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annotate planemo/lib/python3.7/site-packages/cwltool/tests/test_pack.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 import json
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2 from ruamel import yaml
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3 import os
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4 import tempfile
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5 from functools import partial
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6
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7 from six import StringIO
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8 import pytest
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9
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10 import cwltool.pack
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11 import cwltool.workflow
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12 from cwltool import load_tool
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13 from cwltool.load_tool import fetch_document, resolve_and_validate_document
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14 from cwltool.main import main, make_relative, print_pack
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15 from cwltool.pathmapper import adjustDirObjs, adjustFileObjs
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16 from cwltool.resolver import tool_resolver
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17 from cwltool.context import LoadingContext
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18
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19 from .util import get_data, needs_docker
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20
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21
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22 def test_pack():
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23 loadingContext, workflowobj, uri = fetch_document(get_data("tests/wf/revsort.cwl"))
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24 loadingContext.do_update = False
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25 loadingContext, uri = resolve_and_validate_document(
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26 loadingContext, workflowobj, uri)
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27 processobj = loadingContext.loader.resolve_ref(uri)[0]
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28
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29 with open(get_data("tests/wf/expect_packed.cwl")) as packed_file:
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30 expect_packed = yaml.safe_load(packed_file)
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31
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32 packed = cwltool.pack.pack(loadingContext.loader, processobj, uri, loadingContext.metadata)
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33 adjustFileObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))
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34 adjustDirObjs(packed, partial(make_relative, os.path.abspath(get_data("tests/wf"))))
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35
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36 assert "$schemas" in packed
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37 assert len(packed["$schemas"]) == len(expect_packed["$schemas"])
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38 del packed["$schemas"]
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39 del expect_packed["$schemas"]
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40
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41 assert packed == expect_packed
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42
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43
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44 def test_pack_single_tool():
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45 loadingContext, workflowobj, uri = fetch_document(
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46 get_data("tests/wf/formattest.cwl"))
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47 loadingContext.do_update = False
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48 loadingContext, uri = resolve_and_validate_document(
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49 loadingContext, workflowobj, uri)
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50 processobj = loadingContext.loader.resolve_ref(uri)[0]
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51
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52 packed = cwltool.pack.pack(loadingContext.loader, processobj, uri, loadingContext.metadata)
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53 assert "$schemas" in packed
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54
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55 def test_pack_rewrites():
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56 rewrites = {}
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57
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58 loadingContext, workflowobj, uri = fetch_document(get_data("tests/wf/default-wf5.cwl"))
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59 loadingContext.do_update = False
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60 loadingContext, uri = resolve_and_validate_document(
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61 loadingContext, workflowobj, uri)
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62 processobj = loadingContext.loader.resolve_ref(uri)[0]
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63
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64 cwltool.pack.pack(loadingContext.loader, processobj, uri, loadingContext.metadata, rewrite_out=rewrites)
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65
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66 assert len(rewrites) == 6
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67
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68 cwl_missing_version_paths = [
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69 "tests/wf/hello_single_tool.cwl",
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70 "tests/wf/hello-workflow.cwl"
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71 ]
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72
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73 @pytest.mark.parametrize('cwl_path', cwl_missing_version_paths)
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74 def test_pack_missing_cwlVersion(cwl_path):
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75 """Ensure the generated pack output is not missing the `cwlVersion` in case of single tool workflow and single step workflow."""
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76 # Testing single tool workflow
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77 loadingContext, workflowobj, uri = fetch_document(get_data(cwl_path))
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78 loadingContext.do_update = False
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79 loadingContext, uri = resolve_and_validate_document(
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80 loadingContext, workflowobj, uri)
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81 processobj = loadingContext.loader.resolve_ref(uri)[0]
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82
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83 # generate pack output dict
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84 packed = json.loads(print_pack(loadingContext.loader, processobj, uri, loadingContext.metadata))
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85
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86 assert packed["cwlVersion"] == 'v1.0'
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87
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88 def test_pack_idempotence_tool():
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89 """Ensure that pack produces exactly the same document for an already packed CommandLineTool."""
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90 _pack_idempotently("tests/wf/hello_single_tool.cwl")
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91
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92 def test_pack_idempotence_workflow():
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93 """Ensure that pack produces exactly the same document for an already packed workflow."""
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94 _pack_idempotently("tests/wf/count-lines1-wf.cwl")
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95
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96 def _pack_idempotently(document):
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97 loadingContext, workflowobj, uri = fetch_document(
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98 get_data(document))
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99 loadingContext.do_update = False
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100 loadingContext, uri = resolve_and_validate_document(
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101 loadingContext, workflowobj, uri)
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102 processobj = loadingContext.loader.resolve_ref(uri)[0]
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103
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104 # generate pack output dict
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105 packed = json.loads(print_pack(loadingContext.loader, processobj, uri, loadingContext.metadata))
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106
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107 loadingContext, workflowobj, uri2 = fetch_document(packed)
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108 loadingContext.do_update = False
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109 loadingContext, uri2 = resolve_and_validate_document(
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110 loadingContext, workflowobj, uri)
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111 processobj = loadingContext.loader.resolve_ref(uri2)[0]
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112 double_packed = json.loads(print_pack(loadingContext.loader, processobj, uri2, loadingContext.metadata))
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113 assert packed == double_packed
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114
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115 cwl_to_run = [
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116 ("tests/wf/count-lines1-wf.cwl",
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117 "tests/wf/wc-job.json",
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118 False
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119 ),
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120 ("tests/wf/formattest.cwl",
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121 "tests/wf/formattest-job.json",
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122 True
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123 ),
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124 ]
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125
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126 @needs_docker
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127 @pytest.mark.parametrize('wf_path,job_path,namespaced', cwl_to_run)
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128 def test_packed_workflow_execution(wf_path, job_path, namespaced, tmpdir):
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129 loadingContext = LoadingContext()
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130 loadingContext.resolver = tool_resolver
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131 loadingContext, workflowobj, uri = fetch_document(
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132 get_data(wf_path), loadingContext)
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133 loadingContext.do_update = False
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134 loadingContext, uri = resolve_and_validate_document(
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135 loadingContext, workflowobj, uri)
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136 processobj = loadingContext.loader.resolve_ref(uri)[0]
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137 packed = json.loads(print_pack(loadingContext.loader, processobj, uri, loadingContext.metadata))
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138
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139 assert not namespaced or "$namespaces" in packed
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140
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141 wf_packed_handle, wf_packed_path = tempfile.mkstemp()
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142 with open(wf_packed_path, 'w') as temp_file:
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143 json.dump(packed, temp_file)
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144
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145 normal_output = StringIO()
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146 packed_output = StringIO()
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147
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148 normal_params = ['--outdir', str(tmpdir), get_data(wf_path), get_data(job_path)]
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149 packed_params = ['--outdir', str(tmpdir), '--debug', wf_packed_path, get_data(job_path)]
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150
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151 assert main(normal_params, stdout=normal_output) == 0
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152 assert main(packed_params, stdout=packed_output) == 0
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153
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154 assert json.loads(packed_output.getvalue()) == json.loads(normal_output.getvalue())
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155
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156 os.close(wf_packed_handle)
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157 os.remove(wf_packed_path)