MAINT-2145 Add Identiiers to concept JSON

src/main/java/org/snomed/snowstorm/core/data/domain/Concept.java

@@ -1,6 +1,7 @@
 package org.snomed.snowstorm.core.data.domain;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import com.fasterxml.jackson.annotation.JsonView;
 import com.google.common.collect.Sets;
@@ -24,7 +25,7 @@
 
 @Document(indexName = "concept")
 @JsonPropertyOrder({"conceptId", "descendantCount", "fsn", "pt", "active", "effectiveTime", "released", "releasedEffectiveTime",  "inactivationIndicator", "associationTargets",
-		"moduleId", "definitionStatus", "definitionStatusId", "descriptions", "classAxioms", "gciAxioms", "relationships", "validationResults"})
+		"moduleId", "definitionStatus", "definitionStatusId", "descriptions", "classAxioms", "gciAxioms", "relationships", "alternateIdentifiers", "validationResults"})
 public class Concept extends SnomedComponent<Concept> implements ConceptView, SnomedComponentWithInactivationIndicator, SnomedComponentWithAssociations {
 
 	public interface Fields extends SnomedComponent.Fields {
@@ -81,6 +82,9 @@ public interface Fields extends SnomedComponent.Fields {
 	@Transient
 	private Long descendantCount;
 
+	@Transient
+	private List<Identifier> identifiers;
+
 	@Transient
 	private List<InvalidContent> validationResults;
 
@@ -93,6 +97,7 @@ public Concept() {
 		classAxioms = new HashSet<>();
 		generalConceptInclusionAxioms = new HashSet<>();
 		inactivationIndicatorMembers = new ArrayList<>();
+		identifiers = new ArrayList<>();
 		validationResults = new ArrayList<>();
 	}
 
@@ -230,6 +235,11 @@ public Concept addDescription(Description description) {
 		return this;
 	}
 
+	public Concept addIdentifier(Identifier identifier) {
+		identifiers.add(identifier);
+		return this;
+	}
+
 	public Concept addRelationship(String typeId, String destinationId) {
 		return addRelationship(new Relationship(typeId, destinationId));
 	}
@@ -427,6 +437,17 @@ public void setValidationResults(final List<InvalidContent> validationResults) {
 		this.validationResults = validationResults;
 	}
 
+	@JsonProperty("alternateIdentifiers")
+	@JsonView(value = View.Component.class)
+	@Override
+	public List<Identifier> getIdentifiers() {
+		return identifiers;
+	}
+
+	public void setIdentifiers(List<Identifier> identifiers) {
+		this.identifiers = identifiers;
+	}
+
 	public void clone(Concept concept) {
 		setConceptId(concept.getConceptId());
 		setEffectiveTimeI(concept.getEffectiveTimeI());

src/main/java/org/snomed/snowstorm/core/data/domain/ConceptView.java

@@ -33,5 +33,7 @@ public interface ConceptView {
 
 	Set<Axiom> getGciAxioms();
 
+	List<Identifier> getIdentifiers();
+
 	List<InvalidContent> getValidationResults();
 }

src/main/java/org/snomed/snowstorm/core/data/domain/Identifier.java

@@ -4,7 +4,7 @@
 import com.fasterxml.jackson.annotation.JsonPropertyOrder;
 import com.fasterxml.jackson.annotation.JsonView;
 import org.snomed.snowstorm.rest.View;
-import org.springframework.data.annotation.Id;
+import org.springframework.data.annotation.Transient;
 import org.springframework.data.elasticsearch.annotations.Document;
 import org.springframework.data.elasticsearch.annotations.Field;
 import org.springframework.data.elasticsearch.annotations.FieldType;
@@ -14,7 +14,7 @@
 import java.util.Objects;
 
 @Document(indexName = "identifier")
-@JsonPropertyOrder({"alternateIdentifier", "effectiveTime", "active", "moduleId", "identifierSchemeId", "referencedComponentId",  "released", "releasedEffectiveTime"})
+@JsonPropertyOrder({"alternateIdentifier", "effectiveTime", "active", "moduleId", "identifierSchemeId", "identifierScheme", "referencedComponentId",  "released", "releasedEffectiveTime"})
 public class Identifier extends SnomedComponent<Identifier> {
 
 	public interface Fields extends SnomedComponent.Fields {
@@ -44,6 +44,9 @@ public interface Fields extends SnomedComponent.Fields {
 	@Size(min = 5, max = 18)
 	private String referencedComponentId;
 
+	@Transient
+	private ConceptMini identifierScheme;
+
 	public Identifier() {
 		active = true;
 		setModuleId(Concepts.CORE_MODULE);
@@ -100,6 +103,15 @@ public String getIdentifierSchemeId() {
 		return identifierSchemeId;
 	}
 
+	public void setIdentifierScheme(ConceptMini identifierScheme) {
+		this.identifierScheme = identifierScheme;
+	}
+
+	@JsonView(value = View.Component.class)
+	public ConceptMini getIdentifierScheme() {
+		return identifierScheme;
+	}
+
 	@Override
 	protected Object[] getReleaseHashObjects() {
 		return new Object[]{alternateIdentifier, active, getModuleId(), identifierSchemeId, referencedComponentId};

src/main/java/org/snomed/snowstorm/core/data/services/ConceptService.java

@@ -92,6 +92,9 @@ public class ConceptService extends ComponentService {
 	@Autowired
 	private DescriptionService descriptionService;
 
+	@Autowired
+	private IdentifierComponentService identifierComponentService;
+
 	@Autowired
 	@Lazy
 	private ReferenceSetMemberService referenceSetMemberService;
@@ -159,7 +162,7 @@ public Collection<Concept> find(BranchCriteria branchCriteria, String path, Coll
 		if (isEmpty(conceptIds)) {
 			return Collections.emptySet();
 		}
-		return doFind(conceptIds, languageDialects, branchCriteria, PageRequest.of(0, conceptIds.size()), true, true, path).getContent();
+		return doFind(conceptIds, languageDialects, branchCriteria, PageRequest.of(0, conceptIds.size()), true, true, true, path).getContent();
 	}
 
 	public Page<Concept> find(List<Long> conceptIds, List<LanguageDialect> languageDialects, String path, PageRequest pageRequest) {
@@ -271,7 +274,7 @@ public Page<Concept> findAll(String path, List<LanguageDialect> languageDialects
 
 	private Page<Concept> doFind(Collection<?> conceptIds, List<LanguageDialect> languageDialects, BranchTimepoint branchTimepoint, PageRequest pageRequest) {
 		final BranchCriteria branchCriteria = getBranchCriteria(branchTimepoint);
-		return doFind(conceptIds, languageDialects, branchCriteria, pageRequest, true, true, branchTimepoint.getBranchPath());
+		return doFind(conceptIds, languageDialects, branchCriteria, pageRequest, true, true, true, branchTimepoint.getBranchPath());
 	}
 
 	protected BranchCriteria getBranchCriteria(String branchPath) {
@@ -323,7 +326,7 @@ private ResultMapPage<String, ConceptMini> findConceptMinis(BranchCriteria branc
 		if (conceptIds != null && conceptIds.isEmpty()) {
 			return new ResultMapPage<>(new HashMap<>(), 0);
 		}
-		Page<Concept> concepts = doFind(conceptIds, languageDialects, branchCriteria, pageRequest, false, false, null);
+		Page<Concept> concepts = doFind(conceptIds, languageDialects, branchCriteria, pageRequest, false, false, false, null);
 		Map<String, Concept> conceptMap = new HashMap<>();
 		for (Concept concept : concepts) {
 			String id = concept.getId();
@@ -343,7 +346,7 @@ private ResultMapPage<String, ConceptMini> findConceptMinis(BranchCriteria branc
 	private void populateConceptMinis(BranchCriteria branchCriteria, Map<String, ConceptMini> minisToPopulate, List<LanguageDialect> languageDialects) {
 		if (!minisToPopulate.isEmpty()) {
 			Set<String> conceptIds = minisToPopulate.keySet();
-			Page<Concept> concepts = doFind(conceptIds, languageDialects, branchCriteria, PageRequest.of(0, conceptIds.size()), false, false, null);
+			Page<Concept> concepts = doFind(conceptIds, languageDialects, branchCriteria, PageRequest.of(0, conceptIds.size()), false, false, false, null);
 			concepts.getContent().forEach(c -> {
 				ConceptMini conceptMini = minisToPopulate.get(c.getConceptId());
 				conceptMini.setDefinitionStatus(c.getDefinitionStatus());
@@ -359,6 +362,7 @@ private Page<Concept> doFind(
 			PageRequest pageRequest,
 			boolean includeRelationships,
 			boolean includeDescriptionInactivationInfo,
+			boolean includeIdentifiers,
 			String branchPath) {
 
 		final TimerUtil timer = new TimerUtil("Find concept", Level.DEBUG);
@@ -422,6 +426,10 @@ private Page<Concept> doFind(
 			timer.checkpoint("get axioms " + getFetchCount(conceptIdMap.size()));
 		}
 
+		if (includeIdentifiers) {
+			identifierComponentService.joinIdentifiers(branchCriteria, conceptIdMap, conceptMiniMap, languageDialects, timer);
+		}
+
 		// Fetch ConceptMini definition statuses
 		for (List<String> conceptIds : Iterables.partition(conceptMiniMap.keySet(), CLAUSE_LIMIT)) {
 			queryBuilder.withQuery(boolQuery()
@@ -744,7 +752,7 @@ Map<String, Concept> getExistingConceptsForSave(Collection<Concept> concepts, Co
 		if (!conceptIds.isEmpty()) {
 			for (List<String> conceptIdPartition : Iterables.partition(conceptIds, 500)) {
 				final BranchCriteria branchCriteria = versionControlHelper.getBranchCriteriaIncludingOpenCommit(commit);
-				final List<Concept> existingConcepts = doFind(conceptIdPartition, DEFAULT_LANGUAGE_DIALECTS, branchCriteria, PageRequest.of(0, conceptIds.size()), true, true, null).getContent();
+				final List<Concept> existingConcepts = doFind(conceptIdPartition, DEFAULT_LANGUAGE_DIALECTS, branchCriteria, PageRequest.of(0, conceptIds.size()), true, true, true, null).getContent();
 				for (Concept existingConcept : existingConcepts) {
 					existingConceptsMap.put(existingConcept.getConceptId(), existingConcept);
 				}

src/main/java/org/snomed/snowstorm/core/data/services/IdentifierComponentService.java

@@ -1,6 +1,7 @@
 package org.snomed.snowstorm.core.data.services;
 
 import com.google.common.base.Strings;
+import com.google.common.collect.Iterables;
 import io.kaicode.elasticvc.api.BranchCriteria;
 import io.kaicode.elasticvc.api.BranchService;
 import io.kaicode.elasticvc.api.ComponentService;
@@ -12,10 +13,11 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.snomed.snowstorm.config.Config;
-import org.snomed.snowstorm.core.data.domain.Concepts;
-import org.snomed.snowstorm.core.data.domain.Identifier;
+import org.snomed.snowstorm.core.data.domain.*;
 import org.snomed.snowstorm.core.data.repositories.IdentifierRepository;
 import org.snomed.snowstorm.core.data.services.pojo.IdentifierSearchRequest;
+import org.snomed.snowstorm.core.pojo.LanguageDialect;
+import org.snomed.snowstorm.core.util.TimerUtil;
 import org.snomed.snowstorm.ecl.ECLQueryService;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
@@ -24,6 +26,7 @@
 import org.springframework.data.elasticsearch.core.ElasticsearchOperations;
 import org.springframework.data.elasticsearch.core.SearchHit;
 import org.springframework.data.elasticsearch.core.SearchHits;
+import org.springframework.data.elasticsearch.core.SearchHitsIterator;
 import org.springframework.data.elasticsearch.core.query.NativeSearchQuery;
 import org.springframework.data.elasticsearch.core.query.NativeSearchQueryBuilder;
 import org.springframework.stereotype.Service;
@@ -150,4 +153,45 @@ private QueryBuilder buildIdentifierQuery(IdentifierSearchRequest searchRequest,
 
 		return query;
 	}
+	void joinIdentifiers(BranchCriteria branchCriteria, Map<String, Concept> conceptIdMap, Map<String, ConceptMini> conceptMiniMap, List<LanguageDialect> languageDialects, TimerUtil timer) {
+		final NativeSearchQueryBuilder queryBuilder = new NativeSearchQueryBuilder();
+
+		final Set<String> allConceptIds = new HashSet<>();
+		if (conceptIdMap != null) {
+			allConceptIds.addAll(conceptIdMap.keySet());
+		}
+		if (allConceptIds.isEmpty()) {
+			return;
+		}
+
+		// Fetch Identifier
+		for (List<String> conceptIds : Iterables.partition(allConceptIds, CLAUSE_LIMIT)) {
+			queryBuilder.withQuery(boolQuery()
+					.must(branchCriteria.getEntityBranchCriteria(Identifier.class))
+					.must(termQuery(Identifier.Fields.ACTIVE, true))
+					.must(termsQuery(Identifier.Fields.REFERENCED_COMPONENT_ID, conceptIds)))
+					.withPageable(LARGE_PAGE);
+			try (final SearchHitsIterator<Identifier> identifiers = elasticsearchTemplate.searchForStream(queryBuilder.build(), Identifier.class)) {
+				identifiers.forEachRemaining(hit -> {
+					Identifier identifier = hit.getContent();
+					identifier.setIdentifierScheme(getConceptMini(conceptMiniMap, identifier.getIdentifierSchemeId(), languageDialects));
+
+					// Join Identifiers to concepts for loading whole concepts use case.
+					final String referencedComponentId = identifier.getReferencedComponentId();
+					if (conceptIdMap != null) {
+						final Concept concept = conceptIdMap.get(referencedComponentId);
+						if (concept != null) {
+							concept.addIdentifier(identifier);
+						}
+					}
+				});
+			}
+		}
+		if (timer != null) timer.checkpoint("get Identifier " + getFetchCount(allConceptIds.size()));
+	}
+
+	private static ConceptMini getConceptMini(Map<String, ConceptMini> conceptMiniMap, String id, List<LanguageDialect> languageDialects) {
+		if (id == null) return new ConceptMini((String)null, languageDialects);
+		return conceptMiniMap.computeIfAbsent(id, i -> new ConceptMini(id, languageDialects));
+	}
 }

src/test/java/org/snomed/snowstorm/rest/ConceptControllerTest.java

@@ -196,7 +196,7 @@ void testConceptEndpointFields() throws IOException, ServiceException {
 		checkFields(responseBody);
 		LinkedHashMap<String, Object> properties = objectMapper.readValue(responseBody, LinkedHashMap.class);
 		assertEquals("[conceptId, fsn, pt, active, effectiveTime, released, releasedEffectiveTime, moduleId, definitionStatus, " +
-				"descriptions, classAxioms, gciAxioms, relationships, validationResults]", properties.keySet().toString());
+				"descriptions, classAxioms, gciAxioms, relationships, alternateIdentifiers, validationResults]", properties.keySet().toString());
 		Object fsn = properties.get("fsn");
 		assertEquals("LinkedHashMap", fsn.getClass().getSimpleName());
 		assertEquals("{term=Wallace \"69\" side-to-end anastomosis - action (qualifier value), lang=en}", fsn.toString());