Upgrade uses of Jena to 5.3.0

[krauzer]

Hello,

This PR upgrades uses of Apache Jena to 5.3.0 for RDF writing and reading. This resolves #6302.

The main issue is that Jena removed the uses of reader and writer in their read and write methods in version 5, so I modified the utility method to check for StringReader and InputStreamReader on read, and building a OutputStream out of the passed writer. Those readers were the types I could infer that were coming in from HAPI for RDF. Jena only handles a couple types anyway.

Below are the more specific changes I made to accommodate the use of the latest version, as well as removing some unmaintained testing dependencies for RDF.

If there are any adjustments/changes I should make, let me know and I can try to make them. We plan to use HAPI within CMS, where I work, and we'd like to be able to contribute to the code where we can/when needed, such as resolving security issues.

Changes:

-fixes CVE-2024-7254 in dependencies prior to 5.2.0
-hapi-fhir-base: include httpclient dependency which was removed from jena-arq
-hapi-fhir-base RDFParser: init JenaSystem on initialization
-hapi-fhir-base RDFParser: specify signature for null values on methods that are overloaded
-hapi-fhir-base RDFUtil: Jena Riot RDFDataMgr no longer accepts reading and writing into generic reader and writer. Handle reading for StringReader and InputStreamReader. Handle writing by building an output stream from the writer.
-hapi-fhir-structures-r4: Remove shexjava dependency - unmaintained
-hapi-fhir-structures-r4: Use jena-shex for shex validation
-hapi-fhir-structures-r4 RDFParserTest: use jena libraries - compatibile with jena-shex
-hapi-fhir-structures-r4 RDFParserTest: simplify FixedShapeMapEntry by attaching nodes vs recreating them (handles blank nodes)
-hapi-fhir-structures-r4 RDFParserR4Test: jena 5.0.0 defaults to using PREFIX, not @Prefix. Read testing strings and use isomorphic comparison to check for equality. Added extra assertion to test isomorphism check.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 83.48%. Comparing base (46d5809) to head (5f61d35).
Report is 10 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff              @@
##             master    #6704      +/-   ##
============================================
- Coverage     83.50%   83.48%   -0.03%     
+ Complexity    28566    28562       -4     
============================================
  Files          1797     1797              
  Lines        111166   111184      +18     
  Branches      13965    13967       +2     
============================================
- Hits          92828    92818      -10     
- Misses        12351    12375      +24     
- Partials       5987     5991       +4     

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[jamesagnew]

Thanks for the contribution!