Mercurial > repos > gga > apollo_feat_from_gff3

annotate fetch_organism_jbrowse.py @ 6:b6062d33cf13 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit d9f27b297d9a919471c92b02ecf6cc9554457211
author gga
date Tue, 30 Oct 2018 04:29:51 -0400
parents cc098732daf6
children 5d1cf95ade8a
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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 webapollo import GuessOrg, OrgOrGuess, PermissionCheck, WAAuth, WebApolloInstance
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13 logging.basicConfig(level=logging.INFO)
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14 log = logging.getLogger(__name__)
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17 def are_dir_trees_equal(dir1, dir2):
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18 """
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19 Compare two directories recursively. Files in each directory are
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20 assumed to be equal if their names and contents are equal.
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21
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22 @param dir1: First directory path
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23 @param dir2: Second directory path
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24
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25 @return: True if the directory trees are the same and
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26 there were no errors while accessing the directories or files,
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27 False otherwise.
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28
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29 # http://stackoverflow.com/questions/4187564/recursive-dircmp-compare-two-directories-to-ensure-they-have-the-same-files-and/6681395#6681395
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30 """
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32 dirs_cmp = filecmp.dircmp(dir1, dir2)
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33 if len(dirs_cmp.left_only) > 0 or len(dirs_cmp.right_only) > 0 or \
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34 len(dirs_cmp.funny_files) > 0:
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35 print(('LEFT', dirs_cmp.left_only))
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36 print(('RIGHT', dirs_cmp.right_only))
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37 print(('FUNNY', dirs_cmp.funny_files))
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38 return False
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39 (_, mismatch, errors) = filecmp.cmpfiles(
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40 dir1, dir2, dirs_cmp.common_files, shallow=False)
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41 if len(mismatch) > 0 or len(errors) > 0:
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42 print(mismatch)
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43 print(errors)
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44 return False
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45 for common_dir in dirs_cmp.common_dirs:
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46 new_dir1 = os.path.join(dir1, common_dir)
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47 new_dir2 = os.path.join(dir2, common_dir)
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48 if not are_dir_trees_equal(new_dir1, new_dir2):
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49 return False
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50 return True
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51
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52
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53 if __name__ == '__main__':
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54 parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
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55 WAAuth(parser)
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56 OrgOrGuess(parser)
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57 parser.add_argument('target_dir', help='Target directory')
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58 parser.add_argument('email', help='User Email')
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60 args = parser.parse_args()
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61
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62 wa = WebApolloInstance(args.apollo, args.username, args.password)
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63 # User must have an account
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64 org_cn = GuessOrg(args, wa)
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65 if isinstance(org_cn, list):
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66 org_cn = org_cn[0]
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67 org = wa.organisms.findOrganismByCn(org_cn)
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68
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69 # User must have an account, if not, create it
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70 gx_user = wa.users.assertOrCreateUser(args.email)
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72 # User must have READ access
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73
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74 if not PermissionCheck(gx_user, org_cn, "READ"):
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75 raise Exception("READ permissions are required for this action")
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76
0
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77 if not os.path.exists(args.target_dir):
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78 os.makedirs(args.target_dir)
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79
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80 if not os.path.exists(os.path.join(org['directory'], 'seq')):
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81 sys.stderr.write("Missing seq directory BEFORE copy")
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82 sys.exit(1)
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83
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84 cmd = [
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85 'rsync', '-avr',
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86 org['directory'].rstrip('/') + '/',
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87 os.path.join(args.target_dir, 'data', '')
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88 ]
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89 # We run this OBSESSIVELY because my org had a hiccup where the origin
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90 # (silent) cp -R failed at one point. This caused MANY HEADACHES.
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91 #
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92 # Our response is to run this 3 times (in case the issue is temporary),
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93 # with delays in between. And ensure that we have the correct number of
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94 # files / folders before and after.
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95 sys.stderr.write(' '.join(cmd))
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96 sys.stderr.write('\n')
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97 sys.stderr.write(subprocess.check_output(cmd))
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98 if not are_dir_trees_equal(
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99 os.path.join(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 # Not good
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103 time.sleep(5)
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104 sys.stderr.write('\n')
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105 sys.stderr.write(' '.join(cmd))
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106 sys.stderr.write('\n')
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107 sys.stderr.write(subprocess.check_output(cmd))
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108 if not are_dir_trees_equal(
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109 os.path.join(org['directory'].rstrip('/'), 'data'),
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110 os.path.join(args.target_dir, 'data')
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111 ):
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112 time.sleep(5)
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113 sys.stderr.write('\n')
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114 sys.stderr.write(' '.join(cmd))
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115 sys.stderr.write('\n')
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116 sys.stderr.write(subprocess.check_output(cmd))
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117 if not are_dir_trees_equal(
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118 os.path.join(org['directory'].rstrip('/'), 'data'),
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119 os.path.join(args.target_dir, 'data')
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120 ):
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121 sys.stderr.write('FAILED THREE TIMES TO COPY. SOMETHING IS WRONG WRONG WRONG.')
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122 sys.exit(2)