Mercurial > repos > blankenberglab > data_manager_refgenie_pull

annotate data_manager/data_manager_refgenie_pull.py @ 2:2cb1863cd236 draft

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"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 2b81f6b9cadf15796ef7f1f6a0d12f05d3f405d7"
author blankenberglab
date Fri, 01 Oct 2021 14:40:21 +0000
parents aec9bc48cdb7
children b2fa406276e7
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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1 #!/usr/bin/env python
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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4 import argparse
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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5 import logging
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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6 from base64 import urlsafe_b64encode
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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7 from urllib.parse import urljoin
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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9 import refgenconf
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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10 import requests
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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13 log = logging.getLogger("tools.iuc.data_managers.data_manager_refgenie_pull")
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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16 def galaxy_code_get_refgenie_assets(refgenie_config_file):
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2cb1863cd236 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 2b81f6b9cadf15796ef7f1f6a0d12f05d3f405d7"
blankenberglab
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17 try:
2cb1863cd236 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 2b81f6b9cadf15796ef7f1f6a0d12f05d3f405d7"
blankenberglab
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18 rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True)
2cb1863cd236 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 2b81f6b9cadf15796ef7f1f6a0d12f05d3f405d7"
blankenberglab
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19 except refgenconf.exceptions.RefgenconfError as e:
2cb1863cd236 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 2b81f6b9cadf15796ef7f1f6a0d12f05d3f405d7"
blankenberglab
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20 return[{'name': str(e), 'value': 'ERROR', 'options': [], 'selected': False}]
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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21 rval = []
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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22 for urlname, genomes in rgc.listr().items():
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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23 urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8')
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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24 ul = []
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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25 for genome, assets in genomes.items():
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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26 al = []
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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27 for name in assets:
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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28 al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False})
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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29 ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False})
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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30 rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False})
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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31 return rval
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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34 if __name__ == '__main__':
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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35 parser = argparse.ArgumentParser()
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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36 parser.add_argument('-n', '--names', dest='names', action='store', default=None, help='Table names to reload')
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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37 parser.add_argument('-u', '--url', dest='url', action='store', default=None, help='Base url for reload')
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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38 parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key')
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
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aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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40 args = parser.parse_args()
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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41 if not args.names:
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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42 tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json()
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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43 args.names = [d.get('name') for d in tables]
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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44 for name in args.names:
aec9bc48cdb7 "planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/master/data_managers/data_manager_refgenie_pull commit da4cbfcb158b1cf283c5736434fa88b645783306"
blankenberglab
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45 print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json())