Display Ensembl Compara

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RNAcentral website source code

https://rnacentral.org

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Display Ensembl Compara #448

Closed AntonPetrov closed 5 years ago

AntonPetrov commented 5 years ago

Features ✅ links to Ensembl Compara tree ✅ paginates after 50 sequences ✅ identical sequences marked with a badge

Examples

Many related sequences (supports pagination): http://localhost:8000/rna/URS0000001EB3/9606
Only one related sequence: http://localhost:8000/rna/URS0000001A7A/9606
No related sequences (nothing is shown): http://localhost:8000/rna/URS000075D95B/9606

⚠️ Do not merge until the production databases have the Compara tables ⚠️

@blakesweeney Please review on a local machine using the TST database when you get a chance. Thanks!

Fixes #445, closes #342, and closes #32.

blakesweeney commented 5 years ago

The pages display the data nicely enough. There is one change I think we should make though. We need to display something when there is no data available. Specifically we need to distinguish between cases of no data available because it isn't computed:

http://localhost:8000/rna/URS000075D95B/9606

or a genome where this is not yet done. Or cases where there are no related sequences.

AntonPetrov commented 5 years ago

Good point! Will look into it.

AntonPetrov commented 5 years ago

@blakesweeney Now the Compara messages are customised. Test cases:

not an ensembl sequence: http://localhost:8000/rna/URS000075C808/9606
incompatible RNA type (like lncRNA) - when it's in Ensembl but urs_taxid is not in ensembl_compara: http://localhost:8000/rna/URS000025784F/9606
no related sequences (homology_id is unique): http://localhost:8000/rna/URS00008118F7/10090

⚠️ Do not merge until the production databases have the Compara tables ⚠️

blakesweeney commented 5 years ago

Just FYI, prod now has ensembl_compara.

blakesweeney commented 5 years ago

I like how the different cases of no data are explained. It looks good to me. The only issue I see is that the font is a different colour in the Ensembl Compara section. Not sure if that is an issue on my end though. Other than that I think it is ready to merge.