Class default

Specialization of BaseConnector that, in addition to offering ssh connection, supports slurm connections with the HPC.

Hierarchy (view full)

default
- default
  - default

Constructors

constructor

new default(hpcName, jobId?, maintainer?, env?, is_cvmfs?): default
Parameters
- hpcName: string
- jobId: null | string = null
- maintainer: null | default = null
- env: Record<string, unknown> = {}
- is_cvmfs: boolean = false
Returns default
Inherited from default.constructor
- Defined in src/connectors/BaseConnector.ts:31

Properties

connectorConfig

connectorConfig: hpcConfig

config *

`Protected` envCmd

envCmd: string = "#!/bin/bash\n"

hpcName

hpcName: string

isContainer

isContainer: boolean = false

is_cvmfs

is_cvmfs: boolean

jobId

jobId: null | string

properties *

maintainer

maintainer: null | default

parent pointer *

modules

modules: string[] = []

remote_data_folder_path

remote_data_folder_path: null | string

remote_executable_folder_path

remote_executable_folder_path: null | string

remote_result_folder_path

remote_result_folder_path: null | string

slurm_id

slurm_id: string

template

template: string

Methods

cancel

cancel(): Promise<void>
Returns Promise<void>
Async
cancels the job
- Defined in src/connectors/SlurmConnector.ts:253

cat

cat(path, options?): Promise<null | string>
Parameters
- path: string
  specified path with filename
- Optional options: options = {}
  dictionary with string options
Returns Promise<null | string>
command execution output

Async
creates an empty file at specified path
Inherited from default.cat
- Defined in src/connectors/BaseConnector.ts:329

createFile

createFile(content, remotePath, options?, muteEvent?): Promise<void>
Parameters
- content: string | Record<string, unknown>
  file content (either string or dictionary)
- remotePath: string
  specified path with filename
- options: options = {}
  dictionary with string options (not used)
- Optional muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<void>
Async
creates file with specified content
Inherited from default.createFile
- Defined in src/connectors/BaseConnector.ts:528

download

download(from, to, muteEvent?): Promise<void>
Parameters
- from: string
  input file string (input folder to download)
- to: string
  output folder
- muteEvent: boolean = false
  set to True if you want to mute maintainer emitted Event
Returns Promise<void>
Async
Uncompresses the specified zip file to the Local folder (downloads a folder from the HPC to the local machine)

Throws
- Thrown if maintainer emits 'SSH_SCP_DOWNLOAD_ERROR' or if input file not given
Inherited from default.download
- Defined in src/connectors/BaseConnector.ts:169

exec

exec(commands, options?, muteEvent?, muteLog?, continueOnError?): Promise<out>
Parameters
- commands: string | string[]
  command/commands that need to be executed
- options: options = {}
  execution options
- muteEvent: boolean = true
  set to True if you want to mute maintauner emitted Event
- muteLog: boolean = true
  set to True if you want to mute maintainer emitted Log
- continueOnError: boolean = false
  set to True if you want the command/commands to continue despite errors
Returns Promise<out>
out - maintainer output

Async
Executes the command on the maintainer and returns the outpt
Inherited from default.exec
- Defined in src/connectors/BaseConnector.ts:82

getContainerCVMFSFolderPath

getContainerCVMFSFolderPath(providedPath?): string
Get Container CVMFS folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
- Defined in src/connectors/SlurmConnector.ts:333

getContainerDataFolderPath

getContainerDataFolderPath(providedPath?): string
Get Container data folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
- Defined in src/connectors/SlurmConnector.ts:344

getContainerExecutableFolderPath

getContainerExecutableFolderPath(providedPath?): string
Get Container executable folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
- Defined in src/connectors/SlurmConnector.ts:322

getContainerResultFolderPath

getContainerResultFolderPath(providedPath?): string
Get Container result folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
executable path
- Defined in src/connectors/SlurmConnector.ts:355

getRemoteDataFolderPath

getRemoteDataFolderPath(providedPath?): null | string
gets remote data folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns null | string
command execution output
Inherited from default.getRemoteDataFolderPath
- Defined in src/connectors/BaseConnector.ts:593

getRemoteExecutableFolderPath

getRemoteExecutableFolderPath(providedPath?): string
gets remote executable folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
command execution output
Inherited from default.getRemoteExecutableFolderPath
- Defined in src/connectors/BaseConnector.ts:577

getRemoteResultFolderContent

getRemoteResultFolderContent(): Promise<string[]>
Returns Promise<string[]>
file content

Async
Get remote results folder content
- Defined in src/connectors/SlurmConnector.ts:366

getRemoteResultFolderPath

getRemoteResultFolderPath(providedPath?): string
gets remote result folder path
Parameters
- Optional providedPath: null | string = null
  specified path
Returns string
command execution output
Inherited from default.getRemoteResultFolderPath
- Defined in src/connectors/BaseConnector.ts:608

`Private` getSBatchTagsFromArray

getSBatchTagsFromArray(tag, vals): string
Private
Get sbatch tags
Parameters
- tag: string
  sbatch tags
- vals: string[]
  values of sbatch tags
Returns string
sbatch string
- Defined in src/connectors/SlurmConnector.ts:307

getSlurmStderr

getSlurmStderr(): Promise<void>
Returns Promise<void>
Async
gets SlurmStderr and emit it as a log in the maintainer
- Defined in src/connectors/SlurmConnector.ts:290

getSlurmStdout

getSlurmStdout(): Promise<void>
Returns Promise<void>
Async
gets SlurmStdOut and emit it as a log in the maintainer
- Defined in src/connectors/SlurmConnector.ts:277

getStatus

getStatus(): Promise<string>
Returns Promise<string>
job status (RETRY, UNKNOWN, or a slurm job status)

Async
checks job status
- Defined in src/connectors/SlurmConnector.ts:209

getUsage

getUsage(): Promise<Record<string, null | number>>
Get job usage

Returns Promise<Record<string, null | number>>
- usage dictionary
- Defined in src/connectors/SlurmConnector.ts:427

homeDirectory

homeDirectory(options?): Promise<null | string>
Returns the homeDirectory path of the HPC
Parameters
- Optional options: options = {}
  dictionary with string options
Returns Promise<null | string>
returns command execution output
Inherited from default.homeDirectory
- Defined in src/connectors/BaseConnector.ts:268

ls

ls(path?, options?): Promise<null | string>
Parameters
- Optional path: string
- Optional options: options = {}
  dictionary with string options
Returns Promise<null | string>
returns command execution output

Async
Returns all of the files/directories in specified path
Inherited from default.ls
- Defined in src/connectors/BaseConnector.ts:311

mkdir

mkdir(path, options?, muteEvent?): Promise<null | string>
Parameters
- path: string
  specified path with filename
- Optional options: options = {}
  dictionary with string options
- Optional muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<null | string>
command execution output

Async
creates directory at specified path
Inherited from default.mkdir
- Defined in src/connectors/BaseConnector.ts:381

pause

pause(): Promise<void>
Returns Promise<void>
Async
pauses the job
- Defined in src/connectors/SlurmConnector.ts:261

prepare

prepare(cmd, config): void
Creates slurm string with specified configuation. Saves it to this.template.
Parameters
- cmd: string
  command that needs to be executed
- config: slurm
  slurm configuration
Returns void
- Defined in src/connectors/SlurmConnector.ts:34

pwd

pwd(path?, options?): Promise<null | string>
Parameters
- Optional path: string
- Optional options: options = {}
  dictionary with string options
Returns Promise<null | string>
returns command execution output

Async
Returns the specified path
Inherited from default.pwd
- Defined in src/connectors/BaseConnector.ts:293

registerModules

registerModules(modules): void
Registers all of the specified modules
Parameters
- modules: string[]
  Array of strings
Returns void
- Defined in src/connectors/SlurmConnector.ts:24

remoteFsExists

remoteFsExists(path, options?): Promise<boolean>
Parameters
- path: string
  path to test for
- Optional options: options
  options for doing an exec
Returns Promise<boolean>
true if path exists; false if not

Async
Determines whether a passed in (absolute) path exists on the HPC.
Inherited from default.remoteFsExists
- Defined in src/connectors/BaseConnector.ts:346

resume

resume(): Promise<void>
Returns Promise<void>
Async
resumes the job
- Defined in src/connectors/SlurmConnector.ts:269

rm

rm(path, options?, muteEvent?): Promise<null | string>
Parameters
- path: string
  specified path with filename
- Optional options: options = {}
  set to True if you want to mute maintauner emitted Event
- Optional muteEvent: boolean = false
  command execution output
Returns Promise<null | string>
Async
removes the file/folder at specified path
Inherited from default.rm
- Defined in src/connectors/BaseConnector.ts:360

setRemoteDataFolderPath

setRemoteDataFolderPath(providedPath): void
Sets remote data folder path instance variable.
Parameters
- providedPath: string
Returns void
Inherited from default.setRemoteDataFolderPath
- Defined in src/connectors/BaseConnector.ts:632

setRemoteExecutableFolderPath

setRemoteExecutableFolderPath(providedPath): void
Sets remote executable folder path instance variable.
Parameters
- providedPath: string
Returns void
Inherited from default.setRemoteExecutableFolderPath
- Defined in src/connectors/BaseConnector.ts:623

setRemoteResultFolderPath

setRemoteResultFolderPath(providedPath): void
Setes remote reuslt folder path instance variable.
Parameters
- providedPath: string
Returns void
Inherited from default.setRemoteResultFolderPath
- Defined in src/connectors/BaseConnector.ts:641

ssh

ssh(): SSH
Returns ssh connection from maintainer configuration (for community accounts).

Returns SSH
Inherited from default.ssh
- Defined in src/connectors/BaseConnector.ts:62

submit

submit(): Promise<void>
Returns Promise<void>
Async
Submit the slurm job.
- Defined in src/connectors/SlurmConnector.ts:105

tar

tar(from, to, options?, muteEvent?): Promise<null | string>
Parameters
- from: string
  input file/directory path
- to: string
  compress file path with file name
- Optional options: options = {}
  dictionary with string options
- Optional muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<null | string>
command execution output

Async
tars the file/directory at specified path
Inherited from default.tar
- Defined in src/connectors/BaseConnector.ts:469

transferFile

transferFile(from, to, muteEvent?): Promise<void>
Parameters
- from: string
  input file string
- to: string
  output folder
- muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<void>
Async
Transfers a file from the local machine to remote machine

Throws
- Thrown if maintainer emits 'SSH_SCP_DOWNLOAD_ERROR'
Inherited from default.transferFile
- Defined in src/connectors/BaseConnector.ts:211

untar

untar(from, to, options?, muteEvent?): Promise<null | string>
Parameters
- from: string
  input file/directory path
- to: string
  compress file path with file name
- Optional options: options = {}
  dictionary with string options
- Optional muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<null | string>
command execution output

Async
untars the file/directory at specified path
Inherited from default.untar
- Defined in src/connectors/BaseConnector.ts:504

unzip

unzip(from, to, options?, muteEvent?): Promise<null | string>
Parameters
- from: string
  input file/directory path
- to: string
  compress file path with file name
- Optional options: options = {}
  dictionary with string options
- Optional muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<null | string>
command execution output

Async
unzips the file/folder at specified path
Inherited from default.unzip
- Defined in src/connectors/BaseConnector.ts:435

upload

upload(from, to, muteEvent?, unzip?): Promise<void>
Parameters
- from: string
  input file string
- to: string
  output folder
- muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event (unused)
- unzip: boolean = true
  set to True if you want it to unzip and remove on the remote machine; false just uploads
Returns Promise<void>
Async
Uploads a (zipped) folder from the local machine to the target machine. After upload, decompresses the uploaded zip file and then deletes the zip file.

Throws
- Thrown if maintainer emits 'SSH_SCP_DOWNLOAD_ERROR'
Inherited from default.upload
- Defined in src/connectors/BaseConnector.ts:244

whoami

whoami(options?): Promise<null | string>
Parameters
- Optional options: options = {}
  dictionary with string options
Returns Promise<null | string>
returns command execution output

Async
Returns the username
Inherited from default.whoami
- Defined in src/connectors/BaseConnector.ts:280

zip

zip(from, to, options?, muteEvent?): Promise<null | string>
Parameters
- from: string
  input file/directory path
- to: string
  compress file path with file name
- Optional options: options = {}
  dictionary with string options
- Optional muteEvent: boolean = false
  set to True if you want to mute maintauner emitted Event
Returns Promise<null | string>
command execution output

Async
zips the file/directory at specified path
Inherited from default.zip
- Defined in src/connectors/BaseConnector.ts:403

Class default

Hierarchy (view full)

Index

Constructors

Properties

Methods

Constructors

constructor

Parameters

Returns default

Properties

connectorConfig

Protected envCmd

hpcName

isContainer

is_cvmfs

jobId

maintainer

modules

remote_data_folder_path

remote_executable_folder_path

remote_result_folder_path

slurm_id

template

Methods

cancel

Returns Promise<void>

Async

cat

Parameters

Returns Promise<null | string>

Async

createFile

Parameters

Returns Promise<void>

Async

download

Parameters

Returns Promise<void>

Async

Throws

exec

Parameters

Returns Promise<out>

Async

getContainerCVMFSFolderPath

Parameters

Returns string

getContainerDataFolderPath

Parameters

Returns string

getContainerExecutableFolderPath

Parameters

Returns string

getContainerResultFolderPath

Parameters

Returns string

getRemoteDataFolderPath

Parameters

Returns null | string

getRemoteExecutableFolderPath

Parameters

Returns string

getRemoteResultFolderContent

Returns Promise<string[]>

Async

getRemoteResultFolderPath

Parameters

Returns string

Private getSBatchTagsFromArray

Parameters

Returns string

getSlurmStderr

Returns Promise<void>

Async

getSlurmStdout

Returns Promise<void>

Async

getStatus

Returns Promise<string>

`Protected` envCmd

`Private` getSBatchTagsFromArray