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Proteobench / ProteoBench

ProteoBench is an open and collaborative platform for community-curated benchmarks for proteomics data analysis pipelines. Our goal is to allow a continuous, easy, and controlled comparison of proteomics data analysis workflows. https://proteobench.cubimed.rub.de/
https://proteobench.readthedocs.io
Apache License 2.0
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Remove the Proline runs (I did not upload the right ones) #228

Closed mlocardpaulet closed 8 months ago

mlocardpaulet commented 8 months ago

The two proline points: Proline__20240122_190626 and Proline__20240122_190958 are not valid. I did not upload the correct ones. So I want to remove them from the set of public runs and here are my questions:

  1. I can remove the corresponding lines in the file results.json of the module repo: easy!
  2. What do we do about the corresponding files in @julianu repo? (I mean the param and input csvs)
  3. what else do I miss?

Please let me know, I am happy to delete the lines in results.json as soon as you give me the green light. And then we will upload a lot more Proline runs with different parameters etc...

enryH commented 8 months ago

So you would delete if from the results repository? I think it would be good if we create a command to delete if from that json, so that formatting errors are avoided. This should be a simple deletion of a key in a dictionary.

julianu commented 8 months ago

I just need the hash-codes of the datasets you would like to remove. Best pm them to me, as soon as the json is updated. Otherwise, they would just take up some space on the drive, which is also not too much a problem right now. Or should we keep them as an archive somewhere? But probably not necessary, if they are just wrong.

mlocardpaulet commented 8 months ago

So you would delete if from the results repository? I think it would be good if we create a command to delete if from that json, so that formatting errors are avoided. This should be a simple deletion of a key in a dictionary.

that was my plan: to delete the corresponding lines. You make a good point, up to you: shall I delete or do you want to create the command? Not sure exactly how you would want to do that. Or option 3: I delete the 2 data sets for know and we work on a command for the next ones?

enryH commented 8 months ago

I'll create a PR in 5mins...

enryH commented 8 months ago

So dumping the json via pandas is different from the built-in json function per default. Can probably be fixed, but pandas as a dependency is not a big issue.

mlocardpaulet commented 8 months ago

OK, thanks! But I don't think that we should allow anyone to delete points, right?

enryH commented 8 months ago

No, it's only in case there is a mistake. It's maintainer who can submit a PR to delete the points. @RobbinBouwmeester The repository is only for storage and only accessible to maintainers?