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Fix: Integrate offline validation for SBase unit assignments #322

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Merged
draeger merged 9 commits into from
Sep 7, 2026
Merged

Fix: Integrate offline validation for SBase unit assignments #322

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909989d
Fix: Integrate offline validation for SBase unit assignments
dyrpsf Aug 21, 2026
30e796c
Refactor: Split unit validation to distinctly handle syntax (10311) a…
dyrpsf Aug 25, 2026
3b70cc7
Fix: Resolve error factory instantiation and add unit validation test…
dyrpsf Aug 26, 2026
25728ed
Fix: Resolve object state mutation bug and unused import in tests
dyrpsf Sep 3, 2026
75a2d0d
Fix: Remove stray if-statement breaking exception fallback control flow
dyrpsf Sep 4, 2026
9e4ee18
Fix: Align reference validation and error codes with offline constrai…
dyrpsf Sep 7, 2026
e031cb6
Refactor error creation and logging logic
draeger Sep 7, 2026
a4e922b
Fix: Defer reference validation for detached nodes and fix error bloc…
dyrpsf Sep 7, 2026
c5d98bc
Refactor error message handling for clarity
draeger Sep 7, 2026
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32 changes: 22 additions & 10 deletions core/src/org/sbml/jsbml/AbstractNamedSBaseWithUnit.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,8 @@
import org.apache.log4j.Logger;
import org.sbml.jsbml.Unit.Kind;
import org.sbml.jsbml.util.TreeNodeChangeEvent;
import org.sbml.jsbml.validator.SyntaxChecker;
import org.sbml.jsbml.validator.offline.factory.SBMLErrorFactory;

/**
* This simple implementation of the interfaces
Expand Down Expand Up @@ -283,7 +285,7 @@ public void setUnits(Kind unitKind) {
@Override
public void setUnits(String units) {
if ((units != null) && (units.trim().length() == 0)) {
units = null; // If we pass the empty String or null, the value is reset.
units = null;
}

String oldUnits = unitsID;
Expand All @@ -292,24 +294,34 @@ public void setUnits(String units) {
unitsID = null;
} else {
units = units.trim();
unitsID = units;

boolean illegalArgument = false;
// Use the generic SId syntax checker with the current level and version
boolean isSyntaxValid = SyntaxChecker.isValidId(units, getLevel(), getVersion());
boolean isReferenceValid = isSyntaxValid && Unit.isValidUnit(getModel(), units);

if (!Unit.isValidUnit(getModel(), units)) {
illegalArgument = true; // TODO - make use of the offline validation once attributes validation is in place.
}
if (illegalArgument) {
if (!isSyntaxValid || !isReferenceValid) {
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if (!isReadingInProgress()) {
throw new IllegalArgumentException(MessageFormat.format(
JSBML.ILLEGAL_UNIT_EXCEPTION_MSG, units));
SBMLDocument doc = getSBMLDocument();
if (doc != null && doc.getErrorLog() != null) {
int errorCode = !isSyntaxValid ? 10311 : 10313;

doc.getErrorLog().add(SBMLErrorFactory.createError(
errorCode,
getLevel(),
getVersion()
));
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} else {
throw new IllegalArgumentException(MessageFormat.format(
JSBML.ILLEGAL_UNIT_EXCEPTION_MSG, units));
}
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} else {
logger.info(MessageFormat.format(JSBML.ILLEGAL_UNIT_EXCEPTION_MSG, units));
}
}
unitsID = units;
}

if (oldUnits != unitsID) {
if (oldUnits != null ? !oldUnits.equals(unitsID) : unitsID != null) {
firePropertyChange(TreeNodeChangeEvent.units, oldUnits, unitsID);
}
}
Expand Down