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build.sbt
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build.sbt
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// SPDX-License-Identifier: MIT
// Copyright (c) 2020 Hadrien Chauvin
name := "exploratory-pipeline-example"
organization in ThisBuild := "io.hchauvin"
scalaVersion in ThisBuild := "2.12.1"
version in ThisBuild := "0.1"
ThisBuild / fork in Test := true
// Get configuration for R.
lazy val rConfig = {
import sys.process._
val stdout = Seq("Rscript", "-e", "cat(system.file(\"jri\",package=\"rJava\"), \"|\", R.home())")!!
val parts = stdout.split(" \\| ")
println("JRI PATH: " + parts(0).trim)
Map('jriPath -> parts(0).trim, 'rHome -> parts(1).trim)
}
ThisBuild / javaOptions in Test += s"-Djava.library.path=${rConfig('jriPath)}"
ThisBuild / envVars in Test := Map("R_HOME" -> rConfig('rHome))
lazy val global = project
.in(file("."))
.disablePlugins(AssemblyPlugin)
.aggregate(
`spark-r`,
`spark-reflow`,
`bioinformatics`
)
lazy val `spark-r` = project
.settings(
name := "spark-r",
libraryDependencies ++= Seq(
"org.nuiton.thirdparty" % "JRI" % "0.9-9",
"org.apache.spark" %% "spark-core" % "3.0.0-preview2" % "provided",
"org.apache.spark" %% "spark-sql" % "3.0.0-preview2" % "provided",
"org.polynote" %% "polynote-runtime" % "0.3.4" % "provided",
"org.scalatest" %% "scalatest" % "3.1.1" % "test",
"com.holdenkarau" %% "spark-testing-base" % "2.4.5_0.14.0" % "test"
),
assemblyOption in assembly := (assemblyOption in assembly).value.copy(includeScala = false),
test in assembly := {}
)
lazy val `spark-reflow` = project
.settings(
name := "spark-reflow",
libraryDependencies ++= Seq(
"org.apache.spark" %% "spark-core" % "3.0.0-preview2" % "provided",
"org.apache.spark" %% "spark-sql" % "3.0.0-preview2" % "provided",
"org.json4s" %% "json4s-native" % "3.7.0-M2",
"org.apache.hadoop" % "hadoop-aws" % "2.7.4",
"org.scalatest" %% "scalatest" % "3.1.1" % "test",
"com.holdenkarau" %% "spark-testing-base" % "2.4.5_0.14.0" % "test"
),
assemblyOption in assembly := (assemblyOption in assembly).value.copy(includeScala = false),
test in assembly := {},
assemblyMergeStrategy in assembly := {
case PathList("META-INF", xs @ _*) => MergeStrategy.discard
case x => MergeStrategy.first
}
)
lazy val `bioinformatics` = project
.settings(
name := "bioinformatics",
libraryDependencies ++= Seq(
"org.apache.spark" %% "spark-core" % "3.0.0-preview2" % "provided",
"org.apache.spark" %% "spark-sql" % "3.0.0-preview2" % "provided",
"org.scalatest" %% "scalatest" % "3.1.1" % "test",
"org.nuiton.thirdparty" % "JRI" % "0.9-9",
"com.holdenkarau" %% "spark-testing-base" % "2.4.5_0.14.0" % "test"
),
assemblyOption in assembly := (assemblyOption in assembly).value.copy(includeScala = false),
test in assembly := {},
assemblyMergeStrategy in assembly := {
case PathList("META-INF", xs @ _*) => MergeStrategy.discard
case x => MergeStrategy.first
}
).dependsOn(
`spark-r` % "provided",
`spark-reflow` % "provided"
)
ThisBuild / assemblyMergeStrategy in assembly := {
case PathList("META-INF", xs @ _*) => MergeStrategy.discard
case x => MergeStrategy.first
}
ThisBuild / test in assembly := {}