Merge pull request #495 from Breeding-Insight/bug/BI-2786

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

Author: jloux-brapi

src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java

@@ -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";

src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationUnitDAO.java

@@ -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);
                 };
@@ -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);
                 };
@@ -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());
@@ -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);
-            }
-        }
-    }
 }

src/test/java/org/breedinginsight/brapps/importer/daos/BrAPIObservationUnitDAOTest.java

@@ -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)
@@ -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));
@@ -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");
     }
 
 }