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[BI-1189] bug - Season dbId is displayed instead of year for the Env Year of existing studies. #203

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Merged
davedrp merged 1 commit into from
Aug 17, 2022
Merged

[BI-1189] bug - Season dbId is displayed instead of year for the Env Year of existing studies. #203

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9 changes: 9 additions & 0 deletions src/main/java/org/breedinginsight/brapps/importer/daos/BrAPISeasonDAO.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
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.core.response.BrAPISeasonSingleResponse;
import org.brapi.v2.model.pheno.BrAPIObservation;
import org.breedinginsight.brapps.importer.model.ImportUpload;
import org.breedinginsight.daos.ProgramDAO;
Expand Down Expand Up @@ -56,6 +57,14 @@ public List<BrAPISeason> getSeasonByYear(String year, UUID programId) throws Api
return seasons;
}

public BrAPISeason getSeasonById(String id, UUID programId) throws ApiException {
SeasonsApi api = new SeasonsApi(programDAO.getCoreClient(programId));
ApiResponse<BrAPISeasonSingleResponse> apiResponse = api.seasonsSeasonDbIdGet(id);
BrAPISeasonSingleResponse seasonListResponse = apiResponse.getBody();
BrAPISeason season = seasonListResponse.getResult();
return season;
}

public BrAPISeason addOneSeason(BrAPISeason season, UUID programId) throws ApiException {
BrAPISeason resultSeason = null;
SeasonsApi api = new SeasonsApi(programDAO.getCoreClient(programId));
Expand Down
32 changes: 31 additions & 1 deletion ...ain/java/org/breedinginsight/brapps/importer/services/processors/ExperimentProcessor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -75,6 +75,8 @@ public class ExperimentProcessor implements Processor {

// used to make the yearsToSeasonDbId() function more efficient
private Map<String, String > yearToSeasonDbIdCache = new HashMap<>();
// used to make the seasonDbIdtoYear() function more efficient
private Map<String, String > seasonDbIdToYearCache = new HashMap<>();

//These BrapiData-objects are initially populated by the getExistingBrapiData() method,
// then updated by the getNewBrapiData() method.
Expand Down Expand Up @@ -608,6 +610,9 @@ private Map<String, PendingImportObject<BrAPIStudy>> initialize_studyByNameNoSco
try {
existingStudies = brAPIStudyDAO.getStudiesByExperimentID(UUID.fromString(experimentIDStr), program);
existingStudies.forEach(existingStudy -> {
//Swap season DbId with year String
String seasonId = existingStudy.getSeasons().get(0);
existingStudy.setSeasons( List.of( this.seasonDbIdToYear( seasonId, program.getId() ) ) );

existingStudy.setStudyName(Utilities.removeProgramKeyAndUnknownAdditionalData(existingStudy.getStudyName(), program.getKey()));
studyByNameNoScope.put(
Expand Down Expand Up @@ -684,7 +689,7 @@ private String simpleStudyName(String scopedName){
private String yearsToSeasonDbId(List<String> years, UUID programId) {
String year = years.get(0);
String dbID = null;
if (this.yearToSeasonDbIdCache.containsKey(year) ){ // get it from cache if possable
if (this.yearToSeasonDbIdCache.containsKey(year) ){ // get it from cache if possible
dbID = this.yearToSeasonDbIdCache.get(year);
}
else{
Expand All @@ -694,6 +699,18 @@ private String yearsToSeasonDbId(List<String> years, UUID programId) {
return dbID;
}

private String seasonDbIdToYear(String seasonDbId, UUID programId) {
String year = null;
if (this.seasonDbIdToYearCache.containsKey(seasonDbId) ){ // get it from cache if possible
year = this.seasonDbIdToYearCache.get(seasonDbId);
}
else{
year = this.seasonDbIdToYearFromDatabase(seasonDbId,programId);
this.seasonDbIdToYearCache.put(seasonDbId, year);
}
return year;
}

private String yearToSeasonDbIdFromDatabase(String year, UUID programId) {
BrAPISeason targetSeason = null;
List<BrAPISeason> seasons;
Expand All @@ -720,6 +737,19 @@ private String yearToSeasonDbIdFromDatabase(String year, UUID programId) {
return seasonDbId;
}

private String seasonDbIdToYearFromDatabase(String seasonDbId, UUID programId) {
BrAPISeason targetSeason = null;
BrAPISeason season = null;
try {
season = this.brAPISeasonDAO.getSeasonById (seasonDbId, programId);
} catch (ApiException e) {
log.error(e.getResponseBody(), e);;
}
Integer yearInt = (season == null) ? null : season.getYear();;
String yearStr = (yearInt==null) ? "" : yearInt.toString();
return yearStr;
}

private boolean isTrialRefSource(BrAPIExternalReference brAPIExternalReference) {
return brAPIExternalReference.getReferenceSource().equals( String.format("%s/%s", BRAPI_REFERENCE_SOURCE, ExternalReferenceSource.TRIALS.getName()) );
}
Expand Down