Database dir not set

sequenceserver
#1

Hi all,

I encounter an error using SequenceServer in our server. There is no problem by running locally (localhost:4567) but when trying to access it on the server we got a database error.

"Database dir not set. (SequenceServer::DATABASE_DIR_NOT_SET)

#2

Using Apache? Most likely it’s because your database dir has ~ which expand to the user Apache processes are running as. Using absolute path there should work.

— Priyam

#3

Thank you for your answer.

Yes i’m using apache.

I don’t know how to check that?
In the apache.conf I don’t use “~” only absolute path, when doing sequenceserver -l the link to the databases are absolute and ok (works in local).

Thanks again for your help.

#4

No no, I was talking about relative paths in sequenceserver’s config file, which is at ~/.sequenceserver.conf by default. Ah … or maybe it’s the config file that SequenceServer can’t find.

Could you change “SequenceServer.init” in config.ru file to “SequenceServer.init(:config_file => ‘/full/path/to/config/file’)” and see if that works?

– Priyam

#5

Hi,

I have change the config.ru file.

I always can access to SequenceServer using localhost:4567 but there is an error on the server. No “Database dir not set” this time but an “Internal Error”.

In the log file I found lot of errors like “[ 2016-01-13 10:44:00.0195 5923/7f2b0a5fe700 Pool2/Pool.h:777 ]: Process (pid=8808, group=/var/lib/gems/1.9.1/gems/sequenceserver-1.0.6#default) no longer exists! Detaching it from the pool.”

I really don’t understand which may be the problem with the software.

#6

Did you restart the app?

— Priyam

#7

Hi,

Yes we have restart the app.
We have uninstalled and reinstalled all. I think the problem was the default installation directory.

Now there is an other error but maybe easier to fix, I will work on it but if you have an idea?

“Could not spawn process for group /usr/local/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.6#default: An error occured while starting up the preloader.”

"Bundler::PermissionError (Bundler::PermissionError)

#8

It shouldn’t be this hard :(. This one seems to be a permissions issue. seqserv directory and all files in it should be readable by Apache/Passenger.

#9

I really don’t understand what i did not properly so that it doesn’t work.

I have change the permissions, and now it is an error 500…

“Process (pid=5557, group=/usr/local/lib/ruby/gems/2.3.0/gems/sequenceserver-1.0.6#default) no longer exists! Detaching it from the pool.”

Still working using localhost:4567/# so it seems to be a problem from Apache/Passenger…

#10

This is really weird. I am sorry, I have no clue what’s going on. Maybe someone else will know better.

— Priyam

#11

Finally it’s working!

I don’t know what the problem was, but I have deleted the virtual box, reinstall Ubuntu and all the tools to deal with a new and clean install, and it’s ok now!

I have only to customize the tool now.

Thank you very much for your help!