Generates cohort test cases

.gitignore

venv
cohort-cases

README.md

README

Setup

python3 -m venv venv
source venv/bin/activate
pip install PyYAML

Running a Single Chonky From CLI

Command Example

java \
    -Dnamespace=perf \
    -Dcluster=dev0-pinniped \
    -Dkube.config=.kube/config \
    -Ddatabase.username=root \
    -Ddatabase.password=aep  \
    -Demail=dta@aetion.com \
    -Dpassword="glAUtZTOoKe1THQWR5dg33tq6p8NjdPq" \
    -jar dispatcher-performance/target/dispatcher-performance-1.0.0-SNAPSHOT-jar-with-dependencies.jar \
    -c ../cohort-chonky/cohort-cases/cohort-regression-0001.yaml  \
    -r 1

Arguments

Property Definitions ("-D")

Arg	Description
namespace
cluster	dev0-pinniped
kube.config	.kube/config
database.username	root
database.password	aep
email	dta@aetion.com
password	glAUtZTOoKe1THQWR5dg33tq6p8NjdPq

Program Flags

Arg	Description
-c	Filesystem path to chonky file
-r	Number of times to run the test

cohort_chonky.py

#!/bin/env python

from itertools import product
from yaml import safe_load, dump
from copy import deepcopy
from pathlib import Path

case_dir = 'cohort-cases'

measure = {
    'isPatientAttribute':'TRUE',
    'name':'ENROLLMENT'
}

params = {
    'useNewRelativeMeasure': ['TRUE', 'FALSE'],
    'inclusion.newRelativeMeasure': [deepcopy(measure)],
    'inclusion.measure': [deepcopy(measure)],
    'enrollmentMeasure': [deepcopy(measure)],
    'inclusion.priorUsePolicy': ['ALL', 'NEW'],
    'inclusion.newWrtPolicy': ['BOTH', 'MINE'],
    'inclusion.washoutDays': [180],
    'inclusion.episodeType': ['NO_EPISODES', 'EPISODES_WITHOUT_GRACE', 'EPISODES_WITH_GRACE'],
    'inclusion.expRiskDays': [14],
    'inclusion.expGraceDays': [14],
    'inclusion.useBooleansAsEvents': ['TRUE', 'FALSE'],
    'useEntryDates': ['TRUE', 'FALSE'],
    'usePriorEnrollmentDays': ['TRUE', 'FALSE'],
    'priorEnrollmentDays': [0, 180],
    'cohortEntryPolicy': ['FIRST', 'LAST', 'ALL'],
    'applyExclusionPolicy': ['EVENT_BEFORE_EXCLUSIONS', 'EVENT_AFTER_EXCLUSIONS']
}

chonky_yaml = '''
---
version: 0.0.2
project:
  name: Cohort Regression Tests
cohorts:
- name: 
  dataset: SYNPUF_SUBSET
  cohortType: DESCRIPTIVE
  entryParams: 
'''

def main():
    keys, values = zip(*params.items())
    cases = [dict(zip(keys, v)) for v in product(*values)]

    chonky_params = {}
    cnt = 1
    for case in cases:
        chonky = safe_load(chonky_yaml)
        chonky['cohorts'][0]['name'] = f'Cohort regression #{cnt}'
        idx = str(cnt).zfill(4)
        cnt = cnt + 1
        for name, val in case.items():
            if '.' in name:
                k1, k2 = name.split('.')
                if k1 not in chonky_params:
                    chonky_params[k1] = {}
                chonky_params[k1][k2] = val
            else:
                chonky_params[name] = val
        chonky['cohorts'][0]['entryParams'] = chonky_params

        Path(case_dir).mkdir(parents=True, exist_ok=True)        
        with open(f'{case_dir}/cohort-regression-{idx}.yaml', 'w') as outfile:
            dump(chonky, outfile, default_flow_style=False, sort_keys=False)


if __name__ == "__main__":
    main()