Merge remote-tracking branch 'origin/master' into...

Merge remote-tracking branch 'origin/master' into 1455-reactions-overlap-structural-modification-bubbles

.gitlab-ci.yml

@@ -350,6 +350,18 @@ test:dependency_conflict:
     - cat conflicts.txt
     - test 0 = $conflicts
 
+test:code_validation:
+  image: maven:3.6.0-jdk-8
+  stage: test
+  script:
+    - apt-get update
+    - DEBIAN_FRONTEND=noninteractive apt-get install -y curl gnupg git ant
+    - curl -sL https://deb.nodesource.com/setup_9.x | bash -
+    - DEBIAN_FRONTEND=noninteractive apt-get install -y nodejs
+
+    - mvn clean compile validate
+
+
 test:mvn_changelog_version_check:
   image: debian
   stage: test

.project

@@ -30,6 +30,5 @@
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
 		<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
-		<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
 	</natures>
 </projectDescription>

CellDesigner-plugin/.project

@@ -24,6 +24,5 @@
 	<natures>
 		<nature>org.eclipse.jdt.core.javanature</nature>
 		<nature>org.eclipse.m2e.core.maven2Nature</nature>
-		<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
 	</natures>
 </projectDescription>

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyAction.java

@@ -3,7 +3,11 @@ package lcsb.mapviewer.cdplugin.copypaste;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.SystemClipboard;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 
@@ -29,7 +33,7 @@ public class CopyAction extends CopyPasteAbstractAction {
    * @param speciesList
    *          - list of species to annotate
    */
-  public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList) {
+  public void performAnnotation(final CopyPastePlugin plug, final PluginListOf speciesList) {
     SystemClipboard sc = new SystemClipboard();
 
     int size = speciesList.size();
@@ -66,7 +70,7 @@ public class CopyAction extends CopyPasteAbstractAction {
     if (chosenElement != null) {
       try {
         sc.setClipboardContents(getCopyString(chosenElement.getAnnotationString(), chosenElement.getNotesString()));
-      } catch (InvalidXmlSchemaException e) {
+      } catch (final InvalidXmlSchemaException e) {
         logger.warn("Problem with creating copy-paste String", e);
       }
     }

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java

@@ -9,7 +9,9 @@ import org.apache.logging.log4j.Logger;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
-import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamRelationType;
+import lcsb.mapviewer.model.map.MiriamType;
 
 /**
  * This abstract class defines common function for {@link CopyAction} and
@@ -38,7 +40,7 @@ public class CopyPasteAbstractAction {
    *          object to serialize
    * @return string representation of {@link MiriamData}
    */
-  protected String serialize(MiriamData md) {
+  protected String serialize(final MiriamData md) {
     return PREFIX + "\t" + md.getRelationType().getStringRepresentation() + "\t" + md.getDataType().getUris().get(0)
         + "\t" + md.getResource();
   }
@@ -51,7 +53,7 @@ public class CopyPasteAbstractAction {
    *          string representation of {@link MiriamData}
    * @return {@link MiriamData} obtained from input string
    */
-  protected MiriamData deserialize(String string) {
+  protected MiriamData deserialize(final String string) {
     if (string == null) {
       return null;
     }
@@ -86,11 +88,11 @@ public class CopyPasteAbstractAction {
    * @throws InvalidXmlSchemaException
    *           thrown when xmlString is invalid
    */
-  protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
+  protected String getCopyString(final String annotationString, final String notesString) throws InvalidXmlSchemaException {
     XmlAnnotationParser xap = new XmlAnnotationParser();
     Set<MiriamData> set = xap.parse(annotationString, null);
     StringBuilder result = new StringBuilder();
-    for (MiriamData md : set) {
+    for (final MiriamData md : set) {
       result.append(serialize(md) + "\n");
     }
     result.append(notesString);
@@ -106,7 +108,7 @@ public class CopyPasteAbstractAction {
    * 
    * @return {@link Pair} of {@link MiriamData} set and notes string
    */
-  protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(String value) {
+  protected Pair<Set<MiriamData>, String> getAnnotationDataFromClipboardString(final String value) {
     if (value == null) {
       return new Pair<Set<MiriamData>, String>(null, null);
     }

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPastePlugin.java

 package lcsb.mapviewer.cdplugin.copypaste;
 
-import java.awt.*;
+import java.awt.KeyEventDispatcher;
+import java.awt.KeyboardFocusManager;
 import java.awt.event.KeyEvent;
 
 import org.apache.logging.log4j.LogManager;
@@ -13,7 +14,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
 /**
  * This class represent a plugin to cell designer with copy past functionality
  * that allows to copy and paste notes and annotations of species.
- * 
+ * <p>
  * It overrides:
  * <ul>
  * <li>ALT + CTRL + C shortcut - copy annotations from selected element into
@@ -23,6 +24,7 @@ import jp.sbi.celldesigner.plugin.PluginSBase;
  * element(s), if many elements are selected then all elements will be modified,
  * </li>
  * </ul>
+ * </p>
  * 
  * @author Piotr Gawron
  * 
@@ -64,31 +66,31 @@ public class CopyPastePlugin extends CellDesignerPlugin {
       // create keyboard listener for shortcuts
       KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(createKeyEventDispatcher());
 
-    } catch (Exception exception) {
+    } catch (final Exception exception) {
       logger.error(exception, exception);
     }
   }
 
   protected KeyEventDispatcher createKeyEventDispatcher() {
     return new KeyEventDispatcher() {
-      public boolean dispatchKeyEvent(KeyEvent e) {
+      public boolean dispatchKeyEvent(final KeyEvent e) {
         switch (e.getID()) {
-        case KeyEvent.KEY_PRESSED:
-          if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
-              && e.isControlDown()
-              && e.isAltDown()) {
-            getPastePluginAction().myActionPerformed(null);
-            return true;
-          } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
-              && e.isControlDown()
-              && e.isAltDown()) {
-            getCopyPluginAction().myActionPerformed(null);
-            return true;
-          } else {
+          case KeyEvent.KEY_PRESSED:
+            if (e.getKeyCode() == java.awt.event.KeyEvent.VK_V
+                && e.isControlDown()
+                && e.isAltDown()) {
+              getPastePluginAction().myActionPerformed(null);
+              return true;
+            } else if (e.getKeyCode() == java.awt.event.KeyEvent.VK_C
+                && e.isControlDown()
+                && e.isAltDown()) {
+              getCopyPluginAction().myActionPerformed(null);
+              return true;
+            } else {
+              return false;
+            }
+          default:
             return false;
-          }
-        default:
-          return false;
         }
       }
     };
@@ -100,33 +102,33 @@ public class CopyPastePlugin extends CellDesignerPlugin {
 
   // CHECKSTYLE:OFF
   @Override
-  public void SBaseAdded(PluginSBase arg0) {
+  public void SBaseAdded(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void SBaseChanged(PluginSBase arg0) {
+  public void SBaseChanged(final PluginSBase arg0) {
 
   }
 
   // CHECKSTYLE:ON
 
   @Override
-  public void SBaseDeleted(PluginSBase arg0) {
+  public void SBaseDeleted(final PluginSBase arg0) {
   }
 
   @Override
-  public void modelOpened(PluginSBase arg0) {
+  public void modelOpened(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelSelectChanged(PluginSBase arg0) {
+  public void modelSelectChanged(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelClosed(PluginSBase arg0) {
+  public void modelClosed(final PluginSBase arg0) {
 
   }
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPluginAction.java

@@ -39,17 +39,17 @@ public class CopyPluginAction extends PluginAction {
    * @param win
    *          {@link #window}
    */
-  public CopyPluginAction(CopyPastePlugin plugin, MainWindow win) {
+  public CopyPluginAction(final CopyPastePlugin plugin, final MainWindow win) {
     this.plugin = plugin;
   }
 
   @Override
-  public void myActionPerformed(ActionEvent e) {
+  public void myActionPerformed(final ActionEvent e) {
     try {
       CopyAction annotateAction = new CopyAction();
       PluginListOf list = getPlugin().getSelectedAllNode();
       annotateAction.performAnnotation(getPlugin(), list);
-    } catch (Exception ex) {
+    } catch (final Exception ex) {
       logger.error(ex, ex);
     }
   }
@@ -58,7 +58,7 @@ public class CopyPluginAction extends PluginAction {
     return plugin;
   }
 
-  protected void setPlugin(CopyPastePlugin plugin) {
+  protected void setPlugin(final CopyPastePlugin plugin) {
     this.plugin = plugin;
   }
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PasteAction.java

@@ -5,7 +5,11 @@ import java.util.Set;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.SystemClipboard;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
@@ -33,7 +37,7 @@ public class PasteAction extends CopyPasteAbstractAction {
    * @param speciesList
    *          - list of species to annotate
    */
-  public void performAnnotation(CopyPastePlugin plug, PluginListOf speciesList) {
+  public void performAnnotation(final CopyPastePlugin plug, final PluginListOf speciesList) {
     XmlAnnotationParser xap = new XmlAnnotationParser();
 
     SystemClipboard sc = new SystemClipboard();

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/PastePluginAction.java

@@ -39,17 +39,17 @@ public class PastePluginAction extends PluginAction {
    * @param win
    *          {@link #window}
    */
-  public PastePluginAction(CopyPastePlugin plugin, MainWindow win) {
+  public PastePluginAction(final CopyPastePlugin plugin, final MainWindow win) {
     this.setPlugin(plugin);
   }
 
   @Override
-  public void myActionPerformed(ActionEvent e) {
+  public void myActionPerformed(final ActionEvent e) {
     try {
       PasteAction annotateAction = new PasteAction();
       PluginListOf list = getPlugin().getSelectedAllNode();
       annotateAction.performAnnotation(plugin, list);
-    } catch (Exception ex) {
+    } catch (final Exception ex) {
       logger.error(ex, ex);
     }
   }
@@ -58,7 +58,7 @@ public class PastePluginAction extends PluginAction {
     return plugin;
   }
 
-  protected void setPlugin(CopyPastePlugin plugin) {
+  protected void setPlugin(final CopyPastePlugin plugin) {
     this.plugin = plugin;
   }
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoFrame.java

 package lcsb.mapviewer.cdplugin.info;
 
-import java.awt.*;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.GridLayout;
+import java.awt.Toolkit;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.swing.*;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.JFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.JTextField;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -124,7 +136,7 @@ public final class InfoFrame {
     JPanel controlArea = new JPanel(new GridLayout(panels, 1));
     controlArea.setLayout(new BoxLayout(controlArea, BoxLayout.Y_AXIS));
     // for every species create a panel and add it to general form
-    for (PluginSpeciesAlias sp : this.species) {
+    for (final PluginSpeciesAlias sp : this.species) {
       JPanel panel = getPanelViewForSpecies(sp);
       controlArea.add(panel);
     }
@@ -155,7 +167,7 @@ public final class InfoFrame {
    *          CellDesigner species alias
    * @return {@link JPanel} object with information about species
    */
-  private JPanel getPanelViewForSpecies(PluginSpeciesAlias species) {
+  private JPanel getPanelViewForSpecies(final PluginSpeciesAlias species) {
     JPanel result = new JPanel();
     result.setLayout(new BoxLayout(result, BoxLayout.Y_AXIS));
 
@@ -202,7 +214,7 @@ public final class InfoFrame {
    * @param visible
    *          should the frame be visible or not
    */
-  public void setVisible(boolean visible) {
+  public void setVisible(final boolean visible) {
     frame.setVisible(visible);
   }
 
@@ -212,7 +224,7 @@ public final class InfoFrame {
    * @param title
    *          title of the frame
    */
-  public void setTitle(String title) {
+  public void setTitle(final String title) {
     frame.setTitle(title);
   }
 
@@ -231,7 +243,7 @@ public final class InfoFrame {
    * @param type
    *          new {@link JFrame#defaultCloseOperation} value
    */
-  public void setDefaultCloseOperation(int type) {
+  public void setDefaultCloseOperation(final int type) {
     frame.setDefaultCloseOperation(type);
   }
 
@@ -241,7 +253,7 @@ public final class InfoFrame {
    * @param always
    *          new {@link JFrame#isAlwaysOnTop()} value
    */
-  public void setAlwaysOnTop(boolean always) {
+  public void setAlwaysOnTop(final boolean always) {
     frame.setAlwaysOnTop(always);
   }
 
@@ -255,7 +267,7 @@ public final class InfoFrame {
    * @param species
    *          - species to be shown in the form
    */
-  public void setSpecies(List<PluginSpeciesAlias> species) {
+  public void setSpecies(final List<PluginSpeciesAlias> species) {
     this.species = species;
     updateSpecies();
   }

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/info/InfoPlugin.java

 package lcsb.mapviewer.cdplugin.info;
 
-import java.awt.*;
-import java.awt.event.*;
+import java.awt.KeyEventDispatcher;
+import java.awt.KeyboardFocusManager;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.swing.*;
+import javax.swing.Timer;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.CellDesignerPlugin;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginSBase;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 
 /**
  * This class represent a plugin to CellDesigner that add info text box with
  * informations about species. Plugin run in pooling mode (there is no other way
  * in CellDesigner...).
- * 
+ * <p>
  * It overrides <i>CTRL + T shortcut</i> - shows/hide info text window.
+ * </p>
  * 
  * @author Piotr Gawron
  * 
@@ -64,7 +71,7 @@ public class InfoPlugin extends CellDesignerPlugin {
 
       // create keyboard listener for shortcuts
       KeyboardFocusManager.getCurrentKeyboardFocusManager().addKeyEventDispatcher(new KeyEventDispatcher() {
-        public boolean dispatchKeyEvent(KeyEvent e) {
+        public boolean dispatchKeyEvent(final KeyEvent e) {
           if (KeyEvent.KEY_PRESSED == e.getID()) {
             // if someone hits CTRL+T then open/hide info window
             if (e.getKeyCode() == java.awt.event.KeyEvent.VK_T
@@ -81,14 +88,14 @@ public class InfoPlugin extends CellDesignerPlugin {
       onChangeSelectListener = new ActionListener() {
 
         /**
-         * This string contains a simple hash of all species shown in the last run of
-         * this listener. Due to this information we don't have to refresh this
-         * information at every run.
+         * This string contains a simple hash of all species shown in the last
+         * run of this listener. Due to this information we don't have to
+         * refresh this information at every run.
          */
         private String selectedElementsId = "";
 
         @Override
-        public void actionPerformed(ActionEvent arg0) {
+        public void actionPerformed(final ActionEvent arg0) {
           // if there is no open model then getSelectedAllNode() will throw an
           // exception...
           List<PluginSpeciesAlias> aliasList = getListOfAlias();
@@ -107,7 +114,7 @@ public class InfoPlugin extends CellDesignerPlugin {
               selectedElementsId = newId;
               frame.setSpecies(v);
             }
-          } catch (Exception exception) {
+          } catch (final Exception exception) {
             logger.error(exception, exception);
           }
 
@@ -117,7 +124,7 @@ public class InfoPlugin extends CellDesignerPlugin {
       Timer timer = new Timer(DELAY_BETWEEN_ON_SELECT_LISTENER_CHECKS, onChangeSelectListener);
       timer.start();
 
-    } catch (Exception exception) {
+    } catch (final Exception exception) {
       logger.error("Unhandled exception. ", exception);
     }
   }
@@ -128,33 +135,33 @@ public class InfoPlugin extends CellDesignerPlugin {
 
   // CHECKSTYLE:OFF
   @Override
-  public void SBaseAdded(PluginSBase arg0) {
+  public void SBaseAdded(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void SBaseChanged(PluginSBase arg0) {
+  public void SBaseChanged(final PluginSBase arg0) {
 
   }
 
   // CHECKSTYLE:ON
 
   @Override
-  public void SBaseDeleted(PluginSBase arg0) {
+  public void SBaseDeleted(final PluginSBase arg0) {
   }
 
   @Override
-  public void modelOpened(PluginSBase arg0) {
+  public void modelOpened(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelSelectChanged(PluginSBase arg0) {
+  public void modelSelectChanged(final PluginSBase arg0) {
 
   }
 
   @Override
-  public void modelClosed(PluginSBase arg0) {
+  public void modelClosed(final PluginSBase arg0) {
 
   }
 
@@ -169,7 +176,7 @@ public class InfoPlugin extends CellDesignerPlugin {
           result.add(alias);
         }
       }
-    } catch (Exception e) {
+    } catch (final Exception e) {
     }
     return result;
   }

CellDesigner-plugin/src/test/java/lcsb/mapviewer/cdplugin/CdPluginFunctions.java

@@ -3,28 +3,32 @@ package lcsb.mapviewer.cdplugin;
 import java.util.List;
 
 import org.apache.logging.log4j.core.LogEvent;
-import org.junit.*;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Rule;
 import org.mockito.Mockito;
 
-import jp.sbi.celldesigner.plugin.*;
+import jp.sbi.celldesigner.plugin.PluginListOf;
+import jp.sbi.celldesigner.plugin.PluginReaction;
+import jp.sbi.celldesigner.plugin.PluginSpecies;
+import jp.sbi.celldesigner.plugin.PluginSpeciesAlias;
 import lcsb.mapviewer.common.MinervaLoggerAppender;
-import lcsb.mapviewer.common.UnitTestFailedWatcher;
+import lcsb.mapviewer.common.tests.UnitTestFailedWatcher;
 
 public class CdPluginFunctions {
 
   @Rule
   public UnitTestFailedWatcher unitTestFailedWatcher = new UnitTestFailedWatcher();
 
-  String rdfString = "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
-      +
-      "<rdf:Description rdf:about=\"#s3\">\n" +
-      "<bqmodel:is>\n" +
-      "<rdf:Bag>\n" +
-      "<rdf:li rdf:resource=\"urn:miriam:wikipedia.en:1\"/>\n" +
-      "</rdf:Bag>\n" +
-      "</bqmodel:is>\n" +
-      "</rdf:Description>\n" +
-      "</rdf:RDF>\n";
+  private String rdfString = "<rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
+      + "<rdf:Description rdf:about=\"#s3\">\n"
+      + "<bqmodel:is>\n"
+      + "<rdf:Bag>\n"
+      + "<rdf:li rdf:resource=\"urn:miriam:wikipedia.en:1\"/>\n"
+      + "</rdf:Bag>\n"
+      + "</bqmodel:is>\n"
+      + "</rdf:Description>\n"
+      + "</rdf:RDF>\n";
 
   private MinervaLoggerAppender appender;
 
@@ -51,7 +55,7 @@ public class CdPluginFunctions {
     return appender.getFatals();
   }
 
-  protected PluginListOf createPluginListWithSpecies(int size) {
+  protected PluginListOf createPluginListWithSpecies(final int size) {
     PluginListOf list = Mockito.mock(PluginListOf.class);
 
     Mockito.when(list.size()).thenReturn(size);
@@ -62,7 +66,7 @@ public class CdPluginFunctions {