refdb-users

[Refdb-users] Problem setting up refdb

[Olivier F. <oli...@rs...>]

I just installed refdb on a Gentoo-GNU/Linux machine, using SQLite as the=20
database engine. I use 0.9.4-pre1 rather than 0.9.3 since the server in the=
=20
later package terminates with a segfault as soon as a client tries to=20
connect. (I used gcc 3.2.3 for compiling both versions.)

Unfortunately, adding references to a database doesn't seem to work. Whenev=
er=20
I try adding the content of the example ris file provided with the package,=
 I=20
end up with an error (the server log is included in this message). The same=
=20
error happens when I try adding the content of a ris file created by=20
converting a PubMed Medline file.

Does anyone know what is causing this problem or what it relates to ?

Server log :

6:pid=3D22620:Tue Oct 28 20:42:40 2003:server waiting n_max_fd=3D6
6:pid=3D22769:Tue Oct 28 20:42:40 2003:serving client on fd 6 with protocol=
=20
version 1
6:pid=3D22769:Tue Oct 28 20:42:40 2003:dbi is up
4:pid=3D22769:Tue Oct 28 20:42:40 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:40 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:Search ID failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:Search ID failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:insert into t_refdb failed
4:pid=3D22769:Tue Oct 28 20:42:41 2003:failed processing dataset
4:pid=3D22769:Tue Oct 28 20:42:41 2003:keyword query error
6:pid=3D22769:Tue Oct 28 20:42:41 2003:child finished client on fd 6

=2D-=20
Olivier Fisette, B. Sc.

Protein Biosynthesis Research Laboratory
Centre de recherche sur la fonction, la structure
et l'ing=E9nierie des prot=E9ines (CREFSIP)
Department of Biochemistry and Microbiology
Laval University

Office 3208, Charles-Eug=E8ne-Marchand building
Qu=E9bec (Qu=E9bec), Canada, G1K7P4

Telephone : +1 (418) 656-2131, ext. 6273
Electronic mail : oli...@rs...

[Refdb-users] Problem setting up refdb

[Markus H. <mar...@mh...>]

Olivier Fisette writes:
 > I just installed refdb on a Gentoo-GNU/Linux machine, using SQLite as the 
 > database engine. I use 0.9.4-pre1 rather than 0.9.3 since the server in the 
 > later package terminates with a segfault as soon as a client tries to 
 > connect. (I used gcc 3.2.3 for compiling both versions.)
 > 

Yes, this is the now famous
close-nonexistent-file-descriptor-when-logging-to-stderr bug. I
officially recommend to use 0.9.4-pre1 as it fixes a couple of other
bugs as well. It is more stable than 0.9.3.

 > Unfortunately, adding references to a database doesn't seem to work. Whenever 
 > I try adding the content of the example ris file provided with the package, I 
 > end up with an error (the server log is included in this message). The same 
 > error happens when I try adding the content of a ris file created by 
 > converting a PubMed Medline file.
 > 
 > Does anyone know what is causing this problem or what it relates to ?
 > 

I can only guess and ask questions:

Does the createdb command succeed?

If yes, do you get a database file in the expected directory?

Can you open that database with the command-line client sqlite and do
inserts?

Does the whichdb command succeed after selecting the database?

If possible, run all the refdb-related tests with the log level set to 7.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Problem setting up refdb - Solved

[Olivier F. <oli...@rs...>]

Thanks for the tips/questions. The sqlite client didn't work correctly, so =
I=20
recompiled sqlite and created new databases, and that solved the problem.=20

=2D-=20
Olivier Fisette, B. Sc.

Protein Biosynthesis Research Laboratory
Centre de recherche sur la fonction, la structure
et l'ing=E9nierie des prot=E9ines (CREFSIP)
Department of Biochemistry and Microbiology
Laval University

Office 3208, Charles-Eug=E8ne-Marchand building
Qu=E9bec (Qu=E9bec), Canada, G1K7P4

Telephone : +1 (418) 656-2131, ext. 6273
Electronic mail : oli...@rs...