File management

Share:

Description

Functions for uploading and manipulating files in the iPlant infrastructure

Usage

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UploadFile(local.file.name, local.file.path="", filetype=NULL,
           print.curl=FALSE, suppress.Warnings=FALSE)
ShareFile(file.name, file.path="", shared.username, read=TRUE, 
          execute=TRUE, write=TRUE, print.curl=FALSE, suppress.Warnings=FALSE)
PermissionsFile(file.name, file.path="", print.curl=FALSE, suppress.Warnings=FALSE)
RenameFile(file.name, new.file.name, file.path="", print.curl=FALSE,
           suppress.Warnings=FALSE)
CopyFile(file.name, file.path="", end.path="", print.curl=FALSE,
         suppress.Warnings=FALSE)
MoveFile(file.name, file.path="", end.path="", print.curl=FALSE,
         suppress.Warnings=FALSE)
DeleteFile(file.name, file.path="", print.curl=FALSE, suppress.Warnings=FALSE)
SupportFile(print.curl=FALSE, suppress.Warnings=FALSE) 

Arguments

local.file.name

Name of local file on user's computer. This file cannot be an object in the R workspace.

local.file.path

optional path to a sub directory where local file on user's computer is located (include ENTIRE path); default path is empty which leads to a users home directory

filetype

format of file that is to be uploaded. Currently 34 file formats supported. A filetype is not required to upload the file, but some applications require that your data set have a file type assigned to it.

file.name

Name of file to be modified on the iPlant servers.

new.file.name

the new name of the file on the iPlant server to be renamed

file.path

optional path to a sub directory where file on the iPlant server is located; default path is empty which leads to a users home directory

end.path

Path to destination sub directory where file on DE is moved to; default path is empty which leads to a users home directory

read

Gives read permissions for shared file

write

Gives write permissions for shared file

execute

Gives execute permissions for shared file

shared.username

With iPlant you have the ability to share files with other users, their username is the value for the shared.username

print.curl

Prints the curl statement that can be used in the terminal, if curl is installed on your computer

suppress.Warnings

This will turn off the warnings, will speed up run time. Use with caution, if the inputs are incorrect they will not be caught.

Details

The SupportFile function provides a list of the supported file types that can be uploaded onto the iPlant servers. The UploadFile function uploads a file, local.file.name, that is on your computer (i.e. local directory), in the directory local.file.path. If the local.file.path is not specified your working directory is the default path (use getwd() to find that). The filetype is NOT required, but if you do use it then use the SupportFile function to view the 34 file formats that are supported (i.e. for a fasta file use FASTA-0). iPlant offers sharing of files between two (or more) iPlant users, the ShareFile makes it so. Once sharing is done a user can use PermissionsFile on any file to find who the file is shared with. The RenameFile function renames the file.name in file.path (on the iPlant servers), to the new.file.name. The CopyFile function copies a file.name in the file.path to the end.path. The MoveFile function moves a file.name in the file.path to the end.path. The DeleteFile function deletes the file.name in the file.path.

Value

If an error, then a message stating the error should also be reported.

See Also

ListDir

Examples

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# Write .fasta file to home directory
## Not run: data(DNA.fasta)
## Not run: write.fasta(sequences = DNA.fasta, names = names(DNA.fasta), 
                     file.out = "DNA.fasta")
## End(Not run)
## Not run: UploadFile(local.file.name="DNA.fasta", local.file.path="path/to/dir", 
                    filetype="FASTA-0")
## End(Not run)
         
# Upload a file to the DE
## Not run: data(geno_test.tfam)
## Not run: UploadFile(local.file.name="geno_test.tfam")

# Shares the file named "DNA.fasta" with the iPlant user "dude"
## Not run: ShareFile(file.name="DNA.fasta", shared.username="dude")

# Checks permissions on file "DNA.fasta"
## Not run: PermissionsFile(file.name="DNA.fasta")

# Rename a file 
## Not run: RenameFile(file.name="DNA.fasta", new.file.name="lp.fasta")

# Copy a file from the subdirectory 'rPlant' to the home directory
## Not run: CopyFile(file.name="lp.fasta", file.path="", end.path="data")
             
# Move a file from the subdirectory 'rPlant' to the home directory
## Not run: MoveFile(file.name="lp.fasta", file.path="", end.path="data")
     
# Delete a file in the home directory
## Not run: DeleteFile(file.name="lp.fasta", DE.file.path="data")

# Lists file types that are supported
## Not run: SupportFile()