}, indexes = {
|
||||
@Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList = "INDEX_STATUS")
|
||||
@Index(name = "IDX_CONCEPT_INDEXSTATUS", columnList = "INDEX_STATUS"),
|
||||
@Index(name = "IDX_CONCEPT_UPDATED", columnList = "CONCEPT_UPDATED")
|
||||
})
|
||||
public class TermConcept implements Serializable {
|
||||
protected static final int MAX_DESC_LENGTH = 400;
|
||||
|
|
@ -59,15 +60,15 @@ public class TermConcept implements Serializable {
|
|||
@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;
|
||||
|
||||
@Temporal(TemporalType.TIMESTAMP)
|
||||
@Column(name = "CONCEPT_UPDATED", nullable = true)
|
||||
private Date myUpdated;
|
||||
@ManyToOne()
|
||||
@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")})
|
||||
private long myCodeSystemVersionPid;
|
||||
|
||||
@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")),
|
||||
|
|
@ -76,15 +77,12 @@ public class TermConcept implements Serializable {
|
|||
@Field(name = "myDisplayPhonetic", index = org.hibernate.search.annotations.Index.YES, store = Store.NO, analyze = Analyze.YES, analyzer = @Analyzer(definition = "autocompletePhoneticAnalyzer"))
|
||||
})
|
||||
private String myDisplay;
|
||||
|
||||
@OneToMany(mappedBy = "myConcept", orphanRemoval = false)
|
||||
@Field(name = "PROPmyProperties", analyzer = @Analyzer(definition = "termConceptPropertyAnalyzer"))
|
||||
@FieldBridge(impl = TermConceptPropertyFieldBridge.class)
|
||||
private Collection<TermConceptProperty> myProperties;
|
||||
|
||||
@OneToMany(mappedBy = "myConcept", orphanRemoval = false)
|
||||
private Collection<TermConceptDesignation> myDesignations;
|
||||
|
||||
@Id()
|
||||
@SequenceGenerator(name = "SEQ_CONCEPT_PID", sequenceName = "SEQ_CONCEPT_PID")
|
||||
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CONCEPT_PID")
|
||||
|
|
@ -92,18 +90,17 @@ public class TermConcept implements Serializable {
|
|||
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"))
|
||||
@Lob
|
||||
@Column(name="PARENT_PIDS", nullable = true)
|
||||
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();
|
||||
}
|
||||
|
||||
public TermConcept(TermCodeSystemVersion theCs, String theCode) {
|
||||
setCodeSystemVersion(theCs);
|
||||
setCode(theCode);
|
||||
|
|
@ -296,6 +293,14 @@ public class TermConcept implements Serializable {
|
|||
return null;
|
||||
}
|
||||
|
||||
public Date getUpdated() {
|
||||
return myUpdated;
|
||||
}
|
||||
|
||||
public void setUpdated(Date theUpdated) {
|
||||
myUpdated = theUpdated;
|
||||
}
|
||||
|
||||
@Override
|
||||
public int hashCode() {
|
||||
HashCodeBuilder b = new HashCodeBuilder();
|
||||
|
|
|
|||
|
|
@ -327,26 +327,6 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
|
||||
}
|
||||
|
||||
private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
|
||||
int count;
|
||||
ourLog.info(" * Deleting {}", theDescriptor);
|
||||
int totalCount = theCounter.get();
|
||||
StopWatch sw = new StopWatch();
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<T> link = theLoader.get();
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
theDao.deleteInBatch(link);
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} {} deleted - {}/sec - ETA: {}", count, theDescriptor, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
|
||||
}
|
||||
theDao.flush();
|
||||
}
|
||||
|
||||
public void deleteConceptMap(ResourceTable theResourceTable) {
|
||||
// Get existing entity so it can be deleted.
|
||||
Optional<TermConceptMap> optionalExistingTermConceptMapById = myConceptMapDao.findTermConceptMapByResourcePid(theResourceTable.getId());
|
||||
|
|
@ -388,6 +368,26 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
deleteConceptMap(theResourceTable);
|
||||
}
|
||||
|
||||
private <T> void doDelete(String theDescriptor, Supplier<Slice<T>> theLoader, Supplier<Integer> theCounter, JpaRepository<T, ?> theDao) {
|
||||
int count;
|
||||
ourLog.info(" * Deleting {}", theDescriptor);
|
||||
int totalCount = theCounter.get();
|
||||
StopWatch sw = new StopWatch();
|
||||
count = 0;
|
||||
while (true) {
|
||||
Slice<T> link = theLoader.get();
|
||||
if (link.hasContent() == false) {
|
||||
break;
|
||||
}
|
||||
|
||||
theDao.deleteInBatch(link);
|
||||
|
||||
count += link.getNumberOfElements();
|
||||
ourLog.info(" * {} {} deleted - {}/sec - ETA: {}", count, theDescriptor, sw.formatThroughput(count, TimeUnit.SECONDS), sw.getEstimatedTimeRemaining(count, totalCount));
|
||||
}
|
||||
theDao.flush();
|
||||
}
|
||||
|
||||
private int ensureParentsSaved(Collection<TermConceptParentChildLink> theParents) {
|
||||
ourLog.trace("Checking {} parents", theParents.size());
|
||||
int retVal = 0;
|
||||
|
|
@ -397,6 +397,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
TermConcept nextParent = nextLink.getParent();
|
||||
retVal += ensureParentsSaved(nextParent.getParents());
|
||||
if (nextParent.getId() == null) {
|
||||
nextParent.setUpdated(new Date());
|
||||
myConceptDao.saveAndFlush(nextParent);
|
||||
retVal++;
|
||||
ourLog.debug("Saved parent code {} and got id {}", nextParent.getCode(), nextParent.getId());
|
||||
|
|
@ -887,9 +888,11 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
|
||||
for (TermConcept nextConcept : concepts) {
|
||||
|
||||
if (isBlank(nextConcept.getParentPidsAsString())) {
|
||||
StringBuilder parentsBuilder = new StringBuilder();
|
||||
createParentsString(parentsBuilder, nextConcept.getId());
|
||||
nextConcept.setParentPids(parentsBuilder.toString());
|
||||
}
|
||||
|
||||
saveConcept(nextConcept);
|
||||
count++;
|
||||
|
|
@ -923,6 +926,7 @@ public abstract class BaseHapiTerminologySvcImpl implements IHapiTerminologySvc,
|
|||
if (theConcept.getId() == null || theConcept.getIndexStatus() == null) {
|
||||
retVal++;
|
||||
theConcept.setIndexStatus(BaseHapiFhirDao.INDEX_STATUS_INDEXED);
|
||||
theConcept.setUpdated(new Date());
|
||||
myConceptDao.save(theConcept);
|
||||
|
||||
for (TermConceptProperty next : theConcept.getProperties()) {
|
||||
|
|
|
|||
|
|
@ -104,6 +104,8 @@ public abstract class BaseJpaR4Test extends BaseJpaTest {
|
|||
@Qualifier("myConceptMapDaoR4")
|
||||
protected IFhirResourceDaoConceptMap<ConceptMap> myConceptMapDao;
|
||||
@Autowired
|
||||
protected ITermConceptDao myTermConceptDao;
|
||||
@Autowired
|
||||
@Qualifier("myConditionDaoR4")
|
||||
protected IFhirResourceDao<Condition> myConditionDao;
|
||||
@Autowired
|
||||
|
|
|
|||
|
|
@ -1,30 +1,13 @@
|
|||
package ca.uhn.fhir.jpa.dao.r4;
|
||||
|
||||
import static org.hamcrest.Matchers.containsInAnyOrder;
|
||||
import static org.hamcrest.Matchers.containsStringIgnoringCase;
|
||||
import static org.hamcrest.Matchers.empty;
|
||||
import static org.junit.Assert.assertEquals;
|
||||
import static org.junit.Assert.assertThat;
|
||||
import static org.junit.Assert.fail;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
import ca.uhn.fhir.jpa.term.BaseHapiTerminologySvcImpl;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCategory;
|
||||
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.r4.model.ValueSet.*;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.*;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import ca.uhn.fhir.jpa.dao.DaoConfig;
|
||||
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.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.jpa.term.BaseHapiTerminologySvcImpl;
|
||||
import ca.uhn.fhir.jpa.term.IHapiTerminologySvc;
|
||||
import ca.uhn.fhir.parser.IParser;
|
||||
import ca.uhn.fhir.rest.param.TokenParam;
|
||||
|
|
@ -34,13 +17,29 @@ import ca.uhn.fhir.rest.server.exceptions.UnprocessableEntityException;
|
|||
import ca.uhn.fhir.util.TestUtil;
|
||||
import ca.uhn.fhir.validation.FhirValidator;
|
||||
import ca.uhn.fhir.validation.ValidationResult;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.hl7.fhir.r4.model.*;
|
||||
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceCategory;
|
||||
import org.hl7.fhir.r4.model.AllergyIntolerance.AllergyIntoleranceClinicalStatus;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.CodeSystemContentMode;
|
||||
import org.hl7.fhir.r4.model.CodeSystem.ConceptDefinitionComponent;
|
||||
import org.hl7.fhir.r4.model.ValueSet.*;
|
||||
import org.junit.*;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
|
||||
import java.time.Instant;
|
||||
import java.util.ArrayList;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
|
||||
import static org.hamcrest.Matchers.*;
|
||||
import static org.junit.Assert.*;
|
||||
|
||||
public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4TerminologyTest.class);
|
||||
public static final String URL_MY_CODE_SYSTEM = "http://example.com/my_code_system";
|
||||
public static final String URL_MY_VALUE_SET = "http://example.com/my_value_set";
|
||||
|
||||
private static final org.slf4j.Logger ourLog = org.slf4j.LoggerFactory.getLogger(FhirResourceDaoR4TerminologyTest.class);
|
||||
@Autowired
|
||||
private IHapiTerminologySvc myHapiTerminologySvc;
|
||||
|
||||
|
|
@ -96,38 +95,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
TermConcept childCA = new TermConcept(cs, "childCA").setDisplay("Child CA");
|
||||
parentC.addChild(childCA, RelationshipTypeEnum.ISA);
|
||||
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME" , cs);
|
||||
return codeSystem;
|
||||
}
|
||||
|
||||
private CodeSystem createExternalCsLarge() {
|
||||
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.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
|
||||
|
||||
TermCodeSystemVersion cs = new TermCodeSystemVersion();
|
||||
cs.setResource(table);
|
||||
|
||||
TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
|
||||
cs.getConcepts().add(parentA);
|
||||
|
||||
for (int i = 0; i < 450; i++) {
|
||||
TermConcept childI = new TermConcept(cs, "subCodeA"+i).setDisplay("Sub-code A"+i);
|
||||
parentA.addChild(childI, RelationshipTypeEnum.ISA);
|
||||
}
|
||||
|
||||
TermConcept parentB = new TermConcept(cs, "codeB").setDisplay("CodeB");
|
||||
cs.getConcepts().add(parentB);
|
||||
|
||||
for (int i = 0; i < 450; i++) {
|
||||
TermConcept childI = new TermConcept(cs, "subCodeB"+i).setDisplay("Sub-code B"+i);
|
||||
parentB.addChild(childI, RelationshipTypeEnum.ISA);
|
||||
}
|
||||
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME" , cs);
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
|
||||
return codeSystem;
|
||||
}
|
||||
|
||||
|
|
@ -163,7 +131,38 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
TermConcept beagle = new TermConcept(cs, "beagle").setDisplay("Beagle");
|
||||
dogs.addChild(beagle, RelationshipTypeEnum.ISA);
|
||||
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM,"SYSTEM NAME" , cs);
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
|
||||
return codeSystem;
|
||||
}
|
||||
|
||||
private CodeSystem createExternalCsLarge() {
|
||||
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.findById(id.getIdPartAsLong()).orElseThrow(IllegalStateException::new);
|
||||
|
||||
TermCodeSystemVersion cs = new TermCodeSystemVersion();
|
||||
cs.setResource(table);
|
||||
|
||||
TermConcept parentA = new TermConcept(cs, "codeA").setDisplay("CodeA");
|
||||
cs.getConcepts().add(parentA);
|
||||
|
||||
for (int i = 0; i < 450; i++) {
|
||||
TermConcept childI = new TermConcept(cs, "subCodeA" + i).setDisplay("Sub-code A" + i);
|
||||
parentA.addChild(childI, RelationshipTypeEnum.ISA);
|
||||
}
|
||||
|
||||
TermConcept parentB = new TermConcept(cs, "codeB").setDisplay("CodeB");
|
||||
cs.getConcepts().add(parentB);
|
||||
|
||||
for (int i = 0; i < 450; i++) {
|
||||
TermConcept childI = new TermConcept(cs, "subCodeB" + i).setDisplay("Sub-code B" + i);
|
||||
parentB.addChild(childI, RelationshipTypeEnum.ISA);
|
||||
}
|
||||
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), URL_MY_CODE_SYSTEM, "SYSTEM NAME", cs);
|
||||
return codeSystem;
|
||||
}
|
||||
|
||||
|
|
@ -252,6 +251,20 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testConceptTimestamps() {
|
||||
long start = System.currentTimeMillis() - 10;
|
||||
|
||||
createExternalCsDogs();
|
||||
|
||||
runInTransaction(() -> {
|
||||
List<TermConcept> concepts = myTermConceptDao.findAll();
|
||||
for (TermConcept next : concepts) {
|
||||
assertTrue(next.getUpdated().getTime() > start);
|
||||
}
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandInvalid() {
|
||||
createExternalCsAndLocalVs();
|
||||
|
|
@ -300,47 +313,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
// TODO: get this working
|
||||
@Ignore
|
||||
@Test
|
||||
public void testExpandWithOpEquals() {
|
||||
|
||||
|
||||
ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", "");
|
||||
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testExpandWithCodesAndDisplayFilterPartialOnFilter() {
|
||||
CodeSystem codeSystem = createExternalCsDogs();
|
||||
|
||||
ValueSet valueSet = new ValueSet();
|
||||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
valueSet.getCompose()
|
||||
.addInclude()
|
||||
.setSystem(codeSystem.getUrl())
|
||||
.addConcept(new ConceptReferenceComponent().setCode("hello"))
|
||||
.addConcept(new ConceptReferenceComponent().setCode("goodbye"));
|
||||
valueSet.getCompose()
|
||||
.addInclude()
|
||||
.setSystem(codeSystem.getUrl())
|
||||
.addFilter()
|
||||
.setProperty("concept")
|
||||
.setOp(FilterOperator.ISA)
|
||||
.setValue("dogs");
|
||||
|
||||
myValueSetDao.create(valueSet, mySrd);
|
||||
|
||||
ValueSet result = myValueSetDao.expand(valueSet, "lab");
|
||||
logAndValidateValueSet(result);
|
||||
|
||||
assertEquals(1, result.getExpansion().getTotal());
|
||||
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
|
||||
assertThat(codes, containsInAnyOrder("labrador"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandWithCodesAndDisplayFilterPartialOnCodes() {
|
||||
CodeSystem codeSystem = createExternalCsDogs();
|
||||
|
|
@ -389,6 +361,36 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandWithCodesAndDisplayFilterPartialOnFilter() {
|
||||
CodeSystem codeSystem = createExternalCsDogs();
|
||||
|
||||
ValueSet valueSet = new ValueSet();
|
||||
valueSet.setUrl(URL_MY_VALUE_SET);
|
||||
valueSet.getCompose()
|
||||
.addInclude()
|
||||
.setSystem(codeSystem.getUrl())
|
||||
.addConcept(new ConceptReferenceComponent().setCode("hello"))
|
||||
.addConcept(new ConceptReferenceComponent().setCode("goodbye"));
|
||||
valueSet.getCompose()
|
||||
.addInclude()
|
||||
.setSystem(codeSystem.getUrl())
|
||||
.addFilter()
|
||||
.setProperty("concept")
|
||||
.setOp(FilterOperator.ISA)
|
||||
.setValue("dogs");
|
||||
|
||||
myValueSetDao.create(valueSet, mySrd);
|
||||
|
||||
ValueSet result = myValueSetDao.expand(valueSet, "lab");
|
||||
logAndValidateValueSet(result);
|
||||
|
||||
assertEquals(1, result.getExpansion().getTotal());
|
||||
ArrayList<String> codes = toCodesContains(result.getExpansion().getContains());
|
||||
assertThat(codes, containsInAnyOrder("labrador"));
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandWithDisplayInExternalValueSetFuzzyMatching() {
|
||||
createExternalCsAndLocalVs();
|
||||
|
|
@ -543,6 +545,16 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
}
|
||||
}
|
||||
|
||||
// TODO: get this working
|
||||
@Ignore
|
||||
@Test
|
||||
public void testExpandWithOpEquals() {
|
||||
|
||||
|
||||
ValueSet result = myValueSetDao.expandByIdentifier("http://hl7.org/fhir/ValueSet/doc-typecodes", "");
|
||||
ourLog.info(myFhirCtx.newXmlParser().setPrettyPrint(true).encodeResourceToString(result));
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testExpandWithSystemAndCodesAndFilterKeywordInLocalValueSet() {
|
||||
createLocalCsAndVs();
|
||||
|
|
@ -713,7 +725,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
cs.setResource(table);
|
||||
TermConcept parentA = new TermConcept(cs, "ParentA").setDisplay("Parent A");
|
||||
cs.getConcepts().add(parentA);
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct","Snomed CT" , cs);
|
||||
myTermSvc.storeNewCodeSystemVersion(table.getId(), "http://snomed.info/sct", "Snomed CT", cs);
|
||||
|
||||
StringType code = new StringType("ParentA");
|
||||
StringType system = new StringType("http://snomed.info/sct");
|
||||
|
|
@ -818,19 +830,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeInUnknownCodeSystem() {
|
||||
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
|
||||
try {
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unable to find imported value set http://example.com/my_value_set", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeBelowBuiltInCodesystem() {
|
||||
AllergyIntolerance ai1 = new AllergyIntolerance();
|
||||
|
|
@ -918,33 +917,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testSearchCodeBelowLocalCodesystem() {
|
||||
createLocalCsAndVs();
|
||||
|
||||
Observation obsAA = new Observation();
|
||||
obsAA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("AA");
|
||||
IIdType idAA = myObservationDao.create(obsAA, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obsBA = new Observation();
|
||||
obsBA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("BA");
|
||||
IIdType idBA = myObservationDao.create(obsBA, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obsCA = new Observation();
|
||||
obsCA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("CA");
|
||||
IIdType idCA = myObservationDao.create(obsCA, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "A").setModifier(TokenParamModifier.BELOW));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idAA.getValue()));
|
||||
|
||||
params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "AAA").setModifier(TokenParamModifier.BELOW));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeBelowExternalCodesystemLarge() {
|
||||
createExternalCsLarge();
|
||||
|
|
@ -975,6 +947,32 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeBelowLocalCodesystem() {
|
||||
createLocalCsAndVs();
|
||||
|
||||
Observation obsAA = new Observation();
|
||||
obsAA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("AA");
|
||||
IIdType idAA = myObservationDao.create(obsAA, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obsBA = new Observation();
|
||||
obsBA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("BA");
|
||||
IIdType idBA = myObservationDao.create(obsBA, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
Observation obsCA = new Observation();
|
||||
obsCA.getCode().addCoding().setSystem(URL_MY_CODE_SYSTEM).setCode("CA");
|
||||
IIdType idCA = myObservationDao.create(obsCA, mySrd).getId().toUnqualifiedVersionless();
|
||||
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "A").setModifier(TokenParamModifier.BELOW));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), containsInAnyOrder(idAA.getValue()));
|
||||
|
||||
params = new SearchParameterMap();
|
||||
params.add(Observation.SP_CODE, new TokenParam(URL_MY_CODE_SYSTEM, "AAA").setModifier(TokenParamModifier.BELOW));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeInBuiltInValueSet() {
|
||||
AllergyIntolerance ai1 = new AllergyIntolerance();
|
||||
|
|
@ -1093,7 +1091,6 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
assertThat(toUnqualifiedVersionlessIdValues(myAuditEventDao.search(params)), empty());
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testSearchCodeInLocalCodesystem() {
|
||||
createLocalCsAndVs();
|
||||
|
|
@ -1116,6 +1113,19 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeInUnknownCodeSystem() {
|
||||
|
||||
SearchParameterMap params = new SearchParameterMap();
|
||||
|
||||
try {
|
||||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
assertThat(toUnqualifiedVersionlessIdValues(myObservationDao.search(params)), empty());
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unable to find imported value set http://example.com/my_value_set", e.getMessage());
|
||||
}
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testSearchCodeInValueSetThatImportsInvalidCodeSystem() {
|
||||
ValueSet valueSet = new ValueSet();
|
||||
|
|
@ -1131,7 +1141,7 @@ public class FhirResourceDaoR4TerminologyTest extends BaseJpaR4Test {
|
|||
params.add(Observation.SP_CODE, new TokenParam(null, URL_MY_VALUE_SET).setModifier(TokenParamModifier.IN));
|
||||
try {
|
||||
myObservationDao.search(params);
|
||||
} catch(InvalidRequestException e) {
|
||||
} catch (InvalidRequestException e) {
|
||||
assertEquals("Unable to expand imported value set: Unable to find imported value set http://non_existant_VS", e.getMessage());
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue