Feature/bi 2132 a

src/main/java/org/breedinginsight/brapi/v2/services/BrAPITrialService.java

@@ -1,5 +1,8 @@
 package org.breedinginsight.brapi.v2.services;
 
+import com.github.filosganga.geogson.model.Coordinates;
+import com.github.filosganga.geogson.model.positions.SinglePosition;
+import com.google.gson.JsonObject;
 import io.micronaut.context.annotation.Property;
 import io.micronaut.http.MediaType;
 import io.micronaut.http.server.exceptions.InternalServerException;
@@ -465,6 +468,26 @@ private Map<String, Object> createExportRow(
         row.put(ExperimentObservation.Columns.EXP_TYPE, experiment.getAdditionalInfo().getAsJsonObject().get(BrAPIAdditionalInfoFields.EXPERIMENT_TYPE).getAsString());
         row.put(ExperimentObservation.Columns.ENV, Utilities.removeProgramKeyAndUnknownAdditionalData(study.getStudyName(), program.getKey()));
         row.put(ExperimentObservation.Columns.ENV_LOCATION, Utilities.removeProgramKey(study.getLocationName(), program.getKey()));
+
+        // Lat, Long, Elevation
+        Coordinates coordinates = extractCoordinates(ou);
+        Optional.ofNullable(coordinates)
+                .map(c -> doubleToString(c.getLat()))
+                .ifPresent(lat -> row.put(ExperimentObservation.Columns.LAT, lat));
+        Optional.ofNullable(coordinates)
+                .map(c -> doubleToString(c.getLon()))
+                .ifPresent(lon -> row.put(ExperimentObservation.Columns.LONG, lon));
+        Optional.ofNullable(coordinates)
+                .map(c -> doubleToString(c.getAlt()))
+                .ifPresent(elevation -> row.put(ExperimentObservation.Columns.ELEVATION, elevation));
+
+        // RTK
+        JsonObject additionalInfo = ou.getAdditionalInfo();
+        String rtk = ( additionalInfo==null || additionalInfo.get(BrAPIAdditionalInfoFields.RTK) ==null )
+                        ?   null
+                        :   additionalInfo.get(BrAPIAdditionalInfoFields.RTK).getAsString();
+        row.put(ExperimentObservation.Columns.RTK, rtk);
+
         BrAPISeason season = seasonDAO.getSeasonById(study.getSeasons().get(0), program.getId());
         row.put(ExperimentObservation.Columns.ENV_YEAR, season.getYear());
         row.put(ExperimentObservation.Columns.EXP_UNIT_ID, Utilities.removeProgramKeyAndUnknownAdditionalData(ou.getObservationUnitName(), program.getKey()));
@@ -484,11 +507,13 @@ private Map<String, Object> createExportRow(
                 .findFirst();
         blockLevel.ifPresent(brAPIObservationUnitLevelRelationship ->
                 row.put(ExperimentObservation.Columns.BLOCK_NUM, Integer.parseInt(brAPIObservationUnitLevelRelationship.getLevelCode())));
-        if (ou.getObservationUnitPosition() != null && ou.getObservationUnitPosition().getPositionCoordinateX() != null &&
-                ou.getObservationUnitPosition().getPositionCoordinateY() != null) {
+
+        //Row and Column
+        if ( ou.getObservationUnitPosition() != null ) {
             row.put(ExperimentObservation.Columns.ROW, ou.getObservationUnitPosition().getPositionCoordinateX());
             row.put(ExperimentObservation.Columns.COLUMN, ou.getObservationUnitPosition().getPositionCoordinateY());
         }
+
         if (ou.getTreatments() != null && !ou.getTreatments().isEmpty()) {
             row.put(ExperimentObservation.Columns.TREATMENT_FACTORS, ou.getTreatments().get(0).getFactor());
         } else {
@@ -499,7 +524,25 @@ private Map<String, Object> createExportRow(
         return row;
     }
 
-
+    private String doubleToString(double val){
+        return Double.isNaN(val) ? null : String.valueOf( val );
+    }
+    private Coordinates extractCoordinates(BrAPIObservationUnit ou){
+        Coordinates coordinates = null;
+        if (        ou.getObservationUnitPosition()!=null
+                &&  ou.getObservationUnitPosition().getGeoCoordinates()!=null
+                &&  ou.getObservationUnitPosition().getGeoCoordinates().getGeometry()!=null
+                &&  ou.getObservationUnitPosition().getGeoCoordinates().getGeometry().positions()!=null
+        )
+        {
+            Object o = ou.getObservationUnitPosition().getGeoCoordinates().getGeometry().positions();
+            if (o instanceof SinglePosition){
+                SinglePosition sp = (SinglePosition)o;
+                coordinates= sp.coordinates();
+            }
+        }
+        return coordinates;
+    }
 
     private void addObsVarColumns(
             List<Column> columns,

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

@@ -37,7 +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.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;
@@ -214,16 +214,22 @@ public HttpResponse<Response<DataResponse<ImportMapping>>> getSystemMappings(@Nu
     @Produces(MediaType.APPLICATION_JSON)
     @AddMetadata
     @Secured(SecurityRule.IS_ANONYMOUS)
-    public HttpResponse<Response<DataResponse<ImportMappingWorkflow>>> getWorkflowsForSystemMapping(@PathVariable UUID mappingId) {
+    public HttpResponse<Response<DataResponse<ImportWorkflow>>> getWorkflowsForSystemMapping(@PathVariable UUID mappingId) throws Exception {
 
-        List<ImportMappingWorkflow> workflows = fileImportService.getWorkflowsForSystemMapping(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<ImportMappingWorkflow>> response = new Response(metadata, new DataResponse<>(workflows));
+        Response<DataResponse<ImportWorkflow>> response = new Response(metadata, new DataResponse<>(workflows));
         return HttpResponse.ok(response);
     }
 }

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

@@ -163,7 +163,7 @@ public HttpResponse<Response<ImportResponse>> previewData(@PathVariable UUID pro
     @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) {
+                                                              @PathVariable String workflowId, @PathVariable UUID uploadId) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             ImportResponse result = fileImportService.updateUpload(programId, uploadId, workflowId, actingUser, null, false);
@@ -189,7 +189,7 @@ public HttpResponse<Response<ImportResponse>> previewData(@PathVariable UUID pro
     @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,
+                                                             @PathVariable String workflowId, @PathVariable UUID uploadId,
                                                              @Body @Nullable Map<String, Object> userInput) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();

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

@@ -18,10 +18,14 @@
 package org.breedinginsight.brapps.importer.model.imports;
 
 import org.breedinginsight.brapps.importer.model.response.ImportPreviewResponse;
+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);
     }

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

@@ -19,10 +19,10 @@
 
 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
@@ -32,7 +32,7 @@
 @AllArgsConstructor
 @NoArgsConstructor
 public class ImportServiceContext {
-    private Workflow workflow;
+    private String workflowId;
     private List<BrAPIImport> brAPIImports;
     private Table data;
     private Program program;