From 81a24dd5747522766c00adf104d8d9e8e53c7cdc Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 22 Jul 2019 20:24:50 +0200
Subject: [PATCH] map dimension cannot be null
---
.../celldesigner/CellDesignerXmlParser.java | 8 ++--
.../converter/model/sbml/SbmlExporter.java | 7 +--
.../converter/model/sbml/SbmlParser.java | 21 +++------
.../compartment/SbmlCompartmentExporter.java | 2 +-
.../reaction/SbmlReactionExporterTest.java | 4 +-
.../layout/ApplySimpleLayoutModelCommand.java | 43 +++----------------
.../lcsb/mapviewer/model/map/model/Model.java | 8 ++--
.../mapviewer/model/map/model/ModelData.java | 12 +++---
.../model/map/model/ModelFullIndexed.java | 8 ++--
.../model/map/model/ModelFullIndexedTest.java | 28 ++++++------
...20190722_2__size_of_map_cannot_be_null.sql | 5 +++
11 files changed, 55 insertions(+), 91 deletions(-)
create mode 100644 persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190722_2__size_of_map_cannot_be_null.sql
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 26d31a3941..28bd63f9eb 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -621,7 +621,7 @@ public class CellDesignerXmlParser extends Converter {
result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
result.append(unitCollectionXmlParser.toXml(model.getUnits()));
- //notes must be inserted here, but we don't know the warnings yet
+ // notes must be inserted here, but we don't know the warnings yet
int notesPosition = result.length();
result.append(annotationToXml(model, elements));
@@ -633,7 +633,7 @@ public class CellDesignerXmlParser extends Converter {
result.append(parameterCollectionXmlParser.toXml(model.getParameters()));
result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
-
+
if (model.getNotes() != null || !appender.getWarnings().isEmpty()) {
StringBuilder notes = new StringBuilder();
notes.append("<notes>");
@@ -676,8 +676,8 @@ public class CellDesignerXmlParser extends Converter {
result.append("<annotation>\n");
result.append("<celldesigner:extension>\n");
result.append("<celldesigner:modelVersion>4.0</celldesigner:modelVersion>\n");
- result.append("<celldesigner:modelDisplay sizeX=\"" + model.getWidth().intValue() + "\" sizeY=\""
- + model.getHeight().intValue() + "\"/>\n");
+ result.append("<celldesigner:modelDisplay sizeX=\"" + (int) (model.getWidth()) + "\" sizeY=\""
+ + (int) (model.getHeight()) + "\"/>\n");
result.append(speciesCollectionXmlParser.speciesCollectionToXmlIncludedString(model.getSpeciesList()));
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 28c658a78a..6aa238ac2f 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -99,7 +99,8 @@ public class SbmlExporter {
compartmentExporter.setProvideDefaults(provideDefaults);
XmlAnnotationParser parser = new XmlAnnotationParser();
- String rdf = parser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(), model.getCreationDate(), model.getModificationDates(), model.getIdModel());
+ String rdf = parser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(), model.getCreationDate(),
+ model.getModificationDates(), model.getIdModel());
try {
result.setAnnotation(rdf);
} catch (XMLStreamException e1) {
@@ -141,12 +142,12 @@ public class SbmlExporter {
Layout layout = new Layout();
layout.setId("minerva_layout");
Dimensions dimensions = new Dimensions();
- if (model.getHeight() != null) {
+ if (model.getHeight() > 0) {
dimensions.setHeight(model.getHeight());
} else {
dimensions.setHeight(640);
}
- if (model.getWidth() != null) {
+ if (model.getWidth() > 0) {
dimensions.setWidth(model.getWidth());
} else {
dimensions.setWidth(480);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 3769a79627..12344d5b78 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -1,8 +1,6 @@
package lcsb.mapviewer.converter.model.sbml;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.Set;
+import java.util.*;
import javax.xml.stream.XMLStreamException;
@@ -18,12 +16,9 @@ import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import lcsb.mapviewer.commands.CommandExecutionException;
import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
+import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.MimeType;
-import lcsb.mapviewer.converter.Converter;
-import lcsb.mapviewer.converter.ConverterException;
-import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.InvalidInputDataExecption;
-import lcsb.mapviewer.converter.ZIndexPopulator;
+import lcsb.mapviewer.converter.*;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
@@ -33,12 +28,8 @@ import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Modulation;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
@@ -165,7 +156,7 @@ public class SbmlParser extends Converter {
private void createLayout(Model model, Layout layout, boolean resize, SbmlReactionParser parser)
throws InvalidInputDataExecption {
- if (model.getWidth() == null) {
+ if (model.getWidth() <= Configuration.EPSILON) {
double maxY = 1;
double maxX = 1;
for (Element element : model.getElements()) {
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
index 1467cae134..6fdcc5da88 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java
@@ -139,7 +139,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
boundingBox.setPosition(new Point(element.getX(), element.getY(), 0));
Dimensions dimensions = new Dimensions();
- if (getMinervaModel().getWidth() != null) {
+ if (getMinervaModel().getWidth() > 0) {
dimensions.setWidth(getMinervaModel().getWidth());
dimensions.setHeight(getMinervaModel().getHeight());
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
index ce2936868e..278166360e 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionExporterTest.java
@@ -58,12 +58,12 @@ public class SbmlReactionExporterTest {
Layout layout = new Layout();
Dimensions dimensions = new Dimensions();
- if (model.getHeight() != null) {
+ if (model.getHeight() > 0) {
dimensions.setHeight(model.getHeight());
} else {
dimensions.setHeight(640);
}
- if (model.getWidth() != null) {
+ if (model.getWidth() > 0) {
dimensions.setWidth(model.getWidth());
} else {
dimensions.setWidth(480);
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
index a3a81fe456..3d5c0ab39a 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java
@@ -1,16 +1,7 @@
package lcsb.mapviewer.commands.layout;
-import java.awt.geom.Dimension2D;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import java.awt.geom.*;
+import java.util.*;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.Logger;
@@ -27,23 +18,9 @@ import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.reaction.AbstractNode;
-import lcsb.mapviewer.model.map.reaction.AndOperator;
-import lcsb.mapviewer.model.map.reaction.AssociationOperator;
-import lcsb.mapviewer.model.map.reaction.DissociationOperator;
-import lcsb.mapviewer.model.map.reaction.Modifier;
-import lcsb.mapviewer.model.map.reaction.NodeOperator;
-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.SplitOperator;
-import lcsb.mapviewer.model.map.reaction.TruncationOperator;
-import lcsb.mapviewer.model.map.reaction.type.DissociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.HeterodimerAssociationReaction;
-import lcsb.mapviewer.model.map.reaction.type.TruncationReaction;
-import lcsb.mapviewer.model.map.species.Complex;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.reaction.*;
+import lcsb.mapviewer.model.map.reaction.type.*;
+import lcsb.mapviewer.model.map.species.*;
import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.SpeciesWithModificationResidue;
@@ -448,14 +425,8 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
}
protected void modifyModelSize(Model model, Point2D minPoint, Dimension2D dimension) {
- double width = 0;
- double height = 0;
- if (model.getWidth() != null) {
- width = model.getWidth();
- }
- if (model.getHeight() != null) {
- height = model.getHeight();
- }
+ double width = model.getWidth();
+ double height = model.getHeight();
width = Math.max(width, minPoint.getX() + dimension.getWidth());
height = Math.max(height, minPoint.getY() + dimension.getHeight());
model.setWidth(width);
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index 5450b22f0c..05bfbe7f99 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -53,7 +53,7 @@ public interface Model {
*
* @return model width
*/
- Double getWidth();
+ double getWidth();
/**
* Sets model width.
@@ -61,13 +61,13 @@ public interface Model {
* @param width
* new model width
*/
- void setWidth(Double width);
+ void setWidth(double width);
/**
*
* @return model height
*/
- Double getHeight();
+ double getHeight();
/**
* Sets model height.
@@ -75,7 +75,7 @@ public interface Model {
* @param height
* new model height
*/
- void setHeight(Double height);
+ void setHeight(double height);
/**
* Sets model width.
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index eba400c886..0e07da18b9 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -129,12 +129,12 @@ public class ModelData implements Serializable {
/**
* Width of the map.
*/
- private Double width;
+ private double width;
/**
* Height of the map.
*/
- private Double height;
+ private double height;
/**
* X coordinate that should be used when initially showing map.
@@ -550,7 +550,7 @@ public class ModelData implements Serializable {
* @return the width
* @see #width
*/
- public Double getWidth() {
+ public double getWidth() {
return width;
}
@@ -559,7 +559,7 @@ public class ModelData implements Serializable {
* the width to set
* @see #width
*/
- public void setWidth(Double width) {
+ public void setWidth(double width) {
this.width = width;
}
@@ -567,7 +567,7 @@ public class ModelData implements Serializable {
* @return the height
* @see #height
*/
- public Double getHeight() {
+ public double getHeight() {
return height;
}
@@ -576,7 +576,7 @@ public class ModelData implements Serializable {
* the height to set
* @see #height
*/
- public void setHeight(Double height) {
+ public void setHeight(double height) {
this.height = height;
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index bd7085a6b1..0d6a451085 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -122,22 +122,22 @@ public class ModelFullIndexed implements Model {
}
@Override
- public Double getWidth() {
+ public double getWidth() {
return modelData.getWidth();
}
@Override
- public void setWidth(Double width) {
+ public void setWidth(double width) {
modelData.setWidth(width);
}
@Override
- public Double getHeight() {
+ public double getHeight() {
return modelData.getHeight();
}
@Override
- public void setHeight(Double height) {
+ public void setHeight(double height) {
modelData.setHeight(height);
}
diff --git a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
index 371d0d385a..d6eab5e5ce 100644
--- a/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
+++ b/model/src/test/java/lcsb/mapviewer/model/map/model/ModelFullIndexedTest.java
@@ -672,10 +672,10 @@ public class ModelFullIndexedTest {
try {
Model model = new ModelFullIndexed(null);
- Double width = 12.0;
+ double width = 12.0;
int widthInt = 12;
String widthStr = "12.0";
- Double height = 13.0;
+ double height = 13.0;
String heightStr = "13.0";
int heightInt = 13;
Set<Element> elements = new HashSet<>();
@@ -684,26 +684,22 @@ public class ModelFullIndexedTest {
String idModel = "model_ID";
model.setWidth(widthStr);
- assertEquals(width, model.getWidth());
- model.setWidth((Double) null);
- assertNull(model.getWidth());
+ assertEquals(width, model.getWidth(), Configuration.EPSILON);
+ model.setWidth(0.0);
model.setWidth(width);
- assertEquals(width, model.getWidth());
- model.setWidth((Double) null);
- assertNull(model.getWidth());
+ assertEquals(width, model.getWidth(), Configuration.EPSILON);
+ model.setWidth(0.0);
model.setWidth(widthInt);
- assertEquals(width, model.getWidth());
+ assertEquals(width, model.getWidth(), Configuration.EPSILON);
model.setHeight(heightStr);
- assertEquals(height, model.getHeight());
- model.setHeight((Double) null);
- assertNull(model.getHeight());
+ assertEquals(height, model.getHeight(), Configuration.EPSILON);
+ model.setHeight(0.0);
model.setHeight(height);
- assertEquals(height, model.getHeight());
- model.setHeight((Double) null);
- assertNull(model.getHeight());
+ assertEquals(height, model.getHeight(), Configuration.EPSILON);
+ model.setHeight(0.0);
model.setHeight(heightInt);
- assertEquals(height, model.getHeight());
+ assertEquals(height, model.getHeight(), Configuration.EPSILON);
model.setElements(elements);
assertEquals(elements, model.getElements());
diff --git a/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190722_2__size_of_map_cannot_be_null.sql b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190722_2__size_of_map_cannot_be_null.sql
new file mode 100644
index 0000000000..f969d6ae9d
--- /dev/null
+++ b/persist/src/main/resources/db/migration/14.0.0~alpha.0/V14.0.0.20190722_2__size_of_map_cannot_be_null.sql
@@ -0,0 +1,5 @@
+update model_data_table set width = 800 where width is null;
+update model_data_table set height = 600 where height is null;
+
+ALTER TABLE model_data_table ALTER COLUMN width SET NOT NULL;
+ALTER TABLE model_data_table ALTER COLUMN height SET NOT NULL;
--
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