- This topic has 35 replies, 12 voices, and was last updated 7 years, 10 months ago by
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msgParser ExamplesNote01: msgParser splits HL7 messages into fields. I use this script more than any other script. It pains me to see people looking at an HL7 message and counting fields with their fingers. Don’t do that anymore!
Note02: You can use this script on smat .msg files, files generated from msgExtract, and you can pipe data to it from all sorts of places. It’s very flexible.
Note03: The script correctly counts MSH fields starting with the first pipe (|) as MSH.01. So, MSH.02 would normally be “^~&”. For us, 99.99% of the time, the pipe is the field delimiter, so I just hard coded it that way. It’s a simple matter to alter the script to work on messages where there is a different delimiter.
Note04: The script left pads 1-digit number with a zero? Why? so that grep can be more accurate and easier to use, and so the fields line up nicely on the screen. I’ll show some examples.
msgExtract bnd01ms4_in.tin.0809062315.msg | grep ‘TEST^’ > test.hl7-- Max Drown (Infor)
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Max,
Thank you so very much for the scripts and the examples. I find your scripts very helpful and quick to work with when the suits want immediate information. New members of the interface group get a useful education with your example on how to manipulate the output thus empowering them.
Again thank you very much.
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Hey Max,
These scripts are great!
Have you thought about possibly creating an HL7 2.2 or 2.3 field list table and use it to print the names of the fields along with the values for those people who are new to HL7 and may not know the exact location of the field they are looking for?
Just a thought.
Again, all these scripts are excellent and a must have for any Integration deveopler workign in a UNIX platform.
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Hi Max,
I’m not sure why but I had to modify the following lines in msgParser in order to get each field to print on a different line. Maybe a difference with our shell or something. We are using ksh with Perl 5.6 as delivered with QDX 5.4.
print “nMessage $msgnum
n“;print “MSH.01: |
n“;.
print “$name.0$msh_n: $_
n” if $_;.
print “$name.$msh_n: $_
n” if $_;.
print “$name.0$n: $_
n” if $_;.
print “$name.$n: $_
n” if $_;Not sure if anyone else had to make this same change.
Thanks again for the scripts!
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Troy, good catch. The reason you had to add the /n’s was because I forgot to add the -l switch to the header. The -l switch tells perl to always add a newline to the print statements. Sometime this is useful, and sometimes it’s not.
It should be …
Code:#!/usr/bin/perl -lw
I have fixed that above, too.
-- Max Drown (Infor)
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Charlie, that’s a handy utility, but it is not exactly what we’re looking for in this context. To get a clean output, you’d need to scrub the results. For example, single digit numbers are not right padded with a zero which makes grepping results trickier. Searching for PV1(0).#1 would match on PV1(0).#11, too.
-- Max Drown (Infor)
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msgExtract seems to be tailored made for HL7 messages.
Check out the following 3 scripts that will convert any smat file to newline even if messages aren’t HL7
ebcdic_smat_to_nl.ksh
len10_to_nl.pl
ascii_smat_to_nl.ksh
that I previously posted at the following URL
<a href="http://clovertech.infor.com/viewtopic.php?t=1539&” class=”bbcode_url”>http://clovertech.infor.com/viewtopic.php?t=1539&Russ Ross
RussRoss318@gmail.com -
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awk ‘{gsub(/MSH/,”nMSH”);print}’ some_file >temp
puts each message on its own line and stores in file temp
then search or something else
awk ‘/some big reg ex here/’ temp
or to find a field
strings temp >temp1
grep PID temp1 |cut -f 6,20 -d “|”
returns patient_name and ssn from each message in the file
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I re-wrote the msgParser and msgReader perl scripts into one tcl script that does mostly the same thing.
You may need to tweak the regsub lines depending on the format of your HL7 files. While I was developing this script, my files were nl (one HL7 message per line).
By default, msgParser will print HL7 fields. For example, “msgParser *.hl7”.
To get it to print segments instead, use the -seg argument like this: “msgParser -seg *.hl7”.
#!/qdx/qdx5.4/integrator/bin/tclif {[lindex $argv 0] == “-seg”} {
[code]#!/qdx/qdx5.4/integrator/bin/tclif {[lindex $argv 0] == “-seg”} {
-- Max Drown (Infor)
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#### UPDATE 04/08/2011 ####I added support for reading message from a pipe/stdin.I re-wrote the msgParser and msgReader perl scripts into one tcl script that does mostly the same thing.
This script makes the assumption that the input will be one message per line (nl).
By default, msgParser will print HL7 fields. For example, “msgParser *.hl7”.
To get it to print segments instead, use the -seg argument like this: “msgParser -seg *.hl7”.
#!/qdx/qdx5.4/integrator/bin/tcl# Script: msgParser
# Author: Max Drown
# Usage:
# [code]#!/qdx/qdx5.4/integrator/bin/tcl# Script: msgParser
# Author: Max Drown
# Usage:
#-- Max Drown (Infor)
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A Table for HL7 2.2/2.3 names are already in the $HCIROOT/formats/hl7/2.3/etc directory……… so getting them is easy as pie.
I have for years, used some sed functions to do the same things for your scripts………… I’ve had to update it to perl for 5.8…..
readhl7msg () {
cat $1 | perl -pe ‘s/{CONNID.*?}MSH/x0dx0aMSH/g; s/x0d/x0dx0a/g’
}
converthl7msg () {
cat $1 | perl -pe ‘s/{CONNID.*?}MSH/x0dx0aMSH/g; s/{CONNID.*}//g’
}
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I added a new msgExtract script to the original post. This new script uses the .idx file to parse out the messages from the .msg file. There is no consistent way to programmatically remove the metadata at the end of each message in the .msg file, and so using the .idx file gives accurate results. I have placed an enhancement request with R&D to change the way that this meta data is added so that it can be removed predictably by externals scripts.
-- Max Drown (Infor)
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Max Drown wrote:
There is no consistent way to programmatically remove the metadata at the end of each message in the .msg file, and so using the .idx file gives accurate results. I have placed an enhancement request with R&D to change the way that this meta data is added so that it can be removed predictably by externals scripts.
I think the .idx files have always been required to figure out where the messages in the .msg file stop and start. With some message formats (like HL7) it was easy to figure out where the messages start and stop before they added the metadata. Is your request that they change the format of the .msg file so that it can be read without a .idx file?
Edit: I’ve added a script that shows how I got around this problem. It looks like you used the OFFSET and LENGTH fields to figure out where the extra metadata is. I explicitly look for all of the metadata fields that can be present in the file. Either method should work. I think my script works for pre and post-5.8 saved message formats.
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