Combine multiple OBX segments in ORU_R01 message hl7 using python hl7apy

Question

I am trying to create an HL7 RU_R01 message with multiple OBX segments. However, I cannot find a way to merge these segments together into the message.

Here's my code:

message = Message("ORU_R01", validation_level=VALIDATION_LEVEL.STRICT)
has_xxx_formatted = '2'

text_formatted = DEFAULT_HL7_TEXT["EN"]["XXXX"]

## MSH Segment
message.MSH.msh_3 = 'XXXXX'
message.msh.msh_4 = 'XXXXX'
message.msh.msh_9 = "ORU^R01^ORU_R01"
message.msh.msh_10 = ""
message.msh.msh_11 = ""

# patient details
message.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.pid_2 = "patient_id"
message.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.pid_3 = ""
message.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.pid_5 = ""

## OBR Segment -- frature details
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.OBR.obr_4 = "Observations"
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.OBR.obr_7 = f"{datetime.now().strftime('%Y%m%d%H%M%S.%f')[:-2]}"


# obx0
obx0 = Segment('OBX', version='2.5')
obx0.obx_1 = "1"
obx0.obx_2 = "HD"
obx0.obx_3 = "REFInstanceUID"
obx0.obx_5 = "ref_uid"
obx0.obx_11 = "F"

# obx1
obx1 = Segment('OBX', version='2.5')
obx1.obx_1 = "2"
obx1.obx_2 = "TX"
obx1.obx_3 = "Presence"
obx1.obx_5 = "XXXX"
obx1.obx_11 = "F"

# obx2
obx2 = Segment('OBX', version='2.5')
obx2.obx_1 = "3"
obx2.obx_2 = "TX"
obx2.obx_3 = "Result"
obx2.obx_5 = "XXXXX"
obx2.obx_11 = "F"

Now if I add these obx segments using:

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_OBSERVATION.OBX.obx_1 = 1
# adds individual values of obx0
....

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_OBSERVATION.OBX.obx_1 = 2
# adds individual values of obx1
....

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_OBSERVATION.OBX.obx_1 = 3
    # adds individual values of obx2
    ....

It only adds the last OBX segment into the message.

If I try to add the convert the OBX segments into a group as suggested here:

name = 'MDM_T02_OBXNTE_SUPPGRP'
mdm_group = Group(name, version='2.5')
mdm_group.obx = obx0
mdm_group.add(obx1)
mdm_group.add(obx2)

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_ORDER_OBSERVATION = mdm_group

I get the following error:

InvalidName: Invalid name for Group: MDM_T02_OBXNTE_SUPPGRP

I'd like to know how to add these multiple segments into a single message after the OBR. Thank you in advance

Answer 1

It seems that the correct way to add multiple segments is to add each hl7apy.core.Segment to it's individual hl7apy.core.Group. This is explained here, and the documentation from the java version of hl7apy is useful.

message = Message("ORU_R01", validation_level=VALIDATION_LEVEL.TOLERATED)
has_xxx_formatted = '2'

text_formatted = DEFAULT_HL7_TEXT["EN"]["XXXX"]

## MSH Segment
message.MSH.msh_3 = 'XXXXX'
message.msh.msh_4 = 'XXXXX'
message.msh.msh_9 = "ORU^R01^ORU_R01"
message.msh.msh_10 = ""
message.msh.msh_11 = ""

# patient details
message.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.pid_2 = "patient_id"
message.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.pid_3 = ""
message.ORU_R01_PATIENT_RESULT.ORU_R01_PATIENT.PID.pid_5 = ""

## OBR Segment -- frature details
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.OBR.obr_4 = "Observations"
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.OBR.obr_7 = f"{datetime.now().strftime('%Y%m%d%H%M%S.%f')[:-2]}"

obs_name = 'ORU_R01_OBSERVATION'

# obx0
obx0_group = Group(obs_name, version='2.5')
obx0 = Segment('OBX', version='2.5')
obx0.obx_1 = "1"
obx0.obx_2 = "HD"
obx0.obx_3 = "REFInstanceUID"
obx0.obx_5 = "ref_uid"
obx0.obx_11 = "F"
obx0_group.add(obx0)
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.add(obx0_group)

# obx1
name = 'ORU_R01_OBSERVATION'
obx1_group = Group(obs_name, version='2.5')
obx1 = Segment('OBX', version='2.5')
obx1.obx_1 = "2"
obx1.obx_2 = "TX"
obx1.obx_3 = "Presence"
obx1.obx_5 = "XXXX"
obx1.obx_11 = "F"
obx1_group.add(obx1)
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.add(obx1_group)

# obx2
name = 'ORU_R01_OBSERVATION'
obx2_group = Group(obs_name, version='2.5')
obx2 = Segment('OBX', version='2.5')
obx2.obx_1 = "3"
obx2.obx_2 = "TX"
obx2.obx_3 = "Result"
obx2.obx_5 = "XXXXX"
obx2.obx_11 = "F"
obx2_group.add(obx2)
message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.add(obx2_group)

Also note that the validation level is set to tolerated TOLERATED. STRICT mode only works with a single OBX segment.

Now the validation works.

assert hl7.validate() is True

Answer 2

I don't know the python libraries, so I won't be able to give you the exact syntax, but ORU_R01_OBSERVATION is a repeatable field that allows for a single OBX and multiple NTE segments. If I were to guess the code should be something like.

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_OBSERVATION[0].OBX.obx_1 = 1
# adds individual values of obx0
....

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_OBSERVATION[1].OBX.obx_1 = 2
# adds individual values of obx1
....

message.ORU_R01_PATIENT_RESULT.ORU_R01_ORDER_OBSERVATION.ORU_R01_OBSERVATION[2].OBX.obx_1 = 3
    # adds individual values of obx2
    ....