Merge of BI-2093 and BI-2134

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

@@ -295,4 +295,61 @@ public BrAPIObservation updateBrAPIObservation(String dbId, BrAPIObservation obs
             throw new InternalServerException("Unknown error has occurred: " + e.getMessage(), e);
         }
     }
+
+    // This method overloads updateBrAPIObservation(String dbId, BrAPIObservation observation, UUID programId)
+    // It was added to increase efficiency.  It insures that ProgramCache<BrAPIObservation>.populate() is called only once
+    // not once per observation.
+    public List<BrAPIObservation> updateBrAPIObservation(Map<String, BrAPIObservation> mutatedObservationByDbId, UUID programId) throws ApiException {
+        ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
+        var program = programDAO.fetchOneById(programId);
+
+        List <BrAPIObservation> updatedObservations = new ArrayList<>();
+        try {
+            for (Map.Entry<String, BrAPIObservation> entry : mutatedObservationByDbId.entrySet()) {
+                String dbId = entry.getKey();
+                BrAPIObservation observation = entry.getValue();
+                if (observation == null) {
+                    throw new Exception("Null observation");
+                }
+
+                ApiResponse<BrAPIObservationSingleResponse> response = null;
+                try {
+                    response = api.observationsObservationDbIdPut(dbId, observation);
+                } catch (ApiException e) {
+                    throw new RuntimeException(e);
+                }
+                if (response == null) {
+                    throw new ApiException("Response is null", 0, null, null);
+                }
+                BrAPIObservationSingleResponse body = response.getBody();
+                if (body == null) {
+                    throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
+                }
+                BrAPIObservation updatedObservation = body.getResult();
+                if (updatedObservation == null) {
+                    throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
+                }
+                updatedObservations.add(updatedObservation);
+
+                if (!Objects.equals(observation.getValue(), updatedObservation.getValue())
+                        || !Objects.equals(observation.getObservationTimeStamp(), updatedObservation.getObservationTimeStamp())) {
+                    String message;
+                    if (!Objects.equals(observation.getValue(), updatedObservation.getValue())) {
+                        message = String.format("Updated observation, %s, from BrAPI service does not match requested update %s.", updatedObservation.getValue(), observation.getValue());
+                    } else {
+                        message = String.format("Updated observation timestamp, %s, from BrAPI service does not match requested update timestamp %s.", updatedObservation.getObservationTimeStamp(), observation.getObservationTimeStamp());
+                    }
+                    throw new Exception(message);
+                }
+            }
+            Map<String, BrAPIObservation> processedObservations = processObservationsForCache(updatedObservations, program.getKey());
+            return programObservationCache.postThese(programId,processedObservations);
+        } catch (ApiException e) {
+            log.error("Error updating observation: " + Utilities.generateApiExceptionLogMessage(e), e);
+            throw e;
+        } catch (Exception e) {
+            log.error("Error updating observation: ", e);
+            throw new InternalServerException(e.getMessage(), e);
+        }
+    }
 }

src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/appendoverwrite/factory/entity/PendingObservation.java

@@ -31,9 +31,7 @@
 import org.breedinginsight.services.OntologyService;
 import org.breedinginsight.services.exceptions.DoesNotExistException;
 
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 import java.util.stream.Collectors;
 
 @Prototype
@@ -114,14 +112,12 @@ public <U> List<U> brapiPut(List<U> members) throws ApiException, IllegalArgumen
         if (experimentUtilities.isInvalidMemberListForClass(members, BrAPIObservation.class)) {
             return new ArrayList<U>();
         }
+        Map<String, BrAPIObservation> mutatedObservationByDbId = members.stream().collect(Collectors.toMap(
+                m -> ((BrAPIObservation) m).getObservationDbId(),
+                m -> ((BrAPIObservation) m)
+        ));
+        return (List<U>) brAPIObservationDAO.updateBrAPIObservation(mutatedObservationByDbId, importContext.getProgram().getId());
 
-        List<BrAPIObservation> updatedObservations = new ArrayList<>();
-        for (U member : members) {
-            BrAPIObservation observation = (BrAPIObservation) member;
-            Optional.ofNullable(brAPIObservationDAO.updateBrAPIObservation(observation.getObservationDbId(), observation, importContext.getProgram().getId())).ifPresent(updatedObservations::add);
-        }
-
-        return (List<U>) updatedObservations;
     }
 
     /**

src/main/java/org/breedinginsight/daos/cache/ProgramCache.java

@@ -174,16 +174,26 @@ public List<R> post(UUID key, Callable<Map<String, R>> postMethod) throws Except
         Map<String, R> response = null;
         try {
             response = postMethod.call();
+            return postThese(key, response);
+        } catch (Exception e) {
+            log.error("Error posting data and populating the cache", e);
+            invalidate(key);
+            throw e;
+        }
+    }
 
+    public List<R> postThese(UUID key, Map<String, R> toBePosted) throws Exception {
+        log.debug("posting for key: " + generateCacheKey(key));
+        try {
             String cacheKey = generateCacheKey(key);
             RMap<String, String> map = connection.getMap(cacheKey);
-            //temporarily populate the cache with the returned objects from the postMethod so they show in immediate cache requests
-            for(Map.Entry<String, R> obj : response.entrySet()) {
+            //temporarily populate the cache with the returned objects from the postMethod, so they show in immediate cache requests
+            for(Map.Entry<String, R> obj : toBePosted.entrySet()) {
                 map.put(obj.getKey(), gson.toJson(obj.getValue()));
             }
             populate(key);
 
-            return new ArrayList<>(response.values());
+            return new ArrayList<>(toBePosted.values());
         } catch (Exception e) {
             log.error("Error posting data and populating the cache", e);
             invalidate(key);