Mercurial > repos > gga > apollo_feat_from_gff3

annotate fetch_organism_jbrowse.py @ 15:18217f8862ef draft

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"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f742b16e6e4c33b9abdb633405298e05760c84b"
author gga
date Tue, 08 Jun 2021 09:14:38 +0000
parents bb562d95b6cd
children
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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 filecmp
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6 import logging
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7 import os
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8 import subprocess
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9 import sys
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10 import time
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12 from apollo import accessible_organisms
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13 from apollo.util import GuessOrg, OrgOrGuess
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15 from arrow.apollo import get_apollo_instance
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17 from webapollo import UserObj, handle_credentials
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19 logging.basicConfig(level=logging.INFO)
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20 log = logging.getLogger(__name__)
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23 def are_dir_trees_equal(dir1, dir2):
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24 """
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25 Compare two directories recursively. Files in each directory are
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26 assumed to be equal if their names and contents are equal.
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28 @param dir1: First directory path
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29 @param dir2: Second directory path
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30
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31 @return: True if the directory trees are the same and
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32 there were no errors while accessing the directories or files,
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33 False otherwise.
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34
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35 # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395
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36 """
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38 dirs_cmp = filecmp.dircmp(dir1, dir2)
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39 if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \
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40 len(dirs_cmp.funny_files) > 0:
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41 print(('LEFT', dirs_cmp.left_only))
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42 print(('RIGHT', dirs_cmp.right_only))
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43 print(('FUNNY', dirs_cmp.funny_files))
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44 return False
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45 (_, mismatch, errors) = filecmp.cmpfiles(
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46 dir1, dir2, dirs_cmp.common_files, shallow=False)
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47 if len(mismatch) > 0 or len(errors) > 0:
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48 print(mismatch)
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49 print(errors)
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50 return False
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51 for common_dir in dirs_cmp.common_dirs:
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52 new_dir1 = os.path.join(dir1, common_dir)
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53 new_dir2 = os.path.join(dir2, common_dir)
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54 if not are_dir_trees_equal(new_dir1, new_dir2):
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55 return False
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56 return True
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57
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58
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59 if __name__ == '__main__':
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60 parser = argparse.ArgumentParser(description='Script to fetch organism data dir from apollo')
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61 OrgOrGuess(parser)
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62 parser.add_argument('target_dir', help='Target directory')
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63 parser.add_argument('email', help='User Email')
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64
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65 args = parser.parse_args()
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66
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67 wa = get_apollo_instance()
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68 # User must have an account
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69 org_cn = GuessOrg(args, wa)
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70 if isinstance(org_cn, list):
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71 org_cn = org_cn[0]
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72
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73 # User must have an account, if not, create it
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74 gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
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75 handle_credentials(gx_user)
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76
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77 all_orgs = wa.organisms.get_organisms()
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78 if 'error' in all_orgs:
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79 all_orgs = []
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80 all_orgs = [org['commonName'] for org in all_orgs]
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81 if org_cn not in all_orgs:
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82 raise Exception("Could not find organism %s" % org_cn)
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84 # User must have READ access
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85 orgs = accessible_organisms(gx_user, [org_cn], 'READ')
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86 if not orgs:
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87 raise Exception("You do not have write permission on this organism")
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88 org = wa.organisms.show_organism(org_cn)
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89
0
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90 if not os.path.exists(args.target_dir):
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91 os.makedirs(args.target_dir)
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92
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93 if not os.path.exists(os.path.join(org['directory'], 'seq')):
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94 sys.stderr.write("Missing seq directory BEFORE copy")
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95 sys.exit(1)
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96
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97 cmd = [
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98 'rsync', '-avr',
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99 org['directory'].rstrip('/') + '/',
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100 os.path.join(args.target_dir, 'data', '')
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101 ]
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102 # We run this OBSESSIVELY because my org had a hiccup where the origin
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103 # (silent) cp -R failed at one point. This caused MANY HEADACHES.
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104 #
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105 # Our response is to run this 3 times (in case the issue is temporary),
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106 # with delays in between. And ensure that we have the correct number of
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107 # files / folders before and after.
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108 sys.stderr.write(' '.join(cmd))
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109 sys.stderr.write('\n')
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110 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
0
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111 if not are_dir_trees_equal(
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112 os.path.join(org['directory'].rstrip('/')),
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113 os.path.join(args.target_dir, 'data')
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114 ):
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115 # Not good
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116 time.sleep(5)
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117 sys.stderr.write('\n')
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118 sys.stderr.write(' '.join(cmd))
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119 sys.stderr.write('\n')
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120 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
0
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121 if not are_dir_trees_equal(
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122 os.path.join(org['directory'].rstrip('/'), 'data'),
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123 os.path.join(args.target_dir, 'data')
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124 ):
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125 time.sleep(5)
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126 sys.stderr.write('\n')
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127 sys.stderr.write(' '.join(cmd))
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128 sys.stderr.write('\n')
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129 sys.stderr.write(subprocess.check_output(cmd).decode(sys.stderr.encoding))
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130 if not are_dir_trees_equal(
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131 os.path.join(org['directory'].rstrip('/'), 'data'),
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132 os.path.join(args.target_dir, 'data')
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133 ):
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134 sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.')
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135 sys.exit(2)