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1 #!/usr/bin/env python
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2
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3 '''
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4 Test tool for running Galaxy workflows from Refinery
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5
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6 @author: Ilya Sytchev
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7
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8 Input: one or more text files
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9 Output: concatenated input file(s) plus annotation
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10
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11 Requires Python v2.7
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12
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13 '''
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14
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15
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16 import argparse
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17 import random
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18 import sys
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19 import time
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20
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21
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22 def main(args):
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23 time.sleep(args.seconds)
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24
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25 if check_fail(args.p_fail):
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26 cleanup(args)
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27 quit("Processing failed by request", args)
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28
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29 input = read_files(args.input_files)
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30 try:
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31 for out_file in args.output_files:
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8
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32 if args.empty_outfile:
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33 output = ''
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34 else:
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35 output = "Output file name: " + out_file.name + "\n\n" + input
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36 out_file.write(output)
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0
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37 except IOError as e:
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38 cleanup(args)
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39 parser.error(e)
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40 else:
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41 cleanup(args)
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42
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43
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44 def check_fail(p_fail):
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45 '''Determine success/failure state given a probability of failure
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46
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47 '''
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48 random.seed()
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49 if random.random() < p_fail:
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50 return True
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51 else:
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52 return False
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53
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54
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55 def read_files(file_list):
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56 '''Read files from disk into a string
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57
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58 '''
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59 str = ''
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60 for in_file in file_list:
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5
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61 str += "Input file name: " + in_file.name + "\n\n"
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0
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62 str += in_file.read()
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63 return str
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64
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65
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66 def cleanup(args):
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67 '''Close all open file handles
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68
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69 '''
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70 file_list = []
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71 if args.input_files:
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72 file_list.extend(args.input_files)
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73 if args.output_files:
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74 file_list.extend(args.output_files)
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75 for fh in file_list:
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76 try:
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77 fh.close()
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78 except AttributeError:
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79 continue
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80
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81
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82 def quit(message, args):
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83 '''Exit and optionally write to stdout and/or stderr
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84
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85 '''
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86 if args.stdout:
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87 sys.stdout.write(message + '\n')
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88 if args.stderr:
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89 sys.stderr.write(message + '\n')
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90 sys.exit(args.exit_code)
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91
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92
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93 if __name__ == '__main__':
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94 version = "%(prog)s 0.1"
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95 description = "Test tool for running workflows on Galaxy platform from Refinery"
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96 parser = argparse.ArgumentParser(description=description, version=version)
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97
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98 parser.add_argument('-i', '--in-file', dest='input_files', nargs='+',
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99 type=file, metavar='INPUT_FILE', required=True,
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100 help='name of the input file')
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101 parser.add_argument('-o', '--out-file', dest='output_files', nargs='+',
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102 type=argparse.FileType('w'), metavar='OUTPUT_FILE',
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103 required=True, help='name of the output file')
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104 parser.add_argument('-e', '--exit_code', type=int, default=0,
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105 help='code to return on exit, default: %(default)s')
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106 parser.add_argument('--stdout', action='store_true',
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107 help='write a message to stdout')
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108 parser.add_argument('--stderr', action='store_true',
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109 help='write a message to stderr')
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8
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110 parser.add_argument('--empty_outfile', action='store_true',
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111 help='produce empty output file(s)')
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0
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112 parser.add_argument('-p', '--p-fail', type=float, default=0.0,
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113 help='probability of execution failure, default: %(default)s')
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114 parser.add_argument('-s', '--sleep', dest='seconds', type=int, default=0,
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115 metavar='SECONDS',
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116 help='number of seconds to sleep, default: %(default)s')
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117
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118 # check argument values for errors
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119 try:
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120 args = parser.parse_args()
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121 except IOError as e:
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122 parser.error(e)
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123
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124 if args.exit_code < 0 or args.exit_code > 255:
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125 cleanup(args)
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126 parser.error("Exit code value must be between 0 and 255")
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127
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128 if args.p_fail < 0.0 or args.p_fail > 1.0:
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129 cleanup(args)
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130 parser.error("Probability value must be between 0.0 and 1.0 inclusive")
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131
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132 main(args)
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