Merge pull request #41 from TheJacksonLaboratory/feature/search

Feature-search-mp

build.gradle

@@ -5,7 +5,7 @@ plugins {
     id("io.micronaut.test-resources") version "4.1.0"
 }
 
-version = "0.5.6"
+version = "0.5.7"
 group = "org.jacksonlaboratory"
 
 repositories {

config/ontologies.json

@@ -34,5 +34,17 @@
     "api": "https://ontology.jax.org/api/mondo/docs",
     "international": false,
     "description": "The Mondo Disease Ontology (Mondo) aims to harmonize disease definitions across the world. The name Mondo comes from the latin word 'mundus' and means 'for the world.'"
+  },
+  {
+    "name": "Mammalian Phenotype Ontology",
+    "prefix": "mp",
+    "github": {
+      "api":  "https://api.github.com/repos/mgijax/mammalian-phenotype-ontology",
+      "home": "https://github.com/mgijax/mammalian-phenotype-ontology"
+    },
+    "home": "https://www.informatics.jax.org/vocab/mp_ontology",
+    "api": "https://ontology.jax.org/api/mp/docs",
+    "international": false,
+    "description": "The Mammalian Phenotype Ontology (MP) provides a standardized vocabulary of phenotypic abnormalities encountered in Mus musculus."
   }
 ]

src/main/java/org/jacksonlaboratory/controller/SearchController.java

@@ -1,16 +1,19 @@
 package org.jacksonlaboratory.controller;
 
-import com.fasterxml.jackson.annotation.JsonView;
 import io.micronaut.http.annotation.Controller;
 import io.micronaut.http.annotation.Get;
 import io.micronaut.http.annotation.QueryValue;
+import io.micronaut.serde.annotation.SerdeImport;
+import org.jacksonlaboratory.model.dto.SearchDto;
 import org.jacksonlaboratory.model.entity.OntologyTerm;
 import org.jacksonlaboratory.service.TermService;
 import io.swagger.v3.oas.annotations.media.Schema;
 
 import java.util.List;
+import java.util.stream.Collectors;
 
 @Controller("${api-url.prefix}/${ontology}/search")
+@SerdeImport(SearchDto.class)
 public class SearchController {
 
 	private TermService termService;
@@ -24,8 +27,18 @@ public SearchController(TermService termService) {
      * @param query The search value
      * @return List of matching ontology terms
      */
-	@Get(uri="/", produces="application/json")
-	public List<OntologyTerm> search(@QueryValue("q") @Schema(minLength = 3, maxLength = 250, type = "string", pattern = ".*")  String query) {
-		return this.termService.searchOntologyTerm(query);
+	@Get(produces="application/json")
+	public SearchDto search(
+			@QueryValue("q") @Schema(minLength = 3, maxLength = 250, type = "string", pattern = ".*")  String query,
+			@QueryValue(value = "page", defaultValue = "0") @Schema(maxLength = 1000, type = "number") int page,
+			@QueryValue(value = "limit", defaultValue = "10") @Schema(maxLength = 1, type = "number") int limit
+	) {
+		page = page * limit;
+		List<OntologyTerm> terms = this.termService.searchOntologyTerm(query);
+		if (limit == -1) {
+			return new SearchDto(terms,  terms.size());
+		} else {
+			return new SearchDto(terms.stream().skip(page).limit(limit).collect(Collectors.toList()),  terms.size());
+		}
 	}
 }

src/main/java/org/jacksonlaboratory/model/dto/SearchDto.java

@@ -0,0 +1,23 @@
+package org.jacksonlaboratory.model.dto;
+
+import org.jacksonlaboratory.model.entity.OntologyTerm;
+
+import java.util.List;
+
+public class SearchDto {
+	private final List<OntologyTerm> terms;
+	private final int totalCount;
+
+	public SearchDto(List<OntologyTerm> terms, int totalCount) {
+		this.terms = terms;
+		this.totalCount = totalCount;
+	}
+
+	public List<OntologyTerm> getTerms() {
+		return terms;
+	}
+
+	public int getTotalCount() {
+		return totalCount;
+	}
+}

src/main/java/org/jacksonlaboratory/model/dto/SimpleOntologyTerm.java

@@ -1,6 +1,5 @@
 package org.jacksonlaboratory.model.dto;
 
-import com.fasterxml.jackson.annotation.JsonGetter;
 import io.micronaut.serde.annotation.Serdeable;
 import org.jacksonlaboratory.model.entity.OntologyTerm;
 import org.jacksonlaboratory.model.entity.Translation;
@@ -13,12 +12,15 @@ public class SimpleOntologyTerm {
 	private final String id;
 	private final String name;
 
+	private final int nDescendant;
+
 	private final List<Translation> translations;
 
 	public SimpleOntologyTerm(OntologyTerm ontologyTerm) {
 		this.id = ontologyTerm.getId();
 		this.name = ontologyTerm.getName();
 		this.translations = ontologyTerm.getTranslations();
+		this.nDescendant = ontologyTerm.getDescendantCount();
 	}
 
 	public String getId() {
@@ -29,11 +31,14 @@ public String getName() {
 		return name;
 	}
 
-	@JsonGetter(value = "translations")
 	public List<Translation> getTranslations() {
 		return translations;
 	}
 
+	public int getDescendantCount() {
+		return nDescendant;
+	}
+
 	@Override
 	public String toString() {
 		return "SimpleOntologyTerm{" +

src/main/java/org/jacksonlaboratory/model/entity/OntologyTerm.java

@@ -1,7 +1,6 @@
 package org.jacksonlaboratory.model.entity;
 
-import com.fasterxml.jackson.annotation.JsonGetter;
-import com.fasterxml.jackson.annotation.JsonView;
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import io.micronaut.core.annotation.Creator;
 import io.micronaut.serde.annotation.Serdeable;
 import io.swagger.v3.oas.annotations.media.Schema;
@@ -12,7 +11,6 @@
 import org.monarchinitiative.phenol.ontology.data.Term;
 import org.monarchinitiative.phenol.ontology.data.TermId;
 import org.monarchinitiative.phenol.ontology.data.TermSynonym;
-import org.jacksonlaboratory.view.Views;
 
 import java.util.Arrays;
 import java.util.Collections;
@@ -49,6 +47,9 @@ public class OntologyTerm {
 	@Column(columnDefinition = "text")
 	private String xrefs;
 
+	@Column(columnDefinition = "int")
+	private int nDescendants;
+
 	@Transient
 	private List<Translation> translations;
 
@@ -84,6 +85,11 @@ public String getId() {
 		return id.toString();
 	}
 
+	@JsonIgnore
+	public TermId getTermId() {
+		return id;
+	}
+
 	@Schema(maxLength = 255, type = "string", pattern = ".*")
 	public String getName() {
 		return name;
@@ -99,6 +105,10 @@ public String getComment() {
 		return comment;
 	}
 
+	public int getDescendantCount() {
+		return nDescendants;
+	}
+
 	@ArraySchema(maxItems = 25)
 	public List<String> getSynonyms() {
 		if(this.synonyms == null || this.synonyms.isBlank()){
@@ -127,6 +137,10 @@ public void setTranslation(List<Translation> translations) {
 		this.translations = translations;
 	}
 
+	public void setDescendantCount(int count) {
+		this.nDescendants = count;
+	}
+
 	@Override
 	public boolean equals(Object o) {
 		if (this == o) return true;

src/main/java/org/jacksonlaboratory/service/DataInitializer.java

@@ -52,7 +52,9 @@ public void init() {
 			log.info("Loading ontology terms..");
 			try {
 				this.termRepository.configure();
-				List<OntologyTerm> terms = graphService.getOntology().getTerms().stream().distinct().map(OntologyTerm::new).collect(Collectors.toList());
+				List<OntologyTerm> terms = graphService.getOntology().getTerms().stream().distinct().map(OntologyTerm::new).peek(
+						t -> t.setDescendantCount(graphService.getDescendantCount(t.getTermId()))
+				).collect(Collectors.toList());
 				this.termRepository.saveAll(terms);
 				log.info("Finished loading ontology terms..");
 				if (international){

src/main/java/org/jacksonlaboratory/service/GraphService.java

@@ -1,5 +1,6 @@
 package org.jacksonlaboratory.service;
 
+import com.fasterxml.jackson.annotation.JsonIgnore;
 import io.micronaut.context.annotation.Property;
 import io.micronaut.context.annotation.Requires;
 import io.micronaut.context.annotation.Value;
@@ -72,6 +73,11 @@ public List<SimpleOntologyTerm> getChildren(TermId termId) {
 		}
 	}
 
+	@JsonIgnore
+	public int getDescendantCount(TermId termId){
+		return (int) this.ontology.graph().getDescendantsStream(termId, false).count();
+	}
+
 	public MinimalOntology getOntology() {
 		return ontology;
 	}

src/test/groovy/org/jacksonlaboratory/controller/SearchControllerSpec.groovy

@@ -27,14 +27,14 @@ class SearchControllerSpec extends Specification {
 
     void "should search #q and return the fake object"() {
         when:
-        def response = client.toBlocking().retrieve(HttpRequest.GET('/api/hp/search?q='+ q), Argument.listOf(Map.class))
+        def response = client.toBlocking().retrieve(HttpRequest.GET('/api/hp/search?q='+ q), Map.class)
         then:
         termService.searchOntologyTerm(q) >> res
-        response.size() == res.size()
-        response.get(0).get("id").equals(res.get(0).getId())
-        response.get(0).get("name").equals(res.get(0).getName())
-        response.get(0).get("definition").equals(res.get(0).getDefinition())
-
+        response.get("terms").size() == res.size();
+        response.get("terms").get(0).get("id").equals(res.get(0).getId())
+        response.get("terms").get(0).get("name").equals(res.get(0).getName())
+        response.get("terms").get(0).get("definition").equals(res.get(0).getDefinition())
+        response.get("terms").get(0).get("comment").equals(res.get(0).getComment())
         where:
         q | res
         "arach" | [new OntologyTerm(TermId.of("HP:000003"), "fake name", "fake def", "comment")]

src/test/groovy/org/jacksonlaboratory/model/OntologyTermSpec.groovy

@@ -18,6 +18,6 @@ class OntologyTermSpec extends Specification {
 
         result.contains("my name")
         result.contains("def")
-        result == "{\"id\":\"HP:000001\",\"name\":\"my name\",\"definition\":\"def\",\"comment\":null,\"synonyms\":[],\"xrefs\":[],\"translations\":null}"
+        result == "{\"id\":\"HP:000001\",\"name\":\"my name\",\"definition\":\"def\",\"comment\":null,\"synonyms\":[],\"xrefs\":[],\"translations\":null,\"descendantCount\":0}"
     }
 }