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Commit 8e4031af authored by Piotr Gawron's avatar Piotr Gawron
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Merge branch '1540-export-error' into 'devel_16.0.x' 

Resolve "MINERVANET - Error Report 326"

See merge request !1335
parents 6122571d b09b2cc4
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CHANGELOG
View file @ 8e4031af
minerva (16.0.0~beta.2) stable; urgency=medium
* Bug fix: problem with export map with submaps fixed (#1540)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 3 Sep 2021 11:00:00 +0200
minerva (16.0.0~beta.1) stable; urgency=medium
* Backward incompatibility: layout parameter in minerva url is not supported
anymore
......
CellDesigner-plugin/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
......@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
......
annotation/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
......@@ -18,7 +18,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
......@@ -34,13 +34,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2 -->
......
commons/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
......
converter-CellDesigner/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
......@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2 -->
......
converter-SBGNML/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
......@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
......
converter-graphics/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
......@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2-->
......
converter-sbml/pom.xml
View file @ 8e4031af
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
......@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2 -->
......@@ -154,7 +154,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
<scope>test</scope>
</dependency>
......
converter/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>converter</artifactId>
......@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
......
frontend-js/pom.xml
View file @ 8e4031af
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
......
model-command/pom.xml
View file @ 8e4031af
......@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
......@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
......@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2-->
......
model-command/src/main/java/lcsb/mapviewer/commands/CopyCommand.java
View file @ 8e4031af
......@@ -142,7 +142,9 @@ public class CopyCommand extends NewModelCommand {
original = connection.getParentModel();
copy = copies.get(original);
if (copy == null) {
throw new InvalidModelException("Original model contain reference to model that wasn't copied");
if (!original.equals(modelCopy)) {
throw new InvalidModelException("Original model contain reference to model that wasn't copied");
}
} else {
connection.setParentModel(copy);
}
......
model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
View file @ 8e4031af
package lcsb.mapviewer.commands;
import static org.junit.Assert.*;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotEquals;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.awt.geom.Point2D;
import java.util.*;
import java.util.ArrayList;
import java.util.Calendar;
import java.util.List;
import org.apache.commons.lang3.mutable.MutableBoolean;
import org.junit.*;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
......@@ -17,11 +24,22 @@ import lcsb.mapviewer.model.map.compartment.SquareCompartment;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.layout.graphics.Layer;
import lcsb.mapviewer.model.map.model.*;
import lcsb.mapviewer.model.map.reaction.*;
import lcsb.mapviewer.model.map.model.Author;
import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.model.ModelSubmodelConnection;
import lcsb.mapviewer.model.map.model.SubmodelType;
import lcsb.mapviewer.model.map.reaction.AbstractNode;
import lcsb.mapviewer.model.map.reaction.Product;
import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
public class CopyCommandTest extends CommandTestFunctions {
......@@ -219,17 +237,6 @@ public class CopyCommandTest extends CommandTestFunctions {
assertEquals(0, comparator.compare(model, copy));
}
@Test(expected = InvalidArgumentException.class)
public void testCopyModelWithSubmodelsThrowException() throws Exception {
Model model = getModel();
Model model2 = getModel();
model2.setNotes("ASDSA2");
model.getElementByElementId("a_id")
.setSubmodel(new ElementSubmodelConnection(model2, SubmodelType.DOWNSTREAM_TARGETS));
new CopyCommand(model).execute();
}
private Model getModel() {
Model model = new ModelFullIndexed(null);
model.setName("nam" + counter++);
......
model/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
......@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Java xml serialization -->
......
pathvisio/pom.xml
View file @ 8e4031af
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
......@@ -77,20 +77,20 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2 -->
......
persist/pom.xml
View file @ 8e4031af
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>persist</artifactId>
......@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- apache ftp -->
......
pom.xml
View file @ 8e4031af
......@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
......
rest-api/pom.xml
View file @ 8e4031af
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
......@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
......
service/pom.xml
View file @ 8e4031af
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>service</artifactId>
......@@ -20,7 +20,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -28,47 +28,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<!-- Log4J2 -->
......
web/pom.xml
View file @ 8e4031af
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</parent>
<artifactId>web</artifactId>
<packaging>war</packaging>
......@@ -33,19 +33,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
<version>16.0.0~beta.1</version>
<version>16.0.0~beta.2</version>
</dependency>
<dependency>
......
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