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‎.github/workflows/build.yml‎

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# Basic ODK workflow
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name: build
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the main branch
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push:
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branches: [*]
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pull_request:
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branches: [*]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "ontology_qc"
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ontology_qc:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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container: obolibrary/odkfull:v1.6
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v4
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- name: Build ontology
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env:
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DEFAULT_BRANCH: main
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run: cd src/ontology && make refresh-imports all_assets ROBOT_ENV='ROBOT_JAVA_ARGS=-Xmx6G'
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- name: Commit files # commit the src folder
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uses: EndBug/add-and-commit@v9
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with:
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message: "updated ontology"
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add: "*.* --force"
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cwd: "./src/"
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default_author: github_actions

‎.github/workflows/docs.yml‎

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# Sample workflow for building and deploying a Jekyll site to GitHub Pages
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name: create widoco documentation
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on:
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# Runs on pushes targeting the default branch
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push:
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branches: ["main"]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
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permissions:
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contents: read
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pages: write
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id-token: write
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# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
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# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
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concurrency:
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group: "pages"
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cancel-in-progress: false
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jobs:
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# Check job
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check:
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runs-on: ubuntu-latest
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outputs:
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ontology-exists: ${{ steps.check.outputs.exists }}
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ontology-file: ${{ steps.check.outputs.file }}
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Check for ontology file
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id: check
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run: |
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ONTOLOGY_FILE=$(find src/ontology/ -name "*-full.owl" -type f | head -1)
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if [ -z "$ONTOLOGY_FILE" ]; then
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echo "No *-full.owl file found in src/ontology/ directory."
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echo "exists=false" >> $GITHUB_OUTPUT
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else
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echo "Found ontology file: $ONTOLOGY_FILE"
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echo "exists=true" >> $GITHUB_OUTPUT
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echo "file=$ONTOLOGY_FILE" >> $GITHUB_OUTPUT
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fi
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# Build job
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build:
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runs-on: ubuntu-latest
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needs: check
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if: needs.check.outputs.ontology-exists == 'true'
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Setup Pages
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uses: actions/configure-pages@v5
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- name: Build HTML for main
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run: |
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wget -O widoco.jar https://github.com/dgarijo/Widoco/releases/download/v1.4.25/widoco-1.4.25-jar-with-dependencies_JDK-11.jar
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mkdir ./_site
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java -jar widoco.jar -ontFile ${{ needs.check.outputs.ontology-file }} -outFolder ./_site -uniteSections -includeAnnotationProperties -lang en-de -getOntologyMetadata -noPlaceHolderText -rewriteAll -webVowl
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- name: add default entry point
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run: |
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cp ./_site/index-en.html ./_site/index.html
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- name: Upload artifact
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uses: actions/upload-pages-artifact@v3
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# Deployment job
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deploy:
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

‎.github/workflows/seed.yml‎

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# SEEDING ODK workflow
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name: seed odk
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# Controls when the action will run.
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on:
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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inputs:
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ontology_id:
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description: 'Ontology ID (replaces id in seed.yaml)'
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required: true
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uribase_suffix:
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description: 'URI base suffix (replaces uribase_suffix in seed.yaml)'
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required: true
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odk_tag:
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description: 'ODK Docker tag to use'
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required: false
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default: 'latest'
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config_file:
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description: 'Configuration file name'
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required: false
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default: 'seed-template.yaml'
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "seed_ontology"
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seed_ontology:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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container: obolibrary/odkfull:${{ github.event.inputs.odk_tag || 'latest' }}
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v4
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- name: Set up Git config
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run: |
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git config --global user.name "${{ github.actor }}"
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git config --global user.email "${{ github.actor }}@users.noreply.github.com"
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- name: Generate unique branch name
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run: |
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BRANCH_NAME="fresh-seed-$(date +%Y%m%d-%H%M%S)"
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echo "BRANCH_NAME=$BRANCH_NAME" >> $GITHUB_ENV
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- name: Verify seed config file exists
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run: |
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if [ ! -f "${{ github.event.inputs.config_file || 'seed-template.yaml' }}" ]; then
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echo "Error: Configuration file ${{ github.event.inputs.config_file || 'seed-template.yaml' }} not found!"
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exit 1
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fi
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echo "Using configuration file: ${{ github.event.inputs.config_file || 'seed-template.yaml' }}"
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- name: Update seed-template.yaml with input values
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run: |
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CONFIG_FILE="${{ github.event.inputs.config_file || 'seed-template.yaml' }}"
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echo "Original seed-template.yaml content:"
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cat "$CONFIG_FILE"
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# Replace id value
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sed -i "s/^id:.*/id: ${{ github.event.inputs.ontology_id }}/" "$CONFIG_FILE"
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# Replace uribase_suffix value
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sed -i "s/^uribase_suffix:.*/uribase_suffix: ${{ github.event.inputs.uribase_suffix }}/" "$CONFIG_FILE"
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echo "Updated seed-template.yaml content:"
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cat "$CONFIG_FILE"
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- name: Run ODK seed
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env:
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ODK_IMAGE: odkfull
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ODK_TAG: ${{ github.event.inputs.odk_tag || 'latest' }}
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ODK_GITNAME: ${{ github.actor }}
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ODK_GITEMAIL: ${{ github.actor }}@users.noreply.github.com
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run: |
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echo "This script only works with ODK 1.3.2 and later. For ODK 1.3.1 or earlier, use https://raw.githubusercontent.com/INCATools/ontology-development-kit/v1.3.1/seed-via-docker.sh"
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/tools/odk.py seed \
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--gitname "$ODK_GITNAME" \
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--gitemail "$ODK_GITEMAIL" \
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-c \
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-C ${{ github.event.inputs.config_file || 'seed-template.yaml' }}
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- name: Copy generated files to root
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run: |
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TARGET_DIR="target/${{ github.event.inputs.ontology_id }}"
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if [ ! -d "$TARGET_DIR" ]; then
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echo "Error: Target directory $TARGET_DIR not found!"
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exit 1
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fi
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echo "Copying files from $TARGET_DIR to root, excluding .git and .github directories..."
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# Copy all files and directories except .git and .github
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find "$TARGET_DIR" -mindepth 1 -maxdepth 1 ! -name '.git' ! -name '.github' -exec cp -r {} . \;
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# List what was copied
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echo "Files copied to root:"
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ls -la
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- name: Clean up target directory
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run: |
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echo "Removing target directory to avoid git conflicts..."
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rm -rf target/
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git status
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- name: Create Pull Request
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uses: peter-evans/create-pull-request@v5
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with:
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branch: ${{ env.BRANCH_NAME }}
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base: main
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title: "ODK Seed: ${{ github.event.inputs.ontology_id }}"
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commit-message: "ODK seed generated files for ${{ github.event.inputs.ontology_id }} using ${{ github.event.inputs.config_file || 'seed.yaml' }}"
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body: |
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## ODK Seed Generated Files
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- **Ontology ID**: `${{ github.event.inputs.ontology_id }}`
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- **URI Base Suffix**: `${{ github.event.inputs.uribase_suffix }}`
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- **Config File**: `${{ github.event.inputs.config_file || 'seed-template.yaml' }}`
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- **ODK Tag**: `${{ github.event.inputs.odk_tag || 'latest' }}`
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This PR contains the generated ontology files from ODK seed.

‎.gitignore‎

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# ODK-managed rules, do not modify
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# If you need to add your own ignore rules, you may do so below
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# the "End ODK-managed rules" marker at the end of this file.
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.DS_Store
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semantic.cache
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bin/
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.trunk/
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*.tmp
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*.tmp.obo
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*.tmp.owl
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*.tmp.json
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*-relation-graph.tsv.gz
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.template.db
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.github/token.txt

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