myGrid
  1. myGrid
  2. TAV-700

Column 'thing' too short in LogBook database schema

    Details

    • Type: Bug Bug
    • Status: Resolved Resolved
    • Priority: Major Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.7.1
    • Component/s: Provenance
    • Labels:
      None

      Description

      Reported by one of our users:

      I am running a workflow with a text file like input and splitting it
      into several lines to finally get a "list of lists" (I'm using local
      processors and regex to do it).

      Results window show everything well, but logbook say in results tab
      window : "Problem Retrieving Data from Store - No Data Matching the
      Given LSID Value"

      Looking at java console appears:

      com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
      column 'thing' at row 1
      at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2868)
      at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
      at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1169)
      at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:693)
      at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1404)
      at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1318)
      at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1303)
      at uk.org.mygrid.provenance.dataservice.AbstractJDBCDataService.storeDataThing(AbstractJDBCDataService.java:345)
      at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.store(ProvenanceGenerator.java:1419)
      at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.processCompletedWithIteration(ProvenanceGenerator.java:518)
      at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:203)
      at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:184)
      at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:250)
      com.mysql.jdbc.MysqlDataTruncation: Data truncation: Data too long for
      column 'thing' at row 1
      at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:2868)
      at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1573)
      at com.mysql.jdbc.ServerPreparedStatement.serverExecute(ServerPreparedStatement.java:1169)
      at com.mysql.jdbc.ServerPreparedStatement.executeInternal(ServerPreparedStatement.java:693)
      at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1404)
      at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1318)
      at com.mysql.jdbc.PreparedStatement.executeUpdate(PreparedStatement.java:1303)
      at uk.org.mygrid.provenance.dataservice.AbstractJDBCDataService.storeDataThing(AbstractJDBCDataService.java:345)
      at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.store(ProvenanceGenerator.java:1419)
      at uk.ac.man.cs.img.mygrid.provenance.knowledge.taverna.ProvenanceGenerator.workflowCompleted(ProvenanceGenerator.java:426)
      at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.sendAnEvent(WorkflowEventDispatcher.java:199)
      at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher.fireEvents(WorkflowEventDispatcher.java:184)
      at org.embl.ebi.escience.scufl.enactor.implementation.WorkflowEventDispatcher$NotifyThread.run(WorkflowEventDispatcher.java:250)

        Activity

        Hide
        Ian Dunlop added a comment -

        I think it works OK now but needs some testing to say for sure

        Show
        Ian Dunlop added a comment - I think it works OK now but needs some testing to say for sure
        Hide
        Ian Dunlop added a comment -

        Changed it to MEDIUMTEXT, need to test it against some meaningful data - any ideas?

        Show
        Ian Dunlop added a comment - Changed it to MEDIUMTEXT, need to test it against some meaningful data - any ideas?
        Hide
        Stuart Owen added a comment -

        I've had a reply that setting the size to MEDIUMTEXT fixed the problem. We need to update the plugin to set this as the default field size.

        This doesn't need to released as part of 1.7.1 but can be released as an independant plugin update.

        Show
        Stuart Owen added a comment - I've had a reply that setting the size to MEDIUMTEXT fixed the problem. We need to update the plugin to set this as the default field size. This doesn't need to released as part of 1.7.1 but can be released as an independant plugin update.
        Hide
        June Finch (Inactive) added a comment -

        Should be considered within 1.7.1 timescales.

        Show
        June Finch (Inactive) added a comment - Should be considered within 1.7.1 timescales.
        Hide
        Ian Dunlop added a comment -

        Looks like the table is using TEXT field(max size 65k in mySQL). Code is in rdf-provenance module, uk.org.mygrid.provenance.dataservice.MySQLDataService createTables method:

        "CREATE TABLE IF NOT EXISTS datathings (id INT UNSIGNED NOT NULL AUTO_INCREMENT,"
        + " thing TEXT NOT NULL,"
        + " PRIMARY KEY(id)) TYPE = InnoDB;"

        Could set the field size to MEDIUMTEXT or LONGTEXT (although there could be performance issues which arise).

        Show
        Ian Dunlop added a comment - Looks like the table is using TEXT field(max size 65k in mySQL). Code is in rdf-provenance module, uk.org.mygrid.provenance.dataservice.MySQLDataService createTables method: "CREATE TABLE IF NOT EXISTS datathings (id INT UNSIGNED NOT NULL AUTO_INCREMENT," + " thing TEXT NOT NULL," + " PRIMARY KEY(id)) TYPE = InnoDB;" Could set the field size to MEDIUMTEXT or LONGTEXT (although there could be performance issues which arise).

          People

          • Assignee:
            Ian Dunlop
            Reporter:
            Stuart Owen
          • Votes:
            0 Vote for this issue
            Watchers:
            0 Start watching this issue

            Dates

            • Created:
              Updated:
              Resolved: