Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/planemo/rscript_parse.py @ 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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1 """Module parses R scripts and sends a yaml file to cmd_bioc_tool_init."""
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2 import os
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3
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4
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5 def read_rscript(path):
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6 """Read the rscript."""
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7 try:
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8 with open(os.path.expanduser(path), 'r') as f:
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9 rscript = f.readlines()
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10 except Exception as e:
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11 print(e)
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12 return rscript
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13
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14
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15 def parse_rscript(script, example_command):
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16 """Parse script."""
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17 rscript = read_rscript(script)
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18 data = {}
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19
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20 # Find libraries
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21 lib = Library(rscript)
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22 library_list = lib.find_library()
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23 data['library'] = library_list
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24
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25 # Find inputs
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26 inputs = Input(rscript, example_command)
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27 input_list = inputs.find_inputs()
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28 data['inputs'] = input_list
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29
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30 # Find outputs
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31 outputs = Output(rscript, example_command)
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32 output_list = outputs.find_outputs()
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33 data['outputs'] = output_list
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34 return data
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35
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36
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37 def parse_example_command(example_command):
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38 """Parse example_command to get inputs.
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39
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40 Each input stored as element in a dictionary list.
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41 """
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42 cmd = example_command.replace("\n", " ")
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43 opts = [i.strip() for i in cmd.split("--")]
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44 opt_dict = {}
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45 for opt in opts:
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46 opt = opt.split(" ")
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47 if not opt[0] in opt_dict.keys():
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48 opt_dict[opt[0]] = [opt[1]]
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49 else:
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50 opt_dict[opt[0]].append(opt[1])
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51 return opt_dict
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52
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53
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54 class Library(object):
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55 """Library class for parsing R scripts."""
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56
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57 def __init__(self, script):
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58 """Initialize class Library."""
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59 self.script = script
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60 self.searchtext = "library"
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61
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62 def _prune_library(self, line):
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63 """Prune line to get the names in library."""
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64 import re
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65 split_words = re.compile(r'\w+').findall(line)
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66 lib = [w for w in split_words if w != "library"]
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67 return lib[0]
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68
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69 def find_library(self):
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70 """Parse library, to find and check requirements."""
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71 lib = []
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72 for i, line in enumerate(self.script):
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73 line = line.strip()
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74 if (self.searchtext in line) and (not line.startswith("#")):
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75 lib_value = self._prune_library(line)
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76 # if lib_value != "getopt": # getopt already exists
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77 lib.append(lib_value)
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78 return lib
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79
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80
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81 class Input(object):
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82 """Input class for parsing inputs."""
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83
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84 def __init__(self, script, example_command):
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85 """Initialize Input with searchtext = input."""
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86 self.script = script
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87 self.example_command = example_command
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88 self.searchtext = "input"
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89
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90 def find_inputs(self):
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91 """Find inputs in example command.
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92
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93 This parses the R script and has NOTHING TO DO WITH kwds
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94 """
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95 opt_dict = parse_example_command(self.example_command)
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96 inputs = {}
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97 for key, value in opt_dict.iteritems():
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98 if self.searchtext in key: # key here is "input"
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99 for i, line in enumerate(self.script):
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100 line = line.strip()
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101 if (key in line) and (not line.startswith("#")):
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102 # print >> sys.stderr, 'Line: %s\nkey: %s\nvalue: %s' % (line,key,value)
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103 inputs[key] = value
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104 else:
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105 continue
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106 # print >> sys.stderr, 'INPUTS: %s' % inputs
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107 if not bool(inputs): # if inputs are empty
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108 print("No inputs found in the Rscript, please specify inputs.")
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109 return inputs
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110
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111
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112 class Output(object):
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113 """Output class for parsing outputs."""
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114
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115 def __init__(self, script, example_command):
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116 """Initialize Input with searchtext - output."""
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117 self.script = script
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118 self.example_command = example_command
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119 self.searchtext = "output"
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120
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121 def find_outputs(self):
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122 """Find outputs in example command."""
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123 opt_dict = parse_example_command(self.example_command)
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124 outputs = {}
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125 for key, value in opt_dict.iteritems():
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126 if self.searchtext in key:
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127 for i, line in enumerate(self.script):
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128 line = line.strip()
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129 if (key in line) and (not line.startswith("#")):
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130 outputs[key] = value
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131 else:
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132 continue
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133 # if not bool(outputs): # if outputs are empty
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134 # print("No explicit outputs found, please specify outputs.")
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135 return outputs
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136
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137
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138 if __name__ == "__main__":
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139 # TODO : Make sure tools with configfile are not used, this is not supported yet
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140 test_file1 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool.R"
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141 test_file2 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool_verbose.R"
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142 test_file3 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool_multi_inputs_outputs.R"
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143 test_file4 = "/Users/nturaga/Documents/galaxyproject/bioc-galaxy-integration/my_r_tool/my_r_tool_fail_case.R"
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144
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145 # Test case with explicit input and outputs
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146 print(" \n === Tool test 1 ==== \n ")
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147 parse_rscript(test_file1, "Rscript my_r_tool.R --input input.csv --output output.csv")
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148
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149 # Test case with NO EXPLICIT OUTPUT
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150 print(" \n === Tool test 2 ==== \n")
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151 parse_rscript(test_file2, "Rscript my_r_tool_verbose.R --verbose TRUE --input intput.csv")
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152
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153 # Test case with tool which has to fail
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154 print("\n == Tool test 4: Fail case ==== \n")
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155 parse_rscript(test_file4, "Rscript my_r_tool_fail_case.R")