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Re: [Gnumed-devel] Re: Lab importing Re: Bootstrap of (test) lab data

From: Dave Cramer
Subject: Re: [Gnumed-devel] Re: Lab importing Re: Bootstrap of (test) lab data
Date: Tue, 22 Jan 2008 05:41:39 -0500

OK, I spent a bit of time on this.

Can someone point me to where the docs suggest you can use java or python as scripting ?

It appears you can use _javascript_, however the documentation is sorely lacking.

On 21-Jan-08, at 1:50 PM, James Busser wrote:

Hi David McKenzie and all

A thread from prior discussion, based around what was then HL7 v2.3, is on the archive at

proposal for HL7 v2.3 to gnumed parsing

concrete mappings of v2.3 messages onto gnumed measurements

simple HL7 parser (in Python)

Possibly the schema has not, in the meantime, changed (?) as far as lab measurements.

I will send the test files to David & David offlist. FWIW there was a music duo in 1987 named David & David. Sadly they released only one album, but it was great

I await a reply from my regional data broker as to whether their version of HL7 has changed in the 18 months since I was last sent some test messages... it could be possible that they are now on HL7 V3.

On 21-Jan-08, at 4:09 AM, David Mackenzie wrote:


If no-one else would like to do this task, I am happy to look into it with your guidance. I was only looking at Mirth (very briefly) the other day. Let me know if you would like me to help out. I am a J2EE/java developer who has been lurking on the GNUMed devel list for a while and thought that it was time that I should contribute something :-) I am familiar with most of the technologies in project Mirth (J2EE, JBoss, Web Services, XSLT, etc...) however, I am not that familiar with HL7 messgages but interested to learn.

Is there someone that can give me a clear picture as to exactly what needs to be done. And I will see how I go. I may have a lot more questions as I go as I am not that familiar with the GNUMed codebase.

David Mackenzie.

On Jan 21, 2008 9:38 PM, Andreas Tille <address@hidden> wrote:
On Sat, 19 Jan 2008, Karsten Hilbert wrote:

>> Have a look at Mirth - - which can be
>> scripted in Java or Python and which can interface directly to database
>> back-ends or via various APIs or Web service interfaces. Might be easier
>> than re-inventing all this within GNUmed
> I fully agree. For importing of lab data we should be using Mirth to parse sources into our database. That would be another helpful thing the Java person could do for us - setup Mirth to parse your HL7 input which will show us where the GNUmed backend lacks fields to support the incoming data. I would see to it that the necessary fields are added. We would then write a fairly simple grid-based viewer as a first iteration.

Just added Mirth as a prospective package for the Debian-Med project.
Even if I'm not over optimistic that we will have packages soon it should
be listed to remind people that there is something useful out there.

Kind regards



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