The documentation is, in my opinion, a bit sparse in this area, but it's actually quite simple.
Firstly, you deploy the application ( as per the documentation ); this involves
a) Download the ZIP file from the Catalog - as webappintegrator.zip
b) Expand the file into /tmp
c) Drill into the expanded contents, and find webappintegrator_for_Portal_6_1.ZIP
d) Expand this file into /tmp
e) Locate the file /tmp/wai_install/deployWebAppIntegrator.xml and copy it into /opt/IBM/WebSphere/ApplicationServer/profiles/wp_profile/ConfigEngine/config/includes
f) Open a command prompt
g) Change to /opt/IBM/WebSphere/ApplicationServer/profiles/wp_profile/ConfigEngine
h) Run the following script to deploy the portlet: -
./ConfigEngine.sh deploy-webAppIntegrator -DWasPassword=<was pwd> -DPortalAdminPwd=<wps pwd> -DWebAppIntegratorLocation=/tmp/wai_install
This enables the WAI element on each portlet page, within the Manage Pages area within the Administration portlet.
However, any Virtual Portals won't have this element deployed.
Therefore, the trick is to manually import the following XML file: -
/tmp/wai_install/addWAItoManagePages.xml
into each Virtual Portal, using the Administration portlet within the Virtual Portal itself.
Having done this, the WAI element appears in Manage Pages on the Virtual Portal, and you're good to go.
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