Tips in timetree are being rendered outside of panel

Looks like this problem is at the level of generating the timetree (visualizing timetree.nwk below):

@GopiGugan I'm running some tests on Paphlagon

Using the following script to extract by_lineage.json file from latest provision:

import covizu
from covizu.utils import gisaid_utils
from covizu.utils.progress_utils import Callback
from covizu.utils.batch_utils import *
import os

cb = Callback()

infile = "data/provision.2024-02-17T00:00:21.json.xz"
ref_file = os.path.join(covizu.__path__[0], "data/NC_045512.fa")
vcf_file = os.path.join(
    covizu.__path__[0],
    "data/ProblematicSites_SARS-CoV2/problematic_sites_sarsCov2.vcf")

loader = gisaid_utils.load_gisaid(infile, minlen=29000, mindate="2019-12-01",
                                  debug=None) #100)
batcher = gisaid_utils.batch_fasta(loader, size=2000)
aligned = gisaid_utils.extract_features(
    batcher, ref_file=ref_file, binpath="minimap2", nthread=16, minlen=29000)
filtered = gisaid_utils.filter_problematic(
    aligned, vcf_file=vcf_file, cutoff=0.001, callback=cb.callback)
by_lineage = gisaid_utils.sort_by_lineage(filtered, callback=cb.callback)

with open("iss512.json", 'w') as outfile:
    json.dump(by_lineage, outfile)

Reproduced the tree. Looks like this is not a backend problem.

Reproduced the tree. Looks like this is not a backend problem.

I'll take a look at the front end

I believe the issue is that we aren't scaling the nwk tree itself. Branch lengths are being assigned with the values in the nwk file:

covizu/server/phylo.js

Lines 59 to 71 in 10a4017

    
           if (nodeinfo.length==1) { 
        
             if (token.startsWith(':')) { 
        
               curnode.label = ""; 
        
               curnode.branchLength = parseFloat(nodeinfo[0]); 
        
             } else { 
        
               curnode.label = nodeinfo[0]; 
        
               curnode.branchLength = null; 
        
             } 
        
           } 
        
           else if (nodeinfo.length==2) { 
        
             curnode.label = nodeinfo[0]; 
        
             curnode.branchLength = parseFloat(nodeinfo[1]); 
        
           }

I believe the issue is that we aren't scaling the nwk tree itself. Branch lengths are being assigned with the values in the nwk file:

I don't think this is the problem, the branch lengths in this tree are scaled in units of time (years), which is what we want to display. I think the problem is that we are not calculating the maximum tip to root distance in this tree correctly, which would be needed to scale to the horizontal dimension of this panel.

I suspect the problem is somewhere here:

covizu/js/drawtree.js

Lines 122 to 138 in 10a4017

    
           // adjust d3 scales to data frame 
        
           if(!redraw) { 
        
             switch($("#display-tree").val()) { 
        
               case "Other Recombinants": 
        
                 xScale.domain([ 
        
                   axis_padding, 
        
                   date_to_xaxis(d3.max(recombinant_tips, function(d) {return d.last_date})) 
        
                 ]); 
        
                 break; 
        
               default: 
        
                 xScale.domain([ 
        
                   d3.min(org_df, xValue)-axis_padding_trees,  
        
                   date_to_xaxis(d3.max(org_df, function(d) {return d.last_date}))  
        
                 ]); 
        
                 break; 
        
             } 
        
           }

	if (nodeinfo.length==1) {
	if (token.startsWith(':')) {
	curnode.label = "";
	curnode.branchLength = parseFloat(nodeinfo[0]);
	} else {
	curnode.label = nodeinfo[0];
	curnode.branchLength = null;
	}
	}
	else if (nodeinfo.length==2) {
	curnode.label = nodeinfo[0];
	curnode.branchLength = parseFloat(nodeinfo[1]);
	}

	// adjust d3 scales to data frame
	if(!redraw) {
	switch($("#display-tree").val()) {
	case "Other Recombinants":
	xScale.domain([
	axis_padding,
	date_to_xaxis(d3.max(recombinant_tips, function(d) {return d.last_date}))
	]);
	break;
	default:
	xScale.domain([
	d3.min(org_df, xValue)-axis_padding_trees,
	date_to_xaxis(d3.max(org_df, function(d) {return d.last_date}))
	]);
	break;
	}
	}