Dynamically creating an HL7 message from IRIS Embedded Python

Written in reply to community post for can Python create HL7 Message dynamically.

Pre-requisites and setup

Use an integration enabled namespace.
Note: USER namespace is not enabled for interoperability by default.
If following suggest create a new interoperatibility namespace to explore functionality.

# Switch to
ZN "[Interoperability Namespace Name]"

# Launch interactive Python shell:
Do $SYSTEM.Python.Shell()

Script start

#Load dependencies

import datetime as dt
import uuid

# Cache current time in CCYYMMDDHHMMss format
hl7_datetime_now=dt.datetime.now().strftime('%Y%m%d%H%M%S')

# Create HL7 Message
hl7=iris.cls("EnsLib.HL7.Message")._New()

# Set the doc type
# 2.5.1:ORU_R01 - Unsolicited transmission of an observation message
hl7.PokeDocType("2.5.1:ORU_R01")

The structures of these messages can be accessed from Management Portal

 

Create MSH (Message Header Segment)

// MSH Segment
hl7.SetValueAt('OutApp','MSH:SendingApplication')
hl7.SetValueAt('OutFac','MSH:SendingFacility')
hl7.SetValueAt('InApp','MSH:ReceivingApplication')
hl7.SetValueAt('InFac','MSH:ReceivingFacility')
hl7.SetValueAt(hl7_datetime_now,'MSH:DateTimeOfMessage')
hl7.SetValueAt('ORU','MSH:MessageType.MessageCode')
hl7.SetValueAt('R01','MSH:MessageType.TriggerEvent')
hl7.SetValueAt('ORU_R01','MSH:MessageType.MessageStructure')
hl7.SetValueAt(str(uuid.uuid4()),'MSH:MessageControlID')
hl7.SetValueAt('2.5.1','MSH:ProcessingID')

Escape and Unescape

HL7 Documents are formatted into segments
Each segment is divided into Elements by delimiter ("|") and Repeating Elements ("~")
Within an element is "^" delimiter and "&" sub-delimiter.
Where the delimiter appears as actual text content it is escaped with "\" and other characters that replace delimiters.
Commonly "&" is problematic as can occur often in messages resulting in truncation when read by receiving system.
An HL7 Segment has a built in method for Escaping content based on the current chosen delimiters for a message.
A common pattern is to get a reference to the first segment

# Do this line the variable "msh" is used later
> msh=hl7.GetSegmentAt(1)

Then can call Escape for example with Python raw string:

> msh.Escape(r"a&b~c^d")
'a\\T\\b\\R\\c\\S\\d'

The segment can also be used to Unescape back for example:

> msh.Unescape('a\\T\\b\\R\\c\\S\\d')
'a&b~c^d'

So when setting content that is anticipated to contain delimiter characters these can be escaped for the message

hl7.SetValueAt(msh.Escape(r"a&b~c^d"),'MSH:ReceivingFacility')

When retrieving content it can be unescaped

msh.Unescape(hl7.GetValueAt('MSH:ReceivingFacility'))

For this example, just resetting msh back to have previous value

hl7.SetValueAt('InFac','MSH:ReceivingFacility')

To Double check segment so far:

> hl7.GetValueAt('MSH')
'MSH|^~\\&|OutApp|OutFac|InApp|InFac|20230610100040||ORU^R01^ORU_R01|2dfab415-51aa-4c75-a7e7-a63aedfb53cc|2.5.1'

Demographic (PID) segment

# Virtual path prefix for PID
seg='PIDgrpgrp(1).PIDgrp.PID:'
hl7.SetValueAt('1',seg+'SetIDPID')
hl7.SetValueAt('12345',seg+'PatientIdentifierList(1).IDNumber')
hl7.SetValueAt('MRN',seg+'PatientIdentifierList(1).AssigningAuthority')
hl7.SetValueAt('MR',seg+'PatientIdentifierList(1).IdentifierTypeCode')
hl7.SetValueAt(msh.Escape('Redfield'), seg+'PatientName(1).FamilyName')
hl7.SetValueAt(msh.Escape('Claire') ,seg+'PatientName(1).GivenName')
hl7.SetValueAt('19640101',seg+'DateTimeofBirth')
hl7.SetValueAt('F',seg+'AdministrativeSex')
hl7.SetValueAt(msh.Escape('Umbrella Corporation') ,seg+'PatientAddress.StreetAddress')
hl7.SetValueAt(msh.Escape('Umbrella Drive') ,seg+'PatientAddress.OtherDesignation')
hl7.SetValueAt(msh.Escape('Raccoon City') ,seg+'PatientAddress.City')
hl7.SetValueAt(msh.Escape('MO') ,seg+'PatientAddress.StateorProvince')
hl7.SetValueAt(msh.Escape('63117') ,seg+'PatientAddress.ZiporPostalCode')

Double check PID segment content

> hl7.GetValueAt(seg[0:-1])
'PID|1||12345^^^MRN^MR||Redfield^Claire||19640101|F|||Umbrella Corporation^Umbrella Drive^Raccoon City^MO^63117'

Order control Segment

seg='PIDgrpgrp(1).ORCgrp(1).ORC:'
hl7.SetValueAt('RE',seg+'OrderControl')
hl7.SetValueAt('10003681',seg+'PlacerOrderNumber')
hl7.SetValueAt('99001725',seg+'FillerOrderNumber')
hl7.SetValueAt('AG104',seg+'OrderingProvider')
hl7.SetValueAt('L43',seg+'EnterersLocation')

Double check ORC segment content

> hl7.GetValueAt(seg[0:-1])
'ORC|RE|10003681|99001725|||||||||AG104|L43'

 

Observation Request
 

seg='PIDgrpgrp(1).ORCgrp(1).OBR:'
hl7.SetValueAt('1',seg+'SetIDOBR')
hl7.SetValueAt('10003681',seg+'PlacerOrderNumber')
hl7.SetValueAt('99001725',seg+'FillerOrderNumber')
hl7.SetValueAt('20210428100729',seg+'ResultsRptStatusChngDateTime')
hl7.SetValueAt('F',seg+'ResultStatus')
hl7.SetValueAt('U',seg+'QuantityTiming.Priority')

 

OBX Observation/Result

seg='PIDgrpgrp(1).ORCgrp(1).OBXgrp(1).OBX:'
hl7.SetValueAt('1',seg+'SetIDOBX')
hl7.SetValueAt('TX',seg+'ValueType')
hl7.SetValueAt('V8132',seg+'ObservationIdentifier.Identifier')
hl7.SetValueAt(msh.Escape('G-Virus') , seg+'ObservationIdentifier.Identifier')
hl7.SetValueAt(msh.Escape('17.8 log10') ,seg+'ObservationValue')
hl7.SetValueAt(msh.Escape('RNA copies/mL') ,seg+'Units')
hl7.SetValueAt('F',seg+'ObservationResultStatus')
hl7.SetValueAt('20210428100729',seg+'DateTimeoftheObservation')
hl7.SetValueAt('AG001',seg+'ResponsibleObserver.IDNumber')
hl7.SetValueAt('Birkin',seg+'ResponsibleObserver.FamilyName')
hl7.SetValueAt('William',seg+'ResponsibleObserver.GivenName')
hl7.SetValueAt('AG001',seg+'ResponsibleObserver.IDNumber')
hl7.SetValueAt('UXL43',seg+'EquipmentInstanceIdentifier')

 

NTE - Notes and Comments

seg='PIDgrpgrp(1).ORCgrp(1).OBXgrp(1).NTE(1):'
hl7.SetValueAt('1',seg+'SetIDNTE')
hl7.SetValueAt(msh.Escape('Expected late onset Hyphema. Contain but do not approach.') ,seg+'Comment')

 

Printing full message to the terminal

> print(hl7.OutputToString())

MSH|^~\&|OutApp|OutFac|InApp|InFac|20230610141201||ORU^R01^ORU_R01|2dfab415-51aa-4c75-a7e7-a63aedfb53cc|2.5.1
PID|1||12345^^^MRN^MR||Redfield^Claire||19640101|F|||Umbrella Corporation^Umbrella Drive^Raccoon City^MO^63117
ORC|RE|10003681|99001725|||||||||AG104|L43
OBR|1|10003681|99001725|||||||||||||||||||20210428100729|||F||^^^^^U
OBX|1|TX|G-Virus||17.8 log10|RNA copies/mL|||||F|||20210428100729||AG001^Birkin^William||UXL43
NTE|1||Expected late onset Hyphema. Contain but do not approach.

Gotchas

If an elements content contains a value such as "8@%SYS.Python" it is probable that the string value or string property was required instead.

For example uuid was wrapped by "str" in MSH construction.