Re: Archie version 0.6.0 released

[Seref Arikan]

Thank you. Please see inline

On Tue, Feb 12, 2019 at 7:02 PM Pieter Bos  wrote:

> I mean OPT2, which is according to the ooenehr specifications a flattened
> archetype with extra operations performed on it, such as including and
> flattening all archetype roots in the same tree, including their
> terminologies,and replacing all use_node with a copy of the tree to be
> used. Very useful. Can be expressed in ADL.
>
I did not realise that opt2 was fully defined. I thought it was ongoing
work. I'll have to go and check it now :)

>
> Archie does not support the 1.4 xml OPT format.
>
Thanks for the clarification.

>
> Note that xml bindings are in place for the AOM, but I wouldn't use them
> for interoperability because they were written before an official xsd has
> been published - I'm actually not sure if an official AOM 2 xsd currently
> exists.
>
Could you please clarify which official XSD you're referring to? AOM2?

>
> Note that there is also the concept of a template, which is also an
> archetype, but is different from an operational template - templates are
> authored, opts are generated, often generated from a template.
>
Hmm. I guess this means opts lose some information regarding their lineage.

>
> Regards,
>

thanks a lot for the detailed response.

All the best
Seref


> Pieter Bos
>
> Op 12 feb. 2019 19:12 schreef Seref Arikan <
> serefari...@kurumsalteknoloji.com>:
>
> Hi Pieter,
>
> Excellent work, many thanks for all the effort your team put into this
> library. Could you clarify something? When you say an operational template,
> do you mean a flattened archetype as per ADL 2.0? (that's the impression I
> got looking at the code)
>
> I'm a bit behind re adl 2.0; does your implementation imply that an opt
> according to 2.0 specs is no different than an archetype? I can see that
> you declared some xml bindings in your OperationalTemplate class which seam
> to refer to type names from opt 1.4 .
>
> In summary I'm a bit confused :) Could you briefly explain how Archie team
> sees the relationship between opt 1.4 and 2.0 ?
>
> All the best
> Seref
>
>
> On Tue, Feb 12, 2019 at 1:04 PM Pieter Bos  wrote:
>
> Today I’m pleased to announce another major release of the Archie library.
> This release brings a number of new features and improvements:
>
>
>
>- A tool that constructs valid json example instances of RM Objects,
>based on an operational template. Can be parsed to RM Objects.
>- Native ODIN serialization of arbitrary java objects using the
>Jackson library, now used in Archetype and P_BMM serialization
>- The library is now supported on Android, Android 8.0/API level 26
>and higher, including faster initialization time
>- The RM implementation has been verified against the 1.0.4 BMM
>models, and fixed where needed
>- A complete rewrite of the P_BMM implementation, with improved
>validation. The new implementation is much easier to understand and 
> maintain
>
>
>
> Because of the last two features, this version may require some changes to
> your existing code. For more information, see
> https://github.com/openEHR/archie/releases/tag/0.6.0 and the readme.
>
>
>
> Regards,
>
>
>
> Pieter Bos
>
> Nedap Healthcare
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Re: Archie version 0.6.0 released

[Seref Arikan]

Hi Pieter,

Excellent work, many thanks for all the effort your team put into this
library. Could you clarify something? When you say an operational template,
do you mean a flattened archetype as per ADL 2.0? (that's the impression I
got looking at the code)

I'm a bit behind re adl 2.0; does your implementation imply that an opt
according to 2.0 specs is no different than an archetype? I can see that
you declared some xml bindings in your OperationalTemplate class which seam
to refer to type names from opt 1.4 .

In summary I'm a bit confused :) Could you briefly explain how Archie team
sees the relationship between opt 1.4 and 2.0 ?

All the best
Seref


On Tue, Feb 12, 2019 at 1:04 PM Pieter Bos  wrote:

> Today I’m pleased to announce another major release of the Archie library.
> This release brings a number of new features and improvements:
>
>
>
>- A tool that constructs valid json example instances of RM Objects,
>based on an operational template. Can be parsed to RM Objects.
>- Native ODIN serialization of arbitrary java objects using the
>Jackson library, now used in Archetype and P_BMM serialization
>- The library is now supported on Android, Android 8.0/API level 26
>and higher, including faster initialization time
>- The RM implementation has been verified against the 1.0.4 BMM
>models, and fixed where needed
>- A complete rewrite of the P_BMM implementation, with improved
>validation. The new implementation is much easier to understand and 
> maintain
>
>
>
> Because of the last two features, this version may require some changes to
> your existing code. For more information, see
> https://github.com/openEHR/archie/releases/tag/0.6.0 and the readme.
>
>
>
> Regards,
>
>
>
> Pieter Bos
>
> Nedap Healthcare
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Re: query writing question 2

[Seref Arikan]

You are way more technical than just a consumer of AQL, so you may consider
adopting semantics from XQuery/XPath/Sparql. It would not really leave you
a million miles from the current AQL semantics. I'll leave it at that since
this is not a technical list as far as I my understanding goes. Feel free
to re-initiate discussion under technical list if you have comments (goes
for everyone) :)

All the best
Seref


On Wed, Oct 10, 2018 at 8:24 PM Pablo Pazos 
wrote:

>
>
> On Wed, Oct 10, 2018, 07:10 David Moner  wrote:
>
>>
>>
>> El mié., 10 oct. 2018 a las 11:52, Seref Arikan (<
>> serefari...@kurumsalteknoloji.com>) escribió:
>>
>>>
>>> Obligatory moaning for the millionth time: All of this confusion stems
>>> from lack of a formal model defining AQL semantics. I used tree pattern
>>> queries in my research so I can use those to explain aql, but as it stands
>>> the standard we have does not have this so users will keep getting
>>> confused.
>>>
>>>>
>>>>
>> This. A query language is more than just a syntax. And probably we don't
>> need to invent different behaviors than technologies that already work
>> (XPath/XQuery, for example)
>>
>
> That is exactly why I didn't implement AQL yet, the spec should include
> syntax, behavior, semantics and result sets defined. And lots of examples
> of those things combined. Because impregnada should include parser+engine
> and the parser is the simple part. Until we have that all implementations
> will have differences when querying the same database.
>
>
>> --
>> David Moner Cano
>>
>> Web: http://www.linkedin.com/in/davidmoner
>> Twitter: @davidmoner
>> Skype: davidmoner
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>>
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Re: query writing question 2

[Seref Arikan]

That query does not look valid to me. There is no 'b' that is defined in
the FROM clause. Once an alias for a node is created in the FROM clause, as
in COMPOSITION a[..] the alias 'a' in the FROM and WHERE clauses refers to
the same matching data node.

I would not assume anything based on the query you've given because that
query is invalid as far as I can see.

On Mon, Oct 8, 2018 at 7:06 PM Georg Fette 
wrote:

> Hello,
> I have another question concerning the semantics of AQL queries:
> In the documentation there are queries of the form
> SELECT a/data[at0001]/items[at0004]/value
> FROM EHR e CONTAINS COMPOSITION a[openEHR-EHR-COMPOSITION.encounter.v1]
> WHERE b/data[at0001]/items[at0004]/value/value >= 140
> What ensures that the identified path in the SELECT section references
> the same data instances that are contrained with the same identified
> path in the WHERE section ? It could be argued that there is only one
> "data[at0001]" in "b" and only one "items[at0004]" in "a/data[at0001]"
> and so on. But is this already the full explanation for the expression
> to be unambiguous ? The aliases used in queries (e.g. "a") ensures that
> a reference to an alias definitely means the same instance. Looking at
> queries like the one above let assume that aliases are only syntactic
> sugar and are not functionally needed. Is this correct ?
> 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: AQL query writing question

[Seref Arikan]

Given the AQL syntax and its current specifications, nothing stops you from
using the WHERE clause. However, you should consider the consequences of
using the WHERE clause to express that constraint.

if you'd like to express any other criteria such as a particular
DV_QUANTITY/magnitude value being greater than x (.../magnitude >= x) this
will go WHERE clause as well. Since multiple constraints in the WHERE
clause have to be connected by logical operators, you now have to write:

WHERE e/ehr_id/value = $ehrId AND c//magnitude >= x

so you'll have to express the implicitly stated (when you use
[ehr_id/value=..] AND condition explicitly and think about that logic. I'd
say it is possible that this will lead to bugs especially in complicated
AQL queries.

the second reason, which is pure speculation: is that some back ends are
likely to have mechanisms that process different constraints in an AQL
query in different ways. Pretty similar to query planners in relational
databases. The back end you're using may end up selecting all ehrs(!) and
then applying a filter due to ehr id constraint being in the WHERE clause.
This may or may not be the case, but I would not risk it.

Finally, to make things even more complicated, as per the predicates
section of aql spec (
https://www.openehr.org/releases/QUERY/latest/docs/AQL/AQL.html#_predicates
), there is nothing that stops you from moving a constraint in the WHERE
clause into the FROm clause (in some cases). Why? Because both archetype
and node predicates are syntactic sugar for standard predicate. So if you
have a standard predicate such as the dv_quantity example I gave you above,
you could move it into FROM clause as follows:

... COMPOSITION c[/bla/bla/bla/magnitude >= x] CONTAINS bla bla

But in that case you would not be able to express boolean operations where
the operands are constrains of the nodes in the FROM clause. That's why I
said in some cases above.

My suggestion: stick to conventions as much as you can, there is quite a
bit of flexibility in the AQL syntax and its semantics is not formally
defined (as in no formal backing model of queries and match operation etc)
and you don't want to fall into those cracks. You may get wrong results due
to interpretation differences between vendors and your queries may lose
portability.

All the best
Seref




On Mon, Oct 8, 2018 at 8:46 AM Georg Fette 
wrote:

> Hello,
> In the AQL documentation there is a query
>
> SELECT c/uid/value, instruction
> FROM EHR e[ehr_id/value=$ehrid]
> CONTAINS COMPOSITION c
> CONTAINS INSTRUCTION instruction[openEHR-EHR-INSTRUCTION.referral.v1]
> WHERE EXISTS
>
> instruction/links[target='ehr://32702/87284370-2D4B-4e3d-A3F3-F303D2F4F34B@latest_trunk_version
> ']
>
> When I reduce this query to
>
> SELECT e FROM EHR e[ehr_id/value=$ehrid]
>
> why is the constraint on the ehr_id done in the FROM section and not in
> the WHERE section like
>
> SELECT e
> FROM EHR e
> WHERE e/ehr_id/value = $ehrid
>
> Greetings
> Geirg
>
> --
> -
> 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: Announcing Archie version 0.4

[Seref Arikan]

Hi Peter,

Presumably via use of a transpiler or a bytecode to js/webassembly
compiler.

On Sat, Feb 3, 2018 at 10:56 AM, Peter Gummer 
wrote:

> On 1 Feb 2018, at 05:13, Thomas Beale  wrote:
>
> ... But the main interest is that we will be able to build new tools such
> as a Java/JS replacement for the ADL Workbench, and of course things like a
> high-quality, BMM-driven runtime archetype validating kernel for EHR
> systems, workflow implementations and many other components.
>
>
> Hi Thomas, does “JS” stand for JavaScript? If so, I don’t understand how
> Archie (written in Java, disappointingly) would enable JavaScript
> implementations. JavaScript has nothing in common with Java (apart from the
> name).
>
> Peter
>
>
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Re: Versioning implementations

[Seref Arikan]

Hi Danny,

You can unsubscribe from the same page you've subscribed.
http://www.openehr.org/community/mailinglists


On Mon, Aug 21, 2017 at 1:11 AM, Danny Nguyen <danny...@gmail.com> wrote:

> Dear All,
>
> Please remove me from this listserv.
>
> Best,
>
> Danny
>
> On Sat, Aug 19, 2017 at 6:18 AM Bert Verhees <bert.verh...@rosa.nl> wrote:
>
>> I agree that merging is (normally) only interesting for persistent
>> compositions, that are the only kind of compositions which are candidat for
>> simultaneously editing (branching), and then afterwards merging of the
>> branches is needed.
>>
>> I think, getting rid of the persistent compositions would solve these
>> problems. I don't see objections against medication-lists in normal
>> compositions. Maybe the persistent composition idea was something from the
>> old days to have all medications handy together?
>>
>> If that is so, than we can consider that this way of preordening  is not
>> anymore needed because modern systems can quickly find medication-entries,
>> and the extra advantage is that branching and merging is then also not
>> needed anymore.
>>
>> Best regards
>> Bert Verhees
>>
>> Op vr 18 aug. 2017 15:18 schreef Thomas Beale <thomas.be...@openehr.org>:
>>
>>>
>>> Naturally I am all for revising the specs (it's what we do ;) and
>>> throwing out dead stuff. But one thing I have realised over the years is
>>> that many of the scenarios (such as multi-system syncing) we thought of in
>>> the 1990s and early 200s are only just coming onto the radar now. Progress
>>> is much slower than many of us thought.
>>>
>>> Consequently, some types of implementation experience gained so far -
>>> particularly anything cross-enterprise or regional - is not going to be an
>>> indicator to the future. Of course, some kinds of experience, say with
>>> using the RM, or ADL 1.4, AQL etc, has been giving us all the feedback that
>>> we needed to make the updates we are currently making to the specifications.
>>>
>>> Probably what we should consider in this case is an update to the Change
>>> control spec that describes a variant or guideline for using the model to
>>> implement linear versioning, while allowing for later addition of branched
>>> versioning when/if needed.
>>>
>>> - thomas
>>>
>>> On 18/08/2017 12:49, Pablo Pazos wrote:
>>>
>>> From Thomas comments, it is clear that we have such last two use cases,
>>> internal versioning and cross-system versioning / sync / consolidation.
>>>
>>> Consider people here is talking about their own experience with the
>>> specs under the use case they implemented. We can argue that internal
>>> versioning is needed in 100% of the implementations while cross-system is a
>>> much less implemented case. This doesn't mean that the current specs are
>>> not usable and useful in abstract, but we should contextualize the
>>> discussion by use case and by the frequency each is implemented.
>>>
>>>  For internal versioning it is clear that distributed versioning spec
>>> generate some friction at implementation time. IMO we need to address both
>>> use cases trying to minimize friction for new developers. That can improve
>>> the quality of the specs without print anything out.
>>>
>>> Also, I would like to hear more about implementations of both use cases
>>> and the challenges implementers had to really validate the idea of
>>> addressing both use cases explicitly in the specs.
>>>
>>> Cheers,
>>> Pablo.
>>>
>>>
>>> On Aug 18, 2017 5:39 AM, "Seref Arikan" <serefarikan@
>>> kurumsalteknoloji.com> wrote:
>>>
>>> I did not realise that this discussion reached the point of suggesting
>>> that distributed versioning is taken out from the specs. I have been
>>> designing and implementing lots of openEHR data syncing functionality which
>>> relies on the distributed versioning specifications. I have heaps of work
>>> pending, which will also use that part of the specs. I can tell you that
>>> the current specs have worked just fine for me so far and they are up to
>>> the same high quality as the rest of the specifications, so they are
>>> absolutely usable and useful.
>>>
>>> The challenges of distributed versioning does not eliminate the need for
>>> them, so I cannot agree with the suggestion to remove them.  Sure, move
>>

Re: Versioning implementations

[Seref Arikan]

I did not realise that this discussion reached the point of suggesting that
distributed versioning is taken out from the specs. I have been designing
and implementing lots of openEHR data syncing functionality which relies on
the distributed versioning specifications. I have heaps of work pending,
which will also use that part of the specs. I can tell you that the current
specs have worked just fine for me so far and they are up to the same high
quality as the rest of the specifications, so they are absolutely usable
and useful.

The challenges of distributed versioning does not eliminate the need for
them, so I cannot agree with the suggestion to remove them.  Sure, move
them around in the specs all you want, but please keep them.

All the best
Seref


On Fri, Aug 18, 2017 at 9:15 AM, Thomas Beale 
wrote:

> Hi,
>
> distributed versioning with branching was included to allow syncing of
> data gathered about the same patient in different EHR repositories. For
> most data, syncing the repos is trivial, since it's different data.
>
> The classic cases of potential clashes is medication list, problem list,
> basic clinical demographic data, etc. If a sync was started and two
> medication lists are found that are forks of a single earlier one, a manual
> merge will be required.
>
> We are only just starting to see the implementation of systems where
> syncing may be a question, so although there may be adjustments to make to
> the branched versioning model, I would not be in favour of throwing it out
> at this point.
>
> We are however going to move it to the BASE component and make it a
> standalone model.
>
> - thomas
>
> On 21/06/2017 09:19, Pablo Pazos wrote:
>
> Hi Bert, see below
>
> On Wed, Jun 21, 2017 at 4:21 AM, Bert Verhees 
> wrote:
>
>> Hi Pablo, I did it a few years ago, just dumped not-current versions in a
>> slow XML database, because, in normal cases they are never queried, and
>> when they need to be queried, there can always be found a faster solution.
>>
>> But of course, this was a linear version system. ExistDB supports
>> distributed versioning on XML out of the box. And you can also use a
>> normal, not OpenEHR, version system like Git or VCL.
>>
>> But when looking at how OpenEHR works, is there ever need of merging? Do
>> people edit concurrently same datasets? I think they are they always
>> working on new versions of datasets, there is only one exception, that is
>> the persistent Composition, there could occur merging problems.
>>
>> The openEHR versioning mechanism is like Git. The problem I see with this
> approach is that real users don't want to deal with that level of
> complexity just to track changes in a distributed way. openEHR allows
> branching, so if there is no merging, each user can be working on a
> different branch, seeing just part of the data. Merging is complex, but
> that is needed only if branching is allowed, so the problem is really
> branching.
>
> With branches, when a query is executed, it is getting data form the
> latest version of the CURRENT branch, potentially missing data from other
> branches. This might have patient safety issues also.
>
> That is the main reason I ask this because it is not clear to me that a
> good technical solution like distributed versioning, is the best for EHRs.
> Moreover considering that most documents will have 1 or 2 versions at most
> (talking about event). Of course there will be more versions for persistent
> compos.
>
> *Thinking out loud, wouldn't be interesting to have an alternative spec
> for versioning where only linear versions are allowed? (IMO that would be
> easier to implement even though the current spec includes that case).*
>
>
>> But I think, you don't need distributed versioning to handle this, a
>> locking system (like databases have) is, I think, good enough. That is how
>> classic EHR builders handle concurrency.
>>
>> Bert
>>
>>
>> On 21-06-17 03:04, Pablo Pazos wrote:
>>
>> Hi all,
>>
>> I had this questions in mind for a long time: did someone implemented the
>> distributed versioning of openEHR?
>>
>> The specs define a great distributed versioning mechanism but it is a
>> little trickier to implement. Also there is no clear who will do the work
>> of managing that, and how that structure will be queried. It is very
>> difficult to me to think of an amendment sent to an EHR and that not being
>> available for all the parties looking at the EHR of the patient.
>>
>> In the case of the EHRServer I built, only linear versioning is possible,
>> there is only one latest version for each compo, and queries only get data
>> from latest versions.
>>
>> Just wondering, what do others did for versioning and what policies do
>> you have if you implemented the distributed approach in terms of branching,
>> merging and querying.
>>
>>
>> Thanks!
>>
>> --
>> Ing. Pablo Pazos Gutiérrez
>> Cel:(00598) 99 043 145 <099%20043%20145>
>> Skype: cabolabs
>>