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1 import gzip
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2 import optparse # using optparse as hydra still python 2.6
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3 import os.path
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4 import shutil
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5 import sys
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6
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7 def report_error(*args):
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8 sys.stderr.write(' '.join(map(str,args)) + '\n')
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9 sys.stderr.flush()
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10 sys.exit(1)
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11
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12
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13 def get_tool_data(name):
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14 root_dir = os.path.dirname((os.path.realpath(__file__)))
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15 path = os.path.join(root_dir,"tool-data",name)
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16 if not(os.path.isfile(path)):
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17 report_error(name,"file not found in tool's tool-data folder. Please ask you galaxy admin to add it back")
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18 return path
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19
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20
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21 def check_white_list(path_to_check):
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22 white_list = get_tool_data("white-list.ini")
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23 with open(white_list, 'r') as white_list_file:
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24 for line in white_list_file:
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25 line = line.strip()
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26 if len(line) >= 1 and path_to_check.startswith(line):
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27 return True
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28 report_error(path_to_check,"has not been included in the white list. Please contact the local galaxy admin to add it.")
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29
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30
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31 def check_black_list(path_to_check):
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32 black_list = get_tool_data("black-list.ini")
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33 with open(black_list, 'r') as black_list_file:
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34 for line in black_list_file:
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35 line = line.strip()
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36 if len(line) >= 1 and line in path_to_check:
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37 report_error(line,"has been black list so",path_to_check,"is not allowed. Please contact the local galaxy admin to change that, or add a symlink.")
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38 return True
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39
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40
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41 def check_pattern_get_new_name(a_file, ending, options):
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42 if options.start:
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43 if not(a_file.startswith(options.start)):
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44 return None
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45 if options.last:
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46 if ending[0] == ".":
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47 last = options.last + ending
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48 else:
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49 if options.last[-1] == ".":
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50 last = options.last + ending
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51 else:
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52 last = options.last + "." + ending
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53 if not(a_file.endswith(last)):
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54 return None
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55 if options.new_ending:
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56 name = a_file[:-len(ending)]
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57 if options.new_ending[0] ==".":
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58 if name[-1] == ".":
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59 name = name[:-1]
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60 return name + options.new_ending
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61 if options.decompress:
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62 if a_file.endswith(".gz"):
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63 return a_file[:-3]
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64 return a_file
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65
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66
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67 def check_and_get_new_name(a_file, options):
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68 for ending in options.endings:
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69 if a_file.endswith(ending):
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70 return check_pattern_get_new_name (a_file, ending, options)
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71 return None
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72
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73
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74 def link(a_file, new_name, path):
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75 file_path = os.path.join(os.path.realpath(path), a_file)
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76 sym_path = os.path.join(os.path.realpath("output"), new_name)
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77 #if not(os.path.exists(sym_path)):
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78 os.link(file_path, sym_path)
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79
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80
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81 def decompress(a_file, new_name, path):
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82 file_path = os.path.join(os.path.realpath(path), a_file)
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83 target_path = os.path.join(os.path.realpath("output"), new_name)
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84 with gzip.open(file_path, 'rb') as f_in, open(target_path, 'wb') as f_out:
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85 shutil.copyfileobj(f_in, f_out)
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86
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87
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88 def copy_and_link(path, options):
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89 os.mkdir("output")
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90 with open(options.list, 'w') as list_file:
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91 files = os.listdir(path)
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92 files.sort()
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93 for a_file in files:
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94 new_name = check_and_get_new_name(a_file, options)
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95 if new_name:
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96 list_file.write(new_name)
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97 list_file.write("\n")
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98 if options.decompress:
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99 if a_file.endswith(".gz"):
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100 decompress(a_file, new_name,path)
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101 else:
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102 link(a_file, new_name, path)
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103 elif options.link:
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104 link(a_file, new_name, path)
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105
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106
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107 if __name__ == '__main__':
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108 parser = optparse.OptionParser()
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109 parser.add_option("--path", action="store", type="string",
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110 help="Path of directory to check. ")
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111 parser.add_option("--ending", action="append", type="string", dest="endings",
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112 help="Ending that can be listed and if requested linked or decompressed. ")
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113 parser.add_option("--start", action="store", type="string",
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114 help="String that must be at the start of the file name ")
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115 parser.add_option("--last", action="store", type="string",
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116 help="String that must be the last bit of the file name before the endings")
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117 parser.add_option("--new_ending", action="store", type="string",
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118 help="New ending to replace any previous ending in list and if required links or decompressions. Note: If not set decompression will auto remove the compressioned part of the ending")
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119 #parser.add_option("--regex", action="store", type="string",
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120 # help="Regex pattern the file name (less . ending) must match before the endings")
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121 parser.add_option("--list", action="store", type="string",
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122 help="Path to where all files should be listed. ")
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123 parser.add_option("--link", action="store_true", default=False,
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124 help="If set will cause links to be added in output directory. ")
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125 parser.add_option("--decompress", action="store_true", default=False,
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126 help="If set will cause gz files to be decompressed or if not a supported decompression ending linked.")
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127 (options, args) = parser.parse_args()
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128
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129
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130 path = options.path.strip()
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131 if path[-1] != '/':
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132 path = path + "/"
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133 check_white_list(path)
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134 print path, "white listed"
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135 check_black_list(path)
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136 print path, "not black listed"
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137 copy_and_link(path, options)
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138
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