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 |
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2,300 | ergoithz/browsepy | browsepy/file.py | generic_filename | def generic_filename(path):
'''
Extract filename of given path os-indepently, taking care of known path
separators.
:param path: path
:return: filename
:rtype: str or unicode (depending on given path)
'''
for sep in common_path_separators:
if sep in path:
_, path = ... | python | def generic_filename(path):
'''
Extract filename of given path os-indepently, taking care of known path
separators.
:param path: path
:return: filename
:rtype: str or unicode (depending on given path)
'''
for sep in common_path_separators:
if sep in path:
_, path = ... | [
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2,301 | ergoithz/browsepy | browsepy/file.py | clean_restricted_chars | def clean_restricted_chars(path, restricted_chars=restricted_chars):
'''
Get path without restricted characters.
:param path: path
:return: path without restricted characters
:rtype: str or unicode (depending on given path)
'''
for character in restricted_chars:
path = path.replace(... | python | def clean_restricted_chars(path, restricted_chars=restricted_chars):
'''
Get path without restricted characters.
:param path: path
:return: path without restricted characters
:rtype: str or unicode (depending on given path)
'''
for character in restricted_chars:
path = path.replace(... | [
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2,302 | ergoithz/browsepy | browsepy/file.py | check_forbidden_filename | def check_forbidden_filename(filename,
destiny_os=os.name,
restricted_names=restricted_names):
'''
Get if given filename is forbidden for current OS or filesystem.
:param filename:
:param destiny_os: destination operative system
:param fs_en... | python | def check_forbidden_filename(filename,
destiny_os=os.name,
restricted_names=restricted_names):
'''
Get if given filename is forbidden for current OS or filesystem.
:param filename:
:param destiny_os: destination operative system
:param fs_en... | [
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2,303 | ergoithz/browsepy | browsepy/file.py | check_path | def check_path(path, base, os_sep=os.sep):
'''
Check if both given paths are equal.
:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:type base: str
:return: wether two path are equal or not
... | python | def check_path(path, base, os_sep=os.sep):
'''
Check if both given paths are equal.
:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:type base: str
:return: wether two path are equal or not
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2,304 | ergoithz/browsepy | browsepy/file.py | check_base | def check_base(path, base, os_sep=os.sep):
'''
Check if given absolute path is under or given base.
:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:return: wether path is under given base or no... | python | def check_base(path, base, os_sep=os.sep):
'''
Check if given absolute path is under or given base.
:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:return: wether path is under given base or no... | [
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:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:return: wether path is under given base or not
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2,305 | ergoithz/browsepy | browsepy/file.py | check_under_base | def check_under_base(path, base, os_sep=os.sep):
'''
Check if given absolute path is under given base.
:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:return: wether file is under given base or... | python | def check_under_base(path, base, os_sep=os.sep):
'''
Check if given absolute path is under given base.
:param path: absolute path
:type path: str
:param base: absolute base path
:type base: str
:param os_sep: path separator, defaults to os.sep
:return: wether file is under given base or... | [
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2,306 | ergoithz/browsepy | browsepy/file.py | secure_filename | def secure_filename(path, destiny_os=os.name, fs_encoding=compat.FS_ENCODING):
'''
Get rid of parent path components and special filenames.
If path is invalid or protected, return empty string.
:param path: unsafe path, only basename will be used
:type: str
:param destiny_os: destination opera... | python | def secure_filename(path, destiny_os=os.name, fs_encoding=compat.FS_ENCODING):
'''
Get rid of parent path components and special filenames.
If path is invalid or protected, return empty string.
:param path: unsafe path, only basename will be used
:type: str
:param destiny_os: destination opera... | [
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2,307 | ergoithz/browsepy | browsepy/file.py | alternative_filename | def alternative_filename(filename, attempt=None):
'''
Generates an alternative version of given filename.
If an number attempt parameter is given, will be used on the alternative
name, a random value will be used otherwise.
:param filename: original filename
:param attempt: optional attempt nu... | python | def alternative_filename(filename, attempt=None):
'''
Generates an alternative version of given filename.
If an number attempt parameter is given, will be used on the alternative
name, a random value will be used otherwise.
:param filename: original filename
:param attempt: optional attempt nu... | [
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2,308 | ergoithz/browsepy | browsepy/file.py | scandir | def scandir(path, app=None):
'''
Config-aware scandir. Currently, only aware of ``exclude_fnc``.
:param path: absolute path
:type path: str
:param app: flask application
:type app: flask.Flask or None
:returns: filtered scandir entries
:rtype: iterator
'''
exclude = app and app.... | python | def scandir(path, app=None):
'''
Config-aware scandir. Currently, only aware of ``exclude_fnc``.
:param path: absolute path
:type path: str
:param app: flask application
:type app: flask.Flask or None
:returns: filtered scandir entries
:rtype: iterator
'''
exclude = app and app.... | [
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2,309 | ergoithz/browsepy | browsepy/file.py | Node.link | def link(self):
'''
Get last widget with place "entry-link".
:returns: widget on entry-link (ideally a link one)
:rtype: namedtuple instance
'''
link = None
for widget in self.widgets:
if widget.place == 'entry-link':
link = widget
... | python | def link(self):
'''
Get last widget with place "entry-link".
:returns: widget on entry-link (ideally a link one)
:rtype: namedtuple instance
'''
link = None
for widget in self.widgets:
if widget.place == 'entry-link':
link = widget
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2,310 | ergoithz/browsepy | browsepy/file.py | Node.can_remove | def can_remove(self):
'''
Get if current node can be removed based on app config's
directory_remove.
:returns: True if current node can be removed, False otherwise.
:rtype: bool
'''
dirbase = self.app.config["directory_remove"]
return bool(dirbase and che... | python | def can_remove(self):
'''
Get if current node can be removed based on app config's
directory_remove.
:returns: True if current node can be removed, False otherwise.
:rtype: bool
'''
dirbase = self.app.config["directory_remove"]
return bool(dirbase and che... | [
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2,311 | ergoithz/browsepy | browsepy/file.py | Node.parent | def parent(self):
'''
Get parent node if available based on app config's directory_base.
:returns: parent object if available
:rtype: Node instance or None
'''
if check_path(self.path, self.app.config['directory_base']):
return None
parent = os.path.d... | python | def parent(self):
'''
Get parent node if available based on app config's directory_base.
:returns: parent object if available
:rtype: Node instance or None
'''
if check_path(self.path, self.app.config['directory_base']):
return None
parent = os.path.d... | [
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2,312 | ergoithz/browsepy | browsepy/file.py | Node.ancestors | def ancestors(self):
'''
Get list of ancestors until app config's directory_base is reached.
:returns: list of ancestors starting from nearest.
:rtype: list of Node objects
'''
ancestors = []
parent = self.parent
while parent:
ancestors.append... | python | def ancestors(self):
'''
Get list of ancestors until app config's directory_base is reached.
:returns: list of ancestors starting from nearest.
:rtype: list of Node objects
'''
ancestors = []
parent = self.parent
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2,313 | ergoithz/browsepy | browsepy/file.py | Node.modified | def modified(self):
'''
Get human-readable last modification date-time.
:returns: iso9008-like date-time string (without timezone)
:rtype: str
'''
try:
dt = datetime.datetime.fromtimestamp(self.stats.st_mtime)
return dt.strftime('%Y.%m.%d %H:%M:%S... | python | def modified(self):
'''
Get human-readable last modification date-time.
:returns: iso9008-like date-time string (without timezone)
:rtype: str
'''
try:
dt = datetime.datetime.fromtimestamp(self.stats.st_mtime)
return dt.strftime('%Y.%m.%d %H:%M:%S... | [
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2,314 | ergoithz/browsepy | browsepy/file.py | Node.from_urlpath | def from_urlpath(cls, path, app=None):
'''
Alternative constructor which accepts a path as taken from URL and uses
the given app or the current app config to get the real path.
If class has attribute `generic` set to True, `directory_class` or
`file_class` will be used as type.
... | python | def from_urlpath(cls, path, app=None):
'''
Alternative constructor which accepts a path as taken from URL and uses
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If class has attribute `generic` set to True, `directory_class` or
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2,315 | brutasse/graphite-api | graphite_api/finders/whisper.py | WhisperFinder._find_paths | def _find_paths(self, current_dir, patterns):
"""Recursively generates absolute paths whose components
underneath current_dir match the corresponding pattern in
patterns"""
pattern = patterns[0]
patterns = patterns[1:]
has_wildcard = is_pattern(pattern)
using_glob... | python | def _find_paths(self, current_dir, patterns):
pattern = patterns[0]
patterns = patterns[1:]
has_wildcard = is_pattern(pattern)
using_globstar = pattern == "**"
# This avoids os.listdir() for performance
if has_wildcard:
entries = [x.name for x in scandir(curr... | [
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2,316 | brutasse/graphite-api | graphite_api/intervals.py | union_overlapping | def union_overlapping(intervals):
"""Union any overlapping intervals in the given set."""
disjoint_intervals = []
for interval in intervals:
if disjoint_intervals and disjoint_intervals[-1].overlaps(interval):
disjoint_intervals[-1] = disjoint_intervals[-1].union(interval)
else:... | python | def union_overlapping(intervals):
disjoint_intervals = []
for interval in intervals:
if disjoint_intervals and disjoint_intervals[-1].overlaps(interval):
disjoint_intervals[-1] = disjoint_intervals[-1].union(interval)
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disjoint_intervals.append(interval)
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2,317 | brutasse/graphite-api | graphite_api/app.py | recurse | def recurse(query, index):
"""
Recursively walk across paths, adding leaves to the index as they're found.
"""
for node in app.store.find(query):
if node.is_leaf:
index.add(node.path)
else:
recurse('{0}.*'.format(node.path), index) | python | def recurse(query, index):
for node in app.store.find(query):
if node.is_leaf:
index.add(node.path)
else:
recurse('{0}.*'.format(node.path), index) | [
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2,318 | brutasse/graphite-api | graphite_api/_vendor/whisper.py | __archive_fetch | def __archive_fetch(fh, archive, fromTime, untilTime):
"""
Fetch data from a single archive. Note that checks for validity of the time
period requested happen above this level so it's possible to wrap around the
archive on a read and request data older than the archive's retention
"""
fromInterval = int( fromTime -... | python | def __archive_fetch(fh, archive, fromTime, untilTime):
fromInterval = int( fromTime - (fromTime % archive['secondsPerPoint']) ) + archive['secondsPerPoint']
untilInterval = int( untilTime - (untilTime % archive['secondsPerPoint']) ) + archive['secondsPerPoint']
if fromInterval == untilInterval:
# Zero-length ... | [
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2,319 | brutasse/graphite-api | graphite_api/_vendor/whisper.py | merge | def merge(path_from, path_to):
""" Merges the data from one whisper file into another. Each file must have
the same archive configuration
"""
fh_from = open(path_from, 'rb')
fh_to = open(path_to, 'rb+')
return file_merge(fh_from, fh_to) | python | def merge(path_from, path_to):
fh_from = open(path_from, 'rb')
fh_to = open(path_to, 'rb+')
return file_merge(fh_from, fh_to) | [
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2,320 | brutasse/graphite-api | graphite_api/_vendor/whisper.py | diff | def diff(path_from, path_to, ignore_empty = False):
""" Compare two whisper databases. Each file must have the same archive configuration """
fh_from = open(path_from, 'rb')
fh_to = open(path_to, 'rb')
diffs = file_diff(fh_from, fh_to, ignore_empty)
fh_to.close()
fh_from.close()
return diffs | python | def diff(path_from, path_to, ignore_empty = False):
fh_from = open(path_from, 'rb')
fh_to = open(path_to, 'rb')
diffs = file_diff(fh_from, fh_to, ignore_empty)
fh_to.close()
fh_from.close()
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2,321 | brutasse/graphite-api | graphite_api/render/datalib.py | DataStore.add_data | def add_data(self, path, time_info, data, exprs):
"""
Stores data before it can be put into a time series
"""
# Dont add if empty
if not nonempty(data):
for d in self.data[path]:
if nonempty(d['values']):
return
# Add data ... | python | def add_data(self, path, time_info, data, exprs):
# Dont add if empty
if not nonempty(data):
for d in self.data[path]:
if nonempty(d['values']):
return
# Add data to path
for expr in exprs:
self.paths[expr].add(path)
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2,322 | brutasse/graphite-api | graphite_api/carbonlink.py | CarbonLinkPool.select_host | def select_host(self, metric):
"""
Returns the carbon host that has data for the given metric.
"""
key = self.keyfunc(metric)
nodes = []
servers = set()
for node in self.hash_ring.get_nodes(key):
server, instance = node
if server in servers... | python | def select_host(self, metric):
key = self.keyfunc(metric)
nodes = []
servers = set()
for node in self.hash_ring.get_nodes(key):
server, instance = node
if server in servers:
continue
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2,323 | brutasse/graphite-api | graphite_api/render/glyph.py | safeArgs | def safeArgs(args):
"""Iterate over valid, finite values in an iterable.
Skip any items that are None, NaN, or infinite.
"""
return (arg for arg in args
if arg is not None and not math.isnan(arg) and not math.isinf(arg)) | python | def safeArgs(args):
return (arg for arg in args
if arg is not None and not math.isnan(arg) and not math.isinf(arg)) | [
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2,324 | brutasse/graphite-api | graphite_api/render/glyph.py | format_units | def format_units(v, step=None, system="si", units=None):
"""Format the given value in standardized units.
``system`` is either 'binary' or 'si'
For more info, see:
http://en.wikipedia.org/wiki/SI_prefix
http://en.wikipedia.org/wiki/Binary_prefix
"""
if v is None:
return 0, ... | python | def format_units(v, step=None, system="si", units=None):
if v is None:
return 0, ''
for prefix, size in UnitSystems[system]:
if condition(v, size, step):
v2 = v / size
if v2 - math.floor(v2) < 0.00000000001 and v > 1:
v2 = float(math.floor(v2))
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2,325 | brutasse/graphite-api | graphite_api/render/glyph.py | _AxisTics.checkFinite | def checkFinite(value, name='value'):
"""Check that value is a finite number.
If it is, return it. If not, raise GraphError describing the
problem, using name in the error message.
"""
if math.isnan(value):
raise GraphError('Encountered NaN %s' % (name,))
eli... | python | def checkFinite(value, name='value'):
if math.isnan(value):
raise GraphError('Encountered NaN %s' % (name,))
elif math.isinf(value):
raise GraphError('Encountered infinite %s' % (name,))
return value | [
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2,326 | brutasse/graphite-api | graphite_api/render/glyph.py | _AxisTics.reconcileLimits | def reconcileLimits(self):
"""If self.minValue is not less than self.maxValue, fix the problem.
If self.minValue is not less than self.maxValue, adjust
self.minValue and/or self.maxValue (depending on which was not
specified explicitly by the user) to make self.minValue <
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if self.minValue < self.maxValue:
# The limits are already OK.
return
minFixed = (self.minValueSource in ['min'])
maxFixed = (self.maxValueSource in ['max', 'limit'])
if minFixed and maxFixed:
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2,327 | brutasse/graphite-api | graphite_api/render/glyph.py | _AxisTics.applySettings | def applySettings(self, axisMin=None, axisMax=None, axisLimit=None):
"""Apply the specified settings to this axis.
Set self.minValue, self.minValueSource, self.maxValue,
self.maxValueSource, and self.axisLimit reasonably based on the
parameters provided.
Arguments:
axi... | python | def applySettings(self, axisMin=None, axisMax=None, axisLimit=None):
if axisMin is not None and not math.isnan(axisMin):
self.minValueSource = 'min'
self.minValue = self.checkFinite(axisMin, 'axis min')
if axisMax == 'max':
self.maxValueSource = 'extremum'
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2,328 | brutasse/graphite-api | graphite_api/render/glyph.py | _AxisTics.makeLabel | def makeLabel(self, value):
"""Create a label for the specified value.
Create a label string containing the value and its units (if any),
based on the values of self.step, self.span, and self.unitSystem.
"""
value, prefix = format_units(value, self.step,
... | python | def makeLabel(self, value):
value, prefix = format_units(value, self.step,
system=self.unitSystem)
span, spanPrefix = format_units(self.span, self.step,
system=self.unitSystem)
if prefix:
prefix += " "
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2,329 | brutasse/graphite-api | graphite_api/render/glyph.py | _LinearAxisTics.generateSteps | def generateSteps(self, minStep):
"""Generate allowed steps with step >= minStep in increasing order."""
self.checkFinite(minStep)
if self.binary:
base = 2.0
mantissas = [1.0]
exponent = math.floor(math.log(minStep, 2) - EPSILON)
else:
bas... | python | def generateSteps(self, minStep):
self.checkFinite(minStep)
if self.binary:
base = 2.0
mantissas = [1.0]
exponent = math.floor(math.log(minStep, 2) - EPSILON)
else:
base = 10.0
mantissas = [1.0, 2.0, 5.0]
exponent = math.fl... | [
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2,330 | brutasse/graphite-api | graphite_api/render/glyph.py | _LinearAxisTics.computeSlop | def computeSlop(self, step, divisor):
"""Compute the slop that would result from step and divisor.
Return the slop, or None if this combination can't cover the full
range. See chooseStep() for the definition of "slop".
"""
bottom = step * math.floor(self.minValue / float(step) ... | python | def computeSlop(self, step, divisor):
bottom = step * math.floor(self.minValue / float(step) + EPSILON)
top = bottom + step * divisor
if top >= self.maxValue - EPSILON * step:
return max(top - self.maxValue, self.minValue - bottom)
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return None | [
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2,331 | brutasse/graphite-api | graphite_api/render/glyph.py | _LinearAxisTics.chooseStep | def chooseStep(self, divisors=None, binary=False):
"""Choose a nice, pretty size for the steps between axis labels.
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size that minimizes the amount of whites... | python | def chooseStep(self, divisors=None, binary=False):
self.binary = binary
if divisors is None:
divisors = [4, 5, 6]
else:
for divisor in divisors:
self.checkFinite(divisor, 'divisor')
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2,332 | brutasse/graphite-api | graphite_api/functions.py | formatPathExpressions | def formatPathExpressions(seriesList):
"""
Returns a comma-separated list of unique path expressions.
"""
pathExpressions = sorted(set([s.pathExpression for s in seriesList]))
return ','.join(pathExpressions) | python | def formatPathExpressions(seriesList):
pathExpressions = sorted(set([s.pathExpression for s in seriesList]))
return ','.join(pathExpressions) | [
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2,333 | brutasse/graphite-api | graphite_api/functions.py | rangeOfSeries | def rangeOfSeries(requestContext, *seriesLists):
"""
Takes a wildcard seriesList.
Distills down a set of inputs into the range of the series
Example::
&target=rangeOfSeries(Server*.connections.total)
"""
if not seriesLists or not any(seriesLists):
return []
seriesList, sta... | python | def rangeOfSeries(requestContext, *seriesLists):
if not seriesLists or not any(seriesLists):
return []
seriesList, start, end, step = normalize(seriesLists)
name = "rangeOfSeries(%s)" % formatPathExpressions(seriesList)
values = (safeSubtract(max(row),
min(row)) for ro... | [
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2,334 | brutasse/graphite-api | graphite_api/functions.py | percentileOfSeries | def percentileOfSeries(requestContext, seriesList, n, interpolate=False):
"""
percentileOfSeries returns a single series which is composed of the
n-percentile values taken across a wildcard series at each point.
Unless `interpolate` is set to True, percentile values are actual values
contained in on... | python | def percentileOfSeries(requestContext, seriesList, n, interpolate=False):
if n <= 0:
raise ValueError(
'The requested percent is required to be greater than 0')
if not seriesList:
return []
name = 'percentileOfSeries(%s,%g)' % (seriesList[0].pathExpression, n)
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2,335 | brutasse/graphite-api | graphite_api/functions.py | weightedAverage | def weightedAverage(requestContext, seriesListAvg, seriesListWeight, *nodes):
"""
Takes a series of average values and a series of weights and
produces a weighted average for all values.
The corresponding values should share one or more zero-indexed nodes.
Example::
&target=weightedAverag... | python | def weightedAverage(requestContext, seriesListAvg, seriesListWeight, *nodes):
if isinstance(nodes, int):
nodes = [nodes]
sortedSeries = {}
for seriesAvg, seriesWeight in zip_longest(
seriesListAvg, seriesListWeight):
key = ''
for node in nodes:
key += series... | [
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2,336 | brutasse/graphite-api | graphite_api/functions.py | scale | def scale(requestContext, seriesList, factor):
"""
Takes one metric or a wildcard seriesList followed by a constant, and
multiplies the datapoint by the constant provided at each point.
Example::
&target=scale(Server.instance01.threads.busy,10)
&target=scale(Server.instance*.threads.bu... | python | def scale(requestContext, seriesList, factor):
for series in seriesList:
series.name = "scale(%s,%g)" % (series.name, float(factor))
series.pathExpression = series.name
for i, value in enumerate(series):
series[i] = safeMul(value, factor)
return seriesList | [
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2,337 | brutasse/graphite-api | graphite_api/functions.py | scaleToSeconds | def scaleToSeconds(requestContext, seriesList, seconds):
"""
Takes one metric or a wildcard seriesList and returns "value per seconds"
where seconds is a last argument to this functions.
Useful in conjunction with derivative or integral function if you want
to normalize its result to a known resolu... | python | def scaleToSeconds(requestContext, seriesList, seconds):
for series in seriesList:
series.name = "scaleToSeconds(%s,%d)" % (series.name, seconds)
series.pathExpression = series.name
factor = seconds * 1.0 / series.step
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2,338 | brutasse/graphite-api | graphite_api/functions.py | pow | def pow(requestContext, seriesList, factor):
"""
Takes one metric or a wildcard seriesList followed by a constant, and
raises the datapoint by the power of the constant provided at each point.
Example::
&target=pow(Server.instance01.threads.busy,10)
&target=pow(Server.instance*.threads... | python | def pow(requestContext, seriesList, factor):
for series in seriesList:
series.name = "pow(%s,%g)" % (series.name, float(factor))
series.pathExpression = series.name
for i, value in enumerate(series):
series[i] = safePow(value, factor)
return seriesList | [
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2,339 | brutasse/graphite-api | graphite_api/functions.py | powSeries | def powSeries(requestContext, *seriesLists):
"""
Takes two or more series and pows their points. A constant line may be
used.
Example::
&target=powSeries(Server.instance01.app.requests,
Server.instance01.app.replies)
"""
if not seriesLists or not any(seriesLi... | python | def powSeries(requestContext, *seriesLists):
if not seriesLists or not any(seriesLists):
return []
seriesList, start, end, step = normalize(seriesLists)
name = "powSeries(%s)" % ','.join([s.name for s in seriesList])
values = []
for row in zip_longest(*seriesList):
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2,340 | brutasse/graphite-api | graphite_api/functions.py | squareRoot | def squareRoot(requestContext, seriesList):
"""
Takes one metric or a wildcard seriesList, and computes the square root
of each datapoint.
Example::
&target=squareRoot(Server.instance01.threads.busy)
"""
for series in seriesList:
series.name = "squareRoot(%s)" % (series.name)
... | python | def squareRoot(requestContext, seriesList):
for series in seriesList:
series.name = "squareRoot(%s)" % (series.name)
for i, value in enumerate(series):
series[i] = safePow(value, 0.5)
return seriesList | [
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2,341 | brutasse/graphite-api | graphite_api/functions.py | absolute | def absolute(requestContext, seriesList):
"""
Takes one metric or a wildcard seriesList and applies the mathematical abs
function to each datapoint transforming it to its absolute value.
Example::
&target=absolute(Server.instance01.threads.busy)
&target=absolute(Server.instance*.thread... | python | def absolute(requestContext, seriesList):
for series in seriesList:
series.name = "absolute(%s)" % (series.name)
series.pathExpression = series.name
for i, value in enumerate(series):
series[i] = safeAbs(value)
return seriesList | [
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2,342 | brutasse/graphite-api | graphite_api/functions.py | offset | def offset(requestContext, seriesList, factor):
"""
Takes one metric or a wildcard seriesList followed by a constant, and adds
the constant to each datapoint.
Example::
&target=offset(Server.instance01.threads.busy,10)
"""
for series in seriesList:
series.name = "offset(%s,%g)... | python | def offset(requestContext, seriesList, factor):
for series in seriesList:
series.name = "offset(%s,%g)" % (series.name, float(factor))
series.pathExpression = series.name
for i, value in enumerate(series):
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2,343 | brutasse/graphite-api | graphite_api/functions.py | offsetToZero | def offsetToZero(requestContext, seriesList):
"""
Offsets a metric or wildcard seriesList by subtracting the minimum
value in the series from each datapoint.
Useful to compare different series where the values in each series
may be higher or lower on average but you're only interested in the
re... | python | def offsetToZero(requestContext, seriesList):
for series in seriesList:
series.name = "offsetToZero(%s)" % (series.name)
minimum = safeMin(series)
for i, value in enumerate(series):
if value is not None:
series[i] = value - minimum
return seriesList | [
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2,344 | brutasse/graphite-api | graphite_api/functions.py | consolidateBy | def consolidateBy(requestContext, seriesList, consolidationFunc):
"""
Takes one metric or a wildcard seriesList and a consolidation function
name.
Valid function names are 'sum', 'average', 'min', and 'max'.
When a graph is drawn where width of the graph size in pixels is smaller
than the numb... | python | def consolidateBy(requestContext, seriesList, consolidationFunc):
for series in seriesList:
# datalib will throw an exception, so it's not necessary to validate
# here
series.consolidationFunc = consolidationFunc
series.name = 'consolidateBy(%s,"%s")' % (series.name,
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2,345 | brutasse/graphite-api | graphite_api/functions.py | integral | def integral(requestContext, seriesList):
"""
This will show the sum over time, sort of like a continuous addition
function. Useful for finding totals or trends in metrics that are
collected per minute.
Example::
&target=integral(company.sales.perMinute)
This would start at zero on th... | python | def integral(requestContext, seriesList):
results = []
for series in seriesList:
newValues = []
current = 0.0
for val in series:
if val is None:
newValues.append(None)
else:
current += val
newValues.append(current)
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2,346 | brutasse/graphite-api | graphite_api/functions.py | areaBetween | def areaBetween(requestContext, *seriesLists):
"""
Draws the vertical area in between the two series in seriesList. Useful for
visualizing a range such as the minimum and maximum latency for a service.
areaBetween expects **exactly one argument** that results in exactly two
series (see example belo... | python | def areaBetween(requestContext, *seriesLists):
if len(seriesLists) == 1:
[seriesLists] = seriesLists
assert len(seriesLists) == 2, ("areaBetween series argument must "
"reference *exactly* 2 series")
lower, upper = seriesLists
if len(lower) == 1:
[lower... | [
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2,347 | brutasse/graphite-api | graphite_api/functions.py | alias | def alias(requestContext, seriesList, newName):
"""
Takes one metric or a wildcard seriesList and a string in quotes.
Prints the string instead of the metric name in the legend.
Example::
&target=alias(Sales.widgets.largeBlue,"Large Blue Widgets")
"""
try:
seriesList.name = ne... | python | def alias(requestContext, seriesList, newName):
try:
seriesList.name = newName
except AttributeError:
for series in seriesList:
series.name = newName
return seriesList | [
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2,348 | brutasse/graphite-api | graphite_api/functions.py | _getFirstPathExpression | def _getFirstPathExpression(name):
"""Returns the first metric path in an expression."""
tokens = grammar.parseString(name)
pathExpression = None
while pathExpression is None:
if tokens.pathExpression:
pathExpression = tokens.pathExpression
elif tokens.expression:
... | python | def _getFirstPathExpression(name):
tokens = grammar.parseString(name)
pathExpression = None
while pathExpression is None:
if tokens.pathExpression:
pathExpression = tokens.pathExpression
elif tokens.expression:
tokens = tokens.expression
elif tokens.call:
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2,349 | brutasse/graphite-api | graphite_api/functions.py | alpha | def alpha(requestContext, seriesList, alpha):
"""
Assigns the given alpha transparency setting to the series. Takes a float
value between 0 and 1.
"""
for series in seriesList:
series.options['alpha'] = alpha
return seriesList | python | def alpha(requestContext, seriesList, alpha):
for series in seriesList:
series.options['alpha'] = alpha
return seriesList | [
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2,350 | brutasse/graphite-api | graphite_api/functions.py | color | def color(requestContext, seriesList, theColor):
"""
Assigns the given color to the seriesList
Example::
&target=color(collectd.hostname.cpu.0.user, 'green')
&target=color(collectd.hostname.cpu.0.system, 'ff0000')
&target=color(collectd.hostname.cpu.0.idle, 'gray')
&target=... | python | def color(requestContext, seriesList, theColor):
for series in seriesList:
series.color = theColor
return seriesList | [
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2,351 | brutasse/graphite-api | graphite_api/functions.py | logarithm | def logarithm(requestContext, seriesList, base=10):
"""
Takes one metric or a wildcard seriesList, a base, and draws the y-axis in
logarithmic format. If base is omitted, the function defaults to base 10.
Example::
&target=log(carbon.agents.hostname.avgUpdateTime,2)
"""
results = []
... | python | def logarithm(requestContext, seriesList, base=10):
results = []
for series in seriesList:
newValues = []
for val in series:
if val is None:
newValues.append(None)
elif val <= 0:
newValues.append(None)
else:
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2,352 | brutasse/graphite-api | graphite_api/functions.py | maximumBelow | def maximumBelow(requestContext, seriesList, n):
"""
Takes one metric or a wildcard seriesList followed by a constant n.
Draws only the metrics with a maximum value below n.
Example::
&target=maximumBelow(system.interface.eth*.packetsSent,1000)
This would only display interfaces which alw... | python | def maximumBelow(requestContext, seriesList, n):
results = []
for series in seriesList:
val = safeMax(series)
if val is None or val <= n:
results.append(series)
return results | [
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2,353 | brutasse/graphite-api | graphite_api/functions.py | minimumBelow | def minimumBelow(requestContext, seriesList, n):
"""
Takes one metric or a wildcard seriesList followed by a constant n.
Draws only the metrics with a minimum value below n.
Example::
&target=minimumBelow(system.interface.eth*.packetsSent,1000)
This would only display interfaces which sen... | python | def minimumBelow(requestContext, seriesList, n):
results = []
for series in seriesList:
val = safeMin(series)
if val is None or val <= n:
results.append(series)
return results | [
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2,354 | brutasse/graphite-api | graphite_api/functions.py | highestMax | def highestMax(requestContext, seriesList, n=1):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
Out of all metrics passed, draws only the N metrics with the highest
maximum value in the time period specified.
Example::
&target=highestMax(server*.instance*.threads.... | python | def highestMax(requestContext, seriesList, n=1):
result_list = sorted(seriesList, key=lambda s: safeMax(s))[-n:]
return sorted(result_list, key=lambda s: max(s), reverse=True) | [
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2,355 | brutasse/graphite-api | graphite_api/functions.py | currentAbove | def currentAbove(requestContext, seriesList, n):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
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at the end of the time period specified.
Example::
&target=currentAbove(server*.instance*.thread... | python | def currentAbove(requestContext, seriesList, n):
results = []
for series in seriesList:
val = safeLast(series)
if val is not None and val >= n:
results.append(series)
return results | [
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2,356 | brutasse/graphite-api | graphite_api/functions.py | averageAbove | def averageAbove(requestContext, seriesList, n):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
Out of all metrics passed, draws only the metrics with an average value
above N for the time period specified.
Example::
&target=averageAbove(server*.instance*.threads.b... | python | def averageAbove(requestContext, seriesList, n):
results = []
for series in seriesList:
val = safeAvg(series)
if val is not None and val >= n:
results.append(series)
return results | [
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2,357 | brutasse/graphite-api | graphite_api/functions.py | nPercentile | def nPercentile(requestContext, seriesList, n):
"""Returns n-percent of each series in the seriesList."""
assert n, 'The requested percent is required to be greater than 0'
results = []
for s in seriesList:
# Create a sorted copy of the TimeSeries excluding None values in the
# values l... | python | def nPercentile(requestContext, seriesList, n):
assert n, 'The requested percent is required to be greater than 0'
results = []
for s in seriesList:
# Create a sorted copy of the TimeSeries excluding None values in the
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s_copy = TimeSeries(s.name, s.start, s.end, s.ste... | [
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2,358 | brutasse/graphite-api | graphite_api/functions.py | averageOutsidePercentile | def averageOutsidePercentile(requestContext, seriesList, n):
"""
Removes functions lying inside an average percentile interval
"""
averages = [safeAvg(s) for s in seriesList]
if n < 50:
n = 100 - n
lowPercentile = _getPercentile(averages, 100 - n)
highPercentile = _getPercentile(av... | python | def averageOutsidePercentile(requestContext, seriesList, n):
averages = [safeAvg(s) for s in seriesList]
if n < 50:
n = 100 - n
lowPercentile = _getPercentile(averages, 100 - n)
highPercentile = _getPercentile(averages, n)
return [s for s in seriesList
if not lowPercentile < s... | [
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2,359 | brutasse/graphite-api | graphite_api/functions.py | removeBetweenPercentile | def removeBetweenPercentile(requestContext, seriesList, n):
"""
Removes lines who do not have an value lying in the x-percentile of all
the values at a moment
"""
if n < 50:
n = 100 - n
transposed = list(zip_longest(*seriesList))
lowPercentiles = [_getPercentile(col, 100-n) for col... | python | def removeBetweenPercentile(requestContext, seriesList, n):
if n < 50:
n = 100 - n
transposed = list(zip_longest(*seriesList))
lowPercentiles = [_getPercentile(col, 100-n) for col in transposed]
highPercentiles = [_getPercentile(col, n) for col in transposed]
return [l for l in seriesList... | [
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2,360 | brutasse/graphite-api | graphite_api/functions.py | removeAboveValue | def removeAboveValue(requestContext, seriesList, n):
"""
Removes data above the given threshold from the series or list of series
provided. Values above this threshold are assigned a value of None.
"""
for s in seriesList:
s.name = 'removeAboveValue(%s, %g)' % (s.name, n)
s.pathExpre... | python | def removeAboveValue(requestContext, seriesList, n):
for s in seriesList:
s.name = 'removeAboveValue(%s, %g)' % (s.name, n)
s.pathExpression = s.name
for (index, val) in enumerate(s):
if val is None:
continue
if val > n:
s[index] = None... | [
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2,361 | brutasse/graphite-api | graphite_api/functions.py | removeBelowPercentile | def removeBelowPercentile(requestContext, seriesList, n):
"""
Removes data below the nth percentile from the series or list of series
provided. Values below this percentile are assigned a value of None.
"""
for s in seriesList:
s.name = 'removeBelowPercentile(%s, %g)' % (s.name, n)
s... | python | def removeBelowPercentile(requestContext, seriesList, n):
for s in seriesList:
s.name = 'removeBelowPercentile(%s, %g)' % (s.name, n)
s.pathExpression = s.name
try:
percentile = nPercentile(requestContext, [s], n)[0][0]
except IndexError:
continue
for ... | [
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2,362 | brutasse/graphite-api | graphite_api/functions.py | useSeriesAbove | def useSeriesAbove(requestContext, seriesList, value, search, replace):
"""
Compares the maximum of each series against the given `value`. If the
series maximum is greater than `value`, the regular expression search and
replace is applied against the series name to plot a related metric.
e.g. given... | python | def useSeriesAbove(requestContext, seriesList, value, search, replace):
newSeries = []
for series in seriesList:
newname = re.sub(search, replace, series.name)
if safeMax(series) > value:
n = evaluateTarget(requestContext, newname)
if n is not None and len(n) > 0:
... | [
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2,363 | brutasse/graphite-api | graphite_api/functions.py | secondYAxis | def secondYAxis(requestContext, seriesList):
"""
Graph the series on the secondary Y axis.
"""
for series in seriesList:
series.options['secondYAxis'] = True
series.name = 'secondYAxis(%s)' % series.name
return seriesList | python | def secondYAxis(requestContext, seriesList):
for series in seriesList:
series.options['secondYAxis'] = True
series.name = 'secondYAxis(%s)' % series.name
return seriesList | [
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2,364 | brutasse/graphite-api | graphite_api/functions.py | holtWintersForecast | def holtWintersForecast(requestContext, seriesList):
"""
Performs a Holt-Winters forecast using the series as input data. Data from
one week previous to the series is used to bootstrap the initial forecast.
"""
previewSeconds = 7 * 86400 # 7 days
# ignore original data and pull new, including o... | python | def holtWintersForecast(requestContext, seriesList):
previewSeconds = 7 * 86400 # 7 days
# ignore original data and pull new, including our preview
newContext = requestContext.copy()
newContext['startTime'] = (requestContext['startTime'] -
timedelta(seconds=previewSeconds... | [
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2,365 | brutasse/graphite-api | graphite_api/functions.py | holtWintersConfidenceBands | def holtWintersConfidenceBands(requestContext, seriesList, delta=3):
"""
Performs a Holt-Winters forecast using the series as input data and plots
upper and lower bands with the predicted forecast deviations.
"""
previewSeconds = 7 * 86400 # 7 days
# ignore original data and pull new, including... | python | def holtWintersConfidenceBands(requestContext, seriesList, delta=3):
previewSeconds = 7 * 86400 # 7 days
# ignore original data and pull new, including our preview
newContext = requestContext.copy()
newContext['startTime'] = (requestContext['startTime'] -
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2,366 | brutasse/graphite-api | graphite_api/functions.py | holtWintersAberration | def holtWintersAberration(requestContext, seriesList, delta=3):
"""
Performs a Holt-Winters forecast using the series as input data and plots
the positive or negative deviation of the series data from the forecast.
"""
results = []
for series in seriesList:
confidenceBands = holtWintersC... | python | def holtWintersAberration(requestContext, seriesList, delta=3):
results = []
for series in seriesList:
confidenceBands = holtWintersConfidenceBands(requestContext, [series],
delta)
lowerBand = confidenceBands[0]
upperBand = confidenceB... | [
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2,367 | brutasse/graphite-api | graphite_api/functions.py | holtWintersConfidenceArea | def holtWintersConfidenceArea(requestContext, seriesList, delta=3):
"""
Performs a Holt-Winters forecast using the series as input data and plots
the area between the upper and lower bands of the predicted forecast
deviations.
"""
bands = holtWintersConfidenceBands(requestContext, seriesList, de... | python | def holtWintersConfidenceArea(requestContext, seriesList, delta=3):
bands = holtWintersConfidenceBands(requestContext, seriesList, delta)
results = areaBetween(requestContext, bands)
for series in results:
series.name = series.name.replace('areaBetween',
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2,368 | brutasse/graphite-api | graphite_api/functions.py | linearRegressionAnalysis | def linearRegressionAnalysis(series):
"""
Returns factor and offset of linear regression function by least
squares method.
"""
n = safeLen(series)
sumI = sum([i for i, v in enumerate(series) if v is not None])
sumV = sum([v for i, v in enumerate(series) if v is not None])
sumII = sum([i... | python | def linearRegressionAnalysis(series):
n = safeLen(series)
sumI = sum([i for i, v in enumerate(series) if v is not None])
sumV = sum([v for i, v in enumerate(series) if v is not None])
sumII = sum([i * i for i, v in enumerate(series) if v is not None])
sumIV = sum([i * v for i, v in enumerate(series)... | [
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2,369 | brutasse/graphite-api | graphite_api/functions.py | linearRegression | def linearRegression(requestContext, seriesList, startSourceAt=None,
endSourceAt=None):
"""
Graphs the liner regression function by least squares method.
Takes one metric or a wildcard seriesList, followed by a quoted string
with the time to start the line and another quoted string... | python | def linearRegression(requestContext, seriesList, startSourceAt=None,
endSourceAt=None):
from .app import evaluateTarget
results = []
sourceContext = requestContext.copy()
if startSourceAt is not None:
sourceContext['startTime'] = parseATTime(startSourceAt)
if endSourceAt... | [
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2,370 | brutasse/graphite-api | graphite_api/functions.py | drawAsInfinite | def drawAsInfinite(requestContext, seriesList):
"""
Takes one metric or a wildcard seriesList.
If the value is zero, draw the line at 0. If the value is above zero, draw
the line at infinity. If the value is null or less than zero, do not draw
the line.
Useful for displaying on/off metrics, suc... | python | def drawAsInfinite(requestContext, seriesList):
for series in seriesList:
series.options['drawAsInfinite'] = True
series.name = 'drawAsInfinite(%s)' % series.name
return seriesList | [
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2,371 | brutasse/graphite-api | graphite_api/functions.py | constantLine | def constantLine(requestContext, value):
"""
Takes a float F.
Draws a horizontal line at value F across the graph.
Example::
&target=constantLine(123.456)
"""
name = "constantLine(%s)" % str(value)
start = int(epoch(requestContext['startTime']))
end = int(epoch(requestContext... | python | def constantLine(requestContext, value):
name = "constantLine(%s)" % str(value)
start = int(epoch(requestContext['startTime']))
end = int(epoch(requestContext['endTime']))
step = int((end - start) / 2.0)
series = TimeSeries(str(value), start, end, step, [value, value, value])
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2,372 | brutasse/graphite-api | graphite_api/functions.py | aggregateLine | def aggregateLine(requestContext, seriesList, func='avg'):
"""
Takes a metric or wildcard seriesList and draws a horizontal line
based on the function applied to each series.
Note: By default, the graphite renderer consolidates data points by
averaging data points over time. If you are using the 'm... | python | def aggregateLine(requestContext, seriesList, func='avg'):
t_funcs = {'avg': safeAvg, 'min': safeMin, 'max': safeMax}
if func not in t_funcs:
raise ValueError("Invalid function %s" % func)
results = []
for series in seriesList:
value = t_funcs[func](series)
if value is not None... | [
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2,373 | brutasse/graphite-api | graphite_api/functions.py | verticalLine | def verticalLine(requestContext, ts, label=None, color=None):
"""
Takes a timestamp string ts.
Draws a vertical line at the designated timestamp with optional
'label' and 'color'. Supported timestamp formats include both
relative (e.g. -3h) and absolute (e.g. 16:00_20110501) strings,
such as th... | python | def verticalLine(requestContext, ts, label=None, color=None):
ts = int(epoch(parseATTime(ts, requestContext['tzinfo'])))
start = int(epoch(requestContext['startTime']))
end = int(epoch(requestContext['endTime']))
if ts < start:
raise ValueError("verticalLine(): timestamp %s exists "
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2,374 | brutasse/graphite-api | graphite_api/functions.py | transformNull | def transformNull(requestContext, seriesList, default=0, referenceSeries=None):
"""
Takes a metric or wildcard seriesList and replaces null values with
the value specified by `default`. The value 0 used if not specified.
The optional referenceSeries, if specified, is a metric or wildcard
series lis... | python | def transformNull(requestContext, seriesList, default=0, referenceSeries=None):
def transform(v, d):
if v is None:
return d
else:
return v
if referenceSeries:
defaults = [default if any(v is not None for v in x) else None
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2,375 | brutasse/graphite-api | graphite_api/functions.py | countSeries | def countSeries(requestContext, *seriesLists):
"""
Draws a horizontal line representing the number of nodes found in the
seriesList.
Example::
&target=countSeries(carbon.agents.*.*)
"""
if not seriesLists or not any(seriesLists):
series = constantLine(requestContext, 0).pop()
... | python | def countSeries(requestContext, *seriesLists):
if not seriesLists or not any(seriesLists):
series = constantLine(requestContext, 0).pop()
series.pathExpression = "countSeries()"
else:
seriesList, start, end, step = normalize(seriesLists)
name = "countSeries(%s)" % formatPathExpre... | [
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2,376 | brutasse/graphite-api | graphite_api/functions.py | group | def group(requestContext, *seriesLists):
"""
Takes an arbitrary number of seriesLists and adds them to a single
seriesList. This is used to pass multiple seriesLists to a function which
only takes one.
"""
seriesGroup = []
for s in seriesLists:
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return serie... | python | def group(requestContext, *seriesLists):
seriesGroup = []
for s in seriesLists:
seriesGroup.extend(s)
return seriesGroup | [
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2,377 | brutasse/graphite-api | graphite_api/functions.py | groupByNode | def groupByNode(requestContext, seriesList, nodeNum, callback):
"""
Takes a serieslist and maps a callback to subgroups within as defined by a
common node.
Example::
&target=groupByNode(ganglia.by-function.*.*.cpu.load5,2,"sumSeries")
Would return multiple series which are each the result... | python | def groupByNode(requestContext, seriesList, nodeNum, callback):
return groupByNodes(requestContext, seriesList, callback, nodeNum) | [
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2,378 | brutasse/graphite-api | graphite_api/functions.py | groupByNodes | def groupByNodes(requestContext, seriesList, callback, *nodes):
"""
Takes a serieslist and maps a callback to subgroups within as defined by
multiple nodes.
Example::
&target=groupByNodes(ganglia.server*.*.cpu.load*,"sumSeries",1,4)
Would return multiple series which are each the result o... | python | def groupByNodes(requestContext, seriesList, callback, *nodes):
from .app import app
metaSeries = {}
keys = []
if isinstance(nodes, int):
nodes = [nodes]
for series in seriesList:
key = '.'.join(series.name.split(".")[n] for n in nodes)
if key not in metaSeries:
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2,379 | brutasse/graphite-api | graphite_api/functions.py | exclude | def exclude(requestContext, seriesList, pattern):
"""
Takes a metric or a wildcard seriesList, followed by a regular expression
in double quotes. Excludes metrics that match the regular expression.
Example::
&target=exclude(servers*.instance*.threads.busy,"server02")
"""
regex = re.... | python | def exclude(requestContext, seriesList, pattern):
regex = re.compile(pattern)
return [s for s in seriesList if not regex.search(s.name)] | [
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2,380 | brutasse/graphite-api | graphite_api/functions.py | summarize | def summarize(requestContext, seriesList, intervalString, func='sum',
alignToFrom=False):
"""
Summarize the data into interval buckets of a certain size.
By default, the contents of each interval bucket are summed together.
This is useful for counters where each increment represents a dis... | python | def summarize(requestContext, seriesList, intervalString, func='sum',
alignToFrom=False):
results = []
delta = parseTimeOffset(intervalString)
interval = to_seconds(delta)
for series in seriesList:
buckets = {}
timestamps = range(int(series.start), int(series.end) + 1,
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2,381 | opencobra/memote | memote/experimental/medium.py | Medium.apply | def apply(self, model):
"""Set the defined medium on the given model."""
model.medium = {row.exchange: row.uptake
for row in self.data.itertuples(index=False)} | python | def apply(self, model):
model.medium = {row.exchange: row.uptake
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2,382 | opencobra/memote | memote/suite/results/result.py | MemoteResult.add_environment_information | def add_environment_information(meta):
"""Record environment information."""
meta["timestamp"] = datetime.utcnow().isoformat(" ")
meta["platform"] = platform.system()
meta["release"] = platform.release()
meta["python"] = platform.python_version()
meta["packages"] = get_pk... | python | def add_environment_information(meta):
meta["timestamp"] = datetime.utcnow().isoformat(" ")
meta["platform"] = platform.system()
meta["release"] = platform.release()
meta["python"] = platform.python_version()
meta["packages"] = get_pkg_info("memote") | [
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2,383 | opencobra/memote | memote/support/helpers.py | find_transported_elements | def find_transported_elements(rxn):
"""
Return a dictionary showing the amount of transported elements of a rxn.
Collects the elements for each metabolite participating in a reaction,
multiplies the amount by the metabolite's stoichiometry in the reaction and
bins the result according to the compar... | python | def find_transported_elements(rxn):
element_dist = defaultdict()
# Collecting elements for each metabolite.
for met in rxn.metabolites:
if met.compartment not in element_dist:
# Multiplication by the metabolite stoichiometry.
element_dist[met.compartment] = \
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2,384 | opencobra/memote | memote/support/helpers.py | find_transport_reactions | def find_transport_reactions(model):
"""
Return a list of all transport reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
A transport reaction is defined as follows:
1. It contains metabolites from at least 2 compartme... | python | def find_transport_reactions(model):
transport_reactions = []
transport_rxn_candidates = set(model.reactions) - set(model.boundary) \
- set(find_biomass_reaction(model))
transport_rxn_candidates = set(
[rxn for rxn in transport_rxn_candidates if len(rxn.compartments) >= 2]
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# Add al... | [
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2,385 | opencobra/memote | memote/support/helpers.py | find_converting_reactions | def find_converting_reactions(model, pair):
"""
Find all reactions which convert a given metabolite pair.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
pair: tuple or list
A pair of metabolite identifiers without compartment suffix.
Retu... | python | def find_converting_reactions(model, pair):
first = set(find_met_in_model(model, pair[0]))
second = set(find_met_in_model(model, pair[1]))
hits = list()
for rxn in model.reactions:
# FIXME: Use `set.issubset` much more idiomatic.
if len(first & set(rxn.reactants)) > 0 and len(
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2,386 | opencobra/memote | memote/support/helpers.py | find_demand_reactions | def find_demand_reactions(model):
u"""
Return a list of demand reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines demand reactions as:
-- 'unbalanced network reactions that allow the accumulation of a compou... | python | def find_demand_reactions(model):
u"""
Return a list of demand reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
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-- 'unbalanced network reactions that allow the accumulation of a compou... | [
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2,387 | opencobra/memote | memote/support/helpers.py | find_sink_reactions | def find_sink_reactions(model):
u"""
Return a list of sink reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines sink reactions as:
-- 'similar to demand reactions' but reversible, thus able to supply the
m... | python | def find_sink_reactions(model):
u"""
Return a list of sink reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines sink reactions as:
-- 'similar to demand reactions' but reversible, thus able to supply the
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2,388 | opencobra/memote | memote/support/helpers.py | find_exchange_rxns | def find_exchange_rxns(model):
u"""
Return a list of exchange reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines exchange reactions as:
-- reactions that 'define the extracellular environment'
-- 'unbala... | python | def find_exchange_rxns(model):
u"""
Return a list of exchange reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
[1] defines exchange reactions as:
-- reactions that 'define the extracellular environment'
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2,389 | opencobra/memote | memote/support/helpers.py | find_interchange_biomass_reactions | def find_interchange_biomass_reactions(model, biomass=None):
"""
Return the set of all transport, boundary, and biomass reactions.
These reactions are either pseudo-reactions, or incorporated to allow
metabolites to pass between compartments. Some tests focus on purely
metabolic reactions and hence... | python | def find_interchange_biomass_reactions(model, biomass=None):
boundary = set(model.boundary)
transporters = find_transport_reactions(model)
if biomass is None:
biomass = set(find_biomass_reaction(model))
return boundary | transporters | biomass | [
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2,390 | opencobra/memote | memote/support/helpers.py | run_fba | def run_fba(model, rxn_id, direction="max", single_value=True):
"""
Return the solution of an FBA to a set objective function.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
rxn_id : string
A string containing the reaction ID of the desired FB... | python | def run_fba(model, rxn_id, direction="max", single_value=True):
model.objective = model.reactions.get_by_id(rxn_id)
model.objective_direction = direction
if single_value:
try:
return model.slim_optimize()
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return np.nan
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try:
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2,391 | opencobra/memote | memote/support/helpers.py | close_boundaries_sensibly | def close_boundaries_sensibly(model):
"""
Return a cobra model with all boundaries closed and changed constraints.
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as such. Instead reactions are constrained according to their
reversibility. This is to prevent the FBA from ... | python | def close_boundaries_sensibly(model):
for rxn in model.reactions:
if rxn.reversibility:
rxn.bounds = -1, 1
else:
rxn.bounds = 0, 1
for boundary in model.boundary:
boundary.bounds = (0, 0) | [
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2,392 | opencobra/memote | memote/support/helpers.py | metabolites_per_compartment | def metabolites_per_compartment(model, compartment_id):
"""
Identify all metabolites that belong to a given compartment.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
compartment_id : string
Model specific compartment identifier.
Returns... | python | def metabolites_per_compartment(model, compartment_id):
return [met for met in model.metabolites
if met.compartment == compartment_id] | [
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2,393 | opencobra/memote | memote/support/helpers.py | largest_compartment_id_met | def largest_compartment_id_met(model):
"""
Return the ID of the compartment with the most metabolites.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
-------
string
Compartment ID of the compartment with the most metabolites.
... | python | def largest_compartment_id_met(model):
# Sort compartments by decreasing size and extract the largest two.
candidate, second = sorted(
((c, len(metabolites_per_compartment(model, c)))
for c in model.compartments), reverse=True, key=itemgetter(1))[:2]
# Compare the size of the compartments.
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2,394 | opencobra/memote | memote/support/helpers.py | find_compartment_id_in_model | def find_compartment_id_in_model(model, compartment_id):
"""
Identify a model compartment by looking up names in COMPARTMENT_SHORTLIST.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
compartment_id : string
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if compartment_id not in COMPARTMENT_SHORTLIST.keys():
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2,395 | opencobra/memote | memote/support/helpers.py | find_met_in_model | def find_met_in_model(model, mnx_id, compartment_id=None):
"""
Return specific metabolites by looking up IDs in METANETX_SHORTLIST.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
mnx_id : string
Memote internal MetaNetX metabolite identifier u... | python | def find_met_in_model(model, mnx_id, compartment_id=None):
def compare_annotation(annotation):
"""
Return annotation IDs that match to METANETX_SHORTLIST references.
Compares the set of METANETX_SHORTLIST references for a given mnx_id
and the annotation IDs stored in a given annotat... | [
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2,396 | opencobra/memote | memote/support/helpers.py | find_bounds | def find_bounds(model):
"""
Return the median upper and lower bound of the metabolic model.
Bounds can vary from model to model. Cobrapy defaults to (-1000, 1000) but
this may not be the case for merged or autogenerated models. In these
cases, this function is used to iterate over all the bounds of... | python | def find_bounds(model):
lower_bounds = np.asarray([rxn.lower_bound for rxn in model.reactions],
dtype=float)
upper_bounds = np.asarray([rxn.upper_bound for rxn in model.reactions],
dtype=float)
lower_bound = np.nanmedian(lower_bounds[lower_bounds !... | [
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2,397 | opencobra/memote | memote/suite/reporting/report.py | Report.render_html | def render_html(self):
"""Render an HTML report."""
return self._template.safe_substitute(
report_type=self._report_type,
results=self.render_json()
) | python | def render_html(self):
return self._template.safe_substitute(
report_type=self._report_type,
results=self.render_json()
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2,398 | opencobra/memote | memote/suite/reporting/report.py | Report.compute_score | def compute_score(self):
"""Calculate the overall test score using the configuration."""
# LOGGER.info("Begin scoring")
cases = self.get_configured_tests() | set(self.result.cases)
scores = DataFrame({"score": 0.0, "max": 1.0},
index=sorted(cases))
self... | python | def compute_score(self):
# LOGGER.info("Begin scoring")
cases = self.get_configured_tests() | set(self.result.cases)
scores = DataFrame({"score": 0.0, "max": 1.0},
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2,399 | opencobra/memote | memote/support/sbo.py | find_components_without_sbo_terms | def find_components_without_sbo_terms(model, components):
"""
Find model components that are not annotated with any SBO terms.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
components : {"metabolites", "reactions", "genes"}
A string denoting ... | python | def find_components_without_sbo_terms(model, components):
return [elem for elem in getattr(model, components) if
elem.annotation is None or 'sbo' not in elem.annotation] | [
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"... | Find model components that are not annotated with any SBO terms.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
components : {"metabolites", "reactions", "genes"}
A string denoting `cobra.Model` components.
Returns
-------
list
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] | 276630fcd4449fb7b914186edfd38c239e7052df | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/sbo.py#L27-L45 |
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