Configurable sample config public image (#102)

doc/howto/configuration.md

@@ -33,6 +33,7 @@ An example manifest entry may look like
       "lifecycle-pre-stop": ["su", "-c", "cd /data; for f in *; do fusermount -u $f; rm -rf $f; done", "-s", "/bin/sh", "jovyan"]
     },
     "nextflow-global": {
+      "sample-config-public-image": "",
       "imagebuilder-reader-role-arn": ""
     },
     "containers": [
@@ -125,6 +126,7 @@ An example manifest entry may look like
     * `command` a string array as the command to run in the container overriding the default.
     * `lifecycle-pre-stop` a string array as the container prestop command.
 * `nextflow-global` is for global configuration specific to Nextflow containers.
+    * `sample-config-public-image`: a publicly-accessible image that any user can pull to test Nextflow workflows. Will be mentioned in the auto-generated sample configuration and documentation when a user launches a Nextflow workspace.
     * `imagebuilder-reader-role-arn`: see the [nextflow-global.imagebuilder-reader-role-arn section](/doc/explanation/nextflow.md#nextflow-globalimagebuilder-reader-role-arn) of the Nextflow workspaces documentation.
 * `containers` is the list of workspaces available to be run by this instance of Hatchery. Each container must be a single image and expose a web server.
     * `target-port` specifies the port that the container is exposing the webserver on.

hatchery/config.go

@@ -14,6 +14,7 @@ import (
 
 // Global configuration shared by all Nextflow containers
 type NextflowGlobalConfig struct {
+	SampleConfigPublicImage   string `json:"sample-config-public-image"`
 	ImageBuilderReaderRoleArn string `json:"imagebuilder-reader-role-arn"`
 }
 

hatchery/hatchery.go

@@ -700,7 +700,7 @@ func getMountFileContents(fileId string, userName string) (string, error) {
 	}
 
 	if fileId == "sample-nextflow-config.txt" {
-		out, err := generateNextflowConfig(userName)
+		out, err := generateNextflowConfig(Config.Config.NextflowGlobalConfig, userName)
 		if err != nil {
 			Config.Logger.Printf("unable to generate Nextflow config: %v", err)
 		}

hatchery/hatchery_test.go

@@ -1065,7 +1065,7 @@ aws {
 	}
 }`
 	originalGenerateNextflowConfig := generateNextflowConfig
-	generateNextflowConfig = func(userName string) (string, error) {
+	generateNextflowConfig = func(nextflowGlobalConfig NextflowGlobalConfig, userName string) (string, error) {
 		return fileContents, nil
 	}
 	defer func() {

hatchery/nextflow.go

@@ -1608,7 +1608,7 @@ var stopSquidInstance = func(hostname string, userName string, ec2svc *ec2.EC2)
 	return nil
 }
 
-var generateNextflowConfig = func(userName string) (string, error) {
+var generateNextflowConfig = func(nextflowGlobalConfig NextflowGlobalConfig, userName string) (string, error) {
 	sess := session.Must(session.NewSession(&aws.Config{
 		Region: aws.String("us-east-1"),
 	}))
@@ -1652,7 +1652,7 @@ var generateNextflowConfig = func(userName string) (string, error) {
 process {
 	executor = 'awsbatch'
 	queue = '%s'
-	container = 'public.ecr.aws/l5b8a5z6/nextflow-approved/public:gen3-amazonlinux-base-AL2023fix'
+	container = '%s'
 }
 aws {
 	batch {
@@ -1662,6 +1662,7 @@ aws {
 }
 workDir = '%s'`,
 		batchJobQueueName,
+		nextflowGlobalConfig.SampleConfigPublicImage,
 		nextflowJobsRoleArn,
 		workDir,
 	)