It is quite often when a file is being downloaded that it downloads incomplete or corrupted; which could lead to unexpected potential problems.

I propose to create one (or two) files beside the target file target.ext, named target.ext.size (and target.ext.sha).

When we need to parse a file, we currently check its presence (e.g. in ScopInstallation.ensureClaInstalled() for SCPR classification DB file). In my proposal, we do not only check for its presence, but also for its size +/- its hash code.

The four functions to store/check size/hash can be implemented centrally in a separate location (most probably in BioJava-core) as public static methods and called only at the respective use places.

This way, we hopefully will not modify in the current code a lot: just adding one (or two) lines to call storeSize(), and storeHash() at the file download location and checkSize() +/- checkHash() method from within the ensureXXXInstalled() functions.