Add ability to upload a file and use it as a non-editable sequence for an assembly - Githubissues

GMOD / Apollo3

JBrowse 2 plugin for editing annotations on an Apollo server

Apache License 2.0

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Add ability to upload a file and use it as a non-editable sequence for an assembly #406

Open garrettjstevens opened 2 weeks ago

garrettjstevens commented 2 weeks ago

Currently we have the options to

upload a file (GFF3 or FASTA) and use it to load an assembly with sequence in the database
use an external URL to create an assembly that doesn't store the sequence in the database

I think we need a third option:

upload a file (FASTA) and use it to create an assembly that doesn't store the sequence in the database

The steps I see are:

Allow user to upload either a FASTA/FAI or FASTA.GZ/FAI/GZI set of files.
Store the file IDs in the assembly (modify assembly.schema.ts) similar to the externalLocation in the assembly (perhaps called fileLocation).
In sequence.service.ts, check to see if the assembly has a fileLocation and if it does, fetch the sequence from the file similar to how the externalLocation fetches from a URL.