refdb-users — List for RefDB users

Re: [Refdb-users] cannot add records!

[Matt P. <mat...@ut...>]

To: ref...@li...
Cc: 
Bcc: 
Subject: Re: [Refdb-users] difficulty with refdba
Reply-To: 
In-Reply-To: <163...@ti...>

On Tue, Jan 20, 2004 at 09:43:20PM +0100, Markus Hoenicka wrote:
> Matt Price writes:
> 
> There's a couple of options, actually:
> 
> - customize (or copy+edit) backend-html.c until it does what you
>   need. This is fairly easy, but you'll have to apply your patches to
>   each new release (and pray the patches *do* apply...)
> 
> - use refdbc to retrieve the datasets as db31x, teix, risx, or
>   xhtml. All of these XML output formats are suitable to be
>   transformed by a nice XSLT stylesheet to whatever format you desire,
>   including straight HTML.
> 
> - use the Perl client module and write your custom client in
>   Perl. This could use e.g. the risx output and mangle it until you
>   like the results. Perl should have an interface to libxslt, so you
>   could do the XML->HTML transformation transparently to the user.
> 
> If you go down any of these paths, I'm sure the readers of this list
> will be interested in the results.

welll..  I guess I need to figure out whether I most want to learn c, XSLT,
or Perl...!  I actually have an interim solution in PHP that I should
be able to throw together pretty quickly (stealing someone else's
code, and adapting it to the refdb db structure; this will be
mysql-specific, but should be readily adaptable to PostgreSQL with a
quick pattern-replace on the php code).  When it's more or
less working I'll let folks know.   

Then maybe later I can, like, hire someone to translate it into Perl
and use the PerlClient functions to interact directly with refdbc.  

best,
matt


> 
> hope this helps
> Markus
> 

[Refdb-users] Problems compiling pre4

[Diwaker G. <dg...@cs...>]

Hi Markus,

I've installed the latest libdbi, and libdbi-driver, and the latest 
libiconv available from GNU.org. But I'm getting lots of warnings and 
some errors when trying to compile:


refdbdref.o(.text+0x775): In function `addref':
/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:345: undefined reference 
to `libiconv_open'
refdbdref.o(.text+0xad2):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:505: 
undefined reference to `libiconv_close'
refdbdref.o(.text+0xc6f):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:377: 
undefined reference to `libiconv_close'
refdbdref.o(.text+0x10b0): In function `read_ris_data':
/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:650: undefined reference 
to `libiconv'
refdbdref.o(.text+0x3c24): In function `getref':
/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:2216: undefined reference 
to `libiconv_open'
refdbdref.o(.text+0x3d97):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:4012: 
undefined reference to `libiconv_close'
refdbdref.o(.text+0x410c):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:4024: 
undefined reference to `libiconv'
refdbdref.o(.text+0x433e):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdref.c:4087: 
undefined reference to `libiconv_close'
refdbdbib.o(.text+0x43b): In function `getbib':
/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdbib.c:267: undefined reference 
to `libiconv_open'
refdbdbib.o(.text+0x4d7):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdbib.c:561: 
undefined reference to `libiconv_close'
refdbdbib.o(.text+0x922):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdbib.c:1033: 
undefined reference to `libiconv_close'
refdbdbib.o(.text+0xff5):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdbib.c:939: 
undefined reference to `libiconv'
risxhandler.o(.text+0x2f20): In function `risx_end_handler':
/tmp/diwaker/refdb-0.9.4-pre4/src/risxhandler.c:672: undefined reference 
to `libiconv'
noteshandler.o(.text+0x1aca): In function `notes_end_handler':
/tmp/diwaker/refdb-0.9.4-pre4/src/noteshandler.c:659: undefined 
reference to `libiconv'
refdbdnote.o(.text+0x17f): In function `addnote':
/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdnote.c:131: undefined reference 
to `libiconv_open'
refdbdnote.o(.text+0x456):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdnote.c:245: 
undefined reference to `libiconv_close'
refdbdnote.o(.text+0x11cf): In function `getnote':
/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdnote.c:700: undefined reference 
to `libiconv_open'
refdbdnote.o(.text+0x133d):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdnote.c:2013: 
undefined reference to `libiconv_close'
refdbdnote.o(.text+0x15c0):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdnote.c:2025: 
undefined reference to `libiconv'
refdbdnote.o(.text+0x1811):/tmp/diwaker/refdb-0.9.4-pre4/src/refdbdnote.c:2090: 
undefined reference to `libiconv_close'
collect2: ld returned 1 exit status
make[2]: *** [refdbd] Error 1
make[2]: Leaving directory `/tmp/diwaker/refdb-0.9.4-pre4/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/tmp/diwaker/refdb-0.9.4-pre4/src'
make: *** [all-recursive] Error 1

-- 
Diwaker Gupta
Graduate Student, Computer Sc. and Engg.
University of California, San Diego
<http://www.cse.ucsd.edu/users/dgupta>

[Refdb-users] ANN: refdb-0.9.4-pre4 available for testing

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

Hi all,

there's a new prerelease available at:

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

We're getting closer to 0.9.4, but there were some substantial changes
compared to the previous prerelease which make another pre seem like a
good idea.

This release requires the brand-new libdbi-0.7.2 and
libdbi-drivers-0.7.1 versions released last weekend. refdbd gained an
additional dependency as it now requires libiconv.

Besides fixing a couple of bugs and memory leaks, this prerelease
improves the character encoding issue. As Marc has found out, the
previous releases worked ok for risx data only if you happened to use
UTF-8 anyway. In all other cases RefDB still worked, but you might
have gotten an incorrect sorting order in the bibliography in border
cases.

The character encoding stuff now works like this (this will go into
the manual eventually):

- you select a suitable character encoding for your
  database. PostgreSQL allows to select an encoding per database, so
  you can use a suitable one by running createdb -E encoding
  dbname. MySQL allows only one encoding per server instance. Set this
  on the mysqld command line or in the config file. SQLite allows only
  two encodings as a compile-time option.

- RIS input can use any encoding that your local libiconv
  understands. If it is not the default (UTF-8), you have to specify
  the input encoding using the addref/updateref -E switch (or set
  fromencoding in refdbcrc accordingly)

- risx and xnote input can use one of these encodings: UTF-8, UTF-16,
  ISO-8859-1, US-ASCII. The encoding must be declared in the
  processing instruction (the first line of the risx file) like this:
  <?xml version="1.0"? encoding="UTF-16">
  unless it is the default (UTF-8).
  If you have to use a different encoding, use the iconv command line
  utility to convert the data to one of the acceptable encodings
  before sending the data to refdbd.

- getref and getnote send back the data in the encoding used by the
  database unless you request a different encoding with the -E
  switch. You can request any output encoding that your local libiconv
  supports. The same applies to the refdbib tool.

- the refdbc:whichdb shows the character encoding of the current
  database.

regards,
Markus


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

Re: [Refdb-users] cannot add records!

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

Diwaker Gupta writes:
 > Thanks, that solved some of the problems, though not all. Now I'm able 
 > to add references using both the web interface and the command line 
 > interface. In the command shell, getau, getes and so on work just fine. 
 > But getref still returns with a "select failed". Any ideas?

Could you please provide a full log output of what you're doing?

- stop refdbd and restart it like this: refdbd -e 2 -l 7 -L
  /path/to/log

- create a new database

- add example ris data

- run getau and getref queries to reproduce the problem

- send the log file to the list please.

thanks,
Markus

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

Re: [Refdb-users] difficulty with refdba

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

Matt Price writes:
 > how it works...  very impressive, very sophisticated.  I was wondering
 > whether it's possible to modify the output of getref -t html... I've
 > looked at the css, that does help.  But mostly I'd like to be able to
 > remove the ID number & some of the paragraph markings, and to put the
 > output into table form (each reference in its own row table cell, &
 > followed by a couple of buttons "edit this reference" "comment on this
 > reference").  I've written some clumsy php which does this already,
 > but I haven't got the energy to deal with complex reference types so
 > it would be way better to use refdb if I can.  
 > 
 >   I just wondered whether there was a straightforward way to do this
 >   or not...  I suppose it would be possible to parse the output using
 >   perl or something, but it somehow seems cleaner to be able to choose
 >   the fields that actually print out...
 > 

There's a couple of options, actually:

- customize (or copy+edit) backend-html.c until it does what you
  need. This is fairly easy, but you'll have to apply your patches to
  each new release (and pray the patches *do* apply...)

- use refdbc to retrieve the datasets as db31x, teix, risx, or
  xhtml. All of these XML output formats are suitable to be
  transformed by a nice XSLT stylesheet to whatever format you desire,
  including straight HTML.

- use the Perl client module and write your custom client in
  Perl. This could use e.g. the risx output and mangle it until you
  like the results. Perl should have an interface to libxslt, so you
  could do the XML->HTML transformation transparently to the user.

If you go down any of these paths, I'm sure the readers of this list
will be interested in the results.

hope this helps
Markus

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

[Refdb-users] cannot add records!

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

Diwaker Gupta writes:
 > Hello,
 > 
 > I'm running refdb 0.9.3 using MySQL 4.0.22 as the backend. I installed 
 > and tested the installation as given in the manual without any problems. 
 > However, there are some issues:
 > 

0.9.3 was not yet able to deal with MySQL > 4.0. As Bruce mentioned,
and as you apparently found out meanwhile, the newer prerelease
autodetect the MySQL version and cooperate a lot better.

 > 3. I am facing several problems with the web interface. First of all, 
 > all the html files in refdb have absolute URLs (like 
 > "/refdbquery.html"). If I create an alias /refdb to refdb's html files, 
 > then no links work. Further, sometimes I get an error saying "error 
 > loading cgi templates"
 > 

This is mainly an issue of a missing URL in the ./configure argument
list. Please see the documentation how to specify the desired URL. The
templates are modified during make to use the proper URLs then.

regards,
Markus

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

Re: [Refdb-users] cannot add records!

[Diwaker G. <dg...@cs...>]

Thanks, that solved some of the problems, though not all. Now I'm able 
to add references using both the web interface and the command line 
interface. In the command shell, getau, getes and so on work just fine. 
But getref still returns with a "select failed". Any ideas?

Bruce D'Arcus wrote:
> 
> On Jan 19, 2004, at 9:27 PM, Diwaker Gupta wrote:
> 
>> I'm running refdb 0.9.3
> 
> 
> I can't help with the other details, but I would suggest updating to the 
> latest 0.9.4-whatever release.
> 
> Bruce
> 

-- 
Diwaker Gupta
Graduate Student, Computer Sc. and Engg.
University of California, San Diego
<http://www.cse.ucsd.edu/users/dgupta>

Re: [Refdb-users] difficulty with refdba

[Matt P. <mat...@ut...>]

On Tue, Jan 20, 2004 at 12:23:39AM +0100, Markus Hoenicka wrote:
> Matt Price writes:
>  > mysql -u matt refdb1 -p
> [...]
>  > ... so I assume the problem is somewhere in my refdb set up.  I know
>  > this should be simple, but if someone can help me with debugging &c
>  > I'd be grateful!  thanks,
> 
> Your analysis is impressive. I hope you won't bang your head against
> your monitor after you find out the reason. Due to a change in the
> database schema of the system database I had to rename it to
> refdb. This way you can run a release version and a prerelease in
> parallel if you need to. All you need to do is to create the system
> database as mentioned in the manual, but make sure to name it "refdb"
> (this was announced on the list and is mentioned in the file
> UPGRADING). I apologize for the inconvenience.

gaah, sorry, didn't read upgrading so carefully as I haven't REALLY 
been using refdb the last little while...   
 
So about 9 months ago I was hoping to start a project to make a
web-accessible shared bibliography for use in my classes.  Now, with
the classes mostly already finished...  I'm trying to start
again.  I I've got refdb running now, so I have a somewhat better idea of
how it works...  very impressive, very sophisticated.  I was wondering
whether it's possible to modify the output of getref -t html... I've
looked at the css, that does help.  But mostly I'd like to be able to
remove the ID number & some of the paragraph markings, and to put the
output into table form (each reference in its own row table cell, &
followed by a couple of buttons "edit this reference" "comment on this
reference").  I've written some clumsy php which does this already,
but I haven't got the energy to deal with complex reference types so
it would be way better to use refdb if I can.  

  I just wondered whether there was a straightforward way to do this
  or not...  I suppose it would be possible to parse the output using
  perl or something, but it somehow seems cleaner to be able to choose
  the fields that actually print out...

anyway, hope this question is cohrent.  getting late here!  alles
beste,
matt

> 
> regards,
> Markus
> 

Re: [Refdb-users] cannot add records!

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

On Jan 19, 2004, at 9:27 PM, Diwaker Gupta wrote:

> I'm running refdb 0.9.3

I can't help with the other details, but I would suggest updating to 
the latest 0.9.4-whatever release.

Bruce

[Refdb-users] cannot add records!

[Diwaker G. <dg...@cs...>]

Hello,

I'm running refdb 0.9.3 using MySQL 4.0.22 as the backend. I installed 
and tested the installation as given in the manual without any problems. 
However, there are some issues:

1. I can add styles, and I can check (using raw sql) that the styles are 
indeed added to the CITSTYLE table. However, when I issue a liststyle, I 
get nothing. Ditto for listuser

2. Whenever I try to add a reference, I get an error from refdb saying:

refdbc: addref /tmp/diwaker/test.ris
try to add set as reference 2
update TY failed
Processing set 0 failed
0 dataset(s) added, 0 skipped, 1 failed
1 dataset(s) sent.

The log gives an error message like:
6:pid=24231:Tue Jan 20 02:24:15 2004:dbi is up
4:pid=24231:Tue Jan 20 02:24:15 2004:update TY failed
4:pid=24231:Tue Jan 20 02:24:15 2004:failed processing dataset
6:pid=24231:Tue Jan 20 02:24:15 2004:no IDs found for keyword scan

At other times, it gives an error saying "cannot lock tables"

3. I am facing several problems with the web interface. First of all, 
all the html files in refdb have absolute URLs (like 
"/refdbquery.html"). If I create an alias /refdb to refdb's html files, 
then no links work. Further, sometimes I get an error saying "error 
loading cgi templates"

I can use all the help! :)

Thanks
-- 
Diwaker Gupta
Graduate Student, Computer Sc. and Engg.
University of California, San Diego
<http://www.cse.ucsd.edu/users/dgupta>

[Refdb-users] difficulty with refdba

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

Matt Price writes:
 > mysql -u matt refdb1 -p
[...]
 > ... so I assume the problem is somewhere in my refdb set up.  I know
 > this should be simple, but if someone can help me with debugging &c
 > I'd be grateful!  thanks,

Your analysis is impressive. I hope you won't bang your head against
your monitor after you find out the reason. Due to a change in the
database schema of the system database I had to rename it to
refdb. This way you can run a release version and a prerelease in
parallel if you need to. All you need to do is to create the system
database as mentioned in the manual, but make sure to name it "refdb"
(this was announced on the list and is mentioned in the file
UPGRADING). I apologize for the inconvenience.

regards,
Markus

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

[Refdb-users] difficulty with refdba

[Matt P. <mat...@ut...>]

Hi there,

u, I'm having a little trouble getting refdba to work with the current
refdb prerelease.  I'm using mysql and and had no trouble creating the
refdb1 database; refdbd starts up fine; and I can connect just fine to
refdb1 using the mysql command-line:

mysql -u matt refdb1 -p

I've edited /etc/refdbarc to include my user name and password, and
I've looked at refdbdrc and everything looks ok there (though I'm not
absolutely sure which port my mysql server runs on, I haven't messed
with it so I assume that's not a problem.  

refdbd starts up fine, fand using the switches suggested in the manual
for installaiton testing, I get the following output: 

[root@anarres<520>/etc/refdb]$ refdbd -s -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
sqlite
mysql
pgsql
application server started
use /tmp/refdbd_fifo15971 as fifo
server waiting n_max_fd=4

---------------------
I then switch to another terminal to run refdba

 refdba -u matt
Please enter your password: 
refdba: set
serverip 127.0.0.1
port 9734
verbose f
pager stdout
username matt
timeout 60
logfile /var/log/refdba.log
logdest 2
loglevel 6
refdblib 
refdba: viewstat
could not connect to database server

-----------------------
looking in the refdbd window, I see: 

parent removing client on fd 5
server waiting n_max_fd=4
try to read from client
serving client on fd 5 with protocol version 1
201-89-34-90
send pseudo-random string to client
viewstat  -u matt -w 093092109054059125064105
dbi is up
localhost
matt
<password deleted>

3306
mysql

refdb
failed to connect to database server
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
server waiting n_max_fd=4
-------------------------

obviously there's some problem with the connectin, but I'm not sure
how to figure out what it is.  mysql seems to be up and accepting tcp
requests:

$ netstat -tlnp  | grep -i mysql 
tcp        0      0 0.0.0.0:3306 0.0.0.0:* LISTEN     1486/mysqld      

... so I assume the problem is somewhere in my refdb set up.  I know
this should be simple, but if someone can help me with debugging &c
I'd be grateful!  thanks,

matt

Re: [Refdb-users] frbr

[Marc H. <mar...@fr...>]

On Fri, 16 Jan 2004, Markus Hoenicka wrote:

>  > >
>  > > The distinction between expression and manifestation is useful for
>  > > works that are performed but usually can be ignored for works that
>  > > have a single expression, like most journal articles. Journal articles
>  > > represent three types of creations: the work, or creative output of
>  > > the author(s); the manifestations, or instantiations of the work in
>  > > print and/or electronic form; and the items, or specific copies of a
>  > > manifestation. An article, for example, could have been published in a
>  > > print and an electronic version. These would be separate
>  > > manifestations, each of which might have multiple items (perhaps
>  > > several hundred copies for the print run, and mirrored online and
>  > > archival copies of the electronic version).

Are these distinctions really relevant for a tool whose purpose is too
manage references? (refdb, BibTeX, Reference Manager, etc.)

I understand that librarians want a tool to track everything down to
physical instances, but is it useful to bibliographers?

Today, I guess most of us handle multiple "manifestations" like
this:
    <title type="full">IEEE Communications Magazine</title>

      <date> <year>1989</year> <month>6</month> </date>
      <volume>27</volume>  <issue>6</issue>

      <url>http://dl.comsoc.org/cocoon/comsoc/servlets/GetPublication?id=111923</url>

Isn't that enough?

Does refdb want to address the needs of librarians too?

Cheers,

Marc.

Re: [Refdb-users] frbr

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

On Jan 16, 2004, at 5:45 PM, Markus Hoenicka wrote:

> Thanks, but... could you explain this in words that an average PhD
> understands?

Am not sure ;-)

It essentially adds a meta-concept of a work, which is an abstraction 
that allow you to group together related items.  This is most clear 
when dealing with things like music.  A Beethoven symphony is a work; 
it has a creator and title.  A performance by some symphony is an 
expression, while an LP album, a CD release, and a later CD remaster of 
the performance are all manifestations.

This is less relevant for personal reference management (thought the 
Pybliographer people want to implement those ideas), but you can 
imagine the utility in a large catalog.  A search would return all of 
those manifestations as part of the same Beethoven symphony, instead of 
say 100 separate records.

Bruce

[Refdb-users] frbr

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

Bruce D'Arcus writes:
 > 
 > > In the IFLA model, a "work" is an abstract conception of some creator. 
 > > Works are realized through "expressions", which are fixed 
 > > spatial/temporal representations of works, such as a performance of a 
 > > play or a symphony. Expressions in turn are embodied in 
 > > "manifestations", physical representations such as printed books or 
 > > recorded CDs, which may or may not be mass-produced. A specific, 
 > > single manifestation is an "item", also called a "copy".
 > >
 > > The European INDECS project has done a careful analysis of these 
 > > distinctions and proposes a categorization that, while somewhat 
 > > different from the IFLA model, is mainly compatible with it [INDECS]. 
 > > Supplementing the IFLA and INDECS terminology, the International DOI 
 > > Foundation (IDF) has contributed "creation" as a useful generic term 
 > > encompassing the work and all of its expressions, manifestations and 
 > > items.
 > >
 > > The distinction between expression and manifestation is useful for 
 > > works that are performed but usually can be ignored for works that 
 > > have a single expression, like most journal articles. Journal articles 
 > > represent three types of creations: the work, or creative output of 
 > > the author(s); the manifestations, or instantiations of the work in 
 > > print and/or electronic form; and the items, or specific copies of a 
 > > manifestation. An article, for example, could have been published in a 
 > > print and an electronic version. These would be separate 
 > > manifestations, each of which might have multiple items (perhaps 
 > > several hundred copies for the print run, and mirrored online and 
 > > archival copies of the electronic version).
 > 

Thanks, but... could you explain this in words that an average PhD
understands?

thanks
Markus

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

[Refdb-users] the real world (prism example)

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

I was just looking at an interesting new RDF spec called PRISM that is  
designed by the publishing industry to allow stuff like RSS feeds for  
journal and magazine articles (a great idea!).  The schema seems  
well-designed, but there is this typical data problem that won't go  
away, and which means the need for algorithms and RegExp handling or  
tedious tuning of the metadata, sadly.  No endPage, no subtitle  
element, and names ... ugh.  I just sent them comments...

Example:

<item  
rdf:about="http://www.sciencedirect.com/science/article/B6THR-48TMY6Y 
-5/1/94f6ab601fa5489db522037d805d2275">
<title>Solid-supported synthesis of oligomeric bioconjugates</title>
<link>http://www.sciencedirect.com/science/article/B6THR-48TMY6Y-5/1/ 
94f6ab601fa5489db522037d805d2275</link>
<description>Solid-supported synthesis of oligomeric bioconjugates,  
Pages 5137-5174
Pasi Virta, Johanna Katajisto, Teija Niittymaki and Harri  
Lonnberg</description>
<dc:title>Solid-supported synthesis of oligomeric  
bioconjugates</dc:title>
<dc:creator>Pasi Virta, </dc:creator>
<dc:creator>Johanna Katajisto, </dc:creator>
<dc:creator>Teija Niittymaki, </dc:creator>
<dc:creator>Harri Lonnberg, </dc:creator>
<prism:publicationName>Tetrahedron</prism:publicationName>
<prism:volume>59</prism:volume>
<prism:number>28</prism:number>
<prism:startingPage>5137</prism:startingPage>
</item>

[Refdb-users] Fwd: xlink and rdf?

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

Here's an interesting proposal for solving the problem of names that 
has been a subject of great contention on the refdb list recently.  In 
short, the question is how do you have an international-friendly 
metadata model and formatting system that knows what to do with "Samuel 
John van Doe, III", where the first name would generally be 
abbreviated, but the second not (e.g. that this person uses the 
"middle" name as their primary given name)?

As Andy (a contributor to the MODS list) notes, however, XSLT v1 may 
not be able to handle this terribly gracefully.  I imagine XSLT 2 is 
better equipped for it with its regular expression support...

Bruce

Begin forwarded message:

> From: "Andrew E Switala" <and...@lo...>
> Date: January 15, 2004 9:13:21 AM EST
> To: <bd...@fa...>
> Subject: Re: xlink and rdf?
>
> Regarding the name issue, I've been thinking <displayForm> might come 
> in
> handy as a hint to the processor for proper formatting.
>
> <name>
>     <namePart type="family">Kraepelin</namePart>
>     <namePart type="given">Emil </namePart>
>     <namePart type="given">Wilhelm </namePart>
>     <namePart type="given">Magnus </namePart>
>     <namePart type="given">Georg</namePart>
>     <displayForm>Emil Kraepelin</displayForm>
> </name>
>
> The <displayForm> indicates Kraepelin signed his articles Emil
> Kraepelin, and the citation information should read "Kraelpelin, Emil"
> or "Kraepelin, E." rather than "Kraepelin, E.W.M.G.", say.
>
> <name>
>     <namePart type="family">Torrey</namePart>
>     <namePart type="given">Exxxxx </namePart>
>     <namePart type="given">Fuller </namePart>
>     <displayForm>E. Fuller Torrey</displayForm>
> </name>
>
> Here it indicates Fuller Torrey goes by his "middle" name (the x's are
> there because I don't actually know what the E. stands for; pretend
> there's his real first name in the <namePart>).
>
> --Andy

[Refdb-users] frbr

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

Experts in bibliographic metadata often mention the FRBR as the future 
of library cataloguing. Wondering about its relevance to my needs in 
part because of a new project based on it called LibDB, I poked around 
and found this document:

http://www.dlib.org/dlib/july99/caplan/07caplan.html#INDECS

Here's an excerpt for Markus to ponder as he thinks about RefDB's 
internal data model:

> In the IFLA model, a "work" is an abstract conception of some creator. 
> Works are realized through "expressions", which are fixed 
> spatial/temporal representations of works, such as a performance of a 
> play or a symphony. Expressions in turn are embodied in 
> "manifestations", physical representations such as printed books or 
> recorded CDs, which may or may not be mass-produced. A specific, 
> single manifestation is an "item", also called a "copy".
>
> The European INDECS project has done a careful analysis of these 
> distinctions and proposes a categorization that, while somewhat 
> different from the IFLA model, is mainly compatible with it [INDECS]. 
> Supplementing the IFLA and INDECS terminology, the International DOI 
> Foundation (IDF) has contributed "creation" as a useful generic term 
> encompassing the work and all of its expressions, manifestations and 
> items.
>
> The distinction between expression and manifestation is useful for 
> works that are performed but usually can be ignored for works that 
> have a single expression, like most journal articles. Journal articles 
> represent three types of creations: the work, or creative output of 
> the author(s); the manifestations, or instantiations of the work in 
> print and/or electronic form; and the items, or specific copies of a 
> manifestation. An article, for example, could have been published in a 
> print and an electronic version. These would be separate 
> manifestations, each of which might have multiple items (perhaps 
> several hundred copies for the print run, and mirrored online and 
> archival copies of the electronic version).

Bruce

Re: [Refdb-users] RE: reversibility patch (cumulative reply)

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

On Jan 14, 2004, at 6:14 PM, Markus Hoenicka wrote:

> I'm not sure whether this helps that much. The data can't be in
> "whatever XML form" as refdb needs to have a chance to parse it. It
> must know the form in advance or you have to send the data through an
> xslt processor before parsing them. However, RefDB could specify an
> authoritative input format (this is probably what you meant anyway).

Yes, I mean "whatever form" from the standpoint of validation.  
Obviously processors (XSLT engines, RefDB input handlers, etc.) need to 
understand that form though.  My vote would be for one of the RDF 
person/org representations, or MADS.

MADS is being designed precisely to be able to link to from MODS 
records.  I don't really know, frankly, how much they're willing to 
parse names, but it is worth noting that MARC (upon which this is 
drawing) already parses names more fully than MODS.  The library people 
in general don't tend to think about these issues in the same way that 
we do, but they've certainly heard from me on it enough over the past 
six months!

Bruce

[Refdb-users] Starter-kit fails on OS X

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

Markus Hoenicka writes:
 >  > btparse-0.33:
 >  > 
 >  > During ./configure, an error is reported in btparse-0.33/src/lex_auxiliary.c 
 >  > line 161.
 >  > 
 >  > The problem is actually on line 162:
 >  > 
 >  > Orig:
 >  >                || (txt[0] == '"' && txt[len-1] == '"'));
 >  > Solution:
 >  >                || (txt[0] == '\"' && txt[len-1] == '\"'));
 >  > 

I've just checked. There's a btparse-0.34 available which fixes this
bug.

 >  > Solution: insert host info into command line, as in:
 >  >      ./configure --host=`echo $HOST` --with-mysql
 > 
 > I thought we had fixed this one. This is a problem of too old
 > config.guess/config.sub files. In any case, libdbi and libdbi-drivers
 > are available as Fink packages.
 > 

Now I remember. Building these packages on OSX requires re-generating
all autotools-related files by running a sequence of commands which
isn't far from the sun dance ritual of the Cherokee. Please see the
libdbi-drivers list archive or the README.osx files in the packages
for the gory details.

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

Re: [Refdb-users] RE: reversibility patch (cumulative reply)

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

Bruce D'Arcus writes:
 > In other words, a MODS record could have a name defined solely like 
 > below and what's on the other end of that link can be in whatever XML 
 > form one would want:
 > 

I'm not sure whether this helps that much. The data can't be in
"whatever XML form" as refdb needs to have a chance to parse it. It
must know the form in advance or you have to send the data through an
xslt processor before parsing them. However, RefDB could specify an
authoritative input format (this is probably what you meant anyway).

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

[Refdb-users] Starter-kit fails on OS X

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

Hi,

Re...@ao... writes:
 > gcc   -g -O2    -o refdbc   refdbc.o pref.o strfncs.o readln.o page.o 
 > refdb-client.o client-commands.o readris.o connect.o tokenize.o getopt.o linklist.o 
 > enigma.o cgi.o atoll.o -lreadline -ltermcap 
 > ld: readln.o illegal reference to symbol: _xmalloc defined in indirectly 
 > referenced dynamic library /System/
 > Library/PrivateFrameworks/liberty.framework/Versions/A/liberty
 > make[1]: *** [refdbc] Error 1
 > make: *** [all-recursive] Error 1
 > 

Horrors! You wouldn't believe that some code that I stole a couple
years ago would now turn against me. I just wonder why it isn't broke
on any other system. The fix is to replace the dupstr() function with
the commonly available strdup(). Stupid, stupid, stupid... It is in
CVS now and will be available as 0.9.4 in a matter of days. I'll send
you the patched versions of readln.c and readln.h via private mail as
drop-in replacements for your current sources.

 > Other starter-kit problems with solutions, based on my OS X build:
 > 

In general you should try to use Fink packages wherever possible. I
don't own a Mac, but I've had ssh access to one of these lovely boxes
and found out the hard way that building stuff on OSX is more than an
art at times.

 > 
 > btparse-0.33:
 > 
 > During ./configure, an error is reported in btparse-0.33/src/lex_auxiliary.c 
 > line 161.
 > 
 > The problem is actually on line 162:
 > 
 > Orig:
 >                || (txt[0] == '"' && txt[len-1] == '"'));
 > Solution:
 >                || (txt[0] == '\"' && txt[len-1] == '\"'));
 > 
 > 
 > make test fails, but cd t; simple_test; suggests all is well?

I can't comment on this. The best thing is to send some test data
through bib2ris and see what happens. I don't know whether btparse is
still being developed but I'll see whether I can contact the
maintainer and get this fixed upstream.

 > 
 > expat-1.95.2 results in me a make error:
 >      ld: can't locate file for: -lcrt0.o
 >      make[1]: *** [xmlwf] Error 1
 >      make: *** [xmlwf] Error 2
 > 
 > Upgrading to expat-1.95.7 sort of fixes it:   make reports mamy error, but 
 > completes.   So maybe it tries other options to get past the many reported 
 > errors.
 > 

expat ought to be available as a Fink package. Better use that one.

 > 
 > libdbi-drivers-0.7.0:
 > 
 > I was getting errors involving incorrect host type. Change:
 > 
 > Problem:
 >      ./configure --with-mysql results in this error:
 > 
 >      checking host system type... configure: error: can not guess host type; 
 > you must specify one
 > 
 > Solution: insert host info into command line, as in:
 >      ./configure --host=`echo $HOST` --with-mysql

I thought we had fixed this one. This is a problem of too old
config.guess/config.sub files. In any case, libdbi and libdbi-drivers
are available as Fink packages.

Please note that in order to upgrade to RefDB 0.9.4 you'll need new
versions of libdbi and libdbi-drivers as well. I hope to talk Peter
into packaging them as soon as the sources are released.

One final note: I know it may be the fault of your AOL software, but
please try to avoid sending HTML mail to public mailing lists. Plain
text is just fine. Thanks.

regards,
Markus

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

Re: [Refdb-users] RE: reversibility patch (cumulative reply)

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

On Jan 14, 2004, at 5:39 PM, Markus Hoenicka wrote:

>   We'll have to push the MODS people a little in order to support the
>   required attributes. The current MODS implementation is about as
>   flawed as RIS in this respect, but as it is an open standard which
>   is still evolving we have at least a chance to get this fixed.

I want to add a note here that may influence this discussion a lot.  
The LoC is currently developing a companion XML Schema for MODS called 
(least at the moment) MADS.  This schema will handle so-called 
authority-data, including, it is my hope, more detailed name parsing.  
I think this, along with the xlink attribute in MODS, could change 
things a lot, and open up a lot of power for personal reference 
management.

In other words, a MODS record could have a name defined solely like 
below and what's on the other end of that link can be in whatever XML 
form one would want:

<name xlink:href="#doej">
    <role>
       <roleTerm type="text">author</roleTerm>
    </role>
</name>

Bruce

[Refdb-users] RE: reversibility patch (cumulative reply)

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

Hi,

it's getting too tedious for me to answer all ramifications of this
discussion in due detail, so I'll try to pick up a few loose ends from
the previous mails. This will hopefully settle a few issues.

- As a meta-note, I believe much of the confusion in this discussion
  is derived from the fact that we have a hard time to keep input
  formats and formatted author names apart. The input format has to
  supply as much information as possible in a parseable format. The
  input format is therefore not a free string. The output formats have
  to stick to the publisher's specifications even if we consider these
  specs stupid at times.

- if the discussion is only about "so-called \"middle names\"" (I
  prefer to call them what they are: either middlenames or middle
  initials), then we can indeed get to a short conclusion. At least in
  the life sciences, the following possibilities to output first and
  middle names are common practice:

  FM, F.M., F. M., First M, First M., First Middle, F, F., First

  This is independent of how the bearer of that name prefers to read
  his name. A reference manager that wants to support all variants
  ideally knows "First" and "Middle" (as separate entities) as all
  other variants can be derived from them. If you can't track down the
  full names (or can't verify whether "M" is a name as such or an
  abbreviation), there's not much you can do but use the abbreviations
  instead.

  It is quite true that Doris J. Delorie and DJ Delorie end up with
  the same formatted name if you use the first output style. However,
  this is not a bug in RefDB, this is a design decision of the
  publisher requiring that format. I can't argue about this, I just
  have to support it.

  The RIS input format is suitable to supply the full names or the
  abbreviations. It is weak in that it can't distinguish abbreviated
  names from one-letter non-abbreviated names. It also doesn't support
  "prime given names" which are not in the first position. These flaws
  will be addressed by switching over to a MODS-based format.

  BTW the Pubmed XML format (the output of the largest literature
  database in the life sciences) uses elements along the lines of
  "first", "middle", "last", "honorific".

- Just like TeX itself, BibTeX has been designed by a mathematician
  for publications in mathematical journals. It is widely used in
  mathematics, computer sciences, and engineering. The BibTeX data
  format is apparently sufficient for publications in these fields. As
  Bruce pointed out though, we should not use BibTeX as a golden
  standard. The input format is flawed compared to what XML
  has to offer. TeX/BibTeX is not accepted by most journals in the
  life sciences anyway, partly because it does not support the
  citation and bibliography requirements of these journals.

- As far as I understood the ALWD format (a legal citation style
  asking for the name "exactly as it appears on the front cover or
  title page") is probably not as flawed as I thought in the first
  moment. All examples shown in the available docs (I don't own the
  actual manual, though) use names in the natural order, that
  is "Franklin D. Roosevelt" or "Luis Lopez Penabad". I think we agree
  that this is entirely unsuitable as an input format as it is not
  parseable in any way. We still have to record this formatted string
  in addition to the parseable data if we want to support
  ALWD. Needless to say that RIS has no means to do this. A MODS-based
  input format will have.

My conclusions are:

- RIS is and remains flawed. There is no point to fiddle with it as
  you don't gain much but break a lot and lose compatibility with
  commercial tools. The best strategy is to accept the limitations and
  treat the current implementation of RefDB as a "compatibility mode".

- XML is the way to go, along with an improved data model. Something
  like the following should be sufficient to handle most names. The
  following examples assume that you don't have the full information
  about all name parts and use some abbreviations instead. If you
  *had* the information, you'd certainly enter "Jessica" instead of
  "J".

  <name>
  <namePart type="primegiven">Doris</namePart>
  <namePart type="given" abbrev="yes">J</namePart>
  <namePart type="family">Delorie</namePart>
  <displayForm>Doris J. Delorie</displayForm>
  </name>

  <name>
  <namePart type="primegiven">DJ</namePart>
  <namePart type="family">Delorie</namePart>
  <displayForm>DJ Delorie</displayForm>
  </name>

  <name>
  <namePart type="given" abbrev="yes">H</namePart>
  <namePart type="given" abbrev="yes">K</namePart>
  <namePart type="primegiven">Jerry</namePart>
  <namePart type="family">Chun</namePart>
  <displayForm>H.K. Jerry Chun</namePart>
  </name>

  <name>
  <namePart type="primegiven">Harry</namePart>
  <namePart type="given">S</namePart>
  <namePart type="family">Truman</namePart>
  <displayForm>Harry S. Truman</displayForm>
  </name>

  The displayForm element is used nowhere except in the ALWD style and
  any other style that wants the name exactly as printed on the cited
  work (this is not necessarily identical with how the author wants
  his name printed - the actual string may follow the conventions of
  the publisher of the cited work rather than the author's
  preference). This is also why Truman has a dot after his middle
  non-initial because it was just so spelled on that particular book.
  
  Please note also that the parseable data make do without any dots.

  We'll have to push the MODS people a little in order to support the
  required attributes. The current MODS implementation is about as
  flawed as RIS in this respect, but as it is an open standard which
  is still evolving we have at least a chance to get this fixed.

regards,
Markus

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

[Refdb-users] html encoding declaration

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

Markus,

Would be nice if you included an encoding declaration in the html 
output of the web interface.

Bruce