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Re: [Gnumed-devel] forms handling / NetEpi

From: Tim Churches
Subject: Re: [Gnumed-devel] forms handling / NetEpi
Date: Thu, 28 Jun 2007 06:41:21 +1000
User-agent: Thunderbird (Windows/20070509)

Karsten Hilbert wrote:
> On Wed, Jun 27, 2007 at 07:02:27AM +1000, Tim Churches wrote:
>>>> Easier extensibility of the form definitions/metadata,
>>> I can see that. Put IOW: it seems safer to update data in
>>> deployed databases rather than requiring the databases
>>> themselves to be modified, eg. when one needs a new "field"
>>> in the form metadata definition.
>>> It *can* be done via ALTER TABLE but I agree it sounds safer
>>> to rather do UPDATE ... WHERE ... ;
>> What if the update to a form which has already been used to collect data
>> involves the removal of a column? If you use ALTER TABLE, all the data
>> collected in that form field/column is now gone... where's the undo button?
> Well, here's one fundamental difference in what we consider
> a form to be:
> In NetEpi forms are used to *collect* data.
> In GNUmed the sort of form we are currently concerned about
> is to *use existing* data to fill in fields on and (mostly)
> print fields out onto paper forms.
> IOW, the disappearing column scenario doesn't exist.
> I tend to believe, even in your scenario, that a form is but
> a puff of smoke and should never endanger existing data. IOW,
> - never *remove* a form definition but rather
>   retire/obsolete/supercede it by (at least a new version
>   of) a form

Yes, that's exactly what we do. Each form version has its own table, and
obsolete versions are not deleted. There is no user interface to
retrieve data from a field/column dropped in a subsequent version of a
form, but the syadmin/dbadmin can easily get the data. We should add a
user interface to it.

> - roll forward "old" form content only where there's a need,
>   eg to print out repeat prescriptions when the prescription
>   form has changed inbetween first and repeat request
>   I do appreciate this doesn't fit with the
>   forms-for-data-capture approach where you may need to be
>   able to process "old" and "new" form content as if it was
>   captured the same way.

Yes, epidemiological data, especially disease outbreak data, is
ephemeral and only has a limited currency and is for a specific purpose.
So although we never throw data away, we are really only interested in
the current data values for the current set of data items. That is a
difference from a clinical medical record.

>>> (COPY these
>>> days is able to dump the result of a SELECT statement :-)
>> That would work. XML is not always best, but if you tell people that
>> your form definitions are shareable as CSV files, they will look at you
>> very strangely, whereas if you say "shareable as XML" then they won't be
>> surprised at all.
> A good social engineering argument.
> I suppose we'd wrap the CSV in minimalist XML to please them
> peoples:
> <xml>
> <fancy_message caption="this is the new fancy form you asked 
> for"></fancy_message>
> <csv>
> the,csv,for,copy,to,insert
> </csv>
> </xml>
> et voila, shareable via XML where GNUmed displays
> $fancy_message and instructs psql-whatnot to go its merry way
> with the CSV data.


>>>> We tested your approach, which is a form of the well-known
>>>> EAV (entity-attribute-value) approach,
>>> Correct.
>>>> i.e. about 250 million rows in the values tables.
>>> Let's see:
>>> Or 8 000 000 form field values over 10 years. Let's double
>>> that up for increase of bureaucracy: 16 million. Double
>>> again just for good measure: 32 million.
>> Sure - at a clinic or individual institution level, the EAV approach is
>> fine performance-wise.
> We are looking at the individual clinic level with GNUmed.
> So the gist of the this exchange seems to be that a)
> implementation-wise (I did look at the cocklebur code by
> now) we have an excellent reference source for how to do it
> but we need not be afraid - performance-wise - to employ an
> EAV style schema where this seems appropriate.

For systems aimed at a single clinic or institution, yes. If you want to
scale up beyond that, do some performance simulations with lots of dummy
data. But I think you'll be fine.

Of course, if you consider the way PostgreSQL (but not other databases)
works internally, it uses a form of EAV anyway. Well, close to it. But
then it wraps SQL DDL around it. So our approach of a table per form
version with a "fixed" schema is really closer to the EAV formulation
when done with PostgreSQL than you might think.

> Directly reusing the cocklebur forms framework doesn't seem
> appropriate :-( as the goals are different, that is
> arbitrary data-capture vs. predefined-form-filling with the
> existing code being geared towards the former.

I agree. Cocklebur is a custom object-relational mapper for NetEpi
Collection, it was not designed to be general.

> We may end up using it anyways.

Happy to help if we can.

Tim C

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