Breeding-Insight · dmeidlin · Jul 11, 2024 · Apr 26, 2024 · Apr 29, 2024 · Apr 29, 2024
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -59,4 +59,4 @@ jobs:
           JWT_SECRET: ${{ secrets.JWT_SECRET }}
           OAUTH_CLIENT_ID: 123abc
           OAUTH_CLIENT_SECRET: asdfljkhalkbaldsfjasdfi238497098asdf
-          BRAPI_REFERENCE_SOURCE: breedinginsight.org
+          BRAPI_REFERENCE_SOURCE: breedinginsight.org
diff --git a/src/main/java/org/breedinginsight/api/model/v1/response/ValidationErrors.java b/src/main/java/org/breedinginsight/api/model/v1/response/ValidationErrors.java
@@ -17,7 +17,9 @@
 
 package org.breedinginsight.api.model.v1.response;
 
-import lombok.*;
+import lombok.Getter;
+import lombok.Setter;
+import lombok.ToString;
 import lombok.experimental.Accessors;
 
 import java.util.ArrayList;

diff --git a/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java b/src/main/java/org/breedinginsight/brapi/v2/dao/BrAPIObservationDAO.java
@@ -183,6 +183,27 @@ public List<BrAPIObservation> getObservationsByStudyName(List<String> studyNames
         );
     }
 
+    /**
+     * Retrieves a list of observations based on their database IDs and a specific program.
+     *
+     * @param dbIds A list of database IDs representing the observations to retrieve.
+     * @param program The Program object for which the observations belong.
+     * @return A List of BrAPIObservation objects filtered by the provided database IDs.
+     * @throws ApiException if an error occurs during the retrieval process.
+     */
+    public List<BrAPIObservation> getObservationsByDbIds(List<String> dbIds, Program program) throws ApiException {
+        // Check if the dbIds list is empty and return an empty list if so
+        if(dbIds.isEmpty()) {
+            return Collections.emptyList();
+        }
+
+        // Filter the observations based on the provided program ID and the provided list of dbIds
+        // Collect the filtered observations into a List and return the result
+        return getProgramObservations(program.getId()).values().stream()
+                .filter(o -> dbIds.contains(o.getObservationDbId()))
+                .collect(Collectors.toList());
+    }
+
     public List<BrAPIObservation> getObservationsByTrialDbId(List<String> trialDbIds, Program program) throws ApiException {
         if(trialDbIds.isEmpty()) {
             return Collections.emptyList();

diff --git a/src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java b/src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java
@@ -588,8 +588,8 @@ private void addObsVarDataToRow(
             Trait var,
             Program program) {
         String varName = Utilities.removeProgramKey(obs.getObservationVariableName(), program.getKey());
-        if (!(obs.getValue().equalsIgnoreCase("NA")) && (var.getScale().getDataType().equals(DataType.NUMERICAL) ||
-                var.getScale().getDataType().equals(DataType.DURATION))) {
+        if (!("NA".equalsIgnoreCase(obs.getValue())) && (DataType.NUMERICAL.equals(var.getScale().getDataType()) ||
+                DataType.DURATION.equals(var.getScale().getDataType()))) {
             row.put(varName, Double.parseDouble(obs.getValue()));
         } else {
             row.put(varName, obs.getValue());

diff --git a/src/main/java/org/breedinginsight/brapps/importer/controllers/ImportController.java b/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;
@@ -76,7 +77,7 @@ public HttpResponse<Response<DataResponse<ImportConfigResponse>>> getImportTypes
         Pagination pagination = new Pagination(configs.size(), 1, 1, 0);
         Metadata metadata = new Metadata(pagination, metadataStatus);
 
-        Response<DataResponse<ImportConfigResponse>> response = new Response(metadata, new DataResponse<>(configs));
+        Response<DataResponse<ImportConfigResponse>> response = new Response<>(metadata, new DataResponse<>(configs));
         return HttpResponse.ok(response);
     }
 
@@ -95,7 +96,7 @@ public HttpResponse<Response<DataResponse<ImportMapping>>> getMappings(@PathVari
             Pagination pagination = new Pagination(result.size(), 1, 1, 0);
             Metadata metadata = new Metadata(pagination, metadataStatus);
 
-            Response<DataResponse<ImportMapping>> response = new Response(metadata, new DataResponse<>(result));
+            Response<DataResponse<ImportMapping>> response = new Response<>(metadata, new DataResponse<>(result));
             return HttpResponse.ok(response);
         } catch (DoesNotExistException e) {
             log.info(e.getMessage());
@@ -116,7 +117,7 @@ public HttpResponse<Response<ImportMapping>> createMapping(@PathVariable UUID pr
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             ImportMapping result = fileImportService.createMapping(programId, actingUser, file);
-            Response<ImportMapping> response = new Response(result);
+            Response<ImportMapping> response = new Response<>(result);
             return HttpResponse.ok(response);
         } catch (DoesNotExistException e) {
             log.info(e.getMessage());
@@ -140,7 +141,7 @@ public HttpResponse<Response<ImportMapping>> editMappingFile(@PathVariable UUID
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             ImportMapping result = fileImportService.updateMappingFile(programId, mappingId, actingUser, file);
-            Response<ImportMapping> response = new Response(result);
+            Response<ImportMapping> response = new Response<>(result);
             return HttpResponse.ok(response);
         } catch (DoesNotExistException e) {
             log.info(e.getMessage());
@@ -165,7 +166,7 @@ public HttpResponse<Response<ImportMapping>> editMapping(@PathVariable UUID prog
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             ImportMapping result = fileImportService.updateMapping(programId, actingUser, mappingId, mapping, validate);
-            Response<ImportMapping> response = new Response(result);
+            Response<ImportMapping> response = new Response<>(result);
             return HttpResponse.ok(response);
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);
@@ -205,7 +206,30 @@ public HttpResponse<Response<DataResponse<ImportMapping>>> getSystemMappings(@Nu
         Pagination pagination = new Pagination(result.size(), result.size(), 1, 0);
         Metadata metadata = new Metadata(pagination, metadataStatus);
 
-        Response<DataResponse<ImportMapping>> response = new Response(metadata, new DataResponse<>(result));
+        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) {
+
+        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);
     }
 }
diff --git a/src/main/java/org/breedinginsight/brapps/importer/controllers/UploadController.java b/src/main/java/org/breedinginsight/brapps/importer/controllers/UploadController.java
@@ -62,7 +62,7 @@ public HttpResponse<Response<ImportResponse>> uploadData(@PathVariable UUID prog
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             ImportResponse result = fileImportService.uploadData(programId, mappingId, actingUser, file);
-            Response<ImportResponse> response = new Response(result);
+            Response<ImportResponse> response = new Response<>(result);
             return HttpResponse.ok(response);
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);
@@ -94,7 +94,7 @@ public HttpResponse<Response<ImportResponse>> getUploadData(@PathVariable UUID p
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             Pair<HttpStatus, ImportResponse> result = fileImportService.getDataUpload(uploadId, mapping);
-            Response<ImportResponse> response = new Response(result.getRight());
+            Response<ImportResponse> response = new Response<>(result.getRight());
             if (result.getLeft().equals(HttpStatus.ACCEPTED)) {
                 return HttpResponse.ok(response).status(result.getLeft());
             } else {
@@ -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) {
@@ -140,8 +140,61 @@ 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);
-            Response<ImportResponse> response = new Response(result);
+            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/{workflow}/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) {
+        try {
+            AuthenticatedUser actingUser = securityService.getUser();
+            ImportResponse result = fileImportService.updateUpload(programId, uploadId, workflow, 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/{workflow}/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,
+                                                             @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);
             return HttpResponse.ok(response).status(HttpStatus.ACCEPTED);
         } catch (DoesNotExistException e) {
             log.error(e.getMessage(), e);

diff --git a/src/main/java/org/breedinginsight/brapps/importer/model/imports/BrAPIImportService.java b/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();
     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;
 }
diff --git a/src/main/java/org/breedinginsight/brapps/importer/model/imports/DomainImportService.java b/src/main/java/org/breedinginsight/brapps/importer/model/imports/DomainImportService.java
@@ -0,0 +1,69 @@
+/*
+ * 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.response.ImportPreviewResponse;
+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 javax.inject.Singleton;
+import java.util.List;
+import java.util.Optional;
+
+@Singleton
+@Slf4j
+public abstract class DomainImportService implements BrAPIImportService {
+    private final Workflow workflowNavigator;
+
+
+    public DomainImportService(Workflow workflowNavigator)
+    {
+        this.workflowNavigator = workflowNavigator;
+    }
+
+    @Override
+    public String getMissingColumnMsg(String columnName) {
+        return "Column heading does not match template or ontology";
+    }
+    @Override
+    public List<ImportWorkflow> getWorkflows() {
+        return workflowNavigator.getWorkflows();
+    }
+
+    @Override
+    public ImportPreviewResponse process(ImportServiceContext context)
+            throws Exception {
+
+        Optional.ofNullable(context.getWorkflow())
+                .filter(workflow -> !workflow.isEmpty())
+                .ifPresent(workflow -> log.info("Workflow: " + workflow));
+
+
+            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);
+    }
+}
+
diff --git a/src/main/java/org/breedinginsight/brapps/importer/model/imports/ImportServiceContext.java b/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 workflow;
+    private List<BrAPIImport> brAPIImports;
+    private Table data;
+    private Program program;
+    private ImportUpload upload;
+    private User user;
+    private boolean commit;
+}