Post-release-2.8.3 (#276)

* update changelog * update version * update dependency versions * enable stdout/stderr forwarding when executing command script * APPS-897 log command to stderr (#280) * cat command file to stderr * update changelog
dnanexus · Jan 11, 2022 · 59c652b · 59c652b
1 parent d6f90bb
commit 59c652b
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diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md
@@ -2,7 +2,21 @@
 
 ## in develop
 
-* Update dxCommon and wdlTools
+* Command file is now echoed to stderr rather than stdout
+
+## 2.8.3 2022-01-07
+
+* Update dxCommon and wdlTools - fixes forwarding of stdout/stderr to job log fpr commands run in docker
+
+### Dependency updates
+
+#### dxCommon 0.11.1
+
+* Fix `SysUtils.runCommand` forwarding of stderr
+
+#### wdlTools 0.17.7
+
+* Correctly attaches to docker stdout/stderr
 
 ## 2.8.2 2022-01-05
 

diff --git a/build.sbt b/build.sbt
@@ -131,11 +131,11 @@ val githubDxCompilerResolver = Resolver.githubPackages("dnanexus", "dxCompiler")
 
 lazy val dependencies =
   new {
-    val dxCommonVersion = "0.11.1-SNAPSHOT"
+    val dxCommonVersion = "0.11.1"
     val dxApiVersion = "0.13.1"
     val dxFileAccessProtocolsVersion = "0.5.3"
     val dxYamlVersion = "0.1.1"
-    val wdlToolsVersion = "0.17.7-SNAPSHOT"
+    val wdlToolsVersion = "0.17.7"
     val cwlScalaVersion = "0.7.4"
     val typesafeVersion = "1.4.1"
     val sprayVersion = "1.3.6"

diff --git a/compiler/src/main/resources/application.conf b/compiler/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxCompiler {
-    version = "2.8.3-SNAPSHOT"
+    version = "2.8.4-SNAPSHOT"
 }
 
 #

diff --git a/compiler/src/main/resources/templates/applet_script.ssp b/compiler/src/main/resources/templates/applet_script.ssp
@@ -93,7 +93,7 @@ ${dockerPreamble.get}
 
 run_command() {
     echo "bash command encapsulation script:"
-    cat "${runtimePathConfig.getCommandFile().toString}"
+    cat "${runtimePathConfig.getCommandFile().toString}" >&2
 
     # Run the shell script generated by instantiateCommand.
     # Capture the stderr/stdout in files

diff --git a/core/src/main/resources/application.conf b/core/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxCompilerCore {
-    version = "2.8.3-SNAPSHOT"
+    version = "2.8.4-SNAPSHOT"
 }
 
 #

diff --git a/executorCommon/src/main/resources/application.conf b/executorCommon/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxExecutorCommon {
-    version = "2.8.3-SNAPSHOT"
+    version = "2.8.4-SNAPSHOT"
 }
 
 #

diff --git a/executorCommon/src/main/scala/dx/executor/TaskExecutor.scala b/executorCommon/src/main/scala/dx/executor/TaskExecutor.scala
@@ -991,7 +991,7 @@ abstract class TaskExecutor(jobMeta: JobMeta,
     val (hasCommand, successCodes) = writeCommandScript(localizedInputs, finalizedDependencies)
     if (hasCommand) {
       // run the command script
-      jobMeta.runJobScriptFunction(TaskExecutor.RunCommand, successCodes)
+      jobMeta.runJobScriptFunction(TaskExecutor.RunCommand, successCodes, forwardStd = true)
     }
 
     // evaluate output expressions

diff --git a/executorCwl/src/main/resources/application.conf b/executorCwl/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxExecutorCwl {
-    version = "2.8.3-SNAPSHOT"
+    version = "2.8.4-SNAPSHOT"
 }
 
 #

diff --git a/executorWdl/src/main/resources/application.conf b/executorWdl/src/main/resources/application.conf
@@ -1,5 +1,5 @@
 dxExecutorWdl {
-    version = "2.8.3-SNAPSHOT"
+    version = "2.8.4-SNAPSHOT"
 }
 
 #