Issue #1638 Made pypies slab reads work in more than 2-d data. Moved DecisionTree to common.dataquery. Merged changes into CAVEApplication.

Amend: Deleted old DecisionTree

Change-Id: Id51a32c42f5485a5261dd73f88f55a6fda3263c8

Former-commit-id: 14dba9a749 [formerly ea2501abbb] [formerly 40c76c2c82 [formerly 4f76cfa7102f2b266bc94dbeb4ed6d2e4028c106]]
Former-commit-id: 40c76c2c82
Former-commit-id: fc27ac4a30

cave/com.raytheon.uf.viz.core/src/com/raytheon/uf/viz/core/rsc/URICatalog.java

@@ -31,13 +31,13 @@ import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.jobs.Job;
 
+import com.raytheon.uf.common.dataquery.DecisionTree;
 import com.raytheon.uf.common.dataquery.requests.RequestConstraint;
 import com.raytheon.uf.common.status.IUFStatusHandler;
 import com.raytheon.uf.common.status.UFStatus;
 import com.raytheon.uf.common.status.UFStatus.Priority;
 import com.raytheon.uf.common.time.DataTime;
 import com.raytheon.uf.viz.core.datastructure.DataCubeContainer;
-import com.raytheon.uf.viz.core.datastructure.DecisionTree;
 import com.raytheon.uf.viz.core.exception.VizException;
 import com.raytheon.uf.viz.core.rsc.URICatalog.IURIRefreshCallback;
 

cave/com.raytheon.uf.viz.core/src/com/raytheon/uf/viz/core/rsc/updater/DataUpdateTree.java

@@ -22,8 +22,8 @@ package com.raytheon.uf.viz.core.rsc.updater;
 
 import java.util.Map;
 
+import com.raytheon.uf.common.dataquery.DecisionTree;
 import com.raytheon.uf.common.dataquery.requests.RequestConstraint;
-import com.raytheon.uf.viz.core.datastructure.DecisionTree;
 import com.raytheon.uf.viz.core.rsc.AbstractVizResource;
 import com.raytheon.uf.viz.core.rsc.IDisposeListener;
 

cave/com.raytheon.uf.viz.personalities.cave/src/com/raytheon/uf/viz/personalities/cave/component/CAVEApplication.java

@@ -55,6 +55,7 @@ import com.raytheon.uf.viz.core.RecordFactory;
 import com.raytheon.uf.viz.core.VizApp;
 import com.raytheon.uf.viz.core.localization.CAVELocalizationNotificationObserver;
 import com.raytheon.uf.viz.core.localization.LocalizationInitializer;
+import com.raytheon.uf.viz.core.notification.jobs.NotificationManagerJob;
 import com.raytheon.uf.viz.personalities.cave.workbench.VizWorkbenchAdvisor;
 import com.raytheon.viz.alerts.jobs.AutoUpdater;
 import com.raytheon.viz.alerts.jobs.MenuUpdater;
@@ -129,11 +130,21 @@ public class CAVEApplication implements IStandaloneComponent {
             // dialog which would break gfeClient-based cron jobs.
             return IApplication.EXIT_OK;
         }
-        initializeSerialization();
+
+        Job serializationJob = initializeSerialization();
         initializeDataStoreFactory();
         initializeObservers();
         initializeSimulatedTime();
 
+        // wait for serialization initialization to complete before
+        // opening JMS connection to avoid deadlock in class loaders
+        if (serializationJob != null) {
+            serializationJob.join();
+        }
+
+        // open JMS connection to allow alerts to be received
+        NotificationManagerJob.connect();
+
         int returnCode = IApplication.EXIT_OK;
 
         try {
@@ -154,6 +165,14 @@ public class CAVEApplication implements IStandaloneComponent {
                 // catch any exceptions to ensure rest of finally block
                 // executes
             }
+
+            try {
+                // disconnect from JMS
+                NotificationManagerJob.disconnect();
+            } catch (RuntimeException e) {
+                // catch any exceptions to ensure rest of finally block
+                // executes
+            }
         }
 
         if (returnCode == PlatformUI.RETURN_RESTART) {
@@ -176,8 +195,8 @@ public class CAVEApplication implements IStandaloneComponent {
                 new PyPiesDataStoreFactory(pypiesProps));
     }
 
-    protected void initializeSerialization() {
-        new Job("Loading Serialization") {
+    protected Job initializeSerialization() {
+        Job job = new Job("Loading Serialization") {
 
             @Override
             protected IStatus run(IProgressMonitor monitor) {
@@ -190,7 +209,9 @@ public class CAVEApplication implements IStandaloneComponent {
                 return Status.OK_STATUS;
             }
 
-        }.schedule();
+        };
+        job.schedule();
+        return job;
     }
 
     /**

cave/com.raytheon.viz.grid/src/com/raytheon/viz/grid/inv/GridMetadataContainer.java

@@ -27,13 +27,13 @@ import java.util.Map;
 import java.util.Set;
 
 import com.raytheon.uf.common.dataplugin.grid.GridRecord;
+import com.raytheon.uf.common.dataquery.DecisionTree;
 import com.raytheon.uf.common.dataquery.requests.DbQueryRequest;
 import com.raytheon.uf.common.dataquery.requests.DbQueryRequestSet;
 import com.raytheon.uf.common.dataquery.requests.RequestConstraint;
 import com.raytheon.uf.common.dataquery.responses.DbQueryResponse;
 import com.raytheon.uf.common.dataquery.responses.DbQueryResponseSet;
 import com.raytheon.uf.viz.core.RecordFactory;
-import com.raytheon.uf.viz.core.datastructure.DecisionTree;
 import com.raytheon.uf.viz.core.exception.VizException;
 import com.raytheon.uf.viz.core.requests.ThriftClient;
 import com.raytheon.uf.viz.derivparam.data.AbstractRequestableData;

edexOsgi/com.raytheon.uf.common.dataquery/META-INF/MANIFEST.MF

@@ -6,7 +6,8 @@ Bundle-Version: 1.0.0.qualifier
 Bundle-Vendor: RAYTHEON
 Bundle-RequiredExecutionEnvironment: JavaSE-1.6
 Eclipse-RegisterBuddy: com.raytheon.uf.common.serialization
-Export-Package: com.raytheon.uf.common.dataquery.db,
+Export-Package: com.raytheon.uf.common.dataquery,
+ com.raytheon.uf.common.dataquery.db,
  com.raytheon.uf.common.dataquery.requests,
  com.raytheon.uf.common.dataquery.responses
 Require-Bundle: com.raytheon.uf.common.serialization;bundle-version="1.12.1173",

edexOsgi/com.raytheon.uf.common.dataquery/src/com/raytheon/uf/common/dataquery/DecisionTree.java

@@ -18,7 +18,7 @@
  * further licensing information.
  **/
 
-package com.raytheon.uf.viz.core.datastructure;
+package com.raytheon.uf.common.dataquery;
 
 import java.util.ArrayList;
 import java.util.Arrays;

pythonPackages/pypies/pypies/impl/HDF5OpManager.py

@@ -95,12 +95,24 @@ def read(ds, request):
     elif rt == 'SLAB':
         minIndex = request.getMinIndexForSlab()
         maxIndex = request.getMaxIndexForSlab()
+        
+        # Get all sizes and slices in reverse order
+        slices = []
+        sizes = []
+        numIndices = len(minIndex)
+         # Get all sizes and slices in reverse order
+        for i in reversed(range(numIndices)):
+            slices.append(slice(minIndex[i], maxIndex[i]))
+            sizes.append(maxIndex[i] - minIndex[i])
+        
         sel = h5py.selections.HyperSelection(ds.shape)
+        # mask the request slices
         sel[()] = False
-        # reverse x and y for hdf5
-        sel[minIndex[1]:maxIndex[1], minIndex[0]:maxIndex[0]] = True        
+        sel[tuple(slices)] = True
+        
+        # Resize data to desired slab size        
         result = ds[sel]
-        result.resize(maxIndex[1]-minIndex[1], maxIndex[0]-minIndex[0])        
+        result.resize(tuple(sizes))
     else:
         raise NotImplementedException('Only read requests supported are ' +
                                       'ALL, POINT, XLINE, YLINE, and SLAB')