Migration to new Nexus, outdated or no-longer available dependencies

[marco-brandizi]

While migrating Ondex to our new Nexus, I've discovered a number of Ondex 3rd-party dependencies that:

• either are very old and cannot be found in any public Maven repository anymore
• or have never been proper Maven projects, but someone made a Jar in more manual ways (eg, via IDE) and uploaded it in the old Nexus.

In the first case, I tried to find more recent versions or replacements. Some of them worked, but we need entensive testing of the new build. In particular, we need to re-run relevant Mini workflows (ara, wheat, etc) and see if the resulting OXL is fine.

In the second case (and in cases where no version or replacement was available), I had to disable modules that depends on those missing components. These are:

Ondex Module ID	Module Name	URL	Lost Deps
nclondexexpression	NCL Ondex Expression	https://github.com/Rothamsted/ondex-opt/tree/master/modules-opt/expression	de.mpg.mpiinf.csb:KPM
psimi2ondex	PSI-MI 2.5 parser for Ondex	https://github.com/Rothamsted/ondex-opt/tree/master/modules-opt/psimi25	uk.ac.ncl.cs:psimi
sbml	sbml	https://github.com/Rothamsted/ondex-opt/tree/master/modules-opt/sbml	org.biojava:biojava:1.0

We need to confirm that the above modules aren't needed anymore. Or to discuss a solution.

[KeywanHP]

I can confirm they are not needed any longer. It might be a good idea to spring clean our plugins and just keep the ones that are used for building KnetMiner knowledge graphs.