Ran scalafmt/scalafix

mbari-org · Feb 18, 2025 · dc67c93 · dc67c93
1 parent f07c5d6
commit dc67c93
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Showing 81 changed files with 208 additions and 387 deletions.
diff --git a/.scalafix.conf b/.scalafix.conf
@@ -0,0 +1,9 @@
+rules = [
+    OrganizeImports
+]
+OrganizeImports {
+    expandRelative = true
+    groupedImports = Merge
+}
+OrganizeImports.targetDialect = Scala3
+OrganizeImports.removeUnused = true
diff --git a/build.sbt b/build.sbt
@@ -20,12 +20,15 @@ ThisBuild / scalacOptions ++= Seq(
     "-language:existentials",
     "-language:higherKinds",
     "-language:implicitConversions",
-    "-unchecked"
-
+    "-unchecked",
+    "-Wunused:imports", // Warn if an import selector is not referenced.
 )
 ThisBuild / startYear        := Some(2024)
 //ThisBuild / updateOptions    := updateOptions.value.withCachedResolution(true)
 ThisBuild / versionScheme    := Some("semver-spec")
+ThisBuild / semanticdbEnabled := true
+ThisBuild / semanticdbVersion := scalafixSemanticdb.revision
+
 
 ThisBuild / Test / fork              := true
 ThisBuild / Test / parallelExecution := false
@@ -80,7 +83,7 @@ lazy val oni = project
         circeGeneric,
         circeParser,
         commonsCodec,
-        // helidonEncodingDeflate, // Adding content encooding cause the swagger-ui to 
+        // helidonEncodingDeflate, // Adding content encooding cause the swagger-ui to
         // helidonEncodingGzip,    // fail to load the docs.yml file when used with nginx proxy
         hibernateCore,
         hibernateJCache,
@@ -151,4 +154,4 @@ lazy val itSqlserver = (project in file("it-sqlserver"))
       slf4jJulBridge,
       testcontainersSqlserver
     )
-  )
+  )
diff --git a/it/src/main/scala/org/mbari/oni/endpoints/AuthorizationEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/AuthorizationEndpointsSuite.scala
@@ -20,14 +20,13 @@ import io.circe.parser.decode
 import org.mbari.oni.domain.{AuthorizationSC, UserAccount, UserAccountRoles}
 import org.mbari.oni.etc.circe.CirceCodecs.given
 import org.mbari.oni.etc.jwt.JwtService
+import org.mbari.oni.etc.sdk.Futures.*
 import org.mbari.oni.jpa.DatabaseFunSuite
 import org.mbari.oni.services.UserAccountService
 import sttp.client3.*
 import sttp.model.StatusCode
-import org.mbari.oni.etc.sdk.Futures.*
 
 import java.util.Base64
-import scala.concurrent.ExecutionContext
 
 trait AuthorizationEndpointsSuite extends DatabaseFunSuite with EndpointsSuite:
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/ConceptEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/ConceptEndpointsSuite.scala
@@ -16,21 +16,16 @@
 
 package org.mbari.oni.endpoints
 
-import org.mbari.oni.domain.{ConceptCreate, ConceptMetadata, ConceptUpdate, SerdeConcept, UserAccount, UserAccountRoles}
-import org.mbari.oni.jpa.DataInitializer
-
-import scala.jdk.CollectionConverters.*
+import org.mbari.oni.domain.{ConceptCreate, ConceptMetadata, ConceptUpdate, Rank}
 import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
-import org.mbari.oni.services.UserAuthMixin
+import org.mbari.oni.jpa.DataInitializer
+import org.mbari.oni.jpa.entities.TestEntityFactory
+import org.mbari.oni.services.{RankValidator, UserAuthMixin}
 import sttp.model.StatusCode
 
-import scala.concurrent.ExecutionContext
-import org.mbari.oni.jpa.entities.TestEntityFactory
-import org.mbari.oni.jpa.entities.TestEntityFactory.randomRankLevelAndName
-import org.mbari.oni.domain.Rank
-import org.mbari.oni.services.RankValidator
+import scala.jdk.CollectionConverters.*
 
 trait ConceptEndpointsSuite extends EndpointsSuite with DataInitializer with UserAuthMixin:
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/ConceptNameEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/ConceptNameEndpointsSuite.scala
@@ -17,13 +17,11 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{ConceptNameCreate, ConceptNameTypes, ConceptNameUpdate, Page, RawConcept}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jpa.DataInitializer
 import org.mbari.oni.services.UserAuthMixin
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
-
-import scala.concurrent.ExecutionContext
 
 trait ConceptNameEndpointsSuite extends EndpointsSuite with DataInitializer with UserAuthMixin:
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/EndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/EndpointsSuite.scala
@@ -18,19 +18,17 @@ package org.mbari.oni.endpoints
 
 import io.circe.*
 import io.circe.parser.*
-import sttp.client3.*
+import org.mbari.oni.etc.jdk.Loggers.given
+import org.mbari.oni.etc.sdk.Futures.*
 import sttp.client3.testing.SttpBackendStub
+import sttp.client3.{SttpBackend, *}
+import sttp.model.StatusCode
 import sttp.tapir.server.ServerEndpoint
-import sttp.tapir.server.stub.TapirStubInterpreter
-import sttp.shared.Identity
-import sttp.tapir.server.interceptor.exception.ExceptionHandler
 import sttp.tapir.server.interceptor.CustomiseInterceptors
-import sttp.model.StatusCode
-import sttp.client3.SttpBackend
+import sttp.tapir.server.interceptor.exception.ExceptionHandler
 import sttp.tapir.server.model.ValuedEndpointOutput
-import org.mbari.oni.etc.jdk.Loggers.given
+import sttp.tapir.server.stub.TapirStubInterpreter
 import sttp.tapir.server.vertx.VertxFutureServerOptions
-import org.mbari.oni.etc.sdk.Futures.*
 
 import scala.concurrent.{ExecutionContext, Future}
 
@@ -146,7 +144,6 @@ trait EndpointsSuite extends munit.FunSuite:
         )
 
         val customOptions: CustomiseInterceptors[Future, VertxFutureServerOptions] =
-            import scala.concurrent.ExecutionContext.Implicits.global
             VertxFutureServerOptions
                 .customiseInterceptors
                 .exceptionHandler(exceptionHandler)

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/HistoryEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/HistoryEndpointsSuite.scala
@@ -16,14 +16,14 @@
 
 package org.mbari.oni.endpoints
 
-import org.mbari.oni.domain.{ConceptUpdate, Count, ExtendedHistory, LinkCreate, Page, UserAccountRoles}
-import org.mbari.oni.jpa.DataInitializer
-import sttp.model.StatusCode
+import org.mbari.oni.domain.{Count, ExtendedHistory, LinkCreate, Page, UserAccountRoles}
 import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jdbc.FastPhylogenyService
-import org.mbari.oni.services.{ConceptService, HistoryService, LinkTemplateService, UserAuthMixin}
+import org.mbari.oni.jpa.DataInitializer
+import org.mbari.oni.services.{HistoryService, LinkTemplateService, UserAuthMixin}
+import sttp.model.StatusCode
 
 trait HistoryEndpointsSuite extends EndpointsSuite with DataInitializer with UserAuthMixin:
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/LinkEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/LinkEndpointsSuite.scala
@@ -17,9 +17,9 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{ExtendedLink, Link}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.jpa.DataInitializer
 import org.mbari.oni.services.{LinkService, UserAuthMixin}
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import sttp.model.StatusCode
 
 import scala.jdk.CollectionConverters.*

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/LinkRealizationEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/LinkRealizationEndpointsSuite.scala
@@ -17,13 +17,13 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{ExtendedLink, ILink, LinkCreate, LinkUpdate}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
+import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jpa.DataInitializer
+import org.mbari.oni.jpa.entities.TestEntityFactory
 import org.mbari.oni.services.UserAuthMixin
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
-import org.mbari.oni.etc.jdk.Strings
-import org.mbari.oni.jpa.entities.TestEntityFactory
 
 import scala.jdk.CollectionConverters.*
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/LinkTemplateEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/LinkTemplateEndpointsSuite.scala
@@ -24,14 +24,13 @@ import org.mbari.oni.domain.{
     LinkRenameToConceptResponse,
     LinkUpdate
 }
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
+import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jpa.DataInitializer
+import org.mbari.oni.jpa.entities.TestEntityFactory
 import org.mbari.oni.services.UserAuthMixin
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
-import org.mbari.oni.etc.jdk.Strings
-import org.mbari.oni.jpa.entities.TestEntityFactory
-import org.mbari.oni.etc.jdk.Loggers.given
 
 import scala.jdk.CollectionConverters.*
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/MediaEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/MediaEndpointsSuite.scala
@@ -17,13 +17,13 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{Media, MediaCreate, MediaTypes, MediaUpdate}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jdbc.FastPhylogenyService
 import org.mbari.oni.jpa.DataInitializer
-import org.mbari.oni.services.{ConceptService, UserAuthMixin}
+import org.mbari.oni.services.UserAuthMixin
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 
 import java.net.URI
 import scala.jdk.CollectionConverters.*

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/PhylogenyEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/PhylogenyEndpointsSuite.scala
@@ -16,18 +16,11 @@
 
 package org.mbari.oni.endpoints
 
-import jakarta.persistence.EntityManagerFactory
 import org.mbari.oni.domain.SerdeConcept
-import org.mbari.oni.jpa.EntityManagerFactories.*
-import org.mbari.oni.jpa.{DataInitializer, DatabaseFunSuite}
-import org.mbari.oni.etc.jdk.Loggers.given
-import org.mbari.oni.jpa.entities.{ConceptEntity, TestEntityFactory}
-import org.mbari.oni.services.ConceptService
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
+import org.mbari.oni.etc.circe.CirceCodecs.given
+import org.mbari.oni.jpa.DataInitializer
 import sttp.model.StatusCode
 
-import java.util.concurrent.atomic.AtomicReference
-
 trait PhylogenyEndpointsSuite extends EndpointsSuite with DataInitializer:
 
     lazy val endpoints = new PhylogenyEndpoints(entityManagerFactory)

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/PrefNodeEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/PrefNodeEndpointsSuite.scala
@@ -17,14 +17,14 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{PrefNode, PrefNodeUpdate}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
+import org.mbari.oni.etc.jdk.Loggers.given
+import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jpa.DataInitializer
 import org.mbari.oni.services.{PrefNodeService, UserAuthMixin}
-import org.mbari.oni.etc.jdk.Loggers.given
-import org.mbari.oni.etc.jdk.Strings
-import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.util.Reflect
+import sttp.model.StatusCode
 
 trait PrefNodeEndpointsSuite extends EndpointsSuite with DataInitializer with UserAuthMixin:
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/RawEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/RawEndpointsSuite.scala
@@ -16,19 +16,17 @@
 
 package org.mbari.oni.endpoints
 
-import jakarta.persistence.EntityManagerFactory
 import org.mbari.oni.domain.RawConcept
+import org.mbari.oni.etc.circe.CirceCodecs.given
 import org.mbari.oni.jpa.DataInitializer
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 
-trait RawEndpointsSuite extends EndpointsSuite with DataInitializer {
+trait RawEndpointsSuite extends EndpointsSuite with DataInitializer:
 
     lazy val endpoints: RawEndpoints = RawEndpoints(entityManagerFactory)
 
-
     test("findRawConceptByName") {
-        val root = init(2, 2)
+        val root  = init(2, 2)
         val child = root.getChildConcepts.iterator().next()
         val name  = child.getPrimaryConceptName.getName
 
@@ -45,4 +43,3 @@ trait RawEndpointsSuite extends EndpointsSuite with DataInitializer {
         )
 
     }
-}
diff --git a/it/src/main/scala/org/mbari/oni/endpoints/ReferenceEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/ReferenceEndpointsSuite.scala
@@ -17,13 +17,13 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{Reference, ReferenceQuery, ReferenceUpdate}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
+import org.mbari.oni.etc.jdk.Loggers.given
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jpa.DataInitializer
 import org.mbari.oni.jpa.entities.TestEntityFactory
 import org.mbari.oni.services.ReferenceService
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
-import org.mbari.oni.etc.jdk.Loggers.given
 
 import scala.util.Random
 

diff --git a/it/src/main/scala/org/mbari/oni/endpoints/UserAccountsEndpointsSuite.scala b/it/src/main/scala/org/mbari/oni/endpoints/UserAccountsEndpointsSuite.scala
@@ -17,14 +17,14 @@
 package org.mbari.oni.endpoints
 
 import org.mbari.oni.domain.{UserAccount, UserAccountRoles, UserAccountUpdate}
+import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
+import org.mbari.oni.etc.jdk.Loggers.given
+import org.mbari.oni.etc.jdk.Strings
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jpa.DataInitializer
 import org.mbari.oni.jpa.entities.TestEntityFactory
-import org.mbari.oni.services.{UserAccountService, UserAuthMixin}
+import org.mbari.oni.services.UserAccountService
 import sttp.model.StatusCode
-import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
-import org.mbari.oni.etc.jdk.Loggers.given
-import org.mbari.oni.etc.jdk.Strings
 
 trait UserAccountsEndpointsSuite extends EndpointsSuite with DataInitializer:
 

diff --git a/it/src/main/scala/org/mbari/oni/etc/jdbc/Scripts.scala b/it/src/main/scala/org/mbari/oni/etc/jdbc/Scripts.scala
@@ -19,9 +19,9 @@ package org.mbari.oni.etc.jdbc
 import jakarta.persistence.EntityManager
 import munit.internal.io.PlatformIO.Path
 import org.mbari.oni.etc.jdk.Files
+import org.mbari.oni.etc.jpa.EntityManagers.*
 
 import java.nio.file.Files as JFiles
-import org.mbari.oni.etc.jpa.EntityManagers.*
 
 object Scripts:
 

diff --git a/it/src/main/scala/org/mbari/oni/issues/Oni7.scala b/it/src/main/scala/org/mbari/oni/issues/Oni7.scala
@@ -16,12 +16,11 @@
 
 package org.mbari.oni.issues
 
-import org.mbari.oni.domain.ConceptUpdate
 import org.mbari.oni.endpoints.{EndpointsSuite, HistoryEndpoints}
 import org.mbari.oni.etc.jwt.JwtService
 import org.mbari.oni.jdbc.FastPhylogenyService
 import org.mbari.oni.jpa.DataInitializer
-import org.mbari.oni.services.{ConceptService, HistoryService, LinkTemplateService, UserAuthMixin}
+import org.mbari.oni.services.{HistoryService, UserAuthMixin}
 
 trait Oni7 extends EndpointsSuite with DataInitializer with UserAuthMixin:
 

diff --git a/it/src/main/scala/org/mbari/oni/jdbc/FastPhylogenyServiceSuite.scala b/it/src/main/scala/org/mbari/oni/jdbc/FastPhylogenyServiceSuite.scala
@@ -17,13 +17,12 @@
 package org.mbari.oni.jdbc
 
 import org.mbari.oni.domain.Concept
-import org.mbari.oni.jpa.DataInitializer
-
-import scala.jdk.CollectionConverters.*
 import org.mbari.oni.etc.circe.CirceCodecs.{*, given}
 import org.mbari.oni.etc.jdk.Loggers.given
+import org.mbari.oni.jpa.DataInitializer
 
 import scala.annotation.tailrec
+import scala.jdk.CollectionConverters.*
 
 trait FastPhylogenyServiceSuite extends DataInitializer:
 

diff --git a/it/src/main/scala/org/mbari/oni/jpa/DataInitializer.scala b/it/src/main/scala/org/mbari/oni/jpa/DataInitializer.scala
@@ -16,10 +16,9 @@
 
 package org.mbari.oni.jpa
 
+import org.mbari.oni.etc.jdk.Loggers.given
 import org.mbari.oni.jpa.entities.{ConceptEntity, TestEntityFactory}
 import org.mbari.oni.services.ConceptService
-import org.mbari.oni.etc.jdk.Loggers.given
-import org.mbari.oni.jdbc.FastPhylogenyService
 
 trait DataInitializer extends DatabaseFunSuite:
 

diff --git a/it/src/main/scala/org/mbari/oni/jpa/DatabaseFunSuite.scala b/it/src/main/scala/org/mbari/oni/jpa/DatabaseFunSuite.scala
@@ -16,10 +16,6 @@
 
 package org.mbari.oni.jpa
 
-import org.mbari.oni.jpa.entities.{ConceptEntity, TestEntityFactory}
-import org.mbari.oni.services.ConceptService
-import org.mbari.oni.etc.jdk.Loggers.given
 
-import java.util.concurrent.atomic.AtomicReference
 
 trait DatabaseFunSuite extends munit.FunSuite with EntityManagerFactoryProvider {}