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nickjj/ansigenome | ansigenome/export.py | Export.dump | def dump(self):
"""
Dump the output to json.
"""
report_as_json_string = utils.dict_to_json(self.report)
if self.out_file:
utils.string_to_file(self.out_file, report_as_json_string)
else:
print report_as_json_string | python | def dump(self):
"""
Dump the output to json.
"""
report_as_json_string = utils.dict_to_json(self.report)
if self.out_file:
utils.string_to_file(self.out_file, report_as_json_string)
else:
print report_as_json_string | [
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SethMMorton/natsort | natsort/compat/fake_fastnumbers.py | fast_float | def fast_float(
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"""
Convert a string to a float quickly, return input as-is if not possible.
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na... | python | def fast_float(
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nan=None,
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_nan_inf=NAN_INF,
_first_char=POTENTIAL_FIRST_CHAR,
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Convert a string to a float quickly, return input as-is if not possible.
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SethMMorton/natsort | natsort/compat/fake_fastnumbers.py | fast_int | def fast_int(
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"""
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Convert a string to a int quickly, return input as-is if not possible.
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SethMMorton/natsort | natsort/__main__.py | check_filters | def check_filters(filters):
"""
Execute range_check for every element of an iterable.
Parameters
----------
filters : iterable
The collection of filters to check. Each element
must be a two-element tuple of floats or ints.
Returns
-------
The input as-is, or None if it ... | python | def check_filters(filters):
"""
Execute range_check for every element of an iterable.
Parameters
----------
filters : iterable
The collection of filters to check. Each element
must be a two-element tuple of floats or ints.
Returns
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SethMMorton/natsort | natsort/__main__.py | keep_entry_range | def keep_entry_range(entry, lows, highs, converter, regex):
"""
Check if an entry falls into a desired range.
Every number in the entry will be extracted using *regex*,
if any are within a given low to high range the entry will
be kept.
Parameters
----------
entry : str
lows : iter... | python | def keep_entry_range(entry, lows, highs, converter, regex):
"""
Check if an entry falls into a desired range.
Every number in the entry will be extracted using *regex*,
if any are within a given low to high range the entry will
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entry : str
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SethMMorton/natsort | natsort/__main__.py | keep_entry_value | def keep_entry_value(entry, values, converter, regex):
"""
Check if an entry does not match a given value.
Every number in the entry will be extracted using *regex*,
if any match a given value the entry will not be kept.
Parameters
----------
entry : str
values : iterable
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"""
Check if an entry does not match a given value.
Every number in the entry will be extracted using *regex*,
if any match a given value the entry will not be kept.
Parameters
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entry : str
values : iterable
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SethMMorton/natsort | natsort/__main__.py | sort_and_print_entries | def sort_and_print_entries(entries, args):
"""Sort the entries, applying the filters first if necessary."""
# Extract the proper number type.
is_float = args.number_type in ("float", "real", "f", "r")
signed = args.signed or args.number_type in ("real", "r")
alg = (
natsort.ns.FLOAT * is_fl... | python | def sort_and_print_entries(entries, args):
"""Sort the entries, applying the filters first if necessary."""
# Extract the proper number type.
is_float = args.number_type in ("float", "real", "f", "r")
signed = args.signed or args.number_type in ("real", "r")
alg = (
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SethMMorton/natsort | natsort/utils.py | regex_chooser | def regex_chooser(alg):
"""
Select an appropriate regex for the type of number of interest.
Parameters
----------
alg : ns enum
Used to indicate the regular expression to select.
Returns
-------
regex : compiled regex object
Regular expression object that matches the de... | python | def regex_chooser(alg):
"""
Select an appropriate regex for the type of number of interest.
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alg : ns enum
Used to indicate the regular expression to select.
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SethMMorton/natsort | natsort/utils.py | _normalize_input_factory | def _normalize_input_factory(alg):
"""
Create a function that will normalize unicode input data.
Parameters
----------
alg : ns enum
Used to indicate how to normalize unicode.
Returns
-------
func : callable
A function that accepts string (unicode) input and returns the... | python | def _normalize_input_factory(alg):
"""
Create a function that will normalize unicode input data.
Parameters
----------
alg : ns enum
Used to indicate how to normalize unicode.
Returns
-------
func : callable
A function that accepts string (unicode) input and returns the... | [
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SethMMorton/natsort | natsort/utils.py | natsort_key | def natsort_key(val, key, string_func, bytes_func, num_func):
"""
Key to sort strings and numbers naturally.
It works by splitting the string into components of strings and numbers,
and then converting the numbers into actual ints or floats.
Parameters
----------
val : str | unicode | byte... | python | def natsort_key(val, key, string_func, bytes_func, num_func):
"""
Key to sort strings and numbers naturally.
It works by splitting the string into components of strings and numbers,
and then converting the numbers into actual ints or floats.
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SethMMorton/natsort | natsort/utils.py | parse_number_factory | def parse_number_factory(alg, sep, pre_sep):
"""
Create a function that will format a number into a tuple.
Parameters
----------
alg : ns enum
Indicate how to format the *bytes*.
sep : str
The string character to be inserted before the number
in the returned tuple.
p... | python | def parse_number_factory(alg, sep, pre_sep):
"""
Create a function that will format a number into a tuple.
Parameters
----------
alg : ns enum
Indicate how to format the *bytes*.
sep : str
The string character to be inserted before the number
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SethMMorton/natsort | natsort/utils.py | sep_inserter | def sep_inserter(iterable, sep):
"""
Insert '' between numbers in an iterable.
Parameters
----------
iterable
sep : str
The string character to be inserted between adjacent numeric objects.
Yields
------
The values of *iterable* in order, with *sep* inserted where adjacent
... | python | def sep_inserter(iterable, sep):
"""
Insert '' between numbers in an iterable.
Parameters
----------
iterable
sep : str
The string character to be inserted between adjacent numeric objects.
Yields
------
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SethMMorton/natsort | natsort/utils.py | input_string_transform_factory | def input_string_transform_factory(alg):
"""
Create a function to transform a string.
Parameters
----------
alg : ns enum
Indicate how to format the *str*.
Returns
-------
func : callable
A function to be used as the *input_transform* argument to
*parse_string_f... | python | def input_string_transform_factory(alg):
"""
Create a function to transform a string.
Parameters
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alg : ns enum
Indicate how to format the *str*.
Returns
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func : callable
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SethMMorton/natsort | natsort/utils.py | string_component_transform_factory | def string_component_transform_factory(alg):
"""
Create a function to either transform a string or convert to a number.
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----------
alg : ns enum
Indicate how to format the *str*.
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-------
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"""
Create a function to either transform a string or convert to a number.
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alg : ns enum
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SethMMorton/natsort | natsort/utils.py | final_data_transform_factory | def final_data_transform_factory(alg, sep, pre_sep):
"""
Create a function to transform a tuple.
Parameters
----------
alg : ns enum
Indicate how to format the *str*.
sep : str
Separator that was passed to *parse_string_factory*.
pre_sep : str
String separator to ins... | python | def final_data_transform_factory(alg, sep, pre_sep):
"""
Create a function to transform a tuple.
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alg : ns enum
Indicate how to format the *str*.
sep : str
Separator that was passed to *parse_string_factory*.
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SethMMorton/natsort | natsort/utils.py | groupletters | def groupletters(x, _low=lower_function):
"""
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Parameters
----------
x : str
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-------
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Examples
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>>> groupletters("Apple")
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"""
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"""
Double all characters, making doubled letters lowercase.
Parameters
----------
x : str
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>>> groupletters("Apple")
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SethMMorton/natsort | natsort/utils.py | chain_functions | def chain_functions(functions):
"""
Chain a list of single-argument functions together and return.
The functions are applied in list order, and the output of the
previous functions is passed to the next function.
Parameters
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functions : list
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"""
Chain a list of single-argument functions together and return.
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SethMMorton/natsort | natsort/utils.py | path_splitter | def path_splitter(s, _d_match=re.compile(r"\.\d").match):
"""
Split a string into its path components.
Assumes a string is a path or is path-like.
Parameters
----------
s : str | pathlib.Path
Returns
-------
split : tuple
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"""
Split a string into its path components.
Assumes a string is a path or is path-like.
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s : str | pathlib.Path
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SethMMorton/natsort | natsort/utils.py | NumericalRegularExpressions._construct_regex | def _construct_regex(cls, fmt):
"""Given a format string, construct the regex with class attributes."""
return re.compile(fmt.format(**vars(cls)), flags=re.U) | python | def _construct_regex(cls, fmt):
"""Given a format string, construct the regex with class attributes."""
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SethMMorton/natsort | natsort/natsort.py | natsort_keygen | def natsort_keygen(key=None, alg=ns.DEFAULT):
"""
Generate a key to sort strings and numbers naturally.
This key is designed for use as the `key` argument to
functions such as the `sorted` builtin.
The user may customize the generated function with the
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"""
Generate a key to sort strings and numbers naturally.
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SethMMorton/natsort | natsort/natsort.py | natsorted | def natsorted(seq, key=None, reverse=False, alg=ns.DEFAULT):
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seq : iterable
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"""
Sorts an iterable naturally.
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seq : iterable
The input to sort.
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SethMMorton/natsort | natsort/natsort.py | humansorted | def humansorted(seq, key=None, reverse=False, alg=ns.DEFAULT):
"""
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Parameters
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seq : iterable
The input to sort.
key : callable, optional
A k... | python | def humansorted(seq, key=None, reverse=False, alg=ns.DEFAULT):
"""
Convenience function to properly sort non-numeric characters.
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SethMMorton/natsort | natsort/natsort.py | realsorted | def realsorted(seq, key=None, reverse=False, alg=ns.DEFAULT):
"""
Convenience function to properly sort signed floats.
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The behavior of :func:`realsorted` for `natsort` version >= 4.0.0
was th... | python | def realsorted(seq, key=None, reverse=False, alg=ns.DEFAULT):
"""
Convenience function to properly sort signed floats.
A signed float in a string could be "a-5.7". This is a wrapper around
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SethMMorton/natsort | natsort/natsort.py | index_natsorted | def index_natsorted(seq, key=None, reverse=False, alg=ns.DEFAULT):
"""
Determine the list of the indexes used to sort the input sequence.
Sorts a sequence naturally, but returns a list of sorted the
indexes and not the sorted list itself. This list of indexes
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"""
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SethMMorton/natsort | natsort/natsort.py | order_by_index | def order_by_index(seq, index, iter=False):
"""
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The output of `index_natsorted` is a
sequence of integers (index) that correspond to how its input
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"""
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vpelletier/pprofile | pprofile.py | run | def run(cmd, filename=None, threads=True, verbose=False):
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vpelletier/pprofile | pprofile.py | runpath | def runpath(path, argv, filename=None, threads=True, verbose=False):
"""
Run code from open-accessible file path with profiling enabled.
"""
_run(threads, verbose, 'runpath', filename, path, argv) | python | def runpath(path, argv, filename=None, threads=True, verbose=False):
"""
Run code from open-accessible file path with profiling enabled.
"""
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vpelletier/pprofile | pprofile.py | pprofile | def pprofile(line, cell=None):
"""
Profile line execution.
"""
if cell is None:
# TODO: detect and use arguments (statistical profiling, ...) ?
return run(line)
return _main(
['%%pprofile', '-m', '-'] + shlex.split(line),
io.StringIO(cell),
) | python | def pprofile(line, cell=None):
"""
Profile line execution.
"""
if cell is None:
# TODO: detect and use arguments (statistical profiling, ...) ?
return run(line)
return _main(
['%%pprofile', '-m', '-'] + shlex.split(line),
io.StringIO(cell),
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vpelletier/pprofile | pprofile.py | _FileTiming.hit | def hit(self, code, line, duration):
"""
A line has finished executing.
code (code)
container function's code object
line (int)
line number of just executed line
duration (float)
duration of the line, in seconds
"""
entry = self.line... | python | def hit(self, code, line, duration):
"""
A line has finished executing.
code (code)
container function's code object
line (int)
line number of just executed line
duration (float)
duration of the line, in seconds
"""
entry = self.line... | [
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vpelletier/pprofile | pprofile.py | _FileTiming.call | def call(self, code, line, callee_file_timing, callee, duration, frame):
"""
A call originating from this file returned.
code (code)
caller's code object
line (int)
caller's line number
callee_file_timing (FileTiming)
callee's FileTiming
cal... | python | def call(self, code, line, callee_file_timing, callee, duration, frame):
"""
A call originating from this file returned.
code (code)
caller's code object
line (int)
caller's line number
callee_file_timing (FileTiming)
callee's FileTiming
cal... | [
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vpelletier/pprofile | pprofile.py | ProfileBase.dump_stats | def dump_stats(self, filename):
"""
Similar to profile.Profile.dump_stats - but different output format !
"""
if _isCallgrindName(filename):
with open(filename, 'w') as out:
self.callgrind(out)
else:
with io.open(filename, 'w', errors='repl... | python | def dump_stats(self, filename):
"""
Similar to profile.Profile.dump_stats - but different output format !
"""
if _isCallgrindName(filename):
with open(filename, 'w') as out:
self.callgrind(out)
else:
with io.open(filename, 'w', errors='repl... | [
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vpelletier/pprofile | pprofile.py | ProfileRunnerBase.runctx | def runctx(self, cmd, globals, locals):
"""Similar to profile.Profile.runctx ."""
with self():
exec(cmd, globals, locals)
return self | python | def runctx(self, cmd, globals, locals):
"""Similar to profile.Profile.runctx ."""
with self():
exec(cmd, globals, locals)
return self | [
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vpelletier/pprofile | pprofile.py | Profile.enable | def enable(self):
"""
Enable profiling.
"""
if self.enabled_start:
warn('Duplicate "enable" call')
else:
self._enable()
sys.settrace(self._global_trace) | python | def enable(self):
"""
Enable profiling.
"""
if self.enabled_start:
warn('Duplicate "enable" call')
else:
self._enable()
sys.settrace(self._global_trace) | [
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vpelletier/pprofile | pprofile.py | Profile._disable | def _disable(self):
"""
Overload this method when subclassing. Called after actually disabling
trace.
"""
self.total_time += time() - self.enabled_start
self.enabled_start = None
del self.stack | python | def _disable(self):
"""
Overload this method when subclassing. Called after actually disabling
trace.
"""
self.total_time += time() - self.enabled_start
self.enabled_start = None
del self.stack | [
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rsinger86/drf-flex-fields | rest_flex_fields/serializers.py | FlexFieldsSerializerMixin._make_expanded_field_serializer | def _make_expanded_field_serializer(
self, name, nested_expand, nested_fields, nested_omit
):
"""
Returns an instance of the dynamically created nested serializer.
"""
field_options = self.expandable_fields[name]
serializer_class = field_options[0]
serializer_... | python | def _make_expanded_field_serializer(
self, name, nested_expand, nested_fields, nested_omit
):
"""
Returns an instance of the dynamically created nested serializer.
"""
field_options = self.expandable_fields[name]
serializer_class = field_options[0]
serializer_... | [
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rsinger86/drf-flex-fields | rest_flex_fields/serializers.py | FlexFieldsSerializerMixin._clean_fields | def _clean_fields(self, omit_fields, sparse_fields, next_level_omits):
"""
Remove fields that are found in omit list, and if sparse names
are passed, remove any fields not found in that list.
"""
sparse = len(sparse_fields) > 0
to_remove = []
if not spars... | python | def _clean_fields(self, omit_fields, sparse_fields, next_level_omits):
"""
Remove fields that are found in omit list, and if sparse names
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"""
sparse = len(sparse_fields) > 0
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rsinger86/drf-flex-fields | rest_flex_fields/serializers.py | FlexFieldsSerializerMixin._can_access_request | def _can_access_request(self):
"""
Can access current request object if all are true
- The serializer is the root.
- A request context was passed in.
- The request method is GET.
"""
if self.parent:
return False
if not hasattr(self, "context")... | python | def _can_access_request(self):
"""
Can access current request object if all are true
- The serializer is the root.
- A request context was passed in.
- The request method is GET.
"""
if self.parent:
return False
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rsinger86/drf-flex-fields | rest_flex_fields/serializers.py | FlexFieldsSerializerMixin._get_expand_input | def _get_expand_input(self, passed_settings):
"""
If expand value is explicitliy passed, just return it.
If parsing from request, ensure that the value complies with
the "permitted_expands" list passed into the context from the
FlexFieldsMixin.
"""
... | python | def _get_expand_input(self, passed_settings):
"""
If expand value is explicitliy passed, just return it.
If parsing from request, ensure that the value complies with
the "permitted_expands" list passed into the context from the
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rsinger86/drf-flex-fields | rest_flex_fields/utils.py | is_expanded | def is_expanded(request, key):
""" Examines request object to return boolean of whether
passed field is expanded.
"""
expand = request.query_params.get("expand", "")
expand_fields = []
for e in expand.split(","):
expand_fields.extend([e for e in e.split(".")])
return "~all" in ... | python | def is_expanded(request, key):
""" Examines request object to return boolean of whether
passed field is expanded.
"""
expand = request.query_params.get("expand", "")
expand_fields = []
for e in expand.split(","):
expand_fields.extend([e for e in e.split(".")])
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chinuno-usami/CuteR | CuteR/CuteR.py | color_replace | def color_replace(image, color):
"""Replace black with other color
:color: custom color (r,g,b,a)
:image: image to replace color
:returns: TODO
"""
pixels = image.load()
size = image.size[0]
for width in range(size):
for height in range(size):
r, g, b, a = pixels[wi... | python | def color_replace(image, color):
"""Replace black with other color
:color: custom color (r,g,b,a)
:image: image to replace color
:returns: TODO
"""
pixels = image.load()
size = image.size[0]
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maroba/findiff | findiff/vector.py | wrap_in_ndarray | def wrap_in_ndarray(value):
"""Wraps the argument in a numpy.ndarray.
If value is a scalar, it is converted in a list first.
If value is array-like, the shape is conserved.
"""
if hasattr(value, "__len__"):
return np.array(value)
else:
return np.array([value]) | python | def wrap_in_ndarray(value):
"""Wraps the argument in a numpy.ndarray.
If value is a scalar, it is converted in a list first.
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"""
if hasattr(value, "__len__"):
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maroba/findiff | findiff/coefs.py | coefficients_non_uni | def coefficients_non_uni(deriv, acc, coords, idx):
"""
Calculates the finite difference coefficients for given derivative order and accuracy order.
Assumes that the underlying grid is non-uniform.
:param deriv: int > 0: The derivative order.
:param acc: even int > 0: The accuracy order.
... | python | def coefficients_non_uni(deriv, acc, coords, idx):
"""
Calculates the finite difference coefficients for given derivative order and accuracy order.
Assumes that the underlying grid is non-uniform.
:param deriv: int > 0: The derivative order.
:param acc: even int > 0: The accuracy order.
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maroba/findiff | findiff/coefs.py | _build_matrix | def _build_matrix(p, q, deriv):
"""Constructs the equation system matrix for the finite difference coefficients"""
A = [([1 for _ in range(-p, q+1)])]
for i in range(1, p + q + 1):
A.append([j**i for j in range(-p, q+1)])
return np.array(A) | python | def _build_matrix(p, q, deriv):
"""Constructs the equation system matrix for the finite difference coefficients"""
A = [([1 for _ in range(-p, q+1)])]
for i in range(1, p + q + 1):
A.append([j**i for j in range(-p, q+1)])
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maroba/findiff | findiff/coefs.py | _build_rhs | def _build_rhs(p, q, deriv):
"""The right hand side of the equation system matrix"""
b = [0 for _ in range(p+q+1)]
b[deriv] = math.factorial(deriv)
return np.array(b) | python | def _build_rhs(p, q, deriv):
"""The right hand side of the equation system matrix"""
b = [0 for _ in range(p+q+1)]
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maroba/findiff | findiff/coefs.py | _build_matrix_non_uniform | def _build_matrix_non_uniform(p, q, coords, k):
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A = [[1] * (p+q+1)]
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"""Constructs the equation matrix for the finite difference coefficients of non-uniform grids at location k"""
A = [[1] * (p+q+1)]
for i in range(1, p + q + 1):
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maroba/findiff | findiff/operators.py | FinDiff.set_accuracy | def set_accuracy(self, acc):
""" Sets the accuracy order of the finite difference scheme.
If the FinDiff object is not a raw partial derivative but a composition of derivatives
the accuracy order will be propagated to the child operators.
"""
self.acc = acc
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self.acc = acc
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maroba/findiff | findiff/operators.py | FinDiff.diff | def diff(self, y, h, deriv, dim, coefs):
"""The core function to take a partial derivative on a uniform grid.
"""
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npts = y.shape[dim]
except AttributeError as err:
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maroba/findiff | findiff/operators.py | FinDiff.diff_non_uni | def diff_non_uni(self, y, coords, dim, coefs):
"""The core function to take a partial derivative on a non-uniform grid"""
yd = np.zeros_like(y)
ndims = len(y.shape)
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ref_multi_slice = [slice(None, None)] * ndims
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"""The core function to take a partial derivative on a non-uniform grid"""
yd = np.zeros_like(y)
ndims = len(y.shape)
multi_slice = [slice(None, None)] * ndims
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maroba/findiff | findiff/operators.py | FinDiff._apply_to_array | def _apply_to_array(self, yd, y, weights, off_slices, ref_slice, dim):
"""Applies the finite differences only to slices along a given axis"""
ndims = len(y.shape)
all = slice(None, None, 1)
ref_multi_slice = [all] * ndims
ref_multi_slice[dim] = ref_slice
for w, s in z... | python | def _apply_to_array(self, yd, y, weights, off_slices, ref_slice, dim):
"""Applies the finite differences only to slices along a given axis"""
ndims = len(y.shape)
all = slice(None, None, 1)
ref_multi_slice = [all] * ndims
ref_multi_slice[dim] = ref_slice
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anchore/anchore | anchore/anchore_auth.py | get_current_user_info | def get_current_user_info(anchore_auth):
"""
Return the metadata about the current user as supplied by the anchore.io service. Includes permissions and tier access.
:return: Dict of user metadata
"""
user_url = anchore_auth['client_info_url'] + '/' + anchore_auth['username']
user_timeout = 60
... | python | def get_current_user_info(anchore_auth):
"""
Return the metadata about the current user as supplied by the anchore.io service. Includes permissions and tier access.
:return: Dict of user metadata
"""
user_url = anchore_auth['client_info_url'] + '/' + anchore_auth['username']
user_timeout = 60
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anchore/anchore | anchore/cli/policybundle.py | show | def show(details):
"""
Show list of Anchore data policies.
"""
ecode = 0
try:
policymeta = anchore_policy.load_policymeta()
if details:
anchore_print(policymeta, do_formatting=True)
else:
output = {}
name = policymeta['name']
... | python | def show(details):
"""
Show list of Anchore data policies.
"""
ecode = 0
try:
policymeta = anchore_policy.load_policymeta()
if details:
anchore_print(policymeta, do_formatting=True)
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output = {}
name = policymeta['name']
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anchore/anchore | anchore/cli/common.py | extended_help_option | def extended_help_option(extended_help=None, *param_decls, **attrs):
"""
Based on the click.help_option code.
Adds a ``--extended-help`` option which immediately ends the program
printing out the extended extended-help page. Defaults to using the
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"""
Based on the click.help_option code.
Adds a ``--extended-help`` option which immediately ends the program
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anchore/anchore | anchore/cli/common.py | anchore_print | def anchore_print(msg, do_formatting=False):
"""
Print to stdout using the proper formatting for the command.
:param msg: output to be printed, either an object or a string. Objects will be serialized according to config
:return:
"""
if do_formatting:
click.echo(formatter(msg))
else... | python | def anchore_print(msg, do_formatting=False):
"""
Print to stdout using the proper formatting for the command.
:param msg: output to be printed, either an object or a string. Objects will be serialized according to config
:return:
"""
if do_formatting:
click.echo(formatter(msg))
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anchore/anchore | anchore/cli/common.py | build_image_list | def build_image_list(config, image, imagefile, all_local, include_allanchore, dockerfile=None, exclude_file=None):
"""Given option inputs from the cli, construct a list of image ids. Includes all found with no exclusion logic"""
if not image and not (imagefile or all_local):
raise click.BadOptionUsage(... | python | def build_image_list(config, image, imagefile, all_local, include_allanchore, dockerfile=None, exclude_file=None):
"""Given option inputs from the cli, construct a list of image ids. Includes all found with no exclusion logic"""
if not image and not (imagefile or all_local):
raise click.BadOptionUsage(... | [
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anchore/anchore | anchore/cli/logs.py | init_output_formatters | def init_output_formatters(output_verbosity='normal', stderr=sys.stderr, logfile=None, debug_logfile=None):
"""
Initialize the CLI logging scheme.
:param output_verbosity: 'quiet','normal','verbose', or 'debug' controls the output to stdout and its format
:param stderr: stream for stderr output, defaul... | python | def init_output_formatters(output_verbosity='normal', stderr=sys.stderr, logfile=None, debug_logfile=None):
"""
Initialize the CLI logging scheme.
:param output_verbosity: 'quiet','normal','verbose', or 'debug' controls the output to stdout and its format
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anchore/anchore | anchore/cli/__init__.py | main_entry | def main_entry(ctx, verbose, debug, quiet, json, plain, html, config_override):
"""
Anchore is a tool to analyze, query, and curate container images. The options at this top level
control stdout and stderr verbosity and format.
After installation, the first command run should be: 'anchore feeds
lis... | python | def main_entry(ctx, verbose, debug, quiet, json, plain, html, config_override):
"""
Anchore is a tool to analyze, query, and curate container images. The options at this top level
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control stdout and stderr verbosity and format.
After installation, the first command run should be: 'anchore feeds
list' to initialize the system and load feed data.
High-level example flows:
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anchore/anchore | anchore/util/resources.py | get_user_agent | def get_user_agent():
"""
Construct and informative user-agent string.
Includes OS version and docker version info
Not thread-safe
:return:
"""
global user_agent_string
if user_agent_string is None:
# get OS type
try:
sysinfo = subprocess.check_output('lsb_r... | python | def get_user_agent():
"""
Construct and informative user-agent string.
Includes OS version and docker version info
Not thread-safe
:return:
"""
global user_agent_string
if user_agent_string is None:
# get OS type
try:
sysinfo = subprocess.check_output('lsb_r... | [
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anchore/anchore | anchore/util/resources.py | normalize_headers | def normalize_headers(headers):
"""
Convert useful headers to a normalized type and return in a new dict
Only processes content-type, content-length, etag, and last-modified
:param headers:
:return:
"""
for (k, v) in headers.items():
headers.pop(k)
headers[k.lower()] = v
... | python | def normalize_headers(headers):
"""
Convert useful headers to a normalized type and return in a new dict
Only processes content-type, content-length, etag, and last-modified
:param headers:
:return:
"""
for (k, v) in headers.items():
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anchore/anchore | anchore/util/resources.py | get_resource_retriever | def get_resource_retriever(url):
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Get the appropriate retriever object for the specified url based on url scheme.
Makes assumption that HTTP urls do not require any special authorization.
For HTTP urls: returns HTTPResourceRetriever
For s3:// urls returns S3ResourceRetriever
:param url: url... | python | def get_resource_retriever(url):
"""
Get the appropriate retriever object for the specified url based on url scheme.
Makes assumption that HTTP urls do not require any special authorization.
For HTTP urls: returns HTTPResourceRetriever
For s3:// urls returns S3ResourceRetriever
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anchore/anchore | anchore/util/resources.py | ResourceCache.get | def get(self, url):
"""
Lookup the given url and return an entry if found. Else return None.
The returned entry is a dict with metadata about the content and a 'content' key with a file path value
:param url:
:return:
"""
self._load(url)
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... | python | def get(self, url):
"""
Lookup the given url and return an entry if found. Else return None.
The returned entry is a dict with metadata about the content and a 'content' key with a file path value
:param url:
:return:
"""
self._load(url)
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anchore/anchore | anchore/util/resources.py | ResourceCache._load | def _load(self, url):
"""
Load from remote, but check local file content to identify duplicate content. If local file is found with
same hash then it is used with metadata from remote object to avoid fetching full content.
:param url:
:return:
"""
self._logger.de... | python | def _load(self, url):
"""
Load from remote, but check local file content to identify duplicate content. If local file is found with
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:param url:
:return:
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anchore/anchore | anchore/util/fs_util.py | calc_file_md5 | def calc_file_md5(filepath, chunk_size=None):
"""
Calculate a file's md5 checksum. Use the specified chunk_size for IO or the
default 256KB
:param filepath:
:param chunk_size:
:return:
"""
if chunk_size is None:
chunk_size = 256 * 1024
md5sum = hashlib.md5()
with io.open... | python | def calc_file_md5(filepath, chunk_size=None):
"""
Calculate a file's md5 checksum. Use the specified chunk_size for IO or the
default 256KB
:param filepath:
:param chunk_size:
:return:
"""
if chunk_size is None:
chunk_size = 256 * 1024
md5sum = hashlib.md5()
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anchore/anchore | anchore/cli/toolbox.py | toolbox | def toolbox(anchore_config, ctx, image, imageid):
"""
A collection of tools for operating on images and containers and building anchore modules.
Subcommands operate on the specified image passed in as --image <imgid>
"""
global config, imagelist, nav
config = anchore_config
ecode = 0
... | python | def toolbox(anchore_config, ctx, image, imageid):
"""
A collection of tools for operating on images and containers and building anchore modules.
Subcommands operate on the specified image passed in as --image <imgid>
"""
global config, imagelist, nav
config = anchore_config
ecode = 0
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anchore/anchore | anchore/cli/toolbox.py | unpack | def unpack(destdir):
"""Unpack and Squash image to local filesystem"""
if not nav:
sys.exit(1)
ecode = 0
try:
anchore_print("Unpacking images: " + ' '.join(nav.get_images()))
result = nav.unpack(destdir=destdir)
if not result:
anchore_print_err("no images un... | python | def unpack(destdir):
"""Unpack and Squash image to local filesystem"""
if not nav:
sys.exit(1)
ecode = 0
try:
anchore_print("Unpacking images: " + ' '.join(nav.get_images()))
result = nav.unpack(destdir=destdir)
if not result:
anchore_print_err("no images un... | [
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anchore/anchore | anchore/cli/toolbox.py | show_analyzer_status | def show_analyzer_status():
"""Show analyzer status for specified image"""
ecode = 0
try:
image=contexts['anchore_allimages'][imagelist[0]]
analyzer_status = contexts['anchore_db'].load_analyzer_manifest(image.meta['imageId'])
result = {image.meta['imageId']:{'result':{'header':['An... | python | def show_analyzer_status():
"""Show analyzer status for specified image"""
ecode = 0
try:
image=contexts['anchore_allimages'][imagelist[0]]
analyzer_status = contexts['anchore_db'].load_analyzer_manifest(image.meta['imageId'])
result = {image.meta['imageId']:{'result':{'header':['An... | [
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anchore/anchore | anchore/cli/toolbox.py | export | def export(outfile):
"""Export image anchore data to a JSON file."""
if not nav:
sys.exit(1)
ecode = 0
savelist = list()
for imageId in imagelist:
try:
record = {}
record['image'] = {}
record['image']['imageId'] = imageId
record['ima... | python | def export(outfile):
"""Export image anchore data to a JSON file."""
if not nav:
sys.exit(1)
ecode = 0
savelist = list()
for imageId in imagelist:
try:
record = {}
record['image'] = {}
record['image']['imageId'] = imageId
record['ima... | [
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anchore/anchore | anchore/cli/toolbox.py | image_import | def image_import(infile, force):
"""Import image anchore data from a JSON file."""
ecode = 0
try:
with open(infile, 'r') as FH:
savelist = json.loads(FH.read())
except Exception as err:
anchore_print_err("could not load input file: " + str(err))
ecode = 1
if... | python | def image_import(infile, force):
"""Import image anchore data from a JSON file."""
ecode = 0
try:
with open(infile, 'r') as FH:
savelist = json.loads(FH.read())
except Exception as err:
anchore_print_err("could not load input file: " + str(err))
ecode = 1
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anchore/anchore | anchore/cli/system.py | status | def status(conf):
"""
Show anchore system status.
"""
ecode = 0
try:
if conf:
if config.cliargs['json']:
anchore_print(config.data, do_formatting=True)
else:
anchore_print(yaml.safe_dump(config.data, indent=True, default_flow_style=Fal... | python | def status(conf):
"""
Show anchore system status.
"""
ecode = 0
try:
if conf:
if config.cliargs['json']:
anchore_print(config.data, do_formatting=True)
else:
anchore_print(yaml.safe_dump(config.data, indent=True, default_flow_style=Fal... | [
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anchore/anchore | anchore/cli/system.py | show_schemas | def show_schemas(schemaname):
"""
Show anchore document schemas.
"""
ecode = 0
try:
schemas = {}
schema_dir = os.path.join(contexts['anchore_config']['pkg_dir'], 'schemas')
for f in os.listdir(schema_dir):
sdata = {}
try:
with open(os.... | python | def show_schemas(schemaname):
"""
Show anchore document schemas.
"""
ecode = 0
try:
schemas = {}
schema_dir = os.path.join(contexts['anchore_config']['pkg_dir'], 'schemas')
for f in os.listdir(schema_dir):
sdata = {}
try:
with open(os.... | [
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anchore/anchore | anchore/cli/system.py | backup | def backup(outputdir):
"""
Backup an anchore installation to a tarfile.
"""
ecode = 0
try:
anchore_print('Backing up anchore system to directory '+str(outputdir)+' ...')
backupfile = config.backup(outputdir)
anchore_print({"anchore_backup_tarball":str(backupfile)}, do_format... | python | def backup(outputdir):
"""
Backup an anchore installation to a tarfile.
"""
ecode = 0
try:
anchore_print('Backing up anchore system to directory '+str(outputdir)+' ...')
backupfile = config.backup(outputdir)
anchore_print({"anchore_backup_tarball":str(backupfile)}, do_format... | [
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anchore/anchore | anchore/cli/system.py | restore | def restore(inputfile, destination_root):
"""
Restore an anchore installation from a previously backed up tar file.
"""
ecode = 0
try:
anchore_print('Restoring anchore system from backup file %s ...' % (str(inputfile.name)))
restoredir = config.restore(destination_root, inputfile)
... | python | def restore(inputfile, destination_root):
"""
Restore an anchore installation from a previously backed up tar file.
"""
ecode = 0
try:
anchore_print('Restoring anchore system from backup file %s ...' % (str(inputfile.name)))
restoredir = config.restore(destination_root, inputfile)
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anchore/anchore | anchore/cli/system.py | exportdb | def exportdb(outdir):
"""Export all anchore images to JSON files"""
ecode = 0
try:
imgdir = os.path.join(outdir, "images")
feeddir = os.path.join(outdir, "feeds")
storedir = os.path.join(outdir, "storedfiles")
for d in [outdir, imgdir, feeddir, storedir]:
if not ... | python | def exportdb(outdir):
"""Export all anchore images to JSON files"""
ecode = 0
try:
imgdir = os.path.join(outdir, "images")
feeddir = os.path.join(outdir, "feeds")
storedir = os.path.join(outdir, "storedfiles")
for d in [outdir, imgdir, feeddir, storedir]:
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anchore/anchore | anchore/apk.py | next_token | def next_token(expected_type, data):
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:param data:
:return: (TokenType, str) tuple where TokenType is the type of the next token expected
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Based on the expected next type, consume the next token returning the type found and an updated buffer with the found token
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anchore/anchore | anchore/cli/feeds.py | show | def show(feed):
"""
Show detailed feed information
"""
ecode = 0
try:
feedmeta = anchore_feeds.load_anchore_feedmeta()
if feed in feedmeta:
result = {}
groups = feedmeta[feed].get('groups',{}).values()
result['name'] = feed
result['acc... | python | def show(feed):
"""
Show detailed feed information
"""
ecode = 0
try:
feedmeta = anchore_feeds.load_anchore_feedmeta()
if feed in feedmeta:
result = {}
groups = feedmeta[feed].get('groups',{}).values()
result['name'] = feed
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anchore/anchore | anchore/cli/feeds.py | list | def list(showgroups):
"""
Show list of Anchore data feeds.
"""
ecode = 0
try:
result = {}
subscribed = {}
available = {}
unavailable = {}
current_user_data = contexts['anchore_auth']['user_info']
feedmeta = anchore_feeds.load_anchore_feedmeta()
... | python | def list(showgroups):
"""
Show list of Anchore data feeds.
"""
ecode = 0
try:
result = {}
subscribed = {}
available = {}
unavailable = {}
current_user_data = contexts['anchore_auth']['user_info']
feedmeta = anchore_feeds.load_anchore_feedmeta()
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anchore/anchore | anchore/analyzer.py | SelectionStrategy.evaluate_familytree | def evaluate_familytree(self, family_tree, image_set):
"""
Evaluate strategy for the given family tree and return a dict of images to analyze that match the strategy
:param family_tree: the family tree to traverse and evaluate
:param image_set: list of all images in the context
... | python | def evaluate_familytree(self, family_tree, image_set):
"""
Evaluate strategy for the given family tree and return a dict of images to analyze that match the strategy
:param family_tree: the family tree to traverse and evaluate
:param image_set: list of all images in the context
... | [
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anchore/anchore | anchore/cli/login.py | logout | def logout(anchore_config):
"""
Log out of Anchore service
"""
ecode = 0
try:
aa = contexts['anchore_auth']
if aa:
anchore_auth.anchore_auth_invalidate(aa)
if 'auth_file' in aa:
os.remove(aa['auth_file'])
print "Logout successful."
... | python | def logout(anchore_config):
"""
Log out of Anchore service
"""
ecode = 0
try:
aa = contexts['anchore_auth']
if aa:
anchore_auth.anchore_auth_invalidate(aa)
if 'auth_file' in aa:
os.remove(aa['auth_file'])
print "Logout successful."
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joanvila/aioredlock | aioredlock/redis.py | Instance.connect | async def connect(self):
"""
Get an connection for the self instance
"""
if isinstance(self.connection, dict):
# a dict like {'host': 'localhost', 'port': 6379,
# 'db': 0, 'password': 'pass'}
kwargs = self.connection.copy()
ad... | python | async def connect(self):
"""
Get an connection for the self instance
"""
if isinstance(self.connection, dict):
# a dict like {'host': 'localhost', 'port': 6379,
# 'db': 0, 'password': 'pass'}
kwargs = self.connection.copy()
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joanvila/aioredlock | aioredlock/redis.py | Instance.close | async def close(self):
"""
Closes connection and resets pool
"""
if self._pool is not None and not isinstance(self.connection, aioredis.Redis):
self._pool.close()
await self._pool.wait_closed()
self._pool = None | python | async def close(self):
"""
Closes connection and resets pool
"""
if self._pool is not None and not isinstance(self.connection, aioredis.Redis):
self._pool.close()
await self._pool.wait_closed()
self._pool = None | [
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joanvila/aioredlock | aioredlock/redis.py | Redis.set_lock | async def set_lock(self, resource, lock_identifier):
"""
Tries to set the lock to all the redis instances
:param resource: The resource string name to lock
:param lock_identifier: The id of the lock. A unique string
:return float: The elapsed time that took to lock the instances... | python | async def set_lock(self, resource, lock_identifier):
"""
Tries to set the lock to all the redis instances
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:param lock_identifier: The id of the lock. A unique string
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joanvila/aioredlock | aioredlock/redis.py | Redis.unset_lock | async def unset_lock(self, resource, lock_identifier):
"""
Tries to unset the lock to all the redis instances
:param resource: The resource string name to lock
:param lock_identifier: The id of the lock. A unique string
:return float: The elapsed time that took to lock the insta... | python | async def unset_lock(self, resource, lock_identifier):
"""
Tries to unset the lock to all the redis instances
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:param lock_identifier: The id of the lock. A unique string
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_info.py | _clean | def _clean(value):
""" Convert numpy numeric types to their python equivalents. """
if isinstance(value, np.ndarray):
if value.dtype.kind == 'S':
return np.char.decode(value).tolist()
else:
return value.tolist()
elif type(value).__module__ == np.__name__:
# h5... | python | def _clean(value):
""" Convert numpy numeric types to their python equivalents. """
if isinstance(value, np.ndarray):
if value.dtype.kind == 'S':
return np.char.decode(value).tolist()
else:
return value.tolist()
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# h5... | [
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nanoporetech/ont_fast5_api | ont_fast5_api/analysis_tools/basecall_2d.py | Basecall2DTools.get_prior_alignment | def get_prior_alignment(self):
""" Return the prior alignment that was used for 2D basecalling.
:return: Alignment data table.
"""
data_group = '{}/HairpinAlign'.format(self.group_name)
data = self.handle.get_analysis_dataset(data_group, 'Alignment')
return data | python | def get_prior_alignment(self):
""" Return the prior alignment that was used for 2D basecalling.
:return: Alignment data table.
"""
data_group = '{}/HairpinAlign'.format(self.group_name)
data = self.handle.get_analysis_dataset(data_group, 'Alignment')
return data | [
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nanoporetech/ont_fast5_api | ont_fast5_api/analysis_tools/basecall_2d.py | Basecall2DTools.get_2d_call_alignment | def get_2d_call_alignment(self):
""" Return the alignment and model_states from the 2D basecall.
:return: Alignment data table.
"""
data_group = '{}/BaseCalled_2D'.format(self.group_name)
data = self.handle.get_analysis_dataset(data_group, 'Alignment')
return data | python | def get_2d_call_alignment(self):
""" Return the alignment and model_states from the 2D basecall.
:return: Alignment data table.
"""
data_group = '{}/BaseCalled_2D'.format(self.group_name)
data = self.handle.get_analysis_dataset(data_group, 'Alignment')
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nanoporetech/ont_fast5_api | ont_fast5_api/analysis_tools/alignment.py | AlignmentTools.get_results | def get_results(self):
""" Get details about the alignments that have been performed.
:return: A dict of dicts.
The keys of the top level are 'template', 'complement' and '2d'.
Each of these dicts contains the following fields:
* status: Can be 'no data', 'no match found',... | python | def get_results(self):
""" Get details about the alignments that have been performed.
:return: A dict of dicts.
The keys of the top level are 'template', 'complement' and '2d'.
Each of these dicts contains the following fields:
* status: Can be 'no data', 'no match found',... | [
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nanoporetech/ont_fast5_api | ont_fast5_api/analysis_tools/alignment.py | AlignmentTools.calculate_speed | def calculate_speed(self, section, alignment_results=None):
""" Calculate speed using alignment information.
:param section: The section (template or complement) we're calculating
speed for.
:param alignment_results: Optional dictionary of the alignment summary,
so that ... | python | def calculate_speed(self, section, alignment_results=None):
""" Calculate speed using alignment information.
:param section: The section (template or complement) we're calculating
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_read.py | Fast5Read.add_raw_data | def add_raw_data(self, data, attrs):
""" Add raw data for a read.
:param data: The raw data DAQ values (16 bit integers).
The read must already exist in the file. It must not already
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"""
self.assert_writeable()
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... | python | def add_raw_data(self, data, attrs):
""" Add raw data for a read.
:param data: The raw data DAQ values (16 bit integers).
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_read.py | Fast5Read.add_channel_info | def add_channel_info(self, attrs, clear=False):
""" Add channel info data to the channel_id group.
:param data: A dictionary of key/value pairs. Keys must be strings.
Values can be strings or numeric values.
:param clear: If set, any existing channel info data will be removed.
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""" Add channel info data to the channel_id group.
:param data: A dictionary of key/value pairs. Keys must be strings.
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:param clear: If set, any existing channel info data will be removed.
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_read.py | Fast5Read.add_analysis | def add_analysis(self, component, group_name, attrs, config=None):
""" Add a new analysis group to the file.
:param component: The component name.
:param group_name: The name to use for the group. Must not already
exist in the file e.g. 'Test_000'.
:param attrs: A dictionary... | python | def add_analysis(self, component, group_name, attrs, config=None):
""" Add a new analysis group to the file.
:param component: The component name.
:param group_name: The name to use for the group. Must not already
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_writer.py | Fast5Writer.write_strand | def write_strand(self, strand):
""" Writes a Strand object to the stream. """
if strand['channel'] != self._current_channel \
or self._strand_counter == self._reads_per_file:
self._start_new_file(strand)
fname = self._write_strand(strand)
self._index.write('{}\t{}\... | python | def write_strand(self, strand):
""" Writes a Strand object to the stream. """
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_file.py | AbstractFast5File.close | def close(self):
""" Closes the object.
"""
if self._is_open:
self.mode = None
if self.handle:
self.handle.close()
self.handle = None
self.filename = None
self._is_open = False
self.status = None | python | def close(self):
""" Closes the object.
"""
if self._is_open:
self.mode = None
if self.handle:
self.handle.close()
self.handle = None
self.filename = None
self._is_open = False
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_file.py | Fast5File.add_chain | def add_chain(self, group_name, component_map):
"""
Adds the component chain to ``group_name`` in the fast5.
These are added as attributes to the group.
:param group_name: The group name you wish to add chaining data to,
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:param component_map: The se... | python | def add_chain(self, group_name, component_map):
"""
Adds the component chain to ``group_name`` in the fast5.
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_file.py | Fast5File.add_read | def add_read(self, read_number, read_id, start_time, duration, mux, median_before):
""" Add a new read to the file.
:param read_number: The read number to assign to the read.
:param read_id: The unique read-id for the read.
:param start_time: The start time (in samples) of the read.
... | python | def add_read(self, read_number, read_id, start_time, duration, mux, median_before):
""" Add a new read to the file.
:param read_number: The read number to assign to the read.
:param read_id: The unique read-id for the read.
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_file.py | Fast5File.set_summary_data | def set_summary_data(self, group_name, section_name, data):
""" Set the summary data for an analysis group.
:param group_name: The name of the analysis group.
:param section_name: The analysis step. This will become a
subfolder in the Summary section.
:param data: A dictiona... | python | def set_summary_data(self, group_name, section_name, data):
""" Set the summary data for an analysis group.
:param group_name: The name of the analysis group.
:param section_name: The analysis step. This will become a
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_file.py | Fast5File.get_analysis_config | def get_analysis_config(self, group_name):
""" Gets any config data saved for the analysis.
:param group_name: The name of the analysis group.
:returns: A dictionary of dictionaries. Each key represents
an analysis step. Each value is a dictionary containing the
analysis... | python | def get_analysis_config(self, group_name):
""" Gets any config data saved for the analysis.
:param group_name: The name of the analysis group.
:returns: A dictionary of dictionaries. Each key represents
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nanoporetech/ont_fast5_api | ont_fast5_api/fast5_file.py | Fast5File.read_summary_data | def read_summary_data(fname, component):
""" Read summary data suitable to encode as a json packet.
:param fname: The fast5 file to pull the summary data from.
:param component: The component name to pull summary data for.
:returns: A dictionary containing the summary data.
"""... | python | def read_summary_data(fname, component):
""" Read summary data suitable to encode as a json packet.
:param fname: The fast5 file to pull the summary data from.
:param component: The component name to pull summary data for.
:returns: A dictionary containing the summary data.
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mrjoes/sockjs-tornado | sockjs/tornado/transports/base.py | BaseTransportMixin.get_conn_info | def get_conn_info(self):
"""Return `ConnectionInfo` object from current transport"""
return session.ConnectionInfo(self.request.remote_ip,
self.request.cookies,
self.request.arguments,
self.... | python | def get_conn_info(self):
"""Return `ConnectionInfo` object from current transport"""
return session.ConnectionInfo(self.request.remote_ip,
self.request.cookies,
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