BI-2132 Failed QA

src/main/java/org/breedinginsight/brapps/importer/controllers/UploadController.java

@@ -158,16 +158,16 @@ public HttpResponse<Response<ImportResponse>> previewData(@PathVariable UUID pro
         }
     }
 
-    @Put("programs/{programId}/import/mappings/{mappingId}/workflows/{workflow}/data/{uploadId}/preview")
+    @Put("programs/{programId}/import/mappings/{mappingId}/workflows/{workflowId}/data/{uploadId}/preview")
     @Produces(MediaType.APPLICATION_JSON)
     @AddMetadata
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER, ProgramSecuredRole.SYSTEM_ADMIN})
     public HttpResponse<Response<ImportResponse>> previewData(@PathVariable UUID programId, @PathVariable UUID mappingId,
-                                                              @PathVariable String workflow, @PathVariable UUID uploadId) {
+                                                              @PathVariable String workflowId, @PathVariable UUID uploadId) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
-            ImportResponse result = fileImportService.updateUpload(programId, uploadId, workflow, actingUser, null, false);
-            Response<ImportResponse> response = new Response<>(result);
+            ImportResponse result = fileImportService.updateUpload(programId, uploadId, workflowId, actingUser, null, false);
+            Response<ImportResponse> response = new Response(result);
             return HttpResponse.ok(response).status(HttpStatus.ACCEPTED);
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);
@@ -184,17 +184,17 @@ public HttpResponse<Response<ImportResponse>> previewData(@PathVariable UUID pro
         }
     }
 
-    @Put("programs/{programId}/import/mappings/{mappingId}/workflows/{workflow}/data/{uploadId}/commit")
+    @Put("programs/{programId}/import/mappings/{mappingId}/workflows/{workflowId}/data/{uploadId}/commit")
     @Produces(MediaType.APPLICATION_JSON)
     @AddMetadata
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER, ProgramSecuredRole.SYSTEM_ADMIN})
     public HttpResponse<Response<ImportResponse>> commitData(@PathVariable UUID programId, @PathVariable UUID mappingId,
-                                                             @PathVariable String workflow, @PathVariable UUID uploadId,
+                                                             @PathVariable String workflowId, @PathVariable UUID uploadId,
                                                              @Body @Nullable Map<String, Object> userInput) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
-            ImportResponse result = fileImportService.updateUpload(programId, uploadId, workflow, actingUser, userInput, true);
-            Response<ImportResponse> response = new Response<>(result);
+            ImportResponse result = fileImportService.updateUpload(programId, uploadId, workflowId, actingUser, userInput, true);
+            Response<ImportResponse> response = new Response(result);
             return HttpResponse.ok(response).status(HttpStatus.ACCEPTED);
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);

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

@@ -51,7 +51,7 @@ public List<ImportWorkflow> getWorkflows() {
     public ImportPreviewResponse process(ImportServiceContext context)
             throws Exception {
 
-        Optional.ofNullable(context.getWorkflow())
+        Optional.ofNullable(context.getWorkflowId())
                 .filter(workflow -> !workflow.isEmpty())
                 .ifPresent(workflow -> log.info("Workflow: " + workflow));
 

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

@@ -32,7 +32,7 @@
 @AllArgsConstructor
 @NoArgsConstructor
 public class ImportServiceContext {
-    private String workflow;
+    private String workflowId;
     private List<BrAPIImport> brAPIImports;
     private Table data;
     private Program program;

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

@@ -44,6 +44,5 @@ public String getImportTypeId() {
         return "ExperimentImport";
     }
 
-
 }
 

src/main/java/org/breedinginsight/brapps/importer/model/workflow/ImportContext.java

@@ -20,6 +20,7 @@
 import lombok.*;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
+import org.breedinginsight.brapps.importer.model.imports.ImportServiceContext;
 import org.breedinginsight.brapps.importer.model.imports.PendingImport;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.User;
@@ -39,10 +40,19 @@ public class ImportContext {
     private UUID workflowId;
     private ImportUpload upload;
     private List<BrAPIImport> importRows;
-    // TODO: move this out potentially
-    //private Map<Integer, PendingImport> mappedBrAPIImport;
     private Table data;
     private Program program;
     private User user;
     private boolean commit;
+
+    public static ImportContext from(ImportServiceContext importServiceContext) {
+        return ImportContext.builder()
+                .program(importServiceContext.getProgram())
+                .user(importServiceContext.getUser())
+                .commit(importServiceContext.isCommit())
+                .data(importServiceContext.getData())
+                .importRows(importServiceContext.getBrAPIImports())
+                .upload(importServiceContext.getUpload())
+                .build();
+    }
 }

src/main/java/org/breedinginsight/brapps/importer/model/workflow/ProcessedData.java

@@ -28,9 +28,5 @@
 @ToString
 @NoArgsConstructor
 public class ProcessedData {
-    // TODO: remove this, already in ImportPreviewResponse
-    //private Map<String, ImportPreviewStatistics> statistics;
-    // TODO
     private Map<Integer, PendingImport> mappedBrAPIImport;
-    private ImportPreviewResponse importPreviewResponse;
 }

src/main/java/org/breedinginsight/brapps/importer/model/workflow/Workflow.java

@@ -24,6 +24,7 @@
 import java.util.List;
 import java.util.Optional;
 
+
 /**
  * This Functional Interface represents a Workflow that can be executed as part of an import process.
  * It extends the Ordered interface to allow workflows to be ordered in a sequence.

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

@@ -420,14 +420,14 @@ public ImportUpload setDynamicColumns(ImportUpload newUpload, Table data, Import
         return newUpload;
     }
 
-    private void processFile(String workflow, List<BrAPIImport> finalBrAPIImportList, Table data, Program program,
+    private void processFile(String workflowId, List<BrAPIImport> finalBrAPIImportList, Table data, Program program,
                              ImportUpload upload, User user, Boolean commit, BrAPIImportService importService,
                              AuthenticatedUser actingUser) {
         // Spin off new process for processing the file
         CompletableFuture.supplyAsync(() -> {
             try {
                 ImportServiceContext context = ImportServiceContext.builder()
-                        .workflow(workflow)
+                        .workflowId(workflowId)
                         .brAPIImports(finalBrAPIImportList)
                         .data(data)
                         .program(program)
@@ -580,6 +580,7 @@ public List<ImportMapping> getSystemMappingByName(String name) {
      */
     public List<ImportWorkflow> getWorkflowsForSystemMapping(UUID mappingId) throws DoesNotExistException {
         // Retrieve the import mapping configuration based on the provided mapping ID
+
         ImportMapping mappingConfig = importMappingDAO.getMapping(mappingId)
                 .orElseThrow(() -> new DoesNotExistException("Cannot find mapping config associated with upload."));
 

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

@@ -32,13 +32,7 @@
 @Singleton
 public class FileMappingUtil {
 
-    public static final String EXPERIMENT_TEMPLATE_NAME = "ExperimentsTemplateMap";
-    private FileImportService fileImportService;
-
-
-    @Inject
-    public FileMappingUtil(FileImportService fileImportService) {
-        this.fileImportService = fileImportService;
+    public FileMappingUtil() {
     }
 
     // Returns a list of integers to identify the target row of the relationship. -1 if no relationship was found

src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/ExperimentWorkflowNavigator.java

@@ -96,6 +96,7 @@ public enum Workflow {
          */
         NEW_OBSERVATION("new-experiment","Create new experiment"),
 
+
         /**
          * Represents an append or overwrite workflow where experimental dataset is appended.
          * ID: "append-dataset"

src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/appendoverwrite/AppendOverwritePhenotypesWorkflow.java

@@ -92,7 +92,7 @@ public Optional<ImportWorkflowResult> process(ImportServiceContext context) {
                 .build());
 
         // Skip this workflow unless appending or overwriting observation data
-        if (context != null && !this.workflow.isEqual(context.getWorkflow())) {
+        if (context != null && !this.workflow.isEqual(context.getWorkflowId())) {
             return Optional.empty();
         }
 

src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/create/model/ProcessedPhenotypeData.java

@@ -23,7 +23,8 @@
 import java.util.List;
 import java.util.Map;
 
-// TODO: move to common higher level location
+// TODO: move to common higher level location, could be used by both append and create workflows so being located
+// in the create namespace won't make sense if we decide to do that in the future.
 @Getter
 @Setter
 @Builder