SBML has one flat namespace; VCell separates physiology from application. An SBML global + * parameter becomes a Model parameter, while a species' initial concentration is a + * {@code SpeciesContextSpec} parameter under the SimulationContext. The two name scopes are + * unrelated roots -- {@code ModelNameScope.getParent()} and + * {@code SimulationContextNameScope.getParent()} both return null and neither is the other's + * peer -- so a Model parameter cannot name an initial concentration and + * {@code getRelativeScopePrefix} yields {@link AbstractNameScope#UNRESOLVED_PREFIX}. That is why + * 31 curated BioModels failed to import with 'UNRESOLVED.initConc' (issue #803). + * + *
Rather than dropping the dependency, this inverts it. Given SBML {@code beta = c1/(N1*s4)} + * where {@code s4} is a species: + * + *
+ * before: s4.initConc = 250000 beta = c1/(N1 * UNRESOLVED.initConc) [broken] + * after: s4_initConc = 250000 (global) s4.initConc = s4_initConc + * beta = c1/(N1 * s4_initConc) [exact] + *+ * + *
Nothing is lost. The relationship stays symbolic, so scanning {@code s4_initConc} moves the + * initial condition and {@code beta} together -- which is what the SBML meant. Everything stays a + * global parameter, which matters because global parameters already round-trip through + * SBMLExporter, whereas {@code SimulationContextParameter} does not (#1984). + * + *
The reference is written as a plain name, deliberately. The species' initial + * condition resolves it through {@code SimulationContext.getLocalEntry()}, which falls through to + * {@code getModel().getLocalEntry()}; writing it as {@code new Expression(ste, namescope)} would + * ask the scope machinery for a prefix and get {@code UNRESOLVED.} straight back. + * + *
Compartment sizes are deliberately NOT handled the same way. A {@code StructureMapping} size
+ * must remain a constant -- {@code StructureSizeSolver}, {@code GeometryContext} and
+ * {@code SBMLExporter} all call {@code evaluateConstant()} on it -- so hoisting a size into a
+ * symbol would break the size solver and export. Those models keep failing, with an explanation.
+ */
+ private static Expression hoistInitialConditionToGlobalParameter(SymbolTableEntry ste){
+ if(!(ste instanceof SpeciesContextSpecParameter)){
+ return null; // compartment sizes and anything else: see the note above
+ }
+ SpeciesContextSpecParameter initialConditionParam = (SpeciesContextSpecParameter) ste;
+ SpeciesContext speciesContext = initialConditionParam.getSpeciesContext();
+ SpeciesContextSpec speciesContextSpec = initialConditionParam.getSpeciesContextSpec();
+ if(speciesContext == null || speciesContextSpec == null || speciesContextSpec.getSimulationContext() == null){
+ return null;
+ }
+ Model vcModel = speciesContextSpec.getSimulationContext().getModel();
+ if(vcModel == null){
+ return null;
+ }
+ Expression initialConditionExpr = initialConditionParam.getExpression();
+ if(initialConditionExpr == null){
+ return null;
+ }
+ try {
+ // Already hoisted for an earlier reference: reuse it, so N parameters depending on the
+ // same species produce one global parameter rather than N.
+ if(initialConditionExpr.getSymbols() != null && initialConditionExpr.getSymbols().length == 1){
+ ModelParameter existing = vcModel.getModelParameter(initialConditionExpr.getSymbols()[0]);
+ if(existing != null && existing.getName().startsWith(speciesContext.getName() + HOISTED_INITIAL_SUFFIX)){
+ return new Expression(existing.getName());
+ }
+ }
+ String name = uniqueGlobalParameterName(vcModel, speciesContext.getName() + HOISTED_INITIAL_SUFFIX);
+ ModelParameter hoisted = vcModel.new ModelParameter(name, new Expression(initialConditionExpr),
+ Model.ROLE_UserDefined, initialConditionParam.getUnitDefinition());
+ hoisted.setDescription("initial condition of species '" + speciesContext.getName()
+ + "', made a global parameter so it can be referenced from the physiology (issue #803)");
+ vcModel.addModelParameter(hoisted);
+ // plain name on purpose -- see the note above
+ initialConditionParam.setExpression(new Expression(name));
+ logger.info("hoisted initial condition of '" + speciesContext.getName() + "' to global parameter '"
+ + name + "' so it can be named from the physiology");
+ return new Expression(name);
+ } catch(Exception e){
+ logger.error("could not hoist initial condition of '" + speciesContext.getName() + "': " + e.getMessage(), e);
+ return null;
+ }
+ }
+
+ private static final String HOISTED_INITIAL_SUFFIX = "_initConc";
+
+ private static String uniqueGlobalParameterName(Model vcModel, String preferred){
+ String candidate = TokenMangler.fixTokenStrict(preferred);
+ int suffix = 0;
+ while(vcModel.getModelParameter(candidate) != null || vcModel.getLocalEntry(candidate) != null){
+ candidate = TokenMangler.fixTokenStrict(preferred) + "_" + suffix++;
+ }
+ return candidate;
+ }
+
private static SBase findSBase(org.sbml.jsbml.Model sbmlModel, String sbmlSid){
if(sbmlSid == null){
throw new RuntimeException("sbmlSid cannot be null");
diff --git a/vcell-core/src/test/java/org/vcell/sbml/BMDB_SBMLImportTest.java b/vcell-core/src/test/java/org/vcell/sbml/BMDB_SBMLImportTest.java
index ea0b31935b..7d76b0460a 100644
--- a/vcell-core/src/test/java/org/vcell/sbml/BMDB_SBMLImportTest.java
+++ b/vcell-core/src/test/java/org/vcell/sbml/BMDB_SBMLImportTest.java
@@ -175,7 +175,9 @@ public static Map