Update cromwell version from 28 to 29

update release WDL (#2399)
Migrate Cromwell from Spray to Akka HTTP. Closes #1243 (#2380)
broadinstitute · Horneth · Horneth · geoffjentry · geoffjentry · Horneth
Unified Split

Showing 304 changed files with 4,238 additions and 3,569 deletions.
diff --git a/.pullapprove.yml b/.pullapprove.yml
@@ -1,16 +1,24 @@
-approve_by_comment: true
-approve_regex: ':\+1:'
-reset_on_push: false
-author_approval: ignored
-reviewers:
+# enabling version 2 turns github reviews on by default
+version: 2
+group_defaults:
+  approve_by_comment:
+    enabled: true
+    approve_regex: ':\+1:'
+  reset_on_push:
+    enabled: false
+groups:
+  reviewers:
     required: 2
-    members:
+    github_reviews:
+      enabled: true
+    author_approval:
+      ignored: true
+    users:
         - Horneth
         - cjllanwarne
         - francares
         - gauravs90
         - geoffjentry
-        - jainh
         - jsotobroad
         - katevoss
         - kcibul
diff --git a/.travis.yml b/.travis.yml
@@ -1,8 +1,10 @@
 sudo: required
 dist: trusty
+services:
+  - docker
 language: scala
 scala:
-  - 2.11.8
+  - 2.12.2
 jdk:
   - oraclejdk8
 cache:
@@ -18,7 +20,6 @@ before_cache:
 before_install:
   # https://github.com/travis-ci/travis-ci/issues/7940#issuecomment-310759657
   - sudo rm -f /etc/boto.cfg
-  - openssl aes-256-cbc -K "$encrypted_5ebd3ff04788_key" -iv "$encrypted_5ebd3ff04788_iv" -in src/bin/travis/resources/jesConf.tar.enc -out jesConf.tar -d || true
 env:
   global:
     - CENTAUR_BRANCH=develop
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,5 +1,26 @@
 # Cromwell Change Log
 
+## 29
+
+### Breaking Changes
+
+* Request timeouts for HTTP requests on the REST API now return a 503 status code instead of 500. The response for a request timeout is no longer in JSON format.
+* The metadata endpoint no longer returns gzipped responses by default. This now needs to be explicitly requested with an `Accept-Encoding: gzip` header 
+
+* Command line usage has been extensively revised for Cromwell 29.  Please see the
+[README](https://github.com/broadinstitute/cromwell#command-line-usage) for details.
+
+* The engine endpoints are now served under `/engine`. Previousely engine endpoints were available under
+`/api/engine`. Workflow endpoints are still served under `/api/workflows`. The setting `api.routeUnwrapped` has been
+retired at the same time.
+
+* The response format of the [callcaching/diff](https://github.com/broadinstitute/cromwell#get-apiworkflowsversioncallcachingdiff) endpoint has been updated.
+
+### Cromwell Server
+
+* Cromwell now attempts to gracefully shutdown when running in server mode and receiving a `SIGINT` (`Ctrl-C`) or `SIGTERM` (`kill`) signal. This includes waiting for all pending Database writes before exiting.
+A detailed explanation and information about how to configure this feature can be found in the [Cromwell Wiki](https://github.com/broadinstitute/cromwell/wiki/DevZone#graceful-server-shutdown).
+
 ## 28
 
 ### Bug Fixes
diff --git a/NOTICE b/NOTICE
@@ -1,4 +0,0 @@
-cromwell.webservice/PerRequest.scala (https://github.com/NET-A-PORTER/spray-actor-per-request)
-is distributed with this software under the Apache License, Version 2.0 (see the LICENSE-ASL file). In accordance
-with that license, that software comes with the following notices:
-    Copyright (C) 2011-2012 Ian Forsey