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71 lines
2.6 KiB
Python
71 lines
2.6 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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from __future__ import print_function
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import argparse
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import os
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import sys
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import time
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import yaml
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import logging
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import requests
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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('-r', '--report-directory', help='Directory in which reports are stored',
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default=os.path.abspath(os.path.join('.', 'reports')))
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parser.add_argument('-c', '--config', help='Path to GRT config file',
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default=default_config)
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parser.add_argument("-l", "--loglevel", choices=['debug', 'info', 'warning', 'error', 'critical'],
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help="Set the logging level", default='warning')
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args = parser.parse_args()
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logging.info('Loading GRT ini...')
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try:
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with open(args.config) as handle:
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config = yaml.load(handle)
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except Exception:
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logging.info('Using default GRT Configuration')
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with open(sample_config) as handle:
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config = yaml.load(handle)
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REPORT_DIR = args.report_directory
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GRT_URL = config['grt']['url']
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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 = {
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'AUTHORIZATION': GRT_INSTANCE_ID + ':' + GRT_API_KEY
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}
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r = requests.post(GRT_URL + 'api/whoami', headers=headers)
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data = r.json()
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# we get back some information about which reports had previously been uploaded.
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remote_reports = data['uploaded_reports']
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# so now we can know which to send.
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local_reports = [x.strip('.json') for x in os.listdir(REPORT_DIR) if x.endswith('.json')]
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for report_id in local_reports:
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if not report_id in remote_reports:
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print("Uploading %s" % report_id)
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files = {
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'meta': open(os.path.join(sys.argv[1], report_id + '.json'), 'rb'),
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'data': open(os.path.join(sys.argv[1], report_id + '.tsv.gz'), 'rb')
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}
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data = {
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'identifier': report_id
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}
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r = requests.post(GRT_URL + 'api/v2/upload', files=files, headers=headers, data=data)
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print(r.json())
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if __name__ == '__main__':
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main(sys.argv)
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