SBML Simulation Feature Improvements

package.json

@@ -29,7 +29,6 @@
     "libsbmljs_stable": "^5.18.0-beta1",
     "mime-types": "^2.1.35",
     "pretty-data": "^0.40.0",
-    "sbgnviz": "github:umut-er/sbgnviz.js#SBML_Simulation",
     "xml2js": "^0.4.17"
   },
   "devDependencies": {

src/index.js

@@ -41,6 +41,7 @@
     var sbmlToSbgnmlConverter = require('./utilities/sbml-to-sbgnml-converter-factory')();
     var sbgnmlToGpmlConverter = require('./utilities/sbgnml-to-gpml-converter-factory')();
     var gpmlToSbgnmlConverter = require('./utilities/gpml-to-sbgnml-converter-factory')();
+    var sbmlSimulationUtilities = require('./utilities/sbml-simulation-utilities-factory')();
     // Fill param object to use it utilities internally
 
     param.optionUtilities = optionUtilities;
@@ -72,6 +73,7 @@
     param.gpmlToSbgnmlConverter = gpmlToSbgnmlConverter;
     param.experimentalDataOverlay = experimentalDataOverlay;
     param.libsbmlInstance = libsbmlInstance;
+    param.sbmlSimulationUtilities = sbmlSimulationUtilities;
 
     // call constructors of objects with param
 
@@ -102,6 +104,7 @@
     sbgnmlToGpmlConverter(param);
     gpmlToSbgnmlConverter(param);    
     experimentalDataOverlay(param);
+    sbmlSimulationUtilities(param);
 
     // set scratch pad for sbgnviz and init sbgnvizParams inside it
     sbgnCyInstance.getCy().scratch('_sbgnviz', {});
@@ -140,6 +143,11 @@
       api[prop] = graphUtilities[prop];
     }
 
+    // Expose each sbgn graph utility seperately
+    for (var prop in sbmlSimulationUtilities) {
+      api[prop] = sbmlSimulationUtilities[prop];
+    }
+
     // Expose createSbml
     api["createSbml"] = jsonToSbmlConverter.createSbml;
 

src/utilities/element-utilities-factory.js

@@ -47,7 +47,7 @@ module.exports = function () {
     ) {
       d += performance.now(); //use high-precision timer if available
     }
-    return "xxxxxxxx-xxxx-4xxx-yxxx-xxxxxxxxxxxx".replace(
+    return "xxxxxxxx_xxxx_4xxx_yxxx_xxxxxxxxxxxx".replace(
       /[xy]/g,
       function (c) {
         var r = (d + Math.random() * 16) % 16 | 0;
@@ -4787,8 +4787,7 @@ module.exports = function () {
     } else if (elementUtilities.processTypes.includes(pureClass)) {  // SBML Process
       return {
         'localParameters': [],  // {name: , value: , unit: }
-        'kineticLaw': "",       // Use ID's of species
-        'kineticLawVisible': "" // Can use labels of species
+        'kineticLaw': "0"
       };
     } else if (elementUtilities.edgeTypes.includes(pureClass)) {  // SBML Edge
       return {

src/utilities/json-to-sbml-converter-factory.js

@@ -10,7 +10,7 @@ var textUtilities = require('./text-utilities');
 var classes = require('./classes');
 
 module.exports = function () {
-    var elementUtilities, graphUtilities, experimentalDataOverlay;
+    var elementUtilities, graphUtilities, experimentalDataOverlay, sbmlSimulationUtilities;
     var cy;
 
     var nodesToSbo = 
@@ -74,6 +74,7 @@ module.exports = function () {
         elementUtilities = param.elementUtilities;
         graphUtilities = param.graphUtilities;
         experimentalDataOverlay = param.experimentalDataOverlay;
+        sbmlSimulationUtilities = param.sbmlSimulationUtilities;
         cy = param.sbgnCyInstance.getCy();
       }
 
@@ -105,6 +106,16 @@ module.exports = function () {
         const box = cy.elements().boundingBox();
         dim.setWidth(box.w); dim.setHeight(box.h);
 
+        // Create Parameters
+        var parameters = sbmlSimulationUtilities.getParameters();
+        for (var p of parameters) {
+            const param = model.createParameter();
+            param.setId(p.id);
+            param.setName(p.name);
+            param.setValue(p.value);
+            param.setConstant(p.constant);
+        }
+
         // Create compartment
         for (let i = 0; i < nodes.length; i++)
         {
@@ -357,14 +368,14 @@ module.exports = function () {
             else
                 rxn.setSBOTerm(176);
 
-            for(var lp in process.data("simulation")["localParameters"]){
-                var localp = rxn.createLocalParameter();
+            const k1 = rxn.createKineticLaw();
+            for(var lp of process.data("simulation")["localParameters"]){
+                var localp = k1.createLocalParameter();
                 localp.setValue(lp.quantity);
                 localp.setName(lp.name.replace(/-/g, '_'));
             }
-            const k1 = rxn.createKineticLaw();
             const parser = new libsbmlInstance.SBMLFormulaParser();
-            const kmath = parser.parseL3Formula( (process.data("simulation")["kineticLaw"].replace(/-/g, '_') || "") );
+            const kmath = parser.parseL3Formula( (process.data("simulation")["kineticLaw"] || "") );
             k1.setMath(kmath);
             // Add Layout Info for Processes
             const glyph = layout.createReactionGlyph();

src/utilities/sbml-simulation-utilities-factory.js

@@ -0,0 +1,69 @@
+module.exports = function () {
+  var parameters = {}; // { id = str: { name = str, value = float, unit = str, constant = bool } }, 
+
+  var cy;
+  var sbmlSimulationUtilities = function (param) {
+      cy = param.sbgnCyInstance.getCy();
+  };
+
+  sbmlSimulationUtilities.generateUUID = function () {
+    // Public Domain/MIT
+    var d = Date.now();
+    if (
+      typeof performance !== "undefined" &&
+      typeof performance.now === "function"
+    ) {
+      d += performance.now(); //use high-precision timer if available
+    }
+    return "xxxxxxxx_xxxx_4xxx_yxxx_xxxxxxxxxxxx".replace(
+      /[xy]/g,
+      function (c) {
+        var r = (d + Math.random() * 16) % 16 | 0;
+        d = Math.floor(d / 16);
+        return (c === "x" ? r : (r & 0x3) | 0x8).toString(16);
+      }
+    );
+  };
+
+  sbmlSimulationUtilities.generateParameterID = function() {
+    return "param_" + sbmlSimulationUtilities.generateUUID();
+  }
+
+  sbmlSimulationUtilities.addParameter = function (name, value, unit, constant) {
+    var id = sbmlSimulationUtilities.generateParameterID();
+    parameters[id] = {
+      name: name,
+      value: value,
+      unit: unit,
+      constant: constant
+    }
+  }
+
+  // Should only be used while importing, not really anything else
+  // Consider using sbmlSimulationUtilities.addParameter(name, value, unit, constant)
+  sbmlSimulationUtilities.addParameterWithId = function(id, name, value, unit, constant){
+    parameters[id] = {
+      name: name,
+      value: value,
+      unit: unit,
+      constant: constant
+    }
+  }
+
+  sbmlSimulationUtilities.removeParameter = function (id) {
+    delete parameters[id];
+  }
+
+  sbmlSimulationUtilities.getParameters = function () {
+    return Object.entries(parameters).map( ([id, {name, value, unit, constant}]) => ({
+      id, name, value, unit, constant
+    }));
+  }
+
+  sbmlSimulationUtilities.setParameter = function (id, field, value) {
+    parameters[id][field] = value;
+  }
+
+  return sbmlSimulationUtilities;
+};
+

src/utilities/sbml-to-json-converter-factory.js

@@ -6,7 +6,7 @@ var jQuery = ($ = libs.jQuery);
 var classes = require("./classes");
 
 module.exports = function () {
-  var elementUtilities, graphUtilities, handledElements, mainUtilities, libsbmlInstance;
+  var elementUtilities, graphUtilities, handledElements, mainUtilities, sbmlSimulationUtilities, libsbmlInstance;
   let resultJson = [];
   let speciesCompartmentMap = new Map;
   let layout;
@@ -17,6 +17,7 @@ module.exports = function () {
     elementUtilities = param.elementUtilities;
     graphUtilities = param.graphUtilities;
     mainUtilities = param.mainUtilities;
+    sbmlSimulationUtilities = param.sbmlSimulationUtilities;
     libsbmlInstance = param.libsbmlInstance;
 
     handledElements = {};
@@ -128,6 +129,7 @@ module.exports = function () {
     let compartmentBoundingBoxes = new Map;
     let containerNodeMap = new Map;
 
+    sbmlToJson.addParameters(model);
     sbmlToJson.addCompartments(model, cytoscapeJsNodes, compartmentBoundingBoxes, containerNodeMap);
     sbmlToJson.addSpecies(model, cytoscapeJsNodes, compartmentBoundingBoxes, containerNodeMap);
     sbmlToJson.addReactions(model, cytoscapeJsEdges,cytoscapeJsNodes);
@@ -147,6 +149,23 @@ module.exports = function () {
     return cytoscapeJsGraph;
   };
 
+// add parameters TODO: implement units
+sbmlToJson.addParameters = function(model) {
+  for(let i = 0; i < model.getNumParameters(); i++){
+    let parameter = model.getParameter(i);
+    var paramId = parameter.getId();
+    var paramName = paramId;
+    if (parameter.isSetName())
+      paramName = parameter.getName();
+    paramValue = 0.0;
+    if (parameter.isSetValue())
+      paramValue = parameter.getValue();
+    paramConstant = true;
+    if (parameter.isSetConstant())
+      paramConstant = parameter.getConstant();
+    sbmlSimulationUtilities.addParameterWithId(paramId, paramName, paramValue, "", paramConstant);
+  }
+}
 
 // add compartment nodes
 sbmlToJson.addCompartments = function (model,cytoscapeJsNodes, compartmentBoundingBoxes, containerNodeMap) {
@@ -240,7 +259,7 @@ sbmlToJson.addSpecies = function(model, cytoscapeJsNodes, compartmentBoundingBox
     })
     speciesCompartmentMap.set(species.getId(), species.getCompartment());
     var sboTerm = species.getSBOTerm();
-    let speciesData = {"id": species.getId(), "label": species.getName() || " ", 
+    let speciesData = {"id": species.getId(), "label": species.getName() || species.getId(), 
                       "parent": species.getCompartment(), "sboTerm": species.getSBOTerm(),
                       "active": active, "multimer": multimer, "hypothetical": hypothetical,
                       "bindingRegion": bindingRegion, "residueVariable": residueVariable, "unitOfInfo": unitOfInfo};