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[BI-1487] trait create/update: account for null method description in method name #191

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Merged
ctucker3 merged 1 commit into from
Jun 14, 2022
Merged

[BI-1487] trait create/update: account for null method description in method name #191

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11 changes: 9 additions & 2 deletions src/main/java/org/breedinginsight/daos/TraitDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@
import org.breedinginsight.services.brapi.BrAPIProvider;
import org.breedinginsight.utilities.BrAPIDAOUtil;
import org.jooq.*;
import org.jooq.tools.StringUtils;

import javax.inject.Inject;
import javax.inject.Singleton;
Expand Down Expand Up @@ -285,7 +286,7 @@ public List<Trait> createTraitsBrAPI(List<Trait> traits, User actingUser, Progra
.referenceID(trait.getMethod().getId().toString())
.referenceSource(referenceSource);
BrAPIMethod brApiMethod = new BrAPIMethod()
.methodName(String.format("%s %s [%s]", trait.getMethod().getDescription(), trait.getMethod().getMethodClass(), program.getKey()))
.methodName(constructMethodName(trait, program))
.externalReferences(List.of(methodReference))
.methodClass(trait.getMethod().getMethodClass())
.description(trait.getMethod().getDescription())
Expand Down Expand Up @@ -405,7 +406,7 @@ public Trait updateTraitBrAPI(Trait trait, Program program) {
BrAPIObservationVariable existingVariable = getBrAPIVariable(variablesAPI, trait.getId());

// Change method
existingVariable.getMethod().setMethodName(String.format("%s %s [%s]", trait.getMethod().getDescription(), trait.getMethod().getMethodClass(), program.getKey()));
existingVariable.getMethod().setMethodName(constructMethodName(trait, program));
existingVariable.getMethod().setMethodClass(trait.getMethod().getMethodClass());
existingVariable.getMethod().setDescription(trait.getMethod().getDescription());
existingVariable.getMethod().setFormula(trait.getMethod().getFormula());
Expand Down Expand Up @@ -453,6 +454,12 @@ public Trait updateTraitBrAPI(Trait trait, Program program) {
return updatedTrait;
}

private String constructMethodName(Trait trait, Program program) {
return !StringUtils.isBlank(trait.getMethod().getDescription()) ?
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@timparsons timparsons Jun 13, 2022

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Up to you: from a reusability perspective, the Utilities.appendProgramKey method could be used to construct the method name

String.format("%s %s [%s]", trait.getMethod().getDescription(), trait.getMethod().getMethodClass(), program.getKey()) :
String.format("%s [%s]", trait.getMethod().getMethodClass(), program.getKey());
}

private BrAPIObservationVariable getBrAPIVariable(ObservationVariablesApi variablesAPI, UUID traitId) {

BrAPIObservationVariable existingVariable;
Expand Down
76 changes: 76 additions & 0 deletions src/test/java/org/breedinginsight/api/v1/controller/TraitControllerIntegrationTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -455,6 +455,82 @@ public void checkBrapiValues() {

}

@Test
@SneakyThrows
@Order(4)
public void postNullMethodDescriptionNotInMethodName() {

Trait trait1 = new Trait();
trait1.setTraitDescription("trait 1 description");
trait1.setEntity("entity1");
trait1.setObservationVariableName("Test M Desc");
trait1.setProgramObservationLevel(ProgramObservationLevel.builder().name("Plant").build());
Scale scale1 = new Scale();
scale1.setScaleName("Test Scale");
scale1.setDataType(DataType.TEXT);
Method method1 = new Method();
trait1.setScale(scale1);
trait1.setMethod(method1);

// Set the brapi properties
setBrAPIProperties(trait1);

// set the synonyms
trait1.setSynonyms(List.of("Test Trait", "test1", "test2"));

// Set the tags
trait1.setTags(List.of("leaf trait"));

// Set method description to null
method1.setDescription(null);

List<Trait> traits = List.of(trait1);

// Call endpoint
Flowable<HttpResponse<String>> call = client.exchange(
POST("/programs/" + validProgram.getId() + "/traits", traits)
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
);
HttpResponse<String> res = call.blockingFirst();
assertEquals(HttpStatus.OK, res.getStatus());

JsonObject result = JsonParser.parseString(res.getBody().get()).getAsJsonObject().getAsJsonObject("result");
JsonArray data = result.getAsJsonArray("data");

for (JsonElement traitJson: data) {
JsonObject trait = (JsonObject) traitJson;
String traitName = trait.get("observationVariableName").getAsString();
if (traitName.equals(trait1.getObservationVariableName())) {
trait1.setId(UUID.fromString(trait.get("id").getAsString()));
}
}

String validProgramKey = validProgram.getKey();
BrAPIObservationVariable variable = getBrapiVariable(trait1.getObservationVariableName(), "Test Program");

String methodName = String.format("%s", trait1.getMethod().getMethodClass());
assertEquals(String.format("%s [%s]", methodName, validProgramKey),
variable.getMethod().getMethodName(), "Unexpected method name");

// update
trait1.getMethod().setMethodClass("Observation");

Flowable<HttpResponse<String>> call2 = client.exchange(
PUT("/programs/" + validProgram.getId() + "/traits", traits)
.contentType(MediaType.APPLICATION_JSON)
.cookie(new NettyCookie("phylo-token", "test-registered-user")), String.class
);
HttpResponse<String> response2 = call2.blockingFirst();
assertEquals(HttpStatus.OK, response2.getStatus());

variable = getBrapiVariable(trait1.getObservationVariableName(), "Test Program");

methodName = String.format("%s", trait1.getMethod().getMethodClass());
assertEquals(String.format("%s [%s]", methodName, validProgramKey),
variable.getMethod().getMethodName(), "Unexpected method name");
}

private BrAPIObservationVariable getBrapiVariable(String variableName, String programName) throws ApiException {
BrAPIClient client2 = new BrAPIClient(getProperties().get("brapi.server.pheno-url"));
ObservationVariablesApi variablesApi = new ObservationVariablesApi(client2);
Expand Down