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brutasse/graphite-api | graphite_api/functions.py | _getPercentile | def _getPercentile(points, n, interpolate=False):
"""
Percentile is calculated using the method outlined in the NIST Engineering
Statistics Handbook:
http://www.itl.nist.gov/div898/handbook/prc/section2/prc252.htm
"""
sortedPoints = sorted(not_none(points))
if len(sortedPoints) == 0:
... | python | def _getPercentile(points, n, interpolate=False):
"""
Percentile is calculated using the method outlined in the NIST Engineering
Statistics Handbook:
http://www.itl.nist.gov/div898/handbook/prc/section2/prc252.htm
"""
sortedPoints = sorted(not_none(points))
if len(sortedPoints) == 0:
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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):
"""Returns n-percent of each series in the seriesList."""
assert n, 'The requested percent is required to be greater than 0'
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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):
"""
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)
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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):
"""
Removes lines who do not have an value lying in the x-percentile of all
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"""
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n = 100 - n
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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
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"""
for s in seriesList:
s.name = 'removeAboveValue(%s, %g)' % (s.name, n)
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"""
Removes data above the given threshold from the series or list of series
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"""
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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):
"""
Removes data below the nth percentile from the series or list of series
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for s in seriesList:
s.name = 'removeBelowPercentile(%s, %g)' % (s.name, n)
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brutasse/graphite-api | graphite_api/functions.py | sortByName | def sortByName(requestContext, seriesList, natural=False):
"""
Takes one metric or a wildcard seriesList.
Sorts the list of metrics by the metric name using either alphabetical
order or natural sorting. Natural sorting allows names containing numbers
to be sorted more naturally, e.g:
- Alphabe... | python | def sortByName(requestContext, seriesList, natural=False):
"""
Takes one metric or a wildcard seriesList.
Sorts the list of metrics by the metric name using either alphabetical
order or natural sorting. Natural sorting allows names containing numbers
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brutasse/graphite-api | graphite_api/functions.py | sortByTotal | def sortByTotal(requestContext, seriesList):
"""
Takes one metric or a wildcard seriesList.
Sorts the list of metrics by the sum of values across the time period
specified.
"""
return list(sorted(seriesList, key=safeSum, reverse=True)) | python | def sortByTotal(requestContext, seriesList):
"""
Takes one metric or a wildcard seriesList.
Sorts the list of metrics by the sum of values across the time period
specified.
"""
return list(sorted(seriesList, key=safeSum, reverse=True)) | [
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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):
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brutasse/graphite-api | graphite_api/functions.py | mostDeviant | def mostDeviant(requestContext, seriesList, n):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
Draws the N most deviant metrics.
To find the deviants, the standard deviation (sigma) of each series
is taken and ranked. The top N standard deviations are returned.
Example:... | python | def mostDeviant(requestContext, seriesList, n):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
Draws the N most deviant metrics.
To find the deviants, the standard deviation (sigma) of each series
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brutasse/graphite-api | graphite_api/functions.py | stdev | def stdev(requestContext, seriesList, points, windowTolerance=0.1):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
Draw the Standard Deviation of all metrics passed for the past N
datapoints. If the ratio of null points in the window is greater than
windowTolerance, skip the... | python | def stdev(requestContext, seriesList, points, windowTolerance=0.1):
"""
Takes one metric or a wildcard seriesList followed by an integer N.
Draw the Standard Deviation of all metrics passed for the past N
datapoints. If the ratio of null points in the window is greater than
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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):
"""
Graph the series on the secondary Y axis.
"""
for series in seriesList:
series.options['secondYAxis'] = True
series.name = 'secondYAxis(%s)' % series.name
return seriesList | [
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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):
"""
Performs a Holt-Winters forecast using the series as input data. Data from
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previewSeconds = 7 * 86400 # 7 days
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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
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"""
Performs a Holt-Winters forecast using the series as input data and plots
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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):
"""
Performs a Holt-Winters forecast using the series as input data and plots
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"""
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brutasse/graphite-api | graphite_api/functions.py | holtWintersConfidenceArea | def holtWintersConfidenceArea(requestContext, seriesList, delta=3):
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"""
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brutasse/graphite-api | graphite_api/functions.py | linearRegressionAnalysis | def linearRegressionAnalysis(series):
"""
Returns factor and offset of linear regression function by least
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"""
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):
"""
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])
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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):
"""
Graphs the liner regression function by least squares method.
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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):
"""
Takes one metric or a wildcard seriesList.
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the line at infinity. If the value is null or less than zero, do not draw
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brutasse/graphite-api | graphite_api/functions.py | lineWidth | def lineWidth(requestContext, seriesList, width):
"""
Takes one metric or a wildcard seriesList, followed by a float F.
Draw the selected metrics with a line width of F, overriding the default
value of 1, or the &lineWidth=X.X parameter.
Useful for highlighting a single metric out of many, or havi... | python | def lineWidth(requestContext, seriesList, width):
"""
Takes one metric or a wildcard seriesList, followed by a float F.
Draw the selected metrics with a line width of F, overriding the default
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brutasse/graphite-api | graphite_api/functions.py | dashed | def dashed(requestContext, seriesList, dashLength=5):
"""
Takes one metric or a wildcard seriesList, followed by a float F.
Draw the selected metrics with a dotted line with segments of length F
If omitted, the default length of the segments is 5.0
Example::
&target=dashed(server01.instan... | python | def dashed(requestContext, seriesList, dashLength=5):
"""
Takes one metric or a wildcard seriesList, followed by a float F.
Draw the selected metrics with a dotted line with segments of length F
If omitted, the default length of the segments is 5.0
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brutasse/graphite-api | graphite_api/functions.py | timeStack | def timeStack(requestContext, seriesList, timeShiftUnit, timeShiftStart,
timeShiftEnd):
"""
Takes one metric or a wildcard seriesList, followed by a quoted string
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"""
Takes one metric or a wildcard seriesList, followed by a quoted string
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brutasse/graphite-api | graphite_api/functions.py | timeShift | def timeShift(requestContext, seriesList, timeShift, resetEnd=True,
alignDST=False):
"""
Takes one metric or a wildcard seriesList, followed by a quoted string
with the length of time (See ``from / until`` in the render\_api_ for
examples of time formats).
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"""
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brutasse/graphite-api | graphite_api/functions.py | timeSlice | def timeSlice(requestContext, seriesList, startSliceAt, endSliceAt='now'):
"""
Takes one metric or a wildcard metric, followed by a quoted
string with the time to start the line and another quoted string
with the time to end the line. The start and end times are
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"""
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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):
"""
Takes a float F.
Draws a horizontal line at value F across the graph.
Example::
&target=constantLine(123.456)
"""
name = "constantLine(%s)" % str(value)
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brutasse/graphite-api | graphite_api/functions.py | aggregateLine | def aggregateLine(requestContext, seriesList, func='avg'):
"""
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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'):
"""
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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):
"""
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brutasse/graphite-api | graphite_api/functions.py | threshold | def threshold(requestContext, value, label=None, color=None):
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Draws a horizontal line at value F across the graph.
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"""
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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):
"""
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brutasse/graphite-api | graphite_api/functions.py | isNonNull | def isNonNull(requestContext, seriesList):
"""
Takes a metric or wild card seriesList and counts up how many
non-null values are specified. This is useful for understanding
which metrics have data at a given point in time (ie, to count
which servers are alive).
Example::
&target=isNonN... | python | def isNonNull(requestContext, seriesList):
"""
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brutasse/graphite-api | graphite_api/functions.py | identity | def identity(requestContext, name, step=60):
"""
Identity function:
Returns datapoints where the value equals the timestamp of the datapoint.
Useful when you have another series where the value is a timestamp, and
you want to compare it to the time of the datapoint, to render an age
Example::
... | python | def identity(requestContext, name, step=60):
"""
Identity function:
Returns datapoints where the value equals the timestamp of the datapoint.
Useful when you have another series where the value is a timestamp, and
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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):
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... | python | def countSeries(requestContext, *seriesLists):
"""
Draws a horizontal line representing the number of nodes found in the
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Example::
&target=countSeries(carbon.agents.*.*)
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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):
"""
Takes an arbitrary number of seriesLists and adds them to a single
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brutasse/graphite-api | graphite_api/functions.py | mapSeries | def mapSeries(requestContext, seriesList, mapNode):
"""
Short form: ``map()``.
Takes a seriesList and maps it to a list of sub-seriesList. Each
sub-seriesList has the given mapNode in common.
Example (note: This function is not very useful alone. It should be used
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"""
Short form: ``map()``.
Takes a seriesList and maps it to a list of sub-seriesList. Each
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brutasse/graphite-api | graphite_api/functions.py | reduceSeries | def reduceSeries(requestContext, seriesLists, reduceFunction, reduceNode,
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"""
Short form: ``reduce()``.
Takes a list of seriesLists and reduces it to a list of series by means of
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brutasse/graphite-api | graphite_api/functions.py | applyByNode | def applyByNode(requestContext, seriesList, nodeNum, templateFunction,
newName=None):
"""
Takes a seriesList and applies some complicated function (described by
a string), replacing templates with unique prefixes of keys from the
seriesList (the key is all nodes up to the index given as ... | python | def applyByNode(requestContext, seriesList, nodeNum, templateFunction,
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"""
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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):
"""
Takes a serieslist and maps a callback to subgroups within as defined by a
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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):
"""
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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):
"""
Takes a metric or a wildcard seriesList, followed by a regular expression
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Example::
&target=exclude(servers*.instance*.threads.busy,"server02")
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brutasse/graphite-api | graphite_api/functions.py | smartSummarize | def smartSummarize(requestContext, seriesList, intervalString, func='sum'):
"""
Smarter experimental version of summarize.
"""
results = []
delta = parseTimeOffset(intervalString)
interval = to_seconds(delta)
# Adjust the start time to fit an entire day for intervals >= 1 day
requestCon... | python | def smartSummarize(requestContext, seriesList, intervalString, func='sum'):
"""
Smarter experimental version of summarize.
"""
results = []
delta = parseTimeOffset(intervalString)
interval = to_seconds(delta)
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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',
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"""
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brutasse/graphite-api | graphite_api/functions.py | hitcount | def hitcount(requestContext, seriesList, intervalString,
alignToInterval=False):
"""
Estimate hit counts from a list of time series.
This function assumes the values in each time series represent
hits per second. It calculates hits per some larger interval
such as per day or per hou... | python | def hitcount(requestContext, seriesList, intervalString,
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"""
Estimate hit counts from a list of time series.
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brutasse/graphite-api | graphite_api/functions.py | timeFunction | def timeFunction(requestContext, name, step=60):
"""
Short Alias: time()
Just returns the timestamp for each X value. T
Example::
&target=time("The.time.series")
This would create a series named "The.time.series" that contains in Y
the same value (in seconds) as X.
A second argu... | python | def timeFunction(requestContext, name, step=60):
"""
Short Alias: time()
Just returns the timestamp for each X value. T
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brutasse/graphite-api | graphite_api/functions.py | sinFunction | def sinFunction(requestContext, name, amplitude=1, step=60):
"""
Short Alias: sin()
Just returns the sine of the current time. The optional amplitude parameter
changes the amplitude of the wave.
Example::
&target=sin("The.time.series", 2)
This would create a series named "The.time.se... | python | def sinFunction(requestContext, name, amplitude=1, step=60):
"""
Short Alias: sin()
Just returns the sine of the current time. The optional amplitude parameter
changes the amplitude of the wave.
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brutasse/graphite-api | graphite_api/functions.py | randomWalkFunction | def randomWalkFunction(requestContext, name, step=60):
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Short Alias: randomWalk()
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Example::
&target=randomWalk("The.time.series")
This would create a series named "The.time.series... | python | def randomWalkFunction(requestContext, name, step=60):
"""
Short Alias: randomWalk()
Returns a random walk starting at 0. This is great for testing when there
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Example::
&target=randomWalk("The.time.series")
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opencobra/memote | memote/experimental/medium.py | Medium.validate | def validate(self, model, checks=[]):
"""Use a defined schema to validate the medium table format."""
custom = [
check_partial(reaction_id_check,
frozenset(r.id for r in model.reactions))
]
super(Medium, self).validate(model=model, checks=checks + cu... | python | def validate(self, model, checks=[]):
"""Use a defined schema to validate the medium table format."""
custom = [
check_partial(reaction_id_check,
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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):
"""Set the defined medium on the given model."""
model.medium = {row.exchange: row.uptake
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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):
"""Record environment information."""
meta["timestamp"] = datetime.utcnow().isoformat(" ")
meta["platform"] = platform.system()
meta["release"] = platform.release()
meta["python"] = platform.python_version()
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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,
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Return a dictionary showing the amount of transported elements of a rxn.
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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):
"""
Return a list of all transport reactions.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
A transport reaction is defined as follows:
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opencobra/memote | memote/support/helpers.py | is_transport_reaction_formulae | def is_transport_reaction_formulae(rxn):
"""
Return boolean if a reaction is a transport reaction (from formulae).
Parameters
----------
rxn: cobra.Reaction
The metabolic reaction under investigation.
"""
# Collecting criteria to classify transporters by.
rxn_reactants = set([m... | python | def is_transport_reaction_formulae(rxn):
"""
Return boolean if a reaction is a transport reaction (from formulae).
Parameters
----------
rxn: cobra.Reaction
The metabolic reaction under investigation.
"""
# Collecting criteria to classify transporters by.
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opencobra/memote | memote/support/helpers.py | is_transport_reaction_annotations | def is_transport_reaction_annotations(rxn):
"""
Return boolean if a reaction is a transport reaction (from annotations).
Parameters
----------
rxn: cobra.Reaction
The metabolic reaction under investigation.
"""
reactants = set([(k, tuple(v)) for met in rxn.reactants
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"""
Return boolean if a reaction is a transport reaction (from annotations).
Parameters
----------
rxn: cobra.Reaction
The metabolic reaction under investigation.
"""
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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):
"""
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.
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opencobra/memote | memote/support/helpers.py | find_biomass_reaction | def find_biomass_reaction(model):
"""
Return a list of the biomass reaction(s) of the model.
This function identifies possible biomass reactions using two steps:
1. Return reactions that include the SBO annotation "SBO:0000629" for
biomass.
If no reactions can be identifies this way:
2. Loo... | python | def find_biomass_reaction(model):
"""
Return a list of the biomass reaction(s) of the model.
This function identifies possible biomass reactions using two steps:
1. Return reactions that include the SBO annotation "SBO:0000629" for
biomass.
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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
-----
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-- 'unbalanced network reactions that allow the accumulation of a compou... | python | def find_demand_reactions(model):
u"""
Return a list of demand reactions.
Parameters
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model : cobra.Model
The metabolic model under investigation.
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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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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.
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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):
"""
Return the set of all transport, boundary, and biomass reactions.
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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):
"""
Return the solution of an FBA to a set objective function.
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model : cobra.Model
The metabolic model under investigation.
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opencobra/memote | memote/support/helpers.py | close_boundaries_sensibly | def close_boundaries_sensibly(model):
"""
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"""
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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):
"""
Identify all metabolites that belong to a given compartment.
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model : cobra.Model
The metabolic model under investigation.
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Model specific compartment identifier.
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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):
"""
Return the ID of the compartment with the most metabolites.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
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Compartment ID of the compartment with the most metabolites.
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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
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model : cobra.Model
The metabolic model under investigation.
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opencobra/memote | memote/support/helpers.py | find_met_in_model | def find_met_in_model(model, mnx_id, compartment_id=None):
"""
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Parameters
----------
model : cobra.Model
The metabolic model under investigation.
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"""
Return specific metabolites by looking up IDs in METANETX_SHORTLIST.
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model : cobra.Model
The metabolic model under investigation.
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opencobra/memote | memote/support/helpers.py | find_bounds | def find_bounds(model):
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"""
Return the median upper and lower bound of the metabolic model.
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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()
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"""Render an HTML report."""
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opencobra/memote | memote/suite/reporting/report.py | Report.compute_score | def compute_score(self):
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"""Calculate the overall test score using the configuration."""
# LOGGER.info("Begin scoring")
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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"}
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Find model components that are not annotated with any SBO terms.
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model : cobra.Model
The metabolic model under investigation.
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opencobra/memote | memote/support/sbo.py | check_component_for_specific_sbo_term | def check_component_for_specific_sbo_term(items, term):
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Identify model components that lack a specific SBO term(s).
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A list of model components i.e. reactions to be checked for a specific
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term : str or list of str
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Identify model components that lack a specific SBO term(s).
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A list of model components i.e. reactions to be checked for a specific
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opencobra/memote | memote/support/thermodynamics.py | get_smallest_compound_id | def get_smallest_compound_id(compounds_identifiers):
"""
Return the smallest KEGG compound identifier from a list.
KEGG identifiers may map to compounds, drugs or glycans prefixed
respectively with "C", "D", and "G" followed by at least 5 digits. We
choose the lowest KEGG identifier with the assump... | python | def get_smallest_compound_id(compounds_identifiers):
"""
Return the smallest KEGG compound identifier from a list.
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opencobra/memote | memote/support/thermodynamics.py | map_metabolite2kegg | def map_metabolite2kegg(metabolite):
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"""
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opencobra/memote | memote/support/thermodynamics.py | translate_reaction | def translate_reaction(reaction, metabolite_mapping):
"""
Return a mapping from KEGG compound identifiers to coefficients.
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----------
reaction : cobra.Reaction
The reaction whose metabolites are to be translated.
metabolite_mapping : dict
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"""
Return a mapping from KEGG compound identifiers to coefficients.
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reaction : cobra.Reaction
The reaction whose metabolites are to be translated.
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opencobra/memote | memote/support/thermodynamics.py | find_thermodynamic_reversibility_index | def find_thermodynamic_reversibility_index(reactions):
u"""
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opencobra/memote | memote/support/consistency.py | check_stoichiometric_consistency | def check_stoichiometric_consistency(model):
"""
Verify the consistency of the model's stoichiometry.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
See [1]_ section 3.1 for a complete description of the algorithm.
.. [1] Gev... | python | def check_stoichiometric_consistency(model):
"""
Verify the consistency of the model's stoichiometry.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
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See [1]_ section 3.1 for a complete description of the algorithm.
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opencobra/memote | memote/support/consistency.py | find_unconserved_metabolites | def find_unconserved_metabolites(model):
"""
Detect unconserved metabolites.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
See [1]_ section 3.2 for a complete description of the algorithm.
.. [1] Gevorgyan, A., M. G Poolman... | python | def find_unconserved_metabolites(model):
"""
Detect unconserved metabolites.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
See [1]_ section 3.2 for a complete description of the algorithm.
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opencobra/memote | memote/support/consistency.py | find_inconsistent_min_stoichiometry | def find_inconsistent_min_stoichiometry(model, atol=1e-13):
"""
Detect inconsistent minimal net stoichiometries.
Parameters
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model : cobra.Model
The metabolic model under investigation.
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opencobra/memote | memote/support/consistency.py | detect_energy_generating_cycles | def detect_energy_generating_cycles(model, metabolite_id):
u"""
Detect erroneous energy-generating cycles for a a single metabolite.
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Detect erroneous energy-generating cycles for a a single metabolite.
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opencobra/memote | memote/support/consistency.py | find_stoichiometrically_balanced_cycles | def find_stoichiometrically_balanced_cycles(model):
u"""
Find metabolic reactions in stoichiometrically balanced cycles (SBCs).
Identify forward and reverse cycles by closing all exchanges and using FVA.
Parameters
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model : cobra.Model
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Find metabolic reactions in stoichiometrically balanced cycles (SBCs).
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opencobra/memote | memote/support/consistency.py | find_orphans | def find_orphans(model):
"""
Return metabolites that are only consumed in reactions.
Metabolites that are involved in an exchange reaction are never
considered to be orphaned.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
exchange =... | python | def find_orphans(model):
"""
Return metabolites that are only consumed in reactions.
Metabolites that are involved in an exchange reaction are never
considered to be orphaned.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
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opencobra/memote | memote/support/consistency.py | find_metabolites_not_produced_with_open_bounds | def find_metabolites_not_produced_with_open_bounds(model):
"""
Return metabolites that cannot be produced with open exchange reactions.
A perfect model should be able to produce each and every metabolite when
all medium components are available.
Parameters
----------
model : cobra.Model
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Return metabolites that cannot be produced with open exchange reactions.
A perfect model should be able to produce each and every metabolite when
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opencobra/memote | memote/support/consistency.py | find_metabolites_not_consumed_with_open_bounds | def find_metabolites_not_consumed_with_open_bounds(model):
"""
Return metabolites that cannot be consumed with open boundary reactions.
When all metabolites can be secreted, it should be possible for each and
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Parameters
----------
model : cobra... | python | def find_metabolites_not_consumed_with_open_bounds(model):
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Return metabolites that cannot be consumed with open boundary reactions.
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opencobra/memote | memote/support/consistency.py | find_reactions_with_unbounded_flux_default_condition | def find_reactions_with_unbounded_flux_default_condition(model):
"""
Return list of reactions whose flux is unbounded in the default condition.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
-------
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Return list of reactions whose flux is unbounded in the default condition.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
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opencobra/memote | memote/experimental/tabular.py | read_tabular | def read_tabular(filename, dtype_conversion=None):
"""
Read a tabular data file which can be CSV, TSV, XLS or XLSX.
Parameters
----------
filename : str or pathlib.Path
The full file path. May be a compressed file.
dtype_conversion : dict
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"""
Read a tabular data file which can be CSV, TSV, XLS or XLSX.
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The full file path. May be a compressed file.
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opencobra/memote | memote/suite/cli/reports.py | snapshot | def snapshot(model, filename, pytest_args, exclusive, skip, solver,
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"""
Take a snapshot of a model's state and generate a report.
MODEL: Path to model file. Can also be supplied via the environment variable
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"""
Take a snapshot of a model's state and generate a report.
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opencobra/memote | memote/suite/cli/reports.py | history | def history(location, model, filename, deployment, custom_config):
"""Generate a report over a model's git commit history."""
callbacks.git_installed()
LOGGER.info("Initialising history report generation.")
if location is None:
raise click.BadParameter("No 'location' given or configured.")
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"""Generate a report over a model's git commit history."""
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opencobra/memote | memote/suite/cli/reports.py | diff | def diff(models, filename, pytest_args, exclusive, skip, solver,
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"""
Take a snapshot of all the supplied models and generate a diff report.
MODELS: List of paths to two or more model files.
"""
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opencobra/memote | memote/suite/results/history_manager.py | HistoryManager.build_branch_structure | def build_branch_structure(self, model, skip):
"""Inspect and record the repo's branches and their history."""
self._history = dict()
self._history["commits"] = commits = dict()
self._history["branches"] = branches = dict()
for branch in self._repo.refs:
LOGGER.debug(... | python | def build_branch_structure(self, model, skip):
"""Inspect and record the repo's branches and their history."""
self._history = dict()
self._history["commits"] = commits = dict()
self._history["branches"] = branches = dict()
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opencobra/memote | memote/suite/results/history_manager.py | HistoryManager.load_history | def load_history(self, model, skip={"gh-pages"}):
"""
Load the entire results history into memory.
Could be a bad idea in a far future.
"""
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Load the entire results history into memory.
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opencobra/memote | memote/suite/results/history_manager.py | HistoryManager.get_result | def get_result(self, commit, default=MemoteResult()):
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assert self._results is not None, \
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opencobra/memote | memote/support/matrix.py | absolute_extreme_coefficient_ratio | def absolute_extreme_coefficient_ratio(model):
"""
Return the maximum and minimum absolute, non-zero coefficients.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
s_matrix, _, _ = con_helpers.stoichiometry_matrix(
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"""
Return the maximum and minimum absolute, non-zero coefficients.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
s_matrix, _, _ = con_helpers.stoichiometry_matrix(
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opencobra/memote | memote/support/matrix.py | number_independent_conservation_relations | def number_independent_conservation_relations(model):
"""
Return the number of conserved metabolite pools.
This number is given by the left null space of the stoichiometric matrix.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
s_matrix,... | python | def number_independent_conservation_relations(model):
"""
Return the number of conserved metabolite pools.
This number is given by the left null space of the stoichiometric matrix.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
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opencobra/memote | memote/support/matrix.py | matrix_rank | def matrix_rank(model):
"""
Return the rank of the model's stoichiometric matrix.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
s_matrix, _, _ = con_helpers.stoichiometry_matrix(
model.metabolites, model.reactions
)
return co... | python | def matrix_rank(model):
"""
Return the rank of the model's stoichiometric matrix.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
s_matrix, _, _ = con_helpers.stoichiometry_matrix(
model.metabolites, model.reactions
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opencobra/memote | memote/support/matrix.py | degrees_of_freedom | def degrees_of_freedom(model):
"""
Return the degrees of freedom, i.e., number of "free variables".
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
This specifically refers to the dimensionality of the (right) null space
of the... | python | def degrees_of_freedom(model):
"""
Return the degrees of freedom, i.e., number of "free variables".
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
This specifically refers to the dimensionality of the (right) null space
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opencobra/memote | memote/experimental/config.py | ExperimentConfiguration.load | def load(self, model):
"""
Load all information from an experimental configuration file.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
self.load_medium(model)
self.load_essentiality(model)
self... | python | def load(self, model):
"""
Load all information from an experimental configuration file.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
self.load_medium(model)
self.load_essentiality(model)
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opencobra/memote | memote/experimental/config.py | ExperimentConfiguration.validate | def validate(self):
"""Validate the configuration file."""
validator = Draft4Validator(self.SCHEMA)
if not validator.is_valid(self.config):
for err in validator.iter_errors(self.config):
LOGGER.error(str(err.message))
validator.validate(self.config) | python | def validate(self):
"""Validate the configuration file."""
validator = Draft4Validator(self.SCHEMA)
if not validator.is_valid(self.config):
for err in validator.iter_errors(self.config):
LOGGER.error(str(err.message))
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opencobra/memote | memote/experimental/config.py | ExperimentConfiguration.load_medium | def load_medium(self, model):
"""Load and validate all media."""
media = self.config.get("medium")
if media is None:
return
definitions = media.get("definitions")
if definitions is None or len(definitions) == 0:
return
path = self.get_path(media, j... | python | def load_medium(self, model):
"""Load and validate all media."""
media = self.config.get("medium")
if media is None:
return
definitions = media.get("definitions")
if definitions is None or len(definitions) == 0:
return
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opencobra/memote | memote/experimental/config.py | ExperimentConfiguration.load_essentiality | def load_essentiality(self, model):
"""Load and validate all data files."""
data = self.config.get("essentiality")
if data is None:
return
experiments = data.get("experiments")
if experiments is None or len(experiments) == 0:
return
path = self.get... | python | def load_essentiality(self, model):
"""Load and validate all data files."""
data = self.config.get("essentiality")
if data is None:
return
experiments = data.get("experiments")
if experiments is None or len(experiments) == 0:
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opencobra/memote | memote/experimental/config.py | ExperimentConfiguration.load_growth | def load_growth(self, model):
"""Load and validate all data files."""
data = self.config.get("growth")
if data is None:
return
experiments = data.get("experiments")
if experiments is None or len(experiments) == 0:
return
path = self.get_path(data,
... | python | def load_growth(self, model):
"""Load and validate all data files."""
data = self.config.get("growth")
if data is None:
return
experiments = data.get("experiments")
if experiments is None or len(experiments) == 0:
return
path = self.get_path(data,
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opencobra/memote | memote/experimental/config.py | ExperimentConfiguration.get_path | def get_path(self, obj, default):
"""Return a relative or absolute path to experimental data."""
path = obj.get("path")
if path is None:
path = join(self._base, default)
if not isabs(path):
path = join(self._base, path)
return path | python | def get_path(self, obj, default):
"""Return a relative or absolute path to experimental data."""
path = obj.get("path")
if path is None:
path = join(self._base, default)
if not isabs(path):
path = join(self._base, path)
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opencobra/memote | memote/support/annotation.py | find_components_without_annotation | def find_components_without_annotation(model, components):
"""
Find model components with empty annotation attributes.
Parameters
----------
model : cobra.Model
A cobrapy metabolic model.
components : {"metabolites", "reactions", "genes"}
A string denoting `cobra.Model` componen... | python | def find_components_without_annotation(model, components):
"""
Find model components with empty annotation attributes.
Parameters
----------
model : cobra.Model
A cobrapy metabolic model.
components : {"metabolites", "reactions", "genes"}
A string denoting `cobra.Model` componen... | [
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model : cobra.Model
A cobrapy metabolic model.
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A string denoting `cobra.Model` components.
Returns
-------
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