The fourth week included a lot of coding and debugging. The main goal was to successfully apply the layout changes to the network in cytoscape using the response from SyBLaRS API.

TODOs

  • Parse the response from SyBLaRS API to get the layout changes.
  • Format the response from the SyBLaRS API to extract the layout changes.
  • Fetch the node information from the network in cytoscape.
  • Apply the layout changes to the network in cytoscape.

Experiments with code

  • Tried to use org.json library to parse the JSON resonse and extract the required details from the response.
    • Using this library with the below given version caused cytoscape to stop detecting my plugin which prompted me to use javax.json package.
    • Eventually with the help of my mentor we figured out the issue, which was a mismatch between versions of the org.json library used in the plugin and the one used in the cytoscape application.
// Parse the JSON string
JSONObject json = new JSONObject(dataToSend);

// Access the value of a specific key
String elements = json.getJSONObject("elements").toString();

dataToSend = elements;

<!-- Incorrect version -->
<dependency>
    <groupId>org.json</groupId>
    <artifactId>json</artifactId>
    <version>20210307</version>
</dependency>

<!-- Correct version -->
<dependency>
    <groupId>org.json</groupId>
    <artifactId>org.json</artifactId>
    <version>chargebee-1.0</version>
</dependency>

Learnings

  • The Cytoscape desktop application uses multiple external dependencies which might conflict with the dependencies used in the plugin.
  • The Cytoscape desktop application maintains a descriptive error log which is very helpful in debugging the issues.
  • SybLaRS expects only the "elements" object of the exported network JSON to be sent as the request body.

Milestones

Successful parsing of the response from SyBLaRS API

  • Parse the JSON response from the SyBLaRS API to extract the layout changes and the node information.
  • Store the new coordinates of the nodes in a map with the node id as the key.
//iterate over response
JSONObject jsonResponse = new JSONObject(response.toString());
JSONObject layoutFromResponse = jsonResponse.getJSONObject("layout");
Iterator<String> nodes = layoutFromResponse.keys();
while(nodes.hasNext()) {
    String node = nodes.next();
    JSONObject value = layoutFromResponse.getJSONObject(node);
    JSONObject position = value.getJSONObject("position");
    try {
        nodePositions.put(node, position);
    } catch (Exception e) {
        System.out.println("Exception: " + e.getMessage());
    }

Successful application of layout changes to the network in Cytoscape

  • Set the node positions by matching the nodes with SUID.
// Set the node positions
final VisualProperty<Double> xLoc = BasicVisualLexicon.NODE_X_LOCATION;
final VisualProperty<Double> yLoc = BasicVisualLexicon.NODE_Y_LOCATION;

for(View<CyNode> nodeView : myView.getNodeViews()) {
    String nodeName = myView.getModel().getRow(nodeView.getModel()).get("name", String.class);
    String nodeId = nodeView.getModel().getSUID().toString();
    JSONObject position = nodePositions.get(nodeId);
    if(position != null) {
        nodeView.setVisualProperty(xLoc, position.getDouble("x"));
        nodeView.setVisualProperty(yLoc, position.getDouble("y"));
    }
}