Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/tests/test_iwdr.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 import tempfile
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2 import os
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3 from cwltool.main import main
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4 from cwltool import load_tool
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5 from .util import (get_data, get_windows_safe_factory, windows_needs_docker,
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6 needs_docker, temp_dir, needs_singularity, get_main_output)
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7
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8 @windows_needs_docker
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9 def test_newline_in_entry():
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10 """Files in a InitialWorkingDirectory are created with a newline character."""
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11 factory = get_windows_safe_factory()
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12 echo = factory.make(get_data("tests/wf/iwdr-entry.cwl"))
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13 assert echo(message="hello") == {"out": "CONFIGVAR=hello\n"}
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14
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15
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16 @needs_docker
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17 def test_empty_file_creation():
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18 """An empty file can be created in InitialWorkingDirectory."""
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19 err_code, _, _ = get_main_output([get_data("tests/wf/iwdr-empty.cwl")])
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20 assert err_code == 0
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21
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22
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23 @needs_docker
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24 def test_iwdr_permutations():
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25 saved_tempdir = tempfile.tempdir
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26 with temp_dir() as misc:
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27 tempfile.tempdir = os.path.realpath(misc)
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28 with temp_dir() as fifth:
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29 with temp_dir() as sixth:
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30 with temp_dir() as seventh:
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31 with temp_dir() as eighth:
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32 with tempfile.NamedTemporaryFile() as first:
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33 with tempfile.NamedTemporaryFile() as second:
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34 with tempfile.NamedTemporaryFile() as third:
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35 with tempfile.NamedTemporaryFile() as fourth:
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36 with temp_dir() as outdir:
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37 assert(main(
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38 ['--outdir', outdir,
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39 get_data("tests/wf/iwdr_permutations.cwl"),
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40 '--first', first.name,
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41 '--second', second.name,
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42 '--third', third.name,
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43 '--fourth', fourth.name,
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44 '--fifth', fifth,
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45 '--sixth', sixth,
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46 '--seventh', seventh,
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47 '--eighth', eighth]) == 0)
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48 tempfile.tempdir = saved_tempdir
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49
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50 @needs_docker
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51 def test_iwdr_permutations_inplace():
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52 saved_tempdir = tempfile.tempdir
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53 with temp_dir() as misc:
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54 tempfile.tempdir = os.path.realpath(misc)
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55 with temp_dir() as fifth:
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56 with temp_dir() as sixth:
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57 with temp_dir() as seventh:
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58 with temp_dir() as eighth:
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59 with tempfile.NamedTemporaryFile() as first:
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60 with tempfile.NamedTemporaryFile() as second:
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61 with tempfile.NamedTemporaryFile() as third:
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62 with tempfile.NamedTemporaryFile() as fourth:
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63 with temp_dir() as outdir:
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64 assert(main(
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65 ['--outdir', outdir,
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66 '--enable-ext',
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67 '--overrides',
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68 get_data("tests/wf/iwdr_permutations_inplace.yml"),
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69 get_data("tests/wf/iwdr_permutations.cwl"),
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70 '--first', first.name,
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71 '--second', second.name,
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72 '--third', third.name,
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73 '--fourth', fourth.name,
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74 '--fifth', fifth,
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75 '--sixth', sixth,
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76 '--seventh', seventh,
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77 '--eighth', eighth]) == 0)
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78 tempfile.tempdir = saved_tempdir
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79
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80 @needs_singularity
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81 def test_iwdr_permutations_singularity():
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82 with temp_dir() as fifth:
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83 with temp_dir() as sixth:
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84 with temp_dir() as seventh:
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85 with temp_dir() as eighth:
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86 with tempfile.NamedTemporaryFile() as first:
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87 with tempfile.NamedTemporaryFile() as second:
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88 with tempfile.NamedTemporaryFile() as third:
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89 with tempfile.NamedTemporaryFile() as fourth:
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90 with temp_dir() as outdir:
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91 assert(main(
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92 ['--outdir', outdir,
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93 '--singularity',
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94 get_data("tests/wf/iwdr_permutations.cwl"),
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95 '--first', first.name,
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96 '--second', second.name,
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97 '--third', third.name,
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98 '--fourth', fourth.name,
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99 '--fifth', fifth,
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100 '--sixth', sixth,
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101 '--seventh', seventh,
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102 '--eighth', eighth]) == 0)
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103
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104 @needs_singularity
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105 def test_iwdr_permutations_singularity_inplace():
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106 with temp_dir() as fifth:
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107 with temp_dir() as sixth:
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108 with temp_dir() as seventh:
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109 with temp_dir() as eighth:
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110 with tempfile.NamedTemporaryFile() as first:
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111 with tempfile.NamedTemporaryFile() as second:
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112 with tempfile.NamedTemporaryFile() as third:
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113 with tempfile.NamedTemporaryFile() as fourth:
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114 with temp_dir() as outdir:
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115 assert(main(
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116 ['--outdir', outdir,
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117 '--singularity',
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118 '--enable-ext',
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119 '--overrides',
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120 get_data("tests/wf/iwdr_permutations_inplace.yml"),
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121 get_data("tests/wf/iwdr_permutations.cwl"),
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122 '--first', first.name,
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123 '--second', second.name,
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124 '--third', third.name,
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125 '--fourth', fourth.name,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
126 '--fifth', fifth,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
127 '--sixth', sixth,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
128 '--seventh', seventh,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
129 '--eighth', eighth]) == 0)