Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Check to see if key is present *and* values are set #144

Merged
merged 1 commit into from
Jun 15, 2023

Conversation

lazear
Copy link
Contributor

@lazear lazear commented Jun 14, 2023

Fix various index out of range failures

Traceback (most recent call last):
  File "/opt/homebrew/bin/parse_sdrf", line 8, in <module>
    sys.exit(main())
  File "/opt/homebrew/lib/python3.10/site-packages/sdrf_pipelines/parse_sdrf.py", line 226, in main
    cli()
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/sdrf_pipelines/parse_sdrf.py", line 101, in maxquant_from_sdrf
    Maxquant().maxquant_convert(
  File "/opt/homebrew/lib/python3.10/site-packages/sdrf_pipelines/maxquant/maxquant.py", line 1429, in maxquant_convert
    first = list(tparam.values())[0]
IndexError: list index out of range

Fix various index out of range failures

```
Traceback (most recent call last):
  File "/opt/homebrew/bin/parse_sdrf", line 8, in <module>
    sys.exit(main())
  File "/opt/homebrew/lib/python3.10/site-packages/sdrf_pipelines/parse_sdrf.py", line 226, in main
    cli()
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/opt/homebrew/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/click/decorators.py", line 26, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/opt/homebrew/lib/python3.10/site-packages/sdrf_pipelines/parse_sdrf.py", line 101, in maxquant_from_sdrf
    Maxquant().maxquant_convert(
  File "/opt/homebrew/lib/python3.10/site-packages/sdrf_pipelines/maxquant/maxquant.py", line 1429, in maxquant_convert
    first = list(tparam.values())[0]
IndexError: list index out of range
```
@ypriverol ypriverol self-requested a review June 15, 2023 05:37
@ypriverol ypriverol merged commit adf9279 into bigbio:master Jun 15, 2023
@github-actions
Copy link

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

  • Install black: pip install black
  • Fix formatting errors in your pipeline: black .
    Once you push these changes the test should pass, and you can hide this comment 👍
    We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
    Thanks again for your contribution!

@lazear
Copy link
Contributor Author

lazear commented Jun 15, 2023

Sorry, it looks like I added an extra colon on most of the lines... I did the editing on the web interface 🫢

Maybe revert or just add another commit to fix it?

@ypriverol
Copy link
Member

Fixed in my PR.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants