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.. jupyter-execute::
:hide-code:
import set_working_directory
Tracking records that could not be processed
============================================
.. _not_completed:
The ``NotCompleted`` object
---------------------------
``NotCompleted`` is a special result type that can be produced by a composable app. These objects evaluate to ``False``.
An app can return a ``NotCompleted`` result for one of 2 reasons. The object contains information regarding the input data, where the issue arose and whatever message was provided by the code (like an exception traceback).
``NotCompleted`` FALSE type
^^^^^^^^^^^^^^^^^^^^^^^^^^^
The results when a condition was not met. For example, below I create an app that will return alignments with 2 specific sequences. I'm applying this to a data set where a "Mouse" sequence does not exist. This will produce a FALSE type.
.. jupyter-execute::
from cogent3 import get_app
reader = get_app("load_aligned", format="fasta")
select_seqs = get_app("take_named_seqs", "Mouse", "Human")
aln = reader("data/primate_brca1.fasta")
result = select_seqs(aln)
assert result == False
result
The ``NotCompleted`` instance has attributes identifying what data failed,
.. jupyter-execute::
result.source
where the failure occurred
.. jupyter-execute::
result.origin
and the reason for the failure
.. jupyter-execute::
result.message
``NotCompleted`` ERROR type
^^^^^^^^^^^^^^^^^^^^^^^^^^^
An ``ERROR`` type is returned if an unexpected condition occurs. This can be an exception raised during the calculation. In our example, we illustrate this by trying to open a file with an incorrect path.
.. jupyter-execute::
:raises:
result = reader("primate_brca1.fasta")
result
Composed functions propagate ``NotCompleted`` results
-----------------------------------------------------
If you have a composed function, with multiple steps and an error occurs then the resulting ``NotCompleted`` result is returned without any of the other steps being applied to it. For example, we make a composed app from both of the above apps.
.. jupyter-execute::
app = reader + select_seqs
result = app("data/primate_brca1.fasta")
result
and
.. jupyter-execute::
:raises:
result = app("primate_brca1.fasta")
result
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