WorkFiles: Functions for working with WorkFiles
In agower/GeneHive: R interface to a GeneHive

WorkFiles

R Documentation

Functions for working with WorkFiles

Description

These functions attempt to add or retrieve a single WorkFile, to list WorkFile records, to add a set of WorkFiles (specified via a set of filenames or in an archive), to pass data between R objects and WorkFiles, or to test whether a character string represents a valid WorkFile identifier.

Usage

addWorkFile(
  filename,
  fileType = file_ext(sub("\\.gz$", "", filename)),
  compress = TRUE,
  group,
  storage,
  token,
  permissions = getOption("GeneHive.permissions"),
  con = hiveConnection(),
  verbose = getOption("GeneHive.verbose")
)

getWorkFile(
  id,
  filename,
  con = hiveConnection(),
  verbose = getOption("GeneHive.verbose")
)

getWorkFileAsObject(
  id,
  con = hiveConnection(),
  verbose = getOption("GeneHive.verbose")
)

importWorkFiles(
  filenames,
  ...,
  permissions = getOption("GeneHive.permissions"),
  con = hiveConnection(),
  verbose = getOption("GeneHive.verbose")
)

importWorkFileArchive(
  filename,
  ...,
  permissions = getOption("GeneHive.permissions"),
  con = hiveConnection(),
  verbose = getOption("GeneHive.verbose")
)

storeObjectAsWorkFile(
  x,
  permissions = getOption("GeneHive.permissions"),
  con = hiveConnection(),
  verbose = getOption("GeneHive.verbose")
)

validWorkFileId(id, con = hiveConnection())

Arguments

`filename`	A character string specifying the full path to a file; for `importWorkFileArchive`, this must be a .tar, .tgz, .tar.gz or .zip file
`fileType`	A character string specifying the file type (e.g., extension) of the `WorkFile`
`compress`	A logical value specifying whether to gzip-compress the `WorkFile` on upload; if the contents of the `WorkFile` are already gzipped, this is ignored
`group`	A character string specifying the name of the `Group` associated with the `WorkFile`. If missing, the group belonging to the user uploading the `WorkFile` is automatically used by the system.
`storage`	A character string specifying the location in which the WorkFile is stored.
`token`	A character string specifying a token that can be used for password-free authentication. Automatically populated when a `WorkFile` is uploaded.
`permissions`	A `hivePermissions` object specifying the permissions to be used when creating the record
`con`	A `hiveConnection` object; if not provided, a new connection will be established
`verbose`	A logical value specifying whether messages should be printed
`id`	A `hiveWorkFileID` object (or coercible to one) specifying the unique identifier of a `WorkFileProperties` record. Automatically populated when a `WorkFile` is uploaded.
`filenames`	A character vector specifying the full path to one or more files
`...`	Additional arguments specifying `WorkFileProperties` fields on which to limit a listing
`x`	An R object to be uploaded as a `WorkFile`

Value

addWorkFile: If a WorkFile exists with the same hash as the input file, it is assumed that they are identical; the existing record will be returned invisibly as a linkS4class{hiveWorkFileProperties} object, and a warning message will be issued. If a WorkFile does not exist with the same MD5 hash as the input file, the file is uploaded and the resulting WorkFile is returned invisibly as a linkS4class{hiveWorkFileProperties} object.
getWorkFile: No value is returned.
importWorkFiles, importWorkFileArchive: If the operation is successful, a hiveWorkFileIDList object is returned invisibly; otherwise, the function terminates with an error message.
storeObjectAsWorkFile: If the operation is successful, a hiveWorkFileProperties object is invisibly returned.
getWorkFileAsObject: If the operation is successful, an R object is invisibly returned: either the R object encoded in the file (if the WorkFile is an RDS file) or the contents of the WorkFile (as a raw vector).
listWorkFiles: A data frame containing one row per record and one column per field.
validWorkFileId: A logical value specifying whether the string corresponds to a WorkFile identifier.
All functions: If an error is encountered, the function terminates with a message.