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Merge pull request #161 from brainlife/hotfix/user-check
Hotfix/user check
2 parents edb8692 + 83c1969 commit 07dfe84

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Lines changed: 46180 additions & 21536 deletions

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‎.dockerignore‎

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ui
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# This file applies only to Docker builds whose context is the repo root (`context: .`),
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# e.g. the api and ui services in docker-compose.yml. (A ui/.dockerignore is not used when
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# context is the repo root — only this file is.) Other services (handler, telemetry)
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# use their own build directories, so ignoring paths here does not affect those images.
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#
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# Shared context rules:
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# - api/ must NOT be listed — the API Dockerfile copies ./api; hiding it breaks that image.
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# - ui/ must NOT be listed — the UI Dockerfile copies ./ui after npm ci.
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#
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# handler/ is safe to exclude here — the handler image is built with context ./handler, not
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# the repo root, so this ignore list does not apply to that build.
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#
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# electron/: npm workspaces only require electron/package.json in context for the root
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# lockfile. Simple patterns like electron/* would also exclude that file. We exclude
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# heavy paths only (node_modules, dist, release); other electron sources may still be
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# sent in the context but are small compared to those directories.
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handler
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workdir
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test
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bids-specification
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node_modules
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ui/node_modules
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electron/node_modules
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electron/dist
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electron/release
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.git

‎.eslintrc.json‎

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"no-empty": "error",
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"no-empty-function": "error",
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"no-floating-decimal": "error"
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}
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},
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"overrides": [
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{
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"files": ["**/*.test.ts"],
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"rules": {
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"max-nested-callbacks": ["warn", { "max": 8 }]
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}
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}
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]
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}

‎.github/workflows/build-desktop.yml‎

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name: Build Desktop App
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on:
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push:
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tags:
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- 'v*'
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permissions:
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contents: write
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jobs:
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create-release:
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runs-on: ubuntu-latest
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steps:
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- name: Create release
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uses: softprops/action-gh-release@v2
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with:
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name: ${{ github.ref_name }}
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draft: false
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prerelease: false
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generate_release_notes: true
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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build:
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needs: create-release
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strategy:
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fail-fast: false
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matrix:
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include:
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- os: macos-latest
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platform: darwin
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arch: arm64
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eb_flags: --mac --arm64
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- os: windows-latest
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platform: windows
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arch: amd64
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eb_flags: --win --x64
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- os: ubuntu-latest
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platform: linux
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arch: amd64
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eb_flags: --linux --x64
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash
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# specify bash for windows
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env:
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npm_config_script_shell: bash
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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with:
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submodules: recursive
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- name: Setup Node.js
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uses: actions/setup-node@v4
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with:
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node-version: '20'
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- name: Install dependencies
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run: npm ci
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- name: Fetch binaries
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run: bash fetch-binaries.sh ${{ matrix.platform }} ${{ matrix.arch }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Remove embedded archives / package test fixtures (mac notarization)
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if: matrix.platform == 'darwin'
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run: |
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PY_SITE="handler/bin/python-runtime/venv/lib/python3.8/site-packages"
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# Some vendored Python packages ship test fixtures as zip/tar archives (and sometimes odd perms).
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# Apple's notarization pipeline can flag these when bundled inside a signed app.
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rm -rf "$PY_SITE/joblib/test"
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rm -rf "$PY_SITE/pooch/tests"
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# remove dcm2niix_binaries to avoid notarization failure. We will point to the bundled dcm2niix in the app.
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# Note that we have pinned pypet2bids to 1.4.6 in requirements.txt, and it uses dcm2niix v1.0.20250505.
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# in the future, if we want to upgrade pypet2bids, we must make sure that our version of dcm2niix is compatible and vice versa.
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rm -rf "$PY_SITE/pypet2bids/dcm2niix_binaries"
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- name: Clean dist
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run: rm -rf electron/dist
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- name: Build JS bundles
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working-directory: electron
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run: |
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npm run build:electron-api
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npm run build:electron-handler
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npm run build:electron-handler-scripts
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- name: Copy Python files, BIDS schema, and templates
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working-directory: electron
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run: |
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npm run build:electron-python
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npm run build:electron-bids-spec
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npm run build:electron-templates
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- name: Build frontend
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working-directory: ui
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run: npm run build:electron
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- name: Transpile main process
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working-directory: electron
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run: |
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npm run build:electron-preload
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npm run build:electron-main
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- name: Validate Apple signing secrets
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if: matrix.platform == 'darwin'
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run: |
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test -n "${{ secrets.APPLE_CERTIFICATE_P12_BASE64 }}"
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test -n "${{ secrets.APPLE_CERTIFICATE_PASSWORD }}"
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test -n "${{ secrets.APPLE_API_KEY_ID }}"
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test -n "${{ secrets.APPLE_API_ISSUER }}"
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test -n "${{ secrets.APPLE_API_KEY_P8_BASE64 }}"
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- name: Import Apple signing certificate
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if: matrix.platform == 'darwin'
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uses: apple-actions/import-codesign-certs@v3
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with:
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p12-file-base64: ${{ secrets.APPLE_CERTIFICATE_P12_BASE64 }}
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p12-password: ${{ secrets.APPLE_CERTIFICATE_PASSWORD }}
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- name: Create Apple API key file
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if: matrix.platform == 'darwin'
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run: |
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API_KEY_PATH="$RUNNER_TEMP/AuthKey_${APPLE_API_KEY_ID}.p8"
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# Support both GNU and BSD base64 flags on GitHub runners.
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if ! printf '%s' "$APPLE_API_KEY_P8_BASE64" | base64 --decode > "$API_KEY_PATH" 2>/dev/null; then
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printf '%s' "$APPLE_API_KEY_P8_BASE64" | base64 -D > "$API_KEY_PATH"
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fi
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env:
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APPLE_API_KEY_P8_BASE64: ${{ secrets.APPLE_API_KEY_P8_BASE64 }}
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APPLE_API_KEY_ID: ${{ secrets.APPLE_API_KEY_ID }}
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- name: Package (macOS signed + notarized)
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if: matrix.platform == 'darwin'
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working-directory: electron
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timeout-minutes: 360
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run: |
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npx electron-builder ${{ matrix.eb_flags }} &
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EB_PID=$!
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while kill -0 "$EB_PID" 2>/dev/null; do
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echo "[heartbeat] electron-builder still running at $(date -u +'%Y-%m-%dT%H:%M:%SZ')"
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ps -axo pid,ppid,etime,command | grep -E "electron-builder|app-builder|codesign|notarytool" | grep -v grep || true
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sleep 60
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done
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wait "$EB_PID"
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env:
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# Verbose logs: builder-util registers `electron-builder`; @electron/notarize registers `electron-notarize`.
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DEBUG: 'electron-builder*,electron-notarize*'
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APPLE_API_KEY: ${{ runner.temp }}/AuthKey_${{ secrets.APPLE_API_KEY_ID }}.p8
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APPLE_API_KEY_ID: ${{ secrets.APPLE_API_KEY_ID }}
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APPLE_API_ISSUER: ${{ secrets.APPLE_API_ISSUER }}
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CSC_KEY_PASSWORD: ${{ secrets.APPLE_CERTIFICATE_PASSWORD }}
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- name: Package (Windows/Linux)
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if: matrix.platform != 'darwin'
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working-directory: electron
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run: npx electron-builder ${{ matrix.eb_flags }}
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- name: Verify macOS code signing and notarization
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if: matrix.platform == 'darwin'
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working-directory: electron
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run: |
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# electron-builder puts the .app under release/mac-<arch>/ (not release/*.app).
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APP_PATH=$(find release -name '*.app' -type d | head -n 1)
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DMG_PATH=$(find release -maxdepth 1 -name '*.dmg' -type f | head -n 1)
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if [[ -z "$APP_PATH" || ! -d "$APP_PATH" ]]; then
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echo "No .app bundle found under electron/release (expected e.g. release/mac-arm64/*.app):"
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find release -maxdepth 4 -type d -print || true
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exit 1
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fi
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if [[ -z "$DMG_PATH" || ! -f "$DMG_PATH" ]]; then
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echo "No .dmg found under electron/release:"
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ls -la release || true
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exit 1
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fi
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echo "Verifying app signature: $APP_PATH"
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codesign --verify --deep --strict --verbose=2 "$APP_PATH"
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codesign -dv --verbose=4 "$APP_PATH" 2>&1
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# electron-notarize staples the .app; the .dmg is built afterward and usually has no separate ticket.
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echo "Validating notarization ticket on app bundle: $APP_PATH"
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xcrun stapler validate "$APP_PATH"
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echo "Gatekeeper assess app bundle: $APP_PATH"
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spctl --assess --verbose=4 "$APP_PATH"
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echo "DMG artifact present (notarization ticket is on the .app, not this wrapper): $DMG_PATH"
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test -f "$DMG_PATH"
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- name: Upload artifacts to release
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uses: softprops/action-gh-release@v2
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with:
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files: |
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electron/release/*.dmg
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electron/release/*.exe
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electron/release/*.AppImage
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electron/release/*.deb
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/unit-tests.yml‎

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---
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name: Jest Unit Tests
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on:
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push:
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branches: [master]
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pull_request:
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branches: [master]
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workflow_dispatch:
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jobs:
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jest:
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name: Run Jest unit tests
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runs-on: ubuntu-latest
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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 Node.js
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uses: actions/setup-node@v4
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with:
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node-version: '20'
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cache: npm
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- name: Install dependencies
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run: npm ci
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- name: Run unit tests
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run: npm test -- --ci

‎.gitignore‎

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handler/container/ROBEXv12.linux64.tar.gz
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api/*.pub
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api/*.key
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api/ezbids.key
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api/*.js
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api/*.js.map
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api/**/*.pub
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api/**/*.key
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api/**/*.key
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api/**/*.js
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api/**/*.js.map
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api/**/*.cjs
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api/**/*.cjs.map
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handler/**/*.js
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handler/**/*.js.map
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handler/**/*.cjs
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handler/**/*.cjs.map
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handler/bin/*
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handler/*.js
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handler/*.js.map
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handler/*.cjs
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handler/*.log
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tmp/*
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electron/node_modules
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electron/dist
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electron/dist/*
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electron/build
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electron/release
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electron/**/*.js
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electron/dist/*
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electron/**/*.js
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electron/**/*.js.map
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electron/**/*.cjs
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electron/**/*.cjs.map
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electron/ezbids.key
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electron/ezbids.pub

‎.lintstagedrc.json‎

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{
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"**/*.{js,json,ts,vue}": ["npm run style-check", "npm run lint-check"]
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"**/*.{js,json,ts,vue}": ["npm run style-check", "npm run lint-check"],
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"**/*.{js,ts,vue}": ["npm run test -- --findRelatedTests --passWithNoTests"]
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}

‎.prettierignore‎

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.vscode/settings.json
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# Auto-generated by unplugin-vue-components (indent does not match repo Prettier).
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ui/components.d.ts
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node_modules
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ui/node_modules
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ui/src/components/modalityForm.vue
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ui/src/libUnsafe.ts
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handler/convert.js
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ui/test/events/*.js
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api/*.ts
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ui/src/Finalize.vue
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ui/src/Finalize.vue
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bids-specification/*

‎Dockerfile‎

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FROM node:20
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COPY . /app
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WORKDIR /app
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RUN npm install -g npm@9.5.1
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RUN npm install -g pm2 typescript tsc-watch
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RUN npm install
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# For npm to work and run npm install with specific workspaces
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COPY package.json package-lock.json ./
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COPY ui/package.json ./ui/
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COPY electron/package.json ./electron/
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# API/runtime only: root deps from the lockfile — not ui or electron workspace packages (avoids
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# pulling Vite, electron, electron-builder, etc. into this image).
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RUN npm ci --workspaces=false
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COPY tsconfig.base.json ./
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COPY api ./api

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