ppazos / edu-openehr-archetypes

openEHR archetypes in software: examples for CaboLabs' training courses

edu-openehr-archetypes

openEHR archetypes in software: examples for CaboLabs' training courses

Build

$ gradle build

Run from Gradle

NOTE: when running with gradle, the current working directory is ./app not ./ so the path to archetype needs an extra ../ if using relative paths.

Try parse an archetype (returns an error if the ADL is not correct)

$ gradle run --args="parse ../../openEHR-ADL/lib/src/test/resources/archetypes/entry/observation/openEHR-EHR-OBSERVATION.blood_pressure.v1.adl"

Show internal structure with paths

$ gradle run --args="traverse src/test/resources/archetypes/openEHR-EHR-OBSERVATION.blood_pressure.v2.adl"

Show constraint at path

$ gradle run --args="constraint src/test/resources/archetypes/openEHR-EHR-OBSERVATION.blood_pressure.v2.adl /data[at0001]/events[at0006]/data[at0003]/items[at0004]/value"

Data validation

NOTE 1: for data validation the given path should correspond to a data value, usualy a path that constraints an ELEMENT.value attribute in the archetype.

NOTE 2: since a data set should be given, and each data value has different attributes, each data valu has it's own format for providing data:

• DV_QUANTITY: magnitude|units (magnitude is a number, units is a string)
• DV_ORDINAL: value or terminology::code or value|terminology::code (code is a string, value is a number, terminology is a string)
• CODE_PHRASE: terminology::code (code and terminology are both strings)
• DV_TEXT: text (text is a string, should be quoted if it has spaces)

$ gradle run --args="validate src/test/resources/archetypes/openEHR-EHR-OBSERVATION.blood_pressure.v2.adl /protocol[at0011]/items[at1038]/value 'hello hello'"

Run from fat JAR

Build fat jar

$ gradle fatJar

Try parsing archetypes

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar parse app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.blood_pressure.v2.adl

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar parse app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.pulse.v2.adl

Show internal structure with paths

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar traverse app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.pulse.v2.adl

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar traverse app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.chest_circumference.v0.adl

Show constraint at path

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar constraint app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.chest_circumference.v0.adl /data[at0001]/events[at0014]/math_function/defining_codeCODE_PHRASE <CCodePhrase>

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar constraint app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.pulse.v2.adl /data[at0002]/events[at0003]/data[at0001]/items[at0004]/value

Data validation

$ java -jar app/build/libs/edu-openehr-archetypes-0.1-all.jar validate app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.chest_circumference.v0.adl /data[at0001]/events[at0014]/math_function/defining_code openehr::147

Run from Docker

Build image

$ docker build -t archetypes .

Run container

$ docker run -d -t archetypes

Get container ID (f06838afdb71)

$ docker ps

CONTAINER ID   IMAGE                           COMMAND                  CREATED         STATUS         PORTS                                                                                            NAMES
f06838afdb71   archetypes                      "/__cacert_entrypoin…"   9 minutes ago   Up 9 minutes                                                                                                    reverent_booth

Run command using container ID

$ docker exec f06838afdb71 java -jar archetypes/app/build/libs/edu-openehr-archetypes-0.1-all.jar parse /archetypes/app/src/test/resources/archetypes/openEHR-EHR-OBSERVATION.blood_pressure.v2.adl