diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 02a4bab5a92ad8b583b68039ca5323b33bc007fd..dc25365bd5359ab440829cdf58041b39655c9ca9 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -48,8 +48,10 @@ cache:
- .m2/repository/
build:
- image: maven:3.6-adoptopenjdk-14
+ image: eclipse-temurin:17-jdk-alpine
stage: build
+ before_script:
+ - apk update && apk add maven
script:
- mvn $MAVEN_OPTS compile
- TRUEVERSION=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)
@@ -81,8 +83,10 @@ build:
- stable
test:
- image: maven:3.6-adoptopenjdk-14
+ image: eclipse-temurin:17-jdk-alpine
stage: test
+ before_script:
+ - apk update && apk add maven
script:
- find . -name "*.class" -exec touch {} \+
- mvn $MAVEN_OPTS clean test
@@ -93,8 +97,10 @@ test:
package:
- image: maven:3.6-adoptopenjdk-14
+ image: eclipse-temurin:17-jdk-alpine
stage: package
+ before_script:
+ - apk update && apk add maven
script:
- mvn $MAVEN_OPTS clean install -DskipTests=true
- cd met4j-toolbox
@@ -128,17 +134,20 @@ deployJar:
- stable
deploySnapshot:
- image: maven:3.6-adoptopenjdk-14
+ image: eclipse-temurin:17-jdk-alpine
stage: deploy
+ before_script:
+ - apk update && apk add maven
script:
- mvn $MAVEN_CLI_OPTS deploy -Dmaven.test.skip=true
only:
- develop
deployCentral:
- image: maven:3.6-adoptopenjdk-14
+ image: eclipse-temurin:17-jdk-alpine
stage: deploy
before_script:
+ - apk update && apk add maven
- 'which ssh-agent || ( apt-get update -qy && apt-get install openssh-client -qqy )'
- 'command -v ssh-agent >/dev/null || ( apt-get update -y && apt-get install openssh-client -y )'
- eval $(ssh-agent -s)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 77f7c26765ceab1cc8dd676a3ff09fc71fd6bec8..aa863107b456c4cd5bd6a8414ca7b52f3ed0239e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## Next Release
+
+
+
+
## 1.5.0
diff --git a/Dockerfile b/Dockerfile
index 3d409a37e69226b1e2286c1d6ca0f4354ca058f3..3c8fd528354b26618c6a1b52e6b02da44f11f204 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,4 +1,6 @@
-FROM adoptopenjdk:11-jdk-hotspot
+FROM eclipse-temurin:17-jdk-alpine
+
+RUN apk update && apk add maven
RUN mkdir -p /opt/bin
diff --git a/coverage/pom.xml b/coverage/pom.xml
index 1e6d76466cc3f298811809e5fac679277716591f..2a539ca26414262d46be2f89b3c6a701326d2efb 100644
--- a/coverage/pom.xml
+++ b/coverage/pom.xml
@@ -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>
diff --git a/met4j-chemUtils/pom.xml b/met4j-chemUtils/pom.xml
index 404dac28b29f1390367e859f6abe2f663b20febb..842b6fdf42820fe3cb1b0ef39b2eab69792ed27d 100644
--- a/met4j-chemUtils/pom.xml
+++ b/met4j-chemUtils/pom.xml
@@ -10,8 +10,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<artifactId>met4j-chemUtils</artifactId>
@@ -24,7 +24,7 @@
<dependency>
<groupId>org.openscience.cdk</groupId>
<artifactId>cdk-bundle</artifactId>
- <version>2.6</version>
+ <version>2.9</version>
</dependency>
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -35,7 +35,7 @@
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
- <version>3.0.0</version>
+ <version>5.7.0</version>
<scope>test</scope>
</dependency>
</dependencies>
@@ -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>
diff --git a/met4j-core/pom.xml b/met4j-core/pom.xml
index 898ae91a34304b4d14a097b7346db4baaed86334..6edc9ba4e9082d42c91df7985a7c2b2e39d14988 100644
--- a/met4j-core/pom.xml
+++ b/met4j-core/pom.xml
@@ -22,8 +22,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
@@ -31,7 +31,7 @@
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
- <version>3.0</version>
+ <version>3.13.0</version>
</dependency>
</dependencies>
@@ -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>
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
index f9ca3e445769f87c7f5bd5e7c0a887b8ee942f97..9c4cd7b34ad163cdb936a376482ca206a5b5fd83 100755
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioParticipant.java
@@ -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)
diff --git a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
index 81e5236a48106efdac0d698b48e03e0c12d0c2ee..5fe8d9d078ac0255b555c080075f9ed78e0e1260 100644
--- a/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
+++ b/met4j-core/src/main/java/fr/inrae/toulouse/metexplore/met4j_core/biodata/BioReactant.java
@@ -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;
}
diff --git a/met4j-graph/pom.xml b/met4j-graph/pom.xml
index 15bca6259e9eee74db5065a708fa1fd16aa9ebd8..790c6a52e6727cac5f3206932c3fd59aa9664170 100644
--- a/met4j-graph/pom.xml
+++ b/met4j-graph/pom.xml
@@ -16,21 +16,21 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-core</artifactId>
- <version>1.5.0</version>
+ <version>1.5.2</version>
<!--memo: once 1.5.2 is available, remove quick-fix in graph.connect.ShortestPath$getShortestPathsUnionList-->
</dependency>
<dependency>
<groupId>org.jgrapht</groupId>
<artifactId>jgrapht-io</artifactId>
- <version>1.5.0</version>
+ <version>1.5.2</version>
</dependency>
<dependency>
<groupId>fr.inrae.toulouse.metexplore</groupId>
@@ -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>
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
index 76381b6b9632ffe245725614f2db361057d26918..17a32a8b2639ffb1d07e0969ed968bc79f2f7d73 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/connect/ShortestPath.java
@@ -310,13 +310,8 @@ public class ShortestPath<V extends BioEntity,E extends Edge<V>, G extends BioGr
for(V start : startNodes){
for(V end : targetNodes){
if(start!=end){
- try{
- GraphPath<V, E> p = paths.getPath(start,end);
- if(p!=null) outputPaths.add(new BioPath<>(p));
- }catch(NullPointerException e){
- //Handle JGraphT error which will be fixed in the next release (1.5.2).
- //See https://github.com/jgrapht/jgrapht/issues/1053
- }
+ GraphPath<V, E> p = paths.getPath(start,end);
+ if(p!=null) outputPaths.add(new BioPath<>(p));
}
}
}
diff --git a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/EdgeMerger.java b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/EdgeMerger.java
index c3a7b08729205727aa84e18a8c755f5b14767fb2..73a4976abf9f007f708bf42c7e12653fbce95235 100644
--- a/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/EdgeMerger.java
+++ b/met4j-graph/src/main/java/fr/inrae/toulouse/metexplore/met4j_graph/computation/transform/EdgeMerger.java
@@ -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)
);
diff --git a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestBioPathUtils.java b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestBioPathUtils.java
index c8756056fa03bd0de3921d1604197e38ec89059a..6cc16894987cb0c0460ba1c92ccf63674ccf3fcf 100644
--- a/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestBioPathUtils.java
+++ b/met4j-graph/src/test/java/fr/inrae/toulouse/metexplore/met4j_graph/TestBioPathUtils.java
@@ -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
diff --git a/met4j-io/pom.xml b/met4j-io/pom.xml
index 18d2878abbb6c147fb3d5b70e46c5aaf0711c185..36c255838f1f0be517944e0e049caaacf0dc0671 100644
--- a/met4j-io/pom.xml
+++ b/met4j-io/pom.xml
@@ -17,8 +17,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
@@ -35,13 +35,13 @@
<dependency>
<groupId>xerces</groupId>
<artifactId>xercesImpl</artifactId>
- <version>2.8.0</version>
+ <version>2.12.2</version>
</dependency>
<!-- https://mvnrepository.com/artifact/xom/xom -->
<dependency>
<groupId>xom</groupId>
<artifactId>xom</artifactId>
- <version>1.2.5</version>
+ <version>1.3.9</version>
</dependency>
<dependency>
<groupId>com.sun.jersey</groupId>
@@ -51,12 +51,12 @@
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
- <version>31.0.1-jre</version>
+ <version>32.1.3-jre</version>
</dependency>
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
- <version>3.0.0</version>
+ <version>5.7.0</version>
</dependency>
</dependencies>
<build>
@@ -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>
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java
index 92f0a6ee047e2186390cf2619b2aa8df87463b47..74a3dd6095fe043932803ec27a5581e751cdd2ba 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/AnnotationParser.java
@@ -36,10 +36,11 @@
package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
-
-
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
+import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.dataTags.AdditionalDataTag;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.tags.ReaderSBML1Compatible;
import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.tags.ReaderSBML2Compatible;
@@ -49,13 +50,10 @@ import org.sbml.jsbml.CVTerm;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.UniqueNamedSBase;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioReaction;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.collection.BioCollection;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioEntity;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioMetabolite;
-import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
-import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.*;
+import static fr.inrae.toulouse.metexplore.met4j_core.utils.StringUtils.isVoid;
/**
* This class is used to parse the MIRIAM annotation of every SBML element.
@@ -88,11 +86,11 @@ public class AnnotationParser implements PackageParser, AdditionalDataTag, Reade
/**
* The default annotation pattern:
* <ul>
- * <li>http://identifiers.org/([^/]+)/(.*)
+ * <li>http://identifiers.org/([^/]+)[/:](.*)
* </ul>
* The first parenthesis group is
*/
- public static final String defaultAnnotationPattern = "https?://identifiers.org/([^/]+)/(.*)";
+ public static final String defaultAnnotationPattern = "https?://identifiers.org/([^/]+)[/:](.*)";
/**
* Constructor
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java
index a49fe3db5fb94058c6ad67098c69c54d7d0775b0..44d998c38aad1e7d5c6649413fd0501a21250df9 100644
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java
@@ -91,6 +91,11 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
*/
public FBCModelPlugin fbcModel;
+ /**
+ * Indicates if the genes are parsed or not
+ */
+ public Boolean parseGenes = true;
+
/** {@inheritDoc} */
@Override
public String getAssociatedPackageName() {
@@ -103,6 +108,17 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
return model.isPackageURIEnabled(PackageNamespace);
}
+
+ public FBCParser(Boolean parseGenes) {
+
+ this.parseGenes = parseGenes;
+ }
+
+ public FBCParser() {
+
+ this.parseGenes = true;
+ }
+
/**
* {@inheritDoc}
*
@@ -129,7 +145,10 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
this.setStrictFromFbcModel();
this.parseParameters();
- this.parseListOfGeneProducts();
+
+ if(parseGenes) {
+ this.parseListOfGeneProducts();
+ }
try {
this.parseFluxReactions();
} catch (GeneSetException | Met4jSbmlReaderException e) {
@@ -239,7 +258,7 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
GeneAssociation geneAssociation = new GeneAssociation();
// System.err.println(rxn.getId());
- if (rxnPlugin.isSetGeneProductAssociation()) {
+ if (parseGenes && rxnPlugin.isSetGeneProductAssociation()) {
geneAssociation = this.computeGeneAssocations(rxnPlugin.getGeneProductAssociation().getAssociation());
}
// System.err.println("out of recursion");
diff --git a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/utils/StringUtils.java b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/utils/StringUtils.java
index 06fe91e25ac75a58e08cf02eb5cc656511ff8b97..71d4bd8dbeeed10115feeabbddd1d15bf34f0f56 100755
--- a/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/utils/StringUtils.java
+++ b/met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/utils/StringUtils.java
@@ -245,7 +245,7 @@ public class StringUtils {
//
// codes.add(new Integer(str));
- int[] codesInt = new int []{new Integer(str)};
+ int[] codesInt = new int []{Integer.valueOf(str)};
String specialCharacter = new String(codesInt,0, codesInt.length);
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributesTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributesTest.java
index 0ea64e6e695c48745d1bcb15232fdc7cee9f087e..a30c7a7969d5a81fe12d922373447be86d9a6cdf 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributesTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/annotations/GenericAttributesTest.java
@@ -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;
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlReaderTest.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlReaderTest.java
index 5681dc1c849bdb24b9fadc15fbf0e40b4c8a1c72..c9142d8b88be3624befd09a5191fe04b781a14ae 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlReaderTest.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlReaderTest.java
@@ -37,11 +37,15 @@
package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader;
import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.FBCParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
import org.junit.Test;
import org.sbml.jsbml.SBMLDocument;
import javax.xml.stream.XMLStreamException;
import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
import static org.junit.Assert.*;
import static org.mockito.Mockito.doReturn;
@@ -65,10 +69,33 @@ public class JsbmlReaderTest {
assertEquals(3, network.getReactionsView().size());
+ assertEquals(2, network.getGenesView().size());
+
// Other tests are done on JsbmlToBioNetwork
}
+ @Test
+ public void readWithoutGenes() throws IOException, XMLStreamException, Met4jSbmlReaderException {
+
+ JsbmlReader reader = spy(new JsbmlReader("test"));
+
+ SbmlDocMock docMockGenerator = new SbmlDocMock();
+ SBMLDocument doc = docMockGenerator.doc;
+
+ doReturn(doc).when(reader).sbmlRead();
+
+ BioNetwork network = reader.read(new ArrayList<PackageParser>(Arrays.asList(new FBCParser(false))));
+
+ assertNotNull(network);
+
+ assertEquals(3, network.getReactionsView().size());
+
+ assertEquals(0, network.getGenesView().size());
+
+
+ }
+
@Test
public void readWithoutNotes() throws IOException, XMLStreamException, Met4jSbmlReaderException {
JsbmlReader reader = spy(new JsbmlReader("test"));
diff --git a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java
index 9054ca48250285baa15fec6370b430cd545d24b0..f60f41a35be1e2be275271c654068603c7831023 100644
--- a/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java
+++ b/met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java
@@ -35,9 +35,13 @@
*/
package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader;
+import fr.inrae.toulouse.metexplore.met4j_io.utils.StringUtils;
import org.sbml.jsbml.*;
+import org.sbml.jsbml.ext.fbc.*;
import javax.xml.stream.XMLStreamException;
+import java.util.ArrayList;
+import java.util.List;
public class SbmlDocMock {
@@ -51,7 +55,7 @@ public class SbmlDocMock {
public SbmlDocMock() {
- doc = new SBMLDocument(3, 1);
+ doc = new SBMLDocument(3, 2);
model = doc.createModel();
@@ -83,6 +87,21 @@ public class SbmlDocMock {
m1.setInitialAmount(2.0);
m2.setInitialAmount(3.0);
+ // Create genes
+ FBCModelPlugin fbcModel = (FBCModelPlugin) model.getPlugin("http://www.sbml.org/sbml/level3/version1/fbc/version2");
+ GeneProduct gene1 = fbcModel.createGeneProduct();
+ gene1.setId("g1");
+ gene1.setName("g1");
+ gene1.setLabel("g1");
+
+ fbcModel.addGeneProduct(gene1);
+
+ GeneProduct gene2 = fbcModel.createGeneProduct();
+ gene2.setId("g2");
+ gene2.setName("g2");
+ gene2.setLabel("g2");
+
+ fbcModel.addGeneProduct(gene2);
r1 = model.createReaction("r1");
r1.setName("name1");
@@ -90,8 +109,22 @@ public class SbmlDocMock {
r1.setSBOTerm("SBO:0000167");
+ GeneProductRef geneRef1 = new GeneProductRef();
+ geneRef1.setGeneProduct(StringUtils.convertToSID("g1"));
+
+ FBCReactionPlugin rxnPlugin = (FBCReactionPlugin) r1.getPlugin("fbc");
+ GeneProductAssociation GPA = rxnPlugin.createGeneProductAssociation();
+ GPA.setAssociation(geneRef1);
+
r2 = model.createReaction("r2");
+ GeneProductRef geneRef2 = new GeneProductRef();
+ geneRef2.setGeneProduct(StringUtils.convertToSID("g2"));
+
+ FBCReactionPlugin rxn2Plugin = (FBCReactionPlugin) r2.getPlugin("fbc");
+ GeneProductAssociation GPA2 = rxnPlugin.createGeneProductAssociation();
+ GPA.setAssociation(geneRef2);
+
SpeciesReference m1Ref = new SpeciesReference(m1);
m1Ref.setStoichiometry(2.0);
diff --git a/met4j-mapping/pom.xml b/met4j-mapping/pom.xml
index ed55e7a08b7086e1a5da3861e460316d49eeb086..937aef96dd70633eb3f079e7674bb720caff3a37 100644
--- a/met4j-mapping/pom.xml
+++ b/met4j-mapping/pom.xml
@@ -10,8 +10,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<artifactId>met4j-mapping</artifactId>
@@ -24,12 +24,12 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.12</version>
+ <version>4.13.2</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-text</artifactId>
- <version>1.8</version>
+ <version>1.11.0</version>
<scope>compile</scope>
</dependency>
</dependencies>
@@ -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>
diff --git a/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/enrichment/PathwayEnrichment.java b/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/enrichment/PathwayEnrichment.java
index 24ff3608d27890046fc0aaac282585dda9314381..2a182a773fd075ad94ebd4c96c24df751adb47b7 100644
--- a/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/enrichment/PathwayEnrichment.java
+++ b/met4j-mapping/src/main/java/fr/inrae/toulouse/metexplore/met4j_mapping/enrichment/PathwayEnrichment.java
@@ -246,7 +246,7 @@ public class PathwayEnrichment {
for(BioPathway p : pvalues.keySet()){
double pval = pvalues.get(p);
double adjPval = pval*pvalues.size();
- adjPvalues.put(p, new Double(adjPval));
+ adjPvalues.put(p, Double.valueOf(adjPval));
}
return adjPvalues;
}
@@ -265,7 +265,7 @@ public class PathwayEnrichment {
BioPathway p = orderedPaths.get(k);
double pval = pvalues.get(p);
double adjPval = pval*pvalues.size()/(k+1);
- adjPvalues.put(p, new Double(adjPval));
+ adjPvalues.put(p, Double.valueOf(adjPval));
}
return adjPvalues;
}
@@ -284,7 +284,7 @@ public class PathwayEnrichment {
BioPathway p = orderedPaths.get(k);
double pval = pvalues.get(p);
double adjPval = pval*(pvalues.size()+1-(k+1));
- adjPvalues.put(p, new Double(adjPval));
+ adjPvalues.put(p, Double.valueOf(adjPval));
}
return adjPvalues;
}
diff --git a/met4j-mathUtils/pom.xml b/met4j-mathUtils/pom.xml
index a89d93b74486436e6ade399bea00165c8bd70fc6..e5e68a0542aefd654049f22e89cc0030df6b5dcf 100644
--- a/met4j-mathUtils/pom.xml
+++ b/met4j-mathUtils/pom.xml
@@ -17,8 +17,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
@@ -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>
diff --git a/met4j-mathUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_mathUtils/similarity/SimilarityComputor.java b/met4j-mathUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_mathUtils/similarity/SimilarityComputor.java
index aa9f9635caeeb15a85680e21069b4aef85f6c151..ba2d9653ceecf98a748ce164f82446765abfd4a2 100644
--- a/met4j-mathUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_mathUtils/similarity/SimilarityComputor.java
+++ b/met4j-mathUtils/src/main/java/fr/inrae/toulouse/metexplore/met4j_mathUtils/similarity/SimilarityComputor.java
@@ -67,9 +67,9 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet intersect = (BitSet) fingerprint1.clone();
intersect.and(fingerprint2);
- double a = new Integer(fingerprint1.cardinality()).doubleValue();
- double b = new Integer(fingerprint2.cardinality()).doubleValue();
- double c = new Integer(intersect.cardinality()).doubleValue();
+ double a = Integer.valueOf(fingerprint1.cardinality()).doubleValue();
+ double b = Integer.valueOf(fingerprint2.cardinality()).doubleValue();
+ double c = Integer.valueOf(intersect.cardinality()).doubleValue();
double dist = c/(a+b-c);
return dist;
}
@@ -89,9 +89,9 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet intersect = (BitSet) fingerprint1.clone();
intersect.and(fingerprint2);
- double a = new Integer(fingerprint1.cardinality()).doubleValue();
- double b = new Integer(fingerprint2.cardinality()).doubleValue();
- double c = new Integer(intersect.cardinality()).doubleValue();
+ double a = Integer.valueOf(fingerprint1.cardinality()).doubleValue();
+ double b = Integer.valueOf(fingerprint2.cardinality()).doubleValue();
+ double c = Integer.valueOf(intersect.cardinality()).doubleValue();
double dist = (2*c)/(a+b);
return dist;
}
@@ -111,9 +111,9 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet intersect = (BitSet) fingerprint1.clone();
intersect.and(fingerprint2);
- double a = new Integer(fingerprint1.cardinality()).doubleValue();
- double b = new Integer(fingerprint2.cardinality()).doubleValue();
- double c = new Integer(intersect.cardinality()).doubleValue();
+ double a = Integer.valueOf(fingerprint1.cardinality()).doubleValue();
+ double b = Integer.valueOf(fingerprint2.cardinality()).doubleValue();
+ double c = Integer.valueOf(intersect.cardinality()).doubleValue();
double dist = c/(Math.sqrt(a*b));
return dist;
}
@@ -133,9 +133,9 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet intersect = (BitSet) fingerprint1.clone();
intersect.and(fingerprint2);
- double a = new Integer(fingerprint1.cardinality()).doubleValue();
- double b = new Integer(fingerprint2.cardinality()).doubleValue();
- double c = new Integer(intersect.cardinality()).doubleValue();
+ double a = Integer.valueOf(fingerprint1.cardinality()).doubleValue();
+ double b = Integer.valueOf(fingerprint2.cardinality()).doubleValue();
+ double c = Integer.valueOf(intersect.cardinality()).doubleValue();
double dist = a+b-(2*c);
return dist;
}
@@ -154,9 +154,9 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet intersect = (BitSet) fingerprint1.clone();
intersect.and(fingerprint2);
- double a = new Integer(fingerprint1.cardinality()).doubleValue();
- double b = new Integer(fingerprint2.cardinality()).doubleValue();
- double c = new Integer(intersect.cardinality()).doubleValue();
+ double a = Integer.valueOf(fingerprint1.cardinality()).doubleValue();
+ double b = Integer.valueOf(fingerprint2.cardinality()).doubleValue();
+ double c = Integer.valueOf(intersect.cardinality()).doubleValue();
double dist = Math.sqrt(a+b-(2*c));
return dist;
}
@@ -177,9 +177,9 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet intersect = (BitSet) fingerprint1.clone();
intersect.and(fingerprint2);
- double a = new Integer(fingerprint1.cardinality()).doubleValue();
- double b = new Integer(fingerprint2.cardinality()).doubleValue();
- double c = new Integer(intersect.cardinality()).doubleValue();
+ double a = Integer.valueOf(fingerprint1.cardinality()).doubleValue();
+ double b = Integer.valueOf(fingerprint2.cardinality()).doubleValue();
+ double c = Integer.valueOf(intersect.cardinality()).doubleValue();
double dist = (a+b-(2*c))/(a+b-c);
return dist;
}
@@ -198,7 +198,7 @@ public class SimilarityComputor {
if(fingerprint1.size()!=fingerprint2.size()) throw new IllegalArgumentException("bitSets must have the same size");
BitSet xor = (BitSet) fingerprint1.clone();
xor.xor(fingerprint2);
- return new Integer(xor.cardinality()).doubleValue();
+ return Integer.valueOf(xor.cardinality()).doubleValue();
}
diff --git a/met4j-reconstruction/pom.xml b/met4j-reconstruction/pom.xml
index d1e7675faab53276a0226ea7e0d2e252a9bac77b..4fc1807001d32338f67b6499902053271c1fa5ab 100644
--- a/met4j-reconstruction/pom.xml
+++ b/met4j-reconstruction/pom.xml
@@ -52,8 +52,8 @@
<url>http://maven.apache.org</url>
<properties>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
</properties>
@@ -66,7 +66,7 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.12</version>
+ <version>4.13.2</version>
</dependency>
</dependencies>
@@ -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>
diff --git a/met4j-toolbox/pom.xml b/met4j-toolbox/pom.xml
index 04f64ec42501a60492228dbe2aa7365fc613dbd6..17f3ac7eb60c68ded9d4696925e81f4d3ff656e0 100644
--- a/met4j-toolbox/pom.xml
+++ b/met4j-toolbox/pom.xml
@@ -14,8 +14,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
</properties>
<dependencies>
@@ -68,7 +68,12 @@
<dependency>
<groupId>org.hibernate.validator</groupId>
<artifactId>hibernate-validator</artifactId>
- <version>6.0.17.Final</version>
+ <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>
@@ -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>
diff --git a/met4j.singularity b/met4j.singularity
index 5fc314cb88eb96c2f2ec32c3ca8aca65d7f8892b..f2d740b47b5cdf9c0d50700673c67aa5b27514ef 100644
--- a/met4j.singularity
+++ b/met4j.singularity
@@ -1,5 +1,5 @@
Bootstrap: docker
-From: adoptopenjdk:11-jdk-hotspot
+From: eclipse-temurin:17-jdk-alpine
%runscript
if [ $# -lt 1 ]
@@ -24,7 +24,7 @@ mvn package
Maintainer Ludovic.Cottret@inrae.fr
%post
-
+ apk update && apk add maven
cd /usr/bin && ln -s /opt/bin/met4j.sh
%environment
diff --git a/pom.xml b/pom.xml
index b4f87a2b985f2d6f1b17f28db9ce6ff84d0a4998..59f27808b63a8710fc0ca352d93579da3967aa98 100644
--- a/pom.xml
+++ b/pom.xml
@@ -64,8 +64,8 @@
<properties>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
- <maven.compiler.source>11</maven.compiler.source>
- <maven.compiler.target>11</maven.compiler.target>
+ <maven.compiler.source>17</maven.compiler.source>
+ <maven.compiler.target>17</maven.compiler.target>
<project.scm.id>forgemia</project.scm.id>
</properties>
@@ -87,8 +87,8 @@
<artifactId>maven-compiler-plugin</artifactId>
<version>3.8.1</version>
<configuration>
- <source>11</source>
- <target>11</target>
+ <source>17</source>
+ <target>17</target>
</configuration>
</plugin>
<plugin>
@@ -105,7 +105,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
- <version>2.19.1</version>
+ <version>3.0.0-M5</version>
</plugin>
</plugins>
</build>
@@ -184,13 +184,13 @@
<dependency>
<groupId>org.codehaus.mojo</groupId>
<artifactId>build-helper-maven-plugin</artifactId>
- <version>3.0.0</version>
+ <version>3.4.0</version>
<type>maven-plugin</type>
</dependency>
<dependency>
<groupId>org.projectlombok</groupId>
<artifactId>lombok</artifactId>
- <version>1.18.22</version>
+ <version>1.18.30</version>
<scope>provided</scope>
</dependency>
<dependency>