refdb-users — List for RefDB users

[Refdb-users] ANN: refdb-svn deb now relects repository revision 107

[David N. <dav...@sw...>]

The RefDB svn Debian package has been updated and now reflects 
repository revision 107.

Regards,
David.

[Refdb-users] ANN: refdb-0.9.8-pre1 available

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

Hi,

I've uploaded a new prerelease of RefDB:

http://refdb.sourceforge.net/pre/refdb-latest.tar.gz

This prerelease tackles the following issues:

Bugfixes:

- using apostrophes in query strings is now possible if they're
  escaped by a backslash


Improvements:

- restored the ability to handle multiple databases in a LaTeX
  document

- changed the citation format in Latex to: \cite{dbname:citekey} (the
  "dbname:" prefix is optional. If it is missing, RefDB uses the
  default database specified for refdbib)

- LaTeX command characters are now properly escaped in all bibtex
  output

- a new script "bib2ris-utf8" simplifies import of bibtex data. The
  script sends the output of bib2ris through the new
  refdb_latex2utf8txt script to convert foreign character commands to
  Unicode characters and to remove all other LaTeX commands

- all character encoding-related defaults should now use UTF-8 

- allow multiple personal reference lists per user. A description of
  the feature is in the manual which is shipped with the tarball, or
  have a look at this brief writeup:
  http://mhoenicka.de/system-cgi/blog/index.php?itemid=792



I'm sure there are a couple of bugs to unearth. Please report any odd
behaviour to the list.

regards,
Markus

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

[Refdb-users] multiple personal reference lists explained

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

Hi,

I've added a brief description of the new mutiple personal reference
lists feature to my blog:

http://mhoenicka.de/system-cgi/blog/index.php?itemid=792

Remember that you need the current svn version to try this
feature. Debian users may use the latest refdb-svn package. Non-Debian
users may wish to wait for the next prerelease if building the app
from the svn sources is not an option. I plan to publish a prerelease
within the next couple of days.

regards,
Markus

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

[Refdb-users] Fwd: Re: ANN: refdb-svn debian package updated to repository revision 96

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

[ forgot to cc the list... ]

----- Weitergeleitete Nachricht von Markus Hoenicka
<mar...@mh...> -----
    Datum: Wed, 02 Aug 2006 13:04:33 +0200
    Von: Markus Hoenicka <mar...@mh...>
Antwort an: Markus Hoenicka <mar...@mh...>
 Betreff: Re: [Refdb-users] ANN: refdb-svn debian package updated to
repository	revision 96
      An: da...@ne...

Hi,

this time the packages are ahead of the sources, it seems! Repository version 96
contains the multiple personal list feature, but the docs are not yet up to
date. I'll post a short writeup later today so you can test this feature. I'll
then fix the docs and prepare a prerelease for those who don't use Debian.

regards,
Markus

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

----- Ende der weitergeleiteten Nachricht -----


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

[Refdb-users] ANN: refdb-svn debian package updated to repository revision 96

[David N. <dav...@sw...>]

Re: [Refdb-users] refdb-elisp Debian package broken?

[David N. <dav...@sw...>]

Hi Justus,

Justus Piater wrote:
> - How about separating the refdb deb package into refdb-server and
>   refdb-clients? Then, many users will just need to install the latter
>   on their machine. And, refdb-elisp should depend on refdb-clients.
>   

That's a good suggestion but, to be honest, it's not one I'm in a hurry 
to implement.  Markus has certainly made the option easier by providing 
the configure switches '--disable-server' and '--disable-clients'.  It 
is still, however, a non-trivial task.  The advantage of splitting them 
is obvious but not really all that significant.  After all, you don't 
have to run the server and you don't have to run the clients.  I'll 
likely get around to doing it when I have some spare time ;-) .  At the 
moment I'm working on updating the vim-docbk-xml packages to work with 
Vim 7.x and then will be working on a vim-latex version of the package.  
If there is significant demand for splitting the refdb package  ("I can 
use that now", not "yeah, sounds like a good idea") I'll get to it sooner.
> - If ted is only needed to display .rtf, I think refdb-elisp should
>   not depend on it (and probably not on xpdf and gv either), as other
>   choices exists.

Other choices do, indeed, exist but let me explain why I am forced to 
make a default choice on behalf of the package user.  Incidentally, this 
is where the limits of packaging become obvious in comparison to 
building from source.  When building from source Markus' configure 
script looks through all the likely rtf, pdf and ps viewers and picks 
the first one it finds.  For example, it looks in turn for the following 
rtf viewers -- openoffice.org, abiword, ted, Ted, kword, TextEdit, 
soffice, oowriter, openoffice.org-2.0.0, openoffice.org-1.1.4 write & 
openoffice.org.  When it finds a match it records it in the 
refdb-mode-config.el file.  If my reading of autotools documentation is 
correct, the build won't actually fail if none of the potential rtf 
viewers is detected by configure, but there will be no rtf viewer 
specified.  Same for the pdf and ps viewers.

That is the situation when building from source.  Obviously, this 
process does not occur on the user's machine when they install from a 
debian package.  I have to decide ahead of time what default viewers to 
set in refdb-mode-config.el and force them to be available on the user's 
machine by declaring a dependency on them.  One of the primary goals of 
creating a package is to provide users with a fully functioning 
application "out of the box".  They will rightly expect all operations 
explained in the manual to work after the install.  The manual says 
certain keypresses will transform their document into pdf, ps or pdf 
format and display it in viewers.  If I follow your advice and specify 
nothing in refdb-mode-config.el that functionality will not be present 
after install.

So, I force dependencies on gv, xpdf and ted to ensure full 
functionality of the application.  Why did I pick them?  Because they 
are the smallest applications I could find that did the job well.  It's 
a trade-off: full functionality "out-of-the-box" at the cost of forcing 
the install of three small apps some people may never use.

In short, I have to follow the application's build and install process 
and ensure the package reflects that.  Since the build process examines 
the user's system and picks certain viewers, I have to do that also.  
The dependencies simply ensure my choice is always valid.

Incidentally, if you want to change the default viewers, all you have to 
do is edit refdb-mode-config.el.  Please note the following extract from 
the README.Debian file included in the package:
---------------------------------------------------------------------------------------
3. Default viewers

The following are the default viewers:

pdf = xpdf
ps  = gv
rtf = ted

These can be changed by editing the configuration file
'/etc/refdb-mode-config.el'.
---------------------------------------------------------------------------------------

At the moment I have no plans to remove the use of these default viewers 
or, therefore, the dependence on these apps' packages.

Regards,
David.

Re: [Refdb-users] phpweb and autotool woes

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

On Sat, July 29, 2006 9:50 pm, Justus Piater wrote:
> Hi -
>
> I've installed refdb-0.9.7 from source and started to play with the
> PHP interface, and it gladly accepts any bogus logins and nonexistent
> databases without complaining. Before digging into the code, I noticed
> that the PHP code has evolved quite a bit since the latest release, so
> I decided to try refdb-svn.

The latest svn version of phpweb is largely a cosmetic change (from the
point of view of the php) from what was there for most of the last year or
so. As far as I am aware, there were no php coding changes. I got rid of
the tables and made the html largely xhtml 1.0 conformant.

As Markus said, I'm in the middle of a fundamental rewrite of the php
version. This new version works with the default php.ini (i.e.
particularly register_globals=off). But it isn't in the SVN yet because it
is no where near being modular year, has not been checked for security,
and is still subject to complete rewrites as I work my way through the
various operations. As soon as I have roughed in the complete set of
essential operations and checked for security issues, I'll put it in svn.

> About phpweb: It requires a rather specific php.ini setup for session
> handling. For example, it requires register_globals to be On, which is
> against the recommendations. Other settings may clash with
> requirements by other sites on the same server. What would it take to
> remove these restrictive session-handling requirements
> (register_globals, cookies, auto_start)?

The register_globals=on setting is there because the current svn version
is not declaring session variables. It is a simple matter to change this,
though a bit of typing. You need to declare all the form variables as
session variables and then you can turn register_globals=off. I'm not sure
what you you mean about the cookies and auto-start. Weren't they default
settings? I guess no longer remember.

>
> Thanks,
> Justus
>
> --
> Justus H. Piater, Ph.D.         http://www.montefiore.ulg.ac.be/~piater/
> Institut Montefiore, B28        Phone: +32-4-366-2279
> Université de Liège, Belgium    Fax:   +32-4-366-2620
>
> -------------------------------------------------------------------------
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>


-- 
Daniel Paul O'Donnell
Director, Digital Medievalist Project (http://www.digitalmedievalist.org/)
Associate Professor of English
University of Lethbridge
Lethbridge AB T1K 3M4
Tel. +1 (403) 329-2377
Fax. +1 (403) 382-7191

(@webmail)

Re: [Refdb-users] refdb-elisp Debian package broken?

[Justus P. <Jus...@UL...>]

David Nebauer <dav...@sw...> wrote on Sun, 30 Jul 2006
09:33:53 +0930:

> I've uploaded the new package and it is now available.  Both Marcus and=20
> I have successfully installed it.  Please note you may have to run Emacs=
=20
> twice after installation before the refdb and ris modes become=20
> available.  If this is necessary it is due to a bootstrapping problem.

Thanks! Installs without problems, and after restarting emacs,
customize-group refdb works as expected. I don't have a local setup
yet to test further, because the server runs on a different machine,
which leads me to the first of the following suggestions:

- How about separating the refdb deb package into refdb-server and
  refdb-clients? Then, many users will just need to install the latter
  on their machine. And, refdb-elisp should depend on refdb-clients.

- If ted is only needed to display .rtf, I think refdb-elisp should
  not depend on it (and probably not on xpdf and gv either), as other
  choices exists.

Great work!
Justus

--=20
Justus H. Piater, Ph.D.         http://www.montefiore.ulg.ac.be/~piater/
Institut Montefiore, B28        Phone: +32-4-366-2279
Universit=C3=A9 de Li=C3=A8ge, Belgium    Fax:   +32-4-366-2620

Re: [Refdb-users] phpweb and autotool woes

[David N. <dav...@sw...>]

Hi Justus,

Justus Piater wrote:
> I decided to try refdb-svn. However, various combinations of different
> versions of the autotools failed for different reasons.
>
> - Which versions of the autotools should I use?
>
> - I suggest you hard-code the proper versions inside the refdb-svn
>   script.

I'll have to echo Markus on this.  On occasions in the past I have 
encountered refdb build problems after doing a bulk package update.  
Lengthy investigation pins the blame on autotools which turns out to 
have been one of the packages updated.  Markus then performs some 
autotools wizardry on the source and the problem is fixed -- for me and 
every other user of that version of autotools.

I don't want to hard-code the required version(s) of autotools in the 
script because:
    1. The required version may differ across platforms,
    2. It becomes a maintenance issue since I have to test every new 
version of autotools
       on every platform to see if refdb builds successfully, and
    3. Since the goal is that refdb builds on every (fairly recent) 
version of autotools
       the problem is with the source and not the autotools themselves.

If you are experiencing build problems due to an autotools 
incompatibility I urge you to work with Markus to fix the root cause.  
This will solve the problem for all users sharing your system configuration.

Regard,
David.

Re: [Refdb-users] refdb-elisp Debian package broken?

[David N. <dav...@sw...>]

Hi Justus,

Justus Piater wrote:
> I attempted to install the latest refdb-elisp deb (1.3-3), and it
> fails to install. The very files refdb-mode.el and ris.el (at least)
> do not appear to be installed.

It's worse then you suspected.  The two '.el' files were not even 
included in the debian package.  It is a mystery to me as to how that 
happened and I apologise for the inconvenience it caused.  I've rebuilt 
the package using the same build system and the new package contains the 
previously missing files.

I've uploaded the new package and it is now available.  Both Marcus and 
I have successfully installed it.  Please note you may have to run Emacs 
twice after installation before the refdb and ris modes become 
available.  If this is necessary it is due to a bootstrapping problem.

Let me know how you go.

Regards,
David.

[Refdb-users] phpweb and autotool woes

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

Hi,

Justus Piater writes:
 > Hi -
 > 
 > I've installed refdb-0.9.7 from source and started to play with the
 > PHP interface, and it gladly accepts any bogus logins and nonexistent
 > databases without complaining. Before digging into the code, I noticed
 > that the PHP code has evolved quite a bit since the latest release, so
 > I decided to try refdb-svn. However, various combinations of different
 > versions of the autotools failed for different reasons.

First of all, we all should give Dan a little leeway while he's
fiddling with the PHP interface. The current svn versions of the PHP
files are more than two weeks old, and Dan has showed off a more
recent version in a previous post which isn't in svn yet. The
interface is simply not done yet.

 > 
 > - Which versions of the autotools should I use?
 > 

I'm not sure about which versions work. It would be easier to find out
if you could provide your versions and the exact error messages. On my
FreeBSD box the following versions work just fine:

autoconf 2.59
automake 1.8.5

 > - I suggest you hard-code the proper versions inside the refdb-svn
 >   script.
 > 

This will cause errors on even more systems which don't have these
versions installed. I'd rather analyze why newer or older versions
fail and fix the autotools-related files in RefDB accordingly.

 > - Can I simply move the phpweb tree from subversion into the 0.9.7
 >   release tree, and configure, make, install?
 > 

As far as I can tell this should work.

 > - It would also be useful to provide snapshot-tarballs to give easy
 >   access to the latest code without having to run the autotools.
 > 

I do this fairly frequently between releases. We sometimes had 7 or 8
prereleases between two official releases. The thing is that my code
is currently not in a state ready for a prerelease. I hope I'll get
round to finish one within a week or so.

 > About phpweb: It requires a rather specific php.ini setup for session
 > handling. For example, it requires register_globals to be On, which is
 > against the recommendations. Other settings may clash with
 > requirements by other sites on the same server. What would it take to
 > remove these restrictive session-handling requirements
 > (register_globals, cookies, auto_start)?
 > 

I'll leave this to Dan.

regards,
Markus

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

[Refdb-users] phpweb and autotool woes

[Justus P. <Jus...@UL...>]

Hi -

I've installed refdb-0.9.7 from source and started to play with the
PHP interface, and it gladly accepts any bogus logins and nonexistent
databases without complaining. Before digging into the code, I noticed
that the PHP code has evolved quite a bit since the latest release, so
I decided to try refdb-svn. However, various combinations of different
versions of the autotools failed for different reasons.

- Which versions of the autotools should I use?

- I suggest you hard-code the proper versions inside the refdb-svn
  script.

- Can I simply move the phpweb tree from subversion into the 0.9.7
  release tree, and configure, make, install?

- It would also be useful to provide snapshot-tarballs to give easy
  access to the latest code without having to run the autotools.

About phpweb: It requires a rather specific php.ini setup for session
handling. For example, it requires register_globals to be On, which is
against the recommendations. Other settings may clash with
requirements by other sites on the same server. What would it take to
remove these restrictive session-handling requirements
(register_globals, cookies, auto_start)?

Thanks,
Justus

--
Justus H. Piater, Ph.D.         http://www.montefiore.ulg.ac.be/~piater/
Institut Montefiore, B28        Phone: +32-4-366-2279
Universit=C3=A9 de Li=C3=A8ge, Belgium    Fax:   +32-4-366-2620

[Refdb-users] ANN: refdb-svn (rev. 94)

[David N. <dav...@sw...>]

The refdb-svn debian package has been updated to repository revision 94.

Regards,
David.

Re: [Refdb-users] refdbib and bibtex

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

Hi,

J.I...@uv... was heard to say:

> Could not set terminal attributes

This is most likely caused by a missing password in your ~/.refdbibrc. runbib
calls refdbib as part of a pipe, and if there is no password specified, or a
"*"  instead of a password, refdbib tries to ask for a password interactively.
This fails because data are sent through stdin. Please enter your password into
~/.refdbibrc, or add an empty entry like:

passwd

as you seem to run sqlite which does not require a password anyway.

> SELECT ID from CITSTYLE where JOURNAL='bibtex-abbrev'
> select failed

It seems like the style "bibtex-abbrev" has not been added to the refdb
database. Please look at the manual section describing the addstyle command,
and add all styles installed in /usr/local/share/refdb/styles to the database.

NB the refdb-init script which ships with the latest version should add these
styles automatically.

regards,
Markus


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

[Refdb-users] escaping apostrophes (partly fixed)

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

Markus Hoenicka writes:
 > I'll have to fix (or at least test) related commands like getkw, getau
 > and so on as well. This is likely to happen over the weekend.
 > 

FYI getkw, getau, getjo et al are now supposed to work as well with values
containing apostrophes, see the latest svn version.

regards,
Markus

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

[Refdb-users] refdb-elisp Debian package broken?

[Justus P. <Jus...@UL...>]

Hi -

I attempted to install the latest refdb-elisp deb (1.3-3), and it
fails to install. The very files refdb-mode.el and ris.el (at least)
do not appear to be installed. Here's the installation log:

Setting up refdb-elisp (1.3-3) ...
emacsen-common: Handling install of emacsen flavor emacs
emacsen-common: Handling install of emacsen flavor emacs21
emacsen-common: byte-compiling for emacs21
Loading 00debian-vars (source)...
Loading 20gnus-init (source)...
Loading 49url (source)...
Loading 50auctex (source)...
Loading auctex.el (source)...
Loading /usr/lib/emacs/21.4/i486-linux-gnu/fns-21.4.1-x.el (source)...
Loading preview-latex.el (source)...
Loading 50autoconf (source)...
Loading 50dictionaries-common (source)...
Loading debian-ispell...
Loading /var/cache/dictionaries-common/emacsen-ispell-default.el (source)...
Loading /var/cache/dictionaries-common/emacsen-ispell-dicts.el (source)...
Loading 50gnuplot-mode (source)...
Loading 50gnuserv (source)...
Loading 50lilypond-data (source)...
Loading 50mmm-mode (source)...
Loading 50octave2.1-emacsen (source)...
Loading 50psgml-init (source)...
Loading 50psvn (source)...
Loading 50pymacs (source)...
Loading 50python-mode (source)...
Loading 50refdb-elisp (source)...
Error while loading 50refdb-elisp
Loading 50tramp (source)...
Loading 50w3m-el (source)...
Wrote /etc/emacs21/site-start.d/00debian-vars.elc
Wrote /usr/share/emacs21/site-lisp/debian-startup.elc
Done
install/refdb-elisp: Handling install for emacsen flavor emacs21
/usr/lib/emacsen-common/packages/install/refdb-elisp: line 34: cd: /usr/sha=
re/emacs/site-lisp/refdb-elisp: No such file or directory
emacs-package-install: /usr/lib/emacsen-common/packages/install/refdb-elisp=
 emacs21 emacs21 failed at /usr/lib/emacsen-common/emacs-package-install li=
ne 30, <TSORT> line 2.
dpkg: error processing refdb-elisp (--configure):
 subprocess post-installation script returned error exit status 1


--=20
Justus H. Piater, Ph.D.         http://www.montefiore.ulg.ac.be/~piater/
Institut Montefiore, B28        Phone: +32-4-366-2279
Universit=C3=A9 de Li=C3=A8ge, Belgium    Fax:   +32-4-366-2620

[Refdb-users] RefDB rpm available for Mandriva

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

I've uploaded it yesterday but since Mandriva has suffered some hw=20
failures (it was really warm in France the last two weeks), it may be=20
delayed on some mirrors.

I've made my best to produce a correct rpm (and done some thorough tests=20
on it), and you can find the rpm spec file at:
http://cvs.mandriva.com/cgi-bin/viewvc.cgi/contrib-SPECS/refdb/refdb.spec=
?revision=3D1.1&view=3Dmarkup

The rpm itself requires some dependancies available on the Mandriva=20
mirrors (you can easily set them up using http://easurpmi.zarb.org) but=20
for the moment, you'll need to use the cooker (development) tree for=20
getting them.

Fortunate Mandriva users will need to setup the mirrors and only do:
urpmi refdb.

For others (RedHat, Suse, ...), you can find below the list of=20
dependancies needed (you'll either need to find them in your=20
distribution of use the below rpms).

I'm going for holidays and i'll be back in the third week of august so=20
don't hesitate to test the rpm!

I'll try do do more specific rpms later (for Release 2006, for RedHat,=20
and may be Suse), but you can give a go to the already existing rpms.

If you find my bugs (i'm sure there are some ...), you can use the=20
Mandriva's bugzilla to report them (http://qa.mandriva.com, juste=20
register and post your complaints ;-))

For RedHat/Suse, you may need to use the trigger --no-scripts for=20
installing it, i.e. :
rpm -ivh --no-scripts refdb-0.9.7-1mdv2007.0.i586.rpm

Have a nice day, see U soon !

St=E9phane T=E9letch=E9a

List of available (and needed rpms):

ftp://ftp.proxad.net/pub/Distributions_Linux/MandrivaLinux/devel/cooker/c=
ooker/media/contrib/release/

You'll need at least:
* refdb-0.9.7-1mdv2007.0.i586.rpm (the server itself)
* refdb-clients-0.9.7-1mdv2007.0.i586.rpm (containing refdba, redbc and=20
refbib, artificial separation
and the dependancies:
* btparse-0.35-3mdv2007.0.i586.rpm
* libdbi-drivers-dbd-pgsql-0.8.0-2mdk.i586.rpm or=20
libdbi-drivers-dbd-sqlite-0.8.0-2mdk.i586.rpm (according to your databse=20
selection)
* libdbi0-0.8.0-1mdk.i586.rpm
* perl-RefDB-perlmod-0.4.1-2mdv2007.0.noarch.rpm
* perl-MARC-Charset-0.95-2mdv2007.0.noarch.rpm
* perl-MARC-Record-1.38-2mdv2007.0.noarch.rpm
* perl-Term-Clui-1.35-2mdv2007.0.noarch.rpm
* perl-Text-Iconv-1.4-3mdv2007.0.i586.rpm
* perl-XML-Parser-EasyTree-0.01-8mdv2007.0.noarch.rpm or=20
perl-XML-Parser-Lite-Tree-0.03-3mdv2007.0.noarch.rpm)

You'll also need:

ftp://ftp.proxad.net/pub/Distributions_Linux/MandrivaLinux/devel/cooker/c=
ooker/media/contrib/release/

* apache-mod_php-5.1.4-2mdv2007.0.i586.rpm

But it also has some prerequisites ...

--=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

[Refdb-users] escaping apostrophes (partly fixed)

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

Hi all,

Dan reported recently that there is a problem running queries
containing e.g. author names with an apostrophe. The tokenizing
functions simply didn't handle escaped apostrophes at all, making this
a bit of a pain.

I've implemented the missing code for the getref command. In order to
query for values containing apostrophes, do the following:

interactive mode:

Putting the value in quotes is not necessary as the backslash is
passed to the server as is. However, it does not hurt, so both of
these work:

refdbc: getref :AU:=E\'ccles,P.
refdbc: getref :AU:="E\'ccles,P."

command line:

Keep in mind that the shell consumes the backslash unless it is
protected by quotes:

refdbc -C getref :AU:="E\'ccles,P."

I'll have to fix (or at least test) related commands like getkw, getau
and so on as well. This is likely to happen over the weekend.

regards,
Markus

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

[Refdb-users] refdbib and bibtex

[<J.I...@uv...>]

Hi.

I have a problem when generating a bibliography in bibtex format. When I
run runbib (runbib -d mydb -E UTF-8 -S bibtex-abbrev -t bibtex -u josep
tesi060721.aux), the following message appears:

Could not set terminal attributes
999:17 retrieved:17 failed

Then, I run refdbib with -e 0 -l 7, and the following message appeared:

refdbib started
gettexbib  -u josep -d arsbiologica -s bibtex-abbrev 291
Marn2002 Altschul1990 Thompson1997 Saitou1987 Yeh2001 Delcher1999
Nicholas1997 Altschul1990 Altschul1990 Edgar2004 Altschul1990
Altschul1990 Altschul1990 Altschul1990 Saitou1987 Thompson1997 Kumar2004
Arnau2006 Zdobnov2001 Quevillon2005 Bateman2004 Finn2006 Wu2006
Orlev2004 Batagelj1998
999:25 retrieved:25 failed
refdbib finished

Why did it fail? The resulting bib file is empty. Below I copy part of
the output in the shell running refdbd. Could anyone please help me? Thanks

J. Ignasi.

refdb
connected to database server using database:
refdb
SELECT ID from CITSTYLE where JOURNAL=3D'bibtex-abbrev'
select failed
SELECT DISTINCT t_refdb.refdb_id, t_refdb.refdb_citekey,
t_refdb.refdb_type, t_refdb.refdb_pubyear, t_refdb.refdb_startpage,
t_refdb.refdb_endpage, t_refdb.refdb_abstract, t_refdb.refdb_title,
t_refdb.refdb_volume, t_refdb.refdb_issue, t_refdb.refdb_booktitle,
t_refdb.refdb_city, t_refdb.refdb_publisher, t_refdb.refdb_title_series,
t_refdb.refdb_address, t_refdb.refdb_issn, t_refdb.refdb_periodical_id,
t_refdb.refdb_pyother_info, t_refdb.refdb_secyear,
t_refdb.refdb_secother_info, t_refdb.refdb_user1, t_refdb.refdb_user2,
t_refdb.refdb_user3, t_refdb.refdb_user4, t_refdb.refdb_user5,
t_refdb.refdb_misc1, t_refdb.refdb_misc2, t_refdb.refdb_misc3 FROM
t_refdb WHERE t_refdb.refdb_citekey=3D'Zdobnov2001'
localhost
josep
*
arsbiologica

sqlite3
/usr/local/var/lib/refdb/db

refdb
connected to database server using database:
refdb
SELECT ID from CITSTYLE where JOURNAL=3D'bibtex-abbrev'
select failed
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
server waiting n_max_fd=3D4

Re: [Refdb-users] phpweb interface HAS a problem for me, and for you ?

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

[...second attempt...]

[cc'ing the list as this might be of common interest...]

Hi Dan,

Daniel O'Donnell writes:
 > I was thinking of setting up a "Preferences" section that would allow
 > users to place some cookies saying how they want certain things to
 > behave. It could be added there. Or we could build an initial "install"
 > page (like mediawiki does) that allows administrators to specify what
 > dbase they are using and other things like that.
 > 

Another option is to use the refdb-init script which could perform
these customizations once it is at it.

 > Actually I was thinking along the same lines and have been debating the
 > best way of doing it. What I was thinking was a) using drop down lists
 > (collected by running getau, getkw, etc) whenever users are supposed to
 > enter information that might already be in the dbase--with a blank text
 > input field beside the drop down list for info that is new to the
 > database. This would be in the addref page and involve AU, JF, JO, KW,
 > and maybe BT.
 > 

Emacs refdb-mode handles this in a similar fashion. You can enter
authors, keywords, and periodical names with tab completion, or just
type in something new.

 > and b) building links so that clicking say on an author name actually
 > runs :AX:<author name>.
 > 

refdb-mode is a little more advanced here, but this is possible only
because it is part of an editor. You can highlight any word or phrase
and use it as the target of a query (author, citation key, title,
keyword, whatever).

 > The second isn't hard, I don't think, though my PHP is still new. The
 > first wouldn't be either, I don't think, but generating them on the fly
 > might cause speed issues. I'm thinking either adding an "update indices"
 > at the beginning and end of the session with perhaps automatic adding
 > whenever something is added or deleted. The drop down lists would then
 > be premade.
 > 

refdb-mode updates teh internal completion lists whenever a command is
run that alters the database (add|update|delete). I don't know whether
these lists can be made persistent in a similar fashion in
PHP. Updating these lists is a speed issue with larger databases and
slow database engines.

 > The only thing that would affect the design of this, I think, is whether
 > or not we decide to allow multiple personal lists (which I'd like, it is
 > a feature of both Procite and Refworks).

I've been thinking about this for a while. I don't think it makes
sense to duplicate a feature that is already possible with extended
notes. Instead, I figured it should be possible to implement personal lists
transparently by abusing extended notes under the hood. Consider the
following command:

pickref 13

This would run the equivalent of the following client commands on the
server side:

addnote <empty template with title=username> (unless that note already
exists)

addlink :NID:=<id where title=username> :ID:=13

dumpref 13 would run the equivalent deletelink command. Up to here,
everything is entirely transparent to the end-user and perfectly
backwards-compatible.

To add a reference to a different personal list we'll need an
extension of the pickref command:

pickref -P mylist 15

This would run the equivalent of these commands on the server:

addnote <empty template with title=mylist> (unless that note already
exists)

addlink :NID:=<id where title=mylist> :ID:=15

So you'd be using extended notes without even having to know how to
write them. However, if you want to, you can of course retrieve these
notes with the getnote command, add a description or a few keywords,
and treat them just like any other extended note.

As easy as it sounds, please don't expect this feature to pop up
tomorrow. There's more to it on the programmer's end, like user
permissions and orphan cleanup.

 > I'm also still not sure how to
 > search (commandline or php) for words with apostrophes in them.

A quick test indicates that there must be some error in the code that
is supposed to escape and unescape apostrophes. I'll investigate this.

 
 > And
 > finally, I'm not sure that call number on AV is working out--sometimes
 > things have both a callnumber and AV. I wonder if we should decide on a
 > user-defined tag for it?
 > 

As always, we could make this a configurable option.

regards,
Markus

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

[Refdb-users] ANN: refdb-svn debian package updated to revision 92

[David N. <dav...@sw...>]

The refdb svn package was updated at approximately Mon Jul 24 10:07:55 
UTC 2006 to revision 92.

[Refdb-users] phpweb interface HAS a problem for me, and for you ?

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

Hi,

St=E9phane T=E9letch=E9a writes:
 > 4 - using the phpweb interface (i've checked my phpini parameters we=
re=20
 > there using phpinfo, apache has the good setup for refdb, i used=20
 > mod=5Fphp5 + php=5Fsession), i can use some functions:
 > =09* i can do some search (for instance Wang,J.P.) if the match is e=
xact=20
 > (it seems :AU:=3DWang,J.P works, :AU:~Wang,J.P doesn't)
 > =09* i'm not able to add references, edit them or remove them.

Both of these work here. Where did you type these queries in=3F

 > sqlite
[...]
 > SELECT DISTINCT t=5Frefdb.refdb=5Fid, t=5Frefdb.refdb=5Ftype,=20
 > t=5Frefdb.refdb=5Fpubyear, t=5Frefdb.refdb=5Fstartpage, t=5Frefdb.re=
fdb=5Fendpage,=20
 > t=5Frefdb.refdb=5Fabstract, t=5Frefdb.refdb=5Ftitle, t=5Frefdb.refdb=
=5Fvolume,=20
 > t=5Frefdb.refdb=5Fissue, t=5Frefdb.refdb=5Fbooktitle, t=5Frefdb.refd=
b=5Fcity,=20
 > t=5Frefdb.refdb=5Fpublisher, t=5Frefdb.refdb=5Ftitle=5Fseries,=20
 > t=5Frefdb.refdb=5Faddress, t=5Frefdb.refdb=5Fissn, t=5Frefdb.refdb=5F=
periodical=5Fid,=20
 > t=5Frefdb.refdb=5Fpyother=5Finfo, t=5Frefdb.refdb=5Fsecyear,=20
 > t=5Frefdb.refdb=5Fsecother=5Finfo, t=5Frefdb.refdb=5Fuser1, t=5Frefd=
b.refdb=5Fuser2,=20
 > t=5Frefdb.refdb=5Fuser3, t=5Frefdb.refdb=5Fuser4, t=5Frefdb.refdb=5F=
user5,=20
 > t=5Frefdb.refdb=5Fmisc1, t=5Frefdb.refdb=5Fmisc2, t=5Frefdb.refdb=5F=
misc3,=20
 > t=5Frefdb.refdb=5Fcitekey FROM t=5Frefdb WHERE refdb=5Ftype!=3D'DUMM=
Y' AND ALL=20
 > :AU:~Wang ORDER BY t=5Frefdb.refdb=5Fid

I'm afraid this query was somehow entered incorrectly into the web
interface as the syntax of the SQL is all wrong. Moreover, if you use
SQLite as backend, the SQL syntax for a regular expression match is
"LIKE", not "~".=20

 > In both case, there is the warning :
 > ""An invalid or out-of-range index was passed to libdbi""
 >=20

This warning is somewhat familiar, but I thought we got rid of it long
ago. Which libdbi version do you use=3F

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-users] phpweb interface HAS a problem for me, and for you ?

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

This time, i've done extensive tests but without more luck for getting=20
all phpweb functions working.

Here is in detail the procedure:
1 - I've uncompressed and installed refdb

2 - i've used the manual setup to install it, using SQLITE as a client=20
to avoid any database interference problem

3 - using refdba and refdbc i can connect to my refdb database (foo) and=20
perform searches, adding and deletions.

4 - using the phpweb interface (i've checked my phpini parameters were=20
there using phpinfo, apache has the good setup for refdb, i used=20
mod_php5 + php_session), i can use some functions:
	* i can do some search (for instance Wang,J.P.) if the match is exact=20
(it seems :AU:=3DWang,J.P works, :AU:~Wang,J.P doesn't)
	* i'm not able to add references, edit them or remove them.

On the web server log, i see 'select failed'.

I tried to run the refdbc in a debug mode (as staed in the manual) and=20
here are two logs where the query failed or was correct:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Failed query:
$$$$$$$$$$$$$
sqlite
/usr/local/var/lib/refdb/db

foo
SELECT meta_app,meta_type,meta_dbversion from t_meta
connected to database server using database:
foo
no character encoding conversion required
output encoding is:
UTF-8
SELECT DISTINCT t_refdb.refdb_id, t_refdb.refdb_type,=20
t_refdb.refdb_pubyear, t_refdb.refdb_startpage, t_refdb.refdb_endpage,=20
t_refdb.refdb_abstract, t_refdb.refdb_title, t_refdb.refdb_volume,=20
t_refdb.refdb_issue, t_refdb.refdb_booktitle, t_refdb.refdb_city,=20
t_refdb.refdb_publisher, t_refdb.refdb_title_series,=20
t_refdb.refdb_address, t_refdb.refdb_issn, t_refdb.refdb_periodical_id,=20
t_refdb.refdb_pyother_info, t_refdb.refdb_secyear,=20
t_refdb.refdb_secother_info, t_refdb.refdb_user1, t_refdb.refdb_user2,=20
t_refdb.refdb_user3, t_refdb.refdb_user4, t_refdb.refdb_user5,=20
t_refdb.refdb_misc1, t_refdb.refdb_misc2, t_refdb.refdb_misc3,=20
t_refdb.refdb_citekey FROM t_refdb WHERE refdb_type!=3D'DUMMY' AND ALL=20
:AU:~Wang ORDER BY t_refdb.refdb_id


select failed
child finished client on fd 5
child exited with code 1
server waiting n_max_fd=3D4

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Correct query:
$$$$$$$$$$$$$$

sqlite
/usr/local/var/lib/refdb/db

foo
SELECT meta_app,meta_type,meta_dbversion from t_meta
connected to database server using database:
foo
no character encoding conversion required
output encoding is:
UTF-8
SELECT DISTINCT t_xauthor.refdb_id FROM t_xauthor, t_author WHERE=20
t_author.author_id=3Dt_xauthor.author_id AND t_xauthor.xauthor_type=3D1 A=
ND=20
t_author.author_name =3D 'Wang,J.P.'
An invalid or out-of-range index was passed to libdbi
SELECT DISTINCT t_refdb.refdb_id, t_refdb.refdb_type,=20
t_refdb.refdb_pubyear, t_refdb.refdb_startpage, t_refdb.refdb_endpage,=20
t_refdb.refdb_abstract, t_refdb.refdb_title, t_refdb.refdb_volume,=20
t_refdb.refdb_issue, t_refdb.refdb_booktitle, t_refdb.refdb_city,=20
t_refdb.refdb_publisher, t_refdb.refdb_title_series,=20
t_refdb.refdb_address, t_refdb.refdb_issn, t_refdb.refdb_periodical_id,=20
t_refdb.refdb_pyother_info, t_refdb.refdb_secyear,=20
t_refdb.refdb_secother_info, t_refdb.refdb_user1, t_refdb.refdb_user2,=20
t_refdb.refdb_user3, t_refdb.refdb_user4, t_refdb.refdb_user5,=20
t_refdb.refdb_misc1, t_refdb.refdb_misc2, t_refdb.refdb_misc3,=20
t_refdb.refdb_citekey FROM t_refdb WHERE refdb_type!=3D'DUMMY' AND=20
t_refdb.refdb_id IN (1) ORDER BY t_refdb.refdb_id
An invalid or out-of-range index was passed to libdbi
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
server waiting n_max_fd=3D4
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

In both case, there is the warning :
""An invalid or out-of-range index was passed to libdbi""

But i may have missed something else ...

If you find something more, i have all the logs, but i don't want to=20
post them on the list until needed.

I've included as attachment some further information (the above logs +=20
refdbc trace, installed rpm for apache) just in case.

Any hint ?

BTW, since it is not a packaging issue, i'll release very soon the rpm=20
for refdb ;-)

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

[Refdb-users] non-refdb DB error messages

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

Hi Damien,

Damien Jade Duff writes:
 > acws-0175% refdbc -C getnote :NID:\>0
 > ERROR:  relation "t_note" does not exist
 > select failed
 > acws-0175%
 > 
 > ........................
 > 
 > ...I think it would be nicer in this case to produce information like in
 > the first case so that I can figure out the source of the error and
 > don't start think about sending silly messages to the refdb-users group...
 > 
 > ...feel free to disagree with me completely!
 > 

I've checked, and the code to do this is (almost) in place
anyway. Currently refdbd checks for a RefDB database only if you use
the selectdb command in an interactive session. Try that, and you
should get an error message which is a bit more informative than what
you saw.

Clearly, this doesn't help if you run the clients in batch mode. I
could make the db check mandatory for each database connection, but
this also means one additional query per client command. I guess I'll
have to figure out some switch which allows experienced users to turn
off this check in order to gain some speed.

regards,
Markus

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

[Refdb-users] non-refdb DB error messages

[Damien J. D. <D.J...@cs...>]

Gidday

Just one more itty-bitty suggestion for improvement.

If I run a command and specify the wrong refdb database so that it is a
database that does not exist, I get a sensible error message...

........................

acws-0175% refdbc -d thisiswrong -C getnote :NID:\>0
FATAL:  database "thisiswrong" does not exist
could not open reference database

........................

...but if I get a database that exists but is not a refdb database (in
this case the default database for this user), the error messages to
come back are table-not-found messages from the sql server...

........................

acws-0175% refdbc -C getnote :NID:\>0
ERROR:  relation "t_note" does not exist
select failed
acws-0175%

........................

...I think it would be nicer in this case to produce information like in
the first case so that I can figure out the source of the error and
don't start think about sending silly messages to the refdb-users group...

...feel free to disagree with me completely!

Peace
Damien