refdb-users — List for RefDB users

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

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

The refdb svn debian package has been updated.

Re: [Refdb-users] TY for webpages?

[Sergio P. <sp_...@ya...>]

Daniel O'Donnell:

> Is there a general RIS Type for webpages that is perhaps not
> documented? I'm finding I need to artificially try to squeeze
> web pages into arbitrary categories.

I'ld try ELEC, i.e. "Electronic Citation", and look to
http://www.apastyle.org/elecgeneral.html.
For example:

TY  - ELEC
A1  - Author, A.A.
T1  - Title of work
PY  - 2000//
UR  - url
N1  - Retrieved month, day, year
ER  - 

HTH

Sergio



Chiacchiera con i tuoi amici in tempo reale! 
 http://it.yahoo.com/mail_it/foot/*http://it.messenger.yahoo.com 

[Refdb-users] TY for webpages?

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

Hi all,

Is there a general RIS Type for webpages that is perhaps not documented?
I'm finding I need to artificially try to squeeze web pages into
arbitrary categories.

-d
-- 
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

[Refdb-users] xnote udpate with no links

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

Hi Damien,

Damien Jade Duff writes:
 > I have an eeny-weeny little problem that you'll probably be able to 
 > solve in the blink of an eye...
 > 

Well, it took me a little longer than that, but you uncovered a real
and stupid bug. While I was at it, I found a few more problems related
to that bug and fixed them too. The current svn version appears to
work ok with the data and the procedure that you described.

 > Incidentally, what are the chances of getting note-note links working so 
 > that I can create trees or even webs to navigate through my references 
 > (this is further to my thoughts on the best way to make a GUI interface 
 > via java/jedit)? I had a look at the t_xnote table and it seems you'd 
 > probably either want an extra table with bidirectional links or you'd 
 > update the existing one to be keyed by a note-link id rather than a note id.
 > 

I didn't really find the time to think about this request. I don't
think it is a big deal to change the databases to allow these links
(afait it boils down to allowing an additional type string in one of
the fields). The real problem is the recursive nature of retrieving
references and notes. If you retrieve stuff linked to a note in a
recursive fashion, you'll get references linked to notes that were
linked to the note that the specified note links to. It is just a
matter of getting this right.

regards,
Markus

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

[Refdb-users] xnote udpate with no links

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

Gidday Markus

I have an eeny-weeny little problem that you'll probably be able to 
solve in the blink of an eye...

I find on my system that if I insert an extended note (xnote) into the 
refdb database that does not have any links to references, the note is 
inserted okay, but I can no longer update it, even if the update is to 
add links to references.

The problem occurred on refdb-0.9.7-pre5 and I upgraded to refdb-0.9.7 
and I still got it.

I hope it's a bug that can be fixed. Details below.

Incidentally, what are the chances of getting note-note links working so 
that I can create trees or even webs to navigate through my references 
(this is further to my thoughts on the best way to make a GUI interface 
via java/jedit)? I had a look at the t_xnote table and it seems you'd 
probably either want an extra table with bidirectional links or you'd 
update the existing one to be keyed by a note-link id rather than a note id.

Thanks again for all your efforts so far!

Peace
Damien

Here is the output from refdbc:

---------------------------------------------

acws-01xx% cat testnotex.xml
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE xnoteset PUBLIC "-//Markus Hoenicka//DTD Xnote V1.2//EN"
"/usr/local/share/refdb/dtd/xnote.dtd"
[
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
]>
<xnoteset>
         <xnote citekey="TEST123" user="djd">
                 <content>
                         This is a very humble note
                 </content>

         </xnote>
</xnoteset>


acws-01xx% cat testnotex.xml  | refdbc -d djdphd -C addnote
406:1:TEST123
408:1
999:1 added:0 skipped:0 failed
acws-01xx% cat testnotex.xml | refdbc -d djdphd -C updatenote
999:0 updated:0 added:0 skipped:0 failed
SELECT t_note.note_id, t_user.user_name FROM t_note, t_user WHERE 
t_note.note_user_id=t_user.user_id AND t_note.note_key='TEST123'acws-01xx%

---------------------------------------------

The corresponding refdbd.log excerpt for both addnote and updatenote 
operations looks like:

---------------------------------------------

6:pid=13881:Tue Jul 18 19:06:39 2006:adding client 127.0.0.1 on fd 6
6:pid=13881:Tue Jul 18 19:06:39 2006:server waiting n_max_fd=6
7:pid=14425:Tue Jul 18 19:06:39 2006:try to read from client
6:pid=14425:Tue Jul 18 19:06:39 2006:serving client on fd 6 with 
protocol version 4
7:pid=14425:Tue Jul 18 19:06:39 2006:102-47-19-05
7:pid=14425:Tue Jul 18 19:06:39 2006:send pseudo-random string to client
7:pid=14425:Tue Jul 18 19:06:39 2006:addnote  -u djd -w 061088052 -d 
djdphd -s ris -E ISO-8859-1
6:pid=14425:Tue Jul 18 19:06:39 2006:dbi is up
7:pid=14425:Tue Jul 18 19:06:39 2006:localhost
7:pid=14425:Tue Jul 18 19:06:39 2006:djd
7:pid=14425:Tue Jul 18 19:06:39 2006:123
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:5432
7:pid=14425:Tue Jul 18 19:06:39 2006:pgsql
7:pid=14425:Tue Jul 18 19:06:39 2006:/usr/local/share/refdb/db
7:pid=14425:Tue Jul 18 19:06:39 2006:ISO-8859-1
7:pid=14425:Tue Jul 18 19:06:39 2006:refdb
7:pid=14425:Tue Jul 18 19:06:39 2006:connected to database server using 
database:
7:pid=14425:Tue Jul 18 19:06:39 2006:refdb
7:pid=14425:Tue Jul 18 19:06:39 2006:Main database looks ok:
7:pid=14425:Tue Jul 18 19:06:39 2006:refdb
7:pid=14425:Tue Jul 18 19:06:39 2006:localhost
7:pid=14425:Tue Jul 18 19:06:39 2006:djd
7:pid=14425:Tue Jul 18 19:06:39 2006:123
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:5432
7:pid=14425:Tue Jul 18 19:06:39 2006:pgsql
7:pid=14425:Tue Jul 18 19:06:39 2006:/usr/local/share/refdb/db
7:pid=14425:Tue Jul 18 19:06:39 2006:ISO-8859-1
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:SELECT 
meta_app,meta_type,meta_dbversion from t_meta
7:pid=14425:Tue Jul 18 19:06:39 2006:connected to database server using 
database:
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:encoding is UTF-8, no conversion 
required
7:pid=14425:Tue Jul 18 19:06:39 2006:BEGIN WORK
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_keyword IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_user IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_xkeyword IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_xuser IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_note IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_xnote IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_link IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:LOCK TABLE t_xlink IN SHARE MODE
7:pid=14425:Tue Jul 18 19:06:39 2006:SELECT t_note.note_id, 
t_user.user_name FROM t_note, t_user WHERE 
t_note.note_user_id=t_user.user_id AND t_note.note_key='TEST123'
7:pid=14425:Tue Jul 18 19:06:39 2006:INSERT INTO t_note (note_key) 
VALUES ('TEST123')
7:pid=14425:Tue Jul 18 19:06:39 2006:SELECT user_id FROM t_user WHERE 
user_name='djd'
7:pid=14425:Tue Jul 18 19:06:39 2006:UPDATE t_note SET note_user_id=1 
WHERE note_id=22
7:pid=14425:Tue Jul 18 19:06:39 2006:UPDATE t_note SET note_share=-1 
WHERE note_id=22
7:pid=14425:Tue Jul 18 19:06:39 2006:UPDATE t_note SET note_content='
			This is a very humble note
		' WHERE note_id=22
7:pid=14425:Tue Jul 18 19:06:39 2006:UPDATE t_note SET 
note_date='2006-07-18' WHERE note_id=22
7:pid=14425:Tue Jul 18 19:06:39 2006:COMMIT WORK
6:pid=14425:Tue Jul 18 19:06:39 2006:chunk added successfully
6:pid=14425:Tue Jul 18 19:06:39 2006:finished transferring data
6:pid=14425:Tue Jul 18 19:06:39 2006:chunk added successfully
7:pid=14425:Tue Jul 18 19:06:39 2006:UPDATE t_meta SET 
meta_modify_date='2006-07-18 19:06:39'
7:pid=14425:Tue Jul 18 19:06:39 2006:command processing done, finish 
dialog now
7:pid=14425:Tue Jul 18 19:06:39 2006:localhost
7:pid=14425:Tue Jul 18 19:06:39 2006:djd
7:pid=14425:Tue Jul 18 19:06:39 2006:123
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:5432
7:pid=14425:Tue Jul 18 19:06:39 2006:pgsql
7:pid=14425:Tue Jul 18 19:06:39 2006:/usr/local/share/refdb/db
7:pid=14425:Tue Jul 18 19:06:39 2006:ISO-8859-1
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:SELECT 
meta_app,meta_type,meta_dbversion from t_meta
7:pid=14425:Tue Jul 18 19:06:39 2006:connected to database server using 
database:
7:pid=14425:Tue Jul 18 19:06:39 2006:djdphd
7:pid=14425:Tue Jul 18 19:06:39 2006:SELECT * FROM t_keyword
7:pid=14425:Tue Jul 18 19:06:39 2006:SELECT 
note_id,note_title,note_content FROM t_note WHERE note_id IN (22)
6:pid=14425:Tue Jul 18 19:06:39 2006:child finished client on fd 6
6:pid=13881:Tue Jul 18 19:06:39 2006:parent removing client on fd 6
6:pid=13881:Tue Jul 18 19:06:39 2006:server waiting n_max_fd=5
6:pid=13881:Tue Jul 18 19:06:39 2006:child exited with code 0
6:pid=13881:Tue Jul 18 19:06:39 2006:server waiting n_max_fd=5
6:pid=13881:Tue Jul 18 19:06:45 2006:adding client 127.0.0.1 on fd 6
6:pid=13881:Tue Jul 18 19:06:45 2006:server waiting n_max_fd=6
7:pid=14433:Tue Jul 18 19:06:45 2006:try to read from client
6:pid=14433:Tue Jul 18 19:06:45 2006:serving client on fd 6 with 
protocol version 4
7:pid=14433:Tue Jul 18 19:06:45 2006:201-92-03-45
7:pid=14433:Tue Jul 18 19:06:45 2006:send pseudo-random string to client
7:pid=14433:Tue Jul 18 19:06:45 2006:updatenote  -u djd -w 033076070 -d 
djdphd -s ris -E ISO-8859-1
6:pid=14433:Tue Jul 18 19:06:45 2006:dbi is up
7:pid=14433:Tue Jul 18 19:06:45 2006:localhost
7:pid=14433:Tue Jul 18 19:06:45 2006:djd
7:pid=14433:Tue Jul 18 19:06:45 2006:123
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:5432
7:pid=14433:Tue Jul 18 19:06:45 2006:pgsql
7:pid=14433:Tue Jul 18 19:06:45 2006:/usr/local/share/refdb/db
7:pid=14433:Tue Jul 18 19:06:45 2006:ISO-8859-1
7:pid=14433:Tue Jul 18 19:06:45 2006:refdb
7:pid=14433:Tue Jul 18 19:06:45 2006:connected to database server using 
database:
7:pid=14433:Tue Jul 18 19:06:45 2006:refdb
7:pid=14433:Tue Jul 18 19:06:45 2006:Main database looks ok:
7:pid=14433:Tue Jul 18 19:06:45 2006:refdb
7:pid=14433:Tue Jul 18 19:06:45 2006:localhost
7:pid=14433:Tue Jul 18 19:06:45 2006:djd
7:pid=14433:Tue Jul 18 19:06:45 2006:123
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:5432
7:pid=14433:Tue Jul 18 19:06:45 2006:pgsql
7:pid=14433:Tue Jul 18 19:06:45 2006:/usr/local/share/refdb/db
7:pid=14433:Tue Jul 18 19:06:45 2006:ISO-8859-1
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT 
meta_app,meta_type,meta_dbversion from t_meta
7:pid=14433:Tue Jul 18 19:06:45 2006:connected to database server using 
database:
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:encoding is UTF-8, no conversion 
required
7:pid=14433:Tue Jul 18 19:06:45 2006:BEGIN WORK
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_keyword IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_user IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_xkeyword IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_xuser IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_note IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_xnote IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_link IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:LOCK TABLE t_xlink IN SHARE MODE
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT t_note.note_id, 
t_user.user_name FROM t_note, t_user WHERE 
t_note.note_user_id=t_user.user_id AND t_note.note_key='TEST123'
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT keyword_id, xkeyword_id FROM 
t_xkeyword WHERE xkeyword_type='NOTE' AND xref_id=22
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT link_id, xlink_id FROM 
t_xlink WHERE xlink_source='NOTE' AND xref_id=22
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT xnote_id FROM t_xnote WHERE 
note_id=22
6:pid=14433:Tue Jul 18 19:06:45 2006:chunk added successfully
6:pid=14433:Tue Jul 18 19:06:45 2006:finished transferring data
6:pid=14433:Tue Jul 18 19:06:45 2006:chunk added successfully
7:pid=14433:Tue Jul 18 19:06:45 2006:ROLLBACK WORK
7:pid=14433:Tue Jul 18 19:06:45 2006:command processing done, finish 
dialog now
7:pid=14433:Tue Jul 18 19:06:45 2006:localhost
7:pid=14433:Tue Jul 18 19:06:45 2006:djd
7:pid=14433:Tue Jul 18 19:06:45 2006:123
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:5432
7:pid=14433:Tue Jul 18 19:06:45 2006:pgsql
7:pid=14433:Tue Jul 18 19:06:45 2006:/usr/local/share/refdb/db
7:pid=14433:Tue Jul 18 19:06:45 2006:ISO-8859-1
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT 
meta_app,meta_type,meta_dbversion from t_meta
7:pid=14433:Tue Jul 18 19:06:45 2006:connected to database server using 
database:
7:pid=14433:Tue Jul 18 19:06:45 2006:djdphd
7:pid=14433:Tue Jul 18 19:06:45 2006:SELECT * FROM t_keyword
6:pid=14433:Tue Jul 18 19:06:45 2006:no IDs found for keyword scan
6:pid=14433:Tue Jul 18 19:06:45 2006:child finished client on fd 6
6:pid=13881:Tue Jul 18 19:06:45 2006:parent removing client on fd 6
6:pid=13881:Tue Jul 18 19:06:45 2006:server waiting n_max_fd=5
6:pid=13881:Tue Jul 18 19:06:45 2006:child exited with code 0
6:pid=13881:Tue Jul 18 19:06:45 2006:server waiting n_max_fd=5
6:pid=13881:Tue Jul 18 19:07:10 2006:server exited gracefully

Re: [Refdb-users] keybindings and LaTeX support for refdb-mode

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

Hi David,

David Nebauer writes:
 > I've just noticed there is no indication anywhere on the refdb website 
 > that refdb-elisp is available as a deb.  It's not mentioned on the emacs 
 > page, the download page, nor is it specifically mentioned on the Debian 
 > installation page.
 > 

Thanks for catching this. I'll upload the updated web pages as soon as
the SF ssh access is back online again. I'll also check in the pages
as soon as the SF svn access is back online again. Something is going
badly wrong over there.

regards,
Markus

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

[Refdb-users] refdb-mode: new commands to insert authors, keywords, periodicals

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

Hi,

I've added three new commands to refdb-mode, the Emacs frontend for RefDB.
refdb-insert-{author|keyword|periodical} allow to insert author names,
keywords, and periodical names into reference data like RIS or risx. The
commands allow minibuffer completion against the lists of author names,
keywords, and periodical names in the current database. This is pretty neat to
avoid typos and off-by-one duplicates. The commands are bound to Ctrl-c Ctrl-r
i {a|k|p}, respectively.

To test the new feature, either update your elisp svn sources, or grab the
refdb-mode.el file right here:

http://svn.sourceforge.net/viewcvs.cgi/refdb/elisp/trunk/refdb-mode.el?view=log

regards,
Markus

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

Re: [Refdb-users] Recovering after errors

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

On Wed, 2006-12-07 at 21:27 +0200, Markus Hoenicka wrote:
> Dan O'Donnell writes:
>  > Shouldn't be I believe it is a pretty straight forward RIS file (in
>  > UTF-8 though).
>  > > 
> 
> What is your setup in refdbdrc regarding the default character encoding of
> incoming RIS data? What encoding do you use in your MySQL database? I
> wonder whether it is possible to confuse refdbd by converting UTF-8
> data once too often?

Well right now nothing, since I'm trying a new install. But it had been
utf8 in and out (BTW, another possibility may lie in how utf8 is
referred to in these rc files? Sometimes it seems to be utf8, sometimes
UTF-8; I never know what to do if I'm indicating it with -E on the
command line).

> 
> regards,
> Markus
> 

Re: [Refdb-users] Recovering after errors

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

Dan O'Donnell writes:
 > Shouldn't be I believe it is a pretty straight forward RIS file (in
 > UTF-8 though).
 > > 

What is your setup in refdbdrc regarding the default character encoding of
incoming RIS data? What encoding do you use in your MySQL database? I
wonder whether it is possible to confuse refdbd by converting UTF-8
data once too often?

regards,
Markus

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

Re: [Refdb-users] Project lists

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

Rich Shepard writes:
 >    Perhaps a more obvious reference in the documentation would make us aware
 > of the technique. It's a great idea.
 > 

It should probably go into the tutorial. It needs an update anyway.

regards,
Markus

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

Re: [Refdb-users] Recovering after errors

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

On Wed, 2006-12-07 at 19:22 +0200, Markus Hoenicka wrote:
> Dan O'Donnell <dan...@ul...> was heard to say:
> 
> > Hi Markus,
> >
> > That log was cut from the end of tail n=500, so it may mean addref is
> > not firing somehow (i.e. there is nothing else in the log). That would
> > agree with what I'm seeing.
> >
> > After the first error, the db became unusable, so I wiped it and refdb
> > out, refreshed mysql, and reinstalled refdb. This lack of action is
> > coming on a fresh install. refdba is building the db and adding users,
> > whichdb can see it, but addref seems to die.
> >
> 
> Is this somehow related to the kind of data you try to add?

Shouldn't be I believe it is a pretty straight forward RIS file (in
UTF-8 though).
> 
> I see from the end of your log that the server receives a connection request
> from a client but nothing else happens. Needless to say I haven't seen this
> before. Is there a chance to get a ssh guest account on this box to debug this?
> 
Sending you one privately.

> regards,
> Markus
> 
> 

Re: [Refdb-users] Recovering after errors

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

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

> Hi Markus,
>
> That log was cut from the end of tail n=500, so it may mean addref is
> not firing somehow (i.e. there is nothing else in the log). That would
> agree with what I'm seeing.
>
> After the first error, the db became unusable, so I wiped it and refdb
> out, refreshed mysql, and reinstalled refdb. This lack of action is
> coming on a fresh install. refdba is building the db and adding users,
> whichdb can see it, but addref seems to die.
>

Is this somehow related to the kind of data you try to add?

I see from the end of your log that the server receives a connection request
from a client but nothing else happens. Needless to say I haven't seen this
before. Is there a chance to get a ssh guest account on this box to debug this?

regards,
Markus


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

Re: [Refdb-users] Recovering after errors

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

Hi Markus,

That log was cut from the end of tail n=500, so it may mean addref is
not firing somehow (i.e. there is nothing else in the log). That would
agree with what I'm seeing.

After the first error, the db became unusable, so I wiped it and refdb
out, refreshed mysql, and reinstalled refdb. This lack of action is
coming on a fresh install. refdba is building the db and adding users,
whichdb can see it, but addref seems to die.

-d

On Wed, 2006-12-07 at 13:24 +0200, Markus Hoenicka wrote:
> Hi Dan,
> 
> Daniel O'Donnell <dan...@ul...> was heard to say:
> 
> > > 7:pid=6429:Tue Jul 11 23:21:35 2006:selectdb refdbib -u dan -w
> > 072035094057068069114113082
> 
> I'm afraid you caught only the selectdb part of the log. I didn't find any hint
> about you running the addref command. Make sure to kill all instances of refdbd
> before looking at the log as there may still be data in the cache as long as one
> process keeps the file open. Can you retrieve datasets from that database?
> 
> regards,
> Markus
> 

Re: [Refdb-users] Project lists

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

On Wed, 12 Jul 2006, Markus Hoenicka wrote:

> Someone already mentioned the extended notes feature in this context. I'd just
> like to know whether this feature is too obscure to be used to compile project
> lists?

Markus,

   Not once you so clearly explain it.

> You basically create a note with a short description what the project list
> is all about (addnote). Then you use addlink to associate references with
> this note. Finally you can retrieve the references linked to that notes
> using the getref command by specifying the note (:NID: or :NCK:). You can
> of course have as many of these "project notes" as you need.

   Perhaps a more obvious reference in the documentation would make us aware
of the technique. It's a great idea.

Thanks,

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] Project lists

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

Bruce D'Arcus <bda...@gm...> was heard to say:

> Exactly my point; it's in this case an interface issue. If one had
> auto-complete tag/keyword entry -- where you can ensure consistency --
> the problem goes away.
>

I was actually planning something like this - add a mechanism to tap into a
RefDB database to get auto-completion while entering RIS data. I don't know how
hard it would be to make this feature work also with nxml-mode.

regards,
Markus

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

Re: [Refdb-users] Project lists

[Bruce D'A. <bda...@gm...>]

On 7/11/06, Rich Shepard <rsh...@ap...> wrote:

>    With appropriate key words it's not an issue. The trick is to have a
> reasonable choice of key words and remember what each encompasses.

Exactly my point; it's in this case an interface issue. If one had
auto-complete tag/keyword entry -- where you can ensure consistency --
the problem goes away.

>    Since Markus has been clever enough to already coded the latter, if it's
> not a hassle to create a modification which is project-specific, why not?

I'm just trying to understand, in part because I'm involved in the
OpenOffice work.

Bruce

Re: [Refdb-users] Project lists

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

Rich Shepard <rsh...@ap...> was heard to say:

>    With appropriate key words it's not an issue. The trick is to have a
> reasonable choice of key words and remember what each encompasses. I can
> certainly live without the feature, but it would be a simpler equivalent of
> creating pseudo users and having each "user" designate a "personal" sub-set
> of references.
>

Someone already mentioned the extended notes feature in this context. I'd just
like to know whether this feature is too obscure to be used to compile project
lists? You basically create a note with a short description what the project
list is all about (addnote). Then you use addlink to associate references with
this note. Finally you can retrieve the references linked to that notes using
the getref command by specifying the note (:NID: or :NCK:). You can of course
have as many of these "project notes" as you need.

regards,
Markus

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

Re: [Refdb-users] Recovering after errors

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

Hi Dan,

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

> > 7:pid=6429:Tue Jul 11 23:21:35 2006:selectdb refdbib -u dan -w
> 072035094057068069114113082

I'm afraid you caught only the selectdb part of the log. I didn't find any hint
about you running the addref command. Make sure to kill all instances of refdbd
before looking at the log as there may still be data in the cache as long as one
process keeps the file open. Can you retrieve datasets from that database?

regards,
Markus

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

Re: [Refdb-users] keybindings and LaTeX support for refdb-mode

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

Hi Markus,

> Better yet, I've added a test to configure which looks for the
> appropriate docbook2texi program. The current svn version should then
> work out of the box on Debian too.

It does, and it makes my life a little easier -- a nice combination.

Thanks,
David.

Re: [Refdb-users] Project lists

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

On Tue, 11 Jul 2006, Bruce D'Arcus wrote:

> To play devil's advocate, aren't feature like project-specific lists or
> databases hacks to get around poor databases and interfaces? E.g. why
> bother with segmenting references when the only reason to do is to quickly
> find stuff?

Bruce,

   Not to get around poor databases or interfaces, but to quickly find
appropriate references.

   With appropriate key words it's not an issue. The trick is to have a
reasonable choice of key words and remember what each encompasses. I can
certainly live without the feature, but it would be a simpler equivalent of
creating pseudo users and having each "user" designate a "personal" sub-set
of references.

   Since Markus has been clever enough to already coded the latter, if it's
not a hassle to create a modification which is project-specific, why not? A
simpler solution to the same end ... but for a single user.

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] Project lists

[Bruce D'A. <bda...@gm...>]

To play devil's advocate, aren't feature like project-specific lists
or databases hacks to get around poor databases and interfaces? E.g.
why bother with segmenting references when the only reason to do is to
quickly find stuff?

Bruce

Re: [Refdb-users] Recovering after errors

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

Here's l=7 output of my last session. I tried to add a single entry in a
text file ~/one.ris using the following in refdbc; things just hung on
me and I had to abort using ^C: 
selectdb refdbib
addref -f one.ris

(I started refdbc in ~/)

refdbd.log:

> 7:pid=6427:Tue Jul 11 23:21:05 2006:dbi_driver_dir went to:
> 7:pid=6427:Tue Jul 11 23:21:05 2006:
> 7:pid=6427:Tue Jul 11 23:21:05 2006:dbi is up using default driver dir
> 6:pid=6427:Tue Jul 11 23:21:05 2006:Available libdbi database drivers:
> 6:pid=6427:Tue Jul 11 23:21:05 2006:mysql
> 6:pid=6427:Tue Jul 11 23:21:05 2006:Requested libdbi driver found
> 6:pid=6427:Tue Jul 11 23:21:05 2006:Database directory:
> 6:pid=6427:Tue Jul 11 23:21:05 2006:/usr/var/lib/refdb/db
> 6:pid=6427:Tue Jul 11 23:21:05 2006:application server started
> 6:pid=6427:Tue Jul 11 23:21:05 2006:share extended notes by default
> 7:pid=6427:Tue Jul 11 23:21:05 2006:use /tmp/refdbd_fifo6427 as fifo
> 6:pid=6427:Tue Jul 11 23:21:05 2006:server waiting n_max_fd=5
> 6:pid=6427:Tue Jul 11 23:21:35 2006:adding client 127.0.0.1 on fd 6
> 6:pid=6427:Tue Jul 11 23:21:35 2006:server waiting n_max_fd=6
> 7:pid=6429:Tue Jul 11 23:21:35 2006:try to read from client
> 6:pid=6429:Tue Jul 11 23:21:35 2006:serving client on fd 6 with protocol version 4
> 7:pid=6429:Tue Jul 11 23:21:35 2006:210-21-04-49
> 7:pid=6429:Tue Jul 11 23:21:35 2006:send pseudo-random string to client
> 7:pid=6429:Tue Jul 11 23:21:35 2006:selectdb refdbib -u dan -w 072035094057068069114113082
> 6:pid=6429:Tue Jul 11 23:21:35 2006:dbi is up
> 7:pid=6429:Tue Jul 11 23:21:35 2006:localhost
> 7:pid=6429:Tue Jul 11 23:21:35 2006:dan
> 7:pid=6429:Tue Jul 11 23:21:35 2006:SecretPassWord
> 7:pid=6429:Tue Jul 11 23:21:35 2006:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:3306
> 7:pid=6429:Tue Jul 11 23:21:35 2006:mysql
> 7:pid=6429:Tue Jul 11 23:21:35 2006:/usr/var/lib/refdb/db
> 7:pid=6429:Tue Jul 11 23:21:35 2006:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:refdb
> 7:pid=6429:Tue Jul 11 23:21:35 2006:connected to database server using database:7:pid=6429:Tue Jul 11 23:21:35 2006:refdb
> 3:pid=6429:Tue Jul 11 23:21:35 2006:could not open version file:
> 3:pid=6429:Tue Jul 11 23:21:35 2006:/usr/local/var/lib/refdb/db/DB_VERSION
> 7:pid=6429:Tue Jul 11 23:21:35 2006:Main database looks ok:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:refdb
> 7:pid=6429:Tue Jul 11 23:21:35 2006:localhost
> 7:pid=6429:Tue Jul 11 23:21:35 2006:dan
> 7:pid=6429:Tue Jul 11 23:21:35 2006:SecretPassWord
> 7:pid=6429:Tue Jul 11 23:21:35 2006:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:3306
> 7:pid=6429:Tue Jul 11 23:21:35 2006:mysql
> 7:pid=6429:Tue Jul 11 23:21:35 2006:/usr/var/lib/refdb/db
> 7:pid=6429:Tue Jul 11 23:21:35 2006:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:refdb
> 7:pid=6429:Tue Jul 11 23:21:35 2006:connected to database server using database:7:pid=6429:Tue Jul 11 23:21:35 2006:refdb
> 7:pid=6429:Tue Jul 11 23:21:35 2006:localhost
> 7:pid=6429:Tue Jul 11 23:21:35 2006:dan
> 7:pid=6429:Tue Jul 11 23:21:35 2006:SecretPassWord
> 7:pid=6429:Tue Jul 11 23:21:35 2006:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:3306
> 7:pid=6429:Tue Jul 11 23:21:35 2006:mysql
> 7:pid=6429:Tue Jul 11 23:21:35 2006:/usr/var/lib/refdb/db
> 7:pid=6429:Tue Jul 11 23:21:35 2006:
> 7:pid=6429:Tue Jul 11 23:21:35 2006:refdbib
> 7:pid=6429:Tue Jul 11 23:21:35 2006:connected to database server using database:7:pid=6429:Tue Jul 11 23:21:35 2006:refdbib
> 7:pid=6429:Tue Jul 11 23:21:35 2006:SELECT meta_app,meta_type,meta_dbversion from t_meta
> 7:pid=6429:Tue Jul 11 23:21:35 2006:command processing done, finish dialog now
> 6:pid=6429:Tue Jul 11 23:21:35 2006:child finished client on fd 6
> 6:pid=6427:Tue Jul 11 23:21:35 2006:parent removing client on fd 6
> 6:pid=6427:Tue Jul 11 23:21:35 2006:server waiting n_max_fd=5
> 6:pid=6427:Tue Jul 11 23:21:35 2006:child exited with code 0
> 6:pid=6427:Tue Jul 11 23:21:35 2006:server waiting n_max_fd=5
> 6:pid=6427:Tue Jul 11 23:21:46 2006:adding client 127.0.0.1 on fd 6
> 6:pid=6427:Tue Jul 11 23:21:46 2006:server waiting n_max_fd=6





On Tue, 2006-11-07 at 23:56 +0200, Markus Hoenicka wrote:
> Hi Dan,
> 
> Dan O'Donnell writes:
>  > I've been having trouble lately with refdb crashing after errors and
>  > then being extremely difficult to restart. A typical cause for something
>  > like this might be an incorrect command-line option (I once used -t for
>  > the file name instead of -f and was forced to use control c to abort).
>  > After an error like this, refdb seems to lose contact with its databases
>  > Mysql, however, is still working.
>  > 
> 
> What command were you trying to run? Do you remember the exact command
> line? I'd like to replay what was going wrong here. It is likely that
> refdbd lacks a few sanity checks for variable values.
> 
>  > I've tried several things to get it running again from using refdbctl to
>  > stop and start, to restarting mysql and apache2, to removing my
>  > configuration files and reinstalling refdb with the installation script
>  > (often when I come to do this there is one or more refdbd sessions not
>  > properly killed off and immune to refdbctl [I kill them manually])
>  > 
> 
> refdbctl kills only the process that registered its PID in the
> appropriate file. If you bypass refdbctl and start refdbd manually,
> you may end up running two processes, one of which can't be killed
> with refdbctl. Also, if something goes grossly wrong, you may have the
> parent and the child around at the same time. If the child hangs
> (which it should never do, of course) you can only kill it manually
> from the process list.
> 
>  > I usually get set and viewstat to work in refdba, and can usually
>  > selectdb and use whichdb in refdbc. But things hang up the moment I try
>  > to add any references.
>  > 
>  > Any ideas what might be making it so unstable? Here's the log of my last
>  > session. I image the problem is the lost version file
>  > at /usr/local/var/lib/refdb/db/DB_VERSION. In refdbdrc this path is
>  > given as /usr/var/lib/refdb/db/ so I'm not sure what is telling it to
>  > look in this (non-existent) directory unless something in the setup has
>  > missed my original prefix parameter:
>  > 
> 
> Is that the log of a failed addref command? You should re-run this
> test with the log level set to 7. The "error" message does not seem to
> have much to do with the DB_VERSION stuff. The latter is only a means
> to give a packaging tool a hint about the database version without
> having to look at the database itself (which might require username
> and password info). If refdbd can't update this file it will continue
> without a hitch. The file or the write attempt has no meaning for the
> running process.
> 
>  > 
>  > > 6:pid=5412:Tue Jul 11 20:13:15 2006:adding client 127.0.0.1 on fd 6
>  > > 6:pid=5412:Tue Jul 11 20:13:15 2006:server waiting n_max_fd=6
>  > > 6:pid=5456:Tue Jul 11 20:13:15 2006:serving client on fd 6 with protocol version 4
>  > > 6:pid=5456:Tue Jul 11 20:13:15 2006:dbi is up
>  > > 3:pid=5456:Tue Jul 11 20:13:15 2006:could not open version file:
>  > > 3:pid=5456:Tue Jul 11 20:13:15 2006:/usr/local/var/lib/refdb/db/DB_VERSION
>  > > 4:pid=5456:Tue Jul 11 20:19:29 2006:error
>  > > 6:pid=5456:Tue Jul 11 20:19:29 2006:child finished client on fd 6
>  > 
> 
> My only advice (until I get more thorough debug info) is to make sure
> that you kill all hanging child processes if things go wrong. On many
> OSes the process IDs count up, so the child is usually the process
> with the higher ID. Other OSes pick random numbers, so you'll have to
> kill them all.
> 
> 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] Recovering after errors

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

Hi Dan,

Dan O'Donnell writes:
 > I've been having trouble lately with refdb crashing after errors and
 > then being extremely difficult to restart. A typical cause for something
 > like this might be an incorrect command-line option (I once used -t for
 > the file name instead of -f and was forced to use control c to abort).
 > After an error like this, refdb seems to lose contact with its databases
 > Mysql, however, is still working.
 > 

What command were you trying to run? Do you remember the exact command
line? I'd like to replay what was going wrong here. It is likely that
refdbd lacks a few sanity checks for variable values.

 > I've tried several things to get it running again from using refdbctl to
 > stop and start, to restarting mysql and apache2, to removing my
 > configuration files and reinstalling refdb with the installation script
 > (often when I come to do this there is one or more refdbd sessions not
 > properly killed off and immune to refdbctl [I kill them manually])
 > 

refdbctl kills only the process that registered its PID in the
appropriate file. If you bypass refdbctl and start refdbd manually,
you may end up running two processes, one of which can't be killed
with refdbctl. Also, if something goes grossly wrong, you may have the
parent and the child around at the same time. If the child hangs
(which it should never do, of course) you can only kill it manually
from the process list.

 > I usually get set and viewstat to work in refdba, and can usually
 > selectdb and use whichdb in refdbc. But things hang up the moment I try
 > to add any references.
 > 
 > Any ideas what might be making it so unstable? Here's the log of my last
 > session. I image the problem is the lost version file
 > at /usr/local/var/lib/refdb/db/DB_VERSION. In refdbdrc this path is
 > given as /usr/var/lib/refdb/db/ so I'm not sure what is telling it to
 > look in this (non-existent) directory unless something in the setup has
 > missed my original prefix parameter:
 > 

Is that the log of a failed addref command? You should re-run this
test with the log level set to 7. The "error" message does not seem to
have much to do with the DB_VERSION stuff. The latter is only a means
to give a packaging tool a hint about the database version without
having to look at the database itself (which might require username
and password info). If refdbd can't update this file it will continue
without a hitch. The file or the write attempt has no meaning for the
running process.

 > 
 > > 6:pid=5412:Tue Jul 11 20:13:15 2006:adding client 127.0.0.1 on fd 6
 > > 6:pid=5412:Tue Jul 11 20:13:15 2006:server waiting n_max_fd=6
 > > 6:pid=5456:Tue Jul 11 20:13:15 2006:serving client on fd 6 with protocol version 4
 > > 6:pid=5456:Tue Jul 11 20:13:15 2006:dbi is up
 > > 3:pid=5456:Tue Jul 11 20:13:15 2006:could not open version file:
 > > 3:pid=5456:Tue Jul 11 20:13:15 2006:/usr/local/var/lib/refdb/db/DB_VERSION
 > > 4:pid=5456:Tue Jul 11 20:19:29 2006:error
 > > 6:pid=5456:Tue Jul 11 20:19:29 2006:child finished client on fd 6
 > 

My only advice (until I get more thorough debug info) is to make sure
that you kill all hanging child processes if things go wrong. On many
OSes the process IDs count up, so the child is usually the process
with the higher ID. Other OSes pick random numbers, so you'll have to
kill them all.

regards,
Markus

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

Re: [Refdb-users] keybindings and LaTeX support for refdb-mode

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

Hi David,

David Nebauer writes:
 > refdb-mode.texi: refdb-mode-manual-stripped.xml
 >     docbook2x-texi --to-stdout refdb-mode-manual-stripped.xml > $@

This form works nicely over here too. I'll check tomorrow if it is
still supported in 0.8.7.
 > 
 > If that form is portable perhaps you could use it in 'Makefile.am'?  
 > Then all I'd have to do is change 'docbook2texi' to 'docbook2x-texi'.
 > 

Better yet, I've added a test to configure which looks for the
appropriate docbook2texi program. The current svn version should then
work out of the box on Debian too.

regards,
Markus

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

[Refdb-users] Recovering after errors

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

I've been having trouble lately with refdb crashing after errors and
then being extremely difficult to restart. A typical cause for something
like this might be an incorrect command-line option (I once used -t for
the file name instead of -f and was forced to use control c to abort).
After an error like this, refdb seems to lose contact with its databases
Mysql, however, is still working.

I've tried several things to get it running again from using refdbctl to
stop and start, to restarting mysql and apache2, to removing my
configuration files and reinstalling refdb with the installation script
(often when I come to do this there is one or more refdbd sessions not
properly killed off and immune to refdbctl [I kill them manually])

I usually get set and viewstat to work in refdba, and can usually
selectdb and use whichdb in refdbc. But things hang up the moment I try
to add any references.

Any ideas what might be making it so unstable? Here's the log of my last
session. I image the problem is the lost version file
at /usr/local/var/lib/refdb/db/DB_VERSION. In refdbdrc this path is
given as /usr/var/lib/refdb/db/ so I'm not sure what is telling it to
look in this (non-existent) directory unless something in the setup has
missed my original prefix parameter:


> 6:pid=5412:Tue Jul 11 20:13:15 2006:adding client 127.0.0.1 on fd 6
> 6:pid=5412:Tue Jul 11 20:13:15 2006:server waiting n_max_fd=6
> 6:pid=5456:Tue Jul 11 20:13:15 2006:serving client on fd 6 with protocol version 4
> 6:pid=5456:Tue Jul 11 20:13:15 2006:dbi is up
> 3:pid=5456:Tue Jul 11 20:13:15 2006:could not open version file:
> 3:pid=5456:Tue Jul 11 20:13:15 2006:/usr/local/var/lib/refdb/db/DB_VERSION
> 4:pid=5456:Tue Jul 11 20:19:29 2006:error
> 6:pid=5456:Tue Jul 11 20:19:29 2006:child finished client on fd 6