Mercurial > repos > eric-rasche > apollo
view delete_organism.py @ 5:7610987e0c48 draft
planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3
author | eric-rasche |
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date | Wed, 01 Mar 2017 22:39:58 -0500 |
parents | |
children | f9a6e151b3b4 |
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#!/usr/bin/env python import argparse from webapollo import WebApolloInstance from webapollo import WAAuth, OrgOrGuess, GuessOrg, AssertUser import logging logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) if __name__ == '__main__': parser = argparse.ArgumentParser(description='Sample script to completely delete an organism') WAAuth(parser) parser.add_argument('email', help='User Email') OrgOrGuess(parser) args = parser.parse_args() wa = WebApolloInstance(args.apollo, args.username, args.password) # User must have an account gx_user = AssertUser(wa.users.loadUsers(email=args.email)) # Get organism org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] # TODO: Check user perms on org. org = wa.organisms.findOrganismByCn(org_cn) # Call setSequence to tell apollo which organism we're working with wa.annotations.setSequence(org['commonName'], org['id']) # Then get a list of features. features = wa.annotations.getFeatures() # For each feature in the features for feature in features['features']: # We see that deleteFeatures wants a uniqueName, and so we pass # is the uniquename field in the feature. print(wa.annotations.deleteFeatures([feature['uniquename']]))