Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/tests/test_toolargparse.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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0
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1 import os
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2 import sys
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3 from tempfile import NamedTemporaryFile
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4 from io import BytesIO, StringIO
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5
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6 import pytest
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7 from cwltool.main import main
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8 import cwltool.executors
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9
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10 from .util import get_data, needs_docker
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11
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12 script_a = '''
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13 #!/usr/bin/env cwl-runner
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14 cwlVersion: v1.0
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15 class: CommandLineTool
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16 doc: "This tool is developed for SMC-RNA Challenge for detecting gene fusions (STAR fusion)"
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17 inputs:
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18 #Give it a list of input files
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19 - id: input
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20 type: File
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21 inputBinding:
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22 position: 0
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23 outputs:
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24 - id: output
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25 type: File
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26 outputBinding:
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27 glob: test.txt
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28 stdout: test.txt
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29 baseCommand: [cat]
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30 '''
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31
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32 script_b = '''
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33 #!/usr/bin/env cwl-runner
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34 cwlVersion: v1.0
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35 class: CommandLineTool
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36 inputs:
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37 - id: bdg
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38 type: "boolean"
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39 outputs:
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40 - id: output
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41 type: File
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42 outputBinding:
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43 glob: foo
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44 baseCommand:
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45 - echo
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46 - "ff"
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47 stdout: foo
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48 '''
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49
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50 script_c = '''
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51 #!/usr/bin/env cwl-runner
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52
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53 cwlVersion: v1.0
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54 class: ExpressionTool
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55
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56 inputs:
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57 foo:
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58 type:
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59 type: record
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60 fields:
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61 one: File
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62 two: string
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63
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64 expression: $(inputs.foo.two)
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65
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66 outputs: []
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67 '''
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68
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69 scripts_argparse_params = [
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70 ('help', script_a,
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71 lambda x: ["--debug", x, '--input', get_data('tests/echo.cwl')]
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72 ),
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73 ('boolean', script_b, lambda x: [x, '--help']
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74 ),
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75 ('help with c', script_c, lambda x: [x, '--help']),
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76 ('foo with c', script_c,
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77 lambda x: [x, '--foo.one', get_data('tests/echo.cwl'), '--foo.two', 'test']
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78 )
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79 ]
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80
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81 @needs_docker
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82 @pytest.mark.parametrize('name,script_contents,params', scripts_argparse_params)
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83 def test_argparse(name, script_contents, params, tmpdir):
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84 script = None
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85 try:
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86 script = NamedTemporaryFile(mode='w', delete=False)
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87 script.write(script_contents)
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88 script.close()
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89
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90 my_params = ["--outdir", str(tmpdir)]
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91 my_params.extend(params(script.name))
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92 assert main(my_params) == 0, name
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93
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94 except SystemExit as err:
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95 assert err.code == 0, name
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96 finally:
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97 if script and script.name and os.path.exists(script.name):
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98 os.unlink(script.name)
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99
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100
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101 class NoopJobExecutor(cwltool.executors.JobExecutor):
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102 def run_jobs(self,
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103 process, # type: Process
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104 job_order_object, # type: Dict[Text, Any]
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105 logger, # type: logging.Logger
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106 runtime_context # type: RuntimeContext
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107 ): # type: (...) -> None
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108 pass
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109
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110 def execute(self,
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111 process, # type: Process
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112 job_order_object, # type: Dict[Text, Any]
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113 runtime_context, # type: RuntimeContext
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114 logger=None, # type: logging.Logger
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115 ): # type: (...) -> Tuple[Optional[Union[Dict[Text, Any], List[Dict[Text, Any]]]], Text]
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116 return {}, "success"
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117
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118 def test_dont_require_inputs():
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119 if sys.version_info[0] < 3:
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120 stream = BytesIO()
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121 else:
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122 stream = StringIO()
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123
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124 script = None
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125 try:
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126 script = NamedTemporaryFile(mode='w', delete=False)
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127 script.write(script_a)
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128 script.close()
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129
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130 assert main(argsl=["--debug", script.name, "--input", script.name], executor=NoopJobExecutor(), stdout=stream) == 0
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131 assert main(argsl=["--debug", script.name], executor=NoopJobExecutor(), stdout=stream) == 2
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132 assert main(argsl=["--debug", script.name], executor=NoopJobExecutor(), input_required=False, stdout=stream) == 0
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133
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134 except SystemExit as err:
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135 assert err.code == 0, name
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136 finally:
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137 if script and script.name and os.path.exists(script.name):
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138 os.unlink(script.name)