arc-sync-scans.py

#!/usr/bin/python
# arc-sync-scans.py
# Copyright (c) 2010,2011 Washington University
# Author: Kevin A. Archie <karchie@wustl.edu>
#
# Usage:
# arc-sync-scans \
#   -h ${XNAT_BASE_URL}  \
#   --proj ${XNAT_PROJECT} \    (NOTE preceding double dash)
#   -u ${XNAT_USER}      \
#   -p ${XNAT_PASSWORD}  \
#      (-u and -p are optional; user will be prompted if these are omitted)
#   -m ${REQUESTED_MODALITIES} \
#      (-m is optional; multiple values separated by commas)
#   -l ${LOCAL_CACHE_DIR} \
#      (-l is optional; defaults to ${PWD}/${XNAT_PROJECT})
#   -s ${REQUESTED_SCAN_TYPES} \
#      (-t is optional; multiple values separated by commas)
#   -v (optional, displays information about scans being retrieved)

import base64, getopt, getpass, json, os, re, shutil, string, sys, urllib2 as u, zipfile as z

# Read and parse command-line arguments
optsl,args = getopt.getopt(sys.argv[1:], 'h:u:p:m:l:s:v', ['proj='])
opts=dict(optsl)

# XNAT base URL can be either -h or the first non-option argument
base=opts['-h'] if '-h' in opts else args[0]

# XNAT user/pass can be -u/-p or prompted
user=opts['-u'] if '-u' in opts else raw_input('username: ')
passwd=opts['-p'] if '-p' in opts else getpass.getpass('password: ')

verbose='-v' in opts

# Build HTTP header for Basic Authorization
auth={'Authorization':'Basic '+base64.encodestring(user+':'+passwd).strip()}

# Requested modalities
if '-m' in opts:
    xsis = map(lambda m: 'xsiType=xnat:' + m.lower() + 'SessionData&',
                   opts['-m'].split(','))
else:
    xsis=['']

# Local data cache; create if it doesn't already exist
cache=opts['-l'] if '-l' in opts else opts['--proj']
try:
    os.makedirs(cache)
except OSError:
    pass

# Requested scan types
types=opts['-s'] if '-s' in opts else 'ALL'

# What sessions are already (at least partially) present in data cache?
existing=os.listdir(cache)

# Copy requested types into a list so we can look for matches
typelist=types.split(',')


def get(uri):
    """Retrieves the resource text from the given URI on the named host."""
    return u.urlopen(u.Request(url=base+uri, headers=auth))

def get_to_fh(uri, fh):
    """Copies the resource text from the given URI to the file handle."""
    uh = u.urlopen(u.Request(url=base+uri, headers=auth))
    shutil.copyfileobj(uh, fh)

def getJSONResults(uri):
    """Retrieves the Result array from an XNAT JSON search result."""
    return json.load(get(uri))['ResultSet']['Result']

def getScanFiles(expt, scans):
    """Retrieves the data files for the given scan names or types from
the given experiment."""
    args = {'URI':'/REST/projects/%(project)s/subjects/%(subject_label)s/experiments/%(label)s' % expt,
            'scans':scans}
    if verbose:
        print 'Getting %(URI)s: %(scans)s' % args
    zfh = os.tmpfile()
    try:
        get_to_fh('%(URI)s/scans/%(scans)s/files?format=zip' % args, zfh)
        zfh.seek(0, os.SEEK_SET)
        z.ZipFile(zfh, 'r').extractall(cache)
    finally:
        zfh.close()



# main
for xsi in xsis:
    opts['xsi']=xsi
    for expt in getJSONResults('/REST/projects/%(--proj)s/experiments?%(xsi)sformat=json&columns=subject_label,label' % opts):
        expt['project']=opts['--proj']
        label = expt['label']
        if label not in existing:
            getScanFiles(expt, types)
        else:
            for scan in getJSONResults('%(URI)s/scans' % expt):
                if types == 'ALL' or scan['type'] in typelist:
                    name=re.sub(r'[^\w\-]', '_', "%(ID)s-%(type)s" % scan)
                    if name not in os.listdir(cache+'/'+label+'/scans'):
                        getScanFiles(expt, scan['ID'])