[BH2024] Update Bioimaging Archive retrieval tool

[B0r1sD]

Related to Project 17: Development of FAIR image analysis workflows & training in Galaxy
Fixes beatrizserrano/galaxy-image-community#11

[kostrykin]

By the way if you write

Fix beatrizserrano/galaxy-image-community#11

into the text of your PR, it will be linked automatically by GitHub :)

[B0r1sD]

Unfortunately, I discovered even the Bioimage -, Core accession numbers do not follow one clear pattern for their FTP link. See ftp://ftp.ebi.ac.uk/biostudies/fire/S-BIAD/S-BIAD0-99/S-BIAD24 that is not following the S-BIAD/000/S-BIAD000 pattern that was assumed previously. IMO this tool should just ask in one line for the whole ftp link that users can find in the 'ftp' button in the study they want in their Galaxy history. This way it will be correct all the time and usable for the whole BIA.
I can quickly prune this wrapper to do exactly that (as the previous version would just fail on these 'exceptions') and then focus on getting a Galaxy button on BIA.

[B0r1sD]

The tool also keeps failing on the datatype .lif which is in a lot of BIA studies. The tool fetches whole studies atm so not only the images (hence the name is a bit misleading?).

Leia Image Format (LIF) images are JPEG images with metadata

If we want the Galaxy button in BIA, I think it is a datatype that should be added to Galaxy. But I've heard this is quite cumbersome for the developers and I also have no idea if there are more datatypes in a similar siutation.

We could introduce a filter to just download .tif/.tiff from studies but that probably drops metadata from the studies. I am leaning towards not spending more time on this refactoring as it exposes too many flaws - the proper solution (the Galaxy button in BIA) has been initatiated but there is no estimation on when it will be there so this tool has to do for now.
Maybe just updating the help text with the explanation of this is enough for now?... Let me know what you think.