Merge pull request #40 from uc-cdis/feat/no-fuse

Feat/no fuse

Docker/engine/Dockerfile

@@ -10,7 +10,7 @@ ADD . .
 RUN go build -ldflags "-linkmode external -extldflags -static" -o bin/mariner
 
 FROM alpine
-COPY --from=build /go/src/github.com/uc-cdis/mariner/bin/mariner /go/src/github.com/uc-cdis/mariner/Docker/engine/engineDockerrun.sh /
+COPY --from=build /go/src/github.com/uc-cdis/mariner/bin/mariner /
 RUN apk update && apk add --no-cache ca-certificates
 
-ENTRYPOINT [ "/bin/sh", "/engineDockerrun.sh" ]
+ENTRYPOINT [ "/mariner", "run", "$RUN_ID" ]

Docker/s3Sidecar/Dockerfile

@@ -1,19 +1,17 @@
 FROM golang:1.12-alpine as build
 
-RUN apk update && apk add --no-cache git 
+# Install SSL certificates
+RUN apk update && apk add --no-cache git ca-certificates gcc musl-dev
 
-# install goofys
-RUN go get github.com/kahing/goofys
-
-# get bash script from mariner repo
+# Build static sidecar binary
 RUN mkdir -p /go/src/github.com/uc-cdis/mariner
 WORKDIR /go/src/github.com/uc-cdis/mariner
 ADD . .
+RUN go build -ldflags "-linkmode external -extldflags -static" -o /sidecar ./sidecar/
 
-# work from small python:alpine image
-FROM python:alpine
-COPY --from=build /go/src/github.com/uc-cdis/mariner/Docker/s3Sidecar/s3sidecarDockerrun.sh /go/bin/goofys /
-RUN apk update && apk add --no-cache fuse jq ca-certificates
-RUN pip install awscli
+# we love small images
+FROM scratch
+COPY --from=build /etc/ssl/certs/ca-certificates.crt /etc/ssl/certs/ca-certificates.crt
+COPY --from=build /sidecar /
 
-ENTRYPOINT [ "/bin/sh", "/s3sidecarDockerrun.sh" ]
+ENTRYPOINT ["/sidecar"]

mariner/command.go

@@ -434,7 +434,7 @@ func (tool *Tool) argVal(arg cwl.Argument) (val []string, err error) {
 		// NOTE: *might* need to check "$(" or "${" instead of just "$"
 		if strings.HasPrefix(arg.Value, "$") {
 			// expression to eval - here `self` is null - no additional context to load - just need to eval in inputsVM
-			result, err := evalExpression(arg.Value, tool.Task.Root.InputsVM)
+			result, err := evalExpression(arg.Value, tool.InputsVM)
 			if err != nil {
 				return nil, tool.Task.errorf("failed to evaluate expression: %v; err: %v", arg.Value, err)
 			}

mariner/config.go

@@ -55,6 +55,7 @@ const (
 	k8sJobAPI     = "k8sJobAPI"
 	k8sPodAPI     = "k8sPodAPI"
 	k8sMetricsAPI = "k8sMetricsAPI"
+	k8sCoreAPI    = "k8sCoreAPI"
 
 	// top-level workflow ID
 	mainProcessID = "#main"
@@ -136,14 +137,6 @@ var envVarHostname = &k8sv1.EnvVarSource{
 	},
 }
 
-var s3PrestopHook = &k8sv1.Lifecycle{
-	PreStop: &k8sv1.Handler{
-		Exec: &k8sv1.ExecAction{
-			Command: Config.Containers.S3sidecar.Lifecycle.Prestop,
-		},
-	},
-}
-
 // could put in manifest
 var gen3fusePrestopHook = &k8sv1.Lifecycle{
 	PreStop: &k8sv1.Handler{
@@ -304,7 +297,7 @@ func (conf *Container) securityContext() (context *k8sv1.SecurityContext) {
 
 func volumeMounts(component string) (v []k8sv1.VolumeMount) {
 	switch component {
-	case marinerEngine, marinerTask:
+	case marinerTask:
 		v = mainVolumeMounts(component)
 	case s3sidecar, gen3fuse:
 		v = sidecarVolumeMounts(component)
@@ -328,10 +321,6 @@ func mainVolumeMounts(component string) (volumeMounts []k8sv1.VolumeMount) {
 		volumeMount := volumeMount(v, component)
 		volumeMounts = append(volumeMounts, *volumeMount)
 	}
-	if component == marinerEngine {
-		configVol := volumeMount(configVolumeName, component)
-		volumeMounts = append(volumeMounts, *configVol)
-	}
 	return volumeMounts
 }