def insert_unmatched_record(record_dictionary):
'''Inserts the record into the clin.incoming_data_unmatched directly into the GNUMed database. Takes in a dictionary containing
the needed data.'''
try:
conn = psycopg2.connect(connection_string)
cursor = conn.cursor()
insert_query = """SET TRANSACTION READ WRITE;
INSERT into clin.incoming_data_unmatched
(external_data_id, lastnames, firstnames, gender, type, requestor, request_id, other_info, data)
VALUES (%s, %s, %s, %s, %s, %s, %s, %s, %s); """
#print insert_query
cursor.execute(insert_query, (record_dictionary['external_id'], record_dictionary['last_name'],
record_dictionary['first_name'], record_dictionary['gender'],
record_dictionary['data_type'], record_dictionary['ordering_provider_information']
, record_dictionary['request_id'], record_dictionary['other_info'],
psycopg2.Binary(record_dictionary['data'])))
conn.commit()
cursor.close()
conn.close()
except:
error_message = "And error occurred trying to insert record with request_id: \'%s\'\t and external_id: \'%s\'. "\
% (record_dictionary['request_id'], record_dictionary['external_id'])
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_CODE_DB_ISSUE)
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 process_xml_directory(input_directory, hl7_directory, processed_file_dir=None):
try:
xml_files = hl7_importer_file_directory_utilities.process_directory("xml", input_directory)
except IOError:
error_message = "An error occurred trying to retrieve the xml file contents of the directory: %s." % (
input_directory
)
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_FILE_OPERATION_ERROR)
else:
# Process each file.
for n in xml_files:
hl7_path = hl7_importer_file_directory_utilities.create_output_path("hl7", n, hl7_directory, True)
process_xml_file(n, hl7_path)
hl7_importer_file_directory_utilities.handle_processed_file(n, processed_file_dir)
def process_xml_file(in_file, out_file, move_file_path=""):
""" Opens the xml file pulls out all of the hl7 messages in the file , then writes them to a text file. If a move_file_path
is provided, it function moves the xml file to the given directory, otherwise it appends '.px' to all XML files that have been processed."""
try:
e_tree = ElementTree.parse(in_file)
except:
gnumed_error_writer.write_error("Not a valid XML file")
exit(gnumed_error_writer.EXIT_CODE_INVALID_XML)
# Grab all messages in the XML document
messages = e_tree.findall(".//Message")
# Check to see if the file is complete.
# Looks at the MessageCount attribute in the root node and compare with the number of Message nodes
stated_number = e_tree._root.attrib["MessageCount"]
if len(messages) != int(stated_number):
error_message = "Number of message in %s do not match: Listed: %s\t Actual: %s" % (
in_file,
(len(messages)),
str(stated_number),
)
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_CODE_MISMATCH)
# Write HL7 messages to an HL7 file
try:
with open(out_file, "w") as hl7_file:
for node in messages:
hl7_file.write(node.text)
except IOError:
error_message = "Could not open file %s" % out_file
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_FILE_OPERATION_ERROR)
def handle_processed_file(file_path, processed_file_dir=None):
if processed_file_dir != None:
try:
move_processed_file(file_path, processed_file_dir)
except IOError:
#Attempt to rename the file so it won't be scanned later
try:
rename_processed_file(file_path)
except IOError:
error_message = "File %s could not be moved or renamed" % (file_path)
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_FILE_OPERATION_ERROR)
else:
error_message = "File %s not moved. File renamed in its current directory with %s extension" % (
file_path, PROCESSED_FILE_EXTENSION)
gnumed_error_writer.write_error(error_message)
exit(gnumed_error_writer.EXIT_FILE_OPERATION_ERROR)
else:
try:
rename_processed_file(file_path)
except IOError:
error_message = "Could not rename file % with extension %s" % (file_path, PROCESSED_FILE_EXTENSION)
