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Refactor: Migrate from JUL to SLF4J API in SBMLinterpreter #110

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Refactor: Migrate from JUL to SLF4J API in SBMLinterpreter #110

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5 changes: 5 additions & 0 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -518,6 +518,11 @@
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>1.7.32</version>
</dependency>
</dependencies>


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13 changes: 5 additions & 8 deletions src/main/java/org/simulator/sbml/SBMLinterpreter.java
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Expand Up @@ -29,8 +29,8 @@
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import fern.network.AmountManager;
import org.apache.commons.math.ode.DerivativeException;
Expand Down Expand Up @@ -69,7 +69,7 @@ public class SBMLinterpreter extends EquationSystem {
/**
* A {@link Logger}.
*/
private static final transient Logger logger = Logger.getLogger(SBMLinterpreter.class.getName());
private static final transient Logger logger = LoggerFactory.getLogger(SBMLinterpreter.class);

/**
* Generated serial version UID
Expand Down Expand Up @@ -810,8 +810,7 @@ public void setParameters(double[] params) {
law.getMath()
.updateVariables(); // make sure references to local parameter values are reflected in the ASTNode
} else {
logger.log(Level.FINE,
"Cannot set local parameters for reaction {0} because of missing kinetic law.",
logger.debug("Cannot set local parameters for reaction {} because of missing kinetic law.",
model.getReaction(reactionNum).getId());
}
}
Expand All @@ -820,9 +819,7 @@ public void setParameters(double[] params) {
init();
} catch (Exception exc) {
// This can never happen
logger
.log(Level.WARNING, "Could not re-initialize the model with the new parameter values.",
exc);
logger.warn("Could not re-initialize the model with the new parameter values.", exc);
}
} else {
int nCompPlusSpec = model.getCompartmentCount() + model.getSpeciesCount();
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