mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
Nicola Soranzo
8cdca0f343
introduced in https://github.com/galaxyproject/galaxy/pull/18003 . In particular, when using requests in the tests to connect to Galaxy or the ToolShed it's not needed to use the modified headers. Also: - Move some imports after conditional imports. - Fix type annotations in `lib/tool_shed/test/base/populators.py` - Fix typo bug in `test/unit/util/test_get_url.py`
63 lines
2.2 KiB
Python
63 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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"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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