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serratus-bio / serratus.io

Front-end code for Serratus project website
https://serratus.io
GNU Affero General Public License v3.0
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Add results from protein and rdrp search #112

Closed victorlin closed 2 years ago

victorlin commented 3 years ago

Currently, Serratus Explorer is only serving the nucleotide search results. There is much more interesting data in the newer search spaces, which should be made explorable via the same interface. The data has already been loaded onto the SQL database.

Prereqs:

  1. Refactor code to not have hardcoded family/genbank code paths (#79). In the end we want a mapping like this:
    • nucleotide
      • family
      • sequence (genbank)
    • protein
      • family
      • protein
      • sequence (genbank)
    • rdrp
      • ~phylum~
      • family
      • rdrp
  2. Design URL routes. /explorer?family=Coronaviridae is currently sufficient for a single search space, but with multiple search spaces it should be something like /explorer/nucleotide?family=Coronaviridae. This goes hand-in-hand with the next task.
  3. Implement API routes for serratus-summary-api.

Implementing 3-level nesting on the SRA run summary charts will be another challenge, since the current one is pretty hard-coded for 2-level nesting only. This is due for refactoring anyways - I'd like to clean this file up before proceeding.

victorlin commented 2 years ago

RdRP search results are up and we are no longer planning to add protein search results. Data is still in the SQL database if anyone has interest in it.