Restructuring

[khoroshevskyi]

Everything that was mention in previous PR is here pepdbagent divided into 5 Modules:

• PEPDatabaseAgent
• BaseConnection
  • PEPDatabaseProject
  • PEPDatabaseAnnotation
  • PEPDatabaseNamespace

Let me know if you have any questions

Few things to add before merging:

• [x] Docs
• [x] Structured tests
• [x] Add error throwing
• [x] Improve sql performance by reducing LIKE statements and creating indexing

[nleroy917]

So, are we going to close the other PR?

[khoroshevskyi]

@nleroy917 @nsheff I've fixed all your comments. I think, now it's on the stage, that we can start implementing this version of pepdbagent into pephub

[nsheff]

Hey @Khoroshevskyi this API is really nice, I really like it. This is way more clear now!

I went through the tutorial and edited it a bit. There are few things that still confused me, and I wasn't sure how to edit it. Can you rephrase these points:

• [x] "- Submitting/editing projects (+editing metadata)" (what is "+ editing metadata"? isn't that what annotation does? Please explain
• [x] can you provide a bit more insight/example onto how agetn.project.edit works? is this how you update a project or just its annotation? can you provide some more examples? Why isnt't there agent.annotation.edit ?
• [x] "retrieves information about namespaces and provides search functionality." -> can you clarify how this differs from the search functionality described earlier? just be a bit more specific about the differences here.
• [x] This is not clear to me: "# Additionally, to get annotations from private projects you should provide # admin or list of admins."
• [x] This is also not clear to me: "# The same way as in annotation you should provide admin list, to have # information about private projects added to information about namespaces"
• [x] For both of the search functionality, can you provide a brief explanation of what the search will return?

[nsheff]

Here are some ideas for word changes, what do you think?

• [x] change agent.project.edit to agent.project.update.
• [x] change agent.project.submit to agent.project.create.

[nleroy917]

+1 for word changes @nsheff suggested.

[nsheff]

"# submit a project" -> "# create a project"

[nsheff]

Why is there only a _by_rp function for annotation.get_by_rp? Do you need functions create_by_rp and update_by_rp, et. and put them on project, annotation, namespace modules?

[nsheff]

Instead of "NamespaceReturnModel" it doesn't make sense to put the word "Return" in this object, because it's not always going to be "Returned" it could be used for lots of other things.

What is this really? Can you name it appropriately?

NamespaceList? Similar for Annotation? AnnotationList object maybe?

[khoroshevskyi]

Why is there only a _by_rp function for annotation.get_by_rp?

I don't really understand this question

Do you need functions create_by_rp and update_by_rp, et. and put them on project, annotation, namespace modules?

If we need I will add it, but I am not sure if we are using it. https://en.wikipedia.org/wiki/You_aren%27t_gonna_need_it

[khoroshevskyi]

Instead of "NamespaceReturnModel" it doesn't make sense to put the word "Return" in this object, because it's not always going to be "Returned" it could be used for lots of other things.

What is this really? Can you name it appropriately?

NamespaceList? Similar for Annotation? AnnotationList object maybe?

Yes, probably we should use different name for it. Your suggestions?? (p.s. In my experience all model naming should end on Model so in will be obvious that it's model)

[nsheff]

The pydantic docs don't suggest ending every model with Model: https://docs.pydantic.dev/usage/models/

I would suggest NamespaceList and AnnotationList ...

[nsheff]

Is this model an Annotation or Annotations ? Can you sync the model name and docstring one way or the other?

https://github.com/pepkit/pepdbagent/blob/9621f05e61e14b11af61e7800ca6c28a2f4288ae/pepdbagent/models.py#L9-L11

[nsheff]

Can you justify why you're prefixing double underscores here? I'm not familiar with that convention, can you explain why you're not just using the single underscore approach that I'm familiar with?

https://github.com/pepkit/pepdbagent/blob/9621f05e61e14b11af61e7800ca6c28a2f4288ae/pepdbagent/pepdbagent.py#L37-L43

[nsheff]

What's the advantage of attaching an object at _project (or __project) and then defining a @property called project that does nothing more than return the item at _project?

How is this superior to just sticking the object on .project in the first place?

https://github.com/pepkit/pepdbagent/blob/9621f05e61e14b11af61e7800ca6c28a2f4288ae/pepdbagent/pepdbagent.py#L39-L47

[khoroshevskyi]

1) two underscore means private object, it means that you can't change it outside of the object. (You can but in different way) 2) if I am using property, no one can change __project or __namespace variable outside pepdbagent

[nleroy917]

The pydantic docs don't suggest ending every model with Model.

I was going to ask also about the naming of the models. For example, what's the difference between NamespaceResultModel and NamespaceReturnModel? I was getting them mixed up a bit.

[khoroshevskyi]

The pydantic docs don't suggest ending every model with Model.

I was going to ask also about the naming of the models. For example, what's the difference between NamespaceResultModel and NamespaceReturnModel? I was getting them mixed up a bit.

Yeah, again naming... I changed it already. so now you will have: NamespaceList: it returns model that has list of ~NamespaceRetrunModel~ Namespace ~NamespaceRetrunModel~ Namespace: is ONE result

AnnotationList: it returns model that has list of Annotation Annotation: is ONE annotation

[nsheff]

Can NamespaceResultModel just be Namespace then, for consistency with Annotation ?