galaxyproject / galaxyproject/pulsar
Is pulsar-check expected to work currently?
- Dominant language
- Python
- Stars
- 46
- Forks
- 62
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 15
Description
```
INFO:pulsar.client.manager:Setting Pulsar client class to standard, non-caching variant.
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/t/script.py] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/dataset_0.dat] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/dataset_0_files/input_subdir/extra] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/metadata/12312231231231.dat] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/w/config.txt] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/m/metadata_test123] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/idx/seq/human_full_seqs] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/idx/bwa/human.fa.fai] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/idx/bwa/human.fa] (action_type: [transfer])
DEBUG:pulsar.client.client:Uploading path [/tmp/pulsar-check-client.grb4stz_/w/config.txt] (action_type: [message])
Traceback (most recent call last):
File "/mnt/pulsar/venv/lib/python3.10/site-packages/pulsar/client/test/check.py", line 318, in run
assert result_status["returncode"] == 4, f"Expected exit code of 4, got {result_status['returncode']} - {std_streams_debug}"
AssertionError: Expected exit code of 4, got 127 - actual stdout [], actual stderr [/mnt/pulsar/files/staging/123456/command.sh: line 112: python: command not found
]
Traceback (most recent call last):
File "/mnt/pulsar/venv/bin/pulsar-check", line 8, in
sys.exit(main())
File "/mnt/pulsar/venv/lib/python3.10/site-packages/pulsar/client/test/check.py", line 607, in main
run(options)
File "/mnt/pulsar/venv/lib/python3.10/site-packages/pulsar/client/test/check.py", line 318, in run
assert result_status["returncode"] == 4, f"Expected exit code of 4, got {result_status['returncode']} - {std_streams_debug}"
AssertionError: Expected exit code of 4, got 127 - actual stdout [], actual stderr [/mnt/pulsar/files/staging/123456/command.sh: line 112: python: command not found
]
```
I keep seeing this and figured i'd report it in case it's useful. `python3` would've worked, or if the `venv` was included on path since that includes a `python`
Contributor guide
Research direction
Inspect pulsar/client/test/check.py around line 318 and the generated command shown in the traceback. Reproduce pulsar-check in an environment where only python3 is available, and determine how the command interpreter is selected. Done means the check reaches its intended exit-code assertion instead of failing with "python: command not found".
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- cli, testing-qa
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100