BI-2132 - Create new experiment workflow

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

@@ -37,6 +37,7 @@
 import org.breedinginsight.api.model.v1.response.metadata.StatusCode;
 import org.breedinginsight.api.v1.controller.metadata.AddMetadata;
 import org.breedinginsight.brapps.importer.model.mapping.ImportMapping;
+import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflow;
 import org.breedinginsight.brapps.importer.services.ImportConfigManager;
 import org.breedinginsight.brapps.importer.model.config.ImportConfigResponse;
 import org.breedinginsight.brapps.importer.services.FileImportService;
@@ -208,4 +209,27 @@ public HttpResponse<Response<DataResponse<ImportMapping>>> getSystemMappings(@Nu
         Response<DataResponse<ImportMapping>> response = new Response(metadata, new DataResponse<>(result));
         return HttpResponse.ok(response);
     }
+
+    @Get("/import/mappings/{mappingId}/workflows")
+    @Produces(MediaType.APPLICATION_JSON)
+    @AddMetadata
+    @Secured(SecurityRule.IS_ANONYMOUS)
+    public HttpResponse<Response<DataResponse<ImportWorkflow>>> getWorkflowsForSystemMapping(@PathVariable UUID mappingId) throws Exception {
+
+        List<ImportWorkflow> workflows = null;
+        try {
+            workflows = fileImportService.getWorkflowsForSystemMapping(mappingId);
+        } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        }
+
+        List<Status> metadataStatus = new ArrayList<>();
+        metadataStatus.add(new Status(StatusCode.INFO, "Successful Query"));
+        Pagination pagination = new Pagination(workflows.size(), workflows.size(), 1, 0);
+        Metadata metadata = new Metadata(pagination, metadataStatus);
+
+        Response<DataResponse<ImportWorkflow>> response = new Response(metadata, new DataResponse<>(workflows));
+        return HttpResponse.ok(response);
+    }
 }

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

@@ -114,7 +114,7 @@ public HttpResponse<Response<ImportResponse>> commitData(@PathVariable UUID prog
                                                              @PathVariable UUID uploadId, @Body @Nullable Map<String, Object> userInput) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
-            ImportResponse result = fileImportService.updateUpload(programId, uploadId, actingUser, userInput, true);
+            ImportResponse result = fileImportService.updateUpload(programId, uploadId, null, actingUser, userInput, true);
             Response<ImportResponse> response = new Response(result);
             return HttpResponse.ok(response).status(HttpStatus.ACCEPTED);
         } catch (DoesNotExistException e) {
@@ -140,7 +140,60 @@ public HttpResponse<Response<ImportResponse>> previewData(@PathVariable UUID pro
                                                               @PathVariable UUID uploadId) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
-            ImportResponse result = fileImportService.updateUpload(programId, uploadId, actingUser, null, false);
+            ImportResponse result = fileImportService.updateUpload(programId, uploadId, null, actingUser, null, false);
+            Response<ImportResponse> response = new Response(result);
+            return HttpResponse.ok(response).status(HttpStatus.ACCEPTED);
+        } catch (DoesNotExistException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.notFound();
+        } catch (AuthorizationException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.FORBIDDEN, e.getMessage());
+        } catch (UnprocessableEntityException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        } catch (HttpStatusException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(e.getStatus(), e.getMessage());
+        }
+    }
+
+    @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 workflowId, @PathVariable UUID uploadId) {
+        try {
+            AuthenticatedUser actingUser = securityService.getUser();
+            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);
+            return HttpResponse.notFound();
+        } catch (AuthorizationException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.FORBIDDEN, e.getMessage());
+        } catch (UnprocessableEntityException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(HttpStatus.UNPROCESSABLE_ENTITY, e.getMessage());
+        } catch (HttpStatusException e) {
+            log.error(e.getMessage(), e);
+            return HttpResponse.status(e.getStatus(), e.getMessage());
+        }
+    }
+
+    @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 workflowId, @PathVariable UUID uploadId,
+                                                             @Body @Nullable Map<String, Object> userInput) {
+        try {
+            AuthenticatedUser actingUser = securityService.getUser();
+            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) {

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

@@ -17,22 +17,15 @@
 
 package org.breedinginsight.brapps.importer.model.imports;
 
-import org.brapi.client.v2.model.exceptions.ApiException;
-import org.breedinginsight.brapps.importer.model.ImportUpload;
 import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
-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 org.breedinginsight.brapps.importer.model.workflow.ImportWorkflow;
 
 import java.util.List;
 
 public interface BrAPIImportService {
     String getImportTypeId();
     BrAPIImport getImportClass();
+    List<ImportWorkflow> getWorkflows() throws Exception;
     default String getInvalidIntegerMsg(String columnName) {
         return String.format("Column name \"%s\" must be integer type, but non-integer type provided.", columnName);
     }
@@ -48,6 +41,6 @@ default String getMissingUserInputMsg(String fieldName) {
     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)
+    ImportPreviewResponse process(ImportServiceContext context)
             throws Exception;
 }

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

@@ -0,0 +1,96 @@
+/*
+ * 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.extern.slf4j.Slf4j;
+import org.breedinginsight.brapps.importer.model.imports.experimentObservation.ExperimentObservation;
+import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
+import org.breedinginsight.brapps.importer.model.workflow.ExperimentWorkflow;
+import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflow;
+import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflowResult;
+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 javax.inject.Inject;
+import javax.inject.Provider;
+import javax.inject.Singleton;
+import java.util.List;
+import java.util.Optional;
+
+@Singleton
+@Slf4j
+public abstract class DomainImportService implements BrAPIImportService {
+
+    // TODO: delete processor fields once WorkflowNavigator is used
+    private final Provider<ExperimentProcessor> experimentProcessorProvider;
+    private final Provider<ProcessorManager> processorManagerProvider;
+    private final Workflow workflowNavigator;
+
+
+    public DomainImportService(Provider<ExperimentProcessor> experimentProcessorProvider,
+                               Provider<ProcessorManager> processorManagerProvider,
+                               Workflow workflowNavigator)
+    {
+        this.experimentProcessorProvider = experimentProcessorProvider;
+        this.processorManagerProvider = processorManagerProvider;
+        this.workflowNavigator = workflowNavigator;
+    }
+
+    @Override
+    public String getMissingColumnMsg(String columnName) {
+        return "Column heading does not match template or ontology";
+    }
+    @Override
+    public List<ImportWorkflow> getWorkflows() throws Exception{
+        return workflowNavigator.getWorkflows();
+    }
+
+    @Override
+    public ImportPreviewResponse process(ImportServiceContext context)
+            throws Exception {
+
+        Optional.ofNullable(context.getWorkflowId())
+                .filter(workflowId -> !workflowId.isEmpty())
+                .ifPresent(workflowId -> log.info("Workflow: " + workflowId));
+
+        // 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())) {
+            Optional<ImportWorkflowResult> result = workflowNavigator.process(context);
+
+            // Throw any exceptions caught during workflow processing
+            if (result.flatMap(ImportWorkflowResult::getCaughtException).isPresent()) {
+                throw result.flatMap(ImportWorkflowResult::getCaughtException).get();
+            }
+
+            return result.flatMap(ImportWorkflowResult::getImportPreviewResponse).orElse(null);
+
+        } else {
+            return processorManagerProvider.get().process(context.getBrAPIImports(),
+                    List.of(experimentProcessorProvider.get()),
+                    context.getData(),
+                    context.getProgram(),
+                    context.getUpload(),
+                    context.getUser(),
+                    context.isCommit());
+        }
+    }
+}
+

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

@@ -0,0 +1,42 @@
+/*
+ * 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.*;
+import org.breedinginsight.brapps.importer.model.ImportUpload;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.model.User;
+import tech.tablesaw.api.Table;
+
+import java.util.List;
+
+@Getter
+@Setter
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+public class ImportServiceContext {
+    private String workflowId;
+    private List<BrAPIImport> brAPIImports;
+    private Table data;
+    private Program program;
+    private ImportUpload upload;
+    private User user;
+    private boolean commit;
+}

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

@@ -18,36 +18,28 @@
 package org.breedinginsight.brapps.importer.model.imports.experimentObservation;
 
 import lombok.extern.slf4j.Slf4j;
-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.model.imports.DomainImportService;
 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 tech.tablesaw.api.Table;
+import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentWorkflowNavigator;
 
 import javax.inject.Inject;
 import javax.inject.Provider;
 import javax.inject.Singleton;
-import java.util.List;
 
 @Singleton
 @Slf4j
-public class ExperimentImportService implements BrAPIImportService {
+public class ExperimentImportService extends DomainImportService {
 
     private final String IMPORT_TYPE_ID = "ExperimentImport";
 
-    private final Provider<ExperimentProcessor> experimentProcessorProvider;
-    private final Provider<ProcessorManager> processorManagerProvider;
-
+    // TODO: delete processor fields once WorkflowNavigator is used
     @Inject
-    public ExperimentImportService(Provider<ExperimentProcessor> experimentProcessorProvider, Provider<ProcessorManager> processorManagerProvider)
+    public ExperimentImportService(Provider<ExperimentProcessor> experimentProcessorProvider,
+                                   Provider<ProcessorManager> processorManagerProvider,
+                                   ExperimentWorkflowNavigator workflowNavigator)
     {
-        this.experimentProcessorProvider = experimentProcessorProvider;
-        this.processorManagerProvider = processorManagerProvider;
+        super(experimentProcessorProvider, processorManagerProvider, workflowNavigator);
     }
 
     @Override
@@ -60,20 +52,5 @@ public String getImportTypeId() {
         return IMPORT_TYPE_ID;
     }
 
-    @Override
-    public String getMissingColumnMsg(String columnName) {
-        return "Column heading does not match template or ontology";
-    }
-
-    @Override
-    public ImportPreviewResponse process(List<BrAPIImport> brAPIImports, Table data, Program program, ImportUpload upload, User user, Boolean commit)
-            throws Exception {
-
-        ImportPreviewResponse response = null;
-        List<Processor> processors = List.of(experimentProcessorProvider.get());
-        response = processorManagerProvider.get().process(brAPIImports, processors, data, program, upload, user, commit);
-        return response;
-
-    }
 }
 

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

@@ -21,7 +21,9 @@
 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.ImportServiceContext;
 import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
+import org.breedinginsight.brapps.importer.model.workflow.ImportWorkflow;
 import org.breedinginsight.brapps.importer.services.processors.GermplasmProcessor;
 import org.breedinginsight.brapps.importer.services.processors.Processor;
 import org.breedinginsight.brapps.importer.services.processors.ProcessorManager;
@@ -32,6 +34,7 @@
 import javax.inject.Inject;
 import javax.inject.Provider;
 import javax.inject.Singleton;
+import java.util.ArrayList;
 import java.util.List;
 
 @Singleton
@@ -56,18 +59,29 @@ public GermplasmImport getImportClass() {
         return new GermplasmImport();
     }
 
+    @Override
+    public List<ImportWorkflow> getWorkflows() {
+        return new ArrayList<>();
+    }
+
     @Override
     public String getImportTypeId() {
         return IMPORT_TYPE_ID;
     }
 
     @Override
-    public ImportPreviewResponse process(List<BrAPIImport> brAPIImports, Table data, Program program, ImportUpload upload, User user, Boolean commit)
+    public ImportPreviewResponse process(ImportServiceContext context)
             throws Exception {
 
         ImportPreviewResponse response = null;
         List<Processor> processors = List.of(germplasmProcessorProvider.get());
-        response = processorManagerProvider.get().process(brAPIImports, processors, data, program, upload, user, commit);
+        response = processorManagerProvider.get().process(context.getBrAPIImports(),
+                processors,
+                context.getData(),
+                context.getProgram(),
+                context.getUpload(),
+                context.getUser(),
+                context.isCommit());
         return response;
     }
 }