From 31037eb1774888d681c349cc46b81f16ae7a88f3 Mon Sep 17 00:00:00 2001 From: Ruchi Munshi Date: Wed, 12 Oct 2016 11:51:52 -0400 Subject: [PATCH 1/4] update wdltool version from 0.6 -> 0.7 --- build.sbt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.sbt b/build.sbt index cced536..3f4b32f 100644 --- a/build.sbt +++ b/build.sbt @@ -9,7 +9,7 @@ organization := "org.broadinstitute" scalaVersion := "2.11.8" // Upcoming release, or current if we're on the master branch -git.baseVersion := "0.6" +git.baseVersion := "0.7" // Shorten the git commit hash git.gitHeadCommit := git.gitHeadCommit.value map { _.take(7) } From 1143dd66c15dc3313ba957a71aa88f84e7bcbe67 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Fri, 18 Nov 2016 20:15:47 -0500 Subject: [PATCH 2/4] Fix pullapprove. Adding ruchim and kcibul to pullapprove. Removing scottfrazer from pullapprove to fix "'scottfrazer' is not a collaborator of this repo" error. --- .pullapprove.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.pullapprove.yml b/.pullapprove.yml index 7eee40d..ceb8dc6 100644 --- a/.pullapprove.yml +++ b/.pullapprove.yml @@ -7,7 +7,8 @@ reviewers: members: - cjllanwarne - Horneth - - scottfrazer - mcovarr - geoffjentry - kshakir + - kcibul + - ruchim From e5f8c9573e9a8a21dbe8c0b33f9eeba03411a497 Mon Sep 17 00:00:00 2001 From: Khalid Shakir Date: Mon, 21 Nov 2016 16:07:33 -0500 Subject: [PATCH 3/4] Publish `SNAPSHOT`s obfuscated as `SNAP` releases. Fixed build issues related to latest wdl4s. --- build.sbt | 21 +++++++++++++-------- src/main/scala/wdltool/Main.scala | 6 +++--- src/test/scala/wdltool/MainSpec.scala | 2 +- 3 files changed, 17 insertions(+), 12 deletions(-) diff --git a/build.sbt b/build.sbt index 3f4b32f..defbc74 100644 --- a/build.sbt +++ b/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 := "0.7" +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" % "0.7-4a9e61e-SNAP", //---------- Test libraries -------------------// "org.scalatest" %% "scalatest" % "2.2.5" % Test ) diff --git a/src/main/scala/wdltool/Main.scala b/src/main/scala/wdltool/Main.scala index d25aaca..7f39d9a 100644 --- a/src/main/scala/wdltool/Main.scala +++ b/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) } diff --git a/src/test/scala/wdltool/MainSpec.scala b/src/test/scala/wdltool/MainSpec.scala index d568a0b..d20317b 100644 --- a/src/test/scala/wdltool/MainSpec.scala +++ b/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:") } } From 8075e9e431c078405edb8706b1ded6dda9ed80d1 Mon Sep 17 00:00:00 2001 From: geoffjentry Date: Mon, 28 Nov 2016 22:09:24 -0500 Subject: [PATCH 4/4] Update to version of wdl4s which allows for meta in workflow --- build.sbt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.sbt b/build.sbt index defbc74..2f1c44d 100644 --- a/build.sbt +++ b/build.sbt @@ -34,7 +34,7 @@ resolvers ++= Seq( ) libraryDependencies ++= Seq( - "org.broadinstitute" %% "wdl4s" % "0.7-4a9e61e-SNAP", + "org.broadinstitute" %% "wdl4s" % "0.7-799567f-SNAP", //---------- Test libraries -------------------// "org.scalatest" %% "scalatest" % "2.2.5" % Test )