annotate create_or_update_organism.py @ 14:a31493bc7952 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"
author gga
date Wed, 19 Aug 2020 06:57:08 -0400
parents f515aa0b0437
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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
7
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7 import os
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8 import re
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9 import shutil
10
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10 import stat
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11 import subprocess
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12 import sys
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13 import tarfile
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14 import tempfile
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15 import time
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16 from pathlib import Path
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18 from apollo import accessible_organisms
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19 from apollo.util import GuessOrg, OrgOrGuess
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21 from arrow.apollo import get_apollo_instance
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23 from webapollo import UserObj, handle_credentials
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24
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25 logging.basicConfig(level=logging.INFO)
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26 log = logging.getLogger(__name__)
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29 def IsBlatEnabled():
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30 if 'BLAT_ENABLED' not in os.environ:
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31 return False
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32 value = os.environ['BLAT_ENABLED']
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33 if value.lower() in ('true', 't', '1'):
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34 return True
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35 else:
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36 return False
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38
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39 def IsOrgCNSuffixEnabled():
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40 if 'GALAXY_APOLLO_ORG_SUFFIX' not in os.environ:
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41 return False
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42 value = os.environ['GALAXY_APOLLO_ORG_SUFFIX'].lower()
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43 if value in ('id', 'email'):
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44 return value
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45
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46 return False
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47
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48
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49 def IsRemote():
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50 return 'GALAXY_SHARED_DIR' not in os.environ or len(os.environ['GALAXY_SHARED_DIR'].lower().strip()) == 0
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51
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52
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53 def zip_data_dir(dataset_data_dir, tar):
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54 tar.add(dataset_data_dir, arcname='./', recursive=False)
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55 for r, d, f in os.walk(dataset_data_dir):
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56 for file_name in f:
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57 abs_file = os.path.join(r, file_name)
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58 rel_dir = os.path.relpath(r, dataset_data_dir)
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59 rel_file = os.path.join(rel_dir, file_name)
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60 if not rel_file.startswith('./'):
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61 rel_file = './' + rel_file
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62 if os.path.islink(abs_file):
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63 target = Path(abs_file).resolve().absolute().as_posix()
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64 if re.match(r'.*/_metadata_files/[0-9]+/metadata_[0-9]+.dat', target):
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65 # This is a metadata file generated by galaxy, symlink would certainly be dead on remote host, resolve it
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66 abs_file = target
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67 tar.add(abs_file, arcname=rel_file)
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68
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69
0
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70 if __name__ == '__main__':
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71 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
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72 parser.add_argument('jbrowse_src', help='Source JBrowse Data Directory')
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73 parser.add_argument('jbrowse', help='Destination JBrowse Data Directory')
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74 parser.add_argument('email', help='User Email')
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75 OrgOrGuess(parser)
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76 parser.add_argument('--genus', help='Organism Genus')
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77 parser.add_argument('--species', help='Organism Species')
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78 parser.add_argument('--public', action='store_true', help='Make organism public')
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79 parser.add_argument('--group', help='Give access to a user group')
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80 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
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81 parser.add_argument('--no_reload_sequences', action='store_true', help='Disable update genome sequence')
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82 parser.add_argument('--userid', help='User unique id')
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83 args = parser.parse_args()
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84 CHUNK_SIZE = 2**20
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85 blat_db = None
0
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86
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87 path_fasta = args.jbrowse_src + '/seq/genome.fasta'
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88
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89 # Cleanup if existing
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90 if not IsRemote():
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91 if(os.path.exists(args.jbrowse)):
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92 shutil.rmtree(args.jbrowse)
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93 # Copy files
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94 shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)
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95
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96 path_2bit = args.jbrowse + '/seq/genome.2bit'
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97 else:
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98 twobittemp = tempfile.NamedTemporaryFile(prefix="genome.2bit")
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99 path_2bit = twobittemp.name
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100 os.chmod(path_2bit, stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IROTH)
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101
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102 # Convert fasta if existing
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103 if IsBlatEnabled() and os.path.exists(path_fasta):
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104 arg = ['faToTwoBit', path_fasta, path_2bit]
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105 proc = subprocess.Popen(args=arg, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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106 out, err = proc.communicate()
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107 if proc.returncode:
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108 print("Error building index:", file=sys.stderr)
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109 sys.stderr.write(err)
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110 sys.exit(proc.returncode)
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111 if not IsRemote():
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112 # No need to send this in remote mode, it will be in the archive
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113 blat_db = path_2bit
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114
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115 wa = get_apollo_instance()
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116
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117 # User must have an account, if not, create it
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118 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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119 handle_credentials(gx_user)
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120
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121 org_cn = GuessOrg(args, wa)
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122 if isinstance(org_cn, list):
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123 org_cn = org_cn[0]
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124
10
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125 if args.org_raw:
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126 suffix = IsOrgCNSuffixEnabled()
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127 if suffix == 'id' and args.userid:
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128 org_cn += ' (gx%s)' % args.userid
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129 elif suffix == 'email':
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130 org_cn += ' (%s)' % args.email
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131
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132 log.info("Determining if add or update required")
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133 try:
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134 org = wa.organisms.show_organism(org_cn)
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135 except Exception:
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136 org = None
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137
10
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138 if org and 'error' not in org:
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139 old_directory = org['directory']
0
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140
10
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141 all_orgs = wa.organisms.get_organisms()
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142 if 'error' in all_orgs:
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143 all_orgs = []
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144 all_orgs = [x['commonName'] for x in all_orgs]
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145 if org_cn not in all_orgs:
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146 raise Exception("Could not find organism %s" % org_cn)
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147
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148 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
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149 if not orgs:
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150 raise Exception("Naming Conflict. You do not have write permission on this organism. Either request permission from the owner, or choose a different name for your organism.")
0
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151
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152 log.info("\tUpdating Organism")
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153 if IsRemote():
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154 with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
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155 with tarfile.open(archive.name, mode="w:gz") as tar:
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156 dataset_data_dir = args.jbrowse_src
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157 zip_data_dir(dataset_data_dir, tar)
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158 if IsBlatEnabled():
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159 tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
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160 data = wa.remote.update_organism(
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161 org['id'],
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162 archive,
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163 # mandatory
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164 blatdb=blat_db,
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165 genus=args.genus,
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166 species=args.species,
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167 public=args.public,
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168 no_reload_sequences=args.no_reload_sequences
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169 )
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170 else:
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171 data = wa.organisms.update_organism(
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172 org['id'],
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173 org_cn,
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174 args.jbrowse,
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175 # mandatory
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176 genus=args.genus,
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177 species=args.species,
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178 public=args.public,
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179 blatdb=blat_db,
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180 no_reload_sequences=args.no_reload_sequences
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181 )
0
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182 time.sleep(2)
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183
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184 if not IsRemote() and args.remove_old_directory and args.jbrowse != old_directory:
0
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185 shutil.rmtree(old_directory)
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186
10
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187 data = wa.organisms.show_organism(org_cn)
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188
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189 else:
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190 # New organism
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191 log.info("\tAdding Organism")
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192
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193 if IsRemote():
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194 with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
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195 with tarfile.open(archive.name, mode="w:gz") as tar:
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196 dataset_data_dir = args.jbrowse_src
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197 zip_data_dir(dataset_data_dir, tar)
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198 if IsBlatEnabled():
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199 with tempfile.TemporaryDirectory() as empty_dir:
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200 os.chmod(empty_dir, stat.S_IRUSR | stat.S_IXUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IXGRP | stat.S_IROTH | stat.S_IXOTH)
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201 tar.add(empty_dir, arcname="./searchDatabaseData/")
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202 tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
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203 data = wa.remote.add_organism(
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204 org_cn,
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205 archive,
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206 blatdb=blat_db,
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207 genus=args.genus,
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208 species=args.species,
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209 public=args.public,
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210 metadata=None
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211 )
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212 if isinstance(data, list) and len(data) > 0:
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213 data = data[0]
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214 else:
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215 data = wa.organisms.add_organism(
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216 org_cn,
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217 args.jbrowse,
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218 blatdb=blat_db,
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219 genus=args.genus,
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220 species=args.species,
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221 public=args.public,
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222 metadata=None
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223 )
0
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224
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225 # Must sleep before we're ready to handle
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226 time.sleep(2)
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227 log.info("Updating permissions for %s on %s", gx_user, org_cn)
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228 wa.users.update_organism_permissions(
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229 gx_user.username,
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230 org_cn,
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231 write=True,
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232 export=True,
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233 read=True,
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234 )
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235
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236 # Group access
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237 if args.group:
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238 group = wa.groups.get_groups(name=args.group)[0]
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239 res = wa.groups.update_organism_permissions(group['name'], org_cn,
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240 administrate=False, write=True, read=True,
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241 export=True)
0
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242
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243 print(json.dumps(data, indent=2))