code stringlengths 51 2.34k | sequence stringlengths 186 3.94k | docstring stringlengths 11 171 |
|---|---|---|
def check_extraneous(config, schema):
if not isinstance(config, dict):
raise ValueError("Config {} is not a dictionary".format(config))
for k in config:
if k not in schema:
raise ValueError("Unexpected config key `{}` not in {}".format(
k, list(schema.keys())))
v, kreq = schema[k]
if v is None:
continue
elif isinstance(v, type):
if not isinstance(config[k], v):
if v is str and isinstance(config[k], string_types):
continue
raise ValueError(
"Config key `{}` has wrong type {}, expected {}".format(
k,
type(config[k]).__name__, v.__name__))
else:
check_extraneous(config[k], v) | module function_definition identifier parameters identifier identifier block if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier for_statement identifier identifier block if_statement comparison_operator identifier identifier block raise_statement call identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier call identifier argument_list call attribute identifier identifier argument_list expression_statement assignment pattern_list identifier identifier subscript identifier identifier if_statement comparison_operator identifier none block continue_statement elif_clause call identifier argument_list identifier identifier block if_statement not_operator call identifier argument_list subscript identifier identifier identifier block if_statement boolean_operator comparison_operator identifier identifier call identifier argument_list subscript identifier identifier identifier block continue_statement raise_statement call identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier attribute call identifier argument_list subscript identifier identifier identifier attribute identifier identifier else_clause block expression_statement call identifier argument_list subscript identifier identifier identifier | Make sure all items of config are in schema |
def bbox2wktpolygon(bbox):
minx = float(bbox[0])
miny = float(bbox[1])
maxx = float(bbox[2])
maxy = float(bbox[3])
return 'POLYGON((%.2f %.2f, %.2f %.2f, %.2f %.2f, %.2f %.2f, %.2f %.2f))' \
% (minx, miny, minx, maxy, maxx, maxy, maxx, miny, minx, miny) | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list subscript identifier integer expression_statement assignment identifier call identifier argument_list subscript identifier integer expression_statement assignment identifier call identifier argument_list subscript identifier integer expression_statement assignment identifier call identifier argument_list subscript identifier integer return_statement binary_operator string string_start string_content string_end line_continuation tuple identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier | Return OGC WKT Polygon of a simple bbox list of strings |
def _validate_class(self, cl):
if cl not in self.schema_def.attributes_by_class:
search_string = self._build_search_string(cl)
err = self.err(
"{0} - invalid class", self._field_name_from_uri(cl),
search_string=search_string)
return ValidationWarning(ValidationResult.ERROR, err['err'],
err['line'], err['num']) | module function_definition identifier parameters identifier identifier block if_statement comparison_operator identifier attribute attribute identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_end call attribute identifier identifier argument_list identifier keyword_argument identifier identifier return_statement call identifier argument_list attribute identifier identifier subscript identifier string string_start string_content string_end subscript identifier string string_start string_content string_end subscript identifier string string_start string_content string_end | return error if class `cl` is not found in the ontology |
def to_unit(self, values, unit, from_unit):
return self._to_unit_base('degC-days', values, unit, from_unit) | module function_definition identifier parameters identifier identifier identifier identifier block return_statement call attribute identifier identifier argument_list string string_start string_content string_end identifier identifier identifier | Return values converted to the unit given the input from_unit. |
def port_ranges():
try:
return _linux_ranges()
except (OSError, IOError):
try:
ranges = _bsd_ranges()
if ranges:
return ranges
except (OSError, IOError):
pass
return [DEFAULT_EPHEMERAL_PORT_RANGE] | module function_definition identifier parameters block try_statement block return_statement call identifier argument_list except_clause tuple identifier identifier block try_statement block expression_statement assignment identifier call identifier argument_list if_statement identifier block return_statement identifier except_clause tuple identifier identifier block pass_statement return_statement list identifier | Returns a list of ephemeral port ranges for current machine. |
def run(self):
global world
self.__is_running = True
while(self.__is_running):
self.__handle_events()
self.__clock.tick(self.preferred_fps)
elapsed_milliseconds = self.__clock.get_time()
if 2 in self.event_flags:
self.elapsed_milliseconds = 0
if self.print_frames:
self.fpsTimer += elapsed_milliseconds
if self.fpsTimer > self.print_fps_frequency:
print "FPS: ", self.__clock.get_fps()
self.fpsTimer = 0.0
if not 0 in self.event_flags:
world.update(elapsed_milliseconds)
if not 1 in self.event_flags:
world.draw(elapsed_milliseconds)
pygame.display.flip() | module function_definition identifier parameters identifier block global_statement identifier expression_statement assignment attribute identifier identifier true while_statement parenthesized_expression attribute identifier identifier block expression_statement call attribute identifier identifier argument_list expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list if_statement comparison_operator integer attribute identifier identifier block expression_statement assignment attribute identifier identifier integer if_statement attribute identifier identifier block expression_statement augmented_assignment attribute identifier identifier identifier if_statement comparison_operator attribute identifier identifier attribute identifier identifier block print_statement string string_start string_content string_end call attribute attribute identifier identifier identifier argument_list expression_statement assignment attribute identifier identifier float if_statement not_operator comparison_operator integer attribute identifier identifier block expression_statement call attribute identifier identifier argument_list identifier if_statement not_operator comparison_operator integer attribute identifier identifier block expression_statement call attribute identifier identifier argument_list identifier expression_statement call attribute attribute identifier identifier identifier argument_list | Start the game loop |
def _default_dict(self):
options = {}
for attr, _, _, default, multi, _ in self._optiondict.values():
if multi and default is None:
options[attr] = []
else:
options[attr] = default
return options | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary for_statement pattern_list identifier identifier identifier identifier identifier identifier call attribute attribute identifier identifier identifier argument_list block if_statement boolean_operator identifier comparison_operator identifier none block expression_statement assignment subscript identifier identifier list else_clause block expression_statement assignment subscript identifier identifier identifier return_statement identifier | Return a dictionary with the default for each option. |
def replace(code, pattern, goal):
finder = similarfinder.RawSimilarFinder(code)
matches = list(finder.get_matches(pattern))
ast = patchedast.get_patched_ast(code)
lines = codeanalyze.SourceLinesAdapter(code)
template = similarfinder.CodeTemplate(goal)
computer = _ChangeComputer(code, ast, lines, template, matches)
result = computer.get_changed()
if result is None:
return code
return result | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call identifier argument_list call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call identifier argument_list identifier identifier identifier identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list if_statement comparison_operator identifier none block return_statement identifier return_statement identifier | used by other refactorings |
def _add_links(self, links, key="href", proxy_key="proxyURL", endpoints=None):
if endpoints is None:
endpoints = ["likes", "replies", "shares", "self", "followers",
"following", "lists", "favorites", "members"]
if links.get("links"):
for endpoint in links['links']:
if isinstance(links['links'][endpoint], dict):
self._add_link(endpoint, links['links'][endpoint]["href"])
else:
self._add_link(endpoint, links["links"][endpoint])
for endpoint in endpoints:
if links.get(endpoint, None) is None:
continue
if "pump_io" in links[endpoint]:
self._add_link(endpoint, links[endpoint]["pump_io"][proxy_key])
elif "url" in links[endpoint]:
self._add_link(endpoint, links[endpoint]["url"])
else:
self._add_link(endpoint, links[endpoint][key])
return self.links | module function_definition identifier parameters identifier identifier default_parameter identifier string string_start string_content string_end default_parameter identifier string string_start string_content string_end default_parameter identifier none block if_statement comparison_operator identifier none block expression_statement assignment identifier list string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end if_statement call attribute identifier identifier argument_list string string_start string_content string_end block for_statement identifier subscript identifier string string_start string_content string_end block if_statement call identifier argument_list subscript subscript identifier string string_start string_content string_end identifier identifier block expression_statement call attribute identifier identifier argument_list identifier subscript subscript subscript identifier string string_start string_content string_end identifier string string_start string_content string_end else_clause block expression_statement call attribute identifier identifier argument_list identifier subscript subscript identifier string string_start string_content string_end identifier for_statement identifier identifier block if_statement comparison_operator call attribute identifier identifier argument_list identifier none none block continue_statement if_statement comparison_operator string string_start string_content string_end subscript identifier identifier block expression_statement call attribute identifier identifier argument_list identifier subscript subscript subscript identifier identifier string string_start string_content string_end identifier elif_clause comparison_operator string string_start string_content string_end subscript identifier identifier block expression_statement call attribute identifier identifier argument_list identifier subscript subscript identifier identifier string string_start string_content string_end else_clause block expression_statement call attribute identifier identifier argument_list identifier subscript subscript identifier identifier identifier return_statement attribute identifier identifier | Parses and adds block of links |
def css_classes(self, extra_classes=None):
if hasattr(extra_classes, 'split'):
extra_classes = extra_classes.split()
extra_classes = set(extra_classes or [])
field_css_classes = getattr(self.form, 'field_css_classes', None)
if hasattr(field_css_classes, 'split'):
extra_classes.update(field_css_classes.split())
elif isinstance(field_css_classes, (list, tuple)):
extra_classes.update(field_css_classes)
elif isinstance(field_css_classes, dict):
extra_field_classes = []
for key in ('*', self.name):
css_classes = field_css_classes.get(key)
if hasattr(css_classes, 'split'):
extra_field_classes = css_classes.split()
elif isinstance(css_classes, (list, tuple)):
if '__default__' in css_classes:
css_classes.remove('__default__')
extra_field_classes.extend(css_classes)
else:
extra_field_classes = css_classes
extra_classes.update(extra_field_classes)
return super(NgBoundField, self).css_classes(extra_classes) | module function_definition identifier parameters identifier default_parameter identifier none block if_statement call identifier argument_list identifier string string_start string_content string_end block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment identifier call identifier argument_list boolean_operator identifier list expression_statement assignment identifier call identifier argument_list attribute identifier identifier string string_start string_content string_end none if_statement call identifier argument_list identifier string string_start string_content string_end block expression_statement call attribute identifier identifier argument_list call attribute identifier identifier argument_list elif_clause call identifier argument_list identifier tuple identifier identifier block expression_statement call attribute identifier identifier argument_list identifier elif_clause call identifier argument_list identifier identifier block expression_statement assignment identifier list for_statement identifier tuple string string_start string_content string_end attribute identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement call identifier argument_list identifier string string_start string_content string_end block expression_statement assignment identifier call attribute identifier identifier argument_list elif_clause call identifier argument_list identifier tuple identifier identifier block if_statement comparison_operator string string_start string_content string_end identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end expression_statement call attribute identifier identifier argument_list identifier else_clause block expression_statement assignment identifier identifier expression_statement call attribute identifier identifier argument_list identifier return_statement call attribute call identifier argument_list identifier identifier identifier argument_list identifier | Returns a string of space-separated CSS classes for the wrapping element of this input field. |
def update_class_by_type(old, new):
autoreload.update_class(old, new)
if isinstance2(old, new, AtomMeta):
update_atom_members(old, new) | module function_definition identifier parameters identifier identifier block expression_statement call attribute identifier identifier argument_list identifier identifier if_statement call identifier argument_list identifier identifier identifier block expression_statement call identifier argument_list identifier identifier | Update declarative classes or fallback on default |
def sentence_spans(self):
if not self.is_tagged(SENTENCES):
self.tokenize_sentences()
return self.spans(SENTENCES) | module function_definition identifier parameters identifier block if_statement not_operator call attribute identifier identifier argument_list identifier block expression_statement call attribute identifier identifier argument_list return_statement call attribute identifier identifier argument_list identifier | The list of spans representing ``sentences`` layer elements. |
def apply_child_computation(self, child_msg: Message) -> 'BaseComputation':
child_computation = self.generate_child_computation(child_msg)
self.add_child_computation(child_computation)
return child_computation | module function_definition identifier parameters identifier typed_parameter identifier type identifier type string string_start string_content string_end block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement call attribute identifier identifier argument_list identifier return_statement identifier | Apply the vm message ``child_msg`` as a child computation. |
def _install_nukeassist(use_threaded_wrapper):
import nuke
if "--nukeassist" not in nuke.rawArgs:
raise ImportError
def threaded_wrapper(func, *args, **kwargs):
return nuke.executeInMainThreadWithResult(
func, args, kwargs)
_common_setup("NukeAssist", threaded_wrapper, use_threaded_wrapper) | module function_definition identifier parameters identifier block import_statement dotted_name identifier if_statement comparison_operator string string_start string_content string_end attribute identifier identifier block raise_statement identifier function_definition identifier parameters identifier list_splat_pattern identifier dictionary_splat_pattern identifier block return_statement call attribute identifier identifier argument_list identifier identifier identifier expression_statement call identifier argument_list string string_start string_content string_end identifier identifier | Helper function to The Foundry NukeAssist support |
def save_genome_fitness(self,
delimiter=' ',
filename='fitness_history.csv',
with_cross_validation=False):
with open(filename, 'w') as f:
w = csv.writer(f, delimiter=delimiter)
best_fitness = [c.fitness for c in self.most_fit_genomes]
avg_fitness = self.get_fitness_mean()
if with_cross_validation:
cv_best_fitness = [c.cross_fitness for c in self.most_fit_genomes]
cv_avg_fitness = self.get_average_cross_validation_fitness()
for best, avg, cv_best, cv_avg in zip(best_fitness,
avg_fitness,
cv_best_fitness,
cv_avg_fitness):
w.writerow([best, avg, cv_best, cv_avg])
else:
for best, avg in zip(best_fitness, avg_fitness):
w.writerow([best, avg]) | module function_definition identifier parameters identifier default_parameter identifier string string_start string_content string_end default_parameter identifier string string_start string_content string_end default_parameter identifier false block with_statement with_clause with_item as_pattern call identifier argument_list identifier string string_start string_content string_end as_pattern_target identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier keyword_argument identifier identifier expression_statement assignment identifier list_comprehension attribute identifier identifier for_in_clause identifier attribute identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list if_statement identifier block expression_statement assignment identifier list_comprehension attribute identifier identifier for_in_clause identifier attribute identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list for_statement pattern_list identifier identifier identifier identifier call identifier argument_list identifier identifier identifier identifier block expression_statement call attribute identifier identifier argument_list list identifier identifier identifier identifier else_clause block for_statement pattern_list identifier identifier call identifier argument_list identifier identifier block expression_statement call attribute identifier identifier argument_list list identifier identifier | Saves the population's best and average fitness. |
def hydra_breakpoints(in_bam, pair_stats):
in_bed = convert_bam_to_bed(in_bam)
if os.path.getsize(in_bed) > 0:
pair_bed = pair_discordants(in_bed, pair_stats)
dedup_bed = dedup_discordants(pair_bed)
return run_hydra(dedup_bed, pair_stats)
else:
return None | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list identifier if_statement comparison_operator call attribute attribute identifier identifier identifier argument_list identifier integer block expression_statement assignment identifier call identifier argument_list identifier identifier expression_statement assignment identifier call identifier argument_list identifier return_statement call identifier argument_list identifier identifier else_clause block return_statement none | Detect structural variation breakpoints with hydra. |
def CreateDialectActions(dialect):
CompAction = SCons.Action.Action('$%sCOM ' % dialect, '$%sCOMSTR' % dialect)
CompPPAction = SCons.Action.Action('$%sPPCOM ' % dialect, '$%sPPCOMSTR' % dialect)
ShCompAction = SCons.Action.Action('$SH%sCOM ' % dialect, '$SH%sCOMSTR' % dialect)
ShCompPPAction = SCons.Action.Action('$SH%sPPCOM ' % dialect, '$SH%sPPCOMSTR' % dialect)
return CompAction, CompPPAction, ShCompAction, ShCompPPAction | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content string_end identifier binary_operator string string_start string_content string_end identifier expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content string_end identifier binary_operator string string_start string_content string_end identifier expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content string_end identifier binary_operator string string_start string_content string_end identifier expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content string_end identifier binary_operator string string_start string_content string_end identifier return_statement expression_list identifier identifier identifier identifier | Create dialect specific actions. |
def create_kernel_manager_and_kernel_client(self, connection_file,
stderr_handle,
is_cython=False,
is_pylab=False,
is_sympy=False):
kernel_spec = self.create_kernel_spec(is_cython=is_cython,
is_pylab=is_pylab,
is_sympy=is_sympy)
try:
kernel_manager = QtKernelManager(connection_file=connection_file,
config=None, autorestart=True)
except Exception:
error_msg = _("The error is:<br><br>"
"<tt>{}</tt>").format(traceback.format_exc())
return (error_msg, None)
kernel_manager._kernel_spec = kernel_spec
kwargs = {}
if os.name == 'nt':
kwargs['close_fds'] = False
try:
kernel_manager.start_kernel(stderr=stderr_handle, **kwargs)
except Exception:
error_msg = _("The error is:<br><br>"
"<tt>{}</tt>").format(traceback.format_exc())
return (error_msg, None)
kernel_client = kernel_manager.client()
kernel_client.hb_channel.time_to_dead = 18.0
return kernel_manager, kernel_client | module function_definition identifier parameters identifier identifier identifier default_parameter identifier false default_parameter identifier false default_parameter identifier false block expression_statement assignment identifier call attribute identifier identifier argument_list keyword_argument identifier identifier keyword_argument identifier identifier keyword_argument identifier identifier try_statement block expression_statement assignment identifier call identifier argument_list keyword_argument identifier identifier keyword_argument identifier none keyword_argument identifier true except_clause identifier block expression_statement assignment identifier call attribute call identifier argument_list concatenated_string string string_start string_content string_end string string_start string_content string_end identifier argument_list call attribute identifier identifier argument_list return_statement tuple identifier none expression_statement assignment attribute identifier identifier identifier expression_statement assignment identifier dictionary if_statement comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment subscript identifier string string_start string_content string_end false try_statement block expression_statement call attribute identifier identifier argument_list keyword_argument identifier identifier dictionary_splat identifier except_clause identifier block expression_statement assignment identifier call attribute call identifier argument_list concatenated_string string string_start string_content string_end string string_start string_content string_end identifier argument_list call attribute identifier identifier argument_list return_statement tuple identifier none expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment attribute attribute identifier identifier identifier float return_statement expression_list identifier identifier | Create kernel manager and client. |
def trunc_list(s: List) -> List:
if len(s) > max_list_size:
i = max_list_size // 2
j = i - 1
s = s[:i] + [ELLIPSIS] + s[-j:]
return s | module function_definition identifier parameters typed_parameter identifier type identifier type identifier block if_statement comparison_operator call identifier argument_list identifier identifier block expression_statement assignment identifier binary_operator identifier integer expression_statement assignment identifier binary_operator identifier integer expression_statement assignment identifier binary_operator binary_operator subscript identifier slice identifier list identifier subscript identifier slice unary_operator identifier return_statement identifier | Truncate lists to maximum length. |
def logWrite(self, string):
logFile = open(self.logFile, 'at')
logFile.write(string + '\n')
logFile.close() | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list attribute identifier identifier string string_start string_content string_end expression_statement call attribute identifier identifier argument_list binary_operator identifier string string_start string_content escape_sequence string_end expression_statement call attribute identifier identifier argument_list | Only write text to the log file, do not print |
def migrate(self, host, port, key, dest_db, timeout, *,
copy=False, replace=False):
if not isinstance(host, str):
raise TypeError("host argument must be str")
if not isinstance(timeout, int):
raise TypeError("timeout argument must be int")
if not isinstance(dest_db, int):
raise TypeError("dest_db argument must be int")
if not host:
raise ValueError("Got empty host")
if dest_db < 0:
raise ValueError("dest_db must be greater equal 0")
if timeout < 0:
raise ValueError("timeout must be greater equal 0")
flags = []
if copy:
flags.append(b'COPY')
if replace:
flags.append(b'REPLACE')
fut = self.execute(b'MIGRATE', host, port,
key, dest_db, timeout, *flags)
return wait_ok(fut) | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier keyword_separator default_parameter identifier false default_parameter identifier false block if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list string string_start string_content string_end if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list string string_start string_content string_end if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list string string_start string_content string_end if_statement not_operator identifier block raise_statement call identifier argument_list string string_start string_content string_end if_statement comparison_operator identifier integer block raise_statement call identifier argument_list string string_start string_content string_end if_statement comparison_operator identifier integer block raise_statement call identifier argument_list string string_start string_content string_end expression_statement assignment identifier list if_statement identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end if_statement identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_end identifier identifier identifier identifier identifier list_splat identifier return_statement call identifier argument_list identifier | Atomically transfer a key from a Redis instance to another one. |
def nvrtcGetErrorString(self, code):
code_int = c_int(code)
res = self._lib.nvrtcGetErrorString(code_int)
return res.decode('utf-8') | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list identifier return_statement call attribute identifier identifier argument_list string string_start string_content string_end | Returns a text identifier for the given NVRTC status code. |
def _elapsed(self):
self.last_time = time.time()
return self.last_time - self.start | module function_definition identifier parameters identifier block expression_statement assignment attribute identifier identifier call attribute identifier identifier argument_list return_statement binary_operator attribute identifier identifier attribute identifier identifier | Returns elapsed time at update. |
def _create_trustdb(cls):
trustdb = os.path.join(cls.homedir, 'trustdb.gpg')
if not os.path.isfile(trustdb):
log.info("GnuPG complained that your trustdb file was missing. %s"
% "This is likely due to changing to a new homedir.")
log.info("Creating trustdb.gpg file in your GnuPG homedir.")
cls.fix_trustdb(trustdb) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list attribute identifier identifier string string_start string_content string_end if_statement not_operator call attribute attribute identifier identifier identifier argument_list identifier block expression_statement call attribute identifier identifier argument_list binary_operator string string_start string_content string_end string string_start string_content string_end expression_statement call attribute identifier identifier argument_list string string_start string_content string_end expression_statement call attribute identifier identifier argument_list identifier | Create the trustdb file in our homedir, if it doesn't exist. |
def parallel_prep_region(samples, run_parallel):
file_key = "work_bam"
split_fn = _split_by_regions("bamprep", "-prep.bam", file_key)
extras = []
torun = []
for data in [x[0] for x in samples]:
if data.get("work_bam"):
data["align_bam"] = data["work_bam"]
if (not dd.get_realign(data) and not dd.get_variantcaller(data)):
extras.append([data])
elif not data.get(file_key):
extras.append([data])
else:
data["config"]["algorithm"]["orig_markduplicates"] = dd.get_mark_duplicates(data)
data = dd.set_mark_duplicates(data, False)
torun.append([data])
return extras + parallel_split_combine(torun, split_fn, run_parallel,
"piped_bamprep", _add_combine_info, file_key, ["config"]) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier string string_start string_content string_end expression_statement assignment identifier call identifier argument_list string string_start string_content string_end string string_start string_content string_end identifier expression_statement assignment identifier list expression_statement assignment identifier list for_statement identifier list_comprehension subscript identifier integer for_in_clause identifier identifier block if_statement call attribute identifier identifier argument_list string string_start string_content string_end block expression_statement assignment subscript identifier string string_start string_content string_end subscript identifier string string_start string_content string_end if_statement parenthesized_expression boolean_operator not_operator call attribute identifier identifier argument_list identifier not_operator call attribute identifier identifier argument_list identifier block expression_statement call attribute identifier identifier argument_list list identifier elif_clause not_operator call attribute identifier identifier argument_list identifier block expression_statement call attribute identifier identifier argument_list list identifier else_clause block expression_statement assignment subscript subscript subscript identifier string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier false expression_statement call attribute identifier identifier argument_list list identifier return_statement binary_operator identifier call identifier argument_list identifier identifier identifier string string_start string_content string_end identifier identifier list string string_start string_content string_end | Perform full pre-variant calling BAM prep work on regions. |
def _event_duration(vevent):
if hasattr(vevent, 'dtend'):
return vevent.dtend.value - vevent.dtstart.value
elif hasattr(vevent, 'duration') and vevent.duration.value:
return vevent.duration.value
return timedelta(0) | module function_definition identifier parameters identifier block if_statement call identifier argument_list identifier string string_start string_content string_end block return_statement binary_operator attribute attribute identifier identifier identifier attribute attribute identifier identifier identifier elif_clause boolean_operator call identifier argument_list identifier string string_start string_content string_end attribute attribute identifier identifier identifier block return_statement attribute attribute identifier identifier identifier return_statement call identifier argument_list integer | unify dtend and duration to the duration of the given vevent |
def __focus(self, item):
cols = self.__get_display_columns()
for col in cols:
self.__event_info =(col,item)
self.event_generate('<<TreeviewInplaceEdit>>')
if col in self._inplace_widgets:
w = self._inplace_widgets[col]
w.bind('<Key-Tab>',
lambda e: w.tk_focusNext().focus_set())
w.bind('<Shift-Key-Tab>',
lambda e: w.tk_focusPrev().focus_set()) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list for_statement identifier identifier block expression_statement assignment attribute identifier identifier tuple identifier identifier expression_statement call attribute identifier identifier argument_list string string_start string_content string_end if_statement comparison_operator identifier attribute identifier identifier block expression_statement assignment identifier subscript attribute identifier identifier identifier expression_statement call attribute identifier identifier argument_list string string_start string_content string_end lambda lambda_parameters identifier call attribute call attribute identifier identifier argument_list identifier argument_list expression_statement call attribute identifier identifier argument_list string string_start string_content string_end lambda lambda_parameters identifier call attribute call attribute identifier identifier argument_list identifier argument_list | Called when focus item has changed |
def _has_expired(self):
expired = False
if hasattr(self, 'Expiration'):
now = datetime.datetime.utcnow()
expiration = datetime.datetime.strptime(self.Expiration, '%Y-%m-%dT%H:%M:%SZ')
expired = (now >= expiration)
else:
raise ValueError("ERROR: Request for expired property, but no Expiration in HIT!")
return expired | module function_definition identifier parameters identifier block expression_statement assignment identifier false if_statement call identifier argument_list identifier string string_start string_content string_end block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list attribute identifier identifier string string_start string_content string_end expression_statement assignment identifier parenthesized_expression comparison_operator identifier identifier else_clause block raise_statement call identifier argument_list string string_start string_content string_end return_statement identifier | Has this HIT expired yet? |
def create_swag_from_ctx(ctx):
swag_opts = {}
if ctx.type == 'file':
swag_opts = {
'swag.type': 'file',
'swag.data_dir': ctx.data_dir,
'swag.data_file': ctx.data_file
}
elif ctx.type == 's3':
swag_opts = {
'swag.type': 's3',
'swag.bucket_name': ctx.bucket_name,
'swag.data_file': ctx.data_file,
'swag.region': ctx.region
}
elif ctx.type == 'dynamodb':
swag_opts = {
'swag.type': 'dynamodb',
'swag.region': ctx.region
}
return SWAGManager(**parse_swag_config_options(swag_opts)) | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary if_statement comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment identifier dictionary pair string string_start string_content string_end string string_start string_content string_end pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier elif_clause comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment identifier dictionary pair string string_start string_content string_end string string_start string_content string_end pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier elif_clause comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment identifier dictionary pair string string_start string_content string_end string string_start string_content string_end pair string string_start string_content string_end attribute identifier identifier return_statement call identifier argument_list dictionary_splat call identifier argument_list identifier | Creates SWAG client from the current context. |
def lock(self, request, *args, **kwargs):
self.object = self.get_object()
success_url = self.get_success_url()
self.object.status = Topic.TOPIC_LOCKED
self.object.save()
messages.success(self.request, self.success_message)
return HttpResponseRedirect(success_url) | module function_definition identifier parameters identifier identifier list_splat_pattern identifier dictionary_splat_pattern identifier block expression_statement assignment attribute identifier identifier call attribute identifier identifier argument_list expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment attribute attribute identifier identifier identifier attribute identifier identifier expression_statement call attribute attribute identifier identifier identifier argument_list expression_statement call attribute identifier identifier argument_list attribute identifier identifier attribute identifier identifier return_statement call identifier argument_list identifier | Locks the considered topic and retirects the user to the success URL. |
def convert_to_utf8(string):
if (isinstance(string, unicode)):
return string.encode('utf-8')
try:
u = unicode(string, 'utf-8')
except TypeError:
return str(string)
utf8 = u.encode('utf-8')
return utf8 | module function_definition identifier parameters identifier block if_statement parenthesized_expression call identifier argument_list identifier identifier block return_statement call attribute identifier identifier argument_list string string_start string_content string_end try_statement block expression_statement assignment identifier call identifier argument_list identifier string string_start string_content string_end except_clause identifier block return_statement call identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list string string_start string_content string_end return_statement identifier | Convert string to UTF8 |
def ungap_sequences(records, gap_chars=GAP_TABLE):
logging.info('Applying _ungap_sequences generator: removing all gap characters')
for record in records:
yield ungap_all(record, gap_chars) | module function_definition identifier parameters identifier default_parameter identifier identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end for_statement identifier identifier block expression_statement yield call identifier argument_list identifier identifier | Remove gaps from sequences, given an alignment. |
def _infer_all_types(self):
self._initialize_graph_status_for_traversing()
for raw_name, initial_type in self.initial_types:
for scope in self.scopes:
if raw_name not in scope.variable_name_mapping:
continue
for onnx_name in scope.variable_name_mapping[raw_name]:
variable = scope.variables[onnx_name]
if variable.is_root:
variable.type = initial_type
for operator in self.topological_operator_iterator():
if operator.type in self.custom_shape_calculators:
self.custom_shape_calculators[operator.type](operator)
elif operator.type in self.custom_conversion_functions:
pass
else:
operator.infer_types() | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list for_statement pattern_list identifier identifier attribute identifier identifier block for_statement identifier attribute identifier identifier block if_statement comparison_operator identifier attribute identifier identifier block continue_statement for_statement identifier subscript attribute identifier identifier identifier block expression_statement assignment identifier subscript attribute identifier identifier identifier if_statement attribute identifier identifier block expression_statement assignment attribute identifier identifier identifier for_statement identifier call attribute identifier identifier argument_list block if_statement comparison_operator attribute identifier identifier attribute identifier identifier block expression_statement call subscript attribute identifier identifier attribute identifier identifier argument_list identifier elif_clause comparison_operator attribute identifier identifier attribute identifier identifier block pass_statement else_clause block expression_statement call attribute identifier identifier argument_list | Infer all variables' shapes in the computational graph. |
def process_topojson(self, name, layer, input_path):
output_path = os.path.join(TEMP_DIRECTORY, '%s.topojson' % name)
topojson_binary = 'node_modules/bin/topojson'
if not os.path.exists(topojson_binary):
topojson_binary = 'topojson'
topo_cmd = [
topojson_binary,
'-o', output_path
]
if 'id-property' in layer:
topo_cmd.extend([
'--id-property', layer['id-property']
])
if layer.get('all-properties', False):
topo_cmd.append('-p')
elif 'properties' in layer:
topo_cmd.extend([
'-p', ','.join(layer['properties'])
])
topo_cmd.extend([
'--',
input_path
])
sys.stdout.write('* Running TopoJSON\n')
if self.args.verbose:
sys.stdout.write(' %s\n' % ' '.join(topo_cmd))
r = envoy.run(' '.join(topo_cmd))
if r.status_code != 0:
sys.stderr.write(r.std_err)
return output_path | module function_definition identifier parameters identifier identifier identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list identifier binary_operator string string_start string_content string_end identifier expression_statement assignment identifier string string_start string_content string_end if_statement not_operator call attribute attribute identifier identifier identifier argument_list identifier block expression_statement assignment identifier string string_start string_content string_end expression_statement assignment identifier list identifier string string_start string_content string_end identifier if_statement comparison_operator string string_start string_content string_end identifier block expression_statement call attribute identifier identifier argument_list list string string_start string_content string_end subscript identifier string string_start string_content string_end if_statement call attribute identifier identifier argument_list string string_start string_content string_end false block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end elif_clause comparison_operator string string_start string_content string_end identifier block expression_statement call attribute identifier identifier argument_list list string string_start string_content string_end call attribute string string_start string_content string_end identifier argument_list subscript identifier string string_start string_content string_end expression_statement call attribute identifier identifier argument_list list string string_start string_content string_end identifier expression_statement call attribute attribute identifier identifier identifier argument_list string string_start string_content escape_sequence string_end if_statement attribute attribute identifier identifier identifier block expression_statement call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content escape_sequence string_end call attribute string string_start string_content string_end identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier if_statement comparison_operator attribute identifier identifier integer block expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier return_statement identifier | Process layer using topojson. |
def annotation_wrapper(annotation, doc=None):
def decorator(attr):
__cache__.setdefault(attr, []).append(annotation)
try:
if not hasattr(attr, '_coaster_annotations'):
setattr(attr, '_coaster_annotations', [])
attr._coaster_annotations.append(annotation)
except AttributeError:
pass
return attr
decorator.__name__ = decorator.name = annotation
decorator.__doc__ = doc
return decorator | module function_definition identifier parameters identifier default_parameter identifier none block function_definition identifier parameters identifier block expression_statement call attribute call attribute identifier identifier argument_list identifier list identifier argument_list identifier try_statement block if_statement not_operator call identifier argument_list identifier string string_start string_content string_end block expression_statement call identifier argument_list identifier string string_start string_content string_end list expression_statement call attribute attribute identifier identifier identifier argument_list identifier except_clause identifier block pass_statement return_statement identifier expression_statement assignment attribute identifier identifier assignment attribute identifier identifier identifier expression_statement assignment attribute identifier identifier identifier return_statement identifier | Defines an annotation, which can be applied to attributes in a database model. |
def ObjectInitializedEventHandler(analysis, event):
wf.doActionFor(analysis, "initialize")
request = analysis.getRequest()
wf.doActionFor(request, "rollback_to_receive")
analysis.reindexObject(idxs="getServiceUID")
return | module function_definition identifier parameters identifier identifier block expression_statement call attribute identifier identifier argument_list identifier string string_start string_content string_end expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement call attribute identifier identifier argument_list identifier string string_start string_content string_end expression_statement call attribute identifier identifier argument_list keyword_argument identifier string string_start string_content string_end return_statement | Actions to be done when an analysis is added in an Analysis Request |
def list_vips(self, retrieve_all=True, **_params):
return self.list('vips', self.vips_path, retrieve_all,
**_params) | module function_definition identifier parameters identifier default_parameter identifier true dictionary_splat_pattern identifier block return_statement call attribute identifier identifier argument_list string string_start string_content string_end attribute identifier identifier identifier dictionary_splat identifier | Fetches a list of all load balancer vips for a project. |
def recentMatches(self, **criteria):
if not self.matches: return []
try:
maxMatches = criteria["maxMatches"]
del criteria["maxMatches"]
except AttributeError:
maxMatches = c.RECENT_MATCHES
alLMatches = self.matchSubset(**criteria)
matchTimes = [(m.endTime, m) for m in matches]
selMatches = sorted(matchTimes)[:maxMatches]
retMatches = [m for endTime,m in selMatches]
return retMatches | module function_definition identifier parameters identifier dictionary_splat_pattern identifier block if_statement not_operator attribute identifier identifier block return_statement list try_statement block expression_statement assignment identifier subscript identifier string string_start string_content string_end delete_statement subscript identifier string string_start string_content string_end except_clause identifier block expression_statement assignment identifier attribute identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list dictionary_splat identifier expression_statement assignment identifier list_comprehension tuple attribute identifier identifier identifier for_in_clause identifier identifier expression_statement assignment identifier subscript call identifier argument_list identifier slice identifier expression_statement assignment identifier list_comprehension identifier for_in_clause pattern_list identifier identifier identifier return_statement identifier | identify all recent matches for player given optional, additional criteria |
def export_datasource_schema(back_references):
data = dict_import_export.export_schema_to_dict(
back_references=back_references)
yaml.safe_dump(data, stdout, default_flow_style=False) | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list keyword_argument identifier identifier expression_statement call attribute identifier identifier argument_list identifier identifier keyword_argument identifier false | Export datasource YAML schema to stdout |
def to_device(b:Tensors, device:torch.device):
"Recursively put `b` on `device`."
device = ifnone(device, defaults.device)
if is_listy(b): return [to_device(o, device) for o in b]
if is_dict(b): return {k: to_device(v, device) for k, v in b.items()}
return b.to(device, non_blocking=True) | module function_definition identifier parameters typed_parameter identifier type identifier typed_parameter identifier type attribute identifier identifier block expression_statement string string_start string_content string_end expression_statement assignment identifier call identifier argument_list identifier attribute identifier identifier if_statement call identifier argument_list identifier block return_statement list_comprehension call identifier argument_list identifier identifier for_in_clause identifier identifier if_statement call identifier argument_list identifier block return_statement dictionary_comprehension pair identifier call identifier argument_list identifier identifier for_in_clause pattern_list identifier identifier call attribute identifier identifier argument_list return_statement call attribute identifier identifier argument_list identifier keyword_argument identifier true | Recursively put `b` on `device`. |
def visit_while(self, node):
whiles = "while %s:\n%s" % (node.test.accept(self), self._stmt_list(node.body))
if node.orelse:
whiles = "%s\nelse:\n%s" % (whiles, self._stmt_list(node.orelse))
return whiles | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier binary_operator string string_start string_content escape_sequence string_end tuple call attribute attribute identifier identifier identifier argument_list identifier call attribute identifier identifier argument_list attribute identifier identifier if_statement attribute identifier identifier block expression_statement assignment identifier binary_operator string string_start string_content escape_sequence escape_sequence string_end tuple identifier call attribute identifier identifier argument_list attribute identifier identifier return_statement identifier | return an astroid.While node as string |
def df(self, src):
return self._getStdOutCmd([self._hadoop_cmd, 'fs', '-df', self._full_hdfs_path(src)], True) | module function_definition identifier parameters identifier identifier block return_statement call attribute identifier identifier argument_list list attribute identifier identifier string string_start string_content string_end string string_start string_content string_end call attribute identifier identifier argument_list identifier true | Perform ``df`` on a path |
def extendMarkdown(self, md, md_globals):
md.registerExtension(self)
md.preprocessors.add('fenced_code_block',
SpecialFencePreprocessor(md),
">normalize_whitespace") | module function_definition identifier parameters identifier identifier identifier block expression_statement call attribute identifier identifier argument_list identifier expression_statement call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end call identifier argument_list identifier string string_start string_content string_end | Add FencedBlockPreprocessor to the Markdown instance. |
def cublasSdgmm(handle, mode, m, n, A, lda, x, incx, C, ldc):
status = _libcublas.cublasSdgmm(handle,
_CUBLAS_SIDE[mode],
m, n,
int(A), lda,
int(x), incx,
int(C), ldc)
cublasCheckStatus(status) | module function_definition identifier parameters identifier identifier identifier identifier identifier identifier identifier identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier subscript identifier identifier identifier identifier call identifier argument_list identifier identifier call identifier argument_list identifier identifier call identifier argument_list identifier identifier expression_statement call identifier argument_list identifier | Matrix-diagonal matrix product for real general matrix. |
def peaks(x, y, lookahead=20, delta=0.00003):
_max, _min = peakdetect(y, x, lookahead, delta)
x_peaks = [p[0] for p in _max]
y_peaks = [p[1] for p in _max]
x_valleys = [p[0] for p in _min]
y_valleys = [p[1] for p in _min]
_peaks = [x_peaks, y_peaks]
_valleys = [x_valleys, y_valleys]
return {"peaks": _peaks, "valleys": _valleys} | module function_definition identifier parameters identifier identifier default_parameter identifier integer default_parameter identifier float block expression_statement assignment pattern_list identifier identifier call identifier argument_list identifier identifier identifier identifier expression_statement assignment identifier list_comprehension subscript identifier integer for_in_clause identifier identifier expression_statement assignment identifier list_comprehension subscript identifier integer for_in_clause identifier identifier expression_statement assignment identifier list_comprehension subscript identifier integer for_in_clause identifier identifier expression_statement assignment identifier list_comprehension subscript identifier integer for_in_clause identifier identifier expression_statement assignment identifier list identifier identifier expression_statement assignment identifier list identifier identifier return_statement dictionary pair string string_start string_content string_end identifier pair string string_start string_content string_end identifier | A wrapper around peakdetect to pack the return values in a nicer format |
def to_type(value, ptype):
if ptype == 'str':
return str(value)
elif ptype == 'int':
return int(value)
elif ptype == 'float':
return float(value)
elif ptype == 'bool':
if value.lower() == 'true':
return True
elif value.lower() == 'false':
return False
raise ValueError('Bad bool value: %s' % value)
elif ptype == 'json':
return json.loads(value)
return ValueError('Unknown type') | module function_definition identifier parameters identifier identifier block if_statement comparison_operator identifier string string_start string_content string_end block return_statement call identifier argument_list identifier elif_clause comparison_operator identifier string string_start string_content string_end block return_statement call identifier argument_list identifier elif_clause comparison_operator identifier string string_start string_content string_end block return_statement call identifier argument_list identifier elif_clause comparison_operator identifier string string_start string_content string_end block if_statement comparison_operator call attribute identifier identifier argument_list string string_start string_content string_end block return_statement true elif_clause comparison_operator call attribute identifier identifier argument_list string string_start string_content string_end block return_statement false raise_statement call identifier argument_list binary_operator string string_start string_content string_end identifier elif_clause comparison_operator identifier string string_start string_content string_end block return_statement call attribute identifier identifier argument_list identifier return_statement call identifier argument_list string string_start string_content string_end | Convert value to ptype |
def dispatch_request(self, req):
log.debug("Dispatching request: {}".format(str(req)))
res = None
try:
req.validate()
except MissingFieldError as e:
res = APIMissingFieldErrorResponse(str(e))
if not res:
try:
res = req.dispatch()
except Exception as e:
msg = "Exception raised while dispatching request: {}".format(repr(e))
log.exception(msg)
res = APIGenericErrorResponse(msg)
log.debug("Response: {}".format(str(res)))
return res | module function_definition identifier parameters identifier identifier block expression_statement call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list call identifier argument_list identifier expression_statement assignment identifier none try_statement block expression_statement call attribute identifier identifier argument_list except_clause as_pattern identifier as_pattern_target identifier block expression_statement assignment identifier call identifier argument_list call identifier argument_list identifier if_statement not_operator identifier block try_statement block expression_statement assignment identifier call attribute identifier identifier argument_list except_clause as_pattern identifier as_pattern_target identifier block expression_statement assignment identifier call attribute string string_start string_content string_end identifier argument_list call identifier argument_list identifier expression_statement call attribute identifier identifier argument_list identifier expression_statement assignment identifier call identifier argument_list identifier expression_statement call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list call identifier argument_list identifier return_statement identifier | Dispatch a request object. |
def keys_values(self):
keys_values = []
for value in self.keys.values():
if isinstance(value, list):
keys_values += value
elif isinstance(value, basestring) and not value.startswith('-'):
keys_values.append(value)
elif isinstance(value, int) and value >= 0:
keys_values.append(str(value))
return keys_values | module function_definition identifier parameters identifier block expression_statement assignment identifier list for_statement identifier call attribute attribute identifier identifier identifier argument_list block if_statement call identifier argument_list identifier identifier block expression_statement augmented_assignment identifier identifier elif_clause boolean_operator call identifier argument_list identifier identifier not_operator call attribute identifier identifier argument_list string string_start string_content string_end block expression_statement call attribute identifier identifier argument_list identifier elif_clause boolean_operator call identifier argument_list identifier identifier comparison_operator identifier integer block expression_statement call attribute identifier identifier argument_list call identifier argument_list identifier return_statement identifier | Key values might be a list or not, always return a list. |
def parse(string, language=None):
if language:
string = replace_word_tokens(string, language)
tokens = tokenize(string)
postfix = to_postfix(tokens)
return evaluate_postfix(postfix) | module function_definition identifier parameters identifier default_parameter identifier none block if_statement identifier block expression_statement assignment identifier call identifier argument_list identifier identifier expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment identifier call identifier argument_list identifier return_statement call identifier argument_list identifier | Return a solution to the equation in the input string. |
def parse_correlation(self, f):
s_names = None
data = list()
for l in f['f'].splitlines():
s = l.strip().split("\t")
if s_names is None:
s_names = [ x for x in s if x != '' ]
else:
data.append(s[1:])
if f['fn'] == 'corrMatrixPearson.txt':
self.rna_seqc_pearson = (s_names, data)
elif f['fn'] == 'corrMatrixSpearman.txt':
self.rna_seqc_spearman = (s_names, data) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier none expression_statement assignment identifier call identifier argument_list for_statement identifier call attribute subscript identifier string string_start string_content string_end identifier argument_list block expression_statement assignment identifier call attribute call attribute identifier identifier argument_list identifier argument_list string string_start string_content escape_sequence string_end if_statement comparison_operator identifier none block expression_statement assignment identifier list_comprehension identifier for_in_clause identifier identifier if_clause comparison_operator identifier string string_start string_end else_clause block expression_statement call attribute identifier identifier argument_list subscript identifier slice integer if_statement comparison_operator subscript identifier string string_start string_content string_end string string_start string_content string_end block expression_statement assignment attribute identifier identifier tuple identifier identifier elif_clause comparison_operator subscript identifier string string_start string_content string_end string string_start string_content string_end block expression_statement assignment attribute identifier identifier tuple identifier identifier | Parse RNA-SeQC correlation matrices |
def xml(self, fn=None, src='word/document.xml', XMLClass=XML, **params):
"return the src with the given transformation applied, if any."
if src in self.xml_cache: return self.xml_cache[src]
if src not in self.zipfile.namelist(): return
x = XMLClass(
fn=fn or (self.fn and self.fn.replace('.docx', '.xml')) or None,
root=self.zipfile.read(src))
self.xml_cache[src] = x
return x | module function_definition identifier parameters identifier default_parameter identifier none default_parameter identifier string string_start string_content string_end default_parameter identifier identifier dictionary_splat_pattern identifier block expression_statement string string_start string_content string_end if_statement comparison_operator identifier attribute identifier identifier block return_statement subscript attribute identifier identifier identifier if_statement comparison_operator identifier call attribute attribute identifier identifier identifier argument_list block return_statement expression_statement assignment identifier call identifier argument_list keyword_argument identifier boolean_operator boolean_operator identifier parenthesized_expression boolean_operator attribute identifier identifier call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end string string_start string_content string_end none keyword_argument identifier call attribute attribute identifier identifier identifier argument_list identifier expression_statement assignment subscript attribute identifier identifier identifier identifier return_statement identifier | return the src with the given transformation applied, if any. |
async def setFormName(self, oldn, newn):
logger.info(f'Migrating [{oldn}] to [{newn}]')
async with self.getTempSlab():
i = 0
async for buid, valu in self.getFormTodo(oldn):
await self.editNodeNdef((oldn, valu), (newn, valu))
i = i + 1
if i and i % _progress == 0:
logger.info(f'Migrated {i} buids.') | module function_definition identifier parameters identifier identifier identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content interpolation identifier string_content interpolation identifier string_content string_end with_statement with_clause with_item call attribute identifier identifier argument_list block expression_statement assignment identifier integer for_statement pattern_list identifier identifier call attribute identifier identifier argument_list identifier block expression_statement await call attribute identifier identifier argument_list tuple identifier identifier tuple identifier identifier expression_statement assignment identifier binary_operator identifier integer if_statement boolean_operator identifier comparison_operator binary_operator identifier identifier integer block expression_statement call attribute identifier identifier argument_list string string_start string_content interpolation identifier string_content string_end | Rename a form within all the layers. |
def error(self, err=None):
if self.state == 'half-open':
self.test_fail_count = min(self.test_fail_count + 1, 16)
self.errors.append(self.clock())
if len(self.errors) > self.maxfail:
time = self.clock() - self.errors.pop(0)
if time < self.time_unit:
if time == 0:
time = 0.0001
self.log.debug('error rate: %f errors per second' % (
float(self.maxfail) / time))
self.open(err) | module function_definition identifier parameters identifier default_parameter identifier none block if_statement comparison_operator attribute identifier identifier string string_start string_content string_end block expression_statement assignment attribute identifier identifier call identifier argument_list binary_operator attribute identifier identifier integer integer expression_statement call attribute attribute identifier identifier identifier argument_list call attribute identifier identifier argument_list if_statement comparison_operator call identifier argument_list attribute identifier identifier attribute identifier identifier block expression_statement assignment identifier binary_operator call attribute identifier identifier argument_list call attribute attribute identifier identifier identifier argument_list integer if_statement comparison_operator identifier attribute identifier identifier block if_statement comparison_operator identifier integer block expression_statement assignment identifier float expression_statement call attribute attribute identifier identifier identifier argument_list binary_operator string string_start string_content string_end parenthesized_expression binary_operator call identifier argument_list attribute identifier identifier identifier expression_statement call attribute identifier identifier argument_list identifier | Update the circuit breaker with an error event. |
def _make_interpolation_node(self, tag_type, tag_key, leading_whitespace):
if tag_type == '!':
return _CommentNode()
if tag_type == '=':
delimiters = tag_key.split()
self._change_delimiters(delimiters)
return _ChangeNode(delimiters)
if tag_type == '':
return _EscapeNode(tag_key)
if tag_type == '&':
return _LiteralNode(tag_key)
if tag_type == '>':
return _PartialNode(tag_key, leading_whitespace)
raise Exception("Invalid symbol for interpolation tag: %s" % repr(tag_type)) | module function_definition identifier parameters identifier identifier identifier identifier block if_statement comparison_operator identifier string string_start string_content string_end block return_statement call identifier argument_list if_statement comparison_operator identifier string string_start string_content string_end block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement call attribute identifier identifier argument_list identifier return_statement call identifier argument_list identifier if_statement comparison_operator identifier string string_start string_end block return_statement call identifier argument_list identifier if_statement comparison_operator identifier string string_start string_content string_end block return_statement call identifier argument_list identifier if_statement comparison_operator identifier string string_start string_content string_end block return_statement call identifier argument_list identifier identifier raise_statement call identifier argument_list binary_operator string string_start string_content string_end call identifier argument_list identifier | Create and return a non-section node for the parse tree. |
def read_fastq(filename):
if not filename:
return itertools.cycle((None,))
if filename == "-":
filename_fh = sys.stdin
elif filename.endswith('gz'):
if is_python3:
filename_fh = gzip.open(filename, mode='rt')
else:
filename_fh = BufferedReader(gzip.open(filename, mode='rt'))
else:
filename_fh = open(filename)
return stream_fastq(filename_fh) | module function_definition identifier parameters identifier block if_statement not_operator identifier block return_statement call attribute identifier identifier argument_list tuple none if_statement comparison_operator identifier string string_start string_content string_end block expression_statement assignment identifier attribute identifier identifier elif_clause call attribute identifier identifier argument_list string string_start string_content string_end block if_statement identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier keyword_argument identifier string string_start string_content string_end else_clause block expression_statement assignment identifier call identifier argument_list call attribute identifier identifier argument_list identifier keyword_argument identifier string string_start string_content string_end else_clause block expression_statement assignment identifier call identifier argument_list identifier return_statement call identifier argument_list identifier | return a stream of FASTQ entries, handling gzipped and empty files |
def GetCountStopTimes(self):
cursor = self._schedule._connection.cursor()
cursor.execute(
'SELECT count(*) FROM stop_times WHERE trip_id=?', (self.trip_id,))
return cursor.fetchone()[0] | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute attribute attribute identifier identifier identifier identifier argument_list expression_statement call attribute identifier identifier argument_list string string_start string_content string_end tuple attribute identifier identifier return_statement subscript call attribute identifier identifier argument_list integer | Return the number of stops made by this trip. |
def trim(self):
for key, value in list(iteritems(self.counters)):
if value.empty():
del self.counters[key] | module function_definition identifier parameters identifier block for_statement pattern_list identifier identifier call identifier argument_list call identifier argument_list attribute identifier identifier block if_statement call attribute identifier identifier argument_list block delete_statement subscript attribute identifier identifier identifier | Clear not used counters |
def _chk_fields(field_data, field_formatter):
if len(field_data) == len(field_formatter):
return
len_dat = len(field_data)
len_fmt = len(field_formatter)
msg = [
"FIELD DATA({d}) != FORMATTER({f})".format(d=len_dat, f=len_fmt),
"DAT({N}): {D}".format(N=len_dat, D=field_data),
"FMT({N}): {F}".format(N=len_fmt, F=field_formatter)]
raise Exception("\n".join(msg)) | module function_definition identifier parameters identifier identifier block if_statement comparison_operator call identifier argument_list identifier call identifier argument_list identifier block return_statement expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment identifier call identifier argument_list identifier expression_statement assignment identifier list call attribute string string_start string_content string_end identifier argument_list keyword_argument identifier identifier keyword_argument identifier identifier call attribute string string_start string_content string_end identifier argument_list keyword_argument identifier identifier keyword_argument identifier identifier call attribute string string_start string_content string_end identifier argument_list keyword_argument identifier identifier keyword_argument identifier identifier raise_statement call identifier argument_list call attribute string string_start string_content escape_sequence string_end identifier argument_list identifier | Check that expected fields are present. |
def on_any_event(self, event):
for delegate in self.delegates:
if hasattr(delegate, "on_any_event"):
delegate.on_any_event(event) | module function_definition identifier parameters identifier identifier block for_statement identifier attribute identifier identifier block if_statement call identifier argument_list identifier string string_start string_content string_end block expression_statement call attribute identifier identifier argument_list identifier | On any event method |
def safe_setattr(obj, name, value):
try:
setattr(obj, name, value)
return True
except AttributeError:
return False | module function_definition identifier parameters identifier identifier identifier block try_statement block expression_statement call identifier argument_list identifier identifier identifier return_statement true except_clause identifier block return_statement false | Attempt to setattr but catch AttributeErrors. |
def _treat_devices_removed(self):
for device in self._removed_ports.copy():
eventlet.spawn_n(self._process_removed_port, device) | module function_definition identifier parameters identifier block for_statement identifier call attribute attribute identifier identifier identifier argument_list block expression_statement call attribute identifier identifier argument_list attribute identifier identifier identifier | Process the removed devices. |
def isAvailable(self, requester, access):
debuglog("%s isAvailable(%s, %s): self.owners=%r"
% (self, requester, access, self.owners))
num_excl, num_counting = self._claimed_excl, self._claimed_counting
for idx, waiter in enumerate(self.waiting):
if waiter[0] is requester:
w_index = idx
break
else:
w_index = len(self.waiting)
ahead = self.waiting[:w_index]
if access.mode == 'counting':
return num_excl == 0 and num_counting + len(ahead) < self.maxCount \
and all([w[1].mode == 'counting' for w in ahead])
return num_excl == 0 and num_counting == 0 and not ahead | module function_definition identifier parameters identifier identifier identifier block expression_statement call identifier argument_list binary_operator string string_start string_content string_end tuple identifier identifier identifier attribute identifier identifier expression_statement assignment pattern_list identifier identifier expression_list attribute identifier identifier attribute identifier identifier for_statement pattern_list identifier identifier call identifier argument_list attribute identifier identifier block if_statement comparison_operator subscript identifier integer identifier block expression_statement assignment identifier identifier break_statement else_clause block expression_statement assignment identifier call identifier argument_list attribute identifier identifier expression_statement assignment identifier subscript attribute identifier identifier slice identifier if_statement comparison_operator attribute identifier identifier string string_start string_content string_end block return_statement boolean_operator boolean_operator comparison_operator identifier integer comparison_operator binary_operator identifier call identifier argument_list identifier attribute identifier identifier line_continuation call identifier argument_list list_comprehension comparison_operator attribute subscript identifier integer identifier string string_start string_content string_end for_in_clause identifier identifier return_statement boolean_operator boolean_operator comparison_operator identifier integer comparison_operator identifier integer not_operator identifier | Return a boolean whether the lock is available for claiming |
def to_json(self):
obj = {
"vertices": [
{
"id": vertex.id,
"annotation": vertex.annotation,
}
for vertex in self.vertices
],
"edges": [
{
"id": edge.id,
"annotation": edge.annotation,
"head": edge.head,
"tail": edge.tail,
}
for edge in self._edges
],
}
return six.text_type(json.dumps(obj, ensure_ascii=False)) | module function_definition identifier parameters identifier block expression_statement assignment identifier dictionary pair string string_start string_content string_end list_comprehension dictionary pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier for_in_clause identifier attribute identifier identifier pair string string_start string_content string_end list_comprehension dictionary pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier pair string string_start string_content string_end attribute identifier identifier for_in_clause identifier attribute identifier identifier return_statement call attribute identifier identifier argument_list call attribute identifier identifier argument_list identifier keyword_argument identifier false | Convert to a JSON string. |
def _from_dict(cls, _dict):
args = {}
if 'entities' in _dict:
args['entities'] = [
RelationEntity._from_dict(x) for x in (_dict.get('entities'))
]
if 'location' in _dict:
args['location'] = _dict.get('location')
if 'text' in _dict:
args['text'] = _dict.get('text')
return cls(**args) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier dictionary if_statement comparison_operator string string_start string_content string_end identifier block expression_statement assignment subscript identifier string string_start string_content string_end list_comprehension call attribute identifier identifier argument_list identifier for_in_clause identifier parenthesized_expression call attribute identifier identifier argument_list string string_start string_content string_end if_statement comparison_operator string string_start string_content string_end identifier block expression_statement assignment subscript identifier string string_start string_content string_end call attribute identifier identifier argument_list string string_start string_content string_end if_statement comparison_operator string string_start string_content string_end identifier block expression_statement assignment subscript identifier string string_start string_content string_end call attribute identifier identifier argument_list string string_start string_content string_end return_statement call identifier argument_list dictionary_splat identifier | Initialize a RelationArgument object from a json dictionary. |
def _apply_cached_indexes(self, cached_indexes, persist=False):
for elt in ['valid_input_index', 'valid_output_index',
'index_array', 'distance_array']:
val = cached_indexes[elt]
if isinstance(val, tuple):
val = cached_indexes[elt][0]
elif isinstance(val, np.ndarray):
val = da.from_array(val, chunks=CHUNK_SIZE)
elif persist and isinstance(val, da.Array):
cached_indexes[elt] = val = val.persist()
setattr(self.resampler, elt, val) | module function_definition identifier parameters identifier identifier default_parameter identifier false block for_statement identifier list string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end string string_start string_content string_end block expression_statement assignment identifier subscript identifier identifier if_statement call identifier argument_list identifier identifier block expression_statement assignment identifier subscript subscript identifier identifier integer elif_clause call identifier argument_list identifier attribute identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier keyword_argument identifier identifier elif_clause boolean_operator identifier call identifier argument_list identifier attribute identifier identifier block expression_statement assignment subscript identifier identifier assignment identifier call attribute identifier identifier argument_list expression_statement call identifier argument_list attribute identifier identifier identifier identifier | Reassign various resampler index attributes. |
def add_toolbars_to_menu(self, menu_title, actions):
view_menu = self.menus[6]
if actions == self.toolbars and view_menu:
toolbars = []
for toolbar in self.toolbars:
action = toolbar.toggleViewAction()
toolbars.append(action)
add_actions(view_menu, toolbars) | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier subscript attribute identifier identifier integer if_statement boolean_operator comparison_operator identifier attribute identifier identifier identifier block expression_statement assignment identifier list for_statement identifier attribute identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement call attribute identifier identifier argument_list identifier expression_statement call identifier argument_list identifier identifier | Add toolbars to a menu. |
def addVariantSet(self, variantSet):
id_ = variantSet.getId()
self._variantSetIdMap[id_] = variantSet
self._variantSetNameMap[variantSet.getLocalId()] = variantSet
self._variantSetIds.append(id_) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list expression_statement assignment subscript attribute identifier identifier identifier identifier expression_statement assignment subscript attribute identifier identifier call attribute identifier identifier argument_list identifier expression_statement call attribute attribute identifier identifier identifier argument_list identifier | Adds the specified variantSet to this dataset. |
def ping_directories(self, request, queryset, messages=True):
for directory in settings.PING_DIRECTORIES:
pinger = DirectoryPinger(directory, queryset)
pinger.join()
if messages:
success = 0
for result in pinger.results:
if not result.get('flerror', True):
success += 1
else:
self.message_user(request,
'%s : %s' % (directory,
result['message']))
if success:
self.message_user(
request,
_('%(directory)s directory succesfully '
'pinged %(success)d entries.') %
{'directory': directory, 'success': success}) | module function_definition identifier parameters identifier identifier identifier default_parameter identifier true block for_statement identifier attribute identifier identifier block expression_statement assignment identifier call identifier argument_list identifier identifier expression_statement call attribute identifier identifier argument_list if_statement identifier block expression_statement assignment identifier integer for_statement identifier attribute identifier identifier block if_statement not_operator call attribute identifier identifier argument_list string string_start string_content string_end true block expression_statement augmented_assignment identifier integer else_clause block expression_statement call attribute identifier identifier argument_list identifier binary_operator string string_start string_content string_end tuple identifier subscript identifier string string_start string_content string_end if_statement identifier block expression_statement call attribute identifier identifier argument_list identifier binary_operator call identifier argument_list concatenated_string string string_start string_content string_end string string_start string_content string_end dictionary pair string string_start string_content string_end identifier pair string string_start string_content string_end identifier | Ping web directories for selected entries. |
def top_view(self):
self.msg.template(78)
print("{0}{1}{2}{3}{4}{5}{6}{7}{8}{9}{10}".format(
"| Package", " " * 17,
"New Version", " " * 8,
"Arch", " " * 4,
"Build", " " * 2,
"Repos", " " * 10,
"Size"))
self.msg.template(78) | module function_definition identifier parameters identifier block expression_statement call attribute attribute identifier identifier identifier argument_list integer expression_statement call identifier argument_list call attribute string string_start string_content string_end identifier argument_list string string_start string_content string_end binary_operator string string_start string_content string_end integer string string_start string_content string_end binary_operator string string_start string_content string_end integer string string_start string_content string_end binary_operator string string_start string_content string_end integer string string_start string_content string_end binary_operator string string_start string_content string_end integer string string_start string_content string_end binary_operator string string_start string_content string_end integer string string_start string_content string_end expression_statement call attribute attribute identifier identifier identifier argument_list integer | Print packages status bar |
def _setup_ipc(self):
log.debug('Setting up the internal IPC proxy')
self.ctx = zmq.Context()
self.sub = self.ctx.socket(zmq.SUB)
self.sub.bind(PUB_PX_IPC_URL)
self.sub.setsockopt(zmq.SUBSCRIBE, b'')
log.debug('Setting HWM for the proxy frontend: %d', self.hwm)
try:
self.sub.setsockopt(zmq.HWM, self.hwm)
except AttributeError:
self.sub.setsockopt(zmq.SNDHWM, self.hwm)
self.pub = self.ctx.socket(zmq.PUB)
self.pub.bind(PUB_IPC_URL)
log.debug('Setting HWM for the proxy backend: %d', self.hwm)
try:
self.pub.setsockopt(zmq.HWM, self.hwm)
except AttributeError:
self.pub.setsockopt(zmq.SNDHWM, self.hwm) | module function_definition identifier parameters identifier block expression_statement call attribute identifier identifier argument_list string string_start string_content string_end expression_statement assignment attribute identifier identifier call attribute identifier identifier argument_list expression_statement assignment attribute identifier identifier call attribute attribute identifier identifier identifier argument_list attribute identifier identifier expression_statement call attribute attribute identifier identifier identifier argument_list identifier expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier string string_start string_end expression_statement call attribute identifier identifier argument_list string string_start string_content string_end attribute identifier identifier try_statement block expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier attribute identifier identifier except_clause identifier block expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier attribute identifier identifier expression_statement assignment attribute identifier identifier call attribute attribute identifier identifier identifier argument_list attribute identifier identifier expression_statement call attribute attribute identifier identifier identifier argument_list identifier expression_statement call attribute identifier identifier argument_list string string_start string_content string_end attribute identifier identifier try_statement block expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier attribute identifier identifier except_clause identifier block expression_statement call attribute attribute identifier identifier identifier argument_list attribute identifier identifier attribute identifier identifier | Setup the IPC PUB and SUB sockets for the proxy. |
def zoom_out_pixel(self, curr_pixel):
low_frag = curr_pixel[0]
high_frag = curr_pixel[1]
level = curr_pixel[2]
str_level = str(level)
if level < self.n_level - 1:
low_super = self.spec_level[str_level]["fragments_dict"][low_frag][
"super_index"
]
high_super = self.spec_level[str_level]["fragments_dict"][
high_frag
]["sub_index"]
new_pix_low = min([low_super, high_super])
new_pix_high = max([low_super, high_super])
new_level = level + 1
new_pixel = [new_pix_low, new_pix_high, new_level]
else:
new_pixel = curr_pixel
return new_pixel | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier subscript identifier integer expression_statement assignment identifier subscript identifier integer expression_statement assignment identifier subscript identifier integer expression_statement assignment identifier call identifier argument_list identifier if_statement comparison_operator identifier binary_operator attribute identifier identifier integer block expression_statement assignment identifier subscript subscript subscript subscript attribute identifier identifier identifier string string_start string_content string_end identifier string string_start string_content string_end expression_statement assignment identifier subscript subscript subscript subscript attribute identifier identifier identifier string string_start string_content string_end identifier string string_start string_content string_end expression_statement assignment identifier call identifier argument_list list identifier identifier expression_statement assignment identifier call identifier argument_list list identifier identifier expression_statement assignment identifier binary_operator identifier integer expression_statement assignment identifier list identifier identifier identifier else_clause block expression_statement assignment identifier identifier return_statement identifier | return the curr_frag at a lower resolution |
def yara_match(file_path, rules):
print('New Extracted File: {:s}'.format(file_path))
print('Mathes:')
pprint(rules.match(file_path)) | module function_definition identifier parameters identifier identifier block expression_statement call identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier expression_statement call identifier argument_list string string_start string_content string_end expression_statement call identifier argument_list call attribute identifier identifier argument_list identifier | Callback for a newly extracted file |
def _on_changed(self):
page = self._get_page()
if not page.flag_autosave:
page.flag_changed = True
self._update_gui_text_tabs() | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list if_statement not_operator attribute identifier identifier block expression_statement assignment attribute identifier identifier true expression_statement call attribute identifier identifier argument_list | Slot for changed events |
def _add_parent_cnt(self, hdr, goobj, c2ps):
if goobj.id in c2ps:
parents = c2ps[goobj.id]
if 'prt_pcnt' in self.present or parents and len(goobj.parents) != len(parents):
assert len(goobj.parents) == len(set(goobj.parents))
hdr.append("p{N}".format(N=len(set(goobj.parents)))) | module function_definition identifier parameters identifier identifier identifier identifier block if_statement comparison_operator attribute identifier identifier identifier block expression_statement assignment identifier subscript identifier attribute identifier identifier if_statement boolean_operator comparison_operator string string_start string_content string_end attribute identifier identifier boolean_operator identifier comparison_operator call identifier argument_list attribute identifier identifier call identifier argument_list identifier block assert_statement comparison_operator call identifier argument_list attribute identifier identifier call identifier argument_list call identifier argument_list attribute identifier identifier expression_statement call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list keyword_argument identifier call identifier argument_list call identifier argument_list attribute identifier identifier | Add the parent count to the GO term box for if not all parents are plotted. |
def use_comparative_hierarchy_view(self):
self._hierarchy_view = COMPARATIVE
for session in self._get_provider_sessions():
try:
session.use_comparative_hierarchy_view()
except AttributeError:
pass | module function_definition identifier parameters identifier block expression_statement assignment attribute identifier identifier identifier for_statement identifier call attribute identifier identifier argument_list block try_statement block expression_statement call attribute identifier identifier argument_list except_clause identifier block pass_statement | Pass through to provider HierarchyLookupSession.use_comparative_hierarchy_view |
def next_bit_address(self):
if self._current_bit_address == "":
if self._is_16bit:
return "{0}.{1}".format(
self.next_address(),
"00")
return "{0}.{1}".format(
self.next_address(),
"0")
if self._is_16bit:
bool_half = int(self._current_bit_address.split(".")[1])
if bool_half < 4:
register_half = self._current_bit_address.split(".")[0]
return "{0}.{1}".format(
register_half,
pad_zeroes(str(bool_half + 1), 2))
self.move_to_next_address(self._size_of_current_register_address)
return "{0}.{1}".format(
self.next_address(),
"00")
bool_half = int(self._current_bit_address.split(".")[1])
if bool_half < 3:
register_half = self._current_bit_address.split(".")[0]
return "{0}.{1}".format(
register_half,
bool_half + 1)
self.move_to_next_address(self._size_of_current_register_address)
return "{0}.{1}".format(
self.next_address(),
"0") | module function_definition identifier parameters identifier block if_statement comparison_operator attribute identifier identifier string string_start string_end block if_statement attribute identifier identifier block return_statement call attribute string string_start string_content string_end identifier argument_list call attribute identifier identifier argument_list string string_start string_content string_end return_statement call attribute string string_start string_content string_end identifier argument_list call attribute identifier identifier argument_list string string_start string_content string_end if_statement attribute identifier identifier block expression_statement assignment identifier call identifier argument_list subscript call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end integer if_statement comparison_operator identifier integer block expression_statement assignment identifier subscript call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end integer return_statement call attribute string string_start string_content string_end identifier argument_list identifier call identifier argument_list call identifier argument_list binary_operator identifier integer integer expression_statement call attribute identifier identifier argument_list attribute identifier identifier return_statement call attribute string string_start string_content string_end identifier argument_list call attribute identifier identifier argument_list string string_start string_content string_end expression_statement assignment identifier call identifier argument_list subscript call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end integer if_statement comparison_operator identifier integer block expression_statement assignment identifier subscript call attribute attribute identifier identifier identifier argument_list string string_start string_content string_end integer return_statement call attribute string string_start string_content string_end identifier argument_list identifier binary_operator identifier integer expression_statement call attribute identifier identifier argument_list attribute identifier identifier return_statement call attribute string string_start string_content string_end identifier argument_list call attribute identifier identifier argument_list string string_start string_content string_end | Gets the next boolean address |
def clamp(self, clampVal):
if self.x > clampVal:
self.x = clampVal
if self.y > clampVal:
self.y = clampVal
if self.z > clampVal:
self.z = clampVal
if self.w > clampVal:
self.w = clampVal | module function_definition identifier parameters identifier identifier block if_statement comparison_operator attribute identifier identifier identifier block expression_statement assignment attribute identifier identifier identifier if_statement comparison_operator attribute identifier identifier identifier block expression_statement assignment attribute identifier identifier identifier if_statement comparison_operator attribute identifier identifier identifier block expression_statement assignment attribute identifier identifier identifier if_statement comparison_operator attribute identifier identifier identifier block expression_statement assignment attribute identifier identifier identifier | Clamps all the components in the vector to the specified clampVal. |
def qual(obj):
return u'{}.{}'.format(obj.__class__.__module__, obj.__class__.__name__) | module function_definition identifier parameters identifier block return_statement call attribute string string_start string_content string_end identifier argument_list attribute attribute identifier identifier identifier attribute attribute identifier identifier identifier | Return fully qualified name of a class. |
def writeString(self, u):
s = self.context.getBytesForString(u)
self.writeBytes(s) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list identifier expression_statement call attribute identifier identifier argument_list identifier | Write a unicode to the data stream. |
def write_pidfile(pidfile):
pid = os.getpid()
if pidfile:
with open(pidfile, "w", encoding="utf-8") as fobj:
fobj.write(six.u(str(pid)))
return pid | module function_definition identifier parameters identifier block expression_statement assignment identifier call attribute identifier identifier argument_list if_statement identifier block with_statement with_clause with_item as_pattern call identifier argument_list identifier string string_start string_content string_end keyword_argument identifier string string_start string_content string_end as_pattern_target identifier block expression_statement call attribute identifier identifier argument_list call attribute identifier identifier argument_list call identifier argument_list identifier return_statement identifier | write current pid to pidfile. |
def _get_temp(self, content):
temp = None
for line in content.splitlines():
if not temp:
match = TEMP_NEEDLE.match(line)
if match:
temp = match.group(1).strip()
continue
else:
match = TEMP_END_NEEDLE.match(line)
if match:
return temp
raise IndexError(self.path) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier none for_statement identifier call attribute identifier identifier argument_list block if_statement not_operator identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement identifier block expression_statement assignment identifier call attribute call attribute identifier identifier argument_list integer identifier argument_list continue_statement else_clause block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement identifier block return_statement identifier raise_statement call identifier argument_list attribute identifier identifier | Get the string that points to a specific base16 scheme. |
def update_records(self, domain, records):
if not isinstance(records, list):
raise TypeError("Expected records of type list")
uri = "/domains/%s/records" % utils.get_id(domain)
resp, resp_body = self._async_call(uri, method="PUT",
body={"records": records},
error_class=exc.DomainRecordUpdateFailed, has_response=False)
return resp_body | module function_definition identifier parameters identifier identifier identifier block if_statement not_operator call identifier argument_list identifier identifier block raise_statement call identifier argument_list string string_start string_content string_end expression_statement assignment identifier binary_operator string string_start string_content string_end call attribute identifier identifier argument_list identifier expression_statement assignment pattern_list identifier identifier call attribute identifier identifier argument_list identifier keyword_argument identifier string string_start string_content string_end keyword_argument identifier dictionary pair string string_start string_content string_end identifier keyword_argument identifier attribute identifier identifier keyword_argument identifier false return_statement identifier | Modifies an existing records for a domain. |
def to_element(self, root_name=None):
if not root_name:
root_name = self.nodename
elem = ElementTreeBuilder.Element(root_name)
for attrname in self.serializable_attributes():
try:
value = self.__dict__[attrname]
except KeyError:
continue
if attrname in self.xml_attribute_attributes:
elem.attrib[attrname] = six.text_type(value)
else:
sub_elem = self.element_for_value(attrname, value)
elem.append(sub_elem)
return elem | module function_definition identifier parameters identifier default_parameter identifier none block if_statement not_operator identifier block expression_statement assignment identifier attribute identifier identifier expression_statement assignment identifier call attribute identifier identifier argument_list identifier for_statement identifier call attribute identifier identifier argument_list block try_statement block expression_statement assignment identifier subscript attribute identifier identifier identifier except_clause identifier block continue_statement if_statement comparison_operator identifier attribute identifier identifier block expression_statement assignment subscript attribute identifier identifier identifier call attribute identifier identifier argument_list identifier else_clause block expression_statement assignment identifier call attribute identifier identifier argument_list identifier identifier expression_statement call attribute identifier identifier argument_list identifier return_statement identifier | Serialize this `Resource` instance to an XML element. |
def check_uniqe(self, obj_class, error_msg=_('Must be unique'), **kwargs):
if obj_class.objects.filter(**kwargs).exclude(pk=self.instance.pk):
raise forms.ValidationError(error_msg) | module function_definition identifier parameters identifier identifier default_parameter identifier call identifier argument_list string string_start string_content string_end dictionary_splat_pattern identifier block if_statement call attribute call attribute attribute identifier identifier identifier argument_list dictionary_splat identifier identifier argument_list keyword_argument identifier attribute attribute identifier identifier identifier block raise_statement call attribute identifier identifier argument_list identifier | check if this object is unique |
def remove(self, spec_or_id, multi=True, *args, **kwargs):
if multi:
return self.delete_many(spec_or_id)
return self.delete_one(spec_or_id) | module function_definition identifier parameters identifier identifier default_parameter identifier true list_splat_pattern identifier dictionary_splat_pattern identifier block if_statement identifier block return_statement call attribute identifier identifier argument_list identifier return_statement call attribute identifier identifier argument_list identifier | Backwards compatibility with remove |
def add_button(self, name, button_class=wtf_fields.SubmitField, **options):
self._buttons[name] = button_class(**options) | module function_definition identifier parameters identifier identifier default_parameter identifier attribute identifier identifier dictionary_splat_pattern identifier block expression_statement assignment subscript attribute identifier identifier identifier call identifier argument_list dictionary_splat identifier | Adds a button to the form. |
def _parse_sacct(sacct_jobs: List[dict], jobs_count: int=None):
failed_jobs = sacct_api.filter_jobs(sacct_jobs, failed=True)
completed_jobs = [job for job in sacct_jobs if job['is_completed']]
last_job_end = completed_jobs[-1]['end'] if len(completed_jobs) > 0 else None
data = {
'jobs': jobs_count,
'completed_jobs': len(completed_jobs),
'progress': (len(completed_jobs) / jobs_count) if jobs_count else None,
'failed_jobs': [{
'slurm_id': job['id'],
'started_at': job['start'],
'elapsed': job['elapsed'],
'status': job['state'].lower(),
'name': job['step'],
'context': job['context'],
} for job in failed_jobs]
}
return data, last_job_end | module function_definition identifier parameters typed_parameter identifier type generic_type identifier type_parameter type identifier typed_default_parameter identifier type identifier none block expression_statement assignment identifier call attribute identifier identifier argument_list identifier keyword_argument identifier true expression_statement assignment identifier list_comprehension identifier for_in_clause identifier identifier if_clause subscript identifier string string_start string_content string_end expression_statement assignment identifier conditional_expression subscript subscript identifier unary_operator integer string string_start string_content string_end comparison_operator call identifier argument_list identifier integer none expression_statement assignment identifier dictionary pair string string_start string_content string_end identifier pair string string_start string_content string_end call identifier argument_list identifier pair string string_start string_content string_end conditional_expression parenthesized_expression binary_operator call identifier argument_list identifier identifier identifier none pair string string_start string_content string_end list_comprehension dictionary pair string string_start string_content string_end subscript identifier string string_start string_content string_end pair string string_start string_content string_end subscript identifier string string_start string_content string_end pair string string_start string_content string_end subscript identifier string string_start string_content string_end pair string string_start string_content string_end call attribute subscript identifier string string_start string_content string_end identifier argument_list pair string string_start string_content string_end subscript identifier string string_start string_content string_end pair string string_start string_content string_end subscript identifier string string_start string_content string_end for_in_clause identifier identifier return_statement expression_list identifier identifier | Parse out info from Sacct log. |
def net_recv(ws, conn):
in_data = conn.recv(RECEIVE_BYTES)
if not in_data:
print('Received 0 bytes (connection closed)')
ws.receive_data(None)
else:
print('Received {} bytes'.format(len(in_data)))
ws.receive_data(in_data) | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier if_statement not_operator identifier block expression_statement call identifier argument_list string string_start string_content string_end expression_statement call attribute identifier identifier argument_list none else_clause block expression_statement call identifier argument_list call attribute string string_start string_content string_end identifier argument_list call identifier argument_list identifier expression_statement call attribute identifier identifier argument_list identifier | Read pending data from network into websocket. |
def userinfo_json(request, user_id):
data = {'first_name': '',
'last_name': '',
'email': '',
'slug': '',
'bio': '',
'phone': '',
'is_active': False}
try:
member = StaffMember.objects.get(pk=user_id)
for key in data.keys():
if hasattr(member, key):
data[key] = getattr(member, key, '')
except StaffMember.DoesNotExist:
pass
return HttpResponse(json.dumps(data),
mimetype='application/json') | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier dictionary pair string string_start string_content string_end string string_start string_end pair string string_start string_content string_end string string_start string_end pair string string_start string_content string_end string string_start string_end pair string string_start string_content string_end string string_start string_end pair string string_start string_content string_end string string_start string_end pair string string_start string_content string_end string string_start string_end pair string string_start string_content string_end false try_statement block expression_statement assignment identifier call attribute attribute identifier identifier identifier argument_list keyword_argument identifier identifier for_statement identifier call attribute identifier identifier argument_list block if_statement call identifier argument_list identifier identifier block expression_statement assignment subscript identifier identifier call identifier argument_list identifier identifier string string_start string_end except_clause attribute identifier identifier block pass_statement return_statement call identifier argument_list call attribute identifier identifier argument_list identifier keyword_argument identifier string string_start string_content string_end | Return the user's information in a json object |
def unique_string(length=UUID_LENGTH):
string = str(uuid4()) * int(math.ceil(length / float(UUID_LENGTH)))
return string[:length] if length else string | module function_definition identifier parameters default_parameter identifier identifier block expression_statement assignment identifier binary_operator call identifier argument_list call identifier argument_list call identifier argument_list call attribute identifier identifier argument_list binary_operator identifier call identifier argument_list identifier return_statement conditional_expression subscript identifier slice identifier identifier identifier | Generate a unique string |
def local_session(factory):
factory_region = getattr(factory, 'region', 'global')
s = getattr(CONN_CACHE, factory_region, {}).get('session')
t = getattr(CONN_CACHE, factory_region, {}).get('time')
n = time.time()
if s is not None and t + (60 * 45) > n:
return s
s = factory()
setattr(CONN_CACHE, factory_region, {'session': s, 'time': n})
return s | module function_definition identifier parameters identifier block expression_statement assignment identifier call identifier argument_list identifier string string_start string_content string_end string string_start string_content string_end expression_statement assignment identifier call attribute call identifier argument_list identifier identifier dictionary identifier argument_list string string_start string_content string_end expression_statement assignment identifier call attribute call identifier argument_list identifier identifier dictionary identifier argument_list string string_start string_content string_end expression_statement assignment identifier call attribute identifier identifier argument_list if_statement boolean_operator comparison_operator identifier none comparison_operator binary_operator identifier parenthesized_expression binary_operator integer integer identifier block return_statement identifier expression_statement assignment identifier call identifier argument_list expression_statement call identifier argument_list identifier identifier dictionary pair string string_start string_content string_end identifier pair string string_start string_content string_end identifier return_statement identifier | Cache a session thread local for up to 45m |
def _get_site_amplification_term(self, C, vs30):
f_s = np.zeros_like(vs30)
idx = np.logical_and(vs30 < 800.0, vs30 >= 360.0)
f_s[idx] = C["eB"]
idx = np.logical_and(vs30 < 360.0, vs30 >= 180.0)
f_s[idx] = C["eC"]
idx = vs30 < 180.0
f_s[idx] = C["eD"]
return f_s | module function_definition identifier parameters identifier identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier expression_statement assignment identifier call attribute identifier identifier argument_list comparison_operator identifier float comparison_operator identifier float expression_statement assignment subscript identifier identifier subscript identifier string string_start string_content string_end expression_statement assignment identifier call attribute identifier identifier argument_list comparison_operator identifier float comparison_operator identifier float expression_statement assignment subscript identifier identifier subscript identifier string string_start string_content string_end expression_statement assignment identifier comparison_operator identifier float expression_statement assignment subscript identifier identifier subscript identifier string string_start string_content string_end return_statement identifier | Returns the site amplification given Eurocode 8 site classification |
def add_permission(self, role, name):
if self.has_permission(role, name):
return True
targetGroup = AuthGroup.objects(role=role, creator=self.client).first()
if not targetGroup:
return False
permission = AuthPermission.objects(name=name).update(
add_to_set__groups=[targetGroup], creator=self.client, upsert=True
)
return True | module function_definition identifier parameters identifier identifier identifier block if_statement call attribute identifier identifier argument_list identifier identifier block return_statement true expression_statement assignment identifier call attribute call attribute identifier identifier argument_list keyword_argument identifier identifier keyword_argument identifier attribute identifier identifier identifier argument_list if_statement not_operator identifier block return_statement false expression_statement assignment identifier call attribute call attribute identifier identifier argument_list keyword_argument identifier identifier identifier argument_list keyword_argument identifier list identifier keyword_argument identifier attribute identifier identifier keyword_argument identifier true return_statement true | authorize a group for something |
def print_user(self, user):
status = "active"
token = user.token
if token in ['finished', 'revoked']:
status = token
if token is None:
token = ''
subid = "%s\t%s[%s]" %(user.id, token, status)
print(subid)
return subid | module function_definition identifier parameters identifier identifier block expression_statement assignment identifier string string_start string_content string_end expression_statement assignment identifier attribute identifier identifier if_statement comparison_operator identifier list string string_start string_content string_end string string_start string_content string_end block expression_statement assignment identifier identifier if_statement comparison_operator identifier none block expression_statement assignment identifier string string_start string_end expression_statement assignment identifier binary_operator string string_start string_content escape_sequence string_end tuple attribute identifier identifier identifier identifier expression_statement call identifier argument_list identifier return_statement identifier | print a relational database user |
def _get_item_class(self, url):
if '/layers/' in url:
return Layer
elif '/tables/' in url:
return Table
elif '/sets/' in url:
return Set
else:
raise NotImplementedError("No support for catalog results of type %s" % url) | module function_definition identifier parameters identifier identifier block if_statement comparison_operator string string_start string_content string_end identifier block return_statement identifier elif_clause comparison_operator string string_start string_content string_end identifier block return_statement identifier elif_clause comparison_operator string string_start string_content string_end identifier block return_statement identifier else_clause block raise_statement call identifier argument_list binary_operator string string_start string_content string_end identifier | Return the model class matching a URL |
def _WriteAttributes(self):
if "w" not in self.mode:
return
if self.urn is None:
raise ValueError("Storing of anonymous AFF4 objects not supported.")
to_set = {}
for attribute_name, value_array in iteritems(self.new_attributes):
to_set_list = to_set.setdefault(attribute_name, [])
for value in value_array:
to_set_list.append((value.SerializeToDataStore(), value.age))
if self._dirty:
if self._new_version:
to_set[self.Schema.TYPE] = [
(utils.SmartUnicode(self.__class__.__name__),
rdfvalue.RDFDatetime.Now())
]
add_child_index = self.Schema.ADD_CHILD_INDEX
if self.object_exists:
add_child_index = False
FACTORY.SetAttributes(
self.urn,
to_set,
self._to_delete,
add_child_index=add_child_index,
mutation_pool=self.mutation_pool) | module function_definition identifier parameters identifier block if_statement comparison_operator string string_start string_content string_end attribute identifier identifier block return_statement if_statement comparison_operator attribute identifier identifier none block raise_statement call identifier argument_list string string_start string_content string_end expression_statement assignment identifier dictionary for_statement pattern_list identifier identifier call identifier argument_list attribute identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier list for_statement identifier identifier block expression_statement call attribute identifier identifier argument_list tuple call attribute identifier identifier argument_list attribute identifier identifier if_statement attribute identifier identifier block if_statement attribute identifier identifier block expression_statement assignment subscript identifier attribute attribute identifier identifier identifier list tuple call attribute identifier identifier argument_list attribute attribute identifier identifier identifier call attribute attribute identifier identifier identifier argument_list expression_statement assignment identifier attribute attribute identifier identifier identifier if_statement attribute identifier identifier block expression_statement assignment identifier false expression_statement call attribute identifier identifier argument_list attribute identifier identifier identifier attribute identifier identifier keyword_argument identifier identifier keyword_argument identifier attribute identifier identifier | Write the dirty attributes to the data store. |
def _remove_lead_trail_false(bool_list):
for i in (0, -1):
while bool_list and not bool_list[i]:
bool_list.pop(i)
return bool_list | module function_definition identifier parameters identifier block for_statement identifier tuple integer unary_operator integer block while_statement boolean_operator identifier not_operator subscript identifier identifier block expression_statement call attribute identifier identifier argument_list identifier return_statement identifier | Remove leading and trailing false's from a list |
def create_shield_layer(shield, hashcode):
return pgnreader.parse_pagan_file(('%s%spgn%s' % (PACKAGE_DIR, os.sep, os.sep)) + shield + '.pgn', hashcode, sym=False, invert=False) | module function_definition identifier parameters identifier identifier block return_statement call attribute identifier identifier argument_list binary_operator binary_operator parenthesized_expression binary_operator string string_start string_content string_end tuple identifier attribute identifier identifier attribute identifier identifier identifier string string_start string_content string_end identifier keyword_argument identifier false keyword_argument identifier false | Creates the layer for shields. |
def isSequence(arg):
if hasattr(arg, "strip"):
return False
if hasattr(arg, "__getslice__"):
return True
if hasattr(arg, "__iter__"):
return True
return False | module function_definition identifier parameters identifier block if_statement call identifier argument_list identifier string string_start string_content string_end block return_statement false if_statement call identifier argument_list identifier string string_start string_content string_end block return_statement true if_statement call identifier argument_list identifier string string_start string_content string_end block return_statement true return_statement false | Check if input is iterable. |
def isVisible(self, instance, mode='view', default="visible", field=None):
vis_dic = getattr(aq_base(self), 'visible', _marker)
state = default
if vis_dic is _marker:
return state
if type(vis_dic) is DictType:
state = vis_dic.get(mode, state)
elif not vis_dic:
state = 'invisible'
elif vis_dic < 0:
state = 'hidden'
if not field:
return state
adapters = sorted(getAdapters([instance], IATWidgetVisibility),
key=lambda adapter: getattr(adapter[1], "sort", 1000),
reverse=True)
for adapter_name, adapter in adapters:
if field.getName() not in getattr(adapter, "field_names", []):
continue
adapter_state = adapter(instance, mode, field, state)
adapter_name = adapter.__class__.__name__
logger.info("IATWidgetVisibility rule {} for {}.{} ({}): {} -> {}"
.format(adapter_name, instance.id, field.getName(), mode, state,
adapter_state))
if adapter_state == state:
continue
return adapter_state
return state | module function_definition identifier parameters identifier identifier default_parameter identifier string string_start string_content string_end default_parameter identifier string string_start string_content string_end default_parameter identifier none block expression_statement assignment identifier call identifier argument_list call identifier argument_list identifier string string_start string_content string_end identifier expression_statement assignment identifier identifier if_statement comparison_operator identifier identifier block return_statement identifier if_statement comparison_operator call identifier argument_list identifier identifier block expression_statement assignment identifier call attribute identifier identifier argument_list identifier identifier elif_clause not_operator identifier block expression_statement assignment identifier string string_start string_content string_end elif_clause comparison_operator identifier integer block expression_statement assignment identifier string string_start string_content string_end if_statement not_operator identifier block return_statement identifier expression_statement assignment identifier call identifier argument_list call identifier argument_list list identifier identifier keyword_argument identifier lambda lambda_parameters identifier call identifier argument_list subscript identifier integer string string_start string_content string_end integer keyword_argument identifier true for_statement pattern_list identifier identifier identifier block if_statement comparison_operator call attribute identifier identifier argument_list call identifier argument_list identifier string string_start string_content string_end list block continue_statement expression_statement assignment identifier call identifier argument_list identifier identifier identifier identifier expression_statement assignment identifier attribute attribute identifier identifier identifier expression_statement call attribute identifier identifier argument_list call attribute string string_start string_content string_end identifier argument_list identifier attribute identifier identifier call attribute identifier identifier argument_list identifier identifier identifier if_statement comparison_operator identifier identifier block continue_statement return_statement identifier return_statement identifier | decide if a field is visible in a given mode -> 'state'. |
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