Fixed issue where ~9 MB sbml file loading caused runtime memory excep…

…tion

Final check in before first release.

docs/index.html

@@ -28,15 +28,18 @@
 var getSBMLInfoMessages;//		"
 var getSBMLWarnings;	//		"
 var freeAll;			//		"
-
+var jsFree;     		// emscripten function
+//var jsMalloc;	   		//      " Not needed
+var jsAllocateUTF8;		//		"
+var jsUTF8ToString; 	//		"
 
 // Load library functions (asynchronous call):
 try {
  libantimony().then((libantimony) => {
  //	Format: libantimony.cwrap( function name, return type, input param array of types).
- loadString = libantimony.cwrap('loadString', 'number', ['string']);
- loadAntimonyString = libantimony.cwrap('loadAntimonyString', 'number', ['string']);
- loadSBMLString = libantimony.cwrap('loadSBMLString', 'number', ['string']);
+ loadString = libantimony.cwrap('loadString', 'number', ['number']);
+ loadAntimonyString = libantimony.cwrap('loadAntimonyString', 'number', ['number']);
+ loadSBMLString = libantimony.cwrap('loadSBMLString', 'number', ['number']);
  getSBMLString = libantimony.cwrap('getSBMLString', 'string', ['null']);
  getAntimonyString = libantimony.cwrap('getAntimonyString', 'string', ['null']);
  getCompSBMLString = libantimony.cwrap('getCompSBMLString', 'string', ['string']); 
@@ -46,15 +49,22 @@
  getSBMLInfoMessages = libantimony.cwrap('getSBMLInfoMessages', 'string', ['string']);
  getSBMLWarnings = libantimony.cwrap('getSBMLWarnings', 'string', ['string']);
  freeAll = libantimony.cwrap('freeAll', 'null', ['null']);
+ // Emscripten funcs (direct calls):
+ jsFree = (strPtr) => libantimony._free(strPtr); 
+ jsAllocateUTF8 = (newStr) =>  libantimony.allocateUTF8(newStr); 
+ // Do not need?:
+ jsUTF8ToString = (strPtr) => libantimony.UTF8ToString(strPtr);
+ //jsMalloc = (strLenPlus1) => libantimony._malloc(strLenPlus1); // Not needed, use jsAllocateUTF8 to reserve space on Emscripten Heap for string.
  });
 }
 catch(err) {
   console.log('Load libantimony error: ', err);
 }
 // Test functionality:
 function runAntimonyCheck() {
-  var intResult = loadString(antString); // TEST loadString()
+  var intResult = loadString( jsAllocateUTF8(antString) ); // TEST loadString()
   var antResult;
+   console.log('** TEST: loadString():');
   if(intResult < 0) {
     console.log('loadString() returned error:' ,intResult);
     console.log(getLastError());
@@ -66,26 +76,41 @@
   clearPreviousLoads();
 
   sbmlResult = 'none';		// TEST loadAntimonyString()
-  intResult = loadAntimonyString(antString);
+  intResult = loadAntimonyString( jsAllocateUTF8(antString) );
   sbmlResult = getSBMLString();
-  console.log('load ant again, return int:' ,intResult);
+  console.log('** TEST: loadAntimonyString(), return int:' ,intResult);
   console.log('SBML again: ' ,sbmlResult);
 
   clearPreviousLoads();		// TEST loadSBMLString()
-  intResult = loadSBMLString(sbmlResult);
-  console.log('getWarnings: ', getWarnings());
+  intResult = loadSBMLString( jsAllocateUTF8(sbmlResult) );
   antResult = getAntimonyString();
-  console.log('load SBML string, return int:' ,intResult);
+  console.log('** TEST: loadSBMLString(), return int:' ,intResult);
   console.log('Antimony string: ' ,antResult);
+  console.log('getWarnings: ', getWarnings());
 
-  clearPreviousLoads();		// TEST getLastError()
+  clearPreviousLoads();		// TEST getLastError(), SBML error
   var errSBMLStr = sbmlResult.replace('id="S1"', 'id="S5"');
-  intResult = loadSBMLString(errSBMLStr);
-  console.log('load bad SBML model, return int:' ,intResult);
-  console.log('getLastError(): ', getLastError());
-  console.log('getSBMLInfoMessages(): ', getSBMLInfoMessages());// none expected
-  console.log('getSBMLWarnings(): ', getSBMLWarnings('example1')); // none expected
+  intResult = loadSBMLString( jsAllocateUTF8(errSBMLStr) );
+  console.log('** TEST: load bad SBML model, return int:' ,intResult);
+  console.log('bad SBML: getLastError(): ', getLastError());
+  console.log('bad SBML: getSBMLInfoMessages(): ', getSBMLInfoMessages());// none expected
+  console.log('bad SBML: getSBMLWarnings(): ', getSBMLWarnings('example1')); // none expected
+
+  clearPreviousLoads();		// TEST getLastError(), Antimony error
+  var errAntStr = "model example1; S1 -> S2; k1*S*S5 S1 > S5*550; S2 = 0;  k1 = 0.1; end";
+  intResult = loadAntimonyString( jsAllocateUTF8(errAntStr) );
+  console.log('** TEST: load Bad Antimony model, return int:' ,intResult);
+  console.log('Bad Antimony: getLastError(): ', getLastError()); // none expected
+  console.log('Bad Antimony: getSBMLInfoMessages(): ', getSBMLInfoMessages());// none expected
+  console.log('Bad Antimony: getSBMLWarnings(): ', getSBMLWarnings('example1')); 
 
+  clearPreviousLoads();		// TEST getSBMLWarnings(), Antimony error
+  var errAntStr = "model example1; S1 -> S2; k1*S*S5 ; S1 > S5*550; S2 = 0;  k1 = 0.1; end";
+  intResult = loadAntimonyString( jsAllocateUTF8(errAntStr) );
+  console.log('** TEST: load Warnings Antimony model, return int:' ,intResult);
+  console.log('Warnings Antimony: getLastError(): ', getLastError()); // none expected
+  console.log(' Warnings Antimony: getSBMLInfoMessages(): ', getSBMLInfoMessages());// none expected
+  console.log(' Warnings Antimony: getSBMLWarnings(): ', getSBMLWarnings('example1')); 
   return sbmlResult;
 }
 </script>
@@ -96,23 +121,26 @@
  antCode = document.getElementById("antimonycode").value;
  clearPreviousLoads();
  //console.log("*** Antimony code: ",antCode);
- var load_int= loadAntimonyString(antCode);
+ var ptrAntCode = jsAllocateUTF8(antCode);
+ var load_int= loadAntimonyString(ptrAntCode);
  console.log("processAntimony: int returned: ", load_int);
  if (load_int > 0) {
    sbmlResult = getSBMLString(); 
    document.getElementById("sbmlcode").value = sbmlResult;
    document.getElementById("procSBMLBtn").disabled = false;
+
  }
  else { 
    var errStr = getLastError();
    window.alert(errStr); }
-
+ jsFree(ptrAntCode);
 }
 
 function processSBML() {
  sbmlCode = document.getElementById("sbmlcode").value;
  clearPreviousLoads();
- var load_int= loadSBMLString(sbmlCode);
+ var ptrSBMLCode = jsAllocateUTF8(sbmlCode);
+ var load_int= loadSBMLString(ptrSBMLCode);
  console.log("processSBML: int returned: ", load_int);
  if (load_int > 0) {
    antResult = getAntimonyString(); 
@@ -123,19 +151,19 @@
    var errStr = getLastError();
    window.alert(errStr); 
    }
-
+ jsFree(ptrSBMLCode);
 
 }
+
  function processFile(fileStr) {
- console.log('Loaded Model str: ', fileStr);
+ //console.log('Loaded Model str: ', fileStr);
  try {
-   if(loadAntimonyString(fileStr) > 0) {
-   //if(loadSBMLString(fileStr) > 0) {
+     var ptrFileStr = jsAllocateUTF8(fileStr);
+     if(loadAntimonyString(ptrFileStr) > 0) {
 	 document.getElementById("antimonycode").value = fileStr; 
 	 document.getElementById("procSBMLBtn").disabled = true;
-	 document.getElementById("sbmlcode").value = "[SBML code here.]";}
-	 else if (loadSBMLString(fileStr) > 0){  
-	// if (loadSBMLString(fileStr) > 0){ 
+	 document.getElementById("sbmlcode").value = "[SBML code here.]";} 
+	 else if (loadSBMLString(ptrFileStr) > 0){
 	   document.getElementById("sbmlcode").value = fileStr; 
 	   document.getElementById("procAntimonyBtn").disabled = true;
 	   document.getElementById("antimonycode").value = "[Antimony code here.]";
@@ -150,6 +178,7 @@
 	  console.log('processing file error: :', err);
 	  window.alert(err);
 	}
+	jsFree(ptrFileStr);
  }
 
 </script>

release/current/ReleaseInfo.txt

@@ -0,0 +1,14 @@
+libAntimonyjs release 1.0.0 info:
+Date: 2023apr18
+libSBML source: 5.19.0
+Antimony source: 2.13.3
+Emscripten SDK version: 3.1.20
+
+Following Methods are available:
+
+From Antimony library:
+_loadString, _loadAntimonyString, _loadSBMLString, _clearPreviousLoads, _getAntimonyString, _freeAll,
+_getSBMLString, _getCompSBMLString, _getLastError, _getWarnings, _getSBMLInfoMessages, _getSBMLWarnings,
+
+From Emscripten:
+_malloc, _free, ccall, cwrap, allocateUTF8, UTF8ToString