Changeset 2945

Timestamp:

Nov 23, 2006, 12:27:49 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Possible fix for BASE 1 disconnection issues

Location:

branches/2.1/src/clients/migrate

Files:

• net/sf/basedb/clients/migrate/Migrater.java (modified) (1 diff)
• net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java (modified) (4 diffs)
• sql/mysql-migration-queries.sql (modified) (2 diffs)

branches/2.1/src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java

@@ -238 +238 @@
     String user = getProperty("db1.user");
     String password = getProperty("db1.password");
-    String url = getProperty("db1.url");
+    String url = getProperty("db1.url") + "&autoReconnect=true";
     String driver = getProperty("db1.driver");
     try

branches/2.1/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java

@@ -138 +138 @@
      */
     cleanUpMemory();
-    PreparedStatement ps = QUICK_TRANSFER ? prepareStatementFromFile("selectMinimumRawBioAssayData")
-        : prepareStatementFromFile("selectRawBioAssayData");
-    try
-    {
-      ps.setInt(1, rawBioAssayId);
+
       RawDataBatcher batcher = rawBioAssay.getRawDataBatcher();
       batcher.setBatchSize(getBatchSize());
-      runRawBioAssay(ps, 0, getBatchSize(), batcher, hasArrayDesign);
+      runRawBioAssay(rawBioAssay, batcher, hasArrayDesign, rawBioAssayId);
       batcher.flush();
       batcher.close();
-    }
-    catch (SQLException e)
-    {
-      stop("transferRawBioAssayData", e);
-    }
   }
 
@@ -159 +150 @@
   values from and size.
   
-  @param ps <code>PreparedStatement</code> which includes a "LIMIT ?,?"
-         at the end.
-  @param from <code>int</code> indicating start position of the
-         ResultSet.
-  @param size <code>int</code> indicating number of rows to include.
+  @param ps <code>PreparedStatement</code>
   @param batcher RawDataBatcher used in this transfer.
   @param hasArrayDesign (Currently not used)
   @see Transfer#prepareStatementFromFile(String)
    */
-  protected void runRawBioAssay(PreparedStatement ps, int from, int size,
-      RawDataBatcher batcher, boolean hasArrayDesign)
+  protected void runRawBioAssay(RawBioAssay rawBioAssay,  
+      RawDataBatcher batcher, boolean hasArrayDesign, int base1RawBioAssayId)
   {
     try
     {
       int rowCount = 0;
-      ps.setInt(2, from);
-      ps.setInt(3, size);
-      ResultSet rs = ps.executeQuery();
+      ResultSet rs = null;
+      Throwable t = null;
+      int numTries = 0;
+      // Fix for unstable BASE 1 server that is randomly losing the connection
+      // For this to work the connection must be created with autoReconnect=true
+      while (rs == null && numTries < 2)
+      {
+        numTries++;
+        try
+        {
+          PreparedStatement ps = QUICK_TRANSFER ? prepareStatementFromFile("selectMinimumRawBioAssayData")
+            : prepareStatementFromFile("selectRawBioAssayData");
+          ps.setInt(1, base1RawBioAssayId);
+          rs = ps.executeQuery();
+          t = null;
+        }
+        catch (Throwable t2)
+        {
+          t = t2;
+          log("Exception when loading BASE 1 data for raw bioassay: " + rawBioAssay, t2);
+          try
+          {
+            Thread.sleep(2000);
+          }
+          catch (InterruptedException ex)
+          {}
+        }
+      }
+      if (rs == null || t != null) throw new BaseException(t);
       DbControl dc = batcher.getDbControl();
       while (rs.next())
@@ -183 +196 @@
         RawData rd = batcher.newRawData();
         rd.setReporter(reporterT.getReporterById(dc, rs.getInt(2)));
-        // This is not verified, do block, row and col numbers start at
-        // 0 or 1?
         rd.setBlock(rs.getInt(3));
         rd.setColumn(rs.getInt(4));
         rd.setRow(rs.getInt(5));
+        rd.setX(rs.getFloat(6));
+        rd.setY(rs.getFloat(7));
         if (!QUICK_TRANSFER)
         {
@@ -213 +226 @@
         progress.increase();
       }
-      if (rowCount == size)
-      {
-        // Fetch next batch
-        runRawBioAssay(ps, from + size, size, batcher, hasArrayDesign);
-      }
     }
     catch (SQLException e)

branches/2.1/src/clients/migrate/sql/mysql-migration-queries.sql

@@ -971 +971 @@
   `flags` 
 FROM  `RawBioAssayData`
-WHERE   `rawBioAssay` = ?
-ORDER BY `position`
-LIMIT   ?,?;
+WHERE   `rawBioAssay` = ?;
 
 
@@ -979 +977 @@
 SELECT `element`, `reporter`, `block`, `numCol`, `numRow`, `x`, `y`
 FROM  `RawBioAssayData`
-WHERE   `rawBioAssay` = ?
-ORDER BY `position`
-LIMIT   ?,?;
+WHERE   `rawBioAssay` = ?;