[Refdb-users] The state of my Debian RefDB/PHPweb confusion

[Doug du B. <dou...@gm...>]

Hi list,

I tried several weeks ago to install the debian-ised packages from 
the /etc/apt/sources.list resource:
     deb http://refdb.sourceforge.net/debian/release unstable main

as per the instructions  on the website:
           http://refdb.sourceforge.net/download

I believe, but am not totally sure that this also gave me 
> dpkg --list | grep libdbi

ii  libdbi0        0.7.2-1        Database Independent Abstraction Layer for C
ii  libdbi0-dev    0.7.2-1        Database Independent Abstraction Layer for C
 - along with 
ii  libdbd-sqlite  0.7.1-3.0.1    SQLite database driver for libdbi
ii  refdb          0.9.6-pre2     Reference database and bibliography tool for

After some initial confusion on my part in creating the database (following 
the instructions in the tutorial "a day with the refdb clients" 
which made no mention of running the refdba command "createdb DBNAME"),
it turned out that certain library incompatabilities were leading to 
segmentation faults.

(I did experiment with replacing  /lib/tls/libc.so.6 with a symlink 
to /lib/libc.so.6  and while the "mv" command still works, "ls" doesn't,
the CPU started to overheat, the fan went a little berzerk and bib2ris and 
refdbc both still segfaulted - so don't try that at home folks).


Sometime thereafter I decided to build from the sources and downloaded 
     refdb-0.9.7-pre1 
Trying to build that highlighted incompatabilities with libdbi-0.7.2.1 
(as well as my libreadline libraries and dev files)
and required an update to 0.8.1 as indicated by Markus 
Re: [Refdb-users] 0.9.6 Compile problem

I downloaded the sources for both libdbi and libdbi-drivers 0.8.1
Although libdbi seemed to build ok, trying to build the libdbi-sqlite driver
was a nonevent because ./configure --with-sqlite fails with
error: Invalid SQLite directory - include files not found
 - presumably that is because I needed libsqlite0-dev  right?

(ii  libsqlite0         2.8.16-1           SQLite shared library)

Anyway, I put it on the backburner for a while until I read Per-Anders' 
recent email and decided to add the following to my apt/sources.list

deb http://refdb.sourceforge.net/debian/release unstable main
deb  http://refdb.sourceforge.net/debian/cvs/ testing main
deb  http://refdb.sourceforge.net/debian/cvs/ unstable main
deb http://libdbi.sourceforge.net/debian unstable main

I dont know what the deal is with the cvs bit, but it added an extra
3.5 megabytes to the packagelist update process and didn't seem to provide any 
hint of libdbi-0.8.1.  So I gave up and manually scrounged around in 

 http://libdbi.sourceforge.net/debian/pool/l/

there I found 
   libdbd-sqlite_0.8.1-1_i386.deb
   libdbi0_0.8.1-1_i386.deb
   libdbi0-dev_0.8.0-1_i386.deb 

The latter one had a 8.0!=8.1 version conflict so I ran
   dpkg -force-depends -i  libdbi0-dev_0.8.0-1_i386.deb 

Then I could build and install refdb-0.9.7-pre1  along with 
RefDB-perlmod-0.4 and RefDBClient-Client-1.13
(a README to the effect of running "perl Makefile.PL" ; make ; make install 
could have been useful info for the latter two),
and now things seem to work, mostly, I think...
Also during ./configure of refdb, I had
a spot of trouble installing from CPAN the MARC-Charset-0.95.tar.gz perl 
module. Fortunately, I was able to install MARC-Charset-0.6.tar.gz from an 
out of date CPAN mirror. 
Are there debian packages for such things or does everyone just use 
perl -MCPAN ... ?

In my subsequent limited testing, it seems that refdbc had some trouble 
producing debugging info and writing it to the log file. Maybe it was because 
of restrictive file permissions? I dunno.
Also both refdbc and refdba produce log file info with time stamps that seem 
to be standard GMT rather than local timezone. 

The reason I was interested in the log file was because I was having 
trouble with the phpweb interface, to the effect that no search results 
were ever forthcoming.

The only debugging info I was getting was in the Apache2/error.log which said
sh: line 1: -c: command not found

I guess this was because the session info wasn't saved because I didn't 
know about the php.ini file settings (so the /usr/local/bin/refdbc command 
wasn't retained and prepended to the command). I tried 
coppying /etc/php4/apache2/php.ini  to the /var/local/share/refdb/www/
directory, and amending the relevant values with those listed in the
refdb/phpweb/INSTALL file. 
I tried to create a /var/local/share/refdb/www/tmp/ directory, in case
the session info needs to be saved in /tmp relative to the 
http://localhost/refdb/ directory. that didn't seem to work.
So I coppied the amended php.ini file back to /etc/php4/apache2/php.ini.
That seemed to do the job because it now creates files like
/tmp/sess_5f278997b0d82e590a8706b6c491110b  owned by nobody of nogroup 
and cures the "command not found" error, but it still fails to return any 
references when I do any kind of search.
(I would like to think there is a better way to make that work, but I have no 
idea what it is)

To figure what was going wrong I set
$_SESSION["refdbc"]="/usr/local/bin/refdbc -l 7 -e 2 -L /var/log/refdbc.log";
in login.php. But without making the log file writeable by all, there 
didn't seem to be any logging output.

Thereafter doing a search for author Wang,J.P. the search command logged was 
apparently:
     getref ALL :AU:~Wang,J.P. 
i.e. a seemingly spurious "ALL" arising from 
function setSearchFields() in refdbsearch.php

Another logged bogus search command was from the refdbkajquery.html form
   getau refs :AU:=Wang,J.P. 
where the database "refs" is prepended to the command. Actually 
that database is populated with the refdb/examples/testrefs.ris data.
Presumably missing a leading "-d" before the database name?




A different problem arose with the commandline interface for 
refdbc where I can't seem to get wildcard/regular expression searches 
to work e.g.
getref :AU:~Wang,J.P. works, but
getref :AU:~Wang*  does not
getref :AU:~"Wang*"  doesn't
getref :AU:~"^Wang*" doesn't 

Is there something wrong with my syntax, 
a configuration error, or a bug?

The only other problem was that the refdb configure script apparently doesn't 
like my debian libbtparse0 library
ii  libbtparse0        0.34-1             A C library to parse BibTeX files
-rw-r--r--  1 root root   65808 Jun 18  2004 /usr/lib/libbtparse.so.0.0.0
> checking for bt_initialize in -lbtparse... no
> libbtparse not found; bib2ris import filter will not be built


Thats about it, I think.
Advice appreciated.
Many thanks
Doug