Database Schema Changes
Historically, performing a major- or minor-version migration in uPortal required a complete database re-initialization. In other words, the only supported way to have a portal database for your chosen minor release (e.g. 3.1, 3.2, or 4.0) was to run $ant initportal or $ant initdb with the correct/same version of the source code. The current intent within the uPortal developer community is for uPortal 4.1 to be the last minor release for which that is the case. (Major releases will still require database re-initialization.)
Migrating from uPortal 3.x to uPortal 4.1 certainly requires database re-initialization. Migrating from uPortal 4.0 to uPortal 4.1 officially requires it, but you may succeed in running uPortal 4.1 against a database that was functioning properly with a late uPortal 4.0.x release (e.g. 4.0.12).
Even if you could run uPortal 4.1 against your existing portal database, it may be a good idea to perform a full migration anyway. Each new major- and minor-version of uPortal brigs exciting new features. More often than not, these features are implemented with data. In addition to the data changes driven by new features you want, there are often data changes driven by old data that you don't need any longer. When you're making a substantial portal update, it's often very pragmatic to choose a fresh start with portal data. uPortal 4.1, moreover, contains some pretty significant updates, including Respondr and Regions for portlets.
Use $ant data-export to get data from your existing portal, then selectively include elements of that data in the new, 4.1 portal.
Topics for uPortal 4.1 Migration
Below are some data migration notes of particular relevance to uPortal 4.1.
Channels
As of uPortal 4.0, IChannel content is no longer supported. If you're migrating from uPortal 3.x – particularly if you've had a uPortal implementation for a long time – some of your content may be in the form of channels. Although there is no automated path for updating channel-based content to portlet-based content, the community-provided IChannel software can quickly be replaced with their Portlet equivalents (e.g. Webproxy, RSS/News Reader, Announcements, etc.).
Entity PAGS
Starting with uPortal 4.1, Person Attributes Group Store (PAGS) comes in 2 flavors: original (configured in PAGSGroupStoreConfig.xml) and Entity (JPA-managed database entities). Both approaches are functional and behave similarly. Consider switching to Entity PAGS now; in the future, Entity PAGS will allow uPortal to support management of PAGS groups through an administrative UI, without a re-build, re-deploy, and re-start of Tomcat.