Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_tmpdir.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 """Test that all temporary directories respect the --tmpdir-prefix and --tmp-outdir-prefix options.""" |
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2 import subprocess |
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3 import sys |
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4 from pathlib import Path |
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5 from typing import List, cast |
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6 |
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7 from _pytest.monkeypatch import MonkeyPatch |
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8 from ruamel.yaml.comments import CommentedMap |
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9 from schema_salad.avro import schema |
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10 from schema_salad.sourceline import cmap |
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11 |
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12 from cwltool.builder import Builder |
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13 from cwltool.command_line_tool import CommandLineTool |
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14 from cwltool.context import LoadingContext, RuntimeContext |
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15 from cwltool.docker import DockerCommandLineJob |
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16 from cwltool.job import JobBase |
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17 from cwltool.pathmapper import MapperEnt, PathMapper |
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18 from cwltool.stdfsaccess import StdFsAccess |
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19 from cwltool.update import INTERNAL_VERSION |
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20 from cwltool.utils import create_tmp_dir |
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21 |
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22 from .util import get_data, needs_docker |
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23 |
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24 |
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25 def test_docker_commandLineTool_job_tmpdir_prefix(tmp_path: Path) -> None: |
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26 """Test that docker enabled CommandLineTool respects temp directory directives.""" |
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27 loading_context = LoadingContext( |
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28 { |
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29 "metadata": { |
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30 "cwlVersion": INTERNAL_VERSION, |
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31 "http://commonwl.org/cwltool#original_cwlVersion": INTERNAL_VERSION, |
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32 } |
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33 } |
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34 ) |
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35 clt = CommandLineTool( |
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36 cast( |
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37 CommentedMap, |
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38 cmap( |
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39 { |
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40 "cwlVersion": INTERNAL_VERSION, |
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41 "class": "CommandLineTool", |
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42 "inputs": [], |
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43 "outputs": [], |
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44 "requirements": [ |
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45 {"class": "DockerRequirement", "dockerPull": "debian:stable"} |
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46 ], |
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47 } |
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48 ), |
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49 ), |
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50 loading_context, |
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51 ) |
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52 tmpdir_prefix = str(tmp_path / "1") |
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53 tmp_outdir_prefix = str(tmp_path / "2") |
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54 runtime_context = RuntimeContext( |
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55 { |
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56 "tmpdir_prefix": tmpdir_prefix, |
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57 "tmp_outdir_prefix": tmp_outdir_prefix, |
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58 } |
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59 ) |
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60 job = next(clt.job({}, None, runtime_context)) |
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61 assert isinstance(job, JobBase) |
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62 assert job.stagedir and job.stagedir.startswith(tmpdir_prefix) |
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63 assert job.tmpdir and job.tmpdir.startswith(tmpdir_prefix) |
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64 assert job.outdir and job.outdir.startswith(tmp_outdir_prefix) |
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65 |
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66 |
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67 def test_commandLineTool_job_tmpdir_prefix(tmp_path: Path) -> None: |
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68 """Test that non-docker enabled CommandLineTool respects temp directory directives.""" |
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69 loading_context = LoadingContext( |
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70 { |
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71 "metadata": { |
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72 "cwlVersion": INTERNAL_VERSION, |
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73 "http://commonwl.org/cwltool#original_cwlVersion": INTERNAL_VERSION, |
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74 } |
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75 } |
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76 ) |
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77 clt = CommandLineTool( |
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78 cast( |
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79 CommentedMap, |
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80 cmap( |
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81 { |
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82 "cwlVersion": INTERNAL_VERSION, |
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83 "class": "CommandLineTool", |
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84 "inputs": [], |
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85 "outputs": [], |
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86 "requirements": [], |
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87 } |
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88 ), |
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89 ), |
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90 loading_context, |
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91 ) |
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92 tmpdir_prefix = str(tmp_path / "1") |
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93 tmp_outdir_prefix = str(tmp_path / "2") |
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94 runtime_context = RuntimeContext( |
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95 { |
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96 "tmpdir_prefix": tmpdir_prefix, |
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97 "tmp_outdir_prefix": tmp_outdir_prefix, |
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98 } |
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99 ) |
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100 job = next(clt.job({}, None, runtime_context)) |
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101 assert isinstance(job, JobBase) |
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102 assert job.stagedir and job.stagedir.startswith(tmpdir_prefix) |
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103 assert job.tmpdir and job.tmpdir.startswith(tmpdir_prefix) |
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104 assert job.outdir and job.outdir.startswith(tmp_outdir_prefix) |
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105 |
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106 |
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107 @needs_docker |
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108 def test_dockerfile_tmpdir_prefix(tmp_path: Path, monkeypatch: MonkeyPatch) -> None: |
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109 """Test that DockerCommandLineJob.get_image respects temp directory directives.""" |
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110 monkeypatch.setattr( |
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111 target=subprocess, name="check_call", value=lambda *args, **kwargs: True |
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112 ) |
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113 tmp_outdir_prefix = tmp_path / "1" |
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114 assert DockerCommandLineJob.get_image( |
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115 { |
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116 "class": "DockerRequirement", |
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117 "dockerFile": "FROM debian:stable", |
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118 "dockerImageId": sys._getframe().f_code.co_name, |
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119 }, |
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120 pull_image=True, |
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121 force_pull=True, |
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122 tmp_outdir_prefix=str(tmp_outdir_prefix), |
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123 ) |
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124 children = sorted(tmp_outdir_prefix.parent.glob("*")) |
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125 assert len(children) == 1 |
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126 subdir = tmp_path / children[0] |
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127 assert len(sorted(subdir.glob("*"))) == 1 |
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128 assert (subdir / "Dockerfile").exists() |
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129 |
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130 |
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131 def test_docker_tmpdir_prefix(tmp_path: Path) -> None: |
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132 """Test that DockerCommandLineJob respects temp directory directives.""" |
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133 (tmp_path / "3").mkdir() |
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134 tmpdir_prefix = str(tmp_path / "3" / "ttmp") |
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135 runtime_context = RuntimeContext( |
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136 {"tmpdir_prefix": tmpdir_prefix, "user_space_docker_cmd": None} |
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137 ) |
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138 builder = Builder( |
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139 {}, |
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140 [], |
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141 [], |
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142 {}, |
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143 schema.Names(), |
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144 [], |
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145 [], |
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146 {}, |
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147 None, |
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148 None, |
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149 StdFsAccess, |
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150 StdFsAccess(""), |
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151 None, |
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152 0.1, |
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153 False, |
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154 False, |
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155 False, |
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156 "", |
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157 runtime_context.get_outdir(), |
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158 runtime_context.get_tmpdir(), |
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159 runtime_context.get_stagedir(), |
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160 INTERNAL_VERSION, |
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161 ) |
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162 job = DockerCommandLineJob(builder, {}, PathMapper, [], [], "") |
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163 runtime: List[str] = [] |
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164 |
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165 volume_writable_file = MapperEnt( |
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166 resolved=get_data("tests/2.fastq"), target="foo", type=None, staged=None |
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167 ) |
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168 (tmp_path / "1").mkdir() |
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169 job.add_writable_file_volume( |
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170 runtime, volume_writable_file, None, str(tmp_path / "1" / "writable_file") |
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171 ) |
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172 children = sorted((tmp_path / "1").glob("*")) |
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173 assert len(children) == 1 |
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174 subdir = tmp_path / children[0] |
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175 assert subdir.name.startswith("writable_file") |
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176 assert len(sorted(subdir.glob("*"))) == 1 |
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177 assert (subdir / "2.fastq").exists() |
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178 |
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179 resolved_writable_dir = tmp_path / "data_orig" |
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180 resolved_writable_dir.mkdir(parents=True) |
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181 volume_dir = MapperEnt( |
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182 resolved=str(resolved_writable_dir), target="bar", type=None, staged=None |
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183 ) |
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184 (tmp_path / "2").mkdir() |
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185 job.add_writable_directory_volume( |
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186 runtime, volume_dir, None, str(tmp_path / "2" / "dir") |
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187 ) |
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188 children = sorted((tmp_path / "2").glob("*")) |
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189 assert len(children) == 1 |
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190 subdir = tmp_path / "2" / children[0] |
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191 assert subdir.name.startswith("dir") |
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192 assert len(sorted(subdir.glob("*"))) == 1 |
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193 assert (subdir / "data_orig").exists() |
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194 |
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195 cidfile = job.create_runtime({}, runtime_context)[1] |
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196 assert cidfile and cidfile.startswith(tmpdir_prefix) |
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197 |
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198 volume_file = MapperEnt(resolved="Hoopla!", target="baz", type=None, staged=None) |
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199 (tmp_path / "4").mkdir() |
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200 job.create_file_and_add_volume( |
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201 runtime, volume_file, None, None, str(tmp_path / "4" / "file") |
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202 ) |
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203 children = sorted((tmp_path / "4").glob("*")) |
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204 assert len(children) == 1 |
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205 subdir = tmp_path / "4" / children[0] |
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206 assert subdir.name.startswith("file") |
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207 assert len(sorted(subdir.glob("*"))) == 1 |
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208 assert (subdir / "baz").exists() |
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209 |
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210 |
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211 def test_runtimeContext_respects_tmpdir_prefix(tmp_path: Path) -> None: |
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212 """Test that RuntimeContext helper methods respects tmpdir_prefix.""" |
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213 tmpdir_prefix = str(tmp_path / "foo") |
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214 runtime_context = RuntimeContext({"tmpdir_prefix": tmpdir_prefix}) |
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215 assert runtime_context.get_tmpdir().startswith(tmpdir_prefix) |
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216 assert runtime_context.get_stagedir().startswith(tmpdir_prefix) |
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217 assert runtime_context.create_tmpdir().startswith(tmpdir_prefix) |
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218 assert create_tmp_dir(tmpdir_prefix).startswith(tmpdir_prefix) |
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219 |
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220 |
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221 def test_runtimeContext_respects_tmp_outdir_prefix(tmp_path: Path) -> None: |
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222 """Test that RuntimeContext helper methods respects tmp_outdir_prefix.""" |
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223 tmpdir_prefix = str(tmp_path / "foo") |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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224 runtime_context = RuntimeContext({"tmp_outdir_prefix": tmpdir_prefix}) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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225 assert runtime_context.get_outdir().startswith(tmpdir_prefix) |
4f3585e2f14b
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
shellac
parents:
diff
changeset
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226 assert runtime_context.create_outdir().startswith(tmpdir_prefix) |