Feature/bi 2132 a di

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

@@ -26,7 +26,7 @@
 import org.breedinginsight.brapps.importer.model.workflow.Workflow;
 import org.breedinginsight.brapps.importer.services.processors.ExperimentProcessor;
 import org.breedinginsight.brapps.importer.services.processors.ProcessorManager;
-import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentWorkflowNavigator;
+import org.breedinginsight.brapps.importer.services.processors.experiment.WorkflowEnum;
 
 import javax.inject.Inject;
 import javax.inject.Provider;
@@ -43,7 +43,7 @@ public abstract class DomainImportService implements BrAPIImportService {
     private final Provider<ProcessorManager> processorManagerProvider;
     private final Workflow workflowNavigator;
 
-
+    @Inject
     public DomainImportService(Provider<ExperimentProcessor> experimentProcessorProvider,
                                Provider<ProcessorManager> processorManagerProvider,
                                Workflow workflowNavigator)
@@ -72,7 +72,7 @@ public ImportPreviewResponse process(ImportServiceContext context)
 
         // TODO: return results from WorkflowNavigator once processing logic is in separate workflows
         // return workflowNavigator.process(context).flatMap(ImportWorkflowResult::getImportPreviewResponse).orElse(null);
-        if (ExperimentWorkflowNavigator.Workflow.NEW_OBSERVATION.getId().equals(context.getWorkflowId())) {
+        if (WorkflowEnum.NEW_OBSERVATION.getId().equals(context.getWorkflowId())) {
             Optional<ImportWorkflowResult> result = workflowNavigator.process(context);
 
             // Throw any exceptions caught during workflow processing

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

@@ -6,6 +6,7 @@
 import org.breedinginsight.brapps.importer.model.workflow.ExperimentWorkflow;
 import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflowResult;
 
+import javax.inject.Inject;
 import javax.inject.Singleton;
 import java.util.List;
 import java.util.Optional;
@@ -16,6 +17,7 @@
 public class ExperimentWorkflowNavigator implements ExperimentWorkflow {
     private final List<ExperimentWorkflow> workflows;
 
+    @Inject
     public ExperimentWorkflowNavigator(List<ExperimentWorkflow> workflows) {
         this.workflows = workflows;
     }
@@ -61,27 +63,4 @@ public List<ImportWorkflow> getWorkflows() {
 
         return workflowSummaryList; // Return the list of workflow metadata
     }
-
-    public enum Workflow {
-        NEW_OBSERVATION("new-experiment","Create new experiment"),
-        APPEND_OVERWRITE("append-dataset", "Append experimental dataset");
-
-        private String id;
-        private String name;
-
-        Workflow(String id, String name) {
-
-            this.id = id;
-            this.name = name;
-        }
-
-        public String getId() {
-            return id;
-        }
-        public String getName() { return name; }
-
-        public boolean isEqual(String value) {
-            return Optional.ofNullable(id.equals(value)).orElse(false);
-        }
-    }
 }

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

@@ -0,0 +1,26 @@
+package org.breedinginsight.brapps.importer.services.processors.experiment;
+
+import java.util.Optional;
+
+public enum WorkflowEnum {
+    NEW_OBSERVATION("new-experiment","Create new experiment"),
+    APPEND_OVERWRITE("append-dataset", "Append experimental dataset");
+
+    private String id;
+    private String name;
+
+    WorkflowEnum(String id, String name) {
+
+        this.id = id;
+        this.name = name;
+    }
+
+    public String getId() {
+        return id;
+    }
+    public String getName() { return name; }
+
+    public boolean isEqual(String value) {
+        return Optional.ofNullable(id.equals(value)).orElse(false);
+    }
+}

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

@@ -5,18 +5,18 @@
 import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflow;
 import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflowResult;
 import org.breedinginsight.brapps.importer.model.workflow.ExperimentWorkflow;
-import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentWorkflowNavigator;
+import org.breedinginsight.brapps.importer.services.processors.experiment.WorkflowEnum;
 
 import javax.inject.Singleton;
 import java.util.Optional;
 
 @Getter
 @Singleton
 public class AppendOverwritePhenotypesWorkflow implements ExperimentWorkflow {
-    private final ExperimentWorkflowNavigator.Workflow workflow;
+    private final WorkflowEnum workflow;
 
     public AppendOverwritePhenotypesWorkflow(){
-        this.workflow = ExperimentWorkflowNavigator.Workflow.APPEND_OVERWRITE;
+        this.workflow = WorkflowEnum.APPEND_OVERWRITE;
     }
 
     public Optional<ImportWorkflowResult> process(ImportServiceContext context) {

src/main/java/org/breedinginsight/brapps/importer/services/processors/experiment/create/workflow/CreateNewExperimentWorkflow.java

@@ -17,11 +17,9 @@
 
 package org.breedinginsight.brapps.importer.services.processors.experiment.create.workflow;
 
-import io.micronaut.context.annotation.Prototype;
 import io.micronaut.http.HttpStatus;
 import io.micronaut.http.exceptions.HttpStatusException;
 import lombok.extern.slf4j.Slf4j;
-import lombok.val;
 import org.apache.commons.lang3.StringUtils;
 import org.brapi.v2.model.pheno.BrAPIObservation;
 import org.breedinginsight.api.model.v1.response.ValidationErrors;
@@ -35,9 +33,9 @@
 import org.breedinginsight.brapps.importer.model.response.PendingImportObject;
 import org.breedinginsight.brapps.importer.model.workflow.ImportContext;
 import org.breedinginsight.brapps.importer.model.workflow.ProcessedData;
-import org.breedinginsight.brapps.importer.model.workflow.Workflow;
 import org.breedinginsight.brapps.importer.services.ImportStatusService;
 import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentUtilities;
+import org.breedinginsight.brapps.importer.services.processors.experiment.WorkflowEnum;
 import org.breedinginsight.brapps.importer.services.processors.experiment.create.model.PendingData;
 import org.breedinginsight.brapps.importer.services.processors.experiment.create.model.ProcessContext;
 import org.breedinginsight.brapps.importer.services.processors.experiment.create.model.ProcessedPhenotypeData;
@@ -49,7 +47,6 @@
 import org.breedinginsight.services.exceptions.ValidatorException;
 
 import javax.inject.Inject;
-import javax.inject.Named;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -60,7 +57,6 @@
 import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflow;
 import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflowResult;
 import org.breedinginsight.brapps.importer.model.workflow.ExperimentWorkflow;
-import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentWorkflowNavigator;
 
 import javax.inject.Singleton;
 import java.util.Optional;
@@ -69,32 +65,33 @@
 @Getter
 @Singleton
 public class CreateNewExperimentWorkflow implements ExperimentWorkflow {
-    private final ExperimentWorkflowNavigator.Workflow workflow;
+    private final WorkflowEnum workflow;
     private final PopulateExistingPendingImportObjectsStep populateExistingPendingImportObjectsStep;
     private final PopulateNewPendingImportObjectsStep populateNewPendingImportObjectsStep;
-    private final CommitPendingImportObjectsStep commitPendingImportObjectsStep;
+    private final CommitPendingImportObjectsStep commitPendingImportObjectsStep;  // BAD
     private final ValidatePendingImportObjectsStep validatePendingImportObjectsStep;
     private final ImportStatusService statusService;
-    private final ExperimentPhenotypeService experimentPhenotypeService;
+    private final ExperimentPhenotypeService experimentPhenotypeService;  // BAD
 
     @Inject
-    public CreateNewExperimentWorkflow(PopulateExistingPendingImportObjectsStep populateExistingPendingImportObjectsStep,
+    public CreateNewExperimentWorkflow(
+            PopulateExistingPendingImportObjectsStep populateExistingPendingImportObjectsStep,
                                        PopulateNewPendingImportObjectsStep populateNewPendingImportObjectsStep,
                                        CommitPendingImportObjectsStep commitPendingImportObjectsStep,
                                        ValidatePendingImportObjectsStep validatePendingImportObjectsStep,
                                        ImportStatusService statusService,
-                                       ExperimentPhenotypeService experimentPhenotypeService) {
+                                       ExperimentPhenotypeService experimentPhenotypeService
+    ) {
         this.populateExistingPendingImportObjectsStep = populateExistingPendingImportObjectsStep;
         this.populateNewPendingImportObjectsStep = populateNewPendingImportObjectsStep;
         this.commitPendingImportObjectsStep = commitPendingImportObjectsStep;
         this.validatePendingImportObjectsStep = validatePendingImportObjectsStep;
         this.statusService = statusService;
         this.experimentPhenotypeService = experimentPhenotypeService;
-        this.workflow = ExperimentWorkflowNavigator.Workflow.NEW_OBSERVATION;
+        this.workflow = WorkflowEnum.NEW_OBSERVATION;
     }
 
     private ImportPreviewResponse runWorkflow(ImportContext context) throws Exception {
-
         ImportUpload upload = context.getUpload();
         boolean commit = context.isCommit();
         List<BrAPIImport> importRows = context.getImportRows();