refdb-users — List for RefDB users

[Refdb-users] risx output problems

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

Ok, with the new release, I'm still having screwed up output with two 
types of references.  This is just stuf that is invalid against the 
DTD; I've not had time to dig deeper.

MPCT
CASE

Examples:

This...

TY  - CASE
ID  - USvDellinger1968
T1  - United States v. David T. Dellinger et al
T2  - U.S. v. Dellinger
T3  - appeal
KW  - anti-riot
PY  - 1968///
ER  -

...yields:

<entry type="CASE" id="15" citekey="USvDellinger1968">
   <part>
     <title>United States v. David T. Dellinger et al</title>
   </part>
   <set>
     <title type="gen">appeal</title>
   </set>
   <libinfo user="darcusb">
     <reprint status="NOTINFILE"/>
   </libinfo>
   <contents>
     <keyword>anti-riot</keyword>
     <keyword>U.S.</keyword>
     <keyword>United States</keyword>
   </contents>
</entry>

And this...

TY  - MPCT
ID  - Bye1979
A2  - Diegues, Carlos
CT  - Bye Bye Brazil
KW  - Brazil
KW  - Latin America
KW  - human rights
PY  - 1979///
ER  -

...yields:

<entry type="MPCT" id="48" citekey="Bye1979">
   <libinfo user="darcusb">
     <reprint status="NOTINFILE"/>
   </libinfo>
   <contents>
     <keyword>Brazil</keyword>
     <keyword>Latin America</keyword>
     <keyword>human rights</keyword>
   </contents>
</entry>

Should CT be T1 above?

Bruce

Re: [Refdb-users] html code (more)

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

On Tuesday, September 9, 2003, at 07:21  PM, Markus Hoenicka wrote:

> I don't mind to fix these issues as you have a point here. But at the
> same time I'd like to point out (again) that this web interface is a
> proof of concept. ... If anyone with a little Perl
> knowledge wants to help out, please do so. Perl is the way to go for
> the web interface, but I can't do it myself right now.

Yeah, that was my first point, of course, and some of the subsequent 
comments could apply to other web clients.

Tom (though that project was PHP, IIRC)?  Alan?

Bruce

Re: [Refdb-users] risx output and encoding?

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

On Tuesday, September 9, 2003, at 07:12  PM, Markus Hoenicka wrote:

> I'm afraid I missed to add this to the declaration. All that refdb
> does to the data is to perform a simple entity replacement. Beyond
> that, it currently works like "garbage in, garbage out": It simply
> sends out whatever the database engine delivers. If this happens to be
> Unicode, all the better. If it's not, you'll have to use iconv to
> translate the results. I might add character encoding conversion on
> the server side, but this would of course add another dependency to a
> library.

Can't there be a way to specify an encoding default somewhere?  In my 
case, it would be utf-8.  The simple solution would thus simply involve 
the understanding that I was feeding it utf data, and then the output 
declaration would be included.  Ideally you'd want to be able to have 
encoding conversion, but that could come later if necessary.

Bruce

[Refdb-users] html code (more)

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

Hi Bruce,

I don't mind to fix these issues as you have a point here. But at the
same time I'd like to point out (again) that this web interface is a
proof of concept. There is a Perl module that should make it a lot
easier to develop a simple and intuitive web interface. This would be
way easier to maintain too, and the C client code could be much
simpler without the CGI functionality. If anyone with a little Perl
knowledge wants to help out, please do so. Perl is the way to go for
the web interface, but I can't do it myself right now.

regards,
Markus

Bruce D'Arcus writes:
 > 
 > I wonder if this:
 > 
 > <p class='citekey'>CITEKEY:Smith1992b</p>
 > 
 > ...would be better as:
 > 
 > <p class="result_header">Citekey</p>
 > <p class="citekey">Smith1992b</p>
 > 
 > That way you can control the presentation better with CSS. For example, 
 > I'd tend to want to have the "citekey" header in bold, and I'd prefer 
 > to leave whether it is all-uppercase or not as a decision handled in 
 > CSS.
 > 
 > Another alternative, I suppose, would be:
 > 
 > <p><span class="result_header">Citekey</span><span 
 > class="citekey">Smith1992b</span></p>
 > 
 > Bruce
 > 
 > PS - Note also the double-quote around the attribute values, which is 
 > mandatory for xhtml; isn't it?
 > 
 > 
 > 
 > -------------------------------------------------------
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 > Welcome to geek heaven.
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 > _______________________________________________
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 > Ref...@li...
 > https://lists.sourceforge.net/lists/listinfo/refdb-users
 > 
 > 

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

Re: [Refdb-users] more on web stuff

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

On Tuesday, September 9, 2003, at 07:08  PM, Markus Hoenicka wrote:

> could you please post the dataset that results in this output? Also
> any optional fields that you requested. This is important to see why
> this happens.

One thing I noticed after sending the note is that the problem shows up 
consistently in book chapters.

Bruce

> Bruce D'Arcus writes:
>>
>> OK, some buggy html output?  Note the first </p> tag should not be
>> there.
>>
>> <p class='chap'>in: Doherty, Joe(ed.), Postmodernism and the Social
>> Sciences; part of: Postmodernism and the Social Sciences</p>
>> <em class='page'>pp. 57-79</em></p>

[Refdb-users] risx output and encoding?

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

Bruce D'Arcus writes:
 > 
 > Markus,
 > 
 > How does refdb deal with the encoding on risx output, and why is that 
 > not specified in the declaration?
 > 

I'm afraid I missed to add this to the declaration. All that refdb
does to the data is to perform a simple entity replacement. Beyond
that, it currently works like "garbage in, garbage out": It simply
sends out whatever the database engine delivers. If this happens to be
Unicode, all the better. If it's not, you'll have to use iconv to
translate the results. I might add character encoding conversion on
the server side, but this would of course add another dependency to a
library.

regards,
Markus

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

[Refdb-users] html code (more)

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

I wonder if this:

<p class='citekey'>CITEKEY:Smith1992b</p>

...would be better as:

<p class="result_header">Citekey</p>
<p class="citekey">Smith1992b</p>

That way you can control the presentation better with CSS. For example, 
I'd tend to want to have the "citekey" header in bold, and I'd prefer 
to leave whether it is all-uppercase or not as a decision handled in 
CSS.

Another alternative, I suppose, would be:

<p><span class="result_header">Citekey</span><span 
class="citekey">Smith1992b</span></p>

Bruce

PS - Note also the double-quote around the attribute values, which is 
mandatory for xhtml; isn't it?

[Refdb-users] more on web stuff

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

Hi Bruce,

could you please post the dataset that results in this output? Also
any optional fields that you requested. This is important to see why
this happens.

Thanks
Markus

Bruce D'Arcus writes:
 > 
 > OK, some buggy html output?  Note the first </p> tag should not be 
 > there.
 > 
 > <p class='chap'>in: Doherty, Joe(ed.), Postmodernism and the Social 
 > Sciences; part of: Postmodernism and the Social Sciences</p>
 > <em class='page'>pp. 57-79</em></p>
 > 

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

[Refdb-users] more on web stuff

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

OK, some buggy html output?  Note the first </p> tag should not be 
there.

<p class='chap'>in: Doherty, Joe(ed.), Postmodernism and the Social 
Sciences; part of: Postmodernism and the Social Sciences</p>
<em class='page'>pp. 57-79</em></p>

Bruce

[Refdb-users] web interface

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

I finally (with a little help from Markus) got refdb + the web 
interface running smoothly!

A couple quick question/observations.

First, I remember various people were working on improved editing and 
entry UIs, related to risx.  Is anyone releasing any of this soon?  
It'd really be nice.

Maybe if Markus adds a paragraph element to notes, we could even have 
the UI separate paragraphs based on a break.  Suffice it to say the 
enclosed screenshot shows why we need this.

[Refdb-users] risx output and encoding?

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

Markus,

How does refdb deal with the encoding on risx output, and why is that 
not specified in the declaration?

Bruce

[Refdb-users] hmm.. -- config issue with 0.9.4 pre

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

Bruce D'Arcus writes:
 > Just tried compiling the latest release and ran into this:
 > 
 > % ./configure --with-libdbi-lib=/sw/lib/libdbi.0.0.5.dylib 
 > --with-expat-lib=/sw/lib/libexpat.0.4.0.dylib 
 > --with-docbook-xsl=/sw/share/xml/xsl/docbook-xsl 
 > --with-refdb-url=http://darcusb.geo.muohio.edu/refdb 
 > --with-db-server=sqlite CFLAGS=-L/sw/lib -I/sw/include
 > configure: error: unrecognized option: -I/sw/include

You need to enclose the CFLAGS string like this:

CFLAGS="-L/sw/lib -I/sw/include"

otherwise the -I/sw/include part will be interpreted as an option to
configure which it isn't.

regards,
Markus

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

[Refdb-users] disregard

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

While the previous config command had worked in the past, the help 
suggested a slight change.  It compiled fine.  Will let you know if 
there are any other problems.

Bruce

[Refdb-users] hmm.. -- config issue with 0.9.4 pre

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

Just tried compiling the latest release and ran into this:

% ./configure --with-libdbi-lib=/sw/lib/libdbi.0.0.5.dylib 
--with-expat-lib=/sw/lib/libexpat.0.4.0.dylib 
--with-docbook-xsl=/sw/share/xml/xsl/docbook-xsl 
--with-refdb-url=http://darcusb.geo.muohio.edu/refdb 
--with-db-server=sqlite CFLAGS=-L/sw/lib -I/sw/include
configure: error: unrecognized option: -I/sw/include

Re: [Refdb-users] Issues and Observations

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

Hi,

the CVS version allows to select the encoding used in the html
backend. Use the refdbc -E command line switch or the "encoding"
config file variable to select a charset. To get something like the
example below, use e.g. refdbc -E "UTF-8".

regards,
Markus

Justus H. Piater writes:
 > Yes, it would be nice to specify a
 >   <META http-equiv="Content-Type" content="text/html; charset=UTF-8">
 > header. BTW, I would love XHTML support...
 > 

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

[Refdb-users] ANN: refdb-0.9.4-pre1 available for testing

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

Hi all,

I've fixed the worst bugs reported after releasing 0.9.3 and added a
couple of features requested lately. See below for the details. I ask
everyone with a little spare time to test drive this prerelease. The
new archive can be found right here:

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

BTW there's also a link on the download page of the RefDB homepage
which always points to the latest prerelease, if there is one.

regards,
Markus

Bugfixes

- fixed a segfault related to log files

- fixed a couple of issues in the risx backend

- fixed missing parentheses around subsequent multiple citations

- fixed the "xsl:call-template : template component.separator not
  found" bug in the DocBook XSLT fo driver file

- fixed some more attribute case mismatches in the DocBook XSLT driver
  files so the output from DocBook XML docs finally seems ok

- fixed a typo in ris.el

- fixed the omission of HEAR in risx.dtd

- fixed handling of CASE references

- fixed missing entity replacement in journal names

Improvements

- added xhtml support for DocBook XML documents

- extended the html backend for the getref command to allow xhtml export

- added support for NEWS to the bib styles

- added support for multiple middle names in risx.dtd and in refdbd

- added support for arbitrary starting number of numbered
  bibliographies

- added a switch to runbib in order to skip ID extraction

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

[Refdb-users] Starting reference numbering from a chosen number ?

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

Marc Baaden writes:
 > Now I wonder whether there's a possibility to start 
 > numbering from something other than one and how that
 > should/could be done.

I've added support for this feature to the CVS version. Both refdbib
and runbib now support a -N number option to specify where the
reference numbering is supposed to start.

I'll whip up a prerelease today or tomorrow to make the latest
improvements available for testing.

regards,
Markus

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

[Refdb-users] Author names with several middle initials ?

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

Hi,

I've added support for multiple middle initials to RefDB. The current
CVS version ought to support this for all sorts of output. Using this
feature with risx data requires an update to the latest DTD. Use the
following PUBID:

<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.1//EN" "http://refdb.sourceforge.net/dtd/risx-1.0.1/risx.dtd">

Please have a look at the CVS version and let me know about problems,
if any. I also intend to finish a new prerelease within a day or two
to simplify testing.

regards,
Markus

Marc Baaden writes:
 > 
 > Hi,
 > 
 > I just wonder what to do about author names with several middle initials.
 > Like eg Mark S. P. Sansom, which gets reduced to M.S. Sansom whereas I'd
 > like M.S.P. Sansom.
 > 
 > Can this be done (without dvelving too deep into the refdb structure) ?

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

Re: [Refdb-users] import problems

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

Hi,

Bruce D'Arcus writes:
 > OK, Markus, I am finding the import REALLY buggy.  I have deleted and 
 > recreated the "refs" DB, and then reimported the same file about 5 
 > times, each with different results.  Sometimes only 200 records are 
 > imported, once 650 or so (at which point it complained about a 
 > duplicate ID), and only one time did it import all 1000+ of them.  If I 
 > get a chance, I'll put it in a place where you can take a look.

Yes, please do. It is also important to create a log file with log
level 7 along with the data (it'll slow down the import but I need to
know what's going on). As we've seen before dozens of times,
some bugs show up only on particular systems. I'll make sure to test
your data on the systems that I have access to.

regards,
Markus

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

Re: [Refdb-users] Starting reference numbering from a chosen number ?

[Marc B. <ba...@sm...>]

>>> "Markus Hoenicka" said:
 >> Marc Baaden writes:
 >>  > But maybe a variable can be set in an XSL file or so ?
 >>  > But in that case one would have to recognize which of
 >>  > the *.bib.xml files is currently processed.

 >> The easiest way would be to add a switch to refdbib/runbib which sets
 >> the number of the first reference. Would that work with your custom
 >> way of processing the documents?

Yes, that sounds like a great idea and should solve my problem.
(probably I'll have a look at it ..)

Marc
-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:ba...@sm...      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217

[Refdb-users] Issues and Observations

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

Hi,

another quick note...

Justus H. Piater writes:
 >    (e) All output formats: I do not understand how THES references are
 >        supposed to work. The output contains superflouous dots. Is the
 >        degree-granting institution to be coded as the publisher? In
 >        that case, the output order would be
 >        unconventional. Eur.J.Pharmacol. adds a trailing "(nd)", even
 >        though the year does show up before.
 > 

The styles are incomplete in that they do not contain specifications
for *all* reference types (I added only those that were important to
me back then). If no matching spec is found, RefDB uses the GEN spec
instead which is a one-size-fits-all fallback. You've found out the
hard way that the results are not convincing.

The solution is to figure out suitable style specifications for THES
and the other missing reference types and add these to the styles.

regards,
Markus

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

[Refdb-users] Starting reference numbering from a chosen number ?

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

Marc Baaden writes:
 > But maybe a variable can be set in an XSL file or so ?
 > But in that case one would have to recognize which of
 > the *.bib.xml files is currently processed.
 > 

The easiest way would be to add a switch to refdbib/runbib which sets
the number of the first reference. Would that work with your custom
way of processing the documents?

regards,
Markus

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

Re: [Refdb-users] risx output problems

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

Bruce D'Arcus writes:
 > 
 > I was seeing it in journal titles; all of them that included an & 
 > character.
 > 

I've indeed forgotten to replace the entities in the periodical
titles. This is fixed in CVS.

 > This is with data exported from Endnote w/Mac Roman encoding, and then 
 > cleaned up with the en2ris script.  So maybe something went wrong there?
 > 

Could you please zip up the data before and after running it through
the en2ris script? I'd like to have a look at the characters.

 > >> I am also getting parser errors about an incorrect reference type of
 > >> HEAR.  Looking at the refdb docs, I realize there is no such reference
 > >> type.  However, if I look here, RefMan itself (at least v10) does
 > >> support this reference type.
 > >
 > > RefDB lacks a couple of features present in RefMan 10. I've been using
 > > my RefMan 8.01 docs so far as I've last used that version. Other
 > > issues are e.g. support for multiple UR fields and  support for L1-L4
 > > fields. I'll work on that.
 > 
 > For the short-term, perhaps you can just add HEAR as an option in the 
 > DTD?
 > 

I have to correct myself. I've simply forgotten HEAR. It was supposed
to be in the DTD in the first place. I've fixed that in CVS. The new
version is available on the RefDB homepage as well. I've added a
version string to the public identifier. The current version should be
invoked like this:

<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.0/risx.dtd">

 > I may put together the schema/dtd myself, as it's going to be needed, 
 > whether in risx or in mods.
 > 

Yes, why don't you go ahead and cobble together a proposal.

regards,
Markus

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

[Refdb-users] risx output problems

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

Hi,

 > TY  - NEWS
 > ID  - Comm1968a
 > T2  - Commonweal
 > T1  - Jailing Hayden?
 > N1  - cited in Dee (1990) @104:
 > =93the government is about to crack down on the New Left by singling=
 Tom=20
 > Hayden out for arrest.  The FBI has been scouring the country for=20=

 > evidence to indict Hayden under the infamous =91Rap Brown=92 law=97c=
rossing=20
 > state lines to incite to riot.=94 @393
 > PY  - 1968/12/20/
 > ER  -

 > Yields this output in risx, and an error from the xml parser (note=20=

 > dropped publication element):

Newspaper articles are treated just like academic journal
articles. That is, the periodical name must be tagged with JF or
JO. The following ought to work, although there might be complaints
about missing authors:

TY  - NEWS
ID  - Comm1968a
JF  - Commonweal
T1  - Jailing Hayden?
N1  - cited in Dee (1990) @104:
=93the government is about to crack down on the New Left by singling To=
m=20
Hayden out for arrest.  The FBI has been scouring the country for=20
evidence to indict Hayden under the infamous =91Rap Brown=92 law=97cros=
sing=20
state lines to incite to riot.=94 @393
PY  - 1968/12/20/
ER  -

 > I have at 10 records that are screwed up enough to yield a parser=20=

 > error.  Here's another:
 >=20
 > TY  - CASE
 > ID  - USvDellinger1968
 > PY  - 1968
 > T1  - United States v. David T. Dellinger et al
 > T2  - U.S. v. Dellinger
 > T3  - appeal
 > KW  - anti-riot
 > ER  -

I believe I've fixed that. Please do not hesitate to send me test
cases off-list. I do require a number of references outside of what I
personally use (mostly JOUR, BOOK, CHAP) to see what happens. I'll try
to compile a test database of the worst and most ugly references and
use that for my test script.

 > I *really* need this, ASAP in the DTD (in case I need to transform t=
he=20
 > data), and soon after in refdb itself.

I'll try to get this into the next prerelease.

regards,
Markus

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

[Refdb-users] Starting reference numbering from a chosen number ?

[Marc B. <ba...@sm...>]

Hi,

as I indicated before on the list, I have managed to
organize my scientific report using several independent
*.id.xml files to include parts of the bibliography.

One remaining problem is that all of them start at 1,
so if I want to refer to a given entry, 1, 2, etc are
quite ambiguous.

Now I wonder whether there's a possibility to start 
numbering from something other than one and how that
should/could be done.

(NB: I am using the same customized style for all these
citations, so anything that would be hardcoded into the 
style is not an option).

But maybe a variable can be set in an XSL file or so ?
But in that case one would have to recognize which of
the *.bib.xml files is currently processed.

Thanks for any help and suggestions,

  Marc Baaden

-- 
 Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
 mailto:ba...@sm...      -      http://www.marc-baaden.de
 FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217