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def variations(word):
"""Create variations of the word based on letter combinations like oo,
sh, etc."""
if len(word) == 1:
return [[word[0]]]
elif word == 'aa':
return [['A']]
elif word == 'ee':
return [['i']]
elif word == 'ei':
return [['ei']]
elif word in ['oo', 'ou']:
return [['u']]
elif word == 'kha':
return [['kha'], ['kh', 'a']]
elif word in ['kh', 'gh', 'ch', 'sh', 'zh', 'ck']:
return [[word]]
elif word in ["'ee", "'ei"]:
return [["'i"]]
elif word in ["'oo", "'ou"]:
return [["'u"]]
elif word in ["a'", "e'", "o'", "i'", "u'", "A'"]:
return [[word[0] + "'"]]
elif word in ["'a", "'e", "'o", "'i", "'u", "'A"]:
return [["'" + word[1]]]
elif len(word) == 2 and word[0] == word[1]:
return [[word[0]]]
if word[:2] == 'aa':
return [['A'] + i for i in variations(word[2:])]
elif word[:2] == 'ee':
return [['i'] + i for i in variations(word[2:])]
elif word[:2] in ['oo', 'ou']:
return [['u'] + i for i in variations(word[2:])]
elif word[:3] == 'kha':
return \
[['kha'] + i for i in variations(word[3:])] + \
[['kh', 'a'] + i for i in variations(word[3:])] + \
[['k', 'h', 'a'] + i for i in variations(word[3:])]
elif word[:2] in ['kh', 'gh', 'ch', 'sh', 'zh', 'ck']:
return \
[[word[:2]] + i for i in variations(word[2:])] + \
[[word[0]] + i for i in variations(word[1:])]
elif word[:2] in ["a'", "e'", "o'", "i'", "u'", "A'"]:
return [[word[:2]] + i for i in variations(word[2:])]
elif word[:3] in ["'ee", "'ei"]:
return [["'i"] + i for i in variations(word[3:])]
elif word[:3] in ["'oo", "'ou"]:
return [["'u"] + i for i in variations(word[3:])]
elif word[:2] in ["'a", "'e", "'o", "'i", "'u", "'A"]:
return [[word[:2]] + i for i in variations(word[2:])]
elif len(word) >= 2 and word[0] == word[1]:
return [[word[0]] + i for i in variations(word[2:])]
else:
return [[word[0]] + i for i in variations(word[1:])] | Create variations of the word based on letter combinations like oo,
sh, etc. | entailment |
def f2p_word(word, max_word_size=15, cutoff=3):
"""Convert a single word from Finglish to Persian.
max_word_size: Maximum size of the words to consider. Words larger
than this will be kept unchanged.
cutoff: The cut-off point. For each word, there could be many
possibilities. By default 3 of these possibilities are considered
for each word. This number can be changed by this argument.
"""
original_word = word
word = word.lower()
c = dictionary.get(word)
if c:
return [(c, 1.0)]
if word == '':
return []
elif len(word) > max_word_size:
return [(original_word, 1.0)]
results = []
for w in variations(word):
results.extend(f2p_word_internal(w, original_word))
# sort results based on the confidence value
results.sort(key=lambda r: r[1], reverse=True)
# return the top three results in order to cut down on the number
# of possibilities.
return results[:cutoff] | Convert a single word from Finglish to Persian.
max_word_size: Maximum size of the words to consider. Words larger
than this will be kept unchanged.
cutoff: The cut-off point. For each word, there could be many
possibilities. By default 3 of these possibilities are considered
for each word. This number can be changed by this argument. | entailment |
def f2p_list(phrase, max_word_size=15, cutoff=3):
"""Convert a phrase from Finglish to Persian.
phrase: The phrase to convert.
max_word_size: Maximum size of the words to consider. Words larger
than this will be kept unchanged.
cutoff: The cut-off point. For each word, there could be many
possibilities. By default 3 of these possibilities are considered
for each word. This number can be changed by this argument.
Returns a list of lists, each sub-list contains a number of
possibilities for each word as a pair of (word, confidence)
values.
"""
# split the phrase into words
results = [w for w in sep_regex.split(phrase) if w]
# return an empty list if no words
if results == []:
return []
# convert each word separately
results = [f2p_word(w, max_word_size, cutoff) for w in results]
return results | Convert a phrase from Finglish to Persian.
phrase: The phrase to convert.
max_word_size: Maximum size of the words to consider. Words larger
than this will be kept unchanged.
cutoff: The cut-off point. For each word, there could be many
possibilities. By default 3 of these possibilities are considered
for each word. This number can be changed by this argument.
Returns a list of lists, each sub-list contains a number of
possibilities for each word as a pair of (word, confidence)
values. | entailment |
def f2p(phrase, max_word_size=15, cutoff=3):
"""Convert a Finglish phrase to the most probable Persian phrase.
"""
results = f2p_list(phrase, max_word_size, cutoff)
return ' '.join(i[0][0] for i in results) | Convert a Finglish phrase to the most probable Persian phrase. | entailment |
def distribution_version(name):
"""try to get the version of the named distribution,
returs None on failure"""
from pkg_resources import get_distribution, DistributionNotFound
try:
dist = get_distribution(name)
except DistributionNotFound:
pass
else:
return dist.version | try to get the version of the named distribution,
returs None on failure | entailment |
def initpkg(pkgname, exportdefs, attr=None, eager=False):
""" initialize given package from the export definitions. """
attr = attr or {}
oldmod = sys.modules.get(pkgname)
d = {}
f = getattr(oldmod, '__file__', None)
if f:
f = _py_abspath(f)
d['__file__'] = f
if hasattr(oldmod, '__version__'):
d['__version__'] = oldmod.__version__
if hasattr(oldmod, '__loader__'):
d['__loader__'] = oldmod.__loader__
if hasattr(oldmod, '__path__'):
d['__path__'] = [_py_abspath(p) for p in oldmod.__path__]
if hasattr(oldmod, '__package__'):
d['__package__'] = oldmod.__package__
if '__doc__' not in exportdefs and getattr(oldmod, '__doc__', None):
d['__doc__'] = oldmod.__doc__
d.update(attr)
if hasattr(oldmod, "__dict__"):
oldmod.__dict__.update(d)
mod = ApiModule(pkgname, exportdefs, implprefix=pkgname, attr=d)
sys.modules[pkgname] = mod
# eagerload in bypthon to avoid their monkeypatching breaking packages
if 'bpython' in sys.modules or eager:
for module in list(sys.modules.values()):
if isinstance(module, ApiModule):
module.__dict__ | initialize given package from the export definitions. | entailment |
def importobj(modpath, attrname):
"""imports a module, then resolves the attrname on it"""
module = __import__(modpath, None, None, ['__doc__'])
if not attrname:
return module
retval = module
names = attrname.split(".")
for x in names:
retval = getattr(retval, x)
return retval | imports a module, then resolves the attrname on it | entailment |
def __makeattr(self, name):
"""lazily compute value for name or raise AttributeError if unknown."""
# print "makeattr", self.__name__, name
target = None
if '__onfirstaccess__' in self.__map__:
target = self.__map__.pop('__onfirstaccess__')
importobj(*target)()
try:
modpath, attrname = self.__map__[name]
except KeyError:
if target is not None and name != '__onfirstaccess__':
# retry, onfirstaccess might have set attrs
return getattr(self, name)
raise AttributeError(name)
else:
result = importobj(modpath, attrname)
setattr(self, name, result)
try:
del self.__map__[name]
except KeyError:
pass # in a recursive-import situation a double-del can happen
return result | lazily compute value for name or raise AttributeError if unknown. | entailment |
def _request(self, http_method, relative_url='', **kwargs):
"""Does actual HTTP request using requests library."""
# It could be possible to call api.resource.get('/index')
# but it would be non-intuitive that the path would resolve
# to root of domain
relative_url = self._remove_leading_slash(relative_url)
# Add default kwargs with possible custom kwargs returned by
# before_request
new_kwargs = self.default_kwargs().copy()
custom_kwargs = self.before_request(
http_method,
relative_url,
kwargs.copy()
)
new_kwargs.update(custom_kwargs)
response = requests.request(
http_method,
self._join_url(relative_url),
**new_kwargs
)
return self.after_request(response) | Does actual HTTP request using requests library. | entailment |
def _new_url(self, relative_url):
"""Create new Url which points to new url."""
return Url(
urljoin(self._base_url, relative_url),
**self._default_kwargs
) | Create new Url which points to new url. | entailment |
def roles(self):
"""gets user groups"""
result = AuthGroup.objects(creator=self.client).only('role')
return json.loads(result.to_json()) | gets user groups | entailment |
def get_permissions(self, role):
"""gets permissions of role"""
target_role = AuthGroup.objects(role=role, creator=self.client).first()
if not target_role:
return '[]'
targets = AuthPermission.objects(groups=target_role, creator=self.client).only('name')
return json.loads(targets.to_json()) | gets permissions of role | entailment |
def get_user_permissions(self, user):
"""get permissions of a user"""
memberShipRecords = AuthMembership.objects(creator=self.client, user=user).only('groups')
results = []
for each in memberShipRecords:
for group in each.groups:
targetPermissionRecords = AuthPermission.objects(creator=self.client,
groups=group).only('name')
for each_permission in targetPermissionRecords:
results.append({'name':each_permission.name})
return results | get permissions of a user | entailment |
def get_user_roles(self, user):
"""get permissions of a user"""
memberShipRecords = AuthMembership.objects(creator=self.client, user=user).only('groups')
results = []
for each in memberShipRecords:
for group in each.groups:
results.append({'role':group.role})
return results | get permissions of a user | entailment |
def get_role_members(self, role):
"""get permissions of a user"""
targetRoleDb = AuthGroup.objects(creator=self.client, role=role)
members = AuthMembership.objects(groups__in=targetRoleDb).only('user')
return json.loads(members.to_json()) | get permissions of a user | entailment |
def which_roles_can(self, name):
"""Which role can SendMail? """
targetPermissionRecords = AuthPermission.objects(creator=self.client, name=name).first()
return [{'role': group.role} for group in targetPermissionRecords.groups] | Which role can SendMail? | entailment |
def which_users_can(self, name):
"""Which role can SendMail? """
_roles = self.which_roles_can(name)
result = [self.get_role_members(i.get('role')) for i in _roles]
return result | Which role can SendMail? | entailment |
def get_role(self, role):
"""Returns a role object
"""
role = AuthGroup.objects(role=role, creator=self.client).first()
return role | Returns a role object | entailment |
def add_role(self, role, description=None):
""" Creates a new group """
new_group = AuthGroup(role=role, creator=self.client)
try:
new_group.save()
return True
except NotUniqueError:
return False | Creates a new group | entailment |
def del_role(self, role):
""" deletes a group """
target = AuthGroup.objects(role=role, creator=self.client).first()
if target:
target.delete()
return True
else:
return False | deletes a group | entailment |
def add_membership(self, user, role):
""" make user a member of a group """
targetGroup = AuthGroup.objects(role=role, creator=self.client).first()
if not targetGroup:
return False
target = AuthMembership.objects(user=user, creator=self.client).first()
if not target:
target = AuthMembership(user=user, creator=self.client)
if not role in [i.role for i in target.groups]:
target.groups.append(targetGroup)
target.save()
return True | make user a member of a group | entailment |
def del_membership(self, user, role):
""" dismember user from a group """
if not self.has_membership(user, role):
return True
targetRecord = AuthMembership.objects(creator=self.client, user=user).first()
if not targetRecord:
return True
for group in targetRecord.groups:
if group.role==role:
targetRecord.groups.remove(group)
targetRecord.save()
return True | dismember user from a group | entailment |
def has_membership(self, user, role):
""" checks if user is member of a group"""
targetRecord = AuthMembership.objects(creator=self.client, user=user).first()
if targetRecord:
return role in [i.role for i in targetRecord.groups]
return False | checks if user is member of a group | entailment |
def add_permission(self, role, name):
""" authorize a group for something """
if self.has_permission(role, name):
return True
targetGroup = AuthGroup.objects(role=role, creator=self.client).first()
if not targetGroup:
return False
# Create or update
permission = AuthPermission.objects(name=name).update(
add_to_set__groups=[targetGroup], creator=self.client, upsert=True
)
return True | authorize a group for something | entailment |
def del_permission(self, role, name):
""" revoke authorization of a group """
if not self.has_permission(role, name):
return True
targetGroup = AuthGroup.objects(role=role, creator=self.client).first()
target = AuthPermission.objects(groups=targetGroup, name=name, creator=self.client).first()
if not target:
return True
target.delete()
return True | revoke authorization of a group | entailment |
def user_has_permission(self, user, name):
""" verify user has permission """
targetRecord = AuthMembership.objects(creator=self.client, user=user).first()
if not targetRecord:
return False
for group in targetRecord.groups:
if self.has_permission(group.role, name):
return True
return False | verify user has permission | entailment |
def bump_version(version, bump='patch'):
"""patch: patch, minor, major"""
try:
parts = map(int, version.split('.'))
except ValueError:
fail('Current version is not numeric')
if bump == 'patch':
parts[2] += 1
elif bump == 'minor':
parts[1] += 1
parts[2] = 0
elif bump == 'major':
parts[0] +=1
parts[1] = 0
parts[2] = 0
return '.'.join(map(str, parts)) | patch: patch, minor, major | entailment |
def handler(event):
"""Signal decorator to allow use of callback functions as class decorators."""
def decorator(fn):
def apply(cls):
event.connect(fn, sender=cls)
return cls
fn.apply = apply
return fn
return decorator | Signal decorator to allow use of callback functions as class decorators. | entailment |
def stringify(req, resp):
"""
dumps all valid jsons
This is the latest after hook
"""
if isinstance(resp.body, dict):
try:
resp.body = json.dumps(resp.body)
except(nameError):
resp.status = falcon.HTTP_500 | dumps all valid jsons
This is the latest after hook | entailment |
def process_response(self, req, resp, resource):
"""Post-processing of the response (after routing).
Args:
req: Request object.
resp: Response object.
resource: Resource object to which the request was
routed. May be None if no route was found
for the request.
"""
if isinstance(resp.body, dict):
try:
resp.body = json.dumps(resp.body)
except(nameError):
resp.status = falcon.HTTP_500 | Post-processing of the response (after routing).
Args:
req: Request object.
resp: Response object.
resource: Resource object to which the request was
routed. May be None if no route was found
for the request. | entailment |
def run(command=None, *arguments):
"""
Run the given command.
Parameters:
:param command: A string describing a command.
:param arguments: A list of strings describing arguments to the command.
"""
if command is None:
sys.exit('django-shortcuts: No argument was supplied, please specify one.')
if command in ALIASES:
command = ALIASES[command]
if command == 'startproject':
return call('django-admin.py startproject %s' % ' '.join(arguments), shell=True)
script_path = os.getcwd()
while not os.path.exists(os.path.join(script_path, 'manage.py')):
base_dir = os.path.dirname(script_path)
if base_dir != script_path:
script_path = base_dir
else:
sys.exit('django-shortcuts: No \'manage.py\' script found in this directory or its parents.')
return call('%(python)s %(script_path)s %(command)s %(arguments)s' % {
'python': sys.executable,
'script_path': os.path.join(script_path, 'manage.py'),
'command': command or '',
'arguments': ' '.join(arguments)
}, shell=True) | Run the given command.
Parameters:
:param command: A string describing a command.
:param arguments: A list of strings describing arguments to the command. | entailment |
def instantiate(self, scope, args, interp):
"""Create a ParamList instance for actual interpretation
:args: TODO
:returns: A ParamList object
"""
param_instances = []
BYREF = "byref"
# TODO are default values for function parameters allowed in 010?
for param_name, param_cls in self._params:
# we don't instantiate a copy of byref params
if getattr(param_cls, "byref", False):
param_instances.append(BYREF)
else:
field = param_cls()
field._pfp__name = param_name
param_instances.append(field)
if len(args) != len(param_instances):
raise errors.InvalidArguments(
self._coords,
[x.__class__.__name__ for x in args],
[x.__class__.__name__ for x in param_instances]
)
# TODO type checking on provided types
for x in six.moves.range(len(args)):
param = param_instances[x]
# arrays are simply passed through into the function. We shouldn't
# have to worry about frozenness/unfrozenness at this point
if param is BYREF or isinstance(param, pfp.fields.Array):
param = args[x]
param_instances[x] = param
scope.add_local(self._params[x][0], param)
else:
param._pfp__set_value(args[x])
scope.add_local(param._pfp__name, param)
param._pfp__interp = interp
return ParamList(param_instances) | Create a ParamList instance for actual interpretation
:args: TODO
:returns: A ParamList object | entailment |
def get_experiments(base, load=False):
''' get_experiments will return loaded json for all valid experiments from an experiment folder
:param base: full path to the base folder with experiments inside
:param load: if True, returns a list of loaded config.json objects. If False (default) returns the paths to the experiments
'''
experiments = find_directories(base)
valid_experiments = [e for e in experiments if validate(e,cleanup=False)]
bot.info("Found %s valid experiments" %(len(valid_experiments)))
if load is True:
valid_experiments = load_experiments(valid_experiments)
#TODO at some point in this workflow we would want to grab instructions from help
# and variables from labels, environment, etc.
return valid_experiments | get_experiments will return loaded json for all valid experiments from an experiment folder
:param base: full path to the base folder with experiments inside
:param load: if True, returns a list of loaded config.json objects. If False (default) returns the paths to the experiments | entailment |
def load_experiments(folders):
'''load_experiments
a wrapper for load_experiment to read multiple experiments
:param experiment_folders: a list of experiment folders to load, full paths
'''
experiments = []
if isinstance(folders,str):
folders = [experiment_folders]
for folder in folders:
exp = load_experiment(folder)
experiments.append(exp)
return experiments | load_experiments
a wrapper for load_experiment to read multiple experiments
:param experiment_folders: a list of experiment folders to load, full paths | entailment |
def load_experiment(folder, return_path=False):
'''load_experiment:
reads in the config.json for a folder, returns None if not found.
:param folder: full path to experiment folder
:param return_path: if True, don't load the config.json, but return it
'''
fullpath = os.path.abspath(folder)
config = "%s/config.json" %(fullpath)
if not os.path.exists(config):
bot.error("config.json could not be found in %s" %(folder))
config = None
if return_path is False and config is not None:
config = read_json(config)
return config | load_experiment:
reads in the config.json for a folder, returns None if not found.
:param folder: full path to experiment folder
:param return_path: if True, don't load the config.json, but return it | entailment |
def get_selection(available, selection, base='/scif/apps'):
'''we compare the basename (the exp_id) of the selection and available,
regardless of parent directories'''
if isinstance(selection, str):
selection = selection.split(',')
available = [os.path.basename(x) for x in available]
selection = [os.path.basename(x) for x in selection]
finalset = [x for x in selection if x in available]
if len(finalset) == 0:
bot.warning("No user experiments selected, providing all %s" %(len(available)))
finalset = available
return ["%s/%s" %(base,x) for x in finalset] | we compare the basename (the exp_id) of the selection and available,
regardless of parent directories | entailment |
def make_lookup(experiment_list, key='exp_id'):
'''make_lookup returns dict object to quickly look up query experiment on exp_id
:param experiment_list: a list of query (dict objects)
:param key_field: the key in the dictionary to base the lookup key (str)
:returns lookup: dict (json) with key as "key_field" from query_list
'''
lookup = dict()
for single_experiment in experiment_list:
if isinstance(single_experiment, str):
single_experiment = load_experiment(single_experiment)
lookup_key = single_experiment[key]
lookup[lookup_key] = single_experiment
return lookup | make_lookup returns dict object to quickly look up query experiment on exp_id
:param experiment_list: a list of query (dict objects)
:param key_field: the key in the dictionary to base the lookup key (str)
:returns lookup: dict (json) with key as "key_field" from query_list | entailment |
def validate(folder=None, cleanup=False):
'''validate
:param folder: full path to experiment folder with config.json. If path begins
with https, we assume to be starting from a repository.
'''
from expfactory.validator import ExperimentValidator
cli = ExperimentValidator()
return cli.validate(folder, cleanup=cleanup) | validate
:param folder: full path to experiment folder with config.json. If path begins
with https, we assume to be starting from a repository. | entailment |
def get_library(lookup=True, key='exp_id'):
''' return the raw library, without parsing'''
library = None
response = requests.get(EXPFACTORY_LIBRARY)
if response.status_code == 200:
library = response.json()
if lookup is True:
return make_lookup(library,key=key)
return library | return the raw library, without parsing | entailment |
def int3(params, ctxt, scope, stream, coord, interp):
"""Define the ``Int3()`` function in the interpreter. Calling
``Int3()`` will drop the user into an interactive debugger.
"""
if interp._no_debug:
return
if interp._int3:
interp.debugger = PfpDbg(interp)
interp.debugger.cmdloop() | Define the ``Int3()`` function in the interpreter. Calling
``Int3()`` will drop the user into an interactive debugger. | entailment |
def initdb(self):
'''initdb will check for writability of the data folder, meaning
that it is bound to the local machine. If the folder isn't bound,
expfactory runs in demo mode (not saving data)
'''
self.database = EXPFACTORY_DATABASE
bot.info("DATABASE: %s" %self.database)
# Supported database options
valid = ('sqlite', 'postgres', 'mysql', 'filesystem')
if not self.database.startswith(valid):
bot.warning('%s is not yet a supported type, saving to filesystem.' % self.database)
self.database = 'filesystem'
# Add functions specific to database type
self.init_db() # uses url in self.database
bot.log("Data base: %s" % self.database) | initdb will check for writability of the data folder, meaning
that it is bound to the local machine. If the folder isn't bound,
expfactory runs in demo mode (not saving data) | entailment |
def setup(self):
''' obtain database and filesystem preferences from defaults,
and compare with selection in container.
'''
self.selection = EXPFACTORY_EXPERIMENTS
self.ordered = len(EXPFACTORY_EXPERIMENTS) > 0
self.data_base = EXPFACTORY_DATA
self.study_id = EXPFACTORY_SUBID
self.base = EXPFACTORY_BASE
self.randomize = EXPFACTORY_RANDOMIZE
self.headless = EXPFACTORY_HEADLESS
# Generate variables, if they exist
self.vars = generate_runtime_vars() or None
available = get_experiments("%s" % self.base)
self.experiments = get_selection(available, self.selection)
self.logger.debug(self.experiments)
self.lookup = make_lookup(self.experiments)
final = "\n".join(list(self.lookup.keys()))
bot.log("Headless mode: %s" % self.headless)
bot.log("User has selected: %s" % self.selection)
bot.log("Experiments Available: %s" %"\n".join(available))
bot.log("Randomize: %s" % self.randomize)
bot.log("Final Set \n%s" % final) | obtain database and filesystem preferences from defaults,
and compare with selection in container. | entailment |
def get_next(self, session):
'''return the name of the next experiment, depending on the user's
choice to randomize. We don't remove any experiments here, that is
done on finish, in the case the user doesn't submit data (and
thus finish). A return of None means the user has completed the
battery of experiments.
'''
next = None
experiments = session.get('experiments', [])
if len(experiments) > 0:
if app.randomize is True:
next = random.choice(range(0,len(experiments)))
next = experiments[next]
else:
next = experiments[0]
return next | return the name of the next experiment, depending on the user's
choice to randomize. We don't remove any experiments here, that is
done on finish, in the case the user doesn't submit data (and
thus finish). A return of None means the user has completed the
battery of experiments. | entailment |
def finish_experiment(self, session, exp_id):
'''remove an experiment from the list after completion.
'''
self.logger.debug('Finishing %s' %exp_id)
experiments = session.get('experiments', [])
experiments = [x for x in experiments if x != exp_id]
session['experiments'] = experiments
return experiments | remove an experiment from the list after completion. | entailment |
def find_subdirectories(basepath):
'''
Return directories (and sub) starting from a base
'''
directories = []
for root, dirnames, filenames in os.walk(basepath):
new_directories = [d for d in dirnames if d not in directories]
directories = directories + new_directories
return directories | Return directories (and sub) starting from a base | entailment |
def find_directories(root,fullpath=True):
'''
Return directories at one level specified by user
(not recursive)
'''
directories = []
for item in os.listdir(root):
# Don't include hidden directories
if not re.match("^[.]",item):
if os.path.isdir(os.path.join(root, item)):
if fullpath:
directories.append(os.path.abspath(os.path.join(root, item)))
else:
directories.append(item)
return directories | Return directories at one level specified by user
(not recursive) | entailment |
def copy_directory(src, dest, force=False):
''' Copy an entire directory recursively
'''
if os.path.exists(dest) and force is True:
shutil.rmtree(dest)
try:
shutil.copytree(src, dest)
except OSError as e:
# If the error was caused because the source wasn't a directory
if e.errno == errno.ENOTDIR:
shutil.copy(src, dest)
else:
bot.error('Directory not copied. Error: %s' % e)
sys.exit(1) | Copy an entire directory recursively | entailment |
def clone(url, tmpdir=None):
'''clone a repository from Github'''
if tmpdir is None:
tmpdir = tempfile.mkdtemp()
name = os.path.basename(url).replace('.git', '')
dest = '%s/%s' %(tmpdir,name)
return_code = os.system('git clone %s %s' %(url,dest))
if return_code == 0:
return dest
bot.error('Error cloning repo.')
sys.exit(return_code) | clone a repository from Github | entailment |
def run_command(cmd):
'''run_command uses subprocess to send a command to the terminal.
:param cmd: the command to send, should be a list for subprocess
'''
output = Popen(cmd,stderr=STDOUT,stdout=PIPE)
t = output.communicate()[0],output.returncode
output = {'message':t[0],
'return_code':t[1]}
return output | run_command uses subprocess to send a command to the terminal.
:param cmd: the command to send, should be a list for subprocess | entailment |
def get_template(name, base=None):
'''read in and return a template file
'''
# If the file doesn't exist, assume relative to base
template_file = name
if not os.path.exists(template_file):
if base is None:
base = get_templatedir()
template_file = "%s/%s" %(base, name)
# Then try again, if it still doesn't exist, bad name
if os.path.exists(template_file):
with open(template_file,"r") as filey:
template = "".join(filey.readlines())
return template
bot.error("%s does not exist." %template_file) | read in and return a template file | entailment |
def sub_template(template,template_tag,substitution):
'''make a substitution for a template_tag in a template
'''
template = template.replace(template_tag,substitution)
return template | make a substitution for a template_tag in a template | entailment |
def get_post_fields(request):
'''parse through a request, and return fields from post in a dictionary
'''
fields = dict()
for field,value in request.form.items():
fields[field] = value
return fields | parse through a request, and return fields from post in a dictionary | entailment |
def getenv(variable_key, default=None, required=False, silent=True):
'''getenv will attempt to get an environment variable. If the variable
is not found, None is returned.
:param variable_key: the variable name
:param required: exit with error if not found
:param silent: Do not print debugging information for variable
'''
variable = os.environ.get(variable_key, default)
if variable is None and required:
bot.error("Cannot find environment variable %s, exiting." %variable_key)
sys.exit(1)
if not silent:
if variable is not None:
bot.verbose2("%s found as %s" %(variable_key,variable))
else:
bot.verbose2("%s not defined (None)" %variable_key)
return variable | getenv will attempt to get an environment variable. If the variable
is not found, None is returned.
:param variable_key: the variable name
:param required: exit with error if not found
:param silent: Do not print debugging information for variable | entailment |
def parse(
data = None,
template = None,
data_file = None,
template_file = None,
interp = None,
debug = False,
predefines = True,
int3 = True,
keep_successful = False,
printf = True,
):
"""Parse the data stream using the supplied template. The data stream
WILL NOT be automatically closed.
:data: Input data, can be either a string or a file-like object (StringIO, file, etc)
:template: template contents (str)
:data_file: PATH to the data to be used as the input stream
:template_file: template file path
:interp: the interpretor to be used (a default one will be created if ``None``)
:debug: if debug information should be printed while interpreting the template (false)
:predefines: if built-in type information should be inserted (true)
:int3: if debugger breaks are allowed while interpreting the template (true)
:keep_successful: return any succesfully parsed data instead of raising an error. If an error occurred and ``keep_successful`` is True, then ``_pfp__error`` will be contain the exception object
:printf: if ``False``, all calls to ``Printf`` (:any:`pfp.native.compat_interface.Printf`) will be noops. (default=``True``)
:returns: pfp DOM
"""
if data is None and data_file is None:
raise Exception("No input data was specified")
if data is not None and data_file is not None:
raise Exception("Only one input data may be specified")
if isinstance(data, six.string_types):
data = six.StringIO(data)
if data_file is not None:
data = open(os.path.expanduser(data_file), "rb")
if template is None and template_file is None:
raise Exception("No template specified!")
if template is not None and template_file is not None:
raise Exception("Only one template may be specified!")
orig_filename = "string"
if template_file is not None:
orig_filename = template_file
try:
with open(os.path.expanduser(template_file), "r") as f:
template = f.read()
except Exception as e:
raise Exception("Could not open template file '{}'".format(template_file))
# the user may specify their own instance of PfpInterp to be
# used
if interp is None:
interp = pfp.interp.PfpInterp(
debug = debug,
parser = PARSER,
int3 = int3,
)
# so we can consume single bits at a time
data = BitwrappedStream(data)
dom = interp.parse(
data,
template,
predefines = predefines,
orig_filename = orig_filename,
keep_successful = keep_successful,
printf = printf,
)
# close the data stream if a data_file was specified
if data_file is not None:
data.close()
return dom | Parse the data stream using the supplied template. The data stream
WILL NOT be automatically closed.
:data: Input data, can be either a string or a file-like object (StringIO, file, etc)
:template: template contents (str)
:data_file: PATH to the data to be used as the input stream
:template_file: template file path
:interp: the interpretor to be used (a default one will be created if ``None``)
:debug: if debug information should be printed while interpreting the template (false)
:predefines: if built-in type information should be inserted (true)
:int3: if debugger breaks are allowed while interpreting the template (true)
:keep_successful: return any succesfully parsed data instead of raising an error. If an error occurred and ``keep_successful`` is True, then ``_pfp__error`` will be contain the exception object
:printf: if ``False``, all calls to ``Printf`` (:any:`pfp.native.compat_interface.Printf`) will be noops. (default=``True``)
:returns: pfp DOM | entailment |
def Checksum(params, ctxt, scope, stream, coord):
"""
Runs a simple checksum on a file and returns the result as a int64. The
algorithm can be one of the following constants:
CHECKSUM_BYTE - Treats the file as a set of unsigned bytes
CHECKSUM_SHORT_LE - Treats the file as a set of unsigned little-endian shorts
CHECKSUM_SHORT_BE - Treats the file as a set of unsigned big-endian shorts
CHECKSUM_INT_LE - Treats the file as a set of unsigned little-endian ints
CHECKSUM_INT_BE - Treats the file as a set of unsigned big-endian ints
CHECKSUM_INT64_LE - Treats the file as a set of unsigned little-endian int64s
CHECKSUM_INT64_BE - Treats the file as a set of unsigned big-endian int64s
CHECKSUM_SUM8 - Same as CHECKSUM_BYTE except result output as 8-bits
CHECKSUM_SUM16 - Same as CHECKSUM_BYTE except result output as 16-bits
CHECKSUM_SUM32 - Same as CHECKSUM_BYTE except result output as 32-bits
CHECKSUM_SUM64 - Same as CHECKSUM_BYTE
CHECKSUM_CRC16
CHECKSUM_CRCCCITT
CHECKSUM_CRC32
CHECKSUM_ADLER32
If start and size are zero, the algorithm is run on the whole file. If
they are not zero then the algorithm is run on size bytes starting at
address start. See the ChecksumAlgBytes and ChecksumAlgStr functions
to run more complex algorithms. crcPolynomial and crcInitValue
can be used to set a custom polynomial and initial value for the
CRC functions. A value of -1 for these parameters uses the default
values as described in the Check Sum/Hash Algorithms topic. A negative
number is returned on error.
"""
checksum_types = {
0: "CHECKSUM_BYTE", # Treats the file as a set of unsigned bytes
1: "CHECKSUM_SHORT_LE", # Treats the file as a set of unsigned little-endian shorts
2: "CHECKSUM_SHORT_BE", # Treats the file as a set of unsigned big-endian shorts
3: "CHECKSUM_INT_LE", # Treats the file as a set of unsigned little-endian ints
4: "CHECKSUM_INT_BE", # Treats the file as a set of unsigned big-endian ints
5: "CHECKSUM_INT64_LE", # Treats the file as a set of unsigned little-endian int64s
6: "CHECKSUM_INT64_BE", # Treats the file as a set of unsigned big-endian int64s
7: "CHECKSUM_SUM8", # Same as CHECKSUM_BYTE except result output as 8-bits
8: "CHECKSUM_SUM16", # Same as CHECKSUM_BYTE except result output as 16-bits
9: "CHECKSUM_SUM32", # Same as CHECKSUM_BYTE except result output as 32-bits
10: "CHECKSUM_SUM64", # Same as CHECKSUM_BYTE
11: "CHECKSUM_CRC16",
12: "CHECKSUM_CRCCCITT",
13: _crc32,
14: _checksum_Adler32
}
if len(params) < 1:
raise errors.InvalidArguments(coord, "at least 1 argument", "{} args".format(len(params)))
alg = PYVAL(params[0])
if alg not in checksum_types:
raise errors.InvalidArguments(coord, "checksum alg must be one of (0-14)", "{}".format(alg))
start = 0
if len(params) > 1:
start = PYVAL(params[1])
size = 0
if len(params) > 2:
size = PYVAL(params[2])
crc_poly = -1
if len(params) > 3:
crc_poly = PYVAL(params[3])
crc_init = -1
if len(params) > 4:
crc_init = PYVAL(params[4])
stream_pos = stream.tell()
if start + size == 0:
stream.seek(0, 0)
data = stream.read()
else:
stream.seek(start, 0)
data = stream.read(size)
try:
return checksum_types[alg](data, crc_init, crc_poly)
finally:
# yes, this does execute even though a return statement
# exists within the try
stream.seek(stream_pos, 0) | Runs a simple checksum on a file and returns the result as a int64. The
algorithm can be one of the following constants:
CHECKSUM_BYTE - Treats the file as a set of unsigned bytes
CHECKSUM_SHORT_LE - Treats the file as a set of unsigned little-endian shorts
CHECKSUM_SHORT_BE - Treats the file as a set of unsigned big-endian shorts
CHECKSUM_INT_LE - Treats the file as a set of unsigned little-endian ints
CHECKSUM_INT_BE - Treats the file as a set of unsigned big-endian ints
CHECKSUM_INT64_LE - Treats the file as a set of unsigned little-endian int64s
CHECKSUM_INT64_BE - Treats the file as a set of unsigned big-endian int64s
CHECKSUM_SUM8 - Same as CHECKSUM_BYTE except result output as 8-bits
CHECKSUM_SUM16 - Same as CHECKSUM_BYTE except result output as 16-bits
CHECKSUM_SUM32 - Same as CHECKSUM_BYTE except result output as 32-bits
CHECKSUM_SUM64 - Same as CHECKSUM_BYTE
CHECKSUM_CRC16
CHECKSUM_CRCCCITT
CHECKSUM_CRC32
CHECKSUM_ADLER32
If start and size are zero, the algorithm is run on the whole file. If
they are not zero then the algorithm is run on size bytes starting at
address start. See the ChecksumAlgBytes and ChecksumAlgStr functions
to run more complex algorithms. crcPolynomial and crcInitValue
can be used to set a custom polynomial and initial value for the
CRC functions. A value of -1 for these parameters uses the default
values as described in the Check Sum/Hash Algorithms topic. A negative
number is returned on error. | entailment |
def FindAll(params, ctxt, scope, stream, coord, interp):
"""
This function converts the argument data into a set of hex bytes
and then searches the current file for all occurrences of those
bytes. data may be any of the basic types or an array of one of
the types. If data is an array of signed bytes, it is assumed to
be a null-terminated string. To search for an array of hex bytes,
create an unsigned char array and fill it with the target value. If
the type being search for is a string, the matchcase and wholeworld
arguments can be used to control the search (see Using Find for more
information). method controls which search method is used from the
following options:
FINDMETHOD_NORMAL=0 - a normal search
FINDMETHOD_WILDCARDS=1 - when searching for strings use wildcards '*' or '?'
FINDMETHOD_REGEX=2 - when searching for strings use Regular Expressions
wildcardMatchLength indicates the maximum number of characters a '*' can match when searching using wildcards. If the target is a float or double, the tolerance argument indicates that values that are only off by the tolerance value still match. If dir is 1 the find direction is down and if dir is 0 the find direction is up. start and size can be used to limit the area of the file that is searched. start is the starting byte address in the file where the search will begin and size is the number of bytes after start that will be searched. If size is zero, the file will be searched from start to the end of the file.
The return value is a TFindResults structure. This structure contains a count variable indicating the number of matches, and a start array holding an array of starting positions, plus a size array which holds an array of target lengths. For example, use the following code to find all occurrences of the ASCII string "Test" in a file:
"""
matches_iter = _find_helper(params, ctxt, scope, stream, coord, interp)
matches = list(matches_iter)
types = interp.get_types()
res = types.TFindResults()
res.count = len(matches)
# python3 map doesn't return a list
starts = list(map(lambda m: m.start()+FIND_MATCHES_START_OFFSET, matches))
res.start = starts
# python3 map doesn't return a list
sizes = list(map(lambda m: m.end()-m.start(), matches))
res.size = sizes
return res | This function converts the argument data into a set of hex bytes
and then searches the current file for all occurrences of those
bytes. data may be any of the basic types or an array of one of
the types. If data is an array of signed bytes, it is assumed to
be a null-terminated string. To search for an array of hex bytes,
create an unsigned char array and fill it with the target value. If
the type being search for is a string, the matchcase and wholeworld
arguments can be used to control the search (see Using Find for more
information). method controls which search method is used from the
following options:
FINDMETHOD_NORMAL=0 - a normal search
FINDMETHOD_WILDCARDS=1 - when searching for strings use wildcards '*' or '?'
FINDMETHOD_REGEX=2 - when searching for strings use Regular Expressions
wildcardMatchLength indicates the maximum number of characters a '*' can match when searching using wildcards. If the target is a float or double, the tolerance argument indicates that values that are only off by the tolerance value still match. If dir is 1 the find direction is down and if dir is 0 the find direction is up. start and size can be used to limit the area of the file that is searched. start is the starting byte address in the file where the search will begin and size is the number of bytes after start that will be searched. If size is zero, the file will be searched from start to the end of the file.
The return value is a TFindResults structure. This structure contains a count variable indicating the number of matches, and a start array holding an array of starting positions, plus a size array which holds an array of target lengths. For example, use the following code to find all occurrences of the ASCII string "Test" in a file: | entailment |
def FindFirst(params, ctxt, scope, stream, coord, interp):
"""
This function is identical to the FindAll function except that the
return value is the position of the first occurrence of the target
found. A negative number is returned if the value could not be found.
"""
global FIND_MATCHES_ITER
FIND_MATCHES_ITER = _find_helper(params, ctxt, scope, stream, coord, interp)
try:
first = six.next(FIND_MATCHES_ITER)
return first.start() + FIND_MATCHES_START_OFFSET
except StopIteration as e:
return -1 | This function is identical to the FindAll function except that the
return value is the position of the first occurrence of the target
found. A negative number is returned if the value could not be found. | entailment |
def FindNext(params, ctxt, scope, stream, coord):
"""
This function returns the position of the next occurrence of the
target value specified with the FindFirst function. If dir is 1, the
find direction is down. If dir is 0, the find direction is up. The
return value is the address of the found data, or -1 if the target
is not found.
"""
if FIND_MATCHES_ITER is None:
raise errors.InvalidState()
direction = 1
if len(params) > 0:
direction = PYVAL(params[0])
if direction != 1:
# TODO maybe instead of storing the iterator in FIND_MATCHES_ITER,
# we should go ahead and find _all the matches in the file and store them
# in a list, keeping track of the idx of the current match.
#
# This would be highly inefficient on large files though.
raise NotImplementedError("Reverse searching is not yet implemented")
try:
next_match = six.next(FIND_MATCHES_ITER)
return next_match.start() + FIND_MATCHES_START_OFFSET
except StopIteration as e:
return -1 | This function returns the position of the next occurrence of the
target value specified with the FindFirst function. If dir is 1, the
find direction is down. If dir is 0, the find direction is up. The
return value is the address of the found data, or -1 if the target
is not found. | entailment |
def generate_subid(self, token=None):
'''assumes a flat (file system) database, organized by experiment id, and
subject id, with data (json) organized by subject identifier
'''
# Not headless auto-increments
if not token:
token = str(uuid.uuid4())
# Headless doesn't use any folder_id, just generated token folder
return "%s/%s" % (self.study_id, token) | assumes a flat (file system) database, organized by experiment id, and
subject id, with data (json) organized by subject identifier | entailment |
def list_users(self):
'''list users, each associated with a filesystem folder
'''
folders = glob('%s/*' %(self.database))
folders.sort()
return [self.print_user(x) for x in folders] | list users, each associated with a filesystem folder | entailment |
def print_user(self, user):
'''print a filesystem database user. A "database" folder that might end with
the participant status (e.g. _finished) is extracted to print in format
[folder] [identifier][studyid]
/scif/data/expfactory/xxxx-xxxx xxxx-xxxx[studyid]
'''
status = "active"
if user.endswith('_finished'):
status = "finished"
elif user.endswith('_revoked'):
status = "revoked"
subid = os.path.basename(user)
for ext in ['_revoked','_finished']:
subid = subid.replace(ext, '')
subid = '%s\t%s[%s]' %(user, subid, status)
print(subid)
return subid | print a filesystem database user. A "database" folder that might end with
the participant status (e.g. _finished) is extracted to print in format
[folder] [identifier][studyid]
/scif/data/expfactory/xxxx-xxxx xxxx-xxxx[studyid] | entailment |
def generate_user(self, subid=None):
'''generate a new user on the filesystem, still session based so we
create a new identifier. This function is called from the users new
entrypoint, and it assumes we want a user generated with a token.
since we don't have a database proper, we write the folder name to
the filesystem
'''
# Only generate token if subid being created
if subid is None:
token = str(uuid.uuid4())
subid = self.generate_subid(token=token)
if os.path.exists(self.data_base): # /scif/data
data_base = "%s/%s" %(self.data_base, subid)
# expfactory/00001
if not os.path.exists(data_base):
mkdir_p(data_base)
return data_base | generate a new user on the filesystem, still session based so we
create a new identifier. This function is called from the users new
entrypoint, and it assumes we want a user generated with a token.
since we don't have a database proper, we write the folder name to
the filesystem | entailment |
def finish_user(self, subid, ext='finished'):
'''finish user will append "finished" (or other) to the data folder when
the user has completed (or been revoked from) the battery.
For headless, this means that the session is ended and the token
will not work again to rewrite the result. If the user needs to update
or redo an experiment, this can be done with a new session. Note that if
this function is called internally by the application at experiment
finish, the subid includes a study id (e.g., expfactory/xxxx-xxxx)
but if called by the user, it may not (e.g., xxxx-xxxx). We check
for this to ensure it works in both places.
'''
if os.path.exists(self.data_base): # /scif/data
# Only relevant to filesystem save - the studyid is the top folder
if subid.startswith(self.study_id):
data_base = "%s/%s" %(self.data_base, subid)
else:
data_base = "%s/%s/%s" %(self.data_base,
self.study_id,
subid)
# The renamed file will be here
finished = "%s_%s" % (data_base, ext)
# Participant already finished
if os.path.exists(finished):
self.logger.warning('[%s] is already finished: %s' % (subid, data_base))
# Exists and can finish
elif os.path.exists(data_base):
os.rename(data_base, finished)
# Not finished, doesn't exist
else:
finished = None
self.logger.warning('%s does not exist, cannot finish. %s' % (data_base, subid))
return finished | finish user will append "finished" (or other) to the data folder when
the user has completed (or been revoked from) the battery.
For headless, this means that the session is ended and the token
will not work again to rewrite the result. If the user needs to update
or redo an experiment, this can be done with a new session. Note that if
this function is called internally by the application at experiment
finish, the subid includes a study id (e.g., expfactory/xxxx-xxxx)
but if called by the user, it may not (e.g., xxxx-xxxx). We check
for this to ensure it works in both places. | entailment |
def restart_user(self, subid):
'''restart user will remove any "finished" or "revoked" extensions from
the user folder to restart the session. This command always comes from
the client users function, so we know subid does not start with the
study identifer first
'''
if os.path.exists(self.data_base): # /scif/data/<study_id>
data_base = "%s/%s" %(self.data_base, subid)
for ext in ['revoked','finished']:
folder = "%s_%s" % (data_base, ext)
if os.path.exists(folder):
os.rename(folder, data_base)
self.logger.info('Restarting %s, folder is %s.' % (subid, data_base))
self.logger.warning('%s does not have revoked or finished folder, no changes necessary.' % (subid))
return data_base
self.logger.warning('%s does not exist, cannot restart. %s' % (self.database, subid)) | restart user will remove any "finished" or "revoked" extensions from
the user folder to restart the session. This command always comes from
the client users function, so we know subid does not start with the
study identifer first | entailment |
def validate_token(self, token):
'''retrieve a subject based on a token. Valid means we return a participant
invalid means we return None
'''
# A token that is finished or revoked is not valid
subid = None
if not token.endswith(('finished','revoked')):
subid = self.generate_subid(token=token)
data_base = "%s/%s" %(self.data_base, subid)
if not os.path.exists(data_base):
subid = None
return subid | retrieve a subject based on a token. Valid means we return a participant
invalid means we return None | entailment |
def refresh_token(self, subid):
'''refresh or generate a new token for a user. If the user is finished,
this will also make the folder available again for using.'''
if os.path.exists(self.data_base): # /scif/data
data_base = "%s/%s" %(self.data_base, subid)
if os.path.exists(data_base):
refreshed = "%s/%s" %(self.database, str(uuid.uuid4()))
os.rename(data_base, refreshed)
return refreshed
self.logger.warning('%s does not exist, cannot rename %s' % (data_base, subid))
else:
self.logger.warning('%s does not exist, cannot rename %s' % (self.database, subid)) | refresh or generate a new token for a user. If the user is finished,
this will also make the folder available again for using. | entailment |
def save_data(self, session, exp_id, content):
'''save data will obtain the current subid from the session, and save it
depending on the database type. Currently we just support flat files'''
subid = session.get('subid')
# We only attempt save if there is a subject id, set at start
data_file = None
if subid is not None:
data_base = "%s/%s" %(self.data_base, subid)
# If not running in headless, ensure path exists
if not self.headless and not os.path.exists(data_base):
mkdir_p(data_base)
# Conditions for saving:
do_save = False
# If headless with token pre-generated OR not headless
if self.headless and os.path.exists(data_base) or not self.headless:
do_save = True
if data_base.endswith(('revoked','finished')):
do_save = False
# If headless with token pre-generated OR not headless
if do_save is True:
data_file = "%s/%s-results.json" %(data_base, exp_id)
if os.path.exists(data_file):
self.logger.warning('%s exists, and is being overwritten.' %data_file)
write_json(content, data_file)
return data_file | save data will obtain the current subid from the session, and save it
depending on the database type. Currently we just support flat files | entailment |
def init_db(self):
'''init_db for the filesystem ensures that the base folder (named
according to the studyid) exists.
'''
self.session = None
if not os.path.exists(self.data_base):
mkdir_p(self.data_base)
self.database = "%s/%s" %(self.data_base, self.study_id)
if not os.path.exists(self.database):
mkdir_p(self.database) | init_db for the filesystem ensures that the base folder (named
according to the studyid) exists. | entailment |
def native(name, ret, interp=None, send_interp=False):
"""Used as a decorator to add the decorated function to the
pfp interpreter so that it can be used from within scripts.
:param str name: The name of the function as it will be exposed in template scripts.
:param pfp.fields.Field ret: The return type of the function (a class)
:param pfp.interp.PfpInterp interp: The specific interpreter to add the function to
:param bool send_interp: If the current interpreter should be passed to the function.
Examples:
The example below defines a ``Sum`` function that will return the sum of
all parameters passed to the function: ::
from pfp.fields import PYVAL
@native(name="Sum", ret=pfp.fields.Int64)
def sum_numbers(params, ctxt, scope, stream, coord):
res = 0
for param in params:
res += PYVAL(param)
return res
The code below is the code for the :any:`Int3 <pfp.native.dbg.int3>` function. Notice that it
requires that the interpreter be sent as a parameter: ::
@native(name="Int3", ret=pfp.fields.Void, send_interp=True)
def int3(params, ctxt, scope, stream, coord, interp):
if interp._no_debug:
return
if interp._int3:
interp.debugger = PfpDbg(interp)
interp.debugger.cmdloop()
"""
def native_decorator(func):
@functools.wraps(func)
def native_wrapper(*args, **kwargs):
return func(*args, **kwargs)
pfp.interp.PfpInterp.add_native(name, func, ret, interp=interp, send_interp=send_interp)
return native_wrapper
return native_decorator | Used as a decorator to add the decorated function to the
pfp interpreter so that it can be used from within scripts.
:param str name: The name of the function as it will be exposed in template scripts.
:param pfp.fields.Field ret: The return type of the function (a class)
:param pfp.interp.PfpInterp interp: The specific interpreter to add the function to
:param bool send_interp: If the current interpreter should be passed to the function.
Examples:
The example below defines a ``Sum`` function that will return the sum of
all parameters passed to the function: ::
from pfp.fields import PYVAL
@native(name="Sum", ret=pfp.fields.Int64)
def sum_numbers(params, ctxt, scope, stream, coord):
res = 0
for param in params:
res += PYVAL(param)
return res
The code below is the code for the :any:`Int3 <pfp.native.dbg.int3>` function. Notice that it
requires that the interpreter be sent as a parameter: ::
@native(name="Int3", ret=pfp.fields.Void, send_interp=True)
def int3(params, ctxt, scope, stream, coord, interp):
if interp._no_debug:
return
if interp._int3:
interp.debugger = PfpDbg(interp)
interp.debugger.cmdloop() | entailment |
def do_peek(self, args):
"""Peek at the next 16 bytes in the stream::
Example:
The peek command will display the next 16 hex bytes in the input
stream::
pfp> peek
89 50 4e 47 0d 0a 1a 0a 00 00 00 0d 49 48 44 52 .PNG........IHDR
"""
s = self._interp._stream
# make a copy of it
pos = s.tell()
saved_bits = collections.deque(s._bits)
data = s.read(0x10)
s.seek(pos, 0)
s._bits = saved_bits
parts = ["{:02x}".format(ord(data[x:x+1])) for x in range(len(data))]
if len(parts) != 0x10:
parts += [" "] * (0x10 - len(parts))
hex_line = " ".join(parts)
res = utils.binary("")
for x in range(len(data)):
char = data[x:x+1]
val = ord(char)
if 0x20 <= val <= 0x7e:
res += char
else:
res += utils.binary(".")
if len(res) < 0x10:
res += utils.binary(" " * (0x10 - len(res)))
res = "{} {}".format(hex_line, utils.string(res))
if len(saved_bits) > 0:
reverse_bits = reversed(list(saved_bits))
print("bits: {}".format(" ".join(str(x) for x in reverse_bits)))
print(res) | Peek at the next 16 bytes in the stream::
Example:
The peek command will display the next 16 hex bytes in the input
stream::
pfp> peek
89 50 4e 47 0d 0a 1a 0a 00 00 00 0d 49 48 44 52 .PNG........IHDR | entailment |
def do_next(self, args):
"""Step over the next statement
"""
self._do_print_from_last_cmd = True
self._interp.step_over()
return True | Step over the next statement | entailment |
def do_step(self, args):
"""Step INTO the next statement
"""
self._do_print_from_last_cmd = True
self._interp.step_into()
return True | Step INTO the next statement | entailment |
def do_continue(self, args):
"""Continue the interpreter
"""
self._do_print_from_last_cmd = True
self._interp.cont()
return True | Continue the interpreter | entailment |
def do_eval(self, args):
"""Eval the user-supplied statement. Note that you can do anything with
this command that you can do in a template.
The resulting value of your statement will be displayed.
"""
try:
res = self._interp.eval(args)
if res is not None:
if hasattr(res, "_pfp__show"):
print(res._pfp__show())
else:
print(repr(res))
except errors.UnresolvedID as e:
print("ERROR: " + e.message)
except Exception as e:
raise
print("ERROR: " + e.message)
return False | Eval the user-supplied statement. Note that you can do anything with
this command that you can do in a template.
The resulting value of your statement will be displayed. | entailment |
def do_show(self, args):
"""Show the current structure of __root (no args),
or show the result of the expression (something that can be eval'd).
"""
args = args.strip()
to_show = self._interp._root
if args != "":
try:
to_show = self._interp.eval(args)
except Exception as e:
print("ERROR: " + e.message)
return False
if hasattr(to_show, "_pfp__show"):
print(to_show._pfp__show())
else:
print(repr(to_show)) | Show the current structure of __root (no args),
or show the result of the expression (something that can be eval'd). | entailment |
def do_quit(self, args):
"""The quit command
"""
self._interp.set_break(self._interp.BREAK_NONE)
return True | The quit command | entailment |
def validate(self, url):
''' takes in a Github repository for validation of preview and
runtime (and possibly tests passing?
'''
# Preview must provide the live URL of the repository
if not url.startswith('http') or not 'github' in url:
bot.error('Test of preview must be given a Github repostitory.')
return False
if not self._validate_preview(url):
return False
return True | takes in a Github repository for validation of preview and
runtime (and possibly tests passing? | entailment |
def mask_dict_password(dictionary, secret='***'):
"""Replace passwords with a secret in a dictionary."""
d = dictionary.copy()
for k in d:
if 'password' in k:
d[k] = secret
return d | Replace passwords with a secret in a dictionary. | entailment |
def save():
'''save is a view to save data. We might want to adjust this to allow for
updating saved data, but given single file is just one post for now
'''
if request.method == 'POST':
exp_id = session.get('exp_id')
app.logger.debug('Saving data for %s' %exp_id)
fields = get_post_fields(request)
result_file = app.save_data(session=session, content=fields, exp_id=exp_id)
experiments = app.finish_experiment(session, exp_id)
app.logger.info('Finished %s, %s remaining.' % (exp_id, len(experiments)))
# Note, this doesn't seem to be enough to trigger ajax success
return json.dumps({'success':True}), 200, {'ContentType':'application/json'}
return json.dumps({'success':False}), 403, {'ContentType':'application/json'} | save is a view to save data. We might want to adjust this to allow for
updating saved data, but given single file is just one post for now | entailment |
def main(args,parser,subparser=None):
'''this is the main entrypoint for a container based web server, with
most of the variables coming from the environment. See the Dockerfile
template for how this function is executed.
'''
# First priority to args.base
base = args.base
if base is None:
base = os.environ.get('EXPFACTORY_BASE')
# Does the base folder exist?
if base is None:
bot.error("You must set a base of experiments with --base" % base)
sys.exit(1)
if not os.path.exists(base):
bot.error("Base folder %s does not exist." % base)
sys.exit(1)
# Export environment variables for the client
experiments = args.experiments
if experiments is None:
experiments = " ".join(glob("%s/*" % base))
os.environ['EXPFACTORY_EXPERIMENTS'] = experiments
# If defined and file exists, set runtime variables
if args.vars is not None:
if os.path.exists(args.vars):
os.environ['EXPFACTORY_RUNTIME_VARS'] = args.vars
os.environ['EXPFACTORY_RUNTIME_DELIM'] = args.delim
else:
bot.warning('Variables file %s not found.' %args.vars)
subid = os.environ.get('EXPFACTORY_STUDY_ID')
if args.subid is not None:
subid = args.subid
os.environ['EXPFACTORY_SUBID'] = subid
os.environ['EXPFACTORY_RANDOM'] = str(args.disable_randomize)
os.environ['EXPFACTORY_BASE'] = base
from expfactory.server import start
start(port=5000) | this is the main entrypoint for a container based web server, with
most of the variables coming from the environment. See the Dockerfile
template for how this function is executed. | entailment |
def save_data(self,session, exp_id, content):
'''save data will obtain the current subid from the session, and save it
depending on the database type.'''
from expfactory.database.models import (
Participant,
Result
)
subid = session.get('subid')
bot.info('Saving data for subid %s' % subid)
# We only attempt save if there is a subject id, set at start
if subid is not None:
p = Participant.query.filter(Participant.id == subid).first() # better query here
# Preference is to save data under 'data', otherwise do all of it
if "data" in content:
content = content['data']
if isinstance(content,dict):
content = json.dumps(content)
result = Result(data=content,
exp_id=exp_id,
participant_id=p.id) # check if changes from str/int
self.session.add(result)
p.results.append(result)
self.session.commit()
bot.info("Participant: %s" %p)
bot.info("Result: %s" %result) | save data will obtain the current subid from the session, and save it
depending on the database type. | entailment |
def init_db(self):
'''initialize the database, with the default database path or custom of
the format sqlite:////scif/data/expfactory.db
'''
# Database Setup, use default if uri not provided
if self.database == 'sqlite':
db_path = os.path.join(EXPFACTORY_DATA, '%s.db' % EXPFACTORY_SUBID)
self.database = 'sqlite:///%s' % db_path
bot.info("Database located at %s" % self.database)
self.engine = create_engine(self.database, convert_unicode=True)
self.session = scoped_session(sessionmaker(autocommit=False,
autoflush=False,
bind=self.engine))
Base.query = self.session.query_property()
# import all modules here that might define models so that
# they will be registered properly on the metadata. Otherwise
# you will have to import them first before calling init_db()
import expfactory.database.models
Base.metadata.create_all(bind=self.engine)
self.Base = Base | initialize the database, with the default database path or custom of
the format sqlite:////scif/data/expfactory.db | entailment |
def reserve_bits(self, num_bits, stream):
"""Used to "reserve" ``num_bits`` amount of bits in order to keep track
of consecutive bitfields (or are the called bitfield groups?).
E.g. ::
struct {
char a:8, b:8;
char c:4, d:4, e:8;
}
:param int num_bits: The number of bits to claim
:param pfp.bitwrap.BitwrappedStream stream: The stream to reserve bits on
:returns: If room existed for the reservation
"""
padded = self.interp.get_bitfield_padded()
num_bits = PYVAL(num_bits)
if padded:
num_bits = PYVAL(num_bits)
if num_bits + self.reserved_bits > self.max_bits:
return False
# if unpadded, always allow it
if not padded:
if self._cls_bits is None:
self._cls_bits = []
# reserve bits will only be called just prior to reading the bits,
# so check to see if we have enough bits in self._cls_bits, else
# read what's missing
diff = len(self._cls_bits) - num_bits
if diff < 0:
self._cls_bits += stream.read_bits(-diff)
self.reserved_bits += num_bits
return True | Used to "reserve" ``num_bits`` amount of bits in order to keep track
of consecutive bitfields (or are the called bitfield groups?).
E.g. ::
struct {
char a:8, b:8;
char c:4, d:4, e:8;
}
:param int num_bits: The number of bits to claim
:param pfp.bitwrap.BitwrappedStream stream: The stream to reserve bits on
:returns: If room existed for the reservation | entailment |
def read_bits(self, stream, num_bits, padded, left_right, endian):
"""Return ``num_bits`` bits, taking into account endianness and
left-right bit directions
"""
if self._cls_bits is None and padded:
raw_bits = stream.read_bits(self.cls.width*8)
self._cls_bits = self._endian_transform(raw_bits, endian)
if self._cls_bits is not None:
if num_bits > len(self._cls_bits):
raise errors.PfpError("BitfieldRW reached invalid state")
if left_right:
res = self._cls_bits[:num_bits]
self._cls_bits = self._cls_bits[num_bits:]
else:
res = self._cls_bits[-num_bits:]
self._cls_bits = self._cls_bits[:-num_bits]
return res
else:
return stream.read_bits(num_bits) | Return ``num_bits`` bits, taking into account endianness and
left-right bit directions | entailment |
def write_bits(self, stream, raw_bits, padded, left_right, endian):
"""Write the bits. Once the size of the written bits is equal
to the number of the reserved bits, flush it to the stream
"""
if padded:
if left_right:
self._write_bits += raw_bits
else:
self._write_bits = raw_bits + self._write_bits
if len(self._write_bits) == self.reserved_bits:
bits = self._endian_transform(self._write_bits, endian)
# if it's padded, and all of the bits in the field weren't used,
# we need to flush out the unused bits
# TODO should we save the value of the unused bits so the data that
# is written out matches exactly what was read?
if self.reserved_bits < self.cls.width * 8:
filler = [0] * ((self.cls.width * 8) - self.reserved_bits)
if left_right:
bits += filler
else:
bits = filler + bits
stream.write_bits(bits)
self._write_bits = []
else:
# if an unpadded field ended up using the same BitfieldRW and
# as a previous padded field, there will be unwritten bits left in
# self._write_bits. These need to be flushed out as well
if len(self._write_bits) > 0:
stream.write_bits(self._write_bits)
self._write_bits = []
stream.write_bits(raw_bits) | Write the bits. Once the size of the written bits is equal
to the number of the reserved bits, flush it to the stream | entailment |
def _pfp__snapshot(self, recurse=True):
"""Save off the current value of the field
"""
if hasattr(self, "_pfp__value"):
self._pfp__snapshot_value = self._pfp__value | Save off the current value of the field | entailment |
def _pfp__process_metadata(self):
"""Process the metadata once the entire struct has been
declared.
"""
if self._pfp__metadata_processor is None:
return
metadata_info = self._pfp__metadata_processor()
if isinstance(metadata_info, list):
for metadata in metadata_info:
if metadata["type"] == "watch":
self._pfp__set_watch(
metadata["watch_fields"],
metadata["update_func"],
*metadata["func_call_info"]
)
elif metadata["type"] == "packed":
del metadata["type"]
self._pfp__set_packer(**metadata)
if self._pfp__can_unpack():
self._pfp__unpack_data(self.raw_data) | Process the metadata once the entire struct has been
declared. | entailment |
def _pfp__watch(self, watcher):
"""Add the watcher to the list of fields that
are watching this field
"""
if self._pfp__parent is not None and isinstance(self._pfp__parent, Union):
self._pfp__parent._pfp__watch(watcher)
else:
self._pfp__watchers.append(watcher) | Add the watcher to the list of fields that
are watching this field | entailment |
def _pfp__set_watch(self, watch_fields, update_func, *func_call_info):
"""Subscribe to update events on each field in ``watch_fields``, using
``update_func`` to update self's value when ``watch_field``
changes"""
self._pfp__watch_fields = watch_fields
for watch_field in watch_fields:
watch_field._pfp__watch(self)
self._pfp__update_func = update_func
self._pfp__update_func_call_info = func_call_info | Subscribe to update events on each field in ``watch_fields``, using
``update_func`` to update self's value when ``watch_field``
changes | entailment |
def _pfp__set_packer(self, pack_type, packer=None, pack=None, unpack=None, func_call_info=None):
"""Set the packer/pack/unpack functions for this field, as
well as the pack type.
:pack_type: The data type of the packed data
:packer: A function that can handle packing and unpacking. First
arg is true/false (to pack or unpack). Second arg is the stream.
Must return an array of chars.
:pack: A function that packs data. It must accept an array of chars and return an
array of chars that is a packed form of the input.
:unpack: A function that unpacks data. It must accept an array of chars and
return an array of chars
"""
self._pfp__pack_type = pack_type
self._pfp__unpack = unpack
self._pfp__pack = pack
self._pfp__packer = packer
self._pfp__pack_func_call_info = func_call_info | Set the packer/pack/unpack functions for this field, as
well as the pack type.
:pack_type: The data type of the packed data
:packer: A function that can handle packing and unpacking. First
arg is true/false (to pack or unpack). Second arg is the stream.
Must return an array of chars.
:pack: A function that packs data. It must accept an array of chars and return an
array of chars that is a packed form of the input.
:unpack: A function that unpacks data. It must accept an array of chars and
return an array of chars | entailment |
def _pfp__pack_data(self):
"""Pack the nested field
"""
if self._pfp__pack_type is None:
return
tmp_stream = six.BytesIO()
self._._pfp__build(bitwrap.BitwrappedStream(tmp_stream))
raw_data = tmp_stream.getvalue()
unpack_func = self._pfp__packer
unpack_args = []
if self._pfp__packer is not None:
unpack_func = self._pfp__packer
unpack_args = [true(), raw_data]
elif self._pfp__pack is not None:
unpack_func = self._pfp__pack
unpack_args = [raw_data]
# does not need to be converted to a char array
if not isinstance(unpack_func, functions.NativeFunction):
io_stream = bitwrap.BitwrappedStream(six.BytesIO(raw_data))
unpack_args[-1] = Array(len(raw_data), Char, io_stream)
res = unpack_func.call(unpack_args, *self._pfp__pack_func_call_info, no_cast=True)
if isinstance(res, Array):
res = res._pfp__build()
io_stream = six.BytesIO(res)
tmp_stream = bitwrap.BitwrappedStream(io_stream)
self._pfp__no_unpack = True
self._pfp__parse(tmp_stream)
self._pfp__no_unpack = False | Pack the nested field | entailment |
def _pfp__unpack_data(self, raw_data):
"""Means that the field has already been parsed normally,
and that it now needs to be unpacked.
:raw_data: A string of the data that the field consumed while parsing
"""
if self._pfp__pack_type is None:
return
if self._pfp__no_unpack:
return
unpack_func = self._pfp__packer
unpack_args = []
if self._pfp__packer is not None:
unpack_func = self._pfp__packer
unpack_args = [false(), raw_data]
elif self._pfp__unpack is not None:
unpack_func = self._pfp__unpack
unpack_args = [raw_data]
# does not need to be converted to a char array
if not isinstance(unpack_func, functions.NativeFunction):
io_stream = bitwrap.BitwrappedStream(six.BytesIO(raw_data))
unpack_args[-1] = Array(len(raw_data), Char, io_stream)
res = unpack_func.call(unpack_args, *self._pfp__pack_func_call_info, no_cast=True)
if isinstance(res, Array):
res = res._pfp__build()
io_stream = six.BytesIO(res)
tmp_stream = bitwrap.BitwrappedStream(io_stream)
tmp_stream.padded = self._pfp__interp.get_bitfield_padded()
self._ = self._pfp__parsed_packed = self._pfp__pack_type(tmp_stream)
self._._pfp__watch(self) | Means that the field has already been parsed normally,
and that it now needs to be unpacked.
:raw_data: A string of the data that the field consumed while parsing | entailment |
def _pfp__handle_updated(self, watched_field):
"""Handle the watched field that was updated
"""
self._pfp__no_notify = True
# nested data has been changed, so rebuild the
# nested data to update the field
# TODO a global setting to determine this behavior?
# could slow things down a bit for large nested structures
# notice the use of _is_ here - 'is' != '=='. '==' uses
# the __eq__ operator, while is compares id(object) results
if watched_field is self._:
self._pfp__pack_data()
elif self._pfp__update_func is not None:
self._pfp__update_func.call(
[self] + self._pfp__watch_fields,
*self._pfp__update_func_call_info
)
self._pfp__no_notify = False | Handle the watched field that was updated | entailment |
def _pfp__width(self):
"""Return the width of the field (sizeof)
"""
raw_output = six.BytesIO()
output = bitwrap.BitwrappedStream(raw_output)
self._pfp__build(output)
output.flush()
return len(raw_output.getvalue()) | Return the width of the field (sizeof) | entailment |
def _pfp__set_value(self, new_val):
"""Set the new value if type checking is passes, potentially
(TODO? reevaluate this) casting the value to something else
:new_val: The new value
:returns: TODO
"""
if self._pfp__frozen:
raise errors.UnmodifiableConst()
self._pfp__value = self._pfp__get_root_value(new_val)
self._pfp__notify_parent() | Set the new value if type checking is passes, potentially
(TODO? reevaluate this) casting the value to something else
:new_val: The new value
:returns: TODO | entailment |
def _pfp__snapshot(self, recurse=True):
"""Save off the current value of the field
"""
super(Struct, self)._pfp__snapshot(recurse=recurse)
if recurse:
for child in self._pfp__children:
child._pfp__snapshot(recurse=recurse) | Save off the current value of the field | entailment |
def _pfp__restore_snapshot(self, recurse=True):
"""Restore the snapshotted value without triggering any events
"""
super(Struct, self)._pfp__restore_snapshot(recurse=recurse)
if recurse:
for child in self._pfp__children:
child._pfp__restore_snapshot(recurse=recurse) | Restore the snapshotted value without triggering any events | entailment |
def _pfp__set_value(self, value):
"""Initialize the struct. Value should be an array of
fields, one each for each struct member.
:value: An array of fields to initialize the struct with
:returns: None
"""
if self._pfp__frozen:
raise errors.UnmodifiableConst()
if len(value) != len(self._pfp__children):
raise errors.PfpError("struct initialization has wrong number of members")
for x in six.moves.range(len(self._pfp__children)):
self._pfp__children[x]._pfp__set_value(value[x]) | Initialize the struct. Value should be an array of
fields, one each for each struct member.
:value: An array of fields to initialize the struct with
:returns: None | entailment |
def _pfp__add_child(self, name, child, stream=None, overwrite=False):
"""Add a child to the Struct field. If multiple consecutive fields are
added with the same name, an implicit array will be created to store
all fields of that name.
:param str name: The name of the child
:param pfp.fields.Field child: The field to add
:param bool overwrite: Overwrite existing fields (False)
:param pfp.bitwrap.BitwrappedStream stream: unused, but her for compatability with Union._pfp__add_child
:returns: The resulting field added
"""
if not overwrite and self._pfp__is_non_consecutive_duplicate(name, child):
return self._pfp__handle_non_consecutive_duplicate(name, child)
elif not overwrite and name in self._pfp__children_map:
return self._pfp__handle_implicit_array(name, child)
else:
child._pfp__parent = self
self._pfp__children.append(child)
child._pfp__name = name
self._pfp__children_map[name] = child
return child | Add a child to the Struct field. If multiple consecutive fields are
added with the same name, an implicit array will be created to store
all fields of that name.
:param str name: The name of the child
:param pfp.fields.Field child: The field to add
:param bool overwrite: Overwrite existing fields (False)
:param pfp.bitwrap.BitwrappedStream stream: unused, but her for compatability with Union._pfp__add_child
:returns: The resulting field added | entailment |
def _pfp__handle_non_consecutive_duplicate(self, name, child, insert=True):
"""This new child, and potentially one already existing child, need to
have a numeric suffix appended to their name.
An entry will be made for this name in ``self._pfp__name_collisions`` to keep
track of the next available suffix number"""
if name in self._pfp__children_map:
previous_child = self._pfp__children_map[name]
# DO NOT cause __eq__ to be called, we want to test actual objects, not comparison
# operators
if previous_child is not child:
self._pfp__handle_non_consecutive_duplicate(name, previous_child, insert=False)
del self._pfp__children_map[name]
next_suffix = self._pfp__name_collisions.setdefault(name, 0)
new_name = "{}_{}".format(name, next_suffix)
child._pfp__name = new_name
self._pfp__name_collisions[name] = next_suffix + 1
self._pfp__children_map[new_name] = child
child._pfp__parent = self
if insert:
self._pfp__children.append(child)
return child | This new child, and potentially one already existing child, need to
have a numeric suffix appended to their name.
An entry will be made for this name in ``self._pfp__name_collisions`` to keep
track of the next available suffix number | entailment |
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