Replaced TDB with HDT

[svandenhoek]

Changes

• Vibe now uses a HDT database instead of a TDB.
• TDB code has been removed, but can be reverted through commit fa97f91.
• Minor overhaul of shared test resources to reduce chance of overlapping test resources (now individual modules should only not have a shared directory themselves).
• Creation of HDT was done using the vibe-3.1.0 TTL files (so not from the start), so output should be identical (except perhaps the order of diseases with the same score within the results of a single gene).
• Readme is updated.

Testing notes

• New HDT still gives same results as original TDB (script was adjusted to use the optimized HDT instead of optimized TDB):

$ sh TestOptimizedQueries.sh -or ~/Programming/data/vibe/database_creation/vibe-5.0.0-sources-tdb/ -op ~/Programming/data/vibe/database_creation/vibe-5.0.0-hdt/vibe-5.0.0.hdt
### Running original TDB/query.
Time: 74,405 sec
### Running optimized HDT/query.
### Validating if optimized TDB/query output files are equal to their original counterparts.
test/genes_for_hpo-optimized.tsv: OK

• Some new tests are not supported on Jenkins (due to changing file/dir permissions within a unit test), so a tag skipOnJenkins has been created and -DexcludedGroups='skipOnJenkins' was added to the Jenkinsfile on several places. These tests are still run locally by default and mvn clean install did not cause any issues.
• md5 of the final .tsv files seem to differ between the TDB & HDT files, though multiple runs for a single format do not differ. It seems however that the cause of this might be that certain genes (or diseases for a single gene) with the same score are outputted in a different order.

[sonarcloud]

Kudos, SonarCloud Quality Gate passed!

0 Bugs
0 Vulnerabilities
0 Security Hotspots
3 Code Smells

81.4% Coverage
0.0% Duplication

[bartcharbon]

when I try to run with these arguments, I get an error: Missing arguments: -w

when adding the missing argument it works fine

[bartcharbon]

seems like a documentation error that already existed before this PR