From 614fcfdbc27a3be2f4923603bd49b7ae10aa4fe4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Mon, 15 Oct 2018 17:01:38 +0200
Subject: [PATCH] hibernate upgraded
---
model/pom.xml | 81 +-
.../mapviewer/model/map/OverviewImage.java | 386 ++++-----
.../model/map/OverviewModelLink.java | 2 +-
.../model/map/layout/graphics/Layer.java | 736 +++++++++---------
.../model/map/layout/graphics/LayerRect.java | 439 +++++------
.../mapviewer/model/map/model/ModelData.java | 8 +-
persist/pom.xml | 22 +
.../java/lcsb/mapviewer/persist/DbUtils.java | 62 +-
.../lcsb/mapviewer/persist/dao/BaseDao.java | 4 +-
.../mapviewer/persist/dao/ProjectDao.java | 5 +-
.../persist/mapper/Point2DMapper.java | 213 ++---
.../resources/applicationContext-persist.xml | 6 +-
.../mapviewer/persist/dao/AllDaoTests.java | 1 -
.../mapviewer/persist/dao/BaseDaoTest.java | 45 --
.../mapviewer/persist/dao/ProjectDaoTest.java | 557 +++++++------
.../dao/graphics/PolylineDataTest.java | 89 ++-
.../persist/dao/map/LayoutDaoTest.java | 4 +-
.../persist/dao/map/ModelDaoTest.java | 6 +-
pom.xml | 8 +-
19 files changed, 1313 insertions(+), 1361 deletions(-)
delete mode 100644 persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java
diff --git a/model/pom.xml b/model/pom.xml
index 34cd348b50..c98001ebd1 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -1,22 +1,25 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>parent</artifactId>
- <version>1.0</version>
- </parent>
- <artifactId>model</artifactId>
- <name>model MapViewer</name>
- <description>Data model</description>
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>parent</artifactId>
+ <version>1.0</version>
+ </parent>
+ <artifactId>model</artifactId>
+ <name>model MapViewer</name>
+ <description>Data model</description>
<dependencies>
<dependency>
- <groupId>lcsb.mapviewer</groupId>
- <artifactId>commons</artifactId>
- <version>1.0</version>
- </dependency>
+ <groupId>lcsb.mapviewer</groupId>
+ <artifactId>commons</artifactId>
+ <version>1.0</version>
+ </dependency>
- <dependency>
+ <!-- Hibernate -->
+ <dependency>
<groupId>org.hibernate</groupId>
<artifactId>hibernate-core</artifactId>
<version>${hibernate.version}</version>
@@ -25,42 +28,64 @@
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
+ <exclusion>
+ <groupId>org.jboss.logging</groupId>
+ <artifactId>jboss-logging</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.bytebuddy</groupId>
+ <artifactId>byte-buddy</artifactId>
+ </exclusion>
</exclusions>
- </dependency>
-
- <!-- Library excluded from above; it was in conflict with Xerces -->
- <dependency>
+ </dependency>
+
+ <!-- https://mvnrepository.com/artifact/net.bytebuddy/byte-buddy -->
+ <dependency>
+ <groupId>net.bytebuddy</groupId>
+ <artifactId>byte-buddy</artifactId>
+ <version>${byte-buddy.version}</version>
+ </dependency>
+
+ <!-- https://mvnrepository.com/artifact/org.jboss.logging/jboss-logging -->
+ <dependency>
+ <groupId>org.jboss.logging</groupId>
+ <artifactId>jboss-logging</artifactId>
+ <version>${jboss-logging.version}</version>
+ </dependency>
+
+ <!-- Library excluded from above; it was in conflict with Xerces -->
+ <dependency>
<groupId>xml-apis</groupId>
<artifactId>xml-apis</artifactId>
<version>${xml-apis.version}</version>
</dependency>
-
- <!-- Log4j - logging -->
+
+ <!-- Log4j - logging -->
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
<version>${log4j.version}</version>
</dependency>
-
+
<dependency>
- <groupId>org.reflections</groupId>
- <artifactId>reflections</artifactId>
+ <groupId>org.reflections</groupId>
+ <artifactId>reflections</artifactId>
<version>${reflections.version}</version>
<exclusions>
<exclusion>
- <groupId>org.javassist</groupId>
- <artifactId>javassist</artifactId>
+ <groupId>org.javassist</groupId>
+ <artifactId>javassist</artifactId>
</exclusion>
</exclusions>
</dependency>
-<!-- mockito used for testing -->
+ <!-- mockito used for testing -->
<dependency>
<groupId>org.mockito</groupId>
<artifactId>mockito-core</artifactId>
<version>${mockito.version}</version>
<scope>test</scope>
</dependency>
-
+
</dependencies>
</project>
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
index ae22a55c8d..8d7ac37fff 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewImage.java
@@ -35,197 +35,197 @@ import lcsb.mapviewer.model.map.model.ModelData;
@Table(name = "overview_image_table")
public class OverviewImage implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * The image belongs to this {@link Project}. Links can point to any
- * (sub)model in this project.
- */
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private Project project;
-
- /**
- * Name of the file in file system that reresent this overview image.
- */
- private String filename;
-
- /**
- * Width of the image.
- */
- private Integer width;
-
- /**
- * Height of the image.
- */
- private Integer height;
-
- /**
- * List of links that should redirect from this image. They can refer to
- * another {@link OverviewImage} or {@link ModelData Model}.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "overviewImage", orphanRemoval = true)
- @OrderBy("id")
- private List<OverviewLink> links = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public OverviewImage() {
-
- }
-
- /**
- * Default constructor with original {@link OverviewImage} as a source of
- * data.
- *
- * @param overviewImage
- * original {@link OverviewImage}
- */
- public OverviewImage(OverviewImage overviewImage) {
- this.setId(overviewImage.getId());
- this.setProject(overviewImage.getProject());
- this.setFilename(overviewImage.getFilename());
- this.setWidth(overviewImage.getWidth());
- this.setHeight(overviewImage.getHeight());
- for (OverviewLink ol : overviewImage.getLinks()) {
- this.addLink(ol.copy());
- }
- }
-
- /**
- * @return the filename
- * @see #filename
- */
- public String getFilename() {
- return filename;
- }
-
- /**
- * @param filename
- * the filename to set
- * @see #filename
- */
- public void setFilename(String filename) {
- this.filename = filename;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Integer width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Integer height) {
- this.height = height;
- }
-
- /**
- * @return the links
- * @see #links
- */
- public List<OverviewLink> getLinks() {
- return links;
- }
-
- /**
- * @param links
- * the links to set
- * @see #links
- */
- public void setLinks(List<OverviewLink> links) {
- this.links = links;
- }
-
- /**
- * @return the id
- * @see #id
- */
- public int getId() {
- return id;
- }
-
- /**
- * @param id
- * the id to set
- * @see #id
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- * Adds {@link OverviewLink link } to {@link #links}.
- *
- * @param oml
- * object to add
- */
- public void addLink(OverviewLink oml) {
- links.add(oml);
- oml.setOverviewImage(this);
- }
-
- /**
- * Creates a copy of the object.
- *
- * @return copy of the object
- */
- public OverviewImage copy() {
- if (this.getClass() == OverviewImage.class) {
- return new OverviewImage(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the project
- * @see #project
- */
- public Project getProject() {
- return project;
- }
-
- /**
- * @param project the project to set
- * @see #project
- */
- public void setProject(Project project) {
- this.project = project;
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * The image belongs to this {@link Project}. Links can point to any (sub)model
+ * in this project.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private Project project;
+
+ /**
+ * Name of the file in file system that represent this overview image.
+ */
+ private String filename;
+
+ /**
+ * Width of the image.
+ */
+ private Integer width;
+
+ /**
+ * Height of the image.
+ */
+ private Integer height;
+
+ /**
+ * List of links that should redirect from this image. They can refer to another
+ * {@link OverviewImage} or {@link ModelData Model}.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "overviewImage")
+ @OrderBy("id")
+ private List<OverviewLink> links = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public OverviewImage() {
+
+ }
+
+ /**
+ * Default constructor with original {@link OverviewImage} as a source of data.
+ *
+ * @param overviewImage
+ * original {@link OverviewImage}
+ */
+ public OverviewImage(OverviewImage overviewImage) {
+ this.setId(overviewImage.getId());
+ this.setProject(overviewImage.getProject());
+ this.setFilename(overviewImage.getFilename());
+ this.setWidth(overviewImage.getWidth());
+ this.setHeight(overviewImage.getHeight());
+ for (OverviewLink ol : overviewImage.getLinks()) {
+ this.addLink(ol.copy());
+ }
+ }
+
+ /**
+ * @return the filename
+ * @see #filename
+ */
+ public String getFilename() {
+ return filename;
+ }
+
+ /**
+ * @param filename
+ * the filename to set
+ * @see #filename
+ */
+ public void setFilename(String filename) {
+ this.filename = filename;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Integer width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Integer height) {
+ this.height = height;
+ }
+
+ /**
+ * @return the links
+ * @see #links
+ */
+ public List<OverviewLink> getLinks() {
+ return links;
+ }
+
+ /**
+ * @param links
+ * the links to set
+ * @see #links
+ */
+ public void setLinks(List<OverviewLink> links) {
+ this.links = links;
+ }
+
+ /**
+ * @return the id
+ * @see #id
+ */
+ public int getId() {
+ return id;
+ }
+
+ /**
+ * @param id
+ * the id to set
+ * @see #id
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ * Adds {@link OverviewLink link } to {@link #links}.
+ *
+ * @param oml
+ * object to add
+ */
+ public void addLink(OverviewLink oml) {
+ links.add(oml);
+ oml.setOverviewImage(this);
+ }
+
+ /**
+ * Creates a copy of the object.
+ *
+ * @return copy of the object
+ */
+ public OverviewImage copy() {
+ if (this.getClass() == OverviewImage.class) {
+ return new OverviewImage(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the project
+ * @see #project
+ */
+ public Project getProject() {
+ return project;
+ }
+
+ /**
+ * @param project
+ * the project to set
+ * @see #project
+ */
+ public void setProject(Project project) {
+ this.project = project;
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
index 074874ae3e..81c45341ec 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/OverviewModelLink.java
@@ -28,7 +28,7 @@ public class OverviewModelLink extends OverviewLink {
/**
* Model to which this links is going.
*/
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
private ModelData linkedModel;
/**
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
index 1a9237adff..958615af32 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/Layer.java
@@ -11,6 +11,8 @@ import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
+import javax.persistence.JoinColumn;
+import javax.persistence.JoinTable;
import javax.persistence.ManyToOne;
import javax.persistence.OneToMany;
import javax.persistence.Table;
@@ -35,367 +37,375 @@ import lcsb.mapviewer.model.map.model.ModelData;
@Table(name = "layer_table")
public class Layer implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(Layer.class);
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Layer identifier (unique in single model).
- */
- private String layerId;
-
- /**
- * Layer name.
- */
- private String name;
-
- /**
- * Is the layer visible.
- */
- private boolean visible;
-
- /**
- * Is the layer locekd (can be edited).
- */
- private boolean locked;
-
- /**
- * List of text objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<LayerText> texts = new ArrayList<LayerText>();
-
- /**
- * List of line objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<PolylineData> lines = new ArrayList<PolylineData>();
-
- /**
- * List of rectangle objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<LayerRect> rectangles = new ArrayList<LayerRect>();
-
- /**
- * List of oval objects on the layer.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER)
- @IndexColumn(name = "idx")
- private List<LayerOval> ovals = new ArrayList<LayerOval>();
-
- /**
- * ModelData to which layer belongs to.
- */
- @ManyToOne(fetch = FetchType.LAZY)
- private ModelData model;
-
- /**
- * Default constructor.
- */
- public Layer() {
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param layer
- * from this paramter layer data will be copied
- */
- public Layer(Layer layer) {
- layerId = layer.getLayerId();
- name = layer.getName();
- visible = layer.isVisible();
- locked = layer.isLocked();
-
- for (LayerText lt : layer.getTexts()) {
- addLayerText(lt.copy());
- }
-
- for (PolylineData lt : layer.getLines()) {
- addLayerLine(lt.copy());
- }
-
- for (LayerRect lt : layer.getRectangles()) {
- addLayerRect(lt.copy());
- }
-
- for (LayerOval lt : layer.getOvals()) {
- addLayerOval(lt.copy());
- }
-
- model = layer.getModel();
- }
-
- /**
- * Makes copy of the layer.
- *
- * @return copy of the layer
- */
- public Layer copy() {
- if (this.getClass() == Layer.class) {
- return new Layer(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the model
- * @see #model
- */
- public ModelData getModel() {
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- public void setModel(ModelData model) {
- this.model = model;
- }
-
- /**
- * @return the ovals
- * @see #ovals
- */
- public List<LayerOval> getOvals() {
- return ovals;
- }
-
- /**
- * @param ovals
- * the ovals to set
- * @see #ovals
- */
- public void setOvals(List<LayerOval> ovals) {
- this.ovals = ovals;
- }
-
- /**
- * @return the rectangles
- * @see #rectangles
- */
- public List<LayerRect> getRectangles() {
- return rectangles;
- }
-
- /**
- * @param rectangles
- * the rectangles to set
- * @see #rectangles
- */
- public void setRectangles(List<LayerRect> rectangles) {
- this.rectangles = rectangles;
- }
-
- /**
- * @return the lines
- * @see #lines
- */
- public List<PolylineData> getLines() {
- return lines;
- }
-
- /**
- * @param lines
- * the lines to set
- * @see #lines
- */
- public void setLines(List<PolylineData> lines) {
- this.lines = lines;
- }
-
- /**
- * @return the texts
- * @see #texts
- */
- public List<LayerText> getTexts() {
- return texts;
- }
-
- /**
- * @param texts
- * the texts to set
- * @see #texts
- */
- public void setTexts(List<LayerText> texts) {
- this.texts = texts;
- }
-
- /**
- * @return the locked
- * @see #locked
- */
- public boolean isLocked() {
- return locked;
- }
-
- /**
- * @param locked
- * the locked to set
- * @see #locked
- */
- public void setLocked(boolean locked) {
- this.locked = locked;
- }
-
- /**
- * @return the visible
- * @see #visible
- */
- public boolean isVisible() {
- return visible;
- }
-
- /**
- * @param visible
- * the visible to set
- * @see #visible
- */
- public void setVisible(boolean visible) {
- this.visible = visible;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Sets locked param from the text input.
- *
- * @param param
- * text representing true/false
- * @see #locked
- */
- public void setLocked(String param) {
- locked = param.equalsIgnoreCase("TRUE");
- }
-
- /**
- * Sets visible param from the text input.
- *
- * @param param
- * text representing true/false
- * @see #visible
- */
- public void setVisible(String param) {
- visible = param.equalsIgnoreCase("TRUE");
- }
-
- /**
- * Adds text to the layer.
- *
- * @param layerText
- * text to add
- */
- public void addLayerText(LayerText layerText) {
- texts.add(layerText);
- }
-
- /**
- * Adds rectangle to the layer.
- *
- * @param layerRect
- * rectangle to add
- */
- public void addLayerRect(LayerRect layerRect) {
- rectangles.add(layerRect);
- }
-
- /**
- * Adds oval to the layer.
- *
- * @param layerOval
- * oval to add
- */
- public void addLayerOval(LayerOval layerOval) {
- ovals.add(layerOval);
- }
-
- /**
- * Adds line to the layer.
- *
- * @param layerLine
- * line to add
- */
- public void addLayerLine(PolylineData layerLine) {
- lines.add(layerLine);
- }
-
- /**
- * @return the layerId
- * @see #layerId
- */
- public String getLayerId() {
- return layerId;
- }
-
- /**
- * @param layerId
- * the layerId to set
- * @see #layerId
- */
- public void setLayerId(String layerId) {
- this.layerId = layerId;
- }
-
- /**
- * Adds lines to the layer.
- *
- * @param lines
- * lines to add
- */
- public void addLayerLines(Collection<PolylineData> lines) {
- for (PolylineData layerLine : lines) {
- addLayerLine(layerLine);
- }
- }
-
- /**
- * Removes {@link LayerText} from {@link Layer}.
- *
- * @param toRemove
- * object to remove
- */
- public void removeLayerText(LayerText toRemove) {
- texts.remove(toRemove);
- }
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(Layer.class);
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Layer identifier (unique in single model).
+ */
+ private String layerId;
+
+ /**
+ * Layer name.
+ */
+ private String name;
+
+ /**
+ * Is the layer visible.
+ */
+ private boolean visible;
+
+ /**
+ * Is the layer locked (can be edited).
+ */
+ private boolean locked;
+
+ /**
+ * List of text objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ @JoinTable( joinColumns = {
+ @JoinColumn(name = "layer_table_iddb", referencedColumnName = "idDb", nullable = false, updatable = false) })
+ private List<LayerText> texts = new ArrayList<>();
+
+ /**
+ * List of line objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ @JoinTable( joinColumns = {
+ @JoinColumn(name = "layer_table_iddb", referencedColumnName = "idDb", nullable = false, updatable = false) })
+ private List<PolylineData> lines = new ArrayList<>();
+
+ /**
+ * List of rectangle objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ @JoinTable( joinColumns = {
+ @JoinColumn(name = "layer_table_iddb", referencedColumnName = "idDb", nullable = false, updatable = false) })
+ private List<LayerRect> rectangles = new ArrayList<>();
+
+ /**
+ * List of oval objects on the layer.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER)
+ @IndexColumn(name = "idx")
+ @JoinTable( joinColumns = {
+ @JoinColumn(name = "layer_table_iddb", referencedColumnName = "idDb", nullable = false, updatable = false) })
+ private List<LayerOval> ovals = new ArrayList<>();
+
+ /**
+ * ModelData to which layer belongs to.
+ */
+ @ManyToOne(fetch = FetchType.LAZY)
+ private ModelData model;
+
+ /**
+ * Default constructor.
+ */
+ public Layer() {
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param layer
+ * from this parameter layer data will be copied
+ */
+ public Layer(Layer layer) {
+ layerId = layer.getLayerId();
+ name = layer.getName();
+ visible = layer.isVisible();
+ locked = layer.isLocked();
+
+ for (LayerText lt : layer.getTexts()) {
+ addLayerText(lt.copy());
+ }
+
+ for (PolylineData lt : layer.getLines()) {
+ addLayerLine(lt.copy());
+ }
+
+ for (LayerRect lt : layer.getRectangles()) {
+ addLayerRect(lt.copy());
+ }
+
+ for (LayerOval lt : layer.getOvals()) {
+ addLayerOval(lt.copy());
+ }
+
+ model = layer.getModel();
+ }
+
+ /**
+ * Makes copy of the layer.
+ *
+ * @return copy of the layer
+ */
+ public Layer copy() {
+ if (this.getClass() == Layer.class) {
+ return new Layer(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ public ModelData getModel() {
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModel(ModelData model) {
+ this.model = model;
+ }
+
+ /**
+ * @return the ovals
+ * @see #ovals
+ */
+ public List<LayerOval> getOvals() {
+ return ovals;
+ }
+
+ /**
+ * @param ovals
+ * the ovals to set
+ * @see #ovals
+ */
+ public void setOvals(List<LayerOval> ovals) {
+ this.ovals = ovals;
+ }
+
+ /**
+ * @return the rectangles
+ * @see #rectangles
+ */
+ public List<LayerRect> getRectangles() {
+ return rectangles;
+ }
+
+ /**
+ * @param rectangles
+ * the rectangles to set
+ * @see #rectangles
+ */
+ public void setRectangles(List<LayerRect> rectangles) {
+ this.rectangles = rectangles;
+ }
+
+ /**
+ * @return the lines
+ * @see #lines
+ */
+ public List<PolylineData> getLines() {
+ return lines;
+ }
+
+ /**
+ * @param lines
+ * the lines to set
+ * @see #lines
+ */
+ public void setLines(List<PolylineData> lines) {
+ this.lines = lines;
+ }
+
+ /**
+ * @return the texts
+ * @see #texts
+ */
+ public List<LayerText> getTexts() {
+ return texts;
+ }
+
+ /**
+ * @param texts
+ * the texts to set
+ * @see #texts
+ */
+ public void setTexts(List<LayerText> texts) {
+ this.texts = texts;
+ }
+
+ /**
+ * @return the locked
+ * @see #locked
+ */
+ public boolean isLocked() {
+ return locked;
+ }
+
+ /**
+ * @param locked
+ * the locked to set
+ * @see #locked
+ */
+ public void setLocked(boolean locked) {
+ this.locked = locked;
+ }
+
+ /**
+ * @return the visible
+ * @see #visible
+ */
+ public boolean isVisible() {
+ return visible;
+ }
+
+ /**
+ * @param visible
+ * the visible to set
+ * @see #visible
+ */
+ public void setVisible(boolean visible) {
+ this.visible = visible;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * Sets locked param from the text input.
+ *
+ * @param param
+ * text representing true/false
+ * @see #locked
+ */
+ public void setLocked(String param) {
+ locked = param.equalsIgnoreCase("TRUE");
+ }
+
+ /**
+ * Sets visible param from the text input.
+ *
+ * @param param
+ * text representing true/false
+ * @see #visible
+ */
+ public void setVisible(String param) {
+ visible = param.equalsIgnoreCase("TRUE");
+ }
+
+ /**
+ * Adds text to the layer.
+ *
+ * @param layerText
+ * text to add
+ */
+ public void addLayerText(LayerText layerText) {
+ texts.add(layerText);
+ }
+
+ /**
+ * Adds rectangle to the layer.
+ *
+ * @param layerRect
+ * rectangle to add
+ */
+ public void addLayerRect(LayerRect layerRect) {
+ rectangles.add(layerRect);
+ }
+
+ /**
+ * Adds oval to the layer.
+ *
+ * @param layerOval
+ * oval to add
+ */
+ public void addLayerOval(LayerOval layerOval) {
+ ovals.add(layerOval);
+ }
+
+ /**
+ * Adds line to the layer.
+ *
+ * @param layerLine
+ * line to add
+ */
+ public void addLayerLine(PolylineData layerLine) {
+ lines.add(layerLine);
+ }
+
+ /**
+ * @return the layerId
+ * @see #layerId
+ */
+ public String getLayerId() {
+ return layerId;
+ }
+
+ /**
+ * @param layerId
+ * the layerId to set
+ * @see #layerId
+ */
+ public void setLayerId(String layerId) {
+ this.layerId = layerId;
+ }
+
+ /**
+ * Adds lines to the layer.
+ *
+ * @param lines
+ * lines to add
+ */
+ public void addLayerLines(Collection<PolylineData> lines) {
+ for (PolylineData layerLine : lines) {
+ addLayerLine(layerLine);
+ }
+ }
+
+ /**
+ * Removes {@link LayerText} from {@link Layer}.
+ *
+ * @param toRemove
+ * object to remove
+ */
+ public void removeLayerText(LayerText toRemove) {
+ texts.remove(toRemove);
+ }
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
index 5950e68801..6ad9b5ce74 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/layout/graphics/LayerRect.java
@@ -5,9 +5,11 @@ import java.io.Serializable;
import javax.persistence.Column;
import javax.persistence.Entity;
+import javax.persistence.FetchType;
import javax.persistence.GeneratedValue;
import javax.persistence.GenerationType;
import javax.persistence.Id;
+import javax.persistence.ManyToOne;
import org.apache.log4j.Logger;
@@ -23,223 +25,222 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
@Entity
public class LayerRect implements Serializable {
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(LayerRect.class);
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Color of the rectangle.
- */
- private Color color;
-
- /**
- * X coordinate of top left corner.
- */
- private Double x = 0.0;
-
- /**
- * Y coordinate of top left corner.
- */
- private Double y = 0.0;
-
- /**
- * Width of the rectangle.
- */
- private Double width = 0.0;
-
- /**
- * Height of the rectangle.
- */
- private Double height = 0.0;
-
- /**
- * Default constructor.
- */
- public LayerRect() {
-
- }
-
- /**
- * Constructor that copies data from the parameter.
- *
- * @param layerRect
- * from this paramter line data will be copied
- */
- public LayerRect(LayerRect layerRect) {
- color = layerRect.getColor();
- x = layerRect.getX();
- y = layerRect.getY();
- width = layerRect.getWidth();
- height = layerRect.getHeight();
- }
-
- /**
- * Set x from string containing double value.
- *
- * @param param
- * x of the line in text format
- */
- public void setX(String param) {
- try {
- x = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid x value: " + param, e);
- }
- }
-
- /**
- * Set y from string containing double value.
- *
- * @param param
- * y of the line in text format
- */
- public void setY(String param) {
- try {
- y = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid y value: " + param, e);
- }
- }
-
- /**
- * Set width from string containing double value.
- *
- * @param param
- * width of the line in text format
- */
- public void setWidth(String param) {
- try {
- width = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid width value: " + param, e);
- }
- }
-
- /**
- * Set height from string containing double value.
- *
- * @param param
- * height of the line in text format
- */
- public void setHeight(String param) {
- try {
- height = Double.parseDouble(param);
- } catch (NumberFormatException e) {
- throw new InvalidArgumentException("Invalid height value: " + param, e);
- }
- }
-
- /**
- * Prepares a copy of the object.
- *
- * @return copy of LayerRect
- */
- public LayerRect copy() {
- if (this.getClass() == LayerRect.class) {
- return new LayerRect(this);
- } else {
- throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
- }
- }
-
- /**
- * @return the color
- * @see #color
- */
- public Color getColor() {
- return color;
- }
-
- /**
- * @param color
- * the color to set
- * @see #color
- */
- public void setColor(Color color) {
- this.color = color;
- }
-
- /**
- * @return the x
- * @see #x
- */
- public Double getX() {
- return x;
- }
-
- /**
- * @param x
- * the x to set
- * @see #x
- */
- public void setX(Double x) {
- this.x = x;
- }
-
- /**
- * @return the y
- * @see #y
- */
- public Double getY() {
- return y;
- }
-
- /**
- * @param y
- * the y to set
- * @see #y
- */
- public void setY(Double y) {
- this.y = y;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(LayerRect.class);
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Color of the rectangle.
+ */
+ private Color color;
+
+ /**
+ * X coordinate of top left corner.
+ */
+ private Double x = 0.0;
+
+ /**
+ * Y coordinate of top left corner.
+ */
+ private Double y = 0.0;
+
+ /**
+ * Width of the rectangle.
+ */
+ private Double width = 0.0;
+
+ /**
+ * Height of the rectangle.
+ */
+ private Double height = 0.0;
+
+ /**
+ * Default constructor.
+ */
+ public LayerRect() {
+
+ }
+
+ /**
+ * Constructor that copies data from the parameter.
+ *
+ * @param layerRect
+ * from this parameter line data will be copied
+ */
+ public LayerRect(LayerRect layerRect) {
+ color = layerRect.getColor();
+ x = layerRect.getX();
+ y = layerRect.getY();
+ width = layerRect.getWidth();
+ height = layerRect.getHeight();
+ }
+
+ /**
+ * Set x from string containing double value.
+ *
+ * @param param
+ * x of the line in text format
+ */
+ public void setX(String param) {
+ try {
+ x = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid x value: " + param, e);
+ }
+ }
+
+ /**
+ * Set y from string containing double value.
+ *
+ * @param param
+ * y of the line in text format
+ */
+ public void setY(String param) {
+ try {
+ y = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid y value: " + param, e);
+ }
+ }
+
+ /**
+ * Set width from string containing double value.
+ *
+ * @param param
+ * width of the line in text format
+ */
+ public void setWidth(String param) {
+ try {
+ width = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid width value: " + param, e);
+ }
+ }
+
+ /**
+ * Set height from string containing double value.
+ *
+ * @param param
+ * height of the line in text format
+ */
+ public void setHeight(String param) {
+ try {
+ height = Double.parseDouble(param);
+ } catch (NumberFormatException e) {
+ throw new InvalidArgumentException("Invalid height value: " + param, e);
+ }
+ }
+
+ /**
+ * Prepares a copy of the object.
+ *
+ * @return copy of LayerRect
+ */
+ public LayerRect copy() {
+ if (this.getClass() == LayerRect.class) {
+ return new LayerRect(this);
+ } else {
+ throw new NotImplementedException("Method copy() should be overriden in class " + this.getClass());
+ }
+ }
+
+ /**
+ * @return the color
+ * @see #color
+ */
+ public Color getColor() {
+ return color;
+ }
+
+ /**
+ * @param color
+ * the color to set
+ * @see #color
+ */
+ public void setColor(Color color) {
+ this.color = color;
+ }
+
+ /**
+ * @return the x
+ * @see #x
+ */
+ public Double getX() {
+ return x;
+ }
+
+ /**
+ * @param x
+ * the x to set
+ * @see #x
+ */
+ public void setX(Double x) {
+ this.x = x;
+ }
+
+ /**
+ * @return the y
+ * @see #y
+ */
+ public Double getY() {
+ return y;
+ }
+
+ /**
+ * @param y
+ * the y to set
+ * @see #y
+ */
+ public void setY(Double y) {
+ this.y = y;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
}
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 b913f2a50d..f54259d9e0 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
@@ -30,6 +30,7 @@ import org.hibernate.annotations.CascadeType;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.OverviewModelLink;
import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -194,7 +195,7 @@ public class ModelData implements Serializable {
/**
* Project to which this model belong to.
*/
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ @ManyToOne(fetch = FetchType.LAZY)
private Project project;
// This field should be transient in hibernate and during the transformation
@@ -221,6 +222,11 @@ public class ModelData implements Serializable {
@OneToMany(fetch = FetchType.LAZY, mappedBy = "submodel")
private Set<SubmodelConnection> parentModels = new HashSet<>();
+
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.LAZY, mappedBy = "linkedModel")
+ private Set<OverviewModelLink> imageLinks = new HashSet<>();
+
/**
* Default constructor.
*/
diff --git a/persist/pom.xml b/persist/pom.xml
index 5a6cd0fff2..b23f71d657 100644
--- a/persist/pom.xml
+++ b/persist/pom.xml
@@ -47,9 +47,31 @@
<artifactId>xml-apis</artifactId>
<groupId>xml-apis</groupId>
</exclusion>
+ <exclusion>
+ <groupId>org.jboss.logging</groupId>
+ <artifactId>jboss-logging</artifactId>
+ </exclusion>
+ <exclusion>
+ <groupId>net.bytebuddy</groupId>
+ <artifactId>byte-buddy</artifactId>
+ </exclusion>
</exclusions>
</dependency>
+ <!-- https://mvnrepository.com/artifact/net.bytebuddy/byte-buddy -->
+ <dependency>
+ <groupId>net.bytebuddy</groupId>
+ <artifactId>byte-buddy</artifactId>
+ <version>${byte-buddy.version}</version>
+ </dependency>
+
+ <!-- https://mvnrepository.com/artifact/org.jboss.logging/jboss-logging -->
+ <dependency>
+ <groupId>org.jboss.logging</groupId>
+ <artifactId>jboss-logging</artifactId>
+ <version>${jboss-logging.version}</version>
+ </dependency>
+
<!-- Library excluded from above; it was in conflict with Xerces -->
<dependency>
<groupId>xml-apis</groupId>
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
index 6729733e77..8d1e6636fb 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/DbUtils.java
@@ -5,21 +5,12 @@ import java.util.Map;
import java.util.Map.Entry;
import java.util.Observable;
-import javax.management.MBeanServer;
-import javax.management.ObjectName;
-
import org.apache.log4j.Logger;
-import org.flywaydb.core.Flyway;
import org.hibernate.SQLQuery;
import org.hibernate.Session;
import org.hibernate.SessionFactory;
-import org.hibernate.internal.SessionFactoryImpl;
-import org.hibernate.jmx.StatisticsService;
-import org.hibernate.service.jdbc.connections.internal.DatasourceConnectionProviderImpl;
import org.springframework.beans.factory.annotation.Autowired;
-import com.mchange.v2.c3p0.ComboPooledDataSource;
-
import lcsb.mapviewer.common.exception.InvalidStateException;
/**
@@ -28,7 +19,7 @@ import lcsb.mapviewer.common.exception.InvalidStateException;
* <ul>
* <li>default - created and managed by sessionFactory</li>
* <li>custom - created and managed by this class, used only when new thread is
- * created manualy.</li>
+ * created manually.</li>
* </ul>
* Class extends {@link Observable}. Whenever session is created or closed
* observers are notified.
@@ -50,23 +41,6 @@ public class DbUtils extends Observable {
@Autowired
private SessionFactory sessionFactory;
- /**
- * Service used for connection statistics.
- */
- private StatisticsService statisticsService;
-
- /**
- * This flag indicates if the object was initialized or not.
- *
- * @see #init()
- */
- private boolean initialized = false;
-
- /**
- * Bean used for statistics.
- */
- private MBeanServer mbeanServer;
-
/**
* Static map containing opened custom sessions. This object is also used for
* synchronization between threads when accessing informations about sessions.
@@ -85,33 +59,6 @@ public class DbUtils extends Observable {
*/
private static Map<Long, Boolean> autoFlushForThread = new HashMap<>();
- /**
- * This method initialize services responsible for statistics.
- */
- private void init() {
- if (!initialized) {
- if (SpringApplicationContext.getApplicationContext().containsBean("mbeanServer")) {
- logger.info("Hibernate statistics turned on");
- mbeanServer = SpringApplicationContext.getApplicationContext().getBean(MBeanServer.class);
- statisticsService = new StatisticsService();
- statisticsService.setSessionFactory(sessionFactory);
- statisticsService.setStatisticsEnabled(true);
- ObjectName objectName;
- try {
- objectName = new ObjectName("org.hibernate:name=HibernateStatistics");
-
- mbeanServer.registerMBean(statisticsService, objectName);
- } catch (Exception e) {
- logger.error(e, e);
- }
- } else {
- logger.info("Hibernate statistics turned off");
- }
- }
- initialized = true;
-
- }
-
/**
* Executes sql query given in the parameter.
*
@@ -195,9 +142,6 @@ public class DbUtils extends Observable {
Session session = null;
synchronized (sessionForThread) {
session = sessionForThread.get(id);
- if (!initialized) {
- init();
- }
}
// we cannot create two threads for one session
@@ -209,10 +153,6 @@ public class DbUtils extends Observable {
logger.debug("Session opened: " + id);
session.beginTransaction();
logger.debug("Session started: " + id);
- if (statisticsService != null) {
- logger.debug("Opened sessions: " + statisticsService.getSessionOpenCount() + ". Closed sessions: "
- + statisticsService.getSessionCloseCount());
- }
Integer counter = -1;
synchronized (sessionForThread) {
sessionForThread.put(id, session);
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
index 244554d641..e14f32579f 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/BaseDao.java
@@ -251,8 +251,8 @@ public abstract class BaseDao<T> {
@SuppressWarnings("unchecked")
public T getById(int id) {
List<?> list = getSession()
- .createQuery(" from " + this.clazz.getSimpleName() + " where id=? " + removableAndStatemant())
- .setParameter(0, id).list();
+ .createQuery(" from " + this.clazz.getSimpleName() + " where id=:id " + removableAndStatemant())
+ .setParameter("id", id).list();
if (list.size() == 0) {
return null;
} else {
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java b/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java
index d03df93697..66af35c712 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/dao/ProjectDao.java
@@ -8,8 +8,6 @@ import java.util.List;
import org.hibernate.dialect.Dialect;
import org.hibernate.jdbc.ReturningWork;
-import org.hibernate.service.jdbc.dialect.internal.StandardDialectResolver;
-import org.hibernate.service.jdbc.dialect.spi.DialectResolver;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -78,8 +76,7 @@ public class ProjectDao extends BaseDao<Project> {
ReturningWork<Long> maxReturningWork = new ReturningWork<Long>() {
@Override
public Long execute(Connection connection) throws SQLException {
- DialectResolver dialectResolver = new StandardDialectResolver();
- Dialect dialect = dialectResolver.resolveDialect(connection.getMetaData());
+ Dialect dialect = Dialect.getDialect(connection.getClientInfo());
PreparedStatement preparedStatement = null;
ResultSet resultSet = null;
try {
diff --git a/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java b/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
index afab6a1aab..9c1b536705 100644
--- a/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
+++ b/persist/src/main/java/lcsb/mapviewer/persist/mapper/Point2DMapper.java
@@ -6,7 +6,8 @@ import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
-import org.hibernate.engine.spi.SessionImplementor;
+import org.hibernate.HibernateException;
+import org.hibernate.engine.spi.SharedSessionContractImplementor;
import org.hibernate.type.StringType;
import org.hibernate.type.Type;
import org.hibernate.usertype.CompositeUserType;
@@ -19,108 +20,112 @@ import org.hibernate.usertype.CompositeUserType;
*/
public class Point2DMapper implements CompositeUserType {
- @Override
- public String[] getPropertyNames() {
- return new String[] { "val" };
- }
-
- @Override
- public Type[] getPropertyTypes() {
- return new Type[] { StringType.INSTANCE };
- }
-
- @Override
- public Object getPropertyValue(Object component, int property) {
- Object returnValue = null;
- final Point2D point = (Point2D) component;
- if (0 == property) {
- returnValue = point.getX() + "," + point.getY();
- }
- return returnValue;
- }
-
- @Override
- public void setPropertyValue(Object component, int property, Object value) {
- final Point2D point = (Point2D) component;
- if (0 == property) {
- final String[] values = ((String) value).split(",");
- point.setLocation(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
- }
- }
-
- @Override
- public Class<?> returnedClass() {
- return Point2D.class;
- }
-
- @Override
- public boolean equals(Object o1, Object o2) {
- boolean isEqual = false;
- if (o1 == o2) {
- isEqual = false;
- }
- if (null == o1 || null == o2) {
- isEqual = false;
- } else {
- isEqual = o1.equals(o2);
- }
- return isEqual;
- }
-
- @Override
- public int hashCode(Object x) {
- return x.hashCode();
- }
-
- @Override
- public Object nullSafeGet(ResultSet rs, String[] names, SessionImplementor session, Object owner) throws SQLException {
- Point2D point = null;
- final String val = rs.getString(names[0]);
- if (!rs.wasNull()) {
- final String[] values = val.split(",");
- point = new Point2D.Double(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
- }
- return point;
- }
-
- @Override
- public void nullSafeSet(PreparedStatement st, Object value, int property, SessionImplementor session) throws SQLException {
- if (value == null) {
- st.setNull(property, StringType.INSTANCE.sqlType());
- } else {
- final Point2D point = (Point2D) value;
- st.setString(property, point.getX() + "," + point.getY());
- }
- }
-
- @Override
- public Object deepCopy(Object value) {
- if (value == null) {
- return null;
- }
- final Point2D recievedParam = (Point2D) value;
- final Point2D point = new Point2D.Double(recievedParam.getX(), recievedParam.getY());
- return point;
- }
-
- @Override
- public boolean isMutable() {
- return true;
- }
-
- @Override
- public Serializable disassemble(Object value, SessionImplementor session) {
- return (Serializable) value;
- }
-
- @Override
- public Object assemble(Serializable cached, SessionImplementor session, Object owner) {
- return cached;
- }
-
- @Override
- public Object replace(Object original, Object target, SessionImplementor session, Object owner) {
- return this.deepCopy(original);
- }
+ @Override
+ public String[] getPropertyNames() {
+ return new String[] { "val" };
+ }
+
+ @Override
+ public Type[] getPropertyTypes() {
+ return new Type[] { StringType.INSTANCE };
+ }
+
+ @Override
+ public Object getPropertyValue(Object component, int property) {
+ Object returnValue = null;
+ final Point2D point = (Point2D) component;
+ if (0 == property) {
+ returnValue = point.getX() + "," + point.getY();
+ }
+ return returnValue;
+ }
+
+ @Override
+ public void setPropertyValue(Object component, int property, Object value) {
+ final Point2D point = (Point2D) component;
+ if (0 == property) {
+ final String[] values = ((String) value).split(",");
+ point.setLocation(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
+ }
+ }
+
+ @Override
+ public Class<?> returnedClass() {
+ return Point2D.class;
+ }
+
+ @Override
+ public boolean equals(Object o1, Object o2) {
+ boolean isEqual = false;
+ if (o1 == o2) {
+ isEqual = false;
+ }
+ if (null == o1 || null == o2) {
+ isEqual = false;
+ } else {
+ isEqual = o1.equals(o2);
+ }
+ return isEqual;
+ }
+
+ @Override
+ public int hashCode(Object x) {
+ return x.hashCode();
+ }
+
+ @Override
+ public Object deepCopy(Object value) {
+ if (value == null) {
+ return null;
+ }
+ final Point2D recievedParam = (Point2D) value;
+ final Point2D point = new Point2D.Double(recievedParam.getX(), recievedParam.getY());
+ return point;
+ }
+
+ @Override
+ public boolean isMutable() {
+ return true;
+ }
+
+ @Override
+ public Object nullSafeGet(ResultSet rs, String[] names, SharedSessionContractImplementor session, Object owner)
+ throws HibernateException, SQLException {
+ Point2D point = null;
+ final String val = rs.getString(names[0]);
+ if (!rs.wasNull()) {
+ final String[] values = val.split(",");
+ point = new Point2D.Double(Double.parseDouble(values[0]), Double.parseDouble(values[1]));
+ }
+ return point;
+ }
+
+ @Override
+ public void nullSafeSet(PreparedStatement st, Object value, int index, SharedSessionContractImplementor session)
+ throws HibernateException, SQLException {
+ if (value == null) {
+ st.setNull(index, StringType.INSTANCE.sqlType());
+ } else {
+ final Point2D point = (Point2D) value;
+ st.setString(index, point.getX() + "," + point.getY());
+ }
+ }
+
+ @Override
+ public Serializable disassemble(Object value, SharedSessionContractImplementor session) throws HibernateException {
+ return (Serializable) value;
+ }
+
+ @Override
+ public Object assemble(Serializable cached, SharedSessionContractImplementor session, Object owner)
+ throws HibernateException {
+ return cached;
+ }
+
+ @Override
+ public Object replace(Object original, Object target, SharedSessionContractImplementor session, Object owner)
+ throws HibernateException {
+ return this.deepCopy(original);
+ }
}
diff --git a/persist/src/main/resources/applicationContext-persist.xml b/persist/src/main/resources/applicationContext-persist.xml
index 34d97465ab..7cc5c31f49 100644
--- a/persist/src/main/resources/applicationContext-persist.xml
+++ b/persist/src/main/resources/applicationContext-persist.xml
@@ -46,7 +46,7 @@
<bean id="ProjectDao" class="lcsb.mapviewer.persist.dao.ProjectDao" parent="BaseDao"/>
- <bean id="SessionFactory" class="org.springframework.orm.hibernate4.LocalSessionFactoryBean">
+ <bean id="SessionFactory" class="org.springframework.orm.hibernate5.LocalSessionFactoryBean">
<property name="dataSource" ref="DataSource" />
<property name="annotatedClasses">
<list>
@@ -213,11 +213,11 @@
<tx:annotation-driven/>
- <bean id="txManager" class="org.springframework.orm.hibernate4.HibernateTransactionManager">
+ <bean id="txManager" class="org.springframework.orm.hibernate5.HibernateTransactionManager">
<property name="sessionFactory" ref="SessionFactory"/>
</bean>
- <bean id="transactionManager" class="org.springframework.orm.hibernate4.HibernateTransactionManager">
+ <bean id="transactionManager" class="org.springframework.orm.hibernate5.HibernateTransactionManager">
<property name="sessionFactory" ref="SessionFactory"/>
</bean>
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
index 40344ac58c..f18bf7b318 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/AllDaoTests.java
@@ -17,7 +17,6 @@ import lcsb.mapviewer.persist.dao.user.AllUserTests;
AllMapDaoTests.class, //
AllPluginTests.class, //
AllUserTests.class, //
- BaseDaoTest.class, //
ConfigurationDaoTest.class, //
ProjectDaoTest.class, //
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java
deleted file mode 100644
index 7b77f30315..0000000000
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/BaseDaoTest.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package lcsb.mapviewer.persist.dao;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-
-import org.hibernate.Transaction;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.test.annotation.Rollback;
-
-import lcsb.mapviewer.persist.PersistTestFunctions;
-
-@Rollback(false)
-public class BaseDaoTest extends PersistTestFunctions{
-
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testCommit() {
- try {
-
- dbUtils.createSessionForCurrentThread();
- Transaction tr = userDao.getSession().getTransaction();
- userDao.commit();
- assertTrue(tr.equals(tr));
- Transaction tr2 = userDao.getSession().getTransaction();
-
- assertFalse(tr.equals(tr2));
-
- dbUtils.closeSessionForCurrentThread();
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
-}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
index a534023046..efccbc29eb 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/ProjectDaoTest.java
@@ -24,288 +24,279 @@ import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.persist.PersistTestFunctions;
public class ProjectDaoTest extends PersistTestFunctions {
- Logger logger = Logger.getLogger(ProjectDaoTest.class);
- int identifierCounter = 0;
- String projectId = "Some_id";
-
- @Before
- public void setUp() throws Exception {
- Project project = projectDao.getProjectByProjectId(projectId);
- if (project != null) {
- projectDao.delete(project);
- }
- }
-
- @After
- public void tearDown() throws Exception {
- }
-
- @Test
- public void testGetProjectByName() throws Exception {
- try {
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetProjectForModelId() throws Exception {
- try {
- String projectId = "Some name";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- Model model = new ModelFullIndexed(null);
- project.addModel(model);
- modelDao.add(model);
- modelDao.evict(model);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectForModelId(model.getId());
- assertNotNull(project2);
- assertFalse(project2.equals(project));
- assertEquals(project.getId(), project2.getId());
-
- modelDao.delete(modelDao.getById(model.getId()));
- projectDao.delete(project2);
-
- assertNull(projectDao.getProjectForModelId(model.getId()));
-
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testProjectExists() throws Exception {
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
-
- assertFalse(projectDao.isProjectExistsByName(projectId));
-
- projectDao.add(project);
- projectDao.evict(project);
-
- assertTrue(projectDao.isProjectExistsByName(projectId));
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCheckEqualityAfterReload() throws Exception {
- try {
-
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- projectDao.add(project);
- projectDao.flush();
-
- Model model = createModel();
- project.addModel(model);
-
- projectDao.update(project);
- projectDao.evict(project);
-
- ModelComparator comparator = new ModelComparator();
-
- Model model2 = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(projectId, false));
-
- assertEquals(0, comparator.compare(model, model2));
-
- projectDao.delete(projectDao.getById(project.getId()));
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testCheckEqualityAfterReload2() throws Exception {
- try {
- String project_id = "Some_id";
- Project project = new Project();
- project.setProjectId(project_id);
- Model model = createModel();
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(project_id);
-
- ModelComparator comparator = new ModelComparator();
-
- Model fullModel1 = new ModelFullIndexed(project.getModels().iterator().next());
- Model fullModel2 = new ModelFullIndexed(project2.getModels().iterator().next());
- assertEquals(0, comparator.compare(fullModel1, fullModel2));
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- private Model createModel() {
- Model model = new ModelFullIndexed(null);
-
- model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
- model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
- model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
- model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
-
- Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
- Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
- Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
- alias3.addSpecies(alias);
- alias3.addSpecies(alias2);
- alias.setComplex(alias3);
- alias2.setComplex(alias3);
-
- model.addElement(alias);
- model.addElement(alias2);
- model.addElement(alias3);
-
- model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
- model.setWidth(2000);
- model.setHeight(2000);
- return model;
- }
-
- private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
- Compartment alias = new Compartment(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
- Species alias = new SimpleMolecule(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
- Complex alias = new Complex(aliasId);
- alias.setX(x);
- alias.setY(y);
- alias.setWidth(width);
- alias.setHeight(height);
- return alias;
- }
-
- @Test
- public void testAddGetProjectWithOverviewImage() throws Exception {
- try {
- String projectId = "Some_id";
- Project project = new Project();
- project.setProjectId(projectId);
- Model model = new ModelFullIndexed(null);
- OverviewImage oi = new OverviewImage();
- oi.setFilename("test");
- OverviewModelLink oml = new OverviewModelLink();
- oml.setPolygon("10,10 20,20 20,100");
- oml.setxCoord(1);
- oml.setyCoord(2);
- oml.setZoomLevel(3);
- oi.addLink(oml);
- project.addOverviewImage(oi);
- project.addModel(model);
-
- projectDao.add(project);
- projectDao.evict(project);
-
- Project project2 = projectDao.getProjectByProjectId(projectId);
- assertNotNull(project2);
-
- OverviewImage oi2 = project2.getOverviewImages().get(0);
- OverviewModelLink oml2 = (OverviewModelLink) oi2.getLinks().get(0);
-
- assertEquals(oi.getFilename(), oi2.getFilename());
- assertEquals(oml.getPolygon(), oml2.getPolygon());
- assertEquals(oml.getxCoord(), oml2.getxCoord());
- assertEquals(oml.getyCoord(), oml2.getyCoord());
- assertEquals(oml.getZoomLevel(), oml2.getZoomLevel());
- assertNotNull(oml2.getPolygonCoordinates());
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- /**
- * After adding model to db with creation warnings...
- *
- * @throws Exception
- */
- @Test
- public void testCreationWarnings() throws Exception {
- try {
- Project project = new Project();
- project.addWarning("warning A");
- project.addWarning("warning B");
- assertEquals(2, project.getWarnings().size());
-
- projectDao.add(project);
-
- projectDao.evict(project);
- Project project2 = projectDao.getById(project.getId());
-
- assertEquals(2, project2.getWarnings().size());
-
- projectDao.delete(project2);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
-
- @Test
- public void testGetAll() throws Exception {
- try {
-
- long startTime = System.currentTimeMillis();
- double max = 10;
-
- logger.debug("---");
- for (int i = 0; i < max; i++) {
- projectDao.getAll();
- }
- long estimatedTime = System.currentTimeMillis() - startTime;
- logger.debug(estimatedTime/max);
- } catch (Exception e) {
- e.printStackTrace();
- throw e;
- }
- }
+ Logger logger = Logger.getLogger(ProjectDaoTest.class);
+ int identifierCounter = 0;
+ String projectId = "Some_id";
+
+ @Before
+ public void setUp() throws Exception {
+ Project project = projectDao.getProjectByProjectId(projectId);
+ if (project != null) {
+ projectDao.delete(project);
+ }
+ }
+
+ @After
+ public void tearDown() throws Exception {
+ }
+
+ @Test
+ public void testGetProjectByName() throws Exception {
+ try {
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetProjectForModelId() throws Exception {
+ try {
+ Project project = new Project();
+ project.setProjectId(projectId);
+ projectDao.add(project);
+ Model model = new ModelFullIndexed(null);
+ project.addModel(model);
+ modelDao.add(model);
+ modelDao.evict(model);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectForModelId(model.getId());
+ assertNotNull(project2);
+ assertFalse(project2.equals(project));
+ assertEquals(project.getId(), project2.getId());
+
+ modelDao.delete(modelDao.getById(model.getId()));
+ projectDao.delete(project2);
+
+ assertNull(projectDao.getProjectForModelId(model.getId()));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testProjectExists() throws Exception {
+ try {
+ Project project = new Project(projectId);
+
+ assertFalse(projectDao.isProjectExistsByName(projectId));
+
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ assertTrue(projectDao.isProjectExistsByName(projectId));
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCheckEqualityAfterReload() throws Exception {
+ try {
+ Project project = new Project(projectId);
+ projectDao.add(project);
+ projectDao.flush();
+
+ Model model = createModel();
+ project.addModel(model);
+
+ projectDao.update(project);
+ projectDao.evict(project);
+
+ ModelComparator comparator = new ModelComparator();
+
+ Model model2 = new ModelFullIndexed(modelDao.getLastModelForProjectIdentifier(projectId, false));
+
+ assertEquals(0, comparator.compare(model, model2));
+
+ projectDao.delete(projectDao.getById(project.getId()));
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testCheckEqualityAfterReload2() throws Exception {
+ try {
+ Project project = new Project(projectId);
+ Model model = createModel();
+ project.addModel(model);
+
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+
+ ModelComparator comparator = new ModelComparator();
+
+ Model fullModel1 = new ModelFullIndexed(project.getModels().iterator().next());
+ Model fullModel2 = new ModelFullIndexed(project2.getModels().iterator().next());
+ assertEquals(0, comparator.compare(fullModel1, fullModel2));
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ private Model createModel() {
+ Model model = new ModelFullIndexed(null);
+
+ model.addElement(createSpeciesAlias(264.8333333333335, 517.75, 86.0, 46.0, "sa2"));
+ model.addElement(createSpeciesAlias(267.6666666666665, 438.75, 80.0, 40.0, "sa1117"));
+ model.addElement(createSpeciesAlias(261.6666666666665, 600.75, 92.0, 52.0, "sa1119"));
+ model.addElement(createSpeciesAlias(203.666666666667, 687.75, 98.0, 58.0, "sa1121"));
+
+ Species alias = createSpeciesAlias(817.714285714286, 287.642857142859, 80.0, 40.0, "sa1422");
+ Species alias2 = createSpeciesAlias(224.964285714286, 241.392857142859, 80.0, 40.0, "sa1419");
+ Complex alias3 = createComplexAlias(804.714285714286, 182.642857142859, 112.0, 172.0, "csa152");
+ alias3.addSpecies(alias);
+ alias3.addSpecies(alias2);
+ alias.setComplex(alias3);
+ alias2.setComplex(alias3);
+
+ model.addElement(alias);
+ model.addElement(alias2);
+ model.addElement(alias3);
+
+ model.addElement(createCompartmentAlias(380.0, 416.0, 1893.0, 1866.0, "ca1"));
+ model.setWidth(2000);
+ model.setHeight(2000);
+ return model;
+ }
+
+ private Compartment createCompartmentAlias(double x, double y, double width, double height, String aliasId) {
+ Compartment alias = new Compartment(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Species createSpeciesAlias(double x, double y, double width, double height, String aliasId) {
+ Species alias = new SimpleMolecule(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ private Complex createComplexAlias(double x, double y, double width, double height, String aliasId) {
+ Complex alias = new Complex(aliasId);
+ alias.setX(x);
+ alias.setY(y);
+ alias.setWidth(width);
+ alias.setHeight(height);
+ return alias;
+ }
+
+ @Test
+ public void testAddGetProjectWithOverviewImage() throws Exception {
+ try {
+ Project project = new Project(projectId);
+ Model model = new ModelFullIndexed(null);
+ OverviewImage oi = new OverviewImage();
+ oi.setFilename("test");
+ OverviewModelLink oml = new OverviewModelLink();
+ oml.setPolygon("10,10 20,20 20,100");
+ oml.setxCoord(1);
+ oml.setyCoord(2);
+ oml.setZoomLevel(3);
+ oml.setLinkedModel(model);
+ oi.addLink(oml);
+ project.addOverviewImage(oi);
+ project.addModel(model);
+
+ projectDao.add(project);
+ projectDao.evict(project);
+
+ Project project2 = projectDao.getProjectByProjectId(projectId);
+ assertNotNull(project2);
+
+ OverviewImage oi2 = project2.getOverviewImages().get(0);
+ OverviewModelLink oml2 = (OverviewModelLink) oi2.getLinks().get(0);
+
+ assertEquals(oi.getFilename(), oi2.getFilename());
+ assertEquals(oml.getPolygon(), oml2.getPolygon());
+ assertEquals(oml.getxCoord(), oml2.getxCoord());
+ assertEquals(oml.getyCoord(), oml2.getyCoord());
+ assertEquals(oml.getZoomLevel(), oml2.getZoomLevel());
+ assertNotNull(oml2.getPolygonCoordinates());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ /**
+ * After adding model to db with creation warnings...
+ *
+ * @throws Exception
+ */
+ @Test
+ public void testCreationWarnings() throws Exception {
+ try {
+ Project project = new Project("test_project_id");
+ project.addWarning("warning A");
+ project.addWarning("warning B");
+ assertEquals(2, project.getWarnings().size());
+
+ projectDao.add(project);
+
+ projectDao.evict(project);
+ Project project2 = projectDao.getById(project.getId());
+
+ assertEquals(2, project2.getWarnings().size());
+
+ projectDao.delete(project2);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+ @Test
+ public void testGetAll() throws Exception {
+ try {
+
+ long startTime = System.currentTimeMillis();
+ double max = 10;
+
+ logger.debug("---");
+ for (int i = 0; i < max; i++) {
+ projectDao.getAll();
+ }
+ long estimatedTime = System.currentTimeMillis() - startTime;
+ logger.debug(estimatedTime / max);
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
index d30fcf91f5..4edfbf2585 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/graphics/PolylineDataTest.java
@@ -8,62 +8,61 @@ import static org.junit.Assert.fail;
import java.awt.Color;
import java.awt.geom.Point2D;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.LineType;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.persist.PersistTestFunctions;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
public class PolylineDataTest extends PersistTestFunctions {
- @Before
- public void setUp() throws Exception {
- }
-
- @After
- public void tearDown() throws Exception {
- }
+ @Before
+ public void setUp() throws Exception {
+ }
- @Test
- public void test() {
- try {
- PolylineData pd = new PolylineData();
- pd.getBeginAtd().setArrowType(ArrowType.BLANK_CROSSBAR);
- pd.getBeginAtd().setArrowLineType(LineType.DASHED);
- pd.getBeginAtd().setLen(102);
- pd.setColor(Color.CYAN);
- pd.setType(LineType.SOLID_BOLD);
- pd.setWidth(2);
- pd.getPoints().add(new Point2D.Double(1, 1));
- pd.getPoints().add(new Point2D.Double(2, 3));
- pd.getPoints().add(new Point2D.Double(10, 11));
- polylineDao.add(pd);
- assertNotNull(pd.getId());
- PolylineData pd2 = polylineDao.getById(pd.getId());
- assertNotNull(pd2);
+ @After
+ public void tearDown() throws Exception {
+ }
- assertEquals(ArrowType.BLANK_CROSSBAR, pd2.getBeginAtd().getArrowType());
- assertEquals(LineType.DASHED, pd2.getBeginAtd().getArrowLineType());
- assertEquals(102, pd2.getBeginAtd().getLen(), EPSILON);
- assertEquals(Color.CYAN, pd2.getColor());
- assertEquals(LineType.SOLID_BOLD, pd2.getType());
- assertEquals(2, pd2.getWidth(), EPSILON);
- assertEquals(0, pd2.getPoints().get(0).distance(new Point2D.Double(1, 1)), EPSILON);
- assertEquals(0, pd2.getPoints().get(1).distance(new Point2D.Double(2, 3)), EPSILON);
- assertEquals(0, pd2.getPoints().get(2).distance(new Point2D.Double(10, 11)), EPSILON);
+ @Test
+ public void test() {
+ try {
+ PolylineData pd = new PolylineData();
+ pd.getBeginAtd().setArrowType(ArrowType.BLANK_CROSSBAR);
+ pd.getBeginAtd().setArrowLineType(LineType.DASHED);
+ pd.getBeginAtd().setLen(102);
+ pd.setColor(Color.CYAN);
+ pd.setType(LineType.SOLID_BOLD);
+ pd.setWidth(2);
+ pd.getPoints().add(new Point2D.Double(1, 1));
+ pd.getPoints().add(new Point2D.Double(2, 3));
+ pd.getPoints().add(new Point2D.Double(10, 11));
+ polylineDao.add(pd);
+ assertNotNull(pd.getId());
+ PolylineData pd2 = polylineDao.getById(pd.getId());
+ assertNotNull(pd2);
- polylineDao.delete(pd);
- pd2 = polylineDao.getById(pd.getId());
- assertNull(pd2);
+ assertEquals(ArrowType.BLANK_CROSSBAR, pd2.getBeginAtd().getArrowType());
+ assertEquals(LineType.DASHED, pd2.getBeginAtd().getArrowLineType());
+ assertEquals(102, pd2.getBeginAtd().getLen(), EPSILON);
+ assertEquals(Color.CYAN, pd2.getColor());
+ assertEquals(LineType.SOLID_BOLD, pd2.getType());
+ assertEquals(2, pd2.getWidth(), EPSILON);
+ assertEquals(0, pd2.getPoints().get(0).distance(new Point2D.Double(1, 1)), EPSILON);
+ assertEquals(0, pd2.getPoints().get(1).distance(new Point2D.Double(2, 3)), EPSILON);
+ assertEquals(0, pd2.getPoints().get(2).distance(new Point2D.Double(10, 11)), EPSILON);
- } catch (Exception e) {
- e.printStackTrace();
+ polylineDao.delete(pd);
+ pd2 = polylineDao.getById(pd.getId());
+ assertNull(pd2);
- fail("Unknowne exception occured");
- }
- }
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
index 83572545fd..f09a699ebe 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/LayoutDaoTest.java
@@ -62,7 +62,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
try {
Model model = createModel();
- Project project = new Project();
+ Project project = new Project("test_project_id");
project.addModel(model);
projectDao.add(project);
@@ -108,7 +108,7 @@ public class LayoutDaoTest extends PersistTestFunctions {
createUser();
- Project project = new Project();
+ Project project = new Project("test_project_id");
project.addModel(model);
projectDao.add(project);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
index 0d59dd755f..162f85c7ab 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/ModelDaoTest.java
@@ -323,7 +323,7 @@ public class ModelDaoTest extends PersistTestFunctions {
public void testModificationsInProteins() throws Exception {
try {
Model model = createModel();
- Project project = new Project();
+ Project project = new Project("test_project_id");
project.addModel(model);
projectDao.add(project);
@@ -354,7 +354,7 @@ public class ModelDaoTest extends PersistTestFunctions {
public void testMiriamInSpecies() throws Exception {
try {
Model model = createModel();
- Project project = new Project();
+ Project project = new Project("test_project_id");
project.addModel(model);
projectDao.add(project);
@@ -390,7 +390,7 @@ public class ModelDaoTest extends PersistTestFunctions {
layout.setDirectory("tmp");
layout.setTitle("temporary name");
model.addLayout(layout);
- Project project = new Project();
+ Project project = new Project("test_porject_id");
project.addModel(model);
projectDao.add(project);
diff --git a/pom.xml b/pom.xml
index 6e966eda82..84ca0baa89 100644
--- a/pom.xml
+++ b/pom.xml
@@ -47,6 +47,11 @@
<itext.version>5.5.13</itext.version>
+ <libsbgn.version>0.2</libsbgn.version>
+
+ <hibernate.version>5.3.6.Final</hibernate.version>
+ <jboss-logging.version>3.3.2.Final</jboss-logging.version>
+ <byte-buddy.version>1.9.0</byte-buddy.version>
@@ -90,9 +95,6 @@
<celldesigner.version>4.4</celldesigner.version>
- <libsbgn.version>0.2</libsbgn.version>
-
- <hibernate.version>4.1.0.Final</hibernate.version>
<c3p0.version>0.9.1.2</c3p0.version>
--
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