refdb-users — List for RefDB users

[Refdb-users] RisX import

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

Hi,

Couwberghs Tom writes:
 > I've just tested the risx-import (a nifty feature, that I will be happy
 > to use) when I noticed something weird. Apparently if I import a
 > risx-document (with addref -t risx) and try to get it out (with getref
 > -t risx), I get a totally different document.
 > 
 > Could you explain the reason why? Imho, It would make more sense if the
 > risx structure was kept as it was.
 > 

You may spell the reason "incompetence", "stupidity", or maybe
"oversight" :-) While you can't expect that the output is literally
the same as the input, the document object model should of course stay
the same. If it doesn't, it's a bug.

Looks like I can continue to do prereleases. On the other hand I would
have been surprised if this new feature had worked out of the box. I'd
be glad if everyone could test the risx import/export with the
weirdest citations they can find and tell me if the output has gross
errors.

regards,
Markus

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

[Refdb-users] RisX import

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

Hi,

come to think of it, I believe the problem is an incorrect type. Your
reference entry describes a CHAP, but you set the type to BOOK. I
guess that's why RefDB insisted on leaving out the part stuff in the
output. Could you please try again using CHAP as the entry type?

regards,
Markus

Couwberghs Tom writes:
 > <!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris//EN"
 > "http://refdb.sourceforge.net/dtd/risx.dtd">
 > <ris>
 > 	<entry type="BOOK" id="65" citekey="tcb">

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

[Refdb-users] How to create a scientific report with refdb/docbook ?

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

Hi,

Marc Baaden writes:
 > 
 > Hi,
 > 
 > I am currently supposed to write up a full scientific report with
 > complete list of publications, participation at conferences and
 > oral and poster presentations.
 > 
 > I wonder whether this could (?easily?) be done with docbook+refdb ?
 > 

Depends on your definition of "easily" ;-) Basically RefDB was
designed for this purpose, and while I can't exclude some rough edges
(were not yet at 1.0) DocBook+RefDB should just be fine for this
purpose.

 > In particular I wonder about the
 > - participation in conferences
 > - oral presentations
 > - poster presentations
 > 
 > Can (/should) these be put as a bibliographic entry into refdb ? Or is there
 > a better way ?

The idea of using a bibliography tool is to keep the references in a
database to make them reusable for any number of documents. We'd have
to look at your requirements in terms of formatting though. Currently
the number of styles is quite limited, and some general-purpose styles
like Harvard are still missing. I'll be happy to help implementing a
style that suits your needs.

 > 
 > Also, given that I will not cite those things with any number or so,
 > how does one need to write the docbook document for refdb to insert
 > the corresponding references ?
 > 

I'd suggest to have a close look at the tutorial (this is different
from the manual!), available at

http://refdb.sourceforge.net/doc.html

Refer to chapter 3, section "writing documents". The basic idea is to
use the refdbnd script to create a skeleton document along with a
Makefile. Then follow the instructions to insert short-style
citations. If all goes well, "make pdf" or "make html" will give the
desired output.

regards,
Markus

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

[Refdb-users] How to create a scientific report with refdb/docbook ?

[Marc B. <ba...@sm...>]

Hi,

I am currently supposed to write up a full scientific report with
complete list of publications, participation at conferences and
oral and poster presentations.

I wonder whether this could (?easily?) be done with docbook+refdb ?

In particular I wonder about the
- participation in conferences
- oral presentations
- poster presentations

Can (/should) these be put as a bibliographic entry into refdb ? Or is there
a better way ?

Also, given that I will not cite those things with any number or so,
how does one need to write the docbook document for refdb to insert
the corresponding references ?

Thanks in advance,

  Marc Baaden


NB: thanks for releasing 0.9.3 .. and all the ongoing work

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:ba...@sm...      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

[Refdb-users] RisX import

[Couwberghs T. <tco...@sc...>]

Hello all,

it has been a while since my last post here. I'm happy to see that
version 0.9.3 was released yesterday, because I've just continued with
my refdb-based project.

I've just tested the risx-import (a nifty feature, that I will be happy
to use) when I noticed something weird. Apparently if I import a
risx-document (with addref -t risx) and try to get it out (with getref
-t risx), I get a totally different document.

Could you explain the reason why? Imho, It would make more sense if the
risx structure was kept as it was.

Greetz Tom

Ps: You can find the input and output data below:

INPUT:

<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris//EN"
"http://refdb.sourceforge.net/dtd/risx.dtd">
<ris>
	<entry type=3D"BOOK" id=3D"65" citekey=3D"tcb">
		<part>
			<title type=3D"gen">roodkapje en de boze
wolf</title>
			<author>
				<name>hanz grimm</name>
			</author>
		</part>
		<publication>
			<title type=3D"full">de mooiste sprookjes</title>
			<author>
				<firstname>a</firstname>
			=09
				<middlename>b</middlename>

			</author>
			<pubinfo>
				<pubdate type=3D"primary">
					<date>
						<year>2003</year>
						<month>12</month>
						<day>06</day>
					</date>
					<otherinfo>
						met sinterklaas
					</otherinfo>
				</pubdate>
				<volume>5</volume>
				<issue>4</issue>
				<startpage>5</startpage>
				<endpage>100</endpage>
				<city>Mol</city>
				<publisher>SCKCEN</publisher>
				<serial>01545789</serial>
				<address>boertang</address>
				<url>http://google.be</url>
				<userdef type=3D"1">tekstje 1</userdef>
				<userdef type=3D"2">tekstje 2</userdef>
				<userdef type=3D"3">tekstje 3</userdef>
				<userdef type=3D"4">tekstje 4</userdef>
				<userdef type=3D"5">tekstje 5</userdef>
				<misc type=3D"1">pff 1</misc>
				<misc type=3D"2">pff 2</misc>
				<misc type=3D"3">pff 3</misc>
			=09
			</pubinfo>
		</publication>
		<set>
		</set>
		<libinfo user=3D"tom">
			<notes>
				ik vind dees maar een grellig dtd'ke
			</notes>
			<reprint status=3D"ONREQUEST">
				<date>
					<year>1981</year>
					<month>09</month>
					<day>04</day>
				</date>
			</reprint>
			<availability type=3D"full">
				altijd beschikbaar bij mij
			</availability>
		</libinfo>
		<libinfo user=3D"hans">
			<notes>
				ik ook
			</notes>
			<reprint status=3D"NOTINFILE">
				<date>
					<year>1982</year>
					<month>05</month>
					<day>02</day>
				</date>
			</reprint>
			<availability type=3D"useroot">
				ik weet nie wanneer da da beschikbaar is
			</availability>
		</libinfo>
		<contents>
			<abstract>dit boek vertelt het verhaal van
roodkapje</abstract>
			<keyword>roodkapje</keyword>
			<keyword>wolf</keyword>
		</contents>
	</entry>
</ris>

OUTPUT:

<?xml version=3D"1.0"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris//EN"
"http://refdb.sourceforge.net/dtd/risx.dtd" [
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
]>
<ris>



<entry type=3D"BOOK" id=3D"245" citekey=3D"tcb">
  <publication>
    <author><lastname>hanz grimm</lastname></author>
    <author><firstname>a</firstname><middlename>b</middlename></author>
    <pubinfo>
      <pubdate type=3D"primary">
        <date><year>2003</year><month>12</month><day>06</day></date>
        <otherinfo>
                                                met sinterklaas
                                        </otherinfo>
      </pubdate>
      <volume>5</volume>
      <issue>4</issue>
      <startpage>5</startpage>
      <endpage>100</endpage>
      <city>Mol</city>
      <publisher>SCKCEN</publisher>
      <serial>01545789</serial>
      <address>boertang</address>
      <url>http://google.be</url>
      <userdef type=3D"1">tekstje 1</userdef>
      <userdef type=3D"2">tekstje 2</userdef>
      <userdef type=3D"3">tekstje 3</userdef>
      <userdef type=3D"4">tekstje 4</userdef>
      <userdef type=3D"5">tekstje 5</userdef>
      <misc type=3D"1">pff 1</misc>
      <misc type=3D"2">pff 2</misc>
      <misc type=3D"3">pff 3</misc>
    </pubinfo>
  </publication>
  <libinfo user=3D"hans">
    <notes>
                                ik ook
                        </notes>
<reprint status=3D"NOTINFILE"/>
    <availability type=3D"useroot">PATH:
                                ik weet nie wanneer da da beschikbaar is
                        </availability>
  </libinfo>
  <libinfo user=3D"tom">
    <notes>
                                ik vind dees maar een grellig dtd'ke
                        </notes>
    <reprint status=3D"ONREQUEST"/>
    <availability type=3D"full">
                                altijd beschikbaar bij mij
                        </availability>
  </libinfo>
  <contents>
    <abstract>dit boek vertelt het verhaal van roodkapje</abstract>
    <keyword>wolf</keyword>
    <keyword>roodkapje</keyword>
  </contents>
</entry></ris>

[Refdb-users] ANN: refdb-0.9.3 released

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

Hi all,

I've released RefDB version 0.9.3 to the wild a couple of minutes
ago. Get this new release at:

http://sourceforge.net/projects/refdb

along with the support files.

Please send all comments and suggestions to the list.

regards,
Markus

Bugfixes:

- citation key case mismatches fixed for SGML and XML documents

- fixed table locking problem in MySQL 4.02 and later

- work around OSX sprintf() bug

- fixed some build issues on OSX

- fixed SQLite problems on OSX

- assorted fixes in the backends

- queries including journals now use regexp match instead of full
  match

- fixed CGI problem caused by Windoze browsers

- fixed CGI edit problem

- fixed problem with t_periodical entries

- fixed assorted segfaults in the bibliography code

- fixed problems with queries if personal list is empty

Improvements:

- use xsltproc and a XSLT stylesheet to extract IDs/citation keys from
  XML documents

- risx.dtd defines an additional XML reference data input format

- improved support for availability strings

- manual keyword scan

- new risx backend

- med2ris.pl now has full iconv support

- the getref -S option is now honored by most backends

- new RefDBClient::Client Perl module allows to access the
  functionality provided by refdbd through Perl scripts

- refdbjade and refdbxml now use -s instead of -d to specify the
  stylesheet to avoid confusion with the -d switch of runbib

- personal reference list is now also supported by SQLite

- the refdbctl script now uses the reload and restart commands
  according to the LSB specifications

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

RE: [Refdb-users] Redhat testing/installation woes

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

Hi,

Alan Anderson writes:
 > First, you did also download the dbi driver files for MySQL, right?  libdbi requires the drivers to
 > actually communicate with the database.
 > 

I'm afraid this can't be pointed out often enough. When RefDB 0.9.2
was released, the current libdbi version contained the MySQL and
PostgreSQL drivers. This is reflected in the RefDB manual as
well. However, the current version of libdbi provides only the
framework, and we moved all drivers to the libdbi-drivers project. The
next version of the RefDB manual will of course be updated to reflect
this. It will be an intermittent problem I reckon. Moreover, refdbd as
of 0.9.3 will list the available libdbi drivers at startup. The
problem and the solution will then be way more obvious.

And yes, while we're at it: <mantra>You'll have to specify the
driver(s) on the libdbi-drivers configure command line, otherwise
nothing will be built</mantra> ;-)

 > Second, I discovered that RedHat does not seem to set LD_LIBRARY_PATH environment variable.  I had
 > to set this explicitly in my startup script to make RefDB work since the libdbi files are not in
 > /usr/lib.  This probably isn't you're problem if you don't have the actual shared library files.
 > 

Actually LD_LIBRARY_PATH (or an appropriate entry in ld.so.conf) is
required to find libdbi.so. This in turn either uses a compiled-in
path or one provided by the application using the library to locate
the drivers. That is, the directory holding the drivers need not be
listed in LD_LIBRARY_PATH.

regards,
Markus

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

RE: [Refdb-users] Redhat testing/installation woes

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

Jason,

I don't have any direct answers for you, but I have installed RefDB 0.9.2a on RedHat 9 also.  My
installation is only partially working because I had been messing with the CGI client program--the
commandline interface works fine.  However, I did experience similar problems at the start, so I
thought I'd share the little I know and ask a question or two.

First, you did also download the dbi driver files for MySQL, right?  libdbi requires the drivers to
actually communicate with the database.

Second, I discovered that RedHat does not seem to set LD_LIBRARY_PATH environment variable.  I had
to set this explicitly in my startup script to make RefDB work since the libdbi files are not in
/usr/lib.  This probably isn't you're problem if you don't have the actual shared library files.

Third, my RedHat 9 installation has the following in /usr/local/lib.

-rw-r--r--    1 root     root        44746 Jul 29 13:01 libdbi.a
-rwxr-xr-x    1 root     root          708 Jul 29 13:01 libdbi.la
lrwxrwxrwx    1 root     root           15 Jul 29 13:01 libdbi.so -> libdbi.so.0.0.5
lrwxrwxrwx    1 root     root           15 Jul 29 13:01 libdbi.so.0 -> libdbi.so.0.0.5
-rwxr-xr-x    1 root     root        58814 Dec 19  2002 libdbi.so.0.0.4
-rwxr-xr-x    1 root     root        52070 Jul 29 13:01 libdbi.so.0.0.5

And, this in /usr/local/lib/dbd--these are the driver files.

-rw-r--r--    1 root     root        18536 Dec 19  2002 libmysql.a
-rwxr-xr-x    1 root     root          690 Jul 29 13:30 libmysql.la
-rwxr-xr-x    1 root     root        20434 Jul 29 13:30 libmysql.so

I don't know if any of this helps you, but I thought I'd share it with you.  Hopefully, someone else
will have more information.

Al


> -----Original Message-----
> From: ref...@li...
> [mailto:ref...@li...]On Behalf Of Jason
> Schlumbohm
> Sent: Sunday, August 17, 2003 9:47 PM
> To: ref...@li...
> Subject: [Refdb-users] Redhat testing/installation woes
>
>
> Running Redhat 9.0, x86. I slowly worked my way through the refdb
> 0.9.2a + MySQL installation process, and am testing it according to
> this page (http://refdb.sourceforge.net/manual/x1303.html). Running
> tests thus far as root.
>
> The first test, 'refdbctl stop' worked, /usr/local/bin/refdbd is not
> running. That's good.
>
> The second, 'refdb -s -e 0 -1 7', is where I get hung  up. It reports
> back:
>
> "refdbd: error while loading shared libraries: libdbi.so.0: cannot open
> shared object file: No such file or directory"
>
> I went back and made sure that my libdbi installation went ok. I had
> downloaded the libdbi-0.7.1 tarball from sourceforge. It appears to
> make links, but there's no actual files that they link against, AFAIK.
> I searched for libdbi.so.0, and all I get back is the link  in
> /usr/local/lib.
>
> Any hints, links to documentation, &c that might help me iron this one
> out?
>
> Thanks, Jason
>
>
>
> // Jason Schlumbohm <st...@co...>
> // http://hepatic.ath.cx/
> // icq@ 10838181 + YahooIM/AIM/iChat@ jpschlumbohm
>
>
>
> -------------------------------------------------------
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[Refdb-users] Redhat testing/installation woes

[Jason S. <st...@co...>]

Running Redhat 9.0, x86. I slowly worked my way through the refdb 
0.9.2a + MySQL installation process, and am testing it according to 
this page (http://refdb.sourceforge.net/manual/x1303.html). Running 
tests thus far as root.

The first test, 'refdbctl stop' worked, /usr/local/bin/refdbd is not 
running. That's good.

The second, 'refdb -s -e 0 -1 7', is where I get hung  up. It reports 
back:

"refdbd: error while loading shared libraries: libdbi.so.0: cannot open 
shared object file: No such file or directory"

I went back and made sure that my libdbi installation went ok. I had 
downloaded the libdbi-0.7.1 tarball from sourceforge. It appears to 
make links, but there's no actual files that they link against, AFAIK. 
I searched for libdbi.so.0, and all I get back is the link  in 
/usr/local/lib.

Any hints, links to documentation, &c that might help me iron this one 
out?

Thanks, Jason



// Jason Schlumbohm <st...@co...>
// http://hepatic.ath.cx/
// icq@ 10838181 + YahooIM/AIM/iChat@ jpschlumbohm

[Refdb-users] can't edit reference through web interface

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

Hi,

I'd appreciate if you could send me the log output of refdbd (using
log level 7) and the html output by private mail. It might also be a
good idea to try the prerelease that I've announced
yesterday. Compared to 0.9.2 a boatload of bugs are fixed, and yours
might be among them. The web interface works ok here with the current
CVS version.

regards,
Markus

B. Liu writes:
 > 
 > Dear Markus,
 > 
 > I finally have the refdb 0.9.2 installed, and I also have the web
 > interface to do the job. I can serach the reference, but in the query results
 > window, when I started to delete, add, remove and edit the reference, it
 > gave error message saying:
 > 
 > out of memory
 > content-type: text/html
 > Then following shows a html code file, (I didn't copy the html file here,
 > it seems html email caused trouble before. But I can send it to you if you
 > want.)
 > 
 > I am not sure if this is a bug or I didn't have the configure files
 > configured properly.
 > 
 > Thanks
 > 
 > Bin
 > 
 > 
 > 
 > 
 > 
 > 
 > -------------------------------------------------------
 > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
 > Data Reports, E-commerce, Portals, and Forums are available now.
 > Download today and enter to win an XBOX or Visual Studio .NET.
 > http://aspnet.click-url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
 > _______________________________________________
 > Refdb-users mailing list
 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-users
 > 
 > 

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

[Refdb-users] can't edit reference through web interface

[B. L. <bl...@he...>]

Dear Markus,

I finally have the refdb 0.9.2 installed, and I also have the web
interface to do the job. I can serach the reference, but in the query results
window, when I started to delete, add, remove and edit the reference, it
gave error message saying:

out of memory
content-type: text/html
Then following shows a html code file, (I didn't copy the html file here,
it seems html email caused trouble before. But I can send it to you if you
want.)

I am not sure if this is a bug or I didn't have the configure files
configured properly.

Thanks

Bin

[Refdb-users] ANN: refdb-0.9.3-pre9 available for testing

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

Hi,

here's another prerelease for those who like to help testing. This one
mainly fixes some severe problems on the PowerPC platform.

These are the most recent files:

http://refdb.sourceforge.net/pre/refdb-0.9.3-pre9.tar.gz
http://refdb.sourceforge.net/pre/RefDB-perlmod-0.3_pre1.tar.gz
http://refdb.sourceforge.net/pre/RefDBClient-Client-1.6.tar.gz

regards,
Markus

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

Re: [Refdb-users] Problem with installation on Debian

[B. L. <bl...@he...>]

Hi Markus,

> thanks for providing the log. I gather that the crash is pretty close
> to the spot when refdbd first tries to contact the database server. It
> might be some weird incompatibility between the fairly old libdbi and
> the fairly new MySQL version.
>
> You've basically got two ways to find out what's going wrong:
>
> 1) use a different database server. You may try switching to an older
> MySQL version like 3.23. If you're familiar with PostgreSQL,
> use that. SQLite is even easier although I'm not sure whether Debian
> carries packages. For this you'd need libdbi-0.7.1 and
> libdbi-drivers-0.7.0, though.

You are right!! I installed refdb-0.9.2 on debian woody, database:
mysql(3.23.49), libraries: libdbi0, libdbi0-dev, libdbd-mysql (0.6.7), and
the installation testing is fine now :~).

> 2) go ahead and debug the crash. You need three xterms to do the following:
>
> - edit refdbd.c and uncomment the following lines (around 777):
>
> /*  	    printf("child sleeps PID=%d\n", getpid()); */
> /*  	    sleep(10); */
>
> - run make
>
> - run refdb/src/refdbd -e 0 -l 7 -s (don't run the installed version!)
>
> - in the second xterm, cd to refdb/src and run gdb, the debugger
>
> - in the third xterm, run refdba and execute viewstat
>
> - the server process will print the process ID of the child process
>
> - you've got 10 seconds to type "attach <PID>" on the gdb prompt in
> your second xterm
>
> - still on the gdb prompt, type "c" like in continue.
>
> - then watch the child process crash and type "bt" like in backtrace
> on the gdb prompt. This output is what we need.

I did this part as well, but I didn't get the process ID. I can't give you
any output, I'll be very happy to carry on with the debug if you want.

PS. Thanks to Marc, for all the help you offered.

Best Wishes

Bin

Re: [Refdb-users] Problem with installation on Debian

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

Hi,

thanks for providing the log. I gather that the crash is pretty close
to the spot when refdbd first tries to contact the database server. It
might be some weird incompatibility between the fairly old libdbi and
the fairly new MySQL version.

You've basically got two ways to find out what's going wrong:

1) use a different database server. You may try switching to an older
MySQL version like 3.23. If you're familiar with PostgreSQL,
use that. SQLite is even easier although I'm not sure whether Debian
carries packages. For this you'd need libdbi-0.7.1 and
libdbi-drivers-0.7.0, though.

2) go ahead and debug the crash. You need three xterms to do the following:

- edit refdbd.c and uncomment the following lines (around 777):

/*  	    printf("child sleeps PID=%d\n", getpid()); */
/*  	    sleep(10); */

- run make

- run refdb/src/refdbd -e 0 -l 7 -s (don't run the installed version!)

- in the second xterm, cd to refdb/src and run gdb, the debugger

- in the third xterm, run refdba and execute viewstat

- the server process will print the process ID of the child process

- you've got 10 seconds to type "attach <PID>" on the gdb prompt in
your second xterm

- still on the gdb prompt, type "c" like in continue.

- then watch the child process crash and type "bt" like in backtrace
on the gdb prompt. This output is what we need.

regards,
Markus

B. Liu writes:
 > 7:pid=513:Mon Aug 11 10:24:03 2003:try to read from client
 > 6:pid=513:Mon Aug 11 10:24:03 2003:serving client on fd 6 with protocol
 > version 1
 > 7:pid=513:Mon Aug 11 10:24:03 2003:201-24-19-46
 > 7:pid=513:Mon Aug 11 10:24:03 2003:send pseudo-random string to client
 > 7:pid=513:Mon Aug 11 10:24:03 2003:viewstat  -u root -w
 > 050108078040041055080116100
 > 6:pid=513:Mon Aug 11 10:24:03 2003:dbi is up
 > 7:pid=513:Mon Aug 11 10:24:03 2003:localhost
 > 7:pid=513:Mon Aug 11 10:24:03 2003:root
 > 7:pid=513:Mon Aug 11 10:24:03 2003:
 > 7:pid=513:Mon Aug 11 10:24:03 2003:
 > 7:pid=513:Mon Aug 11 10:24:03 2003:3306
 > 

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

Re: [Refdb-users] Problem with installation on Debian

[B. L. <bl...@he...>]

On Sat, 9 Aug 2003, Markus Hoenicka wrote:

> Hi,
>
> Ok, this is something different. Apparently the accept() works but one
> of the processes (parent or child) crashes. To find out which one,
> please send the log output to a file, using something like:
>
> refdbd -s -e 2 -l 7 -L /home/bin/refdbd.log
>
> to start the server.
>
> In addition I'll be back at my Debian box next week. I'll run a few
> tests and see whether I can reproduce the problem on that box.
>
> If this doesn't help, we'll have to figure out something else. What
> are your programming/debugging skills? Do you think you're capable to
> obtain additional debug information with gdb? I'd be happy to lend a
> hand if necessary. Another option is to provide a temporary ssh
> account on your box. Then I could do some debugging myself.

Markus,

Here is the refdbd.log file

7:pid=511:Mon Aug 11 10:23:45 2003:dbi_driver_dir went to:
7:pid=511:Mon Aug 11 10:23:45 2003:
7:pid=511:Mon Aug 11 10:23:45 2003:dbi is up using default driver dir
6:pid=511:Mon Aug 11 10:23:45 2003:Available libdbi database drivers:
6:pid=511:Mon Aug 11 10:23:45 2003:mysql
6:pid=511:Mon Aug 11 10:23:45 2003:application server started
7:pid=511:Mon Aug 11 10:23:45 2003:use /tmp/refdbd_fifo511 as fifo
6:pid=511:Mon Aug 11 10:23:45 2003:server waiting n_max_fd=5
6:pid=511:Mon Aug 11 10:24:03 2003:adding client on fd 6
6:pid=511:Mon Aug 11 10:24:03 2003:server waiting n_max_fd=6
7:pid=513:Mon Aug 11 10:24:03 2003:try to read from client
6:pid=513:Mon Aug 11 10:24:03 2003:serving client on fd 6 with protocol
version 1
7:pid=513:Mon Aug 11 10:24:03 2003:201-24-19-46
7:pid=513:Mon Aug 11 10:24:03 2003:send pseudo-random string to client
7:pid=513:Mon Aug 11 10:24:03 2003:viewstat  -u root -w
050108078040041055080116100
6:pid=513:Mon Aug 11 10:24:03 2003:dbi is up
7:pid=513:Mon Aug 11 10:24:03 2003:localhost
7:pid=513:Mon Aug 11 10:24:03 2003:root
7:pid=513:Mon Aug 11 10:24:03 2003:
7:pid=513:Mon Aug 11 10:24:03 2003:
7:pid=513:Mon Aug 11 10:24:03 2003:3306

In the refdba window, when I used refdba: viewstat
The error message is:
could not connect to database server

I have to say I am not very good at programming, but I can try if you give
me a hand.

Thanks

Bin

Re: [Refdb-users] Problem with installation on Debian

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

Hi,

B. Liu writes:
 > In the refdbd window, it shows:
 > 
 > dbi_driver_dir went to:
 > 
 > dbi is up using default driver dir
 > Available libdbi database drivers:
 > mysql
 > application server started
 > use /tmp/refdbd_fifo4679 as fifo
 > server waiting n_max_fd=4
 > adding client on fd 5
 > server waiting n_max_fd=5
 > Segmentation fault
 > 

Ok, this is something different. Apparently the accept() works but one
of the processes (parent or child) crashes. To find out which one,
please send the log output to a file, using something like:

refdbd -s -e 2 -l 7 -L /home/bin/refdbd.log

to start the server.

In addition I'll be back at my Debian box next week. I'll run a few
tests and see whether I can reproduce the problem on that box.

If this doesn't help, we'll have to figure out something else. What
are your programming/debugging skills? Do you think you're capable to
obtain additional debug information with gdb? I'd be happy to lend a
hand if necessary. Another option is to provide a temporary ssh
account on your box. Then I could do some debugging myself.

regards,

Markus

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

Re: [Refdb-users] building on OS X?

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

Oh, and here's what's in the Fink lib directory (/sw/lib) that seems to 
relate to readline:

libreadline.4.2.dylib -> libreadline.4.3.dylib
libreadline.4.3.dylib
libreadline.4.dylib -> libreadline.4.3.dylib
libreadline.a
libreadline.dylib -> libreadline.4.3.dylib

In the readline include directory, I have:

chardefs.h
history.h
keymaps.h
readline.h
rlconf.h
rlstdc.h
rltypedefs.h
tilde.h

Bruce

Re: [Refdb-users] building on OS X?

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

On Thursday, August 7, 2003, at 06:57  PM, Markus Hoenicka wrote:

> Hi Bruce,
>
> please check whether there's a libreadline-dev fink package. You miss
> the development library and the header files. All you have is the
> runtime library.

OK, there's a problem.

There is no dev package for readline.  However, a discussion with the  
package-maintainer yielded this:

"headers are in 'readline' the rest in 'readline-shlibs'"

Here's the thing: both packages are already installed on my system.

Bruce

> regards,
> Markus
>
> Bruce D'Arcus writes:
>>
>> OK, compiling latest release on OS X, I'm stuck with readline.  I get
>> this error:
>>
>> checking for readline in -lreadline... no
>> Cannot build refdb without libreadline
>>
>> My command:
>>
>> ./configure --with-libdbi-lib="/sw/lib/libdbi.0.0.5.dylib"
>> --with-expat-lib="/sw/lib/libexpat.0.4.0.dylib"
>> --with-docbook-xsl="/sw/share/xml/xsl/docbook-xsl"
>> --with-refdb-url="http://www.users.muohio.edu/darcusb/refdb"
>> --with-db-server=sqlite --libdir="/sw/lib"
>>
>> Path to the library:
>>
>> "/sw/lib/libreadline.4.3.dylib"
>>
>> What now?
>>
>> Bruce
>>
>>
>>
>> -------------------------------------------------------
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>> direct;at.aspnet_072303_01/01
>> _______________________________________________
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>> Ref...@li...
>> https://lists.sourceforge.net/lists/listinfo/refdb-users
>>
>>
>
> -- 
> Markus Hoenicka
> mar...@ca...
> (Spam-protected email: replace the quadrupeds with "mhoenicka")
> http://www.mhoenicka.de
>
>
>
> -------------------------------------------------------
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> Download today and enter to win an XBOX or Visual Studio .NET.
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> direct;at.aspnet_072303_01/01
> _______________________________________________
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> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users

[Refdb-users] Re: [Libdbi-drivers-devel] drivers don't build correctly (was:Re: refdb manual error and question)

[David P. <da...@ne...>]

On Fri, 8 Aug 2003 00:55:23 +0200, Markus Hoenicka wrote:

> the drivers you need are .so files, not .a or .la files. Apparently
> something went wrong when building the shared modules. What platform
> is this again? Can you provide some additional information like the
> config.log and make output?

This is strange, it should always be generating .so files unless specifically
tricked into doing otherwise. In addition to the config.log, 'make' command
line, platform, and make output, can you include the output of
"libtool --version"?

Thanks,
David

-------
David Parker <da...@ne...>
Neon Goat Productions
http://www.neongoat.com
0xF90FFFE5 / F362 51F7 6D51 85EB AF68 75B9 D29B 1AFC F90F FFE5
-------

[Refdb-users] building on OS X?

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

Hi Bruce,

please check whether there's a libreadline-dev fink package. You miss
the development library and the header files. All you have is the
runtime library.

regards,
Markus

Bruce D'Arcus writes:
 > 
 > OK, compiling latest release on OS X, I'm stuck with readline.  I get 
 > this error:
 > 
 > checking for readline in -lreadline... no
 > Cannot build refdb without libreadline
 > 
 > My command:
 > 
 > ./configure --with-libdbi-lib="/sw/lib/libdbi.0.0.5.dylib" 
 > --with-expat-lib="/sw/lib/libexpat.0.4.0.dylib" 
 > --with-docbook-xsl="/sw/share/xml/xsl/docbook-xsl" 
 > --with-refdb-url="http://www.users.muohio.edu/darcusb/refdb" 
 > --with-db-server=sqlite --libdir="/sw/lib"
 > 
 > Path to the library:
 > 
 > "/sw/lib/libreadline.4.3.dylib"
 > 
 > What now?
 > 
 > Bruce
 > 
 > 
 > 
 > -------------------------------------------------------
 > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
 > Data Reports, E-commerce, Portals, and Forums are available now.
 > Download today and enter to win an XBOX or Visual Studio .NET.
 > http://aspnet.click-url.com/go/psa00100003ave/direct;at.aspnet_072303_01/01
 > _______________________________________________
 > Refdb-users mailing list
 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-users
 > 
 > 

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

[Refdb-users] building on OS X?

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

OK, compiling latest release on OS X, I'm stuck with readline.  I get 
this error:

checking for readline in -lreadline... no
Cannot build refdb without libreadline

My command:

./configure --with-libdbi-lib="/sw/lib/libdbi.0.0.5.dylib" 
--with-expat-lib="/sw/lib/libexpat.0.4.0.dylib" 
--with-docbook-xsl="/sw/share/xml/xsl/docbook-xsl" 
--with-refdb-url="http://www.users.muohio.edu/darcusb/refdb" 
--with-db-server=sqlite --libdir="/sw/lib"

Path to the library:

"/sw/lib/libreadline.4.3.dylib"

What now?

Bruce

[Refdb-users] refdb manual error and question

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

Hi,

Nathan Cummings writes:
 > just a note... in the "Testing your installation" section of the 
 > handbook (http://refdb.sourceforge.net/manual/x1303.html) point 3, i 
 > think should have the command:
 > 
 >          #~ refdba -u <dbadmin> -w <dbadmin-passwd>
 > 
 > instead of
 > 
 >          #~ refdba -u <dbadmin> -p <dbadmin-passwd>
 > 
 > It seems the '-p' option is for the port number and not the 
 > password--though it is the right switch to send to the mysql client for 
 > the password. And along those lines, you have any idea quick hints on 

This is indeed a typo. I'll fix that in the next version of the
manual.

 > but when i attempt to do a 'viewstat' from refdba i get this output from 
 > the refdbd process:
 > 
 >         3306
 >         mysql
 >         A@
 >         creating database connection structure failed
 >         command processing done, finish dialog now
 >         child finished client on fd 5
 >         child exited with code 0
 >         server waiting n_max_fd=4
 > 
 > i suspect it has something to do with authentication since i see this in 
 > my mysql log:
 > 
 >         030806 13:25:06  277 Connect Access denied for  \
 >                  user:'root@localhost' (Using password: YES)
 > 

Do you see this log message after each attempt to run refdba:viewstat?
I'd actually be surprised as the "creating database connection
structure failed" usually is a hint that the appropriate libdbi driver
is missing. You'd then have to install libdbi-drivers, specifying
mysql on the configure command line.

regards,
Markus

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

Re: [Refdb-users] Re: Problem with installation on Debian

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

B. Liu writes:
 > Hi Markus,
 > 
 > There is another error message, it shows:
 > 
 > refdbd.c:117: parse error before `gotsignal'
 > refdbd.c:117: warning: data definition has no type or storage class
 > make[1]: *** [refdbd.o] Error 1
 > make[1]: Leaving directory `/home/bl246/refdb/refdb-0.9.2/src'
 > make: *** [all-recursive] Error 1
 > 

I'm afraid you've made some accidental change to the file that screws
up the syntax. In order to speed up things, would you mind trying the
latest prerelease, available at:

http://refdb.sourceforge.net/pre/refdb-0.9.3-pre8.tar.gz

I'll send you a patched refdbd.c by private mail. This one compiles
here so it should be ok for you purposes.

regards,
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.3-pre8 available for testing

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

Hi,

Michael Maechtel writes:
 > On Tuesday 05 August 2003 22:45, Markus Hoenicka wrote:
 > > 1) There seems to be an issue with editing/updating records through
 > > the web interface on some platforms. I can't reproduce it yet, so I'd
 > [...]
 > > do what it should, please send me the log data.
 > Works here, only "Add selected references to Personal List" gives me
 > some HTML code back (see atachment) ... but that might be a
 > config problem of mine ...

Thanks for testing. I'm afraid the message you get when adding refs to
the personal list is related to a misunderstanding of what this
command does. If you added the refs yourself in the first place,
they're in your personal list anyway, so adding them again won't do
you any good. A different user would most likely be able to pick them
without an error message.

 > 
 > > 2) There may be issues left with the XSLT FO driver files. I've fixed
 > [...]
 > > related to printed output from XML documents until the toolchains get
 > > fixed. Yes, and if anyone knows how to fix them, please give
 > > me a call!
 > 
 > Still the same error (with old test.xml .. posted a couple of days before) :
 > ! Missing \endcsname inserted.
 > <to be read again>
 >                    \Odd:
 > l.209 ...ent><fo:flow flow-name="xsl-region-body">
 >                                                   
 > <fo:block><fo:block><fo:bl...
 > 
 > I'm using debian "testing" ... everything works, beside some stylsheet 1.6x 
 > <-> jadetex problems (like A4 paper.size ..) But I got FO output without 
 > errors.
 > 
 > What's broken in your toolchain ?

On Debian 3.0 (stable) I get:

! Undefined control sequence.
l.61 \XMLstringX
                \@staticafter<>xsl-after</>

On FreeBSD 4.7 (all packages current as of approx two weeks ago) I
see:

! Missing number, treated as zero.
<to be read again> 
                   p
l.2 ...egy="character-by-character" language="en">
                                                  <fo:layout-master-set><fo:...

I assume that the XSLT stylesheets do not cooperate well with the TeX
macros. If we include your results, the whole thing is broken in at
least three different ways ... not very reassuring.

I'll think about adding a config option to transform the XML documents
using the Jade/JadeTeX toolchain. This may be a slap in the face of
the XML/XSLT proponents but I need something that works.

regards,
Markus

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

[Refdb-users] how to do this (syllabus)?

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

OK, for my first refdb project, I want to create my syllabii for next 
term.  What I want is to modify the DocBook stylesheets to do this.  
RefDB comes in here:

<row>
   <entry>Week</entry>
   <entry>Dates</entry>
   <entry>Topic</entry>
   <entry>Readings</entry>
</row>
</thead>
<tbody>
<row>
   <entry>1</entry>
   <entry>8/27</entry>
   <entry>Introduction</entry>
   <entry>
	<citation>blah</citation>
	<citation>blah</citation>
	<citation>blah</citation>
</entry>
</row>

I want a table of topics and numbered bib entries.  So the output row 
above would look like:

	1	8/27	Introduction		1, 2, 3

So how do I do this?

And if someone has a better idea of how to deal with syllabi, feel free 
to suggest it.  This seems like a good, easily-maintainable, solution 
to me at the moment...

Bruce