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Reported by KheOps on IRC:

16:06      KheOps ) Quick question: it doesn't seem enough to specifiy a tor_datadir that is empty for the first start of oonib, so that it puts its config 
                    there and reuses it on subsequent launches
16:07      KheOps ) Well the question is, is it supposed to be enough (in which case I may have missed somethng), or has it been thought another way? (like, 
                    having an already filled-up tor datadir from a previous tor run)
16:08      KheOps ) at the moment, oonib basiclly not creates a hidden service
16:08      KheOps ) ("httpo://None")
16:08      KheOps ) The tor_datadir speicifed is existant, accessible for writing, but empty at start
16:10      KheOps ) O_o it seems to be working when specified in an absolute way
16:12      KheOps ) I was intending to have it specified relatively to oonib's run_dir
16:13      KheOps ) rundir, sorry
16:17 [ (isis) ) KheOps: hmm, that is odd. i just set up a couple oonibs on new boxes, and did not experience this, though i did have the problem that if the 
                 directory didn't exist, it wasn't created but instead Tor would get to 100% and then stop because the dir was missing.
16:17 [ (isis) ) KheOps: let me log into one of those boxes and check whether i specified an absolute or relative path
16:22      KheOps ) Thank you :)
16:26 [ (isis) ) KheOps: yep, it seems to be that absolute paths do the trick, my config looks like this:
16:26 Irssi: Pasting 6 lines to #ooni. Press Ctrl-K if you wish to do this or Ctrl-C to cancel.
16:26 [ (isis) ) main: report_dir: '/home/isis/ooni-collector/reports' logfile: '/home/isis/ooni-collector/oonib-collector.log' tor_datadir: 
                 '/home/isis/ooni-collector/tordata' database_uri: 'sqlite://oonib_test_db.db'
16:26      KheOps ) Yes, same here, works with absolute path
16:27 [ (isis) ) whoops, except, obviously spaced according to YAML
16:27      KheOps ) It would be cool if it was possible to have it working relatively to rundir, though
16:30 [ (isis) ) that can be sometimes a bit of a pain to do, because when python apps are installed they go into either '/usr/share/python2.7/dist-packages' 
                 or '$HOME/.virtualenv' or '/usr/share/python2.7/site-packages' and you can't quite be sure how someone is going to install it or where it'll 
                 end up
16:31 [ (isis) ) we should probably just pick a canonical directory and just go with it, like /var/oonib or something
16:32 [ (isis) ) but you're right, as soon as someone specifies something else in the config, everything's going to get jumbled or broken again

KheOps also noted that there is a rundir setting in the config, and that it should be pretty easy to have the other paths respect the rundir config option if it is set.