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If JIRA Portlets are a significant component to your Confluence installation, it's a good idea to consider upgrading both JIRA and Confluence together.
With Confluence 3.1 and JIRA 4.0, Atlassian has introduced gadgets to replace portlets and the jiraissues and jiraportlets macros. Particularly with portlets, it's a good idea to migrate to gadgets. This page includes instructions on how to migrate.

Adding the JIRA Gadgets to Confluence

1. Add the JIRA Saved Filter and JIRA Portlet Gadgets as External Gadgets. See All Atlassian Gadgets for a list of available integration points.
2. Add either trusted communication or OAuth between your instances of JIRA and Confluence.

Migrating the Macros to Gadgets

Because of the wide variety of differences in invocations, this is currently a manual process. Vote for Migration for JIRA Issues and JIRA Portlets to Gadget URLs for a feature to do this automatically.

Workarounds

Several workarounds may help:

1. The Global Search and Replace plugin
2. An update statement to the BODYCONTENT table on the Confluence database. Here's some research contributed by one of our users:
   1. Find the pages that have a jiraportlet macro in it:

      Code Block
      sql sql
      SELECT s.spacekey , s.spacename , c.title , c.lastmoddate , 'https://intranet.company.com/wiki/display/'||s.spacekey||'/'||c.title as url , 'https://intranet.company.com/wiki/pages/editpage.action?pageId='||c.contentid as editurl FROM content c, spaces s WHERE c.contentId IN (SELECT contentId FROM bodycontent WHERE body LIKE '%{jiraportlet%') AND c.spaceid = s.spaceid ORDER BY c.lastmoddate desc, s.spacename, c.title;

   2. Replace the jiraportlet macro:

      Code Block
      {jiraportlet:https://intranet.company.com/jira/secure/RunPortlet.jspa?portletKey=com.atlassian.jira.ext.charting:singlefieldpie&projectOrFilterId=filter-10283&statistictype=statuses}

      With:

      Code Block
      {gadget:url=https://intranet.company.com/jira/rest/gadgets/1.0/g/com.atlassian.jira.gadgets:pie-chart-gadget/gadgets/piechart-gadget.xml|width=500px}projectOrFilterId=filter-10283&statType=statuses&isConfigured=true&refresh=false{gadget}

      
      

      Note
      The previous example assumes your JIRA instance is installed under the /jira/ path. If you're using the standalone edition, you'll need to remove /jira from both the find and replace.