migrate irods pyfilesystem2 filesource to fsspec backed filesource

[PlushZ]

This PR migrates iRODs pyFileSystem2 outdated filesource to fsspec backed with https://gitlab.kuleuven.be/setit/rdm/mango-fsspec
Configuration of file source is not changed.
https://gitlab.kuleuven.be/setit/rdm/mango-fsspec library should be published before merging and changed in conditional requirements.txt

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. Run local iRODS demo server from https://github.com/irods/irods_demo. Start demo server with Docker Compose using the irods-catalog-provider and irods-client-icommands services. Expose the iRODS provider port to the host with a docker-compose.override.yml:

services:
  irods-catalog-provider:
    ports:
      - "1247:1247"

2. Configure local Galaxy instance, use lib/galaxy/files/templates/examples/production_irods.yml as a template in config/file_source_templates.yml
3. Run Galaxy instance, configure Galaxy file source in User Preferences/Manage Your Repositories/Create/iRODS using the demo credentials:

  type: irods
  host: localhost
  port: 1247
  username: rods
  password: rods
  zone: tempZone
  root: /tempZone/home/rods
  writable: true

4. Verifiy through the Galaxy UI that the file source can:

• connect to the iRODS demo server
• browse the configured root collection
• create directories
• upload files into iRODS
• list uploaded files and directories
• import files from the iRODS file source into Galaxy

5. Verifiy the same files from the iRODS side using iCommands inside the demo client container:

docker compose exec irods-client-icommands ils -r /tempZone/home/rods
docker compose exec irods-client-icommands ils -L /tempZone/home/rods/<path>
docker compose exec irods-client-icommands iget -f /tempZone/home/rods/<path>/<file> /tmp/<file>

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[PlushZ]

Ping @hechth

[mvdbeek]

Looks good to me, can you update the PR @PlushZ ?

[mvdbeek]

can you run make format ?

[hechth]

for the time being, we're still testing our implementation of the fsspec here: https://github.com/RECETOX/fs-irods/tree/fsspec

[mvdbeek]

Probably want this resolved before merging.

[PlushZ]

yeah, waiting for the package being tested and published.

[jmchilton]

I'm moving this Draft - can you take it back out of draft once that package has been published and this has been rebased. Also feel free to ping me for a review at that time. Thanks for all the work on these file sources - very exciting!