Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/cwltool/tests/test_provenance.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 json |
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2 import os |
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3 import pickle |
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4 import sys |
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5 import urllib |
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6 from pathlib import Path |
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7 from typing import Any, Generator |
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8 |
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9 import arcp |
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10 import bagit |
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11 import pytest |
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12 from rdflib import Graph, Namespace, URIRef |
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13 from rdflib.namespace import DC, DCTERMS, RDF |
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14 from rdflib.term import Literal |
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15 |
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16 from cwltool import provenance, provenance_constants |
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17 from cwltool.main import main |
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18 from cwltool.provenance import ResearchObject |
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19 from cwltool.stdfsaccess import StdFsAccess |
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20 |
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21 from .util import get_data, needs_docker, working_directory |
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22 |
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23 # RDF namespaces we'll query for later |
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24 ORE = Namespace("http://www.openarchives.org/ore/terms/") |
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25 PROV = Namespace("http://www.w3.org/ns/prov#") |
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26 RO = Namespace("http://purl.org/wf4ever/ro#") |
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27 WFDESC = Namespace("http://purl.org/wf4ever/wfdesc#") |
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28 WFPROV = Namespace("http://purl.org/wf4ever/wfprov#") |
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29 SCHEMA = Namespace("http://schema.org/") |
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30 CWLPROV = Namespace("https://w3id.org/cwl/prov#") |
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31 OA = Namespace("http://www.w3.org/ns/oa#") |
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32 |
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33 |
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34 def cwltool(tmp_path: Path, *args: Any) -> Path: |
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35 prov_folder = tmp_path / "provenance" |
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36 prov_folder.mkdir() |
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37 new_args = ["--provenance", str(prov_folder)] |
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38 new_args.extend(args) |
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39 # Run within a temporary directory to not pollute git checkout |
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40 tmp_dir = tmp_path / "cwltool-run" |
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41 tmp_dir.mkdir() |
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42 with working_directory(tmp_dir): |
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43 status = main(new_args) |
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44 assert status == 0, "Failed: cwltool.main(%r)" % (args) |
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45 return prov_folder |
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46 |
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47 |
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48 @needs_docker |
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49 def test_hello_workflow(tmp_path: Path) -> None: |
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50 check_provenance( |
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51 cwltool( |
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52 tmp_path, |
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53 get_data("tests/wf/hello-workflow.cwl"), |
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54 "--usermessage", |
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55 "Hello workflow", |
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56 ) |
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57 ) |
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58 |
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59 |
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60 @needs_docker |
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61 def test_hello_single_tool(tmp_path: Path) -> None: |
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62 check_provenance( |
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63 cwltool( |
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64 tmp_path, |
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65 get_data("tests/wf/hello_single_tool.cwl"), |
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66 "--message", |
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67 "Hello tool", |
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68 ), |
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69 single_tool=True, |
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70 ) |
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71 |
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72 |
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73 @needs_docker |
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74 def test_revsort_workflow(tmp_path: Path) -> None: |
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75 folder = cwltool( |
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76 tmp_path, |
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77 get_data("tests/wf/revsort.cwl"), |
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78 get_data("tests/wf/revsort-job.json"), |
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79 ) |
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80 check_output_object(folder) |
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81 check_provenance(folder) |
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82 |
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83 |
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84 @needs_docker |
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85 def test_nested_workflow(tmp_path: Path) -> None: |
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86 check_provenance(cwltool(tmp_path, get_data("tests/wf/nested.cwl")), nested=True) |
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87 |
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88 |
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89 @needs_docker |
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90 def test_secondary_files_implicit(tmp_path: Path) -> None: |
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91 file1 = tmp_path / "foo1.txt" |
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92 file1idx = tmp_path / "foo1.txt.idx" |
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93 |
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94 with open(str(file1), "w", encoding="ascii") as f: |
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95 f.write("foo") |
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96 with open(str(file1idx), "w", encoding="ascii") as f: |
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97 f.write("bar") |
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98 |
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99 # secondary will be picked up by .idx |
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100 folder = cwltool(tmp_path, get_data("tests/wf/sec-wf.cwl"), "--file1", str(file1)) |
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101 check_provenance(folder, secondary_files=True) |
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102 check_secondary_files(folder) |
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103 |
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104 |
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105 @needs_docker |
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106 def test_secondary_files_explicit(tmp_path: Path) -> None: |
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107 # Deliberately do NOT have common basename or extension |
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108 file1dir = tmp_path / "foo" |
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109 file1dir.mkdir() |
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110 file1 = file1dir / "foo" |
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111 file1idxdir = tmp_path / "bar" |
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112 file1idxdir.mkdir() |
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113 file1idx = file1idxdir / "bar" |
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114 |
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115 with open(file1, "w", encoding="ascii") as f: |
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116 f.write("foo") |
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117 with open(file1idx, "w", encoding="ascii") as f: |
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118 f.write("bar") |
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119 |
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120 # explicit secondaryFiles |
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121 job = { |
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122 "file1": { |
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123 "class": "File", |
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124 "path": str(file1), |
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125 "basename": "foo1.txt", |
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126 "secondaryFiles": [ |
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127 { |
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128 "class": "File", |
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129 "path": str(file1idx), |
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130 "basename": "foo1.txt.idx", |
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131 } |
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132 ], |
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133 } |
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134 } |
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135 |
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136 jobJson = tmp_path / "job.json" |
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137 with open(jobJson, "wb") as fp: |
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138 j = json.dumps(job, ensure_ascii=True) |
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139 fp.write(j.encode("ascii")) |
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140 |
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141 folder = cwltool(tmp_path, get_data("tests/wf/sec-wf.cwl"), str(jobJson)) |
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142 check_provenance(folder, secondary_files=True) |
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143 check_secondary_files(folder) |
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144 |
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145 |
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146 @needs_docker |
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147 def test_secondary_files_output(tmp_path: Path) -> None: |
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148 # secondary will be picked up by .idx |
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149 folder = cwltool(tmp_path, get_data("tests/wf/sec-wf-out.cwl")) |
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150 check_provenance(folder, secondary_files=True) |
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151 # Skipped, not the same secondary files as above |
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152 # self.check_secondary_files() |
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153 |
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154 |
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155 @needs_docker |
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156 def test_directory_workflow(tmp_path: Path) -> None: |
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157 dir2 = tmp_path / "dir2" |
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158 dir2.mkdir() |
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159 sha1 = { |
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160 # Expected hashes of ASCII letters (no linefeed) |
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161 # as returned from: |
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162 # for x in a b c ; do echo -n $x | sha1sum ; done |
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163 "a": "86f7e437faa5a7fce15d1ddcb9eaeaea377667b8", |
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164 "b": "e9d71f5ee7c92d6dc9e92ffdad17b8bd49418f98", |
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165 "c": "84a516841ba77a5b4648de2cd0dfcb30ea46dbb4", |
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166 } |
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167 for x in "abc": |
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168 # Make test files with predictable hashes |
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169 with open(dir2 / x, "w", encoding="ascii") as f: |
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170 f.write(x) |
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171 |
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172 folder = cwltool(tmp_path, get_data("tests/wf/directory.cwl"), "--dir", str(dir2)) |
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173 check_provenance(folder, directory=True) |
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174 |
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175 # Output should include ls stdout of filenames a b c on each line |
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176 file_list = ( |
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177 folder |
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178 / "data" |
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179 / "3c" |
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180 / "3ca69e8d6c234a469d16ac28a4a658c92267c423" |
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181 # checksum as returned from: |
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182 # echo -e "a\nb\nc" | sha1sum |
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183 # 3ca69e8d6c234a469d16ac28a4a658c92267c423 - |
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184 ) |
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185 assert file_list.is_file() |
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186 |
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187 # Input files should be captured by hash value, |
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188 # even if they were inside a class: Directory |
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189 for (l, l_hash) in sha1.items(): |
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190 prefix = l_hash[:2] # first 2 letters |
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191 p = folder / "data" / prefix / l_hash |
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192 assert p.is_file(), f"Could not find {l} as {p}" |
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193 |
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194 |
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195 def check_output_object(base_path: Path) -> None: |
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196 output_obj = base_path / "workflow" / "primary-output.json" |
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197 compare_checksum = "sha1$b9214658cc453331b62c2282b772a5c063dbd284" |
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198 compare_location = "../data/b9/b9214658cc453331b62c2282b772a5c063dbd284" |
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199 with open(output_obj) as fp: |
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200 out_json = json.load(fp) |
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201 f1 = out_json["sorted_output"] |
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202 assert f1["checksum"] == compare_checksum |
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203 assert f1["location"] == compare_location |
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204 |
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205 |
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206 def check_secondary_files(base_path: Path) -> None: |
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207 foo_data = ( |
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208 base_path |
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209 / "data" |
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210 / "0b" |
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211 / "0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33" |
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212 # checksum as returned from: |
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213 # $ echo -n foo | sha1sum |
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214 # 0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33 - |
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215 ) |
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216 bar_data = base_path / "data" / "62" / "62cdb7020ff920e5aa642c3d4066950dd1f01f4d" |
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217 assert foo_data.is_file(), "Did not capture file.txt 'foo'" |
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218 assert bar_data.is_file(), "Did not capture secondary file.txt.idx 'bar" |
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219 |
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220 primary_job = base_path / "workflow" / "primary-job.json" |
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221 with open(primary_job) as fp: |
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222 job_json = json.load(fp) |
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223 # TODO: Verify secondaryFile in primary-job.json |
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224 f1 = job_json["file1"] |
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225 assert f1["location"] == "../data/0b/0beec7b5ea3f0fdbc95d0dd47f3c5bc275da8a33" |
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226 assert f1["basename"] == "foo1.txt" |
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227 |
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228 secondaries = f1["secondaryFiles"] |
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229 assert secondaries |
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230 f1idx = secondaries[0] |
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231 assert f1idx["location"] == "../data/62/62cdb7020ff920e5aa642c3d4066950dd1f01f4d" |
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232 assert f1idx["basename"], "foo1.txt.idx" |
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233 |
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234 |
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235 def check_provenance( |
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236 base_path: Path, |
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237 nested: bool = False, |
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238 single_tool: bool = False, |
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239 directory: bool = False, |
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240 secondary_files: bool = False, |
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241 ) -> None: |
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242 check_folders(base_path) |
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243 check_bagit(base_path) |
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244 check_ro(base_path, nested=nested) |
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245 check_prov( |
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246 base_path, |
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247 nested=nested, |
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248 single_tool=single_tool, |
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249 directory=directory, |
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250 secondary_files=secondary_files, |
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251 ) |
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252 |
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253 |
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254 def check_folders(base_path: Path) -> None: |
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255 required_folders = [ |
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256 "data", |
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257 "snapshot", |
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258 "workflow", |
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259 "metadata", |
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260 os.path.join("metadata", "provenance"), |
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261 ] |
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262 |
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263 for folder in required_folders: |
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264 assert (base_path / folder).is_dir() |
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265 |
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266 |
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267 def check_bagit(base_path: Path) -> None: |
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268 # check bagit structure |
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269 required_files = [ |
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270 "bagit.txt", |
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271 "bag-info.txt", |
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272 "manifest-sha1.txt", |
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273 "tagmanifest-sha1.txt", |
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274 "tagmanifest-sha256.txt", |
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275 ] |
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276 |
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277 for basename in required_files: |
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278 assert (base_path / basename).is_file() |
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279 |
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280 bag = bagit.Bag(str(base_path)) |
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281 assert bag.has_oxum() |
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282 (only_manifest, only_fs) = bag.compare_manifests_with_fs() |
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283 assert not list(only_manifest), "Some files only in manifest" |
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284 assert not list(only_fs), "Some files only on file system" |
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285 missing_tagfiles = bag.missing_optional_tagfiles() |
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286 assert not list(missing_tagfiles), "Some files only in tagmanifest" |
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287 bag.validate() |
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288 # TODO: Check other bag-info attributes |
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289 assert arcp.is_arcp_uri(bag.info.get("External-Identifier")) |
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290 |
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291 |
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292 def find_arcp(base_path: Path) -> str: |
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293 # First try to find External-Identifier |
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294 bag = bagit.Bag(str(base_path)) |
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295 ext_id = bag.info.get("External-Identifier") |
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296 if arcp.is_arcp_uri(ext_id): |
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297 return str(ext_id) |
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298 raise Exception("Can't find External-Identifier") |
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299 |
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300 |
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301 def _arcp2file(base_path: Path, uri: str) -> Path: |
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302 parsed = arcp.parse_arcp(uri) |
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303 # arcp URIs, ensure they are local to our RO |
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304 assert ( |
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305 parsed.uuid == arcp.parse_arcp(find_arcp(base_path)).uuid |
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306 ), "arcp URI must be local to the research object" |
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307 |
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308 path = parsed.path[1:] # Strip first / |
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309 # Convert to local path, in case it uses \ on Windows |
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310 return base_path / Path(path) |
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311 |
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312 |
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313 def check_ro(base_path: Path, nested: bool = False) -> None: |
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314 manifest_file = base_path / "metadata" / "manifest.json" |
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315 assert manifest_file.is_file(), f"Can't find {manifest_file}" |
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316 arcp_root = find_arcp(base_path) |
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317 base = urllib.parse.urljoin(arcp_root, "metadata/manifest.json") |
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318 g = Graph() |
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319 |
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320 # Avoid resolving JSON-LD context https://w3id.org/bundle/context |
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321 # so this test works offline |
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322 context = Path(get_data("tests/bundle-context.jsonld")).as_uri() |
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323 with open(manifest_file, encoding="UTF-8") as fh: |
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324 jsonld = fh.read() |
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325 # replace with file:/// URI |
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326 jsonld = jsonld.replace("https://w3id.org/bundle/context", context) |
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327 g.parse(data=jsonld, format="json-ld", publicID=base) |
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328 if os.environ.get("DEBUG"): |
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329 print("Parsed manifest:\n\n") |
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330 g.serialize(sys.stdout, format="ttl") |
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331 _ro = None |
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332 |
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333 for _ro in g.subjects(ORE.isDescribedBy, URIRef(base)): |
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334 break |
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335 assert _ro is not None, "Can't find RO with ore:isDescribedBy" |
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336 |
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337 profile = None |
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338 for dc in g.objects(_ro, DCTERMS.conformsTo): |
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339 profile = dc |
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340 break |
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341 assert profile is not None, "Can't find profile with dct:conformsTo" |
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342 assert profile == URIRef(provenance_constants.CWLPROV_VERSION), ( |
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343 "Unexpected cwlprov version " + profile |
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344 ) |
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345 |
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346 paths = [] |
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347 externals = [] |
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348 for aggregate in g.objects(_ro, ORE.aggregates): |
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349 if not arcp.is_arcp_uri(aggregate): |
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350 externals.append(aggregate) |
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351 # Won't check external URIs existence here |
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352 # TODO: Check they are not relative! |
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353 continue |
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354 lfile = _arcp2file(base_path, aggregate) |
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355 paths.append(os.path.relpath(lfile, base_path)) |
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356 assert os.path.isfile(lfile), f"Can't find aggregated {lfile}" |
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357 |
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358 assert paths, "Didn't find any arcp aggregates" |
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359 assert externals, "Didn't find any data URIs" |
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360 |
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361 for ext in ["provn", "xml", "json", "jsonld", "nt", "ttl"]: |
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362 f = "metadata/provenance/primary.cwlprov.%s" % ext |
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363 assert f in paths, "provenance file missing " + f |
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364 |
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365 for f in [ |
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366 "workflow/primary-job.json", |
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367 "workflow/packed.cwl", |
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368 "workflow/primary-output.json", |
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369 ]: |
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370 assert f in paths, "workflow file missing " + f |
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371 # Can't test snapshot/ files directly as their name varies |
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372 |
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373 # TODO: check urn:hash::sha1 thingies |
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374 # TODO: Check OA annotations |
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375 |
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376 packed = urllib.parse.urljoin(arcp_root, "/workflow/packed.cwl") |
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377 primary_job = urllib.parse.urljoin(arcp_root, "/workflow/primary-job.json") |
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378 primary_prov_nt = urllib.parse.urljoin( |
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379 arcp_root, "/metadata/provenance/primary.cwlprov.nt" |
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380 ) |
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381 uuid = arcp.parse_arcp(arcp_root).uuid |
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382 |
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383 highlights = set(g.subjects(OA.motivatedBy, OA.highlighting)) |
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384 assert highlights, "Didn't find highlights" |
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385 for h in highlights: |
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386 assert (h, OA.hasTarget, URIRef(packed)) in g |
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387 |
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388 describes = set(g.subjects(OA.motivatedBy, OA.describing)) |
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389 for d in describes: |
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390 assert (d, OA.hasBody, URIRef(arcp_root)) in g |
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391 assert (d, OA.hasTarget, URIRef(uuid.urn)) in g |
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392 |
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393 linked = set(g.subjects(OA.motivatedBy, OA.linking)) |
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394 for link in linked: |
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395 assert (link, OA.hasBody, URIRef(packed)) in g |
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396 assert (link, OA.hasBody, URIRef(primary_job)) in g |
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397 assert (link, OA.hasTarget, URIRef(uuid.urn)) in g |
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398 |
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399 has_provenance = set(g.subjects(OA.hasBody, URIRef(primary_prov_nt))) |
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400 for p in has_provenance: |
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401 assert (p, OA.hasTarget, URIRef(uuid.urn)) in g |
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402 assert (p, OA.motivatedBy, PROV.has_provenance) in g |
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403 # Check all prov elements are listed |
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404 formats = set() |
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405 for prov in g.objects(p, OA.hasBody): |
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406 assert ( |
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407 prov, |
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408 DCTERMS.conformsTo, |
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409 URIRef(provenance_constants.CWLPROV_VERSION), |
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410 ) in g |
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411 # NOTE: DC.format is a Namespace method and does not resolve like other terms |
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412 formats.update(set(g.objects(prov, DC["format"]))) |
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413 assert formats, "Could not find media types" |
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414 expected = { |
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415 Literal(f) |
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416 for f in ( |
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417 "application/json", |
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418 "application/ld+json", |
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419 "application/n-triples", |
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420 'text/provenance-notation; charset="UTF-8"', |
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421 'text/turtle; charset="UTF-8"', |
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422 "application/xml", |
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423 ) |
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424 } |
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425 assert formats == expected, "Did not match expected PROV media types" |
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426 |
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427 if nested: |
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428 # Check for additional PROVs |
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429 # Let's try to find the other wf run ID |
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430 otherRuns = set() |
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431 for p in g.subjects(OA.motivatedBy, PROV.has_provenance): |
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432 if (p, OA.hasTarget, URIRef(uuid.urn)) in g: |
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433 continue |
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434 otherRuns.update(set(g.objects(p, OA.hasTarget))) |
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435 assert otherRuns, "Could not find nested workflow run prov annotations" |
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436 |
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437 |
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438 def check_prov( |
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439 base_path: Path, |
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440 nested: bool = False, |
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441 single_tool: bool = False, |
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442 directory: bool = False, |
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443 secondary_files: bool = False, |
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444 ) -> None: |
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445 prov_file = base_path / "metadata" / "provenance" / "primary.cwlprov.nt" |
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446 assert prov_file.is_file(), f"Can't find {prov_file}" |
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447 arcp_root = find_arcp(base_path) |
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448 # Note: We don't need to include metadata/provnance in base URI |
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449 # as .nt always use absolute URIs |
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450 g = Graph() |
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451 with open(prov_file, "rb") as f: |
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452 g.parse(file=f, format="nt", publicID=arcp_root) |
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453 if os.environ.get("DEBUG"): |
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454 print("Parsed %s:\n\n" % prov_file) |
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455 g.serialize(sys.stdout, format="ttl") |
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456 runs = set(g.subjects(RDF.type, WFPROV.WorkflowRun)) |
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457 |
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458 # main workflow run URI (as urn:uuid:) should correspond to arcp uuid part |
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459 uuid = arcp.parse_arcp(arcp_root).uuid |
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460 main_run = URIRef(uuid.urn) |
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461 assert main_run in runs, f"Can't find run {main_run} in {runs}" |
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462 # TODO: we should not need to parse arcp, but follow |
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463 # the has_provenance annotations in manifest.json instead |
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464 |
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465 # run should have been started by a wf engine |
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466 |
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467 engines = set(g.subjects(RDF.type, WFPROV.WorkflowEngine)) |
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468 assert engines, "Could not find WorkflowEngine" |
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469 assert len(engines) == 1, "Found too many WorkflowEngines: %s" % engines |
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470 engine = engines.pop() |
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471 |
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472 assert ( |
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473 main_run, |
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474 PROV.wasAssociatedWith, |
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475 engine, |
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476 ) in g, "Wf run not associated with wf engine" |
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477 assert ( |
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478 engine, |
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479 RDF.type, |
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480 PROV.SoftwareAgent, |
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481 ) in g, "Engine not declared as SoftwareAgent" |
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482 |
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483 if single_tool: |
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484 activities = set(g.subjects(RDF.type, PROV.Activity)) |
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485 assert len(activities) == 1, "Too many activities: %s" % activities |
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486 # single tool exec, there should be no other activities |
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487 # than the tool run |
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488 # (NOTE: the WorkflowEngine is also activity, but not declared explicitly) |
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489 else: |
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490 # Check all process runs were started by the main worklow |
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491 stepActivities = set(g.subjects(RDF.type, WFPROV.ProcessRun)) |
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492 # Although semantically a WorkflowEngine is also a ProcessRun, |
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493 # we don't declare that, |
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494 # thus only the step activities should be in this set. |
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495 assert main_run not in stepActivities |
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496 assert stepActivities, "No steps executed in workflow" |
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497 for step in stepActivities: |
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498 # Let's check it was started by the main_run. Unfortunately, unlike PROV-N |
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499 # in PROV-O RDF we have to check through the n-ary qualifiedStart relation |
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500 starts = set(g.objects(step, PROV.qualifiedStart)) |
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501 assert starts, "Could not find qualifiedStart of step %s" % step |
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502 assert len(starts) == 1, "Too many qualifiedStart for step %s" % step |
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503 start = starts.pop() |
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504 assert ( |
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505 start, |
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506 PROV.hadActivity, |
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507 main_run, |
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508 ) in g, "Step activity not started by main activity" |
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509 # Tip: Any nested workflow step executions should not be in this prov file, |
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510 # but in separate file |
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511 if nested: |
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512 # Find some cwlprov.nt the nested workflow is described in |
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513 prov_ids = set(g.objects(predicate=PROV.has_provenance)) |
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514 # FIXME: The above is a bit naive and does not check the subject is |
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515 # one of the steps -- OK for now as this is the only case of prov:has_provenance |
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516 assert prov_ids, "Could not find prov:has_provenance from nested workflow" |
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517 |
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518 nt_uris = [uri for uri in prov_ids if uri.endswith("cwlprov.nt")] |
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519 # TODO: Look up manifest conformsTo and content-type rather than assuming magic filename |
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520 assert nt_uris, "Could not find *.cwlprov.nt" |
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521 # Load into new graph |
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522 g2 = Graph() |
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523 nt_uri = nt_uris.pop() |
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524 with open(_arcp2file(base_path, nt_uri), "rb") as f: |
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525 g2.parse(file=f, format="nt", publicID=nt_uri) |
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526 # TODO: Check g2 statements that it's the same UUID activity inside |
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527 # as in the outer step |
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528 if directory: |
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529 directories = set(g.subjects(RDF.type, RO.Folder)) |
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530 assert directories |
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531 |
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532 for d in directories: |
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533 assert (d, RDF.type, PROV.Dictionary) in g |
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534 assert (d, RDF.type, PROV.Collection) in g |
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535 assert (d, RDF.type, PROV.Entity) in g |
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536 |
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537 files = set() |
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538 for entry in g.objects(d, PROV.hadDictionaryMember): |
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539 assert (entry, RDF.type, PROV.KeyEntityPair) in g |
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540 # We don't check what that filename is here |
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541 assert set(g.objects(entry, PROV.pairKey)) |
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542 |
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543 # RO:Folder aspect |
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544 assert set(g.objects(entry, RO.entryName)) |
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545 assert (d, ORE.aggregates, entry) in g |
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546 assert (entry, RDF.type, RO.FolderEntry) in g |
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547 assert (entry, RDF.type, ORE.Proxy) in g |
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548 assert (entry, ORE.proxyIn, d) in g |
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549 assert (entry, ORE.proxyIn, d) in g |
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550 |
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551 # Which file? |
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552 entities = set(g.objects(entry, PROV.pairEntity)) |
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553 assert entities |
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554 ef = entities.pop() |
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555 files.add(ef) |
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556 assert (entry, ORE.proxyFor, ef) in g |
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557 assert (ef, RDF.type, PROV.Entity) in g |
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558 |
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559 if not files: |
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560 assert (d, RDF.type, PROV.EmptyCollection) in g |
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561 assert (d, RDF.type, PROV.EmptyDictionary) in g |
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562 if secondary_files: |
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563 derivations = set(g.subjects(RDF.type, CWLPROV.SecondaryFile)) |
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564 assert derivations |
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565 for der in derivations: |
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566 sec = set(g.subjects(PROV.qualifiedDerivation, der)).pop() |
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567 prim = set(g.objects(der, PROV.entity)).pop() |
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568 |
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569 # UUID specializes a hash checksum |
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570 assert set(g.objects(sec, PROV.specializationOf)) |
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571 # extensions etc. |
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572 sec_basename = set(g.objects(sec, CWLPROV.basename)).pop() |
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573 sec_nameroot = set(g.objects(sec, CWLPROV.nameroot)).pop() |
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574 sec_nameext = set(g.objects(sec, CWLPROV.nameext)).pop() |
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575 assert str(sec_basename) == f"{sec_nameroot}{sec_nameext}" |
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576 # TODO: Check hash data file exist in RO |
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577 |
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578 # The primary entity should have the same, but different values |
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579 assert set(g.objects(prim, PROV.specializationOf)) |
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580 prim_basename = set(g.objects(prim, CWLPROV.basename)).pop() |
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581 prim_nameroot = set(g.objects(prim, CWLPROV.nameroot)).pop() |
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582 prim_nameext = set(g.objects(prim, CWLPROV.nameext)).pop() |
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583 assert str(prim_basename) == f"{prim_nameroot}{prim_nameext}" |
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584 |
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585 |
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586 @pytest.fixture |
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587 def research_object() -> Generator[ResearchObject, None, None]: |
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588 re_ob = ResearchObject(StdFsAccess("")) |
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589 yield re_ob |
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590 re_ob.close() |
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591 |
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592 |
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593 def test_absolute_path_fails(research_object: ResearchObject) -> None: |
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594 with pytest.raises(ValueError): |
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595 research_object.write_bag_file("/absolute/path/fails") |
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596 |
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597 |
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598 def test_climboutfails(research_object: ResearchObject) -> None: |
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599 with pytest.raises(ValueError): |
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600 research_object.write_bag_file("../../outside-ro") |
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601 |
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602 |
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603 def test_writable_string(research_object: ResearchObject) -> None: |
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604 with research_object.write_bag_file("file.txt") as fh: |
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605 assert fh.writable() |
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606 fh.write("Hello\n") |
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607 # TODO: Check Windows does not modify \n to \r\n here |
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608 |
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609 sha1 = os.path.join(research_object.folder, "tagmanifest-sha1.txt") |
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610 assert os.path.isfile(sha1) |
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611 |
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612 with open(sha1, encoding="UTF-8") as sha_file: |
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613 stripped_sha = sha_file.readline().strip() |
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614 assert stripped_sha.endswith("file.txt") |
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615 # stain@biggie:~/src/cwltool$ echo Hello | sha1sum |
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616 # 1d229271928d3f9e2bb0375bd6ce5db6c6d348d9 - |
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617 assert stripped_sha.startswith("1d229271928d3f9e2bb0375bd6ce5db6c6d348d9") |
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618 |
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619 sha256 = os.path.join(research_object.folder, "tagmanifest-sha256.txt") |
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620 assert os.path.isfile(sha256) |
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621 |
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622 with open(sha256, encoding="UTF-8") as sha_file: |
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623 stripped_sha = sha_file.readline().strip() |
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624 |
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625 assert stripped_sha.endswith("file.txt") |
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626 # stain@biggie:~/src/cwltool$ echo Hello | sha256sum |
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627 # 66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18 - |
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628 assert stripped_sha.startswith( |
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629 "66a045b452102c59d840ec097d59d9467e13a3f34f6494e539ffd32c1bb35f18" |
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630 ) |
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631 |
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632 sha512 = os.path.join(research_object.folder, "tagmanifest-sha512.txt") |
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633 assert os.path.isfile(sha512) |
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634 |
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635 |
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636 def test_writable_unicode_string(research_object: ResearchObject) -> None: |
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637 with research_object.write_bag_file("file.txt") as fh: |
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638 assert fh.writable() |
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639 fh.write("Here is a snowman: \u2603 \n") |
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640 |
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641 |
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642 def test_writable_bytes(research_object: ResearchObject) -> None: |
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643 string = "Here is a snowman: \u2603 \n".encode() |
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644 with research_object.write_bag_file("file.txt", encoding=None) as fh: |
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645 fh.write(string) # type: ignore |
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646 |
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647 |
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648 def test_data(research_object: ResearchObject) -> None: |
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649 with research_object.write_bag_file("data/file.txt") as fh: |
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650 assert fh.writable() |
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651 fh.write("Hello\n") |
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652 # TODO: Check Windows does not modify \n to \r\n here |
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653 |
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654 # Because this is under data/ it should add to manifest |
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655 # rather than tagmanifest |
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656 sha1 = os.path.join(research_object.folder, "manifest-sha1.txt") |
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657 assert os.path.isfile(sha1) |
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658 with open(sha1, encoding="UTF-8") as fh2: |
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659 stripped_sha = fh2.readline().strip() |
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660 assert stripped_sha.endswith("data/file.txt") |
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661 |
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662 |
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663 def test_not_seekable(research_object: ResearchObject) -> None: |
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664 with research_object.write_bag_file("file.txt") as fh: |
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665 assert not fh.seekable() |
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666 with pytest.raises(OSError): |
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667 fh.seek(0) |
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668 |
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669 |
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670 def test_not_readable(research_object: ResearchObject) -> None: |
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671 with research_object.write_bag_file("file.txt") as fh: |
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672 assert not fh.readable() |
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673 with pytest.raises(OSError): |
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674 fh.read() |
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675 |
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676 |
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677 def test_truncate_fails(research_object: ResearchObject) -> None: |
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678 with research_object.write_bag_file("file.txt") as fh: |
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679 fh.write("Hello there") |
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680 fh.truncate() # OK as we're always at end |
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681 # Will fail because the checksum can't rewind |
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682 with pytest.raises(OSError): |
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683 fh.truncate(0) |
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684 |
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685 |
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686 mod_validness = [ |
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687 # Taken from "Some sample ORCID iDs" on |
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688 # https://support.orcid.org/knowledgebase/articles/116780-structure-of-the-orcid-identifier |
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689 ("0000-0002-1825-0097", True), |
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690 ("0000-0001-5109-3700", True), |
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691 ("0000-0002-1694-233X", True), |
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692 # dashes optional |
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693 ("0000000218250097", True), |
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694 ("0000000151093700", True), |
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695 ("000000021694233X", True), |
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696 # do not fail on missing digits |
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697 ("0002-1694-233X", True), |
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698 # Swap check-digits around to force error |
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699 ("0000-0002-1825-009X", False), |
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700 ("0000-0001-5109-3707", False), |
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701 ("0000-0002-1694-2330", False), |
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702 ] |
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703 |
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704 |
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705 @pytest.mark.parametrize("mod11,valid", mod_validness) |
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706 def test_check_mod_11_2(mod11: str, valid: bool) -> None: |
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707 assert provenance._check_mod_11_2(mod11) == valid |
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708 |
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709 |
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710 orcid_uris = [ |
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711 # https://orcid.org/ (Expected form) |
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712 ("https://orcid.org/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X"), |
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713 # orcid.org |
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714 ("http://orcid.org/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X"), |
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715 # just the number |
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716 ("0000-0002-1825-0097", "https://orcid.org/0000-0002-1825-0097"), |
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717 # lower-case X is OK (and fixed) |
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718 ("https://orcid.org/0000-0002-1694-233x", "https://orcid.org/0000-0002-1694-233X"), |
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719 # upper-case ORCID.ORG is OK.. (and fixed) |
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720 ("https://ORCID.ORG/0000-0002-1694-233X", "https://orcid.org/0000-0002-1694-233X"), |
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721 ] |
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722 |
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723 |
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724 @pytest.mark.parametrize("orcid,expected", orcid_uris) |
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725 def test_valid_orcid(orcid: str, expected: str) -> None: |
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726 assert provenance._valid_orcid(orcid) == expected |
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727 |
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728 |
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729 invalid_orcids = [ |
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730 # missing digit fails (even if checksum is correct) |
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731 "0002-1694-2332", |
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732 # Wrong checkdigit fails |
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733 "https://orcid.org/0000-0002-1694-2332", |
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734 "0000-0002-1694-2332", |
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735 # Missing dashes fails (although that's OK for checksum) |
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736 "https://orcid.org/000000021694233X", |
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737 "000000021694233X", |
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738 # Wrong hostname fails |
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739 "https://example.org/0000-0002-1694-233X", |
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740 # Wrong protocol fails |
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741 "ftp://orcid.org/0000-0002-1694-233X", |
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742 # Trying to be clever fails (no URL parsing!) |
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743 "https://orcid.org:443/0000-0002-1694-233X", |
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744 "http://orcid.org:80/0000-0002-1694-233X", |
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745 # Empty string is not really valid |
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746 "", |
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747 ] |
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748 |
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749 |
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750 @pytest.mark.parametrize("orcid", invalid_orcids) |
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751 def test_invalid_orcid(orcid: str) -> None: |
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752 with pytest.raises(ValueError): |
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753 provenance._valid_orcid(orcid) |
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754 |
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755 |
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756 def test_whoami() -> None: |
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757 username, fullname = provenance._whoami() |
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758 assert username and isinstance(username, str) |
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759 assert fullname and isinstance(fullname, str) |
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760 |
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761 |
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762 def test_research_object() -> None: |
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763 # TODO: Test ResearchObject methods |
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764 pass |
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765 |
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766 |
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767 # Reasearch object may need to be pickled (for Toil) |
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768 |
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769 |
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"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
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770 def test_research_object_picklability(research_object: ResearchObject) -> None: |
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771 assert pickle.dumps(research_object) is not None |