Can the function "createViewState" run in nodejs ?

[SeqCrafter]

I try to wrap the JBrowse2 in a Python Reflex app. The React component JBrowseLinearGenomeView can be rendered dynamically, but the function of createViewState can't read compressed files when it is run in a Node.js environment in the backend.

So I want to ask if there are some differences for this function between running in a browser and Node.js.

[cmdcolin]

Hi there,
Sorry I saw your other question about Reflex but I forgot to follow up (xref GMOD/jbrowse-react-linear-genome-view-nextjs-demo#3)

If you share exact errors you get, it might be helpful

The createViewState can be run in a nodejs environment and it shouldn't matter in terms of compressed files as far as I know

An example of createViewState running in a pure node.js non-browser environment is in our @jbrowse/img (aka jb2export) tool

Code snip
https://github.com/GMOD/jbrowse-components/blob/769e28df981faef1930caacfb226aaab0abe801f/products/jbrowse-img/src/renderRegion.tsx#L459-L461

This is used to render static SVG just from node.js
https://www.npmjs.com/package/@jbrowse/img

With that said, JBrowse is primarily a client side app. I can see some interesting examples in the Reflex docs, I dunno if I got time to try it out for time being, but I am happy to help troubleshoot if you have errors you see

[SeqCrafter]

[
{
"type": "FeatureTrack",
"trackId": "genes",
"name": "NCBI RefSeq Genes",
"assemblyNames": ["hg38"],
"category": ["Genes"],
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz"
},
"index": {
"location": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi"
}
}
},
"textSearching": {
"textSearchAdapter": {
"type": "TrixTextSearchAdapter",
"textSearchAdapterId": "gff3tabix_genes-index",
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix",
"assemblyNames": ["GRCh38"]
}
}
}
]

Unfortunately, the same error happened again.

for assembly:

client.ts:59 Error: invalid distance too far back
    at unzip (unzip.ts:31:15)
    at BgzFilehandle._readAndUncompressBlock (bgzFilehandle.ts:59:17)
    at async BgzFilehandle.read (bgzFilehandle.ts:73:34)
    at async BgzipIndexedFasta._fetchFromIndexEntry (indexedFasta.ts:189:15)

for tracks:

Error: invalid distance too far back
    at unzip (unzip.ts:31:15)
    at TabixIndex._parse (tbi.ts:45:30)
    at async TabixIndex.getMetadata (indexFile.ts:40:44)
    at async TabixIndexedFile.getHeaderBuffer (tabixIndexedFile.ts:287:7)
    at async TabixIndexedFile.getHeader (tabixIndexedFile.ts:325:19)
    at async Gff3TabixAdapter.configurePre (Gff3TabixAdapter.js:30:21)
    at async updateStatus (index.js:721:17)
    at async Gff3TabixAdapter.getRefNames (Gff3TabixAdapter.js:47:25)
    at async MainThreadRpcDriver.call (MainThreadRpcDriver.js:28:24)
    at async loadRefNameMap (assembly.js:47:23)

[cmdcolin]

if it still continues it may be due to something about Reflex...not sure exactly what. if you can make a git repo with a readme that shows how to set it up it might help me to reproduce

[SeqCrafter]

Of course, you can test it using this git repo: link

[cmdcolin]

Thank you for making a nice reproducible test case...seriously! it helps a ton

I checked it out

I see reflex uses next.js under the hood. In a hidden directory called .web, there is a full nextjs app. The problem seems to be that it pins to next 15.0.4. After updating to the latest next.js, it works

Specifically, I manually changed the line in .web/package.json

-    "next": "15.0.4",
+    "next": "15.2.3",

Then I ran yarn and ran re-ran the app and it worked

So the issue seems to be with the older version of next.js. not sure if this is the most standard way to fix the issue, maybe reflex needs to update the version of nextjs they use

[SeqCrafter]

Thank you so much for helping find out this unexpected issue, and I will put this issue in the reflex repo.