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<SYSTEM_TASK:> Spy usage of given `fn`. <END_TASK> <USER_TASK:> Description: def spy2(fn): # type: (...) -> None """Spy usage of given `fn`. Patches the module, class or object `fn` lives in, so that all interactions can be recorded; otherwise executes `fn` as before, so that all side effects happen as before. E.g.:: import time spy(time.time) do_work(...) # nothing injected, uses global patched `time` module verify(time).time() Note that builtins often cannot be patched because they're read-only. """
if isinstance(fn, str): answer = get_obj(fn) else: answer = fn when2(fn, Ellipsis).thenAnswer(answer)
<SYSTEM_TASK:> Return a list of templates usable by a model. <END_TASK> <USER_TASK:> Description: def get_templates(model): """ Return a list of templates usable by a model. """
for template_name, template in templates.items(): if issubclass(template.model, model): yield (template_name, template.layout._meta.verbose_name)
<SYSTEM_TASK:> Get required API keys from environment variables. <END_TASK> <USER_TASK:> Description: def get_api_envs(): """Get required API keys from environment variables."""
client_id = os.environ.get('CLIENT_ID') user_id = os.environ.get('USER_ID') if not client_id or not user_id: raise ValueError('API keys are not found in the environment') return client_id, user_id
<SYSTEM_TASK:> Function checkAndCreate <END_TASK> <USER_TASK:> Description: def checkAndCreate(self, key, payload, domainId): """ Function checkAndCreate Check if a subnet exists and create it if not @param key: The targeted subnet @param payload: The targeted subnet description @param domainId: The domainId to be attached wiuth the subnet @return RETURN: The id of the subnet """
if key not in self: self[key] = payload oid = self[key]['id'] if not oid: return False #~ Ensure subnet contains the domain subnetDomainIds = [] for domain in self[key]['domains']: subnetDomainIds.append(domain['id']) if domainId not in subnetDomainIds: subnetDomainIds.append(domainId) self[key]["domain_ids"] = subnetDomainIds if len(self[key]["domains"]) is not len(subnetDomainIds): return False return oid
<SYSTEM_TASK:> Function removeDomain <END_TASK> <USER_TASK:> Description: def removeDomain(self, subnetId, domainId): """ Function removeDomain Delete a domain from a subnet @param subnetId: The subnet Id @param domainId: The domainId to be attached wiuth the subnet @return RETURN: boolean """
subnetDomainIds = [] for domain in self[subnetId]['domains']: subnetDomainIds.append(domain['id']) subnetDomainIds.remove(domainId) self[subnetId]["domain_ids"] = subnetDomainIds return len(self[subnetId]["domains"]) is len(subnetDomainIds)
<SYSTEM_TASK:> Mark a callable as exclusive <END_TASK> <USER_TASK:> Description: def exclusive(via=threading.Lock): """ Mark a callable as exclusive :param via: factory for a Lock to guard the callable Guards the callable against being entered again before completion. Explicitly raises a :py:exc:`RuntimeError` on violation. :note: If applied to a method, it is exclusive across all instances. """
def make_exclusive(fnc): fnc_guard = via() @functools.wraps(fnc) def exclusive_call(*args, **kwargs): if fnc_guard.acquire(blocking=False): try: return fnc(*args, **kwargs) finally: fnc_guard.release() else: raise RuntimeError('exclusive call to %s violated') return exclusive_call return make_exclusive
<SYSTEM_TASK:> r""" <END_TASK> <USER_TASK:> Description: def service(flavour): r""" Mark a class as implementing a Service Each Service class must have a ``run`` method, which does not take any arguments. This method is :py:meth:`~.ServiceRunner.adopt`\ ed after the daemon starts, unless * the Service has been garbage collected, or * the ServiceUnit has been :py:meth:`~.ServiceUnit.cancel`\ ed. For each service instance, its :py:class:`~.ServiceUnit` is available at ``service_instance.__service_unit__``. """
def service_unit_decorator(raw_cls): __new__ = raw_cls.__new__ def __new_service__(cls, *args, **kwargs): if __new__ is object.__new__: self = __new__(cls) else: self = __new__(cls, *args, **kwargs) service_unit = ServiceUnit(self, flavour) self.__service_unit__ = service_unit return self raw_cls.__new__ = __new_service__ if raw_cls.run.__doc__ is None: raw_cls.run.__doc__ = "Service entry point" return raw_cls return service_unit_decorator
<SYSTEM_TASK:> Synchronously run ``payload`` and provide its output <END_TASK> <USER_TASK:> Description: def execute(self, payload, *args, flavour: ModuleType, **kwargs): """ Synchronously run ``payload`` and provide its output If ``*args*`` and/or ``**kwargs`` are provided, pass them to ``payload`` upon execution. """
if args or kwargs: payload = functools.partial(payload, *args, **kwargs) return self._meta_runner.run_payload(payload, flavour=flavour)
<SYSTEM_TASK:> Concurrently run ``payload`` in the background <END_TASK> <USER_TASK:> Description: def adopt(self, payload, *args, flavour: ModuleType, **kwargs): """ Concurrently run ``payload`` in the background If ``*args*`` and/or ``**kwargs`` are provided, pass them to ``payload`` upon execution. """
if args or kwargs: payload = functools.partial(payload, *args, **kwargs) self._meta_runner.register_payload(payload, flavour=flavour)
<SYSTEM_TASK:> Start accepting synchronous, asynchronous and service payloads <END_TASK> <USER_TASK:> Description: def accept(self): """ Start accepting synchronous, asynchronous and service payloads Since services are globally defined, only one :py:class:`ServiceRunner` may :py:meth:`accept` payloads at any time. """
if self._meta_runner: raise RuntimeError('payloads scheduled for %s before being started' % self) self._must_shutdown = False self._logger.info('%s starting', self.__class__.__name__) # force collecting objects so that defunct, migrated and overwritten services are destroyed now gc.collect() self._adopt_services() self.adopt(self._accept_services, flavour=trio) self._meta_runner.run()
<SYSTEM_TASK:> Shutdown the accept loop and stop running payloads <END_TASK> <USER_TASK:> Description: def shutdown(self): """Shutdown the accept loop and stop running payloads"""
self._must_shutdown = True self._is_shutdown.wait() self._meta_runner.stop()
<SYSTEM_TASK:> Transform and push a line to the interpreter. <END_TASK> <USER_TASK:> Description: def push(self, line): """Transform and push a line to the interpreter. The line should not have a trailing newline; it may have internal newlines. The line is appended to a buffer and the interpreter's runsource() method is called with the concatenated contents of the buffer as source. If this indicates that the command was executed or invalid, the buffer is reset; otherwise, the command is incomplete, and the buffer is left as it was after the line was appended. The return value is 1 if more input is required, 0 if the line was dealt with in some way (this is the same as runsource()). """
if transforms.FROM_EXPERIMENTAL.match(line): transforms.add_transformers(line) self.buffer.append("\n") else: self.buffer.append(line) add_pass = False if line.rstrip(' ').endswith(":"): add_pass = True source = "\n".join(self.buffer) if add_pass: source += "pass" source = transforms.transform(source) if add_pass: source = source.rstrip(' ') if source.endswith("pass"): source = source[:-4] # some transformations may strip an empty line meant to end a block if not self.buffer[-1]: source += "\n" try: more = self.runsource(source, self.filename) except SystemExit: os._exit(1) if not more: self.resetbuffer() return more
<SYSTEM_TASK:> Write dict object into file <END_TASK> <USER_TASK:> Description: def dump(obj, f, preserve=False): """Write dict object into file :param obj: the object to be dumped into toml :param f: the file object :param preserve: optional flag to preserve the inline table in result """
if not f.write: raise TypeError('You can only dump an object into a file object') encoder = Encoder(f, preserve=preserve) return encoder.write_dict(obj)
<SYSTEM_TASK:> Stringifies a dict as toml <END_TASK> <USER_TASK:> Description: def dumps(obj, preserve=False): """Stringifies a dict as toml :param obj: the object to be dumped into toml :param preserve: optional flag to preserve the inline table in result """
f = StringIO() dump(obj, f, preserve) return f.getvalue()
<SYSTEM_TASK:> Loads licenses from the given directory. <END_TASK> <USER_TASK:> Description: def license_loader(lic_dir=LIC_DIR): """Loads licenses from the given directory."""
lics = [] for ln in os.listdir(lic_dir): lp = os.path.join(lic_dir, ln) with open(lp) as lf: txt = lf.read() lic = License(txt) lics.append(lic) return lics
<SYSTEM_TASK:> Upload application from file. <END_TASK> <USER_TASK:> Description: def import_app(files, category, overwrite, id, name): """ Upload application from file. By default, file name will be used as application name, with "-vXX.YYY" suffix stripped. Application is looked up by one of these classifiers, in order of priority: app-id, app-name, filename. If app-id is provided, looks up existing application and updates its manifest. If app-id is NOT specified, looks up by name, or creates new application. """
platform = _get_platform() org = platform.get_organization(QUBELL["organization"]) if category: category = org.categories[category] regex = re.compile(r"^(.*?)(-v(\d+)|)\.[^.]+$") if (id or name) and len(files) > 1: raise Exception("--id and --name are supported only for single-file mode") for filename in files: click.echo("Importing " + filename, nl=False) if not name: match = regex.match(basename(filename)) if not match: click.echo(_color("RED", "FAIL") + " unknown filename format") break name = regex.match(basename(filename)).group(1) click.echo(" => ", nl=False) app = None try: app = org.get_application(id=id, name=name) if app and not overwrite: click.echo("%s %s already exists %s" % ( app.id, _color("BLUE", app and app.name or name), _color("RED", "FAIL"))) break except NotFoundError: if id: click.echo("%s %s not found %s" % ( id or "", _color("BLUE", app and app.name or name), _color("RED", "FAIL"))) break click.echo(_color("BLUE", app and app.name or name) + " ", nl=False) try: with file(filename, "r") as f: if app: app.update(name=app.name, category=category and category.id or app.category, manifest=Manifest(content=f.read())) else: app = org.application(id=id, name=name, manifest=Manifest(content=f.read())) if category: app.update(category=category.id) click.echo(app.id + _color("GREEN", " OK")) except IOError as e: click.echo(_color("RED", " FAIL") + " " + e.message) break
<SYSTEM_TASK:> Read the minified CSS file including STATIC_URL in the references <END_TASK> <USER_TASK:> Description: def _chosen_css(self): """Read the minified CSS file including STATIC_URL in the references to the sprite images."""
css = render_to_string(self.css_template, {}) for sprite in self.chosen_sprites: # rewrite path to sprites in the css css = css.replace(sprite, settings.STATIC_URL + "img/" + sprite) return css
<SYSTEM_TASK:> Embed Chosen.js directly in html of the response. <END_TASK> <USER_TASK:> Description: def _embed(self, request, response): """Embed Chosen.js directly in html of the response."""
if self._match(request, response): # Render the <link> and the <script> tags to include Chosen. head = render_to_string( "chosenadmin/_head_css.html", {"chosen_css": self._chosen_css()} ) body = render_to_string( "chosenadmin/_script.html", {"chosen_js": self._chosen_js()} ) # Re-write the Response's content to include our new html content = response.rendered_content content = content.replace('</head>', head) content = content.replace('</body>', body) response.content = content return response
<SYSTEM_TASK:> Writes an 8-bit byte to the specified command register <END_TASK> <USER_TASK:> Description: def write_byte(self, cmd, value): """ Writes an 8-bit byte to the specified command register """
self.bus.write_byte_data(self.address, cmd, value) self.log.debug( "write_byte: Wrote 0x%02X to command register 0x%02X" % ( value, cmd ) )
<SYSTEM_TASK:> Writes a 16-bit word to the specified command register <END_TASK> <USER_TASK:> Description: def write_word(self, cmd, value): """ Writes a 16-bit word to the specified command register """
self.bus.write_word_data(self.address, cmd, value) self.log.debug( "write_word: Wrote 0x%04X to command register 0x%02X" % ( value, cmd ) )
<SYSTEM_TASK:> Writes an 8-bit byte directly to the bus <END_TASK> <USER_TASK:> Description: def write_raw_byte(self, value): """ Writes an 8-bit byte directly to the bus """
self.bus.write_byte(self.address, value) self.log.debug("write_raw_byte: Wrote 0x%02X" % value)
<SYSTEM_TASK:> Writes a block of bytes to the bus using I2C format to the specified <END_TASK> <USER_TASK:> Description: def write_block_data(self, cmd, block): """ Writes a block of bytes to the bus using I2C format to the specified command register """
self.bus.write_i2c_block_data(self.address, cmd, block) self.log.debug( "write_block_data: Wrote [%s] to command register 0x%02X" % ( ', '.join(['0x%02X' % x for x in block]), cmd ) )
<SYSTEM_TASK:> Read an 8-bit byte directly from the bus <END_TASK> <USER_TASK:> Description: def read_raw_byte(self): """ Read an 8-bit byte directly from the bus """
result = self.bus.read_byte(self.address) self.log.debug("read_raw_byte: Read 0x%02X from the bus" % result) return result
<SYSTEM_TASK:> Read a block of bytes from the bus from the specified command register <END_TASK> <USER_TASK:> Description: def read_block_data(self, cmd, length): """ Read a block of bytes from the bus from the specified command register Amount of bytes read in is defined by length """
results = self.bus.read_i2c_block_data(self.address, cmd, length) self.log.debug( "read_block_data: Read [%s] from command register 0x%02X" % ( ', '.join(['0x%02X' % x for x in results]), cmd ) ) return results
<SYSTEM_TASK:> Read an unsigned byte from the specified command register <END_TASK> <USER_TASK:> Description: def read_unsigned_byte(self, cmd): """ Read an unsigned byte from the specified command register """
result = self.bus.read_byte_data(self.address, cmd) self.log.debug( "read_unsigned_byte: Read 0x%02X from command register 0x%02X" % ( result, cmd ) ) return result
<SYSTEM_TASK:> Read an unsigned word from the specified command register <END_TASK> <USER_TASK:> Description: def read_unsigned_word(self, cmd, little_endian=True): """ Read an unsigned word from the specified command register We assume the data is in little endian mode, if it is in big endian mode then set little_endian to False """
result = self.bus.read_word_data(self.address, cmd) if not little_endian: result = ((result << 8) & 0xFF00) + (result >> 8) self.log.debug( "read_unsigned_word: Read 0x%04X from command register 0x%02X" % ( result, cmd ) ) return result
<SYSTEM_TASK:> Attempt to connect to an I2C bus <END_TASK> <USER_TASK:> Description: def __connect_to_bus(self, bus): """ Attempt to connect to an I2C bus """
def connect(bus_num): try: self.log.debug("Attempting to connect to bus %s..." % bus_num) self.bus = smbus.SMBus(bus_num) self.log.debug("Success") except IOError: self.log.debug("Failed") raise # If the bus is not explicitly stated, try 0 and then try 1 if that # fails if bus is None: try: connect(0) return except IOError: pass try: connect(1) return except IOError: raise else: try: connect(bus) return except IOError: raise
<SYSTEM_TASK:> Default user to the current version owner. <END_TASK> <USER_TASK:> Description: def get_formset(self, request, obj=None, **kwargs): """ Default user to the current version owner. """
data = super().get_formset(request, obj, **kwargs) if obj: data.form.base_fields['user'].initial = request.user.id return data
<SYSTEM_TASK:> Function reload <END_TASK> <USER_TASK:> Description: def reload(self): """ Function reload Reload the full object to ensure sync """
realData = self.load() self.clear() self.update(realData)
<SYSTEM_TASK:> Process actions in the publishing schedule. <END_TASK> <USER_TASK:> Description: def process_actions(action_ids=None): """ Process actions in the publishing schedule. Returns the number of actions processed. """
actions_taken = 0 action_list = PublishAction.objects.prefetch_related( 'content_object', ).filter( scheduled_time__lte=timezone.now(), ) if action_ids is not None: action_list = action_list.filter(id__in=action_ids) for action in action_list: action.process_action() action.delete() actions_taken += 1 return actions_taken
<SYSTEM_TASK:> Return a boolean if Celery tasks are enabled for this app. <END_TASK> <USER_TASK:> Description: def celery_enabled(): """ Return a boolean if Celery tasks are enabled for this app. If the ``GLITTER_PUBLISHER_CELERY`` setting is ``True`` or ``False`` - then that value will be used. However if the setting isn't defined, then this will be enabled automatically if Celery is installed. """
enabled = getattr(settings, 'GLITTER_PUBLISHER_CELERY', None) if enabled is None: try: import celery # noqa enabled = True except ImportError: enabled = False return enabled
<SYSTEM_TASK:> Find regexp in activitylog <END_TASK> <USER_TASK:> Description: def find(self, item, description='', event_type=''): """ Find regexp in activitylog find record as if type are in description. """
# TODO: should be refactored, dumb logic if ': ' in item: splited = item.split(': ', 1) if splited[0] in self.TYPES: description = item.split(': ')[1] event_type = item.split(': ')[0] else: description = item else: if not description: description = item if event_type: found = [x['time'] for x in self.log if re.search(description, x['description']) and x['eventTypeText'] == event_type] else: found = [x['time'] for x in self.log if re.search(description, x['description'])] if len(found): return found raise exceptions.NotFoundError("Item '{}' is not found with (description='{}', event_type='{}')". format(item, description, event_type))
<SYSTEM_TASK:> Currently a small stub to create an instance of Checker for the passed <END_TASK> <USER_TASK:> Description: def do_command_line(infile: typing.IO[str]) -> int: """ Currently a small stub to create an instance of Checker for the passed ``infile`` and run its test functions through linting. Args: infile Returns: int: Number of flake8 errors raised. """
lines = infile.readlines() tree = ast.parse(''.join(lines)) checker = Checker(tree, lines, infile.name) checker.load() errors = [] # type: typing.List[AAAError] for func in checker.all_funcs(skip_noqa=True): try: errors = list(func.check_all()) except ValidationError as error: errors = [error.to_aaa()] print(func.__str__(errors), end='') return len(errors)
<SYSTEM_TASK:> Iterate through multiple lists or arrays of equal size <END_TASK> <USER_TASK:> Description: def _izip(*iterables): """ Iterate through multiple lists or arrays of equal size """
# This izip routine is from itertools # izip('ABCD', 'xy') --> Ax By iterators = map(iter, iterables) while iterators: yield tuple(map(next, iterators))
<SYSTEM_TASK:> Check and convert any input scalar or array to numpy array <END_TASK> <USER_TASK:> Description: def _checkinput(zi, Mi, z=False, verbose=None): """ Check and convert any input scalar or array to numpy array """
# How many halo redshifts provided? zi = np.array(zi, ndmin=1, dtype=float) # How many halo masses provided? Mi = np.array(Mi, ndmin=1, dtype=float) # Check the input sizes for zi and Mi make sense, if not then exit unless # one axis is length one, then replicate values to the size of the other if (zi.size > 1) and (Mi.size > 1): if(zi.size != Mi.size): print("Error ambiguous request") print("Need individual redshifts for all haloes provided ") print("Or have all haloes at same redshift ") return(-1) elif (zi.size == 1) and (Mi.size > 1): if verbose: print("Assume zi is the same for all Mi halo masses provided") # Replicate redshift for all halo masses zi = np.ones_like(Mi)*zi[0] elif (Mi.size == 1) and (zi.size > 1): if verbose: print("Assume Mi halo masses are the same for all zi provided") # Replicate redshift for all halo masses Mi = np.ones_like(zi)*Mi[0] else: if verbose: print("A single Mi and zi provided") # Very simple test for size / type of incoming array # just in case numpy / list given if z is False: # Didn't pass anything, set zi = z lenzout = 1 else: # If something was passed, convert to 1D NumPy array z = np.array(z, ndmin=1, dtype=float) lenzout = z.size return(zi, Mi, z, zi.size, Mi.size, lenzout)
<SYSTEM_TASK:> Find cosmological parameters for named cosmo in cosmology.py list <END_TASK> <USER_TASK:> Description: def getcosmo(cosmology): """ Find cosmological parameters for named cosmo in cosmology.py list """
defaultcosmologies = {'dragons': cg.DRAGONS(), 'wmap1': cg.WMAP1_Mill(), 'wmap3': cg.WMAP3_ML(), 'wmap5': cg.WMAP5_mean(), 'wmap7': cg.WMAP7_ML(), 'wmap9': cg.WMAP9_ML(), 'wmap1_lss': cg.WMAP1_2dF_mean(), 'wmap3_mean': cg.WMAP3_mean(), 'wmap5_ml': cg.WMAP5_ML(), 'wmap5_lss': cg.WMAP5_BAO_SN_mean(), 'wmap7_lss': cg.WMAP7_BAO_H0_mean(), 'planck13': cg.Planck_2013(), 'planck15': cg.Planck_2015()} if isinstance(cosmology, dict): # User providing their own variables cosmo = cosmology if 'A_scaling' not in cosmology.keys(): A_scaling = getAscaling(cosmology, newcosmo=True) cosmo.update({'A_scaling': A_scaling}) # Add extra variables by hand that cosmolopy requires # note that they aren't used (set to zero) for paramnames in cg.WMAP5_mean().keys(): if paramnames not in cosmology.keys(): cosmo.update({paramnames: 0}) elif cosmology.lower() in defaultcosmologies.keys(): # Load by name of cosmology instead cosmo = defaultcosmologies[cosmology.lower()] A_scaling = getAscaling(cosmology) cosmo.update({'A_scaling': A_scaling}) else: print("You haven't passed a dict of cosmological parameters ") print("OR a recognised cosmology, you gave %s" % (cosmology)) # No idea why this has to be done by hand but should be O_k = 0 cosmo = cp.distance.set_omega_k_0(cosmo) # Use the cosmology as **cosmo passed to cosmolopy routines return(cosmo)
<SYSTEM_TASK:> Output the cosmology to a string for writing to file <END_TASK> <USER_TASK:> Description: def _getcosmoheader(cosmo): """ Output the cosmology to a string for writing to file """
cosmoheader = ("# Cosmology (flat) Om:{0:.3f}, Ol:{1:.3f}, h:{2:.2f}, " "sigma8:{3:.3f}, ns:{4:.2f}".format( cosmo['omega_M_0'], cosmo['omega_lambda_0'], cosmo['h'], cosmo['sigma_8'], cosmo['n'])) return(cosmoheader)
<SYSTEM_TASK:> NFW conc from Duffy 08 Table 1 for halo mass and redshift <END_TASK> <USER_TASK:> Description: def cduffy(z, M, vir='200crit', relaxed=True): """ NFW conc from Duffy 08 Table 1 for halo mass and redshift"""
if(vir == '200crit'): if relaxed: params = [6.71, -0.091, -0.44] else: params = [5.71, -0.084, -0.47] elif(vir == 'tophat'): if relaxed: params = [9.23, -0.090, -0.69] else: params = [7.85, -0.081, -0.71] elif(vir == '200mean'): if relaxed: params = [11.93, -0.090, -0.99] else: params = [10.14, -0.081, -1.01] else: print("Didn't recognise the halo boundary definition provided %s" % (vir)) return(params[0] * ((M/(2e12/0.72))**params[1]) * ((1+z)**params[2]))
<SYSTEM_TASK:> Returns integral of the linear growth factor from z=200 to z=z <END_TASK> <USER_TASK:> Description: def _int_growth(z, **cosmo): """ Returns integral of the linear growth factor from z=200 to z=z """
zmax = 200 if hasattr(z, "__len__"): for zval in z: assert(zval < zmax) else: assert(z < zmax) y, yerr = scipy.integrate.quad( lambda z: (1 + z)/(cosmo['omega_M_0']*(1 + z)**3 + cosmo['omega_lambda_0'])**(1.5), z, zmax) return(y)
<SYSTEM_TASK:> Returns linear growth factor at a given redshift, normalised to z=0 <END_TASK> <USER_TASK:> Description: def growthfactor(z, norm=True, **cosmo): """ Returns linear growth factor at a given redshift, normalised to z=0 by default, for a given cosmology Parameters ---------- z : float or numpy array The redshift at which the growth factor should be calculated norm : boolean, optional If true then normalise the growth factor to z=0 case defaults True cosmo : dict Dictionary of cosmological parameters, similar in format to: {'N_nu': 0,'Y_He': 0.24, 'h': 0.702, 'n': 0.963,'omega_M_0': 0.275, 'omega_b_0': 0.0458,'omega_lambda_0': 0.725,'omega_n_0': 0.0, 'sigma_8': 0.816, 't_0': 13.76, 'tau': 0.088,'z_reion': 10.6} Returns ------- float or numpy array The growth factor at a range of redshifts 'z' Raises ------ """
H = np.sqrt(cosmo['omega_M_0'] * (1 + z)**3 + cosmo['omega_lambda_0']) growthval = H * _int_growth(z, **cosmo) if norm: growthval /= _int_growth(0, **cosmo) return(growthval)
<SYSTEM_TASK:> Calculate growth rate indices a_tilde and b_tilde <END_TASK> <USER_TASK:> Description: def calc_ab(zi, Mi, **cosmo): """ Calculate growth rate indices a_tilde and b_tilde Parameters ---------- zi : float Redshift Mi : float Halo mass at redshift 'zi' cosmo : dict Dictionary of cosmological parameters, similar in format to: {'N_nu': 0,'Y_He': 0.24, 'h': 0.702, 'n': 0.963,'omega_M_0': 0.275, 'omega_b_0': 0.0458,'omega_lambda_0': 0.725,'omega_n_0': 0.0, 'sigma_8': 0.816, 't_0': 13.76, 'tau': 0.088,'z_reion': 10.6} Returns ------- (a_tilde, b_tilde) : float """
# When zi = 0, the a_tilde becomes alpha and b_tilde becomes beta # Eqn 23 of Correa et al 2015a (analytically solve from Eqn 16 and 17) # Arbitray formation redshift, z_-2 in COM is more physically motivated zf = -0.0064 * (np.log10(Mi))**2 + 0.0237 * (np.log10(Mi)) + 1.8837 # Eqn 22 of Correa et al 2015a q = 4.137 * zf**(-0.9476) # Radius of a mass Mi R_Mass = cp.perturbation.mass_to_radius(Mi, **cosmo) # [Mpc] # Radius of a mass Mi/q Rq_Mass = cp.perturbation.mass_to_radius(Mi/q, **cosmo) # [Mpc] # Mass variance 'sigma' evaluate at z=0 to a good approximation sig, err_sig = cp.perturbation.sigma_r(R_Mass, 0, **cosmo) # [Mpc] sigq, err_sigq = cp.perturbation.sigma_r(Rq_Mass, 0, **cosmo) # [Mpc] f = (sigq**2 - sig**2)**(-0.5) # Eqn 9 and 10 from Correa et al 2015c # (generalised to zi from Correa et al 2015a's z=0 special case) # a_tilde is power law growth rate a_tilde = (np.sqrt(2/np.pi) * 1.686 * _deriv_growth(zi, **cosmo) / growthfactor(zi, norm=True, **cosmo)**2 + 1)*f # b_tilde is exponential growth rate b_tilde = -f return(a_tilde, b_tilde)
<SYSTEM_TASK:> Calculate accretion rate and mass history of a halo at any <END_TASK> <USER_TASK:> Description: def acc_rate(z, zi, Mi, **cosmo): """ Calculate accretion rate and mass history of a halo at any redshift 'z' with mass 'Mi' at a lower redshift 'z' Parameters ---------- z : float Redshift to solve acc_rate / mass history. Note zi<z zi : float Redshift Mi : float Halo mass at redshift 'zi' cosmo : dict Dictionary of cosmological parameters, similar in format to: {'N_nu': 0,'Y_He': 0.24, 'h': 0.702, 'n': 0.963,'omega_M_0': 0.275, 'omega_b_0': 0.0458,'omega_lambda_0': 0.725,'omega_n_0': 0.0, 'sigma_8': 0.816, 't_0': 13.76, 'tau': 0.088,'z_reion': 10.6} Returns ------- (dMdt, Mz) : float Accretion rate [Msol/yr], halo mass [Msol] at redshift 'z' """
# Find parameters a_tilde and b_tilde for initial redshift # use Eqn 9 and 10 of Correa et al. (2015c) a_tilde, b_tilde = calc_ab(zi, Mi, **cosmo) # Halo mass at z, in Msol # use Eqn 8 in Correa et al. (2015c) Mz = Mi * ((1 + z - zi)**a_tilde) * (np.exp(b_tilde * (z - zi))) # Accretion rate at z, Msol yr^-1 # use Eqn 11 from Correa et al. (2015c) dMdt = 71.6 * (Mz/1e12) * (cosmo['h']/0.7) *\ (-a_tilde / (1 + z - zi) - b_tilde) * (1 + z) *\ np.sqrt(cosmo['omega_M_0']*(1 + z)**3+cosmo['omega_lambda_0']) return(dMdt, Mz)
<SYSTEM_TASK:> Calculate mass accretion history by looping function acc_rate <END_TASK> <USER_TASK:> Description: def MAH(z, zi, Mi, **cosmo): """ Calculate mass accretion history by looping function acc_rate over redshift steps 'z' for halo of mass 'Mi' at redshift 'zi' Parameters ---------- z : float / numpy array Redshift to output MAH over. Note zi<z always zi : float Redshift Mi : float Halo mass at redshift 'zi' cosmo : dict Dictionary of cosmological parameters, similar in format to: {'N_nu': 0,'Y_He': 0.24, 'h': 0.702, 'n': 0.963,'omega_M_0': 0.275, 'omega_b_0': 0.0458,'omega_lambda_0': 0.725,'omega_n_0': 0.0, 'sigma_8': 0.816, 't_0': 13.76, 'tau': 0.088,'z_reion': 10.6} Returns ------- (dMdt, Mz) : float / numpy arrays of equivalent size to 'z' Accretion rate [Msol/yr], halo mass [Msol] at redshift 'z' """
# Ensure that z is a 1D NumPy array z = np.array(z, ndmin=1, dtype=float) # Create a full array dMdt_array = np.empty_like(z) Mz_array = np.empty_like(z) for i_ind, zval in enumerate(z): # Solve the accretion rate and halo mass at each redshift step dMdt, Mz = acc_rate(zval, zi, Mi, **cosmo) dMdt_array[i_ind] = dMdt Mz_array[i_ind] = Mz return(dMdt_array, Mz_array)
<SYSTEM_TASK:> Calculate concentration for halo of mass 'M' at redshift 'z' <END_TASK> <USER_TASK:> Description: def COM(z, M, **cosmo): """ Calculate concentration for halo of mass 'M' at redshift 'z' Parameters ---------- z : float / numpy array Redshift to find concentration of halo M : float / numpy array Halo mass at redshift 'z'. Must be same size as 'z' cosmo : dict Dictionary of cosmological parameters, similar in format to: {'N_nu': 0,'Y_He': 0.24, 'h': 0.702, 'n': 0.963,'omega_M_0': 0.275, 'omega_b_0': 0.0458,'omega_lambda_0': 0.725,'omega_n_0': 0.0, 'sigma_8': 0.816, 't_0': 13.76, 'tau': 0.088,'z_reion': 10.6} Returns ------- (c_array, sig_array, nu_array, zf_array) : float / numpy arrays of equivalent size to 'z' and 'M'. Variables are Concentration, Mass Variance 'sigma' this corresponds too, the dimnesionless fluctuation this represents and formation redshift """
# Check that z and M are arrays z = np.array(z, ndmin=1, dtype=float) M = np.array(M, ndmin=1, dtype=float) # Create array c_array = np.empty_like(z) sig_array = np.empty_like(z) nu_array = np.empty_like(z) zf_array = np.empty_like(z) for i_ind, (zval, Mval) in enumerate(_izip(z, M)): # Evaluate the indices at each redshift and mass combination # that you want a concentration for, different to MAH which # uses one a_tilde and b_tilde at the starting redshift only a_tilde, b_tilde = calc_ab(zval, Mval, **cosmo) # Minimize equation to solve for 1 unknown, 'c' c = scipy.optimize.brentq(_minimize_c, 2, 1000, args=(zval, a_tilde, b_tilde, cosmo['A_scaling'], cosmo['omega_M_0'], cosmo['omega_lambda_0'])) if np.isclose(c, 0): print("Error solving for concentration with given redshift and " "(probably) too small a mass") c = -1 sig = -1 nu = -1 zf = -1 else: # Calculate formation redshift for this concentration, # redshift at which the scale radius = virial radius: z_-2 zf = formationz(c, zval, Ascaling=cosmo['A_scaling'], omega_M_0=cosmo['omega_M_0'], omega_lambda_0=cosmo['omega_lambda_0']) R_Mass = cp.perturbation.mass_to_radius(Mval, **cosmo) sig, err_sig = cp.perturbation.sigma_r(R_Mass, 0, **cosmo) nu = 1.686/(sig*growthfactor(zval, norm=True, **cosmo)) c_array[i_ind] = c sig_array[i_ind] = sig nu_array[i_ind] = nu zf_array[i_ind] = zf return(c_array, sig_array, nu_array, zf_array)
<SYSTEM_TASK:> Load a configuration and keep it alive for the given context <END_TASK> <USER_TASK:> Description: def load(config_path: str): """ Load a configuration and keep it alive for the given context :param config_path: path to a configuration file """
# we bind the config to _ to keep it alive if os.path.splitext(config_path)[1] in ('.yaml', '.yml'): _ = load_yaml_configuration(config_path, translator=PipelineTranslator()) elif os.path.splitext(config_path)[1] == '.py': _ = load_python_configuration(config_path) else: raise ValueError('Unknown configuration extension: %r' % os.path.splitext(config_path)[1]) yield
<SYSTEM_TASK:> Assets for a given release <END_TASK> <USER_TASK:> Description: def release_assets(self, release): """Assets for a given release """
release = self.as_id(release) return self.get_list(url='%s/%s/assets' % (self, release))
<SYSTEM_TASK:> Upload a file to a release <END_TASK> <USER_TASK:> Description: def upload(self, release, filename, content_type=None): """Upload a file to a release :param filename: filename to upload :param content_type: optional content type :return: json object from github """
release = self.as_id(release) name = os.path.basename(filename) if not content_type: content_type, _ = mimetypes.guess_type(name) if not content_type: raise ValueError('content_type not known') inputs = {'name': name} url = '%s%s/%s/assets' % (self.uploads_url, urlsplit(self.api_url).path, release) info = os.stat(filename) size = info[stat.ST_SIZE] response = self.http.post( url, data=stream_upload(filename), auth=self.auth, params=inputs, headers={'content-type': content_type, 'content-length': str(size)}) response.raise_for_status() return response.json()
<SYSTEM_TASK:> Validate ``tag_name`` with the latest tag from github <END_TASK> <USER_TASK:> Description: def validate_tag(self, tag_name, prefix=None): """Validate ``tag_name`` with the latest tag from github If ``tag_name`` is a valid candidate, return the latest tag from github """
new_version = semantic_version(tag_name) current = self.latest() if current: tag_name = current['tag_name'] if prefix: tag_name = tag_name[len(prefix):] tag_name = semantic_version(tag_name) if tag_name >= new_version: what = 'equal to' if tag_name == new_version else 'older than' raise GithubException( 'Your local version "%s" is %s ' 'the current github version "%s".\n' 'Bump the local version to ' 'continue.' % ( str(new_version), what, str(tag_name) ) ) return current
<SYSTEM_TASK:> Return the full reddit URL associated with the usernote. <END_TASK> <USER_TASK:> Description: def full_url(self): """Return the full reddit URL associated with the usernote. Arguments: subreddit: the subreddit name for the note (PRAW Subreddit object) """
if self.link == '': return None else: return Note._expand_url(self.link, self.subreddit)
<SYSTEM_TASK:> Convert a reddit URL into the short-hand used by usernotes. <END_TASK> <USER_TASK:> Description: def _compress_url(link): """Convert a reddit URL into the short-hand used by usernotes. Arguments: link: a link to a comment, submission, or message (str) Returns a String of the shorthand URL """
comment_re = re.compile(r'/comments/([A-Za-z\d]{2,})(?:/[^\s]+/([A-Za-z\d]+))?') message_re = re.compile(r'/message/messages/([A-Za-z\d]+)') matches = re.findall(comment_re, link) if len(matches) == 0: matches = re.findall(message_re, link) if len(matches) == 0: return None else: return 'm,' + matches[0] else: if matches[0][1] == '': return 'l,' + matches[0][0] else: return 'l,' + matches[0][0] + ',' + matches[0][1]
<SYSTEM_TASK:> Convert a usernote's URL short-hand into a full reddit URL. <END_TASK> <USER_TASK:> Description: def _expand_url(short_link, subreddit=None): """Convert a usernote's URL short-hand into a full reddit URL. Arguments: subreddit: the subreddit the URL is for (PRAW Subreddit object or str) short_link: the compressed link from a usernote (str) Returns a String of the full URL. """
# Some URL structures for notes message_scheme = 'https://reddit.com/message/messages/{}' comment_scheme = 'https://reddit.com/r/{}/comments/{}/-/{}' post_scheme = 'https://reddit.com/r/{}/comments/{}/' if short_link == '': return None else: parts = short_link.split(',') if parts[0] == 'm': return message_scheme.format(parts[1]) if parts[0] == 'l' and subreddit: if len(parts) > 2: return comment_scheme.format(subreddit, parts[1], parts[2]) else: return post_scheme.format(subreddit, parts[1]) elif not subreddit: raise ValueError('Subreddit name must be provided') else: return None
<SYSTEM_TASK:> Get the JSON stored on the usernotes wiki page. <END_TASK> <USER_TASK:> Description: def get_json(self): """Get the JSON stored on the usernotes wiki page. Returns a dict representation of the usernotes (with the notes BLOB decoded). Raises: RuntimeError if the usernotes version is incompatible with this version of puni. """
try: usernotes = self.subreddit.wiki[self.page_name].content_md notes = json.loads(usernotes) except NotFound: self._init_notes() else: if notes['ver'] != self.schema: raise RuntimeError( 'Usernotes schema is v{0}, puni requires v{1}'. format(notes['ver'], self.schema) ) self.cached_json = self._expand_json(notes) return self.cached_json
<SYSTEM_TASK:> Set up the UserNotes page with the initial JSON schema. <END_TASK> <USER_TASK:> Description: def _init_notes(self): """Set up the UserNotes page with the initial JSON schema."""
self.cached_json = { 'ver': self.schema, 'users': {}, 'constants': { 'users': [x.name for x in self.subreddit.moderator()], 'warnings': Note.warnings } } self.set_json('Initializing JSON via puni', True)
<SYSTEM_TASK:> Send the JSON from the cache to the usernotes wiki page. <END_TASK> <USER_TASK:> Description: def set_json(self, reason='', new_page=False): """Send the JSON from the cache to the usernotes wiki page. Arguments: reason: the change reason that will be posted to the wiki changelog (str) Raises: OverflowError if the new JSON data is greater than max_page_size """
compressed_json = json.dumps(self._compress_json(self.cached_json)) if len(compressed_json) > self.max_page_size: raise OverflowError( 'Usernotes page is too large (>{0} characters)'. format(self.max_page_size) ) if new_page: self.subreddit.wiki.create( self.page_name, compressed_json, reason ) # Set the page as hidden and available to moderators only self.subreddit.wiki[self.page_name].mod.update(False, permlevel=2) else: self.subreddit.wiki[self.page_name].edit( compressed_json, reason )
<SYSTEM_TASK:> Return a list of Note objects for the given user. <END_TASK> <USER_TASK:> Description: def get_notes(self, user): """Return a list of Note objects for the given user. Return an empty list if no notes are found. Arguments: user: the user to search for in the usernotes (str) """
# Try to search for all notes on a user, return an empty list if none # are found. try: users_notes = [] for note in self.cached_json['users'][user]['ns']: users_notes.append(Note( user=user, note=note['n'], subreddit=self.subreddit, mod=self._mod_from_index(note['m']), link=note['l'], warning=self._warning_from_index(note['w']), note_time=note['t'] )) return users_notes except KeyError: # User not found return []
<SYSTEM_TASK:> Decompress the BLOB portion of the usernotes. <END_TASK> <USER_TASK:> Description: def _expand_json(self, j): """Decompress the BLOB portion of the usernotes. Arguments: j: the JSON returned from the wiki page (dict) Returns a Dict with the 'blob' key removed and a 'users' key added """
decompressed_json = copy.copy(j) decompressed_json.pop('blob', None) # Remove BLOB portion of JSON # Decode and decompress JSON compressed_data = base64.b64decode(j['blob']) original_json = zlib.decompress(compressed_data).decode('utf-8') decompressed_json['users'] = json.loads(original_json) # Insert users return decompressed_json
<SYSTEM_TASK:> Compress the BLOB data portion of the usernotes. <END_TASK> <USER_TASK:> Description: def _compress_json(self, j): """Compress the BLOB data portion of the usernotes. Arguments: j: the JSON in Schema v5 format (dict) Returns a dict with the 'users' key removed and 'blob' key added """
compressed_json = copy.copy(j) compressed_json.pop('users', None) compressed_data = zlib.compress( json.dumps(j['users']).encode('utf-8'), self.zlib_compression_strength ) b64_data = base64.b64encode(compressed_data).decode('utf-8') compressed_json['blob'] = b64_data return compressed_json
<SYSTEM_TASK:> Add a note to the usernotes wiki page. <END_TASK> <USER_TASK:> Description: def add_note(self, note): """Add a note to the usernotes wiki page. Arguments: note: the note to be added (Note) Returns the update message for the usernotes wiki Raises: ValueError when the warning type of the note can not be found in the stored list of warnings. """
notes = self.cached_json if not note.moderator: note.moderator = self.r.user.me().name # Get index of moderator in mod list from usernotes # Add moderator to list if not already there try: mod_index = notes['constants']['users'].index(note.moderator) except ValueError: notes['constants']['users'].append(note.moderator) mod_index = notes['constants']['users'].index(note.moderator) # Get index of warning type from warnings list # Add warning type to list if not already there try: warn_index = notes['constants']['warnings'].index(note.warning) except ValueError: if note.warning in Note.warnings: notes['constants']['warnings'].append(note.warning) warn_index = notes['constants']['warnings'].index(note.warning) else: raise ValueError('Warning type not valid: ' + note.warning) new_note = { 'n': note.note, 't': note.time, 'm': mod_index, 'l': note.link, 'w': warn_index } try: notes['users'][note.username]['ns'].insert(0, new_note) except KeyError: notes['users'][note.username] = {'ns': [new_note]} return '"create new note on user {}" via puni'.format(note.username)
<SYSTEM_TASK:> Remove a single usernote from the usernotes. <END_TASK> <USER_TASK:> Description: def remove_note(self, username, index): """Remove a single usernote from the usernotes. Arguments: username: the user that for whom you're removing a note (str) index: the index of the note which is to be removed (int) Returns the update message for the usernotes wiki """
self.cached_json['users'][username]['ns'].pop(index) # Go ahead and remove the user's entry if they have no more notes left if len(self.cached_json['users'][username]['ns']) == 0: del self.cached_json['users'][username] return '"delete note #{} on user {}" via puni'.format(index, username)
<SYSTEM_TASK:> Return the first matching target application in this version range. <END_TASK> <USER_TASK:> Description: def get_related_targetApplication(vR, app_id, app_ver): """Return the first matching target application in this version range. Returns None if there are no target applications or no matching ones."""
targetApplication = vR.get('targetApplication') if not targetApplication: return None for tA in targetApplication: guid = tA.get('guid') if not guid or guid == app_id: if not app_ver: return tA # We purposefully use maxVersion only, so that the blocklist contains items # whose minimum version is ahead of the version we get passed. This means # the blocklist we serve is "future-proof" for app upgrades. if between(version_int(app_ver), '0', tA.get('maxVersion', '*')): return tA return None
<SYSTEM_TASK:> Generate the addons blocklists. <END_TASK> <USER_TASK:> Description: def write_addons_items(xml_tree, records, app_id, api_ver=3, app_ver=None): """Generate the addons blocklists. <emItem blockID="i372" id="[email protected]"> <versionRange minVersion="0" maxVersion="*" severity="3"> <targetApplication id="{ec8030f7-c20a-464f-9b0e-13a3a9e97384}"> <versionRange minVersion="39.0a1" maxVersion="*"/> </targetApplication> </versionRange> <prefs> <pref>browser.startup.homepage</pref> <pref>browser.search.defaultenginename</pref> </prefs> </emItem> """
if not records: return emItems = etree.SubElement(xml_tree, 'emItems') groupby = {} for item in records: if is_related_to(item, app_id, app_ver): if item['guid'] in groupby: emItem = groupby[item['guid']] # When creating new records from the Kinto Admin we don't have proper blockID. if 'blockID' in item: # Remove the first caracter which is the letter i to # compare the numeric value i45 < i356. current_blockID = int(item['blockID'][1:]) previous_blockID = int(emItem.attrib['blockID'][1:]) # Group by and keep the biggest blockID in the XML file. if current_blockID > previous_blockID: emItem.attrib['blockID'] = item['blockID'] else: # If the latest entry does not have any blockID attribute, its # ID should be used. (the list of records is sorted by ascending # last_modified). # See https://bugzilla.mozilla.org/show_bug.cgi?id=1473194 emItem.attrib['blockID'] = item['id'] else: emItem = etree.SubElement(emItems, 'emItem', blockID=item.get('blockID', item['id'])) groupby[item['guid']] = emItem prefs = etree.SubElement(emItem, 'prefs') for p in item['prefs']: pref = etree.SubElement(prefs, 'pref') pref.text = p # Set the add-on ID emItem.set('id', item['guid']) for field in ['name', 'os']: if field in item: emItem.set(field, item[field]) build_version_range(emItem, item, app_id)
<SYSTEM_TASK:> Create or update a label <END_TASK> <USER_TASK:> Description: def label(self, name, color, update=True): """Create or update a label """
url = '%s/labels' % self data = dict(name=name, color=color) response = self.http.post( url, json=data, auth=self.auth, headers=self.headers ) if response.status_code == 201: return True elif response.status_code == 422 and update: url = '%s/%s' % (url, name) response = self.http.patch( url, json=data, auth=self.auth, headers=self.headers ) response.raise_for_status() return False
<SYSTEM_TASK:> Check a plaintext password against a hashed password. <END_TASK> <USER_TASK:> Description: def check_password(password: str, encrypted: str) -> bool: """ Check a plaintext password against a hashed password. """
# some old passwords have {crypt} in lower case, and passlib wants it to be # in upper case. if encrypted.startswith("{crypt}"): encrypted = "{CRYPT}" + encrypted[7:] return pwd_context.verify(password, encrypted)
<SYSTEM_TASK:> Check if version of repository is semantic <END_TASK> <USER_TASK:> Description: def validate(ctx, sandbox): """Check if version of repository is semantic """
m = RepoManager(ctx.obj['agile']) if not sandbox or m.can_release('sandbox'): click.echo(m.validate_version())
<SYSTEM_TASK:> Reset transaction back to original state, discarding all <END_TASK> <USER_TASK:> Description: def reset(self, force_flush_cache: bool = False) -> None: """ Reset transaction back to original state, discarding all uncompleted transactions. """
super(LDAPwrapper, self).reset() if len(self._transactions) == 0: raise RuntimeError("reset called outside a transaction.") self._transactions[-1] = []
<SYSTEM_TASK:> Object state is cached. When an update is required the update will be <END_TASK> <USER_TASK:> Description: def _cache_get_for_dn(self, dn: str) -> Dict[str, bytes]: """ Object state is cached. When an update is required the update will be simulated on this cache, so that rollback information can be correct. This function retrieves the cached data. """
# no cached item, retrieve from ldap self._do_with_retry( lambda obj: obj.search( dn, '(objectclass=*)', ldap3.BASE, attributes=['*', '+'])) results = self._obj.response if len(results) < 1: raise NoSuchObject("No results finding current value") if len(results) > 1: raise RuntimeError("Too many results finding current value") return results[0]['raw_attributes']
<SYSTEM_TASK:> Attempt to commit all changes to LDAP database. i.e. forget all <END_TASK> <USER_TASK:> Description: def commit(self) -> None: """ Attempt to commit all changes to LDAP database. i.e. forget all rollbacks. However stay inside transaction management. """
if len(self._transactions) == 0: raise RuntimeError("commit called outside transaction") # If we have nested transactions, we don't actually commit, but push # rollbacks up to previous transaction. if len(self._transactions) > 1: for on_rollback in reversed(self._transactions[-1]): self._transactions[-2].insert(0, on_rollback) _debug("commit") self.reset()
<SYSTEM_TASK:> Roll back to previous database state. However stay inside transaction <END_TASK> <USER_TASK:> Description: def rollback(self) -> None: """ Roll back to previous database state. However stay inside transaction management. """
if len(self._transactions) == 0: raise RuntimeError("rollback called outside transaction") _debug("rollback:", self._transactions[-1]) # if something goes wrong here, nothing we can do about it, leave # database as is. try: # for every rollback action ... for on_rollback in self._transactions[-1]: # execute it _debug("--> rolling back", on_rollback) self._do_with_retry(on_rollback) except: # noqa: E722 _debug("--> rollback failed") exc_class, exc, tb = sys.exc_info() raise tldap.exceptions.RollbackError( "FATAL Unrecoverable rollback error: %r" % exc) finally: # reset everything to clean state _debug("--> rollback success") self.reset()
<SYSTEM_TASK:> for testing purposes only. always fail in commit <END_TASK> <USER_TASK:> Description: def fail(self) -> None: """ for testing purposes only. always fail in commit """
_debug("fail") # on commit carry out action; on rollback reverse rename def on_commit(_obj): raise_testfailure("commit") def on_rollback(_obj): raise_testfailure("rollback") return self._process(on_commit, on_rollback)
<SYSTEM_TASK:> Spits out the timedelta in days. <END_TASK> <USER_TASK:> Description: def get_interval_timedelta(self): """ Spits out the timedelta in days. """
now_datetime = timezone.now() current_month_days = monthrange(now_datetime.year, now_datetime.month)[1] # Two weeks if self.interval == reminders_choices.INTERVAL_2_WEEKS: interval_timedelta = datetime.timedelta(days=14) # One month elif self.interval == reminders_choices.INTERVAL_ONE_MONTH: interval_timedelta = datetime.timedelta(days=current_month_days) # Three months elif self.interval == reminders_choices.INTERVAL_THREE_MONTHS: three_months = now_datetime + relativedelta(months=+3) interval_timedelta = three_months - now_datetime # Six months elif self.interval == reminders_choices.INTERVAL_SIX_MONTHS: six_months = now_datetime + relativedelta(months=+6) interval_timedelta = six_months - now_datetime # One year elif self.interval == reminders_choices.INTERVAL_ONE_YEAR: one_year = now_datetime + relativedelta(years=+1) interval_timedelta = one_year - now_datetime return interval_timedelta
<SYSTEM_TASK:> Execute a runner without blocking the event loop <END_TASK> <USER_TASK:> Description: async def awaitable_runner(runner: BaseRunner): """Execute a runner without blocking the event loop"""
runner_thread = CapturingThread(target=runner.run) runner_thread.start() delay = 0.0 while not runner_thread.join(timeout=0): await asyncio.sleep(delay) delay = min(delay + 0.1, 1.0)
<SYSTEM_TASK:> Create an ``asyncio`` event loop running in the main thread and watching runners <END_TASK> <USER_TASK:> Description: def asyncio_main_run(root_runner: BaseRunner): """ Create an ``asyncio`` event loop running in the main thread and watching runners Using ``asyncio`` to handle suprocesses requires a specific loop type to run in the main thread. This function sets up and runs the correct loop in a portable way. In addition, it runs a single :py:class:`~.BaseRunner` until completion or failure. .. seealso:: The `issue #8 <https://github.com/MatterMiners/cobald/issues/8>`_ for details. """
assert threading.current_thread() == threading.main_thread(), 'only main thread can accept asyncio subprocesses' if sys.platform == 'win32': event_loop = asyncio.ProactorEventLoop() asyncio.set_event_loop(event_loop) else: event_loop = asyncio.get_event_loop() asyncio.get_child_watcher().attach_loop(event_loop) event_loop.run_until_complete(awaitable_runner(root_runner))
<SYSTEM_TASK:> Dump initialized object structure to yaml <END_TASK> <USER_TASK:> Description: def dump(node): """ Dump initialized object structure to yaml """
from qubell.api.private.platform import Auth, QubellPlatform from qubell.api.private.organization import Organization from qubell.api.private.application import Application from qubell.api.private.instance import Instance from qubell.api.private.revision import Revision from qubell.api.private.environment import Environment from qubell.api.private.zone import Zone from qubell.api.private.manifest import Manifest # Exclude keys from dump # Format: { 'ClassName': ['fields', 'to', 'exclude']} exclusion_list = { Auth: ['cookies'], QubellPlatform:['auth', ], Organization: ['auth', 'organizationId', 'zone'], Application: ['auth', 'applicationId', 'organization'], Instance: ['auth', 'instanceId', 'application'], Manifest: ['name', 'content'], Revision: ['auth', 'revisionId'], Environment: ['auth', 'environmentId', 'organization'], Zone: ['auth', 'zoneId', 'organization'], } def obj_presenter(dumper, obj): for x in exclusion_list.keys(): if isinstance(obj, x): # Find class fields = obj.__dict__.copy() for excl_item in exclusion_list[x]: try: fields.pop(excl_item) except: log.warn('No item %s in object %s' % (excl_item, x)) return dumper.represent_mapping('tag:yaml.org,2002:map', fields) return dumper.represent_mapping('tag:yaml.org,2002:map', obj.__dict__) noalias_dumper = yaml.dumper.Dumper noalias_dumper.ignore_aliases = lambda self, data: True yaml.add_representer(unicode, lambda dumper, value: dumper.represent_scalar(u'tag:yaml.org,2002:str', value)) yaml.add_multi_representer(object, obj_presenter) serialized = yaml.dump(node, default_flow_style=False, Dumper=noalias_dumper) return serialized
<SYSTEM_TASK:> Function list <END_TASK> <USER_TASK:> Description: def list(self, obj, filter=False, only_id=False, limit=20): """ Function list Get the list of an object @param obj: object name ('hosts', 'puppetclasses'...) @param filter: filter for objects @param only_id: boolean to only return dict with name/id @return RETURN: the list of the object """
self.url = '{}{}/?per_page={}'.format(self.base_url, obj, limit) self.method = 'GET' if filter: self.url += '&search={}'.format(filter) self.resp = requests.get(url=self.url, auth=self.auth, headers=self.headers, cert=self.ca_cert) if only_id: if self.__process_resp__(obj) is False: return False if type(self.res['results']) is list: return dict((x['name'], x['id']) for x in self.res['results']) elif type(self.res['results']) is dict: r = {} for v in self.res['results'].values(): for vv in v: r[vv['name']] = vv['id'] return r else: return False else: return self.__process_resp__(obj)
<SYSTEM_TASK:> Function get <END_TASK> <USER_TASK:> Description: def get(self, obj, id, sub_object=None): """ Function get Get an object by id @param obj: object name ('hosts', 'puppetclasses'...) @param id: the id of the object (name or id) @return RETURN: the targeted object """
self.url = '{}{}/{}'.format(self.base_url, obj, id) self.method = 'GET' if sub_object: self.url += '/' + sub_object self.resp = requests.get(url=self.url, auth=self.auth, headers=self.headers, cert=self.ca_cert) if self.__process_resp__(obj): return self.res return False
<SYSTEM_TASK:> Function get_id_by_name <END_TASK> <USER_TASK:> Description: def get_id_by_name(self, obj, name): """ Function get_id_by_name Get the id of an object @param obj: object name ('hosts', 'puppetclasses'...) @param id: the id of the object (name or id) @return RETURN: the targeted object """
list = self.list(obj, filter='name = "{}"'.format(name), only_id=True, limit=1) return list[name] if name in list.keys() else False
<SYSTEM_TASK:> Function set <END_TASK> <USER_TASK:> Description: def set(self, obj, id, payload, action='', async=False): """ Function set Set an object by id @param obj: object name ('hosts', 'puppetclasses'...) @param id: the id of the object (name or id) @param action: specific action of an object ('power'...) @param payload: the dict of the payload @param async: should this request be async, if true use return.result() to get the response @return RETURN: the server response """
self.url = '{}{}/{}'.format(self.base_url, obj, id) self.method = 'PUT' if action: self.url += '/{}'.format(action) self.payload = json.dumps(payload) if async: session = FuturesSession() return session.put(url=self.url, auth=self.auth, headers=self.headers, data=self.payload, cert=self.ca_cert) else: self.resp = requests.put(url=self.url, auth=self.auth, headers=self.headers, data=self.payload, cert=self.ca_cert) if self.__process_resp__(obj): return self.res return False
<SYSTEM_TASK:> Function create <END_TASK> <USER_TASK:> Description: def create(self, obj, payload, async=False): """ Function create Create an new object @param obj: object name ('hosts', 'puppetclasses'...) @param payload: the dict of the payload @param async: should this request be async, if true use return.result() to get the response @return RETURN: the server response """
self.url = self.base_url + obj self.method = 'POST' self.payload = json.dumps(payload) if async: self.method = 'POST(Async)' session = FuturesSession() self.resp = session.post(url=self.url, auth=self.auth, headers=self.headers, data=self.payload, cert=self.ca_cert) return self.resp else: self.resp = requests.post(url=self.url, auth=self.auth, headers=self.headers, data=self.payload, cert=self.ca_cert) return self.__process_resp__(obj)
<SYSTEM_TASK:> Function delete <END_TASK> <USER_TASK:> Description: def delete(self, obj, id): """ Function delete Delete an object by id @param obj: object name ('hosts', 'puppetclasses'...) @param id: the id of the object (name or id) @return RETURN: the server response """
self.url = '{}{}/{}'.format(self.base_url, obj, id) self.method = 'DELETE' self.resp = requests.delete(url=self.url, auth=self.auth, headers=self.headers, cert=self.ca_cert) return self.__process_resp__(obj)
<SYSTEM_TASK:> Modified ``run`` that captures return value and exceptions from ``target`` <END_TASK> <USER_TASK:> Description: def run(self): """Modified ``run`` that captures return value and exceptions from ``target``"""
try: if self._target: return_value = self._target(*self._args, **self._kwargs) if return_value is not None: self._exception = OrphanedReturn(self, return_value) except BaseException as err: self._exception = err finally: # Avoid a refcycle if the thread is running a function with # an argument that has a member that points to the thread. del self._target, self._args, self._kwargs
<SYSTEM_TASK:> Decorate functions that modify the internally stored usernotes JSON. <END_TASK> <USER_TASK:> Description: def update_cache(func): """Decorate functions that modify the internally stored usernotes JSON. Ensures that updates are mirrored onto reddit. Arguments: func: the function being decorated """
@wraps(func) def wrapper(self, *args, **kwargs): """The wrapper function.""" lazy = kwargs.get('lazy', False) kwargs.pop('lazy', None) if not lazy: self.get_json() ret = func(self, *args, **kwargs) # If returning a string assume it is an update message if isinstance(ret, str) and not lazy: self.set_json(ret) else: return ret return wrapper
<SYSTEM_TASK:> Return a tuple for authenticating a user <END_TASK> <USER_TASK:> Description: def get_auth(): """Return a tuple for authenticating a user If not successful raise ``AgileError``. """
auth = get_auth_from_env() if auth[0] and auth[1]: return auth home = os.path.expanduser("~") config = os.path.join(home, '.gitconfig') if not os.path.isfile(config): raise GithubException('No .gitconfig available') parser = configparser.ConfigParser() parser.read(config) if 'user' in parser: user = parser['user'] if 'username' not in user: raise GithubException('Specify username in %s user ' 'section' % config) if 'token' not in user: raise GithubException('Specify token in %s user section' % config) return user['username'], user['token'] else: raise GithubException('No user section in %s' % config)
<SYSTEM_TASK:> Function checkAndCreate <END_TASK> <USER_TASK:> Description: def checkAndCreate(self, key, payload, osIds): """ Function checkAndCreate Check if an architectures exists and create it if not @param key: The targeted architectures @param payload: The targeted architectures description @param osIds: The list of os ids liked with this architecture @return RETURN: The id of the object """
if key not in self: self[key] = payload oid = self[key]['id'] if not oid: return False #~ To be sure the OS list is good, we ensure our os are in the list for os in self[key]['operatingsystems']: osIds.add(os['id']) self[key]["operatingsystem_ids"] = list(osIds) if (len(self[key]['operatingsystems']) is not len(osIds)): return False return oid
<SYSTEM_TASK:> Find the common prefix of two or more paths. <END_TASK> <USER_TASK:> Description: def find_common_prefix( paths: Sequence[Union[str, pathlib.Path]] ) -> Optional[pathlib.Path]: """ Find the common prefix of two or more paths. :: >>> import pathlib >>> one = pathlib.Path('foo/bar/baz') >>> two = pathlib.Path('foo/quux/biz') >>> three = pathlib.Path('foo/quux/wuux') :: >>> import uqbar.io >>> str(uqbar.io.find_common_prefix([one, two, three])) 'foo' :param paths: paths to inspect """
counter: collections.Counter = collections.Counter() for path in paths: path = pathlib.Path(path) counter.update([path]) counter.update(path.parents) valid_paths = sorted( [path for path, count in counter.items() if count >= len(paths)], key=lambda x: len(x.parts), ) if valid_paths: return valid_paths[-1] return None
<SYSTEM_TASK:> r"""Finds executable `name`. <END_TASK> <USER_TASK:> Description: def find_executable(name: str, flags=os.X_OK) -> List[str]: r"""Finds executable `name`. Similar to Unix ``which`` command. Returns list of zero or more full paths to `name`. """
result = [] extensions = [x for x in os.environ.get("PATHEXT", "").split(os.pathsep) if x] path = os.environ.get("PATH", None) if path is None: return [] for path in os.environ.get("PATH", "").split(os.pathsep): path = os.path.join(path, name) if os.access(path, flags): result.append(path) for extension in extensions: path_extension = path + extension if os.access(path_extension, flags): result.append(path_extension) return result
<SYSTEM_TASK:> Walks a directory tree. <END_TASK> <USER_TASK:> Description: def walk( root_path: Union[str, pathlib.Path], top_down: bool = True ) -> Generator[ Tuple[pathlib.Path, Sequence[pathlib.Path], Sequence[pathlib.Path]], None, None ]: """ Walks a directory tree. Like :py:func:`os.walk` but yielding instances of :py:class:`pathlib.Path` instead of strings. :param root_path: foo :param top_down: bar """
root_path = pathlib.Path(root_path) directory_paths, file_paths = [], [] for path in sorted(root_path.iterdir()): if path.is_dir(): directory_paths.append(path) else: file_paths.append(path) if top_down: yield root_path, directory_paths, file_paths for directory_path in directory_paths: yield from walk(directory_path, top_down=top_down) if not top_down: yield root_path, directory_paths, file_paths
<SYSTEM_TASK:> Writes ``contents`` to ``path``. <END_TASK> <USER_TASK:> Description: def write( contents: str, path: Union[str, pathlib.Path], verbose: bool = False, logger_func=None, ) -> bool: """ Writes ``contents`` to ``path``. Checks if ``path`` already exists and only write out new contents if the old contents do not match. Creates any intermediate missing directories. :param contents: the file contents to write :param path: the path to write to :param verbose: whether to print output """
print_func = logger_func or print path = pathlib.Path(path) if path.exists(): with path.open("r") as file_pointer: old_contents = file_pointer.read() if old_contents == contents: if verbose: print_func("preserved {}".format(path)) return False else: with path.open("w") as file_pointer: file_pointer.write(contents) if verbose: print_func("rewrote {}".format(path)) return True elif not path.exists(): if not path.parent.exists(): path.parent.mkdir(parents=True) with path.open("w") as file_pointer: file_pointer.write(contents) if verbose: print_func("wrote {}".format(path)) return True
<SYSTEM_TASK:> Send command without return value, wait for completion, verify success. <END_TASK> <USER_TASK:> Description: def sendQueryVerify(self, cmd): """ Send command without return value, wait for completion, verify success. :param cmd: command to send """
cmd = cmd.strip() self.logger.debug("sendQueryVerify(%s)", cmd) if not self.is_connected(): raise socket.error("sendQueryVerify on a disconnected socket") resp = self.__sendQueryReply(cmd) if resp != self.reply_ok: raise XenaCommandException('Command {} Fail Expected {} Actual {}'.format(cmd, self.reply_ok, resp)) self.logger.debug("SendQueryVerify(%s) Succeed", cmd)
<SYSTEM_TASK:> Modify a changes to add an automatically generated uidNumber. <END_TASK> <USER_TASK:> Description: def save_account(changes: Changeset, table: LdapObjectClass, database: Database) -> Changeset: """ Modify a changes to add an automatically generated uidNumber. """
d = {} settings = database.settings uid_number = changes.get_value_as_single('uidNumber') if uid_number is None: scheme = settings['NUMBER_SCHEME'] first = settings.get('UID_FIRST', 10000) d['uidNumber'] = Counters.get_and_increment( scheme, "uidNumber", first, lambda n: not _check_exists(database, table, 'uidNumber', n) ) changes = changes.merge(d) return changes
<SYSTEM_TASK:> Search for entries in LDAP database. <END_TASK> <USER_TASK:> Description: def search(self, base, scope, filterstr='(objectClass=*)', attrlist=None, limit=None) -> Generator[Tuple[str, dict], None, None]: """ Search for entries in LDAP database. """
_debug("search", base, scope, filterstr, attrlist, limit) # first results if attrlist is None: attrlist = ldap3.ALL_ATTRIBUTES elif isinstance(attrlist, set): attrlist = list(attrlist) def first_results(obj): _debug("---> searching ldap", limit) obj.search( base, filterstr, scope, attributes=attrlist, paged_size=limit) return obj.response # get the 1st result result_list = self._do_with_retry(first_results) # Loop over list of search results for result_item in result_list: # skip searchResRef for now if result_item['type'] != "searchResEntry": continue dn = result_item['dn'] attributes = result_item['raw_attributes'] # did we already retrieve this from cache? _debug("---> got ldap result", dn) _debug("---> yielding", result_item) yield (dn, attributes) # we are finished - return results, eat cake _debug("---> done") return
<SYSTEM_TASK:> Example shows how to configure environment from scratch <END_TASK> <USER_TASK:> Description: def prepare_env(org): """ Example shows how to configure environment from scratch """
# Add services key_service = org.service(type='builtin:cobalt_secure_store', name='Keystore') wf_service = org.service(type='builtin:workflow_service', name='Workflow', parameters='{}') # Add services to environment env = org.environment(name='default') env.clean() env.add_service(key_service) env.add_service(wf_service) env.add_policy( {"action": "provisionVms", "parameter": "publicKeyId", "value": key_service.regenerate()['id']}) # Add cloud provider account access = { "provider": "aws-ec2", "usedEnvironments": [], "ec2SecurityGroup": "default", "providerCopy": "aws-ec2", "name": "test-provider", "jcloudsIdentity": KEY, "jcloudsCredential": SECRET_KEY, "jcloudsRegions": "us-east-1" } prov = org.provider(access) env.add_provider(prov) return org.organizationId
<SYSTEM_TASK:> Commands for devops operations <END_TASK> <USER_TASK:> Description: def start(ctx, debug, version, config): """Commands for devops operations"""
ctx.obj = {} ctx.DEBUG = debug if os.path.isfile(config): with open(config) as fp: agile = json.load(fp) else: agile = {} ctx.obj['agile'] = agile if version: click.echo(__version__) ctx.exit(0) if not ctx.invoked_subcommand: click.echo(ctx.get_help())
<SYSTEM_TASK:> Duplicate all related objects of obj setting <END_TASK> <USER_TASK:> Description: def duplicate(obj, value=None, field=None, duplicate_order=None): """ Duplicate all related objects of obj setting field to value. If one of the duplicate objects has an FK to another duplicate object update that as well. Return the duplicate copy of obj. duplicate_order is a list of models which specify how the duplicate objects are saved. For complex objects this can matter. Check to save if objects are being saved correctly and if not just pass in related objects in the order that they should be saved. """
using = router.db_for_write(obj._meta.model) collector = CloneCollector(using=using) collector.collect([obj]) collector.sort() related_models = list(collector.data.keys()) data_snapshot = {} for key in collector.data.keys(): data_snapshot.update({ key: dict(zip( [item.pk for item in collector.data[key]], [item for item in collector.data[key]])) }) root_obj = None # Sometimes it's good enough just to save in reverse deletion order. if duplicate_order is None: duplicate_order = reversed(related_models) for model in duplicate_order: # Find all FKs on model that point to a related_model. fks = [] for f in model._meta.fields: if isinstance(f, ForeignKey) and f.rel.to in related_models: fks.append(f) # Replace each `sub_obj` with a duplicate. if model not in collector.data: continue sub_objects = collector.data[model] for obj in sub_objects: for fk in fks: fk_value = getattr(obj, "%s_id" % fk.name) # If this FK has been duplicated then point to the duplicate. fk_rel_to = data_snapshot[fk.rel.to] if fk_value in fk_rel_to: dupe_obj = fk_rel_to[fk_value] setattr(obj, fk.name, dupe_obj) # Duplicate the object and save it. obj.id = None if field is not None: setattr(obj, field, value) obj.save() if root_obj is None: root_obj = obj return root_obj
<SYSTEM_TASK:> Enters transaction management for a running thread. It must be balanced <END_TASK> <USER_TASK:> Description: def enter_transaction_management(using=None): """ Enters transaction management for a running thread. It must be balanced with the appropriate leave_transaction_management call, since the actual state is managed as a stack. The state and dirty flag are carried over from the surrounding block or from the settings, if there is no surrounding block (dirty is always false when no current block is running). """
if using is None: for using in tldap.backend.connections: connection = tldap.backend.connections[using] connection.enter_transaction_management() return connection = tldap.backend.connections[using] connection.enter_transaction_management()
<SYSTEM_TASK:> Returns True if the current transaction requires a commit for changes to <END_TASK> <USER_TASK:> Description: def is_dirty(using=None): """ Returns True if the current transaction requires a commit for changes to happen. """
if using is None: dirty = False for using in tldap.backend.connections: connection = tldap.backend.connections[using] if connection.is_dirty(): dirty = True return dirty connection = tldap.backend.connections[using] return connection.is_dirty()
<SYSTEM_TASK:> Checks whether the transaction manager is in manual or in auto state. <END_TASK> <USER_TASK:> Description: def is_managed(using=None): """ Checks whether the transaction manager is in manual or in auto state. """
if using is None: managed = False for using in tldap.backend.connections: connection = tldap.backend.connections[using] if connection.is_managed(): managed = True return managed connection = tldap.backend.connections[using] return connection.is_managed()
<SYSTEM_TASK:> Does the commit itself and resets the dirty flag. <END_TASK> <USER_TASK:> Description: def commit(using=None): """ Does the commit itself and resets the dirty flag. """
if using is None: for using in tldap.backend.connections: connection = tldap.backend.connections[using] connection.commit() return connection = tldap.backend.connections[using] connection.commit()
<SYSTEM_TASK:> This function does the rollback itself and resets the dirty flag. <END_TASK> <USER_TASK:> Description: def rollback(using=None): """ This function does the rollback itself and resets the dirty flag. """
if using is None: for using in tldap.backend.connections: connection = tldap.backend.connections[using] connection.rollback() return connection = tldap.backend.connections[using] connection.rollback()
<SYSTEM_TASK:> This decorator activates commit on response. This way, if the view function <END_TASK> <USER_TASK:> Description: def commit_on_success(using=None): """ This decorator activates commit on response. This way, if the view function runs successfully, a commit is made; if the viewfunc produces an exception, a rollback is made. This is one of the most common ways to do transaction control in Web apps. """
def entering(using): enter_transaction_management(using=using) def exiting(exc_value, using): try: if exc_value is not None: if is_dirty(using=using): rollback(using=using) else: commit(using=using) finally: leave_transaction_management(using=using) return _transaction_func(entering, exiting, using)
<SYSTEM_TASK:> Reloads glitter URL patterns if page URLs change. <END_TASK> <USER_TASK:> Description: def process_request(self, request): """ Reloads glitter URL patterns if page URLs change. Avoids having to restart the server to recreate the glitter URLs being used by Django. """
global _urlconf_pages page_list = list( Page.objects.exclude(glitter_app_name='').values_list('id', 'url').order_by('id') ) with _urlconf_lock: if page_list != _urlconf_pages: glitter_urls = 'glitter.urls' if glitter_urls in sys.modules: importlib.reload(sys.modules[glitter_urls]) _urlconf_pages = page_list