diff --git a/CHANGELOG b/CHANGELOG
index 6cb73ed408253580a902451e1da882ef33b90e1e..f27a7bc28207ddf045d46d604301709bb912c1cf 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -2,6 +2,9 @@ minerva (18.0.8) stable; urgency=medium
* Bug fix: don't create duplicated refresh jobs (#2165)
* Bug fix: performance issues with caching suggested query list for chemicals
(#2168)
+ * Bug fix: information about species pathway/compartment has not been
+ separated. This caused to export the model into incorrect SBML - species are
+ separated using compartment (#2169)
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 19 Dec 2024 13:00:00 +0200
diff --git a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
index 305c7a799ccb661e230ff59555bdb2faa684f9ad..9db57b4061672e6de5512e362c745ed4468d6409 100644
--- a/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
+++ b/model-command/src/main/java/lcsb/mapviewer/commands/CreateHierarchyCommand.java
@@ -1,15 +1,5 @@
package lcsb.mapviewer.commands;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-
-import org.apache.commons.lang3.math.NumberUtils;
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-
import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.common.exception.NotImplementedException;
@@ -25,14 +15,21 @@ import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
+import org.apache.commons.lang3.math.NumberUtils;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
/**
* This {@link ModelCommand command} class allows to transform model into
* multilevel (nested) component structure. Some artificial compartments will
* appear. All compartments have information about children compartments. All
* objects have information about parents.
- *
- *
*/
public class CreateHierarchyCommand extends ModelCommand {
@@ -54,25 +51,22 @@ public class CreateHierarchyCommand extends ModelCommand {
* Default class logger.
*/
@SuppressWarnings("unused")
- private static Logger logger = LogManager.getLogger();
+ private static final Logger logger = LogManager.getLogger();
/**
* How many levels are possible.
*/
- private int zoomLevels;
+ private final int zoomLevels;
/**
* What is the maximum zoom factor in the view.
*/
- private double maxZoomFactor;
+ private final double maxZoomFactor;
/**
* Default constructor that initializes data.
*
- * @param model
- * model on which command will be executed
- * @param maxZoomFactor
- * what is the maximum zoom out factor
- * @param zoomLevels
- * how many levels are possible
+ * @param model model on which command will be executed
+ * @param maxZoomFactor what is the maximum zoom out factor
+ * @param zoomLevels how many levels are possible
*/
public CreateHierarchyCommand(final Model model, final int zoomLevels, final double maxZoomFactor) {
super(model);
@@ -229,7 +223,7 @@ public class CreateHierarchyCommand extends ModelCommand {
}
private String extractNotesFromText(final String notes) {
- if (notes.indexOf("\n") >= 0) {
+ if (notes.contains("\n")) {
return notes.substring(notes.indexOf("\n"));
} else {
return "";
@@ -237,7 +231,7 @@ public class CreateHierarchyCommand extends ModelCommand {
}
private String extractNameFromText(final String notes) {
- if (notes.indexOf("\n") >= 0) {
+ if (notes.contains("\n")) {
return notes.substring(0, notes.indexOf("\n"));
} else {
return notes;
@@ -272,15 +266,14 @@ public class CreateHierarchyCommand extends ModelCommand {
}
return logValue;
} else {
- return Integer.valueOf(alias.getVisibilityLevel());
+ return Integer.parseInt(alias.getVisibilityLevel());
}
}
/**
* Sets transparency level in hierarchical view for compartment alias.
*
- * @param compartment
- * compartment alias
+ * @param compartment compartment alias
*/
private void settingTransparencyLevelForCompartment(final Compartment compartment) {
if (compartment.getTransparencyLevel() == null || compartment.getTransparencyLevel().isEmpty()) {
@@ -288,7 +281,7 @@ public class CreateHierarchyCommand extends ModelCommand {
double rate = computeRate(compartment, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
for (final Element child : compartment.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(computeVisibility(child)));
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, computeVisibility(child));
}
if (maxVisibilityLevel >= zoomLevels) {
maxVisibilityLevel = zoomLevels;
@@ -308,8 +301,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Sets transparency level in hierarchical view for complex alias.
*
- * @param complex
- * complex alias
+ * @param complex complex alias
*/
private void settingTransparencyLevelForComplex(final Complex complex) {
if (complex.getTransparencyLevel() == null || complex.getTransparencyLevel().isEmpty()) {
@@ -317,7 +309,7 @@ public class CreateHierarchyCommand extends ModelCommand {
double rate = computeRate(complex, Configuration.MAX_VISIBLE_OBJECT_SIZE);
maxVisibilityLevel = (int) ((int) Math.ceil(Math.log(rate)) / LOG_4);
for (final Element child : complex.getElements()) {
- maxVisibilityLevel = Math.min(maxVisibilityLevel, Integer.valueOf(computeVisibility(child)));
+ maxVisibilityLevel = Math.min(maxVisibilityLevel, computeVisibility(child));
}
if (maxVisibilityLevel >= zoomLevels) {
maxVisibilityLevel = zoomLevels;
@@ -337,8 +329,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Sets transparency level in hierarchical view for all elements.
*
- * @param sortedAliases
- * list of aliases
+ * @param sortedAliases list of aliases
*/
private void settingOfTransparencyLevel(final List<Element> sortedAliases) {
for (final Element alias : sortedAliases) {
@@ -357,8 +348,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Removes invalid compartment children.
*
- * @param sortedAliases
- * list of aliases
+ * @param sortedAliases list of aliases
*/
private void setChildrening(final List<Element> sortedAliases) {
for (final Element compartment : sortedAliases) {
@@ -377,8 +367,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Sets parent for elements.
*
- * @param sortedAliases
- * list of aliases
+ * @param sortedAliases list of aliases
*/
private void setParentingOfNonComplexChildrens(final List<Element> sortedAliases) {
for (final Element element : getModel().getElements()) {
@@ -410,8 +399,7 @@ public class CreateHierarchyCommand extends ModelCommand {
/**
* Set parents for the elements in hierarchical view.
*
- * @param sortedAliases
- * list of aliases
+ * @param sortedAliases list of aliases
*/
private void setParentingAndChildreningOfNonComplexChildrens(final List<Element> sortedAliases) {
setParentingOfNonComplexChildrens(sortedAliases);
@@ -427,14 +415,22 @@ public class CreateHierarchyCommand extends ModelCommand {
nullCompartment.setHeight(Double.MAX_VALUE);
for (final Element element : getModel().getElements()) {
Compartment supposedParent = nullCompartment;
- for (final Compartment alias : getModel().getCompartments()) {
- if (alias.contains(element) && alias.getSize() < supposedParent.getSize()) {
- supposedParent = alias;
+ PathwayCompartment supposedPathway = null;
+ for (final Compartment compartment : getModel().getCompartments()) {
+ if (compartment instanceof PathwayCompartment) {
+ if (compartment.contains(element)) {
+ if (supposedPathway == null || compartment.getSize() < supposedPathway.getSize()) {
+ supposedPathway = (PathwayCompartment) compartment;
+ }
+ }
+ } else if (compartment.contains(element) && compartment.getSize() < supposedParent.getSize()) {
+ supposedParent = compartment;
}
}
if (supposedParent != nullCompartment) {
supposedParent.addElement(element);
}
+ element.setPathway(supposedPathway);
}
}
@@ -442,12 +438,9 @@ public class CreateHierarchyCommand extends ModelCommand {
* Computes the ratio between the minimal object that should be visible, and
* alias visible on the top level.
*
- * @param alias
- * alias for which computation is done
- * @param limit
- * size of the minimal visible object
- * @return ratio between the minimal object that should be visible, and alias
- * visible on the top level
+ * @param alias alias for which computation is done
+ * @param limit size of the minimal visible object
+ * @return ratio between the minimal object that should be visible, and alias visible on the top level
*/
private double computeRate(final Element alias, final double limit) {
double length = alias.getWidth() / maxZoomFactor;
diff --git a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
index 438e274b013dca6908805c65d0720409da449480..c9d4eeb036f26bd1da4cddec937eb61797703b1d 100644
--- a/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
+++ b/model-command/src/test/java/lcsb/mapviewer/commands/CopyCommandTest.java
@@ -1,21 +1,5 @@
package lcsb.mapviewer.commands;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.awt.geom.Point2D;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.List;
-
-import org.apache.commons.lang3.mutable.MutableBoolean;
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.MiriamData;
@@ -40,10 +24,25 @@ import lcsb.mapviewer.model.map.reaction.type.TransportReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
+import org.apache.commons.lang3.mutable.MutableBoolean;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.awt.geom.Point2D;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.List;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
public class CopyCommandTest extends CommandTestFunctions {
- private ModelComparator comparator = new ModelComparator();
+ private final ModelComparator comparator = new ModelComparator();
@Before
public void setUp() throws Exception {
@@ -148,7 +147,7 @@ public class CopyCommandTest extends CommandTestFunctions {
}
@Test
- public void testCopyModelWithArtifitialAliases() throws Exception {
+ public void testCopyModelWithArtificialAliases() throws Exception {
Model model = getModelForFile("testFiles/artifitial_compartments.xml", false);
new CreateHierarchyCommand(model, 2, 2).execute();
@@ -292,17 +291,17 @@ public class CopyCommandTest extends CommandTestFunctions {
model.addReaction(reaction);
- assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
- assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+ assertEquals(s1, reaction.getReactants().get(0).getElement());
+ assertEquals(s2, reaction.getProducts().get(0).getElement());
Model model2 = new CopyCommand(model).execute();
Reaction reaction2 = model2.getReactions().iterator().next();
- assertTrue(s1.equals(reaction.getReactants().get(0).getElement()));
- assertTrue(s2.equals(reaction.getProducts().get(0).getElement()));
+ assertEquals(s1, reaction.getReactants().get(0).getElement());
+ assertEquals(s2, reaction.getProducts().get(0).getElement());
- assertFalse(s1.equals(reaction2.getReactants().get(0).getElement()));
- assertFalse(s2.equals(reaction2.getProducts().get(0).getElement()));
+ assertNotEquals(s1, reaction2.getReactants().get(0).getElement());
+ assertNotEquals(s2, reaction2.getProducts().get(0).getElement());
assertNotNull(reaction2.getReactants().get(0).getElement().getCompartment());
assertNotNull(reaction2.getProducts().get(0).getElement().getCompartment());
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
index 6de2dcc99e1079a9ce32cfa5b1f7b467e14f78ba..8f06c45f1471fd924cae31d1696bad2370b0902f 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/species/Element.java
@@ -1,15 +1,31 @@
package lcsb.mapviewer.model.map.species;
-import java.awt.Color;
-import java.awt.geom.Point2D;
-import java.awt.geom.Rectangle2D;
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonSerialize;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
+import lcsb.mapviewer.model.graphics.HorizontalAlign;
+import lcsb.mapviewer.model.graphics.VerticalAlign;
+import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
+import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
+import lcsb.mapviewer.model.map.layout.graphics.Glyph;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.modelutils.serializer.model.map.ElementAsIdSerializer;
+import lcsb.mapviewer.modelutils.serializer.model.map.ModelAsIdSerializer;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+import org.hibernate.annotations.Fetch;
+import org.hibernate.annotations.FetchMode;
+import org.hibernate.annotations.Type;
import javax.persistence.CollectionTable;
import javax.persistence.Column;
@@ -32,34 +48,16 @@ import javax.persistence.ManyToMany;
import javax.persistence.ManyToOne;
import javax.persistence.OrderColumn;
import javax.xml.bind.annotation.XmlTransient;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.hibernate.annotations.Fetch;
-import org.hibernate.annotations.FetchMode;
-import org.hibernate.annotations.Type;
-
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
-import com.fasterxml.jackson.databind.annotation.JsonSerialize;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.common.exception.NotImplementedException;
-import lcsb.mapviewer.model.graphics.HorizontalAlign;
-import lcsb.mapviewer.model.graphics.VerticalAlign;
-import lcsb.mapviewer.model.map.BioEntity;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.compartment.Compartment;
-import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
-import lcsb.mapviewer.model.map.layout.graphics.Glyph;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
-import lcsb.mapviewer.model.map.model.ElementSubmodelConnection;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.modelutils.serializer.model.map.ElementAsIdSerializer;
-import lcsb.mapviewer.modelutils.serializer.model.map.ModelAsIdSerializer;
+import java.awt.Color;
+import java.awt.geom.Point2D;
+import java.awt.geom.Rectangle2D;
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Comparator;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
/**
* Abstract class representing objects in the model. Elements are objects that
@@ -67,7 +65,6 @@ import lcsb.mapviewer.modelutils.serializer.model.map.ModelAsIdSerializer;
* element (like symbol, name, etc.).
*
* @author Piotr Gawron
- *
*/
@Entity
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@@ -137,14 +134,19 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
private ElementSubmodelConnection submodel;
/**
- * {@link Compartment} where element is located. When element lies outside of
+ * {@link Compartment} where element is located. When element lies outside
* every compartment then null value is assigned.
*/
@ManyToOne(fetch = FetchType.LAZY)
- @Cascade({ CascadeType.SAVE_UPDATE })
+ @Cascade({CascadeType.SAVE_UPDATE})
@JsonSerialize(using = ElementAsIdSerializer.class)
private Compartment compartment;
+ @ManyToOne(fetch = FetchType.LAZY)
+ @Cascade({CascadeType.SAVE_UPDATE})
+ @JsonSerialize(using = ElementAsIdSerializer.class)
+ private PathwayCompartment pathway;
+
/**
* Unique string identifier within one model object (usually imported from
* external source from which map was imported).
@@ -206,8 +208,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* From which level element should be visible.
*
* @see #transparencyLevel
- * @see lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params#level
- * AbstractImageGenerator.Params#level
+ * @see lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params#level AbstractImageGenerator.Params#level
*/
private String visibilityLevel = "";
@@ -283,7 +284,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
@CollectionTable(name = "element_synonyms", joinColumns = @JoinColumn(name = "id"))
@Column(name = "synonym", length = 512)
@OrderColumn(name = "idx")
- @Cascade({ org.hibernate.annotations.CascadeType.ALL })
+ @Cascade({org.hibernate.annotations.CascadeType.ALL})
private List<String> synonyms = new ArrayList<>();
/**
@@ -294,27 +295,26 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
@CollectionTable(name = "element_former_symbols", joinColumns = @JoinColumn(name = "id"))
@Column(name = "symbol", length = 255)
@OrderColumn(name = "idx")
- @Cascade({ org.hibernate.annotations.CascadeType.ALL })
+ @Cascade({org.hibernate.annotations.CascadeType.ALL})
private List<String> formerSymbols = new ArrayList<>();
/**
* Set of miriam annotations for this element.
*/
- @Cascade({ CascadeType.ALL })
+ @Cascade({CascadeType.ALL})
@Fetch(FetchMode.SUBSELECT)
@ManyToMany(fetch = FetchType.EAGER)
@JoinTable(name = "element_miriam", joinColumns = {
- @JoinColumn(name = "element_id", referencedColumnName = "id", nullable = false, updatable = false) },
+ @JoinColumn(name = "element_id", referencedColumnName = "id", nullable = false, updatable = false)},
inverseJoinColumns = {
- @JoinColumn(name = "miriam_id", referencedColumnName = "id", nullable = true, updatable = true) })
+ @JoinColumn(name = "miriam_id", referencedColumnName = "id", nullable = true, updatable = true)})
@JsonProperty(value = "references")
private Set<MiriamData> miriamData = new HashSet<>();
/**
* Constructor that creates a copy of the element given in the parameter.
*
- * @param original
- * original object that will be used for creating copy
+ * @param original original object that will be used for creating copy
*/
protected Element(final Element original) {
this.id = original.id;
@@ -373,8 +373,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Adds list of former symbol to the object.
*
- * @param formerSymbols
- * list of former symbols to add
+ * @param formerSymbols list of former symbols to add
*/
public void addFormerSymbols(final List<String> formerSymbols) {
this.formerSymbols.addAll(formerSymbols);
@@ -414,8 +413,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* Methods that increase size of the element by increaseSize. It influence x, y,
* width and height fields of the element.
*
- * @param increaseSize
- * by how many units we want to increase size of the element
+ * @param increaseSize by how many units we want to increase size of the element
*/
public void increaseBorder(final double increaseSize) {
x -= increaseSize;
@@ -428,8 +426,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* This method computes the distance between point and the element. It assumes
* that element is a rectangle.
*
- * @param point
- * point from which we are looking for a distance
+ * @param point point from which we are looking for a distance
* @return distance between point and this element
*/
public double getDistanceFromPoint(final Point2D point) {
@@ -451,25 +448,19 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Checks if element contains a point. It assumes that element is a rectangle.
*
- * @param point
- * point to check
+ * @param point point to check
* @return <i>true</i> if point belongs to the element, <i>false</i> otherwise
*/
public boolean contains(final Point2D point) {
- if (getX() <= point.getX() && getY() <= point.getY() && getX() + getWidth() >= point.getX()
- && getY() + getHeight() >= point.getY()) {
- return true;
- }
- return false;
+ return getX() <= point.getX() && getY() <= point.getY() && getX() + getWidth() >= point.getX()
+ && getY() + getHeight() >= point.getY();
}
/**
* Checks if element contains a {@link LayerText}.
*
- * @param lt
- * text to check
- * @return <i>true</i> if {@link LayerText} belongs to the element, <i>false</i>
- * otherwise
+ * @param lt text to check
+ * @return <i>true</i> if {@link LayerText} belongs to the element, <i>false</i> otherwise
*/
public boolean contains(final LayerText lt) {
return getX() < lt.getX() && getY() < lt.getY() && getX() + getWidth() > lt.getX() + lt.getWidth()
@@ -481,8 +472,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
* This method should be overridden by all inheriting classes - it should
* properly handle other shapes than rectangle.
*
- * @param element2
- * object to be checked
+ * @param element2 object to be checked
* @return true if element2 lies in this object, false otherwise
*/
public boolean contains(final Element element2) {
@@ -492,12 +482,11 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
Point2D p3 = new Point2D.Double(element2.getX() + element2.getWidth(), element2.getY());
Point2D p4 = new Point2D.Double(element2.getX() + element2.getWidth(), element2.getY() + element2.getHeight());
return contains(p1) || contains(p2) || contains(p3) || contains(p4);
- } else if (getX() < element2.getX() && getY() < element2.getY()
- && getX() + getWidth() > element2.getX() + element2.getWidth()
- && getY() + getHeight() > element2.getY() + element2.getHeight()) {
- return true;
+ } else {
+ return getX() < element2.getX() && getY() < element2.getY()
+ && getX() + getWidth() > element2.getX() + element2.getWidth()
+ && getY() + getHeight() > element2.getY() + element2.getHeight();
}
- return false;
}
/**
@@ -545,79 +534,34 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
return x;
}
- /**
- * Parse and set x coordinate from string.
- *
- * @param string
- * text representing x coordinate
- * @see x
- */
public void setX(final String string) {
setX(Double.parseDouble(string));
}
- /**
- *
- * @param x
- * the x value to set
- * @see x
- */
public void setX(final int x) {
setX((double) x);
}
- /**
- * @param x
- * the x to set
- * @see #x
- */
public void setX(final Double x) {
this.x = x;
}
- /**
- * @return the y
- * @see #y
- */
public Double getY() {
return y;
}
- /**
- * Parse and set y coordinate from string.
- *
- * @param string
- * text representing y coordinate
- * @see y
- */
public void setY(final String string) {
this.y = Double.parseDouble(string);
}
- /**
- *
- * @param y
- * the y value to set
- * @see y
- */
public void setY(final int y) {
setY((double) y);
}
- /**
- * @param y
- * the y to set
- * @see #y
- */
public void setY(final Double y) {
this.y = y;
}
- /**
- * Makes a copy of the element.
- *
- * @return copy of the element
- */
@Override
public abstract Element copy();
@@ -632,9 +576,8 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Parse and set width.
*
- * @param string
- * text representing width
- * @see width
+ * @param string text representing width
+ * @see #width
*/
public void setWidth(final String string) {
try {
@@ -645,9 +588,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- *
- * @param width
- * the width value to set
+ * @param width the width value to set
* @see #width
*/
public void setWidth(final int width) {
@@ -655,8 +596,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param width
- * the width to set
+ * @param width the width to set
* @see #width
*/
public void setWidth(final Double width) {
@@ -674,9 +614,8 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Parse and set height.
*
- * @param string
- * text representing height
- * @see height
+ * @param string text representing height
+ * @see #height
*/
public void setHeight(final String string) {
try {
@@ -687,9 +626,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- *
- * @param height
- * the height value to set
+ * @param height the height value to set
* @see #height
*/
public void setHeight(final int height) {
@@ -697,8 +634,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param height
- * the height to set
+ * @param height the height to set
* @see #height
*/
public void setHeight(final Double height) {
@@ -716,17 +652,15 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Parse and set font size.
*
- * @param string
- * text representing font size
- * @see fontSize
+ * @param string text representing font size
+ * @see #fontSize
*/
public void setFontSize(final String string) {
this.fontSize = Double.parseDouble(string);
}
/**
- * @param fontSize
- * the fontSize to set
+ * @param fontSize the fontSize to set
* @see #fontSize
*/
public void setFontSize(final Double fontSize) {
@@ -734,8 +668,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param fontSize
- * the fontSize to set
+ * @param fontSize the fontSize to set
* @see #fontSize
*/
public void setFontSize(final int fontSize) {
@@ -753,8 +686,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param model
- * the model to set
+ * @param model the model to set
* @see #model
*/
public void setModelData(final ModelData model) {
@@ -769,17 +701,23 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
return compartment;
}
+ public PathwayCompartment getPathway() {
+ return pathway;
+ }
+
@Override
public String getVisibilityLevel() {
return visibilityLevel;
}
/**
- * @param compartment
- * the compartment to set
+ * @param compartment the compartment to set
* @see #compartment
*/
public void setCompartment(final Compartment compartment) {
+ if (compartment instanceof PathwayCompartment) {
+ throw new InvalidArgumentException("Pathway cannot be set as a parent compartment");
+ }
if (this.compartment != null && compartment != this.compartment) {
Compartment formerCompartment = this.compartment;
this.compartment = null;
@@ -788,6 +726,10 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
this.compartment = compartment;
}
+ public void setPathway(final PathwayCompartment pathway) {
+ this.pathway = pathway;
+ }
+
@Override
public void setVisibilityLevel(final Integer visibilityLevel) {
if (visibilityLevel == null) {
@@ -811,8 +753,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param color
- * the color to set
+ * @param color the color to set
* @see #fillColor
*/
public void setFillColor(final Color color) {
@@ -828,8 +769,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param transparencyLevel
- * the transparencyLevel to set
+ * @param transparencyLevel the transparencyLevel to set
* @see #transparencyLevel
*/
public void setTransparencyLevel(final String transparencyLevel) {
@@ -845,8 +785,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param submodel
- * the submodel to set
+ * @param submodel the submodel to set
* @see #submodel
*/
public void setSubmodel(final ElementSubmodelConnection submodel) {
@@ -865,8 +804,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param fullName
- * the fullName to set
+ * @param fullName the fullName to set
* @see #fullName
*/
public void setFullName(final String fullName) {
@@ -892,8 +830,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param model
- * the model to set
+ * @param model the model to set
* @see #model
*/
public void setModel(final Model model) {
@@ -901,8 +838,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param formerSymbols
- * the formerSymbols to set
+ * @param formerSymbols the formerSymbols to set
* @see #formerSymbols
*/
public void setFormerSymbols(final List<String> formerSymbols) {
@@ -919,8 +855,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param miriamData
- * the miriamData to set
+ * @param miriamData the miriamData to set
* @see #miriamData
*/
public void setMiriamData(final Set<MiriamData> miriamData) {
@@ -964,8 +899,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param id
- * the id to set
+ * @param id the id to set
* @see #id
*/
public void setId(final int id) {
@@ -997,8 +931,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param symbol
- * the symbol to set
+ * @param symbol the symbol to set
* @see #symbol
*/
@Override
@@ -1025,8 +958,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param synonyms
- * the synonyms to set
+ * @param synonyms the synonyms to set
* @see #synonyms
*/
@Override
@@ -1035,8 +967,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param formula
- * the formula to set
+ * @param formula the formula to set
* @see #formula
*/
@Override
@@ -1054,8 +985,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param abbreviation
- * the abbreviation to set
+ * @param abbreviation the abbreviation to set
* @see #abbreviation
*/
@Override
@@ -1066,8 +996,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Adds synonyms to the element.
*
- * @param synonyms
- * list of synonyms to be added
+ * @param synonyms list of synonyms to be added
*/
public void addSynonyms(final List<String> synonyms) {
for (final String string : synonyms) {
@@ -1084,8 +1013,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Adds former symbol to the object.
*
- * @param formerSymbol
- * former symbol to add
+ * @param formerSymbol former symbol to add
*/
public void addFormerSymbol(final String formerSymbol) {
formerSymbols.add(formerSymbol);
@@ -1094,8 +1022,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
/**
* Adds synonym to object.
*
- * @param synonym
- * synonym to be added
+ * @param synonym synonym to be added
*/
public void addSynonym(final String synonym) {
synonyms.add(synonym);
@@ -1136,8 +1063,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
}
/**
- * @param elementId
- * the elementId to set
+ * @param elementId the elementId to set
* @see #elementId
*/
public void setElementId(final String elementId) {
diff --git a/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql b/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
new file mode 100644
index 0000000000000000000000000000000000000000..d69460f18a8fbc7f7edec8f85b60587d41bee205
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
@@ -0,0 +1,31 @@
+update element_table child
+set compartment_id = null
+where element_type_db = 'PATHWAY';
+
+update element_table child
+set compartment_id =
+ (select id
+ from element_table parent
+ where parent.element_type_db like '%COMPARTMENT'
+ and parent.model_id = child.model_id
+ and parent.x < child.x + child.width
+ and parent.x + parent.width > child.x
+ and parent.y < child.y + child.height
+ and parent.y + parent.height > child.y
+ order by parent.width * parent.height
+ limit 1)
+where element_type_db <> 'PATHWAY';
+;
+
+update element_table child
+set pathway_id =
+ (select id
+ from element_table parent
+ where parent.element_type_db = 'PATHWAY'
+ and parent.model_id = child.model_id
+ and parent.x < child.x + child.width
+ and parent.x + parent.width > child.x
+ and parent.y < child.y + child.height
+ and parent.y + parent.height > child.y
+ order by parent.width * parent.height
+ limit 1);
diff --git a/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql b/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql
new file mode 100644
index 0000000000000000000000000000000000000000..fc251495f2400b37a78496bb45f450c2c42728b8
--- /dev/null
+++ b/persist/src/main/resources/db/migration/hsql/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql
@@ -0,0 +1,5 @@
+alter table element_table
+ add column pathway_id integer;
+
+ALTER TABLE element_table
+ ADD CONSTRAINT element_table_pathway_fk FOREIGN KEY (pathway_id) REFERENCES public.element_table (id);
diff --git a/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql b/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
new file mode 100644
index 0000000000000000000000000000000000000000..d69460f18a8fbc7f7edec8f85b60587d41bee205
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230.2__set_proper_pathway_and_compartment.sql
@@ -0,0 +1,31 @@
+update element_table child
+set compartment_id = null
+where element_type_db = 'PATHWAY';
+
+update element_table child
+set compartment_id =
+ (select id
+ from element_table parent
+ where parent.element_type_db like '%COMPARTMENT'
+ and parent.model_id = child.model_id
+ and parent.x < child.x + child.width
+ and parent.x + parent.width > child.x
+ and parent.y < child.y + child.height
+ and parent.y + parent.height > child.y
+ order by parent.width * parent.height
+ limit 1)
+where element_type_db <> 'PATHWAY';
+;
+
+update element_table child
+set pathway_id =
+ (select id
+ from element_table parent
+ where parent.element_type_db = 'PATHWAY'
+ and parent.model_id = child.model_id
+ and parent.x < child.x + child.width
+ and parent.x + parent.width > child.x
+ and parent.y < child.y + child.height
+ and parent.y + parent.height > child.y
+ order by parent.width * parent.height
+ limit 1);
diff --git a/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql b/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql
new file mode 100644
index 0000000000000000000000000000000000000000..fc251495f2400b37a78496bb45f450c2c42728b8
--- /dev/null
+++ b/persist/src/main/resources/db/migration/postgres/18.0.8/V18.0.8.20241230__add_pathway_to_element.sql
@@ -0,0 +1,5 @@
+alter table element_table
+ add column pathway_id integer;
+
+ALTER TABLE element_table
+ ADD CONSTRAINT element_table_pathway_fk FOREIGN KEY (pathway_id) REFERENCES public.element_table (id);
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctionsNoTransaction.java b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctionsNoTransaction.java
index d4078c8e1ecc0f12fe3e954914d222352061f4d1..826d9aee4c2fe5e21000e78c1bf0b2761573abd1 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctionsNoTransaction.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/PersistTestFunctionsNoTransaction.java
@@ -1,13 +1,5 @@
package lcsb.mapviewer.persist;
-import java.awt.Color;
-import java.awt.geom.Point2D;
-
-import org.junit.Rule;
-import org.junit.runner.RunWith;
-import org.springframework.test.context.ContextConfiguration;
-import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
-
import lcsb.mapviewer.common.geometry.PointTransformation;
import lcsb.mapviewer.common.tests.TestUtils;
import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
@@ -38,17 +30,24 @@ import lcsb.mapviewer.model.map.species.field.ModificationResidue;
import lcsb.mapviewer.model.map.species.field.ModificationSite;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.Residue;
+import org.junit.Rule;
+import org.junit.runner.RunWith;
+import org.springframework.test.context.ContextConfiguration;
+import org.springframework.test.context.junit4.SpringJUnit4ClassRunner;
+
+import java.awt.Color;
+import java.awt.geom.Point2D;
@ContextConfiguration(classes = SpringPersistTestConfig.class)
@RunWith(SpringJUnit4ClassRunner.class)
-public class PersistTestFunctionsNoTransaction extends TestUtils {
+public abstract class PersistTestFunctionsNoTransaction extends TestUtils {
@Rule
public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
private static int identifierCounter = 0;
- private PointTransformation pt = new PointTransformation();
+ private final PointTransformation pt = new PointTransformation();
private static int z = 0;
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
index 343374f35cef6307a76e009e579d07b05ac8897e..4589a948d912fce5a7d1bd5eaf7aec97b7905301 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/AllLayoutTests.java
@@ -4,10 +4,8 @@ import org.junit.runner.RunWith;
import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
-import lcsb.mapviewer.persist.dao.map.layout.alias.AllAliasTests;
-
@RunWith(Suite.class)
-@SuiteClasses({ AllAliasTests.class,
+@SuiteClasses({
ReferenceGenomeDaoTest.class,
ReferenceGenomeGeneMappingDaoTest.class,
})
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
deleted file mode 100644
index ff90f895e38e5d5d572169e595fe25c87f87b686..0000000000000000000000000000000000000000
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AllAliasTests.java
+++ /dev/null
@@ -1,15 +0,0 @@
-package lcsb.mapviewer.persist.dao.map.layout.alias;
-
-import org.junit.runner.RunWith;
-import org.junit.runners.Suite;
-import org.junit.runners.Suite.SuiteClasses;
-
-@RunWith(Suite.class)
-@SuiteClasses({ AntisenseRnaTest.class,
- ElementDaoTest.class,
- ElementDaoGetByQueryTest.class,
- RnaTest.class,
-})
-public class AllAliasTests {
-
-}
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
index 8807f4d53dc0a25c338ea96eaa780e6440e0d0df..f950c5984786b157525251c2080cfb814177bc42 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/AntisenseRnaTest.java
@@ -1,14 +1,5 @@
package lcsb.mapviewer.persist.dao.map.layout.alias;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -18,6 +9,14 @@ import lcsb.mapviewer.model.map.species.field.CodingRegion;
import lcsb.mapviewer.model.user.User;
import lcsb.mapviewer.persist.PersistTestFunctions;
import lcsb.mapviewer.persist.dao.ProjectDao;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
public class AntisenseRnaTest extends PersistTestFunctions {
@@ -25,7 +24,7 @@ public class AntisenseRnaTest extends PersistTestFunctions {
@Autowired
private ProjectDao projectDao;
-
+
@Before
public void setUp() throws Exception {
admin = userDao.getUserByLogin(BUILT_IN_TEST_ADMIN_LOGIN);
@@ -48,7 +47,7 @@ public class AntisenseRnaTest extends PersistTestFunctions {
Project project2 = projectDao.getProjectByProjectId(TEST_PROJECT_ID);
assertNotNull(project2);
- assertFalse(project2.equals(project));
+ assertNotEquals(project2, project);
assertEquals(project.getId(), project2.getId());
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoGetByQueryTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoGetByQueryTest.java
index 052bfe179d2ffbfd8f1bdeebcadc4b07f06dbb98..255e923374ea11f991ed9f3179af92139f437249 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoGetByQueryTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoGetByQueryTest.java
@@ -1,28 +1,5 @@
package lcsb.mapviewer.persist.dao.map.layout.alias;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import org.apache.logging.log4j.LogManager;
-import org.apache.logging.log4j.Logger;
-import org.junit.AfterClass;
-import org.junit.BeforeClass;
-import org.junit.Test;
-import org.junit.runner.RunWith;
-import org.junit.runners.Parameterized;
-import org.junit.runners.Parameterized.Parameters;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.annotation.AnnotationConfigApplicationContext;
-import org.springframework.data.domain.PageRequest;
-
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelData;
@@ -37,6 +14,29 @@ import lcsb.mapviewer.persist.SpringPersistTestConfig;
import lcsb.mapviewer.persist.dao.map.species.ElementProperty;
import lcsb.mapviewer.persist.utils.TransactionalElementDao;
import lcsb.mapviewer.persist.utils.TransactionalModelDao;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.springframework.context.ApplicationContext;
+import org.springframework.context.annotation.AnnotationConfigApplicationContext;
+import org.springframework.data.domain.PageRequest;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
@RunWith(Parameterized.class)
public class ElementDaoGetByQueryTest extends PersistTestFunctions {
@@ -44,24 +44,21 @@ public class ElementDaoGetByQueryTest extends PersistTestFunctions {
private static ApplicationContext applicationContext;
@SuppressWarnings("unused")
- private Logger logger = LogManager.getLogger();
-
- private TransactionalElementDao elementDao;
+ private static final Logger logger = LogManager.getLogger();
- private List<ModelData> maps;
+ private final TransactionalElementDao elementDao;
private static List<ModelData> testMaps;
- private String query;
+ private final String query;
- private boolean perfect;
+ private final boolean perfect;
- private List<Element> expectedResult;
+ private final List<Element> expectedResult;
- private List<Class<? extends BioEntity>> types;
+ private final List<Class<? extends BioEntity>> types;
public ElementDaoGetByQueryTest(final String testName, final Model map, final String query, final boolean perfect, final Object result) {
- maps = Arrays.asList(map.getModelData());
this.query = query;
this.perfect = perfect;
this.expectedResult = new ArrayList<>();
@@ -69,7 +66,7 @@ public class ElementDaoGetByQueryTest extends PersistTestFunctions {
this.types = new ElementUtils().getClassesByStringTypes(new ElementUtils().getBioEntityStringTypes());
} else if (result instanceof Element) {
Element bioEntity = (Element) result;
- this.types = Arrays.asList(bioEntity.getClass());
+ this.types = Collections.singletonList(bioEntity.getClass());
this.expectedResult.add(bioEntity);
} else {
this.types = new ArrayList<>();
@@ -109,35 +106,35 @@ public class ElementDaoGetByQueryTest extends PersistTestFunctions {
applicationContext = new AnnotationConfigApplicationContext(SpringPersistTestConfig.class);
- Collection<Object[]> data = new ArrayList<Object[]>();
- data.add(new Object[] { "existing name perfect match", map, protein.getName(), true, protein });
- data.add(new Object[] { "existing name not-perfect match", map, "snn", false, protein });
- data.add(new Object[] { "not existing name perfect match", map, "snn", true, null });
- data.add(new Object[] { "not existing name not-perfect match", map, "bla", false, null });
+ Collection<Object[]> data = new ArrayList<>();
+ data.add(new Object[]{"existing name perfect match", map, protein.getName(), true, protein});
+ data.add(new Object[]{"existing name not-perfect match", map, "snn", false, protein});
+ data.add(new Object[]{"not existing name perfect match", map, "snn", true, null});
+ data.add(new Object[]{"not existing name not-perfect match", map, "bla", false, null});
- data.add(new Object[] { "existing full name perfect match", map, protein.getFullName(), true, protein });
- data.add(new Object[] { "existing full name not-perfect match", map, "BTR5", false, protein });
- data.add(new Object[] { "not existing full name perfect match", map, "BTR5", true, null });
+ data.add(new Object[]{"existing full name perfect match", map, protein.getFullName(), true, protein});
+ data.add(new Object[]{"existing full name not-perfect match", map, "BTR5", false, protein});
+ data.add(new Object[]{"not existing full name perfect match", map, "BTR5", true, null});
- data.add(new Object[] { "existing element id perfect match", map, protein.getElementId(), true, protein });
- data.add(new Object[] { "existing element id not-perfect match", map, protein.getElementId().substring(1), false,
- protein });
+ data.add(new Object[]{"existing element id perfect match", map, protein.getElementId(), true, protein});
+ data.add(new Object[]{"existing element id not-perfect match", map, protein.getElementId().substring(1), false,
+ protein});
- data.add(new Object[] { "existing synonym perfect match", map, "fancy synonym", true, protein });
- data.add(new Object[] { "existing synonym not-perfect match", map, "synonym", false, protein });
- data.add(new Object[] { "not existing synonym perfect match", map, "synonym", true, null });
+ data.add(new Object[]{"existing synonym perfect match", map, "fancy synonym", true, protein});
+ data.add(new Object[]{"existing synonym not-perfect match", map, "synonym", false, protein});
+ data.add(new Object[]{"not existing synonym perfect match", map, "synonym", true, null});
- data.add(new Object[] { "existing former symbol perfect match", map, "former symbol2", true, protein });
- data.add(new Object[] { "existing former symbol not-perfect match", map, "symbol2", false, protein });
- data.add(new Object[] { "not existing former symbol perfect match", map, "symbol2", true, null });
+ data.add(new Object[]{"existing former symbol perfect match", map, "former symbol2", true, protein});
+ data.add(new Object[]{"existing former symbol not-perfect match", map, "symbol2", false, protein});
+ data.add(new Object[]{"not existing former symbol perfect match", map, "symbol2", true, null});
- data.add(new Object[] { "element without synonym and former symbol ", map, ion.getElementId(), false, ion });
+ data.add(new Object[]{"element without synonym and former symbol ", map, ion.getElementId(), false, ion});
- data.add(new Object[] { "type selection", map, "ion", false, ion });
+ data.add(new Object[]{"type selection", map, "ion", false, ion});
- data.add(new Object[] { "sort order", map, "ion", false, Arrays.asList(falseIon, falseIon2, ion) });
+ data.add(new Object[]{"sort order", map, "ion", false, Arrays.asList(falseIon, falseIon2, ion)});
- testMaps = Arrays.asList(map.getModelData());
+ testMaps = Collections.singletonList(map.getModelData());
return data;
}
@@ -150,7 +147,7 @@ public class ElementDaoGetByQueryTest extends PersistTestFunctions {
}
@AfterClass
- public static void shutdown() throws Exception {
+ public static void shutdown() {
TransactionalModelDao modelDao = applicationContext.getBean(TransactionalModelDao.class);
for (final ModelData map : testMaps) {
modelDao.delete(map);
@@ -159,12 +156,12 @@ public class ElementDaoGetByQueryTest extends PersistTestFunctions {
@Test
public void test() throws Exception {
- Map<ElementProperty, List<? extends Object>> filter = new HashMap<>();
- filter.put(ElementProperty.MAP, maps);
+ Map<ElementProperty, List<?>> filter = new HashMap<>();
+ filter.put(ElementProperty.MAP, testMaps);
if (perfect) {
- filter.put(ElementProperty.PERFECT_TEXT, Arrays.asList(query));
+ filter.put(ElementProperty.PERFECT_TEXT, Collections.singletonList(query));
} else {
- filter.put(ElementProperty.TEXT, Arrays.asList(query));
+ filter.put(ElementProperty.TEXT, Collections.singletonList(query));
}
filter.put(ElementProperty.CLASS, types);
List<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), filter).getContent();
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoTest.java
index bf1133aaa3df1fa75e91d1cbb716e6f560256db5..0f6ebe00c97fe6df86560592976dab12d82bde9a 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/ElementDaoTest.java
@@ -39,6 +39,7 @@ import org.springframework.data.domain.Pageable;
import java.awt.geom.Point2D;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -60,13 +61,13 @@ public class ElementDaoTest extends PersistTestFunctions {
@Autowired
private ProjectDao projectDao;
- private Integer testChargeVal = 1;
- private String testIdAlias = "a";
- private Double testInitialAmount = 2.0;
- private Double testInitialConcentration = 3.0;
- private String testName = "d";
- private String testNotes = "e";
- private Boolean testOnlySubstanceunits = true;
+ private final Integer testChargeVal = 1;
+ private final String testIdAlias = "a";
+ private final Double testInitialAmount = 2.0;
+ private final Double testInitialConcentration = 3.0;
+ private final String testName = "d";
+ private final String testNotes = "e";
+ private final Boolean testOnlySubstanceunits = true;
@Before
public void setUp() throws Exception {
@@ -474,7 +475,7 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
List<Element> elements = elementDao.getByCoordinates(map.getModelData(), new Point2D.Double(150, 150), 3,
- Arrays.asList(Ion.class));
+ Collections.singletonList(Ion.class));
assertNotNull(elements);
assertEquals(1, elements.size());
@@ -504,8 +505,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -524,8 +525,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "snca")));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "snca")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -547,7 +548,7 @@ public class ElementDaoTest extends PersistTestFunctions {
Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData(), map2.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -566,8 +567,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<? extends Object>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -585,8 +586,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -605,8 +606,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "snca")));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "snca")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -628,7 +629,7 @@ public class ElementDaoTest extends PersistTestFunctions {
Map<ElementProperty, List<?>> properties = new HashMap<>();
properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData(), map2.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -647,8 +648,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.ANNOTATION, Arrays.asList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.ANNOTATION, Collections.singletonList(new MiriamData(MiriamType.HGNC_SYMBOL, "SNCA")));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -666,8 +667,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.NAME, Arrays.asList("BLA"));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.NAME, Collections.singletonList("BLA"));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -689,12 +690,12 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.SUBMAP_CONNECTION, Arrays.asList(Boolean.TRUE));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.SUBMAP_CONNECTION, Collections.singletonList(Boolean.TRUE));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
- assertEquals(Arrays.asList(protein), elements.getContent());
+ assertEquals(Collections.singletonList(protein), elements.getContent());
}
@Test
@@ -707,8 +708,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.NAME, Arrays.asList("BL"));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.NAME, Collections.singletonList("BL"));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -733,7 +734,7 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
- List<String> elements = elementDao.getSuggestedQueries(Arrays.asList(map.getModelData()));
+ List<String> elements = elementDao.getSuggestedQueries(Collections.singletonList(map.getModelData()));
assertEquals(Arrays.asList("fname", "name1", "symb1", "symb2", "syn1", "syn2"), elements);
}
@@ -758,7 +759,7 @@ public class ElementDaoTest extends PersistTestFunctions {
projectDao.add(project2);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.PROJECT, Arrays.asList(map.getProject()));
+ properties.put(ElementProperty.PROJECT, Collections.singletonList(map.getProject()));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -776,7 +777,7 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.CLASS, Arrays.asList(Ion.class));
+ properties.put(ElementProperty.CLASS, Collections.singletonList(Ion.class));
Page<Element> elements = elementDao.getByFilter(PageRequest.of(0, 10), properties);
@@ -794,8 +795,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.ID, Arrays.asList(ion.getId()));
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
+ properties.put(ElementProperty.ID, Collections.singletonList(ion.getId()));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
Page<Element> element = elementDao.getByFilter(Pageable.unpaged(), properties);
@@ -814,9 +815,9 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(model);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.ID, Arrays.asList(ion.getId()));
- properties.put(ElementProperty.MAP, Arrays.asList(model.getModelData()));
- properties.put(ElementProperty.PROJECT, Arrays.asList(project));
+ properties.put(ElementProperty.ID, Collections.singletonList(ion.getId()));
+ properties.put(ElementProperty.MAP, Collections.singletonList(model.getModelData()));
+ properties.put(ElementProperty.PROJECT, Collections.singletonList(project));
Page<Element> element = elementDao.getByFilter(Pageable.unpaged(), properties);
@@ -833,8 +834,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.PERFECT_TEXT, Arrays.asList(ion.getId() + ""));
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
+ properties.put(ElementProperty.PERFECT_TEXT, Collections.singletonList(ion.getId() + ""));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
Page<Element> element = elementDao.getByFilter(Pageable.unpaged(), properties);
@@ -855,8 +856,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.INCLUDED_IN_COMPARTMENT, Arrays.asList(compartment.getId()));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.INCLUDED_IN_COMPARTMENT, Collections.singletonList(compartment.getId()));
Page<Element> elements = elementDao.getByFilter(Pageable.unpaged(), properties);
assertEquals(1, elements.getContent().size());
@@ -878,8 +879,8 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.MAP, Arrays.asList(map.getModelData()));
- properties.put(ElementProperty.EXCLUDED_FROM_COMPARTMENT, Arrays.asList(compartment.getId()));
+ properties.put(ElementProperty.MAP, Collections.singletonList(map.getModelData()));
+ properties.put(ElementProperty.EXCLUDED_FROM_COMPARTMENT, Collections.singletonList(compartment.getId()));
Page<Element> elements = elementDao.getByFilter(Pageable.unpaged(), properties);
assertEquals(2, elements.getContent().size());
@@ -896,7 +897,7 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
Map<ElementProperty, List<?>> properties = new HashMap<>();
- properties.put(ElementProperty.ID, Arrays.asList(ion.getId()));
+ properties.put(ElementProperty.ID, Collections.singletonList(ion.getId()));
Page<Element> element = elementDao.getByFilter(Pageable.unpaged(), properties);
@@ -920,7 +921,7 @@ public class ElementDaoTest extends PersistTestFunctions {
modelDao.add(map);
- Map<MiriamType, Integer> result = elementDao.getAnnotationStatistics(Arrays.asList(map.getModelData()));
+ Map<MiriamType, Integer> result = elementDao.getAnnotationStatistics(Collections.singletonList(map.getModelData()));
assertEquals((Integer) 4, result.get(MiriamType.HGNC_SYMBOL));
assertEquals((Integer) 1, result.get(MiriamType.HGNC));
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
index cad5536e4abfcd58c0c6e8fb0a307d8c9f27a3dc..e4c0b009068b658b11075bb3b47d3fe081afb8b7 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/map/layout/alias/RnaTest.java
@@ -1,14 +1,5 @@
package lcsb.mapviewer.persist.dao.map.layout.alias;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-
-import org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
-import org.springframework.beans.factory.annotation.Autowired;
-
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
@@ -16,6 +7,14 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Rna;
import lcsb.mapviewer.persist.PersistTestFunctions;
import lcsb.mapviewer.persist.dao.ProjectDao;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotEquals;
+import static org.junit.Assert.assertNotNull;
public class RnaTest extends PersistTestFunctions {
@@ -43,7 +42,7 @@ public class RnaTest extends PersistTestFunctions {
Project project2 = projectDao.getProjectByProjectId(TEST_PROJECT_ID);
assertNotNull(project2);
- assertFalse(project2.equals(project));
+ assertNotEquals(project2, project);
assertEquals(project.getId(), project2.getId());
Model model2 = new ModelFullIndexed(project2.getModels().iterator().next());
diff --git a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
index 3f6b1a2084d87ff86df142a81b71efbe41af8aea..62ad21b1637c23c0a76ceb99b37f52ae8350a251 100644
--- a/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
+++ b/web/src/test/java/lcsb/mapviewer/web/api/NewApiDocs.java
@@ -149,7 +149,7 @@ public class NewApiDocs {
.optional()
.type(JsonFieldType.NUMBER),
fieldWithPath(prefix + "color")
- .description("color that shoyld be used when drawing overlay entry")
+ .description("color that should be used when drawing overlay entry")
.optional()
.type(JsonFieldType.OBJECT),
fieldWithPath(prefix + "description")
@@ -163,8 +163,7 @@ public class NewApiDocs {
}
private List<FieldDescriptor> getReactionCsvFields() {
- final List<FieldDescriptor> result = new ArrayList<>();
- result.addAll(Arrays.asList(
+ return new ArrayList<>(Arrays.asList(
fieldWithPath("elementTypes")
.description("list of element types")
.type(JsonFieldType.ARRAY),
@@ -186,12 +185,10 @@ public class NewApiDocs {
fieldWithPath("excludedCompartmentIds")
.description("list of compartment identifiers where all participant should not be present")
.type(JsonFieldType.ARRAY)));
- return result;
}
private List<FieldDescriptor> getElementCsvFields() {
- final List<FieldDescriptor> result = new ArrayList<>();
- result.addAll(Arrays.asList(
+ return new ArrayList<>(Arrays.asList(
fieldWithPath("types")
.description("list of element types")
.type(JsonFieldType.ARRAY),
@@ -210,7 +207,6 @@ public class NewApiDocs {
fieldWithPath("excludedCompartmentIds")
.description("list of compartment identifiers from which elements should be excluded")
.type(JsonFieldType.ARRAY)));
- return result;
}
private List<FieldDescriptor> getBioEntityFields(final String prefix) {
@@ -310,8 +306,7 @@ public class NewApiDocs {
}
private List<FieldDescriptor> getSpeciesSpecificFields(final String prefix) {
- final List<FieldDescriptor> result = new ArrayList<>();
- result.addAll(Arrays.asList(
+ final List<FieldDescriptor> result = new ArrayList<>(Arrays.asList(
fieldWithPath(prefix + "nameX")
.description("x coordinate of the element name on the map")
.type(JsonFieldType.NUMBER)
@@ -452,6 +447,11 @@ public class NewApiDocs {
.type(JsonFieldType.NUMBER)
.optional(),
+ fieldWithPath(prefix + "pathway")
+ .description("identifier of a pathway in which element is located")
+ .type(JsonFieldType.NUMBER)
+ .optional(),
+
fieldWithPath(prefix + "compartmentName")
.description("name of a compartment in which element is located")
.type(JsonFieldType.STRING)
@@ -549,7 +549,7 @@ public class NewApiDocs {
final List<FieldDescriptor> result = new ArrayList<>();
result.addAll(Arrays.asList(
fieldWithPath(prefix + "idReaction")
- .description("resction identifier taken from source file")
+ .description("reaction identifier taken from source file")
.type(JsonFieldType.STRING)
.optional(),
fieldWithPath(prefix + "reversible")