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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.__getSequenceVariants | def __getSequenceVariants(self, x1, polyStart, polyStop, listSequence) :
"""polyStop, is the polymorphisme at wixh number where the calcul of combinaisons stops"""
if polyStart < len(self.polymorphisms) and polyStart < polyStop:
sequence = copy.copy(listSequence)
ret = []
pk = self.polymorphisms[polyS... | python | def __getSequenceVariants(self, x1, polyStart, polyStop, listSequence) :
"""polyStop, is the polymorphisme at wixh number where the calcul of combinaisons stops"""
if polyStart < len(self.polymorphisms) and polyStart < polyStop:
sequence = copy.copy(listSequence)
ret = []
pk = self.polymorphisms[polyS... | [
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.getSequenceVariants | def getSequenceVariants(self, x1 = 0, x2 = -1, maxVariantNumber = 128) :
"""returns the sequences resulting from all combinaisons of all polymorphismes between x1 and x2. The results is a couple (bool, variants of sequence between x1 and x2), bool == true if there's more combinaisons than maxVariantNumber"""
if x2 ... | python | def getSequenceVariants(self, x1 = 0, x2 = -1, maxVariantNumber = 128) :
"""returns the sequences resulting from all combinaisons of all polymorphismes between x1 and x2. The results is a couple (bool, variants of sequence between x1 and x2), bool == true if there's more combinaisons than maxVariantNumber"""
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.getNbVariants | def getNbVariants(self, x1, x2 = -1) :
"""returns the nb of variants of sequences between x1 and x2"""
if x2 == -1 :
xx2 = len(self.defaultSequence)
else :
xx2 = x2
nbP = 1
for p in self.polymorphisms:
if x1 <= p[0] and p[0] <= xx2 :
nbP *= len(p[1])
return nbP | python | def getNbVariants(self, x1, x2 = -1) :
"""returns the nb of variants of sequences between x1 and x2"""
if x2 == -1 :
xx2 = len(self.defaultSequence)
else :
xx2 = x2
nbP = 1
for p in self.polymorphisms:
if x1 <= p[0] and p[0] <= xx2 :
nbP *= len(p[1])
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence._dichFind | def _dichFind(self, needle, currHaystack, offset, lst = None) :
"""dichotomic search, if lst is None, will return the first position found. If it's a list, will return a list of all positions in lst. returns -1 or [] if no match found"""
if len(currHaystack) == 1 :
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"""dichotomic search, if lst is None, will return the first position found. If it's a list, will return a list of all positions in lst. returns -1 or [] if no match found"""
if len(currHaystack) == 1 :
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence._kmp_construct_next | def _kmp_construct_next(self, pattern):
"""the helper function for KMP-string-searching is to construct the DFA. pattern should be an integer array. return a 2D array representing the DFA for moving the pattern."""
next = [[0 for state in pattern] for input_token in self.ALPHABETA_KMP]
... | python | def _kmp_construct_next(self, pattern):
"""the helper function for KMP-string-searching is to construct the DFA. pattern should be an integer array. return a 2D array representing the DFA for moving the pattern."""
next = [[0 for state in pattern] for input_token in self.ALPHABETA_KMP]
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence._kmp_search_first | def _kmp_search_first(self, pInput_sequence, pPattern):
"""use KMP algorithm to search the first occurrence in the input_sequence of the pattern. both arguments are integer arrays. return the position of the occurence if found; otherwise, -1."""
input_sequence, pattern = pInput_sequence,... | python | def _kmp_search_first(self, pInput_sequence, pPattern):
"""use KMP algorithm to search the first occurrence in the input_sequence of the pattern. both arguments are integer arrays. return the position of the occurence if found; otherwise, -1."""
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence._kmp_search_all | def _kmp_search_all(self, pInput_sequence, pPattern):
"""use KMP algorithm to search all occurrence in the input_sequence of the pattern. both arguments are integer arrays. return a list of the positions of the occurences if found; otherwise, []."""
r = []
input_sequence,... | python | def _kmp_search_all(self, pInput_sequence, pPattern):
"""use KMP algorithm to search all occurrence in the input_sequence of the pattern. both arguments are integer arrays. return a list of the positions of the occurences if found; otherwise, []."""
r = []
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence._kmp_find | def _kmp_find(self, needle, haystack, lst = None):
"""find with KMP-searching. needle is an integer array, reprensenting a pattern. haystack is an integer array, reprensenting the input sequence. if lst is None, return the first position found or -1 if no match found. If it's a list, will return a list of all positio... | python | def _kmp_find(self, needle, haystack, lst = None):
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.findByBiSearch | def findByBiSearch(self, strSeq) :
"""returns the first occurence of strSeq in self. Takes polymorphisms into account"""
arr = self.encode(strSeq)
return self._dichFind(arr[0], self, 0, lst = None) | python | def findByBiSearch(self, strSeq) :
"""returns the first occurence of strSeq in self. Takes polymorphisms into account"""
arr = self.encode(strSeq)
return self._dichFind(arr[0], self, 0, lst = None) | [
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.findAllByBiSearch | def findAllByBiSearch(self, strSeq) :
"""Same as find but returns a list of all occurences"""
arr = self.encode(strSeq)
lst = []
self._dichFind(arr[0], self, 0, lst)
return lst | python | def findAllByBiSearch(self, strSeq) :
"""Same as find but returns a list of all occurences"""
arr = self.encode(strSeq)
lst = []
self._dichFind(arr[0], self, 0, lst)
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.find | def find(self, strSeq) :
"""returns the first occurence of strSeq in self. Takes polymorphisms into account"""
arr = self.encode(strSeq)
return self._kmp_find(arr[0], self) | python | def find(self, strSeq) :
"""returns the first occurence of strSeq in self. Takes polymorphisms into account"""
arr = self.encode(strSeq)
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.findAll | def findAll(self, strSeq) :
"""Same as find but returns a list of all occurences"""
arr = self.encode(strSeq)
lst = []
lst = self._kmp_find(arr[0], self, lst)
return lst | python | def findAll(self, strSeq) :
"""Same as find but returns a list of all occurences"""
arr = self.encode(strSeq)
lst = []
lst = self._kmp_find(arr[0], self, lst)
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tariqdaouda/pyGeno | pyGeno/tools/BinarySequence.py | BinarySequence.decode | def decode(self, binSequence):
"""decodes a binary sequence to return a string"""
try:
binSeq = iter(binSequence[0])
except TypeError, te:
binSeq = binSequence
ret = ''
for b in binSeq :
ch = ''
for c in self.charToBin :
if b & self.forma[self.charToBin[c]] > 0 :
ch += c +'/'
if c... | python | def decode(self, binSequence):
"""decodes a binary sequence to return a string"""
try:
binSeq = iter(binSequence[0])
except TypeError, te:
binSeq = binSequence
ret = ''
for b in binSeq :
ch = ''
for c in self.charToBin :
if b & self.forma[self.charToBin[c]] > 0 :
ch += c +'/'
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tariqdaouda/pyGeno | pyGeno/tools/parsers/VCFTools.py | VCFFile.parse | def parse(self, filename, gziped = False, stream = False) :
"""opens a file"""
self.stream = stream
if gziped :
self.f = gzip.open(filename)
else :
self.f = open(filename)
self.filename = filename
self.gziped = gziped
lineId = 0
inLegend = True
while inLegend :
ll = self.f.readline()... | python | def parse(self, filename, gziped = False, stream = False) :
"""opens a file"""
self.stream = stream
if gziped :
self.f = gzip.open(filename)
else :
self.f = open(filename)
self.filename = filename
self.gziped = gziped
lineId = 0
inLegend = True
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appknox/pyaxmlparser | pyaxmlparser/stringblock.py | StringBlock._decode8 | def _decode8(self, offset):
"""
Decode an UTF-8 String at the given offset
:param offset: offset of the string inside the data
:return: str
"""
# UTF-8 Strings contain two lengths, as they might differ:
# 1) the UTF-16 length
str_len, skip = self._decode_... | python | def _decode8(self, offset):
"""
Decode an UTF-8 String at the given offset
:param offset: offset of the string inside the data
:return: str
"""
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appknox/pyaxmlparser | pyaxmlparser/stringblock.py | StringBlock._decode16 | def _decode16(self, offset):
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Decode an UTF-16 String at the given offset
:param offset: offset of the string inside the data
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appknox/pyaxmlparser | pyaxmlparser/axmlprinter.py | AXMLPrinter._fix_name | def _fix_name(self, name):
"""
Apply some fixes to element named and attribute names.
Try to get conform to:
> Like element names, attribute names are case-sensitive and must start with a letter or underscore.
> The rest of the name can contain letters, digits, hyphens, underscor... | python | def _fix_name(self, name):
"""
Apply some fixes to element named and attribute names.
Try to get conform to:
> Like element names, attribute names are case-sensitive and must start with a letter or underscore.
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appknox/pyaxmlparser | pyaxmlparser/axmlprinter.py | AXMLPrinter._fix_value | def _fix_value(self, value):
"""
Return a cleaned version of a value
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> Char ::= #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
See https://www.w3.org/TR/xml/#charsets
:param value: a value to clean
:r... | python | def _fix_value(self, value):
"""
Return a cleaned version of a value
according to the specification:
> Char ::= #x9 | #xA | #xD | [#x20-#xD7FF] | [#xE000-#xFFFD] | [#x10000-#x10FFFF]
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK._apk_analysis | def _apk_analysis(self):
"""
Run analysis on the APK file.
This method is usually called by __init__ except if skip_analysis is False.
It will then parse the AndroidManifest.xml and set all fields in the APK class which can be
extracted from the Manifest.
"""
i =... | python | def _apk_analysis(self):
"""
Run analysis on the APK file.
This method is usually called by __init__ except if skip_analysis is False.
It will then parse the AndroidManifest.xml and set all fields in the APK class which can be
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK._get_file_magic_name | def _get_file_magic_name(self, buffer):
"""
Return the filetype guessed for a buffer
:param buffer: bytes
:return: str of filetype
"""
default = "Unknown"
ftype = None
try:
# Magic is optional
import magic
except ImportErro... | python | def _get_file_magic_name(self, buffer):
"""
Return the filetype guessed for a buffer
:param buffer: bytes
:return: str of filetype
"""
default = "Unknown"
ftype = None
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK.get_files_types | def get_files_types(self):
"""
Return the files inside the APK with their associated types (by using python-magic)
:rtype: a dictionnary
"""
if self._files == {}:
# Generate File Types / CRC List
for i in self.get_files():
buffer = self.zi... | python | def get_files_types(self):
"""
Return the files inside the APK with their associated types (by using python-magic)
:rtype: a dictionnary
"""
if self._files == {}:
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK._patch_magic | def _patch_magic(self, buffer, orig):
"""
Overwrite some probably wrong detections by mime libraries
:param buffer: bytes of the file to detect
:param orig: guess by mime libary
:return: corrected guess
"""
if ("Zip" in orig) or ('(JAR)' in orig):
val... | python | def _patch_magic(self, buffer, orig):
"""
Overwrite some probably wrong detections by mime libraries
:param buffer: bytes of the file to detect
:param orig: guess by mime libary
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK.get_files_crc32 | def get_files_crc32(self):
"""
Calculates and returns a dictionary of filenames and CRC32
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"""
if self.files_crc32 == {}:
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buffer = self.zip.read(i)
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"""
Calculates and returns a dictionary of filenames and CRC32
:return: dict of filename: CRC32
"""
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK.is_multidex | def is_multidex(self):
"""
Test if the APK has multiple DEX files
:return: True if multiple dex found, otherwise False
"""
dexre = re.compile("^classes(\d+)?.dex$")
return len([instance for instance in self.get_files() if dexre.search(instance)]) > 1 | python | def is_multidex(self):
"""
Test if the APK has multiple DEX files
:return: True if multiple dex found, otherwise False
"""
dexre = re.compile("^classes(\d+)?.dex$")
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK.get_elements | def get_elements(self, tag_name, attribute, with_namespace=True):
"""
Deprecated: use `get_all_attribute_value()` instead
Return elements in xml files which match with the tag name and the specific attribute
:param tag_name: a string which specify the tag name
:param attribute: a... | python | def get_elements(self, tag_name, attribute, with_namespace=True):
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK._format_value | def _format_value(self, value):
"""
Format a value with packagename, if not already set
:param value:
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"""
if len(value) > 0:
if value[0] == ".":
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... | python | def _format_value(self, value):
"""
Format a value with packagename, if not already set
:param value:
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:Deprecated: use `get_attribute_value()` instead
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:param tag_name: specify the tag name
:type tag_name: string
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appknox/pyaxmlparser | pyaxmlparser/core.py | APK.is_tag_matched | def is_tag_matched(self, tag, **attribute_filter):
"""
Return true if the attributes matches in attribute filter
:param tag: specify the tag element
:type tag: Element
:param attribute: specify the attribute
:type attribute: string
"""
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"""
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.name | def name(self):
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeNamespace | def getAttributeNamespace(self, index):
"""
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# No Namespace
if uri == 0xFFFFFFFF:
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeName | def getAttributeName(self, index):
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Returns the String which represents the attribute name
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offset = self._get_attribute_offset(index)
name = self.m_attributes[offset + const.ATTRIBUTE_IX_NAME]
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Returns the String which represents the attribute name
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeValueType | def getAttributeValueType(self, index):
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appknox/pyaxmlparser | pyaxmlparser/axmlparser.py | AXMLParser.getAttributeValueData | def getAttributeValueData(self, index):
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appknox/pyaxmlparser | pyaxmlparser/arscutil.py | ARSCResTableConfig.get_qualifier | def get_qualifier(self):
"""
Return resource name qualifier for the current configuration.
for example
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* `hdpi-v4`
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"""
Return resource name qualifier for the current configuration.
for example
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Kyria/EsiPy | esipy/utils.py | make_cache_key | def make_cache_key(request):
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headers = frozenset(request._p['header'].items())
path = frozenset(request._p['path'].items())
query = frozenset(request._p['query'])
return (request.url, headers, path, query) | python | def make_cache_key(request):
""" Generate a cache key from request object data """
headers = frozenset(request._p['header'].items())
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query = frozenset(request._p['query'])
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Kyria/EsiPy | esipy/utils.py | check_cache | def check_cache(cache):
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Kyria/EsiPy | esipy/utils.py | get_cache_time_left | def get_cache_time_left(expires_header):
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Kyria/EsiPy | esipy/utils.py | generate_code_verifier | def generate_code_verifier(n_bytes=64):
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source: https://github.com/openstack/deb-python-oauth2client
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Kyria/EsiPy | esipy/utils.py | generate_code_challenge | def generate_code_challenge(verifier):
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source: https://github.com/openstack/deb-python-oauth2client
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Kyria/EsiPy | esipy/events.py | Signal.add_receiver | def add_receiver(self, receiver):
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Kyria/EsiPy | esipy/events.py | Signal.remove_receiver | def remove_receiver(self, receiver):
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Kyria/EsiPy | esipy/events.py | Signal.send_robust | def send_robust(self, **kwargs):
""" Trigger all receiver and pass them the parameters
If an exception is raised it will be catched and displayed as error
in the logger (if defined).
:param kwargs: all arguments from the event.
"""
for receiver in self.event_recei... | python | def send_robust(self, **kwargs):
""" Trigger all receiver and pass them the parameters
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:param kwargs: all arguments from the event.
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Kyria/EsiPy | esipy/app.py | EsiApp.__get_or_create_app | def __get_or_create_app(self, url, cache_key):
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Because app object doesn't have etag/expiry, we have to make
a head() call before, to have these informations first... """
headers = {"Accept": "application/json"}
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""" Get the app from cache or generate a new one if required
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Kyria/EsiPy | esipy/app.py | EsiApp.clear_cached_endpoints | def clear_cached_endpoints(self, prefix=None):
""" Invalidate all cached endpoints, meta included
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invalidate each of them. Doing it this way will prevent the
app not finding keys as the user may change its prefixes
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Kyria/EsiPy | esipy/security.py | EsiSecurity.__get_jwks_key | def __get_jwks_key(self, jwks_uri, **kwargs):
"""Get from jwks_ui all the JWK keys required to decode JWT Token.
Parameters
----------
jwks_uri : string
The URL where to gather JWKS key
kwargs : Dict
The constructor parameters
"""
... | python | def __get_jwks_key(self, jwks_uri, **kwargs):
"""Get from jwks_ui all the JWK keys required to decode JWT Token.
Parameters
----------
jwks_uri : string
The URL where to gather JWKS key
kwargs : Dict
The constructor parameters
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Kyria/EsiPy | esipy/security.py | EsiSecurity.__get_basic_auth_header | def __get_basic_auth_header(self):
"""Return the Basic Authorization header for oauth if secret_key exists
Returns
-------
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A dictionary that contains the Basic Authorization key/value,
or {} if secret_key is None
"""
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Returns
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A dictionary that contains the Basic Authorization key/value,
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Kyria/EsiPy | esipy/security.py | EsiSecurity.__prepare_token_request | def __prepare_token_request(self, params, url=None):
"""Generate the request parameters to execute the POST call to
get or refresh a token.
Parameters
----------
params : dictionary
Contains the parameters that will be given as data to the oauth
e... | python | def __prepare_token_request(self, params, url=None):
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Kyria/EsiPy | esipy/security.py | EsiSecurity.get_auth_uri | def get_auth_uri(self, state, scopes=None, implicit=False):
"""Constructs the full auth uri and returns it..
Parameters
----------
state : string
The state to pass through the auth process
scopes : list (optional)
The list of scope to have
... | python | def get_auth_uri(self, state, scopes=None, implicit=False):
"""Constructs the full auth uri and returns it..
Parameters
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state : string
The state to pass through the auth process
scopes : list (optional)
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Kyria/EsiPy | esipy/security.py | EsiSecurity.get_refresh_token_params | def get_refresh_token_params(self, scope_list=None):
""" Return the param object for the post() call to get the access_token
from the refresh_token
:param code: the refresh token
:return: a dict with the url, params and header
"""
if self.refresh_token is None:
... | python | def get_refresh_token_params(self, scope_list=None):
""" Return the param object for the post() call to get the access_token
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:param code: the refresh token
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Kyria/EsiPy | esipy/security.py | EsiSecurity.update_token | def update_token(self, response_json, **kwargs):
""" Update access_token, refresh_token and token_expiry from the
response body.
The response must be converted to a json object before being passed as
a parameter
:param response_json: the response body to use.
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""" Update access_token, refresh_token and token_expiry from the
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Kyria/EsiPy | esipy/security.py | EsiSecurity.is_token_expired | def is_token_expired(self, offset=0):
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- positive value decrease the time (sooner)
- negative value increase the time (later)
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Kyria/EsiPy | esipy/security.py | EsiSecurity.refresh | def refresh(self, scope_list=None):
""" Update the auth data (tokens) using the refresh token in auth.
"""
request_data = self.get_refresh_token_params(scope_list)
res = self._session.post(**request_data)
if res.status_code != 200:
raise APIException(
... | python | def refresh(self, scope_list=None):
""" Update the auth data (tokens) using the refresh token in auth.
"""
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res = self._session.post(**request_data)
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Kyria/EsiPy | esipy/security.py | EsiSecurity.auth | def auth(self, code):
""" Request the token to the /oauth/token endpoint.
Update the security tokens.
:param code: the code you get from the auth process
"""
request_data = self.get_access_token_params(code)
res = self._session.post(**request_data)
if r... | python | def auth(self, code):
""" Request the token to the /oauth/token endpoint.
Update the security tokens.
:param code: the code you get from the auth process
"""
request_data = self.get_access_token_params(code)
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Kyria/EsiPy | esipy/security.py | EsiSecurity.revoke | def revoke(self):
"""Revoke the current tokens then empty all stored tokens
This returns nothing since the endpoint return HTTP/200
whatever the result is...
Currently not working with JWT, left here for compatibility.
"""
if not self.refresh_token and not self.ac... | python | def revoke(self):
"""Revoke the current tokens then empty all stored tokens
This returns nothing since the endpoint return HTTP/200
whatever the result is...
Currently not working with JWT, left here for compatibility.
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Kyria/EsiPy | esipy/security.py | EsiSecurity.verify | def verify(self, kid='JWT-Signature-Key', options=None):
"""Decode and verify the token and return the decoded informations
Parameters
----------
kid : string
The JWKS key id to identify the key to decode the token.
Default is 'JWT-Signature-Key'. Only cha... | python | def verify(self, kid='JWT-Signature-Key', options=None):
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kid : string
The JWKS key id to identify the key to decode the token.
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Kyria/EsiPy | esipy/client.py | EsiClient._retry_request | def _retry_request(self, req_and_resp, _retry=0, **kwargs):
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Kyria/EsiPy | esipy/client.py | EsiClient.multi_request | def multi_request(self, reqs_and_resps, threads=20, **kwargs):
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Kyria/EsiPy | esipy/client.py | EsiClient.head | def head(self, req_and_resp, **kwargs):
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Kyria/EsiPy | esipy/client.py | EsiClient.__cache_response | def __cache_response(self, cache_key, res, method):
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"""
if ('expires' in res.headers
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Kyria/EsiPy | esipy/client.py | EsiClient.__make_request | def __make_request(self, request, opt, cache_key=None, method=None):
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Kyria/EsiPy | esipy/cache.py | _hash | def _hash(data):
""" generate a hash from data object to be used as cache key """
hash_algo = hashlib.new('md5')
hash_algo.update(pickle.dumps(data))
# prefix allows possibility of multiple applications
# sharing same keyspace
return 'esi_' + hash_algo.hexdigest() | python | def _hash(data):
""" generate a hash from data object to be used as cache key """
hash_algo = hashlib.new('md5')
hash_algo.update(pickle.dumps(data))
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mjirik/imcut | imcut/models.py | Model3D.fit_from_image | def fit_from_image(self, data, voxelsize, seeds, unique_cls):
"""
This Method allows computes feature vector and train model.
:cls: list of index number of requested classes in seeds
"""
fvs, clsselected = self.features_from_image(data, voxelsize, seeds, unique_cls)
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"""
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"""
fvs, clsselected = self.features_from_image(data, voxelsize, seeds, unique_cls)
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mjirik/imcut | imcut/models.py | Model3D.save | def save(self, filename):
"""
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"""
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"""
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mjirik/imcut | imcut/models.py | Model3D.load | def load(self, mdl_file):
"""
load model from file. fv_type is not set with this function. It is expected to set it before.
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mdl_file_e = op.expanduser(mdl_file)
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# sel... | python | def load(self, mdl_file):
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"""
import dill as pickle
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mjirik/imcut | imcut/models.py | Model.features_from_image | def features_from_image(
self, data, voxelsize, seeds=None, unique_cls=None
): # , voxels=None):
"""
Input data is 3d image
:param data: is 3d image
:param seeds: ndimage with same shape as data, nonzero values means seeds.
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self, data, voxelsize, seeds=None, unique_cls=None
): # , voxels=None):
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mjirik/imcut | imcut/models.py | Model._fit_one_class | def _fit_one_class(self, clx, cl):
""" Train clas number cl with data clx.
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as an input.
clx: data, 2d matrix
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mjirik/imcut | imcut/models.py | Model.likelihood | def likelihood(self, x, cl):
"""
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# we have data 2x3 with fature vector with 4 fatures
Use likelihoodFromImage() function for 3d image input
m.likelihood(X,0)
"""
# sha = x.shape
# xr = x.reshape(-1, sha[-1])
# out... | python | def likelihood(self, x, cl):
"""
X = numpy.random.random([2,3,4])
# we have data 2x3 with fature vector with 4 fatures
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m.likelihood(X,0)
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mjirik/imcut | imcut/pycut.py | inspect_node_neighborhood | def inspect_node_neighborhood(nlinks, msinds, node_msindex):
"""
Get information about one node in graph
:param nlinks: neighboorhood edges
:param msinds: indexes in 3d image
:param node_msindex: int, multiscale index of selected voxel
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"""
Get information about one node in graph
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:param nlinks: neighboorhood edges
:param msinds: indexes in 3d image
:param node_msindex: int, multiscale index of selected voxel
:return: node_neighboor_edges_and_weights, node_neighboor_seeds | [
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mjirik/imcut | imcut/pycut.py | inspect_node | def inspect_node(nlinks, unariesalt, msinds, node_msindex):
"""
Get information about one node in graph
:param nlinks: neighboorhood edges
:param unariesalt: weights
:param msinds: indexes in 3d image
:param node_msindex: msindex of selected node. See get_node_msindex()
:return: node_unarie... | python | def inspect_node(nlinks, unariesalt, msinds, node_msindex):
"""
Get information about one node in graph
:param nlinks: neighboorhood edges
:param unariesalt: weights
:param msinds: indexes in 3d image
:param node_msindex: msindex of selected node. See get_node_msindex()
:return: node_unarie... | [
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mjirik/imcut | imcut/pycut.py | get_node_msindex | def get_node_msindex(msinds, node_seed):
"""
Convert seeds-like selection of voxel to multiscale index.
:param msinds: ndarray with indexes
:param node_seed: ndarray with 1 where selected pixel is, or list of indexes in this array
:return: multiscale index of first found seed
"""
if type(nod... | python | def get_node_msindex(msinds, node_seed):
"""
Convert seeds-like selection of voxel to multiscale index.
:param msinds: ndarray with indexes
:param node_seed: ndarray with 1 where selected pixel is, or list of indexes in this array
:return: multiscale index of first found seed
"""
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mjirik/imcut | imcut/pycut.py | relabel_squeeze | def relabel_squeeze(data):
""" Makes relabeling of data if there are unused values. """
palette, index = np.unique(data, return_inverse=True)
data = index.reshape(data.shape)
# realy slow solution
# unq = np.unique(data)
# actual_label = 0
# for lab in unq:
# ... | python | def relabel_squeeze(data):
""" Makes relabeling of data if there are unused values. """
palette, index = np.unique(data, return_inverse=True)
data = index.reshape(data.shape)
# realy slow solution
# unq = np.unique(data)
# actual_label = 0
# for lab in unq:
# ... | [
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mjirik/imcut | imcut/pycut.py | ImageGraphCut.load | def load(self, filename, fv_extern=None):
"""
Read model stored in the file.
:param filename: Path to file with model
:param fv_extern: external feature vector function is passed here
:return:
"""
self.modelparams["mdl_stored_file"] = filename
if fv_exter... | python | def load(self, filename, fv_extern=None):
"""
Read model stored in the file.
:param filename: Path to file with model
:param fv_extern: external feature vector function is passed here
:return:
"""
self.modelparams["mdl_stored_file"] = filename
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mjirik/imcut | imcut/pycut.py | ImageGraphCut.__ms_npenalty_fcn | def __ms_npenalty_fcn(self, axis, mask, orig_shape):
"""
:param axis: direction of edge
:param mask: 3d ndarray with ones where is fine resolution
Neighboorhood penalty between small pixels should be smaller then in
bigger tiles. This is the way how to set it.
"""
... | python | def __ms_npenalty_fcn(self, axis, mask, orig_shape):
"""
:param axis: direction of edge
:param mask: 3d ndarray with ones where is fine resolution
Neighboorhood penalty between small pixels should be smaller then in
bigger tiles. This is the way how to set it.
"""
... | [
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mjirik/imcut | imcut/pycut.py | ImageGraphCut.__msgc_step12_low_resolution_segmentation | def __msgc_step12_low_resolution_segmentation(self):
"""
Get the segmentation and the
:return:
"""
import scipy
start = self._start_time
# ===== low resolution data processing
# default parameters
# TODO segparams_lo and segparams_hi je tam asi zb... | python | def __msgc_step12_low_resolution_segmentation(self):
"""
Get the segmentation and the
:return:
"""
import scipy
start = self._start_time
# ===== low resolution data processing
# default parameters
# TODO segparams_lo and segparams_hi je tam asi zb... | [
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