Symptoms

Viewing particular issues shows the following error:

The following appears in the atlassian-jira.log:

2015-01-26 15:09:11,209 http-bio-8014-exec-21 ERROR matheus 909x54x1 1fg0cr8 192.168.10.239 /browse/DEMO-1 [jira.web.component.ModuleWebComponentImpl] An exception occured while rendering the web panel: com.atlassian.jira.jira-view-issue-plugin:timetrackingmodule (null)
java.lang.NullPointerException
        at com.atlassian.jira.security.DefaultPermissionManager.doIssuePermissionCheck(DefaultPermissionManager.java:284)
        at com.atlassian.jira.security.DefaultPermissionManager.hasPermission(DefaultPermissionManager.java:207)
        at com.atlassian.jira.security.WorkflowBasedPermissionManager.hasPermission(WorkflowBasedPermissionManager.java:111)
        at com.atlassian.jira.security.DefaultPermissionManager.hasPermission(DefaultPermissionManager.java:202)
        at com.atlassian.jira.security.WorkflowBasedPermissionManager.hasPermission(WorkflowBasedPermissionManager.java:104)
        at sun.reflect.GeneratedMethodAccessor263.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)

Diagnosis

Run the following queries in JIRA's database - if anything is returning, please continue to the "Workaround" section:

SELECT il.* FROM issuelink il LEFT JOIN jiraissue ji ON ji.id = il.destination WHERE ji.issuenum IS NULL;

SELECT il.* FROM issuelink il LEFT JOIN jiraissue ji ON ji.id = il.source WHERE ji.issuenum IS NULL;

You can see with the queries below which issues are being affected by this problem:

• SELECT p.pkey, ji.issuenum FROM jiraissue ji
    JOIN (SELECT il.* FROM issuelink il LEFT JOIN jiraissue ji ON ji.id = il.destination WHERE ji.issuenum IS NULL) AS pl ON pl.source = ji.id
    JOIN project p ON ji.project = p.id;
  

• SELECT p.pkey, ji.issuenum FROM jiraissue ji
    JOIN (SELECT il.* FROM issuelink il LEFT JOIN jiraissue ji ON ji.id = il.source WHERE ji.issuenum IS NULL) AS pl ON pl.destination = ji.id
    JOIN project p ON ji.project = p.id;
  

  The issues returned with this second query will not display the same errors described above, but still are part of orphaned links that should be removed.

Workaround

1. Backup JIRA!
2. Stop JIRA.

3. Run the following SQL statements in JIRA's database:

   DELETE FROM issuelink WHERE id IN (SELECT il.id FROM issuelink il LEFT JOIN jiraissue ji ON ji.id = il.destination WHERE ji.issuenum IS NULL);
   DELETE FROM issuelink WHERE id IN (SELECT il.id FROM issuelink il LEFT JOIN jiraissue ji ON ji.id = il.source WHERE ji.issuenum IS NULL);

4. Restart JIRA.

After that you should no longer see problems viewing those issues.