code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
if daynum is None:
return None
try:
daycount = int(daynum)
except ValueError:
return None
if daycount > max_days:
# Using default: some time in the 48th century, clearly bogus.
daycount = max_days
return date(1970, 1, 1) + timedelta(daycount) | def daynum_to_date(daynum, max_days=1000000) | Convert a number of days to a date. If it's out of range, default to a
max date. If it is not a number (or a numeric string), return None. Using
a max_days of more than 2932896 (9999-12-31) will throw an exception if the
specified daynum exceeds the max.
:param daynum: A number of days since Jan 1, 1970 | 4.69396 | 5.029387 | 0.933307 |
target_day_date = datetime.strptime(target_day, date_format)
# Compute activity over `past_days` days leading up to target_day
min_activity_date = target_day_date - timedelta(past_days)
min_activity = unix_time_nanos(min_activity_date)
max_activity = unix_time_nanos(target_day_date + timedelta... | def mau(dataframe, target_day, past_days=28, future_days=10, date_format="%Y%m%d") | Compute Monthly Active Users (MAU) from the Executive Summary dataset.
See https://bugzilla.mozilla.org/show_bug.cgi?id=1240849 | 3.551221 | 3.429773 | 1.03541 |
delta_days = ((day.weekday() + 1) % 7) if weekday_start is "Sunday" else day.weekday()
return day - timedelta(days=delta_days) | def snap_to_beginning_of_week(day, weekday_start="Sunday") | Get the first day of the current week.
:param day: The input date to snap.
:param weekday_start: Either "Monday" or "Sunday", indicating the first day of the week.
:returns: A date representing the first day of the current week. | 3.227523 | 3.642044 | 0.886185 |
today = date.today()
# Get the first day of the past complete week.
start_of_week = snap_to_beginning_of_week(today, weekday_start) - timedelta(weeks=1)
end_of_week = start_of_week + timedelta(days=6)
return (start_of_week, end_of_week) | def get_last_week_range(weekday_start="Sunday") | Gets the date for the first and the last day of the previous complete week.
:param weekday_start: Either "Monday" or "Sunday", indicating the first day of the week.
:returns: A tuple containing two date objects, for the first and the last day of the week
respectively. | 3.1646 | 3.090706 | 1.023908 |
today = date.today()
# Get the last day for the previous month.
end_of_last_month = snap_to_beginning_of_month(today) - timedelta(days=1)
start_of_last_month = snap_to_beginning_of_month(end_of_last_month)
return (start_of_last_month, end_of_last_month) | def get_last_month_range() | Gets the date for the first and the last day of the previous complete month.
:returns: A tuple containing two date objects, for the first and the last day of the month
respectively. | 2.50426 | 2.580172 | 0.970579 |
base_path = path
# Specifying basePath retains the partition fields even
# if we read a bunch of paths separately.
reader = spark.read.option("basePath", base_path)
if mergeSchema:
reader = reader.option("mergeSchema", "true")
if submission_date_s3 is not None and sample_id is Non... | def read_main_summary(spark,
submission_date_s3=None,
sample_id=None,
mergeSchema=True,
path='s3://telemetry-parquet/main_summary/v4') | Efficiently read main_summary parquet data.
Read data from the given path, optionally filtering to a
specified set of partition values first. This can save a
time, particularly if `mergeSchema` is True.
Args:
spark: Spark session
submission_date_s3: Optional list of values to filter th... | 3.130224 | 3.110915 | 1.006207 |
return dataframe \
.withColumn(
"sampler",
udf(lambda key: (crc32(key or "") & 0xffffffff) % modulo)(column),
).where("sampler = %s" % sample_id).drop("sampler") | def sampler(dataframe, modulo, column="client_id", sample_id=42) | Collect a sample of clients given an input column
Filter dataframe based on the modulus of the CRC32 of a given string
column matching a given sample_id. if dataframe has already been filtered
by sample_id, then modulo should be a multiple of 100, column should be
"client_id", and the given sample_id s... | 6.379107 | 7.058437 | 0.903756 |
if 'delete' in request.GET:
models.MachineCache.objects.all().delete()
models.InstituteCache.objects.all().delete()
models.PersonCache.objects.all().delete()
models.ProjectCache.objects.all().delete()
return render(
template_name='main.html',
cont... | def progress(request) | Check status of task. | 3.102523 | 3.029329 | 1.024162 |
def inner(request, *args):
lock_id = '%s-%s-built-%s' % (
datetime.date.today(), func.__name__,
",".join([str(a) for a in args]))
if cache.add(lock_id, 'true', LOCK_EXPIRE):
result = func(request, *args)
cache.set(lock_id, result.task_id)
... | def synchronise(func) | If task already queued, running, or finished, don't restart. | 3.445159 | 3.584586 | 0.961104 |
sorted_list = sorted(obj_list, key=lambda x: x['size'], reverse=True)
groups = [[] for _ in range(tot_groups)]
for index, obj in enumerate(sorted_list):
current_group = groups[index % len(groups)]
current_group.append(obj)
return groups | def _group_by_size_greedy(obj_list, tot_groups) | Partition a list of objects in even buckets
The idea is to choose the bucket for an object in a round-robin fashion.
The list of objects is sorted to also try to keep the total size in bytes
as balanced as possible.
:param obj_list: a list of dict-like objects with a 'size' property
:param tot_grou... | 2.042919 | 2.313663 | 0.88298 |
sorted_obj_list = sorted([(obj['size'], obj) for obj in obj_list], reverse=True)
groups = [(random.random(), []) for _ in range(tot_groups)]
if tot_groups <= 1:
groups = _group_by_size_greedy(obj_list, tot_groups)
return groups
heapq.heapify(groups)
for obj in sorted_obj_list:
... | def _group_by_equal_size(obj_list, tot_groups, threshold=pow(2, 32)) | Partition a list of objects evenly and by file size
Files are placed according to largest file in the smallest bucket. If the
file is larger than the given threshold, then it is placed in a new bucket
by itself.
:param obj_list: a list of dict-like objects with a 'size' property
:param tot_groups: ... | 2.403015 | 2.345761 | 1.024407 |
if not (properties or aliased_properties):
return self
merged_properties = dict(zip(properties, properties))
merged_properties.update(aliased_properties)
for prop_name in (merged_properties.keys()):
if prop_name in self.selection:
raise E... | def select(self, *properties, **aliased_properties) | Specify which properties of the dataset must be returned
Property extraction is based on `JMESPath <http://jmespath.org>`_ expressions.
This method returns a new Dataset narrowed down by the given selection.
:param properties: JMESPath to use for the property extraction.
... | 2.878233 | 3.055767 | 0.941902 |
clauses = copy(self.clauses)
for dimension, condition in kwargs.items():
if dimension in self.clauses:
raise Exception('There should be only one clause for {}'.format(dimension))
if dimension not in self.schema:
raise Exception('The dimens... | def where(self, **kwargs) | Return a new Dataset refined using the given condition
:param kwargs: a map of `dimension` => `condition` to filter the elements
of the dataset. `condition` can either be an exact value or a
callable returning a boolean value. If `condition` is a value, it is
converted to a ... | 4.463199 | 4.105113 | 1.087229 |
clauses = copy(self.clauses)
schema = self.schema
if self.prefix:
schema = ['prefix'] + schema
# Add a clause for the prefix that always returns True, in case
# the output is not filtered at all (so that we do a scan/filter
# on the prefi... | def summaries(self, sc, limit=None) | Summary of the files contained in the current dataset
Every item in the summary is a dict containing a key name and the corresponding size of
the key item in bytes, e.g.::
{'key': 'full/path/to/my/key', 'size': 200}
:param limit: Max number of objects to retrieve
:return: An it... | 8.289002 | 7.919995 | 1.046592 |
decode = decode or message_parser.parse_heka_message
summaries = summaries or self.summaries(sc, limit)
# Calculate the sample if summaries is not empty and limit is not set
if summaries and limit is None and sample != 1:
if sample < 0 or sample > 1:
... | def records(self, sc, group_by='greedy', limit=None, sample=1, seed=42, decode=None, summaries=None) | Retrieve the elements of a Dataset
:param sc: a SparkContext object
:param group_by: specifies a partition strategy for the objects
:param limit: maximum number of objects to retrieve
:param decode: an optional transformation to apply to the objects retrieved
:param sample: perc... | 4.452113 | 4.523128 | 0.9843 |
rdd = self.records(spark.sparkContext, group_by, limit, sample, seed, decode, summaries)
if not schema:
df = rdd.map(lambda d: Row(**d)).toDF()
else:
df = spark.createDataFrame(rdd, schema=schema)
if table_name:
df.createOrReplaceTempView(tabl... | def dataframe(self, spark, group_by='greedy', limit=None, sample=1, seed=42, decode=None, summaries=None, schema=None, table_name=None) | Convert RDD returned from records function to a dataframe
:param spark: a SparkSession object
:param group_by: specifies a paritition strategy for the objects
:param limit: maximum number of objects to retrieve
:param decode: an optional transformation to apply to the objects retrieved
... | 2.365294 | 2.307108 | 1.02522 |
meta_bucket = 'net-mozaws-prod-us-west-2-pipeline-metadata'
store = S3Store(meta_bucket)
try:
source = json.loads(store.get_key('sources.json').read().decode('utf-8'))[source_name]
except KeyError:
raise Exception('Unknown source {}'.format(source_name))... | def from_source(source_name) | Create a Dataset configured for the given source_name
This is particularly convenient when the user doesn't know
the list of dimensions or the bucket name, but only the source name.
Usage example::
records = Dataset.from_source('telemetry').where(
docType='main',
... | 4.61199 | 4.479352 | 1.029611 |
application.reopen()
link, is_secret = base.get_email_link(application)
emails.send_invite_email(application, link, is_secret)
messages.success(
request,
"Sent an invitation to %s."
% application.applicant.email)
return 'success' | def get_next_action(self, request, application, roles) | Retrieve the next state. | 7.1569 | 7.321252 | 0.977551 |
# Check for serious errors in submission.
# Should only happen in rare circumstances.
errors = application.check_valid()
if len(errors) > 0:
for error in errors:
messages.error(request, error)
return 'error'
# mark as submitted
... | def get_next_action(self, request, application, roles) | Retrieve the next state. | 5.817771 | 5.8749 | 0.990276 |
# Check for serious errors in submission.
# Should only happen in rare circumstances.
errors = application.check_valid()
if len(errors) > 0:
for error in errors:
messages.error(request, error)
return 'error'
# approve application
... | def get_next_action(self, request, application, roles) | Retrieve the next state. | 5.747974 | 5.690089 | 1.010173 |
context = CONTEXT.copy()
context['person'] = person
for lp in leader_list:
leader = lp['leader']
context['project'] = lp['project']
context['receiver'] = leader
to_email = leader.email
subject = render_to_string(
'karaage/people/emails/bounced_emai... | def send_bounced_warning(person, leader_list) | Sends an email to each project leader for person
informing them that person's email has bounced | 3.993962 | 3.830463 | 1.042684 |
uid = urlsafe_base64_encode(force_bytes(person.pk)).decode("ascii")
token = default_token_generator.make_token(person)
url = '%s/persons/reset/%s/%s/' % (
settings.REGISTRATION_BASE_URL, uid, token)
context = CONTEXT.copy()
context.update({
'url': url,
'receiver': perso... | def send_reset_password_email(person) | Sends an email to user allowing them to set their password. | 2.754282 | 2.78622 | 0.988537 |
url = '%s/profile/login/%s/' % (
settings.REGISTRATION_BASE_URL, person.username)
context = CONTEXT.copy()
context.update({
'url': url,
'receiver': person,
})
to_email = person.email
subject, body = render_email('confirm_password', context)
send_mail(subject, ... | def send_confirm_password_email(person) | Sends an email to user allowing them to confirm their password. | 3.774283 | 3.712901 | 1.016532 |
try:
authorised_persons = self.get_authorised_persons(application)
authorised_persons.get(pk=request.user.pk)
return True
except Person.DoesNotExist:
return False | def check_can_approve(self, request, application, roles) | Check the person's authorization. | 4.022116 | 3.354771 | 1.198924 |
authorised_persons = self.get_email_persons(application)
link, is_secret = self.get_request_email_link(application)
emails.send_request_email(
self.authorised_text,
self.authorised_role,
authorised_persons,
application,
link, i... | def enter_state(self, request, application) | This is becoming the new current state. | 7.634563 | 7.702968 | 0.99112 |
actions = self.get_actions(request, application, roles)
if label == "approve" and 'approve' in actions:
application_form = self.get_approve_form(
request, application, roles)
form = application_form(request.POST or None, instance=application)
... | def get_next_action(self, request, application, label, roles) | Django view method. | 2.580814 | 2.575269 | 1.002153 |
actions = self.get_actions(request, application, roles)
if label is None and 'is_applicant' in roles:
assert application.content_type.model == 'person'
if application.applicant.has_usable_password():
form = forms.PersonVerifyPassword(
... | def get_next_action(self, request, application, label, roles) | Django view method. | 3.555031 | 3.552015 | 1.000849 |
actions = self.get_actions(request, application, roles)
if label is None and \
'is_applicant' in roles and 'is_admin' not in roles:
# applicant, admin, leader can reopen an application
for action in actions:
if action in request.POST:
... | def get_next_action(self, request, application, label, roles) | Django view method. | 5.129138 | 5.294881 | 0.968698 |
assert step_id not in self._steps
assert step_id not in self._order
assert isinstance(step, Step)
self._steps[step_id] = step
self._order.append(step_id) | def add_step(self, step, step_id) | Add a step to the list. The first step added becomes the initial
step. | 2.613456 | 2.589551 | 1.009231 |
actions = self.get_actions(request, application, roles)
# if the user is not the applicant, the steps don't apply.
if 'is_applicant' not in roles:
return super(StateWithSteps, self).get_next_action(
request, application, label, roles)
# was label su... | def get_next_action(self, request, application, label, roles) | Process the get_next_action request at the current step. | 2.969851 | 2.971716 | 0.999372 |
actions = self.get_actions(request, application, roles)
if label is None and \
'is_applicant' in roles and 'is_admin' not in roles:
for action in actions:
if action in request.POST:
return action
link, is_secret = base.... | def get_next_action(self, request, application, label, roles) | Django get_next_action method. | 4.71068 | 4.806142 | 0.980137 |
global _DATASTORES
array = settings.DATASTORES
for config in array:
cls = _lookup(config['ENGINE'])
ds = _get_datastore(cls, DataStore, config)
_DATASTORES.append(ds)
legacy_settings = getattr(settings, 'MACHINE_CATEGORY_DATASTORES', None)
if legacy_settings is not None:... | def _init_datastores() | Initialize all datastores. | 3.454866 | 3.425854 | 1.008469 |
for datastore in _get_datastores():
datastore.set_account_username(account, old_username, new_username) | def set_account_username(account, old_username, new_username) | Account's username was changed. | 3.63568 | 3.988141 | 0.911623 |
result = []
for datastore in _get_datastores():
value = datastore.get_account_details(account)
value['datastore'] = datastore.config['DESCRIPTION']
result.append(value)
return result | def get_account_details(account) | Get the account details. | 5.154035 | 5.012274 | 1.028283 |
for datastore in _get_datastores():
datastore.set_group_name(group, old_name, new_name) | def set_group_name(group, old_name, new_name) | Group was renamed. | 3.74323 | 3.896836 | 0.960582 |
result = []
for datastore in _get_datastores():
value = datastore.get_group_details(group)
value['datastore'] = datastore.config['DESCRIPTION']
result.append(value)
return result | def get_group_details(group) | Get group details. | 5.061508 | 4.967289 | 1.018968 |
result = []
for datastore in _get_datastores():
value = datastore.get_project_details(project)
value['datastore'] = datastore.config['DESCRIPTION']
result.append(value)
return result | def get_project_details(project) | Get details for this user. | 5.262213 | 4.987798 | 1.055017 |
for datastore in _get_datastores():
datastore.save_project(project)
datastore.set_project_pid(project, old_pid, new_pid) | def set_project_pid(project, old_pid, new_pid) | Project's PID was changed. | 3.781592 | 3.852005 | 0.981721 |
result = []
for datastore in _get_datastores():
value = datastore.get_institute_details(institute)
value['datastore'] = datastore.config['DESCRIPTION']
result.append(value)
return result | def get_institute_details(institute) | Get details for this user. | 5.282612 | 5.172475 | 1.021293 |
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_group(account, group) | def add_accounts_to_group(accounts_query, group) | Add accounts to group. | 4.130945 | 3.918875 | 1.054115 |
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_group(account, group) | def remove_accounts_from_group(accounts_query, group) | Remove accounts from group. | 4.065225 | 4.02835 | 1.009154 |
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_project(account, project) | def add_accounts_to_project(accounts_query, project) | Add accounts to project. | 4.173965 | 3.88287 | 1.074969 |
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_project(account, project) | def remove_accounts_from_project(accounts_query, project) | Remove accounts from project. | 4.007971 | 3.912637 | 1.024366 |
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_institute(account, institute) | def add_accounts_to_institute(accounts_query, institute) | Add accounts to institute. | 4.252379 | 3.956775 | 1.074708 |
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_institute(account, institute) | def remove_accounts_from_institute(accounts_query, institute) | Remove accounts from institute. | 4.126776 | 3.906324 | 1.056435 |
status = None
applicant = application.applicant
attrs = []
saml_session = saml.is_saml_session(request)
# certain actions are supported regardless of what else happens
if 'cancel' in request.POST:
return "cancel"
if 'prev' in request.POST:
... | def view(self, request, application, label, roles, actions) | Django view method. | 3.746727 | 3.74094 | 1.001547 |
# Get the appropriate form
status = None
form = None
if application.content_type.model != 'applicant':
status = "You are already registered in the system."
elif application.content_type.model == 'applicant':
if application.applicant.saml_id is no... | def view(self, request, application, label, roles, actions) | Django view method. | 3.794319 | 3.781347 | 1.003431 |
if 'ajax' in request.POST:
resp = self.handle_ajax(request, application)
return HttpResponse(
json.dumps(resp), content_type="application/json")
form_models = {
'common': forms.CommonApplicationForm,
'new': forms.NewProjectApplica... | def view(self, request, application, label, roles, actions) | Django view method. | 2.81203 | 2.801774 | 1.003661 |
if application.content_type.model == 'applicant':
if not application.applicant.email_verified:
application.applicant.email_verified = True
application.applicant.save()
for action in actions:
if action in request.POST:
retur... | def view(self, request, application, label, roles, actions) | Django get_next_action method. | 5.298023 | 5.268657 | 1.005574 |
# if user is logged and and not applicant, steal the
# application
if 'is_applicant' in roles:
# if we got this far, then we either we are logged in as applicant,
# or we know the secret for this application.
new_person = None
reason = N... | def get_next_action(self, request, application, label, roles) | Process the get_next_action request at the current step. | 4.416718 | 4.464361 | 0.989328 |
if value is None:
value = ""
# replace whitespace with space
value = value.replace("\n", " ")
value = value.replace("\t", " ")
# CSV seperator
value = value.replace("|", " ")
# remove leading/trailing whitespace
value = value.strip(... | def _filter_string(value) | Filter the string so MAM doesn't have heart failure. | 4.723532 | 4.181101 | 1.129734 |
length = int(arg)
if value is None:
value = ""
if len(value) > length:
return value[:length] + "..."
else:
return value | def _truncate(value, arg) | Truncates a string after a given number of chars
Argument: Number of chars to _truncate after | 2.706641 | 2.916084 | 0.928176 |
if ignore_errors is None:
ignore_errors = []
command = self._get_command(command)
logger.debug("Cmd %s" % command)
null = open('/dev/null', 'w')
retcode = subprocess.call(command, stdout=null, stderr=null)
null.close()
if retcode in ignore_e... | def _call(self, command, ignore_errors=None) | Call remote command with logging. | 2.601331 | 2.55262 | 1.019083 |
cmd = ["glsuser", "-u", username, "--raw"]
results = self._read_output(cmd)
if len(results) == 0:
return None
elif len(results) > 1:
logger.error(
"Command returned multiple results for '%s'." % username)
raise RuntimeError(
... | def get_user(self, username) | Get the user details from MAM. | 2.735298 | 2.701616 | 1.012467 |
cmd = ["gbalance", "-u", username, "--raw"]
results = self._read_output(cmd)
if len(results) == 0:
return None
return results | def get_user_balance(self, username) | Get the user balance details from MAM. | 7.029948 | 7.281066 | 0.965511 |
ds_project = self.get_project(projectname)
if ds_project is None:
logger.error(
"Project '%s' does not exist in MAM" % projectname)
raise RuntimeError(
"Project '%s' does not exist in MAM" % projectname)
user_list = []
if ... | def get_users_in_project(self, projectname) | Get list of users in project from MAM. | 3.073046 | 2.644537 | 1.162035 |
ds_balance = self.get_user_balance(username)
if ds_balance is None:
return []
project_list = []
for bal in ds_balance:
project_list.append(bal["Name"])
return project_list | def get_projects_in_user(self, username) | Get list of projects in user from MAM. | 4.244335 | 3.883008 | 1.093053 |
# retrieve default project, or use null project if none
default_project_name = self._null_project
if account.default_project is not None:
default_project_name = account.default_project.pid
# account created
# account updated
ds_user = self.get_user... | def _save_account(self, account, username) | Called when account is created/updated. With username override. | 4.421744 | 4.39222 | 1.006722 |
# account deleted
ds_user = self.get_user(username)
if ds_user is not None:
self._call(["grmuser", "-u", username], ignore_errors=[8])
return | def _delete_account(self, account, username) | Called when account is deleted. With username override. | 12.738533 | 12.436432 | 1.024292 |
self._delete_account(account, old_username)
self._save_account(account, new_username) | def set_account_username(self, account, old_username, new_username) | Account's username was changed. | 3.330949 | 3.245698 | 1.026266 |
result = self.get_user(account.username)
if result is None:
result = {}
return result | def get_account_details(self, account) | Get the account details | 6.230832 | 6.409808 | 0.972078 |
pid = project.pid
# project created
# project updated
if project.is_active:
# project is not deleted
logger.debug("project is active")
ds_project = self.get_project(pid)
if ds_project is None:
self._create_project... | def save_project(self, project) | Called when project is saved/updated. | 3.683806 | 3.565391 | 1.033213 |
pid = project.pid
# project deleted
ds_project = self.get_project(pid)
if ds_project is not None:
self._delete_project(pid)
return | def delete_project(self, project) | Called when project is deleted. | 6.459061 | 5.751119 | 1.123096 |
result = self.get_project(project.pid)
if result is None:
result = {}
return result | def get_project_details(self, project) | Get the project details. | 6.476202 | 5.509205 | 1.175524 |
name = institute.name
logger.debug("save_institute '%s'" % name)
# institute created
# institute updated
if institute.is_active:
# date_deleted is not set, user should exist
logger.debug("institute is active")
self._call(
... | def save_institute(self, institute) | Called when institute is created/updated. | 6.789681 | 6.612779 | 1.026752 |
name = institute.name
logger.debug("institute_deleted '%s'" % name)
# institute deleted
self._call(["goldsh", "Organization", "Delete", "Name==%s" % name])
logger.debug("returning")
return | def delete_institute(self, institute) | Called when institute is deleted. | 13.885927 | 12.401295 | 1.119716 |
username = account.username
projectname = project.pid
self._call([
"gchproject",
"--add-user", username,
"-p", projectname],
ignore_errors=[74]) | def add_account_to_project(self, account, project) | Add account to project. | 10.7485 | 10.181634 | 1.055675 |
img = StringIO()
fig.savefig(img, format='svg')
img.seek(0)
print("%html <div style='width:{}px'>{}</div>".format(width, img.buf)) | def show(fig, width=600) | Renders a Matplotlib figure in Zeppelin.
:param fig: a Matplotlib figure
:param width: the width in pixel of the rendered figure, defaults to 600
Usage example::
import matplotlib.pyplot as plt
from moztelemetry.zeppelin import show
fig = plt.figure()
plt.plot([1, 2, 3])
... | 5.788017 | 6.304012 | 0.918148 |
if short_label is None:
short_label = hub_name
if long_label is None:
long_label = short_label
hub = Hub(
hub=hub_name,
short_label=short_label,
long_label=long_label,
email=email)
genome = Genome(genome)
genomes_file = GenomesFile()
trackdb... | def default_hub(hub_name, genome, email, short_label=None, long_label=None) | Returns a fully-connected set of hub components using default filenames.
Parameters
----------
hub_name : str
Name of the hub
genome : str
Assembly name (hg38, dm6, etc)
email : str
Email to include with hub.
short_label : str
Short label for the hub. If None... | 2.20307 | 2.504105 | 0.879784 |
assert machine.name == machine_name
year, month, day = date.split('-')
date = datetime.date(int(year), int(month), int(day))
return parse_logs(usage, date, machine_name, log_type) | def parse_usage(machine, usage, date, machine_name, log_type) | Parses usage | 2.727144 | 2.883681 | 0.945716 |
if strict_type_checks:
load_whitelist()
all_histograms = OrderedDict()
for filename in filenames:
parser = FILENAME_PARSERS[os.path.basename(filename)]
histograms = parser(filename, strict_type_checks)
# OrderedDicts are important, because then the iteration order over... | def from_files(filenames, strict_type_checks=True) | Return an iterator that provides a sequence of Histograms for
the histograms defined in filenames. | 3.708221 | 3.660244 | 1.013108 |
bucket_fns = {
'boolean': linear_buckets,
'flag': linear_buckets,
'count': linear_buckets,
'enumerated': linear_buckets,
'categorical': linear_buckets,
'linear': linear_buckets,
'exponential': exponential_buckets,
... | def ranges(self) | Return an array of lower bounds for each bucket in the histogram. | 4.009372 | 3.656266 | 1.096575 |
number = '0001'
prefix = 'p%s' % institute.name.replace(' ', '')[:4]
found = True
while found:
try:
Project.objects.get(pid=prefix + number)
number = str(int(number) + 1)
if len(number) == 1:
number = '000' + number
elif len(n... | def get_new_pid(institute) | Return a new Project ID
Keyword arguments:
institute_id -- Institute id | 2.1608 | 2.326231 | 0.928885 |
for key, value in six.iteritems(extra_context):
if callable(value):
context[key] = value()
else:
context[key] = value | def apply_extra_context(extra_context, context) | Adds items from extra_context dict to context. If a value in extra_context
is callable, then it is called and the result is added to context. | 2.140525 | 2.004549 | 1.067834 |
if form_class:
return form_class._meta.model, form_class
if model:
# The inner Meta class fails if model = model is used for some reason.
tmp_model = model
# TODO: we should be able to construct a ModelForm without creating
# and passing in a temporary inner class.
... | def get_model_and_form_class(model, form_class) | Returns a model and form class based on the model and form_class
parameters that were passed to the generic view.
If ``form_class`` is given then its associated model will be returned along
with ``form_class`` itself. Otherwise, if ``model`` is given, ``model``
itself will be returned along with a ``M... | 5.466657 | 5.219431 | 1.047366 |
if post_save_redirect:
return HttpResponseRedirect(post_save_redirect % obj.__dict__)
elif hasattr(obj, 'get_absolute_url'):
return HttpResponseRedirect(obj.get_absolute_url())
else:
raise ImproperlyConfigured(
"No URL to redirect to. Either pass a post_save_redirec... | def redirect(post_save_redirect, obj) | Returns a HttpResponseRedirect to ``post_save_redirect``.
``post_save_redirect`` should be a string, and can contain named string-
substitution place holders of ``obj`` field names.
If ``post_save_redirect`` is None, then redirect to ``obj``'s URL returned
by ``get_absolute_url()``. If ``obj`` has no... | 2.480356 | 2.484176 | 0.998462 |
lookup_kwargs = {}
if object_id:
lookup_kwargs['%s__exact' % model._meta.pk.name] = object_id
elif slug and slug_field:
lookup_kwargs['%s__exact' % slug_field] = slug
else:
raise GenericViewError(
"Generic view must be called with either an object_id or a"
... | def lookup_object(model, object_id, slug, slug_field) | Return the ``model`` object with the passed ``object_id``. If
``object_id`` is None, then return the object whose ``slug_field``
equals the passed ``slug``. If ``slug`` and ``slug_field`` are not passed,
then raise Http404 exception. | 2.186583 | 2.172728 | 1.006377 |
if extra_context is None:
extra_context = {}
if login_required and not request.user.is_authenticated:
return redirect_to_login(request.path)
model, form_class = get_model_and_form_class(model, form_class)
if request.method == 'POST':
form = form_class(request.POST, request.... | def create_object(
request, model=None, template_name=None,
template_loader=loader, extra_context=None, post_save_redirect=None,
login_required=False, context_processors=None, form_class=None) | Generic object-creation function.
Templates: ``<app_label>/<model_name>_form.html``
Context:
form
the form for the object | 1.92048 | 1.970511 | 0.97461 |
if extra_context is None:
extra_context = {}
if login_required and not request.user.is_authenticated:
return redirect_to_login(request.path)
model, form_class = get_model_and_form_class(model, form_class)
obj = lookup_object(model, object_id, slug, slug_field)
if request.metho... | def update_object(
request, model=None, object_id=None, slug=None,
slug_field='slug', template_name=None, template_loader=loader,
extra_context=None, post_save_redirect=None, login_required=False,
context_processors=None, template_object_name='object',
form_class=None) | Generic object-update function.
Templates: ``<app_label>/<model_name>_form.html``
Context:
form
the form for the object
object
the original object being edited | 1.740685 | 1.791243 | 0.971775 |
if extra_context is None:
extra_context = {}
if login_required and not request.user.is_authenticated:
return redirect_to_login(request.path)
obj = lookup_object(model, object_id, slug, slug_field)
if request.method == 'POST':
obj.delete()
msg = ugettext("The %(verb... | def delete_object(
request, model, post_delete_redirect, object_id=None,
slug=None, slug_field='slug', template_name=None,
template_loader=loader, extra_context=None, login_required=False,
context_processors=None, template_object_name='object') | Generic object-delete function.
The given template will be used to confirm deletetion if this view is
fetched using GET; for safty, deletion will only be performed if this
view is POSTed.
Templates: ``<app_label>/<model_name>_confirm_delete.html``
Context:
object
the original o... | 1.850918 | 1.999486 | 0.925697 |
for k, v in kw.items():
if k not in self.params:
raise ValidationError(
'"%s" is not a valid parameter for %s'
% (k, self.__class__.__name__))
self.params[k].validate(v)
self._orig_kwargs.update(kw)
self.kw... | def add_params(self, **kw) | Add [possibly many] parameters to the Assembly.
Parameters will be checked against known UCSC parameters and their
supported formats. | 2.838918 | 2.954912 | 0.960746 |
for a in args:
self._orig_kwargs.pop(a)
self.kwargs = self._orig_kwargs.copy() | def remove_params(self, *args) | Remove [possibly many] parameters from the Assembly.
E.g.,
remove_params('color', 'visibility') | 5.214046 | 8.07528 | 0.64568 |
if action == "post_remove":
if not reverse:
group = instance
for person in model.objects.filter(pk__in=pk_set):
_remove_group(group, person)
else:
person = instance
for group in model.objects.filter(pk__in=pk_set):
... | def _members_changed(
sender, instance, action, reverse, model, pk_set, **kwargs) | Hook that executes whenever the group members are changed. | 2.404257 | 2.476063 | 0.971 |
# Check username looks ok
if not username.islower():
raise UsernameInvalid(six.u('Username must be all lowercase'))
if len(username) < 2:
raise UsernameInvalid(six.u('Username must be at least 2 characters'))
if not username_re.search(username):
raise UsernameInvalid(setti... | def validate_username(username) | Validate the new username. If the username is invalid, raises
:py:exc:`UsernameInvalid`.
:param username: Username to validate. | 4.153903 | 4.0955 | 1.01426 |
# is the username valid?
validate_username(username)
# Check for existing people
count = Person.objects.filter(username__exact=username).count()
if count >= 1:
raise UsernameTaken(six.u(
'The username is already taken. Please choose another. '
'If this was th... | def validate_username_for_new_person(username) | Validate the new username for a new person. If the username is invalid
or in use, raises :py:exc:`UsernameInvalid` or :py:exc:`UsernameTaken`.
:param username: Username to validate. | 4.299368 | 4.257079 | 1.009934 |
# This is much the same as validate_username_for_new_person, except
# we don't care if the username is used by the person owning the account
# is the username valid?
validate_username(username)
# Check for existing people
query = Person.objects.filter(username__exact=username)
coun... | def validate_username_for_new_account(person, username) | Validate the new username for a new account. If the username is invalid
or in use, raises :py:exc:`UsernameInvalid` or :py:exc:`UsernameTaken`.
:param person: Owner of new account.
:param username: Username to validate. | 4.051078 | 4.070564 | 0.995213 |
query = Account.objects.filter(
username__exact=username,
date_deleted__isnull=True)
if query.count() > 0:
raise UsernameTaken(
six.u('Username already in use.')
)
if account_exists(username):
raise UsernameTaken(
six.u('Username is alr... | def check_username_for_new_account(person, username) | Check the new username for a new account. If the username is
in use, raises :py:exc:`UsernameTaken`.
:param person: Owner of new account.
:param username: Username to validate. | 5.012465 | 5.019757 | 0.998547 |
# is the username valid?
validate_username(username)
# Check for existing people
count = Person.objects.filter(username__exact=username) \
.exclude(pk=person.pk).count()
if count >= 1:
raise UsernameTaken(
six.u('The username is already taken by an existing perso... | def validate_username_for_rename_person(username, person) | Validate the new username to rename a person. If the username is
invalid or in use, raises :py:exc:`UsernameInvalid` or
:py:exc:`UsernameTaken`.
:param username: Username to validate.
:param person: We exclude this person when checking for duplicates. | 4.174518 | 4.073938 | 1.024689 |
args = []
if label is not None:
args.append(label)
# don't use secret_token unless we have to
if 'is_admin' in roles:
# Administrators can access anything without secrets
require_secret = False
elif 'is_applicant' not in roles:
# we never give secrets to anybody... | def get_url(request, application, roles, label=None) | Retrieve a link that will work for the current user. | 5.541098 | 5.432573 | 1.019977 |
url = '%s/applications/%d/' % (settings.ADMIN_BASE_URL, application.pk)
is_secret = False
return url, is_secret | def get_admin_email_link(application) | Retrieve a link that can be emailed to the administrator. | 5.623045 | 5.074729 | 1.108048 |
url = '%s/applications/%d/' % (
settings.REGISTRATION_BASE_URL, application.pk)
is_secret = False
return url, is_secret | def get_registration_email_link(application) | Retrieve a link that can be emailed to the logged other users. | 6.046971 | 5.669547 | 1.06657 |
# don't use secret_token unless we have to
if (application.content_type.model == 'person'
and application.applicant.has_usable_password()):
url = '%s/applications/%d/' % (
settings.REGISTRATION_BASE_URL, application.pk)
is_secret = False
else:
url = '%s/a... | def get_email_link(application) | Retrieve a link that can be emailed to the applicant. | 4.042095 | 3.948942 | 1.023589 |
# Get the authentication of the current user
roles = self._get_roles_for_request(request, application)
if extra_roles is not None:
roles.update(extra_roles)
# Ensure current user is authenticated. If user isn't applicant,
# leader, delegate or admin, they pr... | def start(self, request, application, extra_roles=None) | Continue the state machine at first state. | 5.585286 | 5.181215 | 1.077988 |
# Get the authentication of the current user
roles = self._get_roles_for_request(request, application)
if extra_roles is not None:
roles.update(extra_roles)
# Ensure current user is authenticated. If user isn't applicant,
# leader, delegate or admin, they p... | def process(
self, request, application,
expected_state, label, extra_roles=None) | Process the view request at the current state. | 4.778763 | 4.778389 | 1.000078 |
roles = application.get_roles_for_person(request.user)
if common.is_admin(request):
roles.add("is_admin")
roles.add('is_authorised')
return roles | def _get_roles_for_request(request, application) | Check the authentication of the current user. | 6.434752 | 5.509366 | 1.167966 |
# we only support state changes for POST requests
if request.method == "POST":
key = None
# If next state is a transition, process it
while True:
# We do not expect to get a direct state transition here.
assert next_config['ty... | def _next(self, request, application, roles, next_config) | Continue the state machine at given state. | 5.01686 | 4.99499 | 1.004378 |
# We only provide a view for when no label provided
if label is not None:
return HttpResponseBadRequest("<h1>Bad Request</h1>")
# only certain actions make sense for default view
actions = self.get_actions(request, application, roles)
# process the request... | def get_next_action(self, request, application, label, roles) | Django view method. We provide a default detail view for
applications. | 4.642588 | 4.473961 | 1.037691 |
if not request.user.is_authenticated:
raise PermissionDenied
if not is_admin(request):
raise PermissionDenied | def check_auth(self, request) | to ensure that nobody can get your data via json simply by knowing the
URL. public facing forms should write a custom LookupChannel to
implement as you wish. also you could choose to return
HttpResponseForbidden("who are you?") instead of raising
PermissionDenied (401 response) | 3.938124 | 3.393795 | 1.160389 |
return Institute.objects.filter(
Q(name__icontains=q)
) | def get_query(self, q, request) | return a query set searching for the query string q
either implement this method yourself or set the search_field
in the LookupChannel class definition | 7.137414 | 6.090198 | 1.171951 |
if not autocast:
return self.buckets
if self.kind in ["exponential", "linear", "enumerated", "boolean"]:
return float(self.percentile(50)) if only_median else self.buckets
elif self.kind == "categorical" and not only_median:
return self.buckets
... | def get_value(self, only_median=False, autocast=True) | Returns a scalar for flag and count histograms. Otherwise it returns either the
raw histogram represented as a pandas Series or just the median if only_median
is True.
If autocast is disabled the underlying pandas series is always returned as is. | 4.318466 | 3.802747 | 1.135617 |
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