Mercurial > repos > shellac > guppy_basecaller

annotate env/bin/lss3 @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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1 #!/Users/pldms/Development/Projects/2020/david-matthews-galaxy/guppy_basecaller/env/bin/python3
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2 import boto
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3 from boto.exception import S3ResponseError
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4 from boto.s3.connection import OrdinaryCallingFormat
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5
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6
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7 def sizeof_fmt(num):
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8 for x in ['b ', 'KB', 'MB', 'GB', 'TB', 'XB']:
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9 if num < 1024.0:
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10 return "%3.1f %s" % (num, x)
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11 num /= 1024.0
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12 return "%3.1f %s" % (num, x)
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13
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14
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15 def list_bucket(b, prefix=None, marker=None):
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16 """List everything in a bucket"""
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17 from boto.s3.prefix import Prefix
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18 from boto.s3.key import Key
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19 total = 0
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20
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21 if prefix:
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22 if not prefix.endswith("/"):
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23 prefix = prefix + "/"
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24 query = b.list(prefix=prefix, delimiter="/", marker=marker)
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25 print("%s" % prefix)
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26 else:
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27 query = b.list(delimiter="/", marker=marker)
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28
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29 num = 0
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30 for k in query:
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31 num += 1
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32 mode = "-rwx---"
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33 if isinstance(k, Prefix):
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34 mode = "drwxr--"
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35 size = 0
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36 else:
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37 size = k.size
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38 for g in k.get_acl().acl.grants:
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39 if g.id == None:
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40 if g.permission == "READ":
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41 mode = "-rwxr--"
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42 elif g.permission == "FULL_CONTROL":
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43 mode = "-rwxrwx"
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44 if isinstance(k, Key):
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45 print("%s\t%s\t%010s\t%s" % (mode, k.last_modified,
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46 sizeof_fmt(size), k.name))
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47 else:
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48 #If it's not a Key object, it doesn't have a last_modified time, so
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49 #print nothing instead
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50 print("%s\t%s\t%010s\t%s" % (mode, ' ' * 24,
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51 sizeof_fmt(size), k.name))
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52 total += size
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53 print ("=" * 80)
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54 print ("\t\tTOTAL: \t%010s \t%i Files" % (sizeof_fmt(total), num))
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55
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56
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57 def list_buckets(s3, display_tags=False):
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58 """List all the buckets"""
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59 for b in s3.get_all_buckets():
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60 print(b.name)
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61 if display_tags:
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62 try:
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63 tags = b.get_tags()
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64 for tag in tags[0]:
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65 print(" %s:%s" % (tag.key, tag.value))
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66 except S3ResponseError as e:
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67 if e.status != 404:
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68 raise
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69
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70
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71 def main():
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72 import optparse
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73 import sys
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74
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75 usage = "usage: %prog [options] [BUCKET1] [BUCKET2]"
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76 description = "List all S3 buckets OR list keys in the named buckets"
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77 parser = optparse.OptionParser(description=description, usage=usage)
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78 parser.add_option('-m', '--marker',
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79 help='The S3 key where the listing starts after it.')
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80 parser.add_option('-t', '--tags', action='store_true',
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81 help='Display tags when listing all buckets.')
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82 options, buckets = parser.parse_args()
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83 marker = options.marker
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84
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85 if not buckets:
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86 list_buckets(boto.connect_s3(), options.tags)
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87 sys.exit(0)
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88
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89 if options.tags:
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90 print("-t option only works for the overall bucket list")
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91 sys.exit(1)
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92
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93 pairs = []
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94 mixedCase = False
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95 for name in buckets:
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96 if "/" in name:
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97 pairs.append(name.split("/", 1))
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98 else:
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99 pairs.append([name, None])
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100 if pairs[-1][0].lower() != pairs[-1][0]:
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101 mixedCase = True
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102
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103 if mixedCase:
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104 s3 = boto.connect_s3(calling_format=OrdinaryCallingFormat())
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105 else:
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106 s3 = boto.connect_s3()
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107
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108 for name, prefix in pairs:
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109 list_bucket(s3.get_bucket(name), prefix, marker=marker)
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110
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111
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112 if __name__ == "__main__":
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113 main()