[BI-1830] Overwrite entity dataset

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

@@ -47,6 +47,7 @@ public final class BrAPIAdditionalInfoFields {
     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";
     public static final String GERMPLASM_UUID = "germplasmId";
     public static final String SAMPLE_ORGANISM = "organism";

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

@@ -16,6 +16,7 @@
  */
 package org.breedinginsight.brapps.importer.daos;
 
+import lombok.extern.slf4j.Slf4j;
 import org.apache.commons.lang3.tuple.Pair;
 import org.brapi.client.v2.ApiResponse;
 import org.brapi.client.v2.model.exceptions.ApiException;
@@ -24,11 +25,13 @@
 import org.brapi.v2.model.pheno.BrAPIObservation;
 import org.brapi.v2.model.pheno.request.BrAPIObservationSearchRequest;
 import org.brapi.v2.model.pheno.response.BrAPIObservationListResponse;
+import org.brapi.v2.model.pheno.response.BrAPIObservationSingleResponse;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.daos.ProgramDAO;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.services.brapi.BrAPIEndpointProvider;
 import org.breedinginsight.utilities.BrAPIDAOUtil;
+import org.breedinginsight.utilities.Utilities;
 import org.jetbrains.annotations.NotNull;
 
 import javax.inject.Inject;
@@ -38,6 +41,7 @@
 import static org.brapi.v2.model.BrAPIWSMIMEDataTypes.APPLICATION_JSON;
 
 @Singleton
+@Slf4j
 public class BrAPIObservationDAO {
 
     private ProgramDAO programDAO;
@@ -113,4 +117,25 @@ public List<BrAPIObservation> createBrAPIObservations(List<BrAPIObservation> brA
         return brAPIDAOUtil.post(brAPIObservationList, upload, api::observationsPost, importDAO::update);
     }
 
+    public BrAPIObservation updateBrAPIObservation(String dbId, BrAPIObservation observation, UUID programId) throws ApiException {
+        ObservationsApi api = brAPIEndpointProvider.get(programDAO.getCoreClient(programId), ObservationsApi.class);
+        ApiResponse<BrAPIObservationSingleResponse> response;
+        BrAPIObservation updatedObservation = null;
+        try {
+            response = api.observationsObservationDbIdPut(dbId, observation);
+            if (response != null) {
+                BrAPIObservationSingleResponse body = response.getBody();
+                if (body == null) {
+                    throw new ApiException("Response is missing body", 0, response.getHeaders(), null);
+                }
+                updatedObservation = body.getResult();
+                if (updatedObservation == null) {
+                    throw new ApiException("Response body is missing result", 0, response.getHeaders(), response.getBody().toString());
+                }
+            }
+        } catch (ApiException e) {
+            log.error(Utilities.generateApiExceptionLogMessage(e));
+        }
+        return updatedObservation;
+    }
 }

src/main/java/org/breedinginsight/brapps/importer/model/config/ImportFieldTypeEnum.java

@@ -21,6 +21,7 @@
 
 @Getter
 public enum ImportFieldTypeEnum {
+    BOOLEAN("BOOLEAN"),
     TEXT("TEXT"),
     NUMERICAL("NUMERICAL"),
     INTEGER("INTEGER"),

src/main/java/org/breedinginsight/brapps/importer/model/imports/BrAPIImportService.java

@@ -49,5 +49,5 @@ default String getWrongUserInputDataTypeMsg(String fieldName, String typeName) {
         return String.format("User input, \"%s\" must be an %s", fieldName, typeName);
     }
     ImportPreviewResponse process(List<BrAPIImport> brAPIImports, Table data, Program program, ImportUpload upload, User user, Boolean commit)
-            throws UnprocessableEntityException, DoesNotExistException, ValidatorException, ApiException, MissingRequiredInfoException;
+            throws Exception;
 }

src/main/java/org/breedinginsight/brapps/importer/model/imports/ChangeLogEntry.java

@@ -0,0 +1,39 @@
+/*
+ * See the NOTICE file distributed with this work for additional information
+ * regarding copyright ownership.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.breedinginsight.brapps.importer.model.imports;
+
+import lombok.Getter;
+import lombok.Setter;
+
+import java.util.UUID;
+
+@Getter
+@Setter
+public class ChangeLogEntry {
+    private String originalValue;
+    private String reasonForChange;
+    private UUID changedBy;
+    private String dateOfChange;
+
+    public ChangeLogEntry(String originalValue, String reasonForChange, UUID changedBy, String dateOfChange) {
+        this.originalValue = originalValue;
+        this.reasonForChange = reasonForChange;
+        this.changedBy = changedBy;
+        this.dateOfChange = dateOfChange;
+    }
+}

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

@@ -18,18 +18,15 @@
 package org.breedinginsight.brapps.importer.model.imports.experimentObservation;
 
 import lombok.extern.slf4j.Slf4j;
-import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImportService;
-import org.breedinginsight.brapps.importer.model.imports.germplasm.GermplasmImport;
 import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
-import org.breedinginsight.brapps.importer.services.processors.*;
+import org.breedinginsight.brapps.importer.services.processors.ExperimentProcessor;
+import org.breedinginsight.brapps.importer.services.processors.Processor;
+import org.breedinginsight.brapps.importer.services.processors.ProcessorManager;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.User;
-import org.breedinginsight.services.exceptions.MissingRequiredInfoException;
-import org.breedinginsight.services.exceptions.UnprocessableEntityException;
-import org.breedinginsight.services.exceptions.ValidatorException;
 import tech.tablesaw.api.Table;
 
 import javax.inject.Inject;
@@ -70,7 +67,7 @@ public String getMissingColumnMsg(String columnName) {
 
     @Override
     public ImportPreviewResponse process(List<BrAPIImport> brAPIImports, Table data, Program program, ImportUpload upload, User user, Boolean commit)
-            throws UnprocessableEntityException, ValidatorException, ApiException, MissingRequiredInfoException {
+            throws Exception {
 
         ImportPreviewResponse response = null;
         List<Processor> processors = List.of(experimentProcessorProvider.get());

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

@@ -47,6 +47,13 @@
 @ImportConfigMetadata(id = "ExperimentImport", name = "Experiment Import",
         description = "This import is used to create Observation Unit and Experiment data")
 public class ExperimentObservation implements BrAPIImport {
+    @ImportFieldType(type = ImportFieldTypeEnum.BOOLEAN, collectTime = ImportCollectTimeEnum.UPLOAD)
+    @ImportFieldMetadata(id = "overwrite", name = "Overwrite", description = "Boolean flag to overwrite existing observation")
+    private String overwrite;
+
+    @ImportFieldType(type = ImportFieldTypeEnum.TEXT, collectTime = ImportCollectTimeEnum.UPLOAD)
+    @ImportFieldMetadata(id="overwriteReason", name="Overwrite Reason", description="Description of the reason for overwriting existing observations")
+    private String overwriteReason;
 
     @ImportFieldType(type = ImportFieldTypeEnum.TEXT)
     @ImportFieldMetadata(id = "germplasmName", name = Columns.GERMPLASM_NAME, description = "Name of germplasm")

src/main/java/org/breedinginsight/brapps/importer/model/imports/germplasm/GermplasmImportService.java

@@ -18,24 +18,21 @@
 package org.breedinginsight.brapps.importer.model.imports.germplasm;
 
 import lombok.extern.slf4j.Slf4j;
-import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImportService;
 import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
-import org.breedinginsight.brapps.importer.services.processors.*;
+import org.breedinginsight.brapps.importer.services.processors.GermplasmProcessor;
+import org.breedinginsight.brapps.importer.services.processors.Processor;
+import org.breedinginsight.brapps.importer.services.processors.ProcessorManager;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.User;
-import org.breedinginsight.services.exceptions.DoesNotExistException;
-import org.breedinginsight.services.exceptions.MissingRequiredInfoException;
-import org.breedinginsight.services.exceptions.UnprocessableEntityException;
-import org.breedinginsight.services.exceptions.ValidatorException;
 import tech.tablesaw.api.Table;
 
 import javax.inject.Inject;
 import javax.inject.Provider;
 import javax.inject.Singleton;
-import java.util.*;
+import java.util.List;
 
 @Singleton
 @Slf4j
@@ -66,7 +63,7 @@ public String getImportTypeId() {
 
     @Override
     public ImportPreviewResponse process(List<BrAPIImport> brAPIImports, Table data, Program program, ImportUpload upload, User user, Boolean commit)
-            throws UnprocessableEntityException, DoesNotExistException, ValidatorException, ApiException, MissingRequiredInfoException {
+            throws Exception {
 
         ImportPreviewResponse response = null;
         List<Processor> processors = List.of(germplasmProcessorProvider.get());

src/main/java/org/breedinginsight/brapps/importer/model/imports/sample/SampleSubmissionImportService.java

@@ -18,7 +18,6 @@
 package org.breedinginsight.brapps.importer.model.imports.sample;
 
 import lombok.extern.slf4j.Slf4j;
-import org.brapi.client.v2.model.exceptions.ApiException;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImportService;
@@ -28,10 +27,6 @@
 import org.breedinginsight.brapps.importer.services.processors.SampleSubmissionProcessor;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.User;
-import org.breedinginsight.services.exceptions.DoesNotExistException;
-import org.breedinginsight.services.exceptions.MissingRequiredInfoException;
-import org.breedinginsight.services.exceptions.UnprocessableEntityException;
-import org.breedinginsight.services.exceptions.ValidatorException;
 import tech.tablesaw.api.Table;
 
 import javax.inject.Inject;
@@ -69,7 +64,7 @@ public ImportPreviewResponse process(List<BrAPIImport> brAPIImports,
                                          Program program,
                                          ImportUpload upload,
                                          User user,
-                                         Boolean commit) throws UnprocessableEntityException, DoesNotExistException, ValidatorException, ApiException, MissingRequiredInfoException {
+                                         Boolean commit) throws Exception {
         List<Processor> processors = List.of(sampleProcessorProvider.get());
         return processorManagerProvider.get().process(brAPIImports, processors, data, program, upload, user, commit);
     }

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

@@ -53,6 +53,12 @@ public class MappingManager {
 
     private ImportConfigManager configManager;
 
+    public static String wrongDataTypeMsg = "Column name \"%s\" must be integer type, but non-integer type provided.";
+    public static String blankRequiredField = "Required field \"%s\" cannot contain empty values";
+    public static String missingColumn = "Column name \"%s\" does not exist in file";
+    public static String missingUserInput = "User input, \"%s\" is required";
+    public static String wrongUserInputDataType = "User input, \"%s\" must be an %s";
+
     @Inject
     MappingManager(ImportConfigManager configManager) {
         this.configManager = configManager;
@@ -339,13 +345,13 @@ private void mapUserInputField(Object parent, Field field, Map<String, Object> u
 
         // Only supports user input at the top level of an object at the moment. No nested objects. Map<String, String>
         String fieldId = metadata.id();
-        if (!userInput.containsKey(fieldId) && required != null) {
+        if ((userInput == null || !userInput.containsKey(fieldId)) && required != null) {
             throw new UnprocessableEntityException(importService.getMissingUserInputMsg(metadata.name()));
         }
         else if (required != null && userInput.containsKey(fieldId) && userInput.get(fieldId).toString().isBlank()) {
             throw new UnprocessableEntityException(importService.getMissingUserInputMsg(metadata.name()));
         }
-        else if (userInput.containsKey(fieldId)) {
+        else if (userInput != null && userInput.containsKey(fieldId)) {
             String value = userInput.get(fieldId).toString();
             if (!isCorrectType(type.type(), value)) {
                 throw new UnprocessableEntityException(importService.getWrongUserInputDataTypeMsg(metadata.name(), type.type().toString().toLowerCase()));
@@ -371,11 +377,14 @@ private Boolean isCorrectType(ImportFieldTypeEnum expectedType, String value) {
         if (!value.isBlank()) {
             if (expectedType == ImportFieldTypeEnum.INTEGER) {
                 try {
-                    Integer d = Integer.parseInt(value);
+                    Integer.parseInt(value);
                 } catch (NumberFormatException nfe) {
                     return false;
                 }
             }
+            if (expectedType == ImportFieldTypeEnum.BOOLEAN && !String.valueOf(Boolean.parseBoolean(value)).equals(value)) {
+                return false;
+            }
         }
         return true;
     }