How to correctly parse an HL7 message using python HL7Apy?
Question:
Here is my code:
from hl7apy.parser import parse_message
hl7 = open("hl7.txt", "r").read()
msg = parse_message(hl7)
print(msg.children)
result:
[<Segment MSH>]
It shows only the first segment, seems simple but I don’t know what i’m doing wrong.
I’ve tried from a text file, passing the message directly or even with another HL7 message, but always got same results.
Here is the message:
MSH|^~&|SendingAPP|TEST|||20080617143943||ORU^R01|1|P|2.3.1||||||UNICODE
PID|1||7393670^^^^MR||Joan^JIang||19900804000000|Female
PV1|1||nk^^001
OBR|1||20071207011|00001^Automated Count^99MRC||20080508140600|20080508150616|||John||||20080508150000||||||||||HM||||||||TEST
Here is my message in notepad++ where all characters are shown:
Answers:
I think your issue is the the MLLP constant for HL7apy is a Carriage return r. If you replace the new line characters n the groups will parse out fine
from hl7apy.parser import parse_message
from hl7apy.core import Group, Segment
hl7 = """
MSH|^~&|SendingAPP|TEST|||20080617143943||ORU^R01|1|P|2.3.1||||||UNICODE
PID|1||7393670^^^^MR||Joan^JIang||19900804000000|Female PV1|1||nk^^001
OBR|1||20071207011|00001^Automated
Count^99MRC||20080508140600|20080508150616|||John||||20080508150000||||||||||HM||||||||TEST
"""
msg = parse_message(hl7.replace('n', 'r'), find_groups=True, validation_level=2)
print(msg.children)
print(msg.children[1].children)
for segment in msg.children:
if isinstance(segment, Segment):
for attribute in segment.children:
print(attribute, attribute.value)
if isinstance(segment, Group):
for group in segment.children:
for group_segment in group.children:
for attribute in group_segment.children:
print(attribute, attribute.value)
Additionaly to the answer above you can use an exception handler
from hl7apy import parser
from hl7apy.core import Group, Segment
from hl7apy.exceptions import UnsupportedVersion
and use it like this
try:
msg = parser.parse_message(hl7)
except UnsupportedVersion:
msg = parser.parse_message(hl7.replace("n", "r"))
If your message is correct you can acces the contents of fields like this
print(msg.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.PID_7.value)
print(msg.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.ORU_R01_VISIT.PV1.PV1_1.value)
print(msg.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.OBR.OBR_3.value)
So an enhanced answer showing all groups and subgroups – but still not perfect – can be e.g.
from hl7apy import parser
from hl7apy.core import Group, Segment
from hl7apy.exceptions import UnsupportedVersion
hl7 = open("hl7.txt", "r").read()
try:
msg = parser.parse_message(hl7.replace('n', 'r'), find_groups=True, validation_level=2)
except UnsupportedVersion:
msg = parser.parse_message(hl7.replace('n', 'r'), find_groups=True, validation_level=2)
indent = " "
indent_seg = " "
indent_fld = " "
def subgroup (group, indent):
indent = indent + " "
print (indent , group)
for group_segment in group.children:
if isinstance(group_segment, Group):
subgroup (group_segment)
else:
print(indent_seg, indent ,group_segment)
for attribute in group_segment.children:
print(indent_fld, indent ,attribute, attribute.value)
def showmsg (msg):
print(msg.children[1])
for segment in msg.children:
if isinstance(segment, Segment):
print (indent ,segment)
for attribute in segment.children:
print(indent_fld, indent, attribute, attribute.value)
if isinstance(segment, Group):
for group in segment.children:
print (indent,group)
for group_segment in group.children:
if isinstance (group_segment, Group):
subgroup (group_segment, indent)
else:
print(indent_seg, indent ,group_segment)
for attribute in group_segment.children:
print(indent_fld, indent, attribute, attribute.value)
showmsg (msg)
can give a result like this
<Group ORU_R01_PATIENT_RESULT>
<Segment MSH>
<Field MSH_1 (FIELD_SEPARATOR) of type ST> |
<Field MSH_2 (ENCODING_CHARACTERS) of type ST> ^~&
<Field MSH_3 (SENDING_APPLICATION) of type HD> SendingAPP
<Field MSH_4 (SENDING_FACILITY) of type HD> TEST
<Field MSH_7 (DATE_TIME_OF_MESSAGE) of type TS> 20080617143943
<Field MSH_9 (MESSAGE_TYPE) of type MSG> ORU^R01
<Field MSH_10 (MESSAGE_CONTROL_ID) of type ST> 1
<Field MSH_11 (PROCESSING_ID) of type PT> P
<Field MSH_12 (VERSION_ID) of type VID> 2.3.1
<Field MSH_18 (CHARACTER_SET) of type ID> UNICODE
<Group ORU_R01_PATIENT>
<Segment PID>
<Field PID_1 (SET_ID_PID) of type SI> 1
<Field PID_3 (PATIENT_IDENTIFIER_LIST) of type CX> 7393670^^^^MR
<Field PID_5 (PATIENT_NAME) of type XPN> Joan^JIang
<Field PID_7 (DATE_TIME_OF_BIRTH) of type TS> 19900804000000
<Field PID_8 (SEX) of type IS> Female
<Group ORU_R01_VISIT>
<Segment PV1>
<Field PV1_1 (SET_ID_PV1) of type SI> 1
<Field PV1_3 (ASSIGNED_PATIENT_LOCATION) of type PL> nk^^001
<Group ORU_R01_ORDER_OBSERVATION>
<Segment OBR>
<Field OBR_1 (SET_ID_OBR) of type SI> 1
<Field OBR_3 (FILLER_ORDER_NUMBER) of type EI> 20071207011
<Field OBR_4 (UNIVERSAL_SERVICE_ID) of type CE> 00001^Automated Count^99MRC
<Field OBR_6 (REQUESTED_DATE_TIME) of type TS> 20080508140600
<Field OBR_7 (OBSERVATION_DATE_TIME) of type TS> 20080508150616
<Field OBR_10 (COLLECTOR_IDENTIFIER) of type XCN> John
<Field OBR_14 (SPECIMEN_RECEIVED_DATE_TIME) of type TS> 20080508150000
<Field OBR_24 (DIAGNOSTIC_SERV_SECT_ID) of type ID> HM
<Field OBR_32 (PRINCIPAL_RESULT_INTERPRETER) of type NDL> TEST1
<Group ORU_R01_ORDER_OBSERVATION>
<Segment OBR>
<Field OBR_1 (SET_ID_OBR) of type SI> 2
<Field OBR_3 (FILLER_ORDER_NUMBER) of type EI> 20071207011
<Field OBR_4 (UNIVERSAL_SERVICE_ID) of type CE> 00001^Automated Count^99MRC
<Field OBR_6 (REQUESTED_DATE_TIME) of type TS> 20080508140600
<Field OBR_7 (OBSERVATION_DATE_TIME) of type TS> 20080508150616
<Field OBR_10 (COLLECTOR_IDENTIFIER) of type XCN> John
<Field OBR_14 (SPECIMEN_RECEIVED_DATE_TIME) of type TS> 20080508150000
<Field OBR_24 (DIAGNOSTIC_SERV_SECT_ID) of type ID> HM
<Field OBR_32 (PRINCIPAL_RESULT_INTERPRETER) of type NDL> TEST2
<Group ORU_R01_OBSERVATION>
<Segment OBX>
<Field OBX_1 (SET_ID_OBX) of type SI> 1
<Field OBX_2 (VALUE_TYPE) of type ID> 2
by disabling find_groups like this msg = parser.parse_message(hl7, find_groups=False) My messages are now parsed correctly.
Thx to @sqlab and @badger0053 for help, i was able to make a progression.
Here is my code:
from hl7apy.parser import parse_message
hl7 = open("hl7.txt", "r").read()
msg = parse_message(hl7)
print(msg.children)
result:
[<Segment MSH>]
It shows only the first segment, seems simple but I don’t know what i’m doing wrong.
I’ve tried from a text file, passing the message directly or even with another HL7 message, but always got same results.
Here is the message:
MSH|^~&|SendingAPP|TEST|||20080617143943||ORU^R01|1|P|2.3.1||||||UNICODE
PID|1||7393670^^^^MR||Joan^JIang||19900804000000|Female
PV1|1||nk^^001
OBR|1||20071207011|00001^Automated Count^99MRC||20080508140600|20080508150616|||John||||20080508150000||||||||||HM||||||||TEST
Here is my message in notepad++ where all characters are shown:
I think your issue is the the MLLP constant for HL7apy is a Carriage return r. If you replace the new line characters n the groups will parse out fine
from hl7apy.parser import parse_message
from hl7apy.core import Group, Segment
hl7 = """
MSH|^~&|SendingAPP|TEST|||20080617143943||ORU^R01|1|P|2.3.1||||||UNICODE
PID|1||7393670^^^^MR||Joan^JIang||19900804000000|Female PV1|1||nk^^001
OBR|1||20071207011|00001^Automated
Count^99MRC||20080508140600|20080508150616|||John||||20080508150000||||||||||HM||||||||TEST
"""
msg = parse_message(hl7.replace('n', 'r'), find_groups=True, validation_level=2)
print(msg.children)
print(msg.children[1].children)
for segment in msg.children:
if isinstance(segment, Segment):
for attribute in segment.children:
print(attribute, attribute.value)
if isinstance(segment, Group):
for group in segment.children:
for group_segment in group.children:
for attribute in group_segment.children:
print(attribute, attribute.value)
Additionaly to the answer above you can use an exception handler
from hl7apy import parser
from hl7apy.core import Group, Segment
from hl7apy.exceptions import UnsupportedVersion
and use it like this
try:
msg = parser.parse_message(hl7)
except UnsupportedVersion:
msg = parser.parse_message(hl7.replace("n", "r"))
If your message is correct you can acces the contents of fields like this
print(msg.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.PID_7.value)
print(msg.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.ORU_R01_VISIT.PV1.PV1_1.value)
print(msg.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.OBR.OBR_3.value)
So an enhanced answer showing all groups and subgroups – but still not perfect – can be e.g.
from hl7apy import parser
from hl7apy.core import Group, Segment
from hl7apy.exceptions import UnsupportedVersion
hl7 = open("hl7.txt", "r").read()
try:
msg = parser.parse_message(hl7.replace('n', 'r'), find_groups=True, validation_level=2)
except UnsupportedVersion:
msg = parser.parse_message(hl7.replace('n', 'r'), find_groups=True, validation_level=2)
indent = " "
indent_seg = " "
indent_fld = " "
def subgroup (group, indent):
indent = indent + " "
print (indent , group)
for group_segment in group.children:
if isinstance(group_segment, Group):
subgroup (group_segment)
else:
print(indent_seg, indent ,group_segment)
for attribute in group_segment.children:
print(indent_fld, indent ,attribute, attribute.value)
def showmsg (msg):
print(msg.children[1])
for segment in msg.children:
if isinstance(segment, Segment):
print (indent ,segment)
for attribute in segment.children:
print(indent_fld, indent, attribute, attribute.value)
if isinstance(segment, Group):
for group in segment.children:
print (indent,group)
for group_segment in group.children:
if isinstance (group_segment, Group):
subgroup (group_segment, indent)
else:
print(indent_seg, indent ,group_segment)
for attribute in group_segment.children:
print(indent_fld, indent, attribute, attribute.value)
showmsg (msg)
can give a result like this
<Group ORU_R01_PATIENT_RESULT>
<Segment MSH>
<Field MSH_1 (FIELD_SEPARATOR) of type ST> |
<Field MSH_2 (ENCODING_CHARACTERS) of type ST> ^~&
<Field MSH_3 (SENDING_APPLICATION) of type HD> SendingAPP
<Field MSH_4 (SENDING_FACILITY) of type HD> TEST
<Field MSH_7 (DATE_TIME_OF_MESSAGE) of type TS> 20080617143943
<Field MSH_9 (MESSAGE_TYPE) of type MSG> ORU^R01
<Field MSH_10 (MESSAGE_CONTROL_ID) of type ST> 1
<Field MSH_11 (PROCESSING_ID) of type PT> P
<Field MSH_12 (VERSION_ID) of type VID> 2.3.1
<Field MSH_18 (CHARACTER_SET) of type ID> UNICODE
<Group ORU_R01_PATIENT>
<Segment PID>
<Field PID_1 (SET_ID_PID) of type SI> 1
<Field PID_3 (PATIENT_IDENTIFIER_LIST) of type CX> 7393670^^^^MR
<Field PID_5 (PATIENT_NAME) of type XPN> Joan^JIang
<Field PID_7 (DATE_TIME_OF_BIRTH) of type TS> 19900804000000
<Field PID_8 (SEX) of type IS> Female
<Group ORU_R01_VISIT>
<Segment PV1>
<Field PV1_1 (SET_ID_PV1) of type SI> 1
<Field PV1_3 (ASSIGNED_PATIENT_LOCATION) of type PL> nk^^001
<Group ORU_R01_ORDER_OBSERVATION>
<Segment OBR>
<Field OBR_1 (SET_ID_OBR) of type SI> 1
<Field OBR_3 (FILLER_ORDER_NUMBER) of type EI> 20071207011
<Field OBR_4 (UNIVERSAL_SERVICE_ID) of type CE> 00001^Automated Count^99MRC
<Field OBR_6 (REQUESTED_DATE_TIME) of type TS> 20080508140600
<Field OBR_7 (OBSERVATION_DATE_TIME) of type TS> 20080508150616
<Field OBR_10 (COLLECTOR_IDENTIFIER) of type XCN> John
<Field OBR_14 (SPECIMEN_RECEIVED_DATE_TIME) of type TS> 20080508150000
<Field OBR_24 (DIAGNOSTIC_SERV_SECT_ID) of type ID> HM
<Field OBR_32 (PRINCIPAL_RESULT_INTERPRETER) of type NDL> TEST1
<Group ORU_R01_ORDER_OBSERVATION>
<Segment OBR>
<Field OBR_1 (SET_ID_OBR) of type SI> 2
<Field OBR_3 (FILLER_ORDER_NUMBER) of type EI> 20071207011
<Field OBR_4 (UNIVERSAL_SERVICE_ID) of type CE> 00001^Automated Count^99MRC
<Field OBR_6 (REQUESTED_DATE_TIME) of type TS> 20080508140600
<Field OBR_7 (OBSERVATION_DATE_TIME) of type TS> 20080508150616
<Field OBR_10 (COLLECTOR_IDENTIFIER) of type XCN> John
<Field OBR_14 (SPECIMEN_RECEIVED_DATE_TIME) of type TS> 20080508150000
<Field OBR_24 (DIAGNOSTIC_SERV_SECT_ID) of type ID> HM
<Field OBR_32 (PRINCIPAL_RESULT_INTERPRETER) of type NDL> TEST2
<Group ORU_R01_OBSERVATION>
<Segment OBX>
<Field OBX_1 (SET_ID_OBX) of type SI> 1
<Field OBX_2 (VALUE_TYPE) of type ID> 2
by disabling find_groups like this msg = parser.parse_message(hl7, find_groups=False) My messages are now parsed correctly.
Thx to @sqlab and @badger0053 for help, i was able to make a progression.