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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
True
>>> result.type
'FALSE'
>>> 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...

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...

If you write results into a tinydb data store, NotCompleted objects are saved. After an analysis, you can get a summary of those using methods on the WritableTinyDbDataStore instance.