MGG ( Microbetag Gui )
MGG Progress Documentation
WEEK 13 & WEEK 14
- CreateNetworkTaskTask
- CreateNetworkTaskTaskFactory
They are responsible for parsing the table and constructing a network model based on it. Additionally, the class generates a visual style for the nodes and edges of the network
CreateNetworkTask
**
* This class represents a task for creating a network in Cytoscape based on a
* JSON response from a server.
*
* The JSON response contain information about the nodes and edges of the
* network. For each node and edge, the task creates a corresponding node or
* edge in the Cytoscape network. The task also sets various attributes for the
* nodes and edges based on the JSON data.
*
* The task uses the CyNetworkFactory service to create a new network, and the
* CyNetworkManager service to add the network to Cytoscape through the
* MGGmanager class
*
*/
public class CreateNetworkTask extends AbstractTask {
final MGGManager mggManager;
// Cytoscape services used by the task
final CyNetworkFactory networkFactory;
final CyNetworkManager networkManager;
final CyNetworkViewFactory networkViewFactory;
final CyNetworkViewManager networkViewManager;
final VisualStyleFactory visualStyleFactory;
final VisualMappingFunctionFactory discreteMappingFactory;
final VisualMappingFunctionFactory vmfFactoryP;
final VisualMappingManager vmmServiceRef;
final CyLayoutAlgorithmManager layoutAlgorithmManager;
final PaletteProviderManager paletteManager;
// final PaletteProvider paletteProvider;
public CreateNetworkTask(MGGManager mggManager) {
this.mggManager = mggManager;
this.networkFactory = mggManager.getService(CyNetworkFactory.class);
this.networkManager = mggManager.getService(CyNetworkManager.class);
this.networkViewFactory = mggManager.getService(CyNetworkViewFactory.class);
this.networkViewManager = mggManager.getService(CyNetworkViewManager.class);
this.visualStyleFactory = mggManager.getService(VisualStyleFactory.class);
this.discreteMappingFactory = mggManager.getService(VisualMappingFunctionFactory.class,
"(mapping.type=discrete)");
this.vmfFactoryP = mggManager.getService(VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
this.vmmServiceRef = mggManager.getService(VisualMappingManager.class);
this.layoutAlgorithmManager = mggManager.getService(CyLayoutAlgorithmManager.class);
this.paletteManager = mggManager.getService(PaletteProviderManager.class);
// this.paletteProvider=mggManager.getService(PaletteProvider.class);
// paletteProvider=Palette.getPalette("ColorBrewer");
// paletteProvider=Palette.getPalette("ColorBrewer");
// PaletteProvider paletteProvider=Palette.getPalette("ColorBrewer");
// PaletteProvider paletteProvider = new PaletteProvider();
}
@Override
public void run(TaskMonitor taskMonitor) {
taskMonitor.setTitle("Creating the network");
taskMonitor.setStatusMessage("Creating the network...");
JSONObject jsonResponse = mggManager.getServerResponse();
JSONObject elements = (JSONObject) jsonResponse.get("elements");
// Create a new network
CyNetwork network = networkFactory.createNetwork();
// Add the network to the network manager
networkManager.addNetwork(network);
// default node table
CyTable nodeTable = network.getDefaultNodeTable();
// Create columns if they don't exist for 'data' attributes if
if (nodeTable.getColumn("id") == null) {
nodeTable.createColumn("id", String.class, false);
}
if (nodeTable.getColumn("taxonomy") == null){
nodeTable.createColumn("taxonomy", String.class, false);
}
if (nodeTable.getColumn("NCBI-Tax-Id") == null) {
nodeTable.createColumn("NCBI-Tax-Id", String.class, false);
}
if
(nodeTable.getColumn("GTDB-representative") == null) {
nodeTable.createColumn("GTDB-representative", String.class, false); }
if
(nodeTable.getColumn("taxonomy-level") == null) {
nodeTable.createColumn("taxonomy-level", String.class, false); }
if
(nodeTable.getColumn("degree_layout") == null) {
nodeTable.createColumn("degree_layout", Long.class, false); }
if
(nodeTable.getColumn("name") == null){
nodeTable.createColumn("name", String.class, false);
}
// if (nodeTable.getColumn("phenotypic_traits") == null) {
// nodeTable.createColumn("phenotypic_traits", String.class, false);
// }
// Add nodes
JSONArray nodes = (JSONArray) elements.get("nodes");
for (Object nodeObj : nodes) {
JSONObject nodeData = (JSONObject) ((JSONObject) nodeObj).get("data");
// String id = (String) nodeData.get("id");
CyNode node = network.addNode();
network.getRow(node).set(CyNetwork.NAME, (String) nodeData.get("id"));
network.getRow(node).set("selected", (Boolean) nodeData.get("selected"));
network.getRow(node).set("taxonomy", (String) nodeData.get("taxonomy"));
network.getRow(node).set("NCBI-Tax-Id", (String) nodeData.get("NCBI-Tax-Id"));
network.getRow(node).set("GTDB-representative", (String) nodeData.get("GTDB-representative"));
network.getRow(node).set("taxonomy-level", (String) nodeData.get("taxonomy-level"));
network.getRow(node).set("degree_layout", (Long) nodeData.get("degree_layout"));
//network.getRow(node).set("name", (String) nodeData.get("name"));
/*
* network.getRow(node).set(CyNetwork.NAME, (String) nodeData.get("id"));
* network.getRow(node).set("selected", (Boolean) nodeData.get("selected"));
* network.getRow(node).set("taxonomy", (String) nodeData.get("taxonomy"));
* network.getRow(node).set("NCBI-Tax-Id", (String)
* nodeData.get("NCBI-Tax-Id")); network.getRow(node).set("GTDB-representative",
* (String) nodeData.get("GTDB-representative"));
* network.getRow(node).set("taxonomy-level", (String)
* nodeData.get("taxonomy-level"));
*/
}
// default edge table
CyTable edgeTable = network.getDefaultEdgeTable();
// Create columns if they don't exist
/*
* if (edgeTable.getColumn(CyNetwork.NAME) == null) {
* edgeTable.createColumn(CyNetwork.NAME, String.class, false); }
*/
if (edgeTable.getColumn("shared_name") == null) {
edgeTable.createColumn("shared_name", String.class, false); }
if
(edgeTable.getColumn("flashweave-score") == null) {
edgeTable.createColumn("flashweave-score", Double.class, false); }
if
(edgeTable.getColumn("SUID") == null) { edgeTable.createColumn("SUID",
Long.class, false); }
if (edgeTable.getColumn("source-ncbi-tax-id") ==
null) { edgeTable.createColumn("source-ncbi-tax-id", String.class, false); }
if (edgeTable.getColumn("target-ncbi-tax-id") == null) {
edgeTable.createColumn("target-ncbi-tax-id", String.class, false); }
if
(edgeTable.getColumn("selected") == null) {
edgeTable.createColumn("selected", Boolean.class, false);
}
if
(edgeTable.getColumn("source") == null) {
edgeTable.createColumn("source", String.class, false);
}
if (edgeTable.getColumn("target") == null) {
edgeTable.createColumn("target", String.class, false);
}
/*
* // Create columns if they don't exist if
* (edgeTable.getColumn("shared_interaction") == null) {
* edgeTable.createColumn("shared_interaction", String.class, false); } if
* (edgeTable.getColumn("interaction") == null) {
* edgeTable.createColumn("interaction", String.class, false); } if
* (edgeTable.getColumn("shared_name") == null) {
* edgeTable.createColumn("shared_name", String.class, false); } if
* (edgeTable.getColumn("source") == null) { edgeTable.createColumn("source",
* String.class, false); } if (edgeTable.getColumn("target") == null) {
* edgeTable.createColumn("target", String.class, false); } if
* (edgeTable.getColumn("selected") == null) {
* edgeTable.createColumn("selected", Boolean.class, false); }
*/
// Add edges
JSONArray edges = (JSONArray) elements.get("edges");
for (Object edgeObj : edges) {
JSONObject edgeData = (JSONObject) ((JSONObject) edgeObj).get("data");
String sourceId = (String) edgeData.get("source");
String targetId = (String) edgeData.get("target");
CyNode sourceNode = getNodeById(network, sourceId);
CyNode targetNode = getNodeById(network, targetId);
if (sourceNode != null && targetNode != null) {
CyEdge edge = network.addEdge(sourceNode, targetNode, false);
network.getRow(edge).set(CyNetwork.NAME, (String) edgeData.get("id"));
network.getRow(edge).set("shared_name", (String) edgeData.get("shared_name"));
String flashweaveScoreStr = (String) edgeData.get("flashweave-score");
double flashweaveScore = Double.parseDouble(flashweaveScoreStr);
network.getRow(edge).set("flashweave-score", flashweaveScore);
//network.getRow(edge).set("flashweave-score", (Double) edgeData.get("flashweave-score")); // Parsing string to long
network.getRow(edge).set("SUID", Long.parseLong((String) edgeData.get("SUID"))); // Parsing string to long
network.getRow(edge).set("source-ncbi-tax-id", (String) edgeData.get("source-ncbi-tax-id"));
network.getRow(edge).set("target-ncbi-tax-id", (String) edgeData.get("target-ncbi-tax-id"));
network.getRow(edge).set("selected", (Boolean) edgeData.get("selected"));
}
/*
* if (sourceNode != null && targetNode != null) { CyEdge edge
* =network.addEdge(sourceNode, targetNode, false);
*
* network.getRow(edge).set(CyNetwork.NAME, (String) edgeData.get("id"));
* network.getRow(edge).set("shared_interaction",
* (String)edgeData.get("shared_interaction"));
*
* network.getRow(edge).set("interaction",(String) edgeData.get("interaction"));
*
* network.getRow(edge).set("shared_name", (String)edgeData.get("shared_name"));
*
* network.getRow(edge).set("source", (String)edgeData.get("source"));
*
* network.getRow(edge).set("target", (String)edgeData.get("target"));
*
* network.getRow(edge).set("selected", (Boolean)edgeData.get("selected")); }
*/
}
// create a network view
CyNetworkView networkView = networkViewFactory.createNetworkView(network);
networkViewManager.addNetworkView(networkView);
// ----------------------------------------------------------------------------------------------------
// VISUAL STYLE
VisualStyle style = visualStyleFactory.createVisualStyle("MGG");
String columnName = "taxonomy-level";
// VisualProperty for node fill color
VisualProperty<?> vp = BasicVisualLexicon.NODE_FILL_COLOR;
style.setDefaultValue(BasicVisualLexicon.NODE_SHAPE, NodeShapeVisualProperty.ELLIPSE);
// Node Borders
style.setDefaultValue(BasicVisualLexicon.NODE_BORDER_WIDTH, 2.0);
style.setDefaultValue(BasicVisualLexicon.NODE_BORDER_PAINT, Color.DARK_GRAY);
// VisualProperty for node shape
VisualProperty<NodeShape> nodeShapeVP = BasicVisualLexicon.NODE_SHAPE;
// Create a discrete mapping function for node shape
DiscreteMapping<String, NodeShape> shapeMapping = (DiscreteMapping<String, NodeShape>) discreteMappingFactory
.createVisualMappingFunction(columnName, String.class, nodeShapeVP);
// Map taxonomy-level to shapes
Map<String, NodeShape> taxonomyShapeMap = getTaxonomyShapeMap();
// Set taxonomy-level to shape pairs
for (Map.Entry<String, NodeShape> entry : taxonomyShapeMap.entrySet()) {
shapeMapping.putMapValue(entry.getKey(), entry.getValue());
}
// Add mapping function to the visual style
style.addVisualMappingFunction(shapeMapping);
// Node Labels
style.setDefaultValue(BasicVisualLexicon.NODE_LABEL, "");
PassthroughMapping<String, String> labelMapping = (PassthroughMapping<String, String>) vmfFactoryP
.createVisualMappingFunction("name", String.class, BasicVisualLexicon.NODE_LABEL);
style.addVisualMappingFunction(labelMapping);
// Discrete mapping function
DiscreteMapping<String, Paint> mapping = (DiscreteMapping<String, Paint>) discreteMappingFactory
.createVisualMappingFunction(columnName, String.class, vp);
// Map species to colors
Map<String, Paint> speciesColorMap = getSpeciesColorMap();
// Set the species-color pairs
for (Map.Entry<String, Paint> entry : speciesColorMap.entrySet()) {
mapping.putMapValue(entry.getKey(), entry.getValue());
}
// Add the mapping function to the visual style
style.addVisualMappingFunction(mapping);
// Apply the visual style to a network view
style.apply(networkView);
vmmServiceRef.addVisualStyle(style);
vmmServiceRef.setCurrentVisualStyle(style);
networkView.updateView();
// layout ( "force-directed")
CyLayoutAlgorithm layout = layoutAlgorithmManager.getLayout("force-directed");
if (layout == null) {
// layout is not found, use the default layout
layout = layoutAlgorithmManager.getDefaultLayout();
}
// Create a task iterator for the layout
insertTasksAfterCurrentTask(layout.createTaskIterator(networkView, layout.getDefaultLayoutContext(),
CyLayoutAlgorithm.ALL_NODE_VIEWS, null));
}
/*
* private CyNode getNodeById(CyNetwork network, String id) { for (CyNode node :
* network.getNodeList()) { if (network.getRow(node).get(CyNetwork.NAME,
* String.class).equals(id)) { return node; } } return null; }
*/
private CyNode getNodeById(CyNetwork network, String nodeId) {
for (CyNode node : network.getNodeList()) {
String id = network.getRow(node).get(CyNetwork.NAME, String.class);
if (nodeId.equals(id)) {
return node;
}
}
return null;
}
private Map<String, NodeShape> getTaxonomyShapeMap() {
Map<String, NodeShape> taxonomyShapeMap = new HashMap<>();
taxonomyShapeMap.put("genus", NodeShapeVisualProperty.DIAMOND);
taxonomyShapeMap.put("family", NodeShapeVisualProperty.ROUND_RECTANGLE);
taxonomyShapeMap.put("mspecies", NodeShapeVisualProperty.ELLIPSE);
taxonomyShapeMap.put("null", NodeShapeVisualProperty.OCTAGON);
taxonomyShapeMap.put("species", NodeShapeVisualProperty.HEXAGON);
// Add more taxonomy-level to shape mappings as needed
return taxonomyShapeMap;
}
private Map<String, Paint> getSpeciesColorMap() {
Map<String, Paint> speciesColorMap = new HashMap<>();
}
PaletteProvider colorBrewerPaletteProvider = paletteManager.getPaletteProvider("ColorBrewer");
Palette set1 = colorBrewerPaletteProvider.getPalette("Set1 colors");
// Palette set1= paletteProvider.getPalette("Set1 colors");
Color[] set1Palette = set1.getColors(9);
speciesColorMap.put("genus", set1Palette[4]);
speciesColorMap.put("family", set1Palette[1]);
speciesColorMap.put("mspecies", set1Palette[2]);
speciesColorMap.put("null", set1Palette[8]);
speciesColorMap.put("species", set1Palette[0]);
// speciesColorMap.put("GRC5", set1Palette[5]);
return speciesColorMap;
}
}
}
CreateNetworkTaskFactory
public class CreateNetworkTaskFactory implements TaskFactory {
private final MGGManager mggManager;
public CreateNetworkTaskFactory(MGGManager mggManager) {
this.mggManager = mggManager;
}
@Override
public TaskIterator createTaskIterator() {
return new TaskIterator(new CreateNetworkTask(mggManager));
}
@Override
public boolean isReady() {
// add any conditions that need to be met before the task can be executed.
// For example, check the JSON response is not null.
return mggManager.getServerResponse() != null;
}
}