Feature/bi 1189 - 4.0 Exp Preview & Commit: Create Exp Independent Variables

src/main/java/org/breedinginsight/brapi/v2/constants/BrAPIAdditionalInfoFields.java

@@ -32,4 +32,8 @@ public final class BrAPIAdditionalInfoFields {
     public static final String GERMPLASM_BREEDING_METHOD_ID = "breedingMethodId";
     public static final String GERMPLASM_BREEDING_METHOD = "breedingMethod";
     public static final String CREATED_DATE = "createdDate";
+	public static final String DEFAULT_OBSERVATION_LEVEL = "defaultObservationLevel";
+    public static final String OBSERVATION_LEVEL = "observationLevel";
+    public static final String EXPERIMENT_TYPE = "experimentType";
+    public static final String EXPERIMENT_NUMBER = "experimentNumber";
 }

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

@@ -35,6 +35,7 @@
 import org.breedinginsight.brapps.importer.services.FileImportService;
 import org.breedinginsight.services.exceptions.*;
 
+import javax.annotation.Nullable;
 import javax.inject.Inject;
 import java.util.Map;
 import java.util.UUID;
@@ -110,7 +111,7 @@ public HttpResponse<Response<ImportResponse>> getUploadData(@PathVariable UUID p
     @AddMetadata
     @ProgramSecured(roles = {ProgramSecuredRole.BREEDER, ProgramSecuredRole.SYSTEM_ADMIN})
     public HttpResponse<Response<ImportResponse>> commitData(@PathVariable UUID programId, @PathVariable UUID mappingId,
-                                                             @PathVariable UUID uploadId, @Body Map<String, Object> userInput) {
+                                                             @PathVariable UUID uploadId, @Body @Nullable Map<String, Object> userInput) {
         try {
             AuthenticatedUser actingUser = securityService.getUser();
             ImportResponse result = fileImportService.updateUpload(programId, uploadId, actingUser, userInput, true);

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPISeasonDAO.java

@@ -0,0 +1,73 @@
+package org.breedinginsight.brapps.importer.daos;
+
+import lombok.extern.slf4j.Slf4j;
+import org.brapi.client.v2.ApiResponse;
+import org.brapi.client.v2.model.exceptions.ApiException;
+import org.brapi.client.v2.model.queryParams.core.SeasonQueryParams;
+import org.brapi.client.v2.modules.core.ListsApi;
+import org.brapi.client.v2.modules.core.SeasonsApi;
+import org.brapi.v2.model.BrAPIExternalReference;
+import org.brapi.v2.model.BrAPIResponse;
+import org.brapi.v2.model.BrAPIResponseResult;
+import org.brapi.v2.model.core.BrAPIListSummary;
+import org.brapi.v2.model.core.BrAPIListTypes;
+import org.brapi.v2.model.core.BrAPISeason;
+import org.brapi.v2.model.core.request.BrAPIListNewRequest;
+import org.brapi.v2.model.core.request.BrAPIListSearchRequest;
+import org.brapi.v2.model.core.response.BrAPIListsSingleResponse;
+import org.brapi.v2.model.core.response.BrAPISeasonListResponse;
+import org.brapi.v2.model.core.response.BrAPISeasonListResponseResult;
+import org.brapi.v2.model.pheno.BrAPIObservation;
+import org.breedinginsight.brapps.importer.model.ImportUpload;
+import org.breedinginsight.daos.ProgramDAO;
+import org.breedinginsight.utilities.BrAPIDAOUtil;
+
+import javax.inject.Inject;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.UUID;
+
+@Slf4j
+public class BrAPISeasonDAO {
+
+    private ProgramDAO programDAO;
+    private ImportDAO importDAO;
+
+    @Inject
+    public BrAPISeasonDAO(ProgramDAO programDAO, ImportDAO importDAO) {
+        this.programDAO = programDAO;
+        this.importDAO = importDAO;
+    }
+
+    public List<BrAPISeason> getSeasonByYear(String year, UUID programId) throws ApiException {
+        SeasonsApi api = new SeasonsApi(programDAO.getCoreClient(programId));
+        SeasonQueryParams queryParams =
+                SeasonQueryParams.builder()
+                        .year( year )
+                        .pageSize( 10000 )
+                        .build();
+        List<BrAPISeason> seasons = new ArrayList<>();
+        ApiResponse<BrAPISeasonListResponse> apiResponse = api.seasonsGet( queryParams );
+        BrAPISeasonListResponse seasonListResponse = apiResponse.getBody();
+        BrAPISeasonListResponseResult result = seasonListResponse.getResult();
+        seasons = result.getData();
+
+        return seasons;
+    }
+
+    public BrAPISeason addOneSeason(BrAPISeason season, UUID programId) throws ApiException {
+        BrAPISeason resultSeason = null;
+        SeasonsApi api = new SeasonsApi(programDAO.getCoreClient(programId));
+
+        ApiResponse<BrAPISeasonListResponse> apiResponse = api.seasonsPost(Arrays.asList(season));
+        BrAPISeasonListResponse seasonListResponse = apiResponse.getBody();
+        BrAPISeasonListResponseResult result = seasonListResponse.getResult();
+        List<BrAPISeason> seasons = result.getData();
+        if (seasons.size() > 0) {
+            resultSeason = seasons.get(0);
+        }
+        return resultSeason;
+    }
+
+}

src/main/java/org/breedinginsight/brapps/importer/daos/BrAPIStudyDAO.java

@@ -16,6 +16,7 @@
  */
 package org.breedinginsight.brapps.importer.daos;
 
+import io.micronaut.context.annotation.Property;
 import org.brapi.client.v2.model.exceptions.ApiException;
 import org.brapi.client.v2.modules.core.StudiesApi;
 import org.brapi.v2.model.core.BrAPIStudy;
@@ -32,6 +33,8 @@
 
 @Singleton
 public class BrAPIStudyDAO {
+    @Property(name = "brapi.server.reference-source")
+    private String BRAPI_REFERENCE_SOURCE;
 
     private ProgramDAO programDAO;
     private ImportDAO importDAO;
@@ -54,6 +57,19 @@ public List<BrAPIStudy> getStudyByName(List<String> studyNames, Program program)
         );
     }
 
+    public List<BrAPIStudy> getStudiesByExperimentID(UUID experimentID, Program program ) throws ApiException {
+        BrAPIStudySearchRequest studySearch = new BrAPIStudySearchRequest();
+        studySearch.programDbIds(List.of(program.getBrapiProgram().getProgramDbId()));
+        studySearch.addExternalReferenceIDsItem(experimentID.toString());
+        studySearch.addExternalReferenceSourcesItem(BRAPI_REFERENCE_SOURCE + "/trials");
+        StudiesApi api = new StudiesApi(programDAO.getCoreClient(program.getId()));
+        return BrAPIDAOUtil.search(
+                api::searchStudiesPost,
+                api::searchStudiesSearchResultsDbIdGet,
+                studySearch
+        );
+    }
+
     public List<BrAPIStudy> createBrAPIStudy(List<BrAPIStudy> brAPIStudyList, UUID programId, ImportUpload upload) throws ApiException {
         StudiesApi api = new StudiesApi(programDAO.getCoreClient(programId));
         return BrAPIDAOUtil.post(brAPIStudyList, upload, api::studiesPost, importDAO::update);

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

@@ -20,10 +20,14 @@
 import lombok.Getter;
 import lombok.NoArgsConstructor;
 import lombok.Setter;
+import org.brapi.v2.model.BrAPIExternalReference;
 import org.brapi.v2.model.core.*;
 import org.brapi.v2.model.pheno.*;
+import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapps.importer.model.config.*;
 import org.breedinginsight.brapps.importer.model.imports.BrAPIImport;
+import org.breedinginsight.brapps.importer.services.ExternalReferenceSource;
+import org.breedinginsight.model.BrAPIConstants;
 import org.breedinginsight.model.Program;
 import org.breedinginsight.utilities.Utilities;
 
@@ -106,11 +110,14 @@ public class ExperimentObservation implements BrAPIImport {
     @ImportFieldMetadata(id="ObsUnitID", name="Observation Unit ID", description = "A database generated unique identifier for experimental observation units")
     private String ObsUnitID;
 
-    public BrAPITrial constructBrAPITrial(Program program, boolean commit) {
+    public BrAPITrial constructBrAPITrial(Program program, boolean commit, String referenceSource, UUID id, String expSeqValue) {
         BrAPIProgram brapiProgram = program.getBrapiProgram();
         BrAPITrial trial = new BrAPITrial();
         if( commit ){
-            trial.setTrialName( getTrialNameWithProgramKey( program ));
+            trial.setTrialName( Utilities.appendProgramKey(getExpTitle(), program.getKey() ));
+
+            // Set external reference
+            trial.setExternalReferences(getTrialExternalReferences(program, referenceSource, id));
         }
         else{
             trial.setTrialName( getExpTitle() );
@@ -120,14 +127,11 @@ public BrAPITrial constructBrAPITrial(Program program, boolean commit) {
         trial.setProgramDbId(brapiProgram.getProgramDbId());
         trial.setProgramName(brapiProgram.getProgramName());
 
-        // TODO: Get to a constant
-        trial.putAdditionalInfoItem("defaultObservationLevel", getExpUnit());
-        trial.putAdditionalInfoItem("experimentType", getExpType());
-        return trial;
-    }
+        trial.putAdditionalInfoItem( BrAPIAdditionalInfoFields.DEFAULT_OBSERVATION_LEVEL, getExpUnit());
+        trial.putAdditionalInfoItem( BrAPIAdditionalInfoFields.EXPERIMENT_TYPE, getExpType());
+        trial.putAdditionalInfoItem( BrAPIAdditionalInfoFields.EXPERIMENT_NUMBER, expSeqValue);
 
-    public String getTrialNameWithProgramKey(Program program){
-        return String.format("%s [%s]", getExpTitle(), program.getKey());
+        return trial;
     }
 
     public BrAPILocation constructBrAPILocation() {
@@ -136,10 +140,19 @@ public BrAPILocation constructBrAPILocation() {
         return location;
     }
 
-    public BrAPIStudy constructBrAPIStudy(Program program, Supplier<BigInteger> nextVal, boolean commit) {
+    public BrAPIStudy constructBrAPIStudy(
+            Program program,
+            boolean commit,
+            String referenceSource,
+            String expSequenceValue,
+            UUID trialId,
+            UUID id) {
         BrAPIStudy study = new BrAPIStudy();
         if ( commit ){
-            study.setStudyName(Utilities.appendProgramKey(getEnv(), program.getKey(), nextVal.get().toString()));
+            study.setStudyName(Utilities.appendProgramKey(getEnv(), program.getKey(), expSequenceValue));
+
+            // Set external reference
+            study.setExternalReferences(getStudyExternalReferences(program, referenceSource, trialId, id));
         }
         else {
             study.setStudyName(getEnv());
@@ -149,51 +162,69 @@ public BrAPIStudy constructBrAPIStudy(Program program, Supplier<BigInteger> next
         study.setLocationName(getEnvLocation());
         study.setTrialName(getExpTitle());
 
-        List<String> seasonsList= new ArrayList<>();
-        seasonsList.add(getEnvYear());
-        study.setSeasons(seasonsList);
-        /*
-        TODO: Not used
+        List<String> seasonList = new ArrayList<>();
+        seasonList.add( getEnvYear() );
+        study.setSeasons( seasonList );
+
+        String designType = "Analysis"; // to support the BRApi server, the design type must be one of the following:
+                                        // 'CRD','Alpha','MAD','Lattice','Augmented','RCBD','p-rep','splitplot','greenhouse','Westcott', or 'Analysis'
+                                        // For now it will be hardcoded to 'Analysis'
         BrAPIStudyExperimentalDesign design = new BrAPIStudyExperimentalDesign();
-        design.setPUI(getExperimentalDesignPUI());
+        design.setPUI(designType);
+        design.setDescription(designType);
         study.setExperimentalDesign(design);
-        */
 
         return study;
     }
 
-    public BrAPIObservationUnit constructBrAPIObservationUnit(Program program, Supplier<BigInteger> nextVal, boolean commit) {
+    public BrAPIObservationUnit constructBrAPIObservationUnit(
+            Program program,
+            Supplier<BigInteger> nextVal,
+            boolean commit,
+            String germplasmName,
+            String referenceSource,
+            UUID trialID,
+            UUID studyID,
+            UUID id
+    ) {
 
         BrAPIObservationUnit observationUnit = new BrAPIObservationUnit();
         if( commit){
             observationUnit.setObservationUnitName( Utilities.appendProgramKey(getExpUnitId(), program.getKey(), nextVal.get().toString()));
+
+            // Set external reference
+            observationUnit.setExternalReferences(getObsUnitExternalReferences(program, referenceSource, trialID, studyID, id));
         }
         else {
             observationUnit.setObservationUnitName(getExpUnitId());
         }
         observationUnit.setStudyName(getEnv());
 
-        // TODO: Set the germplasm
-        //observationUnit.setGermplasmName(getGermplasm().getReferenceValue());
+        if(germplasmName==null){
+            germplasmName = getGermplasmName();
+        }
+        observationUnit.setGermplasmName(germplasmName);
 
         BrAPIObservationUnitPosition position = new BrAPIObservationUnitPosition();
         BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
-        level.setLevelName(getExpUnit());
+        level.setLevelName("plot");  //BreedBase only accepts "plot" or "plant"
+        level.setLevelCode( getExpUnitId() );
         position.setObservationLevel(level);
+        observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.OBSERVATION_LEVEL, getExpUnit());
 
         // Exp Unit
         List<BrAPIObservationUnitLevelRelationship> levelRelationships = new ArrayList<>();
         if( getExpReplicateNo() !=null ) {
             BrAPIObservationUnitLevelRelationship repLvl = new BrAPIObservationUnitLevelRelationship();
-            repLvl.setLevelName("replicate");
+            repLvl.setLevelName(BrAPIConstants.REPLICATE.getValue());
             repLvl.setLevelCode(getExpReplicateNo());
             levelRelationships.add(repLvl);
         }
 
         // Block number
         if( getExpBlockNo() != null ) {
             BrAPIObservationUnitLevelRelationship repLvl = new BrAPIObservationUnitLevelRelationship();
-            repLvl.setLevelName("block");
+            repLvl.setLevelName( BrAPIConstants.REPLICATE.getValue() );
             repLvl.setLevelCode(getExpBlockNo());
             levelRelationships.add(repLvl);
         }
@@ -227,4 +258,39 @@ public BrAPIObservationUnit constructBrAPIObservationUnit(Program program, Suppl
         return observationUnit;
     }
 
+    private List<BrAPIExternalReference> getBrAPIExternalReferences(
+            Program program, String referenceSourceBaseName, UUID trialId, UUID studyId, UUID obsUnitId) {
+        List<BrAPIExternalReference> refs = new ArrayList<>();
+
+        addReference(refs, program.getId(), referenceSourceBaseName, ExternalReferenceSource.PROGRAMS);
+        if( trialId   != null ) { addReference(refs, trialId, referenceSourceBaseName, ExternalReferenceSource.TRIALS); }
+        if( studyId   != null ) { addReference(refs, studyId, referenceSourceBaseName, ExternalReferenceSource.STUDIES); }
+        if( obsUnitId != null ) { addReference(refs, obsUnitId, referenceSourceBaseName, ExternalReferenceSource.OBSERVATION_UNITS); }
+
+        return refs;
+    }
+
+    private List<BrAPIExternalReference> getTrialExternalReferences(
+            Program program, String referenceSourceBaseName, UUID trialId) {
+        return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, null, null);
+    }
+    private List<BrAPIExternalReference> getStudyExternalReferences(
+            Program program, String referenceSourceBaseName, UUID trialId, UUID studyId) {
+        return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, null);
+    }
+    private List<BrAPIExternalReference> getObsUnitExternalReferences(
+            Program program, String referenceSourceBaseName, UUID trialId, UUID studyId, UUID obsUnitId) {
+        return getBrAPIExternalReferences(program, referenceSourceBaseName, trialId, studyId, null);
+    }
+
+
+    private void addReference(List<BrAPIExternalReference> refs, UUID uuid, String referenceBaseNameSource, ExternalReferenceSource refSourceName) {
+        BrAPIExternalReference reference;
+        reference = new BrAPIExternalReference();
+        reference.setReferenceSource( String.format("%s/%s", referenceBaseNameSource, refSourceName.getName()) );
+        reference.setReferenceID(uuid.toString());
+        refs.add(reference);
+    }
+
 }
+

src/main/java/org/breedinginsight/brapps/importer/model/response/PendingImportObject.java

@@ -30,9 +30,12 @@ public class PendingImportObject<T> {
     private T brAPIObject;
     private UUID id;
 
-    public PendingImportObject(ImportObjectState state, T brAPIObject) {
+    public PendingImportObject(ImportObjectState state, T brAPIObject, UUID id) {
         this.state = state;
         this.brAPIObject = brAPIObject;
-        this.id = UUID.randomUUID();
+        this.id = id;
+    }
+    public PendingImportObject(ImportObjectState state, T brAPIObject) {
+        this(state, brAPIObject, UUID.randomUUID());
     }
 }

src/main/java/org/breedinginsight/brapps/importer/services/ExternalReferenceSource.java

@@ -0,0 +1,18 @@
+package org.breedinginsight.brapps.importer.services;
+
+import lombok.Getter;
+
+@Getter
+public enum ExternalReferenceSource {
+    PROGRAMS("programs"),
+    TRIALS("trials"),
+    STUDIES("studies"),
+    OBSERVATION_UNITS("observationunits");
+
+    private String name;
+
+    ExternalReferenceSource(String name) {
+        this.name = name;
+    }
+}
+