HL7 Swiss FHIR Implementation Guide for generic laboratory order forms

CI Build

• CI Build master
• CI Build develop
• CI Build 2.0.0-STU-ballot

This is a HL7 Swiss FHIR implementation guide. It describes mainly two use cases of laboratory orders. The first one composes the order by the choices given from the Laboratory Information System (LIS) and stores them in the FHIR resource ServiceRequest. The second use case offers Questionnaire (Form) curated by the responsible laboratory, which can be prepopulated with administratives informations by the clinic or pracice information system; the client, mostly the ordering practitioner, may complete the Questionnaire with the informations needed to fullfill the request of laboratory tests and test panels. He may add supplementary clinical informations from his information system, such as a problem list, or a medication list. The second use case is based on CH_ORF Order & Referral by Form - Implementation Guide (CH:ORF) http://fhir.ch/ig/ch-orf/index.html

Swiss Laboratory professional societies

• FAMH --The medical Laboratories of Schweiz https://www.famh.ch/
• SULM SULM Swiss Union of Laboratory Medicine https://sulm.ch/d/
• SSAI Swiss Society for Allergologie and Immunology https://ssai.ch/
• SSCC Swiss Society for Clinical Chemistry http://www.sscc.ch/
• SGH-SSH Swiss Society of Hematologie https://www.sgh-ssh.ch/
• SGM-SSM Swiss Society for Microbiology https://www.swissmicrobiology.ch/

Prerequisites

• Oracle JDK: https://fedoraproject.org/wiki/JDK_on_Fedora

Installation of JDK Oracle for Fedora 31

Download JDK from Oracle website:

https://www.oracle.com/java/technologies/downloads/

cat /etc/fedora-release   or $ cat /usr/lib/os-release
Fedora release 38 (Thirty Eight)
java --version
java 20.0.1 2023-04-18
Java(TM) SE Runtime Environment (build 20.0.1+9-29)
Java HotSpot(TM) 64-Bit Server VM (build 20.0.1+9-29, mixed mode, sharing)

$ sudo alternatives --config java

There are 3 programs which provide 'java'.

  Selection    Command
-----------------------------------------------
   1           /usr/lib/jvm/jdk-17-oracle-x64/bin/java
   2           java-17-openjdk.x86_64 (/usr/lib/jvm/java-17-openjdk-17.0.7.0.7-5.fc38.x86_64/bin/java)
*+ 3           /usr/lib/jvm/jdk-20-oracle-x64/bin/java

Enter to keep the current selection[+], or type selection number: 

IG Publisher

Look at https://confluence.hl7.org/display/FHIR/IG+Publisher+Documentation Get the IG Publisher at https://github.com/HL7/fhir-ig-publisher/releases/latest/download/publisher.jar

Running in workspace/ch-lab-order/ in command line mode: Make sure you use the latest version of publisher.

java --version
java 20.0.1 2023-04-18
Java(TM) SE Runtime Environment (build 20.0.1+9-29)
Java HotSpot(TM) 64-Bit Server VM (build 20.0.1+9-29, mixed mode, sharing)


java -jar input-cache/publisher.jar -ig ig.ini

if Terminology server not available:

java -jar input-cache/publisher.jar -ig ig.ini -tx n/a

Checks folders, installs hl7.fhir.r4.core#4.0.1, builds IG

Visit your static pages powered by jekyll

web

http://build.fhir.org/ig/hl7ch/ch-lab-order/branches/master/index.html

local

• navigate to the root directory 'ch-lab-order'

after running IG publisher:

• cd output (This directory is build by IG Publisher and doesn't exist in the repository)

• open a new Gemfile (e.g. 'vi Gemfile')

• add the following two lines:

  source 'https://rubygems.org'
  
  gem 'github-pages', group: :jekyll_plugins

• run bundle install and bundle exec jekyll serve

• visite in your browser 127.0.0.1:4000/index.html

further procedure

look at 'https://fhirblog.com/clinicians-on-fhir-workshop/'

1. Description of Problem (use cases from CDA-CH)

2. Build Information models based on use cases

3. Build 'Resources model' and References Graph'

4. Build all FHIR Artifacts:

   • Profiles on resources (extenstions and constraints)

   • ValueSets and CodeSystem resources

   • Documentation

   • Other possible Resources

Installation of environment on mac

1. Install Homebrew

   /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"

2. Install ruby for user (do not install globally)

3. And add it to your bash profile

   brew install ruby
   echo 'export PATH="/usr/local/opt/ruby/bin:$PATH"' >> ~/.bash_profile

4. Relaunch terminal and check install path and version

   which ruby
   ruby -v

5. Install Jeykll and add your path file

   gem install --user-install bundler jekyll
   echo 'export PATH="$HOME/.gem/ruby/X.X.0/bin:$PATH"' >> ~/.bash_profile

   Important: X.X are the first two Numbers of the version checked previously in step 3.

6. Check if gem path points to correct directory

   gem env

7. Download IG Publisher

8. Copy .jar file into main directory of your project

9. Execute .jar file with

   java -jar publisher.jar -ig ig.ini

10. Let the pages be generated ♺

Worflow for Repository

The process is a simplified adaption of Git Flow.

Branching

The project has two locked branches:

• master: The master branch only contains the source code of the LATEST STABLE release.

• develop: This branch is the mainbranch for creating the feature branches. The develop branch does not contain untested code!

For every feature or issue in the github repo create a sepparate branch. The branch should be named with the pattern [ISSUE_ID]-[ISSUE_NAME]. Whereas the [ISSUE_ID] could be something like #10 and the [ISSUE_NAME] could be create-worflow-documentation. So the final branch name would be #10-create-worflow-documentation.

IF there is an issue that needs a hotfix, we will create the issue branch from the master and merge it back to master with no develop involvement.

If a new release is ready, it needs to be tested again on the develop branch. Before the testing do update the version number. After successfully testing merge it into master and it can be released.

Useful Links

LOINC for in vitro Diagnostics (LLIVD)

DSTU2 U.S. Data Access Framework (DAF) DiagnosticOrder Profile 'https://www.hl7.org/fhir/dstu2/daf/diagnosticorder-daf.html'

Digital Format for Publication of LOINC to Vendor IVD Test Results by IICC:

'http://ivdconnectivity.org/wp-content/uploads/delightful-downloads/2017/06/IICC_LIVD_Digital_Format_2017_06_01_R2.pdf'

LIVD example bundle

'http://hl7.org/fhir/uv/livd/2019Sep/livd-example.html'

Roche qualitative LIVD example bundle 'http://hl7.org/fhir/uv/livd/2019Sep/livd-example-roche-qual.html#root'

Structured data capture

'https://wiki.ihe.net/index.php/Retrieve_Form_for_Data_Capture'

ITI QRPH Supplement – Structured Data Capture: 'https://ihe.net/uploadedFiles/Documents/QRPH/IHE_QRPH_Suppl_SDC.pdf'

HL7 FHIR Implementation guide: 'http://hl7.org/fhir/uv/sdc/2018Sep/index.html'

Request for diagnostic report 'http://hl7.org/fhir/servicerequest.html'

Laboratory ask at order entry panel Universal Lab Orders Value Set from LOINC

Order and Referral by Form (ORF)

'http://build.fhir.org/ig/ahdis/ch-orf/'

LOINC Document Ontology

Matchbox

Questionnaires

[0-generic]https://test.ahdis.ch/matchbox/#/questionnaire/0-generic

[0-generic]https://test.ahdis.ch/matchbox/#/questionnaire/0-generic [1-tvt]https://test.ahdis.ch/matchbox/#/questionnaire/1-tvt [2-pertussis]https://test.ahdis.ch/matchbox/#/questionnaire/2-pertussis [3-gyn]https://test.ahdis.ch/matchbox/#/questionnaire/3-gyn [4-sepsis]https://test.ahdis.ch/matchbox/#/questionnaire/4-sepsis [5-biol-monit]https://test.ahdis.ch/matchbox/#/questionnaire/5-biol-monit [6-histopath]https://test.ahdis.ch/matchbox/#/questionnaire/6-histopath-Questionnaire

Matchbox: file doesn't load [LabOrder-form]https://test.ahdis.ch/matchbox/#/questionnaire/LabOrder-form-0 [sdc-sample]https://test.ahdis.ch/matchbox/#/questionnaire/sdc-sample [sdc-pathology]https://test.ahdis.ch/matchbox/#/questionnaire/sdc-pathology

IG

[package]http://build.fhir.org/ig/hl7ch/ch-lab-order/branches/develop/package.tgz