def test_write_read_files(self):
'''test_write_read_files will test the functions
write_file and read_file
'''
print("Testing utils.write_file...")
from deid.utils import write_file
tmpfile = tempfile.mkstemp()[1]
os.remove(tmpfile)
write_file(tmpfile, "blaaahumbug")
self.assertTrue(os.path.exists(tmpfile))
print("Testing utils.read_file...")
from deid.utils import read_file
content = read_file(tmpfile)[0]
self.assertEqual("blaaahumbug", content)
from deid.utils import write_json
print("Testing utils.write_json...")
print("Case 1: Providing bad json")
bad_json = {"Wakkawakkawakka'}": [{True}, "2", 3]}
tmpfile = tempfile.mkstemp()[1]
os.remove(tmpfile)
with self.assertRaises(TypeError) as cm:
write_json(bad_json, tmpfile)
print("Case 2: Providing good json")
good_json = {"Wakkawakkawakka": [True, "2", 3]}
tmpfile = tempfile.mkstemp()[1]
os.remove(tmpfile)
write_json(good_json, tmpfile)
content = json.load(open(tmpfile, 'r'))
self.assertTrue(isinstance(content, dict))
self.assertTrue("Wakkawakkawakka" in content)
def load_deid(path=None):
'''load_deid will return a loaded in (user) deid configuration file
that can be used to update a default config.json. If a file path is
specified, it is loaded directly. If a folder is specified, we look
for a deid file in the folder. If nothing is specified, we assume
the user wants to load a deid file in the present working directory.
If the user wants to have multiple deid files in a directory, this
can be done with an extension that specifies the module, eg;
deid.dicom
deid.nifti
Parameters
==========
path: a path to a deid file
Returns
=======
config: a parsed deid (dictionary) with valid sections
'''
path = find_deid(path)
# Read in spec, clean up extra spaces and newlines
spec = [
x.strip('\n').strip(' ') for x in read_file(path)
if x.strip('\n').strip(' ') not in ['']
]
spec = [x for x in spec if x not in ['', None]]
config = OrderedDict()
section = None
while len(spec) > 0:
# Clean up white trailing/leading space
line = spec.pop(0).strip()
# Comment
if line.startswith("#"):
continue
# Starts with Format?
elif bool(re.match('format', line, re.I)):
fmt = re.sub('FORMAT|(\s+)', '', line).lower()
if fmt not in formats:
bot.error("%s is not a valid format." % fmt)
sys.exit(1)
# Set format
config['format'] = fmt
bot.debug("FORMAT set to %s" % fmt)
# A new section?
elif line.startswith('%'):
# Remove any comments
line = line.split('#', 1)[0].strip()
# Is there a section name?
section_name = None
parts = line.split(' ')
if len(parts) > 1:
section_name = ' '.join(parts[1:])
section = re.sub('[%]|(\s+)', '', parts[0]).lower()
if section not in sections:
bot.error("%s is not a valid section." % section)
sys.exit(1)
config = add_section(config=config,
section=section,
section_name=section_name)
# An action (replace, blank, remove, keep, jitter)
elif line.upper().startswith(actions):
# Start of a filter group
if line.upper().startswith('LABEL') and section == "filter":
members = []
keep_going = True
while keep_going is True:
next_line = spec[0]
if next_line.upper().strip().startswith('LABEL'):
keep_going = False
elif next_line.upper().strip().startswith("%"):
keep_going = False
else:
new_member = spec.pop(0)
members.append(new_member)
if len(spec) == 0:
keep_going = False
# Add the filter label to the config
config = parse_label(config=config,
section=section,
label=line,
section_name=section_name,
members=members)
# Parse the action
else:
config = parse_action(section=section,
section_name=section_name,
line=line,
config=config)
else:
bot.debug("%s not recognized to be in valid format, skipping." %
line)
return config
def load_deid(path=None):
"""load_deid will return a loaded in (user) deid configuration file
that can be used to update a default config.json. If a file path is
specified, it is loaded directly. If a folder is specified, we look
for a deid file in the folder. If nothing is specified, we assume
the user wants to load a deid file in the present working directory.
If the user wants to have multiple deid files in a directory, this
can be done with an extension that specifies the module, eg;
deid.dicom
deid.nifti
Parameters
==========
path: a path to a deid file
Returns
=======
config: a parsed deid (dictionary) with valid sections
"""
path = find_deid(path)
# Read in spec, clean up extra spaces and newlines
spec = [
x.strip("\n").strip(" ") for x in read_file(path)
if x.strip("\n").strip(" ") not in [""]
]
spec = [x for x in spec if x not in ["", None]]
config = OrderedDict()
section = None
while spec:
# Clean up white trailing/leading space
line = spec.pop(0).strip()
# Comment
if line.startswith("#"):
continue
# Set format
elif bool(re.match("^format", line, re.I)):
config["format"] = parse_format(line)
# A new section?
elif line.startswith("%"):
# Remove any comments
line = line.split("#", 1)[0].strip()
# Is there a section name?
section_name = None
parts = line.split(" ")
if len(parts) > 1:
section_name = " ".join(parts[1:])
section = re.sub("[%]|(\s+)", "", parts[0]).lower()
if section not in sections:
bot.exit("%s is not a valid section." % section)
config = add_section(config=config,
section=section,
section_name=section_name)
# A %fields action (only field allowed), %values allows split
elif line.upper().startswith(group_actions) and section in groups:
config = parse_group_action(section=section,
section_name=section_name,
line=line,
config=config)
# An action (ADD, BLANK, JITTER, KEEP, REPLACE, REMOVE, LABEL)
elif line.upper().startswith(actions):
# Start of a filter group
if line.upper().startswith("LABEL") and section == "filter":
members = parse_filter_group(spec)
# Add the filter label to the config
config = parse_label(
config=config,
section=section,
label=line,
section_name=section_name,
members=members,
)
# Parse the action
else:
config = parse_config_action(section=section,
section_name=section_name,
line=line,
config=config)
else:
bot.warning("%s not recognized to be in valid format, skipping." %
line)
return config
