rapids/docs/usage/quick_rule.rst

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Minimal Working Example
=======================
The following is a quick guide for creating and running a simple pipeline to extract Call metrics for daily and night epochs of one participant monitored on the US East coast.
#. Make sure your database connection credentials in ``.env`` are correct. See step 1 of :ref:`Usage Section <db-configuration>`.
#. Create at least one participant file ``p01`` under ``data/external/``. See step 2 of :ref:`Usage Section <db-configuration>`.
#. Make sure your Conda (python) environment is active. See step 6 of :ref:`install-page`.
#. Replace the contents of the ``Snakefile`` with the following snippet
::
configfile: "config.yaml"
include: "rules/renv.snakefile"
include: "rules/preprocessing.snakefile"
include: "rules/features.snakefile"
include: "rules/reports.snakefile"
rule all:
input:
expand("data/processed/{pid}/call_{call_type}_{day_segment}.csv",
pid=config["PIDS"],
call_type=config["CALLS"]["TYPES"],
day_segment = config["CALLS"]["DAY_SEGMENTS"]),
#. Modify the following settings in the ``config.yaml`` file with the values shown below (leave all other settings as they are)
::
SENSORS: [calls]
FITBIT_TABLE: []
FITBIT_SENSORS: []
PIDS: [p01]
DAY_SEGMENTS: &day_segments
[daily, night]
TIMEZONE: &timezone
America/New_York
DATABASE_GROUP: &database_group
MY_GROUP
For more information on the ``calls`` sensor see :ref:`call-sensor-doc`
#. Run the following command to execute RAPIDS
::
snakemake -j1
#. Daily and night call metrics will be found in files under the ``data/processed/p01/`` directory.