From 67780b01dabf4d39d6d08eb7ae12bfd1d74d472c Mon Sep 17 00:00:00 2001
From: Najwa Lakmouri <najwa.lakmouri@inrae.fr>
Date: Wed, 26 Feb 2025 09:53:07 +0100
Subject: [PATCH] Fix GermplasmCriteria TODO in germplasm controller. Fix
GNP-6632
---
.../api/brapi/v2/GermplasmV2Controller.java | 66 ++-----------------
.../faidare/config/ElasticSearchConfig.java | 4 +-
.../domain/brapi/v1/GermplasmV1VO.java | 1 -
.../brapi/v2/GermplasmV2ControllerTest.java | 24 +++++--
4 files changed, 27 insertions(+), 68 deletions(-)
diff --git a/backend/src/main/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2Controller.java b/backend/src/main/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2Controller.java
index 59efba81..addd0439 100644
--- a/backend/src/main/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2Controller.java
+++ b/backend/src/main/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2Controller.java
@@ -11,20 +11,12 @@ import fr.inrae.urgi.faidare.dao.v2.GermplasmMcpdDao;
import fr.inrae.urgi.faidare.dao.v2.GermplasmV2Dao;
import fr.inrae.urgi.faidare.domain.CollPopVO;
import fr.inrae.urgi.faidare.domain.brapi.v2.GermplasmV2VO;
-import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.tags.Tag;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.core.io.Resource;
import org.springframework.data.domain.Pageable;
import org.springframework.util.MultiValueMap;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.ResponseBody;
-import org.springframework.web.bind.annotation.RestController;
+import org.springframework.web.bind.annotation.*;
@Tag(name = "Breeding API", description = "BrAPI endpoint")
@RestController
@@ -61,29 +53,10 @@ public class GermplasmV2Controller {
@GetMapping("/germplasm")
public BrapiListResponse<GermplasmV2VO> germplasm(
- @RequestParam MultiValueMap<String, String> parameters){
- //TODO: this could be replaced with @RequestParam GermplasmCriteria gCrit) to be adjusted/tested
- GermplasmCriteria gCrit = new GermplasmCriteria();
- if (parameters.get("accessionNumber") != null ){ gCrit.setAccessionNumber(parameters.get("accessionNumber")); }
- if (parameters.get("binomialName") != null ){ gCrit.setAccessionNumber(parameters.get("binomialName")); }
- if (parameters.get("genus") != null ){ gCrit.setAccessionNumber(parameters.get("genus")); }
- if (parameters.get("species") != null ){ gCrit.setAccessionNumber(parameters.get("species")); }
- if (parameters.get("synonym") != null ){ gCrit.setAccessionNumber(parameters.get("synonym")); }
- if (parameters.get("parentDbId") != null ){ gCrit.setAccessionNumber(parameters.get("parentDbId")); }
- if (parameters.get("progenyDbIb") != null ){ gCrit.setAccessionNumber(parameters.get("progenyDbIb")); }
- if (parameters.get("commonCropName") != null ){ gCrit.setAccessionNumber(parameters.get("commonCropName")); }
- if (parameters.get("programDbId") != null ){ gCrit.setAccessionNumber(parameters.get("programDbId")); }
- if (parameters.get("trialDbId") != null ){ gCrit.setAccessionNumber(parameters.get("trialDbId")); }
- if (parameters.get("studyDbId") != null ){ gCrit.setAccessionNumber(parameters.get("studyDbId")); }
- if (parameters.get("germplasmDbId") != null ){ gCrit.setAccessionNumber(parameters.get("germplasmDbId")); }
- if (parameters.get("germplasmName") != null ){ gCrit.setAccessionNumber(parameters.get("germplasmName")); }
- if (parameters.get("germplasmPUI") != null ){ gCrit.setAccessionNumber(parameters.get("germplasmPUI")); }
- if (parameters.get("externalReferenceID") != null ){ gCrit.setAccessionNumber(parameters.get("externalReferenceID")); }
- if (parameters.get("externalReferenceId") != null ){ gCrit.setAccessionNumber(parameters.get("externalReferenceId")); }
- if (parameters.get("externalReferenceSource") != null ){ gCrit.setAccessionNumber(parameters.get("externalReferenceSource")); }
-
- if (parameters.get("page") != null ){ gCrit.setPage(Integer.valueOf(parameters.get("page").get(0))); }
- if (parameters.get("pageSize") != null ){ gCrit.setPageSize(Integer.valueOf(parameters.get("pageSize").get(0))); }
+ @ModelAttribute GermplasmCriteria gCrit){
+ // We used @ModelAttribute because GermplasmCriteria is an object.
+ // This allows Spring to bind the request parameters directly to the fields of the GermplasmCriteria object.
+
BrapiListResponse<GermplasmV2VO> germplasmV2VOs = germplasmDao.findGermplasmsByCriteria(gCrit);
return germplasmV2VOs;
@@ -110,33 +83,4 @@ public class GermplasmV2Controller {
return collectionDao.getAllCollections();
}
- /*
- @GetMapping("/germplasmAttribute")
- public List<SearchHit<GermplasmAttributeV2VO>> germplasmAttribute(@RequestParam(value = "attributeValueDbId", defaultValue = "") String attributeValueDbId,
- @RequestParam(value = "attributeDbId", defaultValue = "") String attributeDbId,
- @RequestParam(value = "attributeName", defaultValue = "") String attributeName,
- @RequestParam(value = "commonCropName", defaultValue = "") String commonCropName,
- @RequestParam(value = "programDbId", defaultValue = "") String programDbId,
- @RequestParam(value = "germplasmDbId", defaultValue = "") String germplasmDbId,
- @RequestParam(value = "externalReferenceID", defaultValue = "") String externalReferenceID,
- @RequestParam(value = "externalReferenceId", defaultValue = "") String externalReferenceId,
- @RequestParam(value = "externalReferenceSource", defaultValue = "") String externalReferenceSource,
- @RequestParam MultiValueMap<String, String> parameters){
-
- GermplasmCriteria gCrit = new GermplasmCriteria();
- if (parameters.get("attributeValueDbId") != null ){ gCrit.setAccessionNumber(parameters.get("attributeValueDbId").get(0)); }
- if (parameters.get("attributeDbId") != null ){ gCrit.setAccessionNumber(parameters.get("attributeDbId").get(0)); }
- if (parameters.get("attributeName") != null ){ gCrit.setAccessionNumber(parameters.get("attributeName").get(0)); }
- if (parameters.get("commonCropName") != null ){ gCrit.setAccessionNumber(parameters.get("commonCropName").get(0)); }
- if (parameters.get("programDbId") != null ){ gCrit.setAccessionNumber(parameters.get("programDbId").get(0)); }
- if (parameters.get("germplasmDbId") != null ){ gCrit.setAccessionNumber(parameters.get("germplasmDbId").get(0)); }
- if (parameters.get("externalReferenceID") != null ){ gCrit.setAccessionNumber(parameters.get("externalReferenceID").get(0)); }
- if (parameters.get("externalReferenceId") != null ){ gCrit.setAccessionNumber(parameters.get("externalReferenceId").get(0)); }
- if (parameters.get("externalReferenceSource") != null ){ gCrit.setAccessionNumber(parameters.get("externalReferenceSource").get(0)); }
-
- SearchPage<GermplasmAttributeV2VO> germplasmAttribute = germplasmDao.findGermplasmsByCriteria(gCrit);
-
- return germplasmAttribute.getContent();
- }
- */
}
diff --git a/backend/src/main/java/fr/inrae/urgi/faidare/config/ElasticSearchConfig.java b/backend/src/main/java/fr/inrae/urgi/faidare/config/ElasticSearchConfig.java
index 1e2ee37d..4f624823 100644
--- a/backend/src/main/java/fr/inrae/urgi/faidare/config/ElasticSearchConfig.java
+++ b/backend/src/main/java/fr/inrae/urgi/faidare/config/ElasticSearchConfig.java
@@ -25,7 +25,9 @@ public class ElasticSearchConfig {
/**
* Provides builder for {@link ElasticsearchRestClientAutoConfiguration}
*/
- //TODO: is this deprecated ?
+ //The RestClient.builder() is not deprecated in Elasticsearch 7.x.
+ // However, in newer versions (e.g., 8.x), there may be alternative approaches
+ // or native clients to consider.
@Bean
public RestClientBuilder restClientBuilder() {
// if we are on CI, we use a hardcoded host, else we use the injected value
diff --git a/backend/src/main/java/fr/inrae/urgi/faidare/domain/brapi/v1/GermplasmV1VO.java b/backend/src/main/java/fr/inrae/urgi/faidare/domain/brapi/v1/GermplasmV1VO.java
index 7ba49058..5a843e3e 100644
--- a/backend/src/main/java/fr/inrae/urgi/faidare/domain/brapi/v1/GermplasmV1VO.java
+++ b/backend/src/main/java/fr/inrae/urgi/faidare/domain/brapi/v1/GermplasmV1VO.java
@@ -48,7 +48,6 @@ public final class GermplasmV1VO {
private String genusSpecies; //GnpIS
private String genusSpeciesSubtaxa; //GnpIS
private String germplasmDbId;
- //private List<DonorInfoVO> donorInfo; TODO activate
private String germplasmName;
private String germplasmPUI;
private Long groupId; //GnpIS
diff --git a/backend/src/test/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2ControllerTest.java b/backend/src/test/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2ControllerTest.java
index 75b5945a..dfb7588f 100644
--- a/backend/src/test/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2ControllerTest.java
+++ b/backend/src/test/java/fr/inrae/urgi/faidare/api/brapi/v2/GermplasmV2ControllerTest.java
@@ -87,6 +87,25 @@ class GermplasmV2ControllerTest {
assertThat(accNumber).isEqualTo("29814");
}
+ @Test
+ void should_get_germplasm_by_criteria() throws Exception{
+
+ HttpEntity<String> entity = new HttpEntity<>(null, headers);
+ ResponseEntity<String> response = testRestTemplate.exchange(
+ createURLWithPort("/brapi/v2/germplasm?accessionNumber=13481&genus=Triticum&species=aestivum&page=0&pageSize=1"),
+ HttpMethod.GET, entity, String.class);
+ assertThat(response.getStatusCode().is2xxSuccessful()).isTrue();
+ String accNumber = JsonPath.parse(response.getBody()).read("$.result.data.[0].accessionNumber");
+ assertThat(accNumber).isEqualTo("13481");
+ String genus = JsonPath.parse(response.getBody()).read("$.result.data.[0].genus");
+ assertThat(genus).isEqualTo("Triticum");
+ String species = JsonPath.parse(response.getBody()).read("$.result.data.[0].species");
+ assertThat(species).isEqualTo("aestivum");
+ Integer pageSize = JsonPath.parse(response.getBody()).read("$.metadata.pagination.pageSize");
+ assertThat(pageSize).isEqualTo(1);
+
+ }
+
@Test
@@ -127,11 +146,6 @@ class GermplasmV2ControllerTest {
}
-
- @Test
- void germplasmAttribute() {
- }
-
@Test
void should_get_collection(){
HttpEntity<String> entity = new HttpEntity<>(null, headers);
--
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