Dataset Viewer
code
stringlengths 81
3.79k
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def apply_option(self, cmd, option, active=True):
return re.sub(r'{{{}\:(?P<option>[^}}]*)}}'.format(option),
'\g<option>' if active else '', cmd)
|
def make_local_static_report_files(self):
for static, pkgdir in self.STATIC_FILES:
shutil.copyfile(
data_filename(static, pkgdir),
os.path.join(self.directory, static)
)
if self.extra_css:
shutil.copyfile(
self.config.extra_css,
os.path.join(self.directory, self.extra_css)
)
|
def format_filesize(size):
for suffix in ("bytes", "KB", "MB", "GB", "TB"):
if size < 1024.0:
if suffix in ("GB", "TB"):
return "{0:3.2f} {1}".format(size, suffix)
else:
return "{0:3.1f} {1}".format(size, suffix)
size /= 1024.0
|
def add_lexicon_ref(self, lrid, name, lrtype, url, lexicon_id,
lexicon_name, datcat_id=None, datcat_name=None):
self.lexicon_refs[lrid] = {
'LEX_REF_ID': lrid,
'NAME': name,
'TYPE': lrtype,
'URL': url,
'LEXICON_ID': lexicon_id,
'LEXICON_NAME': lexicon_name,
'DATCAT_ID': datcat_id,
'DATCAT_NAME': datcat_name
}
|
def invert_hash(self, tok_hash):
return [tok_encoded.decode('utf8')
for (_, tok_encoded) in
self.client.scan_keys(HASH_KEYWORD_INDEX_TABLE,
((tok_hash,), (tok_hash,)))]
|
def find_unique_points(explored_parameters):
ranges = [param.f_get_range(copy=False) for param in explored_parameters]
zipped_tuples = list(zip(*ranges))
try:
unique_elements = OrderedDict()
for idx, val_tuple in enumerate(zipped_tuples):
if val_tuple not in unique_elements:
unique_elements[val_tuple] = []
unique_elements[val_tuple].append(idx)
return list(unique_elements.items())
except TypeError:
logger = logging.getLogger('pypet.find_unique')
logger.error('Your parameter entries could not be hashed, '
'now I am sorting slowly in O(N**2).')
unique_elements = []
for idx, val_tuple in enumerate(zipped_tuples):
matches = False
for added_tuple, pos_list in unique_elements:
matches = True
for idx2, val in enumerate(added_tuple):
if not explored_parameters[idx2]._equal_values(val_tuple[idx2], val):
matches = False
break
if matches:
pos_list.append(idx)
break
if not matches:
unique_elements.append((val_tuple, [idx]))
return unique_elements
|
def unfinished(cls):
return [
cls.NONE,
cls.SCHEDULED,
cls.QUEUED,
cls.RUNNING,
cls.SHUTDOWN,
cls.UP_FOR_RETRY,
cls.UP_FOR_RESCHEDULE
]
|
def merge_left(field, local_task, remote_issue, hamming=False):
local_field = local_task.get(field, [])
remote_field = remote_issue.get(field, [])
if field not in local_task:
local_task[field] = []
new_count = 0
for remote in remote_field:
for local in local_field:
if (
(
hamming
and get_annotation_hamming_distance(remote, local) == 0
)
or (
remote == local
)
):
break
else:
log.debug("%s not found in %r" % (remote, local_field))
local_task[field].append(remote)
new_count += 1
if new_count > 0:
log.debug('Added %s new values to %s (total: %s)' % (
new_count, field, len(local_task[field]),))
|
def images(self, query=None):
from sregistry.database.models import Collection, Container
rows = []
if query is not None:
like = "%" + query + "%"
containers = Container.query.filter(or_(Container.name == query,
Container.tag.like(like),
Container.uri.like(like),
Container.name.like(like))).all()
else:
containers = Container.query.all()
if len(containers) > 0:
message = " [date] [client]\t[uri]"
bot.custom(prefix='Containers:', message=message, color="RED")
for c in containers:
uri = c.get_uri()
created_at = c.created_at.strftime('%B %d, %Y')
rows.append([created_at, " [%s]" %c.client, uri])
bot.table(rows)
return containers
|
def set_max_in_flight(self, max_in_flight):
assert isinstance(max_in_flight, int)
self.max_in_flight = max_in_flight
if max_in_flight == 0:
for conn in itervalues(self.conns):
if conn.rdy > 0:
logger.debug('[%s:%s] rdy: %d -> 0', conn.id, self.name, conn.rdy)
self._send_rdy(conn, 0)
self.total_rdy = 0
else:
self.need_rdy_redistributed = True
self._redistribute_rdy_state()
|
def _store(self, lines, buffer=None, store='source'):
if buffer is None:
buffer = self._buffer
if lines.endswith('\n'):
buffer.append(lines)
else:
buffer.append(lines+'\n')
setattr(self, store, self._set_source(buffer))
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def _ast_option_group_to_code(self, option_group, **kwargs):
lines = ["option("]
lines.extend(self._indent(self._ast_to_code(option_group.expression)))
lines.append(")")
return lines
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def add(symbol: str, date, value, currency: str):
symbol = symbol.upper()
currency = currency.upper()
app = PriceDbApplication()
price = PriceModel()
price.symbol.parse(symbol)
price.datum.from_iso_date_string(date)
price.value = Decimal(value)
price.currency = currency
app.add_price(price)
app.save()
click.echo("Price added.")
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def _close(self):
if self.connection:
with self.wrap_database_errors:
self.connection.client.close()
|
def _get_byte_parser(self):
if not self._byte_parser:
self._byte_parser = \
ByteParser(text=self.text, filename=self.filename)
return self._byte_parser
|
def _configureShortcuts(self):
self._upShortcut = QtGui.QShortcut(
QtGui.QKeySequence('Backspace'), self
)
self._upShortcut.setAutoRepeat(False)
self._upShortcut.activated.connect(self._onNavigateUpButtonClicked)
|
def update_message_dict(message_dict,action):
global g_ok_java_messages
allKeys = g_ok_java_messages.keys()
for key in message_dict.keys():
if key in allKeys:
for message in message_dict[key]:
if action == 1:
if message not in g_ok_java_messages[key]:
g_ok_java_messages[key].append(message)
if action == 2:
if message in g_ok_java_messages[key]:
g_ok_java_messages[key].remove(message)
else:
if action == 1:
g_ok_java_messages[key] = message_dict[key]
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def _addHdlProcToRun(self, trigger: SimSignal, proc) -> None:
if not self._applyValPlaned:
self._scheduleApplyValues()
if isEvDependentOn(trigger, proc):
if self.now == 0:
return
self._seqProcsToRun.append(proc)
else:
self._combProcsToRun.append(proc)
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def resolve_backend_name(name, backends, deprecated, aliased):
available = [backend.name() for backend in backends]
resolved_name = deprecated.get(name, aliased.get(name, name))
if isinstance(resolved_name, list):
resolved_name = next((b for b in resolved_name if b in available), "")
if resolved_name not in available:
raise LookupError("backend '{}' not found.".format(name))
if name in deprecated:
logger.warning("WARNING: '%s' is deprecated. Use '%s'.", name, resolved_name)
return resolved_name
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def _rewrite_insert_nothing(self, sql, params, returning):
conflict_target = self._build_conflict_target()
where_clause = ' AND '.join([
'{0} = %s'.format(self._format_field_name(field_name))
for field_name in self.query.conflict_target
])
where_clause_params = [
self._format_field_value(field_name)
for field_name in self.query.conflict_target
]
params = params + tuple(where_clause_params)
return (
(
'WITH insdata AS ('
'{insert} ON CONFLICT {conflict_target} DO UPDATE'
' SET {pk_column} = NULL WHERE FALSE RETURNING {returning})'
' SELECT * FROM insdata UNION ALL'
' SELECT {returning} FROM {table} WHERE {where_clause} LIMIT 1;'
).format(
insert=sql,
conflict_target=conflict_target,
pk_column=self.qn(self.query.model._meta.pk.column),
returning=returning,
table=self.query.objs[0]._meta.db_table,
where_clause=where_clause
),
params
)
|
def get_stores(self, search_term):
params = {'SearchText': search_term}
response = self.__get('/storefindermap/storesearch', params=params)
return Stores(response.json())
|
def list_recommendations(
self, keywords=None, max_domain_recommendations=None, custom_headers=None, raw=False, **operation_config):
parameters = models.DomainRecommendationSearchParameters(keywords=keywords, max_domain_recommendations=max_domain_recommendations)
def internal_paging(next_link=None, raw=False):
if not next_link:
url = self.list_recommendations.metadata['url']
path_format_arguments = {
'subscriptionId': self._serialize.url("self.config.subscription_id", self.config.subscription_id, 'str')
}
url = self._client.format_url(url, **path_format_arguments)
query_parameters = {}
query_parameters['api-version'] = self._serialize.query("self.api_version", self.api_version, 'str')
else:
url = next_link
query_parameters = {}
header_parameters = {}
header_parameters['Accept'] = 'application/json'
header_parameters['Content-Type'] = 'application/json; charset=utf-8'
if self.config.generate_client_request_id:
header_parameters['x-ms-client-request-id'] = str(uuid.uuid1())
if custom_headers:
header_parameters.update(custom_headers)
if self.config.accept_language is not None:
header_parameters['accept-language'] = self._serialize.header("self.config.accept_language", self.config.accept_language, 'str')
body_content = self._serialize.body(parameters, 'DomainRecommendationSearchParameters')
request = self._client.post(url, query_parameters, header_parameters, body_content)
response = self._client.send(request, stream=False, **operation_config)
if response.status_code not in [200]:
raise models.DefaultErrorResponseException(self._deserialize, response)
return response
deserialized = models.NameIdentifierPaged(internal_paging, self._deserialize.dependencies)
if raw:
header_dict = {}
client_raw_response = models.NameIdentifierPaged(internal_paging, self._deserialize.dependencies, header_dict)
return client_raw_response
return deserialized
|
def query_string(self, **params):
return SearchResult(self, self._api.get(self._href, **params))
|
def add_bias(self, name, size, mean=0, std=1):
mean = self.kwargs.get('mean_{}'.format(name), mean)
std = self.kwargs.get('std_{}'.format(name), std)
self._params.append(theano.shared(
util.random_vector(size, mean, std, rng=self.rng),
name=self._fmt(name)))
|
def ancestors(self, lhs, rhs):
def _search(node):
if node in lhs:
return True
if not node.parent:
return False
return _search(node.parent)
return [node for node in rhs if _search(node)]
|
def get_prices_on(self, on_date: str, namespace: str, symbol: str):
repo = self.get_price_repository()
query = (
repo.query.filter(dal.Price.namespace == namespace)
.filter(dal.Price.symbol == symbol)
.filter(dal.Price.date == on_date)
.order_by(dal.Price.time.desc())
)
result = query.first()
return result
|
def getEvents(self):
events = []
for json in self.conn.endpoints["self"].getEvents():
events.append(SkypeEvent.fromRaw(self, json))
return events
|
def prepare(self):
self.output_dim = 10
self.encoder = Chain(self.input_dim).stack(Dense(self.internal_layer_size, 'tanh'))
self.decoder = Chain(self.internal_layer_size).stack(Dense(self.input_dim))
self.classifier = Chain(self.internal_layer_size).stack(Dense(50, 'tanh'),
Dense(self.output_dim),
Softmax())
self.register_inner_layers(self.encoder, self.decoder, self.classifier)
self.target_input = T.ivector('target')
self.register_external_inputs(self.target_input)
|
def _set_configurations(self):
logger.debug("======================")
logger.debug("Setting configurations")
logger.debug("======================")
resources = ""
containers = ""
params = ""
manifest = ""
if self.merge_params:
params += self._get_merged_params_string()
help_list = self._get_merged_params_help()
else:
params += self._get_params_string()
help_list = self._get_params_help()
for p in self.processes:
if not p.directives:
continue
logger.debug("[{}] Adding directives: {}".format(
p.template, p.directives))
resources += self._get_resources_string(p.directives, p.pid)
containers += self._get_container_string(p.directives, p.pid)
manifest = self._get_manifest_string()
self.resources = self._render_config("resources.config", {
"process_info": resources
})
self.containers = self._render_config("containers.config", {
"container_info": containers
})
self.params = self._render_config("params.config", {
"params_info": params
})
self.manifest = self._render_config("manifest.config", {
"manifest_info": manifest
})
self.help = self._render_config("Helper.groovy", {
"nf_file": basename(self.nf_file),
"help_list": help_list,
"version": __version__,
"pipeline_name": " ".join([x.upper() for x in self.pipeline_name])
})
self.user_config = self._render_config("user.config", {})
|
def add_range(self, sequence, begin, end):
sequence.parser_tree = parsing.Range(self.value(begin).strip("'"),
self.value(end).strip("'"))
return True
|
def streams(self):
result = self.db.read(self.path, {"q": "ls"})
if result is None or result.json() is None:
return []
streams = []
for s in result.json():
strm = self[s["name"]]
strm.metadata = s
streams.append(strm)
return streams
|
def truncate_string(data, headers, max_field_width=None, **_):
return (([utils.truncate_string(v, max_field_width) for v in row] for row in data),
[utils.truncate_string(h, max_field_width) for h in headers])
|
def login(self):
if self._session is None:
self._session = requests.session()
self._session.headers.update({'User-agent': str(UserAgent().random)})
return self._post_login_page()
|
def file_read(filename):
fobj = open(filename,'r');
source = fobj.read();
fobj.close()
return source
|
def einsum_vecmul_index(gate_indices, number_of_qubits):
mat_l, mat_r, tens_lin, tens_lout = _einsum_matmul_index_helper(gate_indices,
number_of_qubits)
return "{mat_l}{mat_r}, ".format(mat_l=mat_l, mat_r=mat_r) + \
"{tens_lin}->{tens_lout}".format(tens_lin=tens_lin,
tens_lout=tens_lout)
|
def validate_widget(widget):
if not has_valid_id(widget):
raise InvalidWidget("%s must contain a valid 'id' attribute" % widget.__name__)
if not has_valid_name(widget):
raise InvalidWidget("%s must contain a valid 'name' attribute" % widget.__name__)
if not has_valid_template(widget):
raise InvalidWidget("%s must contain a valid 'template' attribute" % widget.__name__)
if not hasattr(widget, 'zones') or not widget.zones:
raise InvalidWidget("%s must be compatible with at least one zone" % widget.__name__)
|
def institute(context, institute_id, sanger_recipient, coverage_cutoff, frequency_cutoff,
display_name, remove_sanger):
adapter = context.obj['adapter']
LOG.info("Running scout update institute")
try:
adapter.update_institute(
internal_id=institute_id,
sanger_recipient=sanger_recipient,
coverage_cutoff=coverage_cutoff,
frequency_cutoff=frequency_cutoff,
display_name=display_name,
remove_sanger=remove_sanger,
)
except Exception as err:
LOG.warning(err)
context.abort()
|
def get_agency_id(relation):
op = relation.tags.get('operator')
if op:
return int(hashlib.sha256(op.encode('utf-8')).hexdigest(), 16) % 10**8
return -1
|
def writes(nb, format, **kwargs):
format = unicode(format)
if format == u'json' or format == u'ipynb':
return writes_json(nb, **kwargs)
elif format == u'py':
return writes_py(nb, **kwargs)
else:
raise NBFormatError('Unsupported format: %s' % format)
|
def f_add_config_group(self, *args, **kwargs):
return self._nn_interface._add_generic(self, type_name=CONFIG_GROUP,
group_type_name=CONFIG_GROUP,
args=args, kwargs=kwargs)
|
def _get_authorization(self, request, httpclient):
return 'WRAP access_token="' + \
self._get_token(request.host, request.path, httpclient) + '"'
|
def evaluate(self, expression, i1=None, i2=None, out=None, selection=None, delay=False):
expression = _ensure_strings_from_expressions(expression)
result = self.server._call_dataset("evaluate", self, expression=expression, i1=i1, i2=i2, selection=selection, delay=delay)
return result
|
def _get_value(self, key, func=None, split_val=None, as_boolean=False,
exception_default=None):
try:
if as_boolean:
return self.config.getboolean(key[0], key[1])
value = self.config.get(key[0], key[1])
if split_val is not None:
value = value.split(split_val)
if func is not None:
return func(value)
return value
except (KeyError, configparser.NoSectionError, configparser.NoOptionError) as e:
if exception_default is not None:
return exception_default
raise KeyError(e)
|
def get_system_cpu_times():
user, system, idle = 0, 0, 0
for cpu_time in _psutil_mswindows.get_system_cpu_times():
user += cpu_time[0]
system += cpu_time[1]
idle += cpu_time[2]
return _cputimes_ntuple(user, system, idle)
|
def _spark_fit(self, cls, Z, *args, **kwargs):
mapper = lambda X_y: super(cls, self).fit(
X_y[0], X_y[1], *args, **kwargs
)
models = Z.map(mapper)
avg = models.reduce(operator.add) / models.count()
self.__dict__.update(avg.__dict__)
return self
|
def main(sample_id, assembly_file, coverage_file, coverage_bp_file, bam_file,
opts, gsize):
min_assembly_coverage, max_contigs = opts
logger.info("Starting assembly mapping processing")
logger.info("Parsing coverage table")
coverage_info, a_cov = parse_coverage_table(coverage_file)
a_size, contig_size = get_assembly_size(assembly_file)
logger.info("Assembly processed with a total size of '{}' and coverage"
" of '{}'".format(a_size, a_cov))
logger.info("Parsing coverage per bp table")
coverage_bp_data = get_coverage_from_file(coverage_bp_file)
min_coverage = evaluate_min_coverage(min_assembly_coverage, a_cov, a_size)
filtered_assembly = "{}_filt.fasta".format(
os.path.splitext(assembly_file)[0])
filtered_bam = "filtered.bam"
logger.info("Checking filtered assembly")
if check_filtered_assembly(coverage_info, coverage_bp_data, min_coverage,
gsize, contig_size, int(max_contigs),
sample_id):
logger.info("Filtered assembly passed minimum size threshold")
logger.info("Writting filtered assembly")
filter_assembly(assembly_file, min_coverage, coverage_info,
filtered_assembly)
logger.info("Filtering BAM file according to saved contigs")
filter_bam(coverage_info, bam_file, min_coverage, filtered_bam)
else:
shutil.copy(assembly_file, filtered_assembly)
shutil.copy(bam_file, filtered_bam)
shutil.copy(bam_file + ".bai", filtered_bam + ".bai")
with open(".status", "w") as status_fh:
status_fh.write("pass")
|
def fetchmany(self, size=None):
self._check_executed()
r = self._fetch_row(size or self.arraysize)
self.rownumber = self.rownumber + len(r)
if not r:
self._warning_check()
return r
|
def find_source(self, filename):
source = None
base, ext = os.path.splitext(filename)
TRY_EXTS = {
'.py': ['.py', '.pyw'],
'.pyw': ['.pyw'],
}
try_exts = TRY_EXTS.get(ext)
if not try_exts:
return filename, None
for try_ext in try_exts:
try_filename = base + try_ext
if os.path.exists(try_filename):
return try_filename, None
source = self.coverage.file_locator.get_zip_data(try_filename)
if source:
return try_filename, source
raise NoSource("No source for code: '%s'" % filename)
|
def get_document(self, document_id, database_name=None, collection_name=None):
if document_id is None:
raise AirflowBadRequest("Cannot get a document without an id")
try:
return self.get_conn().ReadItem(
get_document_link(
self.__get_database_name(database_name),
self.__get_collection_name(collection_name),
document_id))
except HTTPFailure:
return None
|
def execute_actions(self, cwd):
self._execute_globals(cwd)
for action in self.actions:
logger.info("executing {}".format(action))
p = subprocess.Popen(action, shell=True, cwd=cwd)
p.wait()
|
def __var_find_to_py_ast(
var_name: str, ns_name: str, py_var_ctx: ast.AST
) -> GeneratedPyAST:
return GeneratedPyAST(
node=ast.Attribute(
value=ast.Call(
func=_FIND_VAR_FN_NAME,
args=[
ast.Call(
func=_NEW_SYM_FN_NAME,
args=[ast.Str(var_name)],
keywords=[ast.keyword(arg="ns", value=ast.Str(ns_name))],
)
],
keywords=[],
),
attr="value",
ctx=py_var_ctx,
)
)
|
def create_storage_account(self, service_name, description, label,
affinity_group=None, location=None,
geo_replication_enabled=None,
extended_properties=None,
account_type='Standard_GRS'):
_validate_not_none('service_name', service_name)
_validate_not_none('description', description)
_validate_not_none('label', label)
if affinity_group is None and location is None:
raise ValueError(
'location or affinity_group must be specified')
if affinity_group is not None and location is not None:
raise ValueError(
'Only one of location or affinity_group needs to be specified')
if geo_replication_enabled == False:
account_type = 'Standard_LRS'
return self._perform_post(
self._get_storage_service_path(),
_XmlSerializer.create_storage_service_input_to_xml(
service_name,
description,
label,
affinity_group,
location,
account_type,
extended_properties),
as_async=True)
|
def set_selection(self, selection, name="default", executor=None):
def create(current):
return selection
self._selection(create, name, executor=executor, execute_fully=True)
|
def set_resolved_name(self, ref: dict, type_name2solve: TypeName,
type_name_ref: TypeName):
if self.resolution[type_name2solve.value] is None:
self.resolution[type_name2solve.value] = ref[type_name_ref.value]
|
def format_data(self, data, scale=True):
if len(self.analytes) == 1:
d = nominal_values(data[self.analytes[0]])
ds = np.array(list(zip(d, np.zeros(len(d)))))
else:
d = [nominal_values(data[a]) for a in self.analytes]
ds = np.vstack(d).T
finite = np.isfinite(ds).sum(1) == ds.shape[1]
sampled = np.arange(data[self.analytes[0]].size)[finite]
ds = ds[finite]
if scale:
ds = self.scaler.transform(ds)
return ds, sampled
|
def _referer(self, extension):
iana_record = self.lookup.whois(
PyFunceble.CONFIGURATION["iana_whois_server"], "hello.%s" % extension
)
if iana_record and "refer" in iana_record:
regex_referer = r"(?s)refer\:\s+([a-zA-Z0-9._-]+)\n"
matched = Regex(
iana_record, regex_referer, return_data=True, group=1
).match()
if matched:
return matched
if extension in self.manual_server:
return self.manual_server[extension]
return None
|
def shape_rb_data(raw_rb):
rb_data = []
rb_data.append(np.mean(raw_rb, 0))
rb_data.append(np.std(raw_rb, 0))
return rb_data
|
def update_function(self, name, body, update_mask):
response = self.get_conn().projects().locations().functions().patch(
updateMask=",".join(update_mask),
name=name,
body=body
).execute(num_retries=self.num_retries)
operation_name = response["name"]
self._wait_for_operation_to_complete(operation_name=operation_name)
|
def boolean(ctx, obj):
if hasattr(obj, 'compute'):
obj = next(seq.compute(ctx), '')
else:
obj = seq
yield next(to_boolean(obj), '')
|
def expects_none(options):
if any(options.get(key) is not None for key in ["count", "maximum", "minimum", "between"]):
return matches_count(0, options)
else:
return False
|
def __early_downsample(y, sr, hop_length, res_type, n_octaves,
nyquist, filter_cutoff, scale):
downsample_count = __early_downsample_count(nyquist, filter_cutoff,
hop_length, n_octaves)
if downsample_count > 0 and res_type == 'kaiser_fast':
downsample_factor = 2**(downsample_count)
hop_length //= downsample_factor
if len(y) < downsample_factor:
raise ParameterError('Input signal length={:d} is too short for '
'{:d}-octave CQT'.format(len(y), n_octaves))
new_sr = sr / float(downsample_factor)
y = audio.resample(y, sr, new_sr,
res_type=res_type,
scale=True)
if not scale:
y *= np.sqrt(downsample_factor)
sr = new_sr
return y, sr, hop_length
|
def log_parser(self):
size_stamp = os.path.getsize(self.log_file)
self.log_retry = 0
if size_stamp and size_stamp == self.log_sizestamp:
return
else:
logger.debug("Updating log size stamp to: {}".format(size_stamp))
self.log_sizestamp = size_stamp
r = ".* (.*) \[.*\].*\[(.*)\].*process > (.*) \((.*)\).*"
with open(self.log_file) as fh:
for line in fh:
if "Submitted process >" in line or \
"Re-submitted process >" in line or \
"Cached process >" in line:
m = re.match(r, line)
if not m:
continue
time_start = m.group(1)
workdir = m.group(2)
process = m.group(3)
tag = m.group(4)
if time_start + tag not in self.stored_log_ids:
self.stored_log_ids.append(time_start + tag)
else:
continue
if process not in self.processes:
continue
p = self.processes[process]
if tag in list(p["finished"]) + list(p["retry"]):
continue
if tag in list(p["failed"]) and \
"Re-submitted process >" in line:
p["retry"].add(tag)
self.send = True
continue
p["barrier"] = "R"
if tag not in p["submitted"]:
p["submitted"].add(tag)
if tag not in self.process_tags[process]:
self.process_tags[process][tag] = {
"workdir": self._expand_path(workdir),
"start": time_start
}
self.send = True
elif not self.process_tags[process][tag]["start"]:
self.process_tags[process][tag]["start"] = time_start
self.send = True
self._update_pipeline_status()
|
def _remove_exploration(self):
for param in self._explored_parameters.values():
if param._stored:
try:
self.f_delete_item(param)
except Exception:
self._logger.exception('Could not delete expanded parameter `%s` '
'from disk.' % param.v_full_name)
|
def setup_platform(hass, config, add_entities, discovery_info=None):
host = config.get(CONF_HOST)
token = config.get(CONF_ACCESS_TOKEN)
name = config.get(CONF_NAME)
volume_step = config.get(CONF_VOLUME_STEP)
device_type = config.get(CONF_DEVICE_CLASS)
device = VizioDevice(host, token, name, volume_step, device_type)
if device.validate_setup() is False:
_LOGGER.error("Failed to set up Vizio platform, "
"please check if host and API key are correct")
return
elif (token is None or token == "") and device_type == "tv":
_LOGGER.error("Failed to set up Vizio platform, "
"if device_class is 'tv' then an auth_token needs "
"to be provided, otherwise if device_class is "
"'soundbar' then add the right device_class to config")
return
if config.get(CONF_SUPPRESS_WARNING):
from requests.packages import urllib3
_LOGGER.warning("InsecureRequestWarning is disabled "
"because of Vizio platform configuration")
urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
add_entities([device], True)
|
def handle_oauth2_response(self, args):
client = self.make_client()
remote_args = {
'code': args.get('code'),
'client_secret': self.consumer_secret,
'redirect_uri': session.get('%s_oauthredir' % self.name)
}
log.debug('Prepare oauth2 remote args %r', remote_args)
remote_args.update(self.access_token_params)
headers = copy(self._access_token_headers)
if self.access_token_method == 'POST':
headers.update({'Content-Type': 'application/x-www-form-urlencoded'})
body = client.prepare_request_body(**remote_args)
resp, content = self.http_request(
self.expand_url(self.access_token_url),
headers=headers,
data=to_bytes(body, self.encoding),
method=self.access_token_method,
)
elif self.access_token_method == 'GET':
qs = client.prepare_request_body(**remote_args)
url = self.expand_url(self.access_token_url)
url += ('?' in url and '&' or '?') + qs
resp, content = self.http_request(
url,
headers=headers,
method=self.access_token_method,
)
else:
raise OAuthException(
'Unsupported access_token_method: %s' %
self.access_token_method
)
data = parse_response(resp, content, content_type=self.content_type)
if resp.code not in (200, 201):
raise OAuthException(
'Invalid response from %s' % self.name,
type='invalid_response', data=data
)
return data
|
def decode(self, val):
new_val = self.decode_date(val)
if val != new_val:
return new_val
return json.JSONDecoder.decode(self, val)
|
def extractPrintSaveIntermittens():
global g_summary_dict_intermittents
localtz = time.tzname[0]
for ind in range(len(g_summary_dict_all["TestName"])):
if g_summary_dict_all["TestInfo"][ind]["FailureCount"] >= g_threshold_failure:
addFailedTests(g_summary_dict_intermittents, g_summary_dict_all, ind)
if len(g_summary_dict_intermittents["TestName"]) > 0:
json.dump(g_summary_dict_intermittents, open(g_summary_dict_name, 'w'))
with open(g_summary_csv_filename, 'w') as summaryFile:
for ind in range(len(g_summary_dict_intermittents["TestName"])):
testName = g_summary_dict_intermittents["TestName"][ind]
numberFailure = g_summary_dict_intermittents["TestInfo"][ind]["FailureCount"]
firstFailedTS = parser.parse(time.ctime(min(g_summary_dict_intermittents["TestInfo"][ind]["Timestamp"]))+
' '+localtz)
firstFailedStr = firstFailedTS.strftime("%a %b %d %H:%M:%S %Y %Z")
recentFail = parser.parse(time.ctime(max(g_summary_dict_intermittents["TestInfo"][ind]["Timestamp"]))+
' '+localtz)
recentFailStr = recentFail.strftime("%a %b %d %H:%M:%S %Y %Z")
eachTest = "{0}, {1}, {2}, {3}\n".format(testName, recentFailStr, numberFailure,
g_summary_dict_intermittents["TestInfo"][ind]["TestCategory"][0])
summaryFile.write(eachTest)
print("Intermittent: {0}, Last failed: {1}, Failed {2} times since "
"{3}".format(testName, recentFailStr, numberFailure, firstFailedStr))
|
def _get_rule_source(self, rule):
p = len(self.input_source) + rule.position
source = self.input_source[p:p + rule.consumed].rstrip()
return self._indent(source, depth=self.indent + " ", skip_first_line=True)
|
def _resubscribe(self, soft=False):
if self.bitfinex_config:
self.send(**self.bitfinex_config)
q_list = []
while True:
try:
identifier, q = self.channel_configs.popitem(last=True if soft else False)
except KeyError:
break
q_list.append((identifier, q.copy()))
if identifier == 'auth':
self.send(**q, auth=True)
continue
if soft:
q['event'] = 'unsubscribe'
self.send(**q)
if soft:
for identifier, q in reversed(q_list):
self.channel_configs[identifier] = q
self.send(**q)
else:
for identifier, q in q_list:
self.channel_configs[identifier] = q
|
def _receive_data(self):
while True:
while len(self._buffer) < self.max_size and self.conn.poll():
data = self._read_chunks()
if data is not None:
self._buffer.append(data)
if len(self._buffer) > 0:
return self._buffer.popleft()
|
def _build_purchase_item(course_id, course_url, cost_in_cents, mode, course_data, sku):
item = {
'id': "{}-{}".format(course_id, mode),
'url': course_url,
'price': cost_in_cents,
'qty': 1,
}
if 'title' in course_data:
item['title'] = course_data['title']
else:
item['title'] = 'Course {} mode: {}'.format(course_id, mode)
if 'tags' in course_data:
item['tags'] = course_data['tags']
item['vars'] = dict(course_data.get('vars', {}), mode=mode, course_run_id=course_id)
item['vars']['purchase_sku'] = sku
return item
|
def _vector_matrix(vs, ms):
return tf.reduce_sum(input_tensor=vs[..., tf.newaxis] * ms, axis=-2)
|
def mix_over_posterior_draws(means, variances):
with tf.compat.v1.name_scope(
'mix_over_posterior_draws', values=[means, variances]):
num_posterior_draws = dist_util.prefer_static_value(
tf.shape(input=means))[0]
component_observations = tfd.Independent(
distribution=tfd.Normal(
loc=dist_util.move_dimension(means, 0, -2),
scale=tf.sqrt(dist_util.move_dimension(variances, 0, -2))),
reinterpreted_batch_ndims=1)
return tfd.MixtureSameFamily(
mixture_distribution=tfd.Categorical(
logits=tf.zeros([num_posterior_draws],
dtype=component_observations.dtype)),
components_distribution=component_observations)
|
def DeleteItem(self, item):
"Remove the item from the list and unset the related data"
wx_data = self.GetItemData(item)
py_data = self._py_data_map[wx_data]
del self._py_data_map[wx_data]
del self._wx_data_map[py_data]
wx.ListCtrl.DeleteItem(self, item)
|
def add_route(self, command, adapter):
if not isinstance(adapter, BaseAdapter):
try:
adapter = self.adapter_aliases[adapter]
except KeyError:
self.adapter_aliases[adapter] = adapter = resolve_adapter(
adapter
)
self.routes[command] = adapter
return self
|
def progress(iterator, prefix):
if terminal_width(prefix) > 25:
prefix = (".." + get_cut_prefix(prefix, 23))
speed_updated = start = time()
speed_written = written = 0
speed_history = deque(maxlen=5)
for data in iterator:
yield data
now = time()
elapsed = now - start
written += len(data)
speed_elapsed = now - speed_updated
if speed_elapsed >= 0.5:
speed_history.appendleft((
written - speed_written,
speed_updated,
))
speed_updated = now
speed_written = written
speed_history_written = sum(h[0] for h in speed_history)
speed_history_elapsed = now - speed_history[-1][1]
speed = speed_history_written / speed_history_elapsed
status = create_status_line(
prefix=prefix,
written=format_filesize(written),
elapsed=format_time(elapsed),
speed=format_filesize(speed)
)
print_inplace(status)
sys.stderr.write("\n")
sys.stderr.flush()
|
def get_params(brightness, contrast, saturation, hue):
transforms = []
if brightness is not None:
brightness_factor = random.uniform(brightness[0], brightness[1])
transforms.append(Lambda(lambda img: F.adjust_brightness(img, brightness_factor)))
if contrast is not None:
contrast_factor = random.uniform(contrast[0], contrast[1])
transforms.append(Lambda(lambda img: F.adjust_contrast(img, contrast_factor)))
if saturation is not None:
saturation_factor = random.uniform(saturation[0], saturation[1])
transforms.append(Lambda(lambda img: F.adjust_saturation(img, saturation_factor)))
if hue is not None:
hue_factor = random.uniform(hue[0], hue[1])
transforms.append(Lambda(lambda img: F.adjust_hue(img, hue_factor)))
random.shuffle(transforms)
transform = Compose(transforms)
return transform
|
def panel(context, panel, version, update_date, update_version):
adapter = context.obj['adapter']
panel_obj = adapter.gene_panel(panel, version=version)
if not panel_obj:
LOG.warning("Panel %s (version %s) could not be found" % (panel, version))
context.abort()
date_obj = None
if update_date:
try:
date_obj = get_date(update_date)
except Exception as err:
LOG.warning(err)
context.abort()
update_panel(
adapter,
panel,
panel_version=panel_obj['version'],
new_version=update_version,
new_date=date_obj
)
|
def random_ports(port, n):
for i in range(min(5, n)):
yield port + i
for i in range(n-5):
yield port + random.randint(-2*n, 2*n)
|
def PermissiveDict(fields=None):
if fields:
check_user_facing_fields_dict(fields, 'PermissiveDict')
class _PermissiveDict(_ConfigComposite):
def __init__(self):
key = 'PermissiveDict.' + str(DictCounter.get_next_count())
super(_PermissiveDict, self).__init__(
name=None,
key=key,
fields=fields or dict(),
description='A configuration dictionary with typed fields',
type_attributes=ConfigTypeAttributes(is_builtin=True),
)
@property
def is_permissive_composite(self):
return True
return _PermissiveDict
|
def gravatar_url(user_or_email, size=GRAVATAR_DEFAULT_SIZE):
if hasattr(user_or_email, 'email'):
email = user_or_email.email
else:
email = user_or_email
try:
return escape(get_gravatar_url(email=email, size=size))
except:
return ''
|
def run_as_cmd(cmd, user, shell='bash'):
to_execute = get_shell(shell) + [EXECUTE_SHELL_PARAM, cmd]
if user == 'root':
return to_execute
return ['sudo', '-s', '--set-home', '-u', user] + to_execute
|
def profile_function(self):
with _CodeHeatmapCalculator() as prof:
result = self._run_object(*self._run_args, **self._run_kwargs)
code_lines, start_line = inspect.getsourcelines(self._run_object)
source_lines = []
for line in code_lines:
source_lines.append(('line', start_line, line))
start_line += 1
filename = os.path.abspath(inspect.getsourcefile(self._run_object))
heatmap = prof.heatmap[filename]
run_time = sum(time for time in heatmap.values())
return {
'objectName': self._object_name,
'runTime': run_time,
'result': result,
'timestamp': int(time.time()),
'heatmaps': [{
'name': self._object_name,
'heatmap': heatmap,
'executionCount': prof.execution_count[filename],
'srcCode': source_lines,
'runTime': run_time
}]
}
|
def dashboard(request):
if not isinstance(mc_client, dict):
cache_stats = _get_cache_stats()
else:
cache_stats = None
if cache_stats:
data = _context_data({
'title': _('Memcache Dashboard'),
'cache_stats': cache_stats,
'can_get_slabs': hasattr(mc_client, 'get_slabs'),
'REFRESH_RATE': SETTINGS['REFRESH_RATE'],
},
request)
template = 'memcache_admin/dashboard.html'
else:
data = _context_data({
'title': _('Memcache Dashboard - Error'),
'error_message': _('Unable to connect to a memcache server.'),
},
request)
template = 'memcache_admin/dashboard_error.html'
return render_to_response(template, data, RequestContext(request))
|
def _validate_initial_statevector(self):
if self._initial_statevector is None:
return
length = len(self._initial_statevector)
required_dim = 2 ** self._number_of_qubits
if length != required_dim:
raise BasicAerError('initial statevector is incorrect length: ' +
'{} != {}'.format(length, required_dim))
|
def chatToId(url):
match = re.search(r"conversations/([0-9]+:[^/]+)", url)
return match.group(1) if match else None
|
def prepare_pids(self):
self.pids = []
for fetcher in self.pid_fetchers:
val = fetcher(None, self.revisions[-1][1])
if val:
self.pids.append(val)
|
def use(network=False):
global _engine
__engine = _engine
activated = __engine.active
if activated:
__engine.disable()
_engine = Engine(network=network)
_engine.activate()
yield _engine
_engine.disable()
if network:
_engine.disable_network()
_engine = __engine
if activated:
_engine.activate()
|
def parse_yaml_linenumbers(data, filename):
def compose_node(parent, index):
line = loader.line
node = Composer.compose_node(loader, parent, index)
node.__line__ = line + 1
return node
def construct_mapping(node, deep=False):
if ANSIBLE_VERSION < 2:
mapping = Constructor.construct_mapping(loader, node, deep=deep)
else:
mapping = AnsibleConstructor.construct_mapping(loader, node, deep=deep)
if hasattr(node, '__line__'):
mapping[LINE_NUMBER_KEY] = node.__line__
else:
mapping[LINE_NUMBER_KEY] = mapping._line_number
mapping[FILENAME_KEY] = filename
return mapping
try:
if ANSIBLE_VERSION < 2:
loader = yaml.Loader(data)
else:
import inspect
kwargs = {}
if 'vault_password' in inspect.getargspec(AnsibleLoader.__init__).args:
kwargs['vault_password'] = DEFAULT_VAULT_PASSWORD
loader = AnsibleLoader(data, **kwargs)
loader.compose_node = compose_node
loader.construct_mapping = construct_mapping
data = loader.get_single_data()
except (yaml.parser.ParserError, yaml.scanner.ScannerError) as e:
raise SystemExit("Failed to parse YAML in %s: %s" % (filename, str(e)))
return data
|
def log_cdf_laplace(x, name="log_cdf_laplace"):
with tf.name_scope(name):
x = tf.convert_to_tensor(value=x, name="x")
lower_solution = -np.log(2.) + x
safe_exp_neg_x = tf.exp(-tf.abs(x))
upper_solution = tf.math.log1p(-0.5 * safe_exp_neg_x)
return tf.where(x < 0., lower_solution, upper_solution)
|
def samefile(path1, path2):
info1 = fs.getfileinfo(path1)
info2 = fs.getfileinfo(path2)
return (info1.dwVolumeSerialNumber == info2.dwVolumeSerialNumber and
info1.nFileIndexHigh == info2.nFileIndexHigh and
info1.nFileIndexLow == info2.nFileIndexLow)
|
def add_netnode_plugin_name(plugin_name):
current_names = set(get_netnode_plugin_names())
if plugin_name in current_names:
return
current_names.add(plugin_name)
get_meta_netnode()[PLUGIN_NAMES_KEY] = json.dumps(list(current_names))
|
def set_serial(self, hex_str):
bignum_serial = _ffi.gc(_lib.BN_new(), _lib.BN_free)
bignum_ptr = _ffi.new("BIGNUM**")
bignum_ptr[0] = bignum_serial
bn_result = _lib.BN_hex2bn(bignum_ptr, hex_str)
if not bn_result:
raise ValueError("bad hex string")
asn1_serial = _ffi.gc(
_lib.BN_to_ASN1_INTEGER(bignum_serial, _ffi.NULL),
_lib.ASN1_INTEGER_free)
_lib.X509_REVOKED_set_serialNumber(self._revoked, asn1_serial)
|
def run_samblaster(job, sam):
work_dir = job.fileStore.getLocalTempDir()
job.fileStore.readGlobalFile(sam, os.path.join(work_dir, 'input.sam'))
command = ['/usr/local/bin/samblaster',
'-i', '/data/input.sam',
'-o', '/data/output.sam',
'--ignoreUnmated']
start_time = time.time()
dockerCall(job=job, workDir=work_dir,
parameters=command,
tool='quay.io/biocontainers/samblaster:0.1.24--0')
end_time = time.time()
_log_runtime(job, start_time, end_time, "SAMBLASTER")
return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'output.sam'))
|
def handle_stranded_tasks(self, engine):
lost = self.pending[engine]
for msg_id in lost.keys():
if msg_id not in self.pending[engine]:
continue
raw_msg = lost[msg_id].raw_msg
idents,msg = self.session.feed_identities(raw_msg, copy=False)
parent = self.session.unpack(msg[1].bytes)
idents = [engine, idents[0]]
try:
raise error.EngineError("Engine %r died while running task %r"%(engine, msg_id))
except:
content = error.wrap_exception()
header = dict(
status='error',
engine=engine,
date=datetime.now(),
)
msg = self.session.msg('apply_reply', content, parent=parent, subheader=header)
raw_reply = map(zmq.Message, self.session.serialize(msg, ident=idents))
self.dispatch_result(raw_reply)
self.completed.pop(engine)
self.failed.pop(engine)
|
def get_group_all(group, path=None):
result = []
for config, distro in iter_files_distros(path=path):
if group in config:
for name, epstr in config[group].items():
with BadEntryPoint.err_to_warnings():
result.append(EntryPoint.from_string(epstr, name, distro))
return result
|
def build_filters_and_sizers(self, ppoi_value, create_on_demand):
name = self.name
if not name and self.field.placeholder_image_name:
name = self.field.placeholder_image_name
self.filters = FilterLibrary(
name,
self.storage,
versatileimagefield_registry,
ppoi_value,
create_on_demand
)
for (
attr_name,
sizedimage_cls
) in iteritems(versatileimagefield_registry._sizedimage_registry):
setattr(
self,
attr_name,
sizedimage_cls(
path_to_image=name,
storage=self.storage,
create_on_demand=create_on_demand,
ppoi=ppoi_value
)
)
|
def predict_logit(self, x, **kwargs):
return self.feed_forward(x, **kwargs)[self.layers[-1].full_name('pre')]
|
def get_source_lane(fork_process, pipeline_list):
fork_source = fork_process[-1]
fork_sig = [x for x in fork_process if x != "__init__"]
for position, p in enumerate(pipeline_list[::-1]):
if p["output"]["process"] == fork_source:
lane = p["output"]["lane"]
logger.debug("Possible source match found in position {} in lane"
" {}".format(position, lane))
lane_sequence = [x["output"]["process"] for x in pipeline_list
if x["output"]["lane"] == lane]
logger.debug("Testing lane sequence '{}' against fork signature"
" '{}'".format(lane_sequence, fork_sig))
if lane_sequence == fork_sig:
return p["output"]["lane"]
return 0
|
def article(self, msgid_article=None, decode=None):
args = None
if msgid_article is not None:
args = utils.unparse_msgid_article(msgid_article)
code, message = self.command("ARTICLE", args)
if code != 220:
raise NNTPReplyError(code, message)
parts = message.split(None, 1)
try:
articleno = int(parts[0])
except ValueError:
raise NNTPProtocolError(message)
headers = utils.parse_headers(self.info_gen(code, message))
decode = "yEnc" in headers.get("subject", "")
escape = 0
crc32 = 0
body = []
for line in self.info_gen(code, message):
if decode:
if line.startswith("=y"):
continue
line, escape, crc32 = yenc.decode(line, escape, crc32)
body.append(line)
return articleno, headers, "".join(body)
|
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