From e35b244e78cca7af2b81df6c65b3772b70ededc3 Mon Sep 17 00:00:00 2001
From: jcschaff <schaff.jim@gmail.com>
Date: Tue, 24 Sep 2024 03:42:32 -0400
Subject: [PATCH] roll back math generation abort if units don't match, too
 agressive

---
 .../vcell/mapping/AbstractMathMapping.java    | 57 ++++++-------------
 1 file changed, 17 insertions(+), 40 deletions(-)

diff --git a/vcell-core/src/main/java/cbit/vcell/mapping/AbstractMathMapping.java b/vcell-core/src/main/java/cbit/vcell/mapping/AbstractMathMapping.java
index 7ed22aabe1..0c40980c5e 100644
--- a/vcell-core/src/main/java/cbit/vcell/mapping/AbstractMathMapping.java
+++ b/vcell-core/src/main/java/cbit/vcell/mapping/AbstractMathMapping.java
@@ -1,18 +1,6 @@
 package cbit.vcell.mapping;
 
-import java.beans.PropertyVetoException;
-import java.util.*;
-import java.util.stream.Collectors;
-
 import cbit.vcell.biomodel.ModelUnitConverter;
-import cbit.vcell.math.*;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.vcell.util.*;
-import org.vcell.util.Issue.IssueCategory;
-import org.vcell.util.Issue.IssueSource;
-import org.vcell.util.IssueContext.ContextType;
-
 import cbit.vcell.client.constants.GuiConstants;
 import cbit.vcell.geometry.CompartmentSubVolume;
 import cbit.vcell.geometry.GeometryClass;
@@ -26,43 +14,32 @@
 import cbit.vcell.mapping.potential.MembraneElectricalDevice;
 import cbit.vcell.mapping.potential.PotentialMapping;
 import cbit.vcell.mapping.spatial.SpatialObject.QuantityComponent;
+import cbit.vcell.math.*;
 import cbit.vcell.math.Variable.Domain;
 import cbit.vcell.matrix.MatrixException;
 import cbit.vcell.matrix.RationalExp;
-import cbit.vcell.model.BioNameScope;
-import cbit.vcell.model.ExpressionContainer;
-import cbit.vcell.model.Kinetics;
+import cbit.vcell.model.*;
 import cbit.vcell.model.Kinetics.KineticsParameter;
-import cbit.vcell.model.Membrane;
 import cbit.vcell.model.Membrane.MembraneVoltage;
-import cbit.vcell.model.Model;
 import cbit.vcell.model.Model.ModelFunction;
 import cbit.vcell.model.Model.ModelParameter;
-import cbit.vcell.model.ModelException;
-import cbit.vcell.model.ModelProcess;
-import cbit.vcell.model.ModelQuantity;
-import cbit.vcell.model.Parameter;
-import cbit.vcell.model.ProxyParameter;
-import cbit.vcell.model.RbmObservable;
-import cbit.vcell.model.ReactionRule;
-import cbit.vcell.model.ReactionStep;
-import cbit.vcell.model.SpeciesContext;
-import cbit.vcell.model.Structure;
 import cbit.vcell.model.Structure.StructureSize;
 import cbit.vcell.parser.ASTFuncNode.FunctionType;
-import cbit.vcell.parser.Expression;
+import cbit.vcell.parser.*;
 import cbit.vcell.parser.Expression.FunctionFilter;
-import cbit.vcell.parser.ExpressionBindingException;
-import cbit.vcell.parser.ExpressionException;
-import cbit.vcell.parser.FunctionInvocation;
-import cbit.vcell.parser.NameScope;
-import cbit.vcell.parser.ScopedSymbolTable;
-import cbit.vcell.parser.SymbolTableEntry;
-import cbit.vcell.parser.VCUnitEvaluator;
 import cbit.vcell.solver.Simulation;
 import cbit.vcell.units.VCUnitDefinition;
 import cbit.vcell.units.VCUnitException;
-import ucar.units_vcell.UnitException;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.vcell.util.*;
+import org.vcell.util.Issue.IssueCategory;
+import org.vcell.util.Issue.IssueSource;
+import org.vcell.util.IssueContext.ContextType;
+
+import java.beans.PropertyVetoException;
+import java.util.*;
+import java.util.stream.Collectors;
 
 public abstract class AbstractMathMapping implements ScopedSymbolTable, UnitFactorProvider, IssueSource, MathMapping {
 
@@ -1761,12 +1738,12 @@ final ProbabilityParameter addProbabilityParameter(String name, Expression expre
             VCUnitEvaluator unitEvaluator = new VCUnitEvaluator(simContext.getModel().getUnitSystem());
             VCUnitDefinition expUnit = unitEvaluator.getUnitDefinition(expression);
             if (unitDefinition != null && !unitDefinition.equals(expUnit)){
-                logger.error("expected unit=" + unitDefinition.getSymbol() + ", found=" + expUnit.getSymbol());
-                throw new VCUnitException("expected unit=" + unitDefinition.getSymbol() + ", found=" + expUnit.getSymbol());
+                logger.warn("expected unit=" + unitDefinition.getSymbol() + ", found=" + expUnit.getSymbol());
+//                throw new VCUnitException("expected unit=" + unitDefinition.getSymbol() + ", found=" + expUnit.getSymbol());
             }
         } catch (ExpressionException e){
-            logger.error("error evaluating units for expression '" + expression + ": " + e.getMessage(), e);
-            throw new VCUnitException("error evaluating units for expression '" + expression + ": " + e.getMessage());
+            logger.warn("error evaluating units for expression '" + expression + ": " + e.getMessage(), e);
+//            throw new VCUnitException("error evaluating units for expression '" + expression + ": " + e.getMessage());
         }
         MathMappingParameter previousParameter = getMathMappingParameter(name);
         if(previousParameter != null){