refdb-users — List for RefDB users

RE: [Refdb-users] refdbc and php4

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

Hi there,

Alan Anderson writes:
 > There are two difficulties with trying to run refdbc from within a CGI application (this includes
 > PHP).  First, refdbc is compiled with CGI support builtin, and it tests the environment to determine
 > whether it is running as a CGI application or a standalone application.  This test is simply the
 > existence of the REQUEST_METHOD environment variable.  Since we are running refdbc from within
 > another CGI application this variable exists, so refdbc assumes it is running in CGI mode.  This
 > test seems to override the -C commandline option (didn't really take the time to find out if this is
 > exactly true).  My solution was to #undef REFDB_CGI at the top of refdbc.c and recompile refdbc to

This analysis is pretty much correct. I've applied the suggested fix,
i.e. checking for -C at the very beginning.

 > The second problem is that refdbc attempts to call fgets in several places regardless of whether it
 > is run in "batch" mode.  Attached is a diff file which should show you where fixes are needed, but
 > you'll have to fight through some garbage changes that I made for debugging.  In two or three places
 > there is a test like
 > 
 > 	if (n_read_file || n_read_stdin) {
 > 
 > If this test succeeds, then fgets is called (not directly, but eventually in each case--I'm not
 > exactly sure what difficulty this causes, but I'm guessing the web server hasn't provided STDOUT or
 > something--in any case, the fgets fails).  If the test fails, then the string sent to the refdbd
 > server is not completed and you get the "unknown command" error in the log.  I changed these lines
 > to also test for batch mode:
 > 
 > 	if ((n_read_file || n_read_stdin) && !n_batchmode) {
 > 
 > In this case, it does not call fgets AND the command string is correctly created and sent to refdbd.
 > 

I'm not sure whether this is the correct fix. Both the com_pickref()
and the com_deleteref() functions accept a list of ID values
(e.g. from a previous getref -s ID call) on either stdin (in batch
mode) or with the -f command line option (interactive mode). Your
suggested fix would preclude the former use. I think we run into
trouble right here:

  if (!isatty(fileno(stdin))) { /* if we receive data on stdin via a redirection or a pipe */
    n_read_stdin = 1;
  }

If a CGI app runs refdbc, stdin won't be a tty, and refdbc incorrectly
assumes that data are waiting at stdin. I'm afraid I'll need another
command line switch to keep refdbc from reading stdin when it's not
supposed to.

 > I hope this makes sense, and I hope Markus doesn't take offense to the "logic" comment above.  I

Don't worry. A flaw is a flaw, and it needs to be fixed. On the
contrary, I appreciate that you've done most of the debugging.

regards,
Markus

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

[Refdb-users] Re: refdbc and php4

[Howard S. <ho...@uk...>]

Hi Alan,

whoooeee! That did it! It works now, thanks a heap!  Maybe
Markus will fix this up for the next release.

Alan Anderson wrote:
.....
> 
> I hope this makes sense, and I hope Markus doesn't take offense to the "logic" comment above.  I
> think RefDB is a great tool, and I use it everyday.
> 
> Hope this helps.
> 
> Al
> 

I'm quite enthusiastic about it, and some other people in the
department would really like to use it as a centralized literature
database system.

-- Howard

--------------------------------------------------------------------
Dipl.-Phys. Howard Schultens                    Tel: +49 551 39-5914
Zentrum Physiologie                             FAX: +49 551 39-5923
Humboldtallee 23
37073 Goettingen      mailto:howard at ukps.gwdg.de
Germany               http://www.neuro-physiol.med.uni-goettingen.de
--------------------------------------------------------------------

RE: [Refdb-users] refdbc and php4

[Alan A. <al...@ru...>]

Howard,

I just ran across a similar thing writing a Perl script to do something specific for me.  There are
two logic flaws in the refdbc client.  I hadn't piped up about them yet because I haven't formalized
the suggested fixes.  Since you're asking, I'll post them here and maybe Markus can integrate the
changes or come up with more suitable suggestions.

There are two difficulties with trying to run refdbc from within a CGI application (this includes
PHP).  First, refdbc is compiled with CGI support builtin, and it tests the environment to determine
whether it is running as a CGI application or a standalone application.  This test is simply the
existence of the REQUEST_METHOD environment variable.  Since we are running refdbc from within
another CGI application this variable exists, so refdbc assumes it is running in CGI mode.  This
test seems to override the -C commandline option (didn't really take the time to find out if this is
exactly true).  My solution was to #undef REFDB_CGI at the top of refdbc.c and recompile refdbc to
create a "nocgi" version.  I named it refdbc-nocgi and copied it into /usr/local/bin.

The second problem is that refdbc attempts to call fgets in several places regardless of whether it
is run in "batch" mode.  Attached is a diff file which should show you where fixes are needed, but
you'll have to fight through some garbage changes that I made for debugging.  In two or three places
there is a test like

	if (n_read_file || n_read_stdin) {

If this test succeeds, then fgets is called (not directly, but eventually in each case--I'm not
exactly sure what difficulty this causes, but I'm guessing the web server hasn't provided STDOUT or
something--in any case, the fgets fails).  If the test fails, then the string sent to the refdbd
server is not completed and you get the "unknown command" error in the log.  I changed these lines
to also test for batch mode:

	if ((n_read_file || n_read_stdin) && !n_batchmode) {

In this case, it does not call fgets AND the command string is correctly created and sent to refdbd.

I hope this makes sense, and I hope Markus doesn't take offense to the "logic" comment above.  I
think RefDB is a great tool, and I use it everyday.

Hope this helps.

Al


> -----Original Message-----
> From: ref...@li...
> [mailto:ref...@li...]On Behalf Of Howard
> Schultens
> Sent: Tuesday, January 28, 2003 8:45 AM
> To: ref...@li...
> Subject: [Refdb-users] refdbc and php4
>
>
> Hello
>
> RefDB works perfectly on my system, and my LAMP system works
> fine, but I need to use refdbc from PHP. I can't use the
> cgi version.  I can't get this to work.  If I try the command
>
> /usr/local/bin/refdbc -C getref :AU:=richter
>
> from the command line, it works correctly and gives me 13
> references.  If I try it in a shell script, it also works.
> But if I try calling this command with the PHP functions 'system'
> 'exec' 'passthru', etc, or with a pipe, it returns an
> error.  The log file for the refdbd daemon has this:
>
> 6:pid=3856:Tue Jan 28 11:49:17 2003:adding client on fd 6
> 6:pid=3856:Tue Jan 28 11:49:17 2003:server waiting n_max_fd=6
> 6:pid=12484:Tue Jan 28 11:49:17 2003:serving client on fd 6 with
> protocol version 0
> 4:pid=12484:Tue Jan 28 11:49:17 2003:unknown command
> 4:pid=12484:Tue Jan 28 11:49:17 2003:no positive ack from client
> 6:pid=12484:Tue Jan 28 11:49:17 2003:child finished client on fd 6
> 6:pid=3856:Tue Jan 28 11:49:17 2003:parent removing client on fd 6
> 6:pid=3856:Tue Jan 28 11:49:17 2003:server waiting n_max_fd=5
> 6:pid=3856:Tue Jan 28 11:49:17 2003:child exited with code 1
>
> If I set the log level to 'debug' (-l7) in refdbc, I get this
> in the log file when calling from PHP:
>
> 7:pid=15100:Tue Jan 28 15:20:35 2003:getref :AU:=richter
>
> If I call the program directly (or from a shell) this
> is
>
> 7:pid=14990:Tue Jan 28 15:14:20 2003:getref ":AU:=richter" -u zmpg -w
> 121069035118125116045057 -d ZMPGlit -R
> /home/local/ZMPG/zmpg/Documents/PDFs -G /usr/local/share/refdb/css/refdb.css
>
> In other words, when I call refdbc from PHP, it ignores both
> the configuration file and most of the command line parameters.
>
> What are the special tricks for getting refdbc to work from PHP?
>
> Thanks,
>
> -- Howard
>
> --------------------------------------------------------------------
> Dipl.-Phys. Howard Schultens                    Tel: +49 551 39-5914
> Zentrum Physiologie                             FAX: +49 551 39-5923
> Humboldtallee 23
> 37073 Goettingen      mailto:howard at ukps.gwdg.de
> Germany               http://www.neuro-physiol.med.uni-goettingen.de
> --------------------------------------------------------------------
>
>
>
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[Refdb-users] refdbc and php4

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

Hi,

I have to admit that my PHP knowledge doesn't get me any further than
creating my (static) personal website. I've never tried using RefDB
from PHP.

Anyway, there's a few thoughts:

- there might be a quoting issue when running commands from PHP that
  contain quoted arguments. Do the PHP docs mention anything like
  this?

- Does PHP cause refdbc to run under an account that is not allowed to
  read the global config file?

- What happens if you pass all configuration parameters on the refdbc
  command line in your PHP code?

I'd be glad if RefDB could be convinced to cooperate with PHP. This
would allow to build a nice user interface, much better than the crude
CGI stuff we've got now.

regards,
Markus

Howard Schultens writes:
 > In other words, when I call refdbc from PHP, it ignores both
 > the configuration file and most of the command line parameters.
 > 
 > What are the special tricks for getting refdbc to work from PHP?
 > 

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

[Refdb-users] refdbc and php4

[Howard S. <ho...@uk...>]

Hello

RefDB works perfectly on my system, and my LAMP system works
fine, but I need to use refdbc from PHP. I can't use the
cgi version.  I can't get this to work.  If I try the command

/usr/local/bin/refdbc -C getref :AU:=richter

from the command line, it works correctly and gives me 13
references.  If I try it in a shell script, it also works.
But if I try calling this command with the PHP functions 'system'
'exec' 'passthru', etc, or with a pipe, it returns an
error.  The log file for the refdbd daemon has this:

6:pid=3856:Tue Jan 28 11:49:17 2003:adding client on fd 6
6:pid=3856:Tue Jan 28 11:49:17 2003:server waiting n_max_fd=6
6:pid=12484:Tue Jan 28 11:49:17 2003:serving client on fd 6 with
protocol version 0
4:pid=12484:Tue Jan 28 11:49:17 2003:unknown command
4:pid=12484:Tue Jan 28 11:49:17 2003:no positive ack from client
6:pid=12484:Tue Jan 28 11:49:17 2003:child finished client on fd 6
6:pid=3856:Tue Jan 28 11:49:17 2003:parent removing client on fd 6
6:pid=3856:Tue Jan 28 11:49:17 2003:server waiting n_max_fd=5
6:pid=3856:Tue Jan 28 11:49:17 2003:child exited with code 1

If I set the log level to 'debug' (-l7) in refdbc, I get this
in the log file when calling from PHP:

7:pid=15100:Tue Jan 28 15:20:35 2003:getref :AU:=richter

If I call the program directly (or from a shell) this
is

7:pid=14990:Tue Jan 28 15:14:20 2003:getref ":AU:=richter" -u zmpg -w 
121069035118125116045057 -d ZMPGlit -R 
/home/local/ZMPG/zmpg/Documents/PDFs -G /usr/local/share/refdb/css/refdb.css

In other words, when I call refdbc from PHP, it ignores both
the configuration file and most of the command line parameters.

What are the special tricks for getting refdbc to work from PHP?

Thanks,

-- Howard

--------------------------------------------------------------------
Dipl.-Phys. Howard Schultens                    Tel: +49 551 39-5914
Zentrum Physiologie                             FAX: +49 551 39-5923
Humboldtallee 23
37073 Goettingen      mailto:howard at ukps.gwdg.de
Germany               http://www.neuro-physiol.med.uni-goettingen.de
--------------------------------------------------------------------

[Refdb-users] Re: templates not found

[Howard S. <ho...@uk...>]

Thanks Markus,

it was a stupid oversight:  I had created rc-files for
everything but refdbd.  When I got your mail, I looked
again at my configuration files -- and fixed the problem.
Everything works fine now.

-- Howard
--------------------------------------------------------------------
Dipl.-Phys. Howard Schultens                    Tel: +49 551 39-5914
Zentrum Physiologie                             FAX: +49 551 39-5923
Humboldtallee 23
37073 Goettingen      mailto:ho...@uk...
Germany               http://www.neuro-physiol.med.uni-goettingen.de
--------------------------------------------------------------------


> From: "Markus Hoenicka" <ma...@mh...>
> Date: Sat, 18 Jan 2003 18:11:04 +0100
> To: ref...@li...
> Subject: [Refdb-users] no cgi templates
> 
> Hi,
> 
> the 6 template files should be in /usr/local/share/refdb/templates on
> the box that runs refdbd (the files in /usr/local/share/refdb/www need
> to be on the box that runs Apache, in case you run these on different
> boxes).
> 
> Your problem might be caused by either refdbd not finding its
> configuration file or by an incorrect setting of refdblib in that file
> (it should be automatically set to the correct value during
> installation, though). One user reported that refdbd (but not the
> clients) fails to read its global configuration file on Cygwin - do
> you happen to use Windows/Cygwin?. In that case, try to use the -y
> command line switch to tell refdbd the location of the config files,
> or to use command line options altogether to configure refdbd.
> 
> regards,
> Markus
> 
> Howard Schultens writes:
>  > I have installed RefDB 0.9.1, and it seems to be running.
>  > The daemon starts, and I can use the clients from the command
>  > line -- everything seems OK but I can't use the web interface.
>  > 
>  > If I try to use the web interface, it also starts up correctly,
>  > but when I try to do a simple query, it hangs.  If I try to
>  > do a query for keywords, authors, etc, it tells me:
>  > 
>  > 	could not load cgi templates
>  > 
>  > The pages are in /usr/local/share/refdb/www, etc.  No error
>  > messages in the system log files.
>  > 
>  > What am I doing wrong?
> 

Re: [Refdb-users] Installed on MacOS X? (and mysqlclient)

[Bruce D'A. <bd...@fa...>]

On Sunday, January 19, 2003, at 05:38  PM, Markus Hoenicka wrote:

> Bruce D'Arcus writes:
>> Hmm...I think maybe they're missing.  I just tried to compile libdbi
>> and got the following error:
>>
>> header file 'dlfcn.h' not found
>>
>
> This one is not a MySQL header. This header is required for the
> dlopen() kind of functions that libdbi uses to load the drivers, which
> are implemented as shared objects. I know that FreeBSD does ship the
> header by default, so I'm a little surprised that OS X (which is
> FreeBSD in disguise, sort of) lacks it. Again, as I'm not an OS X
> experts, others would have to jump in here.

I just came across this:

libdl: AFNI loads plugins using the dlopen() interface (except on 
HP-UX). This is not the OS X way, but Apple has supplied the dlcompat 
library to simulate this interface.  As mentioned earlier, this library 
and its header file dlfcn.h are required for AFNI to compile.

Doing a search on Fink comes up with the following packages:

dlcompat - Dynamic loading compatibility library
dlcompat-dev - headers and static libraries for dlcompat
dlcompat-shlibs - shared libraries for dlcompat

Which should I install?

Bruce

Re: [Refdb-users] Installed on MacOS X? (and mysqlclient)

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

Bruce D'Arcus writes:
 > Hmm...I think maybe they're missing.  I just tried to compile libdbi 
 > and got the following error:
 > 
 > header file 'dlfcn.h' not found
 > 

This one is not a MySQL header. This header is required for the
dlopen() kind of functions that libdbi uses to load the drivers, which
are implemented as shared objects. I know that FreeBSD does ship the
header by default, so I'm a little surprised that OS X (which is
FreeBSD in disguise, sort of) lacks it. Again, as I'm not an OS X
experts, others would have to jump in here.

regards,
Markus

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

Re: [Refdb-users] Installed on MacOS X? (and mysqlclient)

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

If there is a set of headers as well, this should be all it takes. I'm
not familiar with MacOS X, so a little fiddling with library search
paths might be required to successfully build libdbi with these
files. The ./configure shipped with libdbi has ample command-line
options to specify libraries and headers in non-standard locations.

regards,
Markus

Bruce D'Arcus writes:
 > 
 > libdbug.a                               libmysqlclient.la
 > libheap.a                               libmysqlclient_r.10.0.0.dylib
 > libmerge.a                              libmysqlclient_r.10.dylib
 > libmyisam.a                             libmysqlclient_r.a
 > libmyisammrg.a                          libmysqlclient_r.dylib
 > libmysqlclient.10.0.0.dylib             libmysqlclient_r.la
 > libmysqlclient.10.dylib                 libmystrings.a
 > libmysqlclient.a                        libmysys.a
 > libmysqlclient.dylib                    libnisam.a
 > 
 > Is that sufficient Markus?

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

Re: [Refdb-users] Installed on MacOS X? (and mysqlclient)

[Bruce D'A. <bd...@fa...>]

On Saturday, January 18, 2003, at 12:21  PM, Markus Hoenicka wrote:

> I've been in contact with a few people running RefDB/MySQL on MacOS X,
> so in general it should be doable. It is quite possible that binary
> MySQL packages lack the development libraries and headers. Could you
> please check whether there is a separate package for these files,
> something like mysql-devel? Debian Linux uses separate devel packages
> for nearly any package that uses nonstandard libraries.

A new OS X installer package for MySQL was just released 
(http://www.aaronfaby.com/mysql.php).  While I am unsure what the 
previously mentioned package installs, here is what I find in the 
"MySQL/lib/mysql" directory after using the new installer:

libdbug.a                               libmysqlclient.la
libheap.a                               libmysqlclient_r.10.0.0.dylib
libmerge.a                              libmysqlclient_r.10.dylib
libmyisam.a                             libmysqlclient_r.a
libmyisammrg.a                          libmysqlclient_r.dylib
libmysqlclient.10.0.0.dylib             libmysqlclient_r.la
libmysqlclient.10.dylib                 libmystrings.a
libmysqlclient.a                        libmysys.a
libmysqlclient.dylib                    libnisam.a

Is that sufficient Markus?

Bruce

[Refdb-users] Installed on MacOS X? (and mysqlclient)

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

Hi,

I've been in contact with a few people running RefDB/MySQL on MacOS X,
so in general it should be doable. It is quite possible that binary
MySQL packages lack the development libraries and headers. Could you
please check whether there is a separate package for these files,
something like mysql-devel? Debian Linux uses separate devel packages
for nearly any package that uses nonstandard libraries.

If there is no such package, you should be able to build the library
yourself. You need the MySQL sources (preferably from the stable 3.23
branch), available at www.mysql.org. ./configure -h will tell you
about a configure option to build only the clients (something like
--no-server, but I'm not sure) which will also create the
libmysqlclient library and headers.

regards,
Markus

Alexandre Enkerli writes:
 > Did anyone succeed building, installing, and using RefDB on MacOS X?
 > So far, after several attempts, I've succeeded at building some version 
 > of refdb (using Marc Liyanage's MySQL and several fink packages, 
 > including unsupported ones) but I'm missing mysqlclient library for 
 > libdbi's mysql plugin. It seems that Liyanage's MySQL may lack the 
 > mysqlclient library.
 > Installing RefDB on OSX has already been very time-consuming and it 
 > seems that some users have already succeeded. If any of these users 
 > would be so kind as to post a detailed explanation of what they have 
 > done, it would be greatly appreciated.
 > 
 > Thanks!
 > 
 > Alex
 > 

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

[Refdb-users] no cgi templates

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

Hi,

the 6 template files should be in /usr/local/share/refdb/templates on
the box that runs refdbd (the files in /usr/local/share/refdb/www need
to be on the box that runs Apache, in case you run these on different
boxes).

Your problem might be caused by either refdbd not finding its
configuration file or by an incorrect setting of refdblib in that file
(it should be automatically set to the correct value during
installation, though). One user reported that refdbd (but not the
clients) fails to read its global configuration file on Cygwin - do
you happen to use Windows/Cygwin?. In that case, try to use the -y
command line switch to tell refdbd the location of the config files,
or to use command line options altogether to configure refdbd.

regards,
Markus

Howard Schultens writes:
 > I have installed RefDB 0.9.1, and it seems to be running.
 > The daemon starts, and I can use the clients from the command
 > line -- everything seems OK but I can't use the web interface.
 > 
 > If I try to use the web interface, it also starts up correctly,
 > but when I try to do a simple query, it hangs.  If I try to
 > do a query for keywords, authors, etc, it tells me:
 > 
 > 	could not load cgi templates
 > 
 > The pages are in /usr/local/share/refdb/www, etc.  No error
 > messages in the system log files.
 > 
 > What am I doing wrong?

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

[Refdb-users] no cgi templates

[Howard S. <ho...@uk...>]

I have installed RefDB 0.9.1, and it seems to be running.
The daemon starts, and I can use the clients from the command
line -- everything seems OK but I can't use the web interface.

If I try to use the web interface, it also starts up correctly,
but when I try to do a simple query, it hangs.  If I try to
do a query for keywords, authors, etc, it tells me:

	could not load cgi templates

The pages are in /usr/local/share/refdb/www, etc.  No error
messages in the system log files.

What am I doing wrong?

-- Howard

Re: [Refdb-users] Installed on MacOS X? (and mysqlclient)

[Bruce D'A. <bd...@fa...>]

I have not yet tried to install RefDB (was thinking I'd wait for the 
next release, and the new machine I have coming, before tackling this), 
but there has to be a way to make installation easier than it is.

As Alex points out, Marc L. has made available easy-to-use Mac OS X 
installers for both MySQL and PostgreSQL 
(http://www.entropy.ch/software/macosx/welcome.html).  Could someone 
put together a companion package for RefDB?  That way, some who wanted 
to run RefDB on OS X would just need to download the two installers.

I don't really know how to do this myself, but maybe someone out there 
does?

Bruce

[Refdb-users] Installed on MacOS X? (and mysqlclient)

[Alexandre E. <aen...@in...>]

Did anyone succeed building, installing, and using RefDB on MacOS X?
So far, after several attempts, I've succeeded at building some version 
of refdb (using Marc Liyanage's MySQL and several fink packages, 
including unsupported ones) but I'm missing mysqlclient library for 
libdbi's mysql plugin. It seems that Liyanage's MySQL may lack the 
mysqlclient library.
Installing RefDB on OSX has already been very time-consuming and it 
seems that some users have already succeeded. If any of these users 
would be so kind as to post a detailed explanation of what they have 
done, it would be greatly appreciated.

Thanks!

Alex

Re: [Refdb-users] My conclusions regarding RefDB

[Michael B. <mb...@an...>]

Hi Markus,

you wrote:
> We're currently discussing the bibx DTD structure and the requirements
> for various branches in science. If you are knowledgeable about citing
> legal documents your input might help to improve on the
> structure. Please let me know whether you are interested in
> contributing as the bibx development is currently done in a private
> mailing list.

I am willing to help... But I'm not very knowledgeable in terms of
general document structures etc., I could tell you about the kinds of
legal documents I know (in german law) and what I think is
important for referring to them.

Ciao
  Michael

Re: [Refdb-users] My conclusions regarding RefDB

[Michael B. <mb...@an...>]

Hi Bruce, 

you wrote:
 
> If you have any skills, I'd urge you to contribute to improving this
> stuff rather than give up. As far as I'm concerned there isn't much
> alternative, and there's a lot of promise here (not only with RefDB, but
> especially if we can marshal the energy in similar projects around
> standards like bibx and citestylex)!

I'll do both... I have given up using RefDB for my thesis right
now, as I think it's more productive to enter the data into a bibtex
file using emacs. Maybe this will change when I'm done with
gathering literature. On the other hand, I'm willing to help you
to define what's needed for processing german legal literature --
my skills are not in programming and definitely not in database
design.

Ciao
  Michael

Re: [Refdb-users] My conclusions regarding RefDB

[Bruce D'A. <bd...@fa...>]

On Wed, 18 Dec 2002 23:06:22 +0100, mar...@mh... said:
>  > I didn't try RIS-mode, I tried the WWW interface and wrote a
>  > bibtex entry, as bibtex is what I know. I would have liked to see
>  > something like the entry forms for pybliographic, with different
>  > fields according to the type of publication, and configurable for
>  > the needs of the bibtex style I use.
>  > 
> 
> I understand. The web interface is a proof of concept, and I was
> hoping that someone more capable than me in terms of CGI or PHP
> programming would pick up the idea. Well, some did, but there are no
> public versions available to date.

As someone also taking part in helping with bibx, I can say that there is
really a lot of room for collaborative work on these kinds of things. 
Once the data model is nailed down, then it seems to me there ought to be
collaboration on designing an easy input form that'd be appropriate for a
web interface, as well as graphical clients that might link to RefDB (I
myself am interested in BibDesk on Mac OS X).

If you have any skills, I'd urge you to contribute to improving this
stuff rather than give up. As far as I'm concerned there isn't much
alternative, and there's a lot of promise here (not only with RefDB, but
especially if we can marshal the energy in similar projects around
standards like bibx and citestylex)!

Bruce

-- 
http://fastmail.fm - Or how I learned to stop worrying and
                      love email again

Re: [Refdb-users] My conclusions regarding RefDB

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

Michael Below writes:
 > But even with them, it looks like information is lost. If I map
 > e.g. abstracts (like "The author says...") and notes (like "Not
 > yet read") to N1, I won't be able to discern them later on
 > automatically. And it looks like I need to map several bibtex

Well, in this particular case you would map abstracts to N2 and notes
to N1. But in general your impression is correct: BibTeX and RIS are
too far apart for loss-free round-trip conversions.

 > I didn't try RIS-mode, I tried the WWW interface and wrote a
 > bibtex entry, as bibtex is what I know. I would have liked to see
 > something like the entry forms for pybliographic, with different
 > fields according to the type of publication, and configurable for
 > the needs of the bibtex style I use.
 > 

I understand. The web interface is a proof of concept, and I was
hoping that someone more capable than me in terms of CGI or PHP
programming would pick up the idea. Well, some did, but there are no
public versions available to date.

 > Sounds good... As I wrote on http://www.jurawiki.de/LaTeX I think
 > RefDB might become THE solution for bibliography management at
 > some point. But right now, the data structure and the ease of use
 > need improvement.
 > 

We're currently discussing the bibx DTD structure and the requirements
for various branches in science. If you are knowledgeable about citing
legal documents your input might help to improve on the
structure. Please let me know whether you are interested in
contributing as the bibx development is currently done in a private
mailing list.

regards,
Markus

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

[Refdb-users] umlauts

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

Hi Scott,

this depends a lot on what database server you use and how it is
configured. Remember that RefDB passes characters unmodified to the
database server, so you can use any character that the database server
can handle.

Current MySQL versions can handle one charset per server
instance. According to the docs of my version, the following charsets
are available:

big5 	
czech 	
dec8 	
dos 	
german1 
hp8 	
koi8_ru 
latin1	
latin2	
swe7 	
usa7 	
ujis 	
sjis 	
cp1251	
danish	
hebrew	
win1251 
tis620	
euc_kr	
estonia 
hungarian 
koi8_ukr  
win1251ukr
gb2312	  
greek 	  
win1250   
croat 	  
gbk 	  
cp1257	  
latin5	  

PostgreSQL allows to use different charsets for each
database. Available are:

SQL_ASCII
EUC_JP
EUC_CN
EUC_KR
EUC_TW
UNICODE
MULE_INTERNAL
LATIN1
LATIN2
LATIN3
LATIN4
LATIN5
LATIN6
LATIN7
LATIN8
LATIN9
LATIN10
ISO-8859-5
ISO-8859-6
ISO-8859-7
ISO-8859-8
KOI8
WIN
ALT

I suppose that with both databases one of the LATIN charsets would
catch most European "weird" characters. Unicode is not yet available
in the MySQL version that I run here but it should be in versions 4
and later. PostgreSQL does support Unicode, so I'd suggest this to be
on the safe side.

regards,
Markus

Scott Harrison writes:
 > Hi,
 > 
 > Does refdb support umlauts and other "weird" characters
 > for author names?  Reading through the (some) docs and looking
 > at the example testrefs.ris file, it is not immediately clear.
 > 
 > I saw a few tidbits about unicode...
 > 

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

[Refdb-users] umlauts

[Scott H. <sha...@us...>]

Hi,

Does refdb support umlauts and other "weird" characters
for author names?  Reading through the (some) docs and looking
at the example testrefs.ris file, it is not immediately clear.

I saw a few tidbits about unicode...

Thanks.

Regards,
Scott

-- 
Scott Harrison, sha...@us...

[Refdb-users] bibx

[<js...@mi...>]

On Tue, 17 Dec 2002  mar...@mh... wrote:


[...]

> Future releases will support the upcoming bibx DTD. This is a XML DTD
> which is currently under development. 

Very interesting! Who is developing it? Is there any public forum
devoted to it?

> It is supposed to be a common data storage and transfer format
> understood by (hopefully) all open-source bibliography softwares.

Such a standard is definitely needed.

> Once bibx has stabilized and
> support for it has been added to RefDB, you can basically use any XML
> editor to enter data. 

E.g. Emacs :-)

Best regards

Janusz

-- 
                     ,   
dr hab. Janusz S. Bien, prof. UW
Prof. Janusz S. Bien, Warsaw Uniwersity
http://www.orient.uw.edu.pl/~jsbien/
---------------------------------------------------------------------
Na tym koncie czytam i wysylam poczte i wiadomosci offline.
On this account I read/post mail/news offline.

[Refdb-users] My conclusions regarding RefDB

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

Michael Below writes:
 > Hi,
 > 
 > after testing RefDB a bit, I came to the conclusion that it doesn't
 > meet my needs. I thought I should tell you why:
 > 

It is hard to meet everyones needs, so if RefDB doesn't match your
expectations I have to accept this. I try to improve on RefDB
continuously, so I appreciate your comments on the shortcomings of
RefDB.

 > - The database stores only a subset of the contents of my bibtex
 >   files. Certain fields are lost, e.g. abstract, location, type,
 >   dissyear.

bib2ris is highly configurable. By default the converter uses only the
standard bibtex fields (I followed the description of
Daly/Kopka). Support for all other fields must be manually added in
the configuration file. This is the only reasonable way to handle
non-standard data as everyone is free to use non-standard bibtex field
names of his own choice. Please see the manual how to configure
bib2ris.

 > - Data input isn't supported very well. If I want to enter a new
 >   piece of literature, I have to type in field names and their
 >   content. There is no such thing like a data entry form. E.g.
 >   the bibtex mode of emacs is more comfortable, and that's where
 >   I'm coming from (as pybliographer didn't fit my needs).
 > 

What are your main problems with ris-mode? This isn't exactly a form
but should help to enter data fairly rapidly. However, I frankly admit
that RefDB handles the import of existing electronic bibliography data
better than writing entries from scratch.

Future releases will support the upcoming bibx DTD. This is a XML DTD
which is currently under development. It is supposed to be a common
data storage and transfer format understood by (hopefully) all
open-source bibliography softwares. Once bibx has stabilized and
support for it has been added to RefDB, you can basically use any XML
editor to enter data. Most likely someone will also come up with a
graphical bibx editor.

regards,
Markus

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

[Refdb-users] My conclusions regarding RefDB

[Michael B. <mb...@an...>]

Hi,

after testing RefDB a bit, I came to the conclusion that it doesn't
meet my needs. I thought I should tell you why:

- The database stores only a subset of the contents of my bibtex
  files. Certain fields are lost, e.g. abstract, location, type,
  dissyear.

- Data input isn't supported very well. If I want to enter a new
  piece of literature, I have to type in field names and their
  content. There is no such thing like a data entry form. E.g.
  the bibtex mode of emacs is more comfortable, and that's where
  I'm coming from (as pybliographer didn't fit my needs).

I'd be glad to hear that I'm wrong, and I'd be glad to tell you
more about my requirements, as I think they are not too unusual... 

Ciao
  Michael

Re: [Refdb-users] can't connect to server

[Michael B. <mb...@an...>]

Hi Markus,

thanks for your quick reply.  Re-building libdbi solved my
problems with refdba, great!

Now the command line interface seems to work well, I managed to
import my current bibtex database into a refdb database. So I
tried the web interface.  As a web server, I have got boa (Debian
stable version). I think I followed the instructions in the
manual, I am able to call the login page, and I get a confirmation
for a successful login. but if I try to do something, I get an
"500 internal server error", the boa error log says:

[15/Dec/2002:22:03:02 +0000] cgi_header: unable to find LFLF

I had a look at the binaries, but I can't see a difference, both
start with some ELF info. For comparison, file says:

man2html: ELF 32-bit LSB executable, Intel 80386, version 1
(SYSV), dynamically linked (uses shared libs), stripped
/usr/lib/cgi-bin $file bib2ris  
bib2ris: ELF 32-bit LSB executable, Intel 80386, version 1 (SYSV),
dynamically linked (uses shared libs), not stripped

Now I stripped the refdb binaries, but that doesn't help...

Any ideas? I am using boa only locally, so I don't have much
experience with it, and the manuals don't tell me how CGI binaries
should be...

Michael Below