access.js

// Paths come from downloaded assembly metadata, never a guessed repository URL.
function annotationPath(a){return D.loci.paths[a.accession]||null}
function updateDataAccess(a){
 const path=annotationPath(a),known=!!path;
 $('#sel-files').hidden=!known;$('#sel-files').href=known?'https://huggingface.co/buckets/'+D.loci.bucket+'/tree/'+path:'';
 $('#sel-download').textContent=known?'Download code':'Check annotation files ↗';
 $('#sel-availability').textContent=known?'GFF3 · coding sequences · proteins':'Gene files are not recorded in this snapshot.';
}
function annotationCode(a){
 const bucket=D.loci.bucket,path=annotationPath(a);
 const setup=`from pathlib import Path\nfrom huggingface_hub import HfApi\n\napi = HfApi()  # uses your saved Hugging Face login\nbucket = ${JSON.stringify(bucket)}\naccession = ${JSON.stringify(a.accession)}\n`;
 const lookup=path?`prefix = ${JSON.stringify(path)}\n`:`divisions = [\n    "fungi", "invertebrate", "plant", "protozoa",\n    "vertebrate_mammalian", "vertebrate_other",\n]\nmetadata = list(api.get_bucket_paths_info(\n    bucket, [f"cds/{d}/{accession}/metadata.json" for d in divisions]\n))\nif not metadata:\n    raise FileNotFoundError(\n        f"No published gene files found for {accession}."\n    )\nprefix = metadata[0].path.rsplit("/", 1)[0]\n`;
 return setup+lookup+`\noutput = Path(accession)\noutput.mkdir(parents=True, exist_ok=True)\nfiles = [\n    "annotations.gff3.gz",  # predicted gene / CDS coordinates\n    "cds.fna.gz",          # coding nucleotide sequences\n    "proteins.faa.gz",     # predicted protein sequences\n    "metadata.json",       # counts and pipeline provenance\n]\napi.download_bucket_files(\n    bucket,\n    [(f"{prefix}/{name}", output / name) for name in files],\n    raise_on_missing_files=True,\n)\n`;
}
function showDataAccess(a){
 if(!a)return;stopSweep();selectAssembly(a);
 const path=annotationPath(a);
 $('#data-assembly').textContent=a.name+' · '+a.accession;
 $('#data-description').textContent=path?'Download the published predictions for this assembly, with pipeline provenance.':'This snapshot has no published gene-file path for this assembly. The code below checks the current bucket and downloads the files if available.';
 $('#data-browse').href='https://huggingface.co/buckets/'+D.loci.bucket+'/tree/'+(path||'cds');
 $('#data-browse').textContent=path?'Browse this assembly’s files ↗':'Browse published gene files ↗';
 $('#data-code').textContent=annotationCode(a);$('#copy-status').textContent='';$('#data-dialog').showModal();
}
async function copyDataCode(){
 const code=$('#data-code').textContent;
 try{await navigator.clipboard.writeText(code);$('#copy-status').textContent='Copied'}
 catch{const range=document.createRange();range.selectNodeContents($('#data-code'));const selection=window.getSelection();selection.removeAllRanges();selection.addRange(range);$('#copy-status').textContent='Code selected — press Ctrl/Cmd+C'}
}