Mercurial > repos > gga > apollo_feat_from_gff3

annotate create_or_update_organism.py @ 10:5d1cf95ade8a draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"
author gga
date Mon, 02 Dec 2019 05:51:05 -0500
parents 922dd0b252c8
children 1e37bbd4a73b
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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 glob
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6 import json
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7 import logging
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8 import os
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9 import shutil
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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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17 from apollo import accessible_organisms
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18 from apollo.util import GuessOrg, OrgOrGuess
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20 from arrow.apollo import get_apollo_instance
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22 from webapollo import UserObj, handle_credentials
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24 logging.basicConfig(level=logging.INFO)
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25 log = logging.getLogger(__name__)
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28 def IsBlatEnabled():
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29 if 'BLAT_ENABLED' not in os.environ:
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30 return False
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31 value = os.environ['BLAT_ENABLED']
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32 if value.lower() in ('true', 't', '1'):
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33 return True
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34 else:
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35 return False
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38 def IsOrgCNSuffixEnabled():
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39 if 'GALAXY_APOLLO_ORG_SUFFIX' not in os.environ:
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40 return False
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41 value = os.environ['GALAXY_APOLLO_ORG_SUFFIX'].lower()
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42 if value in ('id', 'email'):
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43 return value
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45 return False
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48 def IsRemote():
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49 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 if __name__ == '__main__':
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53 parser = argparse.ArgumentParser(description='Create or update an organism in an Apollo instance')
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54 parser.add_argument('jbrowse_src', help='Source JBrowse Data Directory')
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55 parser.add_argument('jbrowse', help='Destination JBrowse Data Directory')
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56 parser.add_argument('email', help='User Email')
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57 OrgOrGuess(parser)
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58 parser.add_argument('--genus', help='Organism Genus')
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59 parser.add_argument('--species', help='Organism Species')
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60 parser.add_argument('--public', action='store_true', help='Make organism public')
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61 parser.add_argument('--group', help='Give access to a user group')
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62 parser.add_argument('--remove_old_directory', action='store_true', help='Remove old directory')
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63 parser.add_argument('--no_reload_sequences', action='store_true', help='Disable update genome sequence')
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64 parser.add_argument('--userid', help='User unique id')
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65 args = parser.parse_args()
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66 CHUNK_SIZE = 2**20
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67 blat_db = None
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68
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69 path_fasta = args.jbrowse_src + '/seq/genome.fasta'
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70
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71 # Cleanup if existing
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72 if not IsRemote():
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73 if(os.path.exists(args.jbrowse)):
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74 shutil.rmtree(args.jbrowse)
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75 # Copy files
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76 shutil.copytree(args.jbrowse_src, args.jbrowse, symlinks=True)
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77
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78 path_2bit = args.jbrowse + '/seq/genome.2bit'
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79 else:
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80 twobittemp = tempfile.NamedTemporaryFile(prefix="genome.2bit")
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81 path_2bit = twobittemp.name
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82 os.chmod(path_2bit, stat.S_IRUSR | stat.S_IWUSR | stat.S_IRGRP | stat.S_IROTH)
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84 # Convert fasta if existing
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85 if IsBlatEnabled() and os.path.exists(path_fasta):
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86 arg = ['faToTwoBit', path_fasta, path_2bit]
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87 proc = subprocess.Popen(args=arg, shell=False, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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88 out, err = proc.communicate()
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89 if proc.returncode:
7
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90 print("Error building index:", file=sys.stderr)
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91 sys.stderr.write(err)
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92 sys.exit(proc.returncode)
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93 if not IsRemote():
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94 # No need to send this in remote mode, it will be in the archive
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95 blat_db = path_2bit
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96
10
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97 wa = get_apollo_instance()
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98
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99 # User must have an account, if not, create it
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100 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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101 handle_credentials(gx_user)
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102
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103 org_cn = GuessOrg(args, wa)
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104 if isinstance(org_cn, list):
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105 org_cn = org_cn[0]
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106
10
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107 if args.org_raw:
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108 suffix = IsOrgCNSuffixEnabled()
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109 if suffix == 'id' and args.userid:
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110 org_cn += ' (gx%s)' % args.userid
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111 elif suffix == 'email':
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112 org_cn += ' (%s)' % args.email
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113
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114 log.info("Determining if add or update required")
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115 try:
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116 org = wa.organisms.show_organism(org_cn)
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117 except Exception:
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118 org = None
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119
10
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120 if org and 'error' not in org:
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121 old_directory = org['directory']
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122
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123 all_orgs = wa.organisms.get_organisms()
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124 if 'error' in all_orgs:
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125 all_orgs = []
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126 all_orgs = [x['commonName'] for x in all_orgs]
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127 if org_cn not in all_orgs:
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128 raise Exception("Could not find organism %s" % org_cn)
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129
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130 orgs = accessible_organisms(gx_user, [org_cn], 'WRITE')
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131 if not orgs:
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132 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.")
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133
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134 log.info("\tUpdating Organism")
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135 if IsRemote():
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136 with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
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137 with tarfile.open(archive.name, mode="w:gz") as tar:
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138 dataset_data_dir = args.jbrowse_src
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139 for file in glob.glob(dataset_data_dir):
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140 tar.add(file, arcname=file.replace(dataset_data_dir, './'))
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141 if IsBlatEnabled():
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142 tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
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143 data = wa.remote.update_organism(
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144 org['id'],
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145 archive,
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146 # mandatory
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147 blatdb=blat_db,
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148 genus=args.genus,
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149 species=args.species,
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150 public=args.public,
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151 no_reload_sequences=args.no_reload_sequences
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152 )
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153 else:
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154 data = wa.organisms.update_organism(
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155 org['id'],
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156 org_cn,
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157 args.jbrowse,
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158 # mandatory
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159 genus=args.genus,
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160 species=args.species,
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161 public=args.public,
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162 blatdb=blat_db,
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163 no_reload_sequences=args.no_reload_sequences
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164 )
0
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165 time.sleep(2)
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166
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167 if not IsRemote() and args.remove_old_directory and args.jbrowse != old_directory:
0
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168 shutil.rmtree(old_directory)
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169
10
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170 data = wa.organisms.show_organism(org_cn)
0
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171
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172 else:
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173 # New organism
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174 log.info("\tAdding Organism")
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175
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176 if IsRemote():
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177 with tempfile.NamedTemporaryFile(suffix='.tar.gz') as archive:
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178 with tarfile.open(archive.name, mode="w:gz") as tar:
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179 dataset_data_dir = args.jbrowse_src
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180 for file in glob.glob(dataset_data_dir):
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181 tar.add(file, arcname=file.replace(dataset_data_dir, './'))
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182 if IsBlatEnabled():
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183 with tempfile.TemporaryDirectory() as empty_dir:
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184 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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185 tar.add(empty_dir, arcname="./searchDatabaseData/")
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186 tar.add(path_2bit, arcname="./searchDatabaseData/genome.2bit")
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187 data = wa.remote.add_organism(
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188 org_cn,
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189 archive,
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190 blatdb=blat_db,
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191 genus=args.genus,
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192 species=args.species,
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193 public=args.public,
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194 metadata=None
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195 )
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196 if isinstance(data, list) and len(data) > 0:
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197 data = data[0]
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198 else:
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199 data = wa.organisms.add_organism(
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200 org_cn,
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201 args.jbrowse,
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202 blatdb=blat_db,
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203 genus=args.genus,
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204 species=args.species,
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205 public=args.public,
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206 metadata=None
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207 )
0
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208
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209 # Must sleep before we're ready to handle
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210 time.sleep(2)
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211 log.info("Updating permissions for %s on %s", gx_user, org_cn)
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212 wa.users.update_organism_permissions(
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213 gx_user.username,
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214 org_cn,
0
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215 write=True,
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216 export=True,
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217 read=True,
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218 )
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219
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220 # Group access
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221 if args.group:
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222 group = wa.groups.get_groups(name=args.group)[0]
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223 res = wa.groups.update_organism_permissions(group['name'], org_cn,
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224 administrate=False, write=True, read=True,
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225 export=True)
0
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226
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227 print(json.dumps(data, indent=2))