[Backport release/3.6] GPKG: fix issue with StartTransaction() causing features to be omitted when creating background RTree

autotest/ogr/ogr_gpkg.py

@@ -7244,10 +7244,15 @@ def test_ogr_gpkg_background_rtree_build(filename):
     ds = gdaltest.gpkg_dr.CreateDataSource(filename)
     with gdaltest.config_option("OGR_GPKG_THREADED_RTREE_AT_FIRST_FEATURE", "YES"):
         lyr = ds.CreateLayer("foo")
+    assert lyr.StartTransaction() == ogr.OGRERR_NONE
     for i in range(1000):
         f = ogr.Feature(lyr.GetLayerDefn())
         f.SetGeometryDirectly(ogr.CreateGeometryFromWkt("POINT(%d %d)" % (i, i)))
         assert lyr.CreateFeature(f) == ogr.OGRERR_NONE
+        if i == 500:
+            assert lyr.CommitTransaction() == ogr.OGRERR_NONE
+            assert lyr.StartTransaction() == ogr.OGRERR_NONE
+    assert lyr.CommitTransaction() == ogr.OGRERR_NONE
     ds = None
     assert gdal.VSIStatL(filename + ".tmp_rtree_foo.db") is None
 
@@ -7326,6 +7331,45 @@ def test_ogr_gpkg_background_rtree_build(filename):
     gdal.Unlink(filename)
 
 
+###############################################################################
+
+
+def test_ogr_gpkg_detect_broken_rtree_gdal_3_6_0():
+
+    filename = "/vsimem/test_ogr_gpkg_detect_broken_rtree_gdal_3_6_0.gpkg"
+
+    ds = gdaltest.gpkg_dr.CreateDataSource(filename)
+    lyr = ds.CreateLayer("foo")
+    for i in range(100):
+        f = ogr.Feature(lyr.GetLayerDefn())
+        f.SetGeometryDirectly(
+            ogr.CreateGeometryFromWkt("POINT(%d %d)" % (i % 10, i // 10))
+        )
+        lyr.CreateFeature(f)
+    ds = None
+
+    # Voluntary corrupt the RTree by removing the entry for the last feature
+    ds = ogr.Open(filename, update=1)
+    sql_lyr = ds.ExecuteSQL("DELETE FROM rtree_foo_geom WHERE id = 100")
+    ds.ReleaseResultSet(sql_lyr)
+    ds = None
+
+    with gdaltest.config_option("OGR_GPKG_THRESHOLD_DETECT_BROKEN_RTREE", "100"):
+        ds = ogr.Open(filename)
+        lyr = ds.GetLayer(0)
+        with gdaltest.error_handler():
+            gdal.ErrorReset()
+            lyr.SetSpatialFilterRect(8.5, 8.5, 9.5, 9.5)
+            assert (
+                "Spatial index (perhaps created with GDAL 3.6.0) of table foo is corrupted"
+                in gdal.GetLastErrorMsg()
+            )
+        assert lyr.GetFeatureCount() == 1
+        ds = None
+
+    gdal.Unlink(filename)
+
+
 ###############################################################################
 # Test ST_Area()
 

ogr/ogrsf_frmts/gpkg/ogrgeopackagetablelayer.cpp

@@ -2173,6 +2173,10 @@ OGRErr OGRGeoPackageTableLayer::CreateOrUpsertFeature( OGRFeature *poFeature, bo
             else if( !bUpsert && m_bAllowedRTreeThread && !m_bErrorDuringRTreeThread )
             {
                 GPKGRTreeEntry sEntry;
+#ifdef DEBUG_VERBOSE
+                if( m_aoRTreeEntries.empty() )
+                    CPLDebug("GPKG", "Starting to fill m_aoRTreeEntries at FID " CPL_FRMT_GIB, nFID);
+#endif
                 sEntry.nId = nFID;
                 sEntry.fMinX = rtreeValueDown(oEnv.MinX);
                 sEntry.fMaxX = rtreeValueUp(oEnv.MaxX);
@@ -2226,7 +2230,7 @@ void OGRGeoPackageTableLayer::SetDeferredSpatialIndexCreation( bool bFlag )
         // For unit tests
         if( CPLTestBool(CPLGetConfigOption("OGR_GPKG_THREADED_RTREE_AT_FIRST_FEATURE", "NO")) )
         {
-            m_nRTreeBatchSize = 1;
+            m_nRTreeBatchSize = 10;
             m_nRTreeBatchesBeforeStart = 1;
         }
     }
@@ -2363,11 +2367,21 @@ void OGRGeoPackageTableLayer::AsyncRTreeThreadFunction()
     }
 
     SQLCommand(m_hAsyncDBHandle, "BEGIN");
+    GIntBig nCount = 0;
     while( true )
     {
         const auto aoEntries = m_oQueueRTreeEntries.get_and_pop_front();
         if( aoEntries.empty() )
             break;
+#ifdef DEBUG_VERBOSE
+        CPLDebug("GPKG", "AsyncRTreeThreadFunction(): "
+                 "Processing batch of %d features, "
+                 "starting at FID " CPL_FRMT_GIB " and ending "
+                 "at FID " CPL_FRMT_GIB,
+                 static_cast<int>(aoEntries.size()),
+                 aoEntries.front().nId,
+                 aoEntries.back().nId);
+#endif
         for( const auto& entry: aoEntries )
         {
             if( (entry.nId % 500000) == 0 )
@@ -2382,6 +2396,7 @@ void OGRGeoPackageTableLayer::AsyncRTreeThreadFunction()
             }
             sqlite3_reset(hStmt);
 
+            nCount ++;
             sqlite3_bind_int64(hStmt,1,entry.nId);
             sqlite3_bind_double(hStmt,2,entry.fMinX);
             sqlite3_bind_double(hStmt,3,entry.fMaxX);
@@ -2408,6 +2423,7 @@ void OGRGeoPackageTableLayer::AsyncRTreeThreadFunction()
     }
 
     sqlite3_finalize(hStmt);
+    CPLDebug("GPKG", "AsyncRTreeThreadFunction(): " CPL_FRMT_GIB " rows inserted into RTree", nCount);
 
     if( m_bErrorDuringRTreeThread )
     {
@@ -2836,6 +2852,9 @@ OGRErr OGRGeoPackageTableLayer::DeleteFeature(GIntBig nFID)
 
 bool OGRGeoPackageTableLayer::DoJobAtTransactionCommit()
 {
+    if( m_bAllowedRTreeThread )
+        return true;
+
     bool ret = RunDeferredCreationIfNecessary() == OGRERR_NONE &&
                RunDeferredSpatialIndexUpdate();
     m_nCountInsertInTransaction = 0;
@@ -4151,6 +4170,44 @@ bool OGRGeoPackageTableLayer::HasSpatialIndex()
         m_osFIDForRTree = m_pszFidColumn;
     }
 
+    // Add heuristics to try to detect corrupted RTree generated by GDAL 3.6.0
+    // Cf https://github.com/OSGeo/gdal/pull/6911
+    if( m_bHasSpatialIndex )
+    {
+        const auto nFC = GetTotalFeatureCount();
+        if( nFC >= atoi(CPLGetConfigOption(
+                    "OGR_GPKG_THRESHOLD_DETECT_BROKEN_RTREE", "100000")) )
+        {
+            CPLString osSQL = "SELECT 1 FROM \"";
+            osSQL += SQLEscapeName(pszT);
+            osSQL += "\" WHERE \"";
+            osSQL += SQLEscapeName(GetFIDColumn());
+            osSQL += "\" = ";
+            osSQL += CPLSPrintf(CPL_FRMT_GIB, nFC);
+            osSQL += " AND \"";
+            osSQL += SQLEscapeName(pszC);
+            osSQL += "\" IS NOT NULL AND NOT ST_IsEmpty(\"";
+            osSQL += SQLEscapeName(pszC);
+            osSQL += "\")";
+            if( SQLGetInteger(m_poDS->GetDB(), osSQL, nullptr) == 1 )
+            {
+                osSQL = "SELECT 1 FROM \"";
+                osSQL += SQLEscapeName(m_osRTreeName);
+                osSQL += "\" WHERE id = ";
+                osSQL += CPLSPrintf(CPL_FRMT_GIB, nFC);
+                if( SQLGetInteger(m_poDS->GetDB(), osSQL, nullptr) == 0 )
+                {
+                    CPLError(CE_Warning, CPLE_AppDefined,
+                             "Spatial index (perhaps created with GDAL 3.6.0) "
+                             "of table %s is corrupted. Disabling its use. "
+                             "This file should be recreated or its spatial "
+                             "index recreated", m_pszTableName);
+                    m_bHasSpatialIndex = false;
+                }
+            }
+        }
+    }
+
     return CPL_TO_BOOL(m_bHasSpatialIndex);
 }