epicov: empty tips on time-scaled tree

There are bunch of rect elements with width="NaN" and cidx="cidx-undefined"

clusters.json did not get updated in the last run. Similar issue to #464. Commit ba709c4 should have fixed the issue.

Looking into why convert_json failed.
Temporarily replacing the epicov data files with the ones from the last successful run (April 21)

convert_json ran without issues. Looks like the batch.py script terminated earlier. A temporary file with the output from convert_json was created but failed to transfer over to the web server:

covizu/batch.py

Lines 207 to 213 in 7cf87ca

    
           # modify clusters JSON 
        
           epifile = open(clust_file, 'r') 
        
           epicov_data = gisaid_utils.convert_json(epifile, args.infile) 
        
           fp = NamedTemporaryFile('w', delete=False) 
        
           json.dump(epicov_data, fp=fp)  # serialize to temp file 
        
           fp.close() 
        
           subprocess.check_call(['scp', fp.name, '{}/clusters.json'.format(server_epicov)])

This is related to an OOM error - need to upgrade RAM on head node or launch main process on one of the newer compute nodes

Temporary fix is to run the backend on Paphlagon until I can come in to upgrade the RAM on BEVi head node

	# modify clusters JSON
	epifile = open(clust_file, 'r')
	epicov_data = gisaid_utils.convert_json(epifile, args.infile)
	fp = NamedTemporaryFile('w', delete=False)
	json.dump(epicov_data, fp=fp) # serialize to temp file
	fp.close()
	subprocess.check_call(['scp', fp.name, '{}/clusters.json'.format(server_epicov)])