Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_toolargparse.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import argparse |
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2 from io import StringIO |
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3 from pathlib import Path |
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4 from typing import Callable |
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5 |
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6 import pytest |
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7 |
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8 import cwltool.executors |
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9 from cwltool.argparser import generate_parser |
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10 from cwltool.context import LoadingContext |
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11 from cwltool.load_tool import load_tool |
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12 from cwltool.main import main |
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13 |
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14 from .util import get_data, needs_docker |
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15 |
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16 script_a = """ |
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17 #!/usr/bin/env cwl-runner |
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18 cwlVersion: v1.0 |
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19 class: CommandLineTool |
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20 doc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)" |
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21 inputs: |
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22 #Give it a list of input files |
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23 - id: input |
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24 type: File |
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25 inputBinding: |
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26 position: 0 |
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27 outputs: |
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28 - id: output |
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29 type: File |
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30 outputBinding: |
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31 glob: test.txt |
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32 stdout: test.txt |
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33 baseCommand: [cat] |
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34 """ |
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35 |
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36 script_b = """ |
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37 #!/usr/bin/env cwl-runner |
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38 cwlVersion: v1.0 |
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39 class: CommandLineTool |
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40 inputs: |
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41 - id: bdg |
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42 type: "boolean" |
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43 outputs: |
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44 - id: output |
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45 type: File |
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46 outputBinding: |
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47 glob: foo |
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48 baseCommand: |
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49 - echo |
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50 - "ff" |
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51 stdout: foo |
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52 """ |
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53 |
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54 script_c = """ |
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55 #!/usr/bin/env cwl-runner |
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56 |
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57 cwlVersion: v1.0 |
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58 class: ExpressionTool |
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59 |
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60 inputs: |
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61 foo: |
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62 type: |
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63 type: record |
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64 fields: |
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65 one: File |
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66 two: string |
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67 |
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68 expression: $(inputs.foo.two) |
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69 |
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70 outputs: [] |
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71 """ |
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72 |
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73 scripts_argparse_params = [ |
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74 ("help", script_a, lambda x: ["--debug", x, "--input", get_data("tests/echo.cwl")]), |
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75 ("boolean", script_b, lambda x: [x, "--help"]), |
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76 ("help with c", script_c, lambda x: [x, "--help"]), |
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77 ( |
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78 "foo with c", |
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79 script_c, |
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80 lambda x: [x, "--foo.one", get_data("tests/echo.cwl"), "--foo.two", "test"], |
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81 ), |
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82 ] |
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83 |
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84 |
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85 @needs_docker |
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86 @pytest.mark.parametrize("name,script_contents,params", scripts_argparse_params) |
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87 def test_argparse( |
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88 name: str, script_contents: str, params: Callable[[str], str], tmp_path: Path |
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89 ) -> None: |
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90 script_name = tmp_path / "script" |
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91 try: |
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92 with script_name.open(mode="w") as script: |
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93 script.write(script_contents) |
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94 |
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95 my_params = ["--outdir", str(tmp_path / "outdir")] |
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96 my_params.extend(params(script.name)) |
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97 assert main(my_params) == 0, name |
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98 |
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99 except SystemExit as err: |
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100 assert err.code == 0, name |
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101 |
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102 |
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103 def test_dont_require_inputs(tmp_path: Path) -> None: |
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104 stream = StringIO() |
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105 |
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106 script_name = tmp_path / "script" |
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107 try: |
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108 with script_name.open(mode="w") as script: |
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109 script.write(script_a) |
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110 |
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111 assert ( |
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112 main( |
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113 argsl=["--debug", str(script_name), "--input", str(script_name)], |
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114 executor=cwltool.executors.NoopJobExecutor(), |
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115 stdout=stream, |
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116 ) |
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117 == 0 |
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118 ) |
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119 assert ( |
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120 main( |
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121 argsl=["--debug", str(script_name)], |
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122 executor=cwltool.executors.NoopJobExecutor(), |
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123 stdout=stream, |
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124 ) |
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125 == 2 |
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126 ) |
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127 assert ( |
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128 main( |
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129 argsl=["--debug", str(script_name)], |
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130 executor=cwltool.executors.NoopJobExecutor(), |
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131 input_required=False, |
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132 stdout=stream, |
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133 ) |
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134 == 0 |
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135 ) |
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136 |
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137 except SystemExit as err: |
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138 assert err.code == 0, script_name if script else None |
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139 |
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140 |
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141 def test_argparser_with_doc() -> None: |
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142 """The `desription` field is set if `doc` field is provided.""" |
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143 loadingContext = LoadingContext() |
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144 tool = load_tool(get_data("tests/with_doc.cwl"), loadingContext) |
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145 p = argparse.ArgumentParser() |
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146 parser = generate_parser(p, tool, {}, [], False) |
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147 assert parser.description is not None |
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148 |
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149 |
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150 def test_argparser_without_doc() -> None: |
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151 """The `desription` field is None if `doc` field is not provided.""" |
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152 loadingContext = LoadingContext() |
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153 tool = load_tool(get_data("tests/without_doc.cwl"), loadingContext) |
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154 p = argparse.ArgumentParser() |
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155 parser = generate_parser(p, tool, {}, [], False) |
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156 assert parser.description is None |