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79 lines
2.8 KiB
Python
79 lines
2.8 KiB
Python
#!/usr/bin/env python
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"""Script for submitting Galaxy job information to the Galactic Radio Telescope.
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See doc/source/admin/grt.rst for more detailed usage information.
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"""
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import argparse
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import logging
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import os
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import sys
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import requests
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import yaml
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sample_config = os.path.abspath(os.path.join(os.path.dirname(__file__), "grt.yml.sample"))
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default_config = os.path.abspath(os.path.join(os.path.dirname(__file__), "grt.yml"))
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def main(argv):
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parser = argparse.ArgumentParser()
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parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
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parser.add_argument(
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"-r",
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"--report-directory",
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help="Directory in which reports are stored",
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default=os.path.abspath(os.path.join(".", "reports")),
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)
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parser.add_argument("-g", "--grt-config", help="Path to GRT config file", default=default_config)
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parser.add_argument(
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"-l",
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"--loglevel",
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choices=["debug", "info", "warning", "error", "critical"],
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help="Set the logging level",
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default="warning",
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)
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args = parser.parse_args()
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logging.getLogger().setLevel(getattr(logging, args.loglevel.upper()))
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logging.info("Loading GRT configuration...")
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try:
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with open(args.grt_config) as handle:
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config = yaml.safe_load(handle)
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except Exception:
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logging.exception("Could not parse GRT configuration")
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sys.exit(1)
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REPORT_DIR = args.report_directory
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GRT_URL = config["grt"]["url"].rstrip("/") + "/"
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GRT_INSTANCE_ID = config["grt"]["instance_id"]
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GRT_API_KEY = config["grt"]["api_key"]
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# Contact the server and check auth details.
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headers = {"AUTHORIZATION": f"{GRT_INSTANCE_ID}:{GRT_API_KEY}"}
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r = requests.post(GRT_URL + "api/whoami", headers=headers)
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data = r.json()
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# Get back some information about which reports had previously been uploaded.
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remote_reports = data["uploaded_reports"]
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logging.debug("Remote reports: %s", remote_reports)
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local_reports = [x.strip(".json") for x in os.listdir(REPORT_DIR) if x.endswith(".json")]
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logging.debug("Local reports: %s", local_reports)
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# Now we know which to send.
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for report_id in local_reports:
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if report_id not in remote_reports:
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logging.info("Uploading %s", report_id)
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files = {
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"meta": open(os.path.join(REPORT_DIR, report_id + ".json"), "rb"),
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"data": open(os.path.join(REPORT_DIR, report_id + ".tar.gz"), "rb"),
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}
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data = {"identifier": report_id}
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r = requests.post(GRT_URL + "api/v2/upload", files=files, headers=headers, data=data)
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if r.ok:
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logging.info("Uploaded successfully %s", report_id)
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else:
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logging.critical("Non-OK response: %s", r.status_code)
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if __name__ == "__main__":
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main(sys.argv)
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