Invalid GFF crashes apollo server

[dariober]

Describe the bug

The gff file below is invalid because mrna09 in Parent=mrna09 does not exist. Adding an assembly from this file causes the apollo server to crash with error:

Error: some features reference other features that do not exist in the file (or in the same '###' scope). {"mrna09":{"Parent":[[{"seq_id":"chr9","source":null,"type":"CDS","start":7,"end":24,"score":null,"strand":"-","phase":"0","attributes":{"ID":["cds09.1"],"Parent":["mrna09"]},"child_features":[],"derived_features":[]}]],"Derives_from":[]}}
    at Parser._emitAllUnderConstructionFeatures (/workspaces/Apollo3/.yarn/cache/@gmod-gff-npm-1.2.0-4331ffa75f-ec4ad0c57d.zip/node_modules/@gmod/gff/src/parse.ts:223:13)
    at Parser.addLine (/workspaces/Apollo3/.yarn/cache/@gmod-gff-npm-1.2.0-4331ffa75f-ec4ad0c57d.zip/node_modules/@gmod/gff/src/parse.ts:134:18)
    at GFFTransform._addLine (/workspaces/Apollo3/.yarn/cache/@gmod-gff-npm-1.2.0-4331ffa75f-ec4ad0c57d.zip/node_modules/@gmod/gff/src/api.ts:106:19)
    at /workspaces/Apollo3/.yarn/cache/@gmod-gff-npm-1.2.0-4331ffa75f-ec4ad0c57d.zip/node_modules/@gmod/gff/src/api.ts:114:36
    at Array.forEach (<anonymous>)
    at GFFTransform._nextText (/workspaces/Apollo3/.yarn/cache/@gmod-gff-npm-1.2.0-4331ffa75f-ec4ad0c57d.zip/node_modules/@gmod/gff/src/api.ts:114:12)
    at GFFTransform._transform (/workspaces/Apollo3/.yarn/cache/@gmod-gff-npm-1.2.0-4331ffa75f-ec4ad0c57d.zip/node_modules/@gmod/gff/src/api.ts:122:10)
    at GFFTransform.Transform._write (node:internal/streams/transform:171:8)
    at writeOrBuffer (node:internal/streams/writable:572:12)
    at _write (node:internal/streams/writable:501:10)

Note that the database is still updated with a document corresponding to this assembly but Apollo does not see the assembly (e.g. you will not see it in "Delete assembly"). This means that restarting the server and re-loading the file (after fixing it) triggers the "assembly already exists" error.

To Reproduce Steps to reproduce the behavior:

• Write this in file.gff3:

##gff-version 3
chr9	.	gene	1	30	.	-	.	ID=gene09
chr9	.	mRNA	1	30	.	-	.	ID=mrna09.1;Parent=gene09
chr9	.	CDS	7	24	.	-	0	ID=cds09.1;Parent=mrna09
##FASTA
>chr9
TTActaCCCACCAGTACTTTGCGGtcaCATnnnnnnnnnnnnnnnnnnnnn

• On UI or cli add assembly from gff from file.gff3

• Apollo frontend should disconnect from server and server logs should show the error above

Expected behavior

Apollo should gracefully fail to import the file without crashing and without writing to the database.

Version information:

JBrowse 3.0.3
Apollo 0.3.4