Mercurial > repos > gga > apollo_export

annotate create_or_update_organism.py @ 8:ad02f02c75e3 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 2488ac4ea447c45886ce5c7b102fb28c5839d26b
author gga
date Wed, 10 Apr 2019 13:55:49 -0400
parents db216690cbbf
children c3b5bc8b4080
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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 os
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8 import shutil
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9 import subprocess
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10 import sys
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11 import tempfile
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12 import time
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15 from webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
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16 logging.basicConfig(level=logging.INFO)
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17 log = logging.getLogger(__name__)
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20 def IsBlatEnabled():
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21 if 'BLAT_ENABLED' not in os.environ:
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22 return False
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23 value = os.environ['BLAT_ENABLED']
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24 if value.lower() in ('true', 't', '1'):
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25 return True
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26 else:
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27 return False
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29
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30 if __name__ == '__main__':
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31 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
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32 WAAuth(parser)
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33 parser.add_argument('jbrowse_src', help='Old JBrowse Data Directory')
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34 parser.add_argument('jbrowse', help='JBrowse Data Directory')
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35 parser.add_argument('email', help='User Email')
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36 OrgOrGuess(parser)
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37 parser.add_argument('--genus', help='Organism Genus')
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38 parser.add_argument('--species', help='Organism Species')
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39 parser.add_argument('--public', action='store_true', help='Make organism public')
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40 parser.add_argument('--group', help='Give access to a user group')
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41 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
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42 args = parser.parse_args()
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43 CHUNK_SIZE = 2**20
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44 blat_db = None
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45
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46 # Cleanup if existing
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47 if(os.path.exists(args.jbrowse)):
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48 shutil.rmtree(args.jbrowse)
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49 # Copy files
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50 shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)
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51
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52 path_fasta = args.jbrowse + '/seq/genome.fasta'
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53 path_2bit = args.jbrowse + '/seq/genome.2bit'
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54
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55 # Convert fasta if existing
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56 if(IsBlatEnabled() and os.path.exists(path_fasta)):
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57 arg = ['faToTwoBit', path_fasta, path_2bit]
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58 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-twobit-converter-stderr")
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59 proc = subprocess.Popen(args=arg, shell=False, cwd=args.jbrowse, stderr=tmp_stderr.fileno())
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60 return_code = proc.wait()
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61 if return_code:
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62 tmp_stderr.flush()
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63 tmp_stderr.seek(0)
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64 print("Error building index:", file=sys.stderr)
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65 while True:
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66 chunk = tmp_stderr.read(CHUNK_SIZE)
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67 if not chunk:
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68 break
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69 sys.stderr.write(chunk)
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70 sys.exit(return_code)
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71 blat_db = path_2bit
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72 tmp_stderr.close()
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73
0
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74 wa = WebApolloInstance(args.apollo, args.username, args.password)
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75
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76 org_cn = GuessOrg(args, wa)
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77 if isinstance(org_cn, list):
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78 org_cn = org_cn[0]
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79
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80 # User must have an account, if not, create it
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81 gx_user = wa.users.assertOrCreateUser(args.email)
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82
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83 log.info("Determining if add or update required")
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84 try:
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85 org = wa.organisms.findOrganismByCn(org_cn)
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86 except Exception:
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87 org = None
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88
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89 if org:
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90 old_directory = org['directory']
0
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91
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92 if not PermissionCheck(gx_user, org_cn, "WRITE"):
0
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93 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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94 sys.exit(2)
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95
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96 log.info("\tUpdating Organism")
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97 data = wa.organisms.updateOrganismInfo(
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98 org['id'],
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99 org_cn,
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100 args.jbrowse,
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101 # mandatory
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102 genus=args.genus,
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103 species=args.species,
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104 public=args.public,
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105 blatdb=blat_db
0
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106 )
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107 time.sleep(2)
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108 if args.remove_old_directory and args.jbrowse != old_directory:
0
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109 shutil.rmtree(old_directory)
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110
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111 data = [wa.organisms.findOrganismById(org['id'])]
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112
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113 else:
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114 # New organism
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115 log.info("\tAdding Organism")
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116 data = wa.organisms.addOrganism(
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117 org_cn,
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118 args.jbrowse,
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119 genus=args.genus,
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120 species=args.species,
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121 public=args.public,
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122 blatdb=blat_db
0
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123 )
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124
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125 # Must sleep before we're ready to handle
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126 time.sleep(2)
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127 log.info("Updating permissions for %s on %s", gx_user, org_cn)
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128 wa.users.updateOrganismPermission(
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129 gx_user, org_cn,
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130 write=True,
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131 export=True,
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132 read=True,
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133 )
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134
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135 # Group access
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136 if args.group:
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137 group = wa.groups.loadGroupByName(name=args.group)
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138 res = wa.groups.updateOrganismPermission(group, org_cn,
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139 administrate=False, write=True, read=True,
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140 export=True)
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141
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142 data = [o for o in data if o['commonName'] == org_cn]
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143 print(json.dumps(data, indent=2))