Hi Joachim, Sorry for the late reply. The "Update all Schemas" is very slow in MartBuilder. We will improve it in the new release.
For now, please try to update the schema one by one instead of update all, there is a menu "Schema->Update ...". Hope this helps. Yong On 20/02/10 6:08 AM, "Joachim Baran" <[email protected]> wrote: > Hello, > > I have added some data to our customised Ensembl mart and I am trying > to rebuild it now. However, when I update all schemas in MartBuilder, > then accept all changes and finally try to generate the SQL for the > mart, the exceptions as shown below occur. Please note that even > though the top of the call stacks says 'MartScript' rather than > 'MartBuilder', it is the same underlying code of MartBuilder that gets > executed. I just wrote a scripting front-end that takes me through the > mart creation process, which I would otherwise have to do by hand. > > At first I thought there was a network connection problem regarding > the MySQL database, but since this exception reoccurred, I begin to > doubt that. Could this be related to the extended amount of time > MartBuilder needs to pick up the tables that I have added to Ensembl? > It takes about 7h for MartBuilder to calculate the database changes > once I have clicked 'Update all schemas'. > > com.mysql.jdbc.CommunicationsException: Communications link failure > due to underlying exception: > > ** BEGIN NESTED EXCEPTION ** > > java.io.EOFException > > STACKTRACE: > > java.io.EOFException > at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934) > at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) > at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) > at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) > at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) > at > com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) > at > com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) > at > org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java: > 1773) > at > org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema. > java:1787) > at > org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1 > 818) > at > org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) > at > org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter. > java:1662) > at > org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterprete > r.java:273) > at > org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) > at > org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) > at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) > > > ** END NESTED EXCEPTION ** > > > > Last packet sent to the server was 204460 ms ago. > at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) > at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) > at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) > at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) > at > com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) > at > com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) > at > org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java: > 1773) > at > org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema. > java:1787) > at > org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1 > 818) > at > org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) > at > org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter. > java:1662) > at > org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterprete > r.java:273) > at > org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) > at > org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) > at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) > Woops.. the following exception occurred during the script's exception: > java.sql.SQLException: No operations allowed after connection > closed.Connection was implicitly closed due to underlying > exception/error: > > > ** BEGIN NESTED EXCEPTION ** > > com.mysql.jdbc.CommunicationsException > MESSAGE: Communications link failure due to underlying exception: > > ** BEGIN NESTED EXCEPTION ** > > java.io.EOFException > > STACKTRACE: > > java.io.EOFException > at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934) > at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) > at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) > at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) > at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) > at > com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) > at > com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) > at > org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java: > 1773) > at > org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema. > java:1787) > at > org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1 > 818) > at > org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) > at > org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter. > java:1662) > at > org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterprete > r.java:273) > at > org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) > at > org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) > at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) > > > ** END NESTED EXCEPTION ** > > > > Last packet sent to the server was 204460 ms ago. > > STACKTRACE: > > com.mysql.jdbc.CommunicationsException: Communications link failure > due to underlying exception: > > ** BEGIN NESTED EXCEPTION ** > > java.io.EOFException > > STACKTRACE: > > java.io.EOFException > at com.mysql.jdbc.MysqlIO.readFully(MysqlIO.java:1934) > at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2380) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) > at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) > at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) > at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) > at > com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) > at > com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) > at > org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java: > 1773) > at > org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema. > java:1787) > at > org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1 > 818) > at > org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) > at > org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter. > java:1662) > at > org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterprete > r.java:273) > at > org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) > at > org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) > at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) > > > ** END NESTED EXCEPTION ** > > > > Last packet sent to the server was 204460 ms ago. > at com.mysql.jdbc.MysqlIO.reuseAndReadPacket(MysqlIO.java:2592) > at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2909) > at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1600) > at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1695) > at com.mysql.jdbc.Connection.execSQL(Connection.java:3020) > at com.mysql.jdbc.Connection.execSQL(Connection.java:2949) > at com.mysql.jdbc.Statement.executeQuery(Statement.java:959) > at > com.mysql.jdbc.DatabaseMetaData$9.forEach(DatabaseMetaData.java:4450) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4428) > at > com.mysql.jdbc.DatabaseMetaData$2.forEach(DatabaseMetaData.java:1916) > at > com.mysql.jdbc.DatabaseMetaData$IterateBlock.doForAll(DatabaseMetaData.java:79> ) > at > com.mysql.jdbc.DatabaseMetaData.getColumns(DatabaseMetaData.java:1882) > at > org.biomart.builder.model.Schema$JDBCSchema.getTableColumnsFromDB(Schema.java: > 1773) > at > org.biomart.builder.model.Schema$JDBCSchema.getDBTableColumnCollection(Schema. > java:1787) > at > org.biomart.builder.model.Schema$JDBCSchema.findOrphanKeysFromDB(Schema.java:1 > 818) > at > org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1319) > at > org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter. > java:1662) > at > org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterprete > r.java:273) > at > org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) > at > org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) > at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) > > > ** END NESTED EXCEPTION ** > > > at com.mysql.jdbc.Connection.checkClosed(Connection.java:1844) > at com.mysql.jdbc.Connection.createStatement(Connection.java:2872) > at com.mysql.jdbc.Connection.createStatement(Connection.java:2854) > at > com.mysql.jdbc.Connection.getMetadataSafeStatement(Connection.java:3440) > at > com.mysql.jdbc.DatabaseMetaData.getTables(DatabaseMetaData.java:4422) > at > org.biomart.builder.model.Schema$JDBCSchema.synchronise(Schema.java:1409) > at > org.bergmanlab.martscript.MartScriptInterpreter.execute(MartScriptInterpreter. > java:1662) > at > org.bergmanlab.martscript.MartScriptInterpreter.runScript(MartScriptInterprete > r.java:273) > at > org.bergmanlab.martscript.MartScript.processScript(MartScript.java:34) > at > org.bergmanlab.martscript.MartScriptParser.script(MartScriptParser.java:116) > at org.bergmanlab.martscript.MartScript.main(MartScript.java:72) > > BW, > Joachim > > -- > B.1079 Michael Smith Building > Faculty of Life Sciences > The University of Manchester > Oxford Road > Manchester > M13 9PT > United Kingdom
