Mercurial > repos > gga > apollo_export

annotate create_or_update_organism.py @ 5:950fb2bf116d draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 85194fa009ead2c34720faab61a4143fc29d17c2
author gga
date Fri, 31 Aug 2018 09:33:38 -0400
parents 236155b4e5f9
children db216690cbbf
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b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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1 #!/usr/bin/env python
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2 from __future__ import print_function
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4 import argparse
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5 import json
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6 import logging
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7 import shutil
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8 import sys
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9 import time
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11 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
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12 logging.basicConfig(level=logging.INFO)
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13 log = logging.getLogger(__name__)
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15 if __name__ == '__main__':
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16 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
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17 WAAuth(parser)
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19 parser.add_argument('jbrowse', help='JBrowse Data Directory')
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20 parser.add_argument('email', help='User Email')
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21 OrgOrGuess(parser)
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22 parser.add_argument('--genus', help='Organism Genus')
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23 parser.add_argument('--species', help='Organism Species')
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24 parser.add_argument('--public', action='store_true', help='Make organism public')
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25 parser.add_argument('--group', help='Give access to a user group')
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26 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
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28 args = parser.parse_args()
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29 wa = WebApolloInstance(args.apollo, args.username, args.password)
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31 org_cn = GuessOrg(args, wa)
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32 if isinstance(org_cn, list):
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33 org_cn = org_cn[0]
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34
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35 # User must have an account, if not, create it
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36 gx_user = wa.users.assertOrCreateUser(args.email)
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37
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38 log.info("Determining if add or update required")
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39 try:
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40 org = wa.organisms.findOrganismByCn(org_cn)
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41 except Exception:
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42 org = None
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43
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44 if org:
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45 old_directory = org['directory']
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46
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47 if not PermissionCheck(gx_user, org_cn, "WRITE"):
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48 print("Naming Conflict. You do not have permissions to access this organism. Either request permission from the owner, or choose a different name for your organism.")
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49 sys.exit(2)
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50
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51 log.info("\tUpdating Organism")
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52 data = wa.organisms.updateOrganismInfo(
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53 org['id'],
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54 org_cn,
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55 args.jbrowse,
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56 # mandatory
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57 genus=args.genus,
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58 species=args.species,
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59 public=args.public
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60 )
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61 time.sleep(2)
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62 if args.remove_old_directory and args.jbrowse != old_directory:
0
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63 shutil.rmtree(old_directory)
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64
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65 data = [wa.organisms.findOrganismById(org['id'])]
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66
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67 else:
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68 # New organism
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69 log.info("\tAdding Organism")
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70 data = wa.organisms.addOrganism(
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71 org_cn,
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72 args.jbrowse,
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73 genus=args.genus,
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74 species=args.species,
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75 public=args.public
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76 )
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77
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78 # Must sleep before we're ready to handle
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79 time.sleep(2)
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80 log.info("Updating permissions for %s on %s", gx_user, org_cn)
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81 wa.users.updateOrganismPermission(
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82 gx_user, org_cn,
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83 write=True,
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84 export=True,
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85 read=True,
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86 )
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87
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88 # Group access
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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89 if args.group:
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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90 group = wa.groups.loadGroupByName(name=args.group)
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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91 res = wa.groups.updateOrganismPermission(group, org_cn,
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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92 administrate=False, write=True, read=True,
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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93 export=True)
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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94
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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95 data = [o for o in data if o['commonName'] == org_cn]
b4a85d0c85b8 planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268
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96 print(json.dumps(data, indent=2))