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The NotCompleted object

This is an object returned when a composable function did not complete a task. 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 that with 2 specific sequences but I’m including one that does not exist (“Mouse”). So this will fail.

from cogent3.app import io, sample

reader = io.load_aligned(format="fasta")
select_seqs = sample.take_named_seqs("Mouse", "Human")
aln = reader("data/primate_brca1.fasta")
result = select_seqs(aln)
result
NotCompleted(type=FALSE, origin=take_named_seqs, source="data/primate_brca1.fasta", message="named seq(s) {'Mouse'} not in ['Chimpanzee', 'Galago', 'Gorilla', 'HowlerMon', 'Human', 'Orangutan', 'Rhesus']")
result == False
result.type
result.message
"named seq(s) {'Mouse'} not in ['Chimpanzee', 'Galago', 'Gorilla', 'HowlerMon', 'Human', 'Orangutan', 'Rhesus']"

NotCompleted ERROR type

An ERROR type is returned if an exception is raised during the calculation. We trigger it in this case by trying to open a non-existent file.

result = reader("primate_brca1.fasta")
result
NotCompleted(type=ERROR, origin=load_aligned, source="primate_brca1.fasta", message="Traceback (most recent call last):
  File "/Users/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.8/site-packages/cogent3/app/composable.py", line 300, in _trapped_call
    val = func(val, *args, **kwargs)
  File "/Users/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.8/site-packages/cogent3/app/io.py", line 134, in load
    path = SingleReadDataStore(path)[0]
  File "/Users/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.8/site-packages/cogent3/app/data_store.py", line 346, in __init__
    assert path.exists() and path.is_file()
AssertionError
")

Composed functions propagate NotCompleted results

process = reader + select_seqs
result = process("data/primate_brca1.fasta")
result
NotCompleted(type=FALSE, origin=take_named_seqs, source="data/primate_brca1.fasta", message="named seq(s) {'Mouse'} not in ['Chimpanzee', 'Galago', 'Gorilla', 'HowlerMon', 'Human', 'Orangutan', 'Rhesus']")

and

result = process("primate_brca1.fasta")
result
NotCompleted(type=ERROR, origin=load_aligned, source="primate_brca1.fasta", message="Traceback (most recent call last):
  File "/Users/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.8/site-packages/cogent3/app/composable.py", line 300, in _trapped_call
    val = func(val, *args, **kwargs)
  File "/Users/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.8/site-packages/cogent3/app/io.py", line 134, in load
    path = SingleReadDataStore(path)[0]
  File "/Users/runner/work/cogent3.github.io/cogent3.github.io/.venv/lib/python3.8/site-packages/cogent3/app/data_store.py", line 346, in __init__
    assert path.exists() and path.is_file()
AssertionError
")