Makes haddock3 restraints subcommands available as web service

[sverhoeven]

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In the haddock3 webapp I want to make a restraints file (*.tbl) from a list of active residues in 2 models/structures/molecules. I decided not to replicate that algorithm or have a complicated shell script behind a generic web service, but make the web service part of haddock3 repo. As the web service only exposes endpoints that are quick and do not need cns.

With this PR you can do

pip install fastapi uvicorn
uvicorn --port 5000 haddock.clis.restraints.webservice:app

This have the Swagger UI running at http://127.0.0.1:5000/docs#/

[mgiulini]

hi Stefan, I would also expose the other endpoints (restrain_bodies, calc_accessibility), as they can be useful in the webapp (for ex. to target the whole surface)

[sverhoeven]

hi Stefan, I would also expose the other endpoints (restrain_bodies, calc_accessibility), as they can be useful in the webapp (for ex. to target the whole surface)

Other restrain endopoints added and also added a preprocess_pdb endpoint.

[sverhoeven]

@rvhonorato could you have a look at the web service code. @mgiulini could you have a look at the passive_from_active function? I had to move the guts in the cli module to the librestraints module.

[rvhonorato]

hey @sverhoeven I'm out of the loop about the purpose of this. The code lgtm tho

[sverhoeven]

@mgiulini could this PR be merged?

Then I can update the deployments in https://github.com/i-VRESSE/haddock3-webapp to use the main haddock3 branch.

[mgiulini]

hi @sverhoeven no problem for me, but I see it fails the codacy-coverage-reporter-linux, not being able to run the integration tests..@rvhonorato do you know what is happening here?

[rvhonorato]

FYI i've been working on this: https://github.com/rvhonorato/haddock-restraints to add all these functionalities to the frontend via rust/webassembly and also to serve as the base for the GenTBL service. Seems like it overlaps a bit with this here.

[rvhonorato]

@rvhonorato do you know what is happening here?

Yes, it's written in the error message:

2024-05-27 07:52:56.094Z error [CodacyCoverageReporter] Invalid configuration: Either a project or account API token must be provided or available in an environment variable  - (CodacyCoverageReporter.scala:28)

We should figure out a way that external contributors can also run these, but since our continuous integration pipeline is just for show I've added a conditional: https://github.com/haddocking/haddock3/pull/904

@sverhoeven could you please rebase?

[sverhoeven]

thanks @rvhonorato , checks are green now.