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NishaSharma14NishaSharma14
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Merge pull request #1260 from NFDI4Chem/development
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2 parents f2c85bb + 2f13b41 commit 1589c09

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Lines changed: 4350 additions & 1988 deletions

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‎.env.example‎

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Original file line numberDiff line numberDiff line change
@@ -104,6 +104,10 @@ ORCID_CLIENT_SECRET=
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ORCID_REDIRECT_URL=http://localhost/auth/login/orcid/callback
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ORCID_ENVIRONMENT=sandbox
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NFDIAAI_CLIENT_ID=
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NFDIAAI_CLIENT_SECRET=
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NFDIAAI_REDIRECT_URL="${APP_URL}/auth/login/regapp/callback"
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TELESCOPE_ENABLED=false
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#DATACITE Properties
@@ -117,4 +121,6 @@ NMRKIT_URL=https://nodejs.nmrxiv.org
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CAS_URL=https://commonchemistry.cas.org
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PUBCHEM_URL=https://pubchem.ncbi.nlm.nih.gov
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COMMON_CHEMISTRY_URL=https://commonchemistry.cas.org
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CHEMISTRY_STANDARDIZE_URL=https://api.cheminf.studio/latest/chem/standardize
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CHEMISTRY_STANDARDIZE_URL=https://api.cheminf.studio/latest/chem/standardize
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BACKUP_KEEP_DAYS=7

‎.github/workflows/dev-build.yml‎

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@@ -16,11 +16,23 @@ env:
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REPOSITORY_NAMESPACE: nfdi4chem
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jobs:
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lint-security:
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name: Lint & Security (reusable)
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uses: ./.github/workflows/lint-security-check.yml
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permissions:
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contents: read
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security-events: write
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with:
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run_php: true
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run_js: true
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run_secrets: true
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# Build and publish Docker images for the development environment
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setup-build-publish-deploy:
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name: Build & deploy to development
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runs-on: ubuntu-latest
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# Tip: gate deploys on tests with `needs: php-unit-test` once a tests job exists
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needs: [lint-security]
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# Environment provides secrets and protection rules
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environment:
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name: Dev

‎.github/workflows/lint-security-check.yml‎

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name: Lint and Security Checks
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on:
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workflow_call:
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inputs:
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run_php:
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description: "Run PHP lint & security job"
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required: false
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type: boolean
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default: true
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run_js:
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description: "Run JS lint & security job"
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required: false
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type: boolean
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default: true
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run_secrets:
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description: "Run secret leakage detection job"
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required: false
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type: boolean
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default: true
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permissions:
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contents: read
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security-events: write
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concurrency:
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group: lint-security-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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# Lints PHP code style (Pint) and audits Composer dependencies for vulnerabilities
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php:
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if: ${{ inputs.run_php }}
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name: PHP Lint & Security
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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 PHP
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uses: shivammathur/setup-php@v2
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with:
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php-version: '8.3'
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coverage: none
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tools: composer
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extensions: mbstring, intl, pdo, pdo_mysql, pdo_pgsql
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ini-values: memory_limit=512M
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- name: Cache Composer dependencies
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uses: actions/cache@v4
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with:
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path: |
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~/.composer/cache/files
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~/.cache/composer/files
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key: ${{ runner.os }}-composer-${{ hashFiles('**/composer.lock') }}
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restore-keys: |
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${{ runner.os }}-composer-
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- name: Validate composer.json
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run: composer validate --no-check-publish --strict
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- name: Install PHP dependencies
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run: composer install --no-interaction --prefer-dist --no-progress
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- name: PHP code style (Pint)
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run: vendor/bin/pint --test
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- name: Composer security audit
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run: composer audit --no-interaction --locked
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# Runs JS/Vue linting (ESLint), formatting check (Prettier), and npm security audit
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js:
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if: ${{ inputs.run_js }}
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name: JS Lint & Security
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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 Node dependencies
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run: npm ci
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- name: ESLint
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run: npx eslint --ext .js,.vue --ignore-path .gitignore resources/js
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- name: Prettier (check)
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run: npx prettier resources/js --check
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- name: npm audit (high+)
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run: npm audit --audit-level=high
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# Scans the repository for hard-coded secrets using Gitleaks
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secrets:
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if: ${{ inputs.run_secrets }}
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name: Secret Leakage Scan
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Install Gitleaks
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run: |
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set -e
109+
GITLEAKS_VERSION=8.18.4
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curl -sSL -o gitleaks.tar.gz "https://github.com/gitleaks/gitleaks/releases/download/v${GITLEAKS_VERSION}/gitleaks_${GITLEAKS_VERSION}_linux_x64.tar.gz"
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tar -xzf gitleaks.tar.gz gitleaks
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sudo mv gitleaks /usr/local/bin/gitleaks
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gitleaks version
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- name: Gitleaks scan
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id: gitleaks
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run: |
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set +e
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gitleaks detect --source . --no-git --redact --report-format sarif --report-path gitleaks.sarif
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code=$?
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echo "$code" > gitleaks-exit-code.txt
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if [ ! -f gitleaks.sarif ]; then
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echo "Gitleaks did not produce SARIF file; creating empty stub." >&2
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printf '%s\n' '{' \
125+
' "version": "2.1.0",' \
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' "runs": [' \
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' {' \
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' "tool": { "driver": { "name": "Gitleaks", "informationUri": "https://github.com/gitleaks/gitleaks" } },' \
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' "results": []' \
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' }' \
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' ]' \
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'}' > gitleaks.sarif
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fi
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# Always succeed here; we fail after uploading SARIF for annotations
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exit 0
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- name: Upload SARIF (code scanning)
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if: always()
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uses: github/codeql-action/upload-sarif@v3
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with:
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sarif_file: gitleaks.sarif
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- name: Fail if Gitleaks found leaks
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run: |
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code=$(cat gitleaks-exit-code.txt || echo 0)
145+
if [ "$code" -ne 0 ]; then
146+
echo "Gitleaks detected potential secrets (exit code $code). Failing job after SARIF upload." >&2
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exit 1
148+
fi

‎.github/workflows/pr-lint.yml‎

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name: PR Lint & Security
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on:
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pull_request:
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types: [opened, synchronize, reopened, ready_for_review]
6+
branches:
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- development
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- main
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10+
permissions:
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contents: read
12+
security-events: write
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14+
jobs:
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lint-security:
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name: Lint & Security (PR)
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uses: ./.github/workflows/lint-security-check.yml
18+
with:
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run_php: true
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run_js: true
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run_secrets: true

‎.github/workflows/prod-build.yml‎

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@@ -20,10 +20,22 @@ env:
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REPOSITORY_NAMESPACE: nfdi4chem
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jobs:
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lint-security:
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name: Lint & Security (reusable)
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uses: ./.github/workflows/lint-security-check.yml
26+
permissions:
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contents: read
28+
security-events: write
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with:
30+
run_php: true
31+
run_js: true
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run_secrets: true
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2334
# Guard: confirm input and authorize actor
2435
guard:
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name: Access control and confirmation
2637
runs-on: ubuntu-latest
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needs: [lint-security]
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steps:
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- name: Validate actor and confirmation
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shell: bash

‎.github/workflows/test.yml‎

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This file was deleted.

‎.phpunit.cache/test-results‎

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‎app/Console/Commands/CleanupBackups.php‎

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<?php
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namespace App\Console\Commands;
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use App\Jobs\CleanupBackupsJob;
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use Illuminate\Console\Command;
7+
8+
class CleanupBackups extends Command
9+
{
10+
/**
11+
* The name and signature of the console command.
12+
*
13+
* @var string
14+
*/
15+
protected $signature = 'nmrxiv:backup-cleanup';
16+
17+
/**
18+
* The console command description.
19+
*
20+
* @var string
21+
*/
22+
protected $description = 'Cleanup of postgres backups from ceph and retain only last 7 backups.';
23+
24+
/**
25+
* Execute the console command.
26+
*/
27+
public function handle(): void
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{
29+
CleanupBackupsJob::dispatch();
30+
}
31+
}

‎app/Http/Controllers/ApplicationController.php‎

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@@ -21,13 +21,63 @@ class ApplicationController extends Controller
2121
public function compounds(Request $request)
2222
{
2323
$query = $request->get('query');
24-
$limit = $request->get('limit') ? $limit : 24;
24+
$limit = $request->get('limit') ? $request->get('limit') : 24;
2525
$page = $request->query('page');
2626
$tagType = $request->query('tagType') ? $request->query('tagType') : null;
2727

2828
return Inertia::render('Public/Compounds', compact(['query', 'limit', 'page', 'tagType']));
2929
}
3030

31+
/**
32+
* Resolve compound by ID and render the appropriate view
33+
*
34+
* @return Inertia\Inertia
35+
*/
36+
public function resolveCompound(Request $request, $identifier)
37+
{
38+
$resolvedModel = resolveIdentifier($identifier);
39+
$namespace = $resolvedModel['namespace'];
40+
$model = $resolvedModel['model'];
41+
42+
if ($model && $namespace === 'Molecule') {
43+
// Redirect to spectra page with compound parameter for now
44+
// This maintains the current compound viewing functionality
45+
return redirect('/spectra?compound='.substr($identifier, 1));
46+
} else {
47+
abort(404, 'Compound not found');
48+
}
49+
}
50+
51+
/**
52+
* Resolve sample by ID and render the appropriate view
53+
*
54+
* @return Inertia\Inertia
55+
*/
56+
public function resolveSample(Request $request, $identifier)
57+
{
58+
return $this->resolve($request, $identifier);
59+
}
60+
61+
/**
62+
* Resolve project by ID and render the appropriate view
63+
*
64+
* @return Inertia\Inertia
65+
*/
66+
public function resolveProject(Request $request, $identifier)
67+
{
68+
return $this->resolve($request, $identifier);
69+
}
70+
71+
/**
72+
* Resolve dataset by ID and render the appropriate view
73+
*
74+
* @return Inertia\Inertia
75+
*/
76+
public function resolveDataset(Request $request, $identifier)
77+
{
78+
return $this->resolve($request, $identifier);
79+
}
80+
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/**
3282
* Resolve the incoming request into right models and render the
3383
* inertia view

‎app/Http/Middleware/HandleInertiaRequests.php‎

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@@ -63,6 +63,7 @@ public function share(Request $request)
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'twitter' => (env('TWITTER_CLIENT_ID') !== null && env('TWITTER_CLIENT_ID') !== ''),
6464
'github' => (env('GITHUB_CLIENT_ID') !== null && env('GITHUB_CLIENT_ID') !== ''),
6565
'orcid' => (env('ORCID_CLIENT_ID') !== null && env('ORCID_CLIENT_ID') !== ''),
66+
'nfdiaai' => (env('NFDIAAI_CLIENT_ID') !== null && env('NFDIAAI_CLIENT_ID') !== ''),
6667
'config.announcements' => Schema::hasTable('announcements') ? Announcement::active() : null,
6768
'url' => env('APP_URL'),
6869
'nmriumURL' => env('NMRIUM_URL'),

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