Merge branch 'develop'

.pullapprove.yml

@@ -7,7 +7,8 @@ reviewers:
     members:
         - cjllanwarne
         - Horneth
-        - scottfrazer
         - mcovarr
         - geoffjentry
         - kshakir
+        - kcibul
+        - ruchim

build.sbt

@@ -8,16 +8,21 @@ organization := "org.broadinstitute"
 
 scalaVersion := "2.11.8"
 
-// Upcoming release, or current if we're on the master branch
-git.baseVersion := "0.6"
+lazy val versionSettings = Seq(
+  // Upcoming release, or current if we're on the master branch
+  git.baseVersion := "0.7",
 
-// Shorten the git commit hash
-git.gitHeadCommit := git.gitHeadCommit.value map { _.take(7) }
+  // Shorten the git commit hash
+  git.gitHeadCommit := git.gitHeadCommit.value map { _.take(7) },
 
-// Travis will deploy tagged releases, add -SNAPSHOT for all local builds
-git.gitUncommittedChanges := true
+  // Travis will deploy tagged releases, add -SNAPSHOT for all local builds
+  git.gitUncommittedChanges := true,
 
-versionWithGit
+  // For now, obfuscate SNAPSHOTs from sbt's developers: https://github.com/sbt/sbt/issues/2687#issuecomment-236586241
+  git.uncommittedSignifier := Option("SNAP")
+)
+
+versionWithGit ++ versionSettings
 
 assemblyJarName in assembly := "wdltool-" + git.baseVersion.value + ".jar"
 
@@ -29,7 +34,7 @@ resolvers ++= Seq(
 )
 
 libraryDependencies ++= Seq(
-  "org.broadinstitute" %% "wdl4s" % "0.6",
+  "org.broadinstitute" %% "wdl4s" % "0.7-799567f-SNAP",
   //---------- Test libraries -------------------//
   "org.scalatest" %% "scalatest" % "2.2.5" % Test
 )

src/main/scala/wdltool/Main.scala

@@ -3,7 +3,7 @@ package wdltool
 import java.nio.file.Paths
 
 import wdl4s.formatter.{AnsiSyntaxHighlighter, HtmlSyntaxHighlighter, SyntaxFormatter}
-import wdl4s.{AstTools, NamespaceWithWorkflow, WdlNamespace}
+import wdl4s.{AstTools, WdlNamespace, WdlNamespaceWithWorkflow}
 import spray.json._
 
 import scala.util.{Failure, Success, Try}
@@ -57,7 +57,7 @@ object Main extends App {
       loadWdl(args.head) { namespace =>
         import wdl4s.types.WdlTypeJsonFormatter._
         val msg = namespace match {
-          case x: NamespaceWithWorkflow => x.workflow.inputs.toJson.prettyPrint
+          case x: WdlNamespaceWithWorkflow => x.workflow.inputs.toJson.prettyPrint
           case _ => "WDL does not have a local workflow"
         }
 
@@ -75,7 +75,7 @@ object Main extends App {
   private[this] def continueIf(valid: => Boolean)(block: => Termination): Termination = if (valid) block else BadUsageTermination
 
   private[this] def loadWdl(path: String)(f: WdlNamespace => Termination): Termination = {
-    Try(WdlNamespace.load(Paths.get(path))) match {
+    Try(WdlNamespace.loadUsingPath(Paths.get(path), None, None)) match {
       case Success(namespace) => f(namespace)
       case Failure(t) => UnsuccessfulTermination(t.getMessage)
     }

src/test/scala/wdltool/MainSpec.scala

@@ -35,7 +35,7 @@ class MainSpec extends FlatSpec with Matchers with BeforeAndAfterAll {
     testWdl(ThreeStep) { wdlAndInputs =>
       val res = Main.dispatchCommand(Seq("parse", wdlAndInputs.wdl))
       assert(res.isInstanceOf[SuccessfulTermination])
-      res.output should include("(Document:")
+      res.output should include("(Namespace:")
     }
   }