Mercurial > repos > blankenberglab > data_manager_refgenie_pull
annotate data_manager/data_manager_refgenie_pull.py @ 3:b2fa406276e7 draft default tip
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
author | blankenberglab |
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date | Fri, 01 Apr 2022 16:14:13 +0000 |
parents | 2cb1863cd236 |
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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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2 |
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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3 |
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 |
3
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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7 from html import escape |
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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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8 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"
blankenberglab
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9 |
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 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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11 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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12 |
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 |
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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14 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"
blankenberglab
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15 |
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 |
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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17 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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18 try: |
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b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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19 rval = [] |
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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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20 rgc = refgenconf.RefGenConf(refgenie_config_file, writable=False, skip_read_lock=True) |
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b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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21 for urlname, genomes in rgc.listr().items(): |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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22 urlname_64 = urlsafe_b64encode(bytes(urlname, 'utf8')).decode('utf8') |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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23 ul = [] |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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24 for genome, assets in genomes.items(): |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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25 al = [] |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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26 for name in assets: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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27 al.append({'name': name, 'value': '%s/%s/%s' % (urlname_64, genome, name), 'options': [], 'selected': False}) |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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28 ul.append({'name': genome, 'value': genome, 'options': al, 'selected': False}) |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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29 rval.append({'name': urlname, 'value': urlname_64, 'options': ul, 'selected': False}) |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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30 return rval |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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31 except Exception as e: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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32 log.debug("Failed to access refgenie server: %s", e) |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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33 return[{'name': escape(str(e)), 'value': 'ERROR', 'options': [], 'selected': False}] |
0
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 |
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 |
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 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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37 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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38 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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39 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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40 parser.add_argument('-k', '--key', dest='key', action='store', default=None, help='Galaxy API Key') |
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b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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41 parser.add_argument('-g', '--graceful', dest='graceful', action='store_true', help='Fail gracefully') |
0
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 |
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 = parser.parse_args() |
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b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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44 try: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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45 if not args.names: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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46 tables = requests.get(urljoin(args.url, "api/tool_data"), params={'key': args.key}).json() |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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47 args.names = [d.get('name') for d in tables] |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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48 for name in args.names: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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49 print(requests.get(urljoin(args.url, "api/tool_data/%s/reload" % (name)), params={'key': args.key}).json()) |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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50 except Exception as e: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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51 if args.graceful: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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52 print("Failed to reload data tables:\n%s" % (e)) |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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53 else: |
b2fa406276e7
"planemo upload for repository https://github.com/blankenberglab/galaxy-tools-blankenberg/tree/main/data_managers/data_manager_refgenie_pull commit 793d970b919fcfd5f21a2d6e03e825b05dd56b69"
blankenberglab
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54 raise e |