Scala CWL library

cwlScala is a Scala wrapper around cwljava v1.2, the Java parser for the Common Workflow Langauge. Also included is an evaluation engine for CWL expressions (which are ECMAscript 5.1), which is based on the rhinos wrapper of the Mozilla Rhino JavaScript engine.

Examples

Parsing a CWL CommandLineTool

// parsing a CommandLineTool
import java.nio.file.Paths
import dx.cwl.{CommandLineTool, Parser}
object ParserExample {
  val tool: CommandLineTool = Parser.parse(Paths.get("../../test/resources/tools/pass/action.cwl")) match {
    case tool: CommandLineTool => tool
    case _                     => throw new Exception("not a CommandLineTool")
  }
  tool.inputs.map { param =>
    println(s"${param.id.get}: ${param.types}")
  }
}

Evaluating an ECMAscript expression

import dx.cwl._

object EvalutatorExample {
  val evaluator: Evaluator = Evaluator(jsEnabled = true)
  val ctx: EvaluatorContext = EvaluatorContext(inputs = ObjectValue(
      Map(
          "name" -> StringValue("Ned")
      )
  )
  )
  val msg: String = evaluator.applyString("Hello $(inputs.name)!")
  println(msg)
}

Requirements

• JDK 11
• Scala 2.13
• sbt

Using

cwlScala is published in the Maven repository. You can include it in your build.sbt file like so:

val cwlScalaVersion = "0.1.0"
libraryDependencies ++= Seq(
    "com.dnanexus" % "cwlScala" % cwlScalaVersion
)

Building

$ git clone --recurse-submodules https://github.com/dnanexus/cwlScala.git
$ sbt publishLocal

Support

cwlScala is not an official product of DNAnexus. Please do not contact DNAnexus (or any employees thereof) for support. To report a bug or feature request, please open an issue in the issue tracker.