refdbib + latex

Hi,

Damien Jade Duff writes:
 > t_refdb.refdb_citekey='CAWKELL1976,GALLESELAKOFF2005,WILLIAMSSCHNIER1996'
 > 
 > ...which returns no references at all. What you'd want here I suppose is...
 > 
 > WHERE t_refdb.refdb_citekey in
 > ('CAWKELL1976','GALLESELAKOFF2005','WILLIAMSSCHNIER1996')
 > 
 > ...I notice that in readris.c add_id_from_aux the comments say this
 > subroutine is returning a comma separated list but I think that list is
 > just handed straight to the select statement. I really don't envy you
 > all that string stuff you've done in C - it looks like a nightmare of &s
 > and *s and ->s and **s - well, you get used to it I suppose.
 > 

You've got close to the problem. As far as I can tell my code is not
prepared to handle multi-head citations in .aux files at all. The code
simply assumes that each \citation{} block contains a single citation
which it adds to said comma-separated list. Instead, it should inspect
each \citation{} and tokenize it as needed. I'll supply a fix as soon
as time permits.

 > ...yes, so I don't know if you'd consider that a bug given that you may
 > require all users to enter their usernames on the command line (I don't
 > see that putting someones' username in the system-wide rc file is
 > preferrable though).

The manual is apparently a bit unclear about this point. In no case

refdbib + latex

Markus Hoenicka writes:
 > You've got close to the problem. As far as I can tell my code is not
 > prepared to handle multi-head citations in .aux files at all. The code
 > simply assumes that each \citation{} block contains a single citation
 > which it adds to said comma-separated list. Instead, it should inspect
 > each \citation{} and tokenize it as needed. I'll supply a fix as soon
 > as time permits.
 > 

Could you please test the attached file readris.c? I think this should
fix the problem with multi-head TeX citations.

regards
Markus

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: refdbib + latex

Markus Hoenicka wrote:
>
> Could you please test the attached file readris.c? I think this should
> fix the problem with multi-head TeX citations.
> 
> regards
> Markus
> 
> 
> ------------------------------------------------------------------------
> 
> 

Dear Markus

echo "\\citation{HAUFFE1994,MACROBERTS1997}" | refdbib -d djdphd -u djd
-w 123 -S J.Biol.Chem. -t bibtex

...still results in...

7:pid=21669:Mon Jan 02 02:21:48 2006: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,

Re: refdbib + latex

Dear Markus

My comments on your comments below.

 >
 > The manual is apparently a bit unclear about this point. In no case
 > you're supposed to enter usernames or passwords into the system-wide
 > config files. That's the job of the personal config files in your home
 > directory (~/.refdbibrc in this case). Make it read/writable only for
 > yourself and all should be fine.
 >

Oh yes, I'd forgotten about that option. Duh. Apologies.

 >
 > I'll have to check whether there is an error in refdbib which fails to
 > check for missing usernames/passwords. If they're not specified in
 > either a config file or on the command line, it should not attempt to
 > pass them to refdbd, causing the command-line parsing on the server
 > side to fail. I can't explain why it appears to work "sometimes" in
 > your case, unless you use a database engine without password
 > check. I'll investigate this.
 >

Yes, on my experimental system I was indeed using a DB engine without a 
password, allowing only local access, so I guess that could be partially 
it. Though, I always supplied a password even if it's only a dummy one 
otherwise funny things happen during piping. So I guess I'm doing two 
weird things - DB without a password, and supplying a password without a 
username. It would be nice to have error messages in situations like 

Re: refdbib + latex

Hi,

Damien Jade Duff writes:
 > Also, when compiling readris.c my compiler throws up the following (new)
 > warning...
 > 
 > readris.c: In function `wrap_citation':
 > readris.c:386: warning: comparison between pointer and integer
 > 
 > ...so I try changing...
 > 
 >      if (*end == ",") {
 > 
 > ...to...
 > 
 >      if (*end == ',') {
 > 
 > ...and it works on my single test case. I hope that's all there is to
 > it, it seems to work for me.
 > 

Shame on me. I should at least have compiled the code before sending
it out! Anyway, if it works after fixing this more than obvious error
I'll check in this change. And, as you may have noticed, refdbd uses a
whitespace-separated list internally, so the comments in the code are
plain wrong. I'll fix this too while I'm at it.

regards,
Markus

Re: refdbib + latex

Hi,

Damien Jade Duff writes:
 > Yes, on my experimental system I was indeed using a DB engine without a 
 > password, allowing only local access, so I guess that could be partially 
 > it. Though, I always supplied a password even if it's only a dummy one 
 > otherwise funny things happen during piping. So I guess I'm doing two 
 > weird things - DB without a password, and supplying a password without a 
 > username. It would be nice to have error messages in situations like 
 > that I guess.
 > 

Actually, using a DB engine without authentication isn't exactly
weird. RefDB is supposed to work correct with these engines too, and
if it doesn't it's a bug. refdbib indeed did not check for the
presence of a username before assembling the server command. I've
fixed this. refdbib now bails out with an error message (just like
refdba and refdbc, btw) if there is no username. One thing I don't
quite understand is that all tools use a getlogin() call to retrieve
the login name as a fallback if no username is provided. getlogin()
should be able to retrieve your login name unless you do real weird
things.

Feel free to give the current CVS version a try, or wait until the
next prerelease which I'm about to finish.

regards,
Markus

--

-- 

Re: refdbib + latex

 > Anyway, if it works after fixing this more than obvious error
 > I'll check in this change.

readris.c
Thanks Markus. More comprehensive tests have confirmed - it works jut fine.

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RISX Theory

I'm a newcomer to refdb, but am very enthused by its possibilities.  
For one thing, I really like RISX. I like its clean separation of  
analytic, monographic, and serial data (could anyone point me to a  
fuller explanation of those 3 levels?); it seems simple but quite  
close to my "internal model" of a bibliography.

Except for libinfo. The DTD says it is "a wrapper for information  
specific to a particular user of a reference database system". The  
question is, why is "reprint" a required element? In most of my  
bibliographic entries, all I want to put in libinfo is a *note*, and  
it's kind of irritating to have to put in all those empty reprint  
elements. Am I missing something?

  - dam

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RISX Theory

Hi David,

David Mundie writes:
 > I'm a newcomer to refdb, but am very enthused by its possibilities.  
 > For one thing, I really like RISX. I like its clean separation of  
 > analytic, monographic, and serial data (could anyone point me to a  
 > fuller explanation of those 3 levels?); it seems simple but quite  
 > close to my "internal model" of a bibliography.
 > 

I don't have a pointer handy, but this model follows the one used by
TEI (see http://www.tei-c.org). It is explained in some depth in their
DTD documentation.

 > Except for libinfo. The DTD says it is "a wrapper for information  
 > specific to a particular user of a reference database system". The  
 > question is, why is "reprint" a required element? In most of my  
 > bibliographic entries, all I want to put in libinfo is a *note*, and  
 > it's kind of irritating to have to put in all those empty reprint  
 > elements. Am I missing something?
 > 

I'm not religious about this, so I can imagine to make this optional
if this makes sense. But to me RefDB's primary purpose is still to
manage a collection of physical papers, PDF or Postscript files, and
web links relevant to your work. To have a paper in file or to not
have it is a crucial distinction in this context, and it also helps to
keep track of papers that you've ordered in a library or at a reprint
service. All this is recorded in the status attribute and in the
optional date subelement.

refdb-0.9.6 and sqlite3 default database directory ?

Hi list.  I'm new to refdb and installing it for use with sqlite3.  The
default database location cited in manpage and online html documentation
is "/usr/local/share/refdb/db".  Without any arguments to 'configure'
when installing refdb, running 'refdbd -D sqlite3 -s -e 0 -l 7' returns
the following which seems to indicate otherwise:

dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
sqlite3
Requested libdbi driver found
Database directory:
/var/lib/refdb/db
application server started
share extended notes by default
use /tmp/refdbd_fifo1143 as fifo
server waiting n_max_fd=4

Trying to set this to cited location with "with-db-dir" config flag
seems to have not effect.  Furthermore "serverip
/usr/local/share/refdb/db" in refdbcrc seems to have no effect ( if I'm
reading refdbd manpage correctly ).  So, are the powers that be telling
me to use "/var/lib/refdb/db" ?

Sven

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