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[BI-2786] Remove code to add treatments to additional info #495

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Merged
jloux-brapi merged 3 commits into from
Feb 17, 2026
Merged

[BI-2786] Remove code to add treatments to additional info #495

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b85a0e4
[BI-2786] Remove code to add treatments to additional info
jloux-brapi Feb 13, 2026
c475797
Merge branch 'develop' into bug/BI-2786
jloux-brapi Feb 16, 2026
c4539f6
Remove treatments from BrAPIAdditionalFields, update unit test
jloux-brapi Feb 16, 2026
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1 change: 0 additions & 1 deletion src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java
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Expand Up @@ -47,7 +47,6 @@ public final class BrAPIAdditionalInfoFields {
public static final String DATASETS = "datasets";
public static final String FEMALE_PARENT_UNKNOWN = "femaleParentUnknown";
public static final String MALE_PARENT_UNKNOWN = "maleParentUnknown";
public static final String TREATMENTS = "treatments";
public static final String GID = "gid";
public static final String CHANGELOG = "changeLog";
public static final String ENV_YEAR = "envYear";
Expand Down
18 changes: 0 additions & 18 deletions src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java
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Expand Up @@ -176,7 +176,6 @@ public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservat
try {
if (!brAPIObservationUnitList.isEmpty()) {
Callable<Map<String, BrAPIObservationUnit>> postFunction = () -> {
preprocessObservationUnits(brAPIObservationUnitList);
List<BrAPIObservationUnit> ous = brAPIDAOUtil.post(brAPIObservationUnitList, upload, api::observationunitsPost, importDAO::update);
return processObservationUnitsForCache(ous, program, false);
};
Expand All @@ -198,7 +197,6 @@ public List<BrAPIObservationUnit> createBrAPIObservationUnits(List<BrAPIObservat
try {
if (!brAPIObservationUnitList.isEmpty()) {
Callable<Map<String, BrAPIObservationUnit>> postFunction = () -> {
preprocessObservationUnits(brAPIObservationUnitList);
List<BrAPIObservationUnit> ous = brAPIDAOUtil.post(brAPIObservationUnitList, api::observationunitsPost);
return processObservationUnitsForCache(ous, program, false);
};
Expand Down Expand Up @@ -387,15 +385,9 @@ private void processObservationUnits(Program program, List<BrAPIObservationUnit>
this.germplasmService.getGermplasm(program.getId()).forEach((germplasm -> germplasmByDbId.put(germplasm.getGermplasmDbId(), germplasm)));
}

// if has treatments in additionalInfo, copy to treatments property
for (BrAPIObservationUnit ou : brapiObservationUnits) {
JsonObject additionalInfo = ou.getAdditionalInfo();
if (additionalInfo != null) {
JsonElement treatmentsElement = additionalInfo.get(BrAPIAdditionalInfoFields.TREATMENTS);
if (treatmentsElement != null) {
List<BrAPIObservationTreatment> treatments = gson.fromJson(treatmentsElement, treatmentlistType);
ou.setTreatments(treatments);
}
if( withGID ){
BrAPIGermplasm germplasm = germplasmByDbId.get(ou.getGermplasmDbId());
ou.putAdditionalInfoItem(BrAPIAdditionalInfoFields.GID, germplasm.getAccessionNumber());
Expand Down Expand Up @@ -432,14 +424,4 @@ private void processObservationUnits(Program program, List<BrAPIObservationUnit>
}
}
}

private void preprocessObservationUnits(List<BrAPIObservationUnit> brapiObservationUnits) {
// add treatments to additional info
for (BrAPIObservationUnit obsUnit : brapiObservationUnits) {
List<BrAPIObservationTreatment> treatments = obsUnit.getTreatments();
if (treatments != null) {
obsUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.TREATMENTS, treatments);
}
}
}
}
10 changes: 8 additions & 2 deletions src/test/java/org/breedinginsight/brapps/importer/daos/BrAPIObservationUnitDAOTest.java
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Expand Up @@ -36,6 +36,7 @@

import static org.breedinginsight.TestUtils.insertAndFetchTestProgram;
import static org.junit.jupiter.api.Assertions.assertEquals;
import static org.junit.jupiter.api.Assertions.assertNull;

@MicronautTest
@TestInstance(TestInstance.Lifecycle.PER_CLASS)
Expand Down Expand Up @@ -119,12 +120,14 @@ public void setup() {
@SneakyThrows
@Order(1)
public void testCreateObservationUnitAdditionalInfoSingleTreatmentFactor() {
// create observation unit with treatments only in additional info to simulate breedbase not populating
// treatments field
BrAPIObservationUnit ou1 = new BrAPIObservationUnit();
ou1.setObservationUnitName("test1");
ou1.putAdditionalInfoItem(BrAPIAdditionalInfoFields.TREATMENTS, List.of(testTreatment));
ou1.setProgramDbId(validProgram.getBrapiProgram().getProgramDbId());

var treatment = new BrAPIObservationTreatment();
treatment.setFactor("ou1 treatment");
ou1.setTreatments(List.of(treatment));
// Set xref.
BrAPIExternalReference xref = new BrAPIExternalReference();
xref.setReferenceSource(Utilities.generateReferenceSource(referenceSource, ExternalReferenceSource.OBSERVATION_UNITS));
Expand Down Expand Up @@ -153,6 +156,9 @@ private void singleTreatmentAsserts(List<BrAPIObservationUnit> obsUnits, BrAPIOb

BrAPIObservationTreatment treatment = treatments.get(0);
assertEquals(expectedTreatment, treatment, "Expected treatments to be same");

// Storing treatments in additionalInfo is no longer necessary since BrAPI server stores treatments in observation_unit_treatment
assertNull(ou.getAdditionalInfo(), "Expected OU additionalInfo to be null");
}

}