Merge branch 'develop'

.pullapprove.yml

@@ -7,22 +7,30 @@ group_defaults:
   reset_on_push:
     enabled: false
 groups:
-  reviewers:
+  two_reviewers:
     required: 2
     github_reviews:
       enabled: true
     author_approval:
       ignored: true
-    users:
-        - Horneth
-        - cjllanwarne
-        - francares
-        - gauravs90
-        - geoffjentry
-        - jsotobroad
-        - katevoss
-        - kcibul
-        - kshakir
-        - mcovarr
-        - ruchim
-        - danbills
+    teams:
+        - redteam
+    conditions:
+      files:
+        exclude:
+          - wdl/*
+          - centaur/*
+  one_reviewer:
+    required: 1
+    github_reviews:
+      enabled: true
+    author_approval:
+      ignored: true
+    teams:
+        - redteam
+    conditions:
+      files:
+        include:
+          - wdl/*
+          - centaur/*
+

.travis.yml

@@ -1,5 +1,6 @@
 sudo: required
 dist: trusty
+group: deprecated-2017Q4
 services:
   - docker
   - mysql
@@ -13,6 +14,7 @@ cache:
   branch: md5deep
   directories:
     - $HOME/.ivy2/cache
+    - $HOME/.coursier/cache
     - $HOME/.sbt/boot/
 before_cache:
   # Tricks to avoid unnecessary cache updates
@@ -33,7 +35,8 @@ env:
     - BUILD_TYPE=centaurJes
     - BUILD_TYPE=centaurLocal
     - BUILD_TYPE=centaurTes
-    - BUILD_TYPE=centaurCwlConformance
+    - BUILD_TYPE=centaurCwlConformanceLocal
+    - BUILD_TYPE=centaurCwlConformancePAPI
 script:
   - sudo apt-get install procps
   - pip install 'requests[security]'

CHANGELOG.md

@@ -1,5 +1,37 @@
 # Cromwell Change Log
 
+## 31 Release Notes
+
+* **Cromwell server**  
+The Cromwell server source code is now located under `server/src`. `sbt assembly` will build the runnable Cromwell JAR in 
+`server/target/scala-2.12/` with a name like `cromwell-<VERSION>.jar`.
+
+* **Robustness**
+    + The rate at which jobs are being started can now be controlled using the `system.job-rate-control` configuration stanza.  
+    + A load controller service has been added to allow Cromwell to self-monitor and adjust its load accordingly.
+The load controller is currently a simple on/off switch controlling the job start rate. It gathers metrics from different parts of the system
+to inform its decision to stop the creation of jobs.
+You can find relevant configuration in the `services.LoadController` section of the `cromwell.examples.conf` file,
+as well as in the `load-control` section in `reference.conf`.
+The load level of the monitored sub-systems are instrumented and can be found under the `cromwell.load` statsD path.
+    + The statsD metrics have been re-shuffled a bit. If you had a dashboard you might find that you need to update it.
+Changes include: 
+        + Removed artificially inserted "count" and "timing" the path
+        + Added a `load` section
+        + Metrics were prefixed twice with `cromwell` (`cromwell.cromwell.my_metric`), now they're only prefixed once
+        + Added `processed` and `queue` metrics under various metrics monitoring the throughput and amount of queued work respectively
+        + Added a memory metric representing an estimation of the free memory Cromwell thinks it has left
+
+* Added a configuration option under `docker.hash-lookup.enabled` to disable docker hash lookup.
+ Disabling it will also disable call caching for jobs with floating docker tags.
+
+* **API**    
+    + Updated the `/query` response to include the total number of query results returned. See [here](http://cromwell.readthedocs.io/en/develop/api/RESTAPI/#workflowqueryresponse) for more information.
+
+## 30.1 Release Notes
+
+* A set of bug fixes following the migration of Cromwell to WOM (the Workflow Object Model) in version 30.
+
 ## 30 Release Notes
 
 ### Breaking changes
@@ -696,4 +728,4 @@ types](https://github.com/docker/distribution/blob/05b0ab0/docs/spec/manifest-v2
 multiple input files.
 
 * The `/query` endpoint now supports querying by `id`, and submitting
-parameters as a HTTP POST.
+parameters as a HTTP POST.

CromIAM/src/main/resources/application.conf

@@ -0,0 +1,22 @@
+cromiam {
+  interface = "0.0.0.0"
+  port = 8001
+}
+
+sam {
+  interface = "0.0.0.0"
+  port = 443
+  scheme = "https"
+}
+
+cromwell {
+  interface = "0.0.0.0"
+  port = 8000
+  scheme = "http"
+}
+
+swagger_oauth {
+  client_id = "client_id"
+  realm = "realm"
+  app_name = "app_name"
+}