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Add support for at-code coding system in addition to id-code coding system. #16

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48e9b1e
ADL2 with added at-code codesystem
bostjanl-better Mar 2, 2024
83c49b6
Add amendment records to AM and ADL (SPECAM-90)
bostjanl-better Mar 14, 2024
25a95ac
Changes after review from TB (SPECAM-90)
bostjanl-better Mar 15, 2024
a628884
updating specs (by Ian McNicoll) to use asciidoc-tabs for ADL syntax …
sebastian-iancu May 3, 2024
4f0e3fd
fixed typos and some formatting issues; updating Node identification …
freshehr May 5, 2024
5556fa5
ignore .idea directory
sebastian-iancu May 7, 2024
8fe3d6f
updating examples to adl_version=2.4.0 (used replace all) (SPECAM-90)
joostholslag May 7, 2024
b874623
fixing wording around `codedsystem` vs `coding system`; small formatt…
sebastian-iancu Jun 8, 2024
9af323c
Update docs/ADL2/master01-preface.adoc
sebastian-iancu Jun 25, 2024
79fcf14
Update docs/ADL2/master01-preface.adoc
sebastian-iancu Jun 25, 2024
b6ac293
Update docs/AOM2/master01-preface.adoc
sebastian-iancu Jun 25, 2024
ba34661
Remove "The new coding system also carries original id-codes in its a…
bostjanl-better Jul 15, 2024
77a8e1a
Introduce Value_code_leader: String = "at" also for at-coded ADL2
bostjanl-better Jul 15, 2024
e829307
Fix regex pattern for root node description
bostjanl-better Jul 15, 2024
00920d4
Add a note on Root_code_regex_pattern to indicate at-code numbering s…
bostjanl-better Nov 4, 2024
df49b2a
Fix changelog from 2.3 to 2.4 to not include changes from 1.5 to 2.0
bostjanl-better Nov 4, 2024
9f745e0
Fix release version range for changes
bostjanl-better Nov 4, 2024
0752d89
Replace tabs with 4 spaces
bostjanl-better Nov 4, 2024
aca93a3
Fix code in id-system to be +1 of at-code system
bostjanl-better Nov 4, 2024
35a47a5
Fix spelling of "minutes"
bostjanl-better Nov 4, 2024
acc3036
Fix deprecation of 0-padding for at/ac codes
bostjanl-better Nov 4, 2024
e809504
Fix at-coded examples in the last 2 paragraphs
bostjanl-better Nov 4, 2024
4932dc9
Add changelog for new title attribute of the RESOURCE_DESCRIPTION
bostjanl-better Nov 4, 2024
ebf5be1
Rebuild htmls
bostjanl-better Nov 4, 2024
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2 changes: 1 addition & 1 deletion .gitignore
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@@ -1,2 +1,2 @@
*.bak
/.idea
.idea
2 changes: 1 addition & 1 deletion LICENSE
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Expand Up @@ -225,7 +225,7 @@ subject to and limited by the following restrictions:
extent reasonably practicable, the URI, if any, that Licensor
specifies to be associated with the Work, unless such URI does not
refer to the copyright notice or licensing information for the Work;
and (iv) , consistent with Ssection 3(b), in the case of an
and (iv) , consistent with Section 3(b), in the case of an
Adaptation, a credit identifying the use of the Work in the Adaptation
(e.g., "French translation of the Work by Original Author," or
"Screenplay based on original Work by Original Author"). The credit
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54 changes: 54 additions & 0 deletions computable/plantuml/primitive.plantuml
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@@ -0,0 +1,54 @@
@startuml
package primitive_types {
class "<<Value_Type>>\nBoolean " as Boolean
class "<<Value_Type>>\nCharacter " as Character
class "<<Value_Type>>\nOctet " as Octet
class "<<Value_Type>>\nInteger" as Integer
class "<<Value_Type>>\nInteger64" as Integer64
class "<<Value_Type>>\nReal" as Real
class "<<Value_Type>>\nDouble" as Double
class "Ordered Numeric" as OrderedNumeric
class Numeric
class Ordered
class String
class Uri
}

package terminology {
class Terminology_Code
}

package time {
class Temporal
class Iso8601_type
class Iso8601_date
class Iso8601_time
class Iso8601_date_time
class Iso8601_duration
}

Any <|-- Boolean
Any <|-- Numeric
Numeric <|-- OrderedNumeric
Any <|-- Ordered
Ordered <|-- OrderedNumeric
Any <|-- Terminology_Code
Ordered <|-- Character
Ordered <|-- Octet
Ordered <|-- String
String <|-- Uri

OrderedNumeric <|-- Integer
OrderedNumeric <|-- Integer64
OrderedNumeric <|-- Real
OrderedNumeric <|-- Double

Ordered <|-- Temporal
Temporal <|-- Iso8601_type
Iso8601_type <|-- Iso8601_date
Iso8601_type <|-- Iso8601_time
Iso8601_type <|-- Iso8601_date_time
Iso8601_type <|-- Iso8601_duration
@enduml


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2 changes: 1 addition & 1 deletion docs/ADL2/diagrams/adl_text_overview.svg
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15 changes: 13 additions & 2 deletions docs/ADL2/master00-amendment_record.adoc
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Expand Up @@ -4,13 +4,24 @@
|===
|Issue|Details|Raiser, Implementer|Completed

4+^h|*AM Release 2.4.0 (unreleased)*

|[[latest_issue]]2.4.0
|{spec_tickets}/SPECAM-90[SPECAM-90^]. Add support for at-code coding system in addition to id-code coding system. Make the at-code coding system a requirement for openEHR RM compliant implementations.
|B Lah, +
I McNicoll, +
J Holslag, +
S Iancu, +
T Beale
|[[latest_issue_date]]14 Mar 2024

4+^h|*AM Release 2.3.0*

|[[latest_issue]]2.3.0
|2.3.0
|{spec_tickets}/SPECAM-75[SPECAM-75^]. Improve specification of constraint patterns (addresses problem {spec_tickets}/SPECPR-374[SPECPR-374^]). Modified <<#date_time_constraint_patterns>> to include timezone constraints.
|P Pazos, +
T Beale
|[[latest_issue_date]]20 Dec 2022
|20 Dec 2022

|
|{spec_tickets}/SPECAM-76[SPECAM-76^]. Correct VSONCO rule for redefinition of nodes with multiple occurrences; improve text in <<Redefinition Concepts>> and <<Occurrences Redefinition>> (addresses problem {spec_tickets}/SPECPR-374[SPECPR-374^]).
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22 changes: 21 additions & 1 deletion docs/ADL2/master01-preface.adoc
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Expand Up @@ -65,6 +65,26 @@ For existing users of ADL or archetype development tools, the following provides

The object syntax used to represent the description, terminology and annotations sections of an ADL archetype has been historically known as 'dADL' (i.e. 'data ADL'). Since this syntax is completely generic and has no specific dependency on either ADL or openEHR, it has been separated out into its own specification known as Object Data Instance Notation (ODIN).

=== ADL 2.4

==== Changes
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ADL2 was initially released with a new id-coded coding system using id-codes (for nodes), at-codes (for values only) and ac-codes (for value sets).

The primary change in version 2.4 is the introduction of an alternative at-code coding system, identical to that used in ADL1.

Although a conversion algorithm was developed to enable conversion for ADL1 at-codes in archetypes and templates to the new id-codes and coding system, the openEHR implementer community had concerns on the burden and impact and safety risks inherent in converting downstream software artefacts, queries and persisted patient records.

It was decided that the best solution was to allow openEHR-RM based systems and archetypes to continue to use the original ADL1 at-coded coding system instead of the id-coded coding system. This was seen as critical to remove a very significant barrier to transition from ADL1 to ADL2, which in all other respects was widely welcomed by the established openEHR implementer community.

Further information on the choice of coding system is provided at <<_node_identifier_and_coding_systems>>.

NOTE: ADL tools conformant to ADL/AOM 2.3 or earlier will not conform to the at-coded ADL2 archetypes described in ADL 2.4 without additional engineering.

==== Backward Compatibility

When using the AT-coded coding system, this ADL2.4 release is fully backwards compatible with openEHR RM data created based on ADL 1.4 archetypes. But it breaks compatibility with openEHR RM data created using an ID-coded coding system, which was the only option in ADL 2.0 - ADL 2.3 archetypes. So ID-coded ADL2 systems and tools are expected to require additional engineering in order to gain compatibility with at-coded systems.

=== ADL 2.0

==== Changes
Expand Down Expand Up @@ -167,7 +187,7 @@ It is strongly recommended that all tool implementors include this information w

==== dADL (ODIN) Syntax Changes

The dADL (now ODIN) syntax for container attributes has been altered to allow paths and typing to be expressed more clearly, as part of enabling the use of Xpath-style paths. ADL 1.1 dADL had the following appearance:
The dADL (now ODIN) syntax for container attributes has been altered to allow paths and typing to be expressed more clearly, as part of enabling the use of Xpath-style paths. ADL 1.1 dADL had the following appearance:

```
school_schedule = <
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92 changes: 89 additions & 3 deletions docs/ADL2/master02-overview.adoc
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@@ -1,6 +1,10 @@
= Overview

ADL uses three syntaxes, cADL (constraint form of ADL), ODIN (Object Data Instance Notation), and openEHR Expression Language (EL), to express constraints on data which are instances of an underlying information model, which may be expressed in UML, relational form, or in a programming language. ADL itself is a very simple 'glue' syntax, which uses two other syntaxes for expressing structured constraints and data, respectively. The cADL syntax is used to express the archetype `definition` section, while the ODIN syntax is used to express data which appears in the `language`, `description`, and `terminology` sections of an ADL archetype. The top-level structure of an ADL archetype is shown in the figure below.
ADL uses three syntaxes, cADL (constraint form of ADL), ODIN (Object Data Instance Notation), and openEHR Expression Language (EL), to express constraints on data which are instances of an underlying information model, which may be expressed in UML, relational form, or in a programming language.

ADL itself is a very simple 'glue' syntax, which uses two other syntaxes for expressing structured constraints and data, respectively.

The cADL syntax is used to express the archetype `definition` section, while the ODIN syntax is used to express data which appears in the `language`, `description`, and `terminology` sections of an ADL archetype. The top-level structure of an ADL archetype is shown in the figure below.

This main part of this document describes cADL and ADL path syntax, before going on to describe the combined ADL syntax, archetypes, specialisation, terminology integration and templates.

Expand All @@ -10,11 +14,92 @@ image::{diagrams_uri}/adl_text_overview.svg[id=archetype_structure, align="cente

== An Example

The following is an example of a very simple archetype, giving a feel for the syntax. The main point to glean from the following is that the notion of 'guitar' is defined in terms of _constraints_ on a _generic_ model of the concept "INSTRUMENT". The names mentioned down the left-hand side of the definition section (`INSTRUMENT`, `size` etc) are alternately class and attribute names from an object model. Each block of braces encloses a specification for some particular set of instances that conform to a specific concept, such as 'guitar' or 'neck', defined in terms of constraints on types from a generic class model. The leaf pairs of braces enclose constraints on primitive types such as `Integer`, `String`, `Boolean` and so on. 
The following is an example of a very simple archetype, giving a feel for the syntax. The main point to glean from the following is that the notion of 'guitar' is defined in terms of _constraints_ on a _generic_ model of the concept "INSTRUMENT".

The names mentioned down the left-hand side of the definition section (`INSTRUMENT`, `size` etc) are alternately class and attribute names from an object model.

Each block of braces encloses a specification for some particular set of instances that conform to a specific concept, such as 'guitar' or 'neck', defined in terms of constraints on types from a generic class model. The leaf pairs of braces enclose constraints on primitive types such as `Integer`, `String`, `Boolean` and so on.

====
[IMPORTANT]::

ADL 2.4 introduces an option to use the **at-code coding system** of ADL1, as an alternative to the **id-code coding system** introduced in ADL2.

- The **at-code coding system** must be used for systems that need to be conformant to the _openEHR Reference Model (RM)_.
- The **id-code coding system** is recommended for non-openEHR RM information models.

ADL2 syntax examples are provided for both coding systems, as `at-coded ADL2` or `id-coded ADL2`.

Further information on the choice of coding system is provided at <<_node_identifier_and_coding_systems>>.
====

[tabs,sync-group-id=adl-example]
.Simple 'Guitar' archetype ADL2 example
====
at-coded ADL2::
+
[source, adl]
--------
archetype (adl_version=2.4.0; rm_release=1.1.5)
adl-test-instrument.guitar.v1.0.4

language
original_language = <[iso_639-1::en]>

definition
INSTRUMENT[at0000] matches {
size matches {|60..120|} -- size in cm
date_of_manufacture matches {yyyy-mm-??} -- year & month ok
parts matches {
PART[at0001] matches { -- neck
material matches {[ac1]} -- timber or nickel alloy
}
PART[at0002] matches { -- body
material matches {[at3]} -- timber
}
}
}

terminology
term_definitions = <
["en"] = <
["at0000"] = <
text = <"guitar">;
description = <"stringed instrument">
>
["at0001"] = <
text = <"neck">;
description = <"neck of guitar">
>
["at0002"] = <
text = <"body">;
description = <"body of guitar">
>
["at0003"] = <
text = <"timber">;
description = <"straight, seasoned timber">
>
["at0004"] = <
text = <"nickel alloy">;
description = <"frets">
>
>
>

value_sets = <
["ac1"] = <
id = <"ac1">
members = <"at0003", "at0004">
>
>
>
--------

id-coded ADL2::
+
[source, adl]
--------
archetype (adl_version=2.0.5; rm_release=1.1.5)
archetype (adl_version=2.4.0; rm_release=1.1.5)
adl-test-instrument.guitar.v1.0.4

language
Expand Down Expand Up @@ -68,3 +153,4 @@ terminology
>
>
--------
====
46 changes: 45 additions & 1 deletion docs/ADL2/master04.1-cadl_overview.adoc
Original file line number Diff line number Diff line change
@@ -1,9 +1,29 @@
= cADL - Constraint ADL

== Overview

cADL is a block-structured syntax which enables constraints on data defined by object-oriented information models to be expressed in archetypes or other knowledge definition formalisms. It is most useful for defining the specific allowable configurations of data whose instances conform to very general object models. The general appearance of cADL is illustrated by the following example:


[tabs,sync-group-id=adl-example]
====
at-coded ADL2::
+
[source, cadl]
--------
PERSON[at0000] matches { -- constraint on a PERSON instance
name matches { -- constraint on PERSON.name
TEXT[at0001] matches {/.+/} -- any non-empty string
}
addresses cardinality matches {1..*} matches { -- constraint on
ADDRESS[at0002] matches { -- PERSON.addresses
-- etc --
}
}
}
--------

id-coded ADL2::
+
[source, cadl]
--------
PERSON[id1] matches { -- constraint on a PERSON instance
Expand All @@ -17,9 +37,30 @@ cADL is a block-structured syntax which enables constraints on data defined by o
}
}
--------
====

Some of the textual keywords in this example can be more efficiently rendered using common mathematical logic symbols. In the following example, the `matches` keyword have been replaced by an equivalent symbol:

[tabs,sync-group-id=adl-example]

====
at-coded ADL2::
+
[source, cadl]
--------
PERSON[at0000] ∈ { -- constraint on a PERSON instance
name ∈ { -- constraint on PERSON.name
TEXT[at0001] ∈ {/..*/} -- any non-empty string
}
addresses cardinality ∈ {1..*} ∈ { -- constraint on
ADDRESS[at0002] ∈ { -- PERSON.addresses
-- etc --
}
}
}
--------
id-coded ADL2::
+
[source, cadl]
--------
PERSON[id1] ∈ { -- constraint on a PERSON instance
Expand All @@ -33,6 +74,9 @@ Some of the textual keywords in this example can be more efficiently rendered us
}
}
--------
====



The full set of equivalences appears below. Raw cADL is persisted in the text-based form, to remove any difficulties when authoring cADL text in normal text editors, and to aid reading in English. However, the symbolic form might be more widely used for display purposes and in more sophisticated tools, as it is more succinct and less language-dependent. The use of symbols or text is completely a matter of taste, and no meaning whatsoever is lost by completely ignoring one or other format according to one's personal preference. This document uses both conventions.

Expand Down
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