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Currently, you have to be in the D2RQ directory. Removing that restriction would be good for cronjobs etc. (All other scripts should already run from anywhere.)
Fixed issue #80: d2r-server should be launchable from any directory
Clarification: It's actually already possible to call the various scripts from outside of the D2RQ directory, and the dump-rdf and generate-mapping scripts work fine for me from wherever I call them.
The problem is that d2r-server, in JettyLauncher.start, looks for the webapp directory in a path relative to the current directory, and it will throw a FileNotFoundException from inside Jetty if run from somewhere else.
The solution could be to cd into the D2RQ directory before starting the Java call, and back to the original directory afterwards.
@jgeluk's patch unfortunately doesn't solve this issue.