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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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32 out_file.write('\n' + "Output file name: " + out_file.name + '\n')
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33 out_file.write(input)
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34 except IOError as e:
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35 cleanup(args)
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36 parser.error(e)
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37 else:
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38 cleanup(args)
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39
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40
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41 def check_fail(p_fail):
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42 '''Determine success/failure state given a probability of failure
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43
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44 '''
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45 random.seed()
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46 if random.random() < p_fail:
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47 return True
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48 else:
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49 return False
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50
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51
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52 def read_files(file_list):
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53 '''Read files from disk into a string
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54
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55 '''
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56 str = ''
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57 for in_file in file_list:
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58 str += "Input file name: " + in_file.name + '\n'
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59 str += in_file.read()
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60 return str
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61
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62
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63 def cleanup(args):
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64 '''Close all open file handles
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65
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66 '''
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67 file_list = []
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68 if args.input_files:
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69 file_list.extend(args.input_files)
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70 if args.output_files:
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71 file_list.extend(args.output_files)
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72 for fh in file_list:
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73 try:
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74 fh.close()
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75 except AttributeError:
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76 continue
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77
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78
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79 def quit(message, args):
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80 '''Exit and optionally write to stdout and/or stderr
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81
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82 '''
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83 if args.stdout:
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84 sys.stdout.write(message + '\n')
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85 if args.stderr:
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86 sys.stderr.write(message + '\n')
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87 sys.exit(args.exit_code)
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88
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89
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90 if __name__ == '__main__':
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91 version = "%(prog)s 0.1"
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92 description = "Test tool for running workflows on Galaxy platform from Refinery"
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93 parser = argparse.ArgumentParser(description=description, version=version)
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94
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95 parser.add_argument('-i', '--in-file', dest='input_files', nargs='+',
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96 type=file, metavar='INPUT_FILE', required=True,
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97 help='name of the input file')
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98 parser.add_argument('-o', '--out-file', dest='output_files', nargs='+',
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99 type=argparse.FileType('w'), metavar='OUTPUT_FILE',
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100 required=True, help='name of the output file')
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101 parser.add_argument('-e', '--exit_code', type=int, default=0,
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102 help='code to return on exit, default: %(default)s')
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103 parser.add_argument('--stdout', action='store_true',
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104 help='write a message to stdout')
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105 parser.add_argument('--stderr', action='store_true',
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106 help='write a message to stderr')
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107 parser.add_argument('-p', '--p-fail', type=float, default=0.0,
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108 help='probability of execution failure, default: %(default)s')
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109 parser.add_argument('-s', '--sleep', dest='seconds', type=int, default=0,
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110 metavar='SECONDS',
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111 help='number of seconds to sleep, default: %(default)s')
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112
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113 # check argument values for errors
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114 try:
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115 args = parser.parse_args()
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116 except IOError as e:
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117 parser.error(e)
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118
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119 if args.exit_code < 0 or args.exit_code > 255:
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120 cleanup(args)
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121 parser.error("Exit code value must be between 0 and 255")
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122
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123 if args.p_fail < 0.0 or args.p_fail > 1.0:
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124 cleanup(args)
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125 parser.error("Probability value must be between 0.0 and 1.0 inclusive")
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126
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127 main(args)
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