Bug Report: Files with '.' in the name do not have full functionality

[c-barry]

Bug Report: Files with '.' in the name do not have full functionality

Description:

Project files uploaded with '.' in the name are not functioning fully. While the files seem to be processed correctly (alignment and highlighter plot data files are generated as expected), there are specific issues:

• The annotation function does not work for these files on the Phylobook website.
• The highlighter plot is not displayed for these files.

Suspected Cause:

The issue seems to be related to how the URLs are constructed for files with '.' in their names.

Workaround:

This issue is not critical, as users can avoid it by ensuring that files are uploaded without additional periods ('.') in their names.

Steps to Reproduce:

1. Upload a project file with an additional '.' in the filename (e.g., sample.file.fasta).
2. Observe the following:
   • Annotation function is non-functional.
   • Highlighter plot is not displayed.

Expected Behavior:

• The annotation function should work correctly.
• The highlighter plot should be displayed, regardless of periods in the file name.

Additional Context:

Files without extra periods in their names are functioning correctly.

[PeterDarley]

It's not obvious to me why this would be happening. I suspect that the files that are being produced are misnamed for some reason, but I don't currently have a working install to test that on.

The simplest fix would be to update the handle_import_file() function in phylobook/projects/utils/general.py to replace extra periods with underscores.

Since this isn't considered critical it's probably best to mention this issue in the documentation and leave it until there is more active development on Phylobook.

[PeterDarley]

This is not a pipeline bug, it's a Phylobook bug, and should be there.