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Commit 4f9023b

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jloux-brapijloux-brapi
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Merge branch 'germ-importer-opts' into java-21-uuid
2 parents a6ba63f + ab35a5d commit 4f9023b

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11 files changed

+38
-36
lines changed

11 files changed

+38
-36
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‎src/main/java/org/brapi/test/BrAPITestServer/controller/germ/CrossesApiController.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -59,8 +59,8 @@ public ResponseEntity<CrossesListResponse> crossesGet(
5959
validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
6060
validateAcceptHeader(request);
6161
Metadata metadata = generateMetaDataTemplate(page, pageSize);
62-
List<Cross> data = crossService.findCrosses(crossingProjectDbId, crossDbId,
63-
externalReferenceID, externalReferenceSource,
62+
List<Cross> data = crossService.findCrosses(crossingProjectDbId, crossingProjectName, crossDbId, crossName,
63+
commonCropName, programDbId, externalReferenceId, externalReferenceID, externalReferenceSource,
6464
metadata);
6565
return responseOK(new CrossesListResponse(), new CrossesListResponseResult(), data, metadata);
6666
}

‎src/main/java/org/brapi/test/BrAPITestServer/controller/germ/CrossingProjectsApiController.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -60,8 +60,8 @@ public ResponseEntity<CrossingProjectsListResponse> crossingProjectsGet(
6060
validateAcceptHeader(request);
6161
Metadata metadata = generateMetaDataTemplate(page, pageSize);
6262
List<CrossingProject> data = crossingProjectService.findCrossingProjects(crossingProjectDbId,
63-
crossingProjectName, includePotentialParents, commonCropName, programDbId,
64-
externalReferenceID, externalReferenceSource, metadata);
63+
crossingProjectName, includePotentialParents, commonCropName, programDbId, externalReferenceId,
64+
externalReferenceID, externalReferenceSource, metadata);
6565
return responseOK(new CrossingProjectsListResponse(), new CrossingProjectsListResponseResult(), data, metadata);
6666
}
6767

‎src/main/java/org/brapi/test/BrAPITestServer/controller/germ/PlannedCrossesApiController.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -60,8 +60,8 @@ public ResponseEntity<PlannedCrossesListResponse> plannedCrossesGet(
6060
validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
6161
validateAcceptHeader(request);
6262
Metadata metadata = generateMetaDataTemplate(page, pageSize);
63-
List<PlannedCross> data = crossService.findPlannedCrosses(crossingProjectDbId,
64-
plannedCrossDbId,
63+
List<PlannedCross> data = crossService.findPlannedCrosses(crossingProjectDbId, crossingProjectName,
64+
plannedCrossDbId, plannedCrossName, status, commonCropName, programDbId, externalReferenceId,
6565
externalReferenceID, externalReferenceSource, metadata);
6666
return responseOK(new PlannedCrossesListResponse(), new PlannedCrossesListResponseResult(), data, metadata);
6767
}

‎src/main/java/org/brapi/test/BrAPITestServer/controller/germ/SeedLotsApiController.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -66,7 +66,7 @@ public ResponseEntity<SeedLotListResponse> seedlotsGet(
6666
validateAcceptHeader(request);
6767
Metadata metadata = generateMetaDataTemplate(page, pageSize);
6868
List<SeedLot> data = seedLotService.findSeedLots(seedLotDbId, germplasmDbId, germplasmName, crossDbId,
69-
crossName, commonCropName, programDbId, externalReferenceID,
69+
crossName, commonCropName, programDbId, externalReferenceId, externalReferenceID,
7070
externalReferenceSource, metadata);
7171
return responseOK(new SeedLotListResponse(), new SeedLotListResponseResult(), data, metadata);
7272
}
@@ -156,7 +156,7 @@ public ResponseEntity<SeedLotTransactionListResponse> seedlotsTransactionsGet(
156156
validateAcceptHeader(request);
157157
Metadata metadata = generateMetaDataTemplate(page, pageSize);
158158
List<SeedLotTransaction> data = seedLotService.findSeedLotTransactions(transactionDbId, seedLotDbId,
159-
germplasmDbId, germplasmName, crossDbId, crossName, commonCropName, programDbId,
159+
germplasmDbId, germplasmName, crossDbId, crossName, commonCropName, programDbId, externalReferenceId,
160160
externalReferenceID, externalReferenceSource, metadata);
161161
return responseOK(new SeedLotTransactionListResponse(), new SeedLotTransactionListResponseResult(), data,
162162
metadata);

‎src/main/java/org/brapi/test/BrAPITestServer/service/SearchQueryBuilder.java‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,7 @@ public class SearchQueryBuilder<T> {
1414
private String selectClause;
1515
private String selectOnlyIds;
1616
private String whereClause;
17+
private String defaultSort;
1718
private String sortClause;
1819
private Map<String, Object> params;
1920
private Class<T> clazz;
@@ -22,6 +23,7 @@ public SearchQueryBuilder(Class<T> clazz) {
2223
this.selectClause = "SELECT distinct entity FROM " + clazz.getSimpleName() + " entity ";
2324
this.selectOnlyIds = "SELECT entity.id FROM " + clazz.getSimpleName() + " entity ";
2425
this.whereClause = "WHERE 1=1 ";
26+
this.defaultSort = " ORDER BY entity.id ASC ";
2527
this.sortClause = "";
2628
this.params = new HashMap<>();
2729
this.clazz = clazz;
@@ -30,7 +32,7 @@ public SearchQueryBuilder(Class<T> clazz) {
3032
public String getQuery() {
3133
if (sortClause.isEmpty()) {
3234
// By default, sort on entity id to have query result remain idempotent
33-
sortClause = " ORDER BY entity.id ASC ";
35+
sortClause = defaultSort;
3436
}
3537

3638
return selectClause + whereClause + sortClause;
@@ -39,7 +41,7 @@ public String getQuery() {
3941
public String getIdQuery() {
4042
if (sortClause.isEmpty()) {
4143
// By default, sort on entity id to have query result remain idempotent
42-
sortClause = " ORDER BY entity.id ASC ";
44+
sortClause = defaultSort;
4345
}
4446

4547
return selectOnlyIds + whereClause + sortClause;

‎src/main/java/org/brapi/test/BrAPITestServer/service/germ/CrossService.java‎

Lines changed: 14 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -43,29 +43,29 @@ public CrossService(CrossRepository crossRepository, CrossingProjectService cros
4343
this.crossParentService = crossParentService;
4444
}
4545

46-
public List<Cross> findCrosses(String crossingProjectDbId, String crossDbId,
47-
String externalReferenceID, String externalReferenceSource, Metadata metadata)
46+
public List<Cross> findCrosses(String crossingProjectDbId, String crossingProjectName, String crossDbId,
47+
String crossName, String commonCropName, String programDbId, String externalReferenceId,
48+
String externalReferenceID, String externalReferenceSource, Metadata metadata)
4849
throws BrAPIServerException {
49-
List<Cross> crosses = findCrossEntities(crossingProjectDbId, crossDbId,
50-
externalReferenceID, externalReferenceSource, false,
50+
List<Cross> crosses = findCrossEntities(crossingProjectDbId, crossingProjectName, crossDbId, crossName, null,
51+
commonCropName, programDbId, externalReferenceId, externalReferenceID, externalReferenceSource, false,
5152
metadata).map(this::convertToCross).getContent();
5253
return crosses;
5354
}
5455

55-
public List<PlannedCross> findPlannedCrosses(String crossingProjectDbId,
56-
String crossDbId,
57-
String externalReferenceID, String externalReferenceSource,
58-
Metadata metadata)
56+
public List<PlannedCross> findPlannedCrosses(String crossingProjectDbId, String crossingProjectName,
57+
String crossDbId, String crossName, String status, String commonCropName, String programDbId,
58+
String externalReferenceId, String externalReferenceID, String externalReferenceSource, Metadata metadata)
5959
throws BrAPIServerException {
60-
List<PlannedCross> crosses = findCrossEntities(crossingProjectDbId, crossDbId,
61-
externalReferenceID, externalReferenceSource, true,
60+
List<PlannedCross> crosses = findCrossEntities(crossingProjectDbId, crossingProjectName, crossDbId, crossName, status,
61+
commonCropName, programDbId, externalReferenceId, externalReferenceID, externalReferenceSource, true,
6262
metadata).map(this::convertToPlanned).getContent();
6363
return crosses;
6464
}
6565

66-
public Page<CrossEntity> findCrossEntities(String crossingProjectDbId, String crossDbId,
67-
String externalReferenceID, String externalReferenceSource,
68-
Boolean plannedCross, Metadata metadata)
66+
public Page<CrossEntity> findCrossEntities(String crossingProjectDbId, String crossingProjectName, String crossDbId,
67+
String crossName, String status, String commonCropName, String programDbId, String externalReferenceId,
68+
String externalReferenceID, String externalReferenceSource, Boolean plannedCross, Metadata metadata)
6969
throws BrAPIServerException {
7070

7171
Pageable pageReq = PagingUtility.getPageRequest(metadata);
@@ -220,7 +220,7 @@ private void updateEntity(CrossEntity entity, CrossNewRequest cross) throws BrAP
220220
if (cross.getCrossName() != null)
221221
entity.setName(cross.getCrossName());
222222
if (cross.getPlannedCrossDbId() != null) {
223-
List<CrossEntity> plannedEntity = findCrossEntities(null, cross.getPlannedCrossDbId(), null, null, true, null).getContent();
223+
List<CrossEntity> plannedEntity = findCrossEntities(null, null, cross.getPlannedCrossDbId(), null, null, null, null, null, null, null, true, null).getContent();
224224
entity.setPlannedCross(plannedEntity.get(0));
225225
}
226226
if (cross.getPollinationEvents() != null) {

‎src/main/java/org/brapi/test/BrAPITestServer/service/germ/CrossingProjectService.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -38,8 +38,8 @@ public CrossingProjectService(CrossingProjectRepository crossingProjectRepositor
3838
}
3939

4040
public List<CrossingProject> findCrossingProjects(String crossingProjectDbId, String crossingProjectName,
41-
Boolean includePotentialParents, String commonCropName, String programDbId,
42-
String externalReferenceID, String externalReferenceSource, Metadata metadata)
41+
Boolean includePotentialParents, String commonCropName, String programDbId, String externalReferenceId,
42+
String externalReferenceID, String externalReferenceSource, Metadata metadata)
4343
throws BrAPIServerException {
4444
Pageable pageReq = PagingUtility.getPageRequest(metadata);
4545

‎src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -120,7 +120,8 @@ public Page<GermplasmEntity> findGermplasmEntities(@Valid GermplasmSearchRequest
120120

121121
SearchQueryBuilder<GermplasmEntity> searchQuery = buildGermplasmSearchQuery(request);
122122

123-
// First run the query without the fetching all the entities, grabbing the IDs only and paginating and sorting them.
123+
// Since the built searchQuery contains a lazily loaded collection retrieved with a LEFT JOIN FETCH,
124+
// use findAllBySearchPaginatingWithFetches()
124125
Page<GermplasmEntity> germs = germplasmRepository.findAllBySearchPaginatingWithFetches(searchQuery, pageReq);
125126

126127
// Hopefully this retains insertion order in the page?
@@ -336,7 +337,6 @@ private void fetchRemainingGermCollectionsUsingQuery(SearchQueryBuilder<Germplas
336337
searchQuery.leftJoinFetch("externalReferences",
337338
"externalReferences");
338339

339-
// TODO: This method doesn't need to utilize a method that returns a page.
340340
List<GermplasmEntity> xrefs = germplasmRepository.findAllBySearch(searchQuery);
341341

342342
Map<String, List<ExternalReferenceEntity>> xrefByEntity = new HashMap<>();

‎src/main/java/org/brapi/test/BrAPITestServer/service/germ/SeedLotService.java‎

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -56,8 +56,8 @@ public SeedLotService(SeedLotRepository seedLotRepository,
5656
}
5757

5858
public List<SeedLot> findSeedLots(String seedLotDbId, String germplasmDbId, String germplasmName, String crossDbId,
59-
String crossName, String commonCropName, String programDbId,
60-
String externalReferenceID, String externalReferenceSource, Metadata metadata)
59+
String crossName, String commonCropName, String programDbId, String externalReferenceId,
60+
String externalReferenceID, String externalReferenceSource, Metadata metadata)
6161
throws BrAPIServerException {
6262
Pageable pageReq = PagingUtility.getPageRequest(metadata);
6363
SearchQueryBuilder<SeedLotEntity> searchQuery = new SearchQueryBuilder<SeedLotEntity>(SeedLotEntity.class);
@@ -137,16 +137,16 @@ public List<SeedLotTransaction> findSeedLotTransactions(String seedLotDbId, Stri
137137
String transactionDirection, Metadata metadata) throws BrAPIServerException {
138138
SeedLot seedLot = getSeedLot(seedLotDbId);
139139
if (seedLot != null) {
140-
return findSeedLotTransactions(transactionDbId, seedLotDbId, null, null, null, null, null, null, null,
140+
return findSeedLotTransactions(transactionDbId, seedLotDbId, null, null, null, null, null, null, null, null,
141141
null, metadata);
142142
}
143143
return null;
144144
}
145145

146146
public List<SeedLotTransaction> findSeedLotTransactions(String transactionDbId, String seedLotDbId,
147-
String germplasmDbId, String germplasmName, String crossDbId, String crossName, String commonCropName,
148-
String programDbId, String externalReferenceID, String externalReferenceSource,
149-
Metadata metadata)
147+
String germplasmDbId, String germplasmName, String crossDbId, String crossName, String commonCropName,
148+
String programDbId, String externalReferenceId, String externalReferenceID, String externalReferenceSource,
149+
Metadata metadata)
150150
throws BrAPIServerException {
151151
Pageable pageReq = PagingUtility.getPageRequest(metadata);
152152
SearchQueryBuilder<SeedLotTransactionEntity> searchQuery = new SearchQueryBuilder<SeedLotTransactionEntity>(

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

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,7 @@ public List<Scale> findScales(String scaleDbId, String observationVariableDbId,
4545
Pageable pageReq = PagingUtility.getPageRequest(metadata);
4646
SearchQueryBuilder<ScaleEntity> searchQuery = new SearchQueryBuilder<ScaleEntity>(ScaleEntity.class);
4747
if (observationVariableDbId != null) {
48-
searchQuery = searchQuery.join("variables", "variabTle").appendSingle(observationVariableDbId,
48+
searchQuery = searchQuery.join("variables", "variable").appendSingle(observationVariableDbId,
4949
"*variable.id");
5050
}
5151
searchQuery = searchQuery.appendSingle(UUID.fromString(scaleDbId), "id").withExRefs(externalReferenceID,

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