Support Euroscarf as source for plasmids

[dgruano]

I have worked with several plasmids coming from Euroscarf. I think it would be good to support importing these plasmids as a source!

However, note that I opened one of the .dna files from Euroscarf in Share Your Cloning and it gave the error Could not read the file XXX, and the console displayed Failed to load resource: the server responded with a status of 422 () ¨Method not allowed`.

I solved this by changing the extension from .dna to .gb. I am unsure whether we may encounter this problem with .dna files coming from other sources or whether SYC should check this in the background. Happy to open another issue if needed.

[manulera]

Thanks @dgruano, that's a great idea, and we can then contact them and maybe they can do an announcement if they have a mailing list or something similar.

You could do this integration similarly to the one from addgene (scraping). I don't think they have an API from what I can see.

A separate problem is calls to /read_from_file where the extension does not match the format. I opened a separate issue here: https://github.com/manulera/ShareYourCloning_frontend/issues/226

[dgruano]

I'm happy to make the integration. I also think that scraping is the way to go!

[manulera]

Description

Euroscarf support

Checklist

You can do some of these tasks in parallel, specially if you need to wait for approval, but it's good to keep in mind the intended order:

• [x] Make a branch in ShareYourCloning_LinkML where you implement the new source (see extra docs in there) on how to do this.
• [x] Add your branch as a dependency (via commit id) using poetry in this repository, to update shareyourcloning-linkml dependency in pyproject.toml:

  poetry add git+hhttps://github.com/genestorian/ShareYourCloning_LinkML#<commit-id>

• [x] Implement the new source in a branch in this repository. You will need to add a new endpoint in main.py and a new class in pydantic_models.py that will handle the new source. You can use the existing sources as a template. Note that you can add extra validation or methods (see examples as well).
• [x] Write tests for the new source in tests/test_endpoints.py. You can use the existing tests as a template.
• [x] Once the tests pass, merge the PR of the new source in [ShareYourCloning_LinkML] and make a release of the shareyourcloning-linkml package.
• [x] Update the dependency in the branch of this repository repository to the new version.

  # Get version from https://pypi.org/project/shareyourcloning-linkml/
  # For instance, if the version is 0.1.6a0, then:
  poetry add shareyourcloning-linkml@0.1.6a0

• [x] Implement the frontend functionality in a branch, following the frontend wiki.
• [x] Make tests for the frontend functionality.
• [x] Merge the PR in this repository into master.
• [x] Update the backend submodule in the frontend repository to the latest master.
• [x] Merge the PR in the frontend repository into master.
• [x] You are done!