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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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Inconsistent naming between database and website #107

Closed victorlin closed 3 years ago

victorlin commented 3 years ago

There's a small mismatch between the new database and website routes in how they reference SRA run IDs.

We should pick one and be consistent. There are references to serratus.io/explorer?run= in the rebuttal so I want to get this ironed out.

Opinion with example: take an official route https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=ERR2756788. This is logical because it's scoped to sra+run. For Serratus, I think it's reasonable to assume scope of SRA when using run. Having /explorer?sra=ERR2756788 could prompt users to try /explorer?sra=ERX2769781 which doesn't make sense. /explorer?srarun=ERR2756788 could work too.

Also worth noting that database columns family_name/genbank_id are simply family/genbank in Serratus Explorer. Still different, but less of an annoyance to me.

ababaian commented 3 years ago

in the database it would be good to be more descriptive with what run is. I agree sra_id is the wrong name, we should go with run_id. I don't like the term run as it's ambiguous alone but it is the correct choice to use it.

victorlin commented 3 years ago

Yeah run is ambiguous but I suspect any database user should be familiar with Serratus being a SRA search tool, and if not then the column values should give it away. 2 tasks for me here:

  1. update sra_id -> run_id for all tables in the database
  2. add table column names+descriptions to https://github.com/ababaian/serratus/wiki/Serratus-SQL-Database-Management

This isn’t an issue for serratus.io anymore, but I’ll cross reference and close this once the tasks are done.

victorlin commented 3 years ago

Another thought: should database tables nsra/psra/rsra be renamed to nrun/prun/rrun?

ababaian commented 3 years ago

naw that database names are fine because it refers to the actual SRA as a whole