From 8fc80a9cfd775dafb3ba942d72835d1ad12cba36 Mon Sep 17 00:00:00 2001 From: NishiPhalke Date: Thu, 27 May 2021 16:49:20 -0400 Subject: [PATCH] get http input file docker image from config --- src/main/kotlin/krews/config/SlurmConfig.kt | 4 +--- src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt | 6 ------ src/main/kotlin/krews/file/HttpInputFile.kt | 4 ++-- 3 files changed, 3 insertions(+), 11 deletions(-) diff --git a/src/main/kotlin/krews/config/SlurmConfig.kt b/src/main/kotlin/krews/config/SlurmConfig.kt index be25a1d..6aeeb3d 100644 --- a/src/main/kotlin/krews/config/SlurmConfig.kt +++ b/src/main/kotlin/krews/config/SlurmConfig.kt @@ -7,9 +7,7 @@ data class SlurmWorkflowConfig( val jobCompletionPollInterval: Int = 10, // Optional ssh configuration. Will cause all slurm command to be passed through ssh. // Only available for password-less login. - val ssh: SshConfig? = null, - - val httpInputDockerImage: String? = null + val ssh: SshConfig? = null ) data class SshConfig( diff --git a/src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt b/src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt index 979ee0a..9668957 100644 --- a/src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt +++ b/src/main/kotlin/krews/executor/slurm/SlurmExecutor.kt @@ -32,7 +32,6 @@ class SlurmExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirecte private var allShutdown = AtomicBoolean(false) - //private val httpInputDockerImage = workflowConfig.slurm?.httpInputDockerImage override fun downloadFile(fromPath: String, toPath: Path) { val fromFile = workflowBasePath.resolve(fromPath) @@ -139,11 +138,6 @@ class SlurmExecutor(private val workflowConfig: WorkflowConfig) : LocallyDirecte val downloadCommand = remoteDownloadInputFile.downloadFileCommand("/download") var downloadImageName = remoteDownloadInputFile.downloadFileImage() - /*if(httpInputDockerImage != null) - { - downloadImageName= httpInputDockerImage - }*/ - sbatchScript.append("singularity exec --containall docker://$downloadImageName $downloadCommand\n") sbatchScript.append("echo Exit status of download $singUUID: $?\n") } diff --git a/src/main/kotlin/krews/file/HttpInputFile.kt b/src/main/kotlin/krews/file/HttpInputFile.kt index ed31bb1..cf97886 100644 --- a/src/main/kotlin/krews/file/HttpInputFile.kt +++ b/src/main/kotlin/krews/file/HttpInputFile.kt @@ -1,6 +1,6 @@ package krews.file -data class HttpInputFile(val url: String, override val path: String) : InputFile() { - override fun downloadFileImage() = "alpine:3.9" +data class HttpInputFile(val url: String, override val path: String, val dockerimage: String? = "alpine:3.9") : InputFile() { + override fun downloadFileImage() = "$dockerimage" override fun downloadFileCommand(containerBaseDir: String) = "wget $url -O $containerBaseDir/$path" } \ No newline at end of file