define_app(klass=None, *, app_type: AppType = AppType.GENERIC, skip_not_completed: bool = True) type#

decorator for building callable apps


either a class or a function. If a function, it is converted to a class with the function bound as a static method.


what type of app, typically you just want GENERIC.


if True (default), NotCompleted instances are returned without being passed to the app.main() method.


Instances of cogent3 apps are callable. If an exception occurs, the app returns a NotCompleted instance with logging information. Apps defined with app_type LOADER, GENERIC or WRITER can be “composed” (summed together) to produce a single callable that sequentially invokes the composed apps. For example, the independent usage of app instances app1 and app2 as


is equivalent to

combined = app1 + app2

The app_type attribute is used to constrain how apps can be composed. LOADER and WRITER are special cases. If included, a LOADER must always be first, e.g.

app = a_loader + a_generic

If included, a WRITER must always be last, e.g.

app = a_generic + a_writer

Changing the order for either of the above will result in a TypeError.

There are no constraints on ordering of GENERIC aside from compatability of their input and return types (see below).

In order to be decorated with @define_app a class must

  • implement a method called main

  • type hint the first argument of main

  • type hint the return type for main

While you can have more than one argument in main, this is currently not supported in composable apps.

Overlap between the return type hint and first argument hint is required for two apps to be composed together.

define_app adds a __call__ method which checks an input value prior to passing it to app.main() as a positional argument. The data checking results in NotCompleted being returned immediately, unless skip_not_completed==False. If the input value type is consistent with the type hint on the first argument of main it is passed to app.main(). If it does not match, a new NotCompleted instance is returned.


An example app definition.

>>> from typing import Union
>>> from import define_app
>>> from import AlignedSeqsType, SerialisableType
>>> @define_app
... class drop_bad:
...     def __init__(self, quantile=None, gap_fraction=1, moltype="dna"):
...         self.quantile = quantile
...         self.gap_fraction = gap_fraction
...         self.moltype = moltype
...     T = Union[AlignedSeqsType, SerialisableType]
...     def main(self, aln: AlignedSeqsType) -> T:
...         return aln.omit_bad_seqs(
...                                 quantile=self.quantile,
...                                 gap_fraction=self.gap_fraction,
...                                 moltype=self.moltype
...                                 )

drop_bad is a composable app with app_type=GENERIC. The input data must be a sequence alignment instance. It returns the same type, which is also serialisable. (If invalid input data is provided a NotCompleted instance is returned.)

You can also decorate functions. In that case, they will be converted into a class with the same name as the original function. The function itself is bound to this new class as a staticmethod, e.g.

>>> from typing import Union
>>> from import define_app
>>> from import AlignedSeqsType, SerialisableType
>>> T = Union[AlignedSeqsType, SerialisableType]
>>> @define_app
... def omit_seqs(aln: AlignedSeqsType, quantile=None, gap_fraction=1, moltype="dna") -> T:
...     return aln.omit_bad_seqs(
...                             quantile=quantile,
...                             gap_fraction=gap_fraction,
...                             moltype=moltype
...                             )

omit_seqs is now an app, allowing creating different variants which can be composed as per ones defined via a class.

>>> omit_bad = omit_seqs(quantile=0.95)

and omit_bad is an instance of that app.