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Merge pull request #171 from medizininformatik-initiative/release-v3.1.0
Release v3.1.0
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‎.gitattributes

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backend.zip filter=lfs diff=lfs merge=lfs -text
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elastic.zip filter=lfs diff=lfs merge=lfs -text
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mapping.zip filter=lfs diff=lfs merge=lfs -text

‎.github/actions/generate-ontology/action.yml

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name: Generate Ontology
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description: 'Generates ontology files'
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inputs:
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steps_to_run:
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required: false
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description: 'Optional non-empty list of steps of the ontology generation to run. If not supplied all steps
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will be run. The steps to run should be supplied as a JSON array of greater than zero integers
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matching the indices of the steps to run.
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Examples: "[1, 3, 5, 6]"; "[2]"; "[4, 3, 2]"'
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runs:
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using: "composite"
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steps:
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- name: Set default
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shell: bash
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run: echo "GENERATOR_STEPS=--all" >> $GITHUB_ENV
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- name: Parsing generator steps to run
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shell: bash
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if: ${{ inputs.steps_to_run != '' }}
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run: |
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echo "GENERATOR_STEPS=--step ${{ join(fromJSON(inputs.steps_to_run), ' --step ') }}" >> $GITHUB_ENV
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echo "Using generator scripts with arguments $GENERATOR_STEPS"
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- name: Save secret to file
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shell: bash
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id: certificates
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run: |
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echo "$PRIVATE_KEY" > private-key.pem
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echo "$SERVER_CERTIFICATE" > certificate.pem
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echo privateKey=$(readlink -f private-key.pem) >> "$GITHUB_OUTPUT"
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echo certificate=$(readlink -f certificate.pem) >> "$GITHUB_OUTPUT"
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env:
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SERVER_CERTIFICATE: ${{ secrets.FDPGPLUS_ONTO_SERVER_CERT }}
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PRIVATE_KEY: ${{ secrets.FDPGPLUS_ONTO_SERVER_KEY }}
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- name: Run ontology generation
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shell: bash
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env:
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ONTOLOGY_SERVER_ADDRESS: ${{ secrets.FDPGPLUS_ONTO_SERVER_URL }}
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SERVER_CERTIFICATE: ${{ steps.certificates.outputs.certificate }}
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PRIVATE_KEY: ${{ steps.certificates.outputs.privateKey }}
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run: ./generate_full_ontology.sh ${{ GENERATOR_STEPS }}

‎.github/actions/set-locale/action.yml

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name: Set Locale
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description: 'Sets system locale'
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inputs:
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locale:
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required: true
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description: 'Locale code to set as system locale'
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default: 'de_DE.UTF-8'
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runs:
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using: "composite"
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steps:
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- name: Set locale
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shell: bash
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run: |
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sudo apt-get update
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sudo apt-get install tzdata locales -y
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sudo locale-gen ${{ inputs.locale }}
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sudo localectl set-locale LANG="${{ inputs.locale }}"
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export LANG="${{ inputs.locale }}"
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sudo update-locale
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locale -a
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locale
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locale -c -k LC_NUMERIC
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localectl status

‎.github/workflows/ci.yml

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files: |
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example/fdpg-ontology/elastic.zip
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example/fdpg-ontology/backend.zip
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example/fdpg-ontology/mapping.zip
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example/fdpg-ontology/mapping.zip

‎.github/workflows/generate-ontology.yml

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name: Generate ontology
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on:
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workflow_call:
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outputs:
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elastic_zip:
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description: "Path to the generated elastic.zip file"
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value: ${{ steps.save_zips.outputs.elastic_zip }}
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mapping_zip:
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description: "Path to the generated mapping.zip file"
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value: ${{ steps.save_zips.outputs.mapping_zip }}
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backend_zip:
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description: "Path to the generated backend.zip file"
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value: ${{ steps.save_zips.outputs.backend_zip }}
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secrets:
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FDPGPLUS_ONTO_SERVER_CERT:
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required: true
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FDPGPLUS_ONTO_SERVER_KEY:
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required: true
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FDPGPLUS_ONTO_SERVER_URL:
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required: true
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jobs:
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generate_ontology:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set locale
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run: |
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sudo apt-get update
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sudo apt-get install locales -y
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sudo locale-gen de_DE.UTF-8
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export LANG=de_DE.UTF-8
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export LANGUAGE=de_DE.UTF-8
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export LC_ALL=de_DE.UTF-8
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echo "LANG=de_DE.UTF-8" | sudo tee -a /etc/environment
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echo "LC_ALL=de_DE.UTF-8" | sudo tee -a /etc/environment
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locale -a
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locale
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- name: Setup python 3 environment
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uses: actions/setup-python@v5
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with:
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python-version: '3.13'
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cache: 'pip'
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- name: Install required python modules
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run: pip3 install -r requirements.txt
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- name: Save secret to file
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id: certificates
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run: |
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echo "$PRIVATE_KEY" > private-key.pem
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echo "$SERVER_CERTIFICATE" > certificate.pem
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echo privateKey=$(readlink -f private-key.pem) >> "$GITHUB_OUTPUT"
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echo certificate=$(readlink -f certificate.pem) >> "$GITHUB_OUTPUT"
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env:
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SERVER_CERTIFICATE: ${{ secrets.FDPGPLUS_ONTO_SERVER_CERT }}
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PRIVATE_KEY: ${{ secrets.FDPGPLUS_ONTO_SERVER_KEY }}
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- name: Run ontology generation
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env:
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ONTOLOGY_SERVER_ADDRESS: ${{ secrets.FDPGPLUS_ONTO_SERVER_URL }}
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SERVER_CERTIFICATE: ${{ steps.certificates.outputs.certificate }}
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PRIVATE_KEY: ${{ steps.certificates.outputs.privateKey }}
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run: ./generate_full_ontology.sh --all
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- name: Save ZIP file paths
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id: save_zips
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run: |
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echo "elastic_zip=$(readlink -f example/fdpg-ontology/elastic.zip)" >> "$GITHUB_OUTPUT"
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echo "mapping_zip=$(readlink -f example/fdpg-ontology/mapping.zip)" >> "$GITHUB_OUTPUT"
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echo "backend_zip=$(readlink -f example/fdpg-ontology/backend.zip)" >> "$GITHUB_OUTPUT"

‎.github/workflows/run-integration-tests.yml

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name: Integration Test Base Setup
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on:
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push:
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jobs:
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run_integration_tests:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: Set locale
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run: |
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sudo apt-get update
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sudo apt-get install tzdata locales -y
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sudo locale-gen de_DE.UTF-8
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sudo localectl set-locale LANG="de_DE.UTF-8"
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export LANG="de_DE.UTF-8"
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sudo update-locale
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locale -a
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locale
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locale -c -k LC_NUMERIC
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localectl status
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- name: Setup python 3 environment
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uses: actions/setup-python@v5
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with:
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python-version: '3.13'
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cache: 'pip'
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- name: Install required python modules
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run: pip3 install -r requirements.txt
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- name: Save secret to file
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id: certificates
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run: |
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echo "$PRIVATE_KEY" > private-key.pem
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echo "$SERVER_CERTIFICATE" > certificate.pem
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echo privateKey=$(readlink -f private-key.pem) >> "$GITHUB_OUTPUT"
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echo certificate=$(readlink -f certificate.pem) >> "$GITHUB_OUTPUT"
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env:
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SERVER_CERTIFICATE: ${{ secrets.FDPGPLUS_ONTO_SERVER_CERT }}
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PRIVATE_KEY: ${{ secrets.FDPGPLUS_ONTO_SERVER_KEY }}
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- name: Run ontology generation
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env:
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ONTOLOGY_SERVER_ADDRESS: ${{ secrets.FDPGPLUS_ONTO_SERVER_URL }}
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SERVER_CERTIFICATE: ${{ steps.certificates.outputs.certificate }}
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PRIVATE_KEY: ${{ steps.certificates.outputs.privateKey }}
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run: ./generate_full_ontology.sh --all
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- name: Install testing pytest
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run: pip3 install pytest pytest-docker pytest-cov
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- name: Run integration tests
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run: pytest test/integration -v --cov
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- name: Upload Docker logs
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uses: actions/upload-artifact@v4
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if: ${{ failure() }}
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with:
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name: docker_logs
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path: test/integration/backend/docker_logs

‎.gitignore

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/.git/
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availability/*.json
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!availability/stratum-to-context.json
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/.commit
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.commit
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/example/code_systems_translations/*.json
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# FSH
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/fsh/*
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### Own ###
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# Files to edit and store commit messages
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/.commit
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.commit
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# Terminology translations with potentially large size
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/example/code_systems_translations/*.json
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local-onto-gen.sh
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# JetBrains run config export folder
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/.run
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# Directories holding temporary data which are used for example CI during runs or when testing locally
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/test/elastic_search/tmp/
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/temp/
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**/tmp
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**/temp
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/test/**/testdata
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**/.coverage
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# Directories holding docker logs recorded during (intergration) testing
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**/docker_logs/

‎CHANGELOG.md

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### Fixed
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### Security
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## [3.1.0] - 2025-02-13
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| Modul | Version | Changelog |
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|------------------|----------------------------------------------------------------------------|--------------|
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| MII_DIAGNOSE | "de.medizininformatikinitiative.kerndatensatz.diagnose 2025.0.0-alpha2" | |
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| MII_LAB | "de.medizininformatikinitiative.kerndatensatz.laborbefund 2025.0.0-alpha1" | |
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| MII_MEDICATION | "de.medizininformatikinitiative.kerndatensatz.medikation 2025.0.0-alpha5" | |
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| MII_PERSON | "de.medizininformatikinitiative.kerndatensatz.person 2025.0.0-alpha4" | |
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| MII_PROCEDURE | "de.medizininformatikinitiative.kerndatensatz.prozedur 2025.0.0-alpha2" | |
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| MII_FALL | "de.medizininformatikinitiative.kerndatensatz.fall 2025.0.0-alpha4" | |
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| MII_SPECIMEN | "de.medizininformatikinitiative.kerndatensatz.biobank 2025.0.0" | |
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| MII_CONSENT | "de.medizininformatikinitiative.kerndatensatz.consent 1.0.7" | |
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| MII_ICU | "de.medizininformatikinitiative.kerndatensatz.icu 2025.0.1" | Added to DSE |
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| MII_MOLGEN | "de.medizininformatikinitiative.kerndatensatz.molgen 2025.0.0" | Added to DSE |
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| MII_RADIOLOGY | "de.medizininformatikinitiative.kerndatensatz.bildgebung 2025.0.0" | Added to DSE |
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| MII_ONKOLOGY | "de.medizininformatikinitiative.kerndatensatz.onkologie 2025.0.2" | Added to DSE |
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| MII_PATHOLOGY | "de.medizininformatikinitiative.kerndatensatz.patho 2025.0.2" | Added to DSE |
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| MII_MICROBIOLOGY | "de.medizininformatikinitiative.kerndatensatz.mikrobiologie 2025.0.1" | Added to DSE |
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| MII_STUDIES | "de.medizininformatikinitiative.kerndatensatz.studie 2025.0.0" | Added to DSE |
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### Added
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- Added Erweiterungsmodule by @Frontman50 in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/165
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- Add translations for code systems by @Frontman50 in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/121
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- Make display translations searchable by @michael-82 in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/96
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- Extending UI profile for display translations by @Frontman50 in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/139
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- Addressed empty translation array by @Frontman50 in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/151
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- Add flag to update translation files on build by @juliangruendner in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/150
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- Implement type emission for time restriction in CQL mapping by @paulolaup in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/157
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- blacklisting of too general value sets for filter of dse features by @juliangruendner in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/168
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- create integration test base setup by @paulolaup in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/155
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### Fixed
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- fix: only make leaf profile tree profiles in dse selectable @juliangruendner in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/170
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- Index display.original fields in elastic search files by @michael-82 in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/153
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- Fix usage of wrong hash functions for contextualized termcodes by @paulolaup in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/160
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- Fix key error by @paulolaup in https://github.com/medizininformatik-initiative/fhir-ontology-generator/pull/142
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## [3.0.1]
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### Fixed

‎TerminologService/ValueSetResolver.py

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# from dse.generate_dse_files import logger
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from model.TreeMap import ContextualizedTermCodeInfo
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from model.UiDataModel import TermCode
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from util.LoggingUtil import init_logger
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from util.logging.LoggingUtil import init_logger
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from logging import DEBUG
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POSSIBLE_CODE_SYSTEMS = ["http://loinc.org", "http://snomed.info/sct"]

‎TerminologService/valueSetToRoots.py

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import bisect
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import json
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import logging
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import os.path
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from typing import List
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import locale
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from TerminologService.TermServerConstants import TERMINOLOGY_SERVER_ADDRESS, SERVER_CERTIFICATE, PRIVATE_KEY, REQUESTS_SESSION
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from model.UiDataModel import TermCode
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from util.LoggingUtil import init_logger
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from util.logging.LoggingUtil import init_logger
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locale.setlocale(locale.LC_ALL, 'de_DE.UTF-8')
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logger = init_logger("valueSetToRoots", logging.DEBUG)

‎combined-consent-generation.py

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import json
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from model.helper import del_none
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from model.UiDataModel import TermCode
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from model.MappingDataModel import FhirMapping, FixedFHIRCriteria
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from model.MappingDataModel import FhirMapping, FixedFHIRCriteria, CQLTimeRestrictionParameter
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from model.MappingDataModel import CQLMapping, FixedCQLCriteria
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from model.TreeMap import TreeMap, TermEntryNode
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import argparse
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fhir_mapping.timeRestrictionParameter = "date"
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cql_mapping.key = term_code
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cql_mapping.context = context
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cql_mapping.timeRestrictionFhirPath = "Consent.datetime"
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cql_mapping.timeRestriction = CQLTimeRestrictionParameter("Consent.datetime", ["dateTime"])
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cql_mapping.resourceType = "Consent"
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cql_mapping.primaryCode= {
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"code": "57016-8",
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def save_json(filename: str, data):
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with open(filename, "w+") as f:
116+
with open(filename, "w+", encoding='UTF-8') as f:
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json.dump(data, f, default=lambda o: del_none(o.__dict__))
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def append_to_json(filename: str, input_filename: str, data):
121-
with open(input_filename, "r") as f:
121+
with open(input_filename, "r", encoding='UTF-8') as f:
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existing_data = json.load(f)
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existing_data.extend(data)
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save_json(filename, existing_data)
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save_json(f"{consent_input_dir}/consent-mappings_cql.json", consents_cql)
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save_json(f"{consent_input_dir}/consent-mappings-tree.json", consent_mapping_tree.to_dict())
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with open(f"{consent_input_dir}/consent-js-lookup-table.js", "w+") as f:
146+
with open(f"{consent_input_dir}/consent-js-lookup-table.js", "w+", encoding='UTF-8') as f:
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f.write(generate_js_lookup_table(lookup_table))
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if args.merge_mappings:

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