def main(script, task='', case='', output=''):
"""Perform project tasks.
'task' is the project task to run.
'case' is a path to the case to run, optional.
'output' is the output to generate, optional.
Usage: python3 <task> [<case|chapter>] [latex|json]
"""
if not task:
print("Usage: python3 <task> [<case|chapter>] [latex|json]")
sys.exit(2)
if get_empty_indices():
print("Empty indices, run 'python3 index.py build' first!")
sys.exit(1)
if case and case in OUTPUTS:
output = case
case = ''
if output in ('json', 'latex') and not os.path.exists(OUTPUT_FOLDER):
os.mkdir(OUTPUT_FOLDER)
if output not in OUTPUTS:
print("Unknown output %s, valid:" % output, ', '.join(OUTPUTS.keys()))
sys.exit(2)
populate_all()
if task == '5':
task_5()
# Perform a task which uses patient cases as input
elif task in CASE_TASKS:
cases = {name: obj for name, obj in PatientCase.ALL.items()
if (not case or name == case)}
if not cases:
print("Unknown patient case: %s" % case)
sys.exit(2)
_perform_task(task, CASE_TASKS[task], cases, OUTPUTS[output])
# Perform a task which uses chapters as input
elif task in CHAPTER_TASKS:
chapters = {code: obj for code, obj in Therapy.ALL.items()
if (not case or case == obj.code)}
if not chapters:
print("Unknown therapy code: %s" % case)
sys.exit(2)
_perform_task(task, CHAPTER_TASKS[task], chapters,
OUTPUTS[output], progress=True)
else:
print("Unknown task '%s', valid tasks are: %s" % (task,
', '.join(list(CASE_TASKS.keys()) + list(CHAPTER_TASKS.keys()))))
sys.exit(2)
sys.exit(None)
def main(script=None):
"""Test if objects can be populated and indices contains data."""
# Check if json files exists
for cls in (ATC, ICD, PatientCase, Therapy):
if not os.path.isfile(cls._JSON):
print("Missing json file %s, use 'parse.py' to fix" % cls._JSON)
sys.exit(1)
# Load objects from JSON files
now = time.time()
populate_all()
print("Populated ATC %i, ICD %i, Cases %i, Therapy %i in %.2f seconds" % (
len(ATC.ALL), len(ICD.ALL), len(PatientCase.ALL),
len(Therapy.ALL), time.time() - now))
# Check if indices exists and contains documents
import index
empty = index.get_empty_indices()
if empty:
print("Empty indices '%s', run 'python3 index.py build' to fix" %
', '.join(i.__name__ for i in empty))
sys.exit(1)
print("All A-OK")