Fix dependency conflicts

.gitignore

@@ -65,6 +65,7 @@ TAGS
 
 # sbt specific
 .cache
+.coursier-cache
 .history
 .lib/
 dist/*

app-backend/api/src/main/scala/toolrun/Routes.scala

@@ -7,7 +7,6 @@ import com.azavea.rf.datamodel._
 import com.azavea.rf.tool.ast.MapAlgebraAST
 import com.azavea.rf.tool.eval.PureInterpreter
 import com.azavea.rf.database.filter.Filterables._
-import com.azavea.maml.serve.InterpreterExceptionHandling
 import com.lonelyplanet.akka.http.extensions.PaginationDirectives
 import de.heikoseeberger.akkahttpcirce.ErrorAccumulatingCirceSupport._
 import akka.http.scaladsl.model.StatusCodes
@@ -33,8 +32,7 @@ trait ToolRunRoutes extends Authentication
     with PaginationDirectives
     with ToolRunQueryParametersDirective
     with CommonHandlers
-    with UserErrorHandler
-    with InterpreterExceptionHandling {
+    with UserErrorHandler {
 
   val xa: Transactor[IO]
 
@@ -95,7 +93,7 @@ trait ToolRunRoutes extends Authentication
   def createToolRun: Route = authenticate { user =>
     entity(as[ToolRun.Create]) { newRun =>
       onSuccess(ToolRunDao.insertToolRun(newRun, user).transact(xa).unsafeToFuture) { toolRun =>
-        handleExceptions(interpreterExceptionHandler) {
+        {
           complete {
             (StatusCodes.Created, toolRun)
           }

app-backend/api/src/main/scala/tools/Routes.scala

@@ -7,7 +7,6 @@ import com.azavea.rf.datamodel._
 import com.azavea.rf.tool.ast._
 import com.azavea.rf.tool.ast.codec._
 import com.azavea.rf.database.filter.Filterables._
-import com.azavea.maml.serve._
 import io.circe._
 import akka.http.scaladsl.model.StatusCodes
 import akka.http.scaladsl.server.Route
@@ -32,7 +31,6 @@ trait ToolRoutes extends Authentication
     with PaginationDirectives
     with CommonHandlers
     with KamonTraceDirectives
-    with InterpreterExceptionHandling
     with UserErrorHandler {
 
   val xa: Transactor[IO]
@@ -193,7 +191,7 @@ trait ToolRoutes extends Authentication
 
   def validateAST: Route = authenticate { user =>
     entity(as[Json]) { jsonAst =>
-      handleExceptions(interpreterExceptionHandler) {
+      {
         complete {
           jsonAst.as[MapAlgebraAST] match {
             case Right(ast) =>

app-backend/batch/src/main/scala/com/azavea/rf/batch/export/spark/Export.scala

@@ -11,7 +11,6 @@ import com.azavea.rf.batch.util._
 import com.azavea.rf.batch.util.conf._
 import com.azavea.rf.datamodel._
 import com.azavea.rf.tool.ast.MapAlgebraAST
-import com.azavea.maml.serve._
 import com.azavea.maml.eval._
 import io.circe.parser._
 import io.circe.syntax._

app-backend/batch/src/main/scala/com/azavea/rf/batch/ingest/spark/Ingest.scala

@@ -165,7 +165,7 @@ object Ingest extends SparkJob with RollbarNotifier with Config {
         bucket = s3uri.getBucket,
         key = s3uri.getKey,
         client = S3Client.DEFAULT),
-      decompress = false, streaming = true, withOverviews = true, None)
+      streaming = true, withOverviews = true, None)
     }
 
     val info = readInfo

app-backend/batch/src/main/scala/com/azavea/rf/batch/migration/S3ToPostgres.scala

@@ -39,8 +39,8 @@ case class S3ToPostgres(uri: AmazonS3URI, attributeTable: String = "layer_attrib
               val LayerAttributes(header, metadata, keyIndex, schema) = from.readLayerAttributesSafe[S3LayerHeader, TileLayerMetadata[SpatialKey], SpatialKey](layerId)
               to.write(layerId, AttributeStore.Fields.header, header)
               to.write(layerId, AttributeStore.Fields.metadata, metadata)
-              to.write(layerId, AttributeStore.Fields.keyIndex, keyIndex)
-              to.write(layerId, AttributeStore.Fields.schema, schema)
+              to.write(layerId, AttributeStore.AvroLayerFields.keyIndex, keyIndex)
+              to.write(layerId, AttributeStore.AvroLayerFields.schema, schema)
               to.write(layerId, "layerComplete", from.cacheReadSafe[Boolean](layerId, "layerComplete"))
             } else {
               to.write(layerId, "histogram", from.cacheReadSafe[Array[Histogram[Double]]](layerId, "histogram"))

app-backend/batch/src/main/scala/com/azavea/rf/batch/package.scala

@@ -54,8 +54,8 @@ package object batch {
       LayerAttributes(
         blob.fields(AttributeStore.Fields.header).convertTo[H],
         blob.fields(AttributeStore.Fields.metadata).convertTo[M],
-        blob.fields(AttributeStore.Fields.keyIndex).convertTo[KeyIndex[K]],
-        blob.fields(AttributeStore.Fields.schema).convertTo[Schema]
+        blob.fields(AttributeStore.AvroLayerFields.keyIndex).convertTo[KeyIndex[K]],
+        blob.fields(AttributeStore.AvroLayerFields.schema).convertTo[Schema]
       )
     }
   }

app-backend/build.sbt

@@ -335,7 +335,7 @@ lazy val tool = Project("tool", file("tool"))
   .settings(resolvers += Resolver.bintrayRepo("azavea", "maven"))
   .settings({
     libraryDependencies ++= loggingDependencies ++ Seq(
-      Dependencies.spark,
+      Dependencies.sparkCore,
       Dependencies.geotrellisSpark,
       Dependencies.geotrellisRaster,
       Dependencies.geotrellisRasterTestkit,
@@ -346,6 +346,7 @@ lazy val tool = Project("tool", file("tool"))
       Dependencies.circeParser,
       Dependencies.circeOptics,
       Dependencies.scalaCheck,
+      Dependencies.scalaz,
       Dependencies.mamlJvm
     )
   })

app-backend/common/src/main/scala/utils/CogUtils.scala

@@ -45,7 +45,7 @@ object CogUtils {
     }.mapFilter { headerBytes =>
       RangeReaderUtils.fromUri(uri).map { rr =>
         val crr = CacheRangeReader(rr, headerBytes)
-        GeoTiffReader.readMultiband(crr, decompress = false, streaming = true)
+        GeoTiffReader.readMultiband(crr, streaming = true)
       }
     }
   }
@@ -149,7 +149,7 @@ object CogUtils {
   def getTiffExtent(uri: String): Option[Projected[MultiPolygon]] = {
     for {
       rr <- RangeReaderUtils.fromUri(uri)
-      tiff = GeoTiffReader.readMultiband(rr, decompress = false, streaming = true)
+      tiff = GeoTiffReader.readMultiband(rr, streaming = true)
     } yield {
       val crs = tiff.crs
       Projected(MultiPolygon(tiff.extent.reproject(crs, WebMercator).toPolygon()), 3857)

app-backend/datamodel/src/main/scala/com/azavea/rf/datamodel/package.scala

@@ -12,7 +12,7 @@ import io.circe.generic.semiauto._
 
 import com.azavea.rf.bridge._
 
-import geotrellis.vector._
+import geotrellis.vector.{Projected => _, _}
 import geotrellis.vector.io._
 import geotrellis.proj4._
 import geotrellis.slick._

app-backend/db/src/main/scala/com/azavea/rf/database/ProjectDao.scala

@@ -159,7 +159,7 @@ object ProjectDao extends Dao[Project] {
   }
 
   def addScenesToProject(sceneIds: NonEmptyList[UUID], projectId: UUID, user: User, isAccepted: Boolean): ConnectionIO[Int] = {
-    val inClause = fr"scenes.id IN (" ++ Fragment.const(sceneIds.map(_.show).foldSmash("'", "','", "'")) ++ fr")"
+    val inClause = Fragments.in(fr"scenes.id",  sceneIds)
     val sceneIdWithDatasourceF = fr"""
       SELECT scenes.id,
             datasources.id,

app-backend/db/src/main/scala/com/azavea/rf/database/SceneToProjectDao.scala

@@ -50,12 +50,10 @@ object SceneToProjectDao extends Dao[SceneToProject] with LazyLogging {
     val updateF: Fragment =fr"""
       UPDATE scenes_to_projects
       SET accepted = true
-      WHERE
-        project_id = ${projectId}
-        AND
-        scene_id IN (""" ++
-      Fragment.const(sceneIds.map(_.show).foldSmash("'", "','", "'")) ++
-      fr")"
+    """ ++ Fragments.whereAnd(
+      fr"project_id = $projectId",
+      Fragments.in(fr"scene_id", sceneIds)
+    )
     updateF.update.run
   }