Mercurial > repos > gga > apollo_export
view create_or_update_organism.py @ 8:ad02f02c75e3 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 2488ac4ea447c45886ce5c7b102fb28c5839d26b
author | gga |
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date | Wed, 10 Apr 2019 13:55:49 -0400 |
parents | db216690cbbf |
children | c3b5bc8b4080 |
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#!/usr/bin/env python from __future__ import print_function import argparse import json import logging import os import shutil import subprocess import sys import tempfile import time from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance logging.basicConfig(level=logging.INFO) log = logging.getLogger(__name__) def IsBlatEnabled(): if 'BLAT_ENABLED' not in os.environ: return False value = os.environ['BLAT_ENABLED'] if value.lower() in ('true', 't', '1'): return True else: return False if __name__ == '__main__': parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance') WAAuth(parser) parser.add_argument('jbrowse_src', help='Old JBrowse Data Directory') parser.add_argument('jbrowse', help='JBrowse Data Directory') parser.add_argument('email', help='User Email') OrgOrGuess(parser) parser.add_argument('--genus', help='Organism Genus') parser.add_argument('--species', help='Organism Species') parser.add_argument('--public', action='store_true', help='Make organism public') parser.add_argument('--group', help='Give access to a user group') parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory') args = parser.parse_args() CHUNK_SIZE = 2**20 blat_db = None # Cleanup if existing if(os.path.exists(args.jbrowse)): shutil.rmtree(args.jbrowse) # Copy files shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True) path_fasta = args.jbrowse + '/seq/genome.fasta' path_2bit = args.jbrowse + '/seq/genome.2bit' # Convert fasta if existing if(IsBlatEnabled() and os.path.exists(path_fasta)): arg = ['faToTwoBit', path_fasta, path_2bit] tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-twobit-converter-stderr") proc = subprocess.Popen(args=arg, shell=False, cwd=args.jbrowse, stderr=tmp_stderr.fileno()) return_code = proc.wait() if return_code: tmp_stderr.flush() tmp_stderr.seek(0) print("Error building index:", file=sys.stderr) while True: chunk = tmp_stderr.read(CHUNK_SIZE) if not chunk: break sys.stderr.write(chunk) sys.exit(return_code) blat_db = path_2bit tmp_stderr.close() wa = WebApolloInstance(args.apollo, args.username, args.password) org_cn = GuessOrg(args, wa) if isinstance(org_cn, list): org_cn = org_cn[0] # User must have an account, if not, create it gx_user = wa.users.assertOrCreateUser(args.email) log.info("Determining if add or update required") try: org = wa.organisms.findOrganismByCn(org_cn) except Exception: org = None if org: old_directory = org['directory'] if not PermissionCheck(gx_user, org_cn, "WRITE"): 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.") sys.exit(2) log.info("\tUpdating Organism") data = wa.organisms.updateOrganismInfo( org['id'], org_cn, args.jbrowse, # mandatory genus=args.genus, species=args.species, public=args.public, blatdb=blat_db ) time.sleep(2) if args.remove_old_directory and args.jbrowse != old_directory: shutil.rmtree(old_directory) data = [wa.organisms.findOrganismById(org['id'])] else: # New organism log.info("\tAdding Organism") data = wa.organisms.addOrganism( org_cn, args.jbrowse, genus=args.genus, species=args.species, public=args.public, blatdb=blat_db ) # Must sleep before we're ready to handle time.sleep(2) log.info("Updating permissions for %s on %s", gx_user, org_cn) wa.users.updateOrganismPermission( gx_user, org_cn, write=True, export=True, read=True, ) # Group access if args.group: group = wa.groups.loadGroupByName(name=args.group) res = wa.groups.updateOrganismPermission(group, org_cn, administrate=False, write=True, read=True, export=True) data = [o for o in data if o['commonName'] == org_cn] print(json.dumps(data, indent=2))