See: http://www.ibm.com/developerworks/java/library/j-jtp03216.html

[1]  org.sakaiproject.reports.logic.impl.LoadArtifactResultProcessor
Failure to close statement line 274, need to make non anonymous and expressly close in finally

protected void loadArtifactTypes(String artifactIds, Map<String, ArtifactHolder> artifactsToLoad) {
      Connection conn = null;
      ResultSet rs = null;
      try {
         conn = getDataSource().getConnection();
         rs = conn.createStatement().executeQuery(
               "select id, sub_type from dw_resource where id in (" + artifactIds + ")");
         while (rs.next()) {
            String id = rs.getString(1);
            String type = rs.getString(2);
            ArtifactHolder holder = (ArtifactHolder) artifactsToLoad.get(id);
            if (holder != null) {
               holder.artifactType = type;
            }
         }
      }
      catch (SQLException e) {
         logger.error("", e);
         throw new RuntimeException(e);
      }
      finally {
         //ensure that the results set is clsoed
         if (rs != null) {
            try {
               rs.close();
            } catch (SQLException e) {
               if (logger.isDebugEnabled()) {
                  logger.debug("loadArtifactTypes(String, Map) caught " + e);
               }
            }
         }
         //ensure that the connection is closed
         if (conn != null) {
            try {
               conn.close();
            }
            catch (SQLException e) {
               if (logger.isDebugEnabled()) {
                  logger.debug("loadArtifactTypes(String, Map) caught " + e);
            }
            }
         }
      }
   }


[2] org.sakaiproject.reports.logic.impl.ReportsManagerImpl
Line 1271 Useless object creation, result never used
            JDOMResult result = new JDOMResult();


[3] org.sakaiproject.reports.logic.impl.ReportsManagerImpl
NPE if scheduler is null   line 2054
if (scheduler == null) {
            logger.error("Scheduler is down!");
        }
        JobDetail jd = null;
        try {

            JobBeanWrapper job = getJobBeanWrapper();
            if (job != null) {

                jd = scheduler.getJobDetail(report.getReportId().toString(), reportGroup);


[4,5] org.sakaiproject.reports.logic.impl.ReportsManagerImpl

Failure to close InputStream can cause File descriptor leakage

  InputStream stream =  wrapper.getParentClass().getResourceAsStream(wrapper.getDefinitionFileLocation());
 if (wrapper.getParentClass().getResourceAsStream(xsl.getXslLink()) != null){


Wow this is difficult, the whole method should be looked at as by catching Exception with
        catch (Exception e) {
            throw new RuntimeException("Loaded report def failed", e);
        }

You are hidding java.io.Exceptions etc, that have to be closed properly. I would suggest reimplementing the try catch block as a series with a finally. The anonymous creation of streams etc should be removed.