SCRUM-3995 phenotype annotations on gene and allele page by cmpich · Pull Request #1235 · alliance-genome/agr_java_software

cmpich · 2025-02-24T09:35:13Z

No description provided.

…ncluding underscores

… gene records

…ds endpoint

devopsagr

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

checkstyle

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 114 in 8d42342

String phenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 115 in 8d42342

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 116 in 8d42342

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 117 in 8d42342

String sortBy) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 125 in 8d42342

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 126 in 8d42342

boolean excludeNegated,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 127 in 8d42342

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 237 in 8d42342

if (debug) Log.info(sorts);

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 252 in 8d42342

if (gene == null)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 290 in 8d42342

if (size > 0)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 299 in 8d42342

if (CollectionUtils.isEmpty(response.getResults()))

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 305 in 8d42342

if (list == null)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 40 in 8d42342

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 41 in 8d42342

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 80 in 8d42342

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 81 in 8d42342

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 157 in 8d42342

if (debug) Log.info(sorts);

oblodgett · 2025-02-24T13:06:44Z

+
+
+@RequestScoped
+public class ESService {


Most of this code is duplicated from the DiseaseESService please refactor.

oblodgett · 2025-02-24T13:53:03Z

Also if you look at my #1234 you will see that in this PR the unused code got copied and pasted. And now this copy and pasted code is in the ESService

devopsagr

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

checkstyle

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 211 in e6889e7

String hasDisease,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 212 in e6889e7

String hasPhenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 213 in e6889e7

String category,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 214 in e6889e7

String location) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 243 in e6889e7

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 244 in e6889e7

String asc,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 245 in e6889e7

String symbol,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 246 in e6889e7

String synonym,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 247 in e6889e7

String variantType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 248 in e6889e7

String molecularConsequence,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 249 in e6889e7

String phenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 250 in e6889e7

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 251 in e6889e7

String disease) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 276 in e6889e7

String moleculeType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 277 in e6889e7

JoinTypeValue joinType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 278 in e6889e7

String interactorGeneSymbol,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 279 in e6889e7

String interactorSpecies,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 280 in e6889e7

String interactorMoleculeType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 281 in e6889e7

String detectionMethod,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 282 in e6889e7

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 283 in e6889e7

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 284 in e6889e7

String role,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 285 in e6889e7

String geneticPerturbation,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 286 in e6889e7

String interacotorRole,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 287 in e6889e7

String interactorGeneticPerturbation,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 288 in e6889e7

String phenotypes,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 289 in e6889e7

String interactionType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 290 in e6889e7

@Context UriInfo info) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 370 in e6889e7

String geneticEntity,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 371 in e6889e7

String geneticEntityType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 372 in e6889e7

String phenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 373 in e6889e7

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 374 in e6889e7

String asc) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 672 in e6889e7

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 673 in e6889e7

String geneticEntity,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 674 in e6889e7

String geneticEntityType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 675 in e6889e7

String disease,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 676 in e6889e7

String associationType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 677 in e6889e7

String evidenceCode,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 678 in e6889e7

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 679 in e6889e7

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 680 in e6889e7

String asc,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 681 in e6889e7

UriInfo ui) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 714 in e6889e7

Integer limit,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 715 in e6889e7

Integer page,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 716 in e6889e7

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 717 in e6889e7

String alleleSymbol,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 718 in e6889e7

String constructSymbol,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 719 in e6889e7

String constructRegulatedGene,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 720 in e6889e7

String constructTargetedGene,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 721 in e6889e7

String constructExpressedGene,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 722 in e6889e7

String species,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 723 in e6889e7

String hasPhenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 724 in e6889e7

String hasDisease,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 725 in e6889e7

UriInfo ui) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 109 in e6889e7

Integer limit,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 110 in e6889e7

Integer page,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 111 in e6889e7

String phenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 112 in e6889e7

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 113 in e6889e7

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 114 in e6889e7

String sortBy) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 150 in e6889e7

String filterOptions,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 151 in e6889e7

String filterReference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 152 in e6889e7

String diseaseTerm,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 153 in e6889e7

String filterSource,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 154 in e6889e7

String geneticEntity,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 155 in e6889e7

String geneticEntityType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 156 in e6889e7

String associationType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 157 in e6889e7

String diseaseQualifier,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 158 in e6889e7

String evidenceCode,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 159 in e6889e7

Boolean debug,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 160 in e6889e7

Integer limit,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 161 in e6889e7

Integer page,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 162 in e6889e7

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 163 in e6889e7

String asc) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 32 in e6889e7

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 33 in e6889e7

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 72 in e6889e7

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 73 in e6889e7

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 125 in e6889e7

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 126 in e6889e7

boolean excludeNegated,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 127 in e6889e7

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 237 in e6889e7

if (debug) Log.info(sorts);

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 252 in e6889e7

if (gene == null)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 290 in e6889e7

if (size > 0)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 299 in e6889e7

if (CollectionUtils.isEmpty(response.getResults()))

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 305 in e6889e7

if (list == null)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.coding.UnnecessaryParenthesesCheck> _{reported by reviewdog 🐶}
Unnecessary parentheses around lambda value.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 95 in e6889e7

    
           GenePhenotypeAnnotationDocument gpad = lookup.computeIfAbsent(key, (k) -> new GenePhenotypeAnnotationDocument());

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 114 in e6889e7

if (CollectionUtils.isEmpty(crossReferences))

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.coding.UnnecessaryParenthesesCheck> _{reported by reviewdog 🐶}
Unnecessary parentheses around lambda value.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 118 in e6889e7

    
           Optional<CrossReference> opt = crossReferences.stream().filter((reference) -> reference.getReferencedCurie().startsWith(prefix + ":")).findFirst();

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 119 in e6889e7

if (opt.isPresent())

devopsagr

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

checkstyle

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 372 in c8a834e

String phenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 373 in c8a834e

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 374 in c8a834e

String asc) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 672 in c8a834e

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 673 in c8a834e

String geneticEntity,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 674 in c8a834e

String geneticEntityType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 675 in c8a834e

String disease,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 676 in c8a834e

String associationType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 677 in c8a834e

String evidenceCode,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 678 in c8a834e

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 679 in c8a834e

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 680 in c8a834e

String asc,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 681 in c8a834e

UriInfo ui) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 714 in c8a834e

Integer limit,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 715 in c8a834e

Integer page,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 716 in c8a834e

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 717 in c8a834e

String alleleSymbol,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 718 in c8a834e

String constructSymbol,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 719 in c8a834e

String constructRegulatedGene,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 720 in c8a834e

String constructTargetedGene,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 721 in c8a834e

String constructExpressedGene,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 722 in c8a834e

String species,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 723 in c8a834e

String hasPhenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 724 in c8a834e

String hasDisease,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/GeneController.java

Line 725 in c8a834e

UriInfo ui) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 109 in c8a834e

Integer limit,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 110 in c8a834e

Integer page,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 111 in c8a834e

String phenotype,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 112 in c8a834e

String source,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 113 in c8a834e

String reference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 114 in c8a834e

String sortBy) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 150 in c8a834e

String filterOptions,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 151 in c8a834e

String filterReference,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 152 in c8a834e

String diseaseTerm,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 153 in c8a834e

String filterSource,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 154 in c8a834e

String geneticEntity,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 155 in c8a834e

String geneticEntityType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 156 in c8a834e

String associationType,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 157 in c8a834e

String diseaseQualifier,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 158 in c8a834e

String evidenceCode,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 159 in c8a834e

Boolean debug,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 160 in c8a834e

Integer limit,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 161 in c8a834e

Integer page,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 162 in c8a834e

String sortBy,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/controller/AlleleController.java

Line 163 in c8a834e

String asc) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 32 in c8a834e

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 33 in c8a834e

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 72 in c8a834e

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/PhenotypeESService.java

Line 73 in c8a834e

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 125 in c8a834e

Pagination pagination,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 126 in c8a834e

boolean excludeNegated,

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.regexp.RegexpSinglelineJavaCheck> _{reported by reviewdog 🐶}
Indent must use tab characters

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 127 in c8a834e

boolean debug) {

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 237 in c8a834e

if (debug) Log.info(sorts);

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 252 in c8a834e

if (gene == null)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 290 in c8a834e

if (size > 0)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 299 in c8a834e

if (CollectionUtils.isEmpty(response.getResults()))

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_api/src/main/java/org/alliancegenome/api/service/ESService.java

Line 305 in c8a834e

if (list == null)

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.coding.UnnecessaryParenthesesCheck> _{reported by reviewdog 🐶}
Unnecessary parentheses around lambda value.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 95 in c8a834e

    
           GenePhenotypeAnnotationDocument gpad = lookup.computeIfAbsent(key, (k) -> new GenePhenotypeAnnotationDocument());

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 114 in c8a834e

if (CollectionUtils.isEmpty(crossReferences))

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.coding.UnnecessaryParenthesesCheck> _{reported by reviewdog 🐶}
Unnecessary parentheses around lambda value.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 118 in c8a834e

    
           Optional<CrossReference> opt = crossReferences.stream().filter((reference) -> reference.getReferencedCurie().startsWith(prefix + ":")).findFirst();

🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.blocks.NeedBracesCheck> _{reported by reviewdog 🐶}
'if' construct must use '{}'s.

agr_java_software/agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/PhenotypeAnnotationCurationIndexer.java

Line 119 in c8a834e

if (opt.isPresent())

oblodgett · 2025-02-27T19:04:43Z

-		@Parameter(in = ParameterIn.QUERY, name = "filter.reference", description = "Reference number: PUBMED or a Pub ID from the MOD") @QueryParam("filter.reference") String reference,
-		@Parameter(in = ParameterIn.QUERY, name = "sortBy", description = "Field name by which to sort", schema = @Schema(type = SchemaType.STRING)) @DefaultValue("symbol") @QueryParam("sortBy") String sortBy
+	JsonResultResponse<AllelePhenotypeAnnotationDocument> getPhenotypePerAllele(@Parameter(in = ParameterIn.PATH, name = "id", description = "Search for Phenotypes for a given Allele by ID", required = true, schema = @Schema(type = SchemaType.STRING)) @PathParam("id") String id,
+																				@Parameter(in = ParameterIn.QUERY, name = "limit", description = "Number of rows returned", schema = @Schema(type = SchemaType.INTEGER)) @DefaultValue("20") @QueryParam("limit") Integer limit,


Do these really need to be indented in that far?

Yes, so they all a aligned vertically for ease of reading.

They can be lined up much closer to the start of the line.

devopsagr · 2025-02-28T14:15:08Z

+				}
+
+				String key = getConsolidationKey(da);
+				GenePhenotypeAnnotationDocument gpad = lookup.computeIfAbsent(key, (k) -> new GenePhenotypeAnnotationDocument());


🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.coding.UnnecessaryParenthesesCheck> _{reported by reviewdog 🐶}
Unnecessary parentheses around lambda value.

I don't understand this checkstyle rule. I cannot see any unnecessary parenthesis

Don't need the parans around the k

devopsagr · 2025-02-28T14:15:08Z

+		}
+		String[] prefixes = {"PMID", "MGI", "RGD", "ZFIN", "FB", "WB", "MGI"};
+		for (String prefix : prefixes) {
+			Optional<CrossReference> opt = crossReferences.stream().filter((reference) -> reference.getReferencedCurie().startsWith(prefix + ":")).findFirst();


🚫 [checkstyle] <com.puppycrawl.tools.checkstyle.checks.coding.UnnecessaryParenthesesCheck> _{reported by reviewdog 🐶}
Unnecessary parentheses around lambda value.

Don't need parans around the reference

oblodgett

4 Main points left:

The ESService got most all the code from DiseaseESService copied and pasted into it, but the code was not removed from the DiseaseESService please refactor. The following list of methods are now duplicated:

getDiseaseAnnotations
getDiseaseRibbonSummary
populateDiseaseRibbonSummary
getDiseaseAnnotationsWithGenes
getDiseaseAnnotationsWithModels

DiseaseAnnotationCurationIndexer.java had populateImplicatedDA method added but is never used locally please remove.
I removed an unused object mapper "mapper2" if you look at my #1234 you will see that in this PR the unused code got copied and pasted, and now this copy and pasted code is in the ESService again this needs to get removed.
There is still checkstyle cleanups.

cmpich · 2025-03-01T13:00:05Z

I refactored ESService, DiseaseESService and PhenotypeESService with ESService class as the parent class that only contains re-usable code, no disease or phenotype-specific code should be in the parent class.
I don't see any 'mapper2' type of usage of the ObjectMapper in the ESService classes.

oblodgett · 2025-03-02T14:32:12Z

When I download your branch the DiseaseESService contains this method:

	private Map<String, Object> getSupplementalData(String focusTaxonId, boolean useSpeciesAggregation, boolean debug, BoolQueryBuilder unfilteredQuery) {
		// create histogram of select columns of unfiltered query
		Map<String, String> aggregationFields = new HashMap<>();
		if (useSpeciesAggregation) {
			aggregationFields.put("subject.taxon.name.keyword", "species");
		}
		aggregationFields.put("generatedRelationString.keyword", "associationType");
		aggregationFields.put("diseaseQualifiers.keyword", "diseaseQualifiers");
		Map<String, List<String>> distinctFieldValueMap = getAggregations(unfilteredQuery, aggregationFields, focusTaxonId, useSpeciesAggregation, debug);
		Map<String, Object> supplementalData = new LinkedHashMap<>();
		supplementalData.put(DISTINCT_FIELD_VALUES, distinctFieldValueMap);
		return supplementalData;
	}

and the ESService contains this method:

	private Map<String, Object> getSupplementalData(String focusTaxonId, boolean useSpeciesAggregation, boolean debug, BoolQueryBuilder unfilteredQuery) {
		// create histogram of select columns of unfiltered query
		Map<String, String> aggregationFields = new HashMap<>();
		if (useSpeciesAggregation) {
			aggregationFields.put("subject.taxon.name.keyword", "species");
		}
		aggregationFields.put("generatedRelationString.keyword", "associationType");
		aggregationFields.put("diseaseQualifiers.keyword", "diseaseQualifiers");
		Map<String, List<String>> distinctFieldValueMap = getAggregations(unfilteredQuery, aggregationFields, focusTaxonId, useSpeciesAggregation, debug);
		Map<String, Object> supplementalData = new LinkedHashMap<>();
		supplementalData.put(DISTINCT_FIELD_VALUES, distinctFieldValueMap);
		return supplementalData;
	}

How are they different?

And this is the case for the following method's
getAnnotationSorts

Also now the DiseaseESService doesn't even compile as its missing the elasticSearchHelper.

cmpich added 19 commits February 12, 2025 16:58

SCRUM-3995 start of phenotype annotation indexer

a2e405a

small refactor

85df567

small refactor

cfdc86d

small refactor

933a968

SCRUM-3995 create PhenotypeAnnotationIndexer

79e3f0b

make phenotypeStatement sortable with case insensitive

656ece3

create new field with sort directive for phenotype statement

95a88ee

remove unused code

cd290c5

SCRUM-4092 make all disease qualifier names be their original names i…

f303c3e

…ncluding underscores

refactor implicated DAs

1483c9d

remove comments

829678e

add allele phenotype annotations and include inferred gene / asserted…

6169f0c

… gene records

remove debugging code

c4e60ec

rebased on stage, needed changes for the v0.36.1 version, fix downloa…

147b7db

…ds endpoint

add allele indexing to the phenotype annotation indexer

defbee0

SCRUM-4869 populate associated gene to transcript object

b4c1921

Add allele indexing

30b4908

SCRUM-4724 convert phenotype table on allele page

2ac5447

merge SCRUM-3995 int stage

8d42342

devopsagr reviewed Feb 24, 2025

View reviewed changes

fix checkstyle issues

4a0ac4c

oblodgett requested changes Feb 24, 2025

View reviewed changes

merging stage code and optimize classes

e6889e7

devopsagr reviewed Feb 26, 2025

View reviewed changes

Merge branch 'stage' into SCRUM-phenotypeAnnotations

c8a834e

devopsagr reviewed Feb 26, 2025

View reviewed changes

cmpich added 3 commits February 26, 2025 11:12

fix code style recommendations

bfadbee

Merge branch 'stage' into SCRUM-phenotypeAnnotations

b150eac

Merge branch 'stage' into SCRUM-phenotypeAnnotations

f9fb637

Merge branch 'stage' into SCRUM-phenotypeAnnotations

a54cb84

cmpich requested a review from oblodgett February 27, 2025 16:59

oblodgett requested changes Feb 27, 2025

View reviewed changes

cmpich added 2 commits February 28, 2025 15:11

refactor to remove unsued code

524987e

remove unused imports

38f7558

devopsagr reviewed Feb 28, 2025

View reviewed changes

oblodgett requested changes Feb 28, 2025

View reviewed changes

cmpich added 3 commits March 1, 2025 14:01

more refactoring aroudn ESService classes

20bdb64

more refactoring

2d7a852

Merge branch 'stage' into SCRUM-phenotypeAnnotations

5cd14c2

cmpich and others added 6 commits March 2, 2025 18:55

fix merging issues

50ea9aa

fix merging issues

7744c96

remove unused method

ec68508

clear out method from child class

670f8bb

Removed tabs spaces issues

96cd884

Cleaned up indexer config

c9808e3

oblodgett approved these changes Mar 3, 2025

View reviewed changes

cmpich merged commit 94fc82c into stage Mar 3, 2025
4 checks passed

cmpich deleted the SCRUM-phenotypeAnnotations branch March 3, 2025 12:59



		@RequestScoped
		public class ESService {

Conversation

cmpich commented Feb 24, 2025

Uh oh!

devopsagr left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

oblodgett Feb 24, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

oblodgett commented Feb 24, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

devopsagr left a comment

Choose a reason for hiding this comment

Uh oh!

devopsagr left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Choose a reason for hiding this comment

Uh oh!

oblodgett left a comment • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

cmpich commented Mar 1, 2025

Uh oh!

oblodgett commented Mar 2, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

oblodgett Feb 24, 2025 •

edited

Loading

oblodgett commented Feb 24, 2025 •

edited

Loading

oblodgett left a comment •

edited

Loading

oblodgett commented Mar 2, 2025 •

edited

Loading