build.sbt

// multi-project structure Borrowed/Inspired by
// https://github.com/jsuereth/sbt-in-action-examples/blob/master/chapter3/build.sbt
// Project structure
// - smrt-common-models (i.e., pb-common-models)
// - smrt-analysis (i.e., pbscala)
// - smrt-server-base
// - smrt-server-smrtlink
// - smrt-server-analysis
// - smrt-server-sim

name := "smrtflow"

version in ThisBuild := "0.14.0-SNAPSHOT"

organization in ThisBuild := "pacbio.smrt.smrtflow"

// Seeing a lot of evicted calls
scalaVersion in ThisBuild := "2.12.4"

// This is useful, but is really chattery. "-Ywarn-dead-code"
scalacOptions in ThisBuild := Seq(
  "-target:jvm-1.8",
  "-encoding",
  "UTF-8",
  "-unchecked",
  "-deprecation",
  "-feature",
  "-Xfatal-warnings"
  // "-Ywarn-dead-code"
)

// NOT WORKING. This should enables Ctl+C to not exit SBT
// cancelable in Global := true

parallelExecution in ThisBuild := true

fork in ThisBuild := true

javaOptions in ThisBuild += "-Xms256m"

javaOptions in ThisBuild += "-Xmx8g"

// tmp files are written during testing; cannot be mounted noexec because of sqlite
javaOptions in ThisBuild += "-Djava.io.tmpdir=" + (if (sys.env
                                                         .get("TMP")
                                                         .isDefined)
                                                     sys.env("TMP")
                                                   else "/tmp")

// Custom keys for this build.

val gitHeadCommitSha = taskKey[String]("Determines the current git commit SHA")

val makeVersionProperties = taskKey[Seq[File]](
  "Creates a version.properties file we can find at runtime.")

val makePacBioComponentManifest =
  taskKey[Seq[File]]("Creates a pacbio-manifest.json as a managed resource")

val akkaV = "2.4.20"

val akkaHttpV = "10.0.11"

val sprayV = "1.3.3"

val slickV = "3.2.1"

val specs2V = "4.0.2"

val bambooBuildNumberEnv = "bamboo_globalBuildNumber"

scalafmtOnCompile in ThisBuild := true // all projects

resolvers in ThisBuild += "mbilski" at "http://dl.bintray.com/mbilski/maven"

resolvers in ThisBuild += "lightshed-maven" at "http://dl.bintray.com/content/lightshed/maven"

credentials in ThisBuild += Credentials(
  Path.userHome / ".ivy2" / ".credentials")

publishTo in ThisBuild := {
  val nexus = "http://ossnexus.pacificbiosciences.com/repository/"
  if (isSnapshot.value) Some("Nexus snapshots" at nexus + "maven-snapshots")
  else Some("Nexus releases" at nexus + "maven-releases")
}

lazy val baseSettings = Seq(
  "ch.qos.logback" % "logback-classic" % "1.1.7",
  "com.typesafe.akka" %% "akka-http" % akkaHttpV,
  "com.typesafe.akka" %% "akka-http-core" % akkaHttpV,
  "com.typesafe.akka" %% "akka-http-spray-json" % akkaHttpV,
  "com.typesafe.akka" %% "akka-http-xml" % akkaHttpV,
  "ch.megard" %% "akka-http-cors" % "0.2.2",
  "com.typesafe.akka" %% "akka-http-testkit" % akkaHttpV % "test",
  "com.enragedginger" %% "akka-quartz-scheduler" % "1.6.0-akka-2.4.x",
  "com.github.samtools" % "htsjdk" % "1.129",
  "com.google.guava" % "guava" % "23.5-jre", // this is only added for the VisibleForTesting annotation. We should consider removing this
  "com.github.nscala-time" %% "nscala-time" % "2.18.0",
  "com.github.scopt" %% "scopt" % "3.5.0", // Explicitly use this version to be bin compat with ammonite
  "com.github.t3hnar" %% "scala-bcrypt" % "3.1",
  "com.github.tototoshi" %% "slick-joda-mapper" % "2.3.0",
  "com.jason-goodwin" %% "authentikat-jwt" % "0.4.5",
  // "com.pauldijou" %% "jwt-core" % "0.14.0", // We should use this. https://github.com/pauldijou/jwt-scala
  "com.jsuereth" %% "scala-arm" % "2.0",
  "com.lihaoyi" % "ammonite" % "1.0.3" cross CrossVersion.full,
  "com.lihaoyi" %% "scalatags" % "0.6.7",
  "com.novocode" % "junit-interface" % "0.10" % "test",
  "com.typesafe.akka" %% "akka-actor" % akkaV,
  "com.typesafe.akka" %% "akka-slf4j" % akkaV,
  "com.typesafe.scala-logging" %% "scala-logging" % "3.7.2",
  "com.typesafe.slick" %% "slick" % slickV,
  "com.typesafe.slick" %% "slick-hikaricp" % slickV,
  "io.underscore" %% "slickless" % "0.3.2",
  "commons-cli" % "commons-cli" % "1.2",
  "commons-io" % "commons-io" % "2.4",
  "commons-lang" % "commons-lang" % "2.6",
  "org.apache.commons" % "commons-compress" % "1.13",
  "io.spray" %% "spray-json" % "1.3.2",
  "com.github.fommil" %% "spray-json-shapeless" % "1.4.0", // Is this still necessary for 2.12?
  "joda-time" % "joda-time" % "2.9.9",
  "net.sourceforge.saxon" % "saxon" % "9.1.0.8",
  "org.apache.avro" % "avro" % "1.8.0",
  "org.apache.commons" % "commons-dbcp2" % "2.1.1",
  "org.eclipse.persistence" % "eclipselink" % "2.6.0",
  "org.eclipse.persistence" % "org.eclipse.persistence.moxy" % "2.6.0",
  "org.flywaydb" % "flyway-core" % "4.0.3",
  "org.ini4j" % "ini4j" % "0.5.4",
  "org.joda" % "joda-convert" % "1.6",
  "org.scala-lang.modules" %% "scala-xml" % "1.0.6",
  "org.typelevel" %% "cats-core" % "1.0.1",
  "org.specs2" %% "specs2-core" % specs2V % "test,it", // this is the new group for specs2
  "org.specs2" %% "specs2-mock" % specs2V % "test,it",
  "com.novocode" % "junit-interface" % "0.11" % "test,it",
  "org.specs2" %% "specs2-junit" % specs2V % "test,it",
  "org.specs2" %% "specs2-html" % specs2V % "test,it",
  "org.postgresql" % "postgresql" % "42.1.4",
  "org.utgenome.thirdparty" % "picard" % "1.86.0",
  "log4j" % "log4j" % "1.2.17",
  "org.eclipse.jgit" % "org.eclipse.jgit" % "4.6.0.201612231935-r",
  "com.github.zafarkhaja" % "java-semver" % "0.9.0",
//  "mbilski" %% "spray-hmac" % "1.0.1", This probably should just be copied. It's only a few lines of code
  "ch.lightshed" %% "courier" % "0.1.4",
  "javax.mail" % "mail" % "1.4.7"
).map(_.exclude("javax.mail", "mailapi")) // The mailapi is only the interface. This will cause dedupe issues with assembly

gitHeadCommitSha in ThisBuild := scala.sys.process
  .Process("git rev-parse HEAD")
  .lineStream
  .head

def getBuildNumber(): Option[Int] =
  sys.env.get(bambooBuildNumberEnv).map(_.toInt)

// Util to mirror bash clear
def clearConsoleCommand = Command.command("clear") { state =>
  val cr = new jline.console.ConsoleReader()
  cr.clearScreen
  state
}

/**
  * Util func to write the version.properties managed file
  *
  * @param path          Path to the version properties file
  * @param versionString Major.Minor.Patch version string
  * @param gitSha        GIT SHA
  * @param buildNumber   Bamboo Build number or empty string
  * @return
  */
def writeVersionProperties(path: File,
                           versionString: String,
                           gitSha: String,
                           buildNumber: String) = {
  val content = "version=%s\nsha1=%s\nbuildNumber=%s" format (versionString, gitSha, buildNumber)
  IO.write(path, content)
  Seq(path)
}

/**
  * Util func for writing the pacbio-manifest.json Managed file
  *
  * @param path          Path to pacbio-manifest.json
  * @param versionString Major.Minor.Patch version string
  * @param gitSha        Git Short SHA
  * @param buildNumber   Bamboo Build number or empty string
  * @return
  */
def writePacBioManifest(path: File,
                        versionString: String,
                        gitSha: String,
                        buildNumber: String) = {
  val pacbioVersion = "%s+%s%s" format (versionString, buildNumber, gitSha)
  val manifest = s"""
                    |{
                    | "id":"smrtlink_services",
                    | "name": "SMRT Analysis Services",
                    | "version": "$pacbioVersion",
                    | "description":"SMRT Link Analysis Services and Job Orchestration engine",
                    | "dependencies": ["pbsmrtpipe", "sawriter", "gmap", "ngmlr"]
                    |}
              """.stripMargin
  IO.write(path, manifest)
  Seq(path)
}

/**
  * Util to generate a PacBio Project with default Settings
  *
  * @param name subproject name
  * @return
  */
def toPacBioProject(name: String): Project =
  Project(name, file(name))
    .settings(Defaults.itSettings: _*)
    .settings(libraryDependencies ++= baseSettings)
//    .settings(coverageEnabled := false)
    .settings(fork in Test := true)
    .settings(fork in IntegrationTest := true)
    .settings(testOptions in Test += Tests
      .Argument(TestFrameworks.Specs2, "junitxml", "console"))
    .disablePlugins(plugins.JUnitXmlReportPlugin) // MK. Why is this disabled?
    .configs(IntegrationTest)

// Project to use the ammonite repl
lazy val smrtflow = project
  .in(file("."))
  .settings(moduleName := "smrtflow")
  .settings(publish := {})
  .settings(publishLocal := {})
  .settings(publishArtifact := false)
  .settings(fork in Test := true)
  .settings(fork in IntegrationTest := true)
  .settings(fork in run := true)
  .settings(javaOptions in (Test, console) += "-Xmx4G") // Bump for repl usage
  .settings(libraryDependencies ++= baseSettings)
  .settings(exportJars := true)
  // .settings(coverageEnabled := false) // ammonite will disable it because <dataDir> is not defined
  //.settings(parallelExecution in Test := false) // run each Spec sequentially
  .settings(initialCommands in (Test, console) := """ammonite.Main().run()""")
  .settings(Defaults.itSettings: _*)
  .settings(testOptions in Test += Tests
    .Argument(TestFrameworks.Specs2, "junitxml", "console"))
  .disablePlugins(plugins.JUnitXmlReportPlugin) // MK. Why is this disabled?
  .configs(IntegrationTest)
  .dependsOn(common,
             smrtServerLink,
             smrtServerSim,
             smrtServerBundle,
             smrtServerEve)
  .aggregate(common,
             smrtServerLink,
             smrtServerSim,
             smrtServerBundle,
             smrtServerEve)

lazy val common =
  toPacBioProject("smrt-common-models")
    .settings(
      resourceGenerators in Compile += Def.task {
        val propFile = (resourceManaged in Compile).value / "version.properties"
        writeVersionProperties(
          propFile,
          version.value,
          gitHeadCommitSha.value,
          getBuildNumber().map(_.toString).getOrElse("Unknown"))
      }.taskValue
    )
    .settings(
      resourceGenerators in Compile += Def.task {
        val propFile = (resourceManaged in Compile).value / "pacbio-manifest.json"
        val sfVersion = version.value.replace("-SNAPSHOT", "")
        val bambooBuildNumber =
          getBuildNumber().map(number => s"$number.").getOrElse("")
        writePacBioManifest(propFile,
                            sfVersion,
                            gitHeadCommitSha.value.take(7),
                            bambooBuildNumber)
      }.taskValue
    )

lazy val smrtServerLink =
  toPacBioProject("smrt-server-link")
    .dependsOn(common)
    .settings(mainClass in assembly := Some(
                "com.pacbio.secondary.smrtlink.app.SmrtLinkSmrtServer"),
              assemblyJarName in assembly := "smrt-server-link-analysis.jar")

lazy val smrtServerSim =
  toPacBioProject("smrt-server-sim")
    .dependsOn(common, smrtServerLink)
    .settings()

lazy val smrtServerBundle =
  toPacBioProject("smrt-server-bundle")
    .dependsOn(common, smrtServerLink)
    .settings()

lazy val smrtServerEve =
  toPacBioProject("smrt-server-eve")
    .dependsOn(common, smrtServerLink)
    .settings()