chore(deps): bump the minor group across 1 directory with 5 updates (#…

…3196)

* chore(deps): bump the minor group across 1 directory with 5 updates

Bumps the minor group with 5 updates in the /backend directory:

| Package | From | To |
| --- | --- | --- |
| org.flywaydb:flyway-database-postgresql | `10.20.1` | `10.21.0` |
| [org.jetbrains.exposed:exposed-spring-boot-starter](https://github.com/JetBrains/Exposed) | `0.55.0` | `0.56.0` |
| [org.jetbrains.exposed:exposed-jdbc](https://github.com/JetBrains/Exposed) | `0.55.0` | `0.56.0` |
| [org.jetbrains.exposed:exposed-json](https://github.com/JetBrains/Exposed) | `0.55.0` | `0.56.0` |
| [org.jetbrains.exposed:exposed-kotlin-datetime](https://github.com/JetBrains/Exposed) | `0.55.0` | `0.56.0` |



Updates `org.flywaydb:flyway-database-postgresql` from 10.20.1 to 10.21.0

Updates `org.jetbrains.exposed:exposed-spring-boot-starter` from 0.55.0 to 0.56.0
- [Release notes](https://github.com/JetBrains/Exposed/releases)
- [Changelog](https://github.com/JetBrains/Exposed/blob/main/CHANGELOG.md)
- [Commits](JetBrains/Exposed@0.55.0...0.56.0)

Updates `org.jetbrains.exposed:exposed-jdbc` from 0.55.0 to 0.56.0
- [Release notes](https://github.com/JetBrains/Exposed/releases)
- [Changelog](https://github.com/JetBrains/Exposed/blob/main/CHANGELOG.md)
- [Commits](JetBrains/Exposed@0.55.0...0.56.0)

Updates `org.jetbrains.exposed:exposed-json` from 0.55.0 to 0.56.0
- [Release notes](https://github.com/JetBrains/Exposed/releases)
- [Changelog](https://github.com/JetBrains/Exposed/blob/main/CHANGELOG.md)
- [Commits](JetBrains/Exposed@0.55.0...0.56.0)

Updates `org.jetbrains.exposed:exposed-kotlin-datetime` from 0.55.0 to 0.56.0
- [Release notes](https://github.com/JetBrains/Exposed/releases)
- [Changelog](https://github.com/JetBrains/Exposed/blob/main/CHANGELOG.md)
- [Commits](JetBrains/Exposed@0.55.0...0.56.0)

---
updated-dependencies:
- dependency-name: org.flywaydb:flyway-database-postgresql
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
- dependency-name: org.jetbrains.exposed:exposed-spring-boot-starter
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
- dependency-name: org.jetbrains.exposed:exposed-jdbc
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
- dependency-name: org.jetbrains.exposed:exposed-json
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
- dependency-name: org.jetbrains.exposed:exposed-kotlin-datetime
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
...

Signed-off-by: dependabot[bot] <[email protected]>

* fix breaking changes and lints

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Cornelius Roemer <[email protected]>

backend/build.gradle

@@ -37,11 +37,11 @@ dependencies {
     implementation "org.postgresql:postgresql:42.7.4"
     implementation "org.apache.commons:commons-csv:1.12.0"
     implementation "org.springdoc:springdoc-openapi-starter-webmvc-ui:2.6.0"
-    implementation "org.flywaydb:flyway-database-postgresql:10.20.1"
-    implementation "org.jetbrains.exposed:exposed-spring-boot-starter:0.55.0"
-    implementation "org.jetbrains.exposed:exposed-jdbc:0.55.0"
-    implementation "org.jetbrains.exposed:exposed-json:0.55.0"
-    implementation "org.jetbrains.exposed:exposed-kotlin-datetime:0.55.0"
+    implementation "org.flywaydb:flyway-database-postgresql:10.21.0"
+    implementation "org.jetbrains.exposed:exposed-spring-boot-starter:0.56.0"
+    implementation "org.jetbrains.exposed:exposed-jdbc:0.56.0"
+    implementation "org.jetbrains.exposed:exposed-json:0.56.0"
+    implementation "org.jetbrains.exposed:exposed-kotlin-datetime:0.56.0"
     implementation "org.jetbrains.kotlinx:kotlinx-datetime:0.6.1"
     implementation "org.hibernate.validator:hibernate-validator:8.0.1.Final"
     implementation "org.keycloak:keycloak-admin-client:23.0.7"

backend/src/main/kotlin/org/loculus/backend/service/seqsetcitations/SeqSetCitationsDatabaseService.kt

@@ -85,7 +85,7 @@ class SeqSetCitationsDatabaseService(
                 .insert {
                     it[SeqSetRecordsTable.accession] = record.accession
                     it[SeqSetRecordsTable.type] = record.type
-                    it[SeqSetRecordsTable.isFocal] = record.isFocal ?: true
+                    it[SeqSetRecordsTable.isFocal] = record.isFocal
                 }
             SeqSetToRecordsTable
                 .insert {
@@ -119,6 +119,7 @@ class SeqSetCitationsDatabaseService(
             .where { SeqSetsTable.seqSetId eq seqSetId and (SeqSetsTable.createdBy eq username) }
             .firstOrNull()
             ?.get(SeqSetsTable.seqSetVersion.max())
+            as Long?
 
         if (maxVersion == null) {
             throw NotFoundException("SeqSet $seqSetId does not exist")
@@ -158,7 +159,7 @@ class SeqSetCitationsDatabaseService(
                     .insert {
                         it[SeqSetRecordsTable.accession] = record.accession
                         it[SeqSetRecordsTable.type] = record.type
-                        it[SeqSetRecordsTable.isFocal] = record.isFocal ?: true
+                        it[SeqSetRecordsTable.isFocal] = record.isFocal
                     }
                 insertedRecord[SeqSetRecordsTable.seqSetRecordId]
             } else {
@@ -469,7 +470,7 @@ class SeqSetCitationsDatabaseService(
                     val (accession, version) = it.accession.split('.')
                     AccessionVersion(accession, version.toLong())
                 }
-        } catch (e: NumberFormatException) {
+        } catch (_: NumberFormatException) {
             throw UnprocessableEntityException("Accession versions must be integers")
         }