Re: [Froid] Re: Bika Connect to Humacount

[lemoene]

Thank you for the feedback Anousak, and Eid Mubarak all.

I am dialling my reply through the Froid group so we can keep the ball rolling.

This time the Bika Health group, same same but different;-)

Oh and re configuring Senaite, this chapter in the new manual is not quite complete yet, written for LIMS, but it 'll help too I hope, https://www.bikalims.org/manual/setup-and-configuration

Good place start...I can see that it is right step of doing LIS procedures. My staff are not familair how Senaite LIS works, we are doing the best we could. We'll get there.

Is a pity I only arrive end of September...-(  We are always keen to assist on the open forums where it benefits all (and we are under peer pressure to answer quickly;-), please use the Bika Health list for these questions. I am not sure I gave you access to our Health demo at https://health.bikalims.org/, will follow up under separate heading.

This here then

The Health demo configuration is in better shape now. The original configuration data set is a very thorough epidemiology set put together by Dr Chris Larsen during our first outing in the Caribbean and not always suitable for more generic pathology, haematology etc. and I started swinging it round but it is not nearly complete and neither am I knowledgeable enough re clinical analysis.

I expect though that the Haematology Analysis Category at https://health.bikalims.org/bika_setup/bika_analysisservices could be what you are looking to configure for the Humacount?

Please continue posting questions you might have here.

It is also worth noting all, re the rest of the post below, that the Froid instrument middleware project is lifting off. Please subscribe at https://groups.google.com/forum/?hl=en&fromgroups#!forum/freefroid to stay in touch (or contribute;)

Bests, and have good weekend
l

 

Potentially stupid question as I have not had enough time to read the docs: Is the TXT file an example of  the Humacount results Anousak? It opens sweetly as TSV.

Yes, it is Humacount result in plain text.

 

If so, then its parser should be relatively easy, see https://github.com/bikalims/bika.lims/wiki/creating-an-instrument-import-interface (Which has been described as long winded and written for beginners - it is a frequent entry point for new Bika | Senaite coders).  Skilled coders who have done these before, complete and test the easier ones in a day. You'll take a bit longer initially I guess.

The current parsers live at https://github.com/senaite/senaite.core/tree/master/bika/lims/exportimport/instruments and another recommendation I frequently see is that you should simply pick a similar one to yours, then clone and hack it.

Finding a similar one could be difficult, in the tracker you'll find results files attached to instrument interface requests, the ones in the blue 'Instrument Specs' epic has not been don yet. A simple 2D results table, similar to your TXT file, I remember was done in our very first one for the Foss Winescan FT120, its code could be old, https://github.com/senaite/senaite.core/tree/master/bika/lims/exportimport/instruments/foss/winescan.

With Froid then, we'd be looking at the parser outputting REST as per the doc I circulated earlier. I have a longer more detailed version I'll touch up and send on.

Lemoene, these are good info and useful indeed.  I have submitted a request  trough tracker for Humacount interface to LIS on https://jira.bikalabs.com/browse/LIMS-2858.

Thanks for putting it on record, but remember that all free assistance there is voluntary, we have to focus on contracted clients at the moment to sustain the project - the migration of the past 6 months did not deliver much invoicing opportunity. That said, please continue posting your interface questions here where we have I think 27 subscribers already. You're an old hand at FOSS and I am sure knows that well researched questions do a lot better than others;-)

In our own team, Lunga has much experience with these, is subscribed here and I am asking him to keep a lookout for you too. I am still on-site amidst a v tricky implementation and hope to find time over the weekend to assist on the other points you raised.

Have a good one!
l

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