Merge pull request #1345 from virtualcell/sedml-path-or-uri

allow URI or Path refs in SedML, add MathML xor support
virtualcell · Aug 30, 2024 · ec25940 · ec25940
2 parents e5878e8 + fc58fb2
commit ec25940
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Showing 10 changed files with 73 additions and 53 deletions.
diff --git a/vcell-core/src/main/java/org/jlibsedml/Model.java b/vcell-core/src/main/java/org/jlibsedml/Model.java
@@ -8,6 +8,8 @@
 
 import org.jlibsedml.modelsupport.SUPPORTED_LANGUAGE;
 
+import static org.jlibsedml.execution.ArchiveModelResolver.SPACE_URI_ESCAPE_SEQUENCE;
+
 /**
  * Encapsulates a SED-ML Model element. Note that this object is not the
  * computational model itself, but holds information about the model within
@@ -19,7 +21,7 @@
 public final class Model extends AbstractIdentifiableElement {
 
 	private String language = null;
-	private String source = null; 
+	private final String source_path_or_URI_string;
 
 	/**
 	 * Sets the model  language that this element refers to.  This should ideally be a URN, 
@@ -45,21 +47,21 @@ public void setLanguage(String language) {
 	 *            This should ideally be a URN, which may already be defined in
 	 *            {@link SUPPORTED_LANGUAGE}. If no language describes this
 	 *            model, the argument may be <code>null</code>.
-	 * @param source
-	 *            A mandatory URI to the model source.
+	 * @param source_path_or_URI_string
+	 *            A mandatory URI or local path to the model source.
 	 * @throws IllegalArgumentException
 	 *             if any argument except <code>name</code> is null or an empty
 	 *             string.
 	 */
-	public Model(String id, String name, String language, String source) {
+	public Model(String id, String name, String language, String source_path_or_URI_string) {
 		super(id, name);
 		if (SEDMLElementFactory.getInstance().isStrictCreation()) {
-			Assert.checkNoNullArgs(source);
-			Assert.stringsNotEmpty(source);
+			Assert.checkNoNullArgs(source_path_or_URI_string);
+			Assert.stringsNotEmpty(source_path_or_URI_string);
 		}
 
 		this.language = language;
-		this.source = source;
+		this.source_path_or_URI_string = source_path_or_URI_string;
 	}
 
 	/**
@@ -76,7 +78,7 @@ public Model(String id, String name, String language, String source) {
 	 *             if any argument is null
 	 */
 	public Model(Model toCopy, String id) {
-		this(id, toCopy.getName(), toCopy.getLanguage(), toCopy.getSource());
+		this(id, toCopy.getName(), toCopy.getLanguage(), toCopy.getSourcePathOrURIString());
 	}
 
 	/**
@@ -139,9 +141,8 @@ public String getLanguage() {
 	 * 
 	 * @return A <code>String</code>
 	 */
-	public String getSource() {
-
-		return source;
+	public String getSourcePathOrURIString() {
+		return this.source_path_or_URI_string;
 	}
 
 	/**
@@ -231,9 +232,7 @@ public String getSource() {
 	 *             cannot be converted to a URI.
 	 */
 	public URI getSourceURI() throws URISyntaxException {
-
-		return new URI(source);
-
+		return new URI(this.source_path_or_URI_string.replace(" ", SPACE_URI_ESCAPE_SEQUENCE));
 	}
 
 	/**
@@ -269,31 +268,21 @@ public boolean isSourceURIRelative() {
 	 */
 	public boolean isSourceValidURI() {
 		try {
-			new URI(getSource());
+			getSourceURI();
 		} catch (URISyntaxException e) {
 			return false;
 		}
 		return true;
 	}
 
-	/**
-	 * 
-	 * @param srcString
-	 *            A URI of where this model can be retrieved.
-	 *            Attention: if the string is a model reference, it should be prefixed with "#"
-	 */
-	public void setSource(String srcString) {
-		source = srcString;
-	}
-
 	/**
 	 * @see Object#toString()
 	 */
 	public String toString() {
 		return new StringBuffer().append("Model [").append("id=").append(
 				getId()).append(", ").append("name=").append(getName())
 				.append(", ").append("language=").append(language).append(
-				", ").append("src=").append(source).append("]").toString();
+				", ").append("src=").append(this.source_path_or_URI_string).append("]").toString();
 	}
 
 	@Override
@@ -311,6 +300,5 @@ public  boolean accept(SEDMLVisitor visitor){
                 }
             }
             return true;
-
     }
 }
diff --git a/vcell-core/src/main/java/org/jlibsedml/SEDMLWriter.java b/vcell-core/src/main/java/org/jlibsedml/SEDMLWriter.java
@@ -119,7 +119,7 @@ Element getXML(Model sedmlModel) {
             node.setAttribute(SEDMLTags.MODEL_ATTR_LANGUAGE, s); // insert
                                                                  // 'type'
                                                                  // attribute
-        s = sedmlModel.getSource();
+        s = sedmlModel.getSourcePathOrURIString();
         if (s != null)
             node.setAttribute(SEDMLTags.MODEL_ATTR_SOURCE, s); // insert
                                                                // 'source'

diff --git a/vcell-core/src/main/java/org/jlibsedml/SedML.java b/vcell-core/src/main/java/org/jlibsedml/SedML.java
@@ -733,7 +733,7 @@ public final boolean addIdentifiersAsDataGenerators(AbstractTask task,
     public List<Model> getBaseModels() {
         Set<Model> set = new HashSet<Model>();
         for (Model m : getModels()) {
-            if (getModelWithId(m.getSource()) == null) {
+            if (getModelWithId(m.getSourcePathOrURIString()) == null) {
                 set.add(m);
             }
         }

diff --git a/vcell-core/src/main/java/org/jlibsedml/execution/ArchiveModelResolver.java b/vcell-core/src/main/java/org/jlibsedml/execution/ArchiveModelResolver.java
@@ -10,14 +10,16 @@
 import org.jlibsedml.IModelContent;
 
 public class ArchiveModelResolver implements IModelResolver {
+    public final static String SPACE_URI_ESCAPE_SEQUENCE = "%20";
+
   private ArchiveComponents ac;
   private String sedmlPath = "";
     public ArchiveModelResolver(ArchiveComponents ac) {
         this.ac=ac;
     }
     public String getModelXMLFor(URI modelURI) {
         List<IModelContent> children = ac.getModelFiles();
-    	String modelStr = modelURI.toString();
+    	String modelStr = modelURI.toString().replace(SPACE_URI_ESCAPE_SEQUENCE, " ");
     	// try direct match first
         for (IModelContent imc: children) {
             String modelElementStr = imc.getName();

diff --git a/vcell-core/src/main/java/org/jlibsedml/execution/ModelResolver.java b/vcell-core/src/main/java/org/jlibsedml/execution/ModelResolver.java
@@ -121,7 +121,7 @@ public String getModelString(Model m) {
                 srcURI = sedml.getModelWithId(modelRef).getSourceURI();
                 // If we need to recurse to the next level:
                 modelRef = sedml.getModelWithId(modelRef.startsWith("#") ?
-                        modelRef.substring(1): modelRef).getSource();
+                        modelRef.substring(1): modelRef).getSourcePathOrURIString();
             } while (srcURI != null && srcURI.toString().contains("#"));
         } catch (URISyntaxException e) {
             logger.error(MODEL_SRC_NOT_VALID_URI+": "+e.getMessage(), e);
@@ -187,7 +187,7 @@ final String getBaseModel(URI modelSrc) {
     }
 
     void getModelModificationTree(Model m, List<String> modelRefs2) {
-        String modelSrcRef = m.getSource();
+        String modelSrcRef = m.getSourcePathOrURIString();
 
         modelRefs2.add(m.getId());
         if (sedml.getModelWithId(modelSrcRef) != null) {

diff --git a/vcell-core/src/main/java/org/jlibsedml/validation/ModelCyclesDetector.java b/vcell-core/src/main/java/org/jlibsedml/validation/ModelCyclesDetector.java
@@ -39,7 +39,7 @@ public List<SedMLError> validate() throws XMLException {
         List<SedMLError> errs = new ArrayList<SedMLError>();
         List<Model> models = sedml.getModels();
         for (Model model : models) {
-            String src = model.getSource();
+            String src = model.getSourcePathOrURIString();
             String id = model.getId();
             Set<String> ids = new HashSet<String>();
             ids.add(id);
@@ -50,12 +50,12 @@ public List<SedMLError> validate() throws XMLException {
                     errs.add(new SedMLError(line,
                             "Cycles detected in source references for model "
                                     + newID + " and "
-                                    + sedml.getModelWithId(newID).getSource(),
+                                    + sedml.getModelWithId(newID).getSourcePathOrURIString(),
                             ERROR_SEVERITY.ERROR));
                     return errs;
                 } else {
                     ids.add(newID);
-                    src = sedml.getModelWithId(src).getSource();
+                    src = sedml.getModelWithId(src).getSourcePathOrURIString();
                 }
             }
         }

diff --git a/vcell-core/src/main/java/org/jlibsedml/validation/URIValidator.java b/vcell-core/src/main/java/org/jlibsedml/validation/URIValidator.java
@@ -30,9 +30,9 @@ public List<SedMLError> validate()  {
 		for (Model model: models){
 
 				try {
-					URI uri = new URI(model.getSource());
+					URI uri = model.getSourceURI();
 				} catch (URISyntaxException e) {
-					errs.add(new SedMLError(0,"ErrMessageRoot[" + model.getSource() +"]", ERROR_SEVERITY.WARNING ));
+					errs.add(new SedMLError(0,"ErrMessageRoot[" + model.getSourcePathOrURIString() +"]", ERROR_SEVERITY.WARNING ));
 				}
 
 

diff --git a/vcell-core/src/main/java/org/vcell/sedml/SEDMLImporter.java b/vcell-core/src/main/java/org/vcell/sedml/SEDMLImporter.java
@@ -807,7 +807,7 @@ private Map<String, BioModel> createBioModels(List<Model> models) throws SEDMLIm
 
 		// Group models by type for processing order
 		for (Model model : models){
-			if (model.getSource().startsWith("#")){
+			if (model.getSourcePathOrURIString().startsWith("#")){
 				advancedModelsList.get(ADVANCED_MODEL_TYPES.REFERENCING_MODELS.ordinal()).add(model);
 			} else if (!model.getListOfChanges().isEmpty()) {
 				advancedModelsList.get(ADVANCED_MODEL_TYPES.CHANGED_MODELS.ordinal()).add(model);
@@ -866,13 +866,13 @@ private Map<String, BioModel> createBioModels(List<Model> models) throws SEDMLIm
 	}
 
 	private String getReferenceId(Model model){
-		String referenceId = model.getSource();
+		String referenceId = model.getSourcePathOrURIString();
 		return referenceId.startsWith("#") ? referenceId.substring(1) : referenceId;
 	}
 
 	private BioModel getModelReference(String referenceId, Model model, Map<String, BioModel> idToBiomodelMap) throws SEDMLImportException {
 		// Were we given a reference ID? We need to check if the parent was processed yet.
-		if (referenceId != null && !model.getSource().equals(referenceId)){
+		if (referenceId != null && !model.getSourcePathOrURIString().equals(referenceId)){
 			boolean canTranslate;
 			BioModel parentBiomodel = idToBiomodelMap.get(referenceId);
 

diff --git a/vcell-math/src/main/java/cbit/vcell/parser/ExpressionMathMLParser.java b/vcell-math/src/main/java/cbit/vcell/parser/ExpressionMathMLParser.java
@@ -141,6 +141,27 @@ private SimpleNode getRootNode(Element nodeMathML, String timeSymbol) throws Exp
 			vcellOperationNode = new ASTAndNode();
 		} else if (operation.getName().equals(MathMLTags.OR)){
 			vcellOperationNode = new ASTOrNode();
+		} else if (operation.getName().equals(MathMLTags.XOR)){
+			// XOR(A,B) --> OR(AND(A,NOT(B)),AND(NOT(A),B))
+			// NOT(B)
+			ASTNotNode notNode = new ASTNotNode();
+			notNode.jjtAddChild(getRootNode((Element)children.get(2), timeSymbol));
+			// AND(A,NOT(B))
+			ASTAndNode andNode1 = new ASTAndNode();
+			andNode1.jjtAddChild(getRootNode((Element)children.get(1), timeSymbol));
+			andNode1.jjtAddChild(notNode);
+			// NOT(A)
+			ASTNotNode notNode2 = new ASTNotNode();
+			notNode2.jjtAddChild(getRootNode((Element)children.get(1), timeSymbol));
+			// AND(NOT(A),B)
+			ASTAndNode andNode2 = new ASTAndNode();
+			andNode2.jjtAddChild(notNode2);
+			andNode2.jjtAddChild(getRootNode((Element)children.get(2), timeSymbol));
+			// OR(AND(A,NOT(B)),AND(NOT(A),B))
+			ASTOrNode orNode = new ASTOrNode();
+			orNode.jjtAddChild(andNode1);
+			orNode.jjtAddChild(andNode2);
+			return orNode;
 		} else if (operation.getName().equals(MathMLTags.NOT)){
 			vcellOperationNode = new ASTNotNode();
 		} else if (operation.getName().equals(MathMLTags.PLUS)){

diff --git a/.../java/cbit/vcell/parser/MathMLTester.java → ...st/java/cbit/vcell/parser/MathMLTest.java b/.../java/cbit/vcell/parser/MathMLTester.java → ...st/java/cbit/vcell/parser/MathMLTest.java
@@ -14,6 +14,7 @@
 import org.jmathml.ASTNode;
 import org.jmathml.MathMLReader;
 import org.junit.jupiter.api.Tag;
+import org.junit.jupiter.api.Test;
 import org.junit.jupiter.params.ParameterizedTest;
 import org.junit.jupiter.params.provider.MethodSource;
 
@@ -25,13 +26,7 @@
 import static org.junit.jupiter.api.Assertions.fail;
 
 @Tag("Fast")
-public class MathMLTester {
-
-	private Expression expression;
-
-	public MathMLTester(Expression exp) {
-		this.expression = exp;
-	}
+public class MathMLTest {
 
 	public static Collection<Expression> testCases() throws ExpressionException {
 		int depthOfExpressionTree = 2;
@@ -72,9 +67,23 @@ public static Collection<Expression> testCases() throws ExpressionException {
 		return expressions;
 	}
 
+	@Test
+	public void testMathMLParsing_XOR() throws IOException, ExpressionException {
+		// XOR is supported as an SBML operator for importing only
+		Expression exp = new Expression("(x && !y) || (!x && y)");
+		String temp_mathMLStr_with_and = ExpressionMathMLPrinter.getMathML(new Expression("x && y"), true,
+				ExpressionMathMLPrinter.MathType.REAL, ExpressionMathMLPrinter.Dialect.SBML_SUBSET);
+		String mathMLStr_with_xor = temp_mathMLStr_with_and.replace("and", "xor");
+		Expression xor_from_MathML = new ExpressionMathMLParser(null).fromMathML(mathMLStr_with_xor, "t");
+		boolean equiv = ExpressionUtils.functionallyEquivalent(exp, xor_from_MathML, true);
+		String msg = "not equivalent: origExp='"+exp.infix()+"', expMathML='"+xor_from_MathML.infix()+"'";
+		assertTrue(equiv, msg);
+	}
+
+
 	@ParameterizedTest
 	@MethodSource("testCases")
-	public void testMathML_SBMLSubset() throws IOException, ExpressionException {
+	public void testMathML_SBMLSubset(Expression expression) throws IOException, ExpressionException {
 		if (expression.infix().contains("atan")){
 			return;
 		}
@@ -88,7 +97,7 @@ public void testMathML_SBMLSubset() throws IOException, ExpressionException {
 
 	@ParameterizedTest
 	@MethodSource("testCases")
-	public void test_vcell_mathml_jMathML_mathml_vcell() throws IOException, ExpressionException {
+	public void test_vcell_mathml_jMathML_mathml_vcell(Expression expression) throws IOException, ExpressionException {
 		List<String> tokensToAvoid = Arrays.asList(
 				"atan",
 				"sech", "csch", "coth",
@@ -119,7 +128,7 @@ public void test_vcell_mathml_jMathML_mathml_vcell() throws IOException, Express
 
 	@ParameterizedTest
 	@MethodSource("testCases")
-	public void testMathML_GeneralSubset() throws IOException, ExpressionException {
+	public void testMathML_GeneralSubset(Expression expression) throws IOException, ExpressionException {
 		if (expression.infix().contains("atan")){
 			return;
 		}
@@ -133,14 +142,14 @@ public void testMathML_GeneralSubset() throws IOException, ExpressionException {
 
 	@ParameterizedTest
 	@MethodSource("testCases")
-	public void testFlatten() throws ExpressionException {
+	public void testFlatten(Expression expression) throws ExpressionException {
 		Expression expFlattened = expression.flatten();
         assertTrue(functionallyEquivalent(expression, expFlattened, false), "not equivalent: origExp='" + expression.infix() + "', expFlattened='" + expFlattened.infix() + "'");
 	}
 
 	@ParameterizedTest
 	@MethodSource("testCases")
-	public void testJSCLParseInfix() throws ExpressionException, ParseException {
+	public void testJSCLParseInfix(Expression expression) throws ExpressionException, ParseException {
 		List<String> tokensToAvoid = Arrays.asList(
 				"<",">","=","&","|","!"
 		);
@@ -168,7 +177,7 @@ public void testJSCLParseInfix() throws ExpressionException, ParseException {
 
 	@ParameterizedTest
 	@MethodSource("testCases")
-	public void testJSCLSimplifyInfix() {
+	public void testJSCLSimplifyInfix(Expression expression) {
 		Expression expSimplified = null;
 		try {
 			expSimplified = expression.simplifyJSCL(20000, true);