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, command='', index='', field='', *query):
"""Store, clear or search data in whoosh indices.
Can also be used to create vectors needed for task 3.
'command' is either build|store|clean|search|vector
'index' is either atc|icd|therapy|case
Usage: python3 index.py <command> [index] [field] [query]
"""
# Store all objects in index
if command == 'build':
populate_all()
empty = get_empty_indices()
for cls in empty:
store_objects_in_index(cls)
return
classes = [ATC, ICD, PatientCase, Therapy]
if index:
classes = [i for i in classes if i._NAME == index]
if not classes:
print("Unknown index %s, valids: atc|icd|case|therapy" % index)
sys.exit(2)
# Store objects in index, will create duplicates if run several times
if command == 'store':
populate_all()
for cls in classes:
store_objects_in_index(cls)
# Empty index
elif command in ('clean', 'clear'):
for cls in classes:
create_or_open_index(cls)
create_in(INDEX_DIR, SCHEMA_MAP[cls._NAME], cls._NAME)
print("Emptied %s index" % cls.__name__)
# Create vectors
elif command.startswith('vector'):
populate_all()
create_vectors()
# Search in whoosh index
elif command == 'search':
mapping = {'icd': ('short', 'label'), 'atc': ('code', 'title'),
'therapy': ('code', 'title'), 'case': ('code',)}
query = ''.join(query) # Flatten query
cls, = classes # Can only search on one index at a time
print_result(extract(mapping[cls._NAME], search(cls, field, query)))
# Unknown command
else:
print("Unknown command '%s'" % command)
print("Usage: python3 index.py <command> [index] [field] [query]")
print("Command is either build|store|clean|search|vector")
sys.exit(2)
sys.exit(None)
