Merge pull request #77 from TheJacksonLaboratory/76-filter-param

Filter Param
TheJacksonLaboratory · Jan 2, 2025 · 364e8e4 · 364e8e4
2 parents 75d4549 + 2fa1278
commit 364e8e4
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Showing 6 changed files with 29 additions and 10 deletions.
diff --git a/src/main/java/org/jacksonlaboratory/controller/TermController.java b/src/main/java/org/jacksonlaboratory/controller/TermController.java
@@ -1,16 +1,21 @@
 package org.jacksonlaboratory.controller;
 
+import io.micronaut.core.annotation.Nullable;
 import io.micronaut.http.HttpResponse;
 import io.micronaut.http.annotation.*;
+import io.swagger.v3.oas.annotations.Parameter;
 import io.swagger.v3.oas.annotations.media.Schema;
+import jakarta.validation.constraints.Pattern;
 import org.jacksonlaboratory.model.dto.SimpleOntologyTerm;
 import org.jacksonlaboratory.model.entity.OntologyTerm;
 import org.jacksonlaboratory.service.GraphService;
 import org.jacksonlaboratory.service.TermService;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
+import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
+import java.util.stream.Collectors;
 
 @Controller("${api-url.prefix}/${ontology}/terms")
 public class TermController {
@@ -28,8 +33,18 @@ public TermController(TermService termService, GraphService graphService) {
      * @return List of all ontology terms
      */
     @Get(uri="/", produces="application/json")
-    public List<OntologyTerm> all() {
-        return this.termService.getAllOntologyTerms();
+    public List<OntologyTerm> all(
+            @QueryValue(value = "filter")
+            @Nullable
+            @Parameter(schema = @Schema(maxLength = 250, type = "string", pattern = "^(HP:\\d{7})(,HP:\\d{7})*$"), required = false)
+            @Pattern(regexp = "^(HP:\\d{7})(,HP:\\d{7})*$", message = "message = Invalid format. Expected format: HP:0001166 or HP:0001166,HP:0001234") String filter) {
+
+        if (filter == null || filter.isBlank()){
+            return this.termService.getAllOntologyTerms(List.of());
+        } else {
+            List<TermId> termIds = Arrays.stream(filter.split(",")).map(TermId::of).collect(Collectors.toUnmodifiableList());
+            return this.termService.getAllOntologyTerms(termIds);
+        }
     }
 
     /**
@@ -38,7 +53,8 @@ public List<OntologyTerm> all() {
      * @return The term or null.
      */
     @Get(uri="/{id}", produces="application/json")
-    public HttpResponse<?> details(@Schema(minLength = 1, maxLength = 20, type = "string", pattern = ".*") @PathVariable String id) {
+    public HttpResponse<?> details(@Schema(minLength = 1, maxLength = 20, type = "string", pattern = ".*")
+                                       @PathVariable String id) {
         TermId termId = TermId.of(id);
         Optional<TermId> replacement = this.graphService.getMostRecentTermId(termId);
 

diff --git a/src/main/java/org/jacksonlaboratory/repository/TermRepositoryImpl.java b/src/main/java/org/jacksonlaboratory/repository/TermRepositoryImpl.java
@@ -30,18 +30,21 @@ public TermRepositoryImpl(EntityManager entityManager) {
 
 	@Override
 	@ReadOnly
+	@Transactional
 	public List<OntologyTerm> findAll(){
 		return entityManager.createQuery("SELECT t FROM OntologyTerm t", OntologyTerm.class).getResultStream().collect(Collectors.toList());
 	}
 
 	@Override
 	@ReadOnly
+	@Transactional
 	public Optional<OntologyTerm> findByTermId(TermId id) {
 		Optional<OntologyTerm> term = entityManager.createQuery("SELECT t FROM OntologyTerm t WHERE t.id = :param1", OntologyTerm.class).setParameter("param1", id).getResultStream().findFirst();
 		return term;
 	}
 
 	@Override
+	@Transactional
 	public List<OntologyTerm> findByTermIdIn(List<TermId> ids) {
 		List<OntologyTerm> terms = entityManager.createQuery("SELECT t FROM OntologyTerm t WHERE t.id in :param1", OntologyTerm.class).setParameter("param1", ids).getResultList();
 		terms.sort(Comparator.comparing(item -> ids.indexOf(TermId.of(item.getId()))));

diff --git a/src/main/java/org/jacksonlaboratory/service/GraphService.java b/src/main/java/org/jacksonlaboratory/service/GraphService.java
@@ -9,10 +9,7 @@
 import org.jacksonlaboratory.model.entity.OntologyTermBuilder;
 import org.jacksonlaboratory.repository.TermRepository;
 import org.jacksonlaboratory.repository.TranslationRepository;
-import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
 import org.monarchinitiative.phenol.io.OntologyLoader;
-import org.monarchinitiative.phenol.io.OntologyLoaderOptions;
-import org.monarchinitiative.phenol.io.utils.CurieUtilBuilder;
 import org.monarchinitiative.phenol.ontology.data.Identified;
 import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.Term;

diff --git a/src/main/java/org/jacksonlaboratory/service/TermService.java b/src/main/java/org/jacksonlaboratory/service/TermService.java
@@ -46,8 +46,11 @@ public Optional<OntologyTerm> getOntologyTermByTermId(TermId id){
 		return Optional.empty();
 	}
 
-	public List<OntologyTerm> getAllOntologyTerms(){
-		return this.termRepository.findAll();
+	public List<OntologyTerm> getAllOntologyTerms(List<TermId> termIdList){
+		if (termIdList.isEmpty()){
+			return this.termRepository.findAll();
+		}
+		return this.termRepository.findByTermIdIn(termIdList);
 	}
 
 	public List<OntologyTerm> searchOntologyTerm(String q){

diff --git a/src/test/groovy/org/jacksonlaboratory/controller/TermControllerSpec.groovy b/src/test/groovy/org/jacksonlaboratory/controller/TermControllerSpec.groovy
@@ -35,7 +35,7 @@ class TermControllerSpec extends Specification {
         when:
         def response = client.toBlocking().exchange(HttpRequest.GET('/api/hp/terms/'), Argument.listOf(Map.class))
         then:
-        1 * termService.getAllOntologyTerms() >> res
+        1 * termService.getAllOntologyTerms(List.of()) >> res
         response.body().size() == res.size()
         response.status().getCode().toInteger() == 200
         where:

diff --git a/src/test/groovy/org/jacksonlaboratory/repository/TranslationRepositorySpec.groovy b/src/test/groovy/org/jacksonlaboratory/repository/TranslationRepositorySpec.groovy
@@ -24,7 +24,7 @@ class TranslationRepositorySpec extends  Specification {
 
     void "test find all by term"() {
         when:
-            def term = termService.getAllOntologyTerms().find {it -> it.id == "HP:0000002"}.collect()
+            def term = termService.getAllOntologyTerms([]).find {it -> it.id == "HP:0000002"}.collect()
             def res = translationRepository.findAllByTerm(term[0])
         then:
         res.size() == 1