galaxyproject / galaxyproject/pulsar

Is pulsar-check expected to work currently?

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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

Open the contributing 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

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