Merge remote-tracking branch 'origin/develop' into 7239-submods

Conflicts:
	components/insight/ivy.xml

build.xml

@@ -370,13 +370,14 @@ java component.
         </copy>
         <!-- These should eventually be removed in favor of an ivy-based approach -->
         <copy todir="target">
-            <fileset dir="components/insight/target" includes="insight*.zip"/>
+            <fileset dir="components/insight/target" includes="insight*.zip" excludes="*-ij*.zip"/>
             <mapper type="regexp" from="insight(.*).zip"  to="OMERO.insight-${omero.version}\1.zip"/>
         </copy>
         <copy todir="target">
             <fileset dir="components/insight/target" includes="editor*.zip"/>
             <mapper type="regexp" from="editor(.*).zip"  to="OMERO.editor-${omero.version}\1.zip"/>
         </copy>
+       	<copy file="components/insight/target/insight-ij.zip" tofile="target/OMERO.insight-ij-${omero.version}.zip"/>
     </target>
 
     <target name="release-src" description="Zip the git source into OMERO.source-${omero.version}.zip">

components/blitz/resources/ome/services/blitz-servantDefinitions.xml

@@ -332,8 +332,12 @@
   ==============================================================================
   -->
 
-  <bean id="::omero::cmd::Handle" class="omero.cmd.HandleI" singleton="false">
-      <constructor-arg value="${omero.threads.cancel_timeout}"/>
+  <bean id="::omero::cmd::Handle" class="omero.cmd._HandleTie" singleton="false">
+    <constructor-arg>
+        <bean class="omero.cmd.HandleI" singleton="false">
+            <constructor-arg value="${omero.threads.cancel_timeout}"/>
+        </bean>
+    </constructor-arg>
   </bean>
 
   <bean class="omero.cmd.RequestObjectFactoryRegistry">

components/blitz/resources/omero/ServerErrors.ice

@@ -304,14 +304,14 @@ module omero
     {
     };
 
-  exception GroupSecurityViolation extends ServerError
+  exception GroupSecurityViolation extends SecurityViolation
     {
     };
 
-  exception PermissionMismatchGroupSecurityViolation extends ServerError
+  exception PermissionMismatchGroupSecurityViolation extends SecurityViolation
     {
     };
-  exception ReadOnlyGroupSecurityViolation extends ServerError
+  exception ReadOnlyGroupSecurityViolation extends SecurityViolation
     {
     };
 

components/blitz/resources/omero/api/ThumbnailStore.ice

@@ -23,6 +23,7 @@ module omero {
         ["ami", "amd"] interface ThumbnailStore extends StatefulServiceInterface
             {
                 bool setPixelsId(long pixelsId) throws ServerError;
+                bool isInProgress() throws ServerError;
                 void setRenderingDefId(long renderingDefId) throws ServerError;
                 long getRenderingDefId() throws ServerError;
                 Ice::ByteSeq getThumbnail(omero::RInt sizeX, omero::RInt sizeY) throws ServerError;

components/blitz/src/ome/formats/importer/util/IniFileLoader.java

@@ -104,7 +104,7 @@ public IniFileLoader(File userConfigFile) {
             userPrefs = new IniFile(userConfigFile, Mode.RW);
         } catch (BackingStoreException e) {
             log.error(e);
-            throw new RuntimeException("Error accessing ini file", e);
+            //throw new RuntimeException("Error accessing ini file", e);
         }
     }
 
@@ -126,13 +126,15 @@ public void flushPreferences() {
      * Any value lower than null will not call configureDebug.
      */
     public int getDebugLevel() {
+    	if (userPrefs == null) return -1;
         return userPrefs.node("General").getInt("debug", -1);
     }
 
     /**
      * @return if quaqua should be used on mac
      */
     public boolean getUseQuaqua() {
+    	if (userPrefs == null) return true;
         return userPrefs.node("General").getBoolean("useQuaqua", true);
     }
 
@@ -214,6 +216,7 @@ public boolean getStaticDisableHistory()
      */
     public void setUserDisableHistory(boolean b)
     {
+    	if (userPrefs == null) return;
         userPrefs.node("UI").putBoolean("disableHistory", b);
         this.flushPreferences();
     }    
@@ -223,6 +226,7 @@ public void setUserDisableHistory(boolean b)
      */
     public Boolean getUserDisableHistory()
     {
+    	if (userPrefs == null) return true;
     	return userPrefs.node("UI").getBoolean("disableHistory", true);
     }
 
@@ -233,6 +237,7 @@ public Boolean getUserDisableHistory()
      */
     public void setDebugLevel(int level)
     {
+    	if (userPrefs == null) return;
         userPrefs.node("General").putInt("debug", level);
         this.flushPreferences();
     }
@@ -242,6 +247,7 @@ public void setDebugLevel(int level)
      */
     public void setUseQuaqua(boolean b)
     {
+    	if (userPrefs == null) return;
         userPrefs.node("General").putBoolean("useQuaqua", b);
         this.flushPreferences();
     }
@@ -292,6 +298,7 @@ public String getServerPort()
      */
     public void updateFlexReaderServerMaps()
     {
+    	if (userPrefs == null) return;
         Preferences maps = userPrefs.node("FlexReaderServerMaps");
         Map<String, List<String>> values = parseFlexMaps(maps);
         for (Map.Entry<String, List<String>> entry : values.entrySet()) {
@@ -338,7 +345,7 @@ public Map<String, List<String>> parseFlexMaps(Preferences maps)
     }
 
     /**
-     * Append kep to server map
+     * Append keep to server map
      *
      * @param key
      * @param mapValue
@@ -374,7 +381,7 @@ public Boolean isDebugUI() {
     public Rectangle getUIBounds()
     {
         Rectangle rect = new Rectangle();
-
+        if (userPrefs == null) return rect;
         rect.width = userPrefs.node("UI").getInt("width", 980);
         rect.height = userPrefs.node("UI").getInt("height", 580);
         rect.x = userPrefs.node("UI").getInt("xOffset", 10);
@@ -400,6 +407,7 @@ public void setUIBounds(Rectangle bounds)
         if (bounds.height < 100)
             bounds.height = 100;
 
+        if (userPrefs == null) return;
         userPrefs.node("UI").putInt("width", bounds.width);
         userPrefs.node("UI").putInt("height", bounds.height);
         userPrefs.node("UI").putInt("xOffset", bounds.x);
@@ -408,32 +416,38 @@ public void setUIBounds(Rectangle bounds)
 
     public boolean getUserFullPath()
     {
-	return userPrefs.node("UI").getBoolean("userFullPath", true);
+    	if (userPrefs == null) return true;
+	    return userPrefs.node("UI").getBoolean("userFullPath", true);
     }
 
     public void setUserFullPath(boolean b)
     {
-	userPrefs.node("UI").putBoolean("userFullPath", b);
+    	if (userPrefs != null)
+	        userPrefs.node("UI").putBoolean("userFullPath", b);
     }
 
     public boolean getCustomImageNaming()
     {
-	return userPrefs.node("UI").getBoolean("customImageNaming", true);
+    	if (userPrefs == null) return true;
+	    return userPrefs.node("UI").getBoolean("customImageNaming", true);
     }
 
     public void setCustomImageNaming(boolean b)
     {
-	userPrefs.node("UI").putBoolean("customImageNaming", b);
+    	if (userPrefs != null)
+		    userPrefs.node("UI").putBoolean("customImageNaming", b);
     }
 
     public int getNumOfDirectories()
     {
-	return userPrefs.node("UI").getInt("numOfDirectories", 0);
+    	if (userPrefs == null) return 0;
+	    return userPrefs.node("UI").getInt("numOfDirectories", 0);
     }
 
     public void setNumOfDirectories(int i)
     {
-	userPrefs.node("UI").putInt("numOfDirectories", i);
+    	if (userPrefs == null) return;
+	    userPrefs.node("UI").putInt("numOfDirectories", i);
     }
 
     /**

components/blitz/src/ome/services/blitz/gateway/OmeroGateway.java

@@ -437,11 +437,7 @@ public byte[] getPlane(long pixelsId, int z, int c, int t, Ice.Current current)
 	}
 
 	@Override
-	protected void preClose() {
-	    try {
-	        close();
-	    } catch (Exception e) {
-	        log.error("Error on OmeroGateway.close()", e);
-	    }
+	protected void preClose(Ice.Current current) throws Throwable {
+            close();
 	}
 }

components/blitz/src/ome/services/blitz/impl/AbstractAmdServant.java

@@ -222,7 +222,7 @@ public final void close_async(AMD_StatefulServiceInterface_close __cb,
 
         // First we call close on the object
         try {
-            preClose();
+            preClose(__current);
             if (service instanceof StatefulServiceInterface) {
                 StatefulServiceInterface ss = (StatefulServiceInterface) service;
                 ss.close();
@@ -258,8 +258,8 @@ public final void close_async(AMD_StatefulServiceInterface_close __cb,
 
     }
 
-    protected void preClose() {
-
+    protected void preClose(Ice.Current current) throws Throwable {
+        log.debug("No pre-close define");
     }
 
 }

components/blitz/src/ome/services/blitz/impl/DeleteHandleI.java

@@ -14,10 +14,23 @@
 import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.atomic.AtomicReference;
 
+import org.apache.commons.io.filefilter.WildcardFileFilter;
+import org.apache.commons.logging.Log;
+import org.apache.commons.logging.LogFactory;
+import org.hibernate.Session;
+import org.hibernate.exception.ConstraintViolationException;
+import org.perf4j.StopWatch;
+import org.perf4j.commonslog.CommonsLogStopWatch;
+import org.springframework.context.ApplicationContext;
+import org.springframework.transaction.annotation.Transactional;
+
+import Ice.Current;
+
 import ome.conditions.InternalException;
 import ome.io.bioformats.BfPyramidPixelBuffer;
 import ome.io.nio.AbstractFileSystemService;
@@ -30,24 +43,12 @@
 import ome.system.Principal;
 import ome.system.ServiceFactory;
 import ome.util.SqlAction;
+
 import omero.LockTimeout;
 import omero.ServerError;
 import omero.api.delete.DeleteCommand;
 import omero.api.delete.DeleteReport;
-import omero.api.delete._DeleteHandleDisp;
-import omero.util.CloseableServant;
-
-import org.apache.commons.io.filefilter.WildcardFileFilter;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
-import org.hibernate.Session;
-import org.hibernate.exception.ConstraintViolationException;
-import org.perf4j.StopWatch;
-import org.perf4j.commonslog.CommonsLogStopWatch;
-import org.springframework.context.ApplicationContext;
-import org.springframework.transaction.annotation.Transactional;
-
-import Ice.Current;
+import omero.api.delete._DeleteHandleOperations;
 
 /**
  * Servant for the handle proxy from the IDelete service. This is also a
@@ -70,8 +71,8 @@
  * @since 4.2.1
  * @see ome.api.IDelete
  */
-public class DeleteHandleI extends _DeleteHandleDisp implements
-        CloseableServant, Runnable {
+public class DeleteHandleI extends AbstractAmdServant implements
+        _DeleteHandleOperations, Runnable {
 
     private static enum State {
         CREATED, READY, RUNNING, CANCELLING, CANCELLED, FINISHED;
@@ -138,20 +139,34 @@ private static class Report extends DeleteReport {
 
     private final ServiceFactoryI sf;
 
+    private final Map<String, String> callContext;
+
+    /**
+     * Call the main constructor with a null call context.
+     */
+    public DeleteHandleI(final ApplicationContext ctx, final Ice.Identity id, final ServiceFactoryI sf,
+            final AbstractFileSystemService afs, final DeleteCommand[] commands, int cancelTimeoutMs) {
+        this(ctx, id, sf, afs, commands, cancelTimeoutMs, null);
+    }
+
     /**
-     * Create and
+     * Main constructor.
      *
      * @param id
      * @param sf
      * @param factory
      * @param commands
      * @param cancelTimeoutMs
+     * @param callContext
      */
     public DeleteHandleI(final ApplicationContext ctx, final Ice.Identity id, final ServiceFactoryI sf,
-            final AbstractFileSystemService afs, final DeleteCommand[] commands, int cancelTimeoutMs) {
+            final AbstractFileSystemService afs, final DeleteCommand[] commands, int cancelTimeoutMs,
+            Map<String, String> callContext) {
+        super(null, null);
         this.id = id;
         this.sf = sf;
         this.afs = afs;
+        this.callContext = callContext;
         this.principal = sf.getPrincipal();
         this.executor = sf.getExecutor();
         this.cancelTimeoutMs = cancelTimeoutMs;
@@ -297,8 +312,8 @@ public boolean cancel(Current __current) throws ServerError {
     // CloseableServant. See documentation in interface.
     //
 
-    public void close(Ice.Current current) throws ServerError {
-        sf.unregisterServant(id);
+    @Override
+    protected void preClose(Ice.Current current) throws ServerError {
         if (!finished(current)) {
             log.warn("Handle closed before finished! State=" + state.get());
         }
@@ -322,8 +337,9 @@ public void run() {
 
         StopWatch sw = new CommonsLogStopWatch();
         try {
-            executor.execute(principal, new Executor.SimpleWork(this, "run",
-                    Ice.Util.identityToString(id), "size=" + commands.length) {
+            executor.execute(callContext, principal,
+                    new Executor.SimpleWork(this, "run",
+                        Ice.Util.identityToString(id), "size=" + commands.length) {
                 @Transactional(readOnly = false)
                 public Object doWork(Session session, ServiceFactory sf) {
                     try {