repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
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:
... | Percentile is calculated using the method outlined in the NIST Engineering
Statistics Handbook:
http://www.itl.nist.gov/div898/handbook/prc/section2/prc252.htm | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2340-L2368 |
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'
results = []
for s in seriesList:
# Create a sorted copy of the TimeSeries excluding None values in the
# values l... | Returns n-percent of each series in the seriesList. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2371-L2392 |
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)
highPercentile = _getPercentile(av... | Removes functions lying inside an average percentile interval | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2395-L2408 |
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
the values at a moment
"""
if n < 50:
n = 100 - n
transposed = list(zip_longest(*seriesList))
lowPercentiles = [_getPercentile(col, 100-n) for col... | Removes lines who do not have an value lying in the x-percentile of all
the values at a moment | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2411-L2426 |
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):
"""
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... | Removes data above the given threshold from the series or list of series
provided. Values above this threshold are assigned a value of None. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2450-L2464 |
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
provided. Values below this percentile are assigned a value of None.
"""
for s in seriesList:
s.name = 'removeBelowPercentile(%s, %g)' % (s.name, n)
s... | Removes data below the nth percentile from the series or list of series
provided. Values below this percentile are assigned a value of None. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2467-L2485 |
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
to be sorted more naturally, e.g:
- Alphabe... | 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:
- Alphabetical sorting: server1, server11, server12, server2
- Natural sorti... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2526-L2541 |
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)) | Takes one metric or a wildcard seriesList.
Sorts the list of metrics by the sum of values across the time period
specified. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2544-L2551 |
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):
"""
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... | 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 useSeriesAbove(ganglia.metric1.reqs,10,'reqs','time'),
the response time metric... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2585-L2608 |
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
is taken and ranked. The top N standard deviations are returned.
Example:... | 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::
&target=mostDeviant(server*.instance*.memory.free... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2629-L2656 |
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
windowTolerance, skip the... | 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 calculation. The default for windowTolerance is
0.1 (up to 10% of points in... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2659-L2728 |
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 | Graph the series on the secondary Y axis. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2731-L2738 |
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
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... | 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. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2854-L2876 |
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):
"""
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... | Performs a Holt-Winters forecast using the series as input data and plots
upper and lower bands with the predicted forecast deviations. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2879-L2932 |
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
the positive or negative deviation of the series data from the forecast.
"""
results = []
for series in seriesList:
confidenceBands = holtWintersC... | 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. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2935-L2960 |
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):
"""
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... | 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. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2963-L2974 |
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):
"""
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... | Returns factor and offset of linear regression function by least
squares method. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2977-L2995 |
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.
Takes one metric or a wildcard seriesList, followed by a quoted string
with the time to start the line and another quoted string... | 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 with the time
to end the line. The start and end times are inclusive (default range is
from to until). See ``fro... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L2998-L3044 |
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.
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... | 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, such as exit codes. (0 = success,
anything else = failure.)... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3047-L3065 |
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
value of 1, or the &lineWidth=X.X parameter.
Useful for highlighting a single metric out of many, or havi... | 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 having multiple
line widths in one graph.
Example::
... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3068-L3085 |
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
Example::
&target=dashed(server01.instan... | 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.instance01.memory.free,2.5) | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3088-L3103 |
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
with the length of time (See ``from / until`` in the render\_api_ for
examples of time formats). Also takes a start multiplier ... | python | def timeStack(requestContext, seriesList, timeShiftUnit, timeShiftStart,
timeShiftEnd):
"""
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). Also takes a start multiplier ... | 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). Also takes a start multiplier and end
multiplier for the length of time-
Create a seriesList which is composed the original metric seri... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3106-L3151 |
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).
Draws the selected metrics s... | python | 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).
Draws the selected metrics s... | 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).
Draws the selected metrics shifted in time. If no sign is given, a minus
sign ( - ) is implied which will shift the metric back in time... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3158-L3243 |
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
inclusive. See ``from / until`` in th... | python | 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
inclusive. See ``from / until`` in th... | 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
inclusive. See ``from / until`` in the render api for examples of
time formats.
Useful for filtering out a part of ... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3246-L3275 |
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)
start = int(epoch(requestContext['startTime']))
end = int(epoch(requestContext... | Takes a float F.
Draws a horizontal line at value F across the graph.
Example::
&target=constantLine(123.456) | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3278-L3295 |
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'):
"""
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... | 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 'min' or 'max'
function for aggregateLine, this can cause an unusual ... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3298-L3335 |
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):
"""
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... | 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 those used with ``from`` and ``until`` parameters. When
set, the 'label'... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3338-L3373 |
brutasse/graphite-api | graphite_api/functions.py | threshold | def threshold(requestContext, value, label=None, color=None):
"""
Takes a float F, followed by a label (in double quotes) and a color.
(See ``bgcolor`` in the render\_api_ for valid color names & formats.)
Draws a horizontal line at value F across the graph.
Example::
&target=threshold(12... | python | def threshold(requestContext, value, label=None, color=None):
"""
Takes a float F, followed by a label (in double quotes) and a color.
(See ``bgcolor`` in the render\_api_ for valid color names & formats.)
Draws a horizontal line at value F across the graph.
Example::
&target=threshold(12... | Takes a float F, followed by a label (in double quotes) and a color.
(See ``bgcolor`` in the render\_api_ for valid color names & formats.)
Draws a horizontal line at value F across the graph.
Example::
&target=threshold(123.456, "omgwtfbbq", "red") | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3376-L3393 |
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):
"""
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... | 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 list that governs which time intervals nulls should be replaced.
If specified, nulls are re... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3396-L3440 |
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):
"""
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... | 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=isNonNull(webapp.pages.*.views)
Returns a seriesList whe... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3443-L3470 |
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
you want to compare it to the time of the datapoint, to render an age
Example::
... | 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::
&target=identity("The.time.series")
This wou... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3473-L3496 |
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):
"""
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()
... | Draws a horizontal line representing the number of nodes found in the
seriesList.
Example::
&target=countSeries(carbon.agents.*.*) | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3499-L3519 |
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:
seriesGroup.extend(s)
return serie... | python | 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:
seriesGroup.extend(s)
return serie... | 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. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3522-L3532 |
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
with :py:func:`reduceSeries`)... | python | 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
with :py:func:`reduceSeries`)... | 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
with :py:func:`reduceSeries`)::
mapSeries(servers.*.cpu.*,1) =>
[
... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3535-L3562 |
brutasse/graphite-api | graphite_api/functions.py | reduceSeries | def reduceSeries(requestContext, seriesLists, reduceFunction, reduceNode,
*reduceMatchers):
"""
Short form: ``reduce()``.
Takes a list of seriesLists and reduces it to a list of series by means of
the reduceFunction.
Reduction is performed by matching the reduceNode in each series... | python | def reduceSeries(requestContext, seriesLists, reduceFunction, reduceNode,
*reduceMatchers):
"""
Short form: ``reduce()``.
Takes a list of seriesLists and reduces it to a list of series by means of
the reduceFunction.
Reduction is performed by matching the reduceNode in each series... | Short form: ``reduce()``.
Takes a list of seriesLists and reduces it to a list of series by means of
the reduceFunction.
Reduction is performed by matching the reduceNode in each series against
the list of reduceMatchers. The each series is then passed to the
reduceFunction as arguments in the ord... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3565-L3638 |
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,
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 ... | 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 `nodeNum`).
If the `newName` parameter is provided, the name of the resulting series
will be given by tha... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3641-L3677 |
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
common node.
Example::
&target=groupByNode(ganglia.by-function.*.*.cpu.load5,2,"sumSeries")
Would return multiple series which are each the result... | 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 of applying the
"sumSeries" function to groups joined on the second nod... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3680-L3697 |
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):
"""
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... | 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 of applying the
"sumSeries" function to groups joined on the nodes' list ... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3700-L3737 |
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
in double quotes. Excludes metrics that match the regular expression.
Example::
&target=exclude(servers*.instance*.threads.busy,"server02")
"""
regex = re.... | 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") | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3740-L3750 |
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)
# Adjust the start time to fit an entire day for intervals >= 1 day
requestCon... | Smarter experimental version of summarize. | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3767-L3854 |
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):
"""
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... | 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 discrete
event and retrieving a "per X" value requires summing all the events in
that interval.
Specifying... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3857-L3963 |
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,
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... | 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 hour. This function is like summarize(),
except that it compensates automatically for different time s... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L3966-L4066 |
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
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... | 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 argument can be provided as a step parameter (default is 60 secs) | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L4069-L4098 |
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.
Example::
&target=sin("The.time.series", 2)
This would create a series named "The.time.se... | 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.series" that contains sin(x)*2.
A third argument can be provided as a ... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L4101-L4129 |
brutasse/graphite-api | graphite_api/functions.py | randomWalkFunction | def randomWalkFunction(requestContext, name, step=60):
"""
Short Alias: randomWalk()
Returns a random walk starting at 0. This is great for testing when there
is no real data in whisper.
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
is no real data in whisper.
Example::
&target=randomWalk("The.time.series")
This would create a series named "The.time.series... | Short Alias: randomWalk()
Returns a random walk starting at 0. This is great for testing when there
is no real data in whisper.
Example::
&target=randomWalk("The.time.series")
This would create a series named "The.time.series" that contains points
where x(t) == x(t-1)+random()-0.5, and x... | https://github.com/brutasse/graphite-api/blob/0886b7adcf985a1e8bcb084f6dd1dc166a3f3dff/graphite_api/functions.py#L4146-L4175 |
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,
frozenset(r.id for r in model.reactions))
]
super(Medium, self).validate(model=model, checks=checks + cu... | Use a defined schema to validate the medium table format. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/medium.py#L48-L54 |
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
for row in self.data.itertuples(index=False)} | Set the defined medium on the given model. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/medium.py#L56-L59 |
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()
meta["packages"] = get_pk... | Record environment information. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/results/result.py#L46-L52 |
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):
"""
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... | 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 compartment that metabolite is in. This
produces a... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L81-L120 |
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:
1. It contains metabolites from at least 2 compartme... | 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 compartments and
2. at least 1 metabolite undergoes no... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L124-L181 |
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.
rxn_reactants = set([m... | Return boolean if a reaction is a transport reaction (from formulae).
Parameters
----------
rxn: cobra.Reaction
The metabolic reaction under investigation. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L184-L217 |
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
... | python | 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
... | Return boolean if a reaction is a transport reaction (from annotations).
Parameters
----------
rxn: cobra.Reaction
The metabolic reaction under investigation. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L220-L246 |
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.
Retu... | 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.
Returns
-------
frozenset
The set of reactio... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L249-L278 |
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.
If no reactions can be identifies this way:
2. Loo... | 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. Look for the ``buzzwords`` "biomass", "growth" an... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L282-L333 |
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
-----
[1] defines demand reactions as:
-- 'unbalanced network reactions that allow the accumulation of a compou... | 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 compound'
-- reactions that are chiefly ... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L337-L373 |
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
m... | 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
model with metabolites
-- reactio... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L377-L412 |
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'
-- 'unbala... | 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'
-- 'unbalanced, extra-organism reactions that... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L416-L450 |
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.
These reactions are either pseudo-reactions, or incorporated to allow
metabolites to pass between compartments. Some tests focus on purely
metabolic reactions and hence... | 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 exclude this set.
Parameters
----------
model : cobra.Model... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L453-L473 |
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.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
rxn_id : string
A string containing the reaction ID of the desired FB... | 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 FBA objective.
direction: string
A string containing either "max" ... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L476-L511 |
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.
In the returned model previously fixed reactions are no longer constrained
as such. Instead reactions are constrained according to their
reversibility. This is to prevent the FBA from ... | python | def close_boundaries_sensibly(model):
"""
Return a cobra model with all boundaries closed and changed constraints.
In the returned model previously fixed reactions are no longer constrained
as such. Instead reactions are constrained according to their
reversibility. This is to prevent the FBA from ... | Return a cobra model with all boundaries closed and changed constraints.
In the returned model previously fixed reactions are no longer constrained
as such. Instead reactions are constrained according to their
reversibility. This is to prevent the FBA from becoming infeasible when
trying to solve a mod... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L514-L541 |
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.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
compartment_id : string
Model specific compartment identifier.
Returns... | 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
-------
list
List of metabolites belonging to a giv... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L572-L590 |
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
-------
string
Compartment ID of the compartment with the most metabolites.
... | 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. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L593-L618 |
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
Memote internal compartment identifi... | python | 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
Memote internal compartment identifi... | Identify a model compartment by looking up names in COMPARTMENT_SHORTLIST.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
compartment_id : string
Memote internal compartment identifier used to access compartment name
shortlist to look up poten... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L621-L661 |
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):
"""
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... | 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 used to map between
cross-references in the METANETX_SHORTLIST.
... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L664-L764 |
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):
"""
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... | 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 all the
reactions and find the ... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/helpers.py#L781-L809 |
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):
"""Render an HTML report."""
return self._template.safe_substitute(
report_type=self._report_type,
results=self.render_json()
) | Render an HTML report. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/reporting/report.py#L80-L85 |
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):
"""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... | Calculate the overall test score using the configuration. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/reporting/report.py#L114-L164 |
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):
"""
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 ... | 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
Th... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/sbo.py#L27-L45 |
opencobra/memote | memote/support/sbo.py | check_component_for_specific_sbo_term | def check_component_for_specific_sbo_term(items, term):
r"""
Identify model components that lack a specific SBO term(s).
Parameters
----------
items : list
A list of model components i.e. reactions to be checked for a specific
SBO term.
term : str or list of str
A string... | python | def check_component_for_specific_sbo_term(items, term):
r"""
Identify model components that lack a specific SBO term(s).
Parameters
----------
items : list
A list of model components i.e. reactions to be checked for a specific
SBO term.
term : str or list of str
A string... | r"""
Identify model components that lack a specific SBO term(s).
Parameters
----------
items : list
A list of model components i.e. reactions to be checked for a specific
SBO term.
term : str or list of str
A string denoting a valid SBO term matching the regex '^SBO:\d{7}$'
... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/sbo.py#L48-L77 |
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.
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... | 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 assumption that several
identifiers are due to chirality and that t... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/thermodynamics.py#L37-L64 |
opencobra/memote | memote/support/thermodynamics.py | map_metabolite2kegg | def map_metabolite2kegg(metabolite):
"""
Return a KEGG compound identifier for the metabolite if it exists.
First see if there is an unambiguous mapping to a single KEGG compound ID
provided with the model. If not, check if there is any KEGG compound ID in
a list of mappings. KEGG IDs may map to co... | python | def map_metabolite2kegg(metabolite):
"""
Return a KEGG compound identifier for the metabolite if it exists.
First see if there is an unambiguous mapping to a single KEGG compound ID
provided with the model. If not, check if there is any KEGG compound ID in
a list of mappings. KEGG IDs may map to co... | Return a KEGG compound identifier for the metabolite if it exists.
First see if there is an unambiguous mapping to a single KEGG compound ID
provided with the model. If not, check if there is any KEGG compound ID in
a list of mappings. KEGG IDs may map to compounds, drugs and glycans. KEGG
compound IDs... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/thermodynamics.py#L67-L126 |
opencobra/memote | memote/support/thermodynamics.py | translate_reaction | def translate_reaction(reaction, metabolite_mapping):
"""
Return a mapping from KEGG compound identifiers to coefficients.
Parameters
----------
reaction : cobra.Reaction
The reaction whose metabolites are to be translated.
metabolite_mapping : dict
An existing mapping from cobr... | python | def translate_reaction(reaction, metabolite_mapping):
"""
Return a mapping from KEGG compound identifiers to coefficients.
Parameters
----------
reaction : cobra.Reaction
The reaction whose metabolites are to be translated.
metabolite_mapping : dict
An existing mapping from cobr... | Return a mapping from KEGG compound identifiers to coefficients.
Parameters
----------
reaction : cobra.Reaction
The reaction whose metabolites are to be translated.
metabolite_mapping : dict
An existing mapping from cobra.Metabolite to KEGG compound identifier
that may already ... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/thermodynamics.py#L129-L158 |
opencobra/memote | memote/support/thermodynamics.py | find_thermodynamic_reversibility_index | def find_thermodynamic_reversibility_index(reactions):
u"""
Return the reversibility index of the given reactions.
To determine the reversibility index, we calculate
the reversibility index ln_gamma (see [1]_ section 3.5) of each reaction
using the eQuilibrator API [2]_.
Parameters
-------... | python | def find_thermodynamic_reversibility_index(reactions):
u"""
Return the reversibility index of the given reactions.
To determine the reversibility index, we calculate
the reversibility index ln_gamma (see [1]_ section 3.5) of each reaction
using the eQuilibrator API [2]_.
Parameters
-------... | u"""
Return the reversibility index of the given reactions.
To determine the reversibility index, we calculate
the reversibility index ln_gamma (see [1]_ section 3.5) of each reaction
using the eQuilibrator API [2]_.
Parameters
----------
reactions: list of cobra.Reaction
A... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/thermodynamics.py#L161-L234 |
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
-----
See [1]_ section 3.1 for a complete description of the algorithm.
.. [1] Gev... | 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] Gevorgyan, A., M. G Poolman, and D. A Fell.
"Dete... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L63-L110 |
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.
.. [1] Gevorgyan, A., M. G Poolman... | 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, and D. A Fell.
"Detection of Stoichiomet... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L113-L165 |
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
----------
model : cobra.Model
The metabolic model under investigation.
atol : float, optional
Values below the absolute tolerance are treated as zero. Exp... | python | def find_inconsistent_min_stoichiometry(model, atol=1e-13):
"""
Detect inconsistent minimal net stoichiometries.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
atol : float, optional
Values below the absolute tolerance are treated as zero. Exp... | Detect inconsistent minimal net stoichiometries.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
atol : float, optional
Values below the absolute tolerance are treated as zero. Expected to be
very small but larger than zero.
Notes
----... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L170-L246 |
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.
The function will first build a dissipation reaction corresponding to the
input metabolite. This reaction is then set as the objective for
optimization, after closing... | python | def detect_energy_generating_cycles(model, metabolite_id):
u"""
Detect erroneous energy-generating cycles for a a single metabolite.
The function will first build a dissipation reaction corresponding to the
input metabolite. This reaction is then set as the objective for
optimization, after closing... | u"""
Detect erroneous energy-generating cycles for a a single metabolite.
The function will first build a dissipation reaction corresponding to the
input metabolite. This reaction is then set as the objective for
optimization, after closing all exchanges. If the reaction was able to
carry flux, an ... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L277-L369 |
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
----------
model : cobra.Model
The metabolic model under investigation.... | python | 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
----------
model : cobra.Model
The metabolic model under investigation.... | u"""
Find metabolic reactions in stoichiometrically balanced cycles (SBCs).
Identify forward and reverse cycles by closing all exchanges and using FVA.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Notes
-----
"SBCs are artifacts of metabol... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L400-L431 |
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.
"""
exchange =... | 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. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L434-L454 |
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
... | python | 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
... | 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
The metabolic model under investigation.
Returns
-------... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L493-L520 |
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
every metabolite to be consumed in some form.
Parameters
----------
model : cobra... | python | 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
every metabolite to be consumed in some form.
Parameters
----------
model : cobra... | Return metabolites that cannot be consumed with open boundary reactions.
When all metabolites can be secreted, it should be possible for each and
every metabolite to be consumed in some form.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L523-L550 |
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
-------
tuple
list
A li... | python | 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
-------
tuple
list
A li... | Return list of reactions whose flux is unbounded in the default condition.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
-------
tuple
list
A list of reactions that in default modeling conditions are able to
c... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/consistency.py#L553-L612 |
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
Column names as keys and corresponding t... | python | 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
Column names as keys and corresponding t... | 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
Column names as keys and corresponding type for loading the data.
Please take a look at the `pa... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/tabular.py#L25-L60 |
opencobra/memote | memote/suite/cli/reports.py | snapshot | def snapshot(model, filename, pytest_args, exclusive, skip, solver,
experimental, custom_tests, custom_config):
"""
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
MEMOTE_MODEL or configured in 'setup.cf... | python | def snapshot(model, filename, pytest_args, exclusive, skip, solver,
experimental, custom_tests, custom_config):
"""
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
MEMOTE_MODEL or configured in 'setup.cf... | 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
MEMOTE_MODEL or configured in 'setup.cfg' or 'memote.ini'. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/cli/reports.py#L89-L119 |
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.")
t... | python | 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.")
t... | Generate a report over a model's git commit history. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/cli/reports.py#L144-L175 |
opencobra/memote | memote/suite/cli/reports.py | diff | def diff(models, filename, pytest_args, exclusive, skip, solver,
experimental, custom_tests, custom_config):
"""
Take a snapshot of all the supplied models and generate a diff report.
MODELS: List of paths to two or more model files.
"""
if not any(a.startswith("--tb") for a in pytest_args... | python | def diff(models, filename, pytest_args, exclusive, skip, solver,
experimental, custom_tests, custom_config):
"""
Take a snapshot of all the supplied models and generate a diff report.
MODELS: List of paths to two or more model files.
"""
if not any(a.startswith("--tb") for a in pytest_args... | Take a snapshot of all the supplied models and generate a diff report.
MODELS: List of paths to two or more model files. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/cli/reports.py#L226-L287 |
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()
for branch in self._repo.refs:
LOGGER.debug(... | Inspect and record the repo's branches and their history. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/results/history_manager.py#L65-L90 |
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.
"""
if self._history is None:
self.build_branch_structure(model, skip)
self._results = dict()
all_commits = list(s... | python | def load_history(self, model, skip={"gh-pages"}):
"""
Load the entire results history into memory.
Could be a bad idea in a far future.
"""
if self._history is None:
self.build_branch_structure(model, skip)
self._results = dict()
all_commits = list(s... | Load the entire results history into memory.
Could be a bad idea in a far future. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/results/history_manager.py#L100-L116 |
opencobra/memote | memote/suite/results/history_manager.py | HistoryManager.get_result | def get_result(self, commit, default=MemoteResult()):
"""Return an individual result from the history if it exists."""
assert self._results is not None, \
"Please call the method `load_history` first."
return self._results.get(commit, default) | python | def get_result(self, commit, default=MemoteResult()):
"""Return an individual result from the history if it exists."""
assert self._results is not None, \
"Please call the method `load_history` first."
return self._results.get(commit, default) | Return an individual result from the history if it exists. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/suite/results/history_manager.py#L118-L122 |
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(
model.metabolites, mo... | python | 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(
model.metabolites, mo... | Return the maximum and minimum absolute, non-zero coefficients.
Parameters
----------
model : cobra.Model
The metabolic model under investigation. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/matrix.py#L29-L43 |
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.
"""
s_matrix,... | 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. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/matrix.py#L46-L62 |
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
)
return co... | Return the rank of the model's stoichiometric matrix.
Parameters
----------
model : cobra.Model
The metabolic model under investigation. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/matrix.py#L65-L78 |
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
of the... | 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 stoichiometric matrix, as dim(Null(S)) cor... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/matrix.py#L81-L109 |
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)
self... | Load all information from an experimental configuration file.
Parameters
----------
model : cobra.Model
The metabolic model under investigation. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/config.py#L67-L81 |
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))
validator.validate(self.config) | Validate the configuration file. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/config.py#L83-L89 |
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
path = self.get_path(media, j... | Load and validate all media. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/config.py#L91-L111 |
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:
return
path = self.get... | Load and validate all data files. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/config.py#L113-L140 |
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,
... | Load and validate all data files. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/config.py#L142-L169 |
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)
return path | Return a relative or absolute path to experimental data. | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/experimental/config.py#L171-L178 |
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... | Find model components with empty annotation attributes.
Parameters
----------
model : cobra.Model
A cobrapy metabolic model.
components : {"metabolites", "reactions", "genes"}
A string denoting `cobra.Model` components.
Returns
-------
list
The components without an... | https://github.com/opencobra/memote/blob/276630fcd4449fb7b914186edfd38c239e7052df/memote/support/annotation.py#L125-L143 |
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