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Bug #18888
closedError uploading Directory provided on the command line
Start date:
04/19/2022
Due date:
% Done:
100%
Estimated time:
(Total: 0.00 h)
Story points:
-
Release:
Release relationship:
Auto
Description
$ arvados-cwl-runner --debug download_def.cwl --scripts scripts/ INFO /home/peter/work/scripts/venv3/bin/arvados-cwl-runner 2.4.0.dev20220310214858, arvados-python-client 2.4.0.dev20220310214858, cwltool 3.1.20220224085855 INFO Resolved 'download_def.cwl' to 'file:///home/peter/work/3rdparty/alphafold/download_def.cwl' DEBUG Parsed job order from command line: { "id": "download_def.cwl", "scripts": { "class": "Directory", "location": "file:///home/peter/work/3rdparty/alphafold/scripts/" } } INFO Using cluster x1fnz (https://172.17.0.2:3001/) INFO Upload local files: "scripts" DEBUG {'x1fnz-bi6l4-114285986efd63e1': OrderedDict([('href', '/keep_services/x1fnz-bi6l4-114285986efd63e1'), ('kind', 'arvados#keepService'), ('etag', '64emidmw6rnehr2dczxs92c8'), ('uuid', 'x1fnz-bi6l4-114285986efd63e1'), ('owner_uuid', 'x1fnz-tpzed-000000000000000'), ('created_at', '2022-03-17T18:49:24.847116000Z'), ('modified_by_client_uuid', None), ('modified_by_user_uuid', 'x1fnz-tpzed-000000000000000'), ('modified_at', '2022-03-17T18:49:24.847116000Z'), ('service_host', '172.17.0.2'), ('service_port', 25101), ('service_ssl_flag', True), ('service_type', 'proxy'), ('read_only', False), ('_service_root', 'https://172.17.0.2:25101/')])} DEBUG 1f64d06922dd7a09473fe800c510dee8+1354: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/1f64d06922dd7a09473fe800c510dee8 INFO PUT 200: 1354 bytes in 12.429237365722656 msec (0.104 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-1, started daemon 140342110295808)> succeeded 1f64d06922dd7a09473fe800c510dee8+1354 https://172.17.0.2:25101/ DEBUG db9e62b653f5ea04309d2167f70bb43d+1394: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/db9e62b653f5ea04309d2167f70bb43d INFO PUT 200: 1394 bytes in 1.5549659729003906 msec (0.855 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-2, started daemon 140342110295808)> succeeded db9e62b653f5ea04309d2167f70bb43d+1394 https://172.17.0.2:25101/ DEBUG 1026ba07c5dd7fe2272d2f7c58ce59a9+1249: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/1026ba07c5dd7fe2272d2f7c58ce59a9 INFO PUT 200: 1249 bytes in 1.514434814453125 msec (0.787 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-3, started daemon 140342110295808)> succeeded 1026ba07c5dd7fe2272d2f7c58ce59a9+1249 https://172.17.0.2:25101/ DEBUG 50819448fbb1fcc38f12da9f02df12d2+2343: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/50819448fbb1fcc38f12da9f02df12d2 INFO PUT 200: 2343 bytes in 1.6179084777832031 msec (1.381 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-4, started daemon 140342110295808)> succeeded 50819448fbb1fcc38f12da9f02df12d2+2343 https://172.17.0.2:25101/ DEBUG 5cd5abaaf2cbb1ca4337ea61ab789294+1323: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/5cd5abaaf2cbb1ca4337ea61ab789294 INFO PUT 200: 1323 bytes in 1.4336109161376953 msec (0.880 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-5, started daemon 140342110295808)> succeeded 5cd5abaaf2cbb1ca4337ea61ab789294+1323 https://172.17.0.2:25101/ DEBUG a07e65b628577c9af53d64023c2381c0+1509: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/a07e65b628577c9af53d64023c2381c0 INFO PUT 200: 1509 bytes in 1.8351078033447266 msec (0.784 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-6, started daemon 140342110295808)> succeeded a07e65b628577c9af53d64023c2381c0+1509 https://172.17.0.2:25101/ DEBUG 3eaf2718afff27f2dc312166c744c9a0+1439: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/3eaf2718afff27f2dc312166c744c9a0 INFO PUT 200: 1439 bytes in 1.3494491577148438 msec (1.017 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-7, started daemon 140342110295808)> succeeded 3eaf2718afff27f2dc312166c744c9a0+1439 https://172.17.0.2:25101/ DEBUG ecd63ff2d692cbafd4e8e0a811c6f911+1406: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/ecd63ff2d692cbafd4e8e0a811c6f911 INFO PUT 200: 1406 bytes in 1.2781620025634766 msec (1.049 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-8, started daemon 140342110295808)> succeeded ecd63ff2d692cbafd4e8e0a811c6f911+1406 https://172.17.0.2:25101/ DEBUG 22d655f2575b9ad58e46f559603696b6+1522: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/22d655f2575b9ad58e46f559603696b6 INFO PUT 200: 1522 bytes in 1.1749267578125 msec (1.235 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-9, started daemon 140342110295808)> succeeded 22d655f2575b9ad58e46f559603696b6+1522 https://172.17.0.2:25101/ DEBUG aeb3ed2dfc69c0b72b636ff386d407ea+2298: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/aeb3ed2dfc69c0b72b636ff386d407ea INFO PUT 200: 2298 bytes in 1.2860298156738281 msec (1.704 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-10, started daemon 140342110295808)> succeeded aeb3ed2dfc69c0b72b636ff386d407ea+2298 https://172.17.0.2:25101/ DEBUG 1081aba37ccf5eb1295336d8a3ba5879+2051: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/1081aba37ccf5eb1295336d8a3ba5879 INFO PUT 200: 2051 bytes in 2.0923614501953125 msec (0.935 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-11, started daemon 140342110295808)> succeeded 1081aba37ccf5eb1295336d8a3ba5879+2051 https://172.17.0.2:25101/ INFO Using collection d106612c9d08c8e26e40f9909b613198+774 (x1fnz-4zz18-5uxdy2vt9ruf0ro) INFO Upload local files: "scripts" DEBUG 1f64d06922dd7a09473fe800c510dee8+1354: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/1f64d06922dd7a09473fe800c510dee8 INFO PUT 200: 1354 bytes in 1.7938613891601562 msec (0.720 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-12, started daemon 140342110295808)> succeeded 1f64d06922dd7a09473fe800c510dee8+1354 https://172.17.0.2:25101/ DEBUG db9e62b653f5ea04309d2167f70bb43d+1394: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/db9e62b653f5ea04309d2167f70bb43d INFO PUT 200: 1394 bytes in 1.1601448059082031 msec (1.146 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-13, started daemon 140342110295808)> succeeded db9e62b653f5ea04309d2167f70bb43d+1394 https://172.17.0.2:25101/ DEBUG 1026ba07c5dd7fe2272d2f7c58ce59a9+1249: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/1026ba07c5dd7fe2272d2f7c58ce59a9 INFO PUT 200: 1249 bytes in 1.2826919555664062 msec (0.929 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-14, started daemon 140342110295808)> succeeded 1026ba07c5dd7fe2272d2f7c58ce59a9+1249 https://172.17.0.2:25101/ DEBUG 50819448fbb1fcc38f12da9f02df12d2+2343: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/50819448fbb1fcc38f12da9f02df12d2 INFO PUT 200: 2343 bytes in 1.2192726135253906 msec (1.833 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-15, started daemon 140342110295808)> succeeded 50819448fbb1fcc38f12da9f02df12d2+2343 https://172.17.0.2:25101/ DEBUG 5cd5abaaf2cbb1ca4337ea61ab789294+1323: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/5cd5abaaf2cbb1ca4337ea61ab789294 INFO PUT 200: 1323 bytes in 1.186370849609375 msec (1.064 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-16, started daemon 140342110295808)> succeeded 5cd5abaaf2cbb1ca4337ea61ab789294+1323 https://172.17.0.2:25101/ DEBUG a07e65b628577c9af53d64023c2381c0+1509: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/a07e65b628577c9af53d64023c2381c0 INFO PUT 200: 1509 bytes in 1.4586448669433594 msec (0.987 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-17, started daemon 140342110295808)> succeeded a07e65b628577c9af53d64023c2381c0+1509 https://172.17.0.2:25101/ DEBUG 3eaf2718afff27f2dc312166c744c9a0+1439: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/3eaf2718afff27f2dc312166c744c9a0 INFO PUT 200: 1439 bytes in 1.3539791107177734 msec (1.014 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-18, started daemon 140342110295808)> succeeded 3eaf2718afff27f2dc312166c744c9a0+1439 https://172.17.0.2:25101/ DEBUG ecd63ff2d692cbafd4e8e0a811c6f911+1406: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/ecd63ff2d692cbafd4e8e0a811c6f911 INFO PUT 200: 1406 bytes in 1.5573501586914062 msec (0.861 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-19, started daemon 140342110295808)> succeeded ecd63ff2d692cbafd4e8e0a811c6f911+1406 https://172.17.0.2:25101/ DEBUG 22d655f2575b9ad58e46f559603696b6+1522: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/22d655f2575b9ad58e46f559603696b6 INFO PUT 200: 1522 bytes in 1.7366409301757812 msec (0.836 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-20, started daemon 140342110295808)> succeeded 22d655f2575b9ad58e46f559603696b6+1522 https://172.17.0.2:25101/ DEBUG aeb3ed2dfc69c0b72b636ff386d407ea+2298: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/aeb3ed2dfc69c0b72b636ff386d407ea INFO PUT 200: 2298 bytes in 1.3263225555419922 msec (1.652 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-21, started daemon 140342110295808)> succeeded aeb3ed2dfc69c0b72b636ff386d407ea+2298 https://172.17.0.2:25101/ DEBUG 1081aba37ccf5eb1295336d8a3ba5879+2051: ['https://172.17.0.2:25101/'] DEBUG Pool max threads is 1 DEBUG Request: PUT https://172.17.0.2:25101/1081aba37ccf5eb1295336d8a3ba5879 INFO PUT 200: 2051 bytes in 1.2395381927490234 msec (1.578 MiB/sec) DEBUG KeepWriterThread <KeepWriterThread(Thread-22, started daemon 140342110295808)> succeeded 1081aba37ccf5eb1295336d8a3ba5879+2051 https://172.17.0.2:25101/ INFO Using collection d106612c9d08c8e26e40f9909b613198+774 (x1fnz-4zz18-gqx42dl08u9l3c3) ERROR Unhandled error: 'file:///home/peter/work/3rdparty/alphafold/scripts/' Traceback (most recent call last): File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/main.py", line 1343, in main (out, status) = real_executor( File "/home/peter/work/arvados/sdk/cwl/arvados_cwl/executor.py", line 592, in arv_executor merged_map = upload_workflow_deps(self, tool) File "/home/peter/work/arvados/sdk/cwl/arvados_cwl/runner.py", line 606, in upload_workflow_deps tool.visit(upload_tool_deps) File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/process.py", line 1087, in visit op(self.tool) File "/home/peter/work/arvados/sdk/cwl/arvados_cwl/runner.py", line 592, in upload_tool_deps pm = upload_dependencies(arvrunner, File "/home/peter/work/arvados/sdk/cwl/arvados_cwl/runner.py", line 435, in upload_dependencies visit_class(workflowobj, ("File", "Directory"), setloc) File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/utils.py", line 216, in visit_class visit_class(rec[d], cls, op) File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/utils.py", line 219, in visit_class visit_class(d, cls, op) File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/utils.py", line 216, in visit_class visit_class(rec[d], cls, op) File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/utils.py", line 214, in visit_class op(rec) File "/home/peter/work/arvados/sdk/cwl/arvados_cwl/runner.py", line 405, in setloc p["location"] = mapper.mapper(p["location"]).resolved File "/home/peter/work/scripts/venv3/lib/python3.9/site-packages/cwltool/pathmapper.py", line 186, in mapper return self._pathmap[src] KeyError: 'file:///home/peter/work/3rdparty/alphafold/scripts/'
I also had this happen using a Directory default value, but now I can't reproduce it.
Related issues
Updated by Peter Amstutz 11 months ago
- Description updated (diff)
- Subject changed from Error uploading Directory specified as "default" or provided on the command line to Error uploading Directory provided on the command line
Updated by Peter Amstutz 11 months ago
- Related to Story #17848: CWL runner improvements added
Updated by Peter Amstutz 10 months ago
- Target version changed from 2022-03-30 Sprint to 2022-04-13 Sprint
Updated by Peter Amstutz 10 months ago
- Target version changed from 2022-04-13 Sprint to 2022-04-27 Sprint
Updated by Peter Amstutz 10 months ago
The bug was actually not handling the command line, it was due to the "default" value of the Directory using "scripts/" (trailing slash) instead of "script".
File paths are normalized, but the normalization was being skipped for file objects in "default" for some reason.
18888-cwl-dir-arg @ 16628b89b26d26182f66a01a22e91af9307a3e57
Updated by Lucas Di Pentima 10 months ago
Failing test re-run: developer-run-tests-remainder: #3205
Updated by Peter Amstutz 10 months ago
Duh, I changed the status messages but didn't update the tests, of course tests are failing. Sorry.
I was thinking of a different branch, but obviously this one needs to have tests fixed too.
Updated by Peter Amstutz 10 months ago
Updated by Peter Amstutz 10 months ago
- Status changed from In Progress to Resolved
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