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JIRA is Atlassian's issue-tracking and project-management application. You can connect FishEye to JIRA for one or both of the following:

Configuring those two aspects are separate processes, and are described on this page. Note that you can link FishEye with one or more instances of JIRA. If you're linking FishEye to an Atlassian Cloud JIRA instance, please see Linking to server applications from your cloud instance.

On this page:

Your user tiers don't need to match between JIRA and FishEye/Crucible in order to integrate them. JIRA users that are not FishEye users will see the same view as FishEye users within JIRA, but will not be able to log in to FishEye to view the source/reviews.

Initial configuration in JIRA

You should check that the instances of JIRA that you wish to link to FishEye are configured to accept remote API calls; in each JIRA instance, go to Administration > System > General Configuration and turn on Accept remote API calls (under 'Options'). A restart is not required. See JIRA options for more details.

Quick setup with the FishEye Setup Wizard

When you are installing FishEye, the setup wizard allows you to configure the JIRA connection automatically. This is a quick way of setting up integration with JIRA for user management. See Configuring JIRA integration in the Setup Wizard.

If you did not set up JIRA integration during FishEye setup at install time, you can still configure that from the FishEye administration area as described below.

Integrating with JIRA

See JIRA Integration in FishEye for an overview of the benefits you get when FishEye and JIRA are integrated.

Integrating FishEye with JIRA relies on configuring an application link between the FishEye and JIRA servers. See Linking to another application for guidance on doing that.

See also Enabling Smart Commits.

Connecting to JIRA for user management

This option requires JIRA 4.3 and later.

If you want to manage your FishEye users using JIRA, you need to configure a connection in JIRA and then set up the user directory in FishEye. Both steps are described below.

2.1. To configure a new connection for user management in JIRA:

  1. Log in to JIRA as a user with the 'JIRA System Administrators' global permission.
  2. Click Administration on the JIRA top navigation bar.
    1. Go to the JIRA administration screen for configuring the applications that have been set up to use JIRA for user management:
      • In JIRA 4.3: Click 'Other Applications' in the 'Users, Groups & Roles' section of the JIRA administration screen.
      • In JIRA 4.4: Select 'Administration' > 'Users' > 'JIRA User Server'.
    2. Add an application.
    3. Enter the application name and password that your application will use when accessing JIRA.
    4. Enter the IP address or addresses of your application. Valid values are:
      • A full IP address, e.g.
      • A wildcard IP range, using CIDR notation, e.g. For more information, see the introduction to CIDR notation on Wikipedia and RFC 4632.
      • Save the new application.

2.2. To set up the JIRA user directory in FishEye:

  1. Go to your FishEye administration screen.
    1. Click Authentication (under 'Security Settings').
    2. Click Setup JIRA/Crowd authentication. Note, if LDAP authentication has already been set up, you will need to remove that before connecting to JIRA for user management.
    3. Make the following settings:

      Authenticate againstSelect a JIRA instance
      Application name and passwordEnter the values that you defined for your application in the settings on JIRA.
      JIRA URL

      The web address of your JIRA server. Examples:
      Auto-addSelect Create a FishEye user on successful login so that your JIRA users will be automatically added as a FishEye user when they first log in.
      Periodically synchronise users with JIRASelect Yes to ensure that JIRA will synchronize all changes in the user information on a regular basis. Change the value for Synchronise Period if required.
      When Synchronisation HappensSelect an option depending on whether you want to allow changes to user attributes from within FishEye.
      Single Sign OnSelect Disabled. SSO is not available when using JIRA for user management and if enabled will make the integration fail.
    4. Click Next and select at least one user group to be synchronised from JIRA. If necessary, you could create a new group in JIRA, such as 'fisheye-users', and select this group here.
    5. Click Save.

Read more:

We do not recommend the use of project links with FishEye 2.9 and later, if you have JIRA 5.0 or later as well as the latest version of the JIRA FishEye Plugin. This is because application links now provide all of the functionality previously available with project links. However, project links are retained for the following reasons:

  • Setting up project links provides a way to restrict the scope of JIRA searches to a specific FishEye repository. 
  • Legacy configurations can continue to use project links without any need for changes.
  • Third-party plugins may continue to rely on project links for their functionality.


  • JIRA requires FishEye to manually refresh repository cache when repository changes are made — When a repository is removed, or when there has been any change in FishEye repositories, JIRA does not update the FishEye repository list cache automatically. You must manually refresh the repository list cache. This is done in JIRA: 'Administration' > 'FishEye Configuration' > 'Refresh Cache' link (next to 'Repository List Cache')
  • FishEye doesn't check for invalid JIRA issue keys – FishEye doesn't check for invalid issue keys, such as 'UTF-8'. An error will result if FishEye tries to connect to an issue that doesn't exist.
  • FishEye doesn't recognise custom JIRA issue key formats – FishEye assumes that JIRA issue keys are of the default format for JIRA 5.0 and later: that is, up to 10 letters, followed by a hyphen and the issue number (i.e. [a-zA-Z]{10}-[0-9]+), for example FishEye-123
  • If FishEye/Crucible will be running on the same machine as JIRA (already installed), you need to ensure that the URL paths are different for FishEye/Crucible and JIRA. Change the default FishEye/Crucible path as follows:
    • Edit the config.xml in your FishEye/Crucible data directory.
      Add the context attribute to the web-server  element:

      <web-server context="/fisheye">