Merge pull request #29 from antoinetran/fix_envfile_issue27

added alessio/shellescape and changed prepareEnvs to use envfile

go.mod

@@ -5,6 +5,7 @@ go 1.22
 toolchain go1.22.4
 
 require (
+	al.essio.dev/pkg/shellescape v1.5.0
 	github.com/alexellis/go-execute v0.6.0
 	github.com/containerd/containerd v1.7.6
 	github.com/intertwin-eu/interlink v0.0.0-20240829090340-24c45973f3ec

go.sum

@@ -1,3 +1,5 @@
+al.essio.dev/pkg/shellescape v1.5.0 h1:7oTvSsQ5kg9WksA9O58y9wjYnY4jP0CL82/Q8WLUGKk=
+al.essio.dev/pkg/shellescape v1.5.0/go.mod h1:6sIqp7X2P6mThCQ7twERpZTuigpr6KbZWtls1U8I890=
 github.com/alexellis/go-execute v0.6.0 h1:FVGoudJnWSObwf9qmehbvVuvhK6g1UpKOCBjS+OUXEA=
 github.com/alexellis/go-execute v0.6.0/go.mod h1:nlg2F6XdYydUm1xXQMMiuibQCV1mveybBkNWfdNznjk=
 github.com/cenkalti/backoff/v4 v4.3.0 h1:MyRJ/UdXutAwSAT+s3wNd7MfTIcy71VQueUuFK343L8=

pkg/slurm/Create.go

@@ -81,7 +81,7 @@ func (h *SidecarHandler) SubmitHandler(w http.ResponseWriter, r *http.Request) {
 
 		commstr1 := []string{"singularity", "exec", "--containall", "--nv", singularityMounts, singularityOptions}
 
-		envs := prepareEnvs(spanCtx, container)
+		envs := prepareEnvs(spanCtx, h.Config, data, container)
 		image := ""
 
 		CPULimit, _ := container.Resources.Limits.Cpu().AsInt64()

pkg/slurm/prepare.go

@@ -15,6 +15,7 @@ import (
 	"strings"
 	"time"
 
+	"al.essio.dev/pkg/shellescape"
 	exec2 "github.com/alexellis/go-execute/pkg/v1"
 	"github.com/containerd/containerd/log"
 	v1 "k8s.io/api/core/v1"
@@ -184,36 +185,79 @@ func (h *SidecarHandler) LoadJIDs() error {
 	return nil
 }
 
-// prepareEnvs reads all Environment variables from a container and append them to a slice of strings.
-// It returns the slice containing all envs in the form of key=value.
-func prepareEnvs(Ctx context.Context, container v1.Container) []string {
+func createEnvFile(Ctx context.Context, config SlurmConfig, podData commonIL.RetrievedPodData, container v1.Container) ([]string, []string, error) {
+		envs := []string{}
+		// For debugging purpose only
+		envs_data := []string{}
+
+		envfilePath := (config.DataRootFolder + podData.Pod.Namespace + "-" + string(podData.Pod.UID) + "/" + "envfile.properties")
+		log.G(Ctx).Info("-- Appending envs using envfile " + envfilePath)
+		envs = append(envs, "--env-file")
+		envs = append(envs, envfilePath)
+
+		envfile, err := os.Create(envfilePath)
+		if err != nil {
+			log.G(Ctx).Error(err)
+			return nil, nil, err
+		}
+		defer envfile.Close()
+
+		for _, envVar := range container.Env {
+			// The environment variable values can contains all sort of simple/double quote and space and any arbitrary values.
+			// singularity reads the env-file and parse it like a bash string, so shellescape will escape any quote properly.
+			tmpValue :=  shellescape.Quote(envVar.Value)
+			tmp := (envVar.Name + "=" + tmpValue)
+
+			envs_data = append(envs_data, tmp)
+
+			_, err := envfile.WriteString(tmp + "\n")
+			if err != nil {
+				log.G(Ctx).Error(err)
+				return nil, nil, err
+			} else {
+				log.G(Ctx).Debug("---- Written envfile file " + envfilePath + " key " + envVar.Name + " value " + tmpValue)
+			}
+		}
+
+		// All env variables are written, we flush it now. 
+		err = envfile.Sync()
+		if err != nil {
+			log.G(Ctx).Error(err)
+			return nil, nil, err
+		}
+
+		// Calling Close() in case of error. If not error, the defer will close it again but it should be idempotent.
+		envfile.Close()
+
+		return envs, envs_data, nil
+}
+
+// prepareEnvs reads all Environment variables from a container and append them to a envfile.properties. The values are bash-escaped.
+// It returns the slice containing, if there are Environment variables, the arguments for envfile and its path, or else an empty array.
+func prepareEnvs(Ctx context.Context, config SlurmConfig, podData commonIL.RetrievedPodData, container v1.Container) []string {
 	start := time.Now().UnixMicro()
 	span := trace.SpanFromContext(Ctx)
 	span.AddEvent("Preparing ENVs for container " + container.Name)
-	var envs []string
+	var envs []string = []string{}
+	// For debugging purpose only
+	envs_data := []string{}
+	var err error
 
 	if len(container.Env) > 0 {
-		log.G(Ctx).Info("-- Appending envs")
-		envs = append(envs, "--env")
-		env_data := ""
-		for _, envVar := range container.Env {
-			tmp := (envVar.Name + "=" + envVar.Value + ",")
-			env_data += tmp
-		}
-		if last := len(env_data) - 1; last >= 0 && env_data[last] == ',' {
-			env_data = env_data[:last]
-		}
-		if env_data == "" {
-			envs = []string{}
+		envs, envs_data, err = createEnvFile(Ctx, config, podData, container)
+		if err != nil {
+			log.G(Ctx).Error(err)
+			return nil
 		}
-		envs = append(envs, env_data)
 	}
 
 	duration := time.Now().UnixMicro() - start
 	span.AddEvent("Prepared ENVs for container "+container.Name, trace.WithAttributes(
 		attribute.String("prepareenvs.container.name", container.Name),
 		attribute.Int64("prepareenvs.duration", duration),
-		attribute.StringSlice("prepareenvs.container.envs", envs)))
+		attribute.StringSlice("prepareenvs.container.envs", envs),
+		attribute.StringSlice("prepareenvs.container.envs_data", envs_data)))
+
 	return envs
 }