Annotations endpoints

[Fabian-RY]

This pull request adds the first 2 API endpoints for BWS from the annotation endpoints:

• SMART annotation
• ENSEMBL annotation: this also stablish the models and endpoint for the ENSEMBL variant endpoint, which is expected to be ready and tested soon.

They can be tested at:
$(url)/api/annotations/smart/Uniprot/
$(url)/api/annotations/ensembl/annotations/

[adrianq]

@Fabian-RY Can you point this PR to the development branch?

[Fabian-RY]

Done @adrianq

[p3rcypj]

Hi @Fabian-RY, I've been reviewing the PR, but at first glance I can't get Django to run — I'm getting the following error:
ImportError: cannot import name 'source_pfam' from 'api.annotations' (/app/api/annotations/init.py).
It seems like there might be some missing files that haven't been committed...?

I also noticed that the migrations/ folder was in the .gitignore. I hadn't realized that detail.
Could you include them?

Thanks a lot!

[Fabian-RY]

Hi @p3rcypj Done. It seems that I forgot to add it to the commit originally (but of course, it was on my filesystem so i didn't see the error). My fault.

Migrations are also added in the last commit

I've added the files and also all the last changes I made since I opened this pull requests from the last report. This include testing and some other endpoints I'm testing. I have yet to finish some of the tests, though.

[p3rcypj]

No worries! Thanks @Fabian-RY!

[p3rcypj]

Thank you @Fabian-RY for your hard work! I've tested all endpoints functionally after your commit, and here are some things that I notice:

• PFAM: has an extra [ ] on root level, using a protein id that is not in DB returns an HTML
• SMART: consistency -> when an invalid protein id like 'c', it returns { } while on production we return [ ]
• PDB_REDO: has an extra [ ] on root level
• Phosphosite: has an extra [ ] on root level
• IEDB: void, logic not done
• dbptm: has an extra [ ] on root level
• biomuta: has an extra [ ] on root level, it has /dbptm/ prefix before /biomuta/, invalid protein like 'c' returns and error but with message <built-in function ids>...
• dsysmap: has an extra [ ] on root level
• elmdb: void. Is pointing to dsysmap
• ensembl: repeated endpoints with /ENSEMBL/
• lengths: has an extra [ ] on root level, and it's a number -> so answering like { length: 0 } would be more appropiate, if an invalid protein is requested it returns [ 82 ] which is kind of weird... but also happens in production so (but with [ 70 ])... whatever -> likewise could you check why is this happening? <- also it uses BLAST @adrianq
• multi: Django error
• ENSEMBL annotation: it gives error DB all the time, and also the response is the one given by variation
• ENSEMBL variation: has an extra [ ] on root level, it gives the answer that should be in annotation

Thanks!

[Fabian-RY]

I've made a push with several commits fixing as many as your comments as possible. I checked them individually.
I have yet to remove the root extra [], which django creates it due to the fact that a query may have different hits in the db, and each element correspond to a query result. Should proteins ID should be unique in each table? That assumption may change how to focus on that.

Regardless of that, I'll look again at the rest. Maybe I missed still something. Also, note that in ELMD sql insert queries, the "data" element (a list) ended with "\n" which was a source of problems for django, as it could not parse it correctly.

[Fabian-RY]

Also, I think the db have the annotation and variation of ENSEMBL swapped. The content itself, and I looked the sql and it is swapped, probably when I adapted the statements to the new table name convention.