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martensonmartenson
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include uninstaller script, refactor iwc isntaller workflow
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.github/workflows/update-iwc-tools.yml renamed to .github/workflows/dispatch_update_iwc.yml

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Original file line numberDiff line numberDiff line change
@@ -1,22 +1,22 @@
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name: Install and update IWC tools
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on:
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schedule:
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# At 10:00 every day
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- cron: "0 10 * * *"
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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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instance:
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description: 'Galaxy Instance URL'
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required: true
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type: choice
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options:
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- galaxy-qa1.galaxy.cloud.e-infra.cz
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- usegalaxy.cz
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- galaxy-umsa.grid.cesnet.cz
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jobs:
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update-repos:
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permissions:
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contents: write
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pull-requests: write
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runs-on: ubuntu-latest
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strategy:
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matrix:
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toolset: [galaxy-qa1.galaxy.cloud.e-infra.cz]
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steps:
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- uses: actions/setup-python@v5
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with:
@@ -29,16 +29,16 @@ jobs:
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- name: Clone IWC repo
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run: git clone https://github.com/galaxyproject/iwc /tmp/iwc
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- name: Run update script
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run: python scripts/get_iwc_tools.py -w /tmp/iwc -s ${{ matrix.toolset }} -u uncategorized.yml
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run: python scripts/get_iwc_tools.py -w /tmp/iwc -s ${{ inputs.instance }} -u uncategorized.yml
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- name: Get current date
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id: date
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run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
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- name: Create Pull Request
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uses: peter-evans/create-pull-request@v7
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with:
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branch: iwc-update-${{ matrix.toolset }}
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branch: iwc-update-${{ inputs.instance }}
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committer: CESNETbot <[email protected]>
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title: Install IWC tools for ${{ matrix.toolset }}
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title: Install IWC tools for ${{ inputs.instance }}
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commit-message: "output of get_iwc_tools.py"
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labels: automated
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assignees: martenson

‎scripts/uninstaller.py‎

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#!/usr/bin/env python3
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"""
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Galaxy Repository Uninstaller
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Uninstalls repositories from a Galaxy instance using BioBlend.
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"""
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import argparse
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import sys
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import time
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from typing import Dict
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import yaml
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from bioblend.galaxy import GalaxyInstance
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def load_repositories(file_path: str) -> list:
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"""Load and parse YAML file containing repositories."""
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with open(file_path) as f:
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data = yaml.safe_load(f)
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repos = data.get('tools', data) if isinstance(data, dict) else data
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if not repos:
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raise ValueError("No repositories found in file")
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return repos
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def uninstall_repositories(gi: GalaxyInstance, repos: list,
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remove_from_disk: bool, delay: float) -> Dict[str, int]:
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"""Uninstall all repositories and their revisions."""
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results = {'success': 0, 'failed': 0}
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for repo in repos:
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name = repo.get('name')
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owner = repo.get('owner')
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revisions = repo.get('revisions', [])
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tool_shed = repo.get('tool_shed_url', '')
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if not all([name, owner, revisions, tool_shed]):
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print(f"\n✗ Skipping {name or 'unknown'}: missing required fields")
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results['failed'] += 1
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continue
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if not tool_shed.startswith('http'):
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tool_shed = f'https://{tool_shed}'
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print(f"\n{name} (owner: {owner})")
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for revision in revisions:
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print(f" Revision: {revision}")
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try:
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gi.toolshed.uninstall_repository_revision(
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name=name,
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owner=owner,
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changeset_revision=revision,
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tool_shed_url=tool_shed,
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remove_from_disk=remove_from_disk
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)
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print(f" ✓ Successfully uninstalled")
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results['success'] += 1
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except Exception as e:
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print(f" ✗ Failed: {e}")
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results['failed'] += 1
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if delay > 0:
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time.sleep(delay)
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return results
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def dry_run(repos: list):
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"""Display what would be uninstalled without doing it."""
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print("\n[DRY RUN MODE - No changes will be made]")
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print("=" * 60)
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for repo in repos:
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print(f"\n{repo['name']} (owner: {repo['owner']})")
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print(f" Tool shed: {repo['tool_shed_url']}")
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for rev in repo.get('revisions', []):
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print(f" - {rev}")
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def print_statistics(repos: list):
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"""Print statistics about repositories to be uninstalled."""
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from collections import Counter
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owners = Counter(r.get('owner') for r in repos)
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tool_sheds = Counter(r.get('tool_shed_url') for r in repos)
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total_revisions = sum(len(r.get('revisions', [])) for r in repos)
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print("\nStatistics:")
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print(f" Total repositories: {len(repos)}")
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print(f" Total revisions: {total_revisions}")
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print("\n Repositories by owner:")
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for owner, count in sorted(owners.items(), key=lambda x: x[1], reverse=True):
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print(f" {owner}: {count}")
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print("\n Repositories by tool shed:")
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for shed, count in sorted(tool_sheds.items(), key=lambda x: x[1], reverse=True):
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print(f" {shed}: {count}")
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def main():
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parser = argparse.ArgumentParser(
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description='Uninstall repositories from a Galaxy instance using BioBlend',
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formatter_class=argparse.RawDescriptionHelpFormatter,
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epilog="""
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Examples:
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python uninstall_repos.py https://galaxy.example.org API_KEY repos.yaml
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python uninstall_repos.py https://galaxy.example.org API_KEY repos.yaml --dry-run
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python uninstall_repos.py https://galaxy.example.org API_KEY repos.yaml --keep-on-disk
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YAML format:
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tools:
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- name: sra_tools
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owner: iuc
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revisions: [f5ea3ce9b9b0, 8848455c0270]
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tool_shed_url: toolshed.g2.bx.psu.edu
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Requirements: pip install bioblend pyyaml
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"""
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)
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parser.add_argument('galaxy_url', help='Galaxy instance URL')
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parser.add_argument('api_key', help='Galaxy API key')
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parser.add_argument('repo_file', help='YAML file with repositories to uninstall')
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parser.add_argument('--keep-on-disk', action='store_true',
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help='Keep repository files on disk')
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parser.add_argument('--delay', type=float, default=5.0,
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help='Delay between uninstalls in seconds (default: 5.0)')
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parser.add_argument('--dry-run', action='store_true',
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help='Show what would be uninstalled without doing it')
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args = parser.parse_args()
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# Load repositories
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try:
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repos = load_repositories(args.repo_file)
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except FileNotFoundError:
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print(f"Error: File '{args.repo_file}' not found")
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sys.exit(1)
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except Exception as e:
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print(f"Error: {e}")
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sys.exit(1)
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print(f"Galaxy URL: {args.galaxy_url}")
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print_statistics(repos)
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if args.dry_run:
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dry_run(repos)
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sys.exit(0)
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print("=" * 60)
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# Connect and uninstall
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try:
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gi = GalaxyInstance(url=args.galaxy_url, key=args.api_key)
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results = uninstall_repositories(gi, repos, not args.keep_on_disk, args.delay)
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except Exception as e:
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print(f"Error: {e}")
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sys.exit(1)
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# Summary
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print("\n" + "=" * 60)
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print("Uninstall Summary:")
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print(f" Successfully uninstalled: {results['success']}")
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print(f" Failed: {results['failed']}")
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sys.exit(0 if results['failed'] == 0 else 1)
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if __name__ == '__main__':
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main()

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