XNAT file upload in python

xnatUpload.py

#
# Basic XNAT file upload with standard python
#

import httplib, urlparse, mimetypes, io, base64, urllib, os, sys


def createResource(host, selector, auth):
    """
    Create an XNAT resource (directory)
    Return the server's response page.
    """
    body = ''
    h = httplib.HTTP(host)
    h.putrequest('PUT', selector + '?inbody=true')
    h.putheader('Authorization', 'Basic ' + base64.b64encode( auth))
    h.putheader('content-type', 'application/octet-stream')
    h.putheader('content-length', str(len(body)))
    h.endheaders()
    h.send(body)
    errcode, errmsg, headers = h.getreply()
    return h.file.read()


def uploadFile(host, selector, auth, body):
    """
    Upload a file as specified by the selector
    Body is the file contents
    Return the server's response page.
    """
    h = httplib.HTTP(host)
    h.putrequest('PUT', selector + '?inbody=true')
    h.putheader('Authorization', 'Basic ' + base64.b64encode( auth))
    h.putheader('content-type', 'application/octet-stream')
    h.putheader('content-length', str(len(body)))
    h.endheaders()
    h.send(body)
    errcode, errmsg, headers = h.getreply()
    return h.file.read()


##############################################


## XNAT Server Configuration Parameters ##

xnatHost = 'project-xnat.institute.org:8080'  # replace it with actual host
xnatRoot = '/xnat'   # replace it with actual root directory
xnatUser = 'username'  # !replace it with actual username
xnatPw = 'password'  # !replace it with actual password
xnatAuth = xnatUser + ':' + xnatPw 


## File Upload Parameters ##

xnatProject = 'test'
xnatSubject = 'SUB001'
xnatRemoteFile = 'remFile.csv'
localFilename = 'locFile.csv' 


########### upload code #############


xnatPath = '/data/archive/projects/' + xnatProject \
          + '/subjects/' + xnatSubject \
          + '/resources/SIM'

xnatSelector = xnatRoot + xnatPath


if 0:
    deleteResource( xnatHost, xnatSelector, xnatAuth)
    print 'attempting resource deletion'
    print '\t%s'% xnatPath
    exit(0)



# check the resource existence by listing it
#     if fail, create resource
try:
    # get SIM url
    resUrl = 'http://%s@%s%s' \
                        % (xnatAuth, xnatHost, xnatSelector)
    print 'checking resource %s' % xnatSelector
    resObj = urllib.urlopen( resUrl)
    resObj.close()
    if( resObj.getcode() == 404):
        print 'attempting resource creation'
        print '\t%s'% xnatPath
        createResource( xnatHost, xnatSelector, xnatAuth)
except:
    (exc_type, exc_value, exc_traceback) = sys.exc_info()
    print "Problems checking/creating resource"
    print exc_value




# upload file
xnatFileSelector = xnatSelector + '/files/' + xnatRemoteFile

print 'attempting file upload'
print '\t%s' % xnatFileSelector


with open( localFilename, 'rb') as inFile:
    uploadFile( xnatHost, xnatFileSelector, xnatAuth, inFile.read())