ran scalafix + scalafmt

annosaurus/src/main/scala/org/mbari/annosaurus/AppConfig.scala

@@ -87,15 +87,14 @@ case class DatabaseConfig(
     driver: String,
     queryView: String
 ):
-    lazy val dataSource = {
+    lazy val dataSource                      =
         val ds = new com.zaxxer.hikari.HikariDataSource()
         ds.setJdbcUrl(url)
         ds.setUsername(user)
         ds.setPassword(password)
         ds.setDriverClassName(driver)
         ds.setMaximumPoolSize(AppConfig.NumberOfVertxWorkers)
         ds
-    }
     def newConnection(): java.sql.Connection =
         dataSource.getConnection()
         // Class.forName(driver)

annosaurus/src/main/scala/org/mbari/annosaurus/controllers/AnnotationController.scala

@@ -525,8 +525,7 @@ class AnnotationController(
                             .getImageReferences
                             .isEmpty
                     then imDao.delete(imagedMoment)
-                    else
-                        imagedMoment.removeObservation(v)
+                    else imagedMoment.removeObservation(v)
 //                        d.delete(v)
                     true
         )

annosaurus/src/main/scala/org/mbari/annosaurus/controllers/CachedAncillaryDatumController.scala

@@ -81,7 +81,7 @@ class CachedAncillaryDatumController(val daoFactory: JPADAOFactory)
                             )
                         // TODO should this return the existing data?
                         None
-                    else {
+                    else
                         val cad = dao.newPersistentObject(
                             latitude,
                             longitude,
@@ -104,7 +104,6 @@ class CachedAncillaryDatumController(val daoFactory: JPADAOFactory)
 //                        println("---- " + cad)
                         imagedMoment.setAncillaryDatum(cad)
                         Some(cad)
-                    }
 
         for
             entity <- exec(fn)
@@ -126,11 +125,10 @@ class CachedAncillaryDatumController(val daoFactory: JPADAOFactory)
                         throw new RuntimeException(
                             s"ImagedMoment with UUID of $imagedMomentUuid already has ancillary data"
                         )
-                    else {
+                    else
                         val entity = datum.toEntity
                         imagedMoment.setAncillaryDatum(entity)
                         entity
-                    }
 
         for
             entity <- exec(fn)
@@ -289,10 +287,9 @@ class CachedAncillaryDatumController(val daoFactory: JPADAOFactory)
         if im.getAncillaryDatum != null then
             updateValues(im.getAncillaryDatum, d)
             im.getAncillaryDatum
-        else {
+        else
             im.setAncillaryDatum(d)
             im.getAncillaryDatum
-        }
 
     def merge(
         data: Iterable[CachedAncillaryDatum],
@@ -315,7 +312,7 @@ class CachedAncillaryDatumController(val daoFactory: JPADAOFactory)
                 cd.recordedTimestamp.map(_.toEpochMilli).getOrElse(-1L).toDouble
 
             if imagedMoments.isEmpty || usefulData.isEmpty then Seq.empty
-            else {
+            else
                 val mergedData = FastCollator(
                     imagedMoments,
                     imagedMomentToMillis,
@@ -330,7 +327,6 @@ class CachedAncillaryDatumController(val daoFactory: JPADAOFactory)
                 yield
                     val d = dao.newPersistentObject(cad.toEntity)
                     transform(createOrUpdate(d, im))
-            }
 
         exec(fn)
 

annosaurus/src/main/scala/org/mbari/annosaurus/controllers/FastAncillaryDataController.scala

@@ -18,7 +18,7 @@ package org.mbari.annosaurus.controllers
 
 import jakarta.persistence.EntityManager
 import org.mbari.annosaurus.domain.CachedAncillaryDatum
-import org.mbari.annosaurus.etc.jdk.Loggers.{*, given}
+import org.mbari.annosaurus.etc.jdk.Loggers.given
 
 import java.sql.Timestamp
 import java.time.Instant

annosaurus/src/main/scala/org/mbari/annosaurus/controllers/ImageController.scala

@@ -243,8 +243,7 @@ class ImageController(daoFactory: JPADAOFactory):
                     then
                         val imDao = daoFactory.newImagedMomentDAO(d)
                         imDao.delete(imagedMoment)
-                    else
-                        imagedMoment.removeImageReference(imageReference)
+                    else imagedMoment.removeImageReference(imageReference)
 //                        d.delete(imageReference)
                     true
         )

annosaurus/src/main/scala/org/mbari/annosaurus/controllers/ImageReferenceController.scala

@@ -123,8 +123,7 @@ class ImageReferenceController(val daoFactory: JPADAOFactory)
                     then
                         val imDao = daoFactory.newImagedMomentDAO(dao)
                         imDao.delete(imagedMoment)
-                    else
-                        imagedMoment.removeImageReference(imageReference)
+                    else imagedMoment.removeImageReference(imageReference)
 //                        dao.delete(imageReference)
                     true
         exec(fn)

annosaurus/src/main/scala/org/mbari/annosaurus/controllers/ObservationController.scala

@@ -216,8 +216,7 @@ class ObservationController(
                 then
                     val imDao = daoFactory.newImagedMomentDAO(dao)
                     imDao.delete(imagedMoment)
-                else {
+                else
                     imagedMoment.removeObservation(observation)
                     dao.delete(observation)
-                }
                 true

annosaurus/src/main/scala/org/mbari/annosaurus/domain/QueryConstraintsResponse.scala

@@ -16,8 +16,6 @@
 
 package org.mbari.annosaurus.domain
 
-
-
 final case class QueryConstraintsResponse[A](queryConstraints: QueryConstraints, content: A):
     def toSnakeCase: QueryConstraintsResponseSC[A] =
         QueryConstraintsResponseSC(queryConstraints.toSnakeCase, content)

annosaurus/src/main/scala/org/mbari/annosaurus/domain/QueryRequest.scala

@@ -58,17 +58,27 @@ case class QueryRequest(
 /**
  * ConstraintRequest is a case class that represents a constraint to apply to a query. It can have exactly 2 fields:
  * column and one of the following fields: between, contains, equals, in, isnull, like, max, min, minmax.
- * @param column The column to apply the constraint to
- * @param between A list of two numeric, or dat2 (as iso8601) values to apply a between constraint
- * @param contains Maps to a SQL 'LIKE' clause with the value wrapped in '%' characters
- * @param equals A value to apply an equals constraint
- * @param in A list of values to apply an 'IN' constraint
- * @param isnull A boolean value to apply an 'IS NULL' constraint. If true, the constraint is 'IS NULL', if false, the
- *               constraint is 'IS NOT NULL'
- * @param like A value to apply a 'LIKE' constraint. You must apply the '%' characters to the value before passing it
- * @param max The maximum value to apply a '<=' constraint
- * @param min The minimum value to apply a '>=' constraint
- * @param minmax A list of 2 numeric values to apply a 'BETWEEN' constraint
+ * @param column
+ *   The column to apply the constraint to
+ * @param between
+ *   A list of two numeric, or dat2 (as iso8601) values to apply a between constraint
+ * @param contains
+ *   Maps to a SQL 'LIKE' clause with the value wrapped in '%' characters
+ * @param equals
+ *   A value to apply an equals constraint
+ * @param in
+ *   A list of values to apply an 'IN' constraint
+ * @param isnull
+ *   A boolean value to apply an 'IS NULL' constraint. If true, the constraint is 'IS NULL', if false, the constraint is
+ *   'IS NOT NULL'
+ * @param like
+ *   A value to apply a 'LIKE' constraint. You must apply the '%' characters to the value before passing it
+ * @param max
+ *   The maximum value to apply a '<=' constraint
+ * @param min
+ *   The minimum value to apply a '>=' constraint
+ * @param minmax
+ *   A list of 2 numeric values to apply a 'BETWEEN' constraint
  */
 case class ConstraintRequest(
     column: String,

annosaurus/src/main/scala/org/mbari/annosaurus/endpoints/AnnotationEndpoints.scala

@@ -17,7 +17,17 @@
 package org.mbari.annosaurus.endpoints
 
 import org.mbari.annosaurus.controllers.AnnotationController
-import org.mbari.annosaurus.domain.{AnnotationCreateSC, AnnotationSC, AnnotationUpdateSC, BulkAnnotationSC, ConcurrentRequest, ConcurrentRequestCountSC, ErrorMsg, MultiRequest, MultiRequestCountSC}
+import org.mbari.annosaurus.domain.{
+    AnnotationCreateSC,
+    AnnotationSC,
+    AnnotationUpdateSC,
+    BulkAnnotationSC,
+    ConcurrentRequest,
+    ConcurrentRequestCountSC,
+    ErrorMsg,
+    MultiRequest,
+    MultiRequestCountSC
+}
 import org.mbari.annosaurus.endpoints.CustomTapirJsonCirce.*
 import org.mbari.annosaurus.etc.circe.CirceCodecs.given
 import org.mbari.annosaurus.etc.jwt.JwtService

annosaurus/src/main/scala/org/mbari/annosaurus/endpoints/AuthorizationEndpoints.scala

@@ -16,7 +16,15 @@
 
 package org.mbari.annosaurus.endpoints
 
-import org.mbari.annosaurus.domain.{Authorization, AuthorizationSC, BadRequest, ErrorMsg, NotFound, ServerError, Unauthorized}
+import org.mbari.annosaurus.domain.{
+    Authorization,
+    AuthorizationSC,
+    BadRequest,
+    ErrorMsg,
+    NotFound,
+    ServerError,
+    Unauthorized
+}
 import org.mbari.annosaurus.etc.circe.CirceCodecs.given
 import org.mbari.annosaurus.etc.jwt.JwtService
 import sttp.model.StatusCode

annosaurus/src/main/scala/org/mbari/annosaurus/endpoints/Endpoints.scala

@@ -24,10 +24,10 @@ import org.mbari.annosaurus.etc.jdk.Loggers.given
 import org.mbari.annosaurus.etc.jwt.JwtService
 import sttp.model.StatusCode
 import sttp.model.headers.WWWAuthenticateChallenge
+import sttp.tapir.*
 import sttp.tapir.generic.auto.*
 import sttp.tapir.json.circe.*
 import sttp.tapir.server.ServerEndpoint
-import sttp.tapir.*
 
 import java.net.{URI, URL}
 import java.time.Instant

annosaurus/src/main/scala/org/mbari/annosaurus/endpoints/FastAnnotationEndpoints.scala

@@ -16,7 +16,18 @@
 
 package org.mbari.annosaurus.endpoints
 
-import org.mbari.annosaurus.domain.{AnnotationSC, ConcurrentRequestSC, Count, DeleteCountSC, ErrorMsg, GeographicRangeSC, ImageSC, MultiRequestSC, QueryConstraints, QueryConstraintsResponseSC}
+import org.mbari.annosaurus.domain.{
+    AnnotationSC,
+    ConcurrentRequestSC,
+    Count,
+    DeleteCountSC,
+    ErrorMsg,
+    GeographicRangeSC,
+    ImageSC,
+    MultiRequestSC,
+    QueryConstraints,
+    QueryConstraintsResponseSC
+}
 import org.mbari.annosaurus.endpoints.CustomTapirJsonCirce.*
 import org.mbari.annosaurus.etc.circe.CirceCodecs.given
 import org.mbari.annosaurus.etc.jwt.JwtService

annosaurus/src/main/scala/org/mbari/annosaurus/endpoints/QueryEndpoints.scala

@@ -27,7 +27,6 @@ import sttp.tapir.server.ServerEndpoint
 import sttp.tapir.server.ServerEndpoint.Full
 
 import scala.concurrent.{ExecutionContext, Future}
-import java.nio.charset.StandardCharsets
 
 class QueryEndpoints(queryController: QueryController)(using executionContext: ExecutionContext) extends Endpoints:
 
@@ -62,9 +61,9 @@ class QueryEndpoints(queryController: QueryController)(using executionContext: E
             )
         )
 
-    // val runQueryStreaming = 
+    // val runQueryStreaming =
     //     openEndpoint
-    //         .post 
+    //         .post
     //         .in(base / "run")
     //         .in(jsonBody[QueryRequest])
     //         .out(streamTextBody(Fs2Streams[Future]), (CodecFormat.TextPlain(), Some(StandardCharsets.UTF_8)))

annosaurus/src/main/scala/org/mbari/annosaurus/repository/ImagedMomentDAO.scala

@@ -165,7 +165,7 @@ trait ImagedMomentDAO[T <: IPersistentObject] extends DAO[T]:
                 val im0 = elapsedTime.flatMap(findByVideoReferenceUUIDAndElapsedTime(uuid, _))
                 if im0.isEmpty then recordedDate.flatMap(findByVideoReferenceUUIDAndRecordedDate(uuid, _))
                 else im0
-        // This code has bug when resolving timecodes. See M3-15
+            // This code has bug when resolving timecodes. See M3-15
 //    val im0 = timecode.flatMap(findByVideoReferenceUUIDAndTimecode(uuid, _))
 //    val im1 = if (im0.isEmpty) elapsedTime.flatMap(findByVideoReferenceUUIDAndElapsedTime(uuid, _)) else im0
 //    if (im1.isEmpty) recordedDate.flatMap(findByVideoReferenceUUIDAndRecordedDate(uuid, _)) else im1

annosaurus/src/main/scala/org/mbari/annosaurus/repository/jdbc/TimeHistogramSQL.scala

@@ -16,8 +16,6 @@
 
 package org.mbari.annosaurus.repository.jdbc
 
-import io.prometheus.metrics.shaded.com_google_protobuf_3_25_3.Timestamp
-
 import java.time.Instant
 
 object TimeHistogramSQL:

annosaurus/src/main/scala/org/mbari/annosaurus/repository/jpa/BaseDAO.scala

@@ -28,7 +28,7 @@ import java.lang.System.Logger.Level
 import java.util.UUID
 import scala.concurrent.{ExecutionContext, Future}
 import scala.jdk.CollectionConverters.*
-import scala.reflect.{ClassTag, classTag}
+import scala.reflect.{classTag, ClassTag}
 
 /**
  * @author

annosaurus/src/main/scala/org/mbari/annosaurus/repository/jpa/ImagedMomentDAOImpl.scala

@@ -26,7 +26,7 @@ import org.mbari.vcr4j.time.Timecode
 import java.sql.Timestamp
 import java.time.{Duration, Instant}
 import java.util.function.Function
-import java.util.{UUID, stream}
+import java.util.{stream, UUID}
 import scala.jdk.CollectionConverters.*
 
 /**

annosaurus/src/main/scala/org/mbari/annosaurus/repository/jpa/ObservationDAOImpl.scala

@@ -25,7 +25,7 @@ import org.mbari.annosaurus.repository.jpa.entity.ObservationEntity
 
 import java.time.{Duration, Instant}
 import java.util as ju
-import java.util.{UUID, stream}
+import java.util.{stream, UUID}
 import scala.jdk.CollectionConverters.*
 
 /**

annosaurus/src/main/scala/org/mbari/annosaurus/repository/query/PreparedStatementGenerator.scala

@@ -83,7 +83,7 @@ object PreparedStatementGenerator:
         tableName: String,
         query: Query
     ): String =
-        if (query.where.isEmpty) ""
+        if query.where.isEmpty then ""
         else
             val wheres = query.where.map(_.toPreparedStatementTemplate).mkString(" AND ")
             if query.concurrentObservations && query.relatedAssociations then s"""WHERE $ObservationUuid IN (

annosaurus/src/main/scala/org/mbari/annosaurus/repository/query/QueryService.scala

@@ -17,19 +17,16 @@
 package org.mbari.annosaurus.repository.query
 
 import org.mbari.annosaurus.DatabaseConfig
-import org.mbari.annosaurus.domain.Association
 import org.mbari.annosaurus.etc.jdk.Loggers.{*, given}
-import org.mbari.annosaurus.repository.jdbc.*
 
 import java.sql.ResultSet
-import scala.collection.mutable.ListBuffer
 import scala.util.Using
 
 class QueryService(databaseConfig: DatabaseConfig, viewName: String):
 
-    val jdbc               = new JDBC(databaseConfig)
+    val jdbc        = new JDBC(databaseConfig)
 //    val AnnotationViewName = "annotations"
-    private val log        = System.getLogger(getClass.getName)
+    private val log = System.getLogger(getClass.getName)
 
 //    def findAllConceptNames(): Either[Throwable, Seq[String]] =
 //        jdbc.findDistinct(viewName, "concept", stringConverter)

annosaurus/src/main/scala/org/mbari/annosaurus/repository/query/constraints.scala

@@ -37,7 +37,11 @@ case class Query(
 
 object Query:
 
-    def validate(queryRequest: QueryRequest, checkWhere: Boolean = true, checkSelect: Boolean = true): Either[Throwable, Query] =
+    def validate(
+        queryRequest: QueryRequest,
+        checkWhere: Boolean = true,
+        checkSelect: Boolean = true
+    ): Either[Throwable, Query] =
         val query = from(queryRequest)
         if checkWhere && query.where.isEmpty then Left(new IllegalArgumentException("where clause is required"))
         else if checkSelect && query.select.isEmpty then Left(new IllegalArgumentException("select clause is required"))

it/src/main/scala/org/mbari/annosaurus/AssertUtils.scala

@@ -17,7 +17,15 @@
 package org.mbari.annosaurus
 
 import org.junit.Assert.*
-import org.mbari.annosaurus.repository.jpa.entity.{AssociationEntity, CachedAncillaryDatumEntity, CachedVideoReferenceInfoEntity, ImageReferenceEntity, ImagedMomentEntity, IndexEntity, ObservationEntity}
+import org.mbari.annosaurus.repository.jpa.entity.{
+    AssociationEntity,
+    CachedAncillaryDatumEntity,
+    CachedVideoReferenceInfoEntity,
+    ImageReferenceEntity,
+    ImagedMomentEntity,
+    IndexEntity,
+    ObservationEntity
+}
 
 import scala.jdk.CollectionConverters.*
 

it/src/main/scala/org/mbari/annosaurus/controllers/AnnotationControllerSuite.scala

@@ -18,7 +18,6 @@ package org.mbari.annosaurus.controllers
 
 import org.mbari.annosaurus.AssertUtils
 import org.mbari.annosaurus.domain.{Annotation, ConcurrentRequest, MultiRequest}
-import org.mbari.annosaurus.etc.circe.CirceCodecs.*
 import org.mbari.annosaurus.etc.sdk.Futures.*
 import org.mbari.annosaurus.repository.jpa.{BaseDAOSuite, ImagedMomentDAOImpl, JPADAOFactory}
 import org.mbari.vcr4j.time.Timecode

it/src/main/scala/org/mbari/annosaurus/controllers/TestUtils.scala

@@ -30,7 +30,7 @@ import java.sql.Connection
 import java.time.{Duration, Instant}
 import java.util.UUID
 import java.util.concurrent.TimeUnit
-import scala.concurrent.{Await, ExecutionContext, duration}
+import scala.concurrent.{duration, Await, ExecutionContext}
 import scala.util.Random
 
 object TestUtils:

it/src/main/scala/org/mbari/annosaurus/endpoints/AnalysisEndpointsSuite.scala

@@ -72,10 +72,10 @@ trait AnalysisEndpointsSuite extends EndpointsSuite:
 
     // TODO both the depth and time histogram logic needs to be reworked. They can give incorrect results
     test("timeHistogram".flaky) {
-        val xs = TestUtils.create(5, 5, includeData = true)
-        val minTime = xs.map(_.getRecordedTimestamp).min
-        val maxTime = xs.map(_.getRecordedTimestamp).max
-        val expected = xs.flatMap(_.getObservations.asScala).size
+        val xs                  = TestUtils.create(5, 5, includeData = true)
+        val minTime             = xs.map(_.getRecordedTimestamp).min
+        val maxTime             = xs.map(_.getRecordedTimestamp).max
+        val expected            = xs.flatMap(_.getObservations.asScala).size
         val videoReferenceUuids = xs.map(_.getVideoReferenceUuid).distinct
         val qcr                 = QueryConstraints(
             videoReferenceUuids = Seq(xs.head.getVideoReferenceUuid),