Django SIMS (sample information management system) provides centralized logging for distributed computational analyses.
The element of logging is a LogEntry. Each LogEntry instance attaches a
status and timestamp to a rule or expected output for a given pipeline and
sample.
Add Django SIMS calls to existing Python code. The original API was designed for
use within Johannes Köster's
Snakemake, a
Python-based DSL that improves upon GNU Make. See the included Snakefile and
sims/tests.py for examples.
Log an arbitrary status.
from sims.models import Pipeline
pipeline, pipeline_created = Pipeline.objects.get_or_create(name="test", version="0.1")
pipeline.log("my_sample_output.txt", "my_sample", "logged")Alternately, use helper methods for common logging operations like the start and finish of a pipeline's rule.
pipeline.start("my_sample_output.txt", "my_sample")
do_something("my_sample")
pipeline.finish("my_sample_output.txt", "my_sample")