Mercurial > repos > gga > apollo_list_organism
comparison create_or_update_organism.py @ 3:aaf308a49899 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 079b759c21c00200544a6d8d5521617dce8ca70d
| author | gga |
|---|---|
| date | Wed, 20 Sep 2017 09:44:54 -0400 |
| parents | 1f2e360f7554 |
| children | a3000d01c04c |
comparison
equal
deleted
inserted
replaced
| 2:c570db69288b | 3:aaf308a49899 |
|---|---|
| 42 except Exception: | 42 except Exception: |
| 43 org = None | 43 org = None |
| 44 | 44 |
| 45 if org: | 45 if org: |
| 46 has_perms = False | 46 has_perms = False |
| 47 old_directory = org.directory | 47 old_directory = org['directory'] |
| 48 for user_owned_organism in gx_user.organismPermissions: | 48 for user_owned_organism in gx_user.organismPermissions: |
| 49 if 'WRITE' in user_owned_organism['permissions']: | 49 if 'WRITE' in user_owned_organism['permissions']: |
| 50 has_perms = True | 50 has_perms = True |
| 51 break | 51 break |
| 52 | 52 |
| 63 genus=args.genus, | 63 genus=args.genus, |
| 64 species=args.species, | 64 species=args.species, |
| 65 public=args.public | 65 public=args.public |
| 66 ) | 66 ) |
| 67 time.sleep(2) | 67 time.sleep(2) |
| 68 if(args.remove_old_directory): | 68 if args.remove_old_directory and args.jbrowse != old_directory: |
| 69 shutil.rmtree(old_directory) | 69 shutil.rmtree(old_directory) |
| 70 | 70 |
| 71 data = [wa.organisms.findOrganismById(org['id'])] | 71 data = [wa.organisms.findOrganismById(org['id'])] |
| 72 | 72 |
| 73 else: | 73 else: |