id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
|---|---|---|---|---|---|---|---|---|---|---|---|
16,700 | payu-org/payu | payu/manifest.py | PayuManifest.make_link | def make_link(self, filepath):
"""
Payu integration function for creating symlinks in work directories
which point back to the original file.
"""
# Check file exists. It may have been deleted but still in manifest
if not os.path.exists(self.fullpath(filepath)):
print('File not found: {filepath}'.format(
filepath=self.fullpath(filepath)))
if self.contains(filepath):
print('removing from manifest')
self.delete(filepath)
self.needsync = True
else:
try:
destdir = os.path.dirname(filepath)
# Make destination directory if not already exists
# Necessary because sometimes this is called before
# individual model setup
if not os.path.exists(destdir):
os.makedirs(destdir)
if self.copy_file(filepath):
shutil.copy(self.fullpath(filepath), filepath)
perm = (stat.S_IRUSR | stat.S_IRGRP
| stat.S_IROTH | stat.S_IWUSR)
os.chmod(filepath, perm)
else:
make_symlink(self.fullpath(filepath), filepath)
except Exception:
action = 'copying' if self.copy_file else 'linking'
print('payu: error: {action} orig: {orig} '
'local: {local}'.format(action=action,
orig=self.fullpath(filepath),
local=filepath))
raise | python | def make_link(self, filepath):
# Check file exists. It may have been deleted but still in manifest
if not os.path.exists(self.fullpath(filepath)):
print('File not found: {filepath}'.format(
filepath=self.fullpath(filepath)))
if self.contains(filepath):
print('removing from manifest')
self.delete(filepath)
self.needsync = True
else:
try:
destdir = os.path.dirname(filepath)
# Make destination directory if not already exists
# Necessary because sometimes this is called before
# individual model setup
if not os.path.exists(destdir):
os.makedirs(destdir)
if self.copy_file(filepath):
shutil.copy(self.fullpath(filepath), filepath)
perm = (stat.S_IRUSR | stat.S_IRGRP
| stat.S_IROTH | stat.S_IWUSR)
os.chmod(filepath, perm)
else:
make_symlink(self.fullpath(filepath), filepath)
except Exception:
action = 'copying' if self.copy_file else 'linking'
print('payu: error: {action} orig: {orig} '
'local: {local}'.format(action=action,
orig=self.fullpath(filepath),
local=filepath))
raise | [
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16,701 | payu-org/payu | payu/manifest.py | Manifest.add_filepath | def add_filepath(self, manifest, filepath, fullpath, copy=False):
"""
Wrapper to the add_filepath function in PayuManifest. Prevents outside
code from directly calling anything in PayuManifest.
"""
filepath = os.path.normpath(filepath)
if self.manifests[manifest].add_filepath(filepath, fullpath, copy):
# Only link if filepath was added
self.manifests[manifest].make_link(filepath) | python | def add_filepath(self, manifest, filepath, fullpath, copy=False):
filepath = os.path.normpath(filepath)
if self.manifests[manifest].add_filepath(filepath, fullpath, copy):
# Only link if filepath was added
self.manifests[manifest].make_link(filepath) | [
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16,702 | payu-org/payu | payu/runlog.py | commit_hash | def commit_hash(dir='.'):
"""
Return commit hash for HEAD of checked out branch of the
specified directory.
"""
cmd = ['git', 'rev-parse', 'HEAD']
try:
with open(os.devnull, 'w') as devnull:
revision_hash = subprocess.check_output(
cmd,
cwd=dir,
stderr=devnull
)
if sys.version_info.major > 2:
revision_hash = revision_hash.decode('ascii')
return revision_hash.strip()
except subprocess.CalledProcessError:
return None | python | def commit_hash(dir='.'):
cmd = ['git', 'rev-parse', 'HEAD']
try:
with open(os.devnull, 'w') as devnull:
revision_hash = subprocess.check_output(
cmd,
cwd=dir,
stderr=devnull
)
if sys.version_info.major > 2:
revision_hash = revision_hash.decode('ascii')
return revision_hash.strip()
except subprocess.CalledProcessError:
return None | [
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16,703 | payu-org/payu | payu/runlog.py | Runlog.create_manifest | def create_manifest(self):
"""Construct the list of files to be tracked by the runlog."""
config_path = os.path.join(self.expt.control_path,
DEFAULT_CONFIG_FNAME)
self.manifest = []
if os.path.isfile(config_path):
self.manifest.append(config_path)
for model in self.expt.models:
config_files = model.config_files + model.optional_config_files
self.manifest.extend(os.path.join(model.control_path, f)
for f in config_files)
# Add file manifests to runlog manifest
for mf in self.expt.manifest:
self.manifest.append(mf.path) | python | def create_manifest(self):
config_path = os.path.join(self.expt.control_path,
DEFAULT_CONFIG_FNAME)
self.manifest = []
if os.path.isfile(config_path):
self.manifest.append(config_path)
for model in self.expt.models:
config_files = model.config_files + model.optional_config_files
self.manifest.extend(os.path.join(model.control_path, f)
for f in config_files)
# Add file manifests to runlog manifest
for mf in self.expt.manifest:
self.manifest.append(mf.path) | [
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16,704 | payu-org/payu | payu/runlog.py | Runlog.push | def push(self):
"""Push the changes to the remote repository.
Usage: payu push
This command pushes local runlog changes to the remote runlog
repository, currently named `payu`, using the SSH key associated with
this experiment.
For an experiment `test`, it is equivalent to the following command::
ssh-agent bash -c "
ssh-add $HOME/.ssh/payu/id_rsa_payu_test
git push --all payu
"
"""
expt_name = self.config.get('name', self.expt.name)
default_ssh_key = 'id_rsa_payu_' + expt_name
ssh_key = self.config.get('sshid', default_ssh_key)
ssh_key_path = os.path.join(os.path.expanduser('~'), '.ssh', 'payu',
ssh_key)
if not os.path.isfile(ssh_key_path):
print('payu: error: Github SSH key {key} not found.'
''.format(key=ssh_key_path))
print('payu: error: Run `payu ghsetup` to generate a new key.')
sys.exit(-1)
cmd = ('ssh-agent bash -c "ssh-add {key}; git push --all payu"'
''.format(key=ssh_key_path))
subprocess.check_call(shlex.split(cmd), cwd=self.expt.control_path) | python | def push(self):
expt_name = self.config.get('name', self.expt.name)
default_ssh_key = 'id_rsa_payu_' + expt_name
ssh_key = self.config.get('sshid', default_ssh_key)
ssh_key_path = os.path.join(os.path.expanduser('~'), '.ssh', 'payu',
ssh_key)
if not os.path.isfile(ssh_key_path):
print('payu: error: Github SSH key {key} not found.'
''.format(key=ssh_key_path))
print('payu: error: Run `payu ghsetup` to generate a new key.')
sys.exit(-1)
cmd = ('ssh-agent bash -c "ssh-add {key}; git push --all payu"'
''.format(key=ssh_key_path))
subprocess.check_call(shlex.split(cmd), cwd=self.expt.control_path) | [
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For an experiment `test`, it is equivalent to the following command::
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git push --all payu
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16,705 | mozilla/python_moztelemetry | moztelemetry/shared_telemetry_utils.py | add_expiration_postfix | def add_expiration_postfix(expiration):
""" Formats the expiration version and adds a version postfix if needed.
:param expiration: the expiration version string.
:return: the modified expiration string.
"""
if re.match(r'^[1-9][0-9]*$', expiration):
return expiration + ".0a1"
if re.match(r'^[1-9][0-9]*\.0$', expiration):
return expiration + "a1"
return expiration | python | def add_expiration_postfix(expiration):
if re.match(r'^[1-9][0-9]*$', expiration):
return expiration + ".0a1"
if re.match(r'^[1-9][0-9]*\.0$', expiration):
return expiration + "a1"
return expiration | [
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16,706 | mozilla/python_moztelemetry | moztelemetry/shared_telemetry_utils.py | load_yaml_file | def load_yaml_file(filename):
""" Load a YAML file from disk, throw a ParserError on failure."""
try:
with open(filename, 'r') as f:
return yaml.safe_load(f)
except IOError as e:
raise ParserError('Error opening ' + filename + ': ' + e.message)
except ValueError as e:
raise ParserError('Error parsing processes in {}: {}'
.format(filename, e.message)) | python | def load_yaml_file(filename):
try:
with open(filename, 'r') as f:
return yaml.safe_load(f)
except IOError as e:
raise ParserError('Error opening ' + filename + ': ' + e.message)
except ValueError as e:
raise ParserError('Error parsing processes in {}: {}'
.format(filename, e.message)) | [
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16,707 | mozilla/python_moztelemetry | moztelemetry/shared_telemetry_utils.py | StringTable.writeDefinition | def writeDefinition(self, f, name):
"""Writes the string table to a file as a C const char array.
This writes out the string table as one single C char array for memory
size reasons, separating the individual strings with '\0' characters.
This way we can index directly into the string array and avoid the additional
storage costs for the pointers to them (and potential extra relocations for those).
:param f: the output stream.
:param name: the name of the output array.
"""
entries = self.table.items()
entries.sort(key=lambda x: x[1])
# Avoid null-in-string warnings with GCC and potentially
# overlong string constants; write everything out the long way.
def explodeToCharArray(string):
def toCChar(s):
if s == "'":
return "'\\''"
else:
return "'%s'" % s
return ", ".join(map(toCChar, string))
f.write("const char %s[] = {\n" % name)
for (string, offset) in entries:
if "*/" in string:
raise ValueError("String in string table contains unexpected sequence '*/': %s" %
string)
e = explodeToCharArray(string)
if e:
f.write(" /* %5d - \"%s\" */ %s, '\\0',\n"
% (offset, string, explodeToCharArray(string)))
else:
f.write(" /* %5d - \"%s\" */ '\\0',\n" % (offset, string))
f.write("};\n\n") | python | def writeDefinition(self, f, name):
entries = self.table.items()
entries.sort(key=lambda x: x[1])
# Avoid null-in-string warnings with GCC and potentially
# overlong string constants; write everything out the long way.
def explodeToCharArray(string):
def toCChar(s):
if s == "'":
return "'\\''"
else:
return "'%s'" % s
return ", ".join(map(toCChar, string))
f.write("const char %s[] = {\n" % name)
for (string, offset) in entries:
if "*/" in string:
raise ValueError("String in string table contains unexpected sequence '*/': %s" %
string)
e = explodeToCharArray(string)
if e:
f.write(" /* %5d - \"%s\" */ %s, '\\0',\n"
% (offset, string, explodeToCharArray(string)))
else:
f.write(" /* %5d - \"%s\" */ '\\0',\n" % (offset, string))
f.write("};\n\n") | [
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16,708 | Karaage-Cluster/karaage | karaage/templatetags/karaage_tags.py | comments | def comments(context, obj):
""" Render comments for obj. """
content_type = ContentType.objects.get_for_model(obj.__class__)
comment_list = LogEntry.objects.filter(
content_type=content_type,
object_id=obj.pk,
action_flag=COMMENT
)
return {
'obj': obj,
'comment_list': comment_list,
'is_admin': context['is_admin'],
} | python | def comments(context, obj):
content_type = ContentType.objects.get_for_model(obj.__class__)
comment_list = LogEntry.objects.filter(
content_type=content_type,
object_id=obj.pk,
action_flag=COMMENT
)
return {
'obj': obj,
'comment_list': comment_list,
'is_admin': context['is_admin'],
} | [
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16,709 | Karaage-Cluster/karaage | karaage/machines/xmlrpc.py | get_disk_quota | def get_disk_quota(username, machine_name=None):
"""
Returns disk quota for username in KB
"""
try:
ua = Account.objects.get(
username=username,
date_deleted__isnull=True)
except Account.DoesNotExist:
return 'Account not found'
result = ua.get_disk_quota()
if result is None:
return False
return result * 1048576 | python | def get_disk_quota(username, machine_name=None):
try:
ua = Account.objects.get(
username=username,
date_deleted__isnull=True)
except Account.DoesNotExist:
return 'Account not found'
result = ua.get_disk_quota()
if result is None:
return False
return result * 1048576 | [
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16,710 | mozilla/python_moztelemetry | moztelemetry/standards.py | snap_to_beginning_of_week | 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.
"""
delta_days = ((day.weekday() + 1) % 7) if weekday_start is "Sunday" else day.weekday()
return day - timedelta(days=delta_days) | python | def snap_to_beginning_of_week(day, weekday_start="Sunday"):
delta_days = ((day.weekday() + 1) % 7) if weekday_start is "Sunday" else day.weekday()
return day - timedelta(days=delta_days) | [
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... | Get the first day of the current week.
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: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. | [
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] | 09ddf1ec7d953a4308dfdcb0ed968f27bd5921bb | https://github.com/mozilla/python_moztelemetry/blob/09ddf1ec7d953a4308dfdcb0ed968f27bd5921bb/moztelemetry/standards.py#L96-L104 |
16,711 | mozilla/python_moztelemetry | moztelemetry/standards.py | get_last_week_range | 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.
"""
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) | python | def get_last_week_range(weekday_start="Sunday"):
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) | [
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16,712 | mozilla/python_moztelemetry | moztelemetry/standards.py | get_last_month_range | 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.
"""
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) | python | def get_last_month_range():
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) | [
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16,713 | mozilla/python_moztelemetry | moztelemetry/standards.py | read_main_summary | 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 the
`submission_date_s3` partition. Default is to read all
partitions. Each value should be in the form `YYYYMMDD`.
sample_id: Optional list of values to filter the `sample_id`
partition. Default is to read all partitions.
mergeSchema (bool): Determines whether or not to merge the
schemas of the resulting parquet files (ie. whether to
support schema evolution or not). Default is to merge
schemas.
path (str): Location (disk or S3) from which to read data.
Default is to read from the "production" location on S3.
Returns:
A DataFrame loaded from the specified partitions.
"""
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 None:
paths = ["{}/submission_date_s3={}/".format(base_path, s) for s in submission_date_s3]
return reader.parquet(*paths)
if submission_date_s3 is not None and sample_id is not None:
paths = []
for sd in submission_date_s3:
for si in sample_id:
paths.append("{}/submission_date_s3={}/sample_id={}/".format(
base_path, sd, si))
return reader.parquet(*paths)
if submission_date_s3 is None and sample_id is not None:
# Ugh, why? We would have to iterate the entire path to identify
# all the submission_date_s3 partitions, which may end up being
# slower.
data = reader.parquet(base_path)
sids = ["{}".format(s) for s in sample_id]
criteria = "sample_id IN ({})".format(",".join(sids))
return data.where(criteria)
# Neither partition is filtered.
return reader.parquet(base_path) | python | def read_main_summary(spark,
submission_date_s3=None,
sample_id=None,
mergeSchema=True,
path='s3://telemetry-parquet/main_summary/v4'):
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 None:
paths = ["{}/submission_date_s3={}/".format(base_path, s) for s in submission_date_s3]
return reader.parquet(*paths)
if submission_date_s3 is not None and sample_id is not None:
paths = []
for sd in submission_date_s3:
for si in sample_id:
paths.append("{}/submission_date_s3={}/sample_id={}/".format(
base_path, sd, si))
return reader.parquet(*paths)
if submission_date_s3 is None and sample_id is not None:
# Ugh, why? We would have to iterate the entire path to identify
# all the submission_date_s3 partitions, which may end up being
# slower.
data = reader.parquet(base_path)
sids = ["{}".format(s) for s in sample_id]
criteria = "sample_id IN ({})".format(",".join(sids))
return data.where(criteria)
# Neither partition is filtered.
return reader.parquet(base_path) | [
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] | 09ddf1ec7d953a4308dfdcb0ed968f27bd5921bb | https://github.com/mozilla/python_moztelemetry/blob/09ddf1ec7d953a4308dfdcb0ed968f27bd5921bb/moztelemetry/standards.py#L143-L202 |
16,714 | mozilla/python_moztelemetry | moztelemetry/standards.py | 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 should match the value previously
used, optionally plus multiples of 100.
Args:
dataframe: A Dataframe to be sampled
modulo (int): selects a 1/modulo sampling of dataframe
column (str): name of a string column to sample on
sample_id (int): modulus result to select for sampling
Returns:
A DataFrame sampled on the given inputs.
"""
return dataframe \
.withColumn(
"sampler",
udf(lambda key: (crc32(key or "") & 0xffffffff) % modulo)(column),
).where("sampler = %s" % sample_id).drop("sampler") | python | def sampler(dataframe, modulo, column="client_id", sample_id=42):
return dataframe \
.withColumn(
"sampler",
udf(lambda key: (crc32(key or "") & 0xffffffff) % modulo)(column),
).where("sampler = %s" % sample_id).drop("sampler") | [
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16,715 | Karaage-Cluster/karaage | karaage/plugins/kgusage/views.py | progress | def progress(request):
""" Check status of task. """
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',
context={'content': 'Deleted'},
request=request)
if request.method == 'POST':
if 'task_id' in request.POST:
result = Task.AsyncResult(request.POST['task_id'])
if result.failed():
value = {
'info': {},
'ready': result.ready(),
}
else:
value = {
'info': result.info,
'ready': result.ready(),
}
return HttpResponse(
json.dumps(value), content_type="application/json")
return None | python | def progress(request):
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',
context={'content': 'Deleted'},
request=request)
if request.method == 'POST':
if 'task_id' in request.POST:
result = Task.AsyncResult(request.POST['task_id'])
if result.failed():
value = {
'info': {},
'ready': result.ready(),
}
else:
value = {
'info': result.info,
'ready': result.ready(),
}
return HttpResponse(
json.dumps(value), content_type="application/json")
return None | [
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16,716 | Karaage-Cluster/karaage | karaage/plugins/kgusage/views.py | synchronise | def synchronise(func):
""" If task already queued, running, or finished, don't restart. """
def inner(request, *args):
lock_id = '%s-%s-built-%s' % (
datetime.date.today(), func.__name__,
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if cache.add(lock_id, 'true', LOCK_EXPIRE):
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if not task_id:
return None
cache.set(lock_id, "")
result = Task.AsyncResult(task_id)
if result.ready():
result.forget()
return None
return result
return inner | python | def synchronise(func):
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)
else:
task_id = cache.get(lock_id)
if not task_id:
return None
cache.set(lock_id, "")
result = Task.AsyncResult(task_id)
if result.ready():
result.forget()
return None
return result
return inner | [
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16,717 | mozilla/python_moztelemetry | moztelemetry/dataset.py | _group_by_size_greedy | 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_groups: number of partitions to split the data into.
:return: a list of lists, one for each partition.
"""
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 | python | def _group_by_size_greedy(obj_list, tot_groups):
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 | [
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16,718 | mozilla/python_moztelemetry | moztelemetry/dataset.py | _group_by_equal_size | 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: number of partitions to split the data
:param threshold: the maximum size of each bucket
:return: a list of lists, one for each partition
"""
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:
if obj[0] > threshold:
heapq.heappush(groups, (obj[0], [obj[1]]))
else:
size, files = heapq.heappop(groups)
size += obj[0]
files.append(obj[1])
heapq.heappush(groups, (size, files))
groups = [group[1] for group in groups]
return groups | python | def _group_by_equal_size(obj_list, tot_groups, threshold=pow(2, 32)):
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:
if obj[0] > threshold:
heapq.heappush(groups, (obj[0], [obj[1]]))
else:
size, files = heapq.heappop(groups)
size += obj[0]
files.append(obj[1])
heapq.heappush(groups, (size, files))
groups = [group[1] for group in groups]
return groups | [
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16,719 | mozilla/python_moztelemetry | moztelemetry/dataset.py | Dataset.select | 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.
The JMESPath string will be used as a key in the output dictionary.
:param aliased_properties: Same as properties, but the output dictionary will contain
the parameter name instead of the JMESPath string.
"""
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 Exception('The property {} has already been selected'.format(prop_name))
new_selection = self.selection.copy()
new_selection.update(merged_properties)
return self._copy(selection=new_selection) | python | def select(self, *properties, **aliased_properties):
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 Exception('The property {} has already been selected'.format(prop_name))
new_selection = self.selection.copy()
new_selection.update(merged_properties)
return self._copy(selection=new_selection) | [
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] | 09ddf1ec7d953a4308dfdcb0ed968f27bd5921bb | https://github.com/mozilla/python_moztelemetry/blob/09ddf1ec7d953a4308dfdcb0ed968f27bd5921bb/moztelemetry/dataset.py#L174-L197 |
16,720 | mozilla/python_moztelemetry | moztelemetry/dataset.py | Dataset.where | 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 string, then sanitized. If `condition` is a callable, note that it will
be passed sanitized values -- i.e., characters outside [a-zA-Z0-9_.] are converted
to `_`.
"""
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 dimension {} doesn\'t exist'.format(dimension))
if isfunction(condition) or isinstance(condition, functools.partial):
clauses[dimension] = condition
else:
clauses[dimension] = functools.partial((lambda x, y: x == y), self._sanitize_dimension(str(condition)))
return self._copy(clauses=clauses) | python | def where(self, **kwargs):
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 dimension {} doesn\'t exist'.format(dimension))
if isfunction(condition) or isinstance(condition, functools.partial):
clauses[dimension] = condition
else:
clauses[dimension] = functools.partial((lambda x, y: x == y), self._sanitize_dimension(str(condition)))
return self._copy(clauses=clauses) | [
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16,721 | mozilla/python_moztelemetry | moztelemetry/dataset.py | Dataset.summaries | 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 iterable of summaries
"""
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 prefix directory)
clauses['prefix'] = lambda x: True
with futures.ThreadPoolExecutor(self.max_concurrency) as executor:
scanned = self._scan(schema, [self.prefix], clauses, executor)
keys = sc.parallelize(scanned).flatMap(self.store.list_keys)
return keys.take(limit) if limit else keys.collect() | python | def summaries(self, sc, limit=None):
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 prefix directory)
clauses['prefix'] = lambda x: True
with futures.ThreadPoolExecutor(self.max_concurrency) as executor:
scanned = self._scan(schema, [self.prefix], clauses, executor)
keys = sc.parallelize(scanned).flatMap(self.store.list_keys)
return keys.take(limit) if limit else keys.collect() | [
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:param limit: Max number of objects to retrieve
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16,722 | mozilla/python_moztelemetry | moztelemetry/dataset.py | Dataset.records | 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: percentage of results to return. Useful to return a sample
of the dataset. This parameter is ignored when `limit` is set.
:param seed: initialize internal state of the random number generator (42 by default).
This is used to make the dataset sampling reproducible. It can be set to None to obtain
different samples.
:param summaries: an iterable containing a summary for each item in the dataset. If None,
it will computed calling the summaries dataset.
:return: a Spark rdd containing the elements retrieved
"""
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:
raise ValueError('sample must be between 0 and 1')
print(
"WARNING: THIS IS NOT A REPRESENTATIVE SAMPLE.\n"
"This 'sampling' is based on s3 files and is highly\n"
"susceptible to skew. Use only for quicker performance\n"
"while prototyping."
)
# We want this sample to be reproducible.
# See https://bugzilla.mozilla.org/show_bug.cgi?id=1318681
seed_state = random.getstate()
try:
random.seed(seed)
summaries = random.sample(summaries,
int(len(summaries) * sample))
finally:
random.setstate(seed_state)
# Obtain size in MB
total_size = functools.reduce(lambda acc, item: acc + item['size'], summaries, 0)
total_size_mb = total_size / float(1 << 20)
print("fetching %.5fMB in %s files..." % (total_size_mb, len(summaries)))
if group_by == 'equal_size':
groups = _group_by_equal_size(summaries, 10*sc.defaultParallelism)
elif group_by == 'greedy':
groups = _group_by_size_greedy(summaries, 10*sc.defaultParallelism)
else:
raise Exception("group_by specification is invalid")
self._compile_selection()
keys = (
sc.parallelize(groups, len(groups))
.flatMap(lambda x: x)
.map(lambda x: x['key'])
)
file_handles = keys.map(self.store.get_key)
# decode(fp: file-object) -> list[dict]
data = file_handles.flatMap(decode)
return data.map(self._apply_selection) | python | def records(self, sc, group_by='greedy', limit=None, sample=1, seed=42, decode=None, summaries=None):
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:
raise ValueError('sample must be between 0 and 1')
print(
"WARNING: THIS IS NOT A REPRESENTATIVE SAMPLE.\n"
"This 'sampling' is based on s3 files and is highly\n"
"susceptible to skew. Use only for quicker performance\n"
"while prototyping."
)
# We want this sample to be reproducible.
# See https://bugzilla.mozilla.org/show_bug.cgi?id=1318681
seed_state = random.getstate()
try:
random.seed(seed)
summaries = random.sample(summaries,
int(len(summaries) * sample))
finally:
random.setstate(seed_state)
# Obtain size in MB
total_size = functools.reduce(lambda acc, item: acc + item['size'], summaries, 0)
total_size_mb = total_size / float(1 << 20)
print("fetching %.5fMB in %s files..." % (total_size_mb, len(summaries)))
if group_by == 'equal_size':
groups = _group_by_equal_size(summaries, 10*sc.defaultParallelism)
elif group_by == 'greedy':
groups = _group_by_size_greedy(summaries, 10*sc.defaultParallelism)
else:
raise Exception("group_by specification is invalid")
self._compile_selection()
keys = (
sc.parallelize(groups, len(groups))
.flatMap(lambda x: x)
.map(lambda x: x['key'])
)
file_handles = keys.map(self.store.get_key)
# decode(fp: file-object) -> list[dict]
data = file_handles.flatMap(decode)
return data.map(self._apply_selection) | [
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: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: percentage of results to return. Useful to return a sample
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:param seed: initialize internal state of the random number generator (42 by default).
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:param summaries: an iterable containing a summary for each item in the dataset. If None,
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16,723 | mozilla/python_moztelemetry | moztelemetry/dataset.py | Dataset.dataframe | 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
:param sample: percentage of results to return. Useful to return a sample
of the dataset. This parameter is ignored when 'limit' is set.
:param seed: initialize internal state of the random number generator (42 by default).
This is used to make the dataset sampling reproducible. It an be set to None to obtain
different samples.
:param summaries: an iterable containing the summary for each item in the dataset. If None, it
will compute calling the summaries dataset.
:param schema: a Spark schema that overrides automatic conversion to a dataframe
:param table_name: allows resulting dataframe to easily be queried using SparkSQL
:return: a Spark DataFrame
"""
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(table_name)
return df | python | def dataframe(self, spark, group_by='greedy', limit=None, sample=1, seed=42, decode=None, summaries=None, schema=None, table_name=None):
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(table_name)
return df | [
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: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
:param sample: percentage of results to return. Useful to return a sample
of the dataset. This parameter is ignored when 'limit' is set.
:param seed: initialize internal state of the random number generator (42 by default).
This is used to make the dataset sampling reproducible. It an be set to None to obtain
different samples.
:param summaries: an iterable containing the summary for each item in the dataset. If None, it
will compute calling the summaries dataset.
:param schema: a Spark schema that overrides automatic conversion to a dataframe
:param table_name: allows resulting dataframe to easily be queried using SparkSQL
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16,724 | mozilla/python_moztelemetry | moztelemetry/dataset.py | Dataset.from_source | 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',
submissionDate='20160701',
appUpdateChannel='nightly'
)
"""
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))
schema = store.get_key('{}/schema.json'.format(source['metadata_prefix'])).read().decode('utf-8')
dimensions = [f['field_name'] for f in json.loads(schema)['dimensions']]
return Dataset(source['bucket'], dimensions, prefix=source['prefix']) | python | def from_source(source_name):
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))
schema = store.get_key('{}/schema.json'.format(source['metadata_prefix'])).read().decode('utf-8')
dimensions = [f['field_name'] for f in json.loads(schema)['dimensions']]
return Dataset(source['bucket'], dimensions, prefix=source['prefix']) | [
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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',
submissionDate='20160701',
appUpdateChannel='nightly'
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16,725 | Karaage-Cluster/karaage | karaage/people/emails.py | send_bounced_warning | def send_bounced_warning(person, leader_list):
"""Sends an email to each project leader for person
informing them that person's email has bounced"""
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_email_subject.txt', context)
body = render_to_string(
'karaage/people/emails/bounced_email_body.txt', context)
send_mail(
subject.replace('\n', ''), body,
settings.ACCOUNTS_EMAIL, [to_email])
log.change(
leader,
'Sent email about bounced emails from %s' % person) | python | def send_bounced_warning(person, leader_list):
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_email_subject.txt', context)
body = render_to_string(
'karaage/people/emails/bounced_email_body.txt', context)
send_mail(
subject.replace('\n', ''), body,
settings.ACCOUNTS_EMAIL, [to_email])
log.change(
leader,
'Sent email about bounced emails from %s' % person) | [
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16,726 | Karaage-Cluster/karaage | karaage/people/emails.py | send_reset_password_email | def send_reset_password_email(person):
"""Sends an email to user allowing them to set their password."""
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': person,
})
to_email = person.email
subject, body = render_email('reset_password', context)
send_mail(subject, body, settings.ACCOUNTS_EMAIL, [to_email]) | python | def send_reset_password_email(person):
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': person,
})
to_email = person.email
subject, body = render_email('reset_password', context)
send_mail(subject, body, settings.ACCOUNTS_EMAIL, [to_email]) | [
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16,727 | Karaage-Cluster/karaage | karaage/people/emails.py | send_confirm_password_email | def send_confirm_password_email(person):
"""Sends an email to user allowing them to confirm their password."""
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, body, settings.ACCOUNTS_EMAIL, [to_email]) | python | def send_confirm_password_email(person):
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, body, settings.ACCOUNTS_EMAIL, [to_email]) | [
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16,728 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/states.py | StateWaitingForApproval.check_can_approve | def check_can_approve(self, request, application, roles):
""" Check the person's authorization. """
try:
authorised_persons = self.get_authorised_persons(application)
authorised_persons.get(pk=request.user.pk)
return True
except Person.DoesNotExist:
return False | python | def check_can_approve(self, request, application, roles):
try:
authorised_persons = self.get_authorised_persons(application)
authorised_persons.get(pk=request.user.pk)
return True
except Person.DoesNotExist:
return False | [
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] | 2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9 | https://github.com/Karaage-Cluster/karaage/blob/2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9/karaage/plugins/kgapplications/views/states.py#L57-L64 |
16,729 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/states.py | StateWaitingForApproval.enter_state | def enter_state(self, request, application):
""" This is becoming the new current state. """
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, is_secret) | python | def enter_state(self, request, application):
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, is_secret) | [
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16,730 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/states.py | StateWithSteps.add_step | def add_step(self, step, step_id):
""" Add a step to the list. The first step added becomes the initial
step. """
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) | python | def add_step(self, step, step_id):
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) | [
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16,731 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | _init_datastores | def _init_datastores():
""" Initialize all datastores. """
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:
warnings.warn(
"MACHINE_CATEGORY_DATASTORES is deprecated, "
"please change to use DATASTORES",
)
for name in ['ldap']:
array = settings.MACHINE_CATEGORY_DATASTORES.get(name, [])
for config in array:
cls = _lookup(config['ENGINE'])
ds = _get_datastore(cls, DataStore, config)
_DATASTORES.append(ds) | python | def _init_datastores():
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:
warnings.warn(
"MACHINE_CATEGORY_DATASTORES is deprecated, "
"please change to use DATASTORES",
)
for name in ['ldap']:
array = settings.MACHINE_CATEGORY_DATASTORES.get(name, [])
for config in array:
cls = _lookup(config['ENGINE'])
ds = _get_datastore(cls, DataStore, config)
_DATASTORES.append(ds) | [
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16,732 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | get_group_details | def get_group_details(group):
""" Get group details. """
result = []
for datastore in _get_datastores():
value = datastore.get_group_details(group)
value['datastore'] = datastore.config['DESCRIPTION']
result.append(value)
return result | python | def get_group_details(group):
result = []
for datastore in _get_datastores():
value = datastore.get_group_details(group)
value['datastore'] = datastore.config['DESCRIPTION']
result.append(value)
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16,733 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | set_project_pid | def set_project_pid(project, old_pid, new_pid):
""" Project's PID was changed. """
for datastore in _get_datastores():
datastore.save_project(project)
datastore.set_project_pid(project, old_pid, new_pid) | python | def set_project_pid(project, old_pid, new_pid):
for datastore in _get_datastores():
datastore.save_project(project)
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16,734 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | add_accounts_to_group | def add_accounts_to_group(accounts_query, group):
""" Add accounts to group. """
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_group(account, group) | python | def add_accounts_to_group(accounts_query, group):
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_group(account, group) | [
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16,735 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | remove_accounts_from_group | def remove_accounts_from_group(accounts_query, group):
""" Remove accounts from group. """
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_group(account, group) | python | def remove_accounts_from_group(accounts_query, group):
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_group(account, group) | [
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16,736 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | add_accounts_to_project | def add_accounts_to_project(accounts_query, project):
""" Add accounts to project. """
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_project(account, project) | python | def add_accounts_to_project(accounts_query, project):
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
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16,737 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | remove_accounts_from_project | def remove_accounts_from_project(accounts_query, project):
""" Remove accounts from project. """
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_project(account, project) | python | def remove_accounts_from_project(accounts_query, project):
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
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16,738 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | add_accounts_to_institute | def add_accounts_to_institute(accounts_query, institute):
""" Add accounts to institute. """
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
add_account_to_institute(account, institute) | python | def add_accounts_to_institute(accounts_query, institute):
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
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16,739 | Karaage-Cluster/karaage | karaage/datastores/__init__.py | remove_accounts_from_institute | def remove_accounts_from_institute(accounts_query, institute):
""" Remove accounts from institute. """
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
remove_account_from_institute(account, institute) | python | def remove_accounts_from_institute(accounts_query, institute):
query = accounts_query.filter(date_deleted__isnull=True)
for account in query:
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16,740 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase._filter_string | def _filter_string(value):
""" Filter the string so MAM doesn't have heart failure."""
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()
# hack because MAM doesn't quote sql correctly
value = value.replace("\\", "")
# Used for stripping non-ascii characters
value = ''.join(c for c in value if 31 < ord(c) < 127)
return value | python | def _filter_string(value):
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()
# hack because MAM doesn't quote sql correctly
value = value.replace("\\", "")
# Used for stripping non-ascii characters
value = ''.join(c for c in value if 31 < ord(c) < 127)
return value | [
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16,741 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.get_user | def get_user(self, username):
""" Get the user details from MAM. """
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(
"Command returned multiple results for '%s'." % username)
the_result = results[0]
the_name = the_result["Name"]
if username.lower() != the_name.lower():
logger.error(
"We expected username '%s' but got username '%s'."
% (username, the_name))
raise RuntimeError(
"We expected username '%s' but got username '%s'."
% (username, the_name))
return the_result | python | def get_user(self, username):
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(
"Command returned multiple results for '%s'." % username)
the_result = results[0]
the_name = the_result["Name"]
if username.lower() != the_name.lower():
logger.error(
"We expected username '%s' but got username '%s'."
% (username, the_name))
raise RuntimeError(
"We expected username '%s' but got username '%s'."
% (username, the_name))
return the_result | [
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16,742 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.get_user_balance | def get_user_balance(self, username):
""" Get the user balance details from MAM. """
cmd = ["gbalance", "-u", username, "--raw"]
results = self._read_output(cmd)
if len(results) == 0:
return None
return results | python | def get_user_balance(self, username):
cmd = ["gbalance", "-u", username, "--raw"]
results = self._read_output(cmd)
if len(results) == 0:
return None
return results | [
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16,743 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.get_users_in_project | def get_users_in_project(self, projectname):
""" Get list of users in project from MAM. """
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 ds_project["Users"] != "":
user_list = ds_project["Users"].lower().split(",")
return user_list | python | def get_users_in_project(self, projectname):
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 ds_project["Users"] != "":
user_list = ds_project["Users"].lower().split(",")
return user_list | [
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16,744 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.get_projects_in_user | def get_projects_in_user(self, username):
""" Get list of projects in user from MAM. """
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 | python | def get_projects_in_user(self, username):
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 | [
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16,745 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.get_account_details | def get_account_details(self, account):
""" Get the account details """
result = self.get_user(account.username)
if result is None:
result = {}
return result | python | def get_account_details(self, account):
result = self.get_user(account.username)
if result is None:
result = {}
return result | [
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16,746 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.get_project_details | def get_project_details(self, project):
""" Get the project details. """
result = self.get_project(project.pid)
if result is None:
result = {}
return result | python | def get_project_details(self, project):
result = self.get_project(project.pid)
if result is None:
result = {}
return result | [
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16,747 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStoreBase.delete_institute | def delete_institute(self, institute):
""" Called when institute is deleted. """
name = institute.name
logger.debug("institute_deleted '%s'" % name)
# institute deleted
self._call(["goldsh", "Organization", "Delete", "Name==%s" % name])
logger.debug("returning")
return | python | def delete_institute(self, institute):
name = institute.name
logger.debug("institute_deleted '%s'" % name)
# institute deleted
self._call(["goldsh", "Organization", "Delete", "Name==%s" % name])
logger.debug("returning")
return | [
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16,748 | Karaage-Cluster/karaage | karaage/datastores/mam.py | MamDataStore71.add_account_to_project | def add_account_to_project(self, account, project):
""" Add account to project. """
username = account.username
projectname = project.pid
self._call([
"gchproject",
"--add-user", username,
"-p", projectname],
ignore_errors=[74]) | python | def add_account_to_project(self, account, project):
username = account.username
projectname = project.pid
self._call([
"gchproject",
"--add-user", username,
"-p", projectname],
ignore_errors=[74]) | [
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16,749 | mozilla/python_moztelemetry | moztelemetry/zeppelin.py | show | 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])
show(fig)
"""
img = StringIO()
fig.savefig(img, format='svg')
img.seek(0)
print("%html <div style='width:{}px'>{}</div>".format(width, img.buf)) | python | def show(fig, width=600):
img = StringIO()
fig.savefig(img, format='svg')
img.seek(0)
print("%html <div style='width:{}px'>{}</div>".format(width, img.buf)) | [
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import matplotlib.pyplot as plt
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16,750 | daler/trackhub | trackhub/__init__.py | default_hub | 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, defaults to the value of `hub_name`
long_label : str
Long label for the hub. If None, defaults to the value of `short_label`.
"""
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 = TrackDb()
hub.add_genomes_file(genomes_file)
genomes_file.add_genome(genome)
genome.add_trackdb(trackdb)
return hub, genomes_file, genome, trackdb | python | def default_hub(hub_name, genome, email, short_label=None, long_label=None):
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 = TrackDb()
hub.add_genomes_file(genomes_file)
genomes_file.add_genome(genome)
genome.add_trackdb(trackdb)
return hub, genomes_file, genome, trackdb | [
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Email to include with hub.
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Short label for the hub. If None, defaults to the value of `hub_name`
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16,751 | mozilla/python_moztelemetry | moztelemetry/parse_histograms.py | from_files | def from_files(filenames, strict_type_checks=True):
"""Return an iterator that provides a sequence of Histograms for
the histograms defined in filenames.
"""
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
# the parsed histograms is stable, which makes the insertion into
# all_histograms stable, which makes ordering in generated files
# stable, which makes builds more deterministic.
if not isinstance(histograms, OrderedDict):
raise ParserError("Histogram parser did not provide an OrderedDict.")
for name, definition in iteritems(histograms):
if name in all_histograms:
raise ParserError('Duplicate histogram name "%s".' % name)
all_histograms[name] = definition
# We require that all USE_COUNTER2_* histograms be defined in a contiguous
# block.
use_counter_indices = filter(lambda x: x[1].startswith("USE_COUNTER2_"),
enumerate(iterkeys(all_histograms)))
if use_counter_indices:
lower_bound = use_counter_indices[0][0]
upper_bound = use_counter_indices[-1][0]
n_counters = upper_bound - lower_bound + 1
if n_counters != len(use_counter_indices):
raise ParserError("Use counter histograms must be defined in a contiguous block.")
# Check that histograms that were removed from Histograms.json etc.
# are also removed from the whitelists.
if whitelists is not None:
all_whitelist_entries = itertools.chain.from_iterable(whitelists.itervalues())
orphaned = set(all_whitelist_entries) - set(iterkeys(all_histograms))
if len(orphaned) > 0:
msg = 'The following entries are orphaned and should be removed from ' \
'histogram-whitelists.json:\n%s'
raise ParserError(msg % (', '.join(sorted(orphaned))))
for name, definition in iteritems(all_histograms):
yield Histogram(name, definition, strict_type_checks=strict_type_checks) | python | def from_files(filenames, strict_type_checks=True):
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
# the parsed histograms is stable, which makes the insertion into
# all_histograms stable, which makes ordering in generated files
# stable, which makes builds more deterministic.
if not isinstance(histograms, OrderedDict):
raise ParserError("Histogram parser did not provide an OrderedDict.")
for name, definition in iteritems(histograms):
if name in all_histograms:
raise ParserError('Duplicate histogram name "%s".' % name)
all_histograms[name] = definition
# We require that all USE_COUNTER2_* histograms be defined in a contiguous
# block.
use_counter_indices = filter(lambda x: x[1].startswith("USE_COUNTER2_"),
enumerate(iterkeys(all_histograms)))
if use_counter_indices:
lower_bound = use_counter_indices[0][0]
upper_bound = use_counter_indices[-1][0]
n_counters = upper_bound - lower_bound + 1
if n_counters != len(use_counter_indices):
raise ParserError("Use counter histograms must be defined in a contiguous block.")
# Check that histograms that were removed from Histograms.json etc.
# are also removed from the whitelists.
if whitelists is not None:
all_whitelist_entries = itertools.chain.from_iterable(whitelists.itervalues())
orphaned = set(all_whitelist_entries) - set(iterkeys(all_histograms))
if len(orphaned) > 0:
msg = 'The following entries are orphaned and should be removed from ' \
'histogram-whitelists.json:\n%s'
raise ParserError(msg % (', '.join(sorted(orphaned))))
for name, definition in iteritems(all_histograms):
yield Histogram(name, definition, strict_type_checks=strict_type_checks) | [
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16,752 | mozilla/python_moztelemetry | moztelemetry/parse_histograms.py | Histogram.ranges | def ranges(self):
"""Return an array of lower bounds for each bucket in the histogram."""
bucket_fns = {
'boolean': linear_buckets,
'flag': linear_buckets,
'count': linear_buckets,
'enumerated': linear_buckets,
'categorical': linear_buckets,
'linear': linear_buckets,
'exponential': exponential_buckets,
}
if self._kind not in bucket_fns:
raise ParserError('Unknown kind "%s" for histogram "%s".' % (self._kind, self._name))
fn = bucket_fns[self._kind]
return fn(self.low(), self.high(), self.n_buckets()) | python | def ranges(self):
bucket_fns = {
'boolean': linear_buckets,
'flag': linear_buckets,
'count': linear_buckets,
'enumerated': linear_buckets,
'categorical': linear_buckets,
'linear': linear_buckets,
'exponential': exponential_buckets,
}
if self._kind not in bucket_fns:
raise ParserError('Unknown kind "%s" for histogram "%s".' % (self._kind, self._name))
fn = bucket_fns[self._kind]
return fn(self.low(), self.high(), self.n_buckets()) | [
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16,753 | Karaage-Cluster/karaage | karaage/common/create_update.py | apply_extra_context | 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.
"""
for key, value in six.iteritems(extra_context):
if callable(value):
context[key] = value()
else:
context[key] = value | python | def apply_extra_context(extra_context, context):
for key, value in six.iteritems(extra_context):
if callable(value):
context[key] = value()
else:
context[key] = value | [
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16,754 | Karaage-Cluster/karaage | karaage/common/create_update.py | get_model_and_form_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 ``ModelForm`` class created from
``model``.
"""
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.
class Meta:
model = tmp_model
class_name = model.__name__ + 'Form'
form_class = ModelFormMetaclass(
class_name, (ModelForm,), {'Meta': Meta})
return model, form_class
raise GenericViewError("Generic view must be called with either a model or"
" form_class argument.") | python | def get_model_and_form_class(model, form_class):
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.
class Meta:
model = tmp_model
class_name = model.__name__ + 'Form'
form_class = ModelFormMetaclass(
class_name, (ModelForm,), {'Meta': Meta})
return model, form_class
raise GenericViewError("Generic view must be called with either a model or"
" form_class argument.") | [
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] | 2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9 | https://github.com/Karaage-Cluster/karaage/blob/2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9/karaage/common/create_update.py#L24-L50 |
16,755 | Karaage-Cluster/karaage | karaage/common/create_update.py | redirect | 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 ``get_absolute_url`` method,
then raise ImproperlyConfigured.
This function is meant to handle the post_save_redirect parameter to the
``create_object`` and ``update_object`` views.
"""
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_redirect"
" parameter to the generic view or define a get_absolute_url"
" method on the Model.") | python | def redirect(post_save_redirect, obj):
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_redirect"
" parameter to the generic view or define a get_absolute_url"
" method on the Model.") | [
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If ``post_save_redirect`` is None, then redirect to ``obj``'s URL returned
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16,756 | Karaage-Cluster/karaage | karaage/common/create_update.py | lookup_object | 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.
"""
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"
" slug/slug_field.")
try:
return model.objects.get(**lookup_kwargs)
except ObjectDoesNotExist:
raise Http404("No %s found for %s"
% (model._meta.verbose_name, lookup_kwargs)) | python | def lookup_object(model, object_id, slug, slug_field):
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"
" slug/slug_field.")
try:
return model.objects.get(**lookup_kwargs)
except ObjectDoesNotExist:
raise Http404("No %s found for %s"
% (model._meta.verbose_name, lookup_kwargs)) | [
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16,757 | Karaage-Cluster/karaage | karaage/common/create_update.py | create_object | 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
"""
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.FILES)
if form.is_valid():
new_object = form.save()
msg = ugettext("The %(verbose_name)s was created successfully.") %\
{"verbose_name": model._meta.verbose_name}
messages.success(request, msg, fail_silently=True)
return redirect(post_save_redirect, new_object)
else:
form = form_class()
# Create the template, context, response
if not template_name:
template_name = "%s/%s_form.html" % (
model._meta.app_label, model._meta.object_name.lower())
t = template_loader.get_template(template_name)
c = {
'form': form,
}
apply_extra_context(extra_context, c)
return HttpResponse(t.render(context=c, request=request)) | python | 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):
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.FILES)
if form.is_valid():
new_object = form.save()
msg = ugettext("The %(verbose_name)s was created successfully.") %\
{"verbose_name": model._meta.verbose_name}
messages.success(request, msg, fail_silently=True)
return redirect(post_save_redirect, new_object)
else:
form = form_class()
# Create the template, context, response
if not template_name:
template_name = "%s/%s_form.html" % (
model._meta.app_label, model._meta.object_name.lower())
t = template_loader.get_template(template_name)
c = {
'form': form,
}
apply_extra_context(extra_context, c)
return HttpResponse(t.render(context=c, request=request)) | [
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16,758 | Karaage-Cluster/karaage | karaage/common/create_update.py | update_object | 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
"""
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.method == 'POST':
form = form_class(request.POST, request.FILES, instance=obj)
if form.is_valid():
obj = form.save()
msg = ugettext("The %(verbose_name)s was updated successfully.") %\
{"verbose_name": model._meta.verbose_name}
messages.success(request, msg, fail_silently=True)
return redirect(post_save_redirect, obj)
else:
form = form_class(instance=obj)
if not template_name:
template_name = "%s/%s_form.html" % (
model._meta.app_label, model._meta.object_name.lower())
t = template_loader.get_template(template_name)
c = {
'form': form,
template_object_name: obj,
}
apply_extra_context(extra_context, c)
response = HttpResponse(t.render(context=c, request=request))
return response | python | 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):
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.method == 'POST':
form = form_class(request.POST, request.FILES, instance=obj)
if form.is_valid():
obj = form.save()
msg = ugettext("The %(verbose_name)s was updated successfully.") %\
{"verbose_name": model._meta.verbose_name}
messages.success(request, msg, fail_silently=True)
return redirect(post_save_redirect, obj)
else:
form = form_class(instance=obj)
if not template_name:
template_name = "%s/%s_form.html" % (
model._meta.app_label, model._meta.object_name.lower())
t = template_loader.get_template(template_name)
c = {
'form': form,
template_object_name: obj,
}
apply_extra_context(extra_context, c)
response = HttpResponse(t.render(context=c, request=request))
return response | [
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16,759 | Karaage-Cluster/karaage | karaage/common/create_update.py | delete_object | 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 object being deleted
"""
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 %(verbose_name)s was deleted.") %\
{"verbose_name": model._meta.verbose_name}
messages.success(request, msg, fail_silently=True)
return HttpResponseRedirect(post_delete_redirect)
else:
if not template_name:
template_name = "%s/%s_confirm_delete.html" % (
model._meta.app_label, model._meta.object_name.lower())
t = template_loader.get_template(template_name)
c = {
template_object_name: obj,
}
apply_extra_context(extra_context, c)
response = HttpResponse(t.render(context=c, request=request))
return response | python | 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'):
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 %(verbose_name)s was deleted.") %\
{"verbose_name": model._meta.verbose_name}
messages.success(request, msg, fail_silently=True)
return HttpResponseRedirect(post_delete_redirect)
else:
if not template_name:
template_name = "%s/%s_confirm_delete.html" % (
model._meta.app_label, model._meta.object_name.lower())
t = template_loader.get_template(template_name)
c = {
template_object_name: obj,
}
apply_extra_context(extra_context, c)
response = HttpResponse(t.render(context=c, request=request))
return response | [
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Templates: ``<app_label>/<model_name>_confirm_delete.html``
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16,760 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | get_url | def get_url(request, application, roles, label=None):
""" Retrieve a link that will work for the current user. """
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 but the applicant
require_secret = False
elif not request.user.is_authenticated:
# If applicant is not logged in, we redirect them to secret URL
require_secret = True
elif request.user != application.applicant:
# If logged in as different person, we redirect them to secret
# URL. This could happen if the application was open with a different
# email address, and the applicant is logged in when accessing it.
require_secret = True
else:
# otherwise redirect them to URL that requires correct login.
require_secret = False
# return required url
if not require_secret:
url = reverse(
'kg_application_detail',
args=[application.pk, application.state] + args)
else:
url = reverse(
'kg_application_unauthenticated',
args=[application.secret_token, application.state] + args)
return url | python | def get_url(request, application, roles, label=None):
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 but the applicant
require_secret = False
elif not request.user.is_authenticated:
# If applicant is not logged in, we redirect them to secret URL
require_secret = True
elif request.user != application.applicant:
# If logged in as different person, we redirect them to secret
# URL. This could happen if the application was open with a different
# email address, and the applicant is logged in when accessing it.
require_secret = True
else:
# otherwise redirect them to URL that requires correct login.
require_secret = False
# return required url
if not require_secret:
url = reverse(
'kg_application_detail',
args=[application.pk, application.state] + args)
else:
url = reverse(
'kg_application_unauthenticated',
args=[application.secret_token, application.state] + args)
return url | [
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16,761 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | get_admin_email_link | def get_admin_email_link(application):
""" Retrieve a link that can be emailed to the administrator. """
url = '%s/applications/%d/' % (settings.ADMIN_BASE_URL, application.pk)
is_secret = False
return url, is_secret | python | def get_admin_email_link(application):
url = '%s/applications/%d/' % (settings.ADMIN_BASE_URL, application.pk)
is_secret = False
return url, is_secret | [
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16,762 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | get_registration_email_link | def get_registration_email_link(application):
""" Retrieve a link that can be emailed to the logged other users. """
url = '%s/applications/%d/' % (
settings.REGISTRATION_BASE_URL, application.pk)
is_secret = False
return url, is_secret | python | def get_registration_email_link(application):
url = '%s/applications/%d/' % (
settings.REGISTRATION_BASE_URL, application.pk)
is_secret = False
return url, is_secret | [
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16,763 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | get_email_link | def get_email_link(application):
""" Retrieve a link that can be emailed to the applicant. """
# 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/applications/%s/' % (
settings.REGISTRATION_BASE_URL, application.secret_token)
is_secret = True
return url, is_secret | python | def get_email_link(application):
# 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/applications/%s/' % (
settings.REGISTRATION_BASE_URL, application.secret_token)
is_secret = True
return url, is_secret | [
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] | 2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9 | https://github.com/Karaage-Cluster/karaage/blob/2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9/karaage/plugins/kgapplications/views/base.py#L121-L133 |
16,764 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | StateMachine.start | def start(self, request, application, extra_roles=None):
""" Continue the state machine at first state. """
# 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 probably shouldn't be here.
if 'is_authorised' not in roles:
return HttpResponseForbidden('<h1>Access Denied</h1>')
# Go to first state.
return self._next(request, application, roles, self._first_state) | python | def start(self, request, application, extra_roles=None):
# 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 probably shouldn't be here.
if 'is_authorised' not in roles:
return HttpResponseForbidden('<h1>Access Denied</h1>')
# Go to first state.
return self._next(request, application, roles, self._first_state) | [
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16,765 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | StateMachine.process | def process(
self, request, application,
expected_state, label, extra_roles=None):
""" Process the view request at the current state. """
# 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 probably shouldn't be here.
if 'is_authorised' not in roles:
return HttpResponseForbidden('<h1>Access Denied</h1>')
# If user didn't supply state on URL, redirect to full URL.
if expected_state is None:
url = get_url(request, application, roles, label)
return HttpResponseRedirect(url)
# Check that the current state is valid.
if application.state not in self._config:
raise RuntimeError("Invalid current state '%s'" % application.state)
# If state user expected is different to state we are in, warn user
# and jump to expected state.
if expected_state != application.state:
# post data will be lost
if request.method == "POST":
messages.warning(
request,
"Discarding request and jumping to current state.")
# note we discard the label, it probably isn't relevant for new
# state
url = get_url(request, application, roles)
return HttpResponseRedirect(url)
# Get the current state for this application
state_config = self._config[application.state]
# Finally do something
instance = load_state_instance(state_config)
if request.method == "GET":
# if method is GET, state does not ever change.
response = instance.get_next_config(request, application, label, roles)
assert isinstance(response, HttpResponse)
return response
elif request.method == "POST":
# if method is POST, it can return a HttpResponse or a string
response = instance.get_next_config(request, application, label, roles)
if isinstance(response, HttpResponse):
# If it returned a HttpResponse, state not changed, just
# display
return response
else:
# If it returned a string, lookit up in the actions for this
# state
next_config = response
# Go to the next state
return self._next(request, application, roles, next_config)
else:
# Shouldn't happen, user did something weird
return HttpResponseBadRequest("<h1>Bad Request</h1>") | python | def process(
self, request, application,
expected_state, label, extra_roles=None):
# 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 probably shouldn't be here.
if 'is_authorised' not in roles:
return HttpResponseForbidden('<h1>Access Denied</h1>')
# If user didn't supply state on URL, redirect to full URL.
if expected_state is None:
url = get_url(request, application, roles, label)
return HttpResponseRedirect(url)
# Check that the current state is valid.
if application.state not in self._config:
raise RuntimeError("Invalid current state '%s'" % application.state)
# If state user expected is different to state we are in, warn user
# and jump to expected state.
if expected_state != application.state:
# post data will be lost
if request.method == "POST":
messages.warning(
request,
"Discarding request and jumping to current state.")
# note we discard the label, it probably isn't relevant for new
# state
url = get_url(request, application, roles)
return HttpResponseRedirect(url)
# Get the current state for this application
state_config = self._config[application.state]
# Finally do something
instance = load_state_instance(state_config)
if request.method == "GET":
# if method is GET, state does not ever change.
response = instance.get_next_config(request, application, label, roles)
assert isinstance(response, HttpResponse)
return response
elif request.method == "POST":
# if method is POST, it can return a HttpResponse or a string
response = instance.get_next_config(request, application, label, roles)
if isinstance(response, HttpResponse):
# If it returned a HttpResponse, state not changed, just
# display
return response
else:
# If it returned a string, lookit up in the actions for this
# state
next_config = response
# Go to the next state
return self._next(request, application, roles, next_config)
else:
# Shouldn't happen, user did something weird
return HttpResponseBadRequest("<h1>Bad Request</h1>") | [
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16,766 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | StateMachine._get_roles_for_request | def _get_roles_for_request(request, application):
""" Check the authentication of the current user. """
roles = application.get_roles_for_person(request.user)
if common.is_admin(request):
roles.add("is_admin")
roles.add('is_authorised')
return roles | python | def _get_roles_for_request(request, application):
roles = application.get_roles_for_person(request.user)
if common.is_admin(request):
roles.add("is_admin")
roles.add('is_authorised')
return roles | [
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16,767 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | StateMachine._next | def _next(self, request, application, roles, next_config):
""" Continue the state machine at given state. """
# 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['type'] in ['goto', 'transition']
while next_config['type'] == 'goto':
key = next_config['key']
next_config = self._config[key]
instance = load_instance(next_config)
if not isinstance(instance, Transition):
break
next_config = instance.get_next_config(request, application, roles)
# lookup next state
assert key is not None
state_key = key
# enter that state
instance.enter_state(request, application)
application.state = state_key
application.save()
# log details
log.change(application.application_ptr, "state: %s" % instance.name)
# redirect to this new state
url = get_url(request, application, roles)
return HttpResponseRedirect(url)
else:
return HttpResponseBadRequest("<h1>Bad Request</h1>") | python | def _next(self, request, application, roles, next_config):
# 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['type'] in ['goto', 'transition']
while next_config['type'] == 'goto':
key = next_config['key']
next_config = self._config[key]
instance = load_instance(next_config)
if not isinstance(instance, Transition):
break
next_config = instance.get_next_config(request, application, roles)
# lookup next state
assert key is not None
state_key = key
# enter that state
instance.enter_state(request, application)
application.state = state_key
application.save()
# log details
log.change(application.application_ptr, "state: %s" % instance.name)
# redirect to this new state
url = get_url(request, application, roles)
return HttpResponseRedirect(url)
else:
return HttpResponseBadRequest("<h1>Bad Request</h1>") | [
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16,768 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/views/base.py | State.get_next_action | def get_next_action(self, request, application, label, roles):
""" Django view method. We provide a default detail view for
applications. """
# 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 in default view
if request.method == "GET":
context = self.context
context.update({
'application': application,
'actions': actions,
'state': self.name,
'roles': roles})
return render(
template_name='kgapplications/common_detail.html',
context=context,
request=request)
elif request.method == "POST":
for action in actions:
if action in request.POST:
return action
# we don't know how to handle this request.
return HttpResponseBadRequest("<h1>Bad Request</h1>") | python | def get_next_action(self, request, application, label, roles):
# 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 in default view
if request.method == "GET":
context = self.context
context.update({
'application': application,
'actions': actions,
'state': self.name,
'roles': roles})
return render(
template_name='kgapplications/common_detail.html',
context=context,
request=request)
elif request.method == "POST":
for action in actions:
if action in request.POST:
return action
# we don't know how to handle this request.
return HttpResponseBadRequest("<h1>Bad Request</h1>") | [
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16,769 | mozilla/python_moztelemetry | moztelemetry/histogram.py | Histogram.get_value | 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.
"""
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
elif self.kind == "count":
return int(self.buckets[0])
elif self.kind == "flag":
return self.buckets[1] == 1
else:
assert(False) | python | def get_value(self, only_median=False, autocast=True):
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
elif self.kind == "count":
return int(self.buckets[0])
elif self.kind == "flag":
return self.buckets[1] == 1
else:
assert(False) | [
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16,770 | mozilla/python_moztelemetry | moztelemetry/histogram.py | Histogram.percentile | def percentile(self, percentile):
""" Returns the nth percentile of the histogram. """
assert(percentile >= 0 and percentile <= 100)
assert(self.kind in ["exponential", "linear", "enumerated", "boolean"])
fraction = percentile / 100
to_count = fraction * self.buckets.sum()
percentile_bucket = 0
for percentile_bucket in range(len(self.buckets)):
freq = self.buckets.values[percentile_bucket]
if to_count - freq <= 0:
break
to_count -= freq
percentile_lower_boundary = self.buckets.index[percentile_bucket]
percentile_frequency = self.buckets.values[percentile_bucket]
if percentile_bucket == len(self.buckets) - 1 or percentile_frequency == 0:
return percentile_lower_boundary
width = self.buckets.index[percentile_bucket + 1] - self.buckets.index[percentile_bucket]
return percentile_lower_boundary + width * to_count / percentile_frequency | python | def percentile(self, percentile):
assert(percentile >= 0 and percentile <= 100)
assert(self.kind in ["exponential", "linear", "enumerated", "boolean"])
fraction = percentile / 100
to_count = fraction * self.buckets.sum()
percentile_bucket = 0
for percentile_bucket in range(len(self.buckets)):
freq = self.buckets.values[percentile_bucket]
if to_count - freq <= 0:
break
to_count -= freq
percentile_lower_boundary = self.buckets.index[percentile_bucket]
percentile_frequency = self.buckets.values[percentile_bucket]
if percentile_bucket == len(self.buckets) - 1 or percentile_frequency == 0:
return percentile_lower_boundary
width = self.buckets.index[percentile_bucket + 1] - self.buckets.index[percentile_bucket]
return percentile_lower_boundary + width * to_count / percentile_frequency | [
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16,771 | daler/trackhub | trackhub/track.py | BaseTrack.tracktype | def tracktype(self, tracktype):
"""
When setting the track type, the valid parameters for this track type
need to be set as well.
"""
self._tracktype = tracktype
if tracktype is not None:
if 'bed' in tracktype.lower():
tracktype = 'bigBed'
elif 'wig' in tracktype.lower():
tracktype = 'bigWig'
self.params.update(constants.track_typespecific_fields[tracktype]) | python | def tracktype(self, tracktype):
self._tracktype = tracktype
if tracktype is not None:
if 'bed' in tracktype.lower():
tracktype = 'bigBed'
elif 'wig' in tracktype.lower():
tracktype = 'bigWig'
self.params.update(constants.track_typespecific_fields[tracktype]) | [
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16,772 | daler/trackhub | trackhub/track.py | BaseTrack.add_subgroups | def add_subgroups(self, subgroups):
"""
Update the subgroups for this track.
Note that in contrast to :meth:`CompositeTrack`, which takes a list of
:class:`SubGroupDefinition` objects representing the allowed subgroups,
this method takes a single dictionary indicating the particular
subgroups for this track.
Parameters
----------
subgroups : dict
Dictionary of subgroups, e.g., {'celltype': 'K562', 'treatment':
'a'}. Each key must match a SubGroupDefinition name in the
composite's subgroups list. Each value must match a key in that
SubGroupDefinition.mapping dictionary.
"""
if subgroups is None:
subgroups = {}
assert isinstance(subgroups, dict)
self.subgroups.update(subgroups) | python | def add_subgroups(self, subgroups):
if subgroups is None:
subgroups = {}
assert isinstance(subgroups, dict)
self.subgroups.update(subgroups) | [
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16,773 | daler/trackhub | trackhub/track.py | BaseTrack._str_subgroups | def _str_subgroups(self):
"""
helper function to render subgroups as a string
"""
if not self.subgroups:
return ""
return ['subGroups %s'
% ' '.join(['%s=%s' % (k, v) for (k, v) in
self.subgroups.items()])] | python | def _str_subgroups(self):
if not self.subgroups:
return ""
return ['subGroups %s'
% ' '.join(['%s=%s' % (k, v) for (k, v) in
self.subgroups.items()])] | [
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] | e4655f79177822529f80b923df117e38e28df702 | https://github.com/daler/trackhub/blob/e4655f79177822529f80b923df117e38e28df702/trackhub/track.py#L363-L371 |
16,774 | daler/trackhub | trackhub/track.py | CompositeTrack.add_subgroups | def add_subgroups(self, subgroups):
"""
Add a list of SubGroupDefinition objects to this composite.
Note that in contrast to :meth:`BaseTrack`, which takes a single
dictionary indicating the particular subgroups for the track, this
method takes a list of :class:`SubGroupDefinition` objects representing
the allowed subgroups for the composite.
:param subgroups:
List of SubGroupDefinition objects.
"""
if subgroups is None:
subgroups = {}
_subgroups = {}
for sg in subgroups:
assert isinstance(sg, SubGroupDefinition)
_subgroups[sg.name] = sg
self.subgroups = _subgroups | python | def add_subgroups(self, subgroups):
if subgroups is None:
subgroups = {}
_subgroups = {}
for sg in subgroups:
assert isinstance(sg, SubGroupDefinition)
_subgroups[sg.name] = sg
self.subgroups = _subgroups | [
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16,775 | daler/trackhub | trackhub/track.py | CompositeTrack.add_view | def add_view(self, view):
"""
Add a ViewTrack object to this composite.
:param view:
A ViewTrack object.
"""
self.add_child(view)
self.views.append(view) | python | def add_view(self, view):
self.add_child(view)
self.views.append(view) | [
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16,776 | daler/trackhub | trackhub/track.py | CompositeTrack._str_subgroups | def _str_subgroups(self):
"""
renders subgroups to a list of strings
"""
s = []
i = 0
# if there are any views, there must be a subGroup1 view View tag=val
# as the first one. So create it automatically here
if len(self.views) > 0:
mapping = dict((i.view, i.view) for i in self.views)
view_subgroup = SubGroupDefinition(
name='view',
label='Views',
mapping=mapping)
i += 1
s.append('subGroup%s %s' % (i, view_subgroup))
for subgroup in self.subgroups.values():
i += 1
s.append('subGroup%s %s' % (i, subgroup))
return s | python | def _str_subgroups(self):
s = []
i = 0
# if there are any views, there must be a subGroup1 view View tag=val
# as the first one. So create it automatically here
if len(self.views) > 0:
mapping = dict((i.view, i.view) for i in self.views)
view_subgroup = SubGroupDefinition(
name='view',
label='Views',
mapping=mapping)
i += 1
s.append('subGroup%s %s' % (i, view_subgroup))
for subgroup in self.subgroups.values():
i += 1
s.append('subGroup%s %s' % (i, subgroup))
return s | [
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16,777 | daler/trackhub | trackhub/track.py | ViewTrack.add_tracks | def add_tracks(self, subtracks):
"""
Add one or more tracks to this view.
subtracks : Track or iterable of Tracks
A single Track instance or an iterable of them.
"""
if isinstance(subtracks, Track):
subtracks = [subtracks]
for subtrack in subtracks:
subtrack.subgroups['view'] = self.view
self.add_child(subtrack)
self.subtracks.append(subtrack) | python | def add_tracks(self, subtracks):
if isinstance(subtracks, Track):
subtracks = [subtracks]
for subtrack in subtracks:
subtrack.subgroups['view'] = self.view
self.add_child(subtrack)
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16,778 | daler/trackhub | trackhub/track.py | SuperTrack.add_tracks | def add_tracks(self, subtracks):
"""
Add one or more tracks.
subtrack : Track or iterable of Tracks
"""
if isinstance(subtracks, BaseTrack):
subtracks = [subtracks]
for subtrack in subtracks:
self.add_child(subtrack)
self.subtracks.append(subtrack) | python | def add_tracks(self, subtracks):
if isinstance(subtracks, BaseTrack):
subtracks = [subtracks]
for subtrack in subtracks:
self.add_child(subtrack)
self.subtracks.append(subtrack) | [
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16,779 | mozilla/python_moztelemetry | moztelemetry/parse_scalars.py | load_scalars | def load_scalars(filename, strict_type_checks=True):
"""Parses a YAML file containing the scalar definition.
:param filename: the YAML file containing the scalars definition.
:raises ParserError: if the scalar file cannot be opened or parsed.
"""
# Parse the scalar definitions from the YAML file.
scalars = None
try:
with open(filename, 'r') as f:
scalars = yaml.safe_load(f)
except IOError as e:
raise ParserError('Error opening ' + filename + ': ' + e.message)
except ValueError as e:
raise ParserError('Error parsing scalars in {}: {}'
'.\nSee: {}'.format(filename, e.message, BASE_DOC_URL))
scalar_list = []
# Scalars are defined in a fixed two-level hierarchy within the definition file.
# The first level contains the category name, while the second level contains the
# probe name (e.g. "category.name: probe: ...").
for category_name in scalars:
category = scalars[category_name]
# Make sure that the category has at least one probe in it.
if not category or len(category) == 0:
raise ParserError('Category "{}" must have at least one probe in it' +
'.\nSee: {}'.format(category_name, BASE_DOC_URL))
for probe_name in category:
# We found a scalar type. Go ahead and parse it.
scalar_info = category[probe_name]
scalar_list.append(
ScalarType(category_name, probe_name, scalar_info, strict_type_checks))
return scalar_list | python | def load_scalars(filename, strict_type_checks=True):
# Parse the scalar definitions from the YAML file.
scalars = None
try:
with open(filename, 'r') as f:
scalars = yaml.safe_load(f)
except IOError as e:
raise ParserError('Error opening ' + filename + ': ' + e.message)
except ValueError as e:
raise ParserError('Error parsing scalars in {}: {}'
'.\nSee: {}'.format(filename, e.message, BASE_DOC_URL))
scalar_list = []
# Scalars are defined in a fixed two-level hierarchy within the definition file.
# The first level contains the category name, while the second level contains the
# probe name (e.g. "category.name: probe: ...").
for category_name in scalars:
category = scalars[category_name]
# Make sure that the category has at least one probe in it.
if not category or len(category) == 0:
raise ParserError('Category "{}" must have at least one probe in it' +
'.\nSee: {}'.format(category_name, BASE_DOC_URL))
for probe_name in category:
# We found a scalar type. Go ahead and parse it.
scalar_info = category[probe_name]
scalar_list.append(
ScalarType(category_name, probe_name, scalar_info, strict_type_checks))
return scalar_list | [
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16,780 | mozilla/python_moztelemetry | moztelemetry/parse_scalars.py | ScalarType.validate_values | def validate_values(self, definition):
"""This function checks that the fields have the correct values.
:param definition: the dictionary containing the scalar properties.
:raises ParserError: if a scalar definition field contains an unexpected value.
"""
if not self._strict_type_checks:
return
# Validate the scalar kind.
scalar_kind = definition.get('kind')
if scalar_kind not in SCALAR_TYPES_MAP.keys():
raise ParserError(self._name + ' - unknown scalar kind: ' + scalar_kind +
'.\nSee: {}'.format(BASE_DOC_URL))
# Validate the collection policy.
collection_policy = definition.get('release_channel_collection', None)
if collection_policy and collection_policy not in ['opt-in', 'opt-out']:
raise ParserError(self._name + ' - unknown collection policy: ' + collection_policy +
'.\nSee: {}#optional-fields'.format(BASE_DOC_URL))
# Validate the cpp_guard.
cpp_guard = definition.get('cpp_guard')
if cpp_guard and re.match(r'\W', cpp_guard):
raise ParserError(self._name + ' - invalid cpp_guard: ' + cpp_guard +
'.\nSee: {}#optional-fields'.format(BASE_DOC_URL))
# Validate record_in_processes.
record_in_processes = definition.get('record_in_processes', [])
for proc in record_in_processes:
if not utils.is_valid_process_name(proc):
raise ParserError(self._name + ' - unknown value in record_in_processes: ' + proc +
'.\nSee: {}'.format(BASE_DOC_URL))
# Validate the expiration version.
# Historical versions of Scalars.json may contain expiration versions
# using the deprecated format 'N.Na1'. Those scripts set
# self._strict_type_checks to false.
expires = definition.get('expires')
if not utils.validate_expiration_version(expires) and self._strict_type_checks:
raise ParserError('{} - invalid expires: {}.\nSee: {}#required-fields'
.format(self._name, expires, BASE_DOC_URL)) | python | def validate_values(self, definition):
if not self._strict_type_checks:
return
# Validate the scalar kind.
scalar_kind = definition.get('kind')
if scalar_kind not in SCALAR_TYPES_MAP.keys():
raise ParserError(self._name + ' - unknown scalar kind: ' + scalar_kind +
'.\nSee: {}'.format(BASE_DOC_URL))
# Validate the collection policy.
collection_policy = definition.get('release_channel_collection', None)
if collection_policy and collection_policy not in ['opt-in', 'opt-out']:
raise ParserError(self._name + ' - unknown collection policy: ' + collection_policy +
'.\nSee: {}#optional-fields'.format(BASE_DOC_URL))
# Validate the cpp_guard.
cpp_guard = definition.get('cpp_guard')
if cpp_guard and re.match(r'\W', cpp_guard):
raise ParserError(self._name + ' - invalid cpp_guard: ' + cpp_guard +
'.\nSee: {}#optional-fields'.format(BASE_DOC_URL))
# Validate record_in_processes.
record_in_processes = definition.get('record_in_processes', [])
for proc in record_in_processes:
if not utils.is_valid_process_name(proc):
raise ParserError(self._name + ' - unknown value in record_in_processes: ' + proc +
'.\nSee: {}'.format(BASE_DOC_URL))
# Validate the expiration version.
# Historical versions of Scalars.json may contain expiration versions
# using the deprecated format 'N.Na1'. Those scripts set
# self._strict_type_checks to false.
expires = definition.get('expires')
if not utils.validate_expiration_version(expires) and self._strict_type_checks:
raise ParserError('{} - invalid expires: {}.\nSee: {}#required-fields'
.format(self._name, expires, BASE_DOC_URL)) | [
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16,781 | daler/trackhub | trackhub/base.py | HubComponent.add_child | def add_child(self, child):
"""
Adds self as parent to child, and then adds child.
"""
child.parent = self
self.children.append(child)
return child | python | def add_child(self, child):
child.parent = self
self.children.append(child)
return child | [
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16,782 | daler/trackhub | trackhub/base.py | HubComponent.add_parent | def add_parent(self, parent):
"""
Adds self as child of parent, then adds parent.
"""
parent.add_child(self)
self.parent = parent
return parent | python | def add_parent(self, parent):
parent.add_child(self)
self.parent = parent
return parent | [
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16,783 | daler/trackhub | trackhub/base.py | HubComponent.root | def root(self, cls=None, level=0):
"""
Returns the top-most HubComponent in the hierarchy.
If `cls` is not None, then return the top-most attribute HubComponent
that is an instance of class `cls`.
For a fully-constructed track hub (and `cls=None`), this should return
a a Hub object for every component in the hierarchy.
"""
if cls is None:
if self.parent is None:
return self, level
else:
if isinstance(self, cls):
if not isinstance(self.parent, cls):
return self, level
if self.parent is None:
return None, None
return self.parent.root(cls, level - 1) | python | def root(self, cls=None, level=0):
if cls is None:
if self.parent is None:
return self, level
else:
if isinstance(self, cls):
if not isinstance(self.parent, cls):
return self, level
if self.parent is None:
return None, None
return self.parent.root(cls, level - 1) | [
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16,784 | daler/trackhub | trackhub/base.py | HubComponent.leaves | def leaves(self, cls, level=0, intermediate=False):
"""
Returns an iterator of the HubComponent leaves that are of class `cls`.
If `intermediate` is True, then return any intermediate classes as
well.
"""
if intermediate:
if isinstance(self, cls):
yield self, level
elif len(self.children) == 0:
if isinstance(self, cls):
yield self, level
else:
raise StopIteration
for child in self.children:
for leaf, _level in child.leaves(cls, level + 1, intermediate=intermediate):
yield leaf, _level | python | def leaves(self, cls, level=0, intermediate=False):
if intermediate:
if isinstance(self, cls):
yield self, level
elif len(self.children) == 0:
if isinstance(self, cls):
yield self, level
else:
raise StopIteration
for child in self.children:
for leaf, _level in child.leaves(cls, level + 1, intermediate=intermediate):
yield leaf, _level | [
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16,785 | daler/trackhub | trackhub/base.py | HubComponent.render | def render(self, staging=None):
"""
Renders the object to file, returning a list of created files.
Calls validation code, and, as long as each child is also a subclass of
:class:`HubComponent`, the rendering is recursive.
"""
self.validate()
created_files = OrderedDict()
if staging is None:
staging = tempfile.mkdtemp()
this = self._render(staging)
if this:
created_files[repr(self)] = this
for child in self.children:
created_files[repr(child)] = child.render(staging)
return created_files | python | def render(self, staging=None):
self.validate()
created_files = OrderedDict()
if staging is None:
staging = tempfile.mkdtemp()
this = self._render(staging)
if this:
created_files[repr(self)] = this
for child in self.children:
created_files[repr(child)] = child.render(staging)
return created_files | [
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] | e4655f79177822529f80b923df117e38e28df702 | https://github.com/daler/trackhub/blob/e4655f79177822529f80b923df117e38e28df702/trackhub/base.py#L118-L134 |
16,786 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/emails.py | send_request_email | def send_request_email(
authorised_text, authorised_role, authorised_persons, application,
link, is_secret):
"""Sends an email to admin asking to approve user application"""
context = CONTEXT.copy()
context['requester'] = application.applicant
context['link'] = link
context['is_secret'] = is_secret
context['application'] = application
context['authorised_text'] = authorised_text
_send_request_email(
context,
authorised_role, authorised_persons,
"common_request") | python | def send_request_email(
authorised_text, authorised_role, authorised_persons, application,
link, is_secret):
context = CONTEXT.copy()
context['requester'] = application.applicant
context['link'] = link
context['is_secret'] = is_secret
context['application'] = application
context['authorised_text'] = authorised_text
_send_request_email(
context,
authorised_role, authorised_persons,
"common_request") | [
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16,787 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/emails.py | send_invite_email | def send_invite_email(application, link, is_secret):
""" Sends an email inviting someone to create an account"""
if not application.applicant.email:
return
context = CONTEXT.copy()
context['receiver'] = application.applicant
context['application'] = application
context['link'] = link
context['is_secret'] = is_secret
to_email = application.applicant.email
subject, body = render_email('common_invite', context)
send_mail(subject, body, settings.ACCOUNTS_EMAIL, [to_email]) | python | def send_invite_email(application, link, is_secret):
if not application.applicant.email:
return
context = CONTEXT.copy()
context['receiver'] = application.applicant
context['application'] = application
context['link'] = link
context['is_secret'] = is_secret
to_email = application.applicant.email
subject, body = render_email('common_invite', context)
send_mail(subject, body, settings.ACCOUNTS_EMAIL, [to_email]) | [
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16,788 | Karaage-Cluster/karaage | karaage/plugins/kgapplications/emails.py | send_approved_email | def send_approved_email(
application, created_person, created_account, link, is_secret):
"""Sends an email informing person application is approved"""
if not application.applicant.email:
return
context = CONTEXT.copy()
context['receiver'] = application.applicant
context['application'] = application
context['created_person'] = created_person
context['created_account'] = created_account
context['link'] = link
context['is_secret'] = is_secret
subject, body = render_email('common_approved', context)
to_email = application.applicant.email
send_mail(subject, body, settings.ACCOUNTS_EMAIL, [to_email]) | python | def send_approved_email(
application, created_person, created_account, link, is_secret):
if not application.applicant.email:
return
context = CONTEXT.copy()
context['receiver'] = application.applicant
context['application'] = application
context['created_person'] = created_person
context['created_account'] = created_account
context['link'] = link
context['is_secret'] = is_secret
subject, body = render_email('common_approved', context)
to_email = application.applicant.email
send_mail(subject, body, settings.ACCOUNTS_EMAIL, [to_email]) | [
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16,789 | Karaage-Cluster/karaage | karaage/people/models.py | _add_person_to_group | def _add_person_to_group(person, group):
""" Call datastores after adding a person to a group. """
from karaage.datastores import add_accounts_to_group
from karaage.datastores import add_accounts_to_project
from karaage.datastores import add_accounts_to_institute
a_list = person.account_set
add_accounts_to_group(a_list, group)
for project in group.project_set.all():
add_accounts_to_project(a_list, project)
for institute in group.institute_set.all():
add_accounts_to_institute(a_list, institute) | python | def _add_person_to_group(person, group):
from karaage.datastores import add_accounts_to_group
from karaage.datastores import add_accounts_to_project
from karaage.datastores import add_accounts_to_institute
a_list = person.account_set
add_accounts_to_group(a_list, group)
for project in group.project_set.all():
add_accounts_to_project(a_list, project)
for institute in group.institute_set.all():
add_accounts_to_institute(a_list, institute) | [
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16,790 | Karaage-Cluster/karaage | karaage/people/models.py | _remove_person_from_group | def _remove_person_from_group(person, group):
""" Call datastores after removing a person from a group. """
from karaage.datastores import remove_accounts_from_group
from karaage.datastores import remove_accounts_from_project
from karaage.datastores import remove_accounts_from_institute
a_list = person.account_set
remove_accounts_from_group(a_list, group)
for project in group.project_set.all():
remove_accounts_from_project(a_list, project)
for institute in group.institute_set.all():
remove_accounts_from_institute(a_list, institute) | python | def _remove_person_from_group(person, group):
from karaage.datastores import remove_accounts_from_group
from karaage.datastores import remove_accounts_from_project
from karaage.datastores import remove_accounts_from_institute
a_list = person.account_set
remove_accounts_from_group(a_list, group)
for project in group.project_set.all():
remove_accounts_from_project(a_list, project)
for institute in group.institute_set.all():
remove_accounts_from_institute(a_list, institute) | [
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16,791 | daler/trackhub | trackhub/helpers.py | dimensions_from_subgroups | def dimensions_from_subgroups(s):
"""
Given a sorted list of subgroups, return a string appropriate to provide as
a composite track's `dimensions` arg.
Parameters
----------
s : list of SubGroup objects (or anything with a `name` attribute)
"""
letters = 'XYABCDEFGHIJKLMNOPQRSTUVWZ'
return ' '.join(['dim{0}={1}'.format(dim, sg.name) for dim, sg in zip(letters, s)]) | python | def dimensions_from_subgroups(s):
letters = 'XYABCDEFGHIJKLMNOPQRSTUVWZ'
return ' '.join(['dim{0}={1}'.format(dim, sg.name) for dim, sg in zip(letters, s)]) | [
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16,792 | daler/trackhub | trackhub/helpers.py | filter_composite_from_subgroups | def filter_composite_from_subgroups(s):
"""
Given a sorted list of subgroups, return a string appropriate to provide as
the a composite track's `filterComposite` argument
>>> import trackhub
>>> trackhub.helpers.filter_composite_from_subgroups(['cell', 'ab', 'lab', 'knockdown'])
'dimA dimB'
Parameters
----------
s : list
A list representing the ordered subgroups, ideally the same list
provided to `dimensions_from_subgroups`. The values are not actually
used, just the number of items.
"""
dims = []
for letter, sg in zip('ABCDEFGHIJKLMNOPQRSTUVWZ', s[2:]):
dims.append('dim{0}'.format(letter))
if dims:
return ' '.join(dims) | python | def filter_composite_from_subgroups(s):
dims = []
for letter, sg in zip('ABCDEFGHIJKLMNOPQRSTUVWZ', s[2:]):
dims.append('dim{0}'.format(letter))
if dims:
return ' '.join(dims) | [
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----------
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A list representing the ordered subgroups, ideally the same list
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16,793 | daler/trackhub | trackhub/helpers.py | hex2rgb | def hex2rgb(h):
"""
Convert hex colors to RGB tuples
Parameters
----------
h : str
String hex color value
>>> hex2rgb("#ff0033")
'255,0,51'
"""
if not h.startswith('#') or len(h) != 7:
raise ValueError("Does not look like a hex color: '{0}'".format(h))
return ','.join(map(str, (
int(h[1:3], 16),
int(h[3:5], 16),
int(h[5:7], 16),
))) | python | def hex2rgb(h):
if not h.startswith('#') or len(h) != 7:
raise ValueError("Does not look like a hex color: '{0}'".format(h))
return ','.join(map(str, (
int(h[1:3], 16),
int(h[3:5], 16),
int(h[5:7], 16),
))) | [
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String hex color value
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16,794 | daler/trackhub | trackhub/helpers.py | sanitize | def sanitize(s, strict=True):
"""
Sanitize a string.
Spaces are converted to underscore; if strict=True they are then removed.
Parameters
----------
s : str
String to sanitize
strict : bool
If True, only alphanumeric characters are allowed. If False, a limited
set of additional characters (-._) will be allowed.
"""
allowed = ''.join(
[
'ABCDEFGHIJKLMNOPQRSTUVWXYZ',
'abcdefghijklmnopqrstuvwxyz',
'0123456789',
]
)
if not strict:
allowed += '-_.'
s = str(s).replace(' ', '_')
return ''.join([i for i in s if i in allowed]) | python | def sanitize(s, strict=True):
allowed = ''.join(
[
'ABCDEFGHIJKLMNOPQRSTUVWXYZ',
'abcdefghijklmnopqrstuvwxyz',
'0123456789',
]
)
if not strict:
allowed += '-_.'
s = str(s).replace(' ', '_')
return ''.join([i for i in s if i in allowed]) | [
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16,795 | daler/trackhub | trackhub/helpers.py | auto_track_url | def auto_track_url(track):
"""
Automatically sets the bigDataUrl for `track`.
Requirements:
* the track must be fully connected, such that its root is a Hub object
* the root Hub object must have the Hub.url attribute set
* the track must have the `source` attribute set
"""
hub = track.root(cls=Hub)
if hub is None:
raise ValueError(
"track is not fully connected because the root is %s" % repr(hub))
if hub.url is None:
raise ValueError("hub.url is not set")
if track.source is None:
raise ValueError("track.source is not set") | python | def auto_track_url(track):
hub = track.root(cls=Hub)
if hub is None:
raise ValueError(
"track is not fully connected because the root is %s" % repr(hub))
if hub.url is None:
raise ValueError("hub.url is not set")
if track.source is None:
raise ValueError("track.source is not set") | [
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16,796 | daler/trackhub | trackhub/helpers.py | print_rendered_results | def print_rendered_results(results_dict):
"""
Pretty-prints the rendered results dictionary.
Rendered results can be multiply-nested dictionaries; this uses JSON
serialization to print a nice representation.
"""
class _HubComponentEncoder(json.JSONEncoder):
def default(self, o):
if isinstance(o, base.HubComponent):
return repr(o)
return json.JSONEncoder.default(self, o)
formatted = json.dumps(results_dict, indent=4, cls=_HubComponentEncoder)
# the returned string contains lines with trailing spaces, which causes
# doctests to fail. So fix that here.
for s in formatted.splitlines():
print(s.rstrip()) | python | def print_rendered_results(results_dict):
class _HubComponentEncoder(json.JSONEncoder):
def default(self, o):
if isinstance(o, base.HubComponent):
return repr(o)
return json.JSONEncoder.default(self, o)
formatted = json.dumps(results_dict, indent=4, cls=_HubComponentEncoder)
# the returned string contains lines with trailing spaces, which causes
# doctests to fail. So fix that here.
for s in formatted.splitlines():
print(s.rstrip()) | [
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16,797 | daler/trackhub | trackhub/helpers.py | example_bigbeds | def example_bigbeds():
"""
Returns list of example bigBed files
"""
hits = []
d = data_dir()
for fn in os.listdir(d):
fn = os.path.join(d, fn)
if os.path.splitext(fn)[-1] == '.bigBed':
hits.append(os.path.abspath(fn))
return hits | python | def example_bigbeds():
hits = []
d = data_dir()
for fn in os.listdir(d):
fn = os.path.join(d, fn)
if os.path.splitext(fn)[-1] == '.bigBed':
hits.append(os.path.abspath(fn))
return hits | [
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16,798 | Karaage-Cluster/karaage | karaage/plugins/kgusage/graphs.py | get_colour | def get_colour(index):
""" get color number index. """
colours = [
'red', 'blue', 'green', 'pink',
'yellow', 'magenta', 'orange', 'cyan',
]
default_colour = 'purple'
if index < len(colours):
return colours[index]
else:
return default_colour | python | def get_colour(index):
colours = [
'red', 'blue', 'green', 'pink',
'yellow', 'magenta', 'orange', 'cyan',
]
default_colour = 'purple'
if index < len(colours):
return colours[index]
else:
return default_colour | [
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... | get color number index. | [
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] | 2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9 | https://github.com/Karaage-Cluster/karaage/blob/2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9/karaage/plugins/kgusage/graphs.py#L32-L42 |
16,799 | Karaage-Cluster/karaage | karaage/plugins/kgusage/graphs.py | get_project_trend_graph_url | def get_project_trend_graph_url(project, start, end):
"""Generates a bar graph for a project. """
filename = get_project_trend_graph_filename(project, start, end)
urls = {
'graph_url': urlparse.urljoin(GRAPH_URL, filename + ".png"),
'data_url': urlparse.urljoin(GRAPH_URL, filename + ".csv"),
}
return urls | python | def get_project_trend_graph_url(project, start, end):
filename = get_project_trend_graph_filename(project, start, end)
urls = {
'graph_url': urlparse.urljoin(GRAPH_URL, filename + ".png"),
'data_url': urlparse.urljoin(GRAPH_URL, filename + ".csv"),
}
return urls | [
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] | 2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9 | https://github.com/Karaage-Cluster/karaage/blob/2f4c8b4e2d728b3fcbb151160c49000f1c04f5c9/karaage/plugins/kgusage/graphs.py#L102-L111 |
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