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15,600 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | setup_simulation_from_model_specification | def setup_simulation_from_model_specification(model_specification_file: str) -> InteractiveContext:
"""Construct a simulation from a model specification file and call its setup
method.
Parameters
----------
model_specification_file
The path to a model specification file.
Returns
-------
A simulation context that is setup and ready to run.
"""
simulation = initialize_simulation_from_model_specification(model_specification_file)
simulation.setup()
return simulation | python | def setup_simulation_from_model_specification(model_specification_file: str) -> InteractiveContext:
simulation = initialize_simulation_from_model_specification(model_specification_file)
simulation.setup()
return simulation | [
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15,601 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.setup | def setup(self):
"""Setup the simulation and initialize its population."""
super().setup()
self._start_time = self.clock.time
self.initialize_simulants() | python | def setup(self):
super().setup()
self._start_time = self.clock.time
self.initialize_simulants() | [
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15,602 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.initialize_simulants | def initialize_simulants(self):
"""Initialize this simulation's population. Should not be called
directly."""
super().initialize_simulants()
self._initial_population = self.population.get_population(True) | python | def initialize_simulants(self):
super().initialize_simulants()
self._initial_population = self.population.get_population(True) | [
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15,603 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.reset | def reset(self):
"""Reset the simulation to its initial state."""
warnings.warn("This reset method is very crude. It should work for "
"many simple simulations, but we make no guarantees. In "
"particular, if you have components that manage their "
"own state in any way, this might not work.")
self.population._population = self._initial_population
self.clock._time = self._start_time | python | def reset(self):
warnings.warn("This reset method is very crude. It should work for "
"many simple simulations, but we make no guarantees. In "
"particular, if you have components that manage their "
"own state in any way, this might not work.")
self.population._population = self._initial_population
self.clock._time = self._start_time | [
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15,604 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.run | def run(self, with_logging: bool=True) -> int:
"""Run the simulation for the time duration specified in the
configuration
Parameters
----------
with_logging
Whether or not to log the simulation steps. Only works in an ipython
environment.
Returns
-------
The number of steps the simulation took.
"""
return self.run_until(self.clock.stop_time, with_logging=with_logging) | python | def run(self, with_logging: bool=True) -> int:
return self.run_until(self.clock.stop_time, with_logging=with_logging) | [
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15,605 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.run_for | def run_for(self, duration: Timedelta, with_logging: bool=True) -> int:
"""Run the simulation for the given time duration.
Parameters
----------
duration
The length of time to run the simulation for. Should be the same
type as the simulation clock's step size (usually a pandas
Timedelta).
with_logging
Whether or not to log the simulation steps. Only works in an ipython
environment.
Returns
-------
The number of steps the simulation took.
"""
return self.run_until(self.clock.time + duration, with_logging=with_logging) | python | def run_for(self, duration: Timedelta, with_logging: bool=True) -> int:
return self.run_until(self.clock.time + duration, with_logging=with_logging) | [
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15,606 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.run_until | def run_until(self, end_time: Time, with_logging=True) -> int:
"""Run the simulation until the provided end time.
Parameters
----------
end_time
The time to run the simulation until. The simulation will run until
its clock is greater than or equal to the provided end time.
with_logging
Whether or not to log the simulation steps. Only works in an ipython
environment.
Returns
-------
The number of steps the simulation took.
"""
if not isinstance(end_time, type(self.clock.time)):
raise ValueError(f"Provided time must be an instance of {type(self.clock.time)}")
iterations = int(ceil((end_time - self.clock.time)/self.clock.step_size))
self.take_steps(number_of_steps=iterations, with_logging=with_logging)
assert self.clock.time - self.clock.step_size < end_time <= self.clock.time
return iterations | python | def run_until(self, end_time: Time, with_logging=True) -> int:
if not isinstance(end_time, type(self.clock.time)):
raise ValueError(f"Provided time must be an instance of {type(self.clock.time)}")
iterations = int(ceil((end_time - self.clock.time)/self.clock.step_size))
self.take_steps(number_of_steps=iterations, with_logging=with_logging)
assert self.clock.time - self.clock.step_size < end_time <= self.clock.time
return iterations | [
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15,607 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.step | def step(self, step_size: Timedelta=None):
"""Advance the simulation one step.
Parameters
----------
step_size
An optional size of step to take. Must be the same type as the
simulation clock's step size (usually a pandas.Timedelta).
"""
old_step_size = self.clock.step_size
if step_size is not None:
if not isinstance(step_size, type(self.clock.step_size)):
raise ValueError(f"Provided time must be an instance of {type(self.clock.step_size)}")
self.clock._step_size = step_size
super().step()
self.clock._step_size = old_step_size | python | def step(self, step_size: Timedelta=None):
old_step_size = self.clock.step_size
if step_size is not None:
if not isinstance(step_size, type(self.clock.step_size)):
raise ValueError(f"Provided time must be an instance of {type(self.clock.step_size)}")
self.clock._step_size = step_size
super().step()
self.clock._step_size = old_step_size | [
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15,608 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.take_steps | def take_steps(self, number_of_steps: int=1, step_size: Timedelta=None, with_logging: bool=True):
"""Run the simulation for the given number of steps.
Parameters
----------
number_of_steps
The number of steps to take.
step_size
An optional size of step to take. Must be the same type as the
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Whether or not to log the simulation steps. Only works in an ipython
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"""
if not isinstance(number_of_steps, int):
raise ValueError('Number of steps must be an integer.')
if run_from_ipython() and with_logging:
for _ in log_progress(range(number_of_steps), name='Step'):
self.step(step_size)
else:
for _ in range(number_of_steps):
self.step(step_size) | python | def take_steps(self, number_of_steps: int=1, step_size: Timedelta=None, with_logging: bool=True):
if not isinstance(number_of_steps, int):
raise ValueError('Number of steps must be an integer.')
if run_from_ipython() and with_logging:
for _ in log_progress(range(number_of_steps), name='Step'):
self.step(step_size)
else:
for _ in range(number_of_steps):
self.step(step_size) | [
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15,609 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.get_population | def get_population(self, untracked: bool=False) -> pd.DataFrame:
"""Get a copy of the population state table."""
return self.population.get_population(untracked) | python | def get_population(self, untracked: bool=False) -> pd.DataFrame:
return self.population.get_population(untracked) | [
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15,610 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.get_listeners | def get_listeners(self, event_type: str) -> List[Callable]:
"""Get all listeners of a particular type of event."""
if event_type not in self.events:
raise ValueError(f'No event {event_type} in system.')
return self.events.get_listeners(event_type) | python | def get_listeners(self, event_type: str) -> List[Callable]:
if event_type not in self.events:
raise ValueError(f'No event {event_type} in system.')
return self.events.get_listeners(event_type) | [
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15,611 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.get_emitter | def get_emitter(self, event_type: str) -> Callable:
"""Get the callable that emits the given type of events."""
if event_type not in self.events:
raise ValueError(f'No event {event_type} in system.')
return self.events.get_emitter(event_type) | python | def get_emitter(self, event_type: str) -> Callable:
if event_type not in self.events:
raise ValueError(f'No event {event_type} in system.')
return self.events.get_emitter(event_type) | [
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15,612 | ihmeuw/vivarium | src/vivarium/interface/interactive.py | InteractiveContext.get_components | def get_components(self) -> List:
"""Get a list of all components in the simulation."""
return [component for component in self.component_manager._components + self.component_manager._managers] | python | def get_components(self) -> List:
return [component for component in self.component_manager._components + self.component_manager._managers] | [
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15,613 | ihmeuw/vivarium | src/vivarium/framework/lookup.py | LookupTableInterface.build_table | def build_table(self, data, key_columns=('sex',), parameter_columns=(['age', 'age_group_start', 'age_group_end'],
['year', 'year_start', 'year_end']),
value_columns=None) -> LookupTable:
"""Construct a LookupTable from input data.
If data is a ``pandas.DataFrame``, an interpolation function of the specified
order will be calculated for each permutation of the set of key_columns.
The columns in parameter_columns will be used as parameters for the interpolation
functions which will estimate all remaining columns in the table.
If data is a number, time, list, or tuple, a scalar table will be constructed with
the values in data as the values in each column of the table, named according to
value_columns.
Parameters
----------
data : The source data which will be used to build the resulting LookupTable.
key_columns : [str]
Columns used to select between interpolation functions. These
should be the non-continuous variables in the data. For
example 'sex' in data about a population.
parameter_columns : [str]
The columns which contain the parameters to the interpolation functions.
These should be the continuous variables. For example 'age'
in data about a population.
value_columns : [str]
The data columns that will be in the resulting LookupTable. Columns to be
interpolated over if interpolation or the names of the columns in the scalar
table.
Returns
-------
LookupTable
"""
return self._lookup_table_manager.build_table(data, key_columns, parameter_columns, value_columns) | python | def build_table(self, data, key_columns=('sex',), parameter_columns=(['age', 'age_group_start', 'age_group_end'],
['year', 'year_start', 'year_end']),
value_columns=None) -> LookupTable:
return self._lookup_table_manager.build_table(data, key_columns, parameter_columns, value_columns) | [
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key_columns : [str]
Columns used to select between interpolation functions. These
should be the non-continuous variables in the data. For
example 'sex' in data about a population.
parameter_columns : [str]
The columns which contain the parameters to the interpolation functions.
These should be the continuous variables. For example 'age'
in data about a population.
value_columns : [str]
The data columns that will be in the resulting LookupTable. Columns to be
interpolated over if interpolation or the names of the columns in the scalar
table.
Returns
-------
LookupTable | [
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15,614 | ihmeuw/vivarium | src/vivarium/framework/results_writer.py | ResultsWriter.add_sub_directory | def add_sub_directory(self, key, path):
"""Adds a sub-directory to the results directory.
Parameters
----------
key: str
A look-up key for the directory path.
path: str
The relative path from the root of the results directory to the sub-directory.
Returns
-------
str:
The absolute path to the sub-directory.
"""
sub_dir_path = os.path.join(self.results_root, path)
os.makedirs(sub_dir_path, exist_ok=True)
self._directories[key] = sub_dir_path
return sub_dir_path | python | def add_sub_directory(self, key, path):
sub_dir_path = os.path.join(self.results_root, path)
os.makedirs(sub_dir_path, exist_ok=True)
self._directories[key] = sub_dir_path
return sub_dir_path | [
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15,615 | ihmeuw/vivarium | src/vivarium/framework/results_writer.py | ResultsWriter.write_output | def write_output(self, data, file_name, key=None):
"""Writes output data to disk.
Parameters
----------
data: pandas.DataFrame or dict
The data to write to disk.
file_name: str
The name of the file to write.
key: str, optional
The lookup key for the sub_directory to write results to, if any.
"""
path = os.path.join(self._directories[key], file_name)
extension = file_name.split('.')[-1]
if extension == 'yaml':
with open(path, 'w') as f:
yaml.dump(data, f)
elif extension == 'hdf':
# to_hdf breaks with categorical dtypes.
categorical_columns = data.dtypes[data.dtypes == 'category'].index
data.loc[:, categorical_columns] = data.loc[:, categorical_columns].astype('object')
# Writing to an hdf over and over balloons the file size so write to new file and move it over to avoid
data.to_hdf(path + "update", 'data')
if os.path.exists(path):
os.remove(path)
os.rename(path + "update", path)
else:
raise NotImplementedError(
f"Only 'yaml' and 'hdf' file types are supported. You requested {extension}") | python | def write_output(self, data, file_name, key=None):
path = os.path.join(self._directories[key], file_name)
extension = file_name.split('.')[-1]
if extension == 'yaml':
with open(path, 'w') as f:
yaml.dump(data, f)
elif extension == 'hdf':
# to_hdf breaks with categorical dtypes.
categorical_columns = data.dtypes[data.dtypes == 'category'].index
data.loc[:, categorical_columns] = data.loc[:, categorical_columns].astype('object')
# Writing to an hdf over and over balloons the file size so write to new file and move it over to avoid
data.to_hdf(path + "update", 'data')
if os.path.exists(path):
os.remove(path)
os.rename(path + "update", path)
else:
raise NotImplementedError(
f"Only 'yaml' and 'hdf' file types are supported. You requested {extension}") | [
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15,616 | ihmeuw/vivarium | src/vivarium/framework/results_writer.py | ResultsWriter.copy_file | def copy_file(self, src_path, file_name, key=None):
"""Copies a file unmodified to a location inside the ouput directory.
Parameters
----------
src_path: str
Path to the src file
file_name: str
name of the destination file
"""
path = os.path.join(self._directories[key], file_name)
shutil.copyfile(src_path, path) | python | def copy_file(self, src_path, file_name, key=None):
path = os.path.join(self._directories[key], file_name)
shutil.copyfile(src_path, path) | [
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15,617 | ihmeuw/vivarium | src/vivarium/framework/values.py | replace_combiner | def replace_combiner(value, mutator, *args, **kwargs):
"""Replaces the output of the source or mutator with the output
of the subsequent mutator. This is the default combiner.
"""
args = list(args) + [value]
return mutator(*args, **kwargs) | python | def replace_combiner(value, mutator, *args, **kwargs):
args = list(args) + [value]
return mutator(*args, **kwargs) | [
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15,618 | ihmeuw/vivarium | src/vivarium/framework/values.py | set_combiner | def set_combiner(value, mutator, *args, **kwargs):
"""Expects the output of the source to be a set to which
the result of each mutator is added.
"""
value.add(mutator(*args, **kwargs))
return value | python | def set_combiner(value, mutator, *args, **kwargs):
value.add(mutator(*args, **kwargs))
return value | [
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15,619 | ihmeuw/vivarium | src/vivarium/framework/values.py | list_combiner | def list_combiner(value, mutator, *args, **kwargs):
"""Expects the output of the source to be a list to which
the result of each mutator is appended.
"""
value.append(mutator(*args, **kwargs))
return value | python | def list_combiner(value, mutator, *args, **kwargs):
value.append(mutator(*args, **kwargs))
return value | [
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15,620 | ihmeuw/vivarium | src/vivarium/framework/values.py | ValuesInterface.register_value_producer | def register_value_producer(self, value_name: str, source: Callable[..., pd.DataFrame]=None,
preferred_combiner: Callable=replace_combiner,
preferred_post_processor: Callable[..., pd.DataFrame]=None) -> Pipeline:
"""Marks a ``Callable`` as the producer of a named value.
Parameters
----------
value_name :
The name of the new dynamic value pipeline.
source :
A callable source for the dynamic value pipeline.
preferred_combiner :
A strategy for combining the source and the results of any calls to mutators in the pipeline.
``vivarium`` provides the strategies ``replace_combiner`` (the default), ``list_combiner``,
and ``set_combiner`` which are importable from ``vivarium.framework.values``. Client code
may define additional strategies as necessary.
preferred_post_processor :
A strategy for processing the final output of the pipeline. ``vivarium`` provides the strategies
``rescale_post_processor`` and ``joint_value_post_processor`` which are importable from
``vivarium.framework.values``. Client code may define additional strategies as necessary.
Returns
-------
Callable
A callable reference to the named dynamic value pipeline.
"""
return self._value_manager.register_value_producer(value_name, source,
preferred_combiner,
preferred_post_processor) | python | def register_value_producer(self, value_name: str, source: Callable[..., pd.DataFrame]=None,
preferred_combiner: Callable=replace_combiner,
preferred_post_processor: Callable[..., pd.DataFrame]=None) -> Pipeline:
return self._value_manager.register_value_producer(value_name, source,
preferred_combiner,
preferred_post_processor) | [
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15,621 | ihmeuw/vivarium | src/vivarium/framework/values.py | ValuesInterface.register_rate_producer | def register_rate_producer(self, rate_name: str, source: Callable[..., pd.DataFrame]=None) -> Pipeline:
"""Marks a ``Callable`` as the producer of a named rate.
This is a convenience wrapper around ``register_value_producer`` that makes sure
rate data is appropriately scaled to the size of the simulation time step.
It is equivalent to ``register_value_producer(value_name, source,
preferred_combiner=replace_combiner, preferred_post_processor=rescale_post_processor)``
Parameters
----------
rate_name :
The name of the new dynamic rate pipeline.
source :
A callable source for the dynamic rate pipeline.
Returns
-------
Callable
A callable reference to the named dynamic rate pipeline.
"""
return self._value_manager.register_rate_producer(rate_name, source) | python | def register_rate_producer(self, rate_name: str, source: Callable[..., pd.DataFrame]=None) -> Pipeline:
return self._value_manager.register_rate_producer(rate_name, source) | [
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15,622 | ihmeuw/vivarium | src/vivarium/framework/values.py | ValuesInterface.register_value_modifier | def register_value_modifier(self, value_name: str, modifier: Callable, priority: int=5):
"""Marks a ``Callable`` as the modifier of a named value.
Parameters
----------
value_name :
The name of the dynamic value pipeline to be modified.
modifier :
A function that modifies the source of the dynamic value pipeline when called.
If the pipeline has a ``replace_combiner``, the modifier should accept the same
arguments as the pipeline source with an additional last positional argument
for the results of the previous stage in the pipeline. For the ``list_combiner`` and
``set_combiner`` strategies, the pipeline modifiers should have the same signature
as the pipeline source.
priority : {0, 1, 2, 3, 4, 5, 6, 7, 8, 9}
An indication of the order in which pipeline modifiers should be called. Modifiers with
smaller priority values will be called earlier in the pipeline. Modifiers with
the same priority have no guaranteed ordering, and so should be commutative.
"""
self._value_manager.register_value_modifier(value_name, modifier, priority) | python | def register_value_modifier(self, value_name: str, modifier: Callable, priority: int=5):
self._value_manager.register_value_modifier(value_name, modifier, priority) | [
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15,623 | ihmeuw/vivarium | src/vivarium/interface/cli.py | run | def run(model_specification, results_directory, verbose, log, with_debugger):
"""Run a simulation from the command line.
The simulation itself is defined by the given MODEL_SPECIFICATION yaml file.
Within the results directory, which defaults to ~/vivarium_results if none
is provided, a subdirectory will be created with the same name as the
MODEL_SPECIFICATION if one does not exist. Results will be written to a
further subdirectory named after the start time of the simulation run."""
log_level = logging.DEBUG if verbose else logging.ERROR
logging.basicConfig(filename=log, level=log_level)
try:
run_simulation(model_specification, results_directory)
except (BdbQuit, KeyboardInterrupt):
raise
except Exception as e:
if with_debugger:
import pdb
import traceback
traceback.print_exc()
pdb.post_mortem()
else:
logging.exception("Uncaught exception {}".format(e))
raise | python | def run(model_specification, results_directory, verbose, log, with_debugger):
log_level = logging.DEBUG if verbose else logging.ERROR
logging.basicConfig(filename=log, level=log_level)
try:
run_simulation(model_specification, results_directory)
except (BdbQuit, KeyboardInterrupt):
raise
except Exception as e:
if with_debugger:
import pdb
import traceback
traceback.print_exc()
pdb.post_mortem()
else:
logging.exception("Uncaught exception {}".format(e))
raise | [
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15,624 | ihmeuw/vivarium | src/vivarium/interface/cli.py | profile | def profile(model_specification, results_directory, process):
"""Run a simulation based on the provided MODEL_SPECIFICATION and profile
the run.
"""
model_specification = Path(model_specification)
results_directory = Path(results_directory)
out_stats_file = results_directory / f'{model_specification.name}'.replace('yaml', 'stats')
command = f'run_simulation("{model_specification}", "{results_directory}")'
cProfile.runctx(command, globals=globals(), locals=locals(), filename=out_stats_file)
if process:
out_txt_file = results_directory / (out_stats_file.name + '.txt')
with open(out_txt_file, 'w') as f:
p = pstats.Stats(str(out_stats_file), stream=f)
p.sort_stats('cumulative')
p.print_stats() | python | def profile(model_specification, results_directory, process):
model_specification = Path(model_specification)
results_directory = Path(results_directory)
out_stats_file = results_directory / f'{model_specification.name}'.replace('yaml', 'stats')
command = f'run_simulation("{model_specification}", "{results_directory}")'
cProfile.runctx(command, globals=globals(), locals=locals(), filename=out_stats_file)
if process:
out_txt_file = results_directory / (out_stats_file.name + '.txt')
with open(out_txt_file, 'w') as f:
p = pstats.Stats(str(out_stats_file), stream=f)
p.sort_stats('cumulative')
p.print_stats() | [
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15,625 | ihmeuw/vivarium | src/vivarium/framework/event.py | Event.split | def split(self, new_index):
"""Create a new event which is a copy of this one but with a new index.
"""
new_event = Event(new_index, self.user_data)
new_event.time = self.time
new_event.step_size = self.step_size
return new_event | python | def split(self, new_index):
new_event = Event(new_index, self.user_data)
new_event.time = self.time
new_event.step_size = self.step_size
return new_event | [
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15,626 | ihmeuw/vivarium | src/vivarium/framework/event.py | _EventChannel.emit | def emit(self, event):
"""Notifies all listeners to this channel that an event has occurred.
Parameters
----------
event : Event
The event to be emitted.
"""
if hasattr(event, 'time'):
event.step_size = self.manager.step_size()
event.time = self.manager.clock() + self.manager.step_size()
for priority_bucket in self.listeners:
for listener in sorted(priority_bucket, key=lambda x: x.__name__):
listener(event)
return event | python | def emit(self, event):
if hasattr(event, 'time'):
event.step_size = self.manager.step_size()
event.time = self.manager.clock() + self.manager.step_size()
for priority_bucket in self.listeners:
for listener in sorted(priority_bucket, key=lambda x: x.__name__):
listener(event)
return event | [
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15,627 | ihmeuw/vivarium | src/vivarium/framework/event.py | EventManager.setup | def setup(self, builder):
"""Performs this components simulation setup.
Parameters
----------
builder : vivarium.framework.engine.Builder
Object giving access to core framework functionality.
"""
self.clock = builder.time.clock()
self.step_size = builder.time.step_size() | python | def setup(self, builder):
self.clock = builder.time.clock()
self.step_size = builder.time.step_size() | [
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15,628 | ihmeuw/vivarium | src/vivarium/framework/event.py | EventManager.register_listener | def register_listener(self, name, listener, priority=5):
"""Registers a new listener to the named event.
Parameters
----------
name : str
The name of the event.
listener : Callable
The consumer of the named event.
priority : int
Number in range(10) used to assign the ordering in which listeners process the event.
"""
self._event_types[name].listeners[priority].append(listener) | python | def register_listener(self, name, listener, priority=5):
self._event_types[name].listeners[priority].append(listener) | [
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The name of the event.
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15,629 | ihmeuw/vivarium | src/vivarium/framework/event.py | EventInterface.get_emitter | def get_emitter(self, name: str) -> Callable[[Event], Event]:
"""Gets and emitter for a named event.
Parameters
----------
name :
The name of the event he requested emitter will emit.
Users may provide their own named events by requesting an emitter with this function,
but should do so with caution as it makes time much more difficult to think about.
Returns
-------
An emitter for the named event. The emitter should be called by the requesting component
at the appropriate point in the simulation lifecycle.
"""
return self._event_manager.get_emitter(name) | python | def get_emitter(self, name: str) -> Callable[[Event], Event]:
return self._event_manager.get_emitter(name) | [
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15,630 | ihmeuw/vivarium | src/vivarium/framework/event.py | EventInterface.register_listener | def register_listener(self, name: str, listener: Callable[[Event], None], priority: int=5) -> None:
"""Registers a callable as a listener to a events with the given name.
The listening callable will be called with a named ``Event`` as it's only argument any time the
event emitter is invoked from somewhere in the simulation.
The framework creates the following events and emits them at different points in the simulation:
At the end of the setup phase: ``post_setup``
Every time step: ``time_step__prepare``, ``time_step``, ``time_step__cleanup``, ``collect_metrics``
At simulation end: ``simulation_end``
Parameters
----------
name :
The name of the event to listen for.
listener :
The callable to be invoked any time an ``Event`` with the given name is emitted.
priority : {0, 1, 2, 3, 4, 5, 6, 7, 8, 9}
An indication of the order in which event listeners should be called. Listeners with
smaller priority values will be called earlier. Listeners with the same priority have
no guaranteed ordering. This feature should be avoided if possible. Components should
strive to obey the Markov property as they transform the state table (the state of the simulation
at the beginning of the next time step should only depend on the current state of the system).
"""
self._event_manager.register_listener(name, listener, priority) | python | def register_listener(self, name: str, listener: Callable[[Event], None], priority: int=5) -> None:
self._event_manager.register_listener(name, listener, priority) | [
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At the end of the setup phase: ``post_setup``
Every time step: ``time_step__prepare``, ``time_step``, ``time_step__cleanup``, ``collect_metrics``
At simulation end: ``simulation_end``
Parameters
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name :
The name of the event to listen for.
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The callable to be invoked any time an ``Event`` with the given name is emitted.
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An indication of the order in which event listeners should be called. Listeners with
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15,631 | ihmeuw/vivarium | src/vivarium/framework/population.py | PopulationView.get | def get(self, index: pd.Index, query: str='', omit_missing_columns: bool=False) -> pd.DataFrame:
"""For the rows in ``index`` get the columns from the simulation's population which this view is configured.
The result may be further filtered by the view's query.
Parameters
----------
index :
Index of the population to get.
query :
Conditions used to filter the index. May use columns not in the requested view.
omit_missing_columns :
Silently skip loading columns which are not present in the population table. In general you want this to
be False because that situation indicates an error but sometimes, like during population initialization,
it can be convenient to just load whatever data is actually available.
Returns
-------
pd.DataFrame
A table with the subset of the population requested.
"""
pop = self.manager.get_population(True).loc[index]
if self._query:
pop = pop.query(self._query)
if query:
pop = pop.query(query)
if not self._columns:
return pop
else:
if omit_missing_columns:
columns = list(set(self._columns).intersection(pop.columns))
else:
columns = self._columns
try:
return pop[columns].copy()
except KeyError:
non_existent_columns = set(columns) - set(pop.columns)
raise PopulationError(f'Requested column(s) {non_existent_columns} not in population table.') | python | def get(self, index: pd.Index, query: str='', omit_missing_columns: bool=False) -> pd.DataFrame:
pop = self.manager.get_population(True).loc[index]
if self._query:
pop = pop.query(self._query)
if query:
pop = pop.query(query)
if not self._columns:
return pop
else:
if omit_missing_columns:
columns = list(set(self._columns).intersection(pop.columns))
else:
columns = self._columns
try:
return pop[columns].copy()
except KeyError:
non_existent_columns = set(columns) - set(pop.columns)
raise PopulationError(f'Requested column(s) {non_existent_columns} not in population table.') | [
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Index of the population to get.
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Conditions used to filter the index. May use columns not in the requested view.
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Silently skip loading columns which are not present in the population table. In general you want this to
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15,632 | ihmeuw/vivarium | src/vivarium/framework/population.py | PopulationView.update | def update(self, pop: Union[pd.DataFrame, pd.Series]):
"""Update the simulation's state to match ``pop``
Parameters
----------
pop :
The data which should be copied into the simulation's state. If ``pop`` is a DataFrame only those columns
included in the view's columns will be used. If ``pop`` is a Series it must have a name that matches
one of the view's columns unless the view only has one column in which case the Series will be assumed to
refer to that regardless of its name.
"""
if not pop.empty:
if isinstance(pop, pd.Series):
if pop.name in self._columns:
affected_columns = [pop.name]
elif len(self._columns) == 1:
affected_columns = self._columns
else:
raise PopulationError('Cannot update with a Series unless the series name equals a column '
'name or there is only a single column in the view')
else:
affected_columns = set(pop.columns)
affected_columns = set(affected_columns).intersection(self._columns)
state_table = self.manager.get_population(True)
if not self.manager.growing:
affected_columns = set(affected_columns).intersection(state_table.columns)
for c in affected_columns:
if c in state_table:
v = state_table[c].values
if isinstance(pop, pd.Series):
v2 = pop.values
else:
v2 = pop[c].values
v[pop.index] = v2
if v.dtype != v2.dtype:
# This happens when the population is being grown because extending
# the index forces columns that don't have a natural null type
# to become 'object'
if not self.manager.growing:
raise PopulationError('Component corrupting population table. '
'Old column type: {} New column type: {}'.format(v.dtype, v2.dtype))
v = v.astype(v2.dtype)
else:
if isinstance(pop, pd.Series):
v = pop.values
else:
v = pop[c].values
self.manager._population[c] = v | python | def update(self, pop: Union[pd.DataFrame, pd.Series]):
if not pop.empty:
if isinstance(pop, pd.Series):
if pop.name in self._columns:
affected_columns = [pop.name]
elif len(self._columns) == 1:
affected_columns = self._columns
else:
raise PopulationError('Cannot update with a Series unless the series name equals a column '
'name or there is only a single column in the view')
else:
affected_columns = set(pop.columns)
affected_columns = set(affected_columns).intersection(self._columns)
state_table = self.manager.get_population(True)
if not self.manager.growing:
affected_columns = set(affected_columns).intersection(state_table.columns)
for c in affected_columns:
if c in state_table:
v = state_table[c].values
if isinstance(pop, pd.Series):
v2 = pop.values
else:
v2 = pop[c].values
v[pop.index] = v2
if v.dtype != v2.dtype:
# This happens when the population is being grown because extending
# the index forces columns that don't have a natural null type
# to become 'object'
if not self.manager.growing:
raise PopulationError('Component corrupting population table. '
'Old column type: {} New column type: {}'.format(v.dtype, v2.dtype))
v = v.astype(v2.dtype)
else:
if isinstance(pop, pd.Series):
v = pop.values
else:
v = pop[c].values
self.manager._population[c] = v | [
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15,633 | ihmeuw/vivarium | src/vivarium/framework/population.py | PopulationManager.get_view | def get_view(self, columns: Sequence[str], query: str=None) -> PopulationView:
"""Return a configured PopulationView
Notes
-----
Client code should only need this (and only through the version exposed as
``population_view`` on the builder during setup) if it uses dynamically
generated column names that aren't known at definition time. Otherwise
components should use ``uses_columns``.
"""
if 'tracked' not in columns:
query_with_track = query + 'and tracked == True' if query else 'tracked == True'
return PopulationView(self, columns, query_with_track)
return PopulationView(self, columns, query) | python | def get_view(self, columns: Sequence[str], query: str=None) -> PopulationView:
if 'tracked' not in columns:
query_with_track = query + 'and tracked == True' if query else 'tracked == True'
return PopulationView(self, columns, query_with_track)
return PopulationView(self, columns, query) | [
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15,634 | ihmeuw/vivarium | src/vivarium/framework/population.py | PopulationInterface.get_view | def get_view(self, columns: Sequence[str], query: str = None) -> PopulationView:
"""Get a time-varying view of the population state table.
The requested population view can be used to view the current state or to update the state
with new values.
Parameters
----------
columns :
A subset of the state table columns that will be available in the returned view.
query :
A filter on the population state. This filters out particular rows (simulants) based
on their current state. The query should be provided in a way that is understood by
the ``pandas.DataFrame.query`` method and may reference state table columns not
requested in the ``columns`` argument.
Returns
-------
PopulationView
A filtered view of the requested columns of the population state table.
"""
return self._population_manager.get_view(columns, query) | python | def get_view(self, columns: Sequence[str], query: str = None) -> PopulationView:
return self._population_manager.get_view(columns, query) | [
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A subset of the state table columns that will be available in the returned view.
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A filter on the population state. This filters out particular rows (simulants) based
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15,635 | ihmeuw/vivarium | src/vivarium/framework/population.py | PopulationInterface.initializes_simulants | def initializes_simulants(self, initializer: Callable[[SimulantData], None],
creates_columns: Sequence[str]=(),
requires_columns: Sequence[str]=()):
"""Marks a callable as a source of initial state information for new simulants.
Parameters
----------
initializer :
A callable that adds or updates initial state information about new simulants.
creates_columns :
A list of the state table columns that the given initializer provides the initial state information for.
requires_columns :
A list of the state table columns that already need to be present and populated
in the state table before the provided initializer is called.
"""
self._population_manager.register_simulant_initializer(initializer, creates_columns, requires_columns) | python | def initializes_simulants(self, initializer: Callable[[SimulantData], None],
creates_columns: Sequence[str]=(),
requires_columns: Sequence[str]=()):
self._population_manager.register_simulant_initializer(initializer, creates_columns, requires_columns) | [
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15,636 | datosgobar/pydatajson | pydatajson/helpers.py | ensure_dir_exists | def ensure_dir_exists(directory):
"""Se asegura de que un directorio exista."""
if directory and not os.path.exists(directory):
os.makedirs(directory) | python | def ensure_dir_exists(directory):
if directory and not os.path.exists(directory):
os.makedirs(directory) | [
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15,637 | datosgobar/pydatajson | pydatajson/helpers.py | traverse_dict | def traverse_dict(dicc, keys, default_value=None):
"""Recorre un diccionario siguiendo una lista de claves, y devuelve
default_value en caso de que alguna de ellas no exista.
Args:
dicc (dict): Diccionario a ser recorrido.
keys (list): Lista de claves a ser recorrida. Puede contener
índices de listas y claves de diccionarios mezcladas.
default_value: Valor devuelto en caso de que `dicc` no se pueda
recorrer siguiendo secuencialmente la lista de `keys` hasta
el final.
Returns:
object: El valor obtenido siguiendo la lista de `keys` dentro de
`dicc`.
"""
for key in keys:
if isinstance(dicc, dict) and key in dicc:
dicc = dicc[key]
elif (isinstance(dicc, list)
and isinstance(key, int)
and key < len(dicc)):
dicc = dicc[key]
else:
return default_value
return dicc | python | def traverse_dict(dicc, keys, default_value=None):
for key in keys:
if isinstance(dicc, dict) and key in dicc:
dicc = dicc[key]
elif (isinstance(dicc, list)
and isinstance(key, int)
and key < len(dicc)):
dicc = dicc[key]
else:
return default_value
return dicc | [
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15,638 | datosgobar/pydatajson | pydatajson/helpers.py | parse_value | def parse_value(cell):
"""Extrae el valor de una celda de Excel como texto."""
value = cell.value
# stripea espacios en strings
if isinstance(value, string_types):
value = value.strip()
# convierte a texto ISO 8601 las fechas
if isinstance(value, (datetime)):
value = value.isoformat()
return value | python | def parse_value(cell):
value = cell.value
# stripea espacios en strings
if isinstance(value, string_types):
value = value.strip()
# convierte a texto ISO 8601 las fechas
if isinstance(value, (datetime)):
value = value.isoformat()
return value | [
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15,639 | datosgobar/pydatajson | pydatajson/helpers.py | sheet_to_table | def sheet_to_table(worksheet):
"""Transforma una hoja de libro de Excel en una lista de diccionarios.
Args:
worksheet (Workbook.worksheet): Hoja de cálculo de un archivo XLSX
según los lee `openpyxl`
Returns:
list_of_dicts: Lista de diccionarios, con tantos elementos como
registros incluya la hoja, y con tantas claves por diccionario como
campos tenga la hoja.
"""
headers = []
value_rows = []
for row_i, row in enumerate(worksheet.iter_rows()):
# lee los headers y el tamaño máximo de la hoja en columnas en fila 1
if row_i == 0:
for header_cell in row:
if header_cell.value:
headers.append(parse_value(header_cell))
else:
break
continue
# limita la cantidad de celdas a considerar, por la cantidad de headers
row_cells = [parse_value(cell) for index, cell in enumerate(row)
if index < len(headers)]
# agrega las filas siguientes que tengan al menos un campo no nulo
if any(row_cells):
value_rows.append(row_cells)
# no se admiten filas vacías, eso determina el fin de la hoja
else:
break
# convierte las filas en diccionarios con los headers como keys
table = [
# Ignoro los campos con valores nulos (None)
{k: v for (k, v) in zip(headers, row) if v is not None}
for row in value_rows
]
return table | python | def sheet_to_table(worksheet):
headers = []
value_rows = []
for row_i, row in enumerate(worksheet.iter_rows()):
# lee los headers y el tamaño máximo de la hoja en columnas en fila 1
if row_i == 0:
for header_cell in row:
if header_cell.value:
headers.append(parse_value(header_cell))
else:
break
continue
# limita la cantidad de celdas a considerar, por la cantidad de headers
row_cells = [parse_value(cell) for index, cell in enumerate(row)
if index < len(headers)]
# agrega las filas siguientes que tengan al menos un campo no nulo
if any(row_cells):
value_rows.append(row_cells)
# no se admiten filas vacías, eso determina el fin de la hoja
else:
break
# convierte las filas en diccionarios con los headers como keys
table = [
# Ignoro los campos con valores nulos (None)
{k: v for (k, v) in zip(headers, row) if v is not None}
for row in value_rows
]
return table | [
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15,640 | datosgobar/pydatajson | pydatajson/helpers.py | string_to_list | def string_to_list(string, sep=",", filter_empty=False):
"""Transforma una string con elementos separados por `sep` en una lista."""
return [value.strip() for value in string.split(sep)
if (not filter_empty or value)] | python | def string_to_list(string, sep=",", filter_empty=False):
return [value.strip() for value in string.split(sep)
if (not filter_empty or value)] | [
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15,641 | datosgobar/pydatajson | pydatajson/transformation.py | generate_distribution_ids | def generate_distribution_ids(catalog):
"""Genera identificadores para las distribuciones que no los tienen.
Los identificadores de distribuciones se generan concatenando el id del
dataset al que pertenecen con el índice posicional de la distribución en el
dataset: distribution_identifier = "{dataset_identifier}_{index}".
"""
for dataset in catalog.get("dataset", []):
for distribution_index, distribution in enumerate(
dataset.get("distribution", [])):
if "identifier" not in distribution:
distribution["identifier"] = "{}_{}".format(
dataset["identifier"], distribution_index) | python | def generate_distribution_ids(catalog):
for dataset in catalog.get("dataset", []):
for distribution_index, distribution in enumerate(
dataset.get("distribution", [])):
if "identifier" not in distribution:
distribution["identifier"] = "{}_{}".format(
dataset["identifier"], distribution_index) | [
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15,642 | ihmeuw/vivarium | src/vivarium/examples/disease_model/population.py | BasePopulation.on_initialize_simulants | def on_initialize_simulants(self, pop_data: SimulantData):
"""Called by the simulation whenever new simulants are added.
This component is responsible for creating and filling four columns
in the population state table:
'age' :
The age of the simulant in fractional years.
'sex' :
The sex of the simulant. One of {'Male', 'Female'}
'alive' :
Whether or not the simulant is alive. One of {'alive', 'dead'}
'entrance_time' :
The time that the simulant entered the simulation. The 'birthday'
for simulants that enter as newborns. A `pandas.Timestamp`.
Parameters
----------
pop_data :
A record containing the index of the new simulants, the
start of the time step the simulants are added on, the width
of the time step, and the age boundaries for the simulants to
generate.
"""
age_start = self.config.population.age_start
age_end = self.config.population.age_end
if age_start == age_end:
age_window = pop_data.creation_window / pd.Timedelta(days=365)
else:
age_window = age_end - age_start
age_draw = self.age_randomness.get_draw(pop_data.index)
age = age_start + age_draw * age_window
if self.with_common_random_numbers:
population = pd.DataFrame({'entrance_time': pop_data.creation_time,
'age': age.values}, index=pop_data.index)
self.register(population)
population['sex'] = self.sex_randomness.choice(pop_data.index, ['Male', 'Female'])
population['alive'] = 'alive'
else:
population = pd.DataFrame(
{'age': age.values,
'sex': self.sex_randomness.choice(pop_data.index, ['Male', 'Female']),
'alive': pd.Series('alive', index=pop_data.index),
'entrance_time': pop_data.creation_time},
index=pop_data.index)
self.population_view.update(population) | python | def on_initialize_simulants(self, pop_data: SimulantData):
age_start = self.config.population.age_start
age_end = self.config.population.age_end
if age_start == age_end:
age_window = pop_data.creation_window / pd.Timedelta(days=365)
else:
age_window = age_end - age_start
age_draw = self.age_randomness.get_draw(pop_data.index)
age = age_start + age_draw * age_window
if self.with_common_random_numbers:
population = pd.DataFrame({'entrance_time': pop_data.creation_time,
'age': age.values}, index=pop_data.index)
self.register(population)
population['sex'] = self.sex_randomness.choice(pop_data.index, ['Male', 'Female'])
population['alive'] = 'alive'
else:
population = pd.DataFrame(
{'age': age.values,
'sex': self.sex_randomness.choice(pop_data.index, ['Male', 'Female']),
'alive': pd.Series('alive', index=pop_data.index),
'entrance_time': pop_data.creation_time},
index=pop_data.index)
self.population_view.update(population) | [
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The age of the simulant in fractional years.
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The sex of the simulant. One of {'Male', 'Female'}
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Whether or not the simulant is alive. One of {'alive', 'dead'}
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----------
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A record containing the index of the new simulants, the
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15,643 | ihmeuw/vivarium | src/vivarium/examples/disease_model/population.py | BasePopulation.age_simulants | def age_simulants(self, event: Event):
"""Updates simulant age on every time step.
Parameters
----------
event :
An event object emitted by the simulation containing an index
representing the simulants affected by the event and timing
information.
"""
population = self.population_view.get(event.index, query="alive == 'alive'")
population['age'] += event.step_size / pd.Timedelta(days=365)
self.population_view.update(population) | python | def age_simulants(self, event: Event):
population = self.population_view.get(event.index, query="alive == 'alive'")
population['age'] += event.step_size / pd.Timedelta(days=365)
self.population_view.update(population) | [
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15,644 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | random | def random(key: str, index: Index, index_map: IndexMap=None) -> pd.Series:
"""Produces an indexed `pandas.Series` of uniformly distributed random numbers.
The index passed in typically corresponds to a subset of rows in a
`pandas.DataFrame` for which a probabilistic draw needs to be made.
Parameters
----------
key :
A string used to create a seed for the random number generation.
index :
The index used for the returned series.
index_map :
A mapping between the provided index (which may contain ints, floats,
datetimes or any arbitrary combination of them) and an integer index
into the random number array.
Returns
-------
pd.Series
A series of random numbers indexed by the provided index.
"""
if len(index) > 0:
random_state = np.random.RandomState(seed=get_hash(key))
# Generate a random number for every simulant.
#
# NOTE: We generate a full set of random numbers for the population
# even when we may only need a few. This ensures consistency in outcomes
# across simulations.
# See Also:
# 1. https://en.wikipedia.org/wiki/Variance_reduction
# 2. Untangling Uncertainty with Common Random Numbers: A Simulation Study; A.Flaxman, et. al., Summersim 2017
sample_size = index_map.map_size if index_map is not None else index.max() + 1
try:
draw_index = index_map[index]
except (IndexError, TypeError):
draw_index = index
raw_draws = random_state.random_sample(sample_size)
return pd.Series(raw_draws[draw_index], index=index)
return pd.Series(index=index) | python | def random(key: str, index: Index, index_map: IndexMap=None) -> pd.Series:
if len(index) > 0:
random_state = np.random.RandomState(seed=get_hash(key))
# Generate a random number for every simulant.
#
# NOTE: We generate a full set of random numbers for the population
# even when we may only need a few. This ensures consistency in outcomes
# across simulations.
# See Also:
# 1. https://en.wikipedia.org/wiki/Variance_reduction
# 2. Untangling Uncertainty with Common Random Numbers: A Simulation Study; A.Flaxman, et. al., Summersim 2017
sample_size = index_map.map_size if index_map is not None else index.max() + 1
try:
draw_index = index_map[index]
except (IndexError, TypeError):
draw_index = index
raw_draws = random_state.random_sample(sample_size)
return pd.Series(raw_draws[draw_index], index=index)
return pd.Series(index=index) | [
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A string used to create a seed for the random number generation.
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15,645 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | get_hash | def get_hash(key: str) -> int:
"""Gets a hash of the provided key.
Parameters
----------
key :
A string used to create a seed for the random number generator.
Returns
-------
int
A hash of the provided key.
"""
# 4294967295 == 2**32 - 1 which is the maximum allowable seed for a `numpy.random.RandomState`.
return int(hashlib.sha1(key.encode('utf8')).hexdigest(), 16) % 4294967295 | python | def get_hash(key: str) -> int:
# 4294967295 == 2**32 - 1 which is the maximum allowable seed for a `numpy.random.RandomState`.
return int(hashlib.sha1(key.encode('utf8')).hexdigest(), 16) % 4294967295 | [
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15,646 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | _set_residual_probability | def _set_residual_probability(p: np.ndarray) -> np.ndarray:
"""Turns any use of `RESIDUAL_CHOICE` into a residual probability.
Parameters
----------
p :
Array where each row is a set of probability weights and potentially
a `RESIDUAL_CHOICE` placeholder.
Returns
-------
np.ndarray
Array where each row is a set of normalized probability weights.
"""
residual_mask = p == RESIDUAL_CHOICE
if residual_mask.any(): # I.E. if we have any placeholders.
if np.any(np.sum(residual_mask, axis=1) - 1):
raise RandomnessError(
'More than one residual choice supplied for a single set of weights. Weights: {}.'.format(p))
p[residual_mask] = 0
residual_p = 1 - np.sum(p, axis=1) # Probabilities sum to 1.
if np.any(residual_p < 0): # We got un-normalized probability weights.
raise RandomnessError(
'Residual choice supplied with weights that summed to more than 1. Weights: {}.'.format(p))
p[residual_mask] = residual_p
return p | python | def _set_residual_probability(p: np.ndarray) -> np.ndarray:
residual_mask = p == RESIDUAL_CHOICE
if residual_mask.any(): # I.E. if we have any placeholders.
if np.any(np.sum(residual_mask, axis=1) - 1):
raise RandomnessError(
'More than one residual choice supplied for a single set of weights. Weights: {}.'.format(p))
p[residual_mask] = 0
residual_p = 1 - np.sum(p, axis=1) # Probabilities sum to 1.
if np.any(residual_p < 0): # We got un-normalized probability weights.
raise RandomnessError(
'Residual choice supplied with weights that summed to more than 1. Weights: {}.'.format(p))
p[residual_mask] = residual_p
return p | [
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15,647 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | IndexMap.update | def update(self, new_keys: Index):
"""Adds the new keys to the mapping.
Parameters
----------
new_keys :
The new index to hash.
"""
if not self._map.index.intersection(new_keys).empty:
raise KeyError("Non-unique keys in index.")
mapping_update = self.hash_(new_keys)
if self._map.empty:
self._map = mapping_update.drop_duplicates()
else:
self._map = self._map.append(mapping_update).drop_duplicates()
collisions = mapping_update.index.difference(self._map.index)
salt = 1
while not collisions.empty:
mapping_update = self.hash_(collisions, salt)
self._map = self._map.append(mapping_update).drop_duplicates()
collisions = mapping_update.index.difference(self._map.index)
salt += 1 | python | def update(self, new_keys: Index):
if not self._map.index.intersection(new_keys).empty:
raise KeyError("Non-unique keys in index.")
mapping_update = self.hash_(new_keys)
if self._map.empty:
self._map = mapping_update.drop_duplicates()
else:
self._map = self._map.append(mapping_update).drop_duplicates()
collisions = mapping_update.index.difference(self._map.index)
salt = 1
while not collisions.empty:
mapping_update = self.hash_(collisions, salt)
self._map = self._map.append(mapping_update).drop_duplicates()
collisions = mapping_update.index.difference(self._map.index)
salt += 1 | [
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15,648 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | IndexMap.convert_to_ten_digit_int | def convert_to_ten_digit_int(self, column: pd.Series) -> pd.Series:
"""Converts a column of datetimes, integers, or floats into a column of 10 digit integers.
Parameters
----------
column :
A series of datetimes, integers, or floats.
Returns
-------
pd.Series
A series of ten digit integers based on the input data.
Raises
------
RandomnessError :
If the column contains data that is neither a datetime-like nor numeric.
"""
if isinstance(column.iloc[0], datetime.datetime):
column = self.clip_to_seconds(column.astype(int))
elif np.issubdtype(column.iloc[0], np.integer):
if not len(column >= 0) == len(column):
raise RandomnessError("Values in integer columns must be greater than or equal to zero.")
column = self.spread(column)
elif np.issubdtype(column.iloc[0], np.floating):
column = self.shift(column)
else:
raise RandomnessError(f"Unhashable column type {type(column.iloc[0])}. "
"IndexMap accepts datetime like columns and numeric columns.")
return column | python | def convert_to_ten_digit_int(self, column: pd.Series) -> pd.Series:
if isinstance(column.iloc[0], datetime.datetime):
column = self.clip_to_seconds(column.astype(int))
elif np.issubdtype(column.iloc[0], np.integer):
if not len(column >= 0) == len(column):
raise RandomnessError("Values in integer columns must be greater than or equal to zero.")
column = self.spread(column)
elif np.issubdtype(column.iloc[0], np.floating):
column = self.shift(column)
else:
raise RandomnessError(f"Unhashable column type {type(column.iloc[0])}. "
"IndexMap accepts datetime like columns and numeric columns.")
return column | [
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15,649 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | IndexMap.digit | def digit(m: Union[int, pd.Series], n: int) -> Union[int, pd.Series]:
"""Returns the nth digit of each number in m."""
return (m // (10 ** n)) % 10 | python | def digit(m: Union[int, pd.Series], n: int) -> Union[int, pd.Series]:
return (m // (10 ** n)) % 10 | [
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15,650 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | IndexMap.clip_to_seconds | def clip_to_seconds(m: Union[int, pd.Series]) -> Union[int, pd.Series]:
"""Clips UTC datetime in nanoseconds to seconds."""
return m // pd.Timedelta(1, unit='s').value | python | def clip_to_seconds(m: Union[int, pd.Series]) -> Union[int, pd.Series]:
return m // pd.Timedelta(1, unit='s').value | [
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15,651 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | IndexMap.spread | def spread(self, m: Union[int, pd.Series]) -> Union[int, pd.Series]:
"""Spreads out integer values to give smaller values more weight."""
return (m * 111_111) % self.TEN_DIGIT_MODULUS | python | def spread(self, m: Union[int, pd.Series]) -> Union[int, pd.Series]:
return (m * 111_111) % self.TEN_DIGIT_MODULUS | [
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15,652 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | IndexMap.shift | def shift(self, m: Union[float, pd.Series]) -> Union[int, pd.Series]:
"""Shifts floats so that the first 10 decimal digits are significant."""
out = m % 1 * self.TEN_DIGIT_MODULUS // 1
if isinstance(out, pd.Series):
return out.astype(int)
return int(out) | python | def shift(self, m: Union[float, pd.Series]) -> Union[int, pd.Series]:
out = m % 1 * self.TEN_DIGIT_MODULUS // 1
if isinstance(out, pd.Series):
return out.astype(int)
return int(out) | [
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15,653 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | RandomnessStream.copy_with_additional_key | def copy_with_additional_key(self, key: Any) -> 'RandomnessStream':
"""Creates a copy of this stream that combines this streams key with a new one.
Parameters
----------
key :
The additional key to describe the new stream with.
Returns
-------
RandomnessStream
A new RandomnessStream with a combined key.
"""
if self._for_initialization:
raise RandomnessError('Initialization streams cannot be copied.')
elif self._manager:
return self._manager.get_randomness_stream('_'.join([self.key, key]))
else:
return RandomnessStream(self.key, self.clock, self.seed, self.index_map) | python | def copy_with_additional_key(self, key: Any) -> 'RandomnessStream':
if self._for_initialization:
raise RandomnessError('Initialization streams cannot be copied.')
elif self._manager:
return self._manager.get_randomness_stream('_'.join([self.key, key]))
else:
return RandomnessStream(self.key, self.clock, self.seed, self.index_map) | [
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15,654 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | RandomnessStream._key | def _key(self, additional_key: Any=None) -> str:
"""Construct a hashable key from this object's state.
Parameters
----------
additional_key :
Any additional information used to seed random number generation.
Returns
-------
str
A key to seed random number generation.
"""
return '_'.join([self.key, str(self.clock()), str(additional_key), str(self.seed)]) | python | def _key(self, additional_key: Any=None) -> str:
return '_'.join([self.key, str(self.clock()), str(additional_key), str(self.seed)]) | [
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15,655 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | RandomnessStream.get_draw | def get_draw(self, index: Index, additional_key: Any=None) -> pd.Series:
"""Get an indexed sequence of floats pulled from a uniform distribution over [0.0, 1.0)
Parameters
----------
index :
An index whose length is the number of random draws made
and which indexes the returned `pandas.Series`.
additional_key :
Any additional information used to seed random number generation.
Returns
-------
pd.Series
A series of random numbers indexed by the provided `pandas.Index`.
"""
if self._for_initialization:
draw = random(self._key(additional_key), pd.Index(range(len(index))), self.index_map)
draw.index = index
else:
draw = random(self._key(additional_key), index, self.index_map)
return draw | python | def get_draw(self, index: Index, additional_key: Any=None) -> pd.Series:
if self._for_initialization:
draw = random(self._key(additional_key), pd.Index(range(len(index))), self.index_map)
draw.index = index
else:
draw = random(self._key(additional_key), index, self.index_map)
return draw | [
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15,656 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | RandomnessStream.filter_for_rate | def filter_for_rate(self, population: Union[pd.DataFrame, pd.Series, Index],
rate: Array, additional_key: Any=None) -> Index:
"""Decide an event outcome for each individual in a population from rates.
Given a population or its index and an array of associated rates for
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Parameters
----------
population :
A view on the simulants for which we are determining the
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rate :
A 1d list of rates of the event under consideration occurring which
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rate pipeline.
additional_key :
Any additional information used to create the seed.
Returns
-------
Index
The index of the simulants for whom the event occurred.
See Also
--------
framework.values:
Value/rate pipeline management module.
"""
return self.filter_for_probability(population, rate_to_probability(rate), additional_key) | python | def filter_for_rate(self, population: Union[pd.DataFrame, pd.Series, Index],
rate: Array, additional_key: Any=None) -> Index:
return self.filter_for_probability(population, rate_to_probability(rate), additional_key) | [
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A 1d list of rates of the event under consideration occurring which
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population view passed in. The rates must be scaled to the simulation
time-step size either manually or as a post-processing step in a
rate pipeline.
additional_key :
Any additional information used to create the seed.
Returns
-------
Index
The index of the simulants for whom the event occurred.
See Also
--------
framework.values:
Value/rate pipeline management module. | [
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15,657 | ihmeuw/vivarium | src/vivarium/framework/randomness.py | RandomnessManager.register_simulants | def register_simulants(self, simulants: pd.DataFrame):
"""Adds new simulants to the randomness mapping.
Parameters
----------
simulants :
A table with state data representing the new simulants. Each simulant should
pass through this function exactly once.
Raises
------
RandomnessError :
If the provided table does not contain all key columns specified in the configuration.
"""
if not all(k in simulants.columns for k in self._key_columns):
raise RandomnessError("The simulants dataframe does not have all specified key_columns.")
self._key_mapping.update(simulants.set_index(self._key_columns).index) | python | def register_simulants(self, simulants: pd.DataFrame):
if not all(k in simulants.columns for k in self._key_columns):
raise RandomnessError("The simulants dataframe does not have all specified key_columns.")
self._key_mapping.update(simulants.set_index(self._key_columns).index) | [
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15,658 | tjcsl/ion | intranet/apps/groups/models.py | GroupManager.student_visible | def student_visible(self):
"""Return a list of groups that are student-visible.
"""
group_ids = set()
for group in Group.objects.all():
if group.properties.student_visible:
group_ids.add(group.id)
return Group.objects.filter(id__in=group_ids) | python | def student_visible(self):
group_ids = set()
for group in Group.objects.all():
if group.properties.student_visible:
group_ids.add(group.id)
return Group.objects.filter(id__in=group_ids) | [
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15,659 | tjcsl/ion | intranet/apps/preferences/fields.py | PhoneFormField.to_python | def to_python(self, value):
"""Returns a Unicode object."""
if value in self.empty_values:
return ""
value = force_text(value).strip()
return value | python | def to_python(self, value):
if value in self.empty_values:
return ""
value = force_text(value).strip()
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15,660 | agoragames/kairos | kairos/timeseries.py | _resolve_time | def _resolve_time(value):
'''
Resolve the time in seconds of a configuration value.
'''
if value is None or isinstance(value,(int,long)):
return value
if NUMBER_TIME.match(value):
return long(value)
simple = SIMPLE_TIME.match(value)
if SIMPLE_TIME.match(value):
multiplier = long( simple.groups()[0] )
constant = SIMPLE_TIMES[ simple.groups()[1] ]
return multiplier * constant
if value in GREGORIAN_TIMES:
return value
raise ValueError('Unsupported time format %s'%value) | python | def _resolve_time(value):
'''
Resolve the time in seconds of a configuration value.
'''
if value is None or isinstance(value,(int,long)):
return value
if NUMBER_TIME.match(value):
return long(value)
simple = SIMPLE_TIME.match(value)
if SIMPLE_TIME.match(value):
multiplier = long( simple.groups()[0] )
constant = SIMPLE_TIMES[ simple.groups()[1] ]
return multiplier * constant
if value in GREGORIAN_TIMES:
return value
raise ValueError('Unsupported time format %s'%value) | [
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15,661 | agoragames/kairos | kairos/timeseries.py | RelativeTime.step_size | def step_size(self, t0=None, t1=None):
'''
Return the time in seconds of a step. If a begin and end timestamp,
return the time in seconds between them after adjusting for what buckets
they alias to. If t1 and t0 resolve to the same bucket,
'''
if t0!=None and t1!=None:
tb0 = self.to_bucket( t0 )
tb1 = self.to_bucket( t1, steps=1 ) # NOTE: "end" of second bucket
if tb0==tb1:
return self._step
return self.from_bucket( tb1 ) - self.from_bucket( tb0 )
return self._step | python | def step_size(self, t0=None, t1=None):
'''
Return the time in seconds of a step. If a begin and end timestamp,
return the time in seconds between them after adjusting for what buckets
they alias to. If t1 and t0 resolve to the same bucket,
'''
if t0!=None and t1!=None:
tb0 = self.to_bucket( t0 )
tb1 = self.to_bucket( t1, steps=1 ) # NOTE: "end" of second bucket
if tb0==tb1:
return self._step
return self.from_bucket( tb1 ) - self.from_bucket( tb0 )
return self._step | [
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15,662 | agoragames/kairos | kairos/timeseries.py | GregorianTime.to_bucket | def to_bucket(self, timestamp, steps=0):
'''
Calculate the bucket from a timestamp.
'''
dt = datetime.utcfromtimestamp( timestamp )
if steps!=0:
if self._step == 'daily':
dt = dt + timedelta(days=steps)
elif self._step == 'weekly':
dt = dt + timedelta(weeks=steps)
elif self._step == 'monthly':
dt = dt + MonthDelta(steps)
elif self._step == 'yearly':
year = int(dt.strftime( self.FORMATS[self._step] ))
year += steps
dt = datetime(year=year, month=1, day=1)
return int(dt.strftime( self.FORMATS[self._step] )) | python | def to_bucket(self, timestamp, steps=0):
'''
Calculate the bucket from a timestamp.
'''
dt = datetime.utcfromtimestamp( timestamp )
if steps!=0:
if self._step == 'daily':
dt = dt + timedelta(days=steps)
elif self._step == 'weekly':
dt = dt + timedelta(weeks=steps)
elif self._step == 'monthly':
dt = dt + MonthDelta(steps)
elif self._step == 'yearly':
year = int(dt.strftime( self.FORMATS[self._step] ))
year += steps
dt = datetime(year=year, month=1, day=1)
return int(dt.strftime( self.FORMATS[self._step] )) | [
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15,663 | agoragames/kairos | kairos/timeseries.py | GregorianTime.from_bucket | def from_bucket(self, bucket, native=False):
'''
Calculate the timestamp given a bucket.
'''
# NOTE: this is due to a bug somewhere in strptime that does not process
# the week number of '%Y%U' correctly. That bug could be very specific to
# the combination of python and ubuntu that I was testing.
bucket = str(bucket)
if self._step == 'weekly':
year, week = bucket[:4], bucket[4:]
normal = datetime(year=int(year), month=1, day=1) + timedelta(weeks=int(week))
else:
normal = datetime.strptime(bucket, self.FORMATS[self._step])
if native:
return normal
return long(time.mktime( normal.timetuple() )) | python | def from_bucket(self, bucket, native=False):
'''
Calculate the timestamp given a bucket.
'''
# NOTE: this is due to a bug somewhere in strptime that does not process
# the week number of '%Y%U' correctly. That bug could be very specific to
# the combination of python and ubuntu that I was testing.
bucket = str(bucket)
if self._step == 'weekly':
year, week = bucket[:4], bucket[4:]
normal = datetime(year=int(year), month=1, day=1) + timedelta(weeks=int(week))
else:
normal = datetime.strptime(bucket, self.FORMATS[self._step])
if native:
return normal
return long(time.mktime( normal.timetuple() )) | [
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15,664 | agoragames/kairos | kairos/timeseries.py | GregorianTime.normalize | def normalize(self, timestamp, steps=0):
'''
Normalize a timestamp according to the interval configuration. Optionally
can be used to calculate the timestamp N steps away.
'''
# So far, the only commonality with RelativeTime
return self.from_bucket( self.to_bucket(timestamp, steps) ) | python | def normalize(self, timestamp, steps=0):
'''
Normalize a timestamp according to the interval configuration. Optionally
can be used to calculate the timestamp N steps away.
'''
# So far, the only commonality with RelativeTime
return self.from_bucket( self.to_bucket(timestamp, steps) ) | [
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15,665 | agoragames/kairos | kairos/timeseries.py | Timeseries._batch_insert | def _batch_insert(self, inserts, intervals, **kwargs):
'''
Support for batch insert. Default implementation is non-optimized and
is a simple loop over values.
'''
for timestamp,names in inserts.iteritems():
for name,values in names.iteritems():
for value in values:
self._insert( name, value, timestamp, intervals, **kwargs ) | python | def _batch_insert(self, inserts, intervals, **kwargs):
'''
Support for batch insert. Default implementation is non-optimized and
is a simple loop over values.
'''
for timestamp,names in inserts.iteritems():
for name,values in names.iteritems():
for value in values:
self._insert( name, value, timestamp, intervals, **kwargs ) | [
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15,666 | agoragames/kairos | kairos/timeseries.py | Timeseries._normalize_timestamps | def _normalize_timestamps(self, timestamp, intervals, config):
'''
Helper for the subclasses to generate a list of timestamps.
'''
rval = [timestamp]
if intervals<0:
while intervals<0:
rval.append( config['i_calc'].normalize(timestamp, intervals) )
intervals += 1
elif intervals>0:
while intervals>0:
rval.append( config['i_calc'].normalize(timestamp, intervals) )
intervals -= 1
return rval | python | def _normalize_timestamps(self, timestamp, intervals, config):
'''
Helper for the subclasses to generate a list of timestamps.
'''
rval = [timestamp]
if intervals<0:
while intervals<0:
rval.append( config['i_calc'].normalize(timestamp, intervals) )
intervals += 1
elif intervals>0:
while intervals>0:
rval.append( config['i_calc'].normalize(timestamp, intervals) )
intervals -= 1
return rval | [
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15,667 | agoragames/kairos | kairos/timeseries.py | Timeseries._join_results | def _join_results(self, results, coarse, join):
'''
Join a list of results. Supports both get and series.
'''
rval = OrderedDict()
i_keys = set()
for res in results:
i_keys.update( res.keys() )
for i_key in sorted(i_keys):
if coarse:
rval[i_key] = join( [res.get(i_key) for res in results] )
else:
rval[i_key] = OrderedDict()
r_keys = set()
for res in results:
r_keys.update( res.get(i_key,{}).keys() )
for r_key in sorted(r_keys):
rval[i_key][r_key] = join( [res.get(i_key,{}).get(r_key) for res in results] )
return rval | python | def _join_results(self, results, coarse, join):
'''
Join a list of results. Supports both get and series.
'''
rval = OrderedDict()
i_keys = set()
for res in results:
i_keys.update( res.keys() )
for i_key in sorted(i_keys):
if coarse:
rval[i_key] = join( [res.get(i_key) for res in results] )
else:
rval[i_key] = OrderedDict()
r_keys = set()
for res in results:
r_keys.update( res.get(i_key,{}).keys() )
for r_key in sorted(r_keys):
rval[i_key][r_key] = join( [res.get(i_key,{}).get(r_key) for res in results] )
return rval | [
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15,668 | agoragames/kairos | kairos/timeseries.py | Timeseries._process_transform | def _process_transform(self, data, transform, step_size):
'''
Process transforms on the data.
'''
if isinstance(transform, (list,tuple,set)):
return { t : self._transform(data,t,step_size) for t in transform }
elif isinstance(transform, dict):
return { tn : self._transform(data,tf,step_size) for tn,tf in transform.items() }
return self._transform(data,transform,step_size) | python | def _process_transform(self, data, transform, step_size):
'''
Process transforms on the data.
'''
if isinstance(transform, (list,tuple,set)):
return { t : self._transform(data,t,step_size) for t in transform }
elif isinstance(transform, dict):
return { tn : self._transform(data,tf,step_size) for tn,tf in transform.items() }
return self._transform(data,transform,step_size) | [
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15,669 | agoragames/kairos | kairos/timeseries.py | Histogram._condense | def _condense(self, data):
'''
Condense by adding together all of the lists.
'''
rval = {}
for resolution,histogram in data.items():
for value,count in histogram.items():
rval[ value ] = count + rval.get(value,0)
return rval | python | def _condense(self, data):
'''
Condense by adding together all of the lists.
'''
rval = {}
for resolution,histogram in data.items():
for value,count in histogram.items():
rval[ value ] = count + rval.get(value,0)
return rval | [
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15,670 | agoragames/kairos | kairos/timeseries.py | Gauge._condense | def _condense(self, data):
'''
Condense by returning the last real value of the gauge.
'''
if data:
data = filter(None,data.values())
if data:
return data[-1]
return None | python | def _condense(self, data):
'''
Condense by returning the last real value of the gauge.
'''
if data:
data = filter(None,data.values())
if data:
return data[-1]
return None | [
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15,671 | agoragames/kairos | kairos/timeseries.py | Set._condense | def _condense(self, data):
'''
Condense by or-ing all of the sets.
'''
if data:
return reduce(operator.ior, data.values())
return set() | python | def _condense(self, data):
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Condense by or-ing all of the sets.
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15,672 | tjcsl/ion | intranet/apps/api/authentication.py | ApiBasicAuthentication.authenticate_credentials | def authenticate_credentials(self, userid, password, request=None):
"""Authenticate the userid and password."""
user = auth.authenticate(username=userid, password=password)
if user is None or (user and not user.is_active):
raise exceptions.AuthenticationFailed("Invalid username/password.")
return (user, None) | python | def authenticate_credentials(self, userid, password, request=None):
user = auth.authenticate(username=userid, password=password)
if user is None or (user and not user.is_active):
raise exceptions.AuthenticationFailed("Invalid username/password.")
return (user, None) | [
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15,673 | tjcsl/ion | intranet/apps/bus/consumers.py | check_internal_ip | def check_internal_ip(request):
""" request is an AsgiRequest """
remote_addr = (request.META["HTTP_X_FORWARDED_FOR"] if "HTTP_X_FORWARDED_FOR" in request.META else request.META.get("REMOTE_ADDR", ""))
return remote_addr in settings.INTERNAL_IPS | python | def check_internal_ip(request):
remote_addr = (request.META["HTTP_X_FORWARDED_FOR"] if "HTTP_X_FORWARDED_FOR" in request.META else request.META.get("REMOTE_ADDR", ""))
return remote_addr in settings.INTERNAL_IPS | [
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15,674 | tjcsl/ion | intranet/apps/events/views.py | events_view | def events_view(request):
"""Events homepage.
Shows a list of events occurring in the next week, month, and
future.
"""
is_events_admin = request.user.has_admin_permission('events')
if request.method == "POST":
if "approve" in request.POST and is_events_admin:
event_id = request.POST.get('approve')
event = get_object_or_404(Event, id=event_id)
event.rejected = False
event.approved = True
event.approved_by = request.user
event.save()
messages.success(request, "Approved event {}".format(event))
if "reject" in request.POST and is_events_admin:
event_id = request.POST.get('reject')
event = get_object_or_404(Event, id=event_id)
event.approved = False
event.rejected = True
event.rejected_by = request.user
event.save()
messages.success(request, "Rejected event {}".format(event))
if is_events_admin and "show_all" in request.GET:
viewable_events = (Event.objects.all().this_year().prefetch_related("groups"))
else:
viewable_events = (Event.objects.visible_to_user(request.user).this_year().prefetch_related("groups"))
# get date objects for week and month
today = datetime.date.today()
delta = today - datetime.timedelta(days=today.weekday())
this_week = (delta, delta + datetime.timedelta(days=7))
this_month = (this_week[1], this_week[1] + datetime.timedelta(days=31))
events_categories = [{
"title": "This week",
"events": viewable_events.filter(time__gte=this_week[0], time__lt=this_week[1])
}, {
"title": "This month",
"events": viewable_events.filter(time__gte=this_month[0], time__lt=this_month[1])
}, {
"title": "Future",
"events": viewable_events.filter(time__gte=this_month[1])
}]
if is_events_admin:
unapproved_events = (Event.objects.filter(approved=False, rejected=False).prefetch_related("groups"))
events_categories = [{"title": "Awaiting Approval", "events": unapproved_events}] + events_categories
if is_events_admin and "show_all" in request.GET:
events_categories.append({"title": "Past", "events": viewable_events.filter(time__lt=this_week[0])})
context = {
"events": events_categories,
"num_events": sum([x["events"].count() for x in events_categories]),
"is_events_admin": is_events_admin,
"events_admin": is_events_admin,
"show_attend": True,
"show_icon": True
}
return render(request, "events/home.html", context) | python | def events_view(request):
is_events_admin = request.user.has_admin_permission('events')
if request.method == "POST":
if "approve" in request.POST and is_events_admin:
event_id = request.POST.get('approve')
event = get_object_or_404(Event, id=event_id)
event.rejected = False
event.approved = True
event.approved_by = request.user
event.save()
messages.success(request, "Approved event {}".format(event))
if "reject" in request.POST and is_events_admin:
event_id = request.POST.get('reject')
event = get_object_or_404(Event, id=event_id)
event.approved = False
event.rejected = True
event.rejected_by = request.user
event.save()
messages.success(request, "Rejected event {}".format(event))
if is_events_admin and "show_all" in request.GET:
viewable_events = (Event.objects.all().this_year().prefetch_related("groups"))
else:
viewable_events = (Event.objects.visible_to_user(request.user).this_year().prefetch_related("groups"))
# get date objects for week and month
today = datetime.date.today()
delta = today - datetime.timedelta(days=today.weekday())
this_week = (delta, delta + datetime.timedelta(days=7))
this_month = (this_week[1], this_week[1] + datetime.timedelta(days=31))
events_categories = [{
"title": "This week",
"events": viewable_events.filter(time__gte=this_week[0], time__lt=this_week[1])
}, {
"title": "This month",
"events": viewable_events.filter(time__gte=this_month[0], time__lt=this_month[1])
}, {
"title": "Future",
"events": viewable_events.filter(time__gte=this_month[1])
}]
if is_events_admin:
unapproved_events = (Event.objects.filter(approved=False, rejected=False).prefetch_related("groups"))
events_categories = [{"title": "Awaiting Approval", "events": unapproved_events}] + events_categories
if is_events_admin and "show_all" in request.GET:
events_categories.append({"title": "Past", "events": viewable_events.filter(time__lt=this_week[0])})
context = {
"events": events_categories,
"num_events": sum([x["events"].count() for x in events_categories]),
"is_events_admin": is_events_admin,
"events_admin": is_events_admin,
"show_attend": True,
"show_icon": True
}
return render(request, "events/home.html", context) | [
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15,675 | tjcsl/ion | intranet/apps/events/views.py | join_event_view | def join_event_view(request, id):
"""Join event page. If a POST request, actually add or remove the attendance of the current
user. Otherwise, display a page with confirmation.
id: event id
"""
event = get_object_or_404(Event, id=id)
if request.method == "POST":
if not event.show_attending:
return redirect("events")
if "attending" in request.POST:
attending = request.POST.get("attending")
attending = (attending == "true")
if attending:
event.attending.add(request.user)
else:
event.attending.remove(request.user)
return redirect("events")
context = {"event": event, "is_events_admin": request.user.has_admin_permission('events')}
return render(request, "events/join_event.html", context) | python | def join_event_view(request, id):
event = get_object_or_404(Event, id=id)
if request.method == "POST":
if not event.show_attending:
return redirect("events")
if "attending" in request.POST:
attending = request.POST.get("attending")
attending = (attending == "true")
if attending:
event.attending.add(request.user)
else:
event.attending.remove(request.user)
return redirect("events")
context = {"event": event, "is_events_admin": request.user.has_admin_permission('events')}
return render(request, "events/join_event.html", context) | [
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15,676 | tjcsl/ion | intranet/apps/events/views.py | add_event_view | def add_event_view(request):
"""Add event page.
Currently, there is an approval process for events. If a user is an
events administrator, they can create events directly. Otherwise,
their event is added in the system but must be approved.
"""
is_events_admin = request.user.has_admin_permission('events')
if not is_events_admin:
return redirect("request_event")
if request.method == "POST":
form = EventForm(data=request.POST, all_groups=request.user.has_admin_permission('groups'))
logger.debug(form)
if form.is_valid():
obj = form.save()
obj.user = request.user
# SAFE HTML
obj.description = safe_html(obj.description)
# auto-approve if admin
obj.approved = True
obj.approved_by = request.user
messages.success(request, "Because you are an administrator, this event was auto-approved.")
obj.created_hook(request)
obj.save()
return redirect("events")
else:
messages.error(request, "Error adding event.")
else:
form = EventForm(all_groups=request.user.has_admin_permission('groups'))
context = {"form": form, "action": "add", "action_title": "Add" if is_events_admin else "Submit", "is_events_admin": is_events_admin}
return render(request, "events/add_modify.html", context) | python | def add_event_view(request):
is_events_admin = request.user.has_admin_permission('events')
if not is_events_admin:
return redirect("request_event")
if request.method == "POST":
form = EventForm(data=request.POST, all_groups=request.user.has_admin_permission('groups'))
logger.debug(form)
if form.is_valid():
obj = form.save()
obj.user = request.user
# SAFE HTML
obj.description = safe_html(obj.description)
# auto-approve if admin
obj.approved = True
obj.approved_by = request.user
messages.success(request, "Because you are an administrator, this event was auto-approved.")
obj.created_hook(request)
obj.save()
return redirect("events")
else:
messages.error(request, "Error adding event.")
else:
form = EventForm(all_groups=request.user.has_admin_permission('groups'))
context = {"form": form, "action": "add", "action_title": "Add" if is_events_admin else "Submit", "is_events_admin": is_events_admin}
return render(request, "events/add_modify.html", context) | [
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15,677 | tjcsl/ion | intranet/apps/events/views.py | modify_event_view | def modify_event_view(request, id=None):
"""Modify event page. You may only modify an event if you were the creator or you are an
administrator.
id: event id
"""
event = get_object_or_404(Event, id=id)
is_events_admin = request.user.has_admin_permission('events')
if not is_events_admin:
raise exceptions.PermissionDenied
if request.method == "POST":
if is_events_admin:
form = AdminEventForm(data=request.POST, instance=event, all_groups=request.user.has_admin_permission('groups'))
else:
form = EventForm(data=request.POST, instance=event, all_groups=request.user.has_admin_permission('groups'))
logger.debug(form)
if form.is_valid():
obj = form.save()
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully modified event.")
# return redirect("events")
else:
messages.error(request, "Error modifying event.")
else:
if is_events_admin:
form = AdminEventForm(instance=event, all_groups=request.user.has_admin_permission('groups'))
else:
form = EventForm(instance=event, all_groups=request.user.has_admin_permission('groups'))
context = {"form": form, "action": "modify", "action_title": "Modify", "id": id, "is_events_admin": is_events_admin}
return render(request, "events/add_modify.html", context) | python | def modify_event_view(request, id=None):
event = get_object_or_404(Event, id=id)
is_events_admin = request.user.has_admin_permission('events')
if not is_events_admin:
raise exceptions.PermissionDenied
if request.method == "POST":
if is_events_admin:
form = AdminEventForm(data=request.POST, instance=event, all_groups=request.user.has_admin_permission('groups'))
else:
form = EventForm(data=request.POST, instance=event, all_groups=request.user.has_admin_permission('groups'))
logger.debug(form)
if form.is_valid():
obj = form.save()
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully modified event.")
# return redirect("events")
else:
messages.error(request, "Error modifying event.")
else:
if is_events_admin:
form = AdminEventForm(instance=event, all_groups=request.user.has_admin_permission('groups'))
else:
form = EventForm(instance=event, all_groups=request.user.has_admin_permission('groups'))
context = {"form": form, "action": "modify", "action_title": "Modify", "id": id, "is_events_admin": is_events_admin}
return render(request, "events/add_modify.html", context) | [
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15,678 | tjcsl/ion | intranet/apps/events/views.py | delete_event_view | def delete_event_view(request, id):
"""Delete event page. You may only delete an event if you were the creator or you are an
administrator. Confirmation page if not POST.
id: event id
"""
event = get_object_or_404(Event, id=id)
if not request.user.has_admin_permission('events'):
raise exceptions.PermissionDenied
if request.method == "POST":
try:
event.delete()
messages.success(request, "Successfully deleted event.")
except Event.DoesNotExist:
pass
return redirect("events")
else:
return render(request, "events/delete.html", {"event": event}) | python | def delete_event_view(request, id):
event = get_object_or_404(Event, id=id)
if not request.user.has_admin_permission('events'):
raise exceptions.PermissionDenied
if request.method == "POST":
try:
event.delete()
messages.success(request, "Successfully deleted event.")
except Event.DoesNotExist:
pass
return redirect("events")
else:
return render(request, "events/delete.html", {"event": event}) | [
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15,679 | tjcsl/ion | intranet/apps/events/views.py | show_event_view | def show_event_view(request):
""" Unhide an event that was hidden by the logged-in user.
events_hidden in the user model is the related_name for
"users_hidden" in the EventUserMap model.
"""
if request.method == "POST":
event_id = request.POST.get("event_id")
if event_id:
event = Event.objects.get(id=event_id)
event.user_map.users_hidden.remove(request.user)
event.user_map.save()
return http.HttpResponse("Unhidden")
raise http.Http404
else:
return http.HttpResponseNotAllowed(["POST"], "HTTP 405: METHOD NOT ALLOWED") | python | def show_event_view(request):
if request.method == "POST":
event_id = request.POST.get("event_id")
if event_id:
event = Event.objects.get(id=event_id)
event.user_map.users_hidden.remove(request.user)
event.user_map.save()
return http.HttpResponse("Unhidden")
raise http.Http404
else:
return http.HttpResponseNotAllowed(["POST"], "HTTP 405: METHOD NOT ALLOWED") | [
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15,680 | tjcsl/ion | intranet/apps/notifications/views.py | chrome_getdata_view | def chrome_getdata_view(request):
"""Get the data of the last notification sent to the current user.
This is needed because Chrome, as of version 44, doesn't support
sending a data payload to a notification. Thus, information on what
the notification is actually for must be manually fetched.
"""
data = {}
if request.user.is_authenticated:
# authenticated session
notifs = GCMNotification.objects.filter(sent_to__user=request.user).order_by("-time")
if notifs.count() > 0:
notif = notifs.first()
ndata = notif.data
if "title" in ndata and "text" in ndata:
data = {
"title": ndata['title'] if 'title' in ndata else '',
"text": ndata['text'] if 'text' in ndata else '',
"url": ndata['url'] if 'url' in ndata else ''
}
else:
schedule_chk = chrome_getdata_check(request)
if schedule_chk:
data = schedule_chk
else:
schedule_chk = chrome_getdata_check(request)
if schedule_chk:
data = schedule_chk
else:
return HttpResponse("null", content_type="text/json")
else:
schedule_chk = chrome_getdata_check(request)
if schedule_chk:
data = schedule_chk
else:
data = {"title": "Check Intranet", "text": "You have a new notification that couldn't be loaded right now."}
j = json.dumps(data)
return HttpResponse(j, content_type="text/json") | python | def chrome_getdata_view(request):
data = {}
if request.user.is_authenticated:
# authenticated session
notifs = GCMNotification.objects.filter(sent_to__user=request.user).order_by("-time")
if notifs.count() > 0:
notif = notifs.first()
ndata = notif.data
if "title" in ndata and "text" in ndata:
data = {
"title": ndata['title'] if 'title' in ndata else '',
"text": ndata['text'] if 'text' in ndata else '',
"url": ndata['url'] if 'url' in ndata else ''
}
else:
schedule_chk = chrome_getdata_check(request)
if schedule_chk:
data = schedule_chk
else:
schedule_chk = chrome_getdata_check(request)
if schedule_chk:
data = schedule_chk
else:
return HttpResponse("null", content_type="text/json")
else:
schedule_chk = chrome_getdata_check(request)
if schedule_chk:
data = schedule_chk
else:
data = {"title": "Check Intranet", "text": "You have a new notification that couldn't be loaded right now."}
j = json.dumps(data)
return HttpResponse(j, content_type="text/json") | [
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15,681 | tjcsl/ion | intranet/apps/lostfound/views.py | lostitem_add_view | def lostitem_add_view(request):
"""Add a lostitem."""
if request.method == "POST":
form = LostItemForm(request.POST)
logger.debug(form)
if form.is_valid():
obj = form.save()
obj.user = request.user
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully added lost item.")
return redirect("lostitem_view", obj.id)
else:
messages.error(request, "Error adding lost item.")
else:
form = LostItemForm()
return render(request, "lostfound/lostitem_form.html", {"form": form, "action": "add"}) | python | def lostitem_add_view(request):
if request.method == "POST":
form = LostItemForm(request.POST)
logger.debug(form)
if form.is_valid():
obj = form.save()
obj.user = request.user
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully added lost item.")
return redirect("lostitem_view", obj.id)
else:
messages.error(request, "Error adding lost item.")
else:
form = LostItemForm()
return render(request, "lostfound/lostitem_form.html", {"form": form, "action": "add"}) | [
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15,682 | tjcsl/ion | intranet/apps/lostfound/views.py | lostitem_modify_view | def lostitem_modify_view(request, item_id=None):
"""Modify a lostitem.
id: lostitem id
"""
if request.method == "POST":
lostitem = get_object_or_404(LostItem, id=item_id)
form = LostItemForm(request.POST, instance=lostitem)
if form.is_valid():
obj = form.save()
logger.debug(form.cleaned_data)
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully modified lost item.")
return redirect("lostitem_view", obj.id)
else:
messages.error(request, "Error adding lost item.")
else:
lostitem = get_object_or_404(LostItem, id=item_id)
form = LostItemForm(instance=lostitem)
context = {"form": form, "action": "modify", "id": item_id, "lostitem": lostitem}
return render(request, "lostfound/lostitem_form.html", context) | python | def lostitem_modify_view(request, item_id=None):
if request.method == "POST":
lostitem = get_object_or_404(LostItem, id=item_id)
form = LostItemForm(request.POST, instance=lostitem)
if form.is_valid():
obj = form.save()
logger.debug(form.cleaned_data)
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully modified lost item.")
return redirect("lostitem_view", obj.id)
else:
messages.error(request, "Error adding lost item.")
else:
lostitem = get_object_or_404(LostItem, id=item_id)
form = LostItemForm(instance=lostitem)
context = {"form": form, "action": "modify", "id": item_id, "lostitem": lostitem}
return render(request, "lostfound/lostitem_form.html", context) | [
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15,683 | tjcsl/ion | intranet/apps/lostfound/views.py | lostitem_delete_view | def lostitem_delete_view(request, item_id):
"""Delete a lostitem.
id: lostitem id
"""
if request.method == "POST":
try:
a = LostItem.objects.get(id=item_id)
if request.POST.get("full_delete", False):
a.delete()
messages.success(request, "Successfully deleted lost item.")
else:
a.found = True
a.save()
messages.success(request, "Successfully marked lost item as found!")
except LostItem.DoesNotExist:
pass
return redirect("index")
else:
lostitem = get_object_or_404(LostItem, id=item_id)
return render(request, "lostfound/lostitem_delete.html", {"lostitem": lostitem}) | python | def lostitem_delete_view(request, item_id):
if request.method == "POST":
try:
a = LostItem.objects.get(id=item_id)
if request.POST.get("full_delete", False):
a.delete()
messages.success(request, "Successfully deleted lost item.")
else:
a.found = True
a.save()
messages.success(request, "Successfully marked lost item as found!")
except LostItem.DoesNotExist:
pass
return redirect("index")
else:
lostitem = get_object_or_404(LostItem, id=item_id)
return render(request, "lostfound/lostitem_delete.html", {"lostitem": lostitem}) | [
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15,684 | tjcsl/ion | intranet/apps/lostfound/views.py | lostitem_view | def lostitem_view(request, item_id):
"""View a lostitem.
id: lostitem id
"""
lostitem = get_object_or_404(LostItem, id=item_id)
return render(request, "itemreg/item_view.html", {"item": lostitem, "type": "lost"}) | python | def lostitem_view(request, item_id):
lostitem = get_object_or_404(LostItem, id=item_id)
return render(request, "itemreg/item_view.html", {"item": lostitem, "type": "lost"}) | [
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15,685 | tjcsl/ion | intranet/apps/lostfound/views.py | founditem_modify_view | def founditem_modify_view(request, item_id=None):
"""Modify a founditem.
id: founditem id
"""
if request.method == "POST":
founditem = get_object_or_404(FoundItem, id=item_id)
form = FoundItemForm(request.POST, instance=founditem)
if form.is_valid():
obj = form.save()
logger.debug(form.cleaned_data)
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully modified found item.")
return redirect("founditem_view", obj.id)
else:
messages.error(request, "Error adding found item.")
else:
founditem = get_object_or_404(FoundItem, id=item_id)
form = FoundItemForm(instance=founditem)
context = {"form": form, "action": "modify", "id": item_id, "founditem": founditem}
return render(request, "lostfound/founditem_form.html", context) | python | def founditem_modify_view(request, item_id=None):
if request.method == "POST":
founditem = get_object_or_404(FoundItem, id=item_id)
form = FoundItemForm(request.POST, instance=founditem)
if form.is_valid():
obj = form.save()
logger.debug(form.cleaned_data)
# SAFE HTML
obj.description = safe_html(obj.description)
obj.save()
messages.success(request, "Successfully modified found item.")
return redirect("founditem_view", obj.id)
else:
messages.error(request, "Error adding found item.")
else:
founditem = get_object_or_404(FoundItem, id=item_id)
form = FoundItemForm(instance=founditem)
context = {"form": form, "action": "modify", "id": item_id, "founditem": founditem}
return render(request, "lostfound/founditem_form.html", context) | [
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15,686 | tjcsl/ion | intranet/apps/lostfound/views.py | founditem_delete_view | def founditem_delete_view(request, item_id):
"""Delete a founditem.
id: founditem id
"""
if request.method == "POST":
try:
a = FoundItem.objects.get(id=item_id)
if request.POST.get("full_delete", False):
a.delete()
messages.success(request, "Successfully deleted found item.")
else:
a.found = True
a.save()
messages.success(request, "Successfully marked found item as found!")
except FoundItem.DoesNotExist:
pass
return redirect("index")
else:
founditem = get_object_or_404(FoundItem, id=item_id)
return render(request, "lostfound/founditem_delete.html", {"founditem": founditem}) | python | def founditem_delete_view(request, item_id):
if request.method == "POST":
try:
a = FoundItem.objects.get(id=item_id)
if request.POST.get("full_delete", False):
a.delete()
messages.success(request, "Successfully deleted found item.")
else:
a.found = True
a.save()
messages.success(request, "Successfully marked found item as found!")
except FoundItem.DoesNotExist:
pass
return redirect("index")
else:
founditem = get_object_or_404(FoundItem, id=item_id)
return render(request, "lostfound/founditem_delete.html", {"founditem": founditem}) | [
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15,687 | tjcsl/ion | intranet/apps/lostfound/views.py | founditem_view | def founditem_view(request, item_id):
"""View a founditem.
id: founditem id
"""
founditem = get_object_or_404(FoundItem, id=item_id)
return render(request, "itemreg/item_view.html", {"item": founditem, "type": "found"}) | python | def founditem_view(request, item_id):
founditem = get_object_or_404(FoundItem, id=item_id)
return render(request, "itemreg/item_view.html", {"item": founditem, "type": "found"}) | [
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15,688 | tjcsl/ion | intranet/apps/files/views.py | files_view | def files_view(request):
"""The main filecenter view."""
hosts = Host.objects.visible_to_user(request.user)
context = {"hosts": hosts}
return render(request, "files/home.html", context) | python | def files_view(request):
hosts = Host.objects.visible_to_user(request.user)
context = {"hosts": hosts}
return render(request, "files/home.html", context) | [
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15,689 | tjcsl/ion | intranet/apps/files/views.py | files_auth | def files_auth(request):
"""Display authentication for filecenter."""
if "password" in request.POST:
"""
Encrypt the password with AES mode CFB.
Create a random 32 char key, stored in a CLIENT-side cookie.
Create a random 32 char IV, stored in a SERVER-side session.
Store the encrypted ciphertext in a SERVER-side session.
This ensures that neither side can decrypt the password without
the information stored on the other end of the request.
Both the server-side session variables and the client-side cookies
are deleted when the user logs out.
"""
key = Random.new().read(32)
iv = Random.new().read(16)
obj = AES.new(key, AES.MODE_CFB, iv)
message = request.POST.get("password")
if isinstance(message, str):
message = message.encode("utf-8")
ciphertext = obj.encrypt(message)
request.session["files_iv"] = base64.b64encode(iv).decode()
request.session["files_text"] = base64.b64encode(ciphertext).decode()
cookie_key = base64.b64encode(key).decode()
nexturl = request.GET.get("next", None)
if nexturl and nexturl.startswith("/files"):
response = redirect(nexturl)
else:
response = redirect("files")
response.set_cookie(key="files_key", value=cookie_key)
if "username" in request.POST:
request.session["filecenter_username"] = request.POST.get("username")
return response
else:
return render(request, "files/auth.html", {"is_admin": request.user.member_of("admin_all")}) | python | def files_auth(request):
if "password" in request.POST:
"""
Encrypt the password with AES mode CFB.
Create a random 32 char key, stored in a CLIENT-side cookie.
Create a random 32 char IV, stored in a SERVER-side session.
Store the encrypted ciphertext in a SERVER-side session.
This ensures that neither side can decrypt the password without
the information stored on the other end of the request.
Both the server-side session variables and the client-side cookies
are deleted when the user logs out.
"""
key = Random.new().read(32)
iv = Random.new().read(16)
obj = AES.new(key, AES.MODE_CFB, iv)
message = request.POST.get("password")
if isinstance(message, str):
message = message.encode("utf-8")
ciphertext = obj.encrypt(message)
request.session["files_iv"] = base64.b64encode(iv).decode()
request.session["files_text"] = base64.b64encode(ciphertext).decode()
cookie_key = base64.b64encode(key).decode()
nexturl = request.GET.get("next", None)
if nexturl and nexturl.startswith("/files"):
response = redirect(nexturl)
else:
response = redirect("files")
response.set_cookie(key="files_key", value=cookie_key)
if "username" in request.POST:
request.session["filecenter_username"] = request.POST.get("username")
return response
else:
return render(request, "files/auth.html", {"is_admin": request.user.member_of("admin_all")}) | [
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15,690 | tjcsl/ion | intranet/apps/files/views.py | get_authinfo | def get_authinfo(request):
"""Get authentication info from the encrypted message."""
if (("files_iv" not in request.session) or ("files_text" not in request.session) or ("files_key" not in request.COOKIES)):
return False
"""
Decrypt the password given the SERVER-side IV, SERVER-side
ciphertext, and CLIENT-side key.
See note above on why this is done.
"""
iv = base64.b64decode(request.session["files_iv"])
text = base64.b64decode(request.session["files_text"])
key = base64.b64decode(request.COOKIES["files_key"])
obj = AES.new(key, AES.MODE_CFB, iv)
password = obj.decrypt(text)
username = request.session["filecenter_username"] if "filecenter_username" in request.session else request.user.username
return {"username": username, "password": password} | python | def get_authinfo(request):
if (("files_iv" not in request.session) or ("files_text" not in request.session) or ("files_key" not in request.COOKIES)):
return False
"""
Decrypt the password given the SERVER-side IV, SERVER-side
ciphertext, and CLIENT-side key.
See note above on why this is done.
"""
iv = base64.b64decode(request.session["files_iv"])
text = base64.b64decode(request.session["files_text"])
key = base64.b64decode(request.COOKIES["files_key"])
obj = AES.new(key, AES.MODE_CFB, iv)
password = obj.decrypt(text)
username = request.session["filecenter_username"] if "filecenter_username" in request.session else request.user.username
return {"username": username, "password": password} | [
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15,691 | tjcsl/ion | intranet/apps/itemreg/templatetags/texthighlight.py | highlight | def highlight(str1, str2):
"""Highlight str1 with the contents of str2."""
print('------------------------------')
try:
str2 = str2[0]
except IndexError:
str2 = None
if str1 and str2:
return str1.replace(str2, "<b>{}</b>".format(str2))
else:
return str1 | python | def highlight(str1, str2):
print('------------------------------')
try:
str2 = str2[0]
except IndexError:
str2 = None
if str1 and str2:
return str1.replace(str2, "<b>{}</b>".format(str2))
else:
return str1 | [
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15,692 | tjcsl/ion | intranet/apps/eighth/management/commands/import_attendance.py | Command.handle | def handle(self, **options):
"""Exported "eighth_absentees" table in CSV format."""
with open('eighth_absentees.csv', 'r') as absopen:
absences = csv.reader(absopen)
for row in absences:
bid, uid = row
try:
usr = User.objects.get(id=uid)
except User.DoesNotExist:
self.stdout.write("User {} doesn't exist, bid {}".format(usr, bid))
else:
try:
blk = EighthBlock.objects.get(id=bid)
except EighthBlock.DoesNotExist:
self.stdout.write("Block {} doesn't exist, with user {}".format(bid, uid))
else:
usr_signup = EighthSignup.objects.filter(user=usr, scheduled_activity__block=blk)
self.stdout.write("{} signup: {}".format(usr, usr_signup))
if usr_signup.count() == 0:
other_abs_act, _ = EighthActivity.objects.get_or_create(name="z-OTHER ABSENCE (transferred from Iodine)",
administrative=True)
other_abs_sch, _ = EighthScheduledActivity.objects.get_or_create(block=blk, activity=other_abs_act)
other_abs_su = EighthSignup.objects.create(user=usr, scheduled_activity=other_abs_sch, was_absent=True)
self.stdout.write("{} Signup on {} created: {}".format(usr, bid, other_abs_su))
else:
s = usr_signup[0]
s.was_absent = True
s.save()
sa = s.scheduled_activity
sa.attendance_taken = True
sa.save()
self.stdout.write("{} Signup on {} modified: {}".format(usr, bid, usr_signup[0]))
self.stdout.write("Done.") | python | def handle(self, **options):
with open('eighth_absentees.csv', 'r') as absopen:
absences = csv.reader(absopen)
for row in absences:
bid, uid = row
try:
usr = User.objects.get(id=uid)
except User.DoesNotExist:
self.stdout.write("User {} doesn't exist, bid {}".format(usr, bid))
else:
try:
blk = EighthBlock.objects.get(id=bid)
except EighthBlock.DoesNotExist:
self.stdout.write("Block {} doesn't exist, with user {}".format(bid, uid))
else:
usr_signup = EighthSignup.objects.filter(user=usr, scheduled_activity__block=blk)
self.stdout.write("{} signup: {}".format(usr, usr_signup))
if usr_signup.count() == 0:
other_abs_act, _ = EighthActivity.objects.get_or_create(name="z-OTHER ABSENCE (transferred from Iodine)",
administrative=True)
other_abs_sch, _ = EighthScheduledActivity.objects.get_or_create(block=blk, activity=other_abs_act)
other_abs_su = EighthSignup.objects.create(user=usr, scheduled_activity=other_abs_sch, was_absent=True)
self.stdout.write("{} Signup on {} created: {}".format(usr, bid, other_abs_su))
else:
s = usr_signup[0]
s.was_absent = True
s.save()
sa = s.scheduled_activity
sa.attendance_taken = True
sa.save()
self.stdout.write("{} Signup on {} modified: {}".format(usr, bid, usr_signup[0]))
self.stdout.write("Done.") | [
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15,693 | tjcsl/ion | intranet/apps/auth/backends.py | KerberosAuthenticationBackend.kinit_timeout_handle | def kinit_timeout_handle(username, realm):
"""Check if the user exists before we throw an error."""
try:
u = User.objects.get(username__iexact=username)
except User.DoesNotExist:
logger.warning("kinit timed out for {}@{} (invalid user)".format(username, realm))
return
logger.critical("kinit timed out for {}".format(realm), extra={
"stack": True,
"data": {
"username": username
},
"sentry.interfaces.User": {
"id": u.id,
"username": username,
"ip_address": "127.0.0.1"
}
}) | python | def kinit_timeout_handle(username, realm):
try:
u = User.objects.get(username__iexact=username)
except User.DoesNotExist:
logger.warning("kinit timed out for {}@{} (invalid user)".format(username, realm))
return
logger.critical("kinit timed out for {}".format(realm), extra={
"stack": True,
"data": {
"username": username
},
"sentry.interfaces.User": {
"id": u.id,
"username": username,
"ip_address": "127.0.0.1"
}
}) | [
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15,694 | tjcsl/ion | intranet/apps/auth/backends.py | KerberosAuthenticationBackend.get_kerberos_ticket | def get_kerberos_ticket(username, password):
"""Attempts to create a Kerberos ticket for a user.
Args:
username
The username.
password
The password.
Returns:
Boolean indicating success or failure of ticket creation
"""
cache = "/tmp/ion-%s" % uuid.uuid4()
logger.debug("Setting KRB5CCNAME to 'FILE:{}'".format(cache))
os.environ["KRB5CCNAME"] = "FILE:" + cache
try:
realm = settings.CSL_REALM
kinit = pexpect.spawnu("/usr/bin/kinit {}@{}".format(username, realm), timeout=settings.KINIT_TIMEOUT)
kinit.expect(":")
kinit.sendline(password)
returned = kinit.expect([pexpect.EOF, "password:"])
if returned == 1:
logger.debug("Password for {}@{} expired, needs reset".format(username, realm))
return "reset"
kinit.close()
exitstatus = kinit.exitstatus
except pexpect.TIMEOUT:
KerberosAuthenticationBackend.kinit_timeout_handle(username, realm)
exitstatus = 1
if exitstatus != 0:
try:
realm = settings.AD_REALM
kinit = pexpect.spawnu("/usr/bin/kinit {}@{}".format(username, realm), timeout=settings.KINIT_TIMEOUT)
kinit.expect(":")
kinit.sendline(password)
returned = kinit.expect([pexpect.EOF, "password:"])
if returned == 1:
return False
kinit.close()
exitstatus = kinit.exitstatus
except pexpect.TIMEOUT:
KerberosAuthenticationBackend.kinit_timeout_handle(username, realm)
exitstatus = 1
if "KRB5CCNAME" in os.environ:
subprocess.check_call(['kdestroy', '-c', os.environ["KRB5CCNAME"]])
del os.environ["KRB5CCNAME"]
if exitstatus == 0:
logger.debug("Kerberos authorized {}@{}".format(username, realm))
return True
else:
logger.debug("Kerberos failed to authorize {}".format(username))
return False | python | def get_kerberos_ticket(username, password):
cache = "/tmp/ion-%s" % uuid.uuid4()
logger.debug("Setting KRB5CCNAME to 'FILE:{}'".format(cache))
os.environ["KRB5CCNAME"] = "FILE:" + cache
try:
realm = settings.CSL_REALM
kinit = pexpect.spawnu("/usr/bin/kinit {}@{}".format(username, realm), timeout=settings.KINIT_TIMEOUT)
kinit.expect(":")
kinit.sendline(password)
returned = kinit.expect([pexpect.EOF, "password:"])
if returned == 1:
logger.debug("Password for {}@{} expired, needs reset".format(username, realm))
return "reset"
kinit.close()
exitstatus = kinit.exitstatus
except pexpect.TIMEOUT:
KerberosAuthenticationBackend.kinit_timeout_handle(username, realm)
exitstatus = 1
if exitstatus != 0:
try:
realm = settings.AD_REALM
kinit = pexpect.spawnu("/usr/bin/kinit {}@{}".format(username, realm), timeout=settings.KINIT_TIMEOUT)
kinit.expect(":")
kinit.sendline(password)
returned = kinit.expect([pexpect.EOF, "password:"])
if returned == 1:
return False
kinit.close()
exitstatus = kinit.exitstatus
except pexpect.TIMEOUT:
KerberosAuthenticationBackend.kinit_timeout_handle(username, realm)
exitstatus = 1
if "KRB5CCNAME" in os.environ:
subprocess.check_call(['kdestroy', '-c', os.environ["KRB5CCNAME"]])
del os.environ["KRB5CCNAME"]
if exitstatus == 0:
logger.debug("Kerberos authorized {}@{}".format(username, realm))
return True
else:
logger.debug("Kerberos failed to authorize {}".format(username))
return False | [
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Args:
username
The username.
password
The password.
Returns:
Boolean indicating success or failure of ticket creation | [
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15,695 | tjcsl/ion | intranet/apps/dashboard/views.py | get_fcps_emerg | def get_fcps_emerg(request):
"""Return FCPS emergency information."""
try:
emerg = get_emerg()
except Exception:
logger.info("Unable to fetch FCPS emergency info")
emerg = {"status": False}
if emerg["status"] or ("show_emerg" in request.GET):
msg = emerg["message"]
return "{} <span style='display: block;text-align: right'>— FCPS</span>".format(msg)
return False | python | def get_fcps_emerg(request):
try:
emerg = get_emerg()
except Exception:
logger.info("Unable to fetch FCPS emergency info")
emerg = {"status": False}
if emerg["status"] or ("show_emerg" in request.GET):
msg = emerg["message"]
return "{} <span style='display: block;text-align: right'>— FCPS</span>".format(msg)
return False | [
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15,696 | tjcsl/ion | intranet/apps/dashboard/views.py | gen_schedule | def gen_schedule(user, num_blocks=6, surrounding_blocks=None):
"""Generate a list of information about a block and a student's current activity signup.
Returns:
schedule
no_signup_today
"""
no_signup_today = None
schedule = []
if surrounding_blocks is None:
surrounding_blocks = EighthBlock.objects.get_upcoming_blocks(num_blocks)
if len(surrounding_blocks) == 0:
return None, False
# Use select_related to reduce query count
signups = (EighthSignup.objects.filter(user=user, scheduled_activity__block__in=surrounding_blocks).select_related(
"scheduled_activity", "scheduled_activity__block", "scheduled_activity__activity"))
block_signup_map = {s.scheduled_activity.block.id: s.scheduled_activity for s in signups}
for b in surrounding_blocks:
current_sched_act = block_signup_map.get(b.id, None)
if current_sched_act:
current_signup = current_sched_act.title_with_flags
current_signup_cancelled = current_sched_act.cancelled
current_signup_sticky = current_sched_act.activity.sticky
rooms = current_sched_act.get_scheduled_rooms()
else:
current_signup = None
current_signup_cancelled = False
current_signup_sticky = False
rooms = None
# warning flag (red block text and signup link) if no signup today
# cancelled flag (red activity text) if cancelled
flags = "locked" if b.locked else "open"
blk_today = b.is_today()
if blk_today and not current_signup:
flags += " warning"
if current_signup_cancelled:
flags += " cancelled warning"
if current_signup_cancelled:
# don't duplicate this info; already caught
current_signup = current_signup.replace(" (Cancelled)", "")
info = {
"id": b.id,
"block": b,
"block_letter": b.block_letter,
"current_signup": current_signup,
"current_signup_cancelled": current_signup_cancelled,
"current_signup_sticky": current_signup_sticky,
"locked": b.locked,
"date": b.date,
"flags": flags,
"is_today": blk_today,
"signup_time": b.signup_time,
"signup_time_future": b.signup_time_future,
"rooms": rooms
}
schedule.append(info)
if blk_today and not current_signup:
no_signup_today = True
return schedule, no_signup_today | python | def gen_schedule(user, num_blocks=6, surrounding_blocks=None):
no_signup_today = None
schedule = []
if surrounding_blocks is None:
surrounding_blocks = EighthBlock.objects.get_upcoming_blocks(num_blocks)
if len(surrounding_blocks) == 0:
return None, False
# Use select_related to reduce query count
signups = (EighthSignup.objects.filter(user=user, scheduled_activity__block__in=surrounding_blocks).select_related(
"scheduled_activity", "scheduled_activity__block", "scheduled_activity__activity"))
block_signup_map = {s.scheduled_activity.block.id: s.scheduled_activity for s in signups}
for b in surrounding_blocks:
current_sched_act = block_signup_map.get(b.id, None)
if current_sched_act:
current_signup = current_sched_act.title_with_flags
current_signup_cancelled = current_sched_act.cancelled
current_signup_sticky = current_sched_act.activity.sticky
rooms = current_sched_act.get_scheduled_rooms()
else:
current_signup = None
current_signup_cancelled = False
current_signup_sticky = False
rooms = None
# warning flag (red block text and signup link) if no signup today
# cancelled flag (red activity text) if cancelled
flags = "locked" if b.locked else "open"
blk_today = b.is_today()
if blk_today and not current_signup:
flags += " warning"
if current_signup_cancelled:
flags += " cancelled warning"
if current_signup_cancelled:
# don't duplicate this info; already caught
current_signup = current_signup.replace(" (Cancelled)", "")
info = {
"id": b.id,
"block": b,
"block_letter": b.block_letter,
"current_signup": current_signup,
"current_signup_cancelled": current_signup_cancelled,
"current_signup_sticky": current_signup_sticky,
"locked": b.locked,
"date": b.date,
"flags": flags,
"is_today": blk_today,
"signup_time": b.signup_time,
"signup_time_future": b.signup_time_future,
"rooms": rooms
}
schedule.append(info)
if blk_today and not current_signup:
no_signup_today = True
return schedule, no_signup_today | [
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15,697 | tjcsl/ion | intranet/apps/dashboard/views.py | find_birthdays | def find_birthdays(request):
"""Return information on user birthdays."""
today = date.today()
custom = False
yr_inc = 0
if "birthday_month" in request.GET and "birthday_day" in request.GET:
try:
mon = int(request.GET["birthday_month"])
day = int(request.GET["birthday_day"])
yr = today.year
""" If searching a date that already happened this year, skip to the next year. """
if mon < today.month or (mon == today.month and day < today.day):
yr += 1
yr_inc = 1
real_today = today
today = date(yr, mon, day)
if today:
custom = True
else:
today = real_today
except ValueError:
pass
key = "birthdays:{}".format(today)
cached = cache.get(key)
if cached:
logger.debug("Birthdays on {} loaded " "from cache.".format(today))
logger.debug(cached)
return cached
else:
logger.debug("Loading and caching birthday info for {}".format(today))
tomorrow = today + timedelta(days=1)
try:
data = {
"custom": custom,
"today": {
"date": today,
"users": [{
"id": u.id,
"full_name": u.full_name,
"grade": {
"name": u.grade.name
},
"age": (u.age + yr_inc) if u.age is not None else -1,
"public": u.properties.attribute_is_public("show_birthday")
} if u else {} for u in User.objects.users_with_birthday(today.month, today.day)],
"inc": 0,
},
"tomorrow": {
"date": tomorrow,
"users": [{
"id": u.id,
"full_name": u.full_name,
"grade": {
"name": u.grade.name
},
"age": (u.age - 1) if u.age is not None else -1,
"public": u.properties.attribute_is_public("show_birthday")
} for u in User.objects.users_with_birthday(tomorrow.month, tomorrow.day)],
"inc": 1,
},
} # yapf: disable
except AttributeError:
return None
else:
cache.set(key, data, timeout=60 * 60 * 6)
return data | python | def find_birthdays(request):
today = date.today()
custom = False
yr_inc = 0
if "birthday_month" in request.GET and "birthday_day" in request.GET:
try:
mon = int(request.GET["birthday_month"])
day = int(request.GET["birthday_day"])
yr = today.year
""" If searching a date that already happened this year, skip to the next year. """
if mon < today.month or (mon == today.month and day < today.day):
yr += 1
yr_inc = 1
real_today = today
today = date(yr, mon, day)
if today:
custom = True
else:
today = real_today
except ValueError:
pass
key = "birthdays:{}".format(today)
cached = cache.get(key)
if cached:
logger.debug("Birthdays on {} loaded " "from cache.".format(today))
logger.debug(cached)
return cached
else:
logger.debug("Loading and caching birthday info for {}".format(today))
tomorrow = today + timedelta(days=1)
try:
data = {
"custom": custom,
"today": {
"date": today,
"users": [{
"id": u.id,
"full_name": u.full_name,
"grade": {
"name": u.grade.name
},
"age": (u.age + yr_inc) if u.age is not None else -1,
"public": u.properties.attribute_is_public("show_birthday")
} if u else {} for u in User.objects.users_with_birthday(today.month, today.day)],
"inc": 0,
},
"tomorrow": {
"date": tomorrow,
"users": [{
"id": u.id,
"full_name": u.full_name,
"grade": {
"name": u.grade.name
},
"age": (u.age - 1) if u.age is not None else -1,
"public": u.properties.attribute_is_public("show_birthday")
} for u in User.objects.users_with_birthday(tomorrow.month, tomorrow.day)],
"inc": 1,
},
} # yapf: disable
except AttributeError:
return None
else:
cache.set(key, data, timeout=60 * 60 * 6)
return data | [
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... | Return information on user birthdays. | [
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"birthdays",
"."
] | 5d722b0725d572039bb0929fd5715a4070c82c72 | https://github.com/tjcsl/ion/blob/5d722b0725d572039bb0929fd5715a4070c82c72/intranet/apps/dashboard/views.py#L185-L254 |
15,698 | tjcsl/ion | intranet/apps/dashboard/views.py | find_visible_birthdays | def find_visible_birthdays(request, data):
"""Return only the birthdays visible to current user.
"""
if request.user and (request.user.is_teacher or request.user.is_eighthoffice or request.user.is_eighth_admin):
return data
data['today']['users'] = [u for u in data['today']['users'] if u['public']]
data['tomorrow']['users'] = [u for u in data['tomorrow']['users'] if u['public']]
return data | python | def find_visible_birthdays(request, data):
if request.user and (request.user.is_teacher or request.user.is_eighthoffice or request.user.is_eighth_admin):
return data
data['today']['users'] = [u for u in data['today']['users'] if u['public']]
data['tomorrow']['users'] = [u for u in data['tomorrow']['users'] if u['public']]
return data | [
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] | 5d722b0725d572039bb0929fd5715a4070c82c72 | https://github.com/tjcsl/ion/blob/5d722b0725d572039bb0929fd5715a4070c82c72/intranet/apps/dashboard/views.py#L257-L264 |
15,699 | tjcsl/ion | intranet/apps/eighth/models.py | EighthActivity._name_with_flags | def _name_with_flags(self, include_restricted, title=None):
"""Generate the name with flags."""
name = "Special: " if self.special else ""
name += self.name
if title:
name += " - {}".format(title)
if include_restricted and self.restricted:
name += " (R)"
name += " (BB)" if self.both_blocks else ""
name += " (A)" if self.administrative else ""
name += " (S)" if self.sticky else ""
name += " (Deleted)" if self.deleted else ""
return name | python | def _name_with_flags(self, include_restricted, title=None):
name = "Special: " if self.special else ""
name += self.name
if title:
name += " - {}".format(title)
if include_restricted and self.restricted:
name += " (R)"
name += " (BB)" if self.both_blocks else ""
name += " (A)" if self.administrative else ""
name += " (S)" if self.sticky else ""
name += " (Deleted)" if self.deleted else ""
return name | [
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] | 5d722b0725d572039bb0929fd5715a4070c82c72 | https://github.com/tjcsl/ion/blob/5d722b0725d572039bb0929fd5715a4070c82c72/intranet/apps/eighth/models.py#L289-L301 |
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