OpenEHR and Oracle XML DB problems

[Chamorro Gordejuela, Jacobo]

Hi Dimitry,


We are using the same approach as ?Bert (storing compositions, not versions) 
using Oracle 11.2.0.4.0 and it's working fine. We use openEHR schemas 
(Composition, Content, Structure and BaseTypes) with slight modifications 
(datetime regexp, for example).



---

Jacobo


De: openEHR-technical  en 
nombre de pazospablo at hotmail.com 
Enviado: viernes, 17 de abril de 2015 05:25
Para: 79104301700 at yandex.ru; openehr-technical at lists.openehr.org
Asunto: Re: OpenEHR and Oracle XML DB problems


Hi Dmitry, as a side conceptual note, the openEHR IM is not a persistence 
model, and the XSDs are a way to express instances of the IM.


The XSDs would require some refactoring work to express an specific persistence 
model for the Information Model, like simplifying some datatypes of the IM into 
datatypes used/supported by your persistence technology, like dates, texts, 
coded texts, ordinals, etc.


 I would suggest to explore hybrid approaches using relational+xml or 
relational+json persistence technologies. It might make your work easier.


Cheers,

Pablo.


Sent from my LG Mobile

-- Original message--

From: Dmitry Baranov<79104301700 at yandex.ru>

Date: Thu, Apr 16, 2015 04:06

To: For openEHR technical discussions;

Subject:Re: OpenEHR and Oracle XML DB problems

Hi Bert,I give up. The problem appears in 12c as well. And people agree that it 
is an Oracle 
bug.ht<http://bug.ht>tps://community.oracle.com/message/13008017<http://community.oracle.com/message/13008017>>
 You should always follow the standard in your analyses, before you> declare 
one product buggy and another not.> I see in that message that there was a 
patch recommended, did you try> that? Always use the latest patch level.-- 
Regards, DmitryE-mail: baranovda at yandex.ruPh<mailto:%20baranovda at 
yandex.ruPh>: 7 910 
430-17-00___openEHR-technical
 mailing listopenEHR-technical at 
lists.openehr.orghtt<mailto:%20listopenEHR-technical at 
lists.openehr.orghtt>p://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org<http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org>

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a ninguna persona.

 

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a ninguna persona.

 

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OpenEHR and Oracle XML DB problems

[pazospa...@hotmail.com]

Hi Dmitry, as a side conceptual note, the openEHR IM is not a persistence 
model, and the XSDs are a way to express instances of the IM.?
The XSDs would require some refactoring work to express an specific persistence 
model for the Information Model, like simplifying some datatypes of the IM into 
datatypes used/supported by your persistence technology, like dates, texts, 
coded texts, ordinals, etc.
?I would suggest to explore hybrid approaches using relational+xml or 
relational+json persistence technologies. It might make your work easier.
Cheers,Pablo.
Sent from my LG Mobile


-- Original message--From: Dmitry Baranov<79104301700 at 
yandex.ru>Date: Thu, Apr 16, 2015 04:06To: For openEHR technical 
discussions;Subject:Re: OpenEHR and Oracle XML DB problemsHi Bert,I give up. 
The problem appears in 12c as well. And people agree that it is an Oracle 
bug.https://community.oracle.com/message/13008017> You should always follow the 
standard in your analyses, before you> declare one product buggy and another 
not.> I see in that message that there was a patch recommended, did you try> 
that? Always use the latest patch level.-- Regards, DmitryE-mail: baranovda at 
yandex.ruPh: 7 910 
430-17-00___openEHR-technical 
mailing listopenEHR-technical at 
lists.openehr.orghttp://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
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OpenEHR and Oracle XML DB problems

[Dmitry Baranov]

Diego, 
that'll be great. 
Hope that OpenEHR github owners will provide us with an instance samples 
repository some day or other :)

> I can generate random sample instances from current archetypes for you
> if you need them. Generated data may not make much sense as it only
> tries to follow the archetype constraints, but it should be enough for
> application testing and benchmark
-- 
Regards, Dmitry
E-mail: baranovda at yandex.ru
Ph: 7 910 430-17-00

OpenEHR and Oracle XML DB problems

[Dmitry Baranov]

> I regret that I cannot post the XML Schema and XML-instances I use, because 
> they are not of my IP. But they are structured in another way, more dedicated 
> to efficiency.

XML schema is intellectual property, I agree, but why might you or somebody 
else not to provide community with a couple (well, a couple of hundreds will be 
better) of depersonalized sample instance files? :) We'ld appreciate that very 
much. I'm a beginner with OpenEHR and it seems to me that there is a lack of 
OpenEHR instance examples on the Internet; HL7 CDA has plenty of samples and 
their FHIR has an excellent web site with instance samples repository, in 
various formats.  

-- 
Regards, Dmitry
E-mail: baranovda at yandex.ru
Ph: 7 910 430-17-00

OpenEHR and Oracle XML DB problems

[Birger Haarbrandt]

Hi Thomas,

do we really need realistic data sets? At least in the beginning, many 
programmers that are new to openEHR would already be happy with some 
valid data instances.

If anyone likes to do such a synthesier: Katrin Dentler has done some 
work on patient data generation 
(http://www.cs.vu.nl/~frankh/postscript/KR4HC-2013-APDG.pdf)... maybe 
she can provide some existing code and knowledge if anybody wants to 
build such a thing :) (It might be a little out of scope for my department)

Best,

Birger

Am 16.04.2015 um 11:13 schrieb Thomas Beale:
>
> Indeed, it would be a great thing. The reason it doesn't exist so far, 
> is that to be useful we need synthesised data sets that have some 
> realistic statistical spread of values. Since we are talking at 
> multiple levels - not just vital signs measurements, but covariance of 
> all kinds of measurements with assessments (diagnosis etc), plans and 
> orders and actions, the complexity is not trivial.
>
> A data synthesiser to do this for openEHR would be a fantastic 
> Master's project (hint :).
>
> - thomas
>
> On 16/04/2015 10:02, Dmitry Baranov wrote:
>> Diego,
>> that'll be great.
>> Hope that OpenEHR github owners will provide us with an instance 
>> samples repository some day or other :)
>>
>>> I can generate random sample instances from current archetypes for you
>>> if you need them. Generated data may not make much sense as it only
>>> tries to follow the archetype constraints, but it should be enough for
>>> application testing and benchmark
>
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org 
>


-- 
*Birger Haarbrandt, M.Sc.*

Peter L. Reichertz Institut f?r Medizinische Informatik
Technische Universit?t Braunschweig und
Medizinische Hochschule Hannover
M?hlenpfordtstra?e 23
D-38106 Braunschweig

T +49 (0)531 391-2129
F +49 (0)531 391-9502
birger.haarbrandt at plri.de
http://www.plri.de

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OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 16-04-15 11:13, Thomas Beale wrote:
>
> Indeed, it would be a great thing. The reason it doesn't exist so far, 
> is that to be useful we need synthesised data sets that have some 
> realistic statistical spread of values. Since we are talking at 
> multiple levels - not just vital signs measurements, but covariance of 
> all kinds of measurements with assessments (diagnosis etc), plans and 
> orders and actions, the complexity is not trivial.
>
> A data synthesiser to do this for openEHR would be a fantastic 
> Master's project (hint :).

I use Oxygen, it can generate XML instances to XML Schema's, but first 
we need to change the data-element of version to have type Locatable, or 
Composition.
If wanted, I can generate them too, it is only one minute work.

Bert
>
> - thomas
>
> On 16/04/2015 10:02, Dmitry Baranov wrote:
>> Diego,
>> that'll be great.
>> Hope that OpenEHR github owners will provide us with an instance 
>> samples repository some day or other :)
>>
>>> I can generate random sample instances from current archetypes for you
>>> if you need them. Generated data may not make much sense as it only
>>> tries to follow the archetype constraints, but it should be enough for
>>> application testing and benchmark
>
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org 
>

OpenEHR and Oracle XML DB problems

[Ian McNicoll]

As part of NHS Code4Health, we should be able to expose a number of
realistic composition instances, kindly donated by system vendors.

On my Todo list :)

Ian

Dr Ian McNicoll
mobile +44 (0)775 209 7859
office +44 (0)1536 414994
skype: ianmcnicoll
email: ian at freshehr.com
twitter: @ianmcnicoll

Co-Chair, openEHR Foundation Management Board
Director, freshEHR Clinical Informatics
Director, HANDIHealth CIC
Hon. Senior Research Associate, CHIME, UCL

On 16 April 2015 at 10:36, Seref Arikan 
wrote:

> Hi Birger,
> Thanks for link to Katrin's work.
>
> Regards
> Seref
>
>
> On Thu, Apr 16, 2015 at 10:32 AM, Birger Haarbrandt <
> birger.haarbrandt at plri.de> wrote:
>
>>  Hi Thomas,
>>
>> do we really need realistic data sets? At least in the beginning, many
>> programmers that are new to openEHR would already be happy with some valid
>> data instances.
>>
>> If anyone likes to do such a synthesier: Katrin Dentler has done some
>> work on patient data generation (
>> http://www.cs.vu.nl/~frankh/postscript/KR4HC-2013-APDG.pdf)... maybe she
>> can provide some existing code and knowledge if anybody wants to build such
>> a thing :) (It might be a little out of scope for my department)
>>
>> Best,
>>
>> Birger
>>
>> Am 16.04.2015 um 11:13 schrieb Thomas Beale:
>>
>>
>> Indeed, it would be a great thing. The reason it doesn't exist so far, is
>> that to be useful we need synthesised data sets that have some realistic
>> statistical spread of values. Since we are talking at multiple levels - not
>> just vital signs measurements, but covariance of all kinds of measurements
>> with assessments (diagnosis etc), plans and orders and actions, the
>> complexity is not trivial.
>>
>> A data synthesiser to do this for openEHR would be a fantastic Master's
>> project (hint :).
>>
>> - thomas
>>
>> On 16/04/2015 10:02, Dmitry Baranov wrote:
>>
>> Diego,
>> that'll be great.
>> Hope that OpenEHR github owners will provide us with an instance samples
>> repository some day or other :)
>>
>> I can generate random sample instances from current archetypes for you
>> if you need them. Generated data may not make much sense as it only
>> tries to follow the archetype constraints, but it should be enough for
>> application testing and benchmark
>>
>>
>>
>>
>> ___
>> openEHR-technical mailing list
>> openEHR-technical at lists.openehr.org
>>
>> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>>
>>
>>
>> --
>> *Birger Haarbrandt, M.Sc.*
>>
>> Peter L. Reichertz Institut f?r Medizinische Informatik
>> Technische Universit?t Braunschweig und
>> Medizinische Hochschule Hannover
>> M?hlenpfordtstra?e 23
>> D-38106 Braunschweig
>>
>> T +49 (0)531 391-2129
>> F +49 (0)531 391-9502
>> birger.haarbrandt at plri.de
>> http://www.plri.de
>>
>> ___
>> openEHR-technical mailing list
>> openEHR-technical at lists.openehr.org
>>
>> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>>
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
>
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>
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Regarding an openEHR based Data Synthesizer (Was Re: OpenEHR and Oracle XML DB problems)

[Athanasios Anastasiou]

Had to make this a separate discussion about the data synth to 
distinguish it from the Oracle XML DB problems.

If you have access to primary data, e.g. the usual Pat_ID, Timestamp, 
Code, Value, you can create very simple generative models by training a 
neural network to generate sequences with similar statistics. In this 
case, the time parameter, code covariance and code value dynamics (for 
those that have a value attached to them) are all lumped together.

You can set inclusion/exclusion criteria that specify a sub-population 
and have the neural network be trained and generate data for that 
specific population.

As a practical example, in a pilot study of a few thousand elderly 
patients, we found that along with dementia, it was inevitable to be 
getting significant cardiovascular problems and also, a lot of...flu.

It's a crude way to be training a network to produce similar sets of 
codes and values but the dream of specifying patient data as a linear 
mixture of the profiles of different conditions is a bit far off yet :)

Of course, when this is done, we are still left with mapping a given 
clinical encoding scheme to the suitable openEHR archetype. (If we are 
looking at a general solution that is).

All the best
Athanasios






On 16/04/2015 10:22, Bert Verhees wrote:
> On 16-04-15 11:13, Thomas Beale wrote:
>>
>> Indeed, it would be a great thing. The reason it doesn't exist so far,
>> is that to be useful we need synthesised data sets that have some
>> realistic statistical spread of values. Since we are talking at
>> multiple levels - not just vital signs measurements, but covariance of
>> all kinds of measurements with assessments (diagnosis etc), plans and
>> orders and actions, the complexity is not trivial.
>>
>> A data synthesiser to do this for openEHR would be a fantastic
>> Master's project (hint :).
>
> I use Oxygen, it can generate XML instances to XML Schema's, but first
> we need to change the data-element of version to have type Locatable, or
> Composition.
> If wanted, I can generate them too, it is only one minute work.
>
> Bert
>>
>> - thomas
>>
>> On 16/04/2015 10:02, Dmitry Baranov wrote:
>>> Diego,
>>> that'll be great.
>>> Hope that OpenEHR github owners will provide us with an instance
>>> samples repository some day or other :)
>>>
 I can generate random sample instances from current archetypes for you
 if you need them. Generated data may not make much sense as it only
 tries to follow the archetype constraints, but it should be enough for
 application testing and benchmark
>>
>>
>>
>> ___
>> openEHR-technical mailing list
>> openEHR-technical at lists.openehr.org
>> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>>
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>

OpenEHR and Oracle XML DB problems

[Diego Boscá]

I can generate random sample instances from current archetypes for you
if you need them. Generated data may not make much sense as it only
tries to follow the archetype constraints, but it should be enough for
application testing and benchmark

2015-04-16 10:42 GMT+02:00 Dmitry Baranov :
>> I regret that I cannot post the XML Schema and XML-instances I use, because 
>> they are not of my IP. But they are structured in another way, more 
>> dedicated to efficiency.
>
> XML schema is intellectual property, I agree, but why might you or somebody 
> else not to provide community with a couple (well, a couple of hundreds will 
> be better) of depersonalized sample instance files? :) We'ld appreciate that 
> very much. I'm a beginner with OpenEHR and it seems to me that there is a 
> lack of OpenEHR instance examples on the Internet; HL7 CDA has plenty of 
> samples and their FHIR has an excellent web site with instance samples 
> repository, in various formats.
>
> --
> Regards, Dmitry
> E-mail: baranovda at yandex.ru
> Ph: 7 910 430-17-00
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org

OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 16-04-15 10:42, Dmitry Baranov wrote:
>> I regret that I cannot post the XML Schema and XML-instances I use, because 
>> they are not of my IP. But they are structured in another way, more 
>> dedicated to efficiency.
> XML schema is intellectual property, I agree, but why might you or somebody 
> else not to provide community with a couple (well, a couple of hundreds will 
> be better) of depersonalized sample instance files? :) We'ld appreciate that 
> very much. I'm a beginner with OpenEHR and it seems to me that there is a 
> lack of OpenEHR instance examples on the Internet; HL7 CDA has plenty of 
> samples and their FHIR has an excellent web site with instance samples 
> repository, in various formats.
>
Sory Dmitry, I did not explain right. The work I do is not of my IP. I 
work for someone and we agreed he automatically has the IP of my work.

So that is why I can't share the XML Schema's and XML-instances I use.

Bert

OpenEHR and Oracle XML DB problems

[Birger Haarbrandt]

Hi there,

there might be good reasons (as mentioned here) to not like XML but its 
mature and rich technology stack (XSLT, XPath/XQuery, Schematron, 
RelaxNG), available tooling (Mapforce, XML Spy...) and support (Most 
major database vendors...) makes it a working solution in many 
use-cases. I really can't say that we are unhappy with it at our 
persistence layer (though one of my master students currently 
investigates the use of intersystems cach? as an alternative...I'm not 
quite sure if AQL will be possible in an "easy" way as in XML databases 
) Of course, I like the elegance of Json but there is plenty of work to 
do until it's getting a real substitute (if at all)...

Best,

Birger

Am 16.04.2015 um 09:48 schrieb Diego Bosc?:
> In fact, JSON-Schema is only lacking a more detailed typing system to
> replace ADL :)
>
> 2015-04-16 9:29 GMT+02:00 Thomas Beale :
>> On 16/04/2015 06:46, Bert Verhees wrote:
>>>
> I think it is a stupid rule in the XML-Schema standard.

 I just hit this in doing the AOM2 schema. It's a completely senseless
 rule, clearly a hangover from 'document' thinking - nothing to do with
 'data' thinking.  I ended up replacing  with.

 
>>>
>>> It is a poor man's choice, because of the side-effects.
>>> The "choice"-constraint makes the engine ignore the minOccurs/maxOccurs
>>> constraints in the elements under the choice element.
>>>
 I have to say, XML-schema based data looks extremely unattractive as a
 basis for anything except data exchange. I wouldn't try to implement
 anything important inside a system with it, you are too compromised in too
 many ways.
>>>
>>> It is also used, as I wrote yesterday, to tell an XML-database how, in a
>>> specific namespace, the data are arranged, in that way the database can
>>> auto-create indexes, etc.
>>> There is no other way to communicate the structure of XML-documents, and
>>> even if we found another way, or invented it ourselves, we still would need
>>> a broad acceptation.
>>
>> We still need some kind of schema for XML docs/ messages, but I would not
>> even think of making any persistence be based on XML, especially not XML
>> schema. Probably Relax NG would have been the better one for messages etc.
>>
>> Keep XML at the boundaries, that's the key to happiness! I guess JSON with
>> its own schema will replace it in the next couple of years.
>>
>> - thomas
>>
>>
>> ___
>> openEHR-technical mailing list
>> openEHR-technical at lists.openehr.org
>> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org


-- 
*Birger Haarbrandt, M.Sc.*

Peter L. Reichertz Institut f?r Medizinische Informatik
Technische Universit?t Braunschweig und
Medizinische Hochschule Hannover
M?hlenpfordtstra?e 23
D-38106 Braunschweig

T +49 (0)531 391-2129
F +49 (0)531 391-9502
birger.haarbrandt at plri.de
http://www.plri.de

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OpenEHR and Oracle XML DB problems

[Seref Arikan]

Hi Birger,
Thanks for link to Katrin's work.

Regards
Seref


On Thu, Apr 16, 2015 at 10:32 AM, Birger Haarbrandt <
birger.haarbrandt at plri.de> wrote:

>  Hi Thomas,
>
> do we really need realistic data sets? At least in the beginning, many
> programmers that are new to openEHR would already be happy with some valid
> data instances.
>
> If anyone likes to do such a synthesier: Katrin Dentler has done some work
> on patient data generation (
> http://www.cs.vu.nl/~frankh/postscript/KR4HC-2013-APDG.pdf)... maybe she
> can provide some existing code and knowledge if anybody wants to build such
> a thing :) (It might be a little out of scope for my department)
>
> Best,
>
> Birger
>
> Am 16.04.2015 um 11:13 schrieb Thomas Beale:
>
>
> Indeed, it would be a great thing. The reason it doesn't exist so far, is
> that to be useful we need synthesised data sets that have some realistic
> statistical spread of values. Since we are talking at multiple levels - not
> just vital signs measurements, but covariance of all kinds of measurements
> with assessments (diagnosis etc), plans and orders and actions, the
> complexity is not trivial.
>
> A data synthesiser to do this for openEHR would be a fantastic Master's
> project (hint :).
>
> - thomas
>
> On 16/04/2015 10:02, Dmitry Baranov wrote:
>
> Diego,
> that'll be great.
> Hope that OpenEHR github owners will provide us with an instance samples
> repository some day or other :)
>
> I can generate random sample instances from current archetypes for you
> if you need them. Generated data may not make much sense as it only
> tries to follow the archetype constraints, but it should be enough for
> application testing and benchmark
>
>
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
>
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>
>
>
> --
> *Birger Haarbrandt, M.Sc.*
>
> Peter L. Reichertz Institut f?r Medizinische Informatik
> Technische Universit?t Braunschweig und
> Medizinische Hochschule Hannover
> M?hlenpfordtstra?e 23
> D-38106 Braunschweig
>
> T +49 (0)531 391-2129
> F +49 (0)531 391-9502
> birger.haarbrandt at plri.de
> http://www.plri.de
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
>
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>
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OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 16-04-15 09:29, Thomas Beale wrote:
> e still need some kind of schema for XML docs/ messages, but I would 
> not even think of making any persistence be based on XML, especially 
> not XML schema. Probably Relax NG would have been the better one for 
> messages etc.
>
> Keep XML at the boundaries, that's the key to happiness! I guess JSON 
> with its own schema will replace it in the next couple of years. 
With RelaxNG, IMHO, you cannot communicate structure, RelaxNG only 
serves validation.
So, if I am right, optimizing an XML database using RelaxNG is impossible.
You, can say, that if it validates in a RelaxNG-schema, then it must be 
structured right, but learning a structure from a RelaxNG schema seems 
hard to me.

I don't think JSON wll replace XML, JSON has no attribute-mechanism, and 
must treat everything as data. It has its use for wellknown structures. 
It is efficient.
But if you want JSON to be as rich as XML, then it must be restructured 
as XML, and then it will become XML2.
Which is OK for me, but then we still have to solve the problems with 
XML Schema, but then on JSON-Schema

Bert

OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 16-04-15 09:06, Dmitry Baranov wrote:
> Hi Bert,
>
> I give up. The problem appears in 12c as well.
> And people agree that it is an Oracle bug.
> https://community.oracle.com/message/13008017
>
>> You should always follow the standard in your analyses, before you
>> declare one product buggy and another not.
>> I see in that message that there was a patch recommended, did you try
>> that? Always use the latest patch level.
Dmitry, if you read the post carefully, not people, but one person says, 
it *appears* to be a bug
He has to escalate it to engineering, and if it is a confirmed bug, is 
something you must wait for
He says he can reproduce it, this means he used your files.

I checked them also, they validate right in Oxygen.

Oracle in different versions stumbling over your used OpenEHR XML Schema 
with your XML-instances?
That is possible. There is a bug in a particular use of your schema.

I am stressing to this because I am posting all the time Compositions in 
Oracle 12c, and all kind of other XML-instances from several namespaces.
No problem at all.

But I have things structured in another way. For example, when I post a 
Composition, the XML-instance starts with the Document-element called 
Composition. This is allowed because I have an xs:element COMPOSITION on 
top level in the XML-Schema (). I noticed in a glance that you have that too, and 
it is logical that you have, because you flattened the same XML Schema's 
as I did.
When you use that, you have to store your audit and version information 
elsewhere.

When I look at your XML Schema and instance, just a quick glance, then I 
see that you have  at top 
level, and derived from that Original Version, which has as 
child-element data of type xs:anyType. I would not do that, because you 
throw away any optimization. Oracle can't do anything with this.
You could at least have it to be Locatable, because data in version are 
always of type Locatable.
You could even have a original-version of type composition, and one of 
type party, this would help optimization even more.

I regret that I cannot post the XML Schema and XML-instances I use, 
because they are not of my IP. But they are structured in another way, 
more dedicated to efficiency.

Bert


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OpenEHR and Oracle XML DB problems

[Thomas Beale]

Indeed, it would be a great thing. The reason it doesn't exist so far, 
is that to be useful we need synthesised data sets that have some 
realistic statistical spread of values. Since we are talking at multiple 
levels - not just vital signs measurements, but covariance of all kinds 
of measurements with assessments (diagnosis etc), plans and orders and 
actions, the complexity is not trivial.

A data synthesiser to do this for openEHR would be a fantastic Master's 
project (hint :).

- thomas

On 16/04/2015 10:02, Dmitry Baranov wrote:
> Diego,
> that'll be great.
> Hope that OpenEHR github owners will provide us with an instance samples 
> repository some day or other :)
>
>> I can generate random sample instances from current archetypes for you
>> if you need them. Generated data may not make much sense as it only
>> tries to follow the archetype constraints, but it should be enough for
>> application testing and benchmark

OpenEHR and Oracle XML DB problems

[Dmitry Baranov]

Hi Bert,

I give up. The problem appears in 12c as well. 
And people agree that it is an Oracle bug.
https://community.oracle.com/message/13008017

> You should always follow the standard in your analyses, before you
> declare one product buggy and another not.
> I see in that message that there was a patch recommended, did you try
> that? Always use the latest patch level.

-- 
Regards, Dmitry
E-mail: baranovda at yandex.ru
Ph: 7 910 430-17-00

OpenEHR and Oracle XML DB problems

[Diego Boscá]

In fact, JSON-Schema is only lacking a more detailed typing system to
replace ADL :)

2015-04-16 9:29 GMT+02:00 Thomas Beale :
> On 16/04/2015 06:46, Bert Verhees wrote:
>>
>>

 I think it is a stupid rule in the XML-Schema standard.
>>>
>>>
>>> I just hit this in doing the AOM2 schema. It's a completely senseless
>>> rule, clearly a hangover from 'document' thinking - nothing to do with
>>> 'data' thinking.  I ended up replacing  with.
>>>
>>> 
>>
>>
>> It is a poor man's choice, because of the side-effects.
>> The "choice"-constraint makes the engine ignore the minOccurs/maxOccurs
>> constraints in the elements under the choice element.
>>
>>>
>>> I have to say, XML-schema based data looks extremely unattractive as a
>>> basis for anything except data exchange. I wouldn't try to implement
>>> anything important inside a system with it, you are too compromised in too
>>> many ways.
>>
>>
>> It is also used, as I wrote yesterday, to tell an XML-database how, in a
>> specific namespace, the data are arranged, in that way the database can
>> auto-create indexes, etc.
>> There is no other way to communicate the structure of XML-documents, and
>> even if we found another way, or invented it ourselves, we still would need
>> a broad acceptation.
>
>
> We still need some kind of schema for XML docs/ messages, but I would not
> even think of making any persistence be based on XML, especially not XML
> schema. Probably Relax NG would have been the better one for messages etc.
>
> Keep XML at the boundaries, that's the key to happiness! I guess JSON with
> its own schema will replace it in the next couple of years.
>
> - thomas
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical at lists.openehr.org
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org

OpenEHR and Oracle XML DB problems

[Thomas Beale]

On 16/04/2015 06:46, Bert Verhees wrote:
>
>>>
>>> I think it is a stupid rule in the XML-Schema standard.
>>
>> I just hit this in doing the AOM2 schema. It's a completely senseless 
>> rule, clearly a hangover from 'document' thinking - nothing to do 
>> with 'data' thinking.  I ended up replacing  with.
>>
>> 
>
> It is a poor man's choice, because of the side-effects.
> The "choice"-constraint makes the engine ignore the 
> minOccurs/maxOccurs constraints in the elements under the choice element.
>
>>
>> I have to say, XML-schema based data looks extremely unattractive as 
>> a basis for anything except data exchange. I wouldn't try to 
>> implement anything important inside a system with it, you are too 
>> compromised in too many ways.
>
> It is also used, as I wrote yesterday, to tell an XML-database how, in 
> a specific namespace, the data are arranged, in that way the database 
> can auto-create indexes, etc.
> There is no other way to communicate the structure of XML-documents, 
> and even if we found another way, or invented it ourselves, we still 
> would need a broad acceptation.

We still need some kind of schema for XML docs/ messages, but I would 
not even think of making any persistence be based on XML, especially not 
XML schema. Probably Relax NG would have been the better one for 
messages etc.

Keep XML at the boundaries, that's the key to happiness! I guess JSON 
with its own schema will replace it in the next couple of years.

- thomas

OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 15-04-15 23:11, Thomas Beale wrote:
> On 15/04/2015 17:28, Bert Verhees wrote:
>> On 15-04-15 17:19, Dmitry Baranov wrote:
>>> Sorry Bert ) I had to explain that Oracle 11 is a business 
>>> requirement, not a hardware limitation.
>>>
 Just do it, and then it should run fine, although you have to 
 change the
 XML-Schemas (a bit) before registering them to Oracle. I already
 explained to you before what and why.
>>> I remember your advise but not sure that changing all the sequences 
>>> to choices is a right way for many reasons. And I'm almost sure that 
>>> it's an Oracle bug since other XSD validation tools (visual studio, 
>>> netbeans and eclipse) say that my instance files are all OK and 
>>> conform to XML schema.
>>
>> You are right it is a messy solution, but if you use "sequence", like 
>> it is defined in the XML Schema, you have to take care that all the 
>> nodes in your XML are in the right/defined order.
>> I think this is hard to achieve when XML-files are created in 
>> production, but of course, you can arrange that as an alternative.
>>
>> I think it is a stupid rule in the XML-Schema standard.
>
> I just hit this in doing the AOM2 schema. It's a completely senseless 
> rule, clearly a hangover from 'document' thinking - nothing to do with 
> 'data' thinking.  I ended up replacing  with.
>
> 

It is a poor man's choice, because of the side-effects.
The "choice"-constraint makes the engine ignore the minOccurs/maxOccurs 
constraints in the elements under the choice element.

>
> I have to say, XML-schema based data looks extremely unattractive as a 
> basis for anything except data exchange. I wouldn't try to implement 
> anything important inside a system with it, you are too compromised in 
> too many ways.

It is also used, as I wrote yesterday, to tell an XML-database how, in a 
specific namespace, the data are arranged, in that way the database can 
auto-create indexes, etc.
There is no other way to communicate the structure of XML-documents, and 
even if we found another way, or invented it ourselves, we still would 
need a broad acceptation.

I never heard that there is any work going on in the committees, because 
XML Schema 1.1 is almost 15 years old. I believe it is considered finished.

If that is true, it is very sad.

Bert

OpenEHR and Oracle XML DB problems

[Thomas Beale]

On 15/04/2015 17:28, Bert Verhees wrote:
> On 15-04-15 17:19, Dmitry Baranov wrote:
>> Sorry Bert ) I had to explain that Oracle 11 is a business 
>> requirement, not a hardware limitation.
>>
>>> Just do it, and then it should run fine, although you have to change 
>>> the
>>> XML-Schemas (a bit) before registering them to Oracle. I already
>>> explained to you before what and why.
>> I remember your advise but not sure that changing all the sequences 
>> to choices is a right way for many reasons. And I'm almost sure that 
>> it's an Oracle bug since other XSD validation tools (visual studio, 
>> netbeans and eclipse) say that my instance files are all OK and 
>> conform to XML schema.
>
> You are right it is a messy solution, but if you use "sequence", like 
> it is defined in the XML Schema, you have to take care that all the 
> nodes in your XML are in the right/defined order.
> I think this is hard to achieve when XML-files are created in 
> production, but of course, you can arrange that as an alternative.
>
> I think it is a stupid rule in the XML-Schema standard.

I just hit this in doing the AOM2 schema. It's a completely senseless 
rule, clearly a hangover from 'document' thinking - nothing to do with 
'data' thinking.  I ended up replacing  with.



I have to say, XML-schema based data looks extremely unattractive as a 
basis for anything except data exchange. I wouldn't try to implement 
anything important inside a system with it, you are too compromised in 
too many ways.

- thomas

OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 15-04-15 17:19, Dmitry Baranov wrote:
> Sorry Bert ) I had to explain that Oracle 11 is a business requirement, not a 
> hardware limitation.
>
>> Just do it, and then it should run fine, although you have to change the
>> XML-Schemas (a bit) before registering them to Oracle. I already
>> explained to you before what and why.
> I remember your advise but not sure that changing all the sequences to 
> choices is a right way for many reasons. And I'm almost sure that it's an 
> Oracle bug since other XSD validation tools (visual studio, netbeans and 
> eclipse) say that my instance files are all OK and conform to XML schema.

You are right it is a messy solution, but if you use "sequence", like it 
is defined in the XML Schema, you have to take care that all the nodes 
in your XML are in the right/defined order.
I think this is hard to achieve when XML-files are created in 
production, but of course, you can arrange that as an alternative.

I think it is a stupid rule in the XML-Schema standard.
The only alternative is "choice", but then you are not able to have the 
counting of the elements validated.
Check the book written by Priscilla Walmsley, she is the all knowing 
saint regarding XML Schema.
If you don't have it, you can check the w3-website, where the standard 
is published, but less comfortable to read.
So, validating completely against XML Schema is not feasible because of 
weakness in the XML-Schema standard.

So why should you then register the XML-Schema in the database?
There is another reason for that, and that is because Oracle is able to 
optimize the querying by using the structures in the XML-Schema. And for 
that purpose, replacing the "sequence" with "choice" is not a problem.

I don't know if comparing the results with other products is a reason to 
say that your work is done right.
You should always follow the standard in your analyses, before you 
declare one product buggy and another not.

There is a message on Oracle forum, similar symptoms - 
https://community.oracle.com/message/10778556

I see in that message that there was a patch recommended, did you try 
that? Always use the latest patch level.

>
>
> Ok, I'll try 12c this night, thanks.
Maybe on success, you are able to change the business requirement.

good luck.

Bert

OpenEHR and Oracle XML DB problems

[Dmitry Baranov]

Sorry Bert ) I had to explain that Oracle 11 is a business requirement, not a 
hardware limitation.

> Just do it, and then it should run fine, although you have to change the
> XML-Schemas (a bit) before registering them to Oracle. I already
> explained to you before what and why.

I remember your advise but not sure that changing all the sequences to choices 
is a right way for many reasons. And I'm almost sure that it's an Oracle bug 
since other XSD validation tools (visual studio, netbeans and eclipse) say that 
my instance files are all OK and conform to XML schema.

There is a message on Oracle forum, similar symptoms - 
https://community.oracle.com/message/10778556


Ok, I'll try 12c this night, thanks.

--
Regards, Dmitry

OpenEHR and Oracle XML DB problems

[Dmitry Baranov]

Hi everyone,

According Bert experience 
(https://www.linkedin.com/groups/Choice-OpenEHR-persistence-layer-144276.S.208531138),
 one must not try to adopt OpenEHR model to relational storage since almost all 
popular database engines able to process native XML.

So I'm experimenting with Oracle XML DB for almost two weeks, and I'm in 
despair and kindly ask you for help.

Here is a Github repository where I've collected few files - 
https://github.com/da-baranov/openehr-ora :
1) EHR.xsd - flattened OpenEHR XML schema
2) regschema.sql - a script that creates an Oracle directory where test files 
should be copied to, registers XML schema and creates a table with 
XML-schema-based column that matches global "version" element
3) composition_1191_0.xml, composition_1322_0.xml and composition_1531_0.xml 
are test instance files which I borrowed from Pablo Pazos github 
(https://github.com/ppazos/cabolabs-emrapp)
4) I'm using Oracle 11.2.0.2.0 Express (for some reasons can't use 12c). The 
key problem is that Oracle rejects all the instance files producing the 
following error:

insert into versions(x) 
values(
  xmltype(
bfilename('OPENEHR', 'composition_1531_0.xml'),
NLS_CHARSET_ID('AL32UTF8')
  )
)
-
ORA-31079: unable to resolve reference to type "COMPOSITION"
-

5) In other cases I faced same error also related to abstract XML type 
resolution with xsi:type: "ORA-31079: unable to resolve reference to type 
"xsd:string"". Although all XML schema namespaces were OK and Visual Studio 
schema validator gives no errors.

Where am I wrong?


-- 
Regards, Dmitry

OpenEHR and Oracle XML DB problems

[Bert Verhees]

On 15-04-15 15:47, Dmitry Baranov wrote:
> Hi everyone,
>
> According Bert experience 
> (https://www.linkedin.com/groups/Choice-OpenEHR-persistence-layer-144276.S.208531138),
>  one must not try to adopt OpenEHR model to relational storage since almost 
> all popular database engines able to process native XML.
>
> So I'm experimenting with Oracle XML DB for almost two weeks, and I'm in 
> despair and kindly ask you for help.
>
> Here is a Github repository where I've collected few files - 
> https://github.com/da-baranov/openehr-ora :
> 1) EHR.xsd - flattened OpenEHR XML schema
> 2) regschema.sql - a script that creates an Oracle directory where test files 
> should be copied to, registers XML schema and creates a table with 
> XML-schema-based column that matches global "version" element
> 3) composition_1191_0.xml, composition_1322_0.xml and composition_1531_0.xml 
> are test instance files which I borrowed from Pablo Pazos github 
> (https://github.com/ppazos/cabolabs-emrapp)
> 4) I'm using Oracle 11.2.0.2.0 Express (for some reasons can't use 12c). The 
> key problem is that Oracle rejects all the instance files producing the 
> following error:
>
> insert into versions(x)
> values(
>xmltype(
>  bfilename('OPENEHR', 'composition_1531_0.xml'),
>  NLS_CHARSET_ID('AL32UTF8')
>)
> )
> -
> ORA-31079: unable to resolve reference to type "COMPOSITION"
> -
>
> 5) In other cases I faced same error also related to abstract XML type 
> resolution with xsi:type: "ORA-31079: unable to resolve reference to type 
> "xsd:string"". Although all XML schema namespaces were OK and Visual Studio 
> schema validator gives no errors.
>
> Where am I wrong?
>
>
Looks like a namespace-problem. I cannot judge that without seeing your 
XML Schema and XML-file.
And I am not going to look at them. Sorry for sounding harsh, but I am 
not an Oracle specialist.

I use Oracle 12c, so I cannot advise you with your Oracle-version.
You should use 12c, it cannot be an hardware issue.
I have run Oracle 12c on a cheap netbook, with 4G memory.
So, my advise, buy another machine, a cheap one, let it be dedicated for 
Oracle. For developing purpose I have an old Lenovo desktop-machine, I 
bought for 100 Euro as Oracle server.
For demo purpose, as explained, that netbook, runs like hell on both.
For production, of course you need something else.

Install Oracle Linux, Oracle fits best on Oracle Linux.

Just do it, and then it should run fine, although you have to change the 
XML-Schemas (a bit) before registering them to Oracle. I already 
explained to you before what and why.

Anyway, your error-situation may become less ambiguous.

Bert