[FIX] XQuery, db:store: out of bounds. Closes BaseXdb#2100

Author: ChristianGruen

basex-core/src/main/java/org/basex/query/up/ContextModifier.java

@@ -129,9 +129,7 @@ final synchronized void apply(final QueryContext qc) throws QueryException {
     }
 
     // apply remaining updates based on database names
-    for(final NameUpdates up : nameUpdates.values()) {
-      up.apply(false);
-    }
+    for(final NameUpdates up : nameUpdates.values()) up.apply(false);
   }
 
   /**

basex-core/src/main/java/org/basex/query/up/DataUpdates.java

@@ -158,17 +158,16 @@ Data data() {
    * @throws QueryException query exception
    */
   void apply(final QueryContext qc) throws QueryException {
-    // execute database updates
+    // apply initial database operations
+    Collections.sort(dbUpdates);
+    applyDbUpdates(true);
+
+    // execute updates within databases
     auc.execute(true);
     auc = null;
 
-    // execute database operations
-    Collections.sort(dbUpdates);
-    final int sz = dbUpdates.size();
-    for(int i = 0; i < sz; i++) {
-      dbUpdates.get(i).apply();
-      dbUpdates.set(i, null);
-    }
+    // apply remaining database operations
+    applyDbUpdates(false);
 
     // execute fn:put operations
     for(final Put put : puts.values()) put.apply();
@@ -198,6 +197,23 @@ void apply(final QueryContext qc) throws QueryException {
     }
   }
 
+  /**
+   * Applies all database operations.
+   * @param before run updates specified before or after node updates
+   * @throws QueryException query exception
+   */
+  private void applyDbUpdates(final boolean before) throws QueryException {
+    final int pos = UpdateType._NODE_UPDATES_.ordinal();
+    for(final ListIterator<DBUpdate> iter = dbUpdates.listIterator(); iter.hasNext();) {
+      final DBUpdate up = iter.next();
+      final int ord = up.type.ordinal();
+      if(before ? ord < pos : ord > pos) {
+        up.apply();
+        iter.remove();
+      }
+    }
+  }
+
   /**
    * Prepares the {@link NodeUpdate} for execution incl. ordering,
    * and removes the update primitive references to save memory.
@@ -207,17 +223,13 @@ private List<NodeUpdate> preparePrimitives() {
     final List<NodeUpdate> upd = new ArrayList<>();
     for(int i = nodes.size() - 1; i >= 0; i--) {
       final int pre = nodes.get(i);
-      final NodeUpdates n = nodeUpdates.get(pre);
-      for(final NodeUpdate p : n.finish()) {
-        upd.add(p);
-        size += p.size();
+      for(final NodeUpdate up : nodeUpdates.get(pre).finish()) {
+        upd.add(up);
+        size += up.size();
       }
     }
-    for(int i = dbUpdates.size() - 1; i >= 0; i--) {
-      size += dbUpdates.get(i).size();
-    }
-    nodeUpdates = null;
     nodes = null;
+    for(final DBUpdate up : dbUpdates) size += up.size();
     upd.sort(new NodeUpdateComparator());
     return upd;
   }

basex-core/src/main/java/org/basex/query/up/NameUpdates.java

@@ -55,7 +55,9 @@ void apply(final boolean before) throws QueryException {
     final int pos = UpdateType._NODE_UPDATES_.ordinal();
     for(final NameUpdate up : nameUpdates) {
       final int ord = up.type.ordinal();
-      if(before ? ord < pos : ord > pos) up.apply();
+      if(before ? ord < pos : ord > pos) {
+        up.apply();
+      }
     }
   }
 

basex-core/src/main/java/org/basex/query/up/primitives/UpdateType.java

@@ -26,6 +26,8 @@ public enum UpdateType {
   /** Alter backup.         */ BACKUPALTER,
   /** Create backup.        */ BACKUPCREATE,
 
+  /** Add binary resource.  */ DBSTORE,
+
   // Operations on nodes of existing databases
 
   /** Dummy type, indicating start of node updates. */ _NODE_UPDATES_,
@@ -45,7 +47,6 @@ public enum UpdateType {
   // Operations on resources of existing databases
 
   /** Add document.         */ DBADD,
-  /** Add binary resource.  */ DBSTORE,
   /** Rename resource.      */ DBRENAME,
   /** Delete resource.      */ DBDELETE,
   /** Optimize database.    */ DBOPTIMIZE,

basex-core/src/test/java/org/basex/query/expr/MixedTest.java

@@ -277,4 +277,14 @@ public void gh1983() {
     query("db:create('" + NAME + "', json-to-xml('[1]')/*/*, '" + NAME + "')");
     query("db:open('" + NAME + "')/* => namespace-uri()", "http://www.w3.org/2005/xpath-functions");
   }
+
+  /** db:store: out of bounds. */
+  @Test public void gh2100() {
+    query("db:create('x', <x>A</x>, 'x.xml')");
+    query("db:open('x') ! (delete node x, db:store('x', 'x.bin', x))");
+    query("db:retrieve('x', 'x.bin')", "A");
+
+    query("db:create('x', <x>A</x>, 'x.xml')");
+    query("db:open('x') ! (delete node x, db:add('x', x, 'y.xml'))");
+  }
 }