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Changes per code review.

This commit is contained in:
ianmarshall 2020-05-29 23:47:44 -04:00
parent 5cc77b78d4
commit a4811f1508
25 changed files with 428 additions and 507 deletions
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9
hapi-fhir-jpaserver-api/src/main/java/ca/uhn/fhir/jpa/api/dao/IFhirResourceDaoObservation.java
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@ -29,6 +29,15 @@ import javax.servlet.http.HttpServletResponse;
public interface IFhirResourceDaoObservation<T extends IBaseResource> extends IFhirResourceDao<T> {
/**
* Returns a BundleProvider which can be used to implement the $lastn operation.
* @param paramMap Parameters supported include Observation.subject, Observation.patient, Observation.code,
* Observation.category, and max (the maximum number of Observations to return per specified subjects/patients,
* codes, and/or categories.
* @param theRequestDetails
* @param theServletResponse
* @return
*/
IBundleProvider observationsLastN(SearchParameterMap paramMap, RequestDetails theRequestDetails, HttpServletResponse theServletResponse);
}

25
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/BaseHapiFhirResourceDaoObservation.java
View File

@ -22,25 +22,50 @@ package ca.uhn.fhir.jpa.dao;
import ca.uhn.fhir.interceptor.model.RequestPartitionId;
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
import ca.uhn.fhir.jpa.partition.IRequestPartitionHelperSvc;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.api.*;
import ca.uhn.fhir.rest.api.server.*;
import ca.uhn.fhir.rest.api.server.storage.ResourcePersistentId;
import ca.uhn.fhir.rest.api.server.storage.TransactionDetails;
import ca.uhn.fhir.rest.param.ReferenceParam;
import org.hl7.fhir.instance.model.api.*;
import org.springframework.beans.factory.annotation.Autowired;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.TreeMap;
public abstract class BaseHapiFhirResourceDaoObservation<T extends IBaseResource> extends BaseHapiFhirResourceDao<T> implements IFhirResourceDaoObservation<T> {
@Autowired
ObservationLastNIndexPersistSvc myObservationLastNIndexPersistSvc;
@Autowired
private IRequestPartitionHelperSvc myRequestPartitionHelperService;
protected ResourceTable updateObservationEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity,
Date theDeletedTimestampOrNull, boolean thePerformIndexing, boolean theUpdateVersion,
TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion,
theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
// Update indexes here for LastN operation.
myObservationLastNIndexPersistSvc.indexObservation(theResource);
} else {
myObservationLastNIndexPersistSvc.deleteObservationIndex(theEntity);
}
}
return retVal;
}
protected void updateSearchParamsForLastn(SearchParameterMap theSearchParameterMap, RequestDetails theRequestDetails) {
if (!isPagingProviderDatabaseBacked(theRequestDetails)) {
theSearchParameterMap.setLoadSynchronous(true);

114
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/ObservationLastNIndexPersistSvc.java
View File

@ -39,40 +39,46 @@ public class ObservationLastNIndexPersistSvc {
public void indexObservation(IBaseResource theResource) {
String subjectId = null;
List<IBase> subjectReferenceElement = mySearchParameterExtractor.extractValues("Observation.subject", theResource);
if (subjectReferenceElement.size() == 1) {
PathAndRef subjectPathAndRef = mySearchParameterExtractor.extractReferenceLinkFromResource(subjectReferenceElement.get(0), "Observation.subject");
if (subjectPathAndRef != null) {
IBaseReference subjectReference = subjectPathAndRef.getRef();
if (subjectReference != null) {
subjectId = subjectReference.getReferenceElement().getValue();
}
}
}
String subjectId = subjectReferenceElement.stream()
.map(refElement -> mySearchParameterExtractor.extractReferenceLinkFromResource(refElement, "Observation.subject"))
.filter(Objects::nonNull)
.map(PathAndRef::getRef)
.filter(Objects::nonNull)
.map(subjectRef -> subjectRef.getReferenceElement().getValue())
.filter(Objects::nonNull)
.findFirst().orElse(null);
Date effectiveDtm = null;
List<IBase> effectiveDateElement = mySearchParameterExtractor.extractValues("Observation.effective", theResource);
if (effectiveDateElement.size() == 1) {
if (effectiveDateElement.size() > 0) {
effectiveDtm = mySearchParameterExtractor.extractDateFromResource(effectiveDateElement.get(0), "Observation.effective");
}
// Build CodeableConcept entity for Observation.Code.
List<IBase> observationCodeCodeableConcepts = mySearchParameterExtractor.extractValues("Observation.code", theResource);
// Only index for lastn if Observation has a subject, effective date/time and code
if (subjectId == null || effectiveDtm == null || observationCodeCodeableConcepts.size() == 0) {
// Only index for lastn if Observation has a code
if (observationCodeCodeableConcepts.size() == 0) {
return;
}
List<IBase> observationCategoryCodeableConcepts = mySearchParameterExtractor.extractValues("Observation.category", theResource);
String resourcePID = theResource.getIdElement().getIdPart();
createOrUpdateIndexedObservation(resourcePID, effectiveDtm, subjectId, observationCodeCodeableConcepts, observationCategoryCodeableConcepts);
}
private void createOrUpdateIndexedObservation(String resourcePID, Date theEffectiveDtm, String theSubjectId,
List<IBase> theObservationCodeCodeableConcepts,
List<IBase> theObservationCategoryCodeableConcepts) {
// Determine if an index already exists for Observation:
boolean observationIndexUpdate = false;
ObservationIndexedSearchParamLastNEntity indexedObservation = null;
if (resourcePID != null) {
indexedObservation = myResourceIndexedObservationLastNDao.findForIdentifier(resourcePID);
indexedObservation = myResourceIndexedObservationLastNDao.findByIdentifier(resourcePID);
}
if (indexedObservation == null) {
indexedObservation = new ObservationIndexedSearchParamLastNEntity();
@ -80,27 +86,46 @@ public class ObservationLastNIndexPersistSvc {
observationIndexUpdate = true;
}
indexedObservation.setEffectiveDtm(effectiveDtm);
indexedObservation.setEffectiveDtm(theEffectiveDtm);
indexedObservation.setIdentifier(resourcePID);
indexedObservation.setSubject(subjectId);
indexedObservation.setSubject(theSubjectId);
addCodeToObservationIndex(theObservationCodeCodeableConcepts, indexedObservation);
addCategoriesToObservationIndex(theObservationCategoryCodeableConcepts, indexedObservation);
if (observationIndexUpdate) {
myEntityManager.merge(indexedObservation);
} else {
myEntityManager.persist(indexedObservation);
}
}
private void addCodeToObservationIndex(List<IBase> theObservationCodeCodeableConcepts,
ObservationIndexedSearchParamLastNEntity theIndexedObservation) {
// Determine if a Normalized ID was created previously for Observation Code
boolean observationCodeUpdate = false;
String observationCodeNormalizedId = getCodeCodeableConceptIdIfExists(observationCodeCodeableConcepts.get(0));
if (observationCodeNormalizedId != null) {
observationCodeUpdate = true;
}
// Generate a new a normalized ID if necessary
if (observationCodeNormalizedId == null) {
observationCodeNormalizedId = UUID.randomUUID().toString();
}
Optional<String> existingObservationCodeNormalizedId = getCodeCodeableConceptIdIfExists(theObservationCodeCodeableConcepts.get(0));
// Create/update normalized Observation Code index record
ObservationIndexedCodeCodeableConceptEntity codeableConceptField = getCodeCodeableConcept(observationCodeCodeableConcepts.get(0), observationCodeNormalizedId);
ObservationIndexedCodeCodeableConceptEntity codeableConceptField =
getCodeCodeableConcept(theObservationCodeCodeableConcepts.get(0),
existingObservationCodeNormalizedId.orElse(UUID.randomUUID().toString()));
if (existingObservationCodeNormalizedId.isPresent()) {
myEntityManager.merge(codeableConceptField);
} else {
myEntityManager.persist(codeableConceptField);
}
theIndexedObservation.setObservationCode(codeableConceptField);
theIndexedObservation.setCodeNormalizedId(codeableConceptField.getCodeableConceptId());
}
private void addCategoriesToObservationIndex(List<IBase> observationCategoryCodeableConcepts,
ObservationIndexedSearchParamLastNEntity indexedObservation) {
// Build CodeableConcept entities for Observation.Category
List<IBase> observationCategoryCodeableConcepts = mySearchParameterExtractor.extractValues("Observation.category", theResource);
Set<ObservationIndexedCategoryCodeableConceptEntity> categoryCodeableConceptEntities = new HashSet<>();
for (IBase categoryCodeableConcept : observationCategoryCodeableConcepts) {
// Build CodeableConcept entities for each category CodeableConcept
@ -108,20 +133,6 @@ public class ObservationLastNIndexPersistSvc {
}
indexedObservation.setCategoryCodeableConcepts(categoryCodeableConceptEntities);
if (observationCodeUpdate) {
myEntityManager.merge(codeableConceptField);
} else {
myEntityManager.persist(codeableConceptField);
}
indexedObservation.setObservationCode(codeableConceptField);
indexedObservation.setCodeNormalizedId(observationCodeNormalizedId);
if (observationIndexUpdate) {
myEntityManager.merge(indexedObservation);
} else {
myEntityManager.persist(indexedObservation);
}
}
private ObservationIndexedCategoryCodeableConceptEntity getCategoryCodeableConceptEntities(IBase theValue) {
@ -151,29 +162,32 @@ public class ObservationLastNIndexPersistSvc {
return codeCodeableConcept;
}
private String getCodeCodeableConceptIdIfExists(IBase theValue) {
private Optional<String> getCodeCodeableConceptIdIfExists(IBase theValue) {
List<IBase> codings = mySearchParameterExtractor.getCodingsFromCodeableConcept(theValue);
String codeCodeableConceptId = null;
Optional<String> codeCodeableConceptIdOptional = Optional.empty();
for (IBase nextCoding : codings) {
ResourceIndexedSearchParamToken param = mySearchParameterExtractor.createSearchParamForCoding("Observation",
new RuntimeSearchParam(null, null, "code", null, null, null, null, null, null, null),
new RuntimeSearchParam(null, null, "code", null, null, null,
null, null, null, null),
nextCoding);
if (param != null) {
String system = param.getSystem();
String code = param.getValue();
String text = mySearchParameterExtractor.getDisplayTextForCoding(nextCoding);
if (code != null && system != null) {
codeCodeableConceptId = myObservationIndexedCodeCodingSearchParamDao.findForCodeAndSystem(code, system);
codeCodeableConceptIdOptional = Optional.ofNullable(myObservationIndexedCodeCodingSearchParamDao.findByCodeAndSystem(code, system));
} else {
codeCodeableConceptId = myObservationIndexedCodeCodingSearchParamDao.findForDisplay(text);
codeCodeableConceptIdOptional = Optional.ofNullable(myObservationIndexedCodeCodingSearchParamDao.findByDisplay(text));
}
if (codeCodeableConceptId != null) {
if (codeCodeableConceptIdOptional.isPresent()) {
break;
}
}
}
return codeCodeableConceptId;
return codeCodeableConceptIdOptional;
}
private ObservationIndexedCategoryCodingEntity getCategoryCoding(IBase theValue) {
@ -205,7 +219,7 @@ public class ObservationLastNIndexPersistSvc {
}
public void deleteObservationIndex(IBasePersistedResource theEntity) {
ObservationIndexedSearchParamLastNEntity deletedObservationLastNEntity = myResourceIndexedObservationLastNDao.findForIdentifier(theEntity.getIdDt().getIdPart());
ObservationIndexedSearchParamLastNEntity deletedObservationLastNEntity = myResourceIndexedObservationLastNDao.findByIdentifier(theEntity.getIdDt().getIdPart());
if (deletedObservationLastNEntity != null) {
myEntityManager.remove(deletedObservationLastNEntity);
}

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

@ -131,7 +131,7 @@ public class SearchBuilder implements ISearchBuilder {
// NB: keep public
public static final int MAXIMUM_PAGE_SIZE = 800;
public static final int MAXIMUM_PAGE_SIZE_FOR_TESTING = 50;
public static boolean myIsTest = false;
public static boolean myUseMaxPageSize50ForTest = false;
private static final List<ResourcePersistentId> EMPTY_LONG_LIST = Collections.unmodifiableList(new ArrayList<>());
private static final Logger ourLog = LoggerFactory.getLogger(SearchBuilder.class);
@ -184,15 +184,15 @@ public class SearchBuilder implements ISearchBuilder {
}
public static int getMaximumPageSize() {
if (myIsTest) {
if (myUseMaxPageSize50ForTest) {
return MAXIMUM_PAGE_SIZE_FOR_TESTING;
} else {
return MAXIMUM_PAGE_SIZE;
}
}
public static void setIsTest(boolean theIsTest) {
myIsTest = theIsTest;
public static void setMaxPageSize50ForTest(boolean theIsTest) {
myUseMaxPageSize50ForTest = theIsTest;
}
@Override

4
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/data/IObservationIndexedCodeCodingSearchParamDao.java
View File

@ -14,13 +14,13 @@ public interface IObservationIndexedCodeCodingSearchParamDao extends JpaReposito
"WHERE t.myCode = :code " +
"AND t.mySystem = :system " +
"")
String findForCodeAndSystem(@Param("code") String theCode, @Param("system") String theSystem);
String findByCodeAndSystem(@Param("code") String theCode, @Param("system") String theSystem);
@Query("" +
"SELECT t.myCodeableConceptId FROM ObservationIndexedCodeCodingEntity t " +
"WHERE t.myDisplay = :display" +
"")
String findForDisplay(@Param("display") String theDisplay);
String findByDisplay(@Param("display") String theDisplay);
}

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

@ -12,6 +12,6 @@ public interface IObservationIndexedSearchParamLastNDao extends JpaRepository<Ob
"SELECT t FROM ObservationIndexedSearchParamLastNEntity t " +
"WHERE t.myIdentifier = :identifier" +
"")
ObservationIndexedSearchParamLastNEntity findForIdentifier(@Param("identifier") String theIdentifier);
ObservationIndexedSearchParamLastNEntity findByIdentifier(@Param("identifier") String theIdentifier);
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/dstu3/FhirResourceDaoObservationDstu3.java
View File

@ -73,19 +73,9 @@ public class FhirResourceDaoObservationDstu3 extends BaseHapiFhirResourceDaoObse
@Override
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
// Update indexes here for LastN operation.
Observation observation = (Observation) theResource;
myObservationLastNIndexPersistSvc.indexObservation(observation);
} else {
myObservationLastNIndexPersistSvc.deleteObservationIndex(theEntity);
}
}
return retVal;
return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
theCreateNewHistoryEntry);
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoObservationR4.java
View File

@ -80,19 +80,9 @@ public class FhirResourceDaoObservationR4 extends BaseHapiFhirResourceDaoObserva
@Override
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
// Update indexes here for LastN operation.
Observation observation = (Observation) theResource;
myObservationLastNIndexPersistSvc.indexObservation(observation);
} else {
myObservationLastNIndexPersistSvc.deleteObservationIndex(retVal);
}
}
return retVal;
return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
theCreateNewHistoryEntry);
}
}

16
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/r5/FhirResourceDaoObservationR5.java
View File

@ -73,19 +73,9 @@ public class FhirResourceDaoObservationR5 extends BaseHapiFhirResourceDaoObserva
@Override
public ResourceTable updateEntity(RequestDetails theRequest, IBaseResource theResource, IBasePersistedResource theEntity, Date theDeletedTimestampOrNull, boolean thePerformIndexing,
boolean theUpdateVersion, TransactionDetails theTransactionDetails, boolean theForceUpdate, boolean theCreateNewHistoryEntry) {
ResourceTable retVal = super.updateEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull, thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate, theCreateNewHistoryEntry);
if (!retVal.isUnchangedInCurrentOperation()) {
if (retVal.getDeleted() == null) {
// Update indexes here for LastN operation.
Observation observation = (Observation) theResource;
myObservationLastNIndexPersistSvc.indexObservation(observation);
} else {
myObservationLastNIndexPersistSvc.deleteObservationIndex(theEntity);
}
}
return retVal;
return updateObservationEntity(theRequest, theResource, theEntity, theDeletedTimestampOrNull,
thePerformIndexing, theUpdateVersion, theTransactionDetails, theForceUpdate,
theCreateNewHistoryEntry);
}
}

126
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/ElasticsearchSvcImpl.java
View File

@ -1,22 +1,22 @@
package ca.uhn.fhir.jpa.search.lastn;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.jpa.searchparam.util.LastNParameterHelper;
import ca.uhn.fhir.model.api.IQueryParameterType;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.TokenParam;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash;
import ca.uhn.fhir.rest.server.exceptions.InvalidRequestException;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.google.common.annotations.VisibleForTesting;
import org.shadehapi.elasticsearch.action.DocWriteResponse;
import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexRequest;
import org.shadehapi.elasticsearch.action.admin.indices.create.CreateIndexResponse;
import org.shadehapi.elasticsearch.action.admin.indices.get.GetIndexRequest;
import org.shadehapi.elasticsearch.action.DocWriteResponse;
import org.shadehapi.elasticsearch.action.index.IndexRequest;
import org.shadehapi.elasticsearch.action.index.IndexResponse;
import org.shadehapi.elasticsearch.action.search.SearchRequest;
@ -33,7 +33,10 @@ import org.shadehapi.elasticsearch.search.aggregations.AggregationBuilder;
import org.shadehapi.elasticsearch.search.aggregations.AggregationBuilders;
import org.shadehapi.elasticsearch.search.aggregations.Aggregations;
import org.shadehapi.elasticsearch.search.aggregations.BucketOrder;
import org.shadehapi.elasticsearch.search.aggregations.bucket.composite.*;
import org.shadehapi.elasticsearch.search.aggregations.bucket.composite.CompositeAggregationBuilder;
import org.shadehapi.elasticsearch.search.aggregations.bucket.composite.CompositeValuesSourceBuilder;
import org.shadehapi.elasticsearch.search.aggregations.bucket.composite.ParsedComposite;
import org.shadehapi.elasticsearch.search.aggregations.bucket.composite.TermsValuesSourceBuilder;
import org.shadehapi.elasticsearch.search.aggregations.bucket.terms.ParsedTerms;
import org.shadehapi.elasticsearch.search.aggregations.bucket.terms.Terms;
import org.shadehapi.elasticsearch.search.aggregations.bucket.terms.TermsAggregationBuilder;
@ -42,7 +45,9 @@ import org.shadehapi.elasticsearch.search.aggregations.support.ValueType;
import org.shadehapi.elasticsearch.search.builder.SearchSourceBuilder;
import org.shadehapi.elasticsearch.search.sort.SortOrder;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.ArrayList;
import java.util.List;
import java.util.function.Function;
@ -52,9 +57,11 @@ import static org.apache.commons.lang3.StringUtils.isBlank;
public class ElasticsearchSvcImpl implements IElasticsearchSvc {
public static final String OBSERVATION_INDEX = "observation_index";
public static final String CODE_INDEX = "code_index";
public static final String OBSERVATION_CODE_INDEX = "code_index";
public static final String OBSERVATION_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.model.entity.ObservationIndexedSearchParamLastNEntity";
public static final String CODE_DOCUMENT_TYPE = "ca.uhn.fhir.jpa.model.entity.ObservationIndexedCodeCodeableConceptEntity";
public static final String OBSERVATION_INDEX_SCHEMA_FILE = "ObservationIndexSchema.json";
public static final String OBSERVATION_CODE_INDEX_SCHEMA_FILE = "ObservationCodeIndexSchema.json";
private final RestHighLevelClient myRestHighLevelClient;
@ -63,6 +70,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
private final String GROUP_BY_SUBJECT = "group_by_subject";
private final String GROUP_BY_SYSTEM = "group_by_system";
private final String GROUP_BY_CODE = "group_by_code";
private final String OBSERVATION_IDENTIFIER_FIELD_NAME = "identifier";
public ElasticsearchSvcImpl(String theHostname, int thePort, String theUsername, String thePassword) {
@ -70,106 +78,41 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
try {
createObservationIndexIfMissing();
createCodeIndexIfMissing();
createObservationCodeIndexIfMissing();
} catch (IOException theE) {
throw new RuntimeException("Failed to create document index", theE);
}
}
private String getIndexSchema(String theSchemaFileName) throws IOException {
InputStreamReader input = new InputStreamReader(ElasticsearchSvcImpl.class.getResourceAsStream(theSchemaFileName));
BufferedReader reader = new BufferedReader(input);
StringBuilder sb = new StringBuilder();
String str;
while((str = reader.readLine())!= null){
sb.append(str);
}
return sb.toString();
}
private void createObservationIndexIfMissing() throws IOException {
if (indexExists(OBSERVATION_INDEX)) {
return;
}
String observationMapping = "{\n" +
" \"mappings\" : {\n" +
" \"ca.uhn.fhir.jpa.model.entity.ObservationIndexedSearchParamLastNEntity\" : {\n" +
" \"properties\" : {\n" +
" \"codeconceptid\" : {\n" +
" \"type\" : \"keyword\",\n" +
" \"norms\" : true\n" +
" },\n" +
" \"codeconcepttext\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"codeconceptcodingcode\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codeconceptcodingsystem\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codeconceptcodingcode_system_hash\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codeconceptcodingdisplay\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"categoryconcepttext\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"categoryconceptcodingcode\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"categoryconceptcodingsystem\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"categoryconceptcodingcode_system_hash\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"categoryconceptcodingdisplay\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"effectivedtm\" : {\n" +
" \"type\" : \"date\"\n" +
" },\n" +
" \"identifier\" : {\n" +
" \"type\" : \"keyword\",\n" +
" \"store\" : true\n" +
" },\n" +
" \"subject\" : {\n" +
" \"type\" : \"keyword\"\n" +
" }\n" +
" }\n" +
" }\n" +
" }\n" +
"}\n";
String observationMapping = getIndexSchema(OBSERVATION_INDEX_SCHEMA_FILE);
if (!createIndex(OBSERVATION_INDEX, observationMapping)) {
throw new RuntimeException("Failed to create observation index");
}
}
private void createCodeIndexIfMissing() throws IOException {
if (indexExists(CODE_INDEX)) {
private void createObservationCodeIndexIfMissing() throws IOException {
if (indexExists(OBSERVATION_CODE_INDEX)) {
return;
}
String codeMapping = "{\n" +
" \"mappings\" : {\n" +
" \"ca.uhn.fhir.jpa.model.entity.ObservationIndexedCodeCodeableConceptEntity\" : {\n" +
" \"properties\" : {\n" +
" \"codeable_concept_id\" : {\n" +
" \"type\" : \"keyword\",\n" +
" \"store\" : true\n" +
" },\n" +
" \"codingcode\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codingcode_system_hash\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"codingdisplay\" : {\n" +
" \"type\" : \"text\"\n" +
" },\n" +
" \"codingsystem\" : {\n" +
" \"type\" : \"keyword\"\n" +
" },\n" +
" \"text\" : {\n" +
" \"type\" : \"text\"\n" +
" }\n" +
" }\n" +
" }\n" +
" }\n" +
"}\n";
if (!createIndex(CODE_INDEX, codeMapping)) {
throw new RuntimeException("Failed to create code index");
String observationCodeMapping = getIndexSchema(OBSERVATION_CODE_INDEX_SCHEMA_FILE);
if (!createIndex(OBSERVATION_CODE_INDEX, observationCodeMapping)) {
throw new RuntimeException("Failed to create observation code index");
}
}
@ -190,7 +133,6 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
@Override
public List<String> executeLastN(SearchParameterMap theSearchParameterMap, FhirContext theFhirContext, Integer theMaxResultsToFetch) {
String OBSERVATION_IDENTIFIER_FIELD_NAME = "identifier";
String[] topHitsInclude = {OBSERVATION_IDENTIFIER_FIELD_NAME};
return buildAndExecuteSearch(theSearchParameterMap, theFhirContext, topHitsInclude,
ObservationJson::getIdentifier, theMaxResultsToFetch);
@ -557,7 +499,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
@VisibleForTesting
List<CodeJson> queryAllIndexedObservationCodes() throws IOException {
SearchRequest codeSearchRequest = new SearchRequest(CODE_INDEX);
SearchRequest codeSearchRequest = new SearchRequest(OBSERVATION_CODE_INDEX);
SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
// Query
searchSourceBuilder.query(QueryBuilders.matchAllQuery());

8
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/IElasticsearchSvc.java
View File

@ -6,5 +6,13 @@ import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import java.util.List;
public interface IElasticsearchSvc {
/**
* Returns identifiers for the last most recent N observations that meet the specified criteria.
* @param theSearchParameterMap SearchParameterMap containing search parameters used for filtering the last N observations. Supported parameters include Subject, Patient, Code, Category and Max (the parameter used to determine N).
* @param theFhirContext Current FhirContext.
* @param theMaxResultsToFetch The maximum number of results to return for the purpose of paging.
* @return
*/
List<String> executeLastN(SearchParameterMap theSearchParameterMap, FhirContext theFhirContext, Integer theMaxResultsToFetch);
}

2
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/json/CodeJson.java
View File

@ -10,7 +10,7 @@ package ca.uhn.fhir.jpa.search.lastn.json;
* #L%
*/
import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash;
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;

37
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/json/ObservationJson.java
View File

@ -10,7 +10,7 @@ package ca.uhn.fhir.jpa.search.lastn.json;
* #L%
*/
import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash;
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
import com.fasterxml.jackson.annotation.JsonAutoDetect;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.annotation.JsonProperty;
@ -53,29 +53,22 @@ public class ObservationJson {
private String myCode_concept_text;
@JsonProperty(value = "codeconceptcodingcode", required = false)
// TODO: Temporary change until sort out how to deal with multiple observation code codings
// private List<String> myCode_coding_code = new ArrayList<>();
private String myCode_coding_code;
@JsonProperty(value = "codeconceptcodingcode_system_hash", required = false)
// TODO: Temporary change until sort out how to deal with multiple observation code codings
// private List<String> myCode_coding_code_system_hash = new ArrayList<>();
private String myCode_coding_code_system_hash;
@JsonProperty(value = "codeconceptcodingdisplay", required = false)
// TODO: Temporary change until sort out how to deal with multiple observation code codings
// private List<String> myCode_coding_display = new ArrayList<>();
private String myCode_coding_display;
@JsonProperty(value = "codeconceptcodingsystem", required = false)
// TODO: Temporary change until sort out how to deal with multiple observation code codings
// private List<String> myCode_coding_system = new ArrayList<>();
private String myCode_coding_system;
@JsonProperty(value = "effectivedtm", required = true)
private Date myEffectiveDtm;
public ObservationJson() {}
public ObservationJson() {
}
public void setIdentifier(String theIdentifier) {
myIdentifier = theIdentifier;
@ -128,12 +121,6 @@ public class ObservationJson {
public void setCode(CodeableConcept theCode) {
myCode_concept_text = theCode.getText();
for (Coding theCodeCoding : theCode.getCoding()) {
// TODO: Temporary change until address how to manage multiple Observation Code codings.
/* myCode_coding_code_system_hash.add(String.valueOf(CodeSystemHash.hashCodeSystem(theCodeCoding.getSystem(), theCodeCoding.getCode())));
myCode_coding_code.add(theCodeCoding.getCode());
myCode_coding_display.add(theCodeCoding.getDisplay());
myCode_coding_system.add(theCodeCoding.getSystem());
*/
myCode_coding_code_system_hash = String.valueOf(CodeSystemHash.hashCodeSystem(theCodeCoding.getSystem(), theCodeCoding.getCode()));
myCode_coding_code = theCodeCoding.getCode();
myCode_coding_display = theCodeCoding.getDisplay();
@ -146,24 +133,6 @@ public class ObservationJson {
return myCode_concept_text;
}
// TODO: Temporary changes until resolve problem of how to manage Observation Code with multiple codings
/*
public List<String> getCode_coding_code_system_hash() {
return myCode_coding_code_system_hash;
}
public List<String> getCode_coding_code() {
return myCode_coding_code;
}
public List<String> getCode_coding_display() {
return myCode_coding_display;
}
public List<String> getCode_coding_system() {
return myCode_coding_system;
}
*/
public String getCode_coding_code_system_hash() {
return myCode_coding_code_system_hash;
}

33
hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/lastn/util/CodeSystemHash.java
View File

@ -1,33 +0,0 @@
package ca.uhn.fhir.jpa.search.lastn.util;
import ca.uhn.fhir.util.UrlUtil;
import com.google.common.base.Charsets;
import com.google.common.hash.HashCode;
import com.google.common.hash.HashFunction;
import com.google.common.hash.Hasher;
import com.google.common.hash.Hashing;
public class CodeSystemHash {
private static final HashFunction HASH_FUNCTION = Hashing.murmur3_128(0);
private static final byte[] DELIMITER_BYTES = "|".getBytes(Charsets.UTF_8);
static public long hashCodeSystem( String system, String code ) {
Hasher hasher = HASH_FUNCTION.newHasher();
addStringToHasher(hasher, system);
addStringToHasher(hasher, code);
HashCode hashCode = hasher.hash();
return hashCode.asLong();
}
static private void addStringToHasher(Hasher hasher, String next) {
if (next == null) {
hasher.putByte((byte) 0);
} else {
next = UrlUtil.escapeUrlParam(next);
byte[] bytes = next.getBytes(Charsets.UTF_8);
hasher.putBytes(bytes);
}
hasher.putBytes(DELIMITER_BYTES);
}
}

26
hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/search/lastn/ObservationCodeIndexSchema.json Normal file
View File

@ -0,0 +1,26 @@
{
"mappings" : {
"ca.uhn.fhir.jpa.model.entity.ObservationIndexedCodeCodeableConceptEntity" : {
"properties" : {
"codeable_concept_id" : {
"type" : "keyword"
},
"codingcode" : {
"type" : "keyword"
},
"codingcode_system_hash" : {
"type" : "keyword"
},
"codingdisplay" : {
"type" : "keyword"
},
"codingsystem" : {
"type" : "keyword"
},
"text" : {
"type" : "keyword"
}
}
}
}
}

50
hapi-fhir-jpaserver-base/src/main/resources/ca/uhn/fhir/jpa/search/lastn/ObservationIndexSchema.json Normal file
View File

@ -0,0 +1,50 @@
{
"mappings" : {
"ca.uhn.fhir.jpa.model.entity.ObservationIndexedSearchParamLastNEntity" : {
"properties" : {
"codeconceptid" : {
"type" : "keyword"
},
"codeconcepttext" : {
"type" : "text"
},
"codeconceptcodingcode" : {
"type" : "keyword"
},
"codeconceptcodingsystem" : {
"type" : "keyword"
},
"codeconceptcodingcode_system_hash" : {
"type" : "keyword"
},
"codeconceptcodingdisplay" : {
"type" : "keyword"
},
"categoryconcepttext" : {
"type" : "keyword"
},
"categoryconceptcodingcode" : {
"type" : "keyword"
},
"categoryconceptcodingsystem" : {
"type" : "keyword"
},
"categoryconceptcodingcode_system_hash" : {
"type" : "keyword"
},
"categoryconceptcodingdisplay" : {
"type" : "keyword"
},
"effectivedtm" : {
"type" : "date"
},
"identifier" : {
"type" : "keyword"
},
"subject" : {
"type" : "keyword"
}
}
}
}
}

6
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNAsyncIT.java
View File

@ -52,14 +52,14 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
mySmallerPreFetchThresholds.add(-1);
myDaoConfig.setSearchPreFetchThresholds(mySmallerPreFetchThresholds);
SearchBuilder.setIsTest(true);
SearchBuilder.setMaxPageSize50ForTest(true);
}
@After
public void after() {
myDaoConfig.setSearchPreFetchThresholds(originalPreFetchThresholds);
SearchBuilder.setIsTest(false);
SearchBuilder.setMaxPageSize50ForTest(false);
}
@Test
@ -82,7 +82,7 @@ public class FhirResourceDaoR4SearchLastNAsyncIT extends BaseR4SearchLastN {
when(mySrd.getParameters()).thenReturn(requestParameters);
// Set chunk size to 50
SearchBuilder.setIsTest(true);
SearchBuilder.setMaxPageSize50ForTest(true);
// Expand default fetch sizes to ensure all observations are returned in first page:
List<Integer> myBiggerPreFetchThresholds = new ArrayList<>();

4
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchLastNIT.java
View File

@ -23,7 +23,7 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
@After
public void resetMaximumPageSize() {
SearchBuilder.setIsTest(false);
SearchBuilder.setMaxPageSize50ForTest(false);
}
@Test
@ -46,7 +46,7 @@ public class FhirResourceDaoR4SearchLastNIT extends BaseR4SearchLastN {
when(mySrd.getParameters()).thenReturn(requestParameters);
// Set chunk size to 50
SearchBuilder.setIsTest(true);
SearchBuilder.setMaxPageSize50ForTest(true);
myCaptureQueriesListener.clear();
List<String> results = toUnqualifiedVersionlessIdValues(myObservationDao.observationsLastN(params, mockSrd(),null));

24
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/PersistObservationIndexedSearchParamLastNR4IT.java
View File

@ -130,7 +130,6 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
myObservation.setCode(getObservationCode());
//myObservationLastNIndexPersistR4Svc.indexObservation(myObservation);
testObservationPersist.indexObservation(myObservation);
}
@ -139,12 +138,12 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
// Add three CodeableConcepts for category
List<CodeableConcept> categoryConcepts = new ArrayList<>();
// Create three codings and first category CodeableConcept
List<Coding> category1 = new ArrayList<>();
List<Coding> category = new ArrayList<>();
CodeableConcept categoryCodeableConcept1 = new CodeableConcept().setText("Test Codeable Concept Field for first category");
category1.add(new Coding(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE, "test-heart-rate display"));
category1.add(new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-heart-rate", "test-alt-heart-rate display"));
category1.add(new Coding("http://mysecondaltcodes.org/fhir/observation-category", "test-2nd-alt-heart-rate", "test-2nd-alt-heart-rate display"));
categoryCodeableConcept1.setCoding(category1);
category.add(new Coding(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE, "test-heart-rate display"));
category.add(new Coding("http://myalternatecodes.org/fhir/observation-category", "test-alt-heart-rate", "test-alt-heart-rate display"));
category.add(new Coding("http://mysecondaltcodes.org/fhir/observation-category", "test-2nd-alt-heart-rate", "test-2nd-alt-heart-rate display"));
categoryCodeableConcept1.setCoding(category);
categoryConcepts.add(categoryCodeableConcept1);
// Create three codings and second category CodeableConcept
List<Coding> category2 = new ArrayList<>();
@ -169,9 +168,6 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
// Create CodeableConcept for Code with three codings.
CodeableConcept codeableConceptField = new CodeableConcept().setText(SINGLE_OBSERVATION_CODE_TEXT);
codeableConceptField.addCoding(new Coding(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE, "test-code display"));
// TODO: Temporarily limit this to a single Observation Code coding until we sort out how to manage multiple codings
// codeableConceptField.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code", "test-alt-code display"));
// codeableConceptField.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code", "test-second-alt-code display"));
return codeableConceptField;
}
@ -263,8 +259,6 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
Date effectiveDtm = observationDate.getTime();
observation.setEffective(new DateTimeType(effectiveDtm));
// myObservationLastNIndexPersistR4Svc.indexObservation(observation);
testObservationPersist.indexObservation(observation);
}
@ -279,7 +273,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
indexMultipleObservations();
assertEquals(100, myResourceIndexedObservationLastNDao.count());
// Check that fifth observation for fifth patient has been indexed.
ObservationIndexedSearchParamLastNEntity observation = myResourceIndexedObservationLastNDao.findForIdentifier("55");
ObservationIndexedSearchParamLastNEntity observation = myResourceIndexedObservationLastNDao.findByIdentifier("55");
assertNotNull(observation);
SearchParameterMap searchParameterMap = new SearchParameterMap();
@ -295,12 +289,11 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
entity.setResourceType("Observation");
entity.setVersion(0L);
// myObservationLastNIndexPersistR4Svc.deleteObservationIndex(entity);
testObservationPersist.deleteObservationIndex(entity);
// Confirm that observation was deleted.
assertEquals(99, myResourceIndexedObservationLastNDao.count());
observation = myResourceIndexedObservationLastNDao.findForIdentifier("55");
observation = myResourceIndexedObservationLastNDao.findByIdentifier("55");
assertNull(observation);
observationIdsOnly = elasticsearchSvc.executeLastN(searchParameterMap, myFhirCtx, 200);
@ -341,10 +334,9 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
updatedObservation.setCategory(getCategoryCode());
updatedObservation.setCode(getObservationCode());
// myObservationLastNIndexPersistR4Svc.indexObservation(updatedObservation);
testObservationPersist.indexObservation(updatedObservation);
ObservationIndexedSearchParamLastNEntity updatedObservationEntity = myResourceIndexedObservationLastNDao.findForIdentifier(SINGLE_OBSERVATION_PID);
ObservationIndexedSearchParamLastNEntity updatedObservationEntity = myResourceIndexedObservationLastNDao.findByIdentifier(SINGLE_OBSERVATION_PID);
assertEquals("1234", updatedObservationEntity.getSubject());
assertEquals(newEffectiveDtm.getValue(), updatedObservationEntity.getEffectiveDtm());

12
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcMultipleObservationsIT.java
View File

@ -54,7 +54,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
@After
public void after() throws IOException {
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.OBSERVATION_INDEX);
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.CODE_INDEX);
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
}
@Test
@ -307,18 +307,12 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
String codeableConceptId1 = UUID.randomUUID().toString();
CodeableConcept codeableConceptField1 = new CodeableConcept().setText("Test Codeable Concept Field for First Code");
codeableConceptField1.addCoding(new Coding("http://mycodes.org/fhir/observation-code", "test-code-1", "test-code-1 display"));
// TODO: uncomment the following once there is a solution to supporting multiple codings for Observation Code
// codeableConceptField1.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code-1", "test-alt-code-1 display"));
// codeableConceptField1.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code-1", "test-second-alt-code-1 display"));
CodeJson codeJson1 = new CodeJson(codeableConceptField1, codeableConceptId1);
String codeJson1Document = ourMapperNonPrettyPrint.writeValueAsString(codeJson1);
String codeableConceptId2 = UUID.randomUUID().toString();
CodeableConcept codeableConceptField2 = new CodeableConcept().setText("Test Codeable Concept Field for Second Code");
codeableConceptField2.addCoding(new Coding("http://mycodes.org/fhir/observation-code", "test-code-2", "test-code-2 display"));
// TODO: uncomment the following once there is a solution to supporting multiple codings for Observation Code
// codeableConceptField2.addCoding(new Coding("http://myalternatecodes.org/fhir/observation-code", "test-alt-code-2", "test-alt-code-2 display"));
// codeableConceptField2.addCoding(new Coding("http://mysecondaltcodes.org/fhir/observation-code", "test-second-alt-code-2", "test-second-alt-code-2 display"));
CodeJson codeJson2 = new CodeJson(codeableConceptField2, codeableConceptId2);
String codeJson2Document = ourMapperNonPrettyPrint.writeValueAsString(codeJson2);
@ -357,12 +351,12 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
observationJson.setCategories(categoryConcepts1);
observationJson.setCode(codeableConceptField1);
observationJson.setCode_concept_id(codeableConceptId1);
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.CODE_INDEX, codeableConceptId1, codeJson1Document, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX, codeableConceptId1, codeJson1Document, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
} else {
observationJson.setCategories(categoryConcepts2);
observationJson.setCode(codeableConceptField2);
observationJson.setCode_concept_id(codeableConceptId2);
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.CODE_INDEX, codeableConceptId2, codeJson2Document, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX, codeableConceptId2, codeJson2Document, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
}
Calendar observationDate = new GregorianCalendar();

73
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/LastNElasticsearchSvcSingleObservationIT.java
View File

@ -1,27 +1,37 @@
package ca.uhn.fhir.jpa.search.lastn;
import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
import ca.uhn.fhir.jpa.search.lastn.config.TestElasticsearchConfig;
import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
import ca.uhn.fhir.jpa.search.lastn.util.CodeSystemHash;
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
import ca.uhn.fhir.model.dstu2.resource.Observation;
import ca.uhn.fhir.rest.param.*;
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
import ca.uhn.fhir.rest.param.ReferenceParam;
import ca.uhn.fhir.rest.param.TokenAndListParam;
import ca.uhn.fhir.rest.param.TokenOrListParam;
import ca.uhn.fhir.rest.param.TokenParam;
import com.fasterxml.jackson.annotation.JsonInclude;
import com.fasterxml.jackson.core.JsonGenerator;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.databind.SerializationFeature;
import org.hl7.fhir.r4.model.CodeableConcept;
import org.hl7.fhir.r4.model.Coding;
import org.junit.*;
import org.junit.After;
import org.junit.BeforeClass;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.test.context.ContextConfiguration;
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
import java.io.IOException;
import java.util.*;
import java.util.ArrayList;
import java.util.Date;
import java.util.List;
import java.util.UUID;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
@ -68,12 +78,6 @@ public class LastNElasticsearchSvcSingleObservationIT {
final String CODEFIRSTCODINGSYSTEM = "http://mycodes.org/fhir/observation-code";
final String CODEFIRSTCODINGCODE = "test-code";
final String CODEFIRSTCODINGDISPLAY = "test-code display";
// final String CODESECONDCODINGSYSTEM = "http://myalternatecodes.org/fhir/observation-code";
// final String CODESECONDCODINGCODE = "test-alt-code";
// final String CODESECONDCODINGDISPLAY = "test-alt-code display";
// final String CODETHIRDCODINGSYSTEM = "http://mysecondaltcodes.org/fhir/observation-code";
// final String CODETHIRDCODINGCODE = "test-second-alt-code";
// final String CODETHIRDCODINGDISPLAY = "test-second-alt-code display";
final FhirContext myFhirContext = FhirContext.forR4();
@ -89,7 +93,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
@After
public void after() throws IOException {
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.OBSERVATION_INDEX);
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.CODE_INDEX);
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
}
@Test
@ -209,32 +213,6 @@ public class LastNElasticsearchSvcSingleObservationIT {
String code_concept_text_values = observation.getCode_concept_text();
assertEquals(OBSERVATIONCODETEXT, code_concept_text_values);
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
/*
List<String> code_coding_systems = observation.getCode_coding_system();
assertEquals(3,code_coding_systems.size());
assertEquals(CODEFIRSTCODINGSYSTEM, code_coding_systems.get(0));
assertEquals(CODESECONDCODINGSYSTEM, code_coding_systems.get(1));
assertEquals(CODETHIRDCODINGSYSTEM, code_coding_systems.get(2));
List<String> code_coding_codes = observation.getCode_coding_code();
assertEquals(3, code_coding_codes.size());
assertEquals(CODEFIRSTCODINGCODE, code_coding_codes.get(0));
assertEquals(CODESECONDCODINGCODE, code_coding_codes.get(1));
assertEquals(CODETHIRDCODINGCODE, code_coding_codes.get(2));
List<String> code_coding_display = observation.getCode_coding_display();
assertEquals(3, code_coding_display.size());
assertEquals(CODEFIRSTCODINGDISPLAY, code_coding_display.get(0));
assertEquals(CODESECONDCODINGDISPLAY, code_coding_display.get(1));
assertEquals(CODETHIRDCODINGDISPLAY, code_coding_display.get(2));
List<String> code_coding_code_system_hash = observation.getCode_coding_code_system_hash();
assertEquals(3, code_coding_code_system_hash.size());
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE)), code_coding_code_system_hash.get(0));
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE)), code_coding_code_system_hash.get(1));
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE)), code_coding_code_system_hash.get(2));
*/
String code_coding_systems = observation.getCode_coding_system();
assertEquals(CODEFIRSTCODINGSYSTEM, code_coding_systems);
@ -258,36 +236,20 @@ public class LastNElasticsearchSvcSingleObservationIT {
assertEquals(OBSERVATIONCODETEXT, persistedCodeConceptText);
List<String> persistedCodeCodingSystems = persistedObservationCode.getCoding_system();
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
// assertEquals(3,persistedCodeCodingSystems.size());
assertEquals(1, persistedCodeCodingSystems.size());
assertEquals(CODEFIRSTCODINGSYSTEM, persistedCodeCodingSystems.get(0));
// assertEquals(CODESECONDCODINGSYSTEM, persistedCodeCodingSystems.get(1));
// assertEquals(CODETHIRDCODINGSYSTEM, persistedCodeCodingSystems.get(2));
List<String> persistedCodeCodingCodes = persistedObservationCode.getCoding_code();
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
// assertEquals(3, persistedCodeCodingCodes.size());
assertEquals(1, persistedCodeCodingCodes.size());
assertEquals(CODEFIRSTCODINGCODE, persistedCodeCodingCodes.get(0));
// assertEquals(CODESECONDCODINGCODE, persistedCodeCodingCodes.get(1));
// assertEquals(CODETHIRDCODINGCODE, persistedCodeCodingCodes.get(2));
List<String> persistedCodeCodingDisplays = persistedObservationCode.getCoding_display();
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
// assertEquals(3, persistedCodeCodingDisplays.size());
assertEquals(1, persistedCodeCodingDisplays.size());
assertEquals(CODEFIRSTCODINGDISPLAY, persistedCodeCodingDisplays.get(0));
// assertEquals(CODESECONDCODINGDISPLAY, persistedCodeCodingDisplays.get(1));
// assertEquals(CODETHIRDCODINGDISPLAY, persistedCodeCodingDisplays.get(2));
List<String> persistedCodeCodingCodeSystemHashes = persistedObservationCode.getCoding_code_system_hash();
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
// assertEquals(3, persistedCodeCodingCodeSystemHashes.size());
assertEquals(1, persistedCodeCodingCodeSystemHashes.size());
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(0));
// assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(1));
// assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE)), persistedCodeCodingCodeSystemHashes.get(2));
}
@ -330,9 +292,6 @@ public class LastNElasticsearchSvcSingleObservationIT {
indexedObservation.setCode_concept_id(OBSERVATIONSINGLECODEID);
CodeableConcept codeableConceptField = new CodeableConcept().setText(OBSERVATIONCODETEXT);
codeableConceptField.addCoding(new Coding(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE, CODEFIRSTCODINGDISPLAY));
// TODO: Temporary changes until find a solution for addressing Observation Code with multiple codings.
// codeableConceptField.addCoding(new Coding(CODESECONDCODINGSYSTEM, CODESECONDCODINGCODE, CODESECONDCODINGDISPLAY));
// codeableConceptField.addCoding(new Coding(CODETHIRDCODINGSYSTEM, CODETHIRDCODINGCODE, CODETHIRDCODINGDISPLAY));
indexedObservation.setCode(codeableConceptField);
String observationDocument = ourMapperNonPrettyPrint.writeValueAsString(indexedObservation);
@ -340,7 +299,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
CodeJson observationCode = new CodeJson(codeableConceptField, OBSERVATIONSINGLECODEID);
String codeDocument = ourMapperNonPrettyPrint.writeValueAsString(observationCode);
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.CODE_INDEX, OBSERVATIONSINGLECODEID, codeDocument, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX, OBSERVATIONSINGLECODEID, codeDocument, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
try {
Thread.sleep(1000L);

5
hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/search/lastn/config/TestElasticsearchConfig.java
View File

@ -47,9 +47,4 @@ public class TestElasticsearchConfig {
return embeddedElastic;
}
// @PreDestroy
// public void stop() {
// embeddedElasticSearch().stop();
// }
}

9
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ObservationIndexedCodeCodeableConceptEntity.java
View File

@ -24,12 +24,9 @@ public class ObservationIndexedCodeCodeableConceptEntity {
@Column(name = "CODEABLE_CONCEPT_TEXT", nullable = true, length = MAX_LENGTH)
private String myCodeableConceptText;
// TODO: Make coding a Collection. Need to first figure out how to maintain this over time.
@IndexedEmbedded(depth=2, prefix = "coding")
// @OneToMany(mappedBy = "myCodeableConceptId", cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
@JoinColumn(name = "CODEABLE_CONCEPT_ID", nullable = false, updatable = false, foreignKey = @ForeignKey(name = "FK_CONCEPT_CODE"))
@OneToOne(cascade = CascadeType.ALL, fetch = FetchType.LAZY, orphanRemoval = true)
// private Set<ObservationIndexedCodeCodingEntity> myObservationIndexedCodeCodingEntitySet;
private ObservationIndexedCodeCodingEntity myObservationIndexedCodeCodingEntity;
public ObservationIndexedCodeCodeableConceptEntity() {
@ -42,10 +39,6 @@ public class ObservationIndexedCodeCodeableConceptEntity {
}
public void addCoding(ObservationIndexedCodeCodingEntity theObservationIndexedCodeCodingEntity) {
// if (myObservationIndexedCodeCodingEntitySet == null) {
// myObservationIndexedCodeCodingEntitySet = new HashSet<>();
// }
// myObservationIndexedCodeCodingEntitySet.add(theObservationIndexedCodeCodingEntity);
myObservationIndexedCodeCodingEntity = theObservationIndexedCodeCodingEntity;
}
@ -65,6 +58,4 @@ public class ObservationIndexedCodeCodeableConceptEntity {
myCodeableConceptText = theCodeableConceptText;
}
}

9
hapi-fhir-jpaserver-model/src/main/java/ca/uhn/fhir/jpa/model/entity/ObservationIndexedCodeCodingEntity.java
View File

@ -13,12 +13,6 @@ public class ObservationIndexedCodeCodingEntity {
public static final int MAX_LENGTH = 200;
// TODO: Fix this to allow multiple codings for observation code
// @Id
// @SequenceGenerator(name = "SEQ_CODING_FIELD", sequenceName = "SEQ_CODING_FIELD")
// @GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_CODING_FIELD")
// private Long myId;
@Id
@Column(name = "CODEABLE_CONCEPT_ID", length = MAX_LENGTH)
private String myCodeableConceptId;
@ -35,7 +29,8 @@ public class ObservationIndexedCodeCodingEntity {
@Field(name = "display")
private String myDisplay;
public ObservationIndexedCodeCodingEntity() {}
public ObservationIndexedCodeCodingEntity() {
}
public ObservationIndexedCodeCodingEntity(String theSystem, String theCode, String theDisplay, String theCodeableConceptId) {
myCode = theCode;

49
hapi-fhir-jpaserver-searchparam/src/main/java/ca/uhn/fhir/jpa/searchparam/util/LastNParameterHelper.java
View File

@ -10,30 +10,45 @@ public class LastNParameterHelper {
if (theParamName == null) {
return false;
}
if (theContext.getVersion().getVersion() == FhirVersionEnum.R5) {
if (theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_SUBJECT) || theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_PATIENT)
|| theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_CATEGORY) || theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_CODE)) {
FhirVersionEnum version = theContext.getVersion().getVersion();
if (isR5(version) && isLastNParameterR5(theParamName)) {
return true;
} else if (isR4(version) && isLastNParameterR4(theParamName)) {
return true;
} else if (isDstu3(version) && isLastNParameterDstu3(theParamName)) {
return true;
} else {
return false;
}
} else if (theContext.getVersion().getVersion() == FhirVersionEnum.R4) {
if (theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_SUBJECT) || theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_PATIENT)
|| theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_CATEGORY) || theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_CODE)) {
return true;
} else {
return false;
}
} else if (theContext.getVersion().getVersion() == FhirVersionEnum.DSTU3) {
if (theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_SUBJECT) || theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_PATIENT)
|| theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_CATEGORY) || theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_CODE)) {
return true;
} else {
return false;
private static boolean isDstu3(FhirVersionEnum theVersion) {
return (theVersion == FhirVersionEnum.DSTU3);
}
} else {
throw new InvalidRequestException("$lastn operation is not implemented for FHIR Version " + theContext.getVersion().getVersion().getFhirVersionString());
private static boolean isR4(FhirVersionEnum theVersion) {
return (theVersion == FhirVersionEnum.R4);
}
private static boolean isR5(FhirVersionEnum theVersion) {
return (theVersion == FhirVersionEnum.R5);
}
private static boolean isLastNParameterDstu3(String theParamName) {
return (theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_SUBJECT) || theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_PATIENT)
|| theParamName.equals(org.hl7.fhir.dstu3.model.Observation.SP_CATEGORY) || theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_CODE));
}
private static boolean isLastNParameterR4(String theParamName) {
return (theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_SUBJECT) || theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_PATIENT)
|| theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_CATEGORY) || theParamName.equals(org.hl7.fhir.r4.model.Observation.SP_CODE));
}
private static boolean isLastNParameterR5(String theParamName) {
return (theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_SUBJECT) || theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_PATIENT)
|| theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_CATEGORY) || theParamName.equals(org.hl7.fhir.r5.model.Observation.SP_CODE));
}
public static String getSubjectParamName(FhirContext theContext) {