Update commons-codec version and include it in shaded jar

[whikloj]

JIRA Ticket: https://fedora-repository.atlassian.net/browse/FCREPO-3892 and #192

What does this Pull Request do?

Updates the version of commons-codec and adds the ServicesResourceTransformer to the shade plugin to ensure the Jena dependencies end up in the final jar.

How should this be tested?

Make a container with some blank nodes (see linked tickets), then try to index it to a triplestore.

Before PR: get a stacktrace with java.lang.NoClassDefFoundError: org/apache/commons/codec/digest/MurmurHash3 in it.

After PR: resource is indexed to triplestore

Additional Notes:

Example:

• Does this change require documentation to be updated? no
• Does this change add any new dependencies? yes and no
• Does this change require any other modifications to be made to the repository (ie. Regeneration activity, etc.)? no
• Could this change impact execution of existing code? no

Interested parties

Tag (@ mention) interested parties or, if unsure, @fcrepo/committers

[mikejritter]

After rebuilding I can see the commons-codec classes in the jar. Admittedly I don't know how to add a blank node (I tried w/ the resource from the issue but was unable to replicate), which is triggering the exception, but considering the classes were missing from the jar before the exception should no longer occur.

[whikloj]

Just for clarity in the associated Github issue and Jira the blank nodes are identifier by the underscore colon
i.e. _:b1 and _:b0 and _:b2

So this

curl -v -ufedoraAdmin:fedoraAdmin -H"Content-type: text/turtle" -d "<> <http://example.org/somePredicate> _:b0 . _:b0 <http://purl.org/dc/elements/1.1/title> 'Some title' ." -XPOST -H"Slug: testContainer" http://localhost:8080/rest

should generate a resource with a blank node in it.

[mikejritter]

@whikloj I got around to redoing my docker setup this morning for testing this and got the exception to replicate and the verifying the fix. Going to merge this now.