Scala programming language library for parsing WDL, and command-line tools for type-checking, code formatting, and more.
The wdlTools.syntax
package implements an abstract syntax tree (AST) for WDL. It uses the OpenWDL Antlr4 grammar originally created by Patrick Magee.
Currently, WDL draft-2, 1.0, 1.1, and development/2.0 are fully supported (with some limitations).
import wdlTools.syntax.AbstractSyntax._
import wdlTools.syntax.Parsers
import dx.util.{FileNode, FileSourceResolver}
val parsers = Parsers(followImports = true)
val wdl: FileNode = FileSourceResolver.get.resolve("file:///path/to/my/wdl")
val doc: Document = parsers.parseDocument(wdl)
// print the source locations of all tasks in the document
doc.elements.foreach {
case task: Task => println(s"Task ${task.name} is at ${task.loc}")
}
The wdlTools JAR also provides various command line tools to accelerate and simplify the development of WDL workflows. You can get help by running:
$ java -jar wdlTools.jar [command] --help
The following commands are currently available. They should be considered "beta" quality - please report any bugs/enhancements using the issue tracker.
lint
.The java code for the parser is generated by the ANTRL4 tool.
cd GIT_REPO
$HOME/antlr-4.9-complete.jar
generated java code from the grammar by running make
from the toplevel.sbt compile
sbt test
See the documentation for full details.
wdlTools 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.