Merge branch 'develop' into release-2.10.2

dnanexus · May 18, 2022 · 7432519 · 7432519
2 parents 7e07b69 + 4dc45c0
commit 7432519
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Showing 6 changed files with 13 additions and 24 deletions.
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -67,7 +67,7 @@ jobs:
           sudo apt-get install -y apt-transport-https wget git openssh-server tree python3 python3-pip python3-venv
           cwltool=`jq -r '.execDepends.cwl[0].name' scripts/bundled_dependencies.json`
           pip3 install --upgrade pip setuptools pyOpenSSL
-          pip3 install termcolor dxpy $cwltool
+          pip3 install termcolor dxpy==0.323.0 $cwltool
           # install dxda
           sudo wget -O/usr/local/bin/dx-download-agent https://github.com/dnanexus/dxda/releases/download/v0.5.7/dx-download-agent-linux
           sudo chmod +x /usr/local/bin/dx-download-agent

diff --git a/compiler/src/main/scala/dx/compiler/WorkflowCompiler.scala b/compiler/src/main/scala/dx/compiler/WorkflowCompiler.scala
@@ -569,14 +569,8 @@ case class WorkflowCompiler(separateOutputs: Boolean,
                   if (app.kind.getClass == classOf[ExecutableKindWfFragment]) =>
                 "do not override"
               case static: StaticInstanceType => instanceTypeDb.apply(static.req).name
-              case DefaultInstanceType => {
-                logger.trace(
-                    s"Using default instance type for child process. Going to use `${None}`"
-                )
-                "do not override"
-              }
-
-              case _ => instanceTypeDb.defaultInstanceType.name
+              case DefaultInstanceType        => "do not override"
+              case _                          => instanceTypeDb.defaultInstanceType.name
             }
             if (instanceType == "do not override") {
               None
@@ -592,7 +586,6 @@ case class WorkflowCompiler(separateOutputs: Boolean,
 
           case _ => None
         }
-        logger.trace(s"systemRequirements is ${systemRequirements}")
         JsObject(
             Vector(
                 Some("id" -> JsString(stage.dxStage.id)),

diff --git a/compiler/src/main/scala/dx/translator/wdl/RuntimeTranslator.scala b/compiler/src/main/scala/dx/translator/wdl/RuntimeTranslator.scala
@@ -146,6 +146,8 @@ case class RuntimeTranslator(wdlVersion: WdlVersion,
       resolution: InstanceTypeSelection.InstanceTypeSelection
   ): InstanceType = {
     runtime.safeParseInstanceType match {
+      case Some(InstanceTypeRequest.empty) if resolution == InstanceTypeSelection.Dynamic =>
+        DynamicInstanceType
       case Some(InstanceTypeRequest.empty) => DefaultInstanceType
       case Some(req: InstanceTypeRequest)
           if resolution == InstanceTypeSelection.Dynamic && req.dxInstanceType.isDefined =>

diff --git a/compiler/src/test/scala/dx/translator/TranslatorTest.scala b/compiler/src/test/scala/dx/translator/TranslatorTest.scala
@@ -78,18 +78,7 @@ class TranslatorTest extends AnyFlatSpec with Matchers {
       }
       applet.instanceType
     }
-    compile("static") shouldBe StaticInstanceType(
-        InstanceTypeRequest(None,
-                            None,
-                            None,
-                            None,
-                            None,
-                            None,
-                            None,
-                            None,
-                            None,
-                            Some(ExecutionEnvironment("Ubuntu", "20.04", Vector("0"))))
-    )
+    compile("static") shouldBe DefaultInstanceType
     compile("dynamic") shouldBe DynamicInstanceType
   }
 

diff --git a/core/src/main/scala/dx/core/languages/wdl/Runtime.scala b/core/src/main/scala/dx/core/languages/wdl/Runtime.scala
@@ -122,16 +122,19 @@ case class Runtime(wdlVersion: WdlVersion,
           case other =>
             throw new Exception(s"unexpected ${WdlRuntime.GpuKey} value ${other}")
         }
+        val aa = runtimeAttrs.runtime
+        val _ = aa
         val usedGpuDefault: Boolean = gpu match {
           case Some(b) => false
           case None    => true
         }
         val usedOtherSysDefaults: Boolean = {
           runtimeAttrs.runtime.map(_.isDefaultSystemRequirements) match {
             case Some(b) => b
-            case None    => false
+            case None    => true
           }
         }
+
         if (usedOtherSysDefaults && usedGpuDefault) {
           InstanceTypeRequest.empty
         } else {

diff --git a/scripts/run_tests.py b/scripts/run_tests.py
@@ -175,7 +175,9 @@
 ]
 
 static_only = [
-    "apps_1177_native_indirect_override"
+    "apps_1177_native_indirect_override",
+    "apps_1128_frag_native_instance_type_override",
+    "apps_1197_native_frag_default"
 ]
 
 # docker image tests