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mip_hedwig.py
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mip_hedwig.py
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'''
Hedwig wrapper for the HBP medical platform.
@author: anze.vavpetic@ijs.si
'''
import tempfile
import logging
from subprocess import call
from mip_helper import io_helper, parameters
import preprocess
DEFAULT_DOCKER_IMAGE = 'python-jsi-hedwig'
if __name__ == '__main__':
# Configure logging
logging.basicConfig(level=logging.INFO)
# Read inputs
inputs = io_helper.fetch_data()
data = inputs["data"]
beam = parameters.get_param('beam', int, 10)
support = parameters.get_param('support', float, '0.00001')
out_file = 'input.csv'
rules_out_file = 'rules.txt'
matrix, attributes = preprocess.to_matrix(data)
preprocess.dump_to_csv(matrix, attributes, out_file)
# Call hedwig with sensible defaults
examples_file = out_file
empty_bk = tempfile.mkdtemp()
call([
'python', '-m' 'hedwig.__main__',
empty_bk,
examples_file,
'--beam', str(beam),
'--support', str(support),
'-f', 'csv',
'-l',
'-o', rules_out_file,
'--nocache'
])
with open(rules_out_file) as f:
results = f.read()
# TODO: add text/plain to mime types in shapes.Shapes
io_helper.save_results(results.replace('less_than', '<'), 'text/plain')