refdb-users — List for RefDB users

Re: [Refdb-users] Re: nitpicking (element ordering in risx)

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

Bruce D'Arcus writes:
 > > And what is the relation of RIS/RISX/RefDB to Bibliofile?
 > 
 > Markus is involved in development discussions of Bibliofile, as am I.  
 > It is an xslt-based formatting engine designed to be 
 > DTD/schema-independent, both with respect to bib data and document 
 > format.  Noone has done this before, so it's bleeding edge, and Markus 
 > is still skeptical it will work adequately.

xslt is said to be a complete programming language so it will work
eventually, given that someone puts enough sweat in it. I'm skeptical
whether it is  wise to do the raw->cooked transformation in xslt. As
we're not looking at anything specific to XML (in the case of RefDB,
the data to convert are not XML, but SQL query results), any language
with a better signal-to-noise ratio than xslt will provide better and
easier to maintain programs (think C or Perl). For me it is simply a
matter of chosing the right tool for the right job. You can use Emacs
as a web server (google for it, it's fun!) but no one would claim this
stacks up well against Apache.

 >  I really hope it does, and 
 > that RefDB can use it as its formatting engine too.

I strive for compatibility at the stylesheet level.

regards,
Markus

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

[Refdb-users] Re: nitpicking (element ordering in risx)

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

Justus H. Piater writes:
 > Hi,
 > 
 > May I join into the discussion:
 > 

Sure, anytime.


 > Indeed, I am not sure what an input template would provide over and
 > above psgml-mode. Except: In my local copy of risx.dtd, I made the
 > citekey and the type #REQUIRED so that psgml-mode prompts for them.
 > 

This is not a bad idea for entering data from scratch. However, I
didn't want to force this upon users because refdbd can create useful
citekeys if none are provided. Some people may prefer this convenience.

 > Even better, one could convert the DTD to RELAX NG and use it with
 > nxml-mode which does XML validation.
 > 

I'm reluctant to go down this path as currently few tools support
RELAX NG. This is supposed to change eventually.

Before answering the detailed questions below, let me briefly mention
that the risx.dtd was not designed from scratch. Rather it is an XML
representation of the RIS tagged format with all its strengths and
(almost) all its weaknesses. The main purpose of this dtd is to have a
target for SGML/XML transformations. It was by no means written as a
replacement for any serious XML bibliography DTD like e.g. MODS.

 > Here are some questions and comments about risx.dtd:
 > 
 > - There is no editor element. How do I distinguish between authors and
 >   editors, say, for a book?
 > 

I've attempted to get some logic into the RIS author and title
levels. A book author is supposed to be encoded as AU/A1 whereas an
editor is an ED/A2. This does not translate well to the
part/publication/set distinction used in risx. Recent versions of risx
have a role attribute attached to the author element. However, this
may not yet be honored correctly during formatting bibliographies.

 > - I think there should be a way to provide a <url> for a conference
 >   article that's been published in a proceedings volume. This belongs
 >   into the <part>, I think.
 > 

Question to Bruce (he knows MODS better than me): can MODS do this?

 > - This may have been answered elsewhere, but I can't remember right
 >   now: How are full vs. abbreviated journal titles handled by RefDB?
 > 

Journal titles are kept in a separate table. All references encoding
articles from this journal can use either the full or abbreviated name
depending on what the bibliography style requires. There are fallbacks
if one of the titles is missing.

Currently there is no convenience command to maintain the journal
title list. If you have references containing only one type of title,
it is best to retrieve them, add the missing title, and update the
references.

 > - It would be nice to provide an event address for conferences (which
 >   is usually different from the publisher's or organization's
 >   address).
 > 

Bruce: can MODS do this?

 > - I think we need a mechanism to protect individual characters against
 >   automatic case conversion of titles by style sheets (like {G}aussian
 >   and {HMM} in BibTeX).

This would only be a problem if there are styles that force all
lowercase. citestylex.dtd supports this but I don't know whether any
real-life journal requires this. The other possibilities (all caps or
keep as is) would work ok if you supply the titles in proper mixed
case.

If this is not sufficient we'll have a problem. 

 > 
 > - In <libinfo>, why isn't <reprint> optional? Also, the only allowed
 >   content is <date>, not even #CDATA is permitted. This contradicts
 >   the RIS specification of the RP field, doesn't it?

I think you run a reference manager mainly to keep track of your
offprints/electronic copies. The reprint status is kind of essential
to do this. But if this bothers people I won't have a problem changing
this element to optional.

BTW the RIS spec says the RP field can contain one of three status
notes, one of which (ON REQUEST) may be followed by a date. This is
exactly what the reprint element represents: The attribute encodes the
status, the optional child is the date.

 > 
 > - Is there really no established standard for representing references
 >   in XML? By TEI, for example, or something linked to the Dublin
 >   Core... And what is the relation of RIS/RISX/RefDB to Bibliofile?
 > 

The nice thing about standards is that there are so many to choose
from (don't know whom to attribute this to). I'm still evaluating
whether MODS is suitable for the purposes of a reference
manager/bibliography tool. It was clearly not designed for this
purpose but it probably gets closest. 

 > Another issue: I'd like the "master" representation of my references
 > to be an XML file rather than a data base because that allows me to
 > choose and change the format as desired. To make this practical, it
 > would really help if RefDB could optionally identify references by the
 > citekey instead of by the numeric ID. This would allow me to store
 > references from different sources in the same RefDB database, and to
 > update some of them by re-importing manually maintained XML files.
 > 

I don't know what you mean by "choosing and changing the format"? Do
you want to move your data back and forth between different DTDs?
Otherwise XML is plain text that you can (with a few exceptions)
format any way you want, even if it originates from a database. In any
case I don't understand the advantage of maintaining your references
outside of a database. You can retrieve them from the database as XML
files and update them any time. You can even retrieve the full
database as XML periodically and check this into CVS. But the point of
a reference manager is to make the references accessible by simple
queries. If you maintain your data outside the database, you're back
to grep, or you overload your brain with things a database was
designed to remember.

The ID and citekey are mostly interchangeable. Both must be unique in
a database. The ID is automatically created by the database engine and
as such comes for free. But you can of course update references by
providing only the citekey but no ID. The risx import routine always
checks the citekey first, then the ID.

regards,
Markus

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

[Refdb-users] =?iso-8859-1?Q?Re:_[Refdb-users]_Re:_[Refdb-users]_Re:=20?= =?iso-8859-1?Q?[Refdb-users]=20?=

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

[cc'ing to the list]

I'm afraid we'll have to do some serious debugging then. Could you
please provide:

- the refdbdrc settings you used for sqlite and for pgsql
- the full output of refdbd -s -e 0 -l 7 from the start to the point
  where you run a user command (listdb will do).

I'm pretty sure that the configuration is screwed somehow. If you find
the time you can also try to configure refdbd correctly from the start
(i.e. run ./configure --with-db-server=3Dsqlite <other options>) and se=
e
whether this solves your problems (don't forget to copy
refdbdrc.example to refdbdrc after reconfiguring). I'd suggest to
start with sqlite as this does not bother you with user
authentication. Once that works allright you can switch to pgsql.

regards,
Markus

Johan Ekh writes:
 > You were right! However, it did not solve the=20
 > problem. I still cannot connect to the database.
 > I've also tried to use pgsql with the same result.
 > I have a running postmaster and I've used it with
 > other programs.
 > =20
 > Can you think of anthing else?
 >=20
 > Best regards,
 > Johan
 >=20
 > ------- Ursprungligt brev -------
 > Fr=E5n: mar...@mh...
 > Datum: Fri, 21 Nov 2003 23:56:57 +0100
 >=20
 > [cc'ing to the list]
 >=20
 > Seems like I've overlooked something trivial. Can you post the
 > contents of your /usr/local/etc/refdb/refdbdrc config file? I bet th=
e
 > dbserver variable is set to mysql. It should be sqlite in your case.=

 >=20
 > regards,
 > Markus
 >=20
 > Johan Ekh writes:
 >  > Hi again!
 >  > Got the following from running "make check" in the
 >  > libdbi-drivers directory:
 >  >=20
 >  > SUCCESS! All done, disconnecting and shutting down libdbi. Have a=
 nice
 > day.
 >  >=20
 >  > So, it seems ok. But I still cannot connect to the
 >  > database when I try to use refdb.
 >  >=20
 >  > Regards,
 >  > Johan
 >  >=20
 >=20
 > --=20
 > Markus Hoenicka
 > mar...@ca...
 > (Spam-protected email: replace the quadrupeds with "mhoenicka")
 > http://www.mhoenicka.de
 >=20
 >=20
 >=20
 > -------------------------------------------------------
 > This SF.net email is sponsored by: SF.net Giveback Program.
 > Does SourceForge.net help you be more productive?  Does it
 > help you create better code?  SHARE THE LOVE, and help us help
 > YOU!  Click Here: http://sourceforge.net/donate/
 > _______________________________________________
 > Refdb-users mailing list
 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-users
 >=20
 >=20
 >=20
 >=20

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

Re: [Refdb-users] Re: nitpicking (element ordering in risx)

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

I've attached the Relax NG version of RISX.

Looking into this, I can't at the moment see how to properly code a 
book with an editor.

Markus, I thought you had added a way to code "role"?

Anyway, the template package I am talking about is here:

   	http://emacs-template.sourceforge.net/index.html

Here's a template for a book chapter.  I've not included the document 
declaration as I use nxml mode, and RNG has no such concept.

<?xml version="1.0" encoding="utf-8"?>
<ris>
   <entry type="CHAP" citekey="(>>>citekey<<<)">
   <part>
     <title>(>>>title<<<)</title>
     <author>
       <lastname>(>>>authorlast<<<)</lastname>
       <firstname>(>>>authorfirst<<<)</firstname>
     </author>
   </part>
   <publication>
     <title type="full">(>>>ctitle<<<)</title>
     <author>
       <lastname>(>>>cauthorlast<<<)</lastname>
       <firstname>(>>>cauthorfirst<<<)</firstname>
     </author>
     <pubinfo>
       <pubdate type="primary">
	<date><year>(>>>year<<<)</year></date>
       </pubdate>
       <startpage>(>>>start<<<)</startpage>
       <endpage>(>>>end<<<)</endpage>
       <city>(>>>city<<<)</city>
       <publisher>(>>>publisher<<<)</publisher>
     </pubinfo>
   </publication>
   <contents>
     <keyword>(>>>POINT<<<)(>>>MARK<<<)</keyword>
   </contents>
   </entry>
</ris>
 >>>TEMPLATE-DEFINITION-SECTION<<<
("citekey" "Citation Key: ")
("title" "Title: ")
("subtitle"     "Subtitle: ")
("authorfirst"     "Author Firstname: ")
("authorlast"     "Author Lastname: ")
("ctitle" "Book Title: ")
("cauthorfirst"  "Editor Firstname: ")
("cauthorlast"  "Editor Lastname: ")
("year" "Publication Year: ")
("publisher" "Publisher: ")
("city" "City: ")
("start" "Start Page: ")
("end" "End Page: ")

Bruce

Re: [Refdb-users] Re: nitpicking (element ordering in risx)

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

On Nov 24, 2003, at 3:39 AM, Justus H. Piater wrote:

> May I join into the discussion:

Sure!

> Indeed, I am not sure what an input template would provide over and
> above psgml-mode.

It gets to your later question about editor.  It allows you to present 
to the user a more context-specific and unambiguous prompt for entry.  
For example, I have created a template called book-edited, which has a 
prompt to enter "editor."  When the user enters that, it goes in the 
"author" field.

I will post later so you can see for yourself.

> Even better, one could convert the DTD to RELAX NG and use it with
> nxml-mode which does XML validation.

I've been known to argue this.  IMHO, Relax NG is a big leap beyond 
DTDs in both elegance and power, and nxml mode is simple excellent.

But Markus very much wants to maintain compatibility with SGML, so has 
been more reluctant.  Still, it's trivial to convert RISX to RNG with 
Trang.

I'll let Markus answer some of your detail questions.

> - Is there really no established standard for representing references
>   in XML? By TEI, for example, or something linked to the Dublin
>   Core...

No.  My opinion is the new MODS schema from the Library of Congress is 
the most likely to provide this, however.

> And what is the relation of RIS/RISX/RefDB to Bibliofile?

Markus is involved in development discussions of Bibliofile, as am I.  
It is an xslt-based formatting engine designed to be 
DTD/schema-independent, both with respect to bib data and document 
format.  Noone has done this before, so it's bleeding edge, and Markus 
is still skeptical it will work adequately.  I really hope it does, and 
that RefDB can use it as its formatting engine too.  Absent that, 
bibliofile also includes a style specification DTD that can handle 
MODS, and which Markus is interested in too.

> Another issue: I'd like the "master" representation of my references
> to be an XML file rather than a data base because that allows me to
> choose and change the format as desired. To make this practical, it
> would really help if RefDB could optionally identify references by the
> citekey instead of by the numeric ID. This would allow me to store
> references from different sources in the same RefDB database, and to
> update some of them by re-importing manually maintained XML files.

I'm not following here.  RefDB stores the citekey; what more do you 
need it to do?

Bruce

[Refdb-users] Re: nitpicking (element ordering in risx)

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

Hi,

May I join into the discussion:

"Markus Hoenicka" <mar...@mh...> wrote on Fri, 21 Nov
2003 23:52:31 +0100:

> Bruce D'Arcus writes:
>  > I've been working on some input templates for risx for emacs.  The ide=
a=20
>  > is to make entering data much easier than it currently is, since ris i=
s=20
>  > a rather abstract data model.  So, for each variable, the user is=20
>  > prompted for the input with unambiguous prompts: "book title" and so=20
>  > forth.
> ...
> You may then select a suitable mode (M-x ris-mode or M-x psgml-mode or
> whatever you use to edit XML) if you need specific editing support.

Indeed, I am not sure what an input template would provide over and
above psgml-mode. Except: In my local copy of risx.dtd, I made the
citekey and the type #REQUIRED so that psgml-mode prompts for them.

Even better, one could convert the DTD to RELAX NG and use it with
nxml-mode which does XML validation.

Here are some questions and comments about risx.dtd:

- There is no editor element. How do I distinguish between authors and
  editors, say, for a book?

- I think there should be a way to provide a <url> for a conference
  article that's been published in a proceedings volume. This belongs
  into the <part>, I think.

- This may have been answered elsewhere, but I can't remember right
  now: How are full vs. abbreviated journal titles handled by RefDB?

- It would be nice to provide an event address for conferences (which
  is usually different from the publisher's or organization's
  address).

- I think we need a mechanism to protect individual characters against
  automatic case conversion of titles by style sheets (like {G}aussian
  and {HMM} in BibTeX).

- In <libinfo>, why isn't <reprint> optional? Also, the only allowed
  content is <date>, not even #CDATA is permitted. This contradicts
  the RIS specification of the RP field, doesn't it?

- Is there really no established standard for representing references
  in XML? By TEI, for example, or something linked to the Dublin
  Core... And what is the relation of RIS/RISX/RefDB to Bibliofile?

Another issue: I'd like the "master" representation of my references
to be an XML file rather than a data base because that allows me to
choose and change the format as desired. To make this practical, it
would really help if RefDB could optionally identify references by the
citekey instead of by the numeric ID. This would allow me to store
references from different sources in the same RefDB database, and to
update some of them by re-importing manually maintained XML files.

Cheers,
Justus

--=20
Justus H. Piater, Ph.D.         http://www.montefiore.ulg.ac.be/~piater/
Institut Montefiore, B28        Phone: +32-4-366-2279
Universit=E9 de Li=E8ge, Belgium    Fax:   +32-4-366-2620

Re: [Refdb-users] nitpicking (element ordering in risx)

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

Bruce D'Arcus writes:
 > The reverse for both.  First name is, after all, first ;-)
 > 

Yes, except in the place where I grew up. Don't ask me why, but last
name always goes first.

I know that this is cross with the rest of the world, so the DTD will
have the reverse order in the next release.

 > What about using a macro?
 > 

I've been using Emacs for years without ever touching a macro. I'd
simply have to look it up. Don't know whether it is going to work.

regards,
Markus

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

Re: [Refdb-users] nitpicking (element ordering in risx)

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

On Nov 21, 2003, at 5:52 PM, Markus Hoenicka wrote:

>> What is odd for me:
>>
>> 1)  lastname before first
>>
>> 2)  city before publisher
>
> What would then be intuitive? It wouldn't be a big deal to change the
> order.

The reverse for both.  First name is, after all, first ;-)

>> Anyone out there with lisp experience interested in a menu item to 
>> load
>> these records from the buffer directly into refdb?
>
> This would be sweet. For the time being, I was thrilled enough to
> tinker a little with Emacs, trying to find out whether you could do
> the same with built-in functions. A menu (and key bindings) would be
> so much better

What about using a macro?

Bruce

[Refdb-users] =?iso-8859-1?Q?Re:_[Refdb-users]_Re:_[Refdb-users]=20?=

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

[cc'ing to the list]

Seems like I've overlooked something trivial. Can you post the
contents of your /usr/local/etc/refdb/refdbdrc config file? I bet the
dbserver variable is set to mysql. It should be sqlite in your case.

regards,
Markus

Johan Ekh writes:
 > Hi again!
 > Got the following from running "make check" in the
 > libdbi-drivers directory:
 > 
 > SUCCESS! All done, disconnecting and shutting down libdbi. Have a nice day.
 > 
 > So, it seems ok. But I still cannot connect to the
 > database when I try to use refdb.
 > 
 > Regards,
 > Johan
 > 

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

[Refdb-users] nitpicking (element ordering in risx)

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

Hi Bruce,

Bruce D'Arcus writes:
 > I've been working on some input templates for risx for emacs.  The idea 
 > is to make entering data much easier than it currently is, since ris is 
 > a rather abstract data model.  So, for each variable, the user is 
 > prompted for the input with unambiguous prompts: "book title" and so 
 > forth.
 > 

I am very sympathetic to this approach.

 > I have templates now for chapters and articles, and will do another for 
 > book.  In doing so, however, I'm struck by some somewhat unintuitive 
 > element ordering in the risx DTD.  Below's the instance:
 > 
 > What is odd for me:
 > 
 > 1)  lastname before first
 > 
 > 2)  city before publisher
 > 

What would then be intuitive? It wouldn't be a big deal to change the
order.

 > Anyone out there with lisp experience interested in a menu item to load 
 > these records from the buffer directly into refdb?
 > 

This would be sweet. For the time being, I was thrilled enough to
tinker a little with Emacs, trying to find out whether you could do
the same with built-in functions. A menu (and key bindings) would be
so much better, but right now you can do the following:

Generally it is a good idea to run refdbc inside a shell buffer (M-x
shell). It is best to avoid a pager and send the output to stdout
instead. Whatever you retrieve with e.g. getref is editable text.

If you want to import refdbc output into a new buffer, run something
like:

   M-! refdbc -d dbname -t ris -C getref :ID:=1

Remember that if you run M-! again, you can use the argument history
(up arrow) to walk through the previous calls which saves a lot of
typing.

You may then select a suitable mode (M-x ris-mode or M-x psgml-mode or
whatever you use to edit XML) if you need specific editing support.

In order to send new or updated references from a buffer to refdb, mark
the region (go to start of ref, press Ctrl-space, move cursor to end
of ref). Then run something like:

   M-| refdbc -d dbname -C addref

or

   M-| refdbc -d dbname -C updateref

This will send the marked region as input to the addref or updateref
commands. Use the -t risx switch if you deal with risx data.

Keep in mind that the M-! and M-| commands won't give you a chance to
enter a password. You have to set this in your cofiguration file or
use no password.

regards
Markus

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

[Refdb-users] nitpicking (element ordering in risx)

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

I've been working on some input templates for risx for emacs.  The idea 
is to make entering data much easier than it currently is, since ris is 
a rather abstract data model.  So, for each variable, the user is 
prompted for the input with unambiguous prompts: "book title" and so 
forth.

I have templates now for chapters and articles, and will do another for 
book.  In doing so, however, I'm struck by some somewhat unintuitive 
element ordering in the risx DTD.  Below's the instance:

What is odd for me:

1)  lastname before first

2)  city before publisher

Anyone out there with lisp experience interested in a menu item to load 
these records from the buffer directly into refdb?

<?xml version="1.0" encoding="utf-8"?>
<ris>
   <entry type="CHAP" citekey="smith1999c">
   <part>
     <title>Title</title>
     <author>
       <lastname>Smith</lastname>
       <firstname>Jane</firstname>
     </author>
   </part>
   <publication>
     <title type="full">Book</title>
     <pubinfo>
       <pubdate type="primary">
	<date><year>1999</year></date>
       </pubdate>
       <startpage>34</startpage>
       <endpage>45</endpage>
       <city>New York</city>
       <publisher>ABC Publisher</publisher>
     </pubinfo>
   </publication>
   <contents>
     <keyword></keyword>
   </contents>
   </entry>
</ris>

[Refdb-users] =?iso-8859-1?Q?Re:_[Refdb-users]=20?=

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

[cc'ing to the list...]

Johan Ekh writes:
 > Hi Markus!
 > I've used the very same switch.
 > Output from "refdbd -s -e 0 -l 7" is 
 > 
 > dbi is up using default driver dir
 > Available libdbi database drivers:
 > sqlite
 > pgsql
 > application server started
 > use /tmp/refdbd_fifo4059 as fifo
 > server waiting n_max_fd=4
 > 
 > so it seems as if the drivers are OK!
 > 

It seems but a driver failure is still the only thing that can cause
your problem. Can you go back to the libdbi-drivers directory and run
make check? This should tell you whether or not the sqlite driver
works.

regards,
Markus

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

[Refdb-users] =?iso-8859-1?Q?"could_not_connect_to_database_server"?=

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

Hi Johan,

this error is usually caused by a missing libdbi driver. Could you
please restart refdbd with a log level of 7 and have a look at the
beginning of the log output? It should display a list of available and
loadable libdbi drivers. The drivers are part of the libdbi-drivers
package. In order to build the SQLite driver you need to configure
libdbi-drivers with the --with-sqlite switch.

regards,
Markus

Johan Ekh writes:
 > 4:pid=2145:Thu Nov 20 08:53:42 2003:creating database connection structure
 > failed

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

[Refdb-users] =?iso-8859-1?Q?"could_not_connect_to_database_server"?=

[Johan E. <ek...@kt...>]

Hello!
I'm a first time user of refdb and I would like to
use it with SQLite on SuSE 8.1. I've installed all
packages in "refdb-starterkit-0.9.3.tar.gz" 
according to the instructions in the readme file.
SQLite seems to be working, i.e. "sqlite test.db"
creates an empty database. However, when I try to
use refdb I get the message "could not connect to database server". The
"set" command generates the 
following:

serverip 127.0.0.1
port 9734
verbose f
pager less
username johan
timeout 60
logfile /var/log/refdba.log
logdest 1
loglevel INFO
refdblib

The last lines of "refdbd.log" looks like

6:pid=464:Thu Nov 20 08:53:42 2003:adding client on fd 6
6:pid=464:Thu Nov 20 08:53:42 2003:server waiting n_max_fd=6
6:pid=2145:Thu Nov 20 08:53:42 2003:serving client on fd 6 with protocol
version 1
6:pid=2145:Thu Nov 20 08:53:42 2003:dbi is up
4:pid=2145:Thu Nov 20 08:53:42 2003:creating database connection structure
failed
6:pid=2145:Thu Nov 20 08:53:42 2003:child finished client on fd 6

Does anyone know what I have to do?

Regards,
Johan

Re: [Refdb-users] refdb/mysql problems under Cygwin -- please help

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

Gary Lupyan writes:
 > $ ls /usr/local/lib/dbd/
 > total 691
 > -rwxr-xr-x    1 psycomp  None       58130 Jul 15 19:52 libmsql.dll
 > -rwxr-xr-x    1 psycomp  None        39704 Jul 15 19:52 libmsql.dll.a
 > -rwxr-xr-x    1 psycomp  None       146504 Jul 15 19:52 libmysql.dll
 > -rwxr-xr-x    1 psycomp  None       187782 Jul 15 19:52 libmysql.dll.a
 > -rwxr-xr-x    1 psycomp  None        43837 Jul 15 19:52 libpgsql.dll
 > -rwxr-xr-x    1 psycomp  None        14228 Jul 15 19:52 libpgsql.dll.a
 > -rwxr-xr-x    1 psycomp  None         6478 Jul 15 19:35 libmsql.a
 > -rwxr-xr-x    1 psycomp  None          682 Jul 15 19:35 libmsql.la
 > -rwxr-xr-x    1 psycomp  None        21252 Jul 15 19:35 libpgsql.a
 > -rwxr-xr-x    1 psycomp  None          671 Jul 15 19:35 libpgsql.la
 > -rwxr-xr-x    1 psycomp  None        15150 Jul 15 19:35 libmysql.a
 > -rwxr-xr-x    1 psycomp  None          729 Jul 15 19:35 libmysql.la
 > -rwxr-xr-x    1 psycomp  None       167007 Jan  5  2003 libmysqlclient.dll
 > 

[...]

 > Oddly, I also have libmysqlclient.dll in /usr/local/bin and it's a slightly 
 > smaller file.
 > 

The libmysqlclient.dll does not belong into /usr/local/lib/dbd. It is
not part of the libdbi-drivers binary package and must have found
it's way there by some other means. Apparently the MySQL driver
(libmysql.dll) loads the libmysqlclient.dll from the same directory
and thus picks a wrong version. Removing this file should enable the
driver to find the copy in /usr/local/bin.

regards,
Markus

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

[Refdb-users] getnote :LI:=foobar ?

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

Hi,

Marc Herbert writes:
 >  Is there a simple way to get all notes attached to a reference?
 > something like "getnote :LI:=foobar"? If not, do you think is it
 > technically easy to code? Politically?
 > 

You can view the attached notes using the getref -S ALL or getref -S
NX switches. The appropriate getnote extension is under way. I was not
yet able to decide how to distinguish the field selectors referring to
references and those referring to notes. It would probably be best to
use :NID: et al throughout if referring to notes.

 >  Additional question: it is possible/a good idea to give to a note the
 > same CK as a an existing reference ?
 > 

It is possible as these are essentially two separate namespaces. It is
probably not a good idea as you may get confused afterwards.

 > PS: maybe I did not understand the rationale for "xnotes"

xnotes were requested to organize notes along with the references they
belong to. The "one note per reference" was rejected as too rigid for
organizing topics and for compiling related information. It is a means
to enter additional information that you collect to a set of
references and that you intend to use later for e.g. writing a paper.

regards,
Markus

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

[Refdb-users] getnote :LI:=foobar ?

[Marc H. <Mar...@en...>]

Hi,

 Two questions about the new "xnotes".

 Is there a simple way to get all notes attached to a reference?
something like "getnote :LI:=foobar"? If not, do you think is it
technically easy to code? Politically?

 Additional question: it is possible/a good idea to give to a note the
same CK as a an existing reference ?

Thanks in advance.

Cheers,

Marc.


PS: maybe I did not understand the rationale for "xnotes"

Re: [Refdb-users] refdb/mysql problems under Cygwin -- please help

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

Gary Lupyan writes:
 > Markus, I got it to work last night :)  The problem was 
 > several-fold.  First, I created the refdb1 database (as per instructions), 
 > but not the other database.  I realized something was missing when looking 
 > at the logs, I saw it was trying to lock tables that didn't exist.
 >   Secondly, I set serverip to the actual ip of my machine as the readme 
 > file that came with the cygwin release said to do.  Apparently that was the 
 > problem.  When I switched it back to 127.0.0.1, it worked.  I still can't 
 > run mysqlc inside cygwin (although I can run it in DOS when mysqld is 
 > loaded inside cygwin).  The cygwin dll file is in the same place as the 
 > mysql executables.
 > 

Glad it worked out. I'll have to check the serverip thing as I've been
told the opposite previously - I'll check tomorrow what I use at work.

 > I then had some problems with the web interface -- namely the refdbc that 
 > was inside cgi-bin wasn't reading its configuration file, and I couldn't 
 > use the -y switch through the web.  I realized that refdbd, refdba, and the 
 > interactive refdbc all read the config files in my home directory by 
 > default.  This is the precompiled version of refdb I'm talking about-- is 
 > there a way way to change it so that it reads configs from a common 
 > directory?

This is actually the default (/usr/local/etc/refdb/*) but I'm afraid
the prebuilt Cygwin binaries have a problem here. Alan created them
using a virtual root which may have screwed up the compiled-in
defaults. You could try to replace cgi-bin/refdbc with a shell script
that calls refdbc with the appropriate parameter. I've never tried
this, though.

 > Another issue with the web version is that the precompiled .html files had 
 > the wrong links -- I had to add /refdb/ to all the link locations 
 > manually.  That worked fine, but now the only issue is that when I submit a 
 > web request to refdbc, the stuff it prints still has the default links.  Do 
 > you know if I can recompile just refdbc with the appropriate switches?
 > 

This is most likely due to the same problem with the virtual
root. RefDB 0.9.3 and 0.9.4-pre1 build out of the box on Cygwin, so
this might be the cleanest way to fix these things. I'll do another
binary release as soon as time permits.

regards,
Markus

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

Re: [Refdb-users] refdb/mysql problems under Cygwin -- please help

[Gary L. <gl...@cn...>]

Markus, I got it to work last night :)  The problem was 
several-fold.  First, I created the refdb1 database (as per instructions), 
but not the other database.  I realized something was missing when looking 
at the logs, I saw it was trying to lock tables that didn't exist.
  Secondly, I set serverip to the actual ip of my machine as the readme 
file that came with the cygwin release said to do.  Apparently that was the 
problem.  When I switched it back to 127.0.0.1, it worked.  I still can't 
run mysqlc inside cygwin (although I can run it in DOS when mysqld is 
loaded inside cygwin).  The cygwin dll file is in the same place as the 
mysql executables.

I then had some problems with the web interface -- namely the refdbc that 
was inside cgi-bin wasn't reading its configuration file, and I couldn't 
use the -y switch through the web.  I realized that refdbd, refdba, and the 
interactive refdbc all read the config files in my home directory by 
default.  This is the precompiled version of refdb I'm talking about-- is 
there a way way to change it so that it reads configs from a common 
directory?
Another issue with the web version is that the precompiled .html files had 
the wrong links -- I had to add /refdb/ to all the link locations 
manually.  That worked fine, but now the only issue is that when I submit a 
web request to refdbc, the stuff it prints still has the default links.  Do 
you know if I can recompile just refdbc with the appropriate switches?

At 01:15 AM 11/16/2003 +0100, you wrote:
>Hi Gary,
>
>Gary Lupyan writes:
>  > Hi, I've been struggling to get refdb working under Cygwin.  If anyone
>  > could help me get the following issues resolved, I'd be very appreciative.
>  >
>  > The main problem seems to be failure of refdbd to communicate propertly
>  > with mySQL (or to relay information to refdba/refdbc)
>  >
>
>I used to have the Cygwin/MySQL combo at some time at my workplace. It
>did work so we should get yours to work too. However, is there any
>particular reason why you don't use PostgreSQL which is available as a
>Cygwin package? This is what I currently run at work and it was pretty
>smooth to set up.
>
>  > The mysql daemon works fine from dos.  I was able to create the initial
>  > table structures from refb.dump.  Although I can run mysqld in cygwin 
> (and
>  > it loads up fine), I can't get the comman-line mysqlc to work under 
> cygwin
>  > (although strangely it works in dos), but I think that's not the main 
> issue.
>  >
>
>I'm afraid it is an issue. The MySQL command-line client is a wrapper
>around libmysqlclient which is also used by the libdbi driver. If the
>client fails, the libdbi driver is likely to fail too.
>
>  > Finally, I realized that refdbd/a/c weren't reading the configuration 
> files
>  > properly for some reason.  Starting them with the -y switch solved the
>  > problem "-y /usr/local/etc/refdb" I also had to uncomment the 
> dbi_drivedir
>  > option in refdbdcrc :  dbi_driverdir /usr/local/lib/dbd, to get refdbd to
>  > see libdbi.
>
>Which version do you use anyway? I have been told about this problem
>with Cygwin previously but I couldn't reproduce this on my setup.
>
>  >
>  > Now when I run refdbc, I get the following errors for the various 
> commands:
>  >
>  > refdbc: whichdb
>  > cannot get row count
>  >
>  > refdbc: getau
>  > getfoo failed
>  >
>  > refdbc: listdb
>  > could not connect to database server
>  >
>  > refdbc: getref
>  > select failed
>  >
>  >
>
>This is quite inconsistent. Are all results from the same session?
>E.g. the whichdb result means that refdbd could connect to mysqld but
>got a query error. the listdb result means that refdbd couldn't even
>connect to mysqld. This makes me kinda nervous as it should either
>work all the time or fail all the time, but never "once in a while".
>
>Keep also in mind that unless you successfully created a reference
>database and selected that as your current database, most of the above
>commands will fail anyway. A reference database is different from the
>refdb1 system database.
>
>  > The serverip in the config files is set to the ip of my machine.  I 
> checked
>  > the mysql user permissions and they seem fine -- I'm trying to log in 
> as a
>  > superuser so that shouldn't be the problem.
>  >
>
>Could you please compile as much debug info as possible and send it to
>me via private mail? Things I'm interested in are:
>
>/usr/local/etc/refdbd/*
>/var/log/refdb* with a log level set to 7
>the mysqld log (wherever that is)
>a dump of the mysql.user table
>the output of mysql:"SHOW DATABASES"
>the output of mysql:"SHOW TABLES" after selecting your reference
>database
>
>regards,
>Markus

[Refdb-users] refdb/mysql problems under Cygwin -- please help

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

Hi Gary,

Gary Lupyan writes:
 > Hi, I've been struggling to get refdb working under Cygwin.  If anyone 
 > could help me get the following issues resolved, I'd be very appreciative.
 > 
 > The main problem seems to be failure of refdbd to communicate propertly 
 > with mySQL (or to relay information to refdba/refdbc)
 > 

I used to have the Cygwin/MySQL combo at some time at my workplace. It
did work so we should get yours to work too. However, is there any
particular reason why you don't use PostgreSQL which is available as a
Cygwin package? This is what I currently run at work and it was pretty
smooth to set up.

 > The mysql daemon works fine from dos.  I was able to create the initial 
 > table structures from refb.dump.  Although I can run mysqld in cygwin (and 
 > it loads up fine), I can't get the comman-line mysqlc to work under cygwin 
 > (although strangely it works in dos), but I think that's not the main issue.
 > 

I'm afraid it is an issue. The MySQL command-line client is a wrapper
around libmysqlclient which is also used by the libdbi driver. If the
client fails, the libdbi driver is likely to fail too.

 > Finally, I realized that refdbd/a/c weren't reading the configuration files 
 > properly for some reason.  Starting them with the -y switch solved the 
 > problem "-y /usr/local/etc/refdb" I also had to uncomment the dbi_drivedir 
 > option in refdbdcrc :  dbi_driverdir /usr/local/lib/dbd, to get refdbd to 
 > see libdbi.

Which version do you use anyway? I have been told about this problem
with Cygwin previously but I couldn't reproduce this on my setup.

 > 
 > Now when I run refdbc, I get the following errors for the various commands:
 > 
 > refdbc: whichdb
 > cannot get row count
 > 
 > refdbc: getau
 > getfoo failed
 > 
 > refdbc: listdb
 > could not connect to database server
 > 
 > refdbc: getref
 > select failed
 > 
 > 

This is quite inconsistent. Are all results from the same session?
E.g. the whichdb result means that refdbd could connect to mysqld but
got a query error. the listdb result means that refdbd couldn't even
connect to mysqld. This makes me kinda nervous as it should either
work all the time or fail all the time, but never "once in a while".

Keep also in mind that unless you successfully created a reference
database and selected that as your current database, most of the above
commands will fail anyway. A reference database is different from the
refdb1 system database.

 > The serverip in the config files is set to the ip of my machine.  I checked 
 > the mysql user permissions and they seem fine -- I'm trying to log in as a 
 > superuser so that shouldn't be the problem.
 > 

Could you please compile as much debug info as possible and send it to
me via private mail? Things I'm interested in are:

/usr/local/etc/refdbd/*
/var/log/refdb* with a log level set to 7
the mysqld log (wherever that is)
a dump of the mysql.user table
the output of mysql:"SHOW DATABASES"
the output of mysql:"SHOW TABLES" after selecting your reference
database

regards,
Markus

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

[Refdb-users] refdb/mysql problems under Cygwin -- please help

[Gary L. <gl...@cn...>]

Hi, I've been struggling to get refdb working under Cygwin.  If anyone 
could help me get the following issues resolved, I'd be very appreciative.

The main problem seems to be failure of refdbd to communicate propertly 
with mySQL (or to relay information to refdba/refdbc)

The mysql daemon works fine from dos.  I was able to create the initial 
table structures from refb.dump.  Although I can run mysqld in cygwin (and 
it loads up fine), I can't get the comman-line mysqlc to work under cygwin 
(although strangely it works in dos), but I think that's not the main issue.

Finally, I realized that refdbd/a/c weren't reading the configuration files 
properly for some reason.  Starting them with the -y switch solved the 
problem "-y /usr/local/etc/refdb" I also had to uncomment the dbi_drivedir 
option in refdbdcrc :  dbi_driverdir /usr/local/lib/dbd, to get refdbd to 
see libdbi.

Now when I run refdbc, I get the following errors for the various commands:

refdbc: whichdb
cannot get row count

refdbc: getau
getfoo failed

refdbc: listdb
could not connect to database server

refdbc: getref
select failed


when I use redba, I just get "could not connect to database server" errors.
I know that refdbc is communicating with mysql on some level since if 
mysqld isn't running, it also gives me "could not connect to database server"

The serverip in the config files is set to the ip of my machine.  I checked 
the mysql user permissions and they seem fine -- I'm trying to log in as a 
superuser so that shouldn't be the problem.

Does anyone have any ideas?
Thank you.

[Refdb-users] improved DocBook citation support proposal (RFE 810932)

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

Hi,

I would like to draw your attention to RFE 810932 which suggests to
improve the support for citations in scholarly works. The main goal of
the proposed changes is to make the formatting of citations and
bibliographic references according to a publisher-supplied style
specification feasible and to allow DocBook to be used for documents
that have more demanding requirements for citations.

The proposal was discussed at the DocBook TC meeting on October
22. The TC concluded that it requires further discussion. The full
text of the proposal (a collaborative effort of Bruce D'Arcus, Peter
Flynn, and myself) is accessible as one of the followups to RFE
810932:

http://sourceforge.net/tracker/index.php?func=detail&aid=810932&group_id=21935&atid=384107

Please feel free to comment on the proposal, either in the RFE tracker
or on the docbook mailing lists.

regards,
Markus

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

Re: [Refdb-users] RefDB question

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

On Thu, 6 Nov 2003, Markus Hoenicka wrote:

> First of all, I'd recommend to upgrade to 0.9.4-pre1
> (http://refdb.sourceforge.net/pre/refdb-0.9.4-pre1.tar.gz) which fixes
> a couple of bugs still present in 0.9.3.

Markus,

  I'll do that, thank you very much.

> The tags listed are indeed the only ones supported right now. They
> essentially cover whatever RefMan offers.

  I thought that was the case, but I needed to confirm it.

> RefDB currently treats RPRT entries like books. I was just guessing so
> this may be all wrong. Therefore it would not be a good choice for
> circulars. I'd rather use JOUR instead and use JF as the name of the
> circular.

  OK. I don't care what it is as long as it works with your system.

Here are a couple of examples of the type of entries I need to make:

TY  - RPRT
AV  - 113
AU  - Altman,B.
AU  - Henson,C.M.
AU  - Waite,I.R.
PY  - 1997///
TI  - Summary of information on aquatic biota and their habitats in the
Willamette Basin, Oregon, through 1995.
PB  - USGS
JF  - Water Resources Investigations Report 97-4023.
EP  - 174
KW  - aquatic
KW  - biota
KW  - habitats
KW  - willamette
ER  -

  (I'll change this to type JOUR). Otherwise, is this appropriate? I'll also
change EP to SP, or I can use SP  - 1 and EP  - 174.

TY  - NEWS
AV  - 114
PB  - U.S. Department of the Interior.
PY  - 2000///
TI  - NEPA Revised Implementing Procedures; Notice.
JO  - Fed. Reg. Aug. 28, 2000
IS  - 167
SP  - 52211
EP  - 52241
KW  - NEPA
KW  - EIA
KW  - regulations
ER  -

   The "AV" tag is a sequential number. I put everything (but regular books)
in shelf boxes and they're numbered as I process them with no regard for
topics or anything else.

> This would screw up things. You can use SP without EP, but not the other
> way round. Using SP for the total number is probably as close as you can
> get.

  OK. Works for me. :-)

Rich

Dr. Richard B. Shepard, President

                       Applied Ecosystem Services, Inc. (TM)
            2404 SW 22nd Street | Troutdale, OR 97060-1247 | U.S.A.
 + 1 503-667-4517 (voice) | + 1 503-667-8863 (fax) | rshepard@appl-ecosys.com
                         http://www.appl-ecosys.com/

[Refdb-users] RefDB question

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

Hi Rich,

Rich Shepard writes:
 >   I've recently discovered refdb (version 0.9.3) and I'm starting the long,
 > boring process of converting my reference library to the RIS format. Which
 > brings up the question, are the tags listed in the tutorial the only ones
 > allowed?
 > 

First of all, I'd recommend to upgrade to 0.9.4-pre1
(http://refdb.sourceforge.net/pre/refdb-0.9.4-pre1.tar.gz) which fixes
a couple of bugs still present in 0.9.3.

The tags listed are indeed the only ones supported right now. They
essentially cover whatever RefMan offers.

 >   Many of my references are circulars and the like from resource agencies.
 > I give them the TYpe of "RPRT", but I'm not sure what to use for the name of
 > the circular, research report or other type of report. Do I use the JF (full
 > name of journal) or something else? Similarly, these reports -- as well as

RefDB currently treats RPRT entries like books. I was just guessing so
this may be all wrong. Therefore it would not be a good choice for
circulars. I'd rather use JOUR instead and use JF as the name of the
circular.

 > books -- have a total number of pages, not a page range. Is is proper to use
 > the "EP" tag without a "SP" tag?
 > 

This would screw up things. You can use SP without EP, but not the
other way round. Using SP for the total number is probably as close as
you can get.

regards,
Markus

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

[Refdb-users] RefDB question

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

  I've recently discovered refdb (version 0.9.3) and I'm starting the long,
boring process of converting my reference library to the RIS format. Which
brings up the question, are the tags listed in the tutorial the only ones
allowed?

  Many of my references are circulars and the like from resource agencies.
I give them the TYpe of "RPRT", but I'm not sure what to use for the name of
the circular, research report or other type of report. Do I use the JF (full
name of journal) or something else? Similarly, these reports -- as well as
books -- have a total number of pages, not a page range. Is is proper to use
the "EP" tag without a "SP" tag?

Many thanks,

Rich

Dr. Richard B. Shepard, President

                       Applied Ecosystem Services, Inc. (TM)
            2404 SW 22nd Street | Troutdale, OR 97060-1247 | U.S.A.
 + 1 503-667-4517 (voice) | + 1 503-667-8863 (fax) | rshepard@appl-ecosys.com
                         http://www.appl-ecosys.com/