Re: Parsing of Archetypes/Templates

[Bert Verhees]

On 12-11-18 18:40, Bert Verhees wrote:

>> Another very important restriction for using XML Schema, in my opinion,
>> is that you cannot have two or more elements with the same name but a
>> different data type. This data type must be in detail the same. XML Schema
>> regards an Element with a Dv_Text as a different datatype from an Element
>> with a Dv_CodedText.
>>
>> Both elements will be called "items" in an XML schema representing an
>> OpenEhr data structure, and thus is not allowed having them different
>> details in data types.


This already happens in a Item-List, so the constraint is quite easy to 
trigger.



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Re: Parsing of Archetypes/Templates

[Bert Verhees]

On 12-11-18 17:59, Thomas Beale wrote:



On 12/11/2018 16:04, Bert Verhees wrote:

On 12-11-18 16:13, Thomas Beale wrote:
you can, it's called a Template Data Schema (TDS), and is generated 
from the Template Designer and I think the new Marand ADL-designer. 
Its intended exactly for checking data sets...


Of course you can write any validation tool you want,  but you cannot 
do this and still conform to the XML Schema standard, that is why 
Schematron became important. With Schematron you can validate 
anything. As I wrote this morning, LinkEhr also generates Schematron 
for validation purpose.


this already works (for nearly 10 years) and it validates against the 
XML schema standard. What it doesn't do is validate everything you 
want to validate, i.e. not all things in the archetypes. But it's good 
enough most of the time.



I am in the proud possession of the book, "Definitive XML Schema 1.1" by 
Priscilla Walmsley. We had this discussion a few times already

I quote from
https://www.mail-archive.com/search?q=walmsley=openehr-technical%40lists.openehr.org
https://www.mail-archive.com/openehr-technical@lists.openehr.org/msg07405.html


Another very important restriction for using XML Schema, in my opinion,
is that you cannot have two or more elements with the same name but a
different data type. This data type must be in detail the same. XML Schema
regards an Element with a Dv_Text as a different datatype from an Element
with a Dv_CodedText.

Both elements will be called "items" in an XML schema representing an
OpenEhr data structure, and thus is not allowed having them different
details in data types.


Sorry for the funny font,

To do things properly, I agree, you would probably use Schematron + 
XSD, or personally I have always thought that Schematron + Relax-NG 
would be better.


Also I went through that path, with Relax NG, I struggled quite some 
time with this, and not me alone. Ask Diego why LinkEhr does not export 
RelaxNG or XML Schema but Schematron as validation files (although, it 
was like this a few years ago, it still is so in the version I have).


The XSD standard-constraint mentioned above also becomes visible with 
standard XML libraries. If I would have time I would proof it to you in 
a simple way.




whether this is the real requirement being talked about here may be 
another question.


You are right, it was not what was asked, still I thought it would be 
interesting for others to know that there is a JSON Schematron parser 
(instead of an XML Schematron-parser), which can be used to validate 
JSON OpenEhr-datasets against archetypes/templates.


that might be an interesting thing to have in the openEHR toolkit. We 
are just now revising and re-organising all the openEHR XSDs, and also 
adding in some JSON-schemas. Any related artefacts that anyone wants 
to contribute, or fragments that could be used in something larger 
would be appreciated - it will all get posted in the 
specifications-ITS-XML git repo under the usual CC licence.


OpenEhr uses XSD schemas for class descriptions, there is no problem at 
all. It is even an often used methodology in the Java world to 
describe/generate class-interfaces. The problem is when using XML Schema 
for validation of archetyped XML-data. But again, this was not the 
problem the question was initially about. Sorry for the confusion.


Bert


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Re: Parsing of Archetypes/Templates

[Bert Verhees]

On 12-11-18 16:13, Thomas Beale wrote:


On 12/11/2018 09:44, Bert Verhees wrote:


Sorry, I first replied to Pieter Bos only, now to the list. Pieter 
already replied to me that the question was not about XSD to check 
datasets was .


So, read my reply, for those interested in easy validating datasets:

It is possible to have an XSD to describe the AOM, but you cannot 
have an XSD to describe an archetype and check a dataset with it.


you can, it's called a Template Data Schema (TDS), and is generated 
from the Template Designer and I think the new Marand ADL-designer. 
Its intended exactly for checking data sets...


Of course you can write any validation tool you want,  but you cannot do 
this and still conform to the XML Schema standard, that is why 
Schematron became important. With Schematron you can validate anything. 
As I wrote this morning, LinkEhr also generates Schematron for 
validation purpose.




whether this is the real requirement being talked about here may be 
another question.


You are right, it was not what was asked, still I thought it would be 
interesting for others to know that there is a JSON Schematron parser 
(instead of an XML Schematron-parser), which can be used to validate 
JSON OpenEhr-datasets against archetypes/templates.


I wrote an AOM(OpenEhr/CEN13606)-Schematron-validation-generator years 
ago, exactly for this reason, I must have the sourcecode somewhere. Good 
for Marand to have validation too, because checking data-sets before 
storing them is an important responsibility of an OpenEhr-kernel.


Bert



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Re: Parsing of Archetypes/Templates

[Thomas Beale]

On 12/11/2018 16:04, Bert Verhees wrote:

On 12-11-18 16:13, Thomas Beale wrote:
you can, it's called a Template Data Schema (TDS), and is generated 
from the Template Designer and I think the new Marand ADL-designer. 
Its intended exactly for checking data sets...


Of course you can write any validation tool you want,  but you cannot 
do this and still conform to the XML Schema standard, that is why 
Schematron became important. With Schematron you can validate 
anything. As I wrote this morning, LinkEhr also generates Schematron 
for validation purpose.


this already works (for nearly 10 years) and it validates against the 
XML schema standard. What it doesn't do is validate everything you want 
to validate, i.e. not all things in the archetypes. But it's good enough 
most of the time.


To do things properly, I agree, you would probably use Schematron + XSD, 
or personally I have always thought that Schematron + Relax-NG would be 
better.




whether this is the real requirement being talked about here may be 
another question.


You are right, it was not what was asked, still I thought it would be 
interesting for others to know that there is a JSON Schematron parser 
(instead of an XML Schematron-parser), which can be used to validate 
JSON OpenEhr-datasets against archetypes/templates.


that might be an interesting thing to have in the openEHR toolkit. We 
are just now revising and re-organising all the openEHR XSDs, and also 
adding in some JSON-schemas. Any related artefacts that anyone wants to 
contribute, or fragments that could be used in something larger would be 
appreciated - it will all get posted in the specifications-ITS-XML git 
repo under the usual CC licence.


--
Thomas Beale
Principal, Ars Semantica 
Consultant, ABD Project, Intermountain Healthcare 

Management Board, Specifications Program Lead, openEHR Foundation 

Chartered IT Professional Fellow, BCS, British Computer Society 

Health IT blog  | Culture blog 
 | The Objective Stance 

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Re: Parsing of Archetypes/Templates

[Thomas Beale]

On 12/11/2018 09:44, Bert Verhees wrote:


Sorry, I first replied to Pieter Bos only, now to the list. Pieter 
already replied to me that the question was not about XSD to check 
datasets was .


So, read my reply, for those interested in easy validating datasets:

It is possible to have an XSD to describe the AOM, but you cannot have 
an XSD to describe an archetype and check a dataset with it.


you can, it's called a Template Data Schema (TDS), and is generated from 
the Template Designer and I think the new Marand ADL-designer. Its 
intended exactly for checking data sets...


whether this is the real requirement being talked about here may be 
another question.


- thomas



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Re: Parsing of Archetypes/Templates

[Pieter Bos]

Yes, https://github.com/openEHR/java-libs works for ADL 1.4.

If you want the latest and newest, ADL 2 is the way to go. You can convert the 
archetypes to ADL 2 using the ADL workbench and they will parse with Archie. 
The workbench can be found at http://www.openehr.org.

If you want compatibility with existing systems, ADL 1.4 for now – I think most 
EHRs are 1.4 only at the moment.

Regards,

Pieter Bos

From: openEHR-technical  on behalf 
of Diego Boscá 
Reply-To: For openEHR technical discussions 

Date: Monday, 12 November 2018 at 13:44
To: For openEHR technical discussions 
Subject: Re: Parsing of Archetypes/Templates

Hello Georg,

Archie is meant to be used with ADL2 archetypes, if you want to parse 1.4 
archetypes I think java implementation you mentioned before is your current 
best option.

Regards

El lun., 12 nov. 2018 a las 13:40, Georg Fette 
(mailto:georg.fe...@uni-wuerzburg.de>>) escribió:
Hi Peter,
The Archie-Toolkit looks promising.

I tried to parse one of the archetypes from the CKM (BloodPressure) and
tried to parse the exported ADL. However, I got a Exception when trying
this because the exported ADL does not seem to be parseable:
line 1:24 mismatched input '1.4' expecting VERSION_ID
line 2:1 mismatched input 'openEHR-EHR-OBSERVATION.blood_pressure.v1'
expecting ARCHETYPE_HRID

With the exported XML and the try to unmarshal the XML with the JAXBUtil
I also did not succeed. Is there somewhere a testcase were I can see a
working example of a parsed ADL String ?

Greetings
Georg

Hello George,

If you are looking for something to handle ADL 2 archetypes - the most
recent version -, have a look at https://github.com/opener/archie . It
is a java library that can parse archetypes, flatten and validate  them,
create operational templates and more.

Are you using the openehr reference model, or something else like fihr?

Although Archie can parse and serialize archetypes in XML, archetypes
are usually stored as ADL. This is a custom more readable format. Of
course you can then easily convert it to XML or Json to work with them
in other tools where you do not have an ADL parser ready.

Note that for ADL 2 as far as I know there is no official XSD released
yet, so it is possible you run into compatibility problems with XML. For
ADL 1.4 this is not a problem.

Regards,

Pieter Bos

Am 12.11.2018 um 09:18 schrieb Georg Fette:
> Hello,
> For a project we want to create a generic mechanism to transform
> archetypes into FHIR Logical Models, so we can store, retrieve and
> query archetype instance with FHIR tools (CQL, FHIR-REST-API-query).
> At the moment we just want to read/write archetypes and not archetype
> instances. We are looking for existing components to parse and process
> archetypes. I have some questions I encountered related to these issues:
> - I have found several projects that store openEHR-data (archetypes as
> well as archetype instances) into different data substrates (Neo4J,
> ARM (archetype relational mapping), EtherCIS). Although I have not yet
> looked at the code of these projects I assume that they take an
> archetype XML-file, parse it and thus create a runtime object of the
> archetype. That runtime object can then be given as a parameter to a
> persistence layer (e.g. JOOQ, Hibernate, etc.). In order to reuse
> something from already existing projects I am looking for a parser
> that creates a runtime object from an archetype-XML-String, so we can
> write our own components that transform it into a FHIR runtime object.
> The component we are looking for should preferably be written in Java,
> as this is our language of choice in our project.
> - I am not ye sure if we are looking for a method to transform
> archetypes, templates or operational templates into FHIR related
> structures, as I am not yet that familiar with which data structure is
> preferably used for which kind of task. Therefore, component that,
> instead of archetypes, parse templates or operational templates would
> be appreciated as well.
> Greetings
> Georg
>

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-
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Universität WürzburgTel.: +49-(0)931-31-85516
Am Hubland  Fax.: +49-(0)931-31-86732
97074 Würzburg  mail: 
georg.fe...@uni-wuerzburg.de
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Re: Parsing of Archetypes/Templates

[Diego Boscá]

Hello Georg,

Archie is meant to be used with ADL2 archetypes, if you want to parse 1.4
archetypes I think java implementation you mentioned before is your current
best option.

Regards

El lun., 12 nov. 2018 a las 13:40, Georg Fette (<
georg.fe...@uni-wuerzburg.de>) escribió:

> Hi Peter,
> The Archie-Toolkit looks promising.
>
> I tried to parse one of the archetypes from the CKM (BloodPressure) and
> tried to parse the exported ADL. However, I got a Exception when trying
> this because the exported ADL does not seem to be parseable:
> line 1:24 mismatched input '1.4' expecting VERSION_ID
> line 2:1 mismatched input 'openEHR-EHR-OBSERVATION.blood_pressure.v1'
> expecting ARCHETYPE_HRID
>
> With the exported XML and the try to unmarshal the XML with the JAXBUtil
> I also did not succeed. Is there somewhere a testcase were I can see a
> working example of a parsed ADL String ?
>
> Greetings
> Georg
>
> Hello George,
>
> If you are looking for something to handle ADL 2 archetypes - the most
> recent version -, have a look at https://github.com/opener/archie . It
> is a java library that can parse archetypes, flatten and validate  them,
> create operational templates and more.
>
> Are you using the openehr reference model, or something else like fihr?
>
> Although Archie can parse and serialize archetypes in XML, archetypes
> are usually stored as ADL. This is a custom more readable format. Of
> course you can then easily convert it to XML or Json to work with them
> in other tools where you do not have an ADL parser ready.
>
> Note that for ADL 2 as far as I know there is no official XSD released
> yet, so it is possible you run into compatibility problems with XML. For
> ADL 1.4 this is not a problem.
>
> Regards,
>
> Pieter Bos
>
> Am 12.11.2018 um 09:18 schrieb Georg Fette:
> > Hello,
> > For a project we want to create a generic mechanism to transform
> > archetypes into FHIR Logical Models, so we can store, retrieve and
> > query archetype instance with FHIR tools (CQL, FHIR-REST-API-query).
> > At the moment we just want to read/write archetypes and not archetype
> > instances. We are looking for existing components to parse and process
> > archetypes. I have some questions I encountered related to these issues:
> > - I have found several projects that store openEHR-data (archetypes as
> > well as archetype instances) into different data substrates (Neo4J,
> > ARM (archetype relational mapping), EtherCIS). Although I have not yet
> > looked at the code of these projects I assume that they take an
> > archetype XML-file, parse it and thus create a runtime object of the
> > archetype. That runtime object can then be given as a parameter to a
> > persistence layer (e.g. JOOQ, Hibernate, etc.). In order to reuse
> > something from already existing projects I am looking for a parser
> > that creates a runtime object from an archetype-XML-String, so we can
> > write our own components that transform it into a FHIR runtime object.
> > The component we are looking for should preferably be written in Java,
> > as this is our language of choice in our project.
> > - I am not ye sure if we are looking for a method to transform
> > archetypes, templates or operational templates into FHIR related
> > structures, as I am not yet that familiar with which data structure is
> > preferably used for which kind of task. Therefore, component that,
> > instead of archetypes, parse templates or operational templates would
> > be appreciated as well.
> > Greetings
> > Georg
> >
>
> --
> -
> Dipl.-Inf. Georg Fette  Raum: B001
> Universität WürzburgTel.: +49-(0)931-31-85516
> Am Hubland  Fax.: +49-(0)931-31-86732
> 97074 Würzburg  mail: georg.fe...@uni-wuerzburg.de
> -
>
>
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Re: Parsing of Archetypes/Templates

[Georg Fette]

Hi Peter,
The Archie-Toolkit looks promising.

I tried to parse one of the archetypes from the CKM (BloodPressure) and 
tried to parse the exported ADL. However, I got a Exception when trying 
this because the exported ADL does not seem to be parseable:

line 1:24 mismatched input '1.4' expecting VERSION_ID
line 2:1 mismatched input 'openEHR-EHR-OBSERVATION.blood_pressure.v1' 
expecting ARCHETYPE_HRID


With the exported XML and the try to unmarshal the XML with the JAXBUtil 
I also did not succeed. Is there somewhere a testcase were I can see a 
working example of a parsed ADL String ?


Greetings
Georg

Hello George,

If you are looking for something to handle ADL 2 archetypes - the most 
recent version -, have a look at https://github.com/opener/archie . It 
is a java library that can parse archetypes, flatten and validate  them, 
create operational templates and more.


Are you using the openehr reference model, or something else like fihr?

Although Archie can parse and serialize archetypes in XML, archetypes 
are usually stored as ADL. This is a custom more readable format. Of 
course you can then easily convert it to XML or Json to work with them 
in other tools where you do not have an ADL parser ready.


Note that for ADL 2 as far as I know there is no official XSD released 
yet, so it is possible you run into compatibility problems with XML. For 
ADL 1.4 this is not a problem.


Regards,

Pieter Bos

Am 12.11.2018 um 09:18 schrieb Georg Fette:

Hello,
For a project we want to create a generic mechanism to transform 
archetypes into FHIR Logical Models, so we can store, retrieve and 
query archetype instance with FHIR tools (CQL, FHIR-REST-API-query). 
At the moment we just want to read/write archetypes and not archetype 
instances. We are looking for existing components to parse and process 
archetypes. I have some questions I encountered related to these issues:
- I have found several projects that store openEHR-data (archetypes as 
well as archetype instances) into different data substrates (Neo4J, 
ARM (archetype relational mapping), EtherCIS). Although I have not yet 
looked at the code of these projects I assume that they take an 
archetype XML-file, parse it and thus create a runtime object of the 
archetype. That runtime object can then be given as a parameter to a 
persistence layer (e.g. JOOQ, Hibernate, etc.). In order to reuse 
something from already existing projects I am looking for a parser 
that creates a runtime object from an archetype-XML-String, so we can 
write our own components that transform it into a FHIR runtime object. 
The component we are looking for should preferably be written in Java, 
as this is our language of choice in our project.
- I am not ye sure if we are looking for a method to transform 
archetypes, templates or operational templates into FHIR related 
structures, as I am not yet that familiar with which data structure is 
preferably used for which kind of task. Therefore, component that, 
instead of archetypes, parse templates or operational templates would 
be appreciated as well.

Greetings
Georg



--
-
Dipl.-Inf. Georg Fette  Raum: B001
Universität WürzburgTel.: +49-(0)931-31-85516
Am Hubland  Fax.: +49-(0)931-31-86732
97074 Würzburg  mail: georg.fe...@uni-wuerzburg.de
-


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Re: Parsing of Archetypes/Templates

[Bert Verhees]

Sorry, I first replied to Pieter Bos only, now to the list. Pieter 
already replied to me that the question was not about XSD to check 
datasets was .


So, read my reply, for those interested in easy validating datasets:

It is possible to have an XSD to describe the AOM, but you cannot have 
an XSD to describe an archetype and check a dataset with it.


Archetypes can have logical constructs which are not allowed in XSD. It 
has to do with elements with the same name on the same level, that is 
not allowed in XSD, even not when there are different attributes.


You can use Schematron to check an archetyped XML dataset. I believe the 
LinkEHR editor generates such Schematrons.


I also found Schematron validator for JSON, I think that this is very 
interesting for some kernel software developers, because XML is slowly 
becoming something of an previous era.


https://www.npmjs.com/package/jsontron

Good luck with it.

Bert.

On 12-11-18 09:30, Pieter Bos wrote:

Hello George,

If you are looking for something to handle ADL 2 archetypes - the most 
recent version -, have a look at https://github.com/opener/archie . It 
is a java library that can parse archetypes, flatten and validate  
them, create operational  templates and more.


Are you using the openehr reference model, or something else like fihr?

Although Archie can parse and serialize archetypes in XML, archetypes 
are usually stored as ADL. This is a custom more readable format. Of 
course you can then easily convert it to XML or Json to work with them 
in other tools where you do not have an ADL parser ready.


Note that for ADL 2 as far as I know there is no official XSD released 
yet, so it is possible you run into compatibility problems with XML. 
For ADL 1.4 this is not a problem.


Regards,

Pieter Bos


Op 12 nov. 2018 09:18 schreef Georg Fette :
Hello,
For a project we want to create a generic mechanism to transform
archetypes into FHIR Logical Models, so we can store, retrieve and query
archetype instance with FHIR tools (CQL, FHIR-REST-API-query). At the
moment we just want to read/write archetypes and not archetype
instances. We are looking for existing components to parse and process
archetypes. I have some questions I encountered related to these issues:
- I have found several projects that store openEHR-data (archetypes as
well as archetype instances) into different data substrates (Neo4J, ARM
(archetype relational mapping), EtherCIS). Although I have not yet
looked at the code of these projects I assume that they take an
archetype XML-file, parse it and thus create a runtime object of the
archetype. That runtime object can then be given as a parameter to a
persistence layer (e.g. JOOQ, Hibernate, etc.). In order to reuse
something from already existing projects I am looking for a parser that
creates a runtime object from an archetype-XML-String, so we can write
our own components that transform it into a FHIR runtime object. The
component we are looking for should preferably be written in Java, as
this is our language of choice in our project.
- I am not ye sure if we are looking for a method to transform
archetypes, templates or operational templates into FHIR related
structures, as I am not yet that familiar with which data structure is
preferably used for which kind of task. Therefore, component that,
instead of archetypes, parse templates or operational templates would be
appreciated as well.
Greetings
Georg

--
-
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Universität Würzburg    Tel.: +49-(0)931-31-85516
Am Hubland  Fax.: +49-(0)931-31-86732
97074 Würzburg  mail: georg.fe...@uni-wuerzburg.de
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Re: Parsing of Archetypes/Templates

[Pieter Bos]

Hello George,

If you are looking for something to handle ADL 2 archetypes - the most recent 
version -, have a look at https://github.com/opener/archie . It is a java 
library that can parse archetypes, flatten and validate  them, create 
operational  templates and more.

Are you using the openehr reference model, or something else like fihr?

Although Archie can parse and serialize archetypes in XML, archetypes are 
usually stored as ADL. This is a custom more readable format. Of course you can 
then easily convert it to XML or Json to work with them in other tools where 
you do not have an ADL parser ready.

Note that for ADL 2 as far as I know there is no official XSD released yet, so 
it is possible you run into compatibility problems with XML. For ADL 1.4 this 
is not a problem.

Regards,

Pieter Bos


Op 12 nov. 2018 09:18 schreef Georg Fette :
Hello,
For a project we want to create a generic mechanism to transform
archetypes into FHIR Logical Models, so we can store, retrieve and query
archetype instance with FHIR tools (CQL, FHIR-REST-API-query). At the
moment we just want to read/write archetypes and not archetype
instances. We are looking for existing components to parse and process
archetypes. I have some questions I encountered related to these issues:
- I have found several projects that store openEHR-data (archetypes as
well as archetype instances) into different data substrates (Neo4J, ARM
(archetype relational mapping), EtherCIS). Although I have not yet
looked at the code of these projects I assume that they take an
archetype XML-file, parse it and thus create a runtime object of the
archetype. That runtime object can then be given as a parameter to a
persistence layer (e.g. JOOQ, Hibernate, etc.). In order to reuse
something from already existing projects I am looking for a parser that
creates a runtime object from an archetype-XML-String, so we can write
our own components that transform it into a FHIR runtime object. The
component we are looking for should preferably be written in Java, as
this is our language of choice in our project.
- I am not ye sure if we are looking for a method to transform
archetypes, templates or operational templates into FHIR related
structures, as I am not yet that familiar with which data structure is
preferably used for which kind of task. Therefore, component that,
instead of archetypes, parse templates or operational templates would be
appreciated as well.
Greetings
Georg

--
-
Dipl.-Inf. Georg Fette  Raum: B001
Universität WürzburgTel.: +49-(0)931-31-85516
Am Hubland  Fax.: +49-(0)931-31-86732
97074 Würzburg  mail: georg.fe...@uni-wuerzburg.de
-


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Parsing of Archetypes/Templates

[Georg Fette]

Hello,
For a project we want to create a generic mechanism to transform 
archetypes into FHIR Logical Models, so we can store, retrieve and query 
archetype instance with FHIR tools (CQL, FHIR-REST-API-query). At the 
moment we just want to read/write archetypes and not archetype 
instances. We are looking for existing components to parse and process 
archetypes. I have some questions I encountered related to these issues:
- I have found several projects that store openEHR-data (archetypes as 
well as archetype instances) into different data substrates (Neo4J, ARM 
(archetype relational mapping), EtherCIS). Although I have not yet 
looked at the code of these projects I assume that they take an 
archetype XML-file, parse it and thus create a runtime object of the 
archetype. That runtime object can then be given as a parameter to a 
persistence layer (e.g. JOOQ, Hibernate, etc.). In order to reuse 
something from already existing projects I am looking for a parser that 
creates a runtime object from an archetype-XML-String, so we can write 
our own components that transform it into a FHIR runtime object. The 
component we are looking for should preferably be written in Java, as 
this is our language of choice in our project.
- I am not ye sure if we are looking for a method to transform 
archetypes, templates or operational templates into FHIR related 
structures, as I am not yet that familiar with which data structure is 
preferably used for which kind of task. Therefore, component that, 
instead of archetypes, parse templates or operational templates would be 
appreciated as well.

Greetings
Georg

--
-
Dipl.-Inf. Georg Fette  Raum: B001
Universität WürzburgTel.: +49-(0)931-31-85516
Am Hubland  Fax.: +49-(0)931-31-86732
97074 Würzburg  mail: georg.fe...@uni-wuerzburg.de
-


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