refdb-users — List for RefDB users

[Refdb-users] MODS + RefDB

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

Justus H. Piater writes:
 > If I interpret the list traffic correctly, things are converging
 > toward using MODS, and a future version of RefDB will likely be based
 > on MODS instead of RIS. Markus, is this correct?
 > 

Sort of. I've figured the cleanest way is to support two types of
databases, the existing risx type and a new mods type. Most of the
existing infrastructure can be used by both types. This will give
users the choice of a quick and dirty data format like the commercial
tools offer, and a better (though probably slower) MODS-based format.

I've been working on the MODS parser handlers lately and made quite
some progress. Once 0.9.4 is off my chest (it has been delayed due to
some character encoding pitfalls) I'll focus on MODS import and
export.

regards,
Markus

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

[Refdb-users] Bibutils source

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

It turns out Bibutils is GPL, and the source is now available here:

http://www.scripps.edu/~cdputnam/software/bibutils/bibutils_3.4_src.tgz

Markus, can a GPL utility like this be used in an LGPL project like 
OpenOffice?

Bruce

Re: [Refdb-users] MODS + RefDB

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

On Feb 4, 2004, at 3:33 AM, Justus H. Piater wrote:

> Does anybody out there (Bruce, for instance) have practical experience
> with using MODS (as the "master") in conjunction with RefDB?

Let me expand a bit on my problems here:

RefDB does not support extended citations (Smith, 1999:33-34), and they 
are *essential* to my work.  So I can't use it now for processing.

I've hacked Bibliofile (soon to be renamed BiblioX) to handle this 
support with MODS data, and Peter Flynn (the author) is currently 
implementing more comprehensive inline support.

So...I'm in a bind here, and I've got deadlines!   My primary data is 
currently MODS (mostly converted from Endnote), but I really need Peter 
to finish bibliofile, and for RefDB to support, in order of priority:

1)   extended citations (the new biblioref element in DocBook)

2)  MODS import/export

Bruce

Re: [Refdb-users] MODS + RefDB

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

I wrote:

> It would short-term he could somehow use Chris' tools for 
> import/export....

What I meant was:

It might be nice short-term if he could somehow use Chris' tools for 
[MODS] import/export....

Curious question: would it be possible to do that if the tools had an 
LGPL license?  Or must everything be full GPL?

Bruce

Re: [Refdb-users] MODS + RefDB

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

On Feb 4, 2004, at 3:33 AM, Justus H. Piater wrote:

> Does anybody out there (Bruce, for instance) have practical experience
> with using MODS (as the "master") in conjunction with RefDB?

Not exactly.

> How do you import MODS data into RefDB? Do you use Chris Putnam's
> bibutils (MODS->RIS), or do you have an XSLT stylesheet (MODS->RISX)?

v3 of Chris' tools currently do a fantastic job of converting from RIS, 
Endnote and BibTeX (though note, I've not actually test the latter, and 
encourage others to) ---> MODS.  So that provides one mechanism for 
exporting MODS content from RefDB, though I've not tried it yet myself.

Once these tools stabilize (and people testing and sending n bug 
reports will help), Chris will implement conversion out of MODS back to 
those non-XML formats.

> If I interpret the list traffic correctly, things are converging
> toward using MODS

Yes, and with more than one project, I might add.

> , and a future version of RefDB will likely be based
> on MODS instead of RIS. Markus, is this correct?

I'm pretty sure that's the plan, but Markus will have to tackle that.  
It would short-term he could somehow use Chris' tools for 
import/export....

Bruce

[Refdb-users] MODS + RefDB

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

Hi -

Does anybody out there (Bruce, for instance) have practical experience
with using MODS (as the "master") in conjunction with RefDB?

How do you import MODS data into RefDB? Do you use Chris Putnam's
bibutils (MODS->RIS), or do you have an XSLT stylesheet (MODS->RISX)?

Ditto for RefDB->MODS?

I'd like to hear about your experiences.

If I interpret the list traffic correctly, things are converging
toward using MODS, and a future version of RefDB will likely be based
on MODS instead of RIS. Markus, is this correct?

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] Re: interface mockup

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

On Feb 3, 2004, at 12:08 AM, Matt Price wrote:

> On Sat, Jan 31, 2004 at 09:22:32AM -0500, Bruce D'Arcus wrote:
>> On Jan 30, 2004, at 11:26 PM, Matt Price wrote:
>>
>>>> So what would happen if you click on the link?
>>>
>>> you get a page with a full reference, including notes and abstract &
>>> whatever else...
>>
>> How would that then relate to the mark-and-view/export interface, and
>> note pop-up buttons?  Do me a favor and compare what you're thinking
>> about to this example:
>>
>> http://130.83.186.203/exist/xquery/biblio.xm
>
> xquery looks interesting -- I will check it out Real Soon Now.

The thing to look at is just the interface.

>>> when you say 'map natural language', I take it you mean
>>> "take data entered in fields whose names are readily comprehensible
>>> to users, and pass the data on to the database in fields whose names
>>> the db understands." but what's the importance of "template-defined"?
>>
>> OK, you have a pop-up list with reference types of, for example:
>>
>> book
>> edited book
>> journal article
>> legal case
>> film
>> etc.
>>
>> You then choose "create new record" and a form specific to that type  
>> is
>> then displayed.  The template -- maybe an XML configuration file --
>> simply says (using ris stuff):
>>
>> JOUR = "journal article"
>> T1 = "title"
>> t2 = "journal title"
>>
> I think I understand this.  That should be relatively straightforward
> using php...

Take a look here for something like what I'm talking about.

http://216.205.78.164:8001/bw_login2srch? 
edit_loginname=guest&edit_password=guest

For some reason I can't create new references, now, so can't see the  
form.  Otherwise, the interface is pretty nice.

Another thing to look at that I'm quite fond of, which uses Cocoon and  
the XML DB eXist, and whose author is working on updating it to support  
MODS, is the MetaWizard for the SozioNet project out of Germany.   
Screenshots on my blog.

http://netapps.muohio.edu/movabletype/archives/darcusb/darcusb/ 
000129.html

Bruce

Re: [Refdb-users] php/html interface mockup

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

On Feb 1, 2004, at 9:43 AM, Marc Herbert wrote:

>> Interestingly, this Mozilla technology is based on Apple's Sherlock
>> search technology.
>
> Patents anyone=A0? Just wondering...

AFAIK, Sherlock is based on stuff like Javascript and XML.  The Mozilla=20=

page notes, however, that their name choice is to avoid any copyright=20
complaints....

Bruce

[Refdb-users] segfault on server, error on client

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

Rainer Duffner writes:
 > host:/usr/local/share/refdb # refdbd -s -e 0 -l 7
 > dbi_driver_dir went to:
 > 
 > dbi is up using default driver dir
 > Available libdbi database drivers:
 > pgsql
 > application server started
 > use /tmp/refdbd_fifo29127 as fifo
 > server waiting n_max_fd=4
 > adding client on fd 5
 > server waiting n_max_fd=5
 > Segmentation fault
 > 

This looks like the infamous log related segfault in 0.9.3. The
preferred way to fix this is to upgrade to 0.9.4-pre1 (a bugfix
release without new features) which is available here:

http://refdb.sourceforge.net/pre/refdb-0.9.4-pre1.tar.gz

If you want to stick to 0.9.3, do not ask refdbd to write its log
output to stderr. Use -e 1 or -e 2 instead.

HTH,
Markus

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

Re: [Refdb-users] php/html interface mockup

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

On Jan 30, 2004, at 9:45 PM, Matt Price wrote:

> see http://mycroft.mozdev.org; if you don't use this already, I can 
> just about guarantee you will 10 minutes after you check out the 
> website

Interestingly, this Mozilla technology is based on Apple's Sherlock 
search technology.  I presume it'd be possible thus write a plug-in for 
one and have it supported in the other, which would be nice.

Bruce

[Refdb-users] segfault on server, error on client

[Rainer D. <ra...@ul...>]

Hi,

I just installed refdb on a SuSE Enterprise-Server 8.

host:~ # refdba -u postgres
Please enter your password:
refdba: set
serverip 127.0.0.1
port 9734
verbose f
pager stdout
username postgres
timeout 60
logfile /var/log/refdba.log
logdest 2
loglevel 6
refdblib
refdba: viewstat
server error: incorrect scramble string
refdba: viewstat
server error: incorrect scramble string
refdba:


and on the serverside it says:

host:/usr/local/share/refdb # refdbd -s -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
application server started
use /tmp/refdbd_fifo29127 as fifo
server waiting n_max_fd=4
adding client on fd 5
server waiting n_max_fd=5
Segmentation fault



So, what does that mean ? "incorrect scramble string" ?

The postgres-user doesn't have a password ATM, so I assume I can leave 
it blank.




Rainer

Re: [Refdb-users] php frontend to refdb

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

On Wed, Jan 28, 2004 at 11:58:38AM -0500, rob caSSon wrote:
> i've been playing with a php frontend to refdb for a couple of days
> now...nothing fancy, but its a proof of concept...
> 
> right now, its only a search interface, and it interacts with the
> command line client...here's a URL if anyone's interested....bruce has
> helped a bunch with the xslt/css stuff:
> 
>     http://junk.lib.muohio.edu/refdb/
> 
> anyway, take a whack at it, send suggestions, etc....if you want the
> source, just let me know...its pretty trivial stuff at this point, and
> still needs some authentication, input verification, entry facilities...

Hey rob,

so, got the source, tried playing with it, but I'm having trouble with
risx (which is the most interesting part for me, since it turns risx
into html, how cool!!)  I get this error:
Fatal error: Call to undefined function: xslt_create() in
/var/www/derailleur.org/phptest/refdb-php/index.php on line 69

is my php-installation missing something important?  or can this error
be explained some other way? 
 
thx,
matt

Re: [Refdb-users] trying to get refdb up and running on Mac OSX 10.3

[Christian W. <wi...@ka...>]

Christian Wittern <wi...@ka...> writes:

> Hello there, 
>
> I guess this is not specific to the Mac, but anyway, here is my
> problem.  I installed refdb 093 according to the instructions, using
> Postgresql as the database.  I figured out everything, installed the
> database refdb1, and get to the point where I am using refdba to call
> the database.  On a "viewstat" command, all I get is "could not
> connect to database server".  In another terminal, where refdbd is
> running in debug mode, I see the same message.
>
> If I use pgsql on the command-line, however, I am able to connect to
> the database and issue SQL commands without a problem, so pg_hba.conf
> and friends should not cause problems.
>

Well, I found the problem, with the help of Michael Smith.  For the
benefit of those reading this in the archive I will describe what went
wrong:

I had not "configured" the database backend and was using the -D option for refdbd, like so:

refdbd -q -s -e 0 -l 7 -Y /sw/lib/dbd/ -D pgsql 

This failed to switch the database port to the default port for pgsql,
which is 5432, but rather requires the -b option like so:

refdbd -q -s -e 0 -l 7 -Y /sw/lib/dbd/ -D pgsql -b 5432

And bingo, refdba now talks to refdbd.

Now back to setting up refdb...

All the bes,t

Christian

-- 

 Christian Wittern 
 Institute for Research in Humanities, Kyoto University
 47 Higashiogura-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8265, JAPAN

[Refdb-users] Re: interface mockup

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

I like this addition.  I also like the paste-in-the-field thing in the 
current refdb web interface, which is good when doing online searches 
and such.

On Jan 31, 2004, at 12:24 AM, Rob Casson wrote:

> i added an ability to upload ris data via the web the other day..didn't
> send it to the general list, just the refdb-dev...it was more of an
> aside appended to a different concern...anyway, feel free to try it
> out:
>
>     http://junk.lib.muohio.edu/refdb/upload.php

Re: [Refdb-users] Re: interface mockup

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

Matt Price writes:
 > Though I like the way that sounds, it sounds pretty ambitious.  For
 > now it might be much less labour-intensive to write some php that
 > generates bibtex or other simple data structures; though again, my
 > pref would be to have the interesting part abstracted as much as
 > possible from the scripting language.  
 > 

Expressing data in XML is less labour-intensive than you may
think. RefDB (it is written in C, but the principles are the same in
any scripting language) for example uses four helper functions to
create risx XML output:

print_element_x: generates a complete element including contents and
                 attributes. It uses print_elstart_x and print_elend_x
                 internally.

print_elstart_x: generates the start tag including the attributes. It
                 uses print_attribute_x internally.

print_elend_x:   generates the end tag

print_attribute_x: prints out an attribute name/value pair

All you need to figure out is how to call these functions with your
data in order to create valid output. However, the complexity
of risx and xnote is limited. It's doable.

regards,
Markus

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

[Refdb-users] Re: interface mockup

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

 > >> I don't think this made it to the list.  Any feedback?  I can mod the

I'm sorry but the SF mailing lists limit the size of incoming mail. If
a post exceeds this limit, it will be in the loop until I, as the list
administrator, approve it. Hence the delay of up to 24h. If you have
the means to, please put larger files on your web space and post the
link instead.

regards,
Markus

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

[Refdb-users] php/html interface mockup

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

Matt Price writes:
 > Though I can see that other folks might not want this, I'd like to
 > make a plea for a hot-linked title in a short-format list.  This is
 > mostly because once you have an <a href> tag, it's possible to write
 > fully-functional mycroft search engines for mozilla (see
 > http://mycroft.mozdev.org; if you don't use this already, I can just
 > about guarantee you will 10 minutes after you check out the website).
 > I've already done this for a number of libraries and (non-free,
 > subscription based) bibliographical search engines I use.  I would
 > ultimately like to see the development of a fully-functional
 > bibliographical search plugin for mozilla...  Anyway, I'd like to keep
 > the possibility of browser-integration open for this project.
 > 

I haven't heard of this yet, but this sounds exciting.

 > Notes should be relatively simple -- the only hard part is getting the
 > information into the xml format that refdb uses.  If poss I'd like to
 > see this done in xslt again, so that the hard part is abstracted from
 > the scripting language and can be recycled in perl/python/whatever.
 > Bruce, you're the xslt person, how does that shound to you?

I'm not too worried about this. The XML format is so simple that it
wouldn't hurt to do the mapping directly in the scripting
language. But if you figure out an XSLT script that does the job, all
the better.

 > 1) this is important -- choosing a reference format.  Do you think risx/xslt
 > is the way to go again, or would something simple like bibtex be more
 > appropriate?  Once more, the easier it is to move across scripting
 > languages, the happier I'll be with the final product, don't know if
 > this matters to anyone else.  But I do like the idea of refdb as a
 > sort of module for integration with all kinds of projects, so if clean
 > html can be transparently produced with a minimum of hacking by end
 > users, that's a big plus, I think.  
 > 

Like Bruce already said, I'd suggest to avoid BibTeX. This format is
simply odd and next to impossible to parse properly. XML is the best
connector between an input form and a database. risx would be a fairly
simple start, but if well-designed, the interface could easily be
adapted to things like MODS.

 > 2) I'm a bit worried about parsing author fields -- I'd prefer to have
 > each author's name entered on a separate line, but I'm not sure that
 > can be done without making a multiline textarea, which I'd rather not
 > have (I like the simplicity and compactness of my current entry
 > format, even if I don't really like anything else).  
 > 

Definitely the most horrible part. If you use a single input field for
names, you'll have to educate users to stick to a consistent format or
employ a lot of program logic to fix incorrect data. Some users don't
like their data to be fiddled with, as we've seen on this list
recently, so any solution will have to walk a thin line between
usability on the input side and usability of the data on the reference
manager/bibliography tool side.

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

Re: [Refdb-users] Re: interface mockup

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

On Jan 31, 2004, at 9:22 AM, Bruce D'Arcus wrote:

>>>> Though I can see that other folks might not want this, I'd like to
>>>> make a plea for a hot-linked title in a short-format list.
>>> So what would happen if you click on the link?
>>
>> you get a page with a full reference, including notes and abstract &
>> whatever else...
>
> How would that then relate to the mark-and-view/export interface, and 
> note pop-up buttons?

Here's an idea:

Click on the title, and a window a la the Moveable Type comment window 
(e.g. small and plain) pops up with the full display (metadata plus 
notes).   We'd keep the mark facility to handle multiple records.

Another idea following from this (which I'm unsure on) is to also build 
on blog commenting by adding a note field at the bottom of the detailed 
display window (???).  If that was the case, the note buttons on the 
main result display would go away I think.

Bruce

Re: [Refdb-users] trying to get refdb up and running on Mac OSX 10.3

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

Christian Wittern writes:
 > Now trying 094-pre5 it does not even compile...  I configure like so,
 > ld: Undefined symbols:
 > _dbi_conn_get_encoding
 > make[2]: *** [refdbd] Error 1
 > 
 > 
 > It seems to have problems with dbi, which is the latest package from fink: 0.70-1 
 > 

The whole list stuff is a little out of order, so you may already know
the answer. But anyway, dbi_conn_get_encoding is a new function in
libdbi-0.7.2 and libdbi-drivers-0.7.1, so all you need to do is
upgrade to the latest packages.

regards,
Markus

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

Re: [Refdb-users] Re: interface mockup

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

On Jan 30, 2004, at 11:26 PM, Matt Price wrote:

>> So what would happen if you click on the link?
>
> you get a page with a full reference, including notes and abstract &
> whatever else...

How would that then relate to the mark-and-view/export interface, and 
note pop-up buttons?  Do me a favor and compare what you're thinking 
about to this example:

http://130.83.186.203/exist/xquery/biblio.xml

>>> So, missing from here is still the code for _adding_ references and
>>> notes, correct?  How do you think this should be done?
>>
>> A series of template defined fields that map natural language names to
>> underlying metadata model/format.
>
> ...  ok, as marcus said recently, how does that translate into
> language that a plain old PhD like myself can understand?  though I
> actually don't intend any snide overtones that might be inadvertently
> comunicated.

Well ... if you wanted to avoid being snide you could have just said "I 
don't understand; please explain." ;-)

>  when you say 'map natural language', I take it you mean
> "take data entered in fields whose names are readily comprehensible
> to users, and pass the data on to the database in fields whose names
> the db understands." but what's the importance of "template-defined"?

OK, you have a pop-up list with reference types of, for example:

book
edited book
journal article
legal case
film
etc.

You then choose "create new record" and a form specific to that type is 
then displayed.  The template -- maybe an XML configuration file -- 
simply says (using ris stuff):

JOUR = "journal article"
T1 = "title"
t2 = "journal title"

..and so forth.  It's just an abstraction that makes it a) easier for 
the user and b) easier to later modify/add reference types.

>>> 1) this is important -- choosing a reference format.  Do you think 
>>> risx
>>> is hte way to go again, or would something simple like bibtex be more
>>> appropriate?
>>
>> I despise bibtex myself.  I think the input UI should be designed for
>> flexibility; it should work elegantly with risx, but be capable of
>> being moved to handling mods data later.  The trick is to define the
>> key user input fields in a generic way, and then allow configuration.
>> So, the generic fields might be:
>
> Though I like the way that sounds, it sounds pretty ambitious.  For
> now it might be much less labour-intensive to write some php that
> generates bibtex or other simple data structures; though again, my
> pref would be to have the interesting part abstracted as much as
> possible from the scripting language.

Well, if you want to avoid XML, use RIS (it's richer, and 
unicode-possible).  But Rob, doesn't the XML support in PHP allow you 
to basically say "take date in field X and create XML code Y"?  If yes, 
that'd be preferable.

Bruce

[Refdb-users] interface mockup

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

In chatting with Matt, he indicated he'd like a short display, with  
pop-ups for viewing and entering notes.  I've put together a simple  
mockup, a screenshot of which is enclosed.  What do people think?

Note: I've only included authors and title, though ideally the full  
citation would be there, along with hot-linked keywords (as in Rob's  
example).  Also, I don't quite like the rendering right now for the  
view and export button area.

Anyway, here's the code:

<html>
	<head>
		<meta http-equiv="content-type"  
content="text/html;charset=iso-8859-1">
		<meta name="generator" content="Adobe GoLive">
		<title>Untitled Page</title>
		<style type="text/css">
			body {
				background-color: #bdcead;
				font-family: Georgia, serif;
				font-size: 11px;
				line-height: 1.4;
				padding: 10px;
			}
			
			p {
				text-align: justify;
				margin-left: 40px;
			}
			
			.biblio {
				margin-left: 50px;
				margin-top: 30px;
				border: 1px solid gray;
				background-color: white;
			}
			
			.record {
				margin-right: 40px;
				padding: 10px;
			}
			
			.citation {
				
			}
			
			.heading {
				font-weight: bold;
			}
			
			.title {
				font-weight: bold;
				font-size: 12px;
			}
			
			.citekey {
				color: #a69e7d;
				margin-left: 20px;
			}
			
			.note {
				background-color: #bacdce;
				font-size: 9px;
				padding-left: 10px;
				padding-right: 10px;
				border: 1px solid gray;
				font-weight: bold;
				margin-right: 10px;
			}
			
			a {
				color: #add105;
				text-decoration: none;
			}
			
			a.hover {
				color: #bde2da;
			}
			
			input.mark {
				float: left;
				margin-left: -30px;
			}
			input.search {
				margin-left: 40px;
				padding: 10px;
				background-color: transparent;
				font-size: 10px;
				font-weight: bold;
			}
			input.view{
				margin-left: 40px;
				margin-top: 10px;
				font-size: 9px;
			}
			input.search-button{
				margin-left: 20px;
				font-size: 9px;
				width: 70px;
			}
			#header {
				border-bottom: 1px solid gray;
				padding: 10px;
				background: #cecece
			}
			#top {
				margin-top: 20px;
				margin-left: 400px
			}
			select.choose {
				font-size: 9px;
				margin-left: 10px;
				margin-top: 10px;
			}
		</style>
	</head>

	<body bgcolor="#ffffff">
		<div id="top">
		<input class="search" type="text" /><input type="button"  
class="search-button" value="search"/>
		</div>
		<div class="biblio">
		<div id="header">
		    	<input type="button" class="view" value="view marked"/>
		    	<input type="button" class="view" value="export marked"/>
		    	<select name="export" class="choose">
		  <option value="bibtex">bibtex</option>
		  <option value="mods">mods</option>
		  <option value="ris">ris</option>
		  <option value="risx">risx</option>
		</select>
		</div>
		<div class="record">
     <p class="citation">
     	<input type="checkbox" class="mark" value="N1"/>
     <span class="title">Inhibition of deactivation of NO sensitive  
guanylyl cyclase accounts for the sensitizing effect of  
YC-1</span><span class="citekey"> [Russwurm2002]</span></span></p>
     <p class="keywords"><span class="heading">By: </span><a  
href="index.php?format=risx&amp;field=AU&amp;searchText=Russwurm">M  
Russwurm</a>; <a  
href="index.php?format=risx&amp;field=AU&amp;searchText=Mergia">E  
Mergia</a>; <a  
href="index.php?format=risx&amp;field=AU&amp; 
searchText=Mullershausen">F Mullershausen</a>; <a  
href="index.php?format=risx&amp;field=AU&amp;searchText=Koesling">D  
Koesling</a></p>
     <p><span class="note">add note</span><span class="note">view  
notes</span></p>
   </div>
   	<div class="record">
     <p class="citation"><input type="checkbox" class="mark"  
value="N1"/><span class="title">Inhibition of deactivation of NO  
sensitive guanylyl cyclase accounts for the sensitizing effect of  
YC-1</span><span class="citekey"> [Russwurm2002]</span></p>
     <p class="keywords"><span class="heading">By: </span><a  
href="index.php?format=risx&amp;field=AU&amp;searchText=Russwurm">M  
Russwurm</a>; <a  
href="index.php?format=risx&amp;field=AU&amp;searchText=Mergia">E  
Mergia</a>; <a  
href="index.php?format=risx&amp;field=AU&amp; 
searchText=Mullershausen">F Mullershausen</a>; <a  
href="index.php?format=risx&amp;field=AU&amp;searchText=Koesling">D  
Koesling</a></p>
     <p><span class="note">add note</span><span class="note">view  
notes</span></p>
   </div>
   </div>

	</body>

</html>

Bruce

Re: [Refdb-users] trying to get refdb up and running on Mac OSX 10.3

[Christian W. <wi...@ka...>]

Both on and off list I received the advice to use the latest prerelease.


"Bruce D'Arcus" <bd...@fa...> writes:

> On Jan 27, 2004, at 9:27 PM, Christian Wittern wrote:
>
>> I guess this is not specific to the Mac,
>
> Actually, it probably is ...

Well then.

>
>> but anyway, here is my problem. I installed refdb 093 according to the 
>> instructions, using Postgresql as the database.
>
> Try using 0.9.4-pre5 instead.  Both libdbi and refdb needed a lot of 
> changes to compile correctly on Mac OS X, so it's critical you're using 
> the most up-to-date version.  If you have further problems, it may be 
> related to libdbi, for which there is a Fink package that works 
> correctly and is up-to-date.
>

Well, I *got* 093 to compile and install..


Now trying 094-pre5 it does not even compile...  I configure like so,

CFLAGS="-I/sw/include" LDFLAGS="-L/sw/lib" ./configure --with-libdbi-dir=/sw/lib --with-docbook-xsl=/usr/local/TEI/tei-emacs/xml/xsl/docbook/ --with-tei-xsl=/usr/local/share/xsl/tei/ --with-db-server=pgsql

and then make:

gcc  -I/sw/include  -L/sw/lib -o refdbd  refdbd.o refdbdref.o refdbda.o refdbdbib.o pref.o strfncs.o tokenize.o connect.o risdb.o writeris.o getopt.o readris.o backend.o backend-scrn.o backend-ris.o backend-risx.o backend-db31.o backend-teix.o backend-bibtex.o backend-html.o backend-dbib.o backend-dbiba.o linklist.o xmlhandler.o enigma.o cgi.o atoll.o dbfncs.o xmlout.o risxhandler.o authorinfo.o risdata.o noteshandler.o refdbdnote.o writenote.o backendn-scrn.o backendn-notex.o backendn-html.o xmlhelper.o -lltdl -ldbi -lz -lexpat -liconv 
ld: Undefined symbols:
_dbi_conn_get_encoding
make[2]: *** [refdbd] Error 1


It seems to have problems with dbi, which is the latest package from fink: 0.70-1 

Any ideas on how to fix this?  

All the best,

Christian

-- 

 Christian Wittern 
 Institute for Research in Humanities, Kyoto University
 47 Higashiogura-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8265, JAPAN

Re: [Refdb-users] Re: interface mockup

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

On Fri, Jan 30, 2004 at 10:16:30PM -0500, Bruce D'Arcus wrote:
> On Jan 30, 2004, at 9:35 PM, Matt Price wrote:
> 
> >On Fri, Jan 30, 2004 at 12:20:34PM -0500, Bruce D'Arcus wrote:
> >>I don't think this made it to the list.  Any feedback?  I can mod the
> >>xslt once I have a better sense of what we want.
> >Though I can see that other folks might not want this, I'd like to
> >make a plea for a hot-linked title in a short-format list.
> 
> So what would happen if you click on the link?

you get a page with a full reference, including notes and abstract &
whatever else...

> 
> >This is mostly because once you have an <a href> tag, it's possible to 
> >write
> >fully-functional mycroft search engines for mozilla (see
> >http://mycroft.mozdev.org)...
> 
> Interesting; I'd not heard about that.  I wonder if the 
> browser-agnostic bookmarklet might be better though?  E.g.:
> 
> http://webvoy.uwindsor.ca:8080/cocoon/mount/chrysalis/welcome
> 
hmm.  I see the advantages of agnosticism here (and I'm on console
right now, so haven't checked the link) but mycroft has the advantage
of making it possible to combine searches from multiple engines; for
bibliographic information this is not yet especially useful, since
complex queries are rendered with different syntax on different sites;
but eventually I think a more flexible interface will be implemented.
This can be a substantial advantage when data is distributed over a
variety of sites.  

> >So, missing from here is still the code for _adding_ references and
> >notes, correct?  How do you think this should be done?
> 
> A series of template defined fields that map natural language names to 
> underlying metadata model/format.

...  ok, as marcus said recently, how does that translate into
language that a plain old PhD like myself can understand?  though I
actually don't intend any snide overtones that might be inadvertently
comunicated.  when you say 'map natural language', I take it you mean
"take data entered in fields whose names are readily comprehensible
to users, and pass the data on to the database in fields whose names
the db understands." but what's the importance of "template-defined"?

> 
> >Notes should be relatively simple -- the only hard part is getting the
> >information into the xml format that refdb uses.  If poss I'd like to
> >see this done in xslt again, so that the hard part is abstracted from
> >the scripting language and can be recycled in perl/python/whatever.
> >Bruce, you're the xslt person, how does that shound to you?
> 
> I don't do scripting, so maybe Rob has a better sense of the connection 
> between the XML and a form interface.
> 
Rob, tell me what you think -- I think we're interested in similar
goals here, maybe we can divide up the work a bit.  

> >1) this is important -- choosing a reference format.  Do you think risx
> >is hte way to go again, or would something simple like bibtex be more
> >appropriate?
> 
> I despise bibtex myself.  I think the input UI should be designed for 
> flexibility; it should work elegantly with risx, but be capable of 
> being moved to handling mods data later.  The trick is to define the 
> key user input fields in a generic way, and then allow configuration.  
> So, the generic fields might be:
> 

Though I like the way that sounds, it sounds pretty ambitious.  For
now it might be much less labour-intensive to write some php that
generates bibtex or other simple data structures; though again, my
pref would be to have the interesting part abstracted as much as
possible from the scripting language.  

> creator/editor
> title/subtitle
> year
> publisher
> origin place (could be for unpublished sources too)
> location
> keywords
> etc.
> 
> >2) I'm a bit worried about parsing author fields
> 
> There's no doubt this is the trickiest part of any form-based UI for 
> bib data.  I'm not sure how it ought to work.  Anyone have any ideas?  
> Rob?
> 
> Bruce
> 

[Refdb-users] Re: interface mockup

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

On Jan 30, 2004, at 9:35 PM, Matt Price wrote:

> On Fri, Jan 30, 2004 at 12:20:34PM -0500, Bruce D'Arcus wrote:
>> I don't think this made it to the list.  Any feedback?  I can mod the
>> xslt once I have a better sense of what we want.
> Though I can see that other folks might not want this, I'd like to
> make a plea for a hot-linked title in a short-format list.

So what would happen if you click on the link?

> This is mostly because once you have an <a href> tag, it's possible to 
> write
> fully-functional mycroft search engines for mozilla (see
> http://mycroft.mozdev.org)...

Interesting; I'd not heard about that.  I wonder if the 
browser-agnostic bookmarklet might be better though?  E.g.:

http://webvoy.uwindsor.ca:8080/cocoon/mount/chrysalis/welcome

> So, missing from here is still the code for _adding_ references and
> notes, correct?  How do you think this should be done?

A series of template defined fields that map natural language names to 
underlying metadata model/format.

> Notes should be relatively simple -- the only hard part is getting the
> information into the xml format that refdb uses.  If poss I'd like to
> see this done in xslt again, so that the hard part is abstracted from
> the scripting language and can be recycled in perl/python/whatever.
> Bruce, you're the xslt person, how does that shound to you?

I don't do scripting, so maybe Rob has a better sense of the connection 
between the XML and a form interface.

> 1) this is important -- choosing a reference format.  Do you think risx
> is hte way to go again, or would something simple like bibtex be more
> appropriate?

I despise bibtex myself.  I think the input UI should be designed for 
flexibility; it should work elegantly with risx, but be capable of 
being moved to handling mods data later.  The trick is to define the 
key user input fields in a generic way, and then allow configuration.  
So, the generic fields might be:

creator/editor
title/subtitle
year
publisher
origin place (could be for unpublished sources too)
location
keywords
etc.

> 2) I'm a bit worried about parsing author fields

There's no doubt this is the trickiest part of any form-based UI for 
bib data.  I'm not sure how it ought to work.  Anyone have any ideas?  
Rob?

Bruce

[Refdb-users] php/html interface mockup

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

On Fri, Jan 30, 2004 at 12:20:34PM -0500, Bruce D'Arcus wrote:
> I don't think this made it to the list.  Any feedback?  I can mod the  
> xslt once I have a better sense of what we want.
> 

Bruce,  

excuse the topposting -- your code etc included mostly just in case
your mail nevergets to the list....

I think the format is really great, actually -- nice work!  I like
having a nice short format for the cite, this makes it much easier to
integrate this search function into other web pages.  And the look of
the thing is quite pretty.

Though I can see that other folks might not want this, I'd like to
make a plea for a hot-linked title in a short-format list.  This is
mostly because once you have an <a href> tag, it's possible to write
fully-functional mycroft search engines for mozilla (see
http://mycroft.mozdev.org; if you don't use this already, I can just
about guarantee you will 10 minutes after you check out the website).
I've already done this for a number of libraries and (non-free,
subscription based) bibliographical search engines I use.  I would
ultimately like to see the development of a fully-functional
bibliographical search plugin for mozilla...  Anyway, I'd like to keep
the possibility of browser-integration open for this project.

So, missing from here is still the code for _adding_ references and
notes, correct?  How do you think this should be done?  

Notes should be relatively simple -- the only hard part is getting the
information into the xml format that refdb uses.  If poss I'd like to
see this done in xslt again, so that the hard part is abstracted from
the scripting language and can be recycled in perl/python/whatever.
Bruce, you're the xslt person, how does that shound to you?

I have a primitive reference-adding form that I used for my own
purposes before I really got refdb up and runing.  You can see it
working here:  

http://www.derailleur.org/phptest/addrefs.php

the db that it uses is a sort of single-table version of a refdb
database -- much muh less powerful, but easier to access directly via
mysql/postresql.  
The only thing I like about this form is that it allows you to enter
multiple references at the same time.  There are lots of simple ways
in which it can be straightened out and improved, but a couple of
things are fairly iportant:

1) this is important -- choosing a reference format.  Do you think risx/xslt
is the way to go again, or would something simple like bibtex be more
appropriate?  Once more, the easier it is to move across scripting
languages, the happier I'll be with the final product, don't know if
this matters to anyone else.  But I do like the idea of refdb as a
sort of module for integration with all kinds of projects, so if clean
html can be transparently produced with a minimum of hacking by end
users, that's a big plus, I think.  

2) I'm a bit worried about parsing author fields -- I'd prefer to have
each author's name entered on a separate line, but I'm not sure that
can be done without making a multiline textarea, which I'd rather not
have (I like the simplicity and compactness of my current entry
format, even if I don't really like anything else).  


anyway, I'm really psyched at what you've done here, Bruce!  nice job.

matt

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

> 
> In chatting with Matt, he indicated he'd like a short display, with  
> pop-ups for viewing and entering notes.  I've put together a simple  
> mockup, a screenshot of which is enclosed.  What do people think?
> 
> Note: I've only included authors and title, though ideally the full  
> citation would be there, along with hot-linked keywords (as in Rob's  
> example).  Also, I don't quite like the rendering right now for the  
> view and export button area.
> 
> Anyway, here's the code:
> 
> <html>
> 	<head>
> 		<meta http-equiv="content-type"  
> content="text/html;charset=iso-8859-1">
> 		<meta name="generator" content="Adobe GoLive">
> 		<title>Untitled Page</title>
> 		<style type="text/css">
> 			body {
> 				background-color: #bdcead;
> 				font-family: Georgia, serif;
> 				font-size: 11px;
> 				line-height: 1.4;
> 				padding: 10px;
> 			}
> 			
> 			p {
> 				text-align: justify;
> 				margin-left: 40px;
> 			}
> 			
> 			.biblio {
> 				margin-left: 50px;
> 				margin-top: 30px;
> 				border: 1px solid gray;
> 				background-color: white;
> 			}
> 			
> 			.record {
> 				margin-right: 40px;
> 				padding: 10px;
> 			}
> 			
> 			.citation {
> 				
> 			}
> 			
> 			.heading {
> 				font-weight: bold;
> 			}
> 			
> 			.title {
> 				font-weight: bold;
> 				font-size: 12px;
> 			}
> 			
> 			.citekey {
> 				color: #a69e7d;
> 				margin-left: 20px;
> 			}
> 			
> 			.note {
> 				background-color: #bacdce;
> 				font-size: 9px;
> 				padding-left: 10px;
> 				padding-right: 10px;
> 				border: 1px solid gray;
> 				font-weight: bold;
> 				margin-right: 10px;
> 			}
> 			
> 			.note {
> 				background-color: #bacdce;
> 				font-size: 9px;
> 				padding-left: 10px;
> 				padding-right: 10px;
> 				border: 1px solid gray;
> 				font-weight: bold;
> 				margin-right: 10px;
> 			}
> 			
> 			a {
> 				color: #add105;
> 				text-decoration: none;
> 			}
> 			
> 			a.hover {
> 				color: #bde2da;
> 			}
> 			
> 			input.mark {
> 				float: left;
> 				margin-left: -30px;
> 			}
> 			input.search {
> 				margin-left: 40px;
> 				padding: 10px;
> 				background-color: transparent;
> 				font-size: 10px;
> 				font-weight: bold;
> 			}
> 			input.view{
> 				margin-left: 40px;
> 				margin-top: 10px;
> 				font-size: 9px;
> 			}
> 			input.search-button{
> 				margin-left: 20px;
> 				font-size: 9px;
> 				width: 70px;
> 			}
> 			#header {
> 				border-bottom: 1px solid gray;
> 				padding: 10px;
> 				background: #cecece
> 			}
> 			#top {
> 				margin-top: 20px;
> 				margin-left: 400px
> 			}
> 			select.choose {
> 				font-size: 9px;
> 				margin-left: 10px;
> 				margin-top: 10px;
> 			}
> 		</style>
> 	</head>
> 
> 	<body bgcolor="#ffffff">
> 		<div id="top">
> 		<input class="search" type="text" /><input type="button"  
> class="search-button" value="search"/>
> 		</div>
> 		<div class="biblio">
> 		<div id="header">
> 		    	<input type="button" class="view" value="view 
> 		    	marked"/>
> 		    	<input type="button" class="view" value="export 
> 		    	marked"/>
> 		    	<select name="export" class="choose">
> 		  <option value="bibtex">bibtex</option>
> 		  <option value="mods">mods</option>
> 		  <option value="ris">ris</option>
> 		  <option value="risx">risx</option>
> 		</select>
> 		</div>
> 		<div class="record">
>     <p class="citation">
>     	<input type="checkbox" class="mark" value="N1"/>
>     <span class="title">Inhibition of deactivation of NO sensitive  
> guanylyl cyclase accounts for the sensitizing effect of  
> YC-1</span><span class="citekey"> [Russwurm2002]</span></span></p>
>     <p class="keywords"><span class="heading">By: </span><a  
> href="index.php?format=risx&amp;field=AU&amp;searchText=Russwurm">M  
> Russwurm</a>; <a  
> href="index.php?format=risx&amp;field=AU&amp;searchText=Mergia">E  
> Mergia</a>; <a  
> href="index.php?format=risx&amp;field=AU&amp; 
> searchText=Mullershausen">F Mullershausen</a>; <a  
> href="index.php?format=risx&amp;field=AU&amp;searchText=Koesling">D  
> Koesling</a></p>
>     <p><span class="note">add note</span><span class="note">view  
> notes</span></p>
>   </div>
>   	<div class="record">
>     <p class="citation"><input type="checkbox" class="mark"  
> value="N1"/><span class="title">Inhibition of deactivation of NO  
> sensitive guanylyl cyclase accounts for the sensitizing effect of  
> YC-1</span><span class="citekey"> [Russwurm2002]</span></p>
>     <p class="keywords"><span class="heading">By: </span><a  
> href="index.php?format=risx&amp;field=AU&amp;searchText=Russwurm">M  
> Russwurm</a>; <a  
> href="index.php?format=risx&amp;field=AU&amp;searchText=Mergia">E  
> Mergia</a>; <a  
> href="index.php?format=risx&amp;field=AU&amp; 
> searchText=Mullershausen">F Mullershausen</a>; <a  
> href="index.php?format=risx&amp;field=AU&amp;searchText=Koesling">D  
> Koesling</a></p>
>     <p><span class="note">add note</span><span class="note">view  
> notes</span></p>
>   </div>
>   </div>
> 
> 	</body>
> 
> </html>
> 
> Bruce
>