[BI-2813] Set levelNameDbIds in OUs in experiment creation use case

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

@@ -1,49 +1,28 @@
 package org.breedinginsight.brapi.v2.services;
 
 import lombok.extern.slf4j.Slf4j;
-import org.apache.commons.lang3.tuple.ImmutablePair;
-import org.apache.commons.lang3.tuple.Pair;
-import org.brapi.client.v2.ApiResponse;
 import org.brapi.client.v2.model.exceptions.ApiException;
-import org.brapi.client.v2.modules.phenotype.ObservationUnitsApi;
 import org.brapi.v2.model.pheno.BrAPIObservationUnitHierarchyLevel;
-import org.brapi.v2.model.pheno.BrAPIObservationUnitLevelRelationship;
-import org.brapi.v2.model.pheno.response.BrAPIObservationLevelListResponse;
 import org.breedinginsight.brapi.v2.dao.BrAPIObservationLevelDAO;
 import org.breedinginsight.model.DatasetLevel;
 import org.breedinginsight.model.Program;
-import org.breedinginsight.services.ProgramService;
-import org.breedinginsight.services.exceptions.DoesNotExistException;
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
-import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
 
 @Slf4j
 @Singleton
 public class BrAPIObservationLevelService {
     private final BrAPIObservationLevelDAO brAPIObservationLevelDAO;
-    private final ProgramService programService;
-
 
     @Inject
-    public BrAPIObservationLevelService(BrAPIObservationLevelDAO brAPIObservationLevelDAO,
-                                        ProgramService programService) {
+    public BrAPIObservationLevelService(BrAPIObservationLevelDAO brAPIObservationLevelDAO) {
         this.brAPIObservationLevelDAO = brAPIObservationLevelDAO;
-        this.programService = programService;
     }
 
-    /**
-     * @return Pair[GlobalLevelNames, ProgrammaticLevelNames]
-     */
-    public Pair<List<BrAPIObservationUnitHierarchyLevel>, List<BrAPIObservationUnitHierarchyLevel>> getGlobalAndProgrammaticLevelNames(Program program, String brapiProgramDbId) {
-        List<BrAPIObservationUnitHierarchyLevel> globalLevels = brAPIObservationLevelDAO.getGlobalObservationLevelNames(program);
-        List<BrAPIObservationUnitHierarchyLevel> programmaticLevels = brAPIObservationLevelDAO.getObservationLevelNamesByProgramId(program, brapiProgramDbId);
-
-
-        return new ImmutablePair<>(globalLevels, programmaticLevels);
+    public List<BrAPIObservationUnitHierarchyLevel> getGlobalLevelNames(Program program) {
+        return brAPIObservationLevelDAO.getGlobalObservationLevelNames(program);
     }
 
     public List<BrAPIObservationUnitHierarchyLevel> getProgrammaticLevelNames(Program program, String brapiProgramDbId) {

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

@@ -23,6 +23,7 @@
 import org.apache.commons.lang3.StringUtils;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.v2.model.core.BrAPIListSummary;
+import org.brapi.v2.model.core.BrAPIProgram;
 import org.brapi.v2.model.core.BrAPIStudy;
 import org.brapi.v2.model.core.BrAPITrial;
 import org.brapi.v2.model.core.request.BrAPIListNewRequest;
@@ -43,6 +44,7 @@
 import org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentUtilities;
 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.service.DatasetService;
 import org.breedinginsight.model.DatasetLevel;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.model.ProgramLocation;
@@ -55,10 +57,7 @@
 
 import javax.inject.Inject;
 import javax.inject.Singleton;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Map;
-import java.util.Objects;
+import java.util.*;
 import java.util.stream.Collectors;
 
 import static org.breedinginsight.brapps.importer.services.processors.experiment.ExperimentUtilities.PREEXISTING_EXPERIMENT_TITLE;
@@ -74,7 +73,7 @@ public class CommitPendingImportObjectsStep {
     private final BrAPIObservationUnitDAO brAPIObservationUnitDAO;
     private final ProgramLocationService locationService;
     private final OntologyService ontologyService;
-    private final BrAPIObservationLevelDAO brAPIObservationLevelDAO;
+    private final DatasetService datasetService;
 
     @Inject
     public CommitPendingImportObjectsStep(BrAPIListDAO brAPIListDAO,
@@ -84,19 +83,21 @@ public CommitPendingImportObjectsStep(BrAPIListDAO brAPIListDAO,
                                           BrAPIObservationUnitDAO brAPIObservationUnitDAO,
                                           ProgramLocationService locationService,
                                           OntologyService ontologyService,
-                                          BrAPIObservationLevelDAO brAPIObservationLevelDAO) {
+                                          DatasetService datasetService) {
         this.brAPIListDAO = brAPIListDAO;
         this.brapiTrialDAO = brapiTrialDAO;
         this.brAPIStudyDAO = brAPIStudyDAO;
         this.brAPIObservationDAO = brAPIObservationDAO;
         this.brAPIObservationUnitDAO = brAPIObservationUnitDAO;
         this.locationService = locationService;
         this.ontologyService = ontologyService;
-        this.brAPIObservationLevelDAO = brAPIObservationLevelDAO;
+        this.datasetService = datasetService;
     }
 
     // TODO: some common code between workflows here that could be broken out, removed append/update specific code
-    public void process(ProcessContext processContext, ProcessedData processedData) throws UnprocessableEntityException {
+    // TODO: For instance, multiple trials don't really exist in the use case which this code is used for: creating an experiment.
+    // TODO: This means having a Map of trials doesn't really make sense anymore, and should be replaced with a singular PendingImportObject<Trial>
+    public void process(ProcessContext processContext, ProcessedData processedData) throws UnprocessableEntityException, ApiException {
 
         PendingData pendingData = processContext.getPendingData();
         ImportContext importContext = processContext.getImportContext();
@@ -113,6 +114,32 @@ public void process(ProcessContext processContext, ProcessedData processedData)
         Map<String, PendingImportObject<BrAPIObservation>> observationByHash = pendingData.getObservationByHash();
         Map<String, String> expUnitbyTrialName = pendingData.getExpUnitByTrialName();
 
+        // Assume that there's only one expUnit per trial in this workflow.
+        // This should be a safe assumption to make considering this workflow is for the creation of a single experiment.
+        // If that changes in the future, this code will break and need to be dealt with.
+
+        if (expUnitbyTrialName.size() > 1) {
+            throw new InternalServerException("Multiple Experiment names exist during commit stage");
+        }
+
+        String expUnitName = expUnitbyTrialName.values()
+                .stream()
+                .findFirst()
+                .orElse(null);
+
+        if (expUnitName == null) {
+            throw new InternalServerException("Experiment unit name not found during commit stage");
+        }
+
+        String brapiProgramId = Optional.of(program)
+                .map(Program::getBrapiProgram)
+                .map(BrAPIProgram::getProgramDbId)
+                .orElse(null);
+
+        if (brapiProgramId == null) {
+            throw new InternalServerException("BrAPI program not found during commit stage");
+        }
+
         List<BrAPITrial> newTrials = ProcessorData.getNewObjects(pendingData.getTrialByNameNoScope());
 
         List<ProgramLocationRequest> newLocations = ProcessorData.getNewObjects(pendingData.getLocationByName())
@@ -139,6 +166,14 @@ public void process(ProcessContext processContext, ProcessedData processedData)
 
         List<BrAPIObservationUnit> newObservationUnits = ProcessorData.getNewObjects(pendingData.getObservationUnitByNameNoScope());
 
+        // Inject level names here
+        datasetService.updateObservationUnitsWithLevelNameDbIds(newObservationUnits,
+                program,
+                brapiProgramId,
+                expUnitName,
+                DatasetLevel.EXP_UNIT
+                );
+
         // filter out observations with no 'value' so they will not be saved
         List<BrAPIObservation> newObservations = ProcessorData.getNewObjects(observationByHash)
                 .stream()
@@ -176,8 +211,6 @@ public void process(ProcessContext processContext, ProcessedData processedData)
                 trialByNameNoScope.get(createdTrialName)
                         .getBrAPIObject()
                         .setTrialDbId(createdTrial.getTrialDbId());
-
-                createObservationLevel(createdTrialName, expUnitbyTrialName, program);
             }
 
             List<ProgramLocation> createdLocations = new ArrayList<>(locationService.create(actingUser, program.getId(), newLocations));
@@ -251,22 +284,6 @@ public void process(ProcessContext processContext, ProcessedData processedData)
 
     }
 
-    //Check if the experimental unit associated with the trial does not exist in the system and if so create a new observation level
-    private void createObservationLevel(String trialName, Map<String, String> expUnitByTrialName, Program program) throws ApiException, InternalServerException {
-        String expUnit = expUnitByTrialName.get(trialName).toLowerCase();
-        String programDbId = program.getBrapiProgram() != null ? program.getBrapiProgram().getProgramDbId() : null;
-        HttpResponse<String> levelResponse = brAPIObservationLevelDAO.createObservationLevelName(program, expUnit, DatasetLevel.EXP_UNIT, programDbId);
-
-        if (levelResponse.getStatus().getCode() == 409) {
-            log.info(String.format("Level with name=%s, order=%s, programDbId=%s already exists in database", expUnit, DatasetLevel.EXP_UNIT, programDbId));
-        } else if (levelResponse.getStatus().getCode() == 200) {
-            log.info(String.format("Level with name=%s, order=%s, programDbId=%s created in database", expUnit, DatasetLevel.EXP_UNIT, programDbId));
-        } else {
-            log.error("Error saving experiment import: " + levelResponse.getStatus().getReason());
-            throw new InternalServerException("Unable to create observation level: " + levelResponse.getStatus().getReason());
-        }
-    }
-
     private void updateStudyDependencyValues(PendingData pendingData, Map<Integer, PendingImport> mappedBrAPIImport, String programKey) {
         // update location DbIds in studies for all distinct locations
         Map<String, PendingImportObject<BrAPITrial>> trialByNameNoScope = pendingData.getTrialByNameNoScope();

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

@@ -18,6 +18,7 @@
 package org.breedinginsight.brapps.importer.services.processors.experiment.service;
 
 import io.micronaut.context.annotation.Property;
+import io.micronaut.http.server.exceptions.InternalServerException;
 import org.apache.commons.lang3.StringUtils;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.v2.model.BrAPIExternalReference;
@@ -26,14 +27,16 @@
 import org.brapi.v2.model.core.BrAPITrial;
 import org.brapi.v2.model.core.request.BrAPIListNewRequest;
 import org.brapi.v2.model.core.response.BrAPIListDetails;
+import org.brapi.v2.model.pheno.BrAPIObservationUnit;
 import org.brapi.v2.model.pheno.BrAPIObservationUnitHierarchyLevel;
+import org.brapi.v2.model.pheno.BrAPIObservationUnitLevelRelationship;
 import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapi.v2.dao.BrAPIListDAO;
-import org.breedinginsight.brapi.v2.dao.BrAPIObservationLevelDAO;
 import org.breedinginsight.brapi.v2.services.BrAPIObservationLevelService;
 import org.breedinginsight.brapps.importer.model.response.ImportObjectState;
 import org.breedinginsight.brapps.importer.model.response.PendingImportObject;
 import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
+import org.breedinginsight.model.BrAPIConstants;
 import org.breedinginsight.model.DatasetLevel;
 import org.breedinginsight.model.DatasetMetadata;
 import org.breedinginsight.model.Program;
@@ -216,4 +219,42 @@ private String findLevelNameByNameAndOrder(Program program,
 
         return levelNameStreamResult.get(0).getLevelNameDbId();
     }
+
+    public void updateObservationUnitsWithLevelNameDbIds(List<BrAPIObservationUnit> observationUnits,
+                                                         Program program,
+                                                         String brapiProgramDbId,
+                                                         String expUnitName,
+                                                         DatasetLevel levelOrder) throws ApiException {
+        Map<String, String> levelNameDbIdByName = new HashMap<>();
+
+        String expLevelName = expUnitName.toLowerCase();
+
+        String existingLevelNameDbId = getOrCreateLevelNameForDataset(program, brapiProgramDbId, expLevelName, levelOrder);
+        levelNameDbIdByName.put(expLevelName, existingLevelNameDbId);
+
+        List<BrAPIObservationUnitHierarchyLevel> globalLevelNames = observationLevelService.getGlobalLevelNames(program);
+
+        globalLevelNames.forEach(ouln -> levelNameDbIdByName.put(ouln.getLevelName(), ouln.getLevelNameDbId()));
+
+        for (BrAPIObservationUnit observationUnit : observationUnits) {
+
+            String positionLevelName = observationUnit.getObservationUnitPosition().getObservationLevel().getLevelName().toLowerCase();
+
+            observationUnit.getObservationUnitPosition().getObservationLevel().setLevelNameDbId(levelNameDbIdByName.get(positionLevelName));
+
+            for (BrAPIObservationUnitLevelRelationship lvlRelationship : observationUnit.getObservationUnitPosition().getObservationLevelRelationships()) {
+                if (lvlRelationship.getLevelName().equals(BrAPIConstants.BLOCK.getValue())) {
+                    lvlRelationship.setLevelNameDbId(levelNameDbIdByName.get(lvlRelationship.getLevelName()));
+                } else if (lvlRelationship.getLevelName().equals(BrAPIConstants.REPLICATE.getValue())) {
+                    lvlRelationship.setLevelNameDbId(levelNameDbIdByName.get(lvlRelationship.getLevelName()));
+                } else {
+                    throw new InternalServerException(String.format("Level name [%s] detected in OU Level Relationship " +
+                            "for experiment with Exp Unit name [%s].  This is unexpected and the new level " +
+                            "name must be retrieved properly from BrAPI to insert its DbId into BrAPI request for proper creation and assignment.",
+                            lvlRelationship.getLevelName(), expUnitName));
+                }
+            }
+        }
+
+    }
 }