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def _findSubsetProteins(proteins, protToPeps, pepToProts):
"""Find proteins which peptides are a sub-set, but not a same-set to other proteins. :param proteins: ... |
proteinsEqual = lambda prot1, prot2: protToPeps[prot1] == protToPeps[prot2]
subGroups = list()
for protein in proteins:
peptideCounts = Counter()
for peptide in protToPeps[protein]:
proteins = pepToProts[peptide]
peptideCounts.update(proteins)
peptideCount =... |
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def _findRedundantProteins(protToPeps, pepToProts, proteins=None):
"""Returns a set of proteins with redundant peptide evidence. After removing the redundant pro... |
if proteins is None:
proteins = viewkeys(protToPeps)
pepFrequency = _getValueCounts(pepToProts)
protPepCounts = _getValueCounts(protToPeps)
getCount = operator.itemgetter(1)
getProt = operator.itemgetter(0)
#TODO: quick and dirty solution
#NOTE: add a test for merged proteins
... |
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def _mergeProteinEntries(proteinLists, protToPeps):
"""Returns a new "protToPeps" dictionary with entries merged that are present in proteinLists. NOTE: The key ... |
mergedProtToPeps = dict(protToPeps)
for proteins in proteinLists:
for protein in proteins:
peptides = mergedProtToPeps.pop(protein)
mergedProtein = tuple(sorted(proteins))
mergedProtToPeps[mergedProtein] = peptides
return mergedProtToPeps |
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def _reducedProtToPeps(protToPeps, proteins):
"""Returns a new, reduced "protToPeps" dictionary that does not contain entries present in "proteins". :param protT... |
return {k: v for k, v in viewitems(protToPeps) if k not in proteins} |
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def _findUniqueMappingKeys(mapping):
"""Find mapping keys that only have one entry (value length of 1. :param mapping: dict, for each key contains a set of entri... |
uniqueMappingKeys = set()
for key, entries in viewitems(mapping):
if len(entries) == 1:
uniqueMappingKeys.add(key)
return uniqueMappingKeys |
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def _invertMapping(mapping):
"""Converts a protein to peptide or peptide to protein mapping. :param mapping: dict, for each key contains a set of entries :return... |
invertedMapping = ddict(set)
for key, values in viewitems(mapping):
for value in values:
invertedMapping[value].add(key)
return invertedMapping |
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def _mappingGetValueSet(mapping, keys):
"""Return a combined set of values from the mapping. :param mapping: dict, for each key contains a set of entries returns... |
setUnion = set()
for k in keys:
setUnion = setUnion.union(mapping[k])
return setUnion |
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def _flattenMergedProteins(proteins):
"""Return a set where merged protein entries in proteins are flattened. :param proteins: an iterable of proteins, can conta... |
proteinSet = set()
for protein in proteins:
if isinstance(protein, tuple):
proteinSet.update(protein)
else:
proteinSet.add(protein)
return proteinSet |
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def getGroups(self, proteinId):
"""Return a list of protein groups a protein is associated with.""" |
return [self.groups[gId] for gId in self._proteinToGroupIds[proteinId]] |
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def addProteinGroup(self, groupRepresentative):
"""Adds a new protein group and returns the groupId. The groupId is defined using an internal counter, which is i... |
groupId = self._getNextGroupId()
self.groups[groupId] = ProteinGroup(groupId, groupRepresentative)
self.addLeadingToGroups(groupRepresentative, groupId)
return groupId |
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def addLeadingToGroups(self, proteinIds, groupIds):
"""Add one or multiple leading proteins to one or multiple protein groups. :param proteinIds: a proteinId or ... |
for groupId in AUX.toList(groupIds):
self.groups[groupId].addLeadingProteins(proteinIds)
self._addProteinIdsToGroupMapping(proteinIds, groupId) |
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def addSubsetToGroups(self, proteinIds, groupIds):
"""Add one or multiple subset proteins to one or multiple protein groups. :param proteinIds: a proteinId or a ... |
for groupId in AUX.toList(groupIds):
self.groups[groupId].addSubsetProteins(proteinIds)
self._addProteinIdsToGroupMapping(proteinIds, groupId) |
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def addSubsumableToGroups(self, proteinIds, groupIds):
"""Add one or multiple subsumable proteins to one or multiple protein groups. :param proteinIds: a protein... |
for groupId in AUX.toList(groupIds):
self.groups[groupId].addSubsumableProteins(proteinIds)
self._addProteinIdsToGroupMapping(proteinIds, groupId) |
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def _addProteinIdsToGroupMapping(self, proteinIds, groupId):
"""Add a groupId to one or multiple entries of the internal proteinToGroupId mapping. :param protein... |
for proteinId in AUX.toList(proteinIds):
self._proteinToGroupIds[proteinId].add(groupId) |
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def _addProteins(self, proteinIds, containerNames):
"""Add one or multiple proteinIds to the respective container. :param proteinIds: a proteinId or a list of pr... |
proteinIds = AUX.toList(proteinIds)
for containerName in containerNames:
proteinContainer = getattr(self, containerName)
proteinContainer.update(proteinIds) |
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def satisfies(self, other):
"""Check if the capabilities of a primitive are enough to satisfy a requirement. Should be called on a Requirement that is acting as ... |
if other.isnocare:
return True
if self.isnocare:
return False
if self.arbitrary:
return True
if self.constant and not other.arbitrary:
return True
if self.value is other.value and not other.arbitrary\
and not other.const... |
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def _list(self, foldername="INBOX", reverse=False, since=None):
"""Do structured list output. Sorts the list by date, possibly reversed, filtered from 'since'. T... |
folder = self.folder \
if foldername == "INBOX" \
else self._getfolder(foldername)
def sortcmp(d):
try:
return d[1].date
except:
return -1
lst = folder.items() if not since else folder.items_since(since)
s... |
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def ls(self, foldername="INBOX", reverse=False, since=None, grep=None, field=None, stream=sys.stdout):
"""Do standard text list of the folder to the stream. 'fol... |
if foldername == "":
foldername = "INBOX"
msg_list = self._list(foldername, reverse, since)
for folder, mk, m in msg_list:
try:
# I am very unsure about this defaulting of foldername
output_items = (
"%s%s%s" % (folder... |
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def lisp(self, foldername="INBOX", reverse=False, since=None, stream=sys.stdout):
"""Do JSON list of the folder to the stream. 'since' allows the listing to be d... |
def fromval(hdr):
if hdr:
return parseaddr(hdr)
for folder, mk, m in self._list(foldername, reverse, since):
try:
print(json.dumps({
'folder': folder.folder or foldername or "INBOX",
'key': "%s%s%s"... |
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def lsfolders(self, stream=sys.stdout):
"""List the subfolders""" |
for f in self.folder.folders():
print(f.folder.strip("."), file=stream) |
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def _get(self, msgid):
"""Yields the message header against each part from the message.""" |
foldername, msgkey = msgid.split(SEPERATOR)
folder = self.folder if foldername == "INBOX" else self._getfolder(foldername)
# Now look up the message
msg = folder[msgkey]
msg.is_seen = True
hdr = list(msg.items())
for p in msg.walk():
yield hdr,p
... |
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def gettext(self, msgid, stream=sys.stdout, splitter="--text follows this line--\n"):
"""Get the first text part we can find and print it as a message. This is a... |
for hdr,part in self._get(msgid):
if part.get_content_type() == "text/plain":
for name,val in hdr:
# Use the subtype, since we're printing just that - tidy it up first
if name.lower() == "content-type":
val = part["cont... |
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def getrawpart(self, msgid, stream=sys.stdout):
"""Get the first part from the message and print it raw. """ |
for hdr, part in self._get(msgid):
pl = part.get_payload(decode=True)
if pl != None:
print(pl, file=stream)
break |
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def getrawpartid(self, msgid, partid, stream=sys.stdout):
"""Get a specific part from the message and print it raw. """ |
parts = [part for hdr,part in self._get(msgid)]
part = parts[int(partid)]
pl = part.get_payload(decode=True)
if pl != None:
print(pl, file=stream) |
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def getraw(self, msgid, stream=sys.stdout):
"""Get the whole message and print it. """ |
foldername, msgkey = msgid.split(SEPERATOR)
folder = self.folder if foldername == "INBOX" else self._getfolder(foldername)
msg = folder[msgkey]
print(msg.content) |
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def getstruct(self, msgid, as_json=False, stream=sys.stdout):
"""Get and print the whole message. as_json indicates whether to print the part list as JSON or not... |
parts = [part.get_content_type() for hdr, part in self._get(msgid)]
if as_json:
print(json.dumps(parts), file=stream)
else:
for c in parts:
print(c, file=stream) |
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def _extract_alphabet(self, grammar):
""" Extract an alphabet from the given grammar. """ |
alphabet = set([])
for terminal in grammar.Terminals:
alphabet |= set([x for x in terminal])
self.alphabet = list(alphabet) |
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def action(self, column=None, value=None, **kwargs):
""" The underlying GICS table provides codes and descriptions identifying the current status or disposition ... |
return self._resolve_call('GIC_ACTION', column, value, **kwargs) |
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def applicant(self, column=None, value=None, **kwargs):
""" Find the applicant information for a grant. """ |
return self._resolve_call('GIC_APPLICANT', column, value, **kwargs) |
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def authority(self, column=None, value=None, **kwargs):
"""Provides codes and associated authorizing statutes.""" |
return self._resolve_call('GIC_AUTHORITY', column, value, **kwargs) |
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def construction(self, column=None, value=None, **kwargs):
""" Identifies monetary, descriptive, and milestone information for Wastewater Treatment construction ... |
return self._resolve_call('GIC_CONSTRUCTION', column, value, **kwargs) |
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def eligible_cost(self, column=None, value=None, **kwargs):
""" The assistance dollar amounts by eligible cost category. """ |
return self._resolve_call('GIC_ELIGIBLE_COST', column, value, **kwargs) |
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def grant(self, column=None, value=None, **kwargs):
""" Provides various award, project, and grant personnel information. """ |
return self._resolve_call('GIC_GRANT', column, value, **kwargs) |
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def grant_assistance(self, column=None, value=None, **kwargs):
"""Many-to-many table connecting grants and assistance.""" |
return self._resolve_call('GIC_GRANT_ASST_PGM', column, value, **kwargs) |
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def grant_authority(self, column=None, value=None, **kwargs):
"""Many-to-many table connecting grants and authority.""" |
return self._resolve_call('GIC_GRANT_AUTH', column, value, **kwargs) |
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def lab_office(self, column=None, value=None, **kwargs):
"""Abbreviations, names, and locations of labratories and offices.""" |
return self._resolve_call('GIC_LAB_OFFICE', column, value, **kwargs) |
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def milestone(self, column=None, value=None, **kwargs):
""" Status codes and related dates of certain grants, """ |
return self._resolve_call('GIC_MILESTONE', column, value, **kwargs) |
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def record_type(self, column=None, value=None, **kwargs):
""" Codes and descriptions indicating whether an award is for a new project or for the continuation of ... |
return self._resolve_call('GIC_RECORD_TYPE', column, value, **kwargs) |
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def srf_cap(self, column=None, value=None, **kwargs):
""" Fiscal dollar amounts for State Revolving Fund Capitalization Grants. """ |
return self._resolve_call('GIC_SRF_CAP', column, value, **kwargs) |
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def status(self, column=None, value=None, **kwargs):
""" Provides codes and descriptions of project milestones. """ |
return self._resolve_call('GIC_STATUS', column, value, **kwargs) |
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def recRemoveTreeFormating(element):
"""Removes whitespace characters, which are leftovers from previous xml formatting. :param element: an instance of lxml.etre... |
children = element.getchildren()
if len(children) > 0:
for child in children:
recRemoveTreeFormating(child)
if element.text is not None:
if len(element.text.strip()) == 0:
element.text = None
else:
element.text = element.text.strip()
if elemen... |
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def recCopyElement(oldelement):
"""Generates a copy of an xml element and recursively of all child elements. :param oldelement: an instance of lxml.etree._Elemen... |
newelement = ETREE.Element(oldelement.tag, oldelement.attrib)
if len(oldelement.getchildren()) > 0:
for childelement in oldelement.getchildren():
newelement.append(recCopyElement(childelement))
return newelement |
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def getParam(xmlelement):
"""Converts an mzML xml element to a param tuple. :param xmlelement: #TODO docstring :returns: a param tuple or False if the xmlelement... |
elementTag = clearTag(xmlelement.tag)
if elementTag in ['userParam', 'cvParam', 'referenceableParamGroupRef']:
if elementTag == 'cvParam':
param = cvParamFromDict(xmlelement.attrib)
elif elementTag == 'userParam':
param = userParamFromDict(xmlelement.attrib)
else... |
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def xmlAddParams(parentelement, params):
"""Generates new mzML parameter xml elements and adds them to the 'parentelement' as xml children elements. :param paren... |
if not params:
return None
for param in params:
if len(param) == 3:
cvAttrib = {'cvRef': param[0].split(':')[0], 'accession': param[0],
'name':oboTranslator.getNameWithId(param[0])
}
if param[1]:
cvAttrib.up... |
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def interpretBitEncoding(bitEncoding):
"""Returns a floattype string and a numpy array type. :param bitEncoding: Must be either '64' or '32' :returns: (floattype... |
if bitEncoding == '64':
floattype = 'd' # 64-bit
numpyType = numpy.float64
elif bitEncoding == '32':
floattype = 'f' # 32-bit
numpyType = numpy.float32
else:
errorText = ''.join(['bitEncoding \'', bitEncoding, '\' not defined. ',
'Must be... |
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def calc_partition_function(mass, omega_array, temperature_array):
""" Calculates the partition function of your system at each point in time. Parameters mass : ... |
Kappa_t= mass*omega_array**2
return _np.sqrt(4*_np.pi**2*_scipy.constants.Boltzmann**2*temperature_array**2/(mass*Kappa_t)) |
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def calc_mean_and_variance_of_variances(self, NumberOfOscillations):
""" Calculates the mean and variance of a set of varainces. This set is obtained by splittin... |
SplittedArraySize = int(self.SampleFreq/self.FTrap.n) * NumberOfOscillations
VoltageArraySize = len(self.voltage)
SnippetsVariances = _np.var(self.voltage[:VoltageArraySize-_np.mod(VoltageArraySize,SplittedArraySize)].reshape(-1,SplittedArraySize),axis=1)
return _np.mean(SnippetsVarian... |
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def register_template_directory(kb_app: kb, sphinx_app: Sphinx, sphinx_env: BuildEnvironment, docnames=List[str], ):
""" Add this resource's templates dir to tem... |
template_bridge = sphinx_app.builder.templates
actions = ResourceAction.get_callbacks(kb_app)
for action in actions:
f = os.path.dirname(inspect.getfile(action))
template_bridge.loaders.append(SphinxFileSystemLoader(f)) |
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def add_directives(kb_app: kb, sphinx_app: Sphinx, sphinx_env: BuildEnvironment, docnames=List[str], ):
""" For each resource type, register a new Sphinx directi... |
for k, v in list(kb_app.config.resources.items()):
sphinx_app.add_directive(k, ResourceDirective) |
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def stamp_title(kb_app: kb, sphinx_app: Sphinx, doctree: doctree):
""" Walk the tree and extra RST title into resource.title """ |
# First, find out which resource this is. Won't be easy.
resources = sphinx_app.env.resources
confdir = sphinx_app.confdir
source = PurePath(doctree.attributes['source'])
# Get the relative path inside the docs dir, without .rst, then
# get the resource
docname = str(source.relative_to(co... |
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def handle_exception(error):
"""Simple method for handling exceptions raised by `PyBankID`. :param flask_pybankid.FlaskPyBankIDError error: The exception to hand... |
response = jsonify(error.to_dict())
response.status_code = error.status_code
return response |
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def create_from_pybankid_exception(cls, exception):
"""Class method for initiating from a `PyBankID` exception. :param bankid.exceptions.BankIDError exception: :... |
return cls(
"{0}: {1}".format(exception.__class__.__name__, str(exception)),
_exception_class_to_status_code.get(exception.__class__),
) |
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def to_dict(self):
"""Create a dict representation of this exception. :return: The dictionary representation. :rtype: dict """ |
rv = dict(self.payload or ())
rv["message"] = self.message
return rv |
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def integers(num, minimum, maximum, base=10):
# TODO: Ensure numbers within bounds """Random integers within specified interval. The integer generator generates ... |
function = 'integers'
num, minimum, maximum = list(map(int, [num, minimum, maximum]))
# INPUT ERROR CHECKING
# Check input values are within range
if (1 <= num <= 10 ** 4) is False:
print('ERROR: %s is out of range' % num)
return
if (-10 ** 9 <= minimum <= 10 ** 9) is False:
... |
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def sequence(minimum, maximum):
"""Randomize a sequence of integers.""" |
function = 'sequences'
opts = {'min': minimum,
'max': maximum,
'col': 1,
'format': 'plain',
'rnd': 'new'}
deal = get_http(RANDOM_URL, function, opts)
deal_arr = str_to_arr(deal)
return deal_arr |
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def string(num, length, digits=False, upper=True, lower=True, unique=False):
"""Random strings.""" |
function = 'strings'
# Convert arguments to random.org style
# for a discussion on the method see: http://bit.ly/TKGkOF
digits = convert(digits)
upper = convert(upper)
lower = convert(lower)
unique = convert(unique)
opts = {'num': num,
'len': length,
'digits': d... |
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def quota(ip=None):
"""Check your quota.""" |
# TODO: Add arbitrary user defined IP check
url = 'http://www.random.org/quota/?format=plain'
data = urlopen(url)
credit = int(data.read().strip())
if data.code == 200:
return credit
else:
return "ERROR: Server responded with code %s" % data.code |
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def get_http(base_url, function, opts):
"""HTTP request generator.""" |
url = (os.path.join(base_url, function) + '/?' + urlencode(opts))
data = urlopen(url)
if data.code != 200:
raise ValueError("Random.rg returned server code: " + str(data.code))
return data.read() |
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def read(*p):
"""Build a file path from paths and return the contents.""" |
with open(os.path.join(*p), 'r') as fi:
return fi.read() |
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def execute(self, processProtocol, command, env={}, path=None, uid=None, gid=None, usePTY=0, childFDs=None):
"""Form a command and start a process in the desired... |
raise NotImplementedError() |
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def run(self, command, env={}, path=None, uid=None, gid=None, usePTY=0, childFDs=None):
"""Execute a command and return the results of the completed run. """ |
deferred = defer.Deferred()
processProtocol = _SummaryProcessProtocol(deferred)
d = defer.maybeDeferred(self.execute, processProtocol, command, env,
path, uid, gid, usePTY, childFDs)
d.addErrback(deferred.errback)
return deferred |
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def getOutput(self, command, env={}, path=None, uid=None, gid=None, usePTY=0, childFDs=None):
"""Execute a command and get the output of the finished process. ""... |
deferred = defer.Deferred()
processProtocol = _SummaryProcessProtocol(deferred)
self.execute(processProtocol, command, env,
path, uid, gid, usePTY, childFDs)
@deferred.addCallback
def getStdOut(tuple_):
stdout, _stderr, _returnCode = tuple_
... |
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def getExitCode(self, command, env={}, path=None, uid=None, gid=None, usePTY=0, childFDs=None):
"""Execute a command and get the return code of the finished proc... |
deferred = defer.Deferred()
processProtocol = _SummaryProcessProtocol(deferred)
self.execute(processProtocol, command, env, path, uid, gid,
usePTY, childFDs)
@deferred.addCallback
def getStdOut(tuple_):
_stdout, _stderr, exitCode = tuple_
... |
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def validate_task(original_task):
""" Validates task and adds default values for missing options using the following steps. 1. If there is no input list specifie... |
task = original_task._asdict()
# Default values for inputs and outputs
if 'inputs' not in task or task['inputs'] is None:
task['inputs'] = ['*']
# Outputs list cannot be empty
if ('outputs' not in task or
task['outputs'] is None or
len(task['outputs']) == 0):
t... |
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def run_task(task, workspace):
""" Runs the task and updates the workspace with results. Parameters task - dict Task Description Examples: {'task': task_func, 'i... |
data = copy.copy(workspace)
task = validate_task(task)
# Prepare input to task
inputs = [input_parser(key, data) for key in task.inputs]
if inspect.isgeneratorfunction(task.fn):
# Multiple output task
# Assuming number of outputs are equal to number of return values
data.... |
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def run_hook(name, workspace, hooks):
"""Runs all hooks added under the give name. Parameters name - str Name of the hook to invoke workspace - dict Workspace th... |
data = copy.copy(workspace)
for hook_listener in hooks.get(name, []):
# Hook functions may mutate the data and returns nothing
hook_listener(data)
return data |
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def add_task(self, fn, inputs=None, outputs=None):
""" Adds a task to the workflow. Returns self to facilitate chaining method calls """ |
# self.tasks.append({'task': task, 'inputs': inputs, 'outputs': outputs})
self.tasks.append(Task(fn, inputs, outputs))
return self |
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def add_hook(self, name, function):
""" Adds a function to be called for hook of a given name. The function gets entire workspace as input and does not return an... |
if not callable(function):
return ValueError('Hook function should be callable')
if name not in self.hooks:
self.hooks[name] = []
self.hooks[name].append(function)
return self |
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def dns(self):
"""DNS details.""" |
dns = {
'elb': self.dns_elb(),
'elb_region': self.dns_elb_region(),
'global': self.dns_global(),
'region': self.dns_region(),
'instance': self.dns_instance(),
}
return dns |
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def s3_app_bucket(self, include_region=False):
"""Generate s3 application bucket name. Args: include_region (bool):
Include region in the name generation. """ |
if include_region:
s3_app_bucket = self.format['s3_app_region_bucket'].format(**self.data)
else:
s3_app_bucket = self.format['s3_app_bucket'].format(**self.data)
return s3_app_bucket |
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def shared_s3_app_bucket(self, include_region=False):
"""Generate shared s3 application bucket name. Args: include_region (bool):
Include region in the name gen... |
if include_region:
shared_s3_app_bucket = self.format['shared_s3_app_region_bucket'].format(**self.data)
else:
shared_s3_app_bucket = self.format['shared_s3_app_bucket'].format(**self.data)
return shared_s3_app_bucket |
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def iam(self):
"""Generate iam details.""" |
iam = {
'group': self.format['iam_group'].format(**self.data),
'lambda_role': self.format['iam_lambda_role'].format(**self.data),
'policy': self.format['iam_policy'].format(**self.data),
'profile': self.format['iam_profile'].format(**self.data),
'role... |
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def archaius(self):
"""Generate archaius bucket path.""" |
bucket = self.format['s3_bucket'].format(**self.data)
path = self.format['s3_bucket_path'].format(**self.data)
archaius_name = self.format['s3_archaius_name'].format(**self.data)
archaius = {'s3': archaius_name, 'bucket': bucket, 'path': path}
return archaius |
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def jenkins(self):
"""Generate jenkins job details.""" |
job_name = self.format['jenkins_job_name'].format(**self.data)
job = {'name': job_name}
return job |
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def gitlab(self):
"""Generate gitlab details.""" |
main_name = self.format['git_repo'].format(**self.data)
qe_name = self.format['git_repo_qe'].format(**self.data)
config_name = self.format['git_repo_configs'].format(**self.data)
git = {
'config': config_name,
'main': main_name,
'qe': qe_name,
... |
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def get_value_matched_by_regex(field_name, regex_matches, string):
"""Ensure value stored in regex group exists.""" |
try:
value = regex_matches.group(field_name)
if value is not None:
return value
except IndexError:
pass
raise MissingFieldError(string, field_name) |
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def positive_int(val):
"""Parse `val` into a positive integer.""" |
if isinstance(val, float):
raise ValueError('"{}" must not be a float'.format(val))
val = int(val)
if val >= 0:
return val
raise ValueError('"{}" must be positive'.format(val)) |
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def strictly_positive_int_or_none(val):
"""Parse `val` into either `None` or a strictly positive integer.""" |
val = positive_int_or_none(val)
if val is None or val > 0:
return val
raise ValueError('"{}" must be strictly positive'.format(val)) |
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def _attributeLinesToDict(attributeLines):
"""Converts a list of obo 'Term' lines to a dictionary. :param attributeLines: a list of obo 'Term' lines. Each line c... |
attributes = dict()
for line in attributeLines:
attributeId, attributeValue = line.split(':', 1)
attributes[attributeId.strip()] = attributeValue.strip()
return attributes |
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def _termIsObsolete(oboTerm):
"""Determine wheter an obo 'Term' entry is marked as obsolete. :param oboTerm: a dictionary as return by :func:`maspy.ontology._att... |
isObsolete = False
if u'is_obsolete' in oboTerm:
if oboTerm[u'is_obsolete'].lower() == u'true':
isObsolete = True
return isObsolete |
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def discover_handler_classes(handlers_package):
""" Looks for handler classes within handler path module. Currently it's not looking deep into nested module. :pa... |
if handlers_package is None:
return
# Add working directory into PYTHONPATH to import developer packages
sys.path.insert(0, os.getcwd())
package = import_module(handlers_package)
# Continue searching for module if package is not a module
if hasattr(package, '__path__'):
for _... |
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def get_multi_word_keywords(features):
"""This returns an OrderedDict containing the multi word keywords in order of length. This is so the tokenizer will match ... |
keys = {
'is not': Token(TokenTypes.NOT_EQUAL, 'is not'),
}
return OrderedDict(sorted(list(keys.items()), key=lambda t: len(t[0]), reverse=True)) |
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def inside_try(func, options={}):
""" decorator to silence exceptions, for logging we want a "safe" fail of the functions """ |
if six.PY2:
name = func.func_name
else:
name = func.__name__
@wraps(func)
def silenceit(*args, **kwargs):
""" the function func to be silenced is wrapped inside a
try catch and returned, exceptions are logged
exceptions are returned in an error dict
take... |
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def start(self):
""" Start the server and run forever. """ |
Server().start(self.options,self.handler_function, self.__class__.component_type) |
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def sort_entries(self):
"""Get whether reverse is True or False. Return the sorted data.""" |
return sorted(self.data, key=self.sort_func, reverse=self.get_reverse()) |
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def visible_fields(self):
""" Returns the reduced set of visible fields to output from the form. This method respects the provided ``fields`` configuration _and_... |
form_visible_fields = self.form.visible_fields()
if self.render_fields:
fields = self.render_fields
else:
fields = [field.name for field in form_visible_fields]
filtered_fields = [field for field in fields if field not in self.exclude_fields]
return [f... |
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def get_fieldsets(self, fieldsets=None):
""" This method returns a generator which yields fieldset instances. The method uses the optional fieldsets argument to ... |
fieldsets = fieldsets or self.fieldsets
if not fieldsets:
raise StopIteration
# Search for primary marker in at least one of the fieldset kwargs.
has_primary = any(fieldset.get('primary') for fieldset in fieldsets)
for fieldset_kwargs in fieldsets:
fie... |
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def get_chunks(Array, Chunksize):
"""Generator that yields chunks of size ChunkSize""" |
for i in range(0, len(Array), Chunksize):
yield Array[i:i + Chunksize] |
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def read_data_from_bin_file(fileName):
""" Loads the binary data stored in the a binary file and extracts the data for each channel that was saved, along with th... |
with open(fileName, mode='rb') as file: # b is important -> binary
fileContent = file.read()
(ChannelData, LenOf1Channel,
NumOfChannels, SampleTime) = read_data_from_bytes(fileContent)
return ChannelData, LenOf1Channel, NumOfChannels, SampleTime |
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def read_data_from_bytes(fileContent):
""" Takes the binary data stored in the binary string provided and extracts the data for each channel that was saved, alon... |
TotalDataLen = struct.unpack('Q', fileContent[:8])[0] # Unsigned long long
NumOfChannels = struct.unpack('I', fileContent[8:12])[0] # unsigned Long
SampleTime = struct.unpack('d', fileContent[12:20])[0]
AllChannelData = struct.unpack("f" * ((len(fileContent) -20) // 4), fileContent[20:])
# ignor... |
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def get_coord_box(centre_x, centre_y, distance):
"""Get the square boundary coordinates for a given centre and distance""" |
"""Todo: return coordinates inside a circle, rather than a square"""
return {
'top_left': (centre_x - distance, centre_y + distance),
'top_right': (centre_x + distance, centre_y + distance),
'bottom_left': (centre_x - distance, centre_y - distance),
'bottom_right': (centre_x + d... |
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def fleet_ttb(unit_type, quantity, factories, is_techno=False, is_dict=False, stasis_enabled=False):
""" Calculate the time taken to construct a given fleet """ |
unit_weights = {
UNIT_SCOUT: 1,
UNIT_DESTROYER: 13,
UNIT_BOMBER: 10,
UNIT_CRUISER: 85,
UNIT_STARBASE: 1,
}
govt_weight = 80 if is_dict else 100
prod_weight = 85 if is_techno else 100
weighted_qty = unit_weights[unit_type] * quantity
ttb = (weighted_qty... |
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def parse_fasta(data):
# pragma: no cover """ Load sequences in Fasta format. This generator function yields a Sequence object for each sequence record in a GFF3... |
name, seq = None, []
for line in data:
line = line.rstrip()
if line.startswith('>'):
if name:
yield Sequence(name, ''.join(seq))
name, seq = line, []
else:
seq.append(line)
if name:
yield Sequence(name, ''.join(seq)) |
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def _reset(self):
"""Clear internal data structure.""" |
self.records = list()
self.featsbyid = dict()
self.featsbyparent = dict()
self.countsbytype = dict() |
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def get_by_label(self, label):
""" Return the first item with a specific label, or None. """ |
return next((x for x in self if x.label == label), None) |
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def getGenericAnswers(self, name, instruction, prompts):
"""Called when the server requests keyboard interactive authentication """ |
responses = []
for prompt, _echo in prompts:
password = self.getPassword(prompt)
responses.append(password)
return defer.succeed(responses) |
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def pairwise(iterable):
""" Generate consecutive pairs of elements from the given iterable. """ |
iterator = iter(iterable)
try:
first = next(iterator)
except StopIteration:
return
for element in iterator:
yield first, element
first = element |
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def https_policy_from_config(config):
""" Create an ``IPolicyForHTTPS`` which can authenticate a Kubernetes API server. :param KubeConfig config: A Kubernetes co... |
server = config.cluster["server"]
base_url = URL.fromText(native_string_to_unicode(server))
ca_certs = pem.parse(config.cluster["certificate-authority"].bytes())
if not ca_certs:
raise ValueError("No certificate authority certificate found.")
ca_cert = ca_certs[0]
try:
# Valid... |
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def authenticate_with_certificate_chain(reactor, base_url, client_chain, client_key, ca_cert):
""" Create an ``IAgent`` which can issue authenticated requests to... |
if base_url.scheme != u"https":
raise ValueError(
"authenticate_with_certificate() makes sense for HTTPS, not {!r}".format(
base_url.scheme
),
)
netloc = NetLocation(host=base_url.host, port=base_url.port)
policy = ClientCertificatePolicyForHTTPS(
... |
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def authenticate_with_certificate(reactor, base_url, client_cert, client_key, ca_cert):
""" See ``authenticate_with_certificate_chain``. :param pem.Certificate c... |
return authenticate_with_certificate_chain(
reactor, base_url, [client_cert], client_key, ca_cert,
) |
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