Started by timer Running as SYSTEM Building remotely on Ubuntu_18.04_bioeng49 (buildslave Testing) in workspace /home/cmiss/Jenkins/workspace/Segmentation test [WS-CLEANUP] Deleting project workspace... [WS-CLEANUP] Deferred wipeout is used... [WS-CLEANUP] Done The recommended git tool is: NONE No credentials specified Cloning the remote Git repository Cloning repository https://github.com/ABI-Software/scicrunch-knowledge-testing.git > git init /home/cmiss/Jenkins/workspace/Segmentation test # timeout=10 Fetching upstream changes from https://github.com/ABI-Software/scicrunch-knowledge-testing.git > git --version # timeout=10 > git --version # 'git version 2.25.1' > git fetch --tags --force --progress -- https://github.com/ABI-Software/scicrunch-knowledge-testing.git +refs/heads/*:refs/remotes/origin/* # timeout=10 > git config remote.origin.url https://github.com/ABI-Software/scicrunch-knowledge-testing.git # timeout=10 > git config --add remote.origin.fetch +refs/heads/*:refs/remotes/origin/* # timeout=10 Avoid second fetch > git rev-parse refs/remotes/origin/main^{commit} # timeout=10 Checking out Revision d3d7b0041f71b26c4bc267594945f0758e855311 (refs/remotes/origin/main) > git config core.sparsecheckout # timeout=10 > git checkout -f d3d7b0041f71b26c4bc267594945f0758e855311 # timeout=10 Commit message: "Merge pull request #20 from ddjnw1yu/testing-script" > git rev-list --no-walk d3d7b0041f71b26c4bc267594945f0758e855311 # timeout=10 [Segmentation test] $ /bin/sh -xe /tmp/shiningpanda4754258759405792252.sh + export PENNSIEVE_API_HOST=https://api.pennsieve.io/discover + export SCICRUNCH_API_HOST=https://scicrunch.org/api/1/elastic/SPARC_PortalDatasets_pr + pip install -r requirements.txt Collecting mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl (from -r requirements.txt (line 5)) Downloading https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl (18 kB) Requirement already satisfied: requests==2.28.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (2.28.1) Requirement already satisfied: algoliasearch==2.6.2 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 2)) (2.6.2) Requirement already satisfied: boto3==1.17.67 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 3)) (1.17.67) Requirement already satisfied: ftfy==6.1.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from -r requirements.txt (line 4)) (6.1.1) Requirement already satisfied: charset-normalizer<3,>=2 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (2.1.1) Requirement already satisfied: idna<4,>=2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (3.7) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (1.26.19) Requirement already satisfied: certifi>=2017.4.17 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from requests==2.28.1->-r requirements.txt (line 1)) (2024.7.4) Requirement already satisfied: botocore<1.21.0,>=1.20.67 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (1.20.112) Requirement already satisfied: jmespath<1.0.0,>=0.7.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (0.10.0) Requirement already satisfied: s3transfer<0.5.0,>=0.4.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from boto3==1.17.67->-r requirements.txt (line 3)) (0.4.2) Requirement already satisfied: wcwidth>=0.2.5 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from ftfy==6.1.1->-r requirements.txt (line 4)) (0.2.13) Requirement already satisfied: networkx<3.0.0,>=2.8.8 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) (2.8.8) Requirement already satisfied: rdflib<7.0.0,>=6.2.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) (6.3.2) Requirement already satisfied: python-dateutil<3.0.0,>=2.1 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from botocore<1.21.0,>=1.20.67->boto3==1.17.67->-r requirements.txt (line 3)) (2.9.0.post0) Requirement already satisfied: isodate<0.7.0,>=0.6.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from rdflib<7.0.0,>=6.2.0->mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) (0.6.1) Requirement already satisfied: pyparsing<4,>=2.1.0 in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from rdflib<7.0.0,>=6.2.0->mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) (3.1.2) Requirement already satisfied: six in /home/cmiss/Jenkins/shiningpanda/jobs/fccc0fad/virtualenvs/d41d8cd9/lib/python3.8/site-packages (from isodate<0.7.0,>=0.6.0->rdflib<7.0.0,>=6.2.0->mapknowledge@ https://github.com/AnatomicMaps/map-knowledge/releases/download/v0.13.1/mapknowledge-0.13.1-py3-none-any.whl->-r requirements.txt (line 5)) (1.16.0) [notice] A new release of pip is available: 24.1.2 -> 24.3.1 [notice] To update, run: pip install --upgrade pip + python -m unittest tests/slow_tests/segmentation_tests.py Reports generated for 17 Reports generated for 30 Reports generated for 78 Reports generated for 7 Reports generated for 8 Reports generated for 171 Reports generated for 261 Reports generated for 303 Reports generated for 305 Reports generated for 229 Reports generated for 257 Reports generated for 270 Reports generated for 294 Reports generated for 211 Reports generated for 22 Reports generated for 210 Reports generated for 296 Reports generated for 143 Reports generated for 20 Reports generated for 259 Reports generated for 334 Reports generated for 31 Reports generated for 291 Reports generated for 184 Reports generated for 64 Reports generated for 159 Reports generated for 335 Reports generated for 206 Reports generated for 351 Reports generated for 169 Reports generated for 160 Reports generated for 310 Reports generated for 51 Reports generated for 27 Reports generated for 134 Reports generated for 212 Reports generated for 264 Reports generated for 109 Reports generated for 220 Reports generated for 288 Reports generated for 245 Reports generated for 26 Reports generated for 323 Reports generated for 325 Reports generated for 151 Reports generated for 336 Reports generated for 207 Reports generated for 266 Reports generated for 152 Reports generated for 90 Reports generated for 260 Reports generated for 306 Reports generated for 238 Reports generated for 236 Reports generated for 254 Reports generated for 304 Reports generated for 137 Reports generated for 331 Reports generated for 309 Reports generated for 318 Reports generated for 148 Reports generated for 140 Reports generated for 256 Reports generated for 62 Reports generated for 233 Reports generated for 112 Reports generated for 342 Reports generated for 237 Reports generated for 209 Reports generated for 241 Reports generated for 252 Reports generated for 63 Reports generated for 343 Reports generated for 114 Reports generated for 175 Reports generated for 227 Reports generated for 246 Reports generated for 149 Reports generated for 124 Reports generated for 145 Reports generated for 274 Reports generated for 163 Reports generated for 295 Reports generated for 345 Reports generated for 43 Reports generated for 126 Reports generated for 82 Reports generated for 332 Reports generated for 107 Reports generated for 35 Reports generated for 365 Reports generated for 127 Reports generated for 302 Reports generated for 262 Reports generated for 150 Reports generated for 180 Reports generated for 139 Reports generated for 158 Reports generated for 187 Reports generated for 321 Reports generated for 216 Reports generated for 268 Reports generated for 37 Reports generated for 314 Reports generated for 23 Reports generated for 273 Reports generated for 265 Reports generated for 9 Reports generated for 121 Reports generated for 34 Reports generated for 156 Reports generated for 362 Reports generated for 349 Reports generated for 337 Reports generated for 168 Reports generated for 61 Reports generated for 181 Reports generated for 120 Reports generated for 301 Reports generated for 322 Reports generated for 311 Reports generated for 290 Reports generated for 12 Reports generated for 364 Reports generated for 16 Reports generated for 263 Reports generated for 366 Reports generated for 387 Reports generated for 370 Reports generated for 379 Reports generated for 368 Reports generated for 371 Reports generated for 164 Reports generated for 282 Reports generated for 313 Reports generated for 363 Reports generated for 381 Reports generated for 49 Reports generated for 391 Reports generated for 86 Reports generated for 125 Reports generated for 230 Reports generated for 389 Reports generated for 390 Reports generated for 224 Reports generated for 384 Reports generated for 157 Reports generated for 393 Reports generated for 348 Reports generated for 177 Reports generated for 383 Reports generated for 394 Reports generated for 399 Reports generated for 400 Reports generated for 115 Reports generated for 100 Reports generated for 406 Reports generated for 402 Reports generated for 377 Reports generated for 94 Reports generated for 407 Reports generated for 95 Reports generated for 103 Reports generated for 101 Reports generated for 136 Reports generated for 411 Reports generated for 413 Reports generated for 217 Reports generated for 170 Reports generated for 174 Reports generated for 144 Reports generated for 410 Reports generated for 412 Reports generated for 172 Reports generated for 146 Reports generated for 223 Reports generated for 104 Reports generated for 105 Reports generated for 219 Reports generated for 416 Reports generated for 77 Reports generated for 403 Reports generated for 415 Reports generated for 4 Reports generated for 5 Reports generated for 6 Reports generated for 84 Reports generated for 18 Reports generated for 53 Reports generated for 312 Reports generated for 258 Reports generated for 116 Reports generated for 330 Reports generated for 247 Reports generated for 188 Reports generated for 58 Reports generated for 75 Reports generated for 215 Reports generated for 243 Reports generated for 142 Reports generated for 123 Reports generated for 286 Reports generated for 46 Reports generated for 183 Reports generated for 44 Reports generated for 327 Reports generated for 167 Reports generated for 341 Reports generated for 222 Reports generated for 147 Reports generated for 315 Reports generated for 73 Reports generated for 352 Reports generated for 308 Reports generated for 319 Reports generated for 36 Reports generated for 130 Reports generated for 33 Reports generated for 133 Reports generated for 10 Reports generated for 117 Reports generated for 297 Reports generated for 54 Reports generated for 60 Reports generated for 329 Reports generated for 338 Reports generated for 234 Reports generated for 353 Reports generated for 347 Reports generated for 110 Reports generated for 131 Reports generated for 328 Reports generated for 52 Reports generated for 279 Reports generated for 74 Reports generated for 68 Reports generated for 344 Reports generated for 272 Reports generated for 185 Reports generated for 11 Reports generated for 128 Reports generated for 269 Reports generated for 240 Reports generated for 56 Reports generated for 253 Reports generated for 228 Reports generated for 231 Reports generated for 50 Reports generated for 244 Reports generated for 189 Reports generated for 350 Reports generated for 186 Reports generated for 57 Reports generated for 205 Reports generated for 21 Reports generated for 153 Reports generated for 242 Reports generated for 24 Reports generated for 320 Reports generated for 97 Reports generated for 32 Reports generated for 271 Reports generated for 28 Reports generated for 85 Reports generated for 162 Reports generated for 89 Reports generated for 239 Reports generated for 376 Reports generated for 369 Reports generated for 375 Reports generated for 354 Reports generated for 29 Reports generated for 357 Reports generated for 132 Reports generated for 292 Reports generated for 182 Reports generated for 367 Reports generated for 373 Reports generated for 65 Reports generated for 388 Reports generated for 386 Reports generated for 316 Reports generated for 161 Reports generated for 55 Reports generated for 165 Reports generated for 204 Reports generated for 59 Reports generated for 138 Reports generated for 108 Reports generated for 106 Reports generated for 283 Reports generated for 317 Reports generated for 48 Reports generated for 293 Reports generated for 88 Reports generated for 178 Reports generated for 208 Reports generated for 382 Reports generated for 385 Reports generated for 225 Reports generated for 226 Reports generated for 378 Reports generated for 118 Reports generated for 372 Reports generated for 41 Reports generated for 324 Reports generated for 333 Reports generated for 287 Reports generated for 119 Reports generated for 392 Reports generated for 221 Reports generated for 395 Reports generated for 398 Reports generated for 307 Reports generated for 173 Reports generated for 166 Reports generated for 76 Reports generated for 98F ====================================================================== FAIL: test_files_information (tests.slow_tests.segmentation_tests.SegmentationDatasetFilesTest) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/cmiss/Jenkins/workspace/Segmentation test/tests/slow_tests/segmentation_tests.py", line 440, in test_files_information self.assertEqual(0, len(reports['FailedIds'])) AssertionError: 0 != 13 ---------------------------------------------------------------------- Ran 1 test in 514.516s FAILED (failures=1) Reports generated for 232 Reports generated for 99 Reports generated for 155 Reports generated for 102 Reports generated for 218 Reports generated for 409 Reports generated for 380 Reports generated for 154 Reports generated for 135 Reports generated for 396 Reports generated for 397 Number of datasets tested: 329 Number of dataset with erros: 13 Failed Datasets: ['31', '64', '43', '314', '120', '125', '230', '77', '60', '347', '225', '226', '221'] Full report has been generated at reports/segmentation_reports.json Build step 'Virtualenv Builder' marked build as failure Archiving artifacts Finished: FAILURE