Cytoscape: Genetic Links form with nodes that don't have a sequence

[dacowan404]

I loaded the file (the csv version of the file, zenhub doesn't allow CSV files so I had to upload a excel version) and links were forming between each node and nodes (p1, p2, and p3). These three nodes don't have a sequence and they shouldn't have any genetic links. It seems this issue is specific to node files as a CSV, but node files as excel is working.

I believe I have a fix but am testing it further before pushing. Essentially, the empty field (null) is getting converted into a string 'null' by filterXSS function and then the string ('null') is being treated as a genetic sequences. After filterXSS and before calculating genetic distance there is a statement that sets the node.seq to a string of gaps/dashes ('------....') but this is based on if node.seq is falsey. The current fix is to expand the if statement that sets this to include if seq=='null', 'none' or 'na'.

COVID-19_simulated_NodeList.xlsx

[roxycintron]

@dacowan404 How the code has been changed from MT Classic? The network is displayed correctly in MT Classic.

[dacowan404]

@roxycintron essentially one of the functions changed between implementations. The prod version imported this function from a separate package; whereas in the current version a custom version of the function is used. I asked Evan about the switch but it occurred before he joined.

I am pushing the fix discussed in the description today (07/23/25).