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Commit 441814a

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timparsonstimparsons
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[BI-1909] NPE fix, converting sysouts to use Logger
1 parent 7fce804 commit 441814a

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3 files changed

+34
-52
lines changed

3 files changed

+34
-52
lines changed

‎src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationService.java‎

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,8 @@
2121
import org.brapi.test.BrAPITestServer.service.UpdateUtility;
2222
import org.brapi.test.BrAPITestServer.service.core.SeasonService;
2323
import org.brapi.test.BrAPITestServer.service.core.StudyService;
24+
import org.slf4j.Logger;
25+
import org.slf4j.LoggerFactory;
2426
import org.springframework.context.annotation.Lazy;
2527
import org.springframework.data.domain.Page;
2628
import org.springframework.data.domain.Pageable;
@@ -41,6 +43,8 @@
4143
@Service
4244
public class ObservationService {
4345

46+
private static final Logger log = LoggerFactory.getLogger(ObservationService.class);
47+
4448
private final ObservationRepository observationRepository;
4549
private final SeasonService seasonService;
4650
private final ObservationUnitService observationUnitService;
@@ -170,9 +174,9 @@ public ObservationTable findObservationsTable(ObservationSearchRequest obsReques
170174

171175
public List<Observation> findObservations(@Valid ObservationSearchRequest request, Metadata metadata) {
172176
Page<ObservationEntity> page = findObservationEntities(request, metadata);
173-
System.out.println(new Date() + ": converting "+page.getSize()+" entities");
177+
log.debug(new Date() + ": converting "+page.getSize()+" entities");
174178
List<Observation> observations = page.map(this::convertFromEntity).getContent();
175-
System.out.println(new Date() + ": done converting entities");
179+
log.debug(new Date() + ": done converting entities");
176180
PagingUtility.calculateMetaData(metadata, page);
177181
return observations;
178182
}
@@ -250,13 +254,11 @@ public Page<ObservationEntity> findObservationEntities(@Valid ObservationSearchR
250254
.appendList(request.getStudyDbIds(), "study.id").appendList(request.getStudyNames(), "study.studyName")
251255
.appendList(request.getTrialDbIds(), "trial.id").appendList(request.getTrialNames(), "trial.trialName");
252256

253-
System.out.println(new Date() + ": starting search");
257+
log.debug(new Date() + ": starting search");
254258
Page<ObservationEntity> page = observationRepository.findAllBySearch(searchQuery, pageReq);
255-
System.out.println(new Date() + ": search complete");
259+
log.debug(new Date() + ": search complete");
256260

257-
System.out.println("fetching Obs xrefs: " + new Date());
258261
observationRepository.fetchXrefs(page, ObservationEntity.class);
259-
System.out.println("done fetching Obs xrefs: " + new Date());
260262
return page;
261263
}
262264

@@ -327,7 +329,7 @@ public Observation updateObservation(String observationDbId, ObservationNewReque
327329
}
328330

329331
public Observation convertFromEntity(ObservationEntity entity) {
330-
System.out.println(new Date() + ": converting obs: " + entity.getId());
332+
log.trace(new Date() + ": converting obs: " + entity.getId());
331333
Observation observation = new Observation();
332334
if (entity != null) {
333335
UpdateUtility.convertFromEntity(entity, observation);

‎src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java‎

Lines changed: 16 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,8 @@
3131
import org.brapi.test.BrAPITestServer.service.germ.CrossService;
3232
import org.brapi.test.BrAPITestServer.service.germ.GermplasmService;
3333
import org.brapi.test.BrAPITestServer.service.germ.SeedLotService;
34+
import org.slf4j.Logger;
35+
import org.slf4j.LoggerFactory;
3436
import org.springframework.beans.factory.annotation.Autowired;
3537
import org.springframework.data.domain.Page;
3638
import org.springframework.data.domain.PageRequest;
@@ -60,6 +62,8 @@
6062

6163
@Service
6264
public class ObservationUnitService {
65+
66+
private static final Logger log = LoggerFactory.getLogger(ObservationUnitService.class);
6367
private final ObservationUnitRepository observationUnitRepository;
6468

6569
private final EntityManager entityManager;
@@ -197,24 +201,18 @@ public List<ObservationUnit> findObservationUnits(@Valid ObservationUnitSearchRe
197201
boolean includeObservations = request.isIncludeObservations() != null && request.isIncludeObservations();
198202

199203
if(includeObservations) {
200-
System.out.println("Fetching observations for OUs");
204+
log.debug("Fetching observations for OUs");
201205
for(ObservationUnitEntity entity : page) {
202-
System.out.println("Fetching observations for OU: " + entity.getId());
206+
log.trace("Fetching observations for OU: " + entity.getId());
203207
entity.getObservations();
204208
}
205209
}
206210

207-
System.out.println(new Date() + ": converting "+page.getSize()+" entities");
211+
log.debug(new Date() + ": converting "+page.getSize()+" entities");
208212
List<ObservationUnit> observationUnits = page.map(observationUnitEntity -> this.convertFromEntity(observationUnitEntity, includeObservations)).getContent();
209-
System.out.println(new Date() + ": done converting entities");
213+
log.debug(new Date() + ": done converting entities");
210214
PagingUtility.calculateMetaData(metadata, page);
211215

212-
// if (request.isIncludeObservations() == null || !request.isIncludeObservations()) {
213-
// for (ObservationUnit ou : observationUnits) {
214-
// ou.setObservations(null);
215-
// }
216-
// }
217-
218216
return observationUnits;
219217
}
220218

@@ -289,19 +287,13 @@ public Page<ObservationUnitEntity> findObservationUnitEntities(@Valid Observatio
289287
.appendList(request.getStudyNames(), "study.studyName").appendList(request.getTrialDbIds(), "trial.id")
290288
.appendList(request.getTrialNames(), "trial.trailName");
291289

292-
System.out.println("Starting search: " + new Date());
290+
log.debug("Starting search: " + new Date());
293291
Page<ObservationUnitEntity> page = observationUnitRepository.findAllBySearch(searchQuery, pageReq);
294-
System.out.println("Search complete: " + new Date());
292+
log.debug("Search complete: " + new Date());
295293

296-
System.out.println("fetching OU xrefs: " + new Date());
297294
observationUnitRepository.fetchXrefs(page, ObservationUnitEntity.class);
298-
System.out.println("done fetching OU xrefs: " + new Date());
299-
System.out.println("fetching OU treatments: " + new Date());
300295
fetchTreatments(page);
301-
System.out.println("done fetching OU treatments: " + new Date());
302-
System.out.println("fetching OU position levels: " + new Date());
303296
fetchObsUnitLevelRelationships(page);
304-
System.out.println("done fetching OU position levels: " + new Date());
305297
return page;
306298
}
307299

@@ -332,7 +324,11 @@ private void fetchObsUnitLevelRelationships(Page<ObservationUnitEntity> page) {
332324
positions.forEach(ou -> positionByOu.put(ou.getId(), ou.getPosition()));
333325

334326
page.forEach(ou -> {
335-
ou.getPosition().setObservationLevelRelationships(positionByOu.get(ou.getId()).getObservationLevelRelationships());
327+
if(ou.getPosition() != null) {
328+
ou.getPosition()
329+
.setObservationLevelRelationships(positionByOu.get(ou.getId())
330+
.getObservationLevelRelationships());
331+
}
336332
});
337333
}
338334

@@ -455,7 +451,7 @@ private ObservationUnit convertFromEntity(ObservationUnitEntity entity) {
455451
}
456452

457453
private ObservationUnit convertFromEntity(ObservationUnitEntity entity, boolean convertObservations) {
458-
System.out.println(new Date() + ": converting ou: " + entity.getId());
454+
log.trace(new Date() + ": converting ou: " + entity.getId());
459455
ObservationUnit unit = new ObservationUnit();
460456
UpdateUtility.convertFromEntity(entity, unit);
461457

‎src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationVariableService.java‎

Lines changed: 9 additions & 25 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,8 @@
2121
import org.brapi.test.BrAPITestServer.service.SearchQueryBuilder;
2222
import org.brapi.test.BrAPITestServer.service.UpdateUtility;
2323
import org.brapi.test.BrAPITestServer.service.core.CropService;
24+
import org.slf4j.Logger;
25+
import org.slf4j.LoggerFactory;
2426
import org.springframework.beans.factory.annotation.Autowired;
2527
import org.springframework.data.domain.Page;
2628
import org.springframework.data.domain.PageRequest;
@@ -39,6 +41,8 @@
3941

4042
@Service
4143
public class ObservationVariableService {
44+
45+
private static final Logger log = LoggerFactory.getLogger(ObservationVariableService.class);
4246
private final ObservationVariableRepository observationVariableRepository;
4347
private final MethodRepository methodRepository;
4448
private final ScaleRepository scaleRepository;
@@ -137,43 +141,23 @@ public List<ObservationVariable> findObservationVariables(ObservationVariableSea
137141
.appendList(request.getTraitDbIds(), "trait.id")
138142
.appendEnumList(request.getDataTypes(), "scale.dataType");
139143

140-
System.out.println("Starting search: " + new Date());
144+
log.debug("Starting variable search: " + new Date());
141145
Page<ObservationVariableEntity> page = observationVariableRepository.findAllBySearch(searchQuery, pageReq);
142-
System.out.println("Search complete: " + new Date());
143-
System.out.println("fetching var xrefs: " + new Date());
146+
log.debug("Search variable complete: " + new Date());
144147
observationVariableRepository.fetchXrefs(page, ObservationVariableEntity.class);
145-
System.out.println("done fetching var xrefs: " + new Date());
146-
System.out.println("fetching var additionalInfo: " + new Date());
147148
observationVariableRepository.fetchAdditionalInfo(page, ObservationVariableEntity.class);
148-
System.out.println("done fetching var additionalInfo: " + new Date());
149-
System.out.println("fetching var synonyms: " + new Date());
150149
fetchSynonyms(page);
151-
System.out.println("done fetching var synonyms: " + new Date());
152-
System.out.println("fetching method xrefs: " + new Date());
153150
fetchMethodXrefs(page);
154-
System.out.println("done fetching method xrefs: " + new Date());
155-
System.out.println("fetching method additionalInfo: " + new Date());
156151
fetchMethodAdditionalInfo(page);
157-
System.out.println("done fetching method additionalInfo: " + new Date());
158-
System.out.println("fetching scale xrefs: " + new Date());
159152
fetchScaleXrefs(page);
160-
System.out.println("done fetching scale xrefs: " + new Date());
161-
System.out.println("fetching scale additionalInfo: " + new Date());
162153
fetchScaleAdditionalInfo(page);
163-
System.out.println("done fetching scale additionalInfo: " + new Date());
164-
System.out.println("fetching scale valid value categories: " + new Date());
165154
fetchScaleValidValueCategories(page);
166-
System.out.println("done fetching scale valid value categories: " + new Date());
167-
System.out.println("fetching trait xrefs: " + new Date());
168155
fetchTraitXrefs(page);
169-
System.out.println("done fetching trait xrefs: " + new Date());
170-
System.out.println("fetching trait additionalInfo: " + new Date());
171156
fetchTraitAdditionalInfo(page);
172-
System.out.println("done fetching trait additionalInfo: " + new Date());
173157

174-
System.out.println(new Date() + ": converting "+page.getSize()+" entities");
158+
log.debug(new Date() + ": converting "+page.getSize()+" entities");
175159
List<ObservationVariable> observationVariables = page.map(this::convertFromEntity).getContent();
176-
System.out.println(new Date() + ": done converting entities");
160+
log.debug(new Date() + ": done converting entities");
177161
PagingUtility.calculateMetaData(metadata, page);
178162
return observationVariables;
179163
}
@@ -334,7 +318,7 @@ public ObservationVariableEntity getObservationVariableEntity(String observation
334318
}
335319

336320
private ObservationVariable convertFromEntity(ObservationVariableEntity entity) {
337-
System.out.println(new Date() + ": converting variable: " + entity.getId());
321+
log.trace(new Date() + ": converting variable: " + entity.getId());
338322
ObservationVariable var = new ObservationVariable();
339323
convertFromBaseEntity(entity, var);
340324
var.setObservationVariableName(entity.getName());

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