Merge 26.7 to 26.9

Author: labkey-teamcity

api/src/org/labkey/api/data/DbScope.java

@@ -1473,29 +1473,38 @@ public ConnectionWrapper getPooledConnection(ConnectionType type, @Nullable Logg
             throw new ConfigurationException("Can't create a database connection for data source " + getDbScopeLoader().getDsName(), e);
         }
 
-        if (!conn.getAutoCommit())
-            throw new ConfigurationException("A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool.");
+        try
+        {
+            if (!conn.getAutoCommit())
+                throw new ConfigurationException("A database connection is in an unexpected state: auto-commit is false. This indicates a configuration problem with the datasource definition or the database connection pool.");
 
-        //
-        // Handle one time per-connection setup
-        // relies on pool implementation reusing same connection/wrapper instances
-        //
+            //
+            // Handle one time per-connection setup
+            // relies on pool implementation reusing same connection/wrapper instances
+            //
 
-        Connection delegate = getDelegate(conn);
-        Integer spid = _initializedConnections.get(delegate);
+            Connection delegate = getDelegate(conn);
+            Integer spid = _initializedConnections.get(delegate);
 
-        if (null == spid)
-        {
-            if (null != _dialect)
+            if (null == spid)
             {
-                _dialect.prepareConnection(conn);
-                spid = _dialect.getSPID(delegate);
+                if (null != _dialect)
+                {
+                    _dialect.prepareConnection(conn);
+                    spid = _dialect.getSPID(delegate);
+                }
+
+                _initializedConnections.put(delegate, spid == null ? spidUnknown : spid);
             }
 
-            _initializedConnections.put(delegate, spid == null ? spidUnknown : spid);
+            return new ConnectionWrapper(conn, this, spid, type, log);
+        }
+        catch (Throwable t)
+        {
+            // If the ConnectionWrapper didn't get created and returned, nothing else can close the connection
+            closeQuietly(conn, t);
+            throw t;
         }
-
-        return new ConnectionWrapper(conn, this, spid, type, log);
     }
 
     /**
@@ -1513,6 +1522,22 @@ public void releaseConnection(Connection conn)
         }
     }
 
+    /**
+     * Release a connection while an exception is already propagating. Pool implementations can throw unchecked from
+     * close(), which would otherwise replace the failure we're unwinding from.
+     **/
+    public void closeQuietly(Connection conn, Throwable propagating)
+    {
+        try
+        {
+            releaseConnection(conn);
+        }
+        catch (Throwable t)
+        {
+            propagating.addSuppressed(t);
+        }
+    }
+
     @JsonIgnore
     public SqlDialect getSqlDialect()
     {

api/src/org/labkey/api/data/dialect/StandardJdbcMetaDataLocator.java

@@ -37,12 +37,22 @@ public StandardJdbcMetaDataLocator(DbScope scope, String schemaName, String sche
     {
         _scope = scope;
         _connection = getConnection();
-        _dbmd = _connection.getMetaData();
 
-        _schemaName = schemaName;
-        _schemaNamePattern = schemaNamePattern;
-        _tableName = tableName;
-        _tableNamePattern = tableNamePattern;
+        try
+        {
+            _dbmd = _connection.getMetaData();
+
+            _schemaName = schemaName;
+            _schemaNamePattern = schemaNamePattern;
+            _tableName = tableName;
+            _tableNamePattern = tableNamePattern;
+        }
+        catch (Throwable t)
+        {
+            // Nobody else can close the connection for us if we throw from the constructor
+            scope.closeQuietly(_connection, t);
+            throw t;
+        }
     }
 
     protected Connection getConnection() throws SQLException

core/src/org/labkey/core/CoreModule.java

@@ -79,6 +79,7 @@
 import org.labkey.api.data.dialect.BasePostgreSqlDialect;
 import org.labkey.api.data.dialect.PostgreSqlService;
 import org.labkey.api.data.dialect.SqlDialect;
+import org.labkey.api.data.dialect.SqlDialect.DataSourcePropertyReader;
 import org.labkey.api.data.dialect.SqlDialectManager;
 import org.labkey.api.data.dialect.SqlDialectRegistry;
 import org.labkey.api.data.statistics.StatsService;
@@ -349,7 +350,6 @@
 import java.lang.reflect.InvocationTargetException;
 import java.lang.reflect.Method;
 import java.sql.Connection;
-import java.sql.SQLException;
 import java.time.ZonedDateTime;
 import java.util.ArrayList;
 import java.util.Calendar;
@@ -365,6 +365,7 @@
 import java.util.Objects;
 import java.util.Properties;
 import java.util.Set;
+import java.util.concurrent.ConcurrentHashMap;
 import java.util.function.Supplier;
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
@@ -584,6 +585,9 @@ private void deleteTempFiles()
 
     private void registerHealthChecks()
     {
+        // Data sources that were unreachable on the previous check, so we can log transitions instead of every poll
+        Set<String> failedDataSources = ConcurrentHashMap.newKeySet();
+
         HealthCheckRegistry.get().registerHealthCheck("database",  HealthCheckRegistry.DEFAULT_CATEGORY, () ->
             {
                 Map<String, Object> healthValues = new HashMap<>();
@@ -595,11 +599,18 @@ private void registerHealthChecks()
                     {
                         dbConnected = conn != null;
                     }
-                    catch (SQLException e)
+                    // Some failures come as ConfigurationException, not SQLException. Cast a wide net to ensure
+                    // we return a 200 saying we're not healthy instead of a 500
+                    catch (Exception e)
                     {
+                        if (failedDataSources.add(dbScope.getDataSourceName()))
+                            LOG.warn("Failed to get connection for data source {}", dbScope.getDataSourceName(), e);
                         dbConnected = false;
                     }
 
+                    if (dbConnected && failedDataSources.remove(dbScope.getDataSourceName()))
+                        LOG.info("Reconnected to data source {}", dbScope.getDataSourceName());
+
                     healthValues.put(dbScope.getDatabaseName(), dbConnected);
                     allConnected &= dbConnected;
                 }

experiment/src/org/labkey/experiment/ExperimentUpgradeCode.java

@@ -515,7 +515,13 @@ public static void fixContainerForMovedSampleFiles(ModuleContext context)
             LimitedUser admin = new LimitedUser(context.getUpgradeUser(), SiteAdminRole.class);
             int numDuplicates = service.fixContainerForExpDataFiles(admin);
             LOG.info("Fixed {} duplicate data files.", numDuplicates);
+            tx.commit();
+        }
+        catch (Exception e) // Issue 55026
+        {
+            LOG.error("Error while fixing container for moved sample files.", e);
         }
+
     }
 
     /**