/
gnumed_hl7_importer.py
113 lines (85 loc) · 3.77 KB
/
gnumed_hl7_importer.py
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import glob
import os
import shutil
import gnumed_error_writer
__author__ = 'Jeffrey Leegon'
import re
import hl7
import string
import hl7_interface_to_gnumed
import hl7_importer_file_directory_utilities
def process_lab_message(message):
'''Processes and HL7 lab message. Pulls out the necessary data for the clin.incoming_data_unmatched
into a dictionary along with the raw message then passes it on to the interface to be put in the database.
'''
h = hl7.parse(message)
# temp = h.segment('PID')[2][0]
formatter_message = {}
formatter_message['external_id'] = handle_empty(string.rstrip(h.segment('PID')[2][0]))
formatter_message['last_name'] = handle_empty(h.segment('PID')[5][0])
formatter_message['first_name'] = handle_empty(h.segment('PID')[5][1])
#See if the message has a middle name that will also go into the first name column in the table
if len(h.segment('PID')[5]) < 2:
formatter_message['first_name'] += " " + h.segment('PID')[5][2]
#If Gender equals 'U' leave the value null
#temp = h.segment('PID')[8][0]
gender = string.rstrip(h.segment('PID')[8][0])
if (gender.upper() == 'M') or (gender.upper() == 'F'):
formatter_message['gender'] = gender
else:
formatter_message['gender'] = None
formatter_message['data_type'] = 'HL7'
formatter_message['ordering_provider_information'] = handle_empty(" ".join(h.segment('OBR')[16]))
formatter_message['data'] = message
formatter_message['request_id'] = handle_empty(h.segment('ORC')[3][0])
#Build the other info information
temp_list = [h.segment('PID')[2][0], h.segment('PID')[3][0], h.segment('PID')[4][0]]
if len(h.segment('PID')) > 12:
temp_list.append(h.segment('PID')[13][0])
temp_list = [w.strip() for w in temp_list if len(w) != 0]
formatter_message['other_info'] = " ".join(temp_list)
hl7_interface_to_gnumed.insert_unmatched_record(formatter_message)
def handle_empty(segment):
""" Sees if the segment is an empty string. If it is converts the segment to Python's None
"""
if len(segment) == 0:
return None
else:
return segment
def process_hl7_directory(hl7_directory, processed_file_dir=None):
move_files = False
try:
hl7_files = hl7_importer_file_directory_utilities.process_directory('hl7', hl7_directory)
except IOError:
error_message = "An error occurred trying to retrieve the hl7 file contents of the directory: %s." % (input_directory)
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_FILE_OPERATION_ERROR)
# Process each file.
for n in hl7_files:
#TODO Make sure an hl7 file isn't overwritten
gnumed_hl7_importer(n)
hl7_importer_file_directory_utilities.handle_processed_file(n, processed_file_dir)
def gnumed_hl7_importer(file_name):
""" Goes through the file to find each HL7 message then passes it on to process_lab_message to extract t
he specifically needed information from the database to be imported into GNUMed
"""
#TODO ERROR for opening a file
file = open(file_name)
message = ''
find_message_header = re.compile(r"^MSH")
#TODO Have it be able to process both a directory or an individual file
for n in file:
if re.match(find_message_header, n):
if message != '':
process_lab_message(message)
message = n + '\r'
else:
message = message + n + '\r'
if __name__ == '__main__':
import sys
if len(sys.argv) < 2:
print "Syntax is python gnumed_hl7_importer.py hl7_directory_path"
print "or"
print "python gnumed_hl7_importer.py hl7_directory_path process_hl7_directory_path"
else:
process_hl7_directory(sys.argv[1])