[META] State of the union and issue organization

[nleroy917]

I've released PEPhub v0.8.x. Since release, I've gone through and tried to close solved issues, close stale issues, and consolidate issues that seem related/redundant. To wrap up that process, I've organized and identified four main categories that all remaining open issues fall into: 1) Validation, 2) Advanced features, 3) Infrastructure changes, and 4) PEP specification needs.

Validation

The validation support on PEPhub is still lacking. Namely, this includes the validation UI (universal validator) and validating PEPs on the fly throughout the application. I can identify two main reasons for slow development here: 1) the validator endpoints are not very mature, and 2) schema haven't really been considered until very recently.

To progress in this area, I think that we need to 1) severely overhaul the eido/ endpoints, and 2) think about how we want to handle schema now that PEPs are primarily stored in a database.

Related issues:

• Web-based metadata builder UI #94
• Next steps for validation UI #98
• Schema-specific validation on PEP edit page #127

Advanced PEPhub functionality

We've thrown around a lot of ideas to take PEPhub to the next level. This includes things like "groups of PEPs", "staring/favoriting PEPs", "forking PEPs", etc. Some have been implemented and some not. A concerted effort should be made to implement these. They most likely require changes to the way we structure the database and server .

Related issues:

• PEPhub could accommodate pipeline result attributes #91
• Connecting Snakemake and PEPhub #93
• Change namespace search to semantic search #126
• Groups of PEPs #129
• Versioning ideas #130
• Add capability for adding and editing subsample tables #131

Infrastructure changes

Supporting PEPhub longterm might require some big infrastructure changes to the backend. This mostly includes database changes. I've identified issues below that are related to these large sweeping changes to the architecture of the app:

• total projects doesn't match projects list #149
• Database should store samples individually #92
• Testing #134

PEP specification needs

There are specific aspects of the PEP specification that are not fully implemented or supported through PEPhub. This limits the ability to use and share PEPs. Some examples are asterisks in PEPs and passing variables with query params. These should be added to make sure PEPhub is fully compliant with the PEP specification.

Related issues:

• Passing variables with query params #3
• Displaying sample attributes with multiple values #37
• How should pephub handle asterisks? #42

Lingering things

There were a few lingering issues where feedback, testing, and discussion would help decide the state.

Related issues:

• Bugs with the sample table editing #151
• total projects doesn't match projects list #149
• brainstorm pephubclient source link + add copy link button to pephub #138
• Return 401 error for JWT expiration #120
• documentation/tutorial on how to use pephub #106
• Adding example request data to path parameters defined through dependency injection #20