def run():
netrc_path = os.path.join(expanduser("~"), '.netrc')
user = '******'
password = '******'
bad_netrc = """machine dev.xnat.sydney.edu.au
user unittest
password bad_pass"""
try:
shutil.move(netrc_path, netrc_path + '.good')
except IOError as e:
if e.errno != errno.ENOENT:
raise
try:
# Create bad netrc file to test login failure
with open(netrc_path, 'w') as f:
f.write(bad_netrc)
with connect() as login:
print(login.projects)
with connect() as login:
print(login.projects)
finally:
remove_ignore_errors(netrc_path)
shutil.move(netrc_path + '.good', netrc_path)
def test_outer_connect(self):
with connect() as login:
self.assertEqual(ls(self.test_proj, connection=login),
self._subjects)
# Check to see that the context hasn't been closed by the first
# ls call
self.assertEqual(ls(self.test_proj, connection=login),
self._subjects)
def test_outer_connect(self):
with connect() as mbi_xnat:
self.assertEqual(ls(self.test_proj, connection=mbi_xnat),
self._subjects)
# Check to see that the context hasn't been closed by the first
# ls call
self.assertEqual(ls(self.test_proj, connection=mbi_xnat),
self._subjects)
self.assertRaises(AttributeError,
ls,
self.test_proj,
connection=mbi_xnat)
def run():
parser = argparse.ArgumentParser()
parser.add_argument('xnat_id', help="The XNAT session with the duplicates")
parser.add_argument('scan_ids',
nargs='+',
help="The scans to strip enhanced mr images from")
parser.add_argument('--download_dir',
default='.',
help=("A directory to download the scans to"))
parser.add_argument(
'--dry_run',
action='store_true',
default=False,
help=("Don't actually delete anything just display what "
"would be deleted"))
args = parser.parse_args()
ENHANCED_MR_STORAGE = '1.2.840.10008.5.1.4.1.1.4.1'
with xnatutils.connect() as xlogin:
xsession = xlogin.experiments[args.xnat_id] # noqa pylint:disable=no-member
for scan_id in args.scan_ids:
xscan = xsession.scans[scan_id]
xscan.download_dir(args.download_dir)
files_path = op.join(
args.download_dir, args.xnat_id, 'scans',
'{}-{}'.format(xscan.id,
re.sub(r'[^a-zA-Z_0-9]', '_', xscan.type)),
'resources', 'DICOM', 'files')
for fname, xfile in sorted(xscan.files.items(), key=itemgetter(0)):
fpath = op.join(files_path, fname)
with open(fpath, 'rb') as f:
dcm = pydicom.dcmread(fpath)
if dcm.file_meta.MediaStorageSOPClassUID == ENHANCED_MR_STORAGE:
print("Deleting '{}".format(fname))
if not args.dry_run:
xfile.delete()
if args.dry_run:
print(
'Would delete proceeding "Enhanced MR Image Storage" from {}:[{}]'.
format(args.xnat_id, ', '.join(args.scan_ids)))
else:
print('Deleted all "Enhanced MR Image Storage" from {}:[{}]'.format(
args.xnat_id, ', '.join(args.scan_ids)))
from xnatutils import connect
from xnatutils.base import remove_ignore_errors
from os.path import expanduser
import errno
netrc_path = os.path.join(expanduser("~"), '.netrc')
user = '******'
password = '******'
bad_netrc = """machine mbi-xnat.erc.monash.edu.au
user unittest
password bad_pass"""
try:
shutil.move(netrc_path, netrc_path + '.good')
except IOError as e:
if e.errno != errno.ENOENT:
raise
try:
# Create bad netrc file to test login failure
with open(netrc_path, 'w') as f:
f.write(bad_netrc)
with connect() as login:
print(login.projects)
with connect() as login:
print(login.projects)
finally:
remove_ignore_errors(netrc_path)
shutil.move(netrc_path + '.good', netrc_path)
def setUp(self):
self.xnat_login = connect(server=self.server,
loglevel='DEBUG',
logger=logger)
self.delete_subject()
import os
import shutil
from xnatutils import connect
from xnatutils.base import remove_ignore_errors
from os.path import expanduser
import errno
netrc_path = os.path.join(expanduser("~"), '.netrc')
user = '******'
password = '******'
bad_netrc = """machine mbi-xnat.erc.monash.edu.au
user unittest
password bad_pass"""
try:
shutil.move(netrc_path, netrc_path + '.good')
except IOError as e:
if e.errno != errno.ENOENT:
raise
try:
# Create bad netrc file to test login failure
with open(netrc_path, 'w') as f:
f.write(bad_netrc)
with connect() as mbi_xnat:
print(mbi_xnat.projects)
finally:
remove_ignore_errors(netrc_path)
shutil.move(netrc_path + '.good', netrc_path)
def import_():
export_file = app.config['FILEMAKER_EXPORT_FILE']
if not op.exists(export_file):
raise Exception("Could not find an FileMaker export file at {}".format(
export_file))
num_imported = 0
num_prev = 0
skipped = []
malformed = []
no_xnat = []
# Get previous reporters
nick_ferris = User.query.filter_by(
email='*****@*****.**').one()
paul_beech = User.query.filter_by(email='*****@*****.**').one()
axis = User.query.filter_by(name='AXIS Reporting').one()
with xnatutils.connect(server=app.config['XNAT_URL']) as alfred_xnat:
with open(export_file) as f:
for row in csv.DictReader(f):
project_id = row['ProjectID']
if project_id is None:
malformed.append(row)
continue
project_id = project_id.strip()
if not project_id.startswith('M') or project_id[2] == 'A':
skipped.append(row)
continue
mbi_subject_id = row['SubjectID'].strip()
study_id = row['StudyID'].strip()
first_name = row['FirstName'].strip()
last_name = row['LastName'].strip()
try:
subject = Subject.query.filter_by(
mbi_id=mbi_subject_id).one()
except orm.exc.NoResultFound:
subject = Subject(
mbi_subject_id, first_name, last_name,
datetime.strptime(row['DOB'], '%d/%m/%Y'))
db.session.add(subject) # pylint: disable=no-member
if ImagingSession.query.get(study_id) is None:
if row['DarisID']:
_, subject_id, visit_id = daris_id_re.match(
row['DarisID']).groups()
if visit_id is None:
visit_id = '1'
else:
try:
subject_id = row['XnatSubjectID'].strip()
visit_id = row['XnatVisitID'].strip()
except KeyError:
malformed.append(row)
continue
if not subject_id or not visit_id:
malformed.append(row)
continue
try:
subject_id = int(subject_id)
except ValueError:
pass
else:
subject_id = '{:03}'.format(subject_id)
if project_id.startswith('MMH'):
visit_prefix = 'MRPT'
else:
visit_prefix = 'MR'
numeral, suffix = re.match(r'(\d+)(.*)', visit_id).groups()
visit_id = '{}{:02}{}'.format(
visit_prefix, int(numeral),
(suffix if suffix is not None else ''))
xnat_id = '_'.join(
(project_id, subject_id, visit_id)).upper()
try:
exp = alfred_xnat.experiments[xnat_id] # noqa pylint: disable=no-member
except KeyError:
no_xnat.append(row)
continue
avail_scan_types = []
for scan in exp.scans.values():
try:
scan_type = ScanType.query.filter_by(
name=scan.type).one()
except orm.exc.NoResultFound:
scan_type = ScanType(scan.type)
db.session.add(scan_type) # noqa pylint: disable=no-member
avail_scan_types.append(scan_type)
xnat_uri = exp.uri.split('/')[-1]
scan_date = datetime.strptime(row['ScanDate'], '%d/%m/%Y')
priority = LOW
session = ImagingSession(study_id,
subject,
xnat_id,
xnat_uri,
scan_date,
avail_scan_types,
priority=priority)
db.session.add(session) # pylint: disable=no-member
if row['MrReport'] is not None and row['MrReport'].strip():
if 'MSH' in row['MrReport']:
reporter = axis
else:
reporter = nick_ferris
db.session.add(
Report( # noqa pylint: disable=no-member
session.id,
reporter.id,
'',
NOT_RECORDED, [],
MRI,
date=scan_date,
dummy=True))
if (row['PetReport'] is not None
and row['PetReport'].strip()):
db.session.add(
Report( # noqa pylint: disable=no-member
session.id,
paul_beech.id,
'',
NOT_RECORDED, [],
PET,
date=scan_date,
dummy=True)) # noqa pylint: disable=no-member
db.session.commit() # pylint: disable=no-member
num_imported += 1
print(study_id)
else:
num_prev += 1
return render_template('reporting/import.html',
num_imported=num_imported,
num_prev=num_prev,
malformed=malformed,
no_xnat=no_xnat,
skipped=skipped)
def setUp(self):
self.xnat_login = connect()
self.delete_subject()
def setUp(self):
self.mbi_xnat = connect()
self.delete_subject()
parser.add_argument('scan_ids',
nargs='+',
help="The scans to strip enhanced mr images from")
parser.add_argument('--download_dir',
default='.',
help=("A directory to download the scans to"))
parser.add_argument('--dry_run',
action='store_true',
default=False,
help=("Don't actually delete anything just display what "
"would be deleted"))
args = parser.parse_args()
ENHANCED_MR_STORAGE = '1.2.840.10008.5.1.4.1.1.4.1'
with xnatutils.connect() as xlogin:
xsession = xlogin.experiments[args.xnat_id] # noqa pylint:disable=no-member
for scan_id in args.scan_ids:
xscan = xsession.scans[scan_id]
xscan.download_dir(args.download_dir)
files_path = op.join(
args.download_dir, args.xnat_id,
'scans', '{}-{}'.format(xscan.id,
re.sub(r'[^a-zA-Z_0-9]', '_', xscan.type)),
'resources', 'DICOM', 'files')
for fname, xfile in sorted(xscan.files.items(), key=itemgetter(0)):
