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Re: Jim and Logan Logging level fixes
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@CodeByDrescher
CodeByDrescher committed Jan 23, 2025
1 parent 8e5fdc5 commit 9cb0f33
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Showing 11 changed files with 21 additions and 19 deletions.
4 changes: 3 additions & 1 deletion vcell-cli/src/main/java/org/vcell/cli/biosimulation/BiosimulationsCommand.java
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Expand Up @@ -82,7 +82,9 @@ public static int executeVCellBiosimulationsMode(File inFile, File outDir, boole
}
LoggerContext config = (LoggerContext)(LogManager.getContext(false));
config.getConfiguration().getLoggerConfig(LogManager.getLogger("org.vcell").getName()).setLevel(logLevel);
config.getConfiguration().getLoggerConfig(LogManager.getLogger("cbit").getName()).setLevel(logLevel);

config.getConfiguration().getLoggerConfig(LogManager.getLogger("cbit").getName()).setLevel(!bDebug ? Level.WARN : logLevel);
config.getConfiguration().getLoggerConfig(LogManager.getLogger("org.jlibsedml").getName()).setLevel(!bDebug ? Level.WARN : logLevel);
config.updateLoggers();

logger.debug("Biosimulations mode requested");
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8 changes: 4 additions & 4 deletions vcell-core/src/main/java/cbit/vcell/geometry/surface/GeometrySurfaceUtils.java
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Expand Up @@ -85,7 +85,7 @@ public static GeometricRegion[] getUpdatedGeometricRegions(GeometrySurfaceDescri
cbit.vcell.geometry.RegionImage.RegionInfo regionInfos[] = regionImage.getRegionInfos();
for(int i = 0; i < regionInfos.length; i++){
cbit.vcell.geometry.RegionImage.RegionInfo regionInfo = regionInfos[i];
if (lg.isDebugEnabled()) lg.info(regionInfo);
lg.info(regionInfo);
cbit.vcell.geometry.SubVolume subVolume = geometrySpec.getSubVolume(regionInfo.getPixelValue());
String name = subVolume.getName() + regionInfo.getRegionIndex();
int numPixels = regionInfo.getNumPixels();
Expand Down Expand Up @@ -214,15 +214,15 @@ public static GeometricRegion[] getUpdatedGeometricRegions(GeometrySurfaceDescri
}

size -= sizeOfPixel * 0.125 * numOctantsToRemove;
if(lg.isDebugEnabled()) lg.info("size={}", size);
lg.debug("size={}", size);

break;
}
}

VolumeGeometricRegion volumeRegion = new VolumeGeometricRegion(name, size, volumeUnit, subVolume, regionInfo.getRegionIndex());
regionList.add(volumeRegion);
if(lg.isDebugEnabled()) lg.info("added volumeRegion({})", volumeRegion.getName());
lg.info("added volumeRegion({})", volumeRegion.getName());

}
//
Expand Down Expand Up @@ -266,7 +266,7 @@ public static GeometricRegion[] getUpdatedGeometricRegions(GeometrySurfaceDescri
}
surfaceRegion.addAdjacentGeometricRegion(interiorVolumeRegion);
interiorVolumeRegion.addAdjacentGeometricRegion(surfaceRegion);
if(lg.isDebugEnabled()) lg.info("added surfaceRegion({})", surfaceRegion.getName());
lg.info("added surfaceRegion({})", surfaceRegion.getName());

}

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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/cbit/vcell/mapping/DiffEquMathMapping.java
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Expand Up @@ -1454,7 +1454,7 @@ private void refreshMathDescription() throws MappingException, MatrixException,
for(int i = 0; i < mappedSMs.length; i++){
if(mappedSMs[i] instanceof FeatureMapping){
if(mappedFM != null){
if (lg.isDebugEnabled()) lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
lg.info("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping) mappedSMs[i];
}
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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/cbit/vcell/mapping/LangevinMathMapping.java
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Expand Up @@ -415,7 +415,7 @@ protected void refreshMathDescription() throws MappingException, MatrixException
for (int i = 0; i < mappedSMs.length; i++) {
if (mappedSMs[i] instanceof FeatureMapping){
if (mappedFM!=null){
if (lg.isDebugEnabled()) lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
lg.info("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping)mappedSMs[i];
}
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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/cbit/vcell/mapping/ParticleMathMapping.java
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Expand Up @@ -487,7 +487,7 @@ private void refreshMathDescription() throws MappingException, MatrixException,
for (int i = 0; i < mappedSMs.length; i++) {
if (mappedSMs[i] instanceof FeatureMapping){
if (mappedFM!=null){
if (lg.isDebugEnabled()) lg.warn("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
lg.info("WARNING:::: MathMapping.refreshMathDescription() ... assigning boundary condition types not unique");
}
mappedFM = (FeatureMapping)mappedSMs[i];
}
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4 changes: 3 additions & 1 deletion vcell-core/src/main/java/cbit/vcell/solver/SolverUtilities.java
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Expand Up @@ -164,8 +164,10 @@ private static List<SolverDescription> matchByKisaoId(KisaoTerm candidate) {
for (SolverDescription sd : SolverDescription.values()) {
if (sd.getKisao().contains(":") || sd.getKisao().contains("_")) {
logger.trace(sd.getKisao());
} else if ("KISAO".equals(sd.getKisao())){
logger.info("Skipping not-yet-created KiSAO term");
} else {
if (logger.isDebugEnabled()) logger.warn("`{}` is bad KiSAO formating, skipping", sd.getKisao());
logger.warn("`{}` is bad KiSAO formating, skipping", sd.getKisao());
continue;
}
String s1 = candidate.getId();
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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/cbit/vcell/xml/XmlReader.java
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Expand Up @@ -4562,7 +4562,7 @@ public Model getModel(Element param) throws XmlParseException{
if(element != null){
getRbmModelContainer(element, newmodel);
} else {
if (lg.isDebugEnabled()) lg.info("RbmModelContainer is missing.");
lg.info("RbmModelContainer is missing.");
}

//Add SpeciesContexts
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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/org/jlibsedml/SEDMLReader.java
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Expand Up @@ -246,7 +246,7 @@ Algorithm getAlgorithm(Element algorithmElement) {
if (eChild.getName().equals(SEDMLTags.ALGORITHM_PARAMETER_LIST)) {
addAlgorithmParameters(alg, eChild);
} else {
if (log.isDebugEnabled()) log.warn("Unexpected " + eChild);
log.warn("Unexpected " + eChild);
}
}
return alg;
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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/org/jlibsedml/validation/SchemaValidatorImpl.java
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Expand Up @@ -90,7 +90,7 @@ private String getSchema(String xmlAsString) throws JDOMException,
return SEDML_L1_V2_SCHEMA;
} else {
// probably level 3, but trying anyway to interpret with level 2
if (log.isDebugEnabled()) log.warn("SED-ML version level not supported, import may fail");
log.info("WARNING: SED-ML version level not supported, import may fail");
return SEDML_L1_V3_SCHEMA;
// throw new IllegalArgumentException(
// "Invalid level/version combingation - must be 1-1 or 1-2 but was "
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2 changes: 1 addition & 1 deletion vcell-core/src/main/java/org/jlibsedml/validation/SchematronValidator.java
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Expand Up @@ -116,7 +116,7 @@ private String getSchematronXSL() {
} else if (sedml.isL1V2()) {
return "validatorl1v2.xsl";
} else {
if (lg.isDebugEnabled()) lg.warn("Unsupported version, import may fail");
lg.warn("Unsupported version, import may fail");
return "validatorl1v2.xsl";
// throw new UnsupportedOperationException(MessageFormat.format(
// "Invalid level and version - {0}-{1}", sedml.getLevel(),
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10 changes: 4 additions & 6 deletions vcell-core/src/main/java/org/vcell/sedml/SEDMLImporter.java
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Expand Up @@ -195,7 +195,7 @@ public List<BioModel> getBioModels() {
// try to find a match in the ontology tree
SolverDescription solverDescription = SolverUtilities.matchSolverWithKisaoId(kisaoID, this.exactMatchOnly);
if (solverDescription != null) {
if (logger.isDebugEnabled()) logger.info("Task (id='{}') is compatible, solver match found in ontology: '{}' matched to {}", selectedTask.getId(), kisaoID, 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;
Expand Down Expand Up @@ -441,12 +441,10 @@ private List<BioModel> mergeBioModels(List<BioModel> bioModels) {

BioModel bm0 = bioModels.get(0);
for (int i = 1; i < bioModels.size(); i++) {
if (logger.isDebugEnabled())
logger.info("--------------------\ncomparing model from `{}`\n with model from `{}`\n--------------------",
bioModels.get(i), bm0);
logger.debug("--------------------\ncomparing model from `{}`\n with model from `{}`\n--------------------", bioModels.get(i), bm0);
RelationVisitor rvNotStrict = new ModelRelationVisitor(false);
boolean equivalent = bioModels.get(i).getModel().relate(bm0.getModel(),rvNotStrict);
if (logger.isDebugEnabled()) logger.info("Equivalent => {}", equivalent);
logger.debug("Equivalent => {}", equivalent);
if (!equivalent) return bioModels;
}
// all have matchable model, try to merge by pooling SimContexts
Expand Down Expand Up @@ -1087,7 +1085,7 @@ private void translateAlgorithmParams(SolverTaskDescription simTaskDesc, org.jli
NonspatialStochHybridOptions nonspatialSHO = simTaskDesc.getStochHybridOpt();
nonspatialSHO.setSDETolerance(Double.parseDouble(apValue));
} else {
logger.error("Algorithm parameter with kisao id '" + apKisaoID + "' not supported at this time, skipping.");
logger.info("WARNING: Algorithm parameter with kisao id '" + apKisaoID + "' not supported at this time, skipping.");
}
}
simTaskDesc.setErrorTolerance(errorTolerance);
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