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Commit a8c8f63b authored by cfrainay's avatar cfrainay
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I don't know what I'm doing

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coverage/pom.xml
+ 4
− 1
View file @ a8c8f63b
......@@ -54,6 +54,9 @@
<properties>
<maven.deploy.skip>true</maven.deploy.skip>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
......@@ -93,7 +96,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.5</version>
<version>0.8.11</version>
<executions>
<execution>
<id>report-aggregate</id>
......
met4j-chemUtils/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -46,7 +46,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-core/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -40,7 +40,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
+ 3
− 2
View file @ a8c8f63b
......@@ -37,7 +37,8 @@
package fr.inrae.toulouse.metexplore.met4j_core.biodata;
import lombok.Getter;
import javax.annotation.Nonnull;
import lombok.NonNull;
import java.util.Objects;
/**
......@@ -61,7 +62,7 @@ public abstract class BioParticipant extends BioEntity {
* @param quantity number of units of physicalEntity
*/
public BioParticipant(String id, @Nonnull BioPhysicalEntity physicalEntity, Double quantity) {
public BioParticipant(String id, @NonNull BioPhysicalEntity physicalEntity, Double quantity) {
super(id);
this.physicalEntity=physicalEntity;
if(Double.isNaN(quantity) || Double.isInfinite(quantity) || quantity <= 0)
......
met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
+ 2
− 2
View file @ a8c8f63b
......@@ -36,8 +36,8 @@
package fr.inrae.toulouse.metexplore.met4j_core.biodata;
import lombok.Getter;
import lombok.NonNull;
import javax.annotation.Nonnull;
import java.text.DecimalFormat;
import java.text.DecimalFormatSymbols;
import java.text.NumberFormat;
......@@ -61,7 +61,7 @@ public class BioReactant extends BioParticipant {
* @param stoichiometry stoichiometric coefficient
* @param location a {@link fr.inrae.toulouse.metexplore.met4j_core.biodata.BioCompartment}
*/
protected BioReactant(@Nonnull BioMetabolite metabolite, Double stoichiometry, @Nonnull BioCompartment location) {
protected BioReactant(@NonNull BioMetabolite metabolite, Double stoichiometry, @NonNull BioCompartment location) {
super(metabolite.getId()+"__"+stoichiometry+"__"+location.getId(), metabolite, stoichiometry);
this.location = location;
}
......
met4j-graph/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -59,7 +59,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/EdgeMerger.java
+ 5
− 7
View file @ a8c8f63b
......@@ -35,15 +35,13 @@
*/
package fr.inrae.toulouse.metexplore.met4j_graph.computation.transform;
import java.util.*;
import java.util.stream.Collectors;
import com.google.common.primitives.Doubles;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
import fr.inrae.toulouse.metexplore.met4j_graph.core.BioGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.Edge;
import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MergedGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.parallel.MetaEdge;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
import java.util.*;
/**
* Class used to merges parallel edges.
......@@ -222,7 +220,7 @@ public class EdgeMerger {
return new Comparator<E>() {
@Override
public int compare(E e1, E e2) {
return Doubles.compare(
return Double.compare(
g.getEdgeWeight(e2),
g.getEdgeWeight(e1)
);
......@@ -233,7 +231,7 @@ public class EdgeMerger {
return new Comparator<E>() {
@Override
public int compare(E e1, E e2) {
return Doubles.compare(
return Double.compare(
g.getEdgeWeight(e1),
g.getEdgeWeight(e2)
);
......
met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestBioPathUtils.java
+ 7
− 19
View file @ a8c8f63b
......@@ -35,35 +35,23 @@
*/
package fr.inrae.toulouse.metexplore.met4j_graph;
import static org.junit.Assert.*;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Set;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.ShortestPath;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.UnweightedPolicy;
import fr.inrae.toulouse.metexplore.met4j_graph.core.BioPath;
import fr.inrae.toulouse.metexplore.met4j_graph.core.BioPathUtils;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.CompoundGraph;
import fr.inrae.toulouse.metexplore.met4j_graph.core.compound.ReactionEdge;
import fr.inrae.toulouse.metexplore.met4j_graph.io.ExportGraph;
import fr.inrae.toulouse.metexplore.met4j_mathUtils.matrix.BioMatrix;
import fr.inrae.toulouse.metexplore.met4j_mathUtils.matrix.EjmlMatrix;
import fr.inrae.toulouse.metexplore.met4j_graph.computation.connect.weighting.UnweightedPolicy;
import org.apache.bcel.generic.BREAKPOINT;
import org.junit.BeforeClass;
import org.junit.Before;
import org.junit.Test;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.ExpectedException;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import java.util.*;
import static org.junit.Assert.assertEquals;
/**
* test class for {@link BioPathUtils} methods
......
met4j-io/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -64,7 +64,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributesTest.java
+ 1
− 4
View file @ a8c8f63b
......@@ -38,16 +38,13 @@ package fr.inrae.toulouse.metexplore.met4j_io.annotations;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioProtein;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.Notes;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.attributes.SbmlAnnotation;
import org.apache.xalan.trace.GenerateEvent;
import org.junit.Rule;
import org.junit.Test;
import org.junit.rules.ExpectedException;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioProtein;
import java.util.HashSet;
import java.util.Set;
......
met4j-mapping/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -39,7 +39,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-mathUtils/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -39,7 +39,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-reconstruction/pom.xml
+ 1
− 1
View file @ a8c8f63b
......@@ -75,7 +75,7 @@
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
met4j-toolbox/pom.xml
+ 7
− 2
View file @ a8c8f63b
......@@ -70,6 +70,11 @@
<artifactId>hibernate-validator</artifactId>
<version>8.0.1.Final</version>
</dependency>
<dependency>
<groupId>org.apache.maven</groupId>
<artifactId>maven-model</artifactId>
<version>4.0.0-alpha-8</version>
</dependency>
</dependencies>
<description>Bundle of all met4j modules and api</description>
......@@ -121,14 +126,14 @@
<dependency>
<groupId>com.github.edwgiz</groupId>
<artifactId>maven-shade-plugin.log4j2-cachefile-transformer</artifactId>
<version>2.6.1</version>
<version>2.6.2</version>
</dependency>
</dependencies>
</plugin>
<plugin>
<groupId>org.jacoco</groupId>
<artifactId>jacoco-maven-plugin</artifactId>
<version>0.8.7</version>
<version>0.8.11</version>
<executions>
<!-- to avoid bugs in some situations -->
<execution>
......
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