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Merge pull request #40 from uc-cdis/feat/no-fuse
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Feat/no fuse
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mattgarvin1 committed Nov 9, 2020
2 parents de608d1 + b7b1940 commit 434b08c
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Showing 27 changed files with 1,671 additions and 897 deletions.
4 changes: 2 additions & 2 deletions Docker/engine/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -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" ]
8 changes: 0 additions & 8 deletions Docker/engine/engineDockerrun.sh

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20 changes: 9 additions & 11 deletions Docker/s3Sidecar/Dockerfile
Original file line number Diff line number Diff line change
@@ -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"]
61 changes: 0 additions & 61 deletions Docker/s3Sidecar/s3sidecarDockerrun.sh

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2 changes: 1 addition & 1 deletion mariner/command.go
Original file line number Diff line number Diff line change
Expand Up @@ -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)
}
Expand Down
15 changes: 2 additions & 13 deletions mariner/config.go
Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@ const (
k8sJobAPI = "k8sJobAPI"
k8sPodAPI = "k8sPodAPI"
k8sMetricsAPI = "k8sMetricsAPI"
k8sCoreAPI = "k8sCoreAPI"

// top-level workflow ID
mainProcessID = "#main"
Expand Down Expand Up @@ -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{
Expand Down Expand Up @@ -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)
Expand All @@ -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
}

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