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Version: 0.4-4
Date: 2024-04-15
Title: Interface to 'D4Science' 'StorageHub' API
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Depends: R (≥ 3.3.0), methods
Imports: R6, httr, jsonlite, XML, xml2, keyring, tools
Suggests: testthat, parallel
Description: Provides an interface to 'D4Science' 'StorageHub' API (https://dev.d4science.org/). Allows to get user profile, and perform actions over the 'StorageHub' (workspace) including creation of folders, files management (upload/update/deletion/sharing), and listing of stored resources.
License: MIT + file LICENSE
URL: https://github.com/eblondel/d4storagehub4R, https://www.d4science.org/, https://dev.d4science.org/
BugReports: https://github.com/eblondel/d4storagehub4R/issues
LazyLoad: yes
RoxygenNote: 7.3.1
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2024-04-15 07:40:22 UTC; emman
Author: Emmanuel Blondel ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2024-04-15 08:00:02 UTC

Interface to 'D4Science' 'StorageHub' API

Description

Provides an interface to 'D4Science' 'StorageHub' API (<https://dev.d4science.org/>). Allows to get user profile, and perform actions over the 'StorageHub' (workspace) including creation of folders, files management (upload/update/deletion/sharing), and listing of stored resources.

Author(s)

Emmanuel Blondel emmanuel.blondel1@gmail.com

StoragehubManager

Description

StoragehubManager

StoragehubManager

Value

Object of R6Class for modelling a D4Science StoragehubManager

Super class

d4storagehub4R::d4storagehub4RLogger -> StoragehubManager

Methods

Public methods

Inherited methods

Method new()

Method is used to instantiate the StoragehubManager.

Usage
StoragehubManager$new(
  token,
  token_type = "gcube",
  logger = NULL,
  keyring_backend = "env"
)
Arguments
token

user access token

token_type

token type, either 'gcube' (default) or 'jwt'

logger

logger can be either NULL, "INFO" (with minimum logs), or "DEBUG" (for complete curl http calls logs)

keyring_backend

keyring backend to use.it can be set to use a different backend for storing the D4science gcube token with keyring (Default value is 'env').

Method getToken()

Get token

Usage
StoragehubManager$getToken()
Returns

the user access token

Method getUserProfile()

Get user profile

Usage
StoragehubManager$getUserProfile()
Returns

the user profile

Method getUserWorkspace()

Get user workspace

Usage
StoragehubManager$getUserWorkspace()
Returns

the user workspace root path

Method fetchWSEndpoint()

Fetches the workspace endpoint from the D4Science ICProxy service

Usage
StoragehubManager$fetchWSEndpoint()

Method fetchUserProfile()

Fetches the user profile

Usage
StoragehubManager$fetchUserProfile()

Method getWSRoot()

Get workspace root

Usage
StoragehubManager$getWSRoot()
Returns

the workspace root, as list

Method getWSRootID()

Get workspace root ID

Usage
StoragehubManager$getWSRootID()
Returns

the workspace root ID, as character

Method getWSItem()

Get workspace item given a itemPath in a parent folder

Usage
StoragehubManager$getWSItem(
  parentFolderID = NULL,
  itemPath,
  showHidden = FALSE
)
Arguments
parentFolderID

parent folder ID

itemPath

item path

showHidden

show hidden files

Returns

the workspace item, NULL if no workspace item existing

Method getWSItemID()

Get workspace item ID given a itemPath in a parent folder

Usage
StoragehubManager$getWSItemID(
  parentFolderID = NULL,
  itemPath,
  showHidden = FALSE
)
Arguments
parentFolderID

parent folder ID

itemPath

item path

showHidden

show hidden files

Returns

the workspace item ID, NULL if no workspace item existing

Method getWSVREFolder()

Get VRE Folder

Usage
StoragehubManager$getWSVREFolder()
Returns

the VRE folder, as list

Method getWSVREFolderID()

Get VRE Folder ID

Usage
StoragehubManager$getWSVREFolderID()
Returns

the VRE folder ID, as character

Method listWSItems()

Lists workspace items given a parentFolder ID

Usage
StoragehubManager$listWSItems(parentFolderID = NULL, showHidden = FALSE)
Arguments
parentFolderID

parent folder ID

showHidden

show hidden files

Returns

an object of class data.frame

Method listWSItemsByPath()

Lists workspace items given a folder path

Usage
StoragehubManager$listWSItemsByPath(folderPath, showHidden = FALSE)
Arguments
folderPath

folder path where to list items

showHidden

show hidden files

Returns

an object of class data.frame

Method searchWSItem()

Searches for a workspace item given a item path

Usage
StoragehubManager$searchWSItem(
  itemPath,
  includeVreFolder = TRUE,
  showHidden = FALSE
)
Arguments
itemPath

path of the item

includeVreFolder

search also in VRE folder

showHidden

show hidden files

Returns

the item, NULL if nothing found

Method searchWSItemID()

Searches for a workspace item ID given a item path

Usage
StoragehubManager$searchWSItemID(
  itemPath,
  includeVreFolder = TRUE,
  showHidden = FALSE
)
Arguments
itemPath

path of the item

includeVreFolder

search also in VRE folder

showHidden

show hidden files

Returns

the item, NULL if nothing found

Method createFolder()

Creates a folder, given a folder path, a folder name/description. By default recursive = TRUE meaning that a folder path matching nested folders will trigger all nested folders. Setting recursive = FALSE, the folder creation will work only if the folder path matches an existing folder. The hidden (default FALSE) argument can be used to set hidden folders on the workspace. Using folderID, recursive will be set to FALSE.

Usage
StoragehubManager$createFolder(
  folderPath = NULL,
  folderID = NULL,
  name,
  description = "",
  hidden = FALSE,
  recursive = TRUE
)
Arguments
folderPath

parent folder path where to create the folder

folderID

parent folder ID where to create the folder

name

name of the folder

description

description of the folder

hidden

hidden, default is FALSE

recursive

recursive, default is TRUE

Returns

the ID of the created folder

Method uploadFile()

Uploads a file to a folder (given a folder path). The argument description can be used to further describe the file to upload. The argument archive (default = FALSE) indicates the type of item (FILE or ARCHIVE) to be uploaded.

Usage
StoragehubManager$uploadFile(
  folderPath = NULL,
  folderID = NULL,
  file,
  description = basename(file),
  archive = FALSE
)
Arguments
folderPath

folder path where to upload the file

folderID

folder ID where to upload the file

file

file to upload

description

file description, default would be the file basename

archive

archive, default is FALSE

Returns

the ID of the uploaded file

Method deleteItem()

Deletes an item given its path on the workspace

Usage
StoragehubManager$deleteItem(itemPath, force = FALSE)
Arguments
itemPath

item path

force

whether to force deletion, default is FALSE

Returns

TRUE if deleted, FALSE otherwise

Method shareItem()

Shares an item with users

Usage
StoragehubManager$shareItem(itemPath, defaultAccessType, users)
Arguments
itemPath

item path

defaultAccessType

access type to use for sharing, among 'WRITE_ALL', 'WRITE_OWNER', 'READ_ONLY', 'ADMINISTRATOR'

users

one or more user names with whom the item has to be shared

Returns

TRUE if shared, FALSE otherwise

Method unshareItem()

unshare an item

Usage
StoragehubManager$unshareItem(itemPath, users)
Arguments
itemPath

item path

users

users

Returns

TRUE if unshared, FALSE otherwise

Method downloadItem()

Download item

Usage
StoragehubManager$downloadItem(item = NULL, wd = NULL)
Arguments
item

item

wd

working directory where to download the item

Method downloadItemByPath()

Download item by path

Usage
StoragehubManager$downloadItemByPath(path, wd = NULL)
Arguments
path

path

wd

working directory where to download the item

Method getPublicFileLinkByID()

Get public file link by ID

Usage
StoragehubManager$getPublicFileLinkByID(pathID)
Arguments
pathID

file item ID

Returns

the public file URL

Method getPublicFileLink()

Get public file link

Usage
StoragehubManager$getPublicFileLink(path)
Arguments
path

file path

Returns

the public file URL

Method clone()

The objects of this class are cloneable with this method.

Usage
StoragehubManager$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Main user class to be used with d4storagehub4R

Deprecated

Author(s)

Emmanuel Blondel <emmanuel.blondel1@gmail.com>

Examples

## Not run: 
  manager <- StoragehubManager$new(
    token = "<your token>",
    logger = "DEBUG"
  )

## End(Not run)

d4storagehub4RLogger

Description

d4storagehub4RLogger

d4storagehub4RLogger

Format

R6Class object.

Value

Object of R6Class for modelling a simple logger

Abstract Methods

INFO(text)

Logger to report information. Used internally

WARN(text)

Logger to report warnings. Used internally

ERROR(text)

Logger to report errors. Used internally

Public fields

verbose.info

verbose info, default is FALSE

verbose.debug

verbose debug, default is FALSE

loggerType

logger type

Methods

Public methods

Method logger()

Logger function

Usage
d4storagehub4RLogger$logger(type, text)
Arguments
type

type

text

text

Method INFO()

INFO logger function

Usage
d4storagehub4RLogger$INFO(text)
Arguments
text

text

Method WARN()

WARN logger function

Usage
d4storagehub4RLogger$WARN(text)
Arguments
text

text

Method ERROR()

ERROR logger function

Usage
d4storagehub4RLogger$ERROR(text)
Arguments
text

text

Method new()

Initializes a basic logger class

Usage
d4storagehub4RLogger$new(logger = NULL)
Arguments
logger

the type of logger, either NULL (default), INFO, or DEBUG

Method getClassName()

Get class name

Usage
d4storagehub4RLogger$getClassName()
Returns

the class name

Method getClass()

Get class

Usage
d4storagehub4RLogger$getClass()
Returns

the class

Method clone()

The objects of this class are cloneable with this method.

Usage
d4storagehub4RLogger$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Note

Logger class used internally by d4storagehub4R

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.