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[BI-1202] Add sort fields to GET germplasm #157

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Merged
ctucker3 merged 2 commits into from
Mar 3, 2022
Merged

[BI-1202] Add sort fields to GET germplasm #157

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adb3e8e
germplasm get: add germplasm sort fields
Feb 28, 2022
726b453
germplasm get: add test for sorting
Feb 28, 2022
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2 changes: 0 additions & 2 deletions src/main/java/org/breedinginsight/brapi/v2/GermplasmController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -51,8 +51,6 @@ public HttpResponse<Response<DataResponse<List<BrAPIGermplasm>>>> getGermplasm(
@QueryValue @QueryValid(using = GermplasmQueryMapper.class) @Valid BrapiQuery queryParams) {
try {
List<BrAPIGermplasm> germplasm = germplasmService.getGermplasm(programId);
queryParams.setSortField(germplasmQueryMapper.getDefaultSortField());
queryParams.setSortOrder(germplasmQueryMapper.getDefaultSortOrder());
return ResponseUtils.getBrapiQueryResponse(germplasm, germplasmQueryMapper, queryParams);}
catch (ApiException e) {
log.info(e.getMessage());
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23 changes: 22 additions & 1 deletion src/main/java/org/breedinginsight/brapi/v2/model/response/mappers/GermplasmQueryMapper.java
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@@ -1,5 +1,6 @@
package org.breedinginsight.brapi.v2.model.response.mappers;

import com.google.gson.JsonObject;
import lombok.Getter;
import org.brapi.v2.model.germ.BrAPIGermplasm;
import org.breedinginsight.api.v1.controller.metadata.SortOrder;
Expand All @@ -21,7 +22,27 @@ public class GermplasmQueryMapper extends AbstractQueryMapper {

public GermplasmQueryMapper() {
fields = Map.ofEntries(
Map.entry("accessionNumber", BrAPIGermplasm::getAccessionNumber)
Map.entry("accessionNumber", BrAPIGermplasm::getAccessionNumber),
Map.entry("defaultDisplayName", BrAPIGermplasm::getDefaultDisplayName),
Map.entry("additionalInfo.breedingMethod", (germplasm) ->
germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().get("breedingMethod") != null ?
germplasm.getAdditionalInfo().get("breedingMethod").getAsString() : null),
Map.entry("seedSource", BrAPIGermplasm::getSeedSource),
Map.entry("femaleParent", (germplasm) ->
germplasm.getPedigree() != null ? germplasm.getPedigree().split("/")[0] : null),
Map.entry("maleParent", (germplasm) ->
germplasm.getPedigree() != null && germplasm.getPedigree().split("/").length > 1 ? germplasm.getPedigree().split("/")[1] : null),
Map.entry("additionalInfo.createdDate", (germplasm) ->
germplasm.getAdditionalInfo() != null && germplasm.getAdditionalInfo().get("createdDate") != null ?
germplasm.getAdditionalInfo().get("createdDate").getAsString() : null),
Map.entry("additionalInfo.createdBy.userName", (germplasm) -> {
JsonObject additionalInfo = germplasm.getAdditionalInfo();
if (additionalInfo == null) { return null;}
if (!additionalInfo.has("createdBy")) { return null;}
JsonObject createdBy = additionalInfo.getAsJsonObject("createdBy");
if (!createdBy.has("userName")) { return null; }
return createdBy.get("userName").getAsString();
})
);
}

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8 changes: 6 additions & 2 deletions src/test/java/org/breedinginsight/brapi/v2/GermplasmControllerIntegrationTest.java
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Expand Up @@ -153,7 +153,7 @@ public void getAllSuccess() {
// TODO: Parents are updated
// Breeding method is assigned
Flowable<HttpResponse<String>> call = client.exchange(
GET(String.format("/programs/%s/brapi/v2/germplasm",validProgram.getId().toString()))
GET(String.format("/programs/%s/brapi/v2/germplasm?sortField=defaultDisplayName&sortOrder=ASC",validProgram.getId().toString()))
.cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
);
HttpResponse<String> response = call.blockingFirst();
Expand All @@ -164,7 +164,9 @@ public void getAllSuccess() {
JsonArray data = result.getAsJsonArray("data");

assertEquals(6, data.size(), "Wrong number of germplasm were returned");
for (JsonElement jsonGermplasm: data) {
List<String> correctOrder = List.of("Full Germplasm 1", "Full Germplasm 2", "Full Germplasm 3", "Germplasm 1", "Germplasm 2", "Germplasm 3");
for (int i = 0; i < data.size(); i++) {
JsonElement jsonGermplasm = data.get(i);
JsonObject exampleGermplasm = jsonGermplasm.getAsJsonObject();
assertEquals(exampleGermplasm.get("defaultDisplayName").getAsString(), exampleGermplasm.get("germplasmName").getAsString(), "Germplasm name was not set to display name");
if (exampleGermplasm.get("additionalInfo").getAsJsonObject().has("breedingMethodId")){
Expand All @@ -178,6 +180,8 @@ public void getAllSuccess() {
}
}

// Check the correct sort order
assertEquals(correctOrder.get(i), exampleGermplasm.get("defaultDisplayName").getAsString(), "Wrong sort order");
}
}

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