refdb-users — List for RefDB users

[Refdb-users] authors et al

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

Hi,

this is the job of the citation/bibliography styles. Each journal or
publisher has his own ideas how these things should be handled. The
author/year style shipped with RefDB happens to be from a journal that
lists all authors in the citation. Other journal would cite only the
first three, or some journals cite all on the first occurrence and
fewer on all later occurrences. RefDB has support for all this.

If you can't make do with one of the styles shipped with RefDB (I
acknowledge there's not many to choose from currently), you'll have to
tweak your own style specification.

regards,
Markus

Dylan Oliver writes:
 > Hi, 
 > 
 > Any suggestions on making RefDB produce "author et al" in the text rather than
 > "author author author author author author" when citing a work with many
 > authors?
 > 
 > Best,
 > -- 
 > Dylan Oliver 
 > http://bork.hampshire.edu/~dao
 > AIM: l0sang

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

[Refdb-users] Eur.J.Pharmacol.*.xsl

[Dylan O. <lo...@st...>]

Hi again,

Just found that the Eur.J.Pharmacol. stylesheet doesn't work as
configured by refdbnd. Check out the difference in output when I run the
two default stylesheets; refdbib.log doesn't give me anything else to go
on even when set to debug.=20

0708 17:43 steelbend:div3/cep_prop% make html
refdbxp -t db31x < cepprop.short.xml > cepprop.xml
touch cepprop.bib.xml
runbib -d rdbib_dao -S Eur.J.Pharmacol. -t db31x cepprop.xml
POS
refdbxml -d Eur.J.Pharmacol.fo.xsl -t pdf cepprop.xml

0708 17:44 steelbend:div3/cep_prop% make html
refdbxp -t db31x < cepprop.short.xml > cepprop.xml
touch cepprop.bib.xml
runbib -d rdbib_dao -S J.Biol.Chem. -t db31x cepprop.xml
5 reference(s) formatted, 0 failed

refdbxml -d J.Biol.Chem.html.xsl -t html cepprop.xml
--=20
Dylan Oliver=20
http://bork.hampshire.edu/~dao
AIM: l0sang

[Refdb-users] authors et al

[Dylan O. <lo...@st...>]

Hi,=20

Any suggestions on making RefDB produce "author et al" in the text rather t=
han
"author author author author author author" when citing a work with many
authors?

Best,
--=20
Dylan Oliver=20
http://bork.hampshire.edu/~dao
AIM: l0sang

[Refdb-users] ANN: RefDB-0.9.3-pre7 available

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

Hi all,

this is hopefully the final prerelease before 0.9.3 hits the
shelves. I've attempted to fix the remaining issues with citation key
case mismatches in SGML and XML bibliographies. If you find some time,
please install this version and give it some thorough testing.

These are the files to grab:

http://refdb.sourceforge.net/pre/refdb-0.9.3-pre7.tar.gz
http://refdb.sourceforge.net/pre/RefDB-perlmod-0.3_pre1.tar.gz
http://refdb.sourceforge.net/pre/RefDBClient-Client-1.6.tar.gz

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

[Refdb-users] <newbie> 0 reference formatted

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

Hi Matt,

waitaminute - the id file looks all wrong. What you apparently tried
is to run a document using the short citation style through runbib or
refdbib. This is not going to work. You'll have to run the document
through refdbxp first to create the full citation style.

I'd recommend to read about refdbnd which will create skeleton
documents along with a customized Makefile. This will take all the
hassle out of this process.

Let me know if you need further assistance.

regards,
Markus

Matt P. writes:
 > <?xml version="1.0" encoding="UTF-8"?>
 > 
 > <!DOCTYPE citationlist PUBLIC "-//Markus Hoenicka//DTD CitationList//EN" "http://refdb.sourceforge.net/dtd/citationlistx.dtd">
 > <citationlist>
 > 	<citation>2;</citation>
 > 	<citation>2;14;5;</citation>
 > 	<citation>11;</citation>
 > 	<citation>12;</citation>
 > 	<citation>A:2;</citation>
 > 	<citation>Y:2;</citation>
 > 	</citationlist>
 > 
 > 

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

Re: [Refdb-users] <newbie> 0 reference formatted

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

Hi Matt,

I'm sorry but this can't be the case. If nothing changes on the server
side, you'd get a timeout error on the client side instead of an error
message. I assume you have a refdbd process lurking in the background
that happily answers the client requests instead of the foreground
process.

Please make sure to kill all refdbd processes before trying again. I
need to see the server side log output in order to figure out what's
going wrong here.

Thanks,
Markus

Matt P. writes:
 > Another point is that on the server side, nothing changes...
 > I started it as you suggested: refdbd -s -e 0 -l 7, and the terminal
 > doesn't change at all, even when connections are made:
 > 
 > application server started
 > use /tmp/refdbd_fifo29316 as fifo
 > server waiting n_max_fd=4
 > 

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

[Refdb-users] <newbie> 0 reference formatted

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

Hi Matt,

the bibtex-* styles are special styles intended for use with LaTeX
documents only - they don't provide sufficient information to render
an XML bibliography properly. Please try again using either the
J.Biol.Chem. or the Eur.J.Pharmacol. style. This works fine over
here. If it does not work for you, it's a bug and needs to be
fixed. In that case, please provide the debug output created by refdbd
started with a log level of 7.

regards,
Markus

Matt P. writes:
 > Would someone indicate to me what I am doing wrong, or point somewhere
 > in the (extensive and very good) documentation. 
 > 

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

[Refdb-users] <newbie> 0 reference formatted

[Matt P. <mpa...@to...>]

Hello,

Just starting with refdb. 

when using runbib (or refdbib), I systematically get
0 reference(s) formatted, 0 failed.

I am using the version 0.9.3-pre6, with mysql as a backend.
I have successfully created a database reftest, in which I inserted the
content of testrefs.ris

After completion of the command 
  'runbib -d reftest -S "bibtex-full" -t db31x dbxtest.xml',
I get various bibtex-full.*.dsl, dbxtest.id.xml that looks ok:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE citationlist PUBLIC "-//Markus Hoenicka//DTD CitationList//EN" "http://refdb.sourceforge.net/dtd/citationlistx.dtd">
<citationlist>
	<citation>2;</citation>
	<citation>2;14;5;</citation>
	<citation>11;</citation>
	<citation>12;</citation>
	<citation>A:2;</citation>
	<citation>Y:2;</citation>
	</citationlist>


But the dbxtest.bib.xml looks rather empty:

<!-- <?xml version="1.0"?>
<!DOCTYPE bibliography PUBLIC "-//OASIS//DTD DocBook XML V4.1.2//EN" "http://www.oasis-open.org/docbook/xml/4.1.2/docbookx.dtd"> -->
<bibliography role="refdb">
<title>Reference List</title>
<bibliomixed role="multixref"></bibliomixed></bibliography>



I've tried to run the command refdbib
  refdbib -d reftest -S "bibtex-full" dbtest.id.xml > dbxtest.bib.xml

and I conveniently get the same result.

Would someone indicate to me what I am doing wrong, or point somewhere
in the (extensive and very good) documentation. 

Thanks,

Matt

[Refdb-users] =?ISO-8859-3?B?cmVmZGItdXNlcnMsVHVybiBiYWNrIHlvdXIgYm9keSdzIGJpb2xvZ2ljYWwgdGltZSBjbG9jayAxMC0yMCB5ZWFycw==?=

[Carol Alderson<Ho...@ya...>]

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L2MvcmVtb3ZlIj5SZW1vdmUgbWFpbDwvYT48L3A+DQo8L2JvZHk+DQo8L2h0bWw+

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[Queen S. <ny...@ix...>]

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[Refdb-users] Re: [libdbi-users] Re: libdbi/libdbi-drivers prereleases

[Marc <kl...@sa...>]

Hi!

Sorry, I forgot to attach config.h in my previous mail.

Best regards,

Marc
-------------
/* config.h.  Generated automatically by configure.  */
/* config.h.in.  Generated from configure.in by autoheader.  */

/* Specifies the mode of dlopen behavior */
#define DLOPEN_FLAG RTLD_NOW

/* Specifies the filename extension of loadable modules */
#define DRIVER_EXT ".so"

/* Define to 1 if you have the `asprintf' function. */
#define HAVE_ASPRINTF 1

/* Define to 1 if you have the `atoll' function. */
#define HAVE_ATOLL 1

/* Define to 1 if you have the <dlfcn.h> header file. */
/* #undef HAVE_DLFCN_H */

/* Define to 1 if you have the `dlopen' function. */
/* #undef HAVE_DLOPEN */

/* Define to 1 if you have the <inttypes.h> header file. */
/* #undef HAVE_INTTYPES_H */

/* Define to 1 if you have the <ltdl.h> header file. */
#define HAVE_LTDL_H 1

/* Define to 1 if you have the <mach-o/dyld.h> header file. */
/* #undef HAVE_MACH_O_DYLD_H */

/* Define to 1 if you have the <memory.h> header file. */
/* #undef HAVE_MEMORY_H */

/* Define to 1 if you have the `NSLinkModule' function. */
/* #undef HAVE_NSLINKMODULE */

/* Define to 1 if you have the <stdint.h> header file. */
/* #undef HAVE_STDINT_H */

/* Define to 1 if you have the <stdlib.h> header file. */
/* #undef HAVE_STDLIB_H */

/* Define to 1 if you have the <strings.h> header file. */
#define HAVE_STRINGS_H 1

/* Define to 1 if you have the <string.h> header file. */
#define HAVE_STRING_H 1

/* Define to 1 if you have the `strtoll' function. */
#define HAVE_STRTOLL 1

/* Define to 1 if you have the <sys/stat.h> header file. */
/* #undef HAVE_SYS_STAT_H */

/* Define to 1 if you have the <sys/types.h> header file. */
/* #undef HAVE_SYS_TYPES_H */

/* Define to 1 if you have the <unistd.h> header file. */
/* #undef HAVE_UNISTD_H */

/* Define to 1 if you have the `vasprintf' function. */
#define HAVE_VASPRINTF 1

/* Name of package */
#define PACKAGE "libdbi-drivers"

/* Define to the address where bug reports for this package should be sent. */
/* #undef PACKAGE_BUGREPORT */

/* Define to the full name of this package. */
/* #undef PACKAGE_NAME */

/* Define to the full name and version of this package. */
/* #undef PACKAGE_STRING */

/* Define to the one symbol short name of this package. */
/* #undef PACKAGE_TARNAME */

/* Define to the version of this package. */
/* #undef PACKAGE_VERSION */

/* Define to 1 if you have the ANSI C header files. */
/* #undef STDC_HEADERS */

/* Version number of package */
#define VERSION "0.7.0"

Re: [Refdb-users] refdbib segfault

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

Dylan Oliver writes:
 > The big secret, I discovered, is to comment out &bibliography; 
 > from short.xml before running make for the first time, to uncomment it,
 > and finally run make again. voila! Long as I searched through the docs, this
 > was NOT obvious; please spell it out in the tutorial or, better, find a
 > work-around (I tried adding '--novalid' to xsltproc's list of arguments
 > in runbib, but it didn't do the trick).
 > 
I'll use the workaround you suggested in a separate mail. I didn't
bother to fix this in the past as it is a non-fatal error that
shouldn't do any harm except that it doesn't look reassuring to start
with an error.

 > Oh, one more change for the docs: I noticed that the Y:author prefix
 > produces a reference number rather than year in the text - that is, a
 > (1) instead of a (2000). Be nice to have both options, really - maybe
 > the former could be accomplished by prefixing the key with an 'N:'. But
 > 'Y:' should really just print the year.
 > 
This is by design. The year should only be used in author/year
citation styles as far as I can tell from the journals that I read:

...as reported lately (Miller, 1999)
...as reported by Miller (1999)

...as reported lately (5)
...as reported by Miller (5)

Having both options is not a good thing as it would make switching
styles hard. Using prefixes that work only in author/year or only in
numbered citation styles is not a good thing IMHO.

regards,
Markus

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

[Refdb-users] [OT] Problem with emacs/XML mode and refdb citations in XML

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

Hi Marc,

I don't know the XML mode. I use PSGML which does not show this
strange phenomenon. You should probably go ahead and send an example
document to the XML mode maintainer.

regards,
Markus

Marc Baaden writes:
 > 
 > Hi,
 > 
 > this can probably hardly be identified as a refdb problem, but still
 > it is quite annoying if you start writing documents with citations
 > more and more often. I do use emacs and XML mode for editing, and
 > if I re-justify my paragraphs via C-c C-q, it works fine except for
 > the lines where I have a citation.
 > 
 > So most of the lines go to about ...................................|
 > the end indicated by the pipe symbol, but the lines with citations are
 > broken as follows:
 > 
 >     position  du  cation  dans  le complexe <citation
 > 						      role="REFDB">BAADEN01N02</citation>.
 > 
 > and all thereafter is one line until the next </para>.
 > 
 > Any other emacs users here with any hints ?

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

[Refdb-users] addref, nmed2ris

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

Hi,

except memory exhaustion (which I do not assume) the only way to cause
this problem is to drop the leading newline in the RIS file. Each
dataset, including the first one in a file, has to start with a
newline (essentially an empty line). nmed2ris used to create these
newlines when I last checked. It should still do, although I'd
recommend to use med2ris.pl instead. Maybe you lost it during editing?


regards,
Markus

Dylan Oliver writes:
 > Grabbed a reference from PubMed in MEDLINE format and converted it to
 > RIS with nmed2ris; looks good. Enter refdbc and try to addref it, but
 > get only a cryptic 'data read error' with nothing to back it up in the
 > logs (collecting in DEBUG mode). What's that mean? Something wrong with
 > the nmed or ris file? Both are attached.
 > 
 > -- 
 > Dylan Oliver 
 > http://bork.hampshire.edu/~dao
 > AIM: l0sang

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

[Refdb-users] addref, nmed2ris

[Dylan O. <lo...@st...>]

Grabbed a reference from PubMed in MEDLINE format and converted it to
RIS with nmed2ris; looks good. Enter refdbc and try to addref it, but
get only a cryptic 'data read error' with nothing to back it up in the
logs (collecting in DEBUG mode). What's that mean? Something wrong with
the nmed or ris file? Both are attached.

-- 
Dylan Oliver 
http://bork.hampshire.edu/~dao
AIM: l0sang

[Refdb-users] [OT] Problem with emacs/XML mode and refdb citations in XML

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

Hi,

this can probably hardly be identified as a refdb problem, but still
it is quite annoying if you start writing documents with citations
more and more often. I do use emacs and XML mode for editing, and
if I re-justify my paragraphs via C-c C-q, it works fine except for
the lines where I have a citation.

So most of the lines go to about ...................................|
the end indicated by the pipe symbol, but the lines with citations are
broken as follows:

    position  du  cation  dans  le complexe <citation
						      role="REFDB">BAADEN01N02</citation>.

and all thereafter is one line until the next </para>.

Any other emacs users here with any hints ?

Thanks in advance,
  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

Re: [Refdb-users] refdbib segfault

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

Hi,

Markus Hoenicka writes:
 > Fine, then it's a bug. I'll try to run some tests with your data asap
 > and see what happens.
 > 

Done. There's been two issues:

- your XML document was broke. The bibliography entity lacked the
  trailing ";" which causes SGML/XML parsers to barf. The whole line
  needs to read:
  &bibliography;

- RefDB stumbled over the citation key case issue, something that I'm
  currently about to fix thoroughly. Your data now work properly on my
  box, but there's been a couple of changes compared to the last
  release. I'll check in the changes later tonight. You should then be
  able to pull the CVS version (if the SF folks will let you) and get
  things to work. The current version relies on xsltproc to process
  the intermediate XML documents. You better make sure you've
  installed that lest you want to manually fix the bibliography
  scripts.

 >  > How about automatically stripping unmapped tags when importing data
 >  > through the web interface?
 >  > 
 > 
 > Sure this is possible. It never occured to me, that's why it hasn't
 > been done long ago. I'll add a proper default setting to
 > refdbcgirc.example and add some code to the RIS import routine that
 > will skip lines starting with "<unmapped>".
 > 

I've changed the med2riscgirc example config file to ignore unmapped
tags. The import routines actually ignore these lines anyway, they
only result in additional warnings in the log output.

regards,
Markus

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

[Refdb-users] marc2ris.pl and RefDB::Log

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

Hi Dylan,

I assume this is caused by a lack of write permissions to the default
log file. Do you get the same error if you start marc2ris with the
command line parameter -L ~/marc2ris.log, i.e. if you specify a log
file that you do have write permissions for?

If that helps, you might want to create /var/log/marc2ris.log as root
and change the permissions accordingly.

regards,
Markus

Dylan Oliver writes:
 > 'Lo again - 
 > 
 > Trying to convert data from the LOC through yaz to RIS and marc2ris.pl
 > is giving me this error:
 > 
 > 0630 15:09 steelbend:div3/cep_prop% marc2ris.pl bruman.usmarc > bruman.ris
 > Can't use an undefined value as a symbol reference at
 > /usr/local/share/perl/5.8.0/RefDB/Log.pm line 294.
 > 

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

[Refdb-users] marc2ris.pl and RefDB::Log

[Dylan O. <lo...@st...>]

'Lo again - 

Trying to convert data from the LOC through yaz to RIS and marc2ris.pl
is giving me this error:

0630 15:09 steelbend:div3/cep_prop% marc2ris.pl bruman.usmarc > bruman.ris
Can't use an undefined value as a symbol reference at
/usr/local/share/perl/5.8.0/RefDB/Log.pm line 294.

Here's what I did; bruman.usmarc, bruman.ris, and bruman.ris2 are
attached (sorry for the flood; I don't want to leave anything that would
help debugging out):

0630 15:24 steelbend:div3/cep_prop% yaz-client
z3950.loc.gov:7090/Voyager
Connecting...OK.
Sent initrequest.
Connection accepted by v3 target.
ID     : 34
Name   : Voyager LMS - Z39.50 Server
Version: 1.13
Options: search present
Elapsed: 2.126070
Z> set_marcdump bruman.usmarc
Z> format usmarc
Z> f @attr 1=4 "Alcohol in Ancient Mexico"
Sent searchRequest.
Received SearchResponse.
Search was a success.
Number of hits: 1
records returned: 0
Elapsed: 5.014342
Z> show 1+1
Sent presentRequest (1+1).
Records: 1
[VOYAGER]Record type: USmarc
convert from MARC8 to ANSI_X3.4-1968
001 11874980
005 20010515122345.0
008 991222s2000    utuab    b   s001 0 eng
906    $a 7 $b cbc $c orignew $d 1 $e ecip $f 19 $g y-gencatlg
925 0  $a acquire $b 2 shelf copies $x policy default
955    $a sf10 12-22-99; sf12 to CPSO 12-22-99; sf04; to Dewey 01-11-00;
aa11 01-11-00; CIP ver. se40 02-09-01; to BCCD 02-09-01; lj05 sent copy
2 to BCCD 05-15-01
010    $a    99050946
020    $a 0874806585 (hardcover : alk. paper)
040    $a DLC $c DLC $d DLC
042    $a pcc
050 00 $a F1219.3.A42 $b B78 2000
082 00 $a 394.1/3/0972 $2 21
100 1  $a Bruman, Henry J.
245 10 $a Alcohol in Ancient Mexico / $c Henry J. Bruman ; foreword by
Peter T. Furst ; [maps by J. Chase Langford ; all photographs by Henry
J. Bruman unless otherwise noted].
260    $a Salt Lake City : $b University of Utah Press, $c c2000.
300    $a xii, 158 p. : $b ill., maps ; $c 24 cm.
504    $a Includes bibliographical references (p. 136-144) and index.
504    $a "Henry J. Bruman, selected bibliography compiled by Ronald F.
Lockmann": p. 147-148.
650  0 $a Indians of Mexico $x Alcohol use.
650  0 $a Indians of Mexico $x Rites and ceremonies.
650  0 $a Indians of Mexico $x Medicine.
650  0 $a Fermentation $z Mexico $x History.
650  0 $a Drinking of alcoholic beverages $z Mexico $x History.
nextResultSetPosition = 2
Elapsed: 0.073821
Z> quit
See you later, alligator.

0630 15:41 steelbend:div3/cep_prop% marc2ris.pl bruman.usmarc >
bruman.ris
Can't use an undefined value as a symbol reference at
/usr/local/share/perl/5.8.0/RefDB/Log.pm line 271.

0630 15:41 steelbend:div3/cep_prop% marc2ris.pl -l 7 -e stderr
bruman.usmarc > bruman.ris2
marc2ris.pl:converting bruman.usmarc
marc2ris.pl:no type found - assume BOOK
marc2ris.pl:name >>Bruman, Henry J.<< in direct order - leave as is
marc2ris.pl:empty series title field
marc2ris.pl:no issn found
marc2ris.pl:no type found - assume BOOK
marc2ris.pl:name >>Bruman, Henry J.<< in direct order - leave as is
marc2ris.pl:empty series title field
marc2ris.pl:no issn found

-- 
Dylan Oliver 
http://bork.hampshire.edu/~dao
AIM: l0sang

Re: [Refdb-users] refdbib segfault

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

Hi Dylan,

Dylan Oliver writes:
 > I still get the same error after removing the unmapped lines. 
 > 

Fine, then it's a bug. I'll try to run some tests with your data asap
and see what happens.

 > How about automatically stripping unmapped tags when importing data
 > through the web interface?
 > 

Sure this is possible. It never occured to me, that's why it hasn't
been done long ago. I'll add a proper default setting to
refdbcgirc.example and add some code to the RIS import routine that
will skip lines starting with "<unmapped>".

regards,
Markus

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

[Refdb-users] Mapping http://docbook.sourceforge.net identifier (catalogs)

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

I don't have any experience with XEP, but other tools like xsltproc
require a switch like --catalog to use catalogs in the first
place. Frankly, I don't even know whether XEP works with SGML catalogs
at all, or with XML catalogs, or maybe neither? Another issue is the
lack of a mapping. You'd have to write your own catalog file and
either add it manually to your SGML_CATALOG_FILES variable (assuming
that XEP evaluates this) or use the Debian tools to add the catalog to
the Debian master catalog.

In any case I'd suggest to go to comp.text.xml or a similar forum,
people should be way more knowledgeable about these issues than me.

regards,
Markus


Marc Baaden writes:
 > 
 > Hi,
 > 
 > I have some trouble of the sort
 > 
 > {?Could not retrieve image from 'http://docbook.sourceforge.net/release/images/draft.png': java.net.NoRouteToHostException: No route to host}
 > 
 > when trying to render a docbook document translated to fo with XEP. (this is 
 > due to the fact that we are now firewalled and use a proxy). But more 
 > importantly, I would like to avoid fetching things like that, as they are
 > locally installed in my case (eg 
 > /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/images/draft.png).
 > 
 > I thought this would be taken care of by catalog files, but I couldn't find
 > any mapping of docbook.sourceforge.net to local files. Is there a reason ?
 > 
 > (NB: I am using Debian, and until now most things were automagically 
 > catalogued correctly).
 > 
 > Should I add something directly to /etc/catalogs, or how else to properly 
 > setup these things ?
 > 
 > (NB: I have compiled the little java extension from 
 > http://xep.xattic.com/lists/xep-support/0680.html to make catalogs available 
 > to XEP, so that should not be a problem).
 > 
 > Thanks in advance,
 >   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
 > 
 > 
 > 
 > 
 > -------------------------------------------------------
 > This SF.Net email sponsored by: Free pre-built ASP.NET sites including
 > Data Reports, E-commerce, Portals, and Forums are available now.
 > Download today and enter to win an XBOX or Visual Studio .NET.
 > http://aspnet.click-url.com/go/psa00100006ave/direct;at.asp_061203_01/01
 > _______________________________________________
 > Refdb-users mailing list
 > 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

[Refdb-users] cvs

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

Hi Dylan,

all I can suggest is to try again later. The sourceforge folks are
currently fiddling a lot with their setup, e.g. the web cvs runs
against a backup server instead of the live data. I've had similar
access problems lately, but they go away as often as they occur. I
apologize for the inconvenience, but there's not much that I could do
about it.

regards,
Markus

Dylan Oliver writes:
 > I'd like to check out the RefDB source from cvs, but can't log in:
 > 
 > 0630 10:29 steelbend:~# cvs -d
 > :pserver:ano...@cv...:/cvsroot/refdb login
 > Logging in to
 > :pserver:ano...@cv...:2401/cvsroot/refdb
 > CVS password: 
 > cvs [login aborted]: reading from server: Connection reset by peer
 > 
 > hmmm. What's up? I've been able to log in to other cvs servers..
 > 
 > thanks,
 > -- 
 > Dylan Oliver 
 > http://bork.hampshire.edu/~dao
 > AIM: l0sang

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

[Refdb-users] cvs

[Dylan O. <lo...@st...>]

I'd like to check out the RefDB source from cvs, but can't log in:

0630 10:29 steelbend:~# cvs -d
:pserver:ano...@cv...:/cvsroot/refdb login
Logging in to
:pserver:ano...@cv...:2401/cvsroot/refdb
CVS password:=20
cvs [login aborted]: reading from server: Connection reset by peer

hmmm. What's up? I've been able to log in to other cvs servers..

thanks,
--=20
Dylan Oliver=20
http://bork.hampshire.edu/~dao
AIM: l0sang

[Refdb-users] Mapping http://docbook.sourceforge.net identifier (catalogs)

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

Hi,

I have some trouble of the sort

{?Could not retrieve image from 'http://docbook.sourceforge.net/release/images/draft.png': java.net.NoRouteToHostException: No route to host}

when trying to render a docbook document translated to fo with XEP. (this is 
due to the fact that we are now firewalled and use a proxy). But more 
importantly, I would like to avoid fetching things like that, as they are
locally installed in my case (eg 
/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/images/draft.png).

I thought this would be taken care of by catalog files, but I couldn't find
any mapping of docbook.sourceforge.net to local files. Is there a reason ?

(NB: I am using Debian, and until now most things were automagically 
catalogued correctly).

Should I add something directly to /etc/catalogs, or how else to properly 
setup these things ?

(NB: I have compiled the little java extension from 
http://xep.xattic.com/lists/xep-support/0680.html to make catalogs available 
to XEP, so that should not be a problem).

Thanks in advance,
  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

Re: [Refdb-users] refdbib segfault

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

Hi,

I didn't run any tests yet, but I see that your RIS data still contain
the unmapped tags. They're not supposed to be imported into RefDB,
therefore you've got to strip them out (or use the proper switch of
the import filter to suppress them in the first place). Use a command
like:

grep -v "<unmapped" < cepprop.ris > cepprop.fixed.ris

to fix your existing data. Does your problem persist if you use clean
RIS data?

regards,
Markus

Dylan Oliver writes:
 > Sorry for the confusion re: segfaulting; I was running 0.9.2a when I
 > started writing that message and the segfaulting stopped when I upgraded
 > to 0.9.3-pre6 and `make clean`ed. The references were imported from
 > pubmed through RefDB's web interface. Thanks, and let me know if I can
 > be of any further assistance in debugging this.  
 > 

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