Bug/bi 1594

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

@@ -36,4 +36,5 @@ public final class BrAPIAdditionalInfoFields {
     public static final String OBSERVATION_LEVEL = "observationLevel";
     public static final String EXPERIMENT_TYPE = "experimentType";
     public static final String EXPERIMENT_NUMBER = "experimentNumber";
+    public static final String ENVIRONMENT_NUMBER = "environmentNumber";
 }

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

@@ -146,7 +146,8 @@ public BrAPIStudy constructBrAPIStudy(
             String referenceSource,
             String expSequenceValue,
             UUID trialId,
-            UUID id) {
+            UUID id,
+            Supplier<BigInteger> envNextVal) {
         BrAPIStudy study = new BrAPIStudy();
         if ( commit ){
             study.setStudyName(Utilities.appendProgramKey(getEnv(), program.getKey(), expSequenceValue));
@@ -173,13 +174,17 @@ public BrAPIStudy constructBrAPIStudy(
         design.setPUI(designType);
         design.setDescription(designType);
         study.setExperimentalDesign(design);
-
+        String envSequenceValue = null;
+        if( commit ){
+            envSequenceValue = envNextVal.get().toString();
+            study.putAdditionalInfoItem( BrAPIAdditionalInfoFields.ENVIRONMENT_NUMBER, envSequenceValue);
+        }
         return study;
     }
 
     public BrAPIObservationUnit constructBrAPIObservationUnit(
             Program program,
-            Supplier<BigInteger> nextVal,
+            String seqVal,
             boolean commit,
             String germplasmName,
             String referenceSource,
@@ -190,7 +195,7 @@ public BrAPIObservationUnit constructBrAPIObservationUnit(
 
         BrAPIObservationUnit observationUnit = new BrAPIObservationUnit();
         if( commit){
-            observationUnit.setObservationUnitName( Utilities.appendProgramKey(getExpUnitId(), program.getKey(), nextVal.get().toString()));
+            observationUnit.setObservationUnitName( Utilities.appendProgramKey(getExpUnitId(), program.getKey(), seqVal) );
 
             // Set external reference
             observationUnit.setExternalReferences(getObsUnitExternalReferences(program, referenceSource, trialID, studyID, id));
@@ -208,7 +213,7 @@ public BrAPIObservationUnit constructBrAPIObservationUnit(
         BrAPIObservationUnitPosition position = new BrAPIObservationUnitPosition();
         BrAPIObservationUnitLevelRelationship level = new BrAPIObservationUnitLevelRelationship();
         level.setLevelName("plot");  //BreedBase only accepts "plot" or "plant"
-        level.setLevelCode( getExpUnitId() );
+        level.setLevelCode( Utilities.appendProgramKey(getExpUnitId(), program.getKey(), seqVal) );
         position.setObservationLevel(level);
         observationUnit.putAdditionalInfoItem(BrAPIAdditionalInfoFields.OBSERVATION_LEVEL, getExpUnit());
 

src/main/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java

@@ -33,6 +33,7 @@
 import org.brapi.v2.model.pheno.*;
 import org.breedinginsight.api.model.v1.response.ValidationError;
 import org.breedinginsight.api.model.v1.response.ValidationErrors;
+import org.breedinginsight.brapi.v2.constants.BrAPIAdditionalInfoFields;
 import org.breedinginsight.brapi.v2.dao.BrAPIGermplasmDAO;
 import org.breedinginsight.brapps.importer.daos.*;
 import org.breedinginsight.brapps.importer.model.ImportUpload;
@@ -192,37 +193,43 @@ public Map<String, ImportPreviewStatistics> process(
 
     private void getNewBrapiData(List<BrAPIImport> importRows, Program program, boolean commit) {
 
-        String obsUnitSequenceName = program.getObsUnitSequence();
-        if (obsUnitSequenceName == null) {
-            log.error(String.format("Program, %s, is missing a value in the obsUnit sequence column.", program.getName()));
+        String expSequenceName = program.getExpSequence();
+        if (expSequenceName == null) {
+            log.error(String.format("Program, %s, is missing a value in the exp sequence column.", program.getName()));
             throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, "Program is not properly configured for observation unit import");
         }
-        Supplier<BigInteger> obsUnitNextVal = () -> dsl.nextval(obsUnitSequenceName.toLowerCase());
+        Supplier<BigInteger> expNextVal = () -> dsl.nextval(expSequenceName.toLowerCase());
 
-        // It is assumed, at this point, that there is only one experiment per import-file
-        String expSeqValue = null;
-        if (commit) {
-            String expUnitSequenceName = program.getExpSequence();
-            if (expUnitSequenceName == null) {
-                log.error(String.format("Program, %s, is missing a value in the exp sequence column.", program.getName()));
-                throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, "Program is not properly configured for experiment import");
-            }
-            expSeqValue = dsl.nextval(expUnitSequenceName.toLowerCase()).toString();
+        String envSequenceName = program.getEnvSequence();
+        if (envSequenceName == null) {
+            log.error(String.format("Program, %s, is missing a value in the env sequence column.", program.getName()));
+            throw new HttpStatusException(HttpStatus.UNPROCESSABLE_ENTITY, "Program is not properly configured for environment import");
         }
+        Supplier<BigInteger> envNextVal = () -> dsl.nextval(envSequenceName.toLowerCase());
 
         for (BrAPIImport row : importRows) {
             ExperimentObservation importRow = (ExperimentObservation) row;
 
-            PendingImportObject<BrAPITrial> trialPIO = createTrialPIO(program, commit, importRow, expSeqValue);
+            PendingImportObject<BrAPITrial> trialPIO = createTrialPIO(program, commit, importRow, expNextVal);
             this.trialByNameNoScope.put(importRow.getExpTitle(), trialPIO);
 
+            String expSeqValue = null;
+            if(commit) {
+                expSeqValue = trialPIO.getBrAPIObject().getAdditionalInfo().get(BrAPIAdditionalInfoFields.EXPERIMENT_NUMBER).getAsString();
+            }
+
             PendingImportObject<BrAPILocation> locationPIO = createLocationPIO(importRow);
             this.locationByName.put(importRow.getEnvLocation(), locationPIO);
 
-            PendingImportObject<BrAPIStudy> studyPIO = createStudyPIO(program, commit, expSeqValue, importRow);
+            PendingImportObject<BrAPIStudy> studyPIO = createStudyPIO(program, commit, expSeqValue, importRow, envNextVal);
             this.studyByNameNoScope.put(importRow.getEnv(), studyPIO);
 
-            PendingImportObject<BrAPIObservationUnit> obsUnitPIO = createObsUnitPIO(program, commit, obsUnitNextVal, importRow);
+            String envSeqValue = null;
+            if(commit) {
+                envSeqValue = studyPIO.getBrAPIObject().getAdditionalInfo().get(BrAPIAdditionalInfoFields.ENVIRONMENT_NUMBER).getAsString();
+            }
+
+            PendingImportObject<BrAPIObservationUnit> obsUnitPIO = createObsUnitPIO(program, commit, envSeqValue, importRow);
             String key = createObservationUnitKey(importRow);
             this.observationUnitByNameNoScope.put(key, obsUnitPIO);
         }
@@ -381,7 +388,7 @@ private PendingImportObject<BrAPIGermplasm> getGidPOI(ExperimentObservation impo
         }
     }
 
-    private PendingImportObject<BrAPIObservationUnit> createObsUnitPIO(Program program, boolean commit, Supplier<BigInteger> obsUnitNextVal, ExperimentObservation importRow) {
+    private PendingImportObject<BrAPIObservationUnit> createObsUnitPIO(Program program, boolean commit, String seqValue, ExperimentObservation importRow) {
         PendingImportObject<BrAPIObservationUnit> pio = null;
         if( this.observationUnitByNameNoScope.containsKey( createObservationUnitKey( importRow ) ) ) {
             pio = observationUnitByNameNoScope.get( createObservationUnitKey( importRow ) ) ;
@@ -396,13 +403,13 @@ private PendingImportObject<BrAPIObservationUnit> createObsUnitPIO(Program progr
             PendingImportObject<BrAPIStudy> studyPIO = this.studyByNameNoScope.get(importRow.getEnv());
             UUID studyID = studyPIO.getId();
             UUID id = UUID.randomUUID();
-            BrAPIObservationUnit newObservationUnit = importRow.constructBrAPIObservationUnit(program, obsUnitNextVal, commit, germplasmName, BRAPI_REFERENCE_SOURCE, trialID, studyID, id);
+            BrAPIObservationUnit newObservationUnit = importRow.constructBrAPIObservationUnit(program, seqValue, commit, germplasmName, BRAPI_REFERENCE_SOURCE, trialID, studyID, id);
             pio = new PendingImportObject<>(ImportObjectState.NEW, newObservationUnit);
         }
         return pio;
     }
 
-    private PendingImportObject<BrAPIStudy> createStudyPIO(Program program, boolean commit, String expSeqenceValue, ExperimentObservation importRow) {
+    private PendingImportObject<BrAPIStudy> createStudyPIO(Program program, boolean commit, String expSequenceValue, ExperimentObservation importRow, Supplier<BigInteger> envNextVal) {
         PendingImportObject<BrAPIStudy> pio = null;
         if( studyByNameNoScope.containsKey( importRow.getEnv()) ) {
             pio =  studyByNameNoScope.get( importRow.getEnv() ) ;
@@ -411,7 +418,7 @@ private PendingImportObject<BrAPIStudy> createStudyPIO(Program program, boolean
             PendingImportObject<BrAPITrial> trialPIO = this.trialByNameNoScope.get(importRow.getExpTitle());
             UUID trialID = trialPIO.getId();
             UUID id = UUID.randomUUID();
-            BrAPIStudy newStudy = importRow.constructBrAPIStudy(program, commit, BRAPI_REFERENCE_SOURCE, expSeqenceValue, trialID, id);
+            BrAPIStudy newStudy = importRow.constructBrAPIStudy(program, commit, BRAPI_REFERENCE_SOURCE, expSequenceValue, trialID, id, envNextVal);
 
             if( commit) {
                 String seasonID = this.yearsToSeasonDbId(newStudy.getSeasons(), program.getId());
@@ -435,13 +442,17 @@ private PendingImportObject<BrAPILocation> createLocationPIO(ExperimentObservati
         return pio;
     }
 
-    private PendingImportObject<BrAPITrial> createTrialPIO(Program program, boolean commit, ExperimentObservation importRow, String expSeqValue) {
+    private PendingImportObject<BrAPITrial> createTrialPIO(Program program, boolean commit, ExperimentObservation importRow, Supplier<BigInteger> expNextVal) {
         PendingImportObject<BrAPITrial> pio = null;
         if( trialByNameNoScope.containsKey( importRow.getExpTitle()) ) {
             pio = trialByNameNoScope.get( importRow.getExpTitle() ) ;
        }
        else {
             UUID id = UUID.randomUUID();
+            String expSeqValue = null;
+            if(commit){
+                expSeqValue = expNextVal.get().toString();
+            }
             BrAPITrial newTrial = importRow.constructBrAPITrial(program, commit, BRAPI_REFERENCE_SOURCE, id, expSeqValue);
             pio = new PendingImportObject<>(ImportObjectState.NEW, newTrial, id);
         }
@@ -463,7 +474,6 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program
 
         try {
             List<BrAPITrial> createdTrials = new ArrayList<>(brapiTrialDAO.createBrAPITrial(newTrials, program.getId(), upload));
-
             // set the DbId to the for each newly created trial
             for ( BrAPITrial createdTrial: createdTrials ) {
                 String createdTrialName = createdTrial.getTrialName();
@@ -473,7 +483,16 @@ public void postBrapiData(Map<Integer, PendingImport> mappedBrAPIImport, Program
                 String dbid = createdTrial.getTrialDbId();
                 listedTrial.setTrialDbId( dbid );
             }
-            brAPILocationDAO.createBrAPILocation(newLocations, program.getId(), upload);
+
+            List<BrAPILocation> createdLocations = new ArrayList<>(brAPILocationDAO.createBrAPILocation(newLocations, program.getId(), upload));
+            // set the DbId to the for each newly created trial
+            for ( BrAPILocation createdLocation : createdLocations){
+                String createdLocationName = createdLocation.getLocationName();
+                PendingImportObject<BrAPILocation> pi = this.locationByName.get(createdLocationName);
+                BrAPILocation listedLocation = pi.getBrAPIObject();
+                String dbid = createdLocation.getLocationDbId();
+                listedLocation.setLocationDbId(dbid);
+            }
 
             updateStudyDependencyValues(mappedBrAPIImport,program.getKey());
             List<BrAPIStudy> createdStudies = new ArrayList<>();
@@ -546,7 +565,7 @@ private void updateStudyDependencyValues(Map<Integer, PendingImport> mappedBrAPI
 
     private void updateStudyLocationDbId(BrAPILocation location) {
         this.studyByNameNoScope.values().stream()
-                .filter(study -> study.getBrAPIObject().getLocationName().equals(location.getLocationName()))
+                .filter(study -> location.getLocationName().equals( study.getBrAPIObject().getLocationName() ))
                 .forEach(study -> study.getBrAPIObject().setLocationDbId(location.getLocationDbId()));
     }
 
@@ -606,20 +625,12 @@ private Map<String, PendingImportObject<BrAPIStudy>> initialize_studyByNameNoSco
         ExperimentObservation experimentObservation = experimentImportRows.get(0);
 
         PendingImportObject<BrAPITrial> trial = this.trialByNameNoScope.get(experimentObservation.getExpTitle());
-        List<BrAPIExternalReference> experimentRefs = trial.getBrAPIObject().getExternalReferences();
-        Optional <BrAPIExternalReference> experimentIDRef = experimentRefs.stream()
-                .filter(this::isTrialRefSource)
-                .findFirst();
-        if( experimentIDRef.isEmpty()){
-            throw new InternalServerException("An Experiment ID was not found any of the external references");
-        }
 
-        //get experimentID
-        String experimentIDStr = experimentIDRef.get().getReferenceID();
+        UUID experimentId = trial.getId();
 
         List<BrAPIStudy> existingStudies;
         try {
-            existingStudies = brAPIStudyDAO.getStudiesByExperimentID(UUID.fromString(experimentIDStr), program);
+            existingStudies = brAPIStudyDAO.getStudiesByExperimentID(experimentId, program);
             existingStudies.forEach(existingStudy -> {
                 //Swap season DbId with year String
                 String seasonId = existingStudy.getSeasons().get(0);
@@ -672,9 +683,20 @@ private Map<String, PendingImportObject<BrAPITrial>> initialize_trialByNameNoSco
             existingTrials = brapiTrialDAO.getTrialByName(uniqueTrialNames, program);
             existingTrials.forEach(existingTrial -> {
                 existingTrial.setTrialName(Utilities.removeProgramKey(existingTrial.getTrialName(), program.getKey()));
+
+                //get TrialId from existingTrial
+                List<BrAPIExternalReference> experimentRefs = existingTrial.getExternalReferences();
+                Optional <BrAPIExternalReference> experimentIDRef = experimentRefs.stream()
+                        .filter(this::isTrialRefSource)
+                        .findFirst();
+                if( experimentIDRef.isEmpty()){
+                    throw new InternalServerException("An Experiment ID was not found any of the external references");
+                }
+                UUID experimentId = UUID.fromString(  experimentIDRef.get().getReferenceID() );
+
                 trialByNameNoScope.put(
                         existingTrial.getTrialName(),
-                        new PendingImportObject<>(ImportObjectState.EXISTING, existingTrial));
+                        new PendingImportObject<>(ImportObjectState.EXISTING, existingTrial, experimentId));
             });
             return trialByNameNoScope;
         } catch (ApiException e) {

src/main/java/org/breedinginsight/model/Program.java

@@ -91,7 +91,7 @@ public static Program parseSQLRecord(Record record, ProgramTable programTable) {
                 .active(record.getValue(programTable.ACTIVE))
                 .germplasmSequence(record.getValue(programTable.GERMPLASM_SEQUENCE))
                 .expSequence( record.getValue(programTable.EXP_SEQUENCE))
-                .obsUnitSequence(( record.getValue(programTable.OBS_UNIT_SEQUENCE)))
+                .envSequence(( record.getValue(programTable.ENV_SEQUENCE)))
                 .build();
 
         return program;

src/main/java/org/breedinginsight/services/ProgramService.java

@@ -61,6 +61,8 @@ public class ProgramService {
     private static final String GERMPLASM_SEQUENCE_TEMPLATE = "%s_germplasm_sequence";
     private static final String OBS_UNIT_SEQUENCE_TEMPLATE = "%s_obs_unit_sequence";
     private static final String EXP_SEQUENCE_TEMPLATE = "%s_exp_sequence";
+    private static final String ENV_SEQUENCE_TEMPLATE = "%s_env_sequence";
+
 
     @Inject
     public ProgramService(ProgramDAO dao, ProgramOntologyDAO programOntologyDAO, ProgramObservationLevelDAO programObservationLevelDAO,
@@ -171,6 +173,10 @@ public Program create(ProgramRequest programRequest, AuthenticatedUser actingUse
             String obs_unit_sequence_name = String.format(OBS_UNIT_SEQUENCE_TEMPLATE, programRequest.getKey()).toLowerCase();
             dsl.createSequence(obs_unit_sequence_name).execute();
 
+            // Create env sequence
+            String env_sequence_name = String.format(ENV_SEQUENCE_TEMPLATE, programRequest.getKey()).toLowerCase();
+            dsl.createSequence(env_sequence_name).execute();
+
             // Parse and create the program object
             ProgramEntity programEntity = ProgramEntity.builder()
                     .name(programRequest.getName())
@@ -182,7 +188,7 @@ public Program create(ProgramRequest programRequest, AuthenticatedUser actingUse
                     .key(programRequest.getKey())
                     .germplasmSequence(germplasm_sequence_name)
                     .expSequence( exp_sequence_name )
-                    .obsUnitSequence( obs_unit_sequence_name )
+                    .envSequence( env_sequence_name )
                     .createdBy(actingUser.getId())
                     .updatedBy(actingUser.getId())
                     .build();

src/main/resources/db/migration/V1.0.4__create_experiment_sequence.sql

@@ -15,7 +15,7 @@
  * limitations under the License.
  */
 
-alter table program add column exp_sequence text;
+alter table program add column  IF NOT EXISTS exp_sequence text;
 
 do
 $$
@@ -27,7 +27,7 @@ loop
     if f.key is NULL then
        RAISE EXCEPTION 'Programs must have a key associated with them';
     end if;
-    execute format('create sequence %s_exp_sequence',f.key);
+    execute format('create sequence  IF NOT EXISTS %s_exp_sequence',f.key);
     update program set exp_sequence = format('%s_exp_sequence', f.key) where id = f.id;
 end loop;
 end;

src/main/resources/db/migration/V1.0.6__create_environment_sequence.sql

@@ -0,0 +1,34 @@
+/*
+ * 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.
+ */
+
+alter table program add column IF NOT EXISTS env_sequence text;
+
+do
+$$
+declare
+f record;
+begin
+for f in select * from program
+loop
+    if f.key is NULL then
+       RAISE EXCEPTION 'Programs must have a key associated with them';
+    end if;
+    execute format('create sequence IF NOT EXISTS  %s_env_sequence',f.key);
+    update program set env_sequence = format('%s_env_sequence', f.key) where id = f.id;
+end loop;
+end;
+$$