[BI-1193] Associate phenotypes with experiment observation dataset

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

@@ -40,4 +40,5 @@ public final class BrAPIAdditionalInfoFields {
     public static final String EXPERIMENT_NUMBER = "experimentNumber";
     public static final String ENVIRONMENT_NUMBER = "environmentNumber";
     public static final String STUDY_NAME = "studyName";
+    public static final String OBSERVATION_DATASET_ID = "observationDatasetId";
 }

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPIListDAO.java

@@ -12,7 +12,7 @@
 import org.brapi.v2.model.core.BrAPIListTypes;
 import org.brapi.v2.model.core.request.BrAPIListNewRequest;
 import org.brapi.v2.model.core.request.BrAPIListSearchRequest;
-import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
+import org.brapi.v2.model.core.response.*;
 import org.brapi.v2.model.pheno.BrAPIObservation;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.daos.ProgramDAO;
@@ -97,28 +97,69 @@ private List<BrAPIListSummary> processListsForProgram(List<BrAPIListSummary> pro
         }
         return filteredLists;
     }
+    public List<String> updateBrAPIList(String brAPIListDbId, BrAPIListDetails mutatedList, UUID programId) throws ApiException {
+        ListsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ListsApi.class);
+        BrAPIListNewRequest request = new BrAPIListNewRequest();
+        request.setAdditionalInfo(mutatedList.getAdditionalInfo());
+        request.setDateCreated(mutatedList.getDateCreated());
+        request.setDateModified(mutatedList.getDateModified());
+        request.setExternalReferences(mutatedList.getExternalReferences());
+        request.setListDescription(mutatedList.getListDescription());
+        request.setListName(mutatedList.getListName());
+        request.setListOwnerName(mutatedList.getListOwnerName());
+        request.setListOwnerPersonDbId(mutatedList.getListOwnerPersonDbId());
+        request.setListSize(mutatedList.getListSize());
+        request.setListSource(mutatedList.getListSource());
+        request.setListType(mutatedList.getListType());
+        request.setData(mutatedList.getData());
+
+        // Do manually, it doesn't like List<Object> to List<BrAPIListNewRequest> for some reason
+        ApiResponse<BrAPIListsSingleResponse> response;
+        try {
+            response = api.listsListDbIdPut(brAPIListDbId, request);
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e));
+            throw e;
+        }
+        if(response != null) {
+            BrAPIListsSingleResponse body = response.getBody();
+            if (body == null) {
+                throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
+            }
+            BrAPIListDetails result = body.getResult();
+            if (result == null) {
+                throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
+            }
+            if (result.getData() == null) {
+                throw new ApiException("Response result is missing data", 0, response.getHeaders(), response.getBody().toString());
+            }
+            return result.getData();
+        }
+
+        throw new ApiException("No response after creating list");
+    }
 
-    public List<BrAPIObservation> createBrAPILists(List<BrAPIListNewRequest> brapiLists, UUID programId, ImportUpload upload) throws ApiException {
+    public List<BrAPIListSummary> createBrAPILists(List<BrAPIListNewRequest> brapiLists, UUID programId, ImportUpload upload) throws ApiException {
         ListsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ListsApi.class);
         // Do manually, it doesn't like List<Object> to List<BrAPIListNewRequest> for some reason
-        ApiResponse response;
+        ApiResponse<BrAPIListsListResponse> response;
         try {
             response = api.listsPost(brapiLists);
         } catch (ApiException e) {
             log.warn(Utilities.generateApiExceptionLogMessage(e));
             throw e;
         }
         if(response != null) {
-            BrAPIResponse body = (BrAPIResponse) response.getBody();
+            BrAPIResponse<BrAPIListsListResponseResult> body = response.getBody();
             if (body == null) {
-                throw new ApiException("Response is missing body");
+                throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
             }
-            BrAPIResponseResult result = (BrAPIResponseResult) body.getResult();
+            BrAPIResponseResult<BrAPIListSummary> result = body.getResult();
             if (result == null) {
-                throw new ApiException("Response body is missing result");
+                throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
             }
             if (result.getData() == null) {
-                throw new ApiException("Response result is missing data");
+                throw new ApiException("Response result is missing data", 0, response.getHeaders(), response.getBody().toString());
             }
             return result.getData();
         }

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPITrialDAO.java

@@ -21,6 +21,9 @@
 import org.brapi.client.v2.modules.core.TrialsApi;
 import org.brapi.v2.model.core.BrAPITrial;
 import org.brapi.v2.model.core.request.BrAPITrialSearchRequest;
+import org.brapi.v2.model.core.response.BrAPIListDetails;
+import org.brapi.v2.model.core.response.BrAPIListResponse;
+import org.brapi.v2.model.core.response.BrAPITrialSingleResponse;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
 import org.breedinginsight.daos.ProgramDAO;
@@ -76,7 +79,10 @@ public List<BrAPITrial> createBrAPITrials(List<BrAPITrial> brAPITrialList, UUID
         TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), TrialsApi.class);
         return brAPIDAOUtil.post(brAPITrialList, upload, api::trialsPost, importDAO::update);
     }
-
+    public BrAPITrial updateBrAPITrial(String trialDbId, BrAPITrial trial, UUID programId) throws ApiException {
+        TrialsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), TrialsApi.class);
+        return brAPIDAOUtil.put(trialDbId, trial, api::trialsTrialDbIdPut);
+    }
     /**
      * Fetch formatted trials/experiments for this program
      * @param programId

src/main/java/org/breedinginsight/brapps/importer/model/imports/experimentObservation/ExperimentObservation.java

@@ -22,6 +22,7 @@
 import lombok.Setter;
 import org.brapi.v2.model.BrAPIExternalReference;
 import org.brapi.v2.model.core.*;
+import org.brapi.v2.model.core.response.BrAPIListDetails;
 import org.brapi.v2.model.pheno.*;
 import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapps.importer.model.config.*;
@@ -197,6 +198,23 @@ public BrAPIStudy constructBrAPIStudy(
         return study;
     }
 
+    public BrAPIListDetails constructDatasetDetails(
+            String name,
+            UUID datasetId,
+            String referenceSourceBase,
+            Program program, String trialId) {
+        BrAPIListDetails dataSetDetails = new BrAPIListDetails();
+        dataSetDetails.setListName(name);
+        dataSetDetails.setListType(BrAPIListTypes.OBSERVATIONVARIABLES);
+        dataSetDetails.setData(new ArrayList<>());
+        dataSetDetails.putAdditionalInfoItem("datasetType", "observationDataset");
+        List<BrAPIExternalReference> refs = new ArrayList<>();
+        addReference(refs, program.getId(), referenceSourceBase, ExternalReferenceSource.PROGRAMS);
+        addReference(refs, UUID.fromString(trialId), referenceSourceBase, ExternalReferenceSource.TRIALS);
+        addReference(refs, datasetId, referenceSourceBase, ExternalReferenceSource.DATASET);
+        dataSetDetails.setExternalReferences(refs);
+        return dataSetDetails;
+    }
     public BrAPIObservationUnit constructBrAPIObservationUnit(
             Program program,
             String seqVal,
@@ -340,8 +358,7 @@ private List<BrAPIExternalReference> getObsUnitExternalReferences(
 
 
     private void addReference(List<BrAPIExternalReference> refs, UUID uuid, String referenceBaseNameSource, ExternalReferenceSource refSourceName) {
-        BrAPIExternalReference reference;
-        reference = new BrAPIExternalReference();
+        BrAPIExternalReference reference = new BrAPIExternalReference();
         reference.setReferenceSource(String.format("%s/%s", referenceBaseNameSource, refSourceName.getName()));
         reference.setReferenceID(uuid.toString());
         refs.add(reference);

src/main/java/org/breedinginsight/brapps/importer/model/response/ImportObjectState.java

@@ -19,5 +19,6 @@
 
 public enum ImportObjectState {
     NEW,
-    EXISTING
+    EXISTING,
+    MUTATED
 }

src/main/java/org/breedinginsight/brapps/importer/model/response/PendingImportObject.java

@@ -38,4 +38,5 @@ public PendingImportObject(ImportObjectState state, T brAPIObject, UUID id) {
     public PendingImportObject(ImportObjectState state, T brAPIObject) {
         this(state, brAPIObject, UUID.randomUUID());
     }
+
 }

src/main/java/org/breedinginsight/brapps/importer/services/ExternalReferenceSource.java

@@ -8,6 +8,7 @@ public enum ExternalReferenceSource {
     TRIALS("trials"),
     STUDIES("studies"),
     OBSERVATION_UNITS("observationunits"),
+    DATASET("dataset"),
     LISTS("lists");
 
     private String name;