Changed observation indexing to bypass hibernate search and removed Observation index tables.
This commit is contained in:
ianmarshall
parent
6e507bf642
commit
9696af5dc0
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@ -21,36 +21,26 @@ package ca.uhn.fhir.jpa.dao;
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*/
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import ca.uhn.fhir.context.*;
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import ca.uhn.fhir.jpa.dao.data.IObservationIndexedCodeCodingSearchParamDao;
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import ca.uhn.fhir.jpa.dao.data.IObservationIndexedSearchParamLastNDao;
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import ca.uhn.fhir.jpa.model.cross.IBasePersistedResource;
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import ca.uhn.fhir.jpa.model.entity.ResourceIndexedSearchParamToken;
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import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
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import ca.uhn.fhir.jpa.search.lastn.IElasticsearchSvc;
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import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
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import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
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import ca.uhn.fhir.jpa.searchparam.extractor.ISearchParamExtractor;
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import ca.uhn.fhir.jpa.searchparam.extractor.PathAndRef;
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import org.hl7.fhir.instance.model.api.*;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.transaction.annotation.Propagation;
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import org.springframework.transaction.annotation.Transactional;
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import javax.persistence.EntityManager;
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import javax.persistence.PersistenceContext;
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import javax.persistence.PersistenceContextType;
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import java.util.*;
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@Transactional(propagation = Propagation.REQUIRED)
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public class ObservationLastNIndexPersistSvc {
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@PersistenceContext(type = PersistenceContextType.TRANSACTION)
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protected EntityManager myEntityManager;
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@Autowired
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IObservationIndexedSearchParamLastNDao myResourceIndexedObservationLastNDao;
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private ISearchParamExtractor mySearchParameterExtractor;
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@Autowired
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IObservationIndexedCodeCodingSearchParamDao myObservationIndexedCodeCodingSearchParamDao;
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@Autowired
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public ISearchParamExtractor mySearchParameterExtractor;
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@Autowired(required = false)
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private IElasticsearchSvc myElasticsearchSvc;
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public void indexObservation(IBaseResource theResource) {
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@ -95,15 +85,12 @@ public class ObservationLastNIndexPersistSvc {
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List<IBase> theObservationCategoryCodeableConcepts) {
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// Determine if an index already exists for Observation:
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boolean observationIndexUpdate = false;
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ObservationIndexedSearchParamLastNEntity indexedObservation = null;
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ObservationJson indexedObservation = null;
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if (resourcePID != null) {
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indexedObservation = myResourceIndexedObservationLastNDao.findByIdentifier(resourcePID);
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indexedObservation = myElasticsearchSvc.getObservationDocument(resourcePID);
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}
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if (indexedObservation == null) {
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indexedObservation = new ObservationIndexedSearchParamLastNEntity();
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} else {
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observationIndexUpdate = true;
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indexedObservation = new ObservationJson();
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}
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indexedObservation.setEffectiveDtm(theEffectiveDtm);
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@ -114,77 +101,65 @@ public class ObservationLastNIndexPersistSvc {
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addCategoriesToObservationIndex(theObservationCategoryCodeableConcepts, indexedObservation);
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if (observationIndexUpdate) {
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myEntityManager.merge(indexedObservation);
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} else {
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myEntityManager.persist(indexedObservation);
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}
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myElasticsearchSvc.createOrUpdateObservationIndex(resourcePID, indexedObservation);
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}
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private void addCodeToObservationIndex(List<IBase> theObservationCodeCodeableConcepts,
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ObservationIndexedSearchParamLastNEntity theIndexedObservation) {
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ObservationJson theIndexedObservation) {
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// Determine if a Normalized ID was created previously for Observation Code
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Optional<String> existingObservationCodeNormalizedId = getCodeCodeableConceptIdIfExists(theObservationCodeCodeableConcepts.get(0));
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String existingObservationCodeNormalizedId = getCodeCodeableConceptId(theObservationCodeCodeableConcepts.get(0));
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// Create/update normalized Observation Code index record
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ObservationIndexedCodeCodeableConceptEntity codeableConceptField =
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CodeJson codeableConceptField =
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getCodeCodeableConcept(theObservationCodeCodeableConcepts.get(0),
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existingObservationCodeNormalizedId.orElse(UUID.randomUUID().toString()));
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existingObservationCodeNormalizedId);
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if (existingObservationCodeNormalizedId.isPresent()) {
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myEntityManager.merge(codeableConceptField);
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} else {
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myEntityManager.persist(codeableConceptField);
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}
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theIndexedObservation.setObservationCode(codeableConceptField);
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theIndexedObservation.setCodeNormalizedId(codeableConceptField.getCodeableConceptId());
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myElasticsearchSvc.createOrUpdateObservationCodeIndex(codeableConceptField.getCodeableConceptId(), codeableConceptField);
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theIndexedObservation.setCode(codeableConceptField);
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theIndexedObservation.setCode_concept_id(codeableConceptField.getCodeableConceptId());
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}
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private void addCategoriesToObservationIndex(List<IBase> observationCategoryCodeableConcepts,
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ObservationIndexedSearchParamLastNEntity indexedObservation) {
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ObservationJson indexedObservation) {
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// Build CodeableConcept entities for Observation.Category
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Set<ObservationIndexedCategoryCodeableConceptEntity> categoryCodeableConceptEntities = new HashSet<>();
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List<CodeJson> categoryCodeableConceptEntities = new ArrayList<>();
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for (IBase categoryCodeableConcept : observationCategoryCodeableConcepts) {
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// Build CodeableConcept entities for each category CodeableConcept
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categoryCodeableConceptEntities.add(getCategoryCodeableConceptEntities(categoryCodeableConcept));
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}
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indexedObservation.setCategoryCodeableConcepts(categoryCodeableConceptEntities);
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indexedObservation.setCategories(categoryCodeableConceptEntities);
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}
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private ObservationIndexedCategoryCodeableConceptEntity getCategoryCodeableConceptEntities(IBase theValue) {
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private CodeJson getCategoryCodeableConceptEntities(IBase theValue) {
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String text = mySearchParameterExtractor.getDisplayTextFromCodeableConcept(theValue);
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ObservationIndexedCategoryCodeableConceptEntity categoryCodeableConcept = new ObservationIndexedCategoryCodeableConceptEntity(text);
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CodeJson categoryCodeableConcept = new CodeJson();
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categoryCodeableConcept.setCodeableConceptText(text);
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List<IBase> codings = mySearchParameterExtractor.getCodingsFromCodeableConcept(theValue);
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Set<ObservationIndexedCategoryCodingEntity> categoryCodingEntities = new HashSet<>();
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for (IBase nextCoding : codings) {
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categoryCodingEntities.add(getCategoryCoding(nextCoding));
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addCategoryCoding(nextCoding, categoryCodeableConcept);
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}
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categoryCodeableConcept.setObservationIndexedCategoryCodingEntitySet(categoryCodingEntities);
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return categoryCodeableConcept;
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}
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private ObservationIndexedCodeCodeableConceptEntity getCodeCodeableConcept(IBase theValue, String observationCodeNormalizedId) {
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private CodeJson getCodeCodeableConcept(IBase theValue, String observationCodeNormalizedId) {
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String text = mySearchParameterExtractor.getDisplayTextFromCodeableConcept(theValue);
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ObservationIndexedCodeCodeableConceptEntity codeCodeableConcept = new ObservationIndexedCodeCodeableConceptEntity(text, observationCodeNormalizedId);
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CodeJson codeCodeableConcept = new CodeJson();
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codeCodeableConcept.setCodeableConceptText(text);
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codeCodeableConcept.setCodeableConceptId(observationCodeNormalizedId);
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List<IBase> codings = mySearchParameterExtractor.getCodingsFromCodeableConcept(theValue);
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for (IBase nextCoding : codings) {
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codeCodeableConcept.addCoding(getCodeCoding(nextCoding, observationCodeNormalizedId));
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addCodeCoding(nextCoding, codeCodeableConcept);
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}
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return codeCodeableConcept;
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}
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private Optional<String> getCodeCodeableConceptIdIfExists(IBase theValue) {
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private String getCodeCodeableConceptId(IBase theValue) {
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List<IBase> codings = mySearchParameterExtractor.getCodingsFromCodeableConcept(theValue);
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String codeCodeableConceptId = null;
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Optional<String> codeCodeableConceptIdOptional = Optional.empty();
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for (IBase nextCoding : codings) {
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@ -196,52 +171,52 @@ public class ObservationLastNIndexPersistSvc {
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String system = param.getSystem();
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String code = param.getValue();
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String text = mySearchParameterExtractor.getDisplayTextForCoding(nextCoding);
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if (code != null && system != null) {
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codeCodeableConceptIdOptional = Optional.ofNullable(myObservationIndexedCodeCodingSearchParamDao.findByCodeAndSystem(code, system));
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} else {
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codeCodeableConceptIdOptional = Optional.ofNullable(myObservationIndexedCodeCodingSearchParamDao.findByDisplay(text));
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}
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if (codeCodeableConceptIdOptional.isPresent()) {
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String codeSystemHash = String.valueOf(CodeSystemHash.hashCodeSystem(system, code));
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CodeJson codeCodeableConceptDocument = myElasticsearchSvc.getObservationCodeDocument(codeSystemHash, text);
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if (codeCodeableConceptDocument != null) {
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codeCodeableConceptIdOptional = Optional.of(codeCodeableConceptDocument.getCodeableConceptId());
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break;
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}
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}
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}
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return codeCodeableConceptIdOptional;
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return codeCodeableConceptIdOptional.orElse(UUID.randomUUID().toString());
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}
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private ObservationIndexedCategoryCodingEntity getCategoryCoding(IBase theValue) {
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private void addCategoryCoding(IBase theValue, CodeJson theCategoryCodeableConcept) {
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ResourceIndexedSearchParamToken param = mySearchParameterExtractor.createSearchParamForCoding("Observation",
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new RuntimeSearchParam(null, null, "category", null, null, null, null, null, null, null),
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theValue);
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ObservationIndexedCategoryCodingEntity observationIndexedCategoryCodingEntity = null;
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if (param != null) {
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String system = param.getSystem();
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String code = param.getValue();
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String text = mySearchParameterExtractor.getDisplayTextForCoding(theValue);
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observationIndexedCategoryCodingEntity = new ObservationIndexedCategoryCodingEntity(system, code, text);
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theCategoryCodeableConcept.addCoding(system, code, text);
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}
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return observationIndexedCategoryCodingEntity;
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}
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private ObservationIndexedCodeCodingEntity getCodeCoding(IBase theValue, String observationCodeNormalizedId) {
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private void addCodeCoding(IBase theValue, CodeJson theObservationCode) {
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ResourceIndexedSearchParamToken param = mySearchParameterExtractor.createSearchParamForCoding("Observation",
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new RuntimeSearchParam(null, null, "code", null, null, null, null, null, null, null),
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theValue);
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ObservationIndexedCodeCodingEntity observationIndexedCodeCodingEntity = null;
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if (param != null) {
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String system = param.getSystem();
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String code = param.getValue();
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String text = mySearchParameterExtractor.getDisplayTextForCoding(theValue);
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observationIndexedCodeCodingEntity = new ObservationIndexedCodeCodingEntity(system, code, text, observationCodeNormalizedId);
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theObservationCode.addCoding(system, code, text);
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}
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return observationIndexedCodeCodingEntity;
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}
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public void deleteObservationIndex(IBasePersistedResource theEntity) {
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ObservationIndexedSearchParamLastNEntity deletedObservationLastNEntity = myResourceIndexedObservationLastNDao.findByIdentifier(theEntity.getIdDt().getIdPart());
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if (myElasticsearchSvc == null) {
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// Elasticsearch is not enabled and therefore no index needs to be updated.
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return;
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}
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ObservationJson deletedObservationLastNEntity = myElasticsearchSvc.getObservationDocument(theEntity.getIdDt().getIdPart());
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if (deletedObservationLastNEntity != null) {
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myEntityManager.remove(deletedObservationLastNEntity);
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myElasticsearchSvc.deleteObservationDocument(deletedObservationLastNEntity.getIdentifier());
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}
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}
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@ -1,46 +0,0 @@
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package ca.uhn.fhir.jpa.dao.data;
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/*-
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* #%L
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* HAPI FHIR JPA Server
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* %%
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* Copyright (C) 2014 - 2020 University Health Network
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* %%
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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* #L%
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*/
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import ca.uhn.fhir.jpa.model.entity.ObservationIndexedCodeCodingEntity;
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import org.springframework.data.jpa.repository.JpaRepository;
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import org.springframework.data.jpa.repository.Query;
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import org.springframework.data.repository.query.Param;
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import org.springframework.stereotype.Repository;
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@Repository
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public interface IObservationIndexedCodeCodingSearchParamDao extends JpaRepository<ObservationIndexedCodeCodingEntity, Long> {
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@Query("" +
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"SELECT t.myCodeableConceptId FROM ObservationIndexedCodeCodingEntity t " +
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"WHERE t.myCode = :code " +
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"AND t.mySystem = :system " +
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"")
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String findByCodeAndSystem(@Param("code") String theCode, @Param("system") String theSystem);
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@Query("" +
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"SELECT t.myCodeableConceptId FROM ObservationIndexedCodeCodingEntity t " +
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"WHERE t.myDisplay = :display" +
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"")
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String findByDisplay(@Param("display") String theDisplay);
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}
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@ -229,7 +229,7 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
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private CompositeAggregationBuilder createObservationSubjectAggregationBuilder(int theMaxNumberObservationsPerCode, String[] theTopHitsInclude) {
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CompositeValuesSourceBuilder<?> subjectValuesBuilder = new TermsValuesSourceBuilder("subject").field("subject");
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List<CompositeValuesSourceBuilder<?>> compositeAggSubjectSources = new ArrayList();
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List<CompositeValuesSourceBuilder<?>> compositeAggSubjectSources = new ArrayList<>();
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compositeAggSubjectSources.add(subjectValuesBuilder);
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CompositeAggregationBuilder compositeAggregationSubjectBuilder = new CompositeAggregationBuilder(GROUP_BY_SUBJECT, compositeAggSubjectSources);
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compositeAggregationSubjectBuilder.subAggregation(createObservationCodeAggregationBuilder(theMaxNumberObservationsPerCode, theTopHitsInclude));
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@ -514,12 +514,12 @@ public class ElasticsearchSvcImpl implements IElasticsearchSvc {
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}
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@VisibleForTesting
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List<ObservationJson> executeLastNWithAllFields(SearchParameterMap theSearchParameterMap, FhirContext theFhirContext) {
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public List<ObservationJson> executeLastNWithAllFieldsForTest(SearchParameterMap theSearchParameterMap, FhirContext theFhirContext) {
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return buildAndExecuteSearch(theSearchParameterMap, theFhirContext, null, t -> t, 100);
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}
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@VisibleForTesting
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List<CodeJson> queryAllIndexedObservationCodes() throws IOException {
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List<CodeJson> queryAllIndexedObservationCodesForTest() throws IOException {
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SearchRequest codeSearchRequest = new SearchRequest(OBSERVATION_CODE_INDEX);
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SearchSourceBuilder searchSourceBuilder = new SearchSourceBuilder();
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// Query
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@ -21,6 +21,8 @@ package ca.uhn.fhir.jpa.search.lastn;
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*/
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.search.lastn.json.CodeJson;
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import ca.uhn.fhir.jpa.search.lastn.json.ObservationJson;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import java.util.List;
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@ -35,4 +37,42 @@ public interface IElasticsearchSvc {
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* @return
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*/
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List<String> executeLastN(SearchParameterMap theSearchParameterMap, FhirContext theFhirContext, Integer theMaxResultsToFetch);
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/**
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* Returns index document for a single Observation
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* @param theDocumentID Identifier of Observation resource.
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* @return
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*/
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ObservationJson getObservationDocument(String theDocumentID);
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/**
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* Returns index document for a single Observation Code that either has a coding that matches a specified Code value and system or that has a specified text value.
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* @param theCodeSystemHash A hash string constructed from a Code value and Code system used to match to an Observation Code.
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* @param theText A text value used to match to an Observation Code.
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* @return
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*/
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CodeJson getObservationCodeDocument(String theCodeSystemHash, String theText);
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/**
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* Creates or updates index for an Observation Resource.
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* @param theDocumentId Identifier for Observation resource.
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* @param theObservationDocument Indexing document for Observation.
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* @return
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*/
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Boolean createOrUpdateObservationIndex(String theDocumentId, ObservationJson theObservationDocument);
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/**
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* Creates or updates index for an Observation Code.
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* @param theCodeableConceptID Identifier for Observation resource.
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* @param theObservationCodeDocument Indexing document for Observation.
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* @return
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*/
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Boolean createOrUpdateObservationCodeIndex(String theCodeableConceptID, CodeJson theObservationCodeDocument);
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/**
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* Deletes index for an Observation Resource.
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* @param theDocumentId Identifier for Observation resource.
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*/
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void deleteObservationDocument(String theDocumentId);
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}
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@ -24,8 +24,6 @@ import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
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import com.fasterxml.jackson.annotation.JsonAutoDetect;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.annotation.JsonProperty;
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import org.hl7.fhir.r4.model.CodeableConcept;
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import org.hl7.fhir.r4.model.Coding;
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import java.util.ArrayList;
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import java.util.List;
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@ -55,22 +53,26 @@ public class CodeJson {
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public CodeJson(){
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}
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public CodeJson(CodeableConcept theCodeableConcept, String theCodeableConceptId) {
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myCodeableConceptText = theCodeableConcept.getText();
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myCodeableConceptId = theCodeableConceptId;
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for (Coding theCoding : theCodeableConcept.getCoding()) {
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myCoding_code.add(theCoding.getCode());
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myCoding_system.add(theCoding.getSystem());
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myCoding_display.add(theCoding.getDisplay());
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myCoding_code_system_hash.add(String.valueOf(CodeSystemHash.hashCodeSystem(theCoding.getSystem(), theCoding.getCode())));
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}
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}
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public void setCodeableConceptId(String theCodeableConceptId) {
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myCodeableConceptId = theCodeableConceptId;
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}
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public String getCodeableConceptId() {
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public void addCoding(String theCoding_system, String theCoding_code, String theCoding_display) {
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myCoding_code.add(theCoding_code);
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myCoding_system.add(theCoding_system);
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myCoding_display.add(theCoding_display);
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myCoding_code_system_hash.add(String.valueOf(CodeSystemHash.hashCodeSystem(theCoding_system, theCoding_code)));
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}
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public String getCodeableConceptId() {
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return myCodeableConceptId;
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||||
}
|
||||
|
||||
public String getCodeableConceptText() {
|
||||
public void setCodeableConceptText(String theCodeableConceptText) {
|
||||
myCodeableConceptText = theCodeableConceptText;
|
||||
}
|
||||
|
||||
public String getCodeableConceptText() {
|
||||
return myCodeableConceptText;
|
||||
}
|
||||
|
||||
|
|
@ -78,11 +80,11 @@ public class CodeJson {
|
|||
return myCoding_code;
|
||||
}
|
||||
|
||||
public List<String> getCoding_code_system_hash() {
|
||||
public List<String> getCoding_code_system_hash() {
|
||||
return myCoding_code_system_hash;
|
||||
}
|
||||
|
||||
public List<String> getCoding_display() {
|
||||
public List<String> getCoding_display() {
|
||||
return myCoding_display;
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -24,8 +24,6 @@ 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;
|
||||
import org.hl7.fhir.r4.model.CodeableConcept;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
|
||||
import java.util.ArrayList;
|
||||
import java.util.Date;
|
||||
|
|
@ -88,18 +86,24 @@ public class ObservationJson {
|
|||
mySubject = theSubject;
|
||||
}
|
||||
|
||||
public void setCategories(List<CodeableConcept> theCategories) {
|
||||
for (CodeableConcept theConcept : theCategories) {
|
||||
myCategory_concept_text.add(theConcept.getText());
|
||||
public void setCategories(List<CodeJson> theCategories) {
|
||||
for (CodeJson theConcept : theCategories) {
|
||||
myCategory_concept_text.add(theConcept.getCodeableConceptText());
|
||||
List<String> coding_code_system_hashes = new ArrayList<>();
|
||||
List<String> coding_codes = new ArrayList<>();
|
||||
List<String> coding_displays = new ArrayList<>();
|
||||
List<String> coding_systems = new ArrayList<>();
|
||||
for (Coding theCategoryCoding : theConcept.getCoding()) {
|
||||
coding_code_system_hashes.add(String.valueOf(CodeSystemHash.hashCodeSystem(theCategoryCoding.getSystem(), theCategoryCoding.getCode())));
|
||||
coding_codes.add(theCategoryCoding.getCode());
|
||||
coding_displays.add(theCategoryCoding.getDisplay());
|
||||
coding_systems.add(theCategoryCoding.getSystem());
|
||||
for (String theCategoryCoding_code : theConcept.getCoding_code()) {
|
||||
coding_codes.add(theCategoryCoding_code);
|
||||
}
|
||||
for (String theCategoryCoding_system : theConcept.getCoding_system()) {
|
||||
coding_systems.add(theCategoryCoding_system);
|
||||
}
|
||||
for (String theCategoryCoding_code_system_hash : theConcept.getCoding_code_system_hash()) {
|
||||
coding_code_system_hashes.add(theCategoryCoding_code_system_hash);
|
||||
}
|
||||
for (String theCategoryCoding_display : theConcept.getCoding_display()) {
|
||||
coding_displays.add(theCategoryCoding_display);
|
||||
}
|
||||
myCategory_coding_code_system_hash.add(coding_code_system_hashes);
|
||||
myCategory_coding_code.add(coding_codes);
|
||||
|
|
@ -128,14 +132,13 @@ public class ObservationJson {
|
|||
return myCategory_coding_system;
|
||||
}
|
||||
|
||||
public void setCode(CodeableConcept theCode) {
|
||||
myCode_concept_text = theCode.getText();
|
||||
for (Coding theCodeCoding : theCode.getCoding()) {
|
||||
myCode_coding_code_system_hash = String.valueOf(CodeSystemHash.hashCodeSystem(theCodeCoding.getSystem(), theCodeCoding.getCode()));
|
||||
myCode_coding_code = theCodeCoding.getCode();
|
||||
myCode_coding_display = theCodeCoding.getDisplay();
|
||||
myCode_coding_system = theCodeCoding.getSystem();
|
||||
}
|
||||
public void setCode(CodeJson theCode) {
|
||||
myCode_concept_text = theCode.getCodeableConceptText();
|
||||
// Currently can only support one Coding for Observation Code
|
||||
myCode_coding_code_system_hash = theCode.getCoding_code_system_hash().get(0);
|
||||
myCode_coding_code = theCode.getCoding_code().get(0);
|
||||
myCode_coding_display = theCode.getCoding_display().get(0);
|
||||
myCode_coding_system = theCode.getCoding_system().get(0);
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoObservation;
|
|||
import ca.uhn.fhir.jpa.api.dao.IFhirResourceDaoPatient;
|
||||
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticsearchClient;
|
||||
import ca.uhn.fhir.jpa.dao.BaseJpaTest;
|
||||
import ca.uhn.fhir.jpa.dao.SearchBuilder;
|
||||
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||
import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
|
||||
import ca.uhn.fhir.rest.param.ReferenceAndListParam;
|
||||
import ca.uhn.fhir.rest.param.ReferenceOrListParam;
|
||||
|
|
@ -31,6 +31,7 @@ import org.springframework.test.context.ContextConfiguration;
|
|||
import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
|
||||
import org.springframework.transaction.PlatformTransactionManager;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.ArrayList;
|
||||
import java.util.Calendar;
|
||||
import java.util.Date;
|
||||
|
|
@ -61,6 +62,9 @@ public class BaseR4SearchLastN extends BaseJpaTest {
|
|||
@Autowired
|
||||
protected FhirContext myFhirCtx;
|
||||
|
||||
@Autowired
|
||||
private ElasticsearchSvcImpl myElasticsearchSvc;
|
||||
|
||||
@Autowired
|
||||
protected PlatformTransactionManager myPlatformTransactionManager;
|
||||
|
||||
|
|
@ -101,7 +105,7 @@ public class BaseR4SearchLastN extends BaseJpaTest {
|
|||
private static final Map<String, Date> observationEffectiveMap = new HashMap<>();
|
||||
|
||||
@Before
|
||||
public void beforeCreateTestPatientsAndObservations() {
|
||||
public void beforeCreateTestPatientsAndObservations() throws IOException {
|
||||
// Using a static flag to ensure that test data and elasticsearch index is only created once.
|
||||
// Creating this data and the index is time consuming and as such want to avoid having to repeat for each test.
|
||||
// Normally would use a static @BeforeClass method for this purpose, but Autowired objects cannot be accessed in static methods.
|
||||
|
|
@ -120,6 +124,9 @@ public class BaseR4SearchLastN extends BaseJpaTest {
|
|||
createObservationsForPatient(patient2Id);
|
||||
dataLoaded = true;
|
||||
|
||||
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
myElasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,13 +3,12 @@ package ca.uhn.fhir.jpa.dao.r4;
|
|||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.jpa.api.dao.IFhirSystemDao;
|
||||
import ca.uhn.fhir.jpa.config.TestR4ConfigWithElasticsearchClient;
|
||||
import ca.uhn.fhir.jpa.dao.data.IObservationIndexedCodeCodeableConceptSearchParamDao;
|
||||
import ca.uhn.fhir.jpa.dao.ObservationLastNIndexPersistSvc;
|
||||
import ca.uhn.fhir.jpa.model.entity.ObservationIndexedCodeCodeableConceptEntity;
|
||||
import ca.uhn.fhir.jpa.model.entity.ObservationIndexedSearchParamLastNEntity;
|
||||
import ca.uhn.fhir.jpa.dao.data.IObservationIndexedSearchParamLastNDao;
|
||||
import ca.uhn.fhir.jpa.model.entity.ResourceTable;
|
||||
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
|
||||
import ca.uhn.fhir.jpa.search.lastn.ElasticsearchSvcImpl;
|
||||
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.parser.IParser;
|
||||
import ca.uhn.fhir.rest.param.*;
|
||||
|
|
@ -42,12 +41,6 @@ import static org.junit.Assert.assertTrue;
|
|||
@ContextConfiguration(classes = {TestR4ConfigWithElasticsearchClient.class})
|
||||
public class PersistObservationIndexedSearchParamLastNR4IT {
|
||||
|
||||
@Autowired
|
||||
IObservationIndexedSearchParamLastNDao myResourceIndexedObservationLastNDao;
|
||||
|
||||
@Autowired
|
||||
IObservationIndexedCodeCodeableConceptSearchParamDao myCodeableConceptIndexedSearchParamNormalizedDao;
|
||||
|
||||
@Autowired
|
||||
private ElasticsearchSvcImpl elasticsearchSvc;
|
||||
|
||||
|
|
@ -64,11 +57,10 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
protected FhirContext myFhirCtx;
|
||||
|
||||
@Before
|
||||
public void before() {
|
||||
|
||||
myResourceIndexedObservationLastNDao.deleteAll();
|
||||
myCodeableConceptIndexedSearchParamNormalizedDao.deleteAll();
|
||||
public void before() throws IOException {
|
||||
|
||||
elasticsearchSvc.deleteAllDocumentsForTest(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
elasticsearchSvc.deleteAllDocumentsForTest(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
|
||||
}
|
||||
|
||||
private final String SINGLE_SUBJECT_ID = "4567";
|
||||
|
|
@ -85,7 +77,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
private ReferenceAndListParam multiSubjectParams = null;
|
||||
|
||||
@Test
|
||||
public void testIndexObservationSingle() {
|
||||
public void testIndexObservationSingle() throws IOException {
|
||||
indexSingleObservation();
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
searchParameterMap.setLastNMax(10);
|
||||
|
|
@ -124,7 +116,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
assertEquals(SINGLE_OBSERVATION_PID, observationIdsOnly.get(0));
|
||||
}
|
||||
|
||||
private void indexSingleObservation() {
|
||||
private void indexSingleObservation() throws IOException {
|
||||
|
||||
Observation myObservation = new Observation();
|
||||
IdType observationID = new IdType("Observation", SINGLE_OBSERVATION_PID, "1");
|
||||
|
|
@ -139,6 +131,9 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
|
||||
testObservationPersist.indexObservation(myObservation);
|
||||
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
|
||||
|
||||
}
|
||||
|
||||
private List<CodeableConcept> getCategoryCode() {
|
||||
|
|
@ -179,7 +174,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testIndexObservationMultiple() {
|
||||
public void testIndexObservationMultiple() throws IOException {
|
||||
indexMultipleObservations();
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
searchParameterMap.setLastNMax(100);
|
||||
|
|
@ -206,7 +201,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
|
||||
}
|
||||
|
||||
private void indexMultipleObservations() {
|
||||
private void indexMultipleObservations() throws IOException {
|
||||
|
||||
// Create two CodeableConcept values each for a Code with three codings.
|
||||
CodeableConcept codeableConceptField1 = new CodeableConcept().setText("Test Codeable Concept Field for First Code");
|
||||
|
|
@ -275,10 +270,13 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
|
||||
multiSubjectParams = new ReferenceAndListParam().addAnd(subjectParams);
|
||||
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
|
||||
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testDeleteObservation() {
|
||||
public void testDeleteObservation() throws IOException {
|
||||
indexMultipleObservations();
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
searchParameterMap.setLastNMax(100);
|
||||
|
|
@ -302,6 +300,7 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
entity.setVersion(0L);
|
||||
|
||||
testObservationPersist.deleteObservationIndex(entity);
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
|
||||
// Confirm that observation was deleted.
|
||||
searchParameterMap = new SearchParameterMap();
|
||||
|
|
@ -318,14 +317,16 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
}
|
||||
|
||||
@Test
|
||||
public void testUpdateObservation() {
|
||||
public void testUpdateObservation() throws IOException {
|
||||
indexSingleObservation();
|
||||
ObservationIndexedSearchParamLastNEntity observationIndexEntity = myResourceIndexedObservationLastNDao.findAll().get(0);
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
searchParameterMap.setLastNMax(10);
|
||||
ObservationJson observationIndexEntity = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirCtx).get(0);
|
||||
assertEquals(SINGLE_OBSERVATION_PID, observationIndexEntity.getIdentifier());
|
||||
assertEquals(SINGLE_SUBJECT_ID, observationIndexEntity.getSubject());
|
||||
assertEquals(SINGLE_EFFECTIVEDTM, observationIndexEntity.getEffectiveDtm());
|
||||
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
searchParameterMap = new SearchParameterMap();
|
||||
ReferenceParam subjectParam = new ReferenceParam("Patient", "", SINGLE_SUBJECT_ID);
|
||||
searchParameterMap.add(Observation.SP_SUBJECT, new ReferenceAndListParam().addAnd(new ReferenceOrListParam().addOr(subjectParam)));
|
||||
TokenParam categoryParam = new TokenParam(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE);
|
||||
|
|
@ -350,8 +351,9 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
updatedObservation.setCode(getObservationCode());
|
||||
|
||||
testObservationPersist.indexObservation(updatedObservation);
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
|
||||
ObservationIndexedSearchParamLastNEntity updatedObservationEntity = myResourceIndexedObservationLastNDao.findByIdentifier(SINGLE_OBSERVATION_PID);
|
||||
ObservationJson updatedObservationEntity = elasticsearchSvc.getObservationDocument(SINGLE_OBSERVATION_PID);
|
||||
assertEquals("1234", updatedObservationEntity.getSubject());
|
||||
assertEquals(newEffectiveDtm.getValue(), updatedObservationEntity.getEffectiveDtm());
|
||||
|
||||
|
|
@ -413,6 +415,8 @@ public class PersistObservationIndexedSearchParamLastNR4IT {
|
|||
}
|
||||
);
|
||||
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
|
||||
SearchParameterMap searchParameterMap = new SearchParameterMap();
|
||||
|
||||
// execute Observation ID search - Composite Aggregation
|
||||
|
|
|
|||
|
|
@ -12,8 +12,6 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
import com.fasterxml.jackson.databind.SerializationFeature;
|
||||
import org.hl7.fhir.r4.model.Observation;
|
||||
import org.junit.*;
|
||||
import org.hl7.fhir.r4.model.CodeableConcept;
|
||||
import org.hl7.fhir.r4.model.Coding;
|
||||
import org.junit.runner.RunWith;
|
||||
import org.springframework.beans.factory.annotation.Autowired;
|
||||
import org.springframework.test.context.ContextConfiguration;
|
||||
|
|
@ -84,7 +82,7 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
|
|||
searchParameterMap.add(Observation.SP_SUBJECT, buildReferenceAndListParam(subjectParam));
|
||||
searchParameterMap.setLastNMax(3);
|
||||
|
||||
List<ObservationJson> observations = elasticsearchSvc.executeLastNWithAllFields(searchParameterMap, myFhirContext);
|
||||
List<ObservationJson> observations = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirContext);
|
||||
|
||||
assertEquals(60, observations.size());
|
||||
|
||||
|
|
@ -305,16 +303,16 @@ public class LastNElasticsearchSvcMultipleObservationsIT {
|
|||
private void createMultiplePatientsAndObservations() throws IOException {
|
||||
// Create CodeableConcepts for two Codes, each with three codings.
|
||||
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"));
|
||||
CodeJson codeJson1 = new CodeJson(codeableConceptField1, codeableConceptId1);
|
||||
String codeJson1Document = ourMapperNonPrettyPrint.writeValueAsString(codeJson1);
|
||||
CodeJson codeJson1 = new CodeJson();
|
||||
codeJson1.setCodeableConceptText("Test Codeable Concept Field for First Code");
|
||||
codeJson1.setCodeableConceptId(codeableConceptId1);
|
||||
codeJson1.addCoding("http://mycodes.org/fhir/observation-code", "test-code-1", "test-code-1 display");
|
||||
|
||||
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"));
|
||||
CodeJson codeJson2 = new CodeJson(codeableConceptField2, codeableConceptId2);
|
||||
String codeJson2Document = ourMapperNonPrettyPrint.writeValueAsString(codeJson2);
|
||||
CodeJson codeJson2 = new CodeJson();
|
||||
codeJson2.setCodeableConceptText("Test Codeable Concept Field for Second Code");
|
||||
codeJson2.setCodeableConceptId(codeableConceptId1);
|
||||
codeJson2.addCoding("http://mycodes.org/fhir/observation-code", "test-code-2", "test-code-2 display");
|
||||
|
||||
// Create CodeableConcepts for two categories, each with three codings.
|
||||
// Create three codings and first category CodeableConcept
|
||||
|
|
|
|||
|
|
@ -17,8 +17,6 @@ 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.After;
|
||||
import org.junit.BeforeClass;
|
||||
import org.junit.Test;
|
||||
|
|
@ -92,8 +90,8 @@ public class LastNElasticsearchSvcSingleObservationIT {
|
|||
|
||||
@After
|
||||
public void after() throws IOException {
|
||||
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
elasticsearchSvc.deleteAllDocuments(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
|
||||
elasticsearchSvc.deleteAllDocumentsForTest(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
elasticsearchSvc.deleteAllDocumentsForTest(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX);
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -118,7 +116,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
|
|||
assertEquals(RESOURCEPID, observationIdsOnly.get(0));
|
||||
|
||||
// execute Observation search for all search fields
|
||||
List<ObservationJson> observations = elasticsearchSvc.executeLastNWithAllFields(searchParameterMap, myFhirContext);
|
||||
List<ObservationJson> observations = elasticsearchSvc.executeLastNWithAllFieldsForTest(searchParameterMap, myFhirContext);
|
||||
|
||||
validateFullObservationSearch(observations);
|
||||
}
|
||||
|
|
@ -226,7 +224,7 @@ public class LastNElasticsearchSvcSingleObservationIT {
|
|||
assertEquals(String.valueOf(CodeSystemHash.hashCodeSystem(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE)), code_coding_code_system_hash);
|
||||
|
||||
// Retrieve all Observation codes
|
||||
List<CodeJson> codes = elasticsearchSvc.queryAllIndexedObservationCodes();
|
||||
List<CodeJson> codes = elasticsearchSvc.queryAllIndexedObservationCodesForTest();
|
||||
assertEquals(1, codes.size());
|
||||
CodeJson persistedObservationCode = codes.get(0);
|
||||
|
||||
|
|
@ -261,51 +259,44 @@ public class LastNElasticsearchSvcSingleObservationIT {
|
|||
indexedObservation.setEffectiveDtm(EFFECTIVEDTM);
|
||||
|
||||
// Add three CodeableConcepts for category
|
||||
List<CodeableConcept> categoryConcepts = new ArrayList<>();
|
||||
List<CodeJson> categoryConcepts = new ArrayList<>();
|
||||
// Create three codings and first category CodeableConcept
|
||||
List<Coding> category1 = new ArrayList<>();
|
||||
CodeableConcept categoryCodeableConcept1 = new CodeableConcept().setText(FIRSTCATEGORYTEXT);
|
||||
category1.add(new Coding(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE, FIRSTCATEGORYFIRSTCODINGDISPLAY));
|
||||
category1.add(new Coding(CATEGORYSECONDCODINGSYSTEM, FIRSTCATEGORYSECONDCODINGCODE, FIRSTCATEGORYSECONDCODINGDISPLAY));
|
||||
category1.add(new Coding(CATEGORYTHIRDCODINGSYSTEM, FIRSTCATEGORYTHIRDCODINGCODE, FIRSTCATEGORYTHIRDCODINGDISPLAY));
|
||||
categoryCodeableConcept1.setCoding(category1);
|
||||
CodeJson categoryCodeableConcept1 = new CodeJson();
|
||||
categoryCodeableConcept1.setCodeableConceptText(FIRSTCATEGORYTEXT);
|
||||
categoryCodeableConcept1.addCoding(CATEGORYFIRSTCODINGSYSTEM, FIRSTCATEGORYFIRSTCODINGCODE, FIRSTCATEGORYFIRSTCODINGDISPLAY);
|
||||
categoryCodeableConcept1.addCoding(CATEGORYSECONDCODINGSYSTEM, FIRSTCATEGORYSECONDCODINGCODE, FIRSTCATEGORYSECONDCODINGDISPLAY);
|
||||
categoryCodeableConcept1.addCoding(CATEGORYTHIRDCODINGSYSTEM, FIRSTCATEGORYTHIRDCODINGCODE, FIRSTCATEGORYTHIRDCODINGDISPLAY);
|
||||
categoryConcepts.add(categoryCodeableConcept1);
|
||||
// Create three codings and second category CodeableConcept
|
||||
List<Coding> category2 = new ArrayList<>();
|
||||
CodeableConcept categoryCodeableConcept2 = new CodeableConcept().setText(SECONDCATEGORYTEXT);
|
||||
category2.add(new Coding(CATEGORYFIRSTCODINGSYSTEM, SECONDCATEGORYFIRSTCODINGCODE, SECONDCATEGORYFIRSTCODINGDISPLAY));
|
||||
category2.add(new Coding(CATEGORYSECONDCODINGSYSTEM, SECONDCATEGORYSECONDCODINGCODE, SECONDCATEGORYSECONDCODINGDISPLAY));
|
||||
category2.add(new Coding(CATEGORYTHIRDCODINGSYSTEM, SECONDCATEGORYTHIRDCODINGCODE, SECONDCATEGORYTHIRDCODINGDISPLAY));
|
||||
categoryCodeableConcept2.setCoding(category2);
|
||||
CodeJson categoryCodeableConcept2 = new CodeJson();
|
||||
categoryCodeableConcept2.setCodeableConceptText(SECONDCATEGORYTEXT);
|
||||
categoryCodeableConcept2.addCoding(CATEGORYFIRSTCODINGSYSTEM, SECONDCATEGORYFIRSTCODINGCODE, SECONDCATEGORYFIRSTCODINGDISPLAY);
|
||||
categoryCodeableConcept2.addCoding(CATEGORYSECONDCODINGSYSTEM, SECONDCATEGORYSECONDCODINGCODE, SECONDCATEGORYSECONDCODINGDISPLAY);
|
||||
categoryCodeableConcept2.addCoding(CATEGORYTHIRDCODINGSYSTEM, SECONDCATEGORYTHIRDCODINGCODE, SECONDCATEGORYTHIRDCODINGDISPLAY);
|
||||
|
||||
categoryConcepts.add(categoryCodeableConcept2);
|
||||
// Create three codings and third category CodeableConcept
|
||||
List<Coding> category3 = new ArrayList<>();
|
||||
CodeableConcept categoryCodeableConcept3 = new CodeableConcept().setText(THIRDCATEGORYTEXT);
|
||||
category3.add(new Coding(CATEGORYFIRSTCODINGSYSTEM, THIRDCATEGORYFIRSTCODINGCODE, THIRDCATEGORYFIRSTCODINGDISPLAY));
|
||||
category3.add(new Coding(CATEGORYSECONDCODINGSYSTEM, THIRDCATEGORYSECONDCODINGCODE, THIRDCATEGORYSECONDCODINGDISPLAY));
|
||||
category3.add(new Coding(CATEGORYTHIRDCODINGSYSTEM, THIRDCATEGORYTHIRDCODINGCODE, THIRDCATEGORYTHIRDCODINGDISPLAY));
|
||||
categoryCodeableConcept3.setCoding(category3);
|
||||
CodeJson categoryCodeableConcept3 = new CodeJson();
|
||||
categoryCodeableConcept3.setCodeableConceptText(THIRDCATEGORYTEXT);
|
||||
categoryCodeableConcept3.addCoding(CATEGORYFIRSTCODINGSYSTEM, THIRDCATEGORYFIRSTCODINGCODE, THIRDCATEGORYFIRSTCODINGDISPLAY);
|
||||
categoryCodeableConcept3.addCoding(CATEGORYSECONDCODINGSYSTEM, THIRDCATEGORYSECONDCODINGCODE, THIRDCATEGORYSECONDCODINGDISPLAY);
|
||||
categoryCodeableConcept3.addCoding(CATEGORYTHIRDCODINGSYSTEM, THIRDCATEGORYTHIRDCODINGCODE, THIRDCATEGORYTHIRDCODINGDISPLAY);
|
||||
categoryConcepts.add(categoryCodeableConcept3);
|
||||
indexedObservation.setCategories(categoryConcepts);
|
||||
|
||||
// Create CodeableConcept for Code with three codings.
|
||||
indexedObservation.setCode_concept_id(OBSERVATIONSINGLECODEID);
|
||||
CodeableConcept codeableConceptField = new CodeableConcept().setText(OBSERVATIONCODETEXT);
|
||||
codeableConceptField.addCoding(new Coding(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE, CODEFIRSTCODINGDISPLAY));
|
||||
CodeJson codeableConceptField = new CodeJson();
|
||||
codeableConceptField.setCodeableConceptText(OBSERVATIONCODETEXT);
|
||||
codeableConceptField.addCoding(CODEFIRSTCODINGSYSTEM, CODEFIRSTCODINGCODE, CODEFIRSTCODINGDISPLAY);
|
||||
indexedObservation.setCode(codeableConceptField);
|
||||
|
||||
assertTrue(elasticsearchSvc.createOrUpdateObservationIndex(RESOURCEPID, indexedObservation));
|
||||
|
||||
CodeJson observationCode = new CodeJson(codeableConceptField, OBSERVATIONSINGLECODEID);
|
||||
String codeDocument = ourMapperNonPrettyPrint.writeValueAsString(observationCode);
|
||||
assertTrue(elasticsearchSvc.performIndex(ElasticsearchSvcImpl.OBSERVATION_CODE_INDEX, OBSERVATIONSINGLECODEID, codeDocument, ElasticsearchSvcImpl.CODE_DOCUMENT_TYPE));
|
||||
|
||||
try {
|
||||
Thread.sleep(1000L);
|
||||
} catch (InterruptedException theE) {
|
||||
theE.printStackTrace();
|
||||
}
|
||||
codeableConceptField.setCodeableConceptId(OBSERVATIONSINGLECODEID);
|
||||
assertTrue(elasticsearchSvc.createOrUpdateObservationCodeIndex(OBSERVATIONSINGLECODEID, codeableConceptField));
|
||||
|
||||
elasticsearchSvc.refreshIndex(ElasticsearchSvcImpl.OBSERVATION_INDEX);
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,63 +0,0 @@
|
|||
package ca.uhn.fhir.jpa.model.entity;
|
||||
|
||||
/*-
|
||||
* #%L
|
||||
* HAPI FHIR Model
|
||||
* %%
|
||||
* Copyright (C) 2014 - 2020 University Health Network
|
||||
* %%
|
||||
* Licensed under the Apache License, Version 2.0 (the "License");
|
||||
* you may not use this file except in compliance with the License.
|
||||
* You may obtain a copy of the License at
|
||||
*
|
||||
* http://www.apache.org/licenses/LICENSE-2.0
|
||||
*
|
||||
* Unless required by applicable law or agreed to in writing, software
|
||||
* distributed under the License is distributed on an "AS IS" BASIS,
|
||||
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
||||
* See the License for the specific language governing permissions and
|
||||
* limitations under the License.
|
||||
* #L%
|
||||
*/
|
||||
|
||||
import ca.uhn.fhir.jpa.model.util.CodeSystemHash;
|
||||
import org.hibernate.search.annotations.Analyze;
|
||||
import org.hibernate.search.annotations.Field;
|
||||
|
||||
import javax.persistence.*;
|
||||
|
||||
@Entity
|
||||
@Embeddable
|
||||
@Table(name = "HFJ_SPIDX_LASTN_CODING")
|
||||
public class ObservationIndexedCodeCodingEntity {
|
||||
|
||||
public static final int MAX_LENGTH = 200;
|
||||
|
||||
@Id
|
||||
@Column(name = "CODEABLE_CONCEPT_ID", length = MAX_LENGTH)
|
||||
private String myCodeableConceptId;
|
||||
|
||||
@Field(name = "code", analyze = Analyze.NO)
|
||||
private String myCode;
|
||||
|
||||
@Field(name = "system", analyze = Analyze.NO)
|
||||
private String mySystem;
|
||||
|
||||
@Field(name = "code_system_hash", analyze = Analyze.NO)
|
||||
private String myCodeSystemHash;
|
||||
|
||||
@Field(name = "display")
|
||||
private String myDisplay;
|
||||
|
||||
public ObservationIndexedCodeCodingEntity() {
|
||||
}
|
||||
|
||||
public ObservationIndexedCodeCodingEntity(String theSystem, String theCode, String theDisplay, String theCodeableConceptId) {
|
||||
myCode = theCode;
|
||||
mySystem = theSystem;
|
||||
myCodeSystemHash = String.valueOf(CodeSystemHash.hashCodeSystem(theSystem, theCode));
|
||||
myDisplay = theDisplay;
|
||||
myCodeableConceptId = theCodeableConceptId;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue