BI-2115 - Experiment Import Workflows Refactor

src/main/java/org/breedinginsight/api/model/v1/response/ValidationErrors.java

@@ -17,6 +17,7 @@
 
 package org.breedinginsight.api.model.v1.response;
 
+import io.micronaut.http.HttpStatus;
 import lombok.*;
 import lombok.experimental.Accessors;
 
@@ -46,7 +47,6 @@ public void addError(Integer rowNumber, ValidationError validationError){
         newRow.addError(validationError);
         rowErrors.add(newRow);
     }
-
     public void merge(ValidationErrors validationErrors){
         for (RowValidationErrors rowValidationErrors: validationErrors.getRowErrors()){
             for (ValidationError validationError: rowValidationErrors.getErrors()) {

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.ImportMappingWorkflow;
 import org.breedinginsight.brapps.importer.services.ImportConfigManager;
 import org.breedinginsight.brapps.importer.model.config.ImportConfigResponse;
 import org.breedinginsight.brapps.importer.services.FileImportService;
@@ -208,4 +209,21 @@ 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<ImportMappingWorkflow>>> getWorkflowsForSystemMapping(@PathVariable UUID mappingId) {
+
+        List<ImportMappingWorkflow> workflows = fileImportService.getWorkflowsForSystemMapping(mappingId);
+
+        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<ImportMappingWorkflow>> 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 UUID 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 UUID 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/daos/ImportMappingWorkflowDAO.java

@@ -0,0 +1,68 @@
+/*
+ * 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.daos;
+
+import org.breedinginsight.brapps.importer.model.workflow.ImportMappingWorkflow;
+import org.breedinginsight.dao.db.tables.daos.ImporterMappingWorkflowDao;
+import org.jooq.Configuration;
+import org.jooq.DSLContext;
+
+import javax.inject.Inject;
+import java.util.List;
+import java.util.Optional;
+import java.util.UUID;
+
+import static org.breedinginsight.dao.db.Tables.*;
+
+public class ImportMappingWorkflowDAO extends ImporterMappingWorkflowDao {
+
+    private DSLContext dsl;
+
+    @Inject
+    public ImportMappingWorkflowDAO(Configuration config, DSLContext dsl) {
+        super(config);
+        this.dsl = dsl;
+    }
+
+    /**
+     * Retrieves a list of ImportMappingWorkflow objects associated with the given mappingId. They are ordered by
+     * position for proper ordering on the front end.
+     *
+     * @param mappingId The UUID of the mapping to retrieve the workflows for.
+     * @return A list of ImportMappingWorkflow objects.
+     */
+    public List<ImportMappingWorkflow> getWorkflowsByImportMappingId(UUID mappingId) {
+        return dsl.select()
+                .from(IMPORTER_MAPPING_WORKFLOW)
+                .where(IMPORTER_MAPPING_WORKFLOW.MAPPING_ID.eq(mappingId))
+                .orderBy(IMPORTER_MAPPING_WORKFLOW.POSITION.asc())
+                .fetch(ImportMappingWorkflow::parseSQLRecord);
+    }
+
+    /**
+     * Retrieves a workflow by its ID.
+     *
+     * @param workflowId The ID of the workflow to retrieve.
+     * @return An Optional containing the ImportMappingWorkflow if found, otherwise an empty Optional.
+     */
+    public Optional<ImportMappingWorkflow> getWorkflowById(UUID workflowId) {
+        return Optional.ofNullable(fetchOneById(workflowId))
+                .map(ImportMappingWorkflow::new);
+    }
+
+}

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

@@ -17,18 +17,7 @@
 
 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 java.util.List;
 
 public interface BrAPIImportService {
     String getImportTypeId();
@@ -48,6 +37,6 @@ 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/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.brapps.importer.model.workflow.Workflow;
+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 Workflow workflow;
+    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

@@ -21,6 +21,7 @@
 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.services.processors.ExperimentProcessor;
 import org.breedinginsight.brapps.importer.services.processors.Processor;
@@ -66,12 +67,24 @@ public String getMissingColumnMsg(String columnName) {
     }
 
     @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(experimentProcessorProvider.get());
-        response = processorManagerProvider.get().process(brAPIImports, processors, data, program, upload, user, commit);
+
+        if (context.getWorkflow() != null) {
+            log.info("Workflow: " + context.getWorkflow().getName());
+        }
+
+        // TODO: change to calling workflow process instead of processor manager
+        response = processorManagerProvider.get().process(context.getBrAPIImports(),
+                processors,
+                context.getData(),
+                context.getProgram(),
+                context.getUpload(),
+                context.getUser(),
+                context.isCommit());
         return response;
 
     }

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

@@ -21,6 +21,7 @@
 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.services.processors.GermplasmProcessor;
 import org.breedinginsight.brapps.importer.services.processors.Processor;
@@ -62,12 +63,18 @@ public String getImportTypeId() {
     }
 
     @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;
     }
 }

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

@@ -21,6 +21,7 @@
 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.services.processors.Processor;
 import org.breedinginsight.brapps.importer.services.processors.ProcessorManager;
@@ -59,13 +60,14 @@ public BrAPIImport getImportClass() {
     }
 
     @Override
-    public ImportPreviewResponse process(List<BrAPIImport> brAPIImports,
-                                         Table data,
-                                         Program program,
-                                         ImportUpload upload,
-                                         User user,
-                                         Boolean commit) throws Exception {
+    public ImportPreviewResponse process(ImportServiceContext context) throws Exception {
         List<Processor> processors = List.of(sampleProcessorProvider.get());
-        return processorManagerProvider.get().process(brAPIImports, processors, data, program, upload, user, commit);
+        return processorManagerProvider.get().process(context.getBrAPIImports(),
+                processors,
+                context.getData(),
+                context.getProgram(),
+                context.getUpload(),
+                context.getUser(),
+                context.isCommit());
     }
 }

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

@@ -0,0 +1,47 @@
+/*
+ * 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.workflow;
+
+import lombok.*;
+import org.breedinginsight.brapps.importer.model.ImportUpload;
+import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
+import org.breedinginsight.brapps.importer.model.imports.PendingImport;
+import org.breedinginsight.model.Program;
+import org.breedinginsight.model.User;
+import tech.tablesaw.api.Table;
+
+import java.util.List;
+import java.util.Map;
+import java.util.UUID;
+
+@Getter
+@Setter
+@Builder
+@ToString
+@AllArgsConstructor
+@NoArgsConstructor
+public class ImportContext {
+    private UUID workflowId;
+    private ImportUpload upload;
+    private List<BrAPIImport> importRows;
+    private Map<Integer, PendingImport> mappedBrAPIImport;
+    private Table data;
+    private Program program;
+    private User user;
+    private boolean commit;
+}