Merge pull request #1393 from virtualcell/Ontology-update

Updated KiSAO OBO and added parsing for KiSAO_694

vcell-core/src/main/java/cbit/util/kisao/KisaoOntology.java

@@ -10,7 +10,7 @@
 
 public class KisaoOntology {
 
-	private List<KisaoTerm> terms = new ArrayList<>();
+	private final List<KisaoTerm> terms = new ArrayList<>();
 	private static KisaoOntology instance;
 
 
@@ -61,7 +61,7 @@ public static List<KisaoTerm> makeDescendantList(KisaoTerm root) {
 			if(tmpList.size() > 1) {
 				System.err.println("Each kisao term must have no more than 1 descendant");
 			}
-			if(tmpList.size() == 0) {	// we seldom get here
+			if(tmpList.isEmpty()) {	// we seldom get here
 				if(root.getId().equals("KISAO_0000000")) {
 					throw new RuntimeException("Error reaching KISAO_0000000");
 				} else {

vcell-core/src/main/java/cbit/util/kisao/KisaoTermParser.java

@@ -6,8 +6,10 @@
 import java.io.BufferedReader;
 import java.io.InputStream;
 import java.io.InputStreamReader;
+import java.nio.file.Files;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
+import java.util.stream.StreamSupport;
 
 
 public class KisaoTermParser {
@@ -22,16 +24,15 @@ public class KisaoTermParser {
 	final Pattern ISA_PATTERN = Pattern.compile("is_a:\\s*(\\S+)");
 
 	KisaoOntology parse() {
-		InputStream is = KisaoTermParser.class.getClassLoader().getResourceAsStream(Kisao_OBO);
-		BufferedReader isr = new BufferedReader(new InputStreamReader(is));
-		String line = null;
-		boolean inState = false;
 		KisaoOntology ontology = new KisaoOntology();
 		KisaoTerm curr = null;
+		boolean inState = false;
+
+		InputStream is = KisaoTermParser.class.getClassLoader().getResourceAsStream(Kisao_OBO);
+		if (is == null) throw new RuntimeException("Unable to load OBO file necessary for KiSAO!");
 
 		try {
-			while ((line = isr.readLine()) != null) {
-
+			for (String line : (new BufferedReader(new InputStreamReader(is))).lines().toList()){
 				if (line.matches(TERM_PATTERN)) {
 					inState = true;
 					curr = new KisaoTerm();
@@ -41,11 +42,12 @@ KisaoOntology parse() {
 					ontology.addTerm(curr);
 					curr = null;
 				}
-				
+
 				if(inState) {
 					Matcher matcher = ID_PATTERN.matcher(line);
 					if (matcher.find()) {
-						curr.setId(matcher.group(1));
+						String group1 = matcher.group(1);
+						curr.setId(group1.startsWith("kisao:") ? group1.substring(6) : group1);
 					}
 
 					matcher = NAME_PATTERN.matcher(line);
@@ -54,11 +56,12 @@ KisaoOntology parse() {
 					}
 					matcher = ISA_PATTERN.matcher(line);
 					if (matcher.find()) {
-						curr.addIsaRef(matcher.group(1));
+						String group1 = matcher.group(1);
+						curr.addIsaRef(group1.startsWith("kisao:") ? group1.substring(6) : group1);
 					}
 				}
 			}
-		} catch(Exception e) {
+		} catch (Exception e) {
 			lg.error(e.getMessage(), e);
 		}
 

vcell-core/src/main/java/cbit/vcell/solver/SolverUtilities.java

@@ -86,14 +86,14 @@ public static boolean isPowerOf2(int n) {
 
 	/**
 	 * Ensure solvers extracted from resources and registered as property
-	 * @param cf
+	 * @param sd the solver description
 	 * @return array of exes used by provided solver
 	 * @throws IOException, {@link UnsupportedOperationException} if no exe for this solver
 	 */
 	public static File[] getExes(SolverDescription sd) throws IOException {
 		SolverExecutable se = sd.getSolverExecutable(); 
 		if (se != null) {
-			SolverExecutable.NameInfo nameInfos[] = se.getNameInfo(); 
+			SolverExecutable.NameInfo[] nameInfos = se.getNameInfo();
 			File files[] = new File[nameInfos.length];
 			for (int i = 0; i < nameInfos.length; ++i) {
 				SolverExecutable.NameInfo ni = nameInfos[i];
@@ -106,7 +106,7 @@ public static File[] getExes(SolverDescription sd) throws IOException {
 	}
 
 	/**
-	 * calls {@link #getExes(SolverConfig)} if solver requires executables,
+	 * calls {@link #getExes(SolverDescription)} if solver requires executables,
 	 * no-op otherwise
 	 */
 	public static void prepareSolverExecutable(SolverDescription solverDescription) throws IOException {
@@ -179,33 +179,29 @@ private static List<SolverDescription> matchByKisaoId(KisaoTerm candidate) {
 	}
 
 	private static SolverDescription attemptLastResortMatch(KisaoTerm last) {
-		switch(last.getId()) {
-		case "KISAO_0000433":
-			return SolverDescription.CVODE;
-		case "KISAO_0000094":
-			return SolverDescription.CVODE;
-		case "KISAO_0000284":
-			return SolverDescription.CVODE;
-		case "KISAO_0000319":
-			return SolverDescription.StochGibson;
-		case "KISAO_0000408":
-			return SolverDescription.IDA;
-		case "KISAO_0000056":
-			return SolverDescription.Smoldyn;
-		case "KISAO_0000352":
-			return SolverDescription.HybridMilstein;
-		case "KISAO_0000398":
-			return SolverDescription.SundialsPDE;
-		case "KISAO_0000369":
-			return SolverDescription.SundialsPDE;
-		case "KISAO_0000281":
-			return SolverDescription.AdamsMoulton;
-		case "KISAO_0000377":
-			return SolverDescription.RungeKuttaFehlberg;
-		default:
-			logger.error("Failed last resort match for descendant " + last.getId());
-			return null;
-		}
+        return switch (last.getId()) {
+            case "KISAO_0000056" -> SolverDescription.Smoldyn; // Livermore Solver
+            case "KISAO_0000094" /* Livermore Solver */, "KISAO_0000284" /* ? missing ? */,
+				 "KISAO_0000433" /* CVODE-like method */, "KISAO_0000694" /* ODE-solver */ ->
+                    SolverDescription.CVODE;
+            case "KISAO_0000281" /*multi-step method*/ ->
+                    SolverDescription.AdamsMoulton;
+            case "KISAO_0000319" /*Monte-carlo*/ ->
+                    SolverDescription.StochGibson;
+            case "KISAO_0000352" /* Hybrid-method */ ->
+                    SolverDescription.HybridMilstein;
+            case "KISAO_0000369" /* partial differential equation discretization method */,
+				 "KISAO_0000398" /* iterative method for solving a system of equations */ ->
+                    SolverDescription.SundialsPDE;
+            case "KISAO_0000377" /* one-step method */ ->
+                    SolverDescription.RungeKuttaFehlberg;
+            case "KISAO_0000408" /* Newton type method */ ->
+                    SolverDescription.IDA;
+            default -> {
+                logger.error("Failed last resort match for descendant {}", last.getId());
+                yield null;
+            }
+        };
 	}
 
 	private static boolean needsExactMatch(boolean cmdRequestedMatch){

vcell-core/src/main/java/org/vcell/sedml/SEDMLImporter.java

@@ -180,11 +180,11 @@ public List<BioModel> getBioModels() {
 				// try to find a match in the ontology tree
 				SolverDescription solverDescription = SolverUtilities.matchSolverWithKisaoId(kisaoID, this.exactMatchOnly);
 				if (solverDescription != null) {
-					logger.info("Task (id='"+selectedTask.getId()+"') is compatible, solver match found in ontology: '" + kisaoID + "' matched to " + solverDescription);
+                    logger.info("Task (id='{}') is compatible, solver match found in ontology: '{}' matched to {}", selectedTask.getId(), kisaoID, solverDescription);
 				} else {
 					// give it a try anyway with our deterministic default solver
 					solverDescription = SolverDescription.CombinedSundials;
-					logger.error("Task (id='"+selectedTask.getId()+")' is not compatible, no equivalent solver found in ontology for requested algorithm '"+kisaoID + "'; trying with deterministic default solver "+solverDescription);
+                    logger.error("Task (id='{})' is not compatible, no equivalent solver found in ontology for requested algorithm '{}'; trying with deterministic default solver {}", selectedTask.getId(), kisaoID, solverDescription);
 				}
 				// find out everything else we need about the application we're going to use,
 				// as some more info will be needed when we parse the sbml file
@@ -1010,7 +1010,7 @@ private void translateAlgorithmParams(SolverTaskDescription simTaskDesc, org.jli
 		String kisaoID = algorithm.getKisaoID();
 		ErrorTolerance errorTolerance = new ErrorTolerance();
 		List<AlgorithmParameter> sedmlAlgorithmParameters = algorithm.getListOfAlgorithmParameters();
-		for(AlgorithmParameter sedmlAlgorithmParameter : sedmlAlgorithmParameters) {
+		for (AlgorithmParameter sedmlAlgorithmParameter : sedmlAlgorithmParameters) {
 
 			String apKisaoID = sedmlAlgorithmParameter.getKisaoID();
 			String apValue = sedmlAlgorithmParameter.getValue();