refdb-users — List for RefDB users

[Refdb-users] marc2ris problems

[Daniel O'D. <dan...@ul...>]

Hi,

I've been running some marc files through marc2ris (the new version from
the svn). The script is not recognising anything in the input files.
Here's everthing I have:

==Input:==

> 01115cam 22002654a 4500
> 001 13258321
> 005 20040420092439.0
> 008 030701s2003 nyua b 001 0 eng
> 906 $a 7 $b cbc $c orignew $d 1 $e ocip $f 20 $g y-gencatlg
> 925 0 $a acquire $b 2 shelf copies $x policy default
> 955 $a pc24 2003-07-01 to HLCD $i jp99 2003-07-09 $e jp10 2003-07-09
> to
> Dewey $a CAD uf24 2003-11-17 $a uf24 1 copy forwarded to CIP $a px04
> 2004-03-19 1 copy rec'd., to CIP ver. $a jp00 2004-03-24 $f jp99
> 2004-04-06 $g jp10 2004-04-20 to BCCD
> 010 $a 2003057650
> 020 $a 0670030759 (acid-free paper)
> 040 $a DLC $c DLC $d DLC
> 042 $a pcc
> 043 $a e-gx---
> 050 00 $a Q127.G3 $b C67 2003
> 082 00 $a 509.43/09/04 $2 22
> 100 1 $a Cornwell, John, $d 1940-
> 245 10 $a Hitler's scientists : $b science, war, and the devil's
> pact /
> $c John Cornwell.
> 260 $a New York : $b Viking, $c 2003.
> 300 $a xvi, 535 p. : $b ill. ; $c 24 cm.
> 504 $a Includes bibliographical references (p. [501]-512) and index.
> 650 0 $a Science and state $z Germany $x History $y 20th century.
> 650 0 $a World War, 1939-1945 $x Science $z Germany.

==Command==

> marc2ris -e 2 -l 7 -L /home/dan/marc2ris.log -o Desktop/marcoutput2.ris Desktop/marcoutput2.marc


==Output file==
(After several tries):

> TY  - BOOK
> ER  -
> 
> TY  - BOOK
> ER  -
> 
> TY  - BOOK
> ER  -


==Log (l=7):==

> 7:pid:Mon Jul  3 23:18:01 2006:converting Desktop/marcoutput2.marc
> -1:pid:Mon Jul  3 23:18:01 2006:no type found - assume BOOK
> 6:pid:Mon Jul  3 23:18:01 2006:empty title field (245)
> 6:pid:Mon Jul  3 23:18:01 2006:empty series title field
> 6:pid:Mon Jul  3 23:18:01 2006:no isbn found
> 6:pid:Mon Jul  3 23:18:01 2006:no issn found
> 6:pid:Mon Jul  3 23:18:01 2006:no LOC call number found
> 6:pid:Mon Jul  3 23:18:01 2006:no Dewey number found
> 6:pid:Mon Jul  3 23:18:01 2006:no publication information found


Any suggestions?

-d
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] php interface

[Daniel O'D. <dan...@ul...>]

On Sun, 2006-02-07 at 22:03 +0200, Markus Hoenicka wrote:
> Daniel O'Donnell writes:
>  > As far as I can tell--I'm a novice PHPer but experienced XML/XSLT
>  > person, so likely biased--the way to go for importing z3950 put into
>  > refdb is via XML: yaz provides good MARC to MARCXML functionality, and
>  > writing a stylesheet that mimics marc2ris probably wouldn't be to hard
>  > if the target were risx.
>  > 
> 
> I don't want to talk you out of this, but in the end the data have to
> be piped into refdbc anyway. If you convert MARC data internally to
> MARCXML and then to risx, you basically duplicate the existing MARC
> to RIS conversion. This at best duplicates the efforts to get better
> MARC support, but at worst it causes inconsistencies: The SQL data
> should not depend on the path how you import the data (command line
> vs. web interface). I'm not generally opposed to going through
> MARCXML, but if you follow this path, you should provide modular code
> which can be used from the command line as well.

Good point. The only reason for going the other way is that xslt support
is native to php5. But there's certainly lots of room for inconsistency
this way.

> 
>  > The advice on the net seems to be to avoid mixing perl and php; since
>  > xml handling is built into php 5, this seems both a safer and a more
>  > elegant approach.
> 
> We're not talking about mixing Perl and PHP. The PHP code will have to
> pipe data into refdbc (unless someone codes the client networking code
> directly in PHP). PHP will open a shell for this purpose, and PHP does
> not even notice whether the first command in the pipe is a C program
> (refdbc) or a Perl script (marc2ris).

I guess I'm just not knowledgeable enough to know how to do this. Right
now I think I'll work on cleaning up the html and CSS in the web version
of refdb and integrating a PHP_YAZ search page into the stack. Once
that's done, there will be time to learn how to transfer the data from
the external source to refdb.

> 
>  > 
>  > B. 
>  > As part of my experimentation, I thought I'd also play a bit with the
>  > refdb_php. In particular, I'd like to do two things:
>  > 
>  > 1) xhtml-ize the current html (make it well formed, use CSS instead of
>  > tables for positioning)
>  > 
> 
> You should keep in mind that the original web design (which is
> replicated in the current PHP interface) was created by a person not
> very capable of designing user interfaces (I'm talking about
> myself). If you start fiddling with the HTML/XHTML code, you should
> feel free to do a redesign as well, if it helps to improve your
> code. I'd appreciate clean XHTML + CSS code.
> 
>  > 2) change the output to either risx or tei xml (more possibilities for
>  > display and exchange)
>  > 
> 
> You should probably provide several output formats (see the Emacs
> interface). For entering new references we should think about
> designing an interface that does not directly show the underlying data
> format.
> 
>  > Any thoughts on either? I know nothing about making packages, so I'll be
>  > doing all this on my local installation as a hobby. I'm not quite sure
>  > how one posts progress or enables collaboration but I'm happy to do so.
>  > 
> 
> The easiest way is to sign up as a RefDB developer and use the
> subversion repository to publish your work and to collaborate. Let me
> know if you are interested.
> 
> regards,
> Markus
> 
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] Does the edit button actually work in the php version of refdb?

[<ste...@jo...>]

Daniel O'Donnell a =C3=A9crit :
> I had trouble but then got it working. What is your PHP version, Linux
> Distro, and Apache version? I'm assuming you followed the brief readme
> in the package?
>=20

Yes i did, but since i'm packaging it on the devel version of Mandriva=20
(aka cooker), i may have missed something.

I'll check as soon as possible (and permissions too), when i'm back from=20
a congress next week).

Cheers,

St=C3=A9phane

--=20
St=C3=A9phane T=C3=A9letch=C3=A9a, PhD.                  http://www.stele=
tch.org
Unit=C3=A9 Math=C3=A9matique Informatique et G=C3=A9nome http://migale.jo=
uy.inra.fr/mig
INRA, Domaine de Vilvert                  T=C3=A9l : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

[Refdb-users] ANN: refdb-svn

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

Hi all,

David Nebauer asked me to forward the following announcement. The tool
mentioned here is available from the RefDB homepage:

http://refdb.sourceforge.net/download.html#cvseasy

regards,
Markus

-----

Once upon a time there lived a set of scripts known as 'refdb-cvs' for 
automatic installation of refdb from cvs.

Those scripts are outdated now that refdb has migrated to subversion.

I have created the subversion analogue to refdb-cvs -- refdb-svn.  It 
consists of three files:

 - refdb-svn: script, handles checkout, update, switching trees and 
building from source
 - refdb-svn-install: script, called with 'su' to enable installation as 
root
 - refdb-svnrc: configuration file

[A manpage for each file is also included.]

Those with good memories will recall that settings in refdb-cvs were 
handled by editing the script directly; and that the scripts has to be 
installed manually.

refdb-svn behaves more like the basic refdb tools.  There is a global 
configuration file: refdb-svnrc.  It lives in @sysconfdir@.  It can be 
copied to the user's root directory as ~/.refdb-svnrc and settings in 
the local config file override global settings.

It comes packaged as an autotools tarzip for trouble-free installation.  
I have also released a Debian package.

refdb-svn has been fairly well tested, but only on a Debian Linux system 
-- users with other platforms are encouraged to report their experience.


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

[Refdb-users] php interface

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

Daniel O'Donnell writes:
 > As far as I can tell--I'm a novice PHPer but experienced XML/XSLT
 > person, so likely biased--the way to go for importing z3950 put into
 > refdb is via XML: yaz provides good MARC to MARCXML functionality, and
 > writing a stylesheet that mimics marc2ris probably wouldn't be to hard
 > if the target were risx.
 > 

I don't want to talk you out of this, but in the end the data have to
be piped into refdbc anyway. If you convert MARC data internally to
MARCXML and then to risx, you basically duplicate the existing MARC
to RIS conversion. This at best duplicates the efforts to get better
MARC support, but at worst it causes inconsistencies: The SQL data
should not depend on the path how you import the data (command line
vs. web interface). I'm not generally opposed to going through
MARCXML, but if you follow this path, you should provide modular code
which can be used from the command line as well.

 > The advice on the net seems to be to avoid mixing perl and php; since
 > xml handling is built into php 5, this seems both a safer and a more
 > elegant approach.

We're not talking about mixing Perl and PHP. The PHP code will have to
pipe data into refdbc (unless someone codes the client networking code
directly in PHP). PHP will open a shell for this purpose, and PHP does
not even notice whether the first command in the pipe is a C program
(refdbc) or a Perl script (marc2ris).

 > 
 > B. 
 > As part of my experimentation, I thought I'd also play a bit with the
 > refdb_php. In particular, I'd like to do two things:
 > 
 > 1) xhtml-ize the current html (make it well formed, use CSS instead of
 > tables for positioning)
 > 

You should keep in mind that the original web design (which is
replicated in the current PHP interface) was created by a person not
very capable of designing user interfaces (I'm talking about
myself). If you start fiddling with the HTML/XHTML code, you should
feel free to do a redesign as well, if it helps to improve your
code. I'd appreciate clean XHTML + CSS code.

 > 2) change the output to either risx or tei xml (more possibilities for
 > display and exchange)
 > 

You should probably provide several output formats (see the Emacs
interface). For entering new references we should think about
designing an interface that does not directly show the underlying data
format.

 > Any thoughts on either? I know nothing about making packages, so I'll be
 > doing all this on my local installation as a hobby. I'm not quite sure
 > how one posts progress or enables collaboration but I'm happy to do so.
 > 

The easiest way is to sign up as a RefDB developer and use the
subversion repository to publish your work and to collaborate. Let me
know if you are interested.

regards,
Markus

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

[Refdb-users] php interface

[Daniel O'D. <dan...@ul...>]

I've been experimenting with the refdb php interface and phpyaz, with an
eye to incorporating them seamlessly into the same interface.

A. 
As far as I can tell--I'm a novice PHPer but experienced XML/XSLT
person, so likely biased--the way to go for importing z3950 put into
refdb is via XML: yaz provides good MARC to MARCXML functionality, and
writing a stylesheet that mimics marc2ris probably wouldn't be to hard
if the target were risx.

The advice on the net seems to be to avoid mixing perl and php; since
xml handling is built into php 5, this seems both a safer and a more
elegant approach.

B. 
As part of my experimentation, I thought I'd also play a bit with the
refdb_php. In particular, I'd like to do two things:

1) xhtml-ize the current html (make it well formed, use CSS instead of
tables for positioning)

2) change the output to either risx or tei xml (more possibilities for
display and exchange)

Any thoughts on either? I know nothing about making packages, so I'll be
doing all this on my local installation as a hobby. I'm not quite sure
how one posts progress or enables collaboration but I'm happy to do so.

-d
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] Does the edit button actually work in the php version of refdb?

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

Daniel O'Donnell writes:
 > I had trouble but then got it working. What is your PHP version, Linux
 > Distro, and Apache version? I'm assuming you followed the brief readme
 > in the package?
 > 

Same here. I suspect there is a problem with permissions. Do PHP
scripts in general work in your Apache installation?

regards,
Markus

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

Re: [Refdb-users] Does the edit button actually work in the php version of refdb?

[Daniel O'D. <dan...@ul...>]

I had trouble but then got it working. What is your PHP version, Linux
Distro, and Apache version? I'm assuming you followed the brief readme
in the package?

On Fri, 2006-30-06 at 12:27 +0200, Stéphane Téletchéa wrote:
> Daniel O'Donnell a écrit :
> > Been experimenting with the php version of refdb.
> > 
> > Everything seems to work except for the [edit] button, which produces
> > errors. Does anybody know if it is supposed to work? Looking the code,
> > over I'd have said it was a deletion button rather than an edit button!
> > 
> > -d
> 
> Moreover the phpweb interface seems to not work at all :-(
> 
> I've tried to use it and i couldn't get anything working, which is bad 
> since refdb fits all my others needs :-(
> 
> Using refdbc i can browse citations, import, export ones.
> 
>  From the web interface, i can only get errors (see below httpd logs):
> 
> [Thu Jun 29 23:06:11 2006] [notice] Apache/2.2.2 (Mandriva 
> Linux/PREFORK-6mdv2007.0) configured -- resuming normal operations
> [Thu Jun 29 23:11:39 2006] [error] [client 127.0.0.1] File does not 
> exist: /var/www/html/favicon.ico
> [Thu Jun 29 23:12:58 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed-result.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:12:58 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phpTjy7Vz' to 'pubmed-result.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:44:01 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed-result.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:44:01 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phplYBqez' to 'pubmed-result.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:44:17 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed-result.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:44:17 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phpgbuB7q' to 'pubmed-result.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:51:16 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed-result.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:51:16 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phpM0QeWa' to 'pubmed-result.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:51:23 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed-result.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Thu Jun 29 23:51:23 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phpFbRbtg' to 'pubmed-result.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> sh: -c: command not found
> sh: -u: command not found
> sh: -u: command not found
> [Fri Jun 30 00:25:45 2006] [error] [client 127.0.0.1] PHP Warning: 
> session_destroy() [<a 
> href='function.session-destroy'>function.session-destroy</a>]: Trying to 
> destroy uninitialized session in /var/www/refdb/refdblogout.php on line 
> 30, referer: http://localhost/refdb/refdbdbquery.php
> sh: -c: command not found
> sh: -u: command not found
> sh: -u: command not found
> [Fri Jun 30 00:33:46 2006] [error] [client 127.0.0.1] PHP Warning: 
> session_destroy() [<a 
> href='function.session-destroy'>function.session-destroy</a>]: Trying to 
> destroy uninitialized session in /var/www/refdb/refdblogout.php on line 
> 30, referer: http://localhost/refdb/refdbadmin.php
> [Fri Jun 30 00:34:02 2006] [error] [client 127.0.0.1] PHP Warning: 
> session_destroy() [<a 
> href='function.session-destroy'>function.session-destroy</a>]: Trying to 
> destroy uninitialized session in /var/www/refdb/refdblogout.php on line 
> 30, referer: http://localhost/refdb/index.html
> [Fri Jun 30 00:34:07 2006] [error] [client 127.0.0.1] PHP Warning: 
> session_destroy() [<a 
> href='function.session-destroy'>function.session-destroy</a>]: Trying to 
> destroy uninitialized session in /var/www/refdb/refdblogout.php on line 
> 30, referer: http://localhost/refdb/refdbquery.html
> [Fri Jun 30 00:39:57 2006] [error] [client 127.0.0.1] PHP Warning: 
> session_destroy() [<a 
> href='function.session-destroy'>function.session-destroy</a>]: Trying to 
> destroy uninitialized session in /var/www/refdb/refdblogout.php on line 
> 30, referer: http://localhost/refdb/refdbquery.html
> [Fri Jun 30 00:40:34 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Fri Jun 30 00:40:34 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phpYAU50H' to 'pubmed.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> [Fri Jun 30 00:51:03 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file(pubmed.txt) [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> failed to open stream: Permission denied in /var/www/refdb/refdbadd.php 
> on line 111, referer: http://localhost/refdb/refdbadd.html
> [Fri Jun 30 00:51:03 2006] [error] [client 127.0.0.1] PHP Warning: 
> move_uploaded_file() [<a 
> href='function.move-uploaded-file'>function.move-uploaded-file</a>]: 
> Unable to move '/tmp/phposFZ3V' to 'pubmed.txt' in 
> /var/www/refdb/refdbadd.php on line 111, referer: 
> http://localhost/refdb/refdbadd.html
> 
> Any hint ?
> 
> Cheers,
> 
> Stéphane
> 
-- 
Daniel Paul O'Donnell
Associate Professor and Chair of English
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
University of Lethbridge
Lethbridge AB T1K 3M4
Canada

Vox +1 403 329-2377
Fax +1 403 382-7191

:@caedmon/ubuntu

Re: [Refdb-users] Does the edit button actually work in the php version of refdb?

[<ste...@jo...>]

Daniel O'Donnell a =E9crit :
> Been experimenting with the php version of refdb.
>=20
> Everything seems to work except for the [edit] button, which produces
> errors. Does anybody know if it is supposed to work? Looking the code,
> over I'd have said it was a deletion button rather than an edit button!
>=20
> -d

Moreover the phpweb interface seems to not work at all :-(

I've tried to use it and i couldn't get anything working, which is bad=20
since refdb fits all my others needs :-(

Using refdbc i can browse citations, import, export ones.

 From the web interface, i can only get errors (see below httpd logs):

[Thu Jun 29 23:06:11 2006] [notice] Apache/2.2.2 (Mandriva=20
Linux/PREFORK-6mdv2007.0) configured -- resuming normal operations
[Thu Jun 29 23:11:39 2006] [error] [client 127.0.0.1] File does not=20
exist: /var/www/html/favicon.ico
[Thu Jun 29 23:12:58 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed-result.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:12:58 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phpTjy7Vz' to 'pubmed-result.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:44:01 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed-result.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:44:01 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phplYBqez' to 'pubmed-result.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:44:17 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed-result.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:44:17 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phpgbuB7q' to 'pubmed-result.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:51:16 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed-result.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:51:16 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phpM0QeWa' to 'pubmed-result.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:51:23 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed-result.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Thu Jun 29 23:51:23 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phpFbRbtg' to 'pubmed-result.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html
sh: -c: command not found
sh: -u: command not found
sh: -u: command not found
[Fri Jun 30 00:25:45 2006] [error] [client 127.0.0.1] PHP Warning:=20
session_destroy() [<a=20
href=3D'function.session-destroy'>function.session-destroy</a>]: Trying t=
o=20
destroy uninitialized session in /var/www/refdb/refdblogout.php on line=20
30, referer: http://localhost/refdb/refdbdbquery.php
sh: -c: command not found
sh: -u: command not found
sh: -u: command not found
[Fri Jun 30 00:33:46 2006] [error] [client 127.0.0.1] PHP Warning:=20
session_destroy() [<a=20
href=3D'function.session-destroy'>function.session-destroy</a>]: Trying t=
o=20
destroy uninitialized session in /var/www/refdb/refdblogout.php on line=20
30, referer: http://localhost/refdb/refdbadmin.php
[Fri Jun 30 00:34:02 2006] [error] [client 127.0.0.1] PHP Warning:=20
session_destroy() [<a=20
href=3D'function.session-destroy'>function.session-destroy</a>]: Trying t=
o=20
destroy uninitialized session in /var/www/refdb/refdblogout.php on line=20
30, referer: http://localhost/refdb/index.html
[Fri Jun 30 00:34:07 2006] [error] [client 127.0.0.1] PHP Warning:=20
session_destroy() [<a=20
href=3D'function.session-destroy'>function.session-destroy</a>]: Trying t=
o=20
destroy uninitialized session in /var/www/refdb/refdblogout.php on line=20
30, referer: http://localhost/refdb/refdbquery.html
[Fri Jun 30 00:39:57 2006] [error] [client 127.0.0.1] PHP Warning:=20
session_destroy() [<a=20
href=3D'function.session-destroy'>function.session-destroy</a>]: Trying t=
o=20
destroy uninitialized session in /var/www/refdb/refdblogout.php on line=20
30, referer: http://localhost/refdb/refdbquery.html
[Fri Jun 30 00:40:34 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Fri Jun 30 00:40:34 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phpYAU50H' to 'pubmed.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html
[Fri Jun 30 00:51:03 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file(pubmed.txt) [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
failed to open stream: Permission denied in /var/www/refdb/refdbadd.php=20
on line 111, referer: http://localhost/refdb/refdbadd.html
[Fri Jun 30 00:51:03 2006] [error] [client 127.0.0.1] PHP Warning:=20
move_uploaded_file() [<a=20
href=3D'function.move-uploaded-file'>function.move-uploaded-file</a>]:=20
Unable to move '/tmp/phposFZ3V' to 'pubmed.txt' in=20
/var/www/refdb/refdbadd.php on line 111, referer:=20
http://localhost/refdb/refdbadd.html

Any hint ?

Cheers,

St=E9phane

--=20
St=E9phane T=E9letch=E9a, PhD.                  http://www.steletch.org
Unit=E9 Math=E9matique Informatique et G=E9nome http://migale.jouy.inra.f=
r/mig
INRA, Domaine de Vilvert                  T=E9l : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

Re: [Refdb-users] Does the edit button actually work in the php version of refdb?

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

Daniel O'Donnell <dan...@ul...> was heard to say:

> In keeping with the general tone of "let's get the user interfaces up" I
> wouldn't mind working on this as I can--really only learning PHP; my
> only real skills are XML and XSLT.
>

You're more than welcome to tackle this. The PHP web interface is certainly much
easier to extend than the previous C implementation.

> I've been playing with phpyaz as well--though I'm having trouble with
> it ;). I think on the basis of the demos that it might be possible not
> only to build an edit in php for refdb--shouldn't be too hard, I
> think--but also integrate z39.50 searching.
>

Cool.

> The main thing that would need work I think would be the piping. Yaz can
> output in USMARC or an XML equivalent. We'd need something to run the
> yaz output into the refdb dbase.
>

I don't know in which form phpyaz provides the retrieved data, but it should be
possible to send the result to a pipe. You should be able to use marc2ris as a
filter to pipe the data directly into refdbc.

regards,
Markus

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

Re: [Refdb-users] Does the edit button actually work in the php version of refdb?

[Daniel O'D. <dan...@ul...>]

In keeping with the general tone of "let's get the user interfaces up" I
wouldn't mind working on this as I can--really only learning PHP; my
only real skills are XML and XSLT.

I've been playing with phpyaz as well--though I'm having trouble with
it ;). I think on the basis of the demos that it might be possible not
only to build an edit in php for refdb--shouldn't be too hard, I
think--but also integrate z39.50 searching.

The main thing that would need work I think would be the piping. Yaz can
output in USMARC or an XML equivalent. We'd need something to run the
yaz output into the refdb dbase.

-d

On Thu, 2006-29-06 at 22:31 +0200, Markus Hoenicka wrote:
> Daniel O'Donnell writes:
>  > Been experimenting with the php version of refdb.
>  > 
>  > Everything seems to work except for the [edit] button, which produces
>  > errors. Does anybody know if it is supposed to work? Looking the code,
>  > over I'd have said it was a deletion button rather than an edit button!
>  > 
> 
> I'm afraid you're right. There is no "edit" action implemented in
> refdb-prl-del.php which is supposed to handle this request. Tom, are
> you listening? Any chance to get this implemented anytime soon?
> 
> regards,
> Markus
> 
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

[Refdb-users] Does the edit button actually work in the php version of refdb?

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

Daniel O'Donnell writes:
 > Been experimenting with the php version of refdb.
 > 
 > Everything seems to work except for the [edit] button, which produces
 > errors. Does anybody know if it is supposed to work? Looking the code,
 > over I'd have said it was a deletion button rather than an edit button!
 > 

I'm afraid you're right. There is no "edit" action implemented in
refdb-prl-del.php which is supposed to handle this request. Tom, are
you listening? Any chance to get this implemented anytime soon?

regards,
Markus

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

[Refdb-users] Does the edit button actually work in the php version of refdb?

[Daniel O'D. <dan...@ul...>]

Been experimenting with the php version of refdb.

Everything seems to work except for the [edit] button, which produces
errors. Does anybody know if it is supposed to work? Looking the code,
over I'd have said it was a deletion button rather than an edit button!

-d
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] marc2ris.pl

[Daniel O'D. <dan...@ul...>]

It's working Markus, thanks.

-d

On Tue, 2006-27-06 at 22:57 +0200, Markus Hoenicka wrote:
> make && make install
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

[Refdb-users] [Refdb-devel] jEdit interface to RefDB

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

Damien Jade Duff writes:
 > I am planning to make some improvements to my basic jEdit RefDB 
 > interface and since maybe one day this might be useful to someone else, 
 > I think I'm justified in seeing if anyone wants to comment before I get 
 > up to my armpits in the technical details of java GUI building. If 
 > you're interested in jEdit GUIs for RefDB, read on.
 > 

First of all, any attempts at a graphical interface to RefDB are
greatly appreciated. I know that not everyone is fond enough of Emacs
(or vim) to use the existing interfaces.

 > Incidentally, in order to create links directly between xnotes at 
 > present I would have to create dummy references for these to point to. 
 > Is this sensible, or am I trying to push the system too far?  (i.e. as 
 > well as keeping a bibliography I want to use the system to keep notes 
 > and it seems nearly adapted to this in structure). Whaddya reckon?
 > 

You mean linking notes to notes? I'd have to check whether this could
be supported natively.

 > The former has the advantage that it doesn't stretch jEdit's memory and 
 > is has a reasonably straightforward partial-synchronisation strategy. 
 > But it means that I need to impose more structure on my reference 
 > database so that I can browse it in a local fashion. refdbc does provide 
 > a facility for extracting the author list, keyword list, journal list, 
 > etc though unfortunately there is no facility for an anadorned list of 
 > citation keys or note keys (I could probably figure how to do this even 
 > though c gives me a headache, but perhaps it could be included in the 
 > next release...? Also, presumably titles are not indexed fields). I 
 > _think_ refdb should be fast enough if I choose my methods of data 
 > extraction right.
 > 

I could add functions that retrieve lists for citation keys, notes
keys, and essentially any other field that you may be interested
in. It will make the interface a bit clumsier though, as there will be
a variety of fairly specialized commands that are of no interest to
the regular command line user.

One thing that I've always been pondering is server-side paging. I
don't know whether you had something similar in mind, but I feel
refdbd should be able to return the results of queries in chunks of an
arbitrary size. This way, a graphical app could request e.g. the
results 11-20 of a query without having to cache the remaining 5000
hits. This should be doable as long as SQL supports this (I think it
does).

regards,
Markus

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

Re: [Refdb-users] marc2ris.pl

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

Dan O'Donnell writes:
 > Oh that's good to hear (I mean that it wasn't me). I thought I'd messed
 > up the paths perhaps somehow and was about to reinstall everything!
 > 

No complete reinstall required this time :-) I've checked in a fixed
version of marc2ris.in which works with the latest version of
MARC::Charset as of today. If you use the Subversion version, please
update your working copy. If you use a release tarball, please use the
following link to download marc2ris.in:

http://svn.sourceforge.net/viewcvs.cgi/refdb/refdb/trunk/scripts/marc2ris.in?view=markup&rev=43

(all in one long line, glue it back together if your mail agent
chopped it).

Please copy the file into the /scripts subdirectory of your sources
and run make && make install.

regards,
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.7 released

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

Rich Shepard writes:
 >    Are you working over the weekend because your city has been invaded by the
 > World Cup?
 > 

No, the city where I work is not one of the places suffering from
this kind of invasion. However, later this year the Pope is going to
spend a day here, and this (or rather the crowds he is going to
attract) are a good reason to leave town for sure.

regards,
Markus

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

Re: [Refdb-users] marc2ris.pl

[Dan O'D. <dan...@ul...>]

On Tue, 2006-27-06 at 09:30 +0200, Markus Hoenicka wrote:
> Dan O'Donnell <dan...@ul...> was heard to say:
> 
> > > Can't locate object method "new" via package "MARC::Charset"
> > > at /usr/local/bin/marc2ris line 90.
> > >
> >
> 
> I missed that in your original post. I'm afraid the MARC::Charset module was
> rewritten entirely. I've checked out the latest version from CPAN (0.95), and
> it does not have much in common with the version I've got installed here (0.2).
> I think I'll have to rewrite marc2ris using the new version. The module used to
> allow to create a charset object, but the new version only exports two
> conversion functions. Please allow me a day or two to fix this.

Oh that's good to hear (I mean that it wasn't me). I thought I'd messed
up the paths perhaps somehow and was about to reinstall everything!

-d

> 
> > BTW. I don't thank you enough for this software, Markus. It really is
> > quite neat now that I've mostly got it running.
> >
> 
> Much appreciated!
> 
> regards,
> Markus
> 
> 

Re: [Refdb-users] marc2ris.pl

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

Dan O'Donnell <dan...@ul...> was heard to say:

> > Can't locate object method "new" via package "MARC::Charset"
> > at /usr/local/bin/marc2ris line 90.
> >
>

I missed that in your original post. I'm afraid the MARC::Charset module was
rewritten entirely. I've checked out the latest version from CPAN (0.95), and
it does not have much in common with the version I've got installed here (0.2).
I think I'll have to rewrite marc2ris using the new version. The module used to
allow to create a charset object, but the new version only exports two
conversion functions. Please allow me a day or two to fix this.

> BTW. I don't thank you enough for this software, Markus. It really is
> quite neat now that I've mostly got it running.
>

Much appreciated!

regards,
Markus


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

Re: [Refdb-users] marc2ris.pl

[Dan O'D. <dan...@ul...>]

On Mon, 2006-26-06 at 23:06 +0200, Markus Hoenicka wrote:

> 
> I'm sorry for the confusion that I've caused here (once again). The
> Perl scripts used to have a .pl suffix as mentioned in the
> tutorial. However, I've been told that such a suffix causes scripts
> and other stuff to fail if you re-implement a tool in a different
> language. Hence I dropped the .pl suffix.
> 
> You just have to run marc2ris instead of marc2ris.pl (and med2ris,
> en2ris and so on).

Yes, it is working both ways now. But not the new() problem. Any
suggestions?


> Can't locate object method "new" via package "MARC::Charset"
> at /usr/local/bin/marc2ris line 90.
> 

BTW. I don't thank you enough for this software, Markus. It really is
quite neat now that I've mostly got it running.

-d

> 
> regards,
> Markus
> 

Re: [Refdb-users] marc2ris.pl

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

Rich Shepard writes:
 >    Aha! Progress. If you look at /usr/bin/marc2ris (with a pager), does the
 > first line contain:
 > 
 > #!/usr/bin/perl
 > 
 > ? I don't know if the perl interpreter wants the extension on the filename or
 > doesn't care.
 > 
 >    Next thing I'd check is the reaction when I add .pl to /usr/bin/marc2ris. I
 > suspect that perl cannot find or recognize the script you're asking it to
 > run.
 > 

I'm sorry for the confusion that I've caused here (once again). The
Perl scripts used to have a .pl suffix as mentioned in the
tutorial. However, I've been told that such a suffix causes scripts
and other stuff to fail if you re-implement a tool in a different
language. Hence I dropped the .pl suffix.

You just have to run marc2ris instead of marc2ris.pl (and med2ris,
en2ris and so on).

regards,
Markus

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

Re: [Refdb-users] marc2ris.pl

[Rich S. <rsh...@ap...>]

On Mon, 26 Jun 2006, Dan O'Donnell wrote:

> Well no, it isn't showing up with locate, even after updating the database.
> I get /usr/bin/marc2ris, and an example configuration, but no .pl file.

Dan,

   Aha! Progress. If you look at /usr/bin/marc2ris (with a pager), does the
first line contain:

#!/usr/bin/perl

? I don't know if the perl interpreter wants the extension on the filename or
doesn't care.

   Next thing I'd check is the reaction when I add .pl to /usr/bin/marc2ris. I
suspect that perl cannot find or recognize the script you're asking it to
run.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] marc2ris.pl

[Dan O'D. <dan...@ul...>]

On Mon, 2006-26-06 at 12:27 -0700, Rich Shepard wrote:
> On Mon, 26 Jun 2006, Dan O'Donnell wrote:
> 
> Dan,
> 
>    You can use 'locate marc2ris.pl' to find the file on your system, correct?

Well no, it isn't showing up with locate, even after updating the
database. I get /usr/bin/marc2ris, and an example configuration, but
no .pl file. 

> 

>    Did you use CPAN to install that module?

Yes. MARC:Char is installed from CPAN.


>    I've no need to access on-line bibliographies so I've no real world
> experience with marc2ris. But, it looks like a permission or missing module
> problem to me.

I'm thinking it is a module problem too, but can't see how to get round
it if it lies in refdbperlmod.  But, so far everything that's gone wrong
has been my fault ;)!



-d

> 
> Rich
> 

Re: [Refdb-users] marc2ris.pl

[Rich S. <rsh...@ap...>]

On Mon, 26 Jun 2006, Dan O'Donnell wrote:

> 1) Trying the example exactly:
> dan@caedmon:~/downloads/yaz-2.1.22$ marc2ris.pl knuth.loc.usmarc >
> knuth.loc.ris
> -bash: marc2ris.pl: command not found

Dan,

   You can use 'locate marc2ris.pl' to find the file on your system, correct?

> 2) Specifying perl and perl5.8.7
> dan@caedmon:~/downloads/yaz-2.1.22$ perl marc2ris.pl knuth.loc.usmarc >
> knuth.loc.ris
> Can't open perl script "marc2ris.pl": No such file or directory

   The file is marked executable, yes? (chmod a+x marc2fis.pl)

> dan@caedmon:~/downloads/yaz-2.1.22$ perl5.8.7 marc2ris.pl
> knuth.loc.usmarc > knuth.loc.ris
> Can't open perl script "marc2ris.pl": No such file or directory

   You have execute permissions on the directory where the file is located,
yes?

> 3) Trying with /usr/local/bin/marc2ris
> dan@caedmon:~/downloads/yaz-2.1.22$ /usr/local/bin/marc2ris
> knuth.loc.usmarc > knuth.loc.ris
> Can't locate object method "new" via package "MARC::Charset"
> at /usr/local/bin/marc2ris line 90.

   Did you use CPAN to install that module?

   I've no need to access on-line bibliographies so I've no real world
experience with marc2ris. But, it looks like a permission or missing module
problem to me.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] marc2ris.pl

[Dan O'D. <dan...@ul...>]

Hi,

I'm sure this is a question I should be able to answer from the manual,
but I don't seem able to.

I've been going through the Tutorial model for converting marc to ris,
but can't get marc2ris.pl to run. Here's what I get:

1) Trying the example exactly:
dan@caedmon:~/downloads/yaz-2.1.22$ marc2ris.pl knuth.loc.usmarc >
knuth.loc.ris
-bash: marc2ris.pl: command not found

2) Specifying perl and perl5.8.7
dan@caedmon:~/downloads/yaz-2.1.22$ perl marc2ris.pl knuth.loc.usmarc >
knuth.loc.ris
Can't open perl script "marc2ris.pl": No such file or directory

dan@caedmon:~/downloads/yaz-2.1.22$ perl5.8.7 marc2ris.pl
knuth.loc.usmarc > knuth.loc.ris
Can't open perl script "marc2ris.pl": No such file or directory

3) Trying with /usr/local/bin/marc2ris
dan@caedmon:~/downloads/yaz-2.1.22$ /usr/local/bin/marc2ris
knuth.loc.usmarc > knuth.loc.ris
Can't locate object method "new" via package "MARC::Charset"
at /usr/local/bin/marc2ris line 90.

I'm sure I've missed something, but I have done my best to follow the
manual here. Is this evidence of an obvious problem in my installation
that I'm not seeing?

-d