Placing Files in iRODS using python irods client

[Katherine Beaulieu]

Hi everyone,
I am working on placing a file in the iRODS file system using a python script. I just want to place it in the users main collection but am not sure how to go about it following the user guide found here: https://github.com/irods/python-irodsclient.
Here is the script I have so far:
import sys
from irods.session import iRODSSession
sess = iRODSSesssion(host='localhost',port=1247,user='rods',password=XXXXXXXX, zone='tempZone')

with open(sys.argv[1], 'r') as fileToPlace:
     print fileToPlace.read()
     obj = sess.data_objects.create("tempZone/home/rods/" + fileToPlace)

This doesn't work as you can't concatenate a string a file but I don't know how else you would put an already existing file into irods using this API.
Thanks in advance!

[de Torcy, Antoine]

Hi,

You will have to read your local file's content and write it to a new irods object, e.g:

obj = session.data_objects.create(obj_path)
with obj.open('w') as obj_desc:
    obj_desc.write(content)

# refresh object after write
return session.data_objects.get(obj_path) 

You might also want to take a look at the test code in https://github.com/irods/python-irodsclient/tree/master/irods/test for further examples.

AdT

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From: irod...@googlegroups.com <irod...@googlegroups.com> on behalf of Katherine Beaulieu <katherine....@gmail.com>
Sent: Friday, May 27, 2016 9:12 AM
To: iRODS-Chat
Subject: [iROD-Chat:15147] Placing Files in iRODS using python irods client

 

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[Sune Andersen]

Hi !

Have look at my Python script at GitHub : https://github.com/sunadtudk/irods_2_figshare

Just a note : you can use the iCommand to upload/download files - info : https://docs.irods.org/master/icommands/user/

And just do the Python-call:

import os

cmd = 'bin/bar --option'

os.system(cmd) # returns the exit status

-Sune , Denmark