Release 0.8

README.md

@@ -165,6 +165,109 @@ $ java -jar wdltool.jar highlight test.wdl html
 }
 ```
 
+## graph 
+ 
+The syntax of the graph command is:
+```
+wdltool graph [--all] wdlFile.wdl
+```
+
+Given a WDL file input, command generates the data-flow graph through the system in `.dot` format.
+
+For example the fork-join WDL:
+```
+task mkFile {
+  command {
+    for i in `seq 1 1000`
+    do
+      echo $i
+    done
+  }
+  output {
+    File numbers = stdout()
+  }
+  runtime {docker: "ubuntu:latest"}
+}
+
+task grep {
+  String pattern
+  File in_file
+  command {
+    grep '${pattern}' ${in_file} | wc -l
+  }
+  output {
+    Int count = read_int(stdout())
+  }
+  runtime {docker: "ubuntu:latest"}
+}
+
+task wc {
+  File in_file
+  command {
+    cat ${in_file} | wc -l
+  }
+  output {
+    Int count = read_int(stdout())
+  }
+  runtime {docker: "ubuntu:latest"}
+}
+
+task join {
+  Int grepCount
+  Int wcCount
+  command {
+    expr ${wcCount} / ${grepCount}
+  }
+  output {
+    Int proportion = read_int(stdout())
+  }
+  runtime {docker: "ubuntu:latest"}
+}
+
+workflow forkjoin {
+  call mkFile
+  call grep { input: in_file = mkFile.numbers }
+  call wc { input: in_file=mkFile.numbers }
+  call join { input: wcCount = wc.count, grepCount = grep.count }
+  output {
+    join.proportion
+  }
+}
+```
+
+Produces the DAG:
+```
+digraph forkjoin {
+  "call forkjoin.mkFile" -> "call forkjoin.wc"
+  "call forkjoin.mkFile" -> "call forkjoin.grep"
+  "call forkjoin.wc" -> "call forkjoin.join"
+  "call forkjoin.grep" -> "call forkjoin.join"
+}
+```
+
+### The --all flag
+
+If this flag is set, all WDL graph nodes become nodes in the generated DAG, even if they are not "executed". Typically this will mean task declarations and call outputs. 
+For example in the above example, with `--all` you would get:
+
+```
+digraph forkjoin {
+  "call forkjoin.grep" -> "String forkjoin.grep.pattern"
+  "call forkjoin.grep" -> "output { forkjoin.grep.count = read_int(stdout()) }"
+  "call forkjoin.grep" -> "File forkjoin.grep.in_file"
+  "call forkjoin.wc" -> "output { forkjoin.wc.count = read_int(stdout()) }"
+  "call forkjoin.grep" -> "call forkjoin.join"
+  "call forkjoin.wc" -> "File forkjoin.wc.in_file"
+  "call forkjoin.mkFile" -> "call forkjoin.grep"
+  "call forkjoin.join" -> "output { forkjoin.join.proportion = read_int(stdout()) }"
+  "call forkjoin.join" -> "Int forkjoin.join.wcCount"
+  "call forkjoin.wc" -> "call forkjoin.join"
+  "call forkjoin.mkFile" -> "output { forkjoin.mkFile.numbers = stdout() }"
+  "call forkjoin.mkFile" -> "call forkjoin.wc"
+  "call forkjoin.join" -> "Int forkjoin.join.grepCount"
+}
+```
+
 # Getting Started with WDL
 
 For documentation and many examples on how to use WDL see [the WDL website](https://software.broadinstitute.org/wdl/).

build.sbt

@@ -10,7 +10,7 @@ scalaVersion := "2.11.8"
 
 lazy val versionSettings = Seq(
   // Upcoming release, or current if we're on the master branch
-  git.baseVersion := "0.7",
+  git.baseVersion := "0.8",
 
   // Shorten the git commit hash
   git.gitHeadCommit := git.gitHeadCommit.value map { _.take(7) },
@@ -34,7 +34,7 @@ resolvers ++= Seq(
 )
 
 libraryDependencies ++= Seq(
-  "org.broadinstitute" %% "wdl4s" % "0.7-799567f-SNAP",
+  "org.broadinstitute" %% "wdl4s" % "0.8",
   //---------- Test libraries -------------------//
   "org.scalatest" %% "scalatest" % "2.2.5" % Test
 )

src/main/scala/wdltool/GraphPrint.scala

@@ -0,0 +1,77 @@
+package wdltool
+
+import java.nio.file.{Files, Paths}
+
+import wdl4s.{CallOutput, Declaration, If, Scatter, _}
+import scala.collection.JavaConverters._
+
+object GraphPrint {
+
+  case class WorkflowDigraph(workflowName: String, digraph: Set[String])
+
+  def generateWorkflowDigraph(file: String, allNodesMode: Boolean): WorkflowDigraph = {
+    val namespace = WdlNamespaceWithWorkflow.load(Files.readAllLines(Paths.get(file)).asScala.mkString(System.lineSeparator()), Seq(WdlNamespace.fileResolver _))
+
+    val digraph = if (allNodesMode) {
+      listAllGraphNodes(namespace)
+    } else {
+      val executables = GraphPrint.listExecutableGraphNodes(namespace.workflow)
+      listAllGraphNodes(namespace, graphNode => executables.contains(graphNode))
+    }
+
+    WorkflowDigraph(namespace.workflow.unqualifiedName, digraph)
+  }
+
+  private def defaultFilter: GraphNode => Boolean = _ => true
+
+  private def listAllGraphNodes(namespace: WdlNamespaceWithWorkflow, filter: GraphNode => Boolean = defaultFilter): Set[String] = {
+
+    val graphNodes = namespace.descendants collect {
+      case g: GraphNode if filter(g) => g
+    }
+
+    graphNodes flatMap { graphNode =>
+      val name = graphName(graphNode)
+      val initialSet: Set[String] = graphNode match {
+        case c: Call => Set(s""""${dotSafe(name)}"""")
+        case _ => Set.empty
+      }
+      val upstreamLinks = graphNode.upstream collect {
+        case upstream if filter(upstream) =>
+          val upstreamName = graphName(upstream)
+          s""""${dotSafe(upstreamName)}" -> "${dotSafe(name)}""""
+      }
+
+      initialSet ++ upstreamLinks
+    }
+  }
+
+  private def listExecutableGraphNodes(s: Scope): Set[GraphNode] = {
+    s.children.toSet flatMap { child: Scope => child match {
+      case call: Call => Set[GraphNode](call)
+      case scatter: Scatter => Set[GraphNode](scatter) ++ listExecutableGraphNodes(scatter)
+      case i: If => Set[GraphNode](i) ++ listExecutableGraphNodes(i)
+      case declaration: Declaration => Set[GraphNode](declaration)
+      case _ => Set.empty[GraphNode]
+    }}
+  }
+
+
+  private def dotSafe(s: String) = s.replaceAllLiterally("\"", "\\\"")
+
+  private def graphName(g: GraphNode): String = g match {
+    case d: Declaration =>
+      val exprString = d.expression.map(e => " = " + e.toWdlString).getOrElse("")
+      s"${d.wdlType.toWdlString} ${d.fullyQualifiedName}$exprString"
+    case c: Call =>
+      s"call ${c.fullyQualifiedName}"
+    case i: If =>
+      s"if (${i.condition.toWdlString})"
+    case s: Scatter =>
+      s"scatter (${s.item} in ${s.collection.toWdlString})"
+    case c: CallOutput =>
+      val exprString = c.expression.map(e => " = " + e.toWdlString).getOrElse("")
+      s"output { ${c.fullyQualifiedName}$exprString }"
+    case other => s"${other.getClass.getSimpleName}: ${other.fullyQualifiedName}"
+  }
+}

src/main/scala/wdltool/Main.scala

@@ -3,9 +3,10 @@ package wdltool
 import java.nio.file.Paths
 
 import wdl4s.formatter.{AnsiSyntaxHighlighter, HtmlSyntaxHighlighter, SyntaxFormatter}
-import wdl4s.{AstTools, WdlNamespace, WdlNamespaceWithWorkflow}
+import wdl4s._
 import spray.json._
 
+
 import scala.util.{Failure, Success, Try}
 
 object Main extends App {
@@ -33,6 +34,7 @@ object Main extends App {
       case Some(x) if x == Actions.Highlight => highlight(args.tail)
       case Some(x) if x == Actions.Inputs => inputs(args.tail)
       case Some(x) if x == Actions.Parse => parse(args.tail)
+      case Some(x) if x == Actions.Graph => graph(args.tail)
       case _ => BadUsageTermination
     }
   }
@@ -72,6 +74,23 @@ object Main extends App {
     }
   }
 
+  def graph(args: Seq[String]): Termination = {
+    continueIf(args.length == 1 || (args.length == 2 && args.head.equals("--all"))) {
+
+      val (file, allNodesMode) =
+        if (args.size == 1) (args.head, false)
+        else (args(1), true)
+
+      val workflowDigraph = GraphPrint.generateWorkflowDigraph(file, allNodesMode)
+
+      val result = s"""|digraph ${workflowDigraph.workflowName} {
+                       |  ${workflowDigraph.digraph.mkString(System.lineSeparator + "  ")}
+                       |}
+                       |"""
+      SuccessfulTermination(result.stripMargin)
+    }
+  }
+
   private[this] def continueIf(valid: => Boolean)(block: => Termination): Termination = if (valid) block else BadUsageTermination
 
   private[this] def loadWdl(path: String)(f: WdlNamespace => Termination): Termination = {
@@ -88,7 +107,7 @@ object Main extends App {
   } yield action
 
   object Actions extends Enumeration {
-    val Parse, Validate, Highlight, Inputs = Value
+    val Parse, Validate, Highlight, Inputs, Graph = Value
   }
 
   val UsageMessage = """
@@ -119,7 +138,14 @@ object Main extends App {
                        |  abstract syntax tree if it is valid, and a syntax error
                        |  otherwise.  Note that higher-level AST checks are not done
                        |  via this sub-command and the 'validate' subcommand should
-                       |  be used for full validation
+                       |  be used for full validation.
+                       |graph [--all] <WDL file>
+                       |
+                       |  Reads a WDL file against the grammar and prints out a
+                       |  .dot of the DAG if it is valid, and a syntax error
+                       |  otherwise.
+                       |  Use [--all] to show all graph nodes in the WDL spec,
+                       |  even the non-executable nodes.
                      """.stripMargin
 
   val termination = dispatchCommand(args)