def _create_message(self, results, ack_code):
"""
Creates the final RSP_K21 response message. If no errors occurred and some results have been found, the message
will carry as many different PID segments as the number of the results.
:type: results ``list``
:param: results a list providing the Gnuhealth ORM query results
:type: ack_code ``str``
:param: ack_code it is the ack:code to be put in the MSA segment. If no errors occurred, the code wull be of
positive ACK (AA); else, one of the negative acks (AE, AR)
:return: an hl7apy ``Message`` class instance, which is the final RSP_K21 message
"""
try:
qry_ack_code = 'OK'
if len(results) == 0:
qry_ack_code = 'NF'
is_pdqv = self.is_pdqv_message()
logger.debug("Creating response message...")
if is_pdqv:
message_profile = load_message_profile(os.path.join(_get_message_profiles_dir(), "pdqv_response"))
message_structure = PDQV_MESSAGE_STRUCTURE
else:
message_profile = load_message_profile(os.path.join(_get_message_profiles_dir(), "pdq_response"))
message_structure = PDQ_MESSAGE_STRUCTURE
message = Message(message_structure, version='2.5', validation_level=VALIDATION_LEVEL.STRICT,
reference=message_profile)
self._set_msh(message, is_pdqv)
msa = message.add_segment("MSA")
msa.msa_1 = ack_code
msa.msa_2 = self.msg.msh.msh_10.msh_10_1
qak = message.add_segment("QAK")
qak.qak_1 = self.msg.qpd.qpd_2
qak.qak_2 = qry_ack_code
qak.qak_4.qak_4_1 = str(len(results)) # total results
qak.qak_5.qak_5_1 = str(len(results)) # sent results
qak.qak_6.qak_6_1 = "0" # remaining results
message.add_segment("QPD")
message.qpd = self.msg.qpd
message = self._create_pdq_res_list(message, message_structure, results)
return message
except Exception, e:
logger.error('Error during Message Creation, %s' % e)
def setUp(self):
self.rsp_k21 = \
'MSH|^~\&|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.5|||||ITA||EN\r' \
'MSA|AA|26775702551812240|\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH||||\r' \
'PID|1||10101^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009||||||||||||CAGLIARI|||||\r'
# it misses some PID.3 components
self.invalid_rsp_k21 = \
'MSH|^~\&|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.5|||||ITA||EN\r' \
'MSA|AA|26775702551812240|\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH||||\r' \
'PID|1||10101^^^||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009|||||||||||||||||\r'
self.rsp_k21_27 = \
'MSH|^~\&#|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.7|||||ITA||EN\r' \
'MSA|AA|26775702551812240\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH\r' \
'PID|1||10101^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009||||||||||||CAGLIARI'
self.rsp_k21_27_no_truncation = \
'MSH|^~\&|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.7|||||ITA||EN\r' \
'MSA|AA|26775702551812240\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH\r' \
'PID|1||10101^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009||||||||||||CAGLIARI'
base_path = os.path.abspath(os.path.dirname(__file__))
path = os.path.join(base_path, 'profiles/iti_21')
self.rsp_k21_mp = hl7apy.load_message_profile(path)
def setUp(self):
self.rsp_k21 = \
'MSH|^~\&|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.5|||||ITA||EN\r' \
'MSA|AA|26775702551812240|\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH||||\r' \
'PID|1||10101^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009||||||||||||CAGLIARI|||||\r'
# it misses some PID.3 components
self.invalid_rsp_k21 = \
'MSH|^~\&|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.5|||||ITA||EN\r' \
'MSA|AA|26775702551812240|\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH||||\r' \
'PID|1||10101^^^||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009|||||||||||||||||\r'
self.rsp_k21_27 = \
'MSH|^~\&#|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.7|||||ITA||EN\r' \
'MSA|AA|26775702551812240\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH\r' \
'PID|1||10101^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009||||||||||||CAGLIARI'
self.rsp_k21_27_no_truncation = \
'MSH|^~\&|SEND APP|SEND FAC|REC APP|REC FAC|20110708163514||RSP^K22^RSP_K21|1234|D|2.7|||||ITA||EN\r' \
'MSA|AA|26775702551812240\r' \
'QAK|111069|OK||1|1|0\r' \
'QPD|IHE PDQ Query|111069|@PID.3.1^[email protected]^SMITH\r' \
'PID|1||10101^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^100^H^^092009||||||||||||CAGLIARI'
base_path = os.path.abspath(os.path.dirname(__file__))
path = os.path.join(base_path, 'profiles/iti_21')
self.rsp_k21_mp = hl7apy.load_message_profile(path)
def _check_incoming_message(self):
"""
Controls the incoming HL7 message, after parsing, according to some IHE PDQ message request rules.
It checks that:
- All query parameters codes and values are correct in the request message
- The incoming message contains at least one query parameter
- For the birth date query parameter, the date value format is HL7 - compliant
- If the Allowed Application Filter is enabled. checks if the MSH_3 field contains a value included in the
Allowed_application list table
:raises: :exc:`MissingQueryParameters` if the incoming message has not any query parameters
(QPD_3 hl7 message field is empty)
:raises: :exc:`InvalidQueryParameterCode` if the incoming message has a query parameter code
(QPD_3_1) in a not-allowed format
:raises: :exc:`MissingQueryParameterValue` if the incoming message has a query parameter
(QPD_3_1) correct but without the corrispondent value (QPD_3_2)
:raises: :exc:`InvalidDateParameterValue` if the incoming message has a query parameter (QPD_3_1) asking for
the patient birth date, but providing a not allowed date format in the value
:raise: :exc:`InvalidSendingApplicationParameterValue if the Application Filter is enabled and the MSH_3
field of the incoming message is not included into the Allowed Applications list`
"""
try:
message_profiles_dir = _get_message_profiles_dir()
logger.debug("Checking for message profile from dir: %s" % message_profiles_dir)
if self.is_pdq_message():
message_profile = load_message_profile(os.path.join(message_profiles_dir, 'pdq_request'))
elif self.is_pdqv_message():
message_profile = load_message_profile(os.path.join(message_profiles_dir, 'pdqv_request'))
else:
raise MessageProfileNotFound()
self.msg = parse_message(self.raw_msg, validation_level=VALIDATION_LEVEL.STRICT,
message_profile=message_profile)
except MessageProfileNotFound, e: # NO PDQ
logger.error("No message profile found for message: %s -> %s" % (self.raw_msg, str(e)))
raise PDQMessageProfileNotFound
def setUp(self):
self.rsp_k21 = \
'MSH|^~\&|SENDING APP|SENDING FAC|RECEIVING APP|RECEIVING FAC|20140410170011||RSP^K22^RSP_K21|11111111|P|2.5\r' \
'MSA|AA|20140410170015\r' \
'QAK|222222222|OK\r' \
'QPD|IHE PDQ Query|222222222|@PID.3.1.1^3333333|||||^^^IHEFACILITY&1.3.6.1.4.1.21367.3000.1.6&ISO^|\r' \
'PID|1||10101109091948^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^ITA^H^^092009||||||||||||CAGLIARI|||\r'
base_path = os.path.abspath(os.path.dirname(__file__))
path = os.path.join(base_path, 'profiles/iti_21')
self.rsp_k21_mp = hl7apy.load_message_profile(path)
self.report_file = '/tmp/hl7apy_test_rf'
def setUp(self):
self.rsp_k21 = \
'MSH|^~\&|SENDING APP|SENDING FAC|RECEIVING APP|RECEIVING FAC|20140410170011||RSP^K22^RSP_K21|11111111|P|2.5\r' \
'MSA|AA|20140410170015\r' \
'QAK|222222222|OK\r' \
'QPD|IHE PDQ Query|222222222|@PID.3.1.1^3333333|||||^^^IHEFACILITY&1.3.6.1.4.1.21367.3000.1.6&ISO^|\r' \
'PID|1||10101109091948^^^GATEWAY&1.3.6.1.4.1.21367.2011.2.5.17&ISO||JOHN^SMITH^^^^^A||19690113|M|||VIA DELLE VIE^^CAGLIARI^^^ITA^H^^092009||||||||||||CAGLIARI|||\r'
base_path = os.path.abspath(os.path.dirname(__file__))
path = os.path.join(base_path, 'profiles/iti_21')
self.rsp_k21_mp = hl7apy.load_message_profile(path)
self.report_file = '/tmp/hl7apy_test_rf'
def parse_messages(directory,
validation_level=VL.STRICT,
find_groups=True,
limit=-1,
output_file=None,
message_profile=None):
exceptions = {VL.TOLERANT: [], VL.STRICT: []}
msg_per_versions = {
VL.TOLERANT: defaultdict(int),
VL.STRICT: defaultdict(int)
}
msg_per_type = {VL.TOLERANT: defaultdict(int), VL.STRICT: defaultdict(int)}
parsing_time = {VL.TOLERANT: [], VL.STRICT: []}
encoding_time = []
files = _get_files(directory)[:limit] if limit != -1 else _get_files(
directory)
n_messages = {VL.TOLERANT: 0, VL.STRICT: 0}
mp = load_message_profile(
message_profile) if message_profile is not None else None
start = time.time()
for f in sorted(files):
with open(f) as hl7_file:
msg_str = hl7_file.read()
msg_str = msg_str.replace('\r\n', '\r')
msg_str = msg_str.replace('\n', '\r')
error_occurred = False
validations = [VL.STRICT, VL.TOLERANT]
if validation_level == VL.TOLERANT:
validations.remove(VL.STRICT)
for vl in validations:
# it parses TOLERANT only if the user asked (validation_level == VL.TOLERANT)
# or an error occurred
if vl == VL.TOLERANT and (validation_level != VL.TOLERANT
and not error_occurred):
continue
file_base_name = os.path.basename(hl7_file.name)
try:
msg_start = time.time()
msg = parse_message(msg_str,
vl,
find_groups=find_groups,
message_profile=mp)
msg_end = time.time()
msg_per_versions[vl][msg.version] += 1
msg_per_type[vl][msg.msh.msh_9.to_er7()] += 1
parsing_time[vl].append(
(file_base_name, len(msg.children),
msg.msh.msh_9.to_er7(), msg_end - msg_start))
except MessageProfileNotFound:
continue
except InvalidEncodingChars:
if mp is None:
exceptions[vl].append({
'type': 'parsing',
'ex': e,
'file_name': f,
'msg': msg_str
})
if vl == VL.STRICT:
error_occurred = True
else:
continue
except Exception as e:
exceptions[vl].append({
'type': 'parsing',
'ex': e,
'file_name': f,
'msg': msg_str
})
if vl == VL.STRICT:
error_occurred = True
n_messages[vl] += 1
try:
encoding_start = time.time()
msg.to_er7()
encoding_end = time.time()
encoding_time.append((file_base_name, len(msg.children),
msg.msh.msh_9.to_er7(),
encoding_end - encoding_start))
except Exception as e:
exceptions[vl].append({
'type': 'encoding',
'ex': e,
'file_name': f,
'msg': msg_str
})
elapsed_time = time.time() - start
print_report(n_messages, msg_per_versions, msg_per_type, exceptions,
elapsed_time, output_file, parsing_time, encoding_time,
validation_level, message_profile)
def parse_messages(directory, validation_level=VL.STRICT, find_groups=True, limit=-1,
output_file=None, message_profile=None):
exceptions = {VL.TOLERANT: [], VL.STRICT: []}
msg_per_versions = {VL.TOLERANT: defaultdict(int), VL.STRICT: defaultdict(int)}
msg_per_type = {VL.TOLERANT: defaultdict(int), VL.STRICT: defaultdict(int)}
parsing_time = {VL.TOLERANT : [], VL.STRICT : []}
encoding_time = []
files = _get_files(directory)[:limit] if limit != -1 else _get_files(directory)
n_messages = {VL.TOLERANT: 0, VL.STRICT: 0}
mp = load_message_profile(message_profile) if message_profile is not None else None
start = time.time()
for f in sorted(files):
with open(f) as hl7_file:
msg_str = hl7_file.read()
msg_str = msg_str.replace('\r\n', '\r')
msg_str = msg_str.replace('\n', '\r')
error_occurred = False
validations = [VL.STRICT, VL.TOLERANT]
if validation_level == VL.TOLERANT:
validations.remove(VL.STRICT)
for vl in validations:
# it parses TOLERANT only if the user asked (validation_level == VL.TOLERANT)
# or an error occurred
if vl == VL.TOLERANT and (validation_level != VL.TOLERANT and not error_occurred):
continue
file_base_name = os.path.basename(hl7_file.name)
try:
msg_start = time.time()
msg = parse_message(msg_str, vl, find_groups=find_groups, message_profile=mp)
msg_end = time.time()
msg_per_versions[vl][msg.version] += 1
msg_per_type[vl][msg.msh.msh_9.to_er7()] += 1
parsing_time[vl].append((file_base_name, len(msg.children),
msg.msh.msh_9.to_er7(), msg_end - msg_start))
except MessageProfileNotFound:
continue
except InvalidEncodingChars:
if mp is None:
exceptions[vl].append({'type': 'parsing', 'ex': e, 'file_name': f, 'msg': msg_str})
if vl == VL.STRICT:
error_occurred = True
else:
continue
except Exception as e:
exceptions[vl].append({'type': 'parsing', 'ex': e, 'file_name': f, 'msg': msg_str})
if vl == VL.STRICT:
error_occurred = True
n_messages[vl] += 1
try:
encoding_start = time.time()
msg.to_er7()
encoding_end = time.time()
encoding_time.append((file_base_name, len(msg.children), msg.msh.msh_9.to_er7(),
encoding_end - encoding_start))
except Exception as e:
exceptions[vl].append({'type': 'encoding', 'ex': e, 'file_name': f, 'msg': msg_str})
elapsed_time = time.time() - start
print_report(n_messages, msg_per_versions, msg_per_type, exceptions,
elapsed_time, output_file, parsing_time, encoding_time,
validation_level, message_profile)
# See license-GPLv2.txt or license-MIT.txt
import os
import re
import uuid
import socket
import hashlib
from django.conf import settings
from hl7apy import load_message_profile, VALIDATION_LEVEL as VL
from hl7apy.core import Message
from hl7apy.parser import parse_message
_MP_ROOT_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), "hl7_profiles")
_PDQ_REQ_MP = load_message_profile(os.path.join(_MP_ROOT_PATH, "pdq_request"))
_PDQV_REQ_MP = load_message_profile(os.path.join(_MP_ROOT_PATH, "pdqv_request"))
_PDQ_RES_MP = load_message_profile(os.path.join(_MP_ROOT_PATH, "pdq_response"))
_PDQV_RES_MP = load_message_profile(os.path.join(_MP_ROOT_PATH, "pdqv_response"))
def make_new_uid():
return hashlib.sha1(os.urandom(20)).hexdigest()
def json_response():
pass
def send_hl7_message(host, port, er7_message):
sb = "\x0b"
import uuid
import logging
import datetime
from hl7apy.v2_5 import DTM
from hl7apy.utils import check_date
from hl7apy.mllp import AbstractHandler
from hl7apy.parser import parse_message
from hl7apy.core import Message
from hl7apy import load_message_profile
from dao import DAO
_ROOT_PATH = os.path.dirname(os.path.abspath(__file__))
PDQ_REQ_MP = load_message_profile(os.path.join(_ROOT_PATH, './pdq_req'))
PDQ_RES_MP = load_message_profile(os.path.join(_ROOT_PATH, './pdq_res'))
logger = logging.getLogger(__name__)
class PDQHandler(AbstractHandler):
REQ_MP, RES_MP = PDQ_REQ_MP, PDQ_RES_MP
PDQ_FIELD_NAMES = {
'@PID.3.1': "IDENTIFIER",
'@PID.5.1.1': 'SURNAME',
'@PID.5.2': 'NAME',
'@PID.7.1': 'DOB'
}
class PDQSupplier(AbstractHandler):
REQ_MP = load_message_profile(os.path.join(_ROOT_PATH, './pdq_req'))
RES_MP = load_message_profile(os.path.join(_ROOT_PATH, './pdq_res'))
FIELD_NAMES = {
'@PID.5.1.1': 'SURNAME',
'@PID.5.2': 'NAME',
'@PID.7.1': 'DOB'
}
MISSING_PARAMS = 1
def __init__(self, message):
msg = parse_message(message, message_profile=self.REQ_MP)
super(PDQSupplier, self).__init__(msg)
def _create_response(self, ack_code, query_ack_code, patients):
res = Message('RSP_K21', reference=self.RES_MP)
res.msh.msh_5 = self.incoming_message.msh.msh_3
res.msh.msh_6 = self.incoming_message.msh.msh_4
res.msh.msh_7.ts_1 = DTM(datetime.datetime.now())
res.msh.msh_9 = 'RSP^K22^RSP_K21'
res.msh.msh_10 = uuid.uuid4().hex
# MSA creation
res.msa.msa_1 = ack_code
res.msa.msa_2 = self.incoming_message.msh.msh_10.msh_10_1
# QAK creation
res.qak.qak_1 = self.incoming_message.qpd.qpd_2
res.qak.qak_2 = 'OK' if len(patients) > 0 else 'NF'
res.qak.qak_4 = str(len(patients))
# QPD creation
res.qpd = self.incoming_message.qpd
# RSP_K21_QUERY_RESPONSE creation
res.add_group('rsp_k21_query_response')
g = res.rsp_k21_query_response
for i, p in enumerate(patients):
# add a pid segment for every patient
g.add_segment('PID')
g.pid[i].pid_3.cx_1, g.pid[i].pid_5.xpn_1, g.pid[i].pid_5.xpn_2 = p[:]
return res.to_mllp()
def _create_error(self, error_code):
res = self._create_response('AR', 'AR', [])
return res
def reply(self):
print('Received a message')
print(repr(self.incoming_message.to_er7()))
query_params = dict((self.FIELD_NAMES[q.qip_1.value], q.qip_2.value)
for q in self.incoming_message.qpd.qpd_3
if q.qip_1.value in self.FIELD_NAMES)
print("Extracted query params: {}".format(query_params))
if '' in query_params.values():
return self._create_error(1)
else:
patients = [('0001', 'John', 'Smith')]
return self._create_response('AA', 'OK', patients)
