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65 lines
2.2 KiB
Python
65 lines
2.2 KiB
Python
#!/usr/bin/env python3
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import os
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import click
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import requests
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from tusclient import client
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from tusclient.storage import filestorage
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UPLOAD_ENDPOINT = '/api/upload/resumable_upload'
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SUBMISSION_ENDPOINT = '/api/tools/fetch'
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CHUNK_SIZE = 10 ** 7
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@click.command()
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@click.option("--url", default='http://localhost:8080', help="URL of Galaxy instance")
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@click.option("--api_key", envvar="GALAXY_API_KEY", required=True, help="API key for Galaxy instance")
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@click.option('--history_id', type=str, required=True, help="Target History ID")
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@click.option('--file_type', default="auto", type=str, help="Galaxy file type to use")
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@click.option('--dbkey', default="?", type=str, help="Genome Build for dataset")
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@click.option('--filename', type=str, help="Filename to use in Galaxy history, if different from path")
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@click.option('--storage', type=click.Path(), required=False, help="Store URLs to resume here")
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@click.argument('path', type=click.Path())
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def upload_file(url, path, api_key, history_id, file_type='auto', dbkey='?', filename=None, storage=None):
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headers = {'x-api-key': api_key}
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my_client = client.TusClient(f"{url}{UPLOAD_ENDPOINT}", headers=headers)
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filename = filename or os.path.basename(path)
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metadata = {
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'filename': filename,
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'history_id': history_id,
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'file_type': file_type,
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'dbkey': dbkey,
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}
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# Upload a file to a tus server.
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if storage:
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storage = filestorage.FileStorage(storage)
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uploader = my_client.uploader(path, metadata=metadata, url_storage=storage)
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uploader.chunk_size = CHUNK_SIZE
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uploader.upload()
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# Extract session from created upload URL
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session_id = uploader.url.rsplit('/', 1)[1]
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payload = {
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"history_id": history_id,
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"targets":
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[
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{
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"destination": {"type": "hdas"},
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"elements": [{"src": "files", "ext": file_type, "dbkey": dbkey, "name": filename}],
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}
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],
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"files_0|file_data": {"session_id": session_id, "name": filename},
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}
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response = requests.post(
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f"{url}{SUBMISSION_ENDPOINT}",
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json=payload,
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headers=headers,
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)
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response.raise_for_status()
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if __name__ == '__main__':
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upload_file()
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