Merge pull request #4 from KlasJoenssson/Bug3069

Bug3069
bioclipse · Sep 4, 2012 · e908824 · e908824
2 parents 2d222ae + d7a5785
commit e908824
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Showing 3 changed files with 77 additions and 27 deletions.
diff --git a/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/Activator.java b/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/Activator.java
@@ -20,10 +20,12 @@
 import net.bioclipse.usermanager.business.IUserManager;
 
 import org.apache.log4j.Logger;
-import org.eclipse.jface.preference.IPreferenceStore;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
 import org.eclipse.ui.plugin.AbstractUIPlugin;
 import org.opentox.aa.opensso.OpenSSOToken;
 import org.osgi.framework.BundleContext;
+import org.osgi.service.prefs.BackingStoreException;
+import org.osgi.service.prefs.Preferences;
 import org.osgi.util.tracker.ServiceTracker;
 
 /**
@@ -98,31 +100,63 @@ public void start(BundleContext context) throws Exception {
         	}
         }
 
+        Preferences preferences = 
+                ConfigurationScope.INSTANCE
+                .getNode( OpenToxConstants.PLUGIN_ID );
+        List<String[]> toPrefs = ServicesPreferencePage.convertPreferenceStringToArraylist( preferences.get( OpenToxConstants.SERVICES, "n/a" ) );
+
         //Save the, possibly changed, list of services to prefs
         //This way we have the list openToxServices synced with the prefs
-        List<String[]> toPrefs=new ArrayList<String[]>();
+//        List<String[]> toPrefs = new ArrayList<String[]>();
         for (OpenToxService eps : epservices){
-        	String[] entry = new String[3];
-        	entry[0]=eps.getName();
-        	entry[1]=eps.getService();
-        	entry[2]=eps.getServiceSPARQL();
-
-        	toPrefs.add(entry);
+            String[] entry = new String[3];
+            entry[0]=eps.getName();
+            entry[1]=eps.getService();
+            entry[2]=eps.getServiceSPARQL();
+
+            if (!listContains( toPrefs, entry ))
+                toPrefs.add(entry);
         }
+
         String toPrefsString = ServicesPreferencePage.convertToPreferenceString(toPrefs);
-
+        
         //Save the serialized services to preferences
-        IPreferenceStore prefsStore=Activator.getDefault().getPreferenceStore();
-        prefsStore.setValue(OpenToxConstants.SERVICES, toPrefsString);
+        preferences.put( OpenToxConstants.SERVICES, toPrefsString );
+        try {
+            preferences.flush();
+        } catch ( BackingStoreException e ) {
+            logger.error( e.getMessage() );
+            e.printStackTrace();
+        }
 
         logger.debug("Saved the serialized services prefs string: " + toPrefsString);
 
         logger.debug("OpenTox initialization ended");
 
     }
-
-
 
+    /* This method is written 'cos using "toPrefs.contains( entry )" in the if-
+     * statement on line 117 above didn't worked. */
+    private boolean listContains(List<String[]> list, String[] item) {
+        boolean found = false, itemEquals;
+        for (String[] listItem : list) {
+            itemEquals = false;
+            for (int i = 0; i < listItem.length; i++) {
+                if (item[i] == null || item[i].isEmpty()) {
+                    if (listItem[i].equals( "NA" ) || listItem[i].isEmpty() )
+                        itemEquals = true;
+                } else if (listItem[i].equals( item[i] ) )
+                        itemEquals = true;
+                else
+                    itemEquals = false;
+            }
+            if (itemEquals)
+                found = true;
+        }
+
+        return found;    
+    }
+
 	public void stop(BundleContext context) throws Exception {
         plugin = null;
         super.stop(context);

diff --git a/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/OpenToxConstants.java b/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/OpenToxConstants.java
@@ -5,5 +5,6 @@ public class OpenToxConstants {
 	public static final String PREFS_SEPERATOR = "__SEP__";
 	public static final String SERVICES = "opentox.services";
 	public static final String PREFERENCES_OBJECT_DELIMITER = null;
+	public static final String PLUGIN_ID="net.bioclipse.opentox";
 
 }
diff --git a/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/prefs/ServicesPreferencePage.java b/plugins/net.bioclipse.opentox/src/net/bioclipse/opentox/prefs/ServicesPreferencePage.java
@@ -19,6 +19,7 @@
 import net.bioclipse.ui.prefs.IPreferenceConstants;
 
 import org.apache.log4j.Logger;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
 import org.eclipse.jface.dialogs.MessageDialog;
 import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.jface.preference.PreferencePage;
@@ -45,6 +46,8 @@
 import org.eclipse.swt.layout.FormLayout;
 import org.eclipse.swt.layout.FormData;
 import org.eclipse.swt.layout.FormAttachment;
+import org.osgi.service.prefs.BackingStoreException;
+import org.osgi.service.prefs.Preferences;
 
 /**
  * 
@@ -54,10 +57,12 @@
 public class ServicesPreferencePage extends PreferencePage implements
 IWorkbenchPreferencePage {
 
-    private static final Logger logger = Logger.getLogger(ServicesPreferencePage.class.toString());
-
-    private static IPreferenceStore prefsStore=Activator.getDefault().getPreferenceStore();
+    private static final Logger logger = 
+            Logger.getLogger(ServicesPreferencePage.class.toString());
 
+    private static Preferences preferences = 
+            ConfigurationScope.INSTANCE.getNode( OpenToxConstants.PLUGIN_ID );
+
     private List<String[]> appList;
     private TableViewer checkboxTableViewer;
 
@@ -205,7 +210,16 @@ public void mouseUp(MouseEvent e) {
                 }
 
                 String[] chosen = (String[]) obj;
-
+                /* TODO Fix this in a better way. Without the if-statement below
+                 * we'll get an unexpected ArrayIndexOutOfBoundsException in 
+                 * some cases, 'cos the last element is missing in the selection */
+                if (chosen.length < 3) {
+                    String[] temp = {"NA", "NA", "NA"};
+                    for (int i = 0; i < chosen.length; i++) 
+                        temp[i] = chosen[i];   
+                    chosen = temp;
+                }    
+
                 ServicesEditDialog dlg=new ServicesEditDialog(getShell(), chosen[0], chosen[1], chosen[2]);
 
                 dlg.open();
@@ -280,12 +294,15 @@ public boolean performOk() {
 
         String value=convertToPreferenceString(appList);
         logger.debug("Update sites prefs to store: " + value);
-        prefsStore.setValue(OpenToxConstants.SERVICES,value);
-
-
+
         //Save prefs as this must be done explicitly
-        Activator.getDefault().savePluginPreferences();
-
+        preferences.put( OpenToxConstants.SERVICES, value );
+        try {
+            preferences.flush();
+        } catch ( BackingStoreException e ) {
+            logger.error( e.getMessage() );
+            e.printStackTrace();
+        }
         return true;
     }
 
@@ -295,9 +312,8 @@ public boolean performOk() {
      */
     public static List<String[]> getPreferencesFromStore() {
 
-
-        String entireString=prefsStore.getString(OpenToxConstants.SERVICES);
-
+        String entireString=preferences.get( OpenToxConstants.SERVICES, "n/a" );
+
         return convertPreferenceStringToArraylist(entireString);
     }
 
@@ -307,8 +323,7 @@ public static List<String[]> getPreferencesFromStore() {
      * 
      */
     public static List<String[]> getDefaultPreferencesFromStore() {
-        String entireString=prefsStore.getDefaultString(OpenToxConstants.SERVICES);
-
+        String entireString=preferences.get( OpenToxConstants.SERVICES, "n/a" );
         return convertPreferenceStringToArraylist(entireString);
     }