Mercurial > repos > gga > apollo_export

annotate create_or_update_organism.py @ 5:951ee6d268cb draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 70fbb41d4c6b0a08a7bed4849a5ae7c865e1ab1e
author gga
date Mon, 12 Mar 2018 06:28:32 -0400
parents 782a14b83165
children 3d11577d86e8
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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 AssertUser, GuessOrg, OrgOrGuess, 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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16 if __name__ == '__main__':
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17 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
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18 WAAuth(parser)
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20 parser.add_argument('jbrowse', help='JBrowse Data Directory')
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21 parser.add_argument('email', help='User Email')
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22 OrgOrGuess(parser)
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23 parser.add_argument('--genus', help='Organism Genus')
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24 parser.add_argument('--species', help='Organism Species')
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25 parser.add_argument('--public', action='store_true', help='Make organism public')
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26 parser.add_argument('--group', help='Give access to a user group')
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27 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
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29 args = parser.parse_args()
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30 wa = WebApolloInstance(args.apollo, args.username, args.password)
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32 org_cn = GuessOrg(args, wa)
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33 if isinstance(org_cn, list):
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34 org_cn = org_cn[0]
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35
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36 # User must have an account
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37 gx_user = AssertUser(wa.users.loadUsers(email=args.email))
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38
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39 log.info("Determining if add or update required")
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40 try:
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41 org = wa.organisms.findOrganismByCn(org_cn)
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42 except Exception:
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43 org = None
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44
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45 if org:
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46 has_perms = False
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47 old_directory = org['directory']
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48 for user_owned_organism in gx_user.organismPermissions:
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49 if 'WRITE' in user_owned_organism['permissions']:
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50 has_perms = True
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51 break
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52
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53 if not has_perms:
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54 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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55 sys.exit(2)
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56
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57 log.info("\tUpdating Organism")
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58 data = wa.organisms.updateOrganismInfo(
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59 org['id'],
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60 org_cn,
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61 args.jbrowse,
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62 # mandatory
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63 genus=args.genus,
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64 species=args.species,
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65 public=args.public
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66 )
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67 time.sleep(2)
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68 if args.remove_old_directory and args.jbrowse != old_directory:
0
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69 shutil.rmtree(old_directory)
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70
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71 data = [wa.organisms.findOrganismById(org['id'])]
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72
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73 else:
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74 # New organism
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75 log.info("\tAdding Organism")
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76 data = wa.organisms.addOrganism(
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77 org_cn,
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78 args.jbrowse,
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79 genus=args.genus,
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80 species=args.species,
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81 public=args.public
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82 )
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83
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84 # Must sleep before we're ready to handle
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85 time.sleep(2)
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86 log.info("Updating permissions for %s on %s", gx_user, org_cn)
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87 wa.users.updateOrganismPermission(
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88 gx_user, org_cn,
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89 write=True,
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90 export=True,
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91 read=True,
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92 )
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93
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94 # Group access
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95 if args.group:
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96 group = wa.groups.loadGroupByName(name=args.group)
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97 res = wa.groups.updateOrganismPermission(group, org_cn,
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98 administrate=False, write=True, read=True,
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99 export=True)
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100
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101 data = [o for o in data if o['commonName'] == org_cn]
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102 print(json.dumps(data, indent=2))