Noob problems running generate-files

[NBIX-Mark-Southern]

Hi! I really like the idea of this project. I can see that it could make the management of Benchling Schemas much easier and the grand vision of covering other LIMS systems is pretty amazing!

I naively attempted to run liminal generate-files for an existing system. The first time I saw:

ValueError: 'KEEP_NAMES' is not a valid BenchlingNamingStrategy

and as a workaround I added KEEP_NAMES to the BenchlingNamingStrategy enum.

The second time, I then saw:

ValueError: Field type 'BenchlingAPIFieldType.TRANSLATION_LINK' is not supported

From here, and this looks a bit more complex. It may be coming from the in-built AA Sequence schema so not something I could change :-?

Any thoughts on what I could try next? Thank you!

[ndamania00]

Hey Mark,

So sorry for the delayed response, this somehow slipped by me!! Thanks for bringing up these bugs, totally not Noob problems. I included bug fixes for both of these issues in the latest v2.0.4 release. I'd recommend installing the latest version and trying to generate your files again.

Definitely reach out and let me know if it works or if you run into any more issues. I'd also be happy to hop on a call with you to help get your Liminal environment setup, answer any questions, and hear more about your use cases (which would help me drive Liminal's direction).

You can also join our Slack community here!

Best,
Nirmit

[NBIX-Mark-Southern]

Hey! Much appreciated. Unfortunately I ran into another, maybe similar problem:

ValueError: Field type 'BenchlingAPIFieldType.PART_LINK' is not supported.

This is before any Entity schemas are generated. I would love to get past this and look further, thanks!

[ndamania00]

Hey! I made the bug fix here - #112.

I'm in the middle of releasing a major version update with two backwards incompatible additions. One feature has been added and I have one more PR I want to get in with it before cutting a new release. I'll update you when this is released so you can try again but should be by tomorrow!

[ndamania00]

Hey! I've included the bug fix for this in the v3.0.0, the latest release. Let me know how installing the latest version goes for you.