python-hl7 is a simple library for parsing messages of Health Level 7 (HL7) version 2.x into Python objects. python-hl7 includes a simple client that can send HL7 messages to a Minimal Lower Level Protocol (MLLP) server (mllp_send).
HL7 is a communication protocol and message format for health care data. It is the de-facto standard for transmitting data between clinical information systems and between clinical devices. The version 2.x series, which is often is a pipe delimited format is currently the most widely accepted version of HL7 (version 3.0 is an XML-based format).
python-hl7 currently only parses HL7 version 2.x messages into an easy to access data structure. The current implementation does not completely follow the HL7 specification, but is good enough to parse the most commonly seen HL7 messages. The library could potentially evolve into being fully complainant with the spec. The library could eventually also contain the ability to create HL7 v2.x messages.
python-hl7 parses HL7 into a series of wrapped hl7.Container objects. The there are specific subclasses of hl7.Container depending on the part of the HL7 message. The hl7.Container message itself is a subclass of a Python list, thus we can easily access the HL7 message as an n-dimensional list. Specifically, the subclasses of hl7.Container, in order, are hl7.Message, hl7.Segment, and hl7.Field. Eventually additional containers will be added to fully support the HL7 specification.
As an example, let’s create a HL7 message:
>>> message = 'MSH|^~\&|GHH LAB|ELAB-3|GHH OE|BLDG4|200202150930||ORU^R01|CNTRL-3456|P|2.4\r'
>>> message += 'PID|||555-44-4444||EVERYWOMAN^EVE^E^^^^L|JONES|196203520|F|||153 FERNWOOD DR.^^STATESVILLE^OH^35292||(206)3345232|(206)752-121||||AC555444444||67-A4335^OH^20030520\r'
>>> message += 'OBR|1|845439^GHH OE|1045813^GHH LAB|1554-5^GLUCOSE|||200202150730||||||||555-55-5555^PRIMARY^PATRICIA P^^^^MD^^LEVEL SEVEN HEALTHCARE, INC.|||||||||F||||||444-44-4444^HIPPOCRATES^HOWARD H^^^^MD\r'
>>> message += 'OBX|1|SN|1554-5^GLUCOSE^POST 12H CFST:MCNC:PT:SER/PLAS:QN||^182|mg/dl|70_105|H|||F'
We call the hl7.parse() command with string message:
>>> import hl7
>>> h = hl7.parse(message)
We get a hl7.Message object, wrapping a series of hl7.Segment objects:
>>> type(h)
<class 'hl7.Message'>
We can always get the HL7 message back:
>>> unicode(h) == message
True
Interestingly, hl7.Message can be accessed as a list:
>>> isinstance(h, list)
True
There were 4 segments (MSH, PID, OBR, OBX):
>>> len(h)
4
We can extract the hl7.Segment from the hl7.Message instance:
>>> h[3]
[[u'OBX'], [u'1'], [u'SN'], [u'1554-5', u'GLUCOSE', u'POST 12H CFST:MCNC:PT:SER/PLAS:QN'], [u''], [u'', u'182'], [u'mg/dl'], [u'70_105'], [u'H'], [u''], [u''], [u'F']]
We can easily reconstitute this segment as HL7, using the appropriate separators:
>>> unicode(h[3])
u'OBX|1|SN|1554-5^GLUCOSE^POST 12H CFST:MCNC:PT:SER/PLAS:QN||^182|mg/dl|70_105|H|||F'
We can extract individual elements of the message:
>>> h[3][3][1]
u'GLUCOSE'
>>> h[3][5][1]
u'182'
We can look up segments by the segment identifier, either via hl7.Message.segments() or via the traditional dictionary syntax:
>>> h.segments('OBX')[0][3][1]
u'GLUCOSE'
>>> h['OBX'][0][3][1]
u'GLUCOSE'
Since many many types of segments only have a single instance in a message (e.g. PID or MSH), hl7.Message.segment() provides a convienance wrapper around hl7.Message.segments() that returns the first matching hl7.Segment:
>>> h.segment('PID')[3][0]
u'555-44-4444'
python-hl7 features a simple network client, mllp_send, which reads HL7 messages from a file or sys.stdin and posts them to an MLLP server. mllp_send is a command-line wrapper around hl7.client.MLLPClient. mllp_send is a useful tool for testing HL7 interfaces or resending logged messages:
mllp_send --file sample.hl7 --port 6661 mirth.example.com
See mllp_send - MLLP network client for examples and usage instructions.
Returns a instance of the hl7.Message that allows indexed access to the data elements.
Note
HL7 usually contains only ASCII, but can use other character sets (HL7 Standards Document, Section 1.7.1). Therefore, python-hl7 works on Python unicode strings. hl7.parse() will accept ASCII-only strings and automatically convert them into unicode. However, if the message contains non-ASCII characters, it is the responsibility of the caller of hl7.parse() to properly convert the message string to unicode first.
>>> h = hl7.parse(message)
| Return type: | hl7.Message |
|---|
Determines whether a line looks like an HL7 message. This method only does a cursory check and does not fully validate the message.
| Return type: | bool |
|---|
Abstract root class for the parts of the HL7 message.
Join a the child containers into a single string, separated by the self.separator. This method acts recursively, calling the children’s __unicode__ method. Thus unicode() is the approriate method for turning the python-hl7 representation of HL7 into a standard string.
>>> unicode(h) == message
True
Representation of an HL7 message. It contains a list of hl7.Segment instances.
Index or segment-based lookup.
If key is an integer, __getitem__ acts list a list, returning the hl7.Segment held at that index:
>>> h[1]
[[u'PID'], ...]
If the key is a string, __getitem__ acts like a dictionary, returning all segments whose segment_id is key (alias of hl7.Message.segments()).
>>> h['OBX']
[[[u'OBX'], [u'1'], ...]]
| Return type: | hl7.Segment or list of hl7.Segment |
|---|
Gets the first segment with the segment_id from the parsed message.
>>> h.segment('PID')
[[u'PID'], ...]
| Return type: | hl7.Segment |
|---|
Returns the requested segments from the parsed message that are identified by the segment_id (e.g. OBR, MSH, ORC, OBX).
>>> h.segments('OBX')
[[[u'OBX'], [u'1'], ...]]
| Return type: | list of hl7.Segment |
|---|
Second level of an HL7 message, which represents an HL7 Segment. Traditionally this is a line of a message that ends with a carriage return and is separated by pipes. It contains a list of hl7.Field instances.
Third level of an HL7 message, that traditionally is surrounded by pipes and separated by carets. It contains a list of strings.
A basic, blocking, HL7 MLLP client based upon socket.
MLLPClient implements two methods for sending data to the server.
Can be used by the with statement to ensure MLLPClient.close() is called:
with MLLPClient(host, port) as client:
client.send_message('MSH|...')
Release the socket connection
Low-level, direct access to the socket.send (data must be already wrapped in an MLLP container). Blocks until the server returns.
Wraps a str, unicode, or :py:cls:`hl7.Message` in a MLLP container and send the message to the server
python-hl7 features a simple network client, mllp_send, which reads HL7 messages from a file or sys.stdin and posts them to an MLLP server. mllp_send is a command-line wrapper around hl7.client.MLLPClient. mllp_send is a useful tool for testing HL7 interfaces or resending logged messages:
$ mllp_send --file sample.hl7 --port 6661 mirth.example.com
MSH|^~\&|LIS|Example|Hospital|Mirth|20111207105244||ACK^A01|A234244|P|2.3.1|
MSA|AA|234242|Message Received Successfully|
Usage: mllp_send [options] <server>
Options:
-h, --help show this help message and exit
--version print current version and exit
-p PORT, --port=PORT port to connect to
-f FILE, --file=FILE read from FILE instead of stdin
-q, --quiet do not print status messages to stdout
--loose allow file to be a HL7-like object (\r\n instead of
\r). Requires that messages start with "MSH|^~\&|".
Requires --file option (no stdin)
By default, mllp_send expects the FILE or stdin input to be a properly formatted HL7 message (carriage returns separating segments) wrapped in a MLLP stream (<SB>message1<EB><CR><SB>message2<EB><CR>...).
However, it is common, especially if the file has been manually edited in certain text editors, that the ASCII control characters will be lost and the carriage returns will be replaced with the platform’s default line endings. In this case, mllp_send provides the --loose option, which attempts to take something that “looks like HL7” and convert it into a proper HL7 message..
The source code is available at http://github.com/johnpaulett/python-hl7
Please fork and issue pull requests. Generally any changes, bug fixes, or new features should be accompanied by corresponding tests in our test suite.
The test suite is located in tests/ and can be run via setup.py:
$ python setup.py test
...
----------------------------------------------------------------------
Ran 17 tests in 0.005s
OK
Make sure the documentation is still valid:
$ pushd docs && make html man doctest && popd
...
Doctest summary
===============
23 tests
0 failures in tests
0 failures in setup code
...
John Paulett <john -at- paulett.org>
Copyright (C) 2009-2011 John Paulett (john -at- paulett.org)
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python-hl7 is available on PyPi via pip or easy_install:
pip install -U hl7
For recent versions of Debian and Ubuntu, the python-hl7 package is available:
sudo apt-get install python-hl7
HL7 References: