Re: constraining of laboratory_test_analyte Analyte result

[Thomas Beale]

Well, at the risk of stepping on Ian's toes (he has spent a lot more 
time on these particular archetypes and also AQL in general than me), I 
would say that what we need to do is to create a data-type specific 
version of this archetype for each DATA_VALUE descendant, e.g. 
openEHR-EHR-CLUSTER.laboratory_test_analyte_quantity.v1 etc. For 
example, I did these test archetypes some time ago to illustrate just this:


openEHR-EHR-CLUSTER.laboratory_test_analyte_quantity.v1

The definition of this is:

definition
    CLUSTER[id1.1] matches {    -- -
        /items[id2]/value matches {
            DV_QUANTITY[id0.16] matches {
                normal_range matches {
                    DV_INTERVAL[id0.17]
                }
                other_reference_ranges matches {
REFERENCE_RANGE[id0.18]     -- Quantity reference range
                }
            }
        }
    }

You can see a few others here in the ADL2 test archetype Git repo 
.


From my analysis, these subtypes are unavoidable in order to make 
querying work, but also to enable manual specialisations e.g. into 
particular analytes, which is something very useful for creating 
standardised analytes and panels.


- thomas

On 02/05/2019 09:57, Georg Fette wrote:


Hi Thomas,
It depends on what you mean with "specialise". I do not wish to create 
a new archetype but I rather would like to query existing instances of 
the openEHR-EHR-CLUSTER.laboratory_test_analyte.v1 archetype. From 
those instances I would like to query only this with specific 
attributes. One constraint I am able to define is to constrain the 
analyte name:


SELECT e
FROM EHR e CONTAINS CLUSTER 
a[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]

WHERE a/items[at0024]/value/value = 'Calcium'

But how can I manage to as well constrain the value ? The path 
openEHR-EHR-CLUSTER.laboratory_test_analyte.v1/items[at0001] is of the 
type ELEMENT, which has a DATA_VALUE for its field "value". The 
concrete instances of the analytes do have decendents of the 
DATA_VALUE type in the place for ELEMENT[at0001]/value, e.g. 
DV_QUANTITY. Is it possible to use paths to those concrete value types 
in the WHERE-paths, such like:


SELECT e
FROM EHR e CONTAINS CLUSTER 
a[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]
WHERE a/items[at0024]/value/value = 'Calcium' AND 
a/items[at0001]/value/magnitude > 100


From a type checking point of view, this is not allowed, because the 
data type at the path a/items[at0001]/value (which is DATA_VALUE) does 
not contain a field "magnitude". To make this work I would have to 
bind the value to the concrete type, with something like:


SELECT e
FROM EHR e CONTAINS CLUSTER 
a[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]

CONTAINS DV_QUANTITY b
WHERE a/items[at0024]/value/value = 'Calcium' AND 
a/items[at0001]/value = b and b/magnitude > 100


but I don't think this is allowed in AQL. I am not yet that fluent in 
AQL, so I could need a little help in this.

Greetings
Georg


--
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: constraining of laboratory_test_analyte Analyte result

[Georg Fette]

Hi Thomas,
It depends on what you mean with "specialise". I do not wish to create a 
new archetype but I rather would like to query existing instances of the 
openEHR-EHR-CLUSTER.laboratory_test_analyte.v1 archetype. From those 
instances I would like to query only this with specific attributes. One 
constraint I am able to define is to constrain the analyte name:


SELECT e
FROM EHR e CONTAINS CLUSTER 
a[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]

WHERE a/items[at0024]/value/value = 'Calcium'

But how can I manage to as well constrain the value ? The path 
openEHR-EHR-CLUSTER.laboratory_test_analyte.v1/items[at0001] is of the 
type ELEMENT, which has a DATA_VALUE for its field "value". The concrete 
instances of the analytes do have decendents of the DATA_VALUE type in 
the place for ELEMENT[at0001]/value, e.g. DV_QUANTITY. Is it possible to 
use paths to those concrete value types in the WHERE-paths, such like:


SELECT e
FROM EHR e CONTAINS CLUSTER 
a[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]
WHERE a/items[at0024]/value/value = 'Calcium' AND 
a/items[at0001]/value/magnitude > 100


From a type checking point of view, this is not allowed, because the 
data type at the path a/items[at0001]/value (which is DATA_VALUE) does 
not contain a field "magnitude". To make this work I would have to bind 
the value to the concrete type, with something like:


SELECT e
FROM EHR e CONTAINS CLUSTER 
a[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1]

CONTAINS DV_QUANTITY b
WHERE a/items[at0024]/value/value = 'Calcium' AND a/items[at0001]/value 
= b and b/magnitude > 100


but I don't think this is allowed in AQL. I am not yet that fluent in 
AQL, so I could need a little help in this.

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: constraining of laboratory_test_analyte Analyte result

[Seref Arikan]

Hi Georg,

Please note that you can always define your FROM clause with a high level
node such as an OBSERVATION o[archetype_id] and access the particular path
you're interested in using a path starting from o as in o/data[..]/...

Regarding your assumptions re FROM clause, technically there is nothing
stopping you from writing a query such as SELECT x FROM EHR e CONTAINS
DV_CODED_TEXT x. As useless as it may be, this is valid AQL and it asks for
all the DV_CODED_TEXT instances in all compositions under all EHRs
However, it is likely that most AQL implementations won't let you run this
query simply because implementers don't want to pay the multi-dimensional
price for supporting a theoretically possible but useless-in-real-life
use-case. I'm telling this only because your comments sounds like you're
assuming archetype node ids are mandatory in the FROM clause. They're not,
from a syntax standpoint and maybe we should close that gap in the specs.

So use the SELECT clause to define a path from the Observation and the aql
implementation should give you the element you're interested in based on
its archetype node id. Whatever serialisation format the back end uses
(json/xml), you should always get an attribute or a json field telling you
the actual instance type of DATA_VALUE, which you can use to process data.
It is really no different than any subtype based polymorphism
implementation where you're given a base (sometimes abstract) type and you
need to figure out the actual type during runtime.

All the best.
S.



On Mon, Apr 29, 2019 at 11:46 PM Georg Fette 
wrote:

> Hello,
> How do I constrain the Analyte result of a laboratory_test_analyte.v1 ?
> The Analyte result are defined as an ELEMENT that is only constrained by
> a node predicate (i.e. ELEMENT[at0001]). Therefore the results cannot be
> bound with a specialized type and an alias within the FROM part, as in
> the FROM part only archetypeID-predicates are allowed and no node
> predicates. As the result is defined with the abstract ELEMENT type,
> which has an abstract DATA_VALUE as its content, no paths can be defined
> that constrain specific aspects of subclasses of DATA_VALUE that are
> actually stored in the ELEMENT[at0001] field of the test_analyte.
> How can this problem be resolved ?
> 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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>
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Re: constraining of laboratory_test_analyte Analyte result

[Ian McNicoll]

Hi Georg

The instance data will actually have been subclassed to have a specific
datatype and therefore the relevant attributes.

Therefore if you know that a particular analyte is a quantity, you can use
aql to access the data just as if it had originally been modelled
specifically as a quantity.

If you do not know the datatype you should still be able to pull back the
whole element as an object and process it further after figuring out the
datatype.

I'll try to an example when I get to my laptop. Too hard on the phone.

Ian


On Mon, 29 Apr 2019, 23:46 Georg Fette, 
wrote:

> Hello,
> How do I constrain the Analyte result of a laboratory_test_analyte.v1 ?
> The Analyte result are defined as an ELEMENT that is only constrained by
> a node predicate (i.e. ELEMENT[at0001]). Therefore the results cannot be
> bound with a specialized type and an alias within the FROM part, as in
> the FROM part only archetypeID-predicates are allowed and no node
> predicates. As the result is defined with the abstract ELEMENT type,
> which has an abstract DATA_VALUE as its content, no paths can be defined
> that constrain specific aspects of subclasses of DATA_VALUE that are
> actually stored in the ELEMENT[at0001] field of the test_analyte.
> How can this problem be resolved ?
> 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
> -
>
>
> ___
> openEHR-technical mailing list
> openEHR-technical@lists.openehr.org
>
> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
>
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Re: constraining of laboratory_test_analyte Analyte result

[Thomas Beale]

Hi Georg,

Just to be clear, are you trying to specialise the 
openEHR-EHR-CLUSTER.laboratory_test_analyte.v1 archetype for specific 
analytes, e.g. serum sodium, TSH etc?


- thomas

On 29/04/2019 23:46, Georg Fette wrote:

Hello,
How do I constrain the Analyte result of a laboratory_test_analyte.v1 ?
The Analyte result are defined as an ELEMENT that is only constrained 
by a node predicate (i.e. ELEMENT[at0001]). Therefore the results 
cannot be bound with a specialized type and an alias within the FROM 
part, as in the FROM part only archetypeID-predicates are allowed and 
no node predicates. As the result is defined with the abstract ELEMENT 
type, which has an abstract DATA_VALUE as its content, no paths can be 
defined that constrain specific aspects of subclasses of DATA_VALUE 
that are actually stored in the ELEMENT[at0001] field of the 
test_analyte.

How can this problem be resolved ?
Greetings
Georg


--
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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