refdb-cvs — All cvs checkins go to this list

[Refdb-cvs] CVS: refdb/scripts Makefile.am,1.22,1.23

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/scripts
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22459

Modified Files:
	Makefile.am 
Log Message:
updated for latest refdbxml version

Index: Makefile.am
===================================================================
RCS file: /cvsroot/refdb/refdb/scripts/Makefile.am,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -U2 -r1.22 -r1.23
--- Makefile.am	6 Jan 2004 18:11:33 -0000	1.22
+++ Makefile.am	5 Mar 2004 00:10:05 -0000	1.23
@@ -36,4 +36,5 @@
 	sed 's%<tei_root>%$(tei_xsl)%g' | \
 	sed 's%<myshell>%$(myshell)%' | \
+	sed 's%<sysconfdir>%$(sysconfdir)/@PACKAGE@%' | \
 	sed 's%<classpath_root>%$(classpath_root)%' > refdbxml
 	chmod a+x refdbxml

[Refdb-cvs] CVS: refdb/etc refdbxmlrc,NONE,1.1

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/etc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22317

Added Files:
	refdbxmlrc 
Log Message:
initial version

--- NEW FILE ---
# This is an example configuration file for refdbxml, the XML transformation
# tool of RefDB
# RefDB is a reference database and bibliography tool, see
# http://refdb.sourceforge.net for further information

# Syntax rules of this file:
# 1. Each line contains a pair of variable name and variable value, 
#    separated by whitespace.
# 2. The hash (#) denotes the start of a comment, the rest of the line
#    will be ignored
# 3. The line ending must be Unix-style (LF) regardless of the operating
#    system


# Note: Each of these options can be overridden at execution time by
# invoking refdbxml with command line options.
# To see the available options, type 'refdbxml -h' or refer to the manual.


## XSLT processor.
# An xslt processor is used to transform your DocBook xml document to
# (x)html or fo.
# Currently available choices are:
#   xalan
#   xt
#   xsltproc (default)
#   saxon
#   saxon-xerces
# Note: 'saxon-xerces' refers to the saxon xslt processor using the
# xerces xml parser from Apache.
# Note: 'saxon', both with and without 'xerces', will use the Apache resolver.
# Note: _You_ must ensure that the xslt processor is installed and
# correctly configured.  RefDB does not check for processors other than the
# default xsltproc.
#xslt_processor	xsltproc

## XSLT classpath
# You only need to set this variable if your XSLT processor is java-based.
# If it's not java-based (eg. xsltproc), don't set this variable.
# Some XSLT processors _are_ java-based (including xalan, xt and saxon)
# and need to access certain directories and java class files.
# This is done by specifying a classpath.
# Refer to the application's documentation for further information
# about the necessary classpath.
# One approach is to choose a directory and put in it symlinks to
# the required jars, so the classpath may be something like:
#   /usr/share/java
# Do not use backslashes to concatenate lines.
#xslt_classpath	/usr/share/java

## FO processor
# When producing printed output the xslt processor produces a "formatted
# objects" file (.fo).  An FO processor then transforms this to printed
# output.
# Currently available choices are:
#   passivetex (default) -> pdf output
#   fop                  -> pdf output
#   xep                  -> pdf output
#   jfor                 -> rtf output
# Note: _You_ must ensure that the xslt processor is installed and
# correctly configured.  RefDB does not check.
#fo_processor	passivetex

## FO classpath
# You only need to set this variable if your FO processor is java-based.
# If it's not java-based (eg. passivetex), don't set this variable.
# Some FO processors _are_ java-based (including fop, xep and jfor)
# and need to access certain directories and java class files.
# This is done by specifying a classpath.
# Refer to the application's documentation for further information
# about the necessary classpath.
# One approach is to choose a directory and put in it symlinks to
# the required jars, so the classpath may be something like:
#   /usr/share/java
# Do not use backslashes to concatenate lines.
#fo_classpath	/usr/share/java


## Include following variables to cover all command line options
## Not needed with refdbnd/make system

## stylesheet
# refdbxml currently sets no stylesheet default, relying on command line
# option.  I'll do the same.
#stylesheet		

## output format
# The format of the output file.
# Current options are:
#   html (default)
#   pdf
#   rtf
# refdbxml currently sets outformat to html as default. I'll do the same.
#outformat	html

[Refdb-cvs] CVS: refdb configure.in,1.47,1.48

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22233

Modified Files:
	configure.in 
Log Message:
added refdbxmlrc to config files

Index: configure.in
===================================================================
RCS file: /cvsroot/refdb/refdb/configure.in,v
retrieving revision 1.47
retrieving revision 1.48
diff -u -U2 -r1.47 -r1.48
--- configure.in	17 Feb 2004 22:15:51 -0000	1.47
+++ configure.in	5 Mar 2004 00:08:54 -0000	1.48
@@ -123,12 +123,12 @@
 client_bins="refdbib\$(EXEEXT) refdbc\$(EXEEXT) refdba\$(EXEEXT) refdbxp\$(EXEEXT) nmed2ris\$(EXEEXT) eenc\$(EXEEXT)"
 client_scripts="refdbjade runbib tex2mail db2ris refdbxml marc2ris.pl med2ris.pl en2ris.pl refdbnd dos2unix"
-client_etc_objects="bib2risrc.example bib2riscgirc.example db2risrc.example nmed2risrc.example nmed2riscgirc.example refdbarc.example refdbcrc.example refdbcgirc.example refdbibrc.example med2risrc.example med2riscgirc.example marc2risrc.example"
-client_etc_distobjects="bib2risrc bib2riscgirc db2risrc nmed2risrc nmed2riscgirc refdbarc refdbcrc refdbcgirc refdbibrc med2risrc med2riscgirc marc2risrc"
+client_etc_objects="bib2risrc.example bib2riscgirc.example db2risrc.example nmed2risrc.example nmed2riscgirc.example refdbarc.example refdbcrc.example refdbcgirc.example refdbibrc.example med2risrc.example med2riscgirc.example marc2risrc.example refdbxmlrc.example"
+client_etc_distobjects="bib2risrc bib2riscgirc db2risrc nmed2risrc nmed2riscgirc refdbarc refdbcrc refdbcgirc refdbibrc med2risrc med2riscgirc marc2risrc refdbxmlrc"
 elif test "$ac_client" = "YES"; then
 client_subdirs="declarations dsssl dtd etc examples scripts src styles doc xsl"
 client_bins="refdbib refdbc refdba refdbxp nmed2ris eenc"
 client_scripts="refdbjade runbib tex2mail db2ris refdb-bug refdbxml marc2ris.pl med2ris.pl en2ris.pl refdbnd dos2unix"
-client_etc_objects="bib2risrc.example bib2riscgirc.example db2risrc.example nmed2risrc.example nmed2riscgirc.example refdbarc.example refdbcrc.example refdbcgirc.example refdbibrc.example med2risrc.example med2riscgirc.example marc2risrc.example"
-client_etc_distobjects="bib2risrc bib2riscgirc db2risrc nmed2risrc nmed2riscgirc refdbarc refdbcrc refdbcgirc refdbibrc med2risrc med2riscgirc marc2risrc"
+client_etc_objects="bib2risrc.example bib2riscgirc.example db2risrc.example nmed2risrc.example nmed2riscgirc.example refdbarc.example refdbcrc.example refdbcgirc.example refdbibrc.example med2risrc.example med2riscgirc.example marc2risrc.example refdbxmlrc.example"
+client_etc_distobjects="bib2risrc bib2riscgirc db2risrc nmed2risrc nmed2riscgirc refdbarc refdbcrc refdbcgirc refdbibrc med2risrc med2riscgirc marc2risrc refdbxmlrc"
 else
 client_subdirs=""

[Refdb-cvs] CVS: refdb/etc refdbibrc,1.5,1.6

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/etc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv22691

Modified Files:
	refdbibrc 
Log Message:
fixed comment about available output types

Index: refdbibrc
===================================================================
RCS file: /cvsroot/refdb/refdb/etc/refdbibrc,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -U2 -r1.5 -r1.6
--- refdbibrc	8 Feb 2004 00:34:59 -0000	1.5
+++ refdbibrc	3 Mar 2004 23:41:16 -0000	1.6
@@ -44,5 +44,6 @@
 #timeout 60
 
-# Bibliography output type. Currently only "db31" available
+# Bibliography output type. Currently "db31", "db31x", "teix", and "bibtex"
+# are available
 outtype	db31
 

[Refdb-cvs] CVS: refdb/examples Makefile.template,1.7,1.8

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/examples
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23590/examples

Modified Files:
	Makefile.template 
Log Message:
make clean now removes .aux and .fo files

Index: Makefile.template
===================================================================
RCS file: /cvsroot/refdb/refdb/examples/Makefile.template,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -U2 -r1.7 -r1.8
--- Makefile.template	30 Aug 2003 21:18:38 -0000	1.7
+++ Makefile.template	1 Mar 2004 22:14:31 -0000	1.8
@@ -80,8 +80,9 @@
 	rm -f $(basename).dvi
 	rm -f $(basename).rtf
-	rm -f $(basename).aux.*
+	rm -f $(basename).aux*
 	rm -f $(basename).log
 	rm -f $(basename).out
 	rm -f $(basename).tex
+	rm -f $(basename).fo
 	rm -f *.html
 	rm -f *.xhtml

[Refdb-cvs] CVS: refdb/xsl/refdb/docbk-refdb-xsl/docbk-html docbk-refdb-html.xsl.in,1.6,1.7

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/xsl/refdb/docbk-refdb-xsl/docbk-html
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv23388/xsl/refdb/docbk-refdb-xsl/docbk-html

Modified Files:
	docbk-refdb-html.xsl.in 
Log Message:
fixed typo

Index: docbk-refdb-html.xsl.in
===================================================================
RCS file: /cvsroot/refdb/refdb/xsl/refdb/docbk-refdb-xsl/docbk-html/docbk-refdb-html.xsl.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -U2 -r1.6 -r1.7
--- docbk-refdb-html.xsl.in	19 Sep 2003 22:51:21 -0000	1.6
+++ docbk-refdb-html.xsl.in	1 Mar 2004 22:13:53 -0000	1.7
@@ -72,5 +72,5 @@
       <xsl:when test="$reftype='ADVS'">
         <xsl:call-template name="refdb-literal">
-          <xsl:with-param name="style" select="$ADVSTURLSTYLE"/>
+          <xsl:with-param name="style" select="$ADVSURLSTYLE"/>
           <xsl:with-param name="string">
             <xsl:value-of select="."/>

[Refdb-cvs] CVS: refdb ChangeLog,1.10,1.11

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2953

Modified Files:
	ChangeLog 
Log Message:
post-0.9.4 checkin

Index: ChangeLog
===================================================================
RCS file: /cvsroot/refdb/refdb/ChangeLog,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -U2 -r1.10 -r1.11
--- ChangeLog	30 Aug 2003 21:16:58 -0000	1.10
+++ ChangeLog	18 Feb 2004 00:42:50 -0000	1.11
@@ -1,799 +1,1812 @@
-2003-08-17 18:57  mhoenicka
+2004-02-17 23:20  mhoenicka
 
-	* src/refdbdref.c (1.34): getref(): replaced HAVING by AND; fixed
-	query if personal list is empty
+	* NEWS (1.19), README (1.16): updated for 0.9.4
 
-2003-08-17 18:54  mhoenicka
+2004-02-17 23:15  mhoenicka
 
-	* scripts/refdbnd.in (1.5): added support for DocBook XML 4.2
[...2246 lines suppressed...]
+2003-08-30 23:19  mhoenicka
 
-	* src/eenc.c (1.1): initial version
+	* scripts/: refdb.dump (1.4), refdb.dump.pgsql (1.4),
+	refdb.dump.sqlite (1.3): added CRYOBIOLOGY as journal name word
 
-2003-03-17 23:48  mhoenicka
+2003-08-30 23:18  mhoenicka
 
-	* src/Makefile.am (1.11): added eenc
+	* configure.in (1.36), examples/Makefile.template (1.7),
+	scripts/refdbnd.in (1.6), scripts/refdbxml.in (1.6),
+	scripts/runbib.in (1.8): added xhtml support for DocBook XML
 
-2003-03-17 23:45  mhoenicka
+2003-08-30 23:16  mhoenicka
 
-	* configure (1.24), configure.in (1.30): removed spaces after -L
+	* ChangeLog (1.10): post-0.9.3 checkin
 

[Refdb-cvs] CVS: perlmod/RefDBClient test.pl,1.6,1.7

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/perlmod/RefDBClient
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9664

Modified Files:
	test.pl 
Log Message:
updated to new Client.pm version

Index: test.pl
===================================================================
RCS file: /cvsroot/refdb/perlmod/RefDBClient/test.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -U2 -r1.6 -r1.7
--- test.pl	31 Dec 2003 01:21:54 -0000	1.6
+++ test.pl	17 Feb 2004 22:45:41 -0000	1.7
@@ -126,5 +126,5 @@
 $numtest++;
 
-@result = $clienta->refdb_createdb("perltest");
+@result = $clienta->refdb_createdb("perltest", undef);
 
 foreach $line (@result) {
@@ -160,5 +160,5 @@
 $risdata->read_ris("testdata/pubmed.ris");
 
-@result = $clientc->refdb_addref(undef, $risdata, "ris");
+@result = $clientc->refdb_addref(undef, $risdata, "ris", "ISO-8859-1");
 
 foreach $line (@result) {
@@ -178,5 +178,5 @@
 close IN;
 
-@result = $clientc->refdb_addref(undef, $risxstring, "risx");
+@result = $clientc->refdb_addref(undef, $risxstring, "risx", undef);
 
 foreach $line (@result) {
@@ -196,5 +196,5 @@
 close IN;
 
-@result = $clientc->refdb_addnote(undef, $xnotestring, "xnote");
+@result = $clientc->refdb_addnote(undef, $xnotestring);
 
 foreach $line (@result) {
@@ -216,5 +216,5 @@
 $numtest++;
 
-@result = $clientc->refdb_getref("ris", "AB", undef, "f", ":ID:=1");
+@result = $clientc->refdb_getref("ris", "AB", undef, "f", "ISO-8859-1", ":ID:=1");
 
 foreach $line (@result) {
@@ -226,5 +226,5 @@
 $numtest++;
 
-@result = $clientc->refdb_getnote("xnote", "AB", undef, ":ID:=1");
+@result = $clientc->refdb_getnote("xnote", "AB", undef, "UTF-8", ":ID:=1");
 
 foreach $line (@result) {
@@ -277,5 +277,5 @@
 close IN;
 
-@result = $clientc->refdb_dbib("db31", "refdbteststyle", \&read_styledriver, \&read_biblio, $instring);
+@result = $clientc->refdb_dbib("db31", "refdbteststyle", \&read_styledriver, \&read_biblio, "ISO-8859-1", $instring);
 
 foreach $line (@result) {

[Refdb-cvs] CVS: perlmod/RefDBClient Client.pm,1.8,1.9

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/perlmod/RefDBClient
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9416

Modified Files:
	Client.pm 
Log Message:
updated protocol and functions to RefDB version 0.9.4

Index: Client.pm
===================================================================
RCS file: /cvsroot/refdb/perlmod/RefDBClient/Client.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -U2 -r1.8 -r1.9
--- Client.pm	31 Dec 2003 01:22:19 -0000	1.8
+++ Client.pm	17 Feb 2004 22:44:44 -0000	1.9
@@ -197,5 +197,5 @@
 use strict;
 use vars qw($VERSION @ISA @EXPORT @EXPORT_OK);
-use constant REFDB_PROTOCOL_VERSION => 1;
+use constant REFDB_PROTOCOL_VERSION => 2;
 use constant COMMAND_INBUF_LENGTH => 4096;
 use constant OUTBUF_LEN => 4096;
@@ -204,5 +204,4 @@
 use Socket;
 
-
 =head2 new
 
@@ -252,4 +251,7 @@
     $self->{css_url} = undef;
 
+    ## the client/server message terminator
+    $self->{CS_TERM} = "\x00\x00\x00\x00";
+
     bless $self, $class;
     return $self;
@@ -349,7 +351,7 @@
 
     # send protocol version
-    my $proto = REFDB_PROTOCOL_VERSION;
+    my $proto = REFDB_PROTOCOL_VERSION . $self->{CS_TERM};
 
-    syswrite($socket, "$proto\x00");
+    syswrite($socket, "$proto");
 
     # read password scramble string
@@ -383,5 +385,5 @@
     while (sysread($socket, my $line, $len)) {
 	$result .= $line;
-	if ($line =~ /\x00/) {
+	if ($line =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -420,5 +422,5 @@
     my ($self, $sl) = @_;
 
-    syswrite($self->{socket}, $sl->{cmd} . "\x00");
+    syswrite($self->{socket}, $sl->{cmd} . $self->{CS_TERM});
     #print $sl->{cmd};
     my $inbuffer;
@@ -426,5 +428,5 @@
     while (defined($inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$sl->{inbuffer} .= $inbuffer;
-	if ($sl->{inbuffer} =~ s/\x00//) {
+	if ($sl->{inbuffer} =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
@@ -433,5 +435,5 @@
 #    print $sl->{inbuffer};
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     if ($self->{close} eq "t") {
@@ -448,5 +450,5 @@
     my ($self, $cmd, $risdata, $type) = @_;
 
-    syswrite($self->{socket}, $cmd . "\x00");
+    syswrite($self->{socket}, $cmd . $self->{CS_TERM});
 
     my $result;
@@ -455,5 +457,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -469,6 +471,6 @@
 	foreach my $dataset (@{$risdata->{sets}}) {
 	    # Phase 1: transmit length of next dataset
-	    my $datalength = length($dataset) + 1;
-	    syswrite($self->{socket}, "$datalength\x00");
+	    my $datalength = length($dataset) + length($self->{CS_TERM});
+	    syswrite($self->{socket}, "$datalength" . $self->{CS_TERM});
 	    
 	    # Phase 2: read acknowledgement from server
@@ -476,5 +478,5 @@
 	    while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 		$result .= $inbuffer;
-		if ($result =~ s/\x00//) {
+		if ($result =~ s/$self->{CS_TERM}//) {
 		    last;
 		}
@@ -487,5 +489,5 @@
 	    
 	    # Phase 3: send dataset
-	    syswrite($self->{socket}, $dataset . "\x00");
+	    syswrite($self->{socket}, $dataset . $self->{CS_TERM});
 	    
 	    # Phase 4: read server reply
@@ -493,8 +495,9 @@
 	    while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 		$result .= $inbuffer;
-		if ($inbuffer =~ /\x00/) {
+		if ($inbuffer =~ /$self->{CS_TERM}/) {
 		    last;
 		}
 	    }
+	    $result =~ s/$self->{CS_TERM}//;
 
 	    push (@all_results, $result);
@@ -507,8 +510,8 @@
     # Phase 5: signal server that we're done
     if ($type eq "ris") {
-	syswrite($self->{socket}, "0\x00");
+	syswrite($self->{socket}, "0" . $self->{CS_TERM});
     }
     else {
-	syswrite($self->{socket}, "QUIT\x00");
+	syswrite($self->{socket}, "QUIT" . $self->{CS_TERM});
     }
 
@@ -516,12 +519,15 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($inbuffer =~ s/\x00//) {
+	if ($inbuffer =~ /$self->{CS_TERM}/) {
 	    last;
 	}
     }
     #print $result . "\n";
+
+    $result =~ s/$self->{CS_TERM}//;
+
     push (@all_results, $result);
     
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     @all_results;
@@ -534,5 +540,5 @@
     my ($self, $cmd, $xnotedata) = @_;
 
-    syswrite($self->{socket}, $cmd . "\x00");
+    syswrite($self->{socket}, $cmd . $self->{CS_TERM});
 
     my $result;
@@ -541,5 +547,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -554,17 +560,19 @@
 
     # Phase 5: signal server that we're done
-    syswrite($self->{socket}, "QUIT\x00");
+    syswrite($self->{socket}, "QUIT" . $self->{CS_TERM});
 
     $result = undef;
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($inbuffer =~ s/\x00//) {
+	if ($inbuffer =~ /$self->{CS_TERM}/) {
 	    last;
 	}
     }
     #print $result . "\n";
+
+    $result =~ s/$self->{CS_TERM}//;
     push (@all_results, $result);
     
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     @all_results;
@@ -585,5 +593,5 @@
 	# Phase 1: transmit length of next dataset
 	my $datalength = ($stylelength > XMLPARSE_CHUNKSIZE) ? XMLPARSE_CHUNKSIZE : $stylelength;
-	syswrite($self->{socket}, "$datalength\x00");
+	syswrite($self->{socket}, "$datalength" . $self->{CS_TERM});
 
 	# Phase 2: read acknowledgement from server
@@ -591,5 +599,5 @@
 	while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	    $result .= $inbuffer;
-	    if ($result =~ s/\x00//) {
+	    if ($result =~ s/$self->{CS_TERM}//) {
 		last;
 	    }
@@ -608,9 +616,10 @@
 	while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	    $result .= $inbuffer;
-	    if ($inbuffer =~ /\x00/) {
+	    if ($inbuffer =~ /$self->{CS_TERM}/) {
 		last;
 	    }
 	}
 
+	$result =~ s/$self->{CS_TERM}//;
 
 	unless (substr($result, 0, 3) eq "POS") {
@@ -657,5 +666,5 @@
     }
 
-    syswrite($self->{socket}, $cmd . "\x00");
+    syswrite($self->{socket}, $cmd . $self->{CS_TERM});
 
     my $result;
@@ -663,9 +672,11 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
     }
 
+    $result =~ s/$self->{CS_TERM}//;
+
     unless (substr($result, 0, 3) eq "POS") {
 	$result_pool .= $result;
@@ -677,9 +688,9 @@
 
     # Phase 5: signal server that we're done
-    syswrite($self->{socket}, "0\x00");
+    syswrite($self->{socket}, "0" . $self->{CS_TERM});
 
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	my $result .= $inbuffer;
-	if ($inbuffer =~ s/\x00//) {
+	if ($inbuffer =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
@@ -688,15 +699,16 @@
     # this module sends only one XML document, so we need to tell
     # the server again that we're done
-    syswrite($self->{socket}, "QUIT\x00");
+    syswrite($self->{socket}, "QUIT" . $self->{CS_TERM});
 
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result_pool .= $inbuffer;
-	if ($inbuffer =~ s/\x00//) {
+	if ($inbuffer =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
     }
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
+    $result_pool =~ s/$self->{CS_TERM}//;
     $result_pool;
 }
@@ -754,5 +766,5 @@
     }
 
-    syswrite($self->{socket}, $cmd . "\x00");
+    syswrite($self->{socket}, $cmd . $self->{CS_TERM});
 
     my $result;
@@ -760,5 +772,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -779,18 +791,19 @@
     }
 
-    syswrite($self->{socket}, substr($arg, $index) . "\x00");
+    syswrite($self->{socket}, substr($arg, $index) . $self->{CS_TERM});
 
     $result = undef;
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($inbuffer =~ s/\x00//) {
+	if ($inbuffer =~ /$self->{CS_TERM}/) {
 	    last;
 	}
     }
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     close ($self->{socket});
 
+    $result =~ s/$self->{CS_TERM}//;
     split /\n/, $result;
 }
@@ -828,5 +841,5 @@
     }
 
-    syswrite($self->{socket}, $cmd . "\x00");
+    syswrite($self->{socket}, $cmd . $self->{CS_TERM});
 
     my $result;
@@ -834,5 +847,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -845,5 +858,5 @@
 
     my $index = 0;
-    my $arglength = length($arg);
+    my $arglength = length($arg) +length($self->{CS_TERM});
 
     while ($arglength > COMMAND_INBUF_LEN) {
@@ -853,18 +866,19 @@
     }
 
-    syswrite($self->{socket}, substr($arg, $index) . "\x00");
+    syswrite($self->{socket}, substr($arg, $index) . $self->{CS_TERM});
 
     $result = undef;
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($inbuffer =~ s/\x00//) {
+	if ($inbuffer =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
     }
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     close ($self->{socket});
 
+    $result =~ s/$self->{CS_TERM}//;
     split /\n/, $result;
 }
@@ -1079,5 +1093,5 @@
 Title   : refdb_addref
 
-Usage   : @result = $client->refdb_addref($owner, $risdata, $type);
+Usage   : @result = $client->refdb_addref($owner, $risdata, $type, $encoding);
 
 Function: adds references to the database
@@ -1089,5 +1103,5 @@
 ######################################################################
 sub refdb_addref {
-    my ($self, $owner, $risdata, $type) = @_;
+    my ($self, $owner, $risdata, $type, $encoding) = @_;
 
     $self->_init_dialog();
@@ -1107,4 +1121,8 @@
     }
 
+    if (length($encoding) > 0) {
+	$cmd .= "-E $encoding ";
+    }
+
     $cmd .= "-s $type";
 
@@ -1117,5 +1135,5 @@
 Title   : refdb_updateref
 
-Usage   : @result = $client->refdb_updateref($owner, $is_personal, $risdata);
+Usage   : @result = $client->refdb_updateref($owner, $is_personal, $risdata, $type, $encoding);
 
 Function: updates references in the database
@@ -1127,5 +1145,5 @@
 ######################################################################
 sub refdb_updateref {
-    my ($self, $owner, $is_personal, $risdata, $type) = @_;
+    my ($self, $owner, $is_personal, $risdata, $type, $encoding) = @_;
 
     my $cmd = "updateref -d $self->{db} ";
@@ -1145,4 +1163,8 @@
     }
 
+    if (length($encoding) > 0) {
+	$cmd .= "-E $encoding ";
+    }
+
     if ($is_personal eq "t") {
 	$cmd .= "-p ";
@@ -1183,7 +1205,7 @@
     }
 
-    my $arglength = length($arg) + 1;
+    my $arglength = length($arg) + length($self->{CS_TERM});
 
-    syswrite($self->{socket}, $cmd . " $arglength\x00");
+    syswrite($self->{socket}, $cmd . " $arglength" . $self->{CS_TERM});
 
     my $result;
@@ -1191,5 +1213,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1213,5 +1235,5 @@
 Title   : refdb_addnote
 
-Usage   : @result = $client->refdb_addnote($owner, $xnotedata, $type);
+Usage   : @result = $client->refdb_addnote($owner, $xnotedata);
 
 Function: adds notes to the database
@@ -1223,5 +1245,5 @@
 ######################################################################
 sub refdb_addnote {
-    my ($self, $owner, $xnotedata, $type) = @_;
+    my ($self, $owner, $xnotedata) = @_;
 
     $self->_init_dialog();
@@ -1241,6 +1263,4 @@
     }
 
-    $cmd .= "-s $type";
-
     # return result as a list of lines
     $self->_addnote($cmd, $xnotedata);
@@ -1319,5 +1339,5 @@
     my $arglength = length($arg) + 1;
 
-    syswrite($self->{socket}, $cmd . " $arglength\x00");
+    syswrite($self->{socket}, $cmd . " $arglength" . $self->{CS_TERM});
 
     my $result;
@@ -1325,5 +1345,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1571,5 +1591,5 @@
 Title   : refdb_getref
 
-Usage   : @result = $client->refdb_getref($type, $format_string, $sort_string, $is_personal, $query_string);
+Usage   : @result = $client->refdb_getref($type, $format_string, $sort_string, $is_personal, $encoding, $query_string);
 
 Function: retrieves references
@@ -1581,5 +1601,5 @@
 ######################################################################
 sub refdb_getref {
-    my ($self, $type, $format_string, $sort_string, $is_personal, $arg) = @_;
+    my ($self, $type, $format_string, $sort_string, $is_personal, $encoding, $arg) = @_;
 
     my $cmd = "getref -d $self->{db} ";
@@ -1605,4 +1625,8 @@
     }
     
+    if (length($encoding) > 0) {
+	$cmd .= "-E $encoding ";
+    }
+
     if ($is_personal eq "t") {
 	$cmd .= "-P ";
@@ -1646,7 +1670,7 @@
     }
 
-    my $arglength = length($arg) + 1;
+    my $arglength = length($arg) + length($self->{CS_TERM});
 
-    syswrite($self->{socket}, $cmd . " $arglength\x00");
+    syswrite($self->{socket}, $cmd . " $arglength" . $self->{CS_TERM});
 
     my $result;
@@ -1654,5 +1678,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1676,5 +1700,5 @@
 Title   : refdb_getref
 
-Usage   : @result = $client->refdb_getref($type, $format_string, $sort_string, $query_string);
+Usage   : @result = $client->refdb_getref($type, $format_string, $sort_string, $encoding, $query_string);
 
 Function: retrieves references
@@ -1686,5 +1710,5 @@
 ######################################################################
 sub refdb_getnote {
-    my ($self, $type, $format_string, $sort_string, $arg) = @_;
+    my ($self, $type, $format_string, $sort_string, $encoding, $arg) = @_;
 
     my $cmd = "getnote -d $self->{db} ";
@@ -1710,4 +1734,8 @@
     }
     
+    if (length($encoding) > 0) {
+	$cmd .= "-E $encoding ";
+    }
+
     $cmd .= $arg;
 
@@ -1792,5 +1820,5 @@
     my $datalength = length($cite_data) + 1;
 
-    syswrite($self->{socket}, $cmd . " $datalength\x00");
+    syswrite($self->{socket}, $cmd . " $datalength" . $self->{CS_TERM});
 
     my $result;
@@ -1798,5 +1826,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1816,9 +1844,9 @@
     my @the_result = split /\n/, $self->_getsimplelist($sl);
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1839,5 +1867,5 @@
 Title   : refdb_dbib
 
-Usage   : @result = $client->refdb_dbib($type, $style, $cite_data);
+Usage   : @result = $client->refdb_dbib($type, $style, $stylecallback, $bibliocallback, $encoding, $cite_data);
 
 Function: retrieves an XML/SGML bibliography based on citationlistx data
@@ -1849,5 +1877,5 @@
 ######################################################################
 sub refdb_dbib {
-    my ($self, $type, $style, $stylecallback, $bibliocallback, $cite_data) = @_;
+    my ($self, $type, $style, $stylecallback, $bibliocallback, $encoding, $cite_data) = @_;
 
     my $cmd = "getbib -d $self->{db} -t $type -s $style ";
@@ -1863,5 +1891,9 @@
     }
 
-    syswrite($self->{socket}, $cmd . "\x00");
+    if (length($encoding) > 0) {
+	$cmd .= "-E $encoding ";
+    }
+
+    syswrite($self->{socket}, $cmd . $self->{CS_TERM});
 
     my $result;
@@ -1869,5 +1901,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1879,5 +1911,5 @@
     }
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     # read stylesheet driver data
@@ -1886,5 +1918,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$driverdata .= $inbuffer;
-	if ($driverdata =~ s/\x00//) {
+	if ($driverdata =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
@@ -1894,5 +1926,5 @@
     \&{$stylecallback}($style, $type, $driverdata);
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     $result = undef;
@@ -1900,5 +1932,5 @@
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ /\x00/) {
+	if ($result =~ /$self->{CS_TERM}/) {
 	    last;
 	}
@@ -1914,10 +1946,10 @@
 
     # Phase 5: signal server that we're done
-    syswrite($self->{socket}, "0\x00");
+    syswrite($self->{socket}, "0" . $self->{CS_TERM});
 
     $result = undef;
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ s/\x00//) {
+	if ($result =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
@@ -1929,10 +1961,10 @@
     }
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     my $biblio = undef;
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$biblio .= $inbuffer;
-	if ($biblio =~ s/\x00//) {
+	if ($biblio =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
@@ -1941,15 +1973,15 @@
     \&{$bibliocallback}($biblio);
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     $result = undef;
     while (defined(my $inbuffer = $self->_tread(OUTBUF_LEN))) {
 	$result .= $inbuffer;
-	if ($result =~ s/\x00//) {
+	if ($result =~ s/$self->{CS_TERM}//) {
 	    last;
 	}
     }
 
-    syswrite($self->{socket}, "POS\x00");
+    syswrite($self->{socket}, "POS" . $self->{CS_TERM});
 
     close ($self->{socket});

[Refdb-cvs] CVS: perlmod/RefDBClient MANIFEST,1.2,1.3

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/perlmod/RefDBClient
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8959

Modified Files:
	MANIFEST 
Log Message:
added INSTALL

Index: MANIFEST
===================================================================
RCS file: /cvsroot/refdb/perlmod/RefDBClient/MANIFEST,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -U2 -r1.2 -r1.3
--- MANIFEST	28 May 2003 23:50:52 -0000	1.2
+++ MANIFEST	17 Feb 2004 22:42:40 -0000	1.3
@@ -1,3 +1,4 @@
 Changes
+INSTALL
 Client.pm
 Makefile.PL

[Refdb-cvs] CVS: perlmod/RefDBClient INSTALL,NONE,1.1

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/perlmod/RefDBClient
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv8675

Added Files:
	INSTALL 
Log Message:
initial version

--- NEW FILE ---
Installing the RefDBClient Perl module
======================================

1. Create a system-specific Makefile:
perl Makefile.PL

2. Build the module:
make

3. Run a test. This step is optional and requires a running RefDB installation: 
make test

4. Install the module in the default location:
make install

See the test.pl script for an example of how to use this module.

$Id: INSTALL,v 1.1 2004/02/17 22:41:45 mhoenicka Exp $
(c) Markus Hoenicka <ma...@mh...> 2004

[Refdb-cvs] CVS: refdb README,1.15,1.16 NEWS,1.18,1.19

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4327

Modified Files:
	README NEWS 
Log Message:
updated for 0.9.4

Index: README
===================================================================
RCS file: /cvsroot/refdb/refdb/README,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -U2 -r1.15 -r1.16
--- README	31 Dec 2003 00:27:26 -0000	1.15
+++ README	17 Feb 2004 22:20:23 -0000	1.16
@@ -23,5 +23,5 @@
 Linux, and Solaris
 
-refdb uses MySQL or PostgreSQL as external database servers or SQLite
+refdb uses MySQL or PostgreSQL as external database servers, or SQLite
 as an embedded database engine.
 
@@ -51,8 +51,11 @@
 the instructions in UPGRADING.
 
-In contrast to previous releases, refdbd no longer accepts remote
-connections by default. If you want to continue accessing refdbd from
-a different box, make sure to start refdbd with the -I switch or use
-the "remoteconnect" variable in refdbdrc.
+For security reasons refdbd no longer accepts remote connections by
+default. If you want to continue accessing refdbd from a remote
+box, make sure to start refdbd with the -I switch or use the
+"remoteconnect" variable in refdbdrc.
+
+The query language now performs literal string matches by default. Use
+the new operator "~" to request a regular expression match.
 
 _______

Index: NEWS
===================================================================
RCS file: /cvsroot/refdb/refdb/NEWS,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -U2 -r1.18 -r1.19
--- NEWS	31 Dec 2003 00:27:26 -0000	1.18
+++ NEWS	17 Feb 2004 22:20:23 -0000	1.19
@@ -5,16 +5,15 @@
 
 ______________________________
-Version 0.9.4 (December 2003)
+Version 0.9.4 (February 2004)
 
 Bugfixes:
 
-- fixed a serious bug when updating personal information which may
-  lead to data loss
-
 - fixed risx output
 
+- fixed wrong mapping of titles in some risx types
+
 - added publication type HEAR to the risx DTD
 
-- fixed a possible segfault if messages are not logged in a custom file
+- fixed a possible segfault if messages are logged to stderr
 
 - fixed case mismatches in DocBook XML driver files
@@ -28,4 +27,12 @@
   specifying a default database.
 
+- fixed erroneus trailing spaces in middle names
+
+- fixed handling of hyphenated double-initials (K.-H.)
+
+- fixed error in handling of journal custom abbrev2
+
+- fixed bug that would have blocked concurrent addref commands
+
 
 Improvements:
@@ -55,9 +62,28 @@
   refdbc:whichdb command.
 
-- listdb will now only return RefDB reference databases
+- listdb now only returns RefDB reference databases
 
 - the refdbnd script was enhanced to simplify generating a Makefile
   for an existing SGML or XML document
 
+- server and clients can now be built and installed separately
+
+- if a default database is selected in refdbc, the program will try to
+  select this database at startup to test for its presence.
+
+- the getref and getnote query language now uses literal string
+  matches by default. Use the new "~" operator to obtain a regexp
+  match.
+
+- the string quoting was improved to simplify running regexp queries
+  in the batch mode.
+
+- refdbd now has built-in support for character encoding
+  conversions. You can add datasets and notes in several encodings,
+  including Unicode, and retrieve datasets in all encodings that your
+  libiconv supports. Incoming data is automatically converted to the
+  encoding used by the current database.
+
+
 ______________________________
 Version 0.9.3 (August 2003)

[Refdb-cvs] CVS: refdb configure.in,1.46,1.47

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv3436

Modified Files:
	configure.in 
Log Message:
bumped up version number

Index: configure.in
===================================================================
RCS file: /cvsroot/refdb/refdb/configure.in,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -U2 -r1.46 -r1.47
--- configure.in	26 Jan 2004 21:22:10 -0000	1.46
+++ configure.in	17 Feb 2004 22:15:51 -0000	1.47
@@ -6,5 +6,5 @@
 
 dnl Use automake
-AM_INIT_AUTOMAKE(refdb, 0.9.4-pre5)
+AM_INIT_AUTOMAKE(refdb, 0.9.4)
 
 dnl Find out host type

[Refdb-cvs] CVS: refdb/doc refdb-manual-chapter11.sgml,1.13,1.14 refdb-manual-chapter13.sgml,1.15,1.16 refdb-manual-chapter7.sgml,1.15,1.16

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/doc
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2977/doc

Modified Files:
	refdb-manual-chapter11.sgml refdb-manual-chapter13.sgml 
	refdb-manual-chapter7.sgml 
Log Message:
updated for 0.9.4

Index: refdb-manual-chapter11.sgml
===================================================================
RCS file: /cvsroot/refdb/refdb/doc/refdb-manual-chapter11.sgml,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -U2 -r1.13 -r1.14
--- refdb-manual-chapter11.sgml	8 Feb 2004 00:32:45 -0000	1.13
+++ refdb-manual-chapter11.sgml	17 Feb 2004 22:14:40 -0000	1.14
@@ -743,4 +743,70 @@
     <para>An example set of extended notes is installed into <filename class="directory" moreinfo="none">/usr/local/share/refdb/examples</filename>.</para>
   </sect1>
+  <sect1>
+    <title>Input data mangling</title>
+    <para>Input data are not stored as a literal chunk of text by &appname;. If you import a dataset, and later retrieve it using the same format, the dataset is not guaranteed to be the same character by character. Instead, the data are sliced up, sometimes slightly modified, and sometimes &appname; creates additional information. This section tries to explain what happens to your data behind the scenes, and why this is good for you.</para>
+    <sect2>
+      <title>Information that &appname; generates for you</title>
+      <para>In a few cases &appname; fills in some default values if the datasets do not specify them. This happens in the following cases:</para>
+      <itemizedlist>
+	<listitem>
+	  <para>Each reference and extended note will be assigned a unique numeric identifier. This is mainly used internally, but you can also retrieve references and extended notes by their ID. The ID is always created by the database server, there is no way to enforce specific IDs for your datasets.</para>
+	</listitem>
+	<listitem>
+	  <para>Both references and datasets require a unique alphanumeric key. With a few limitations this is an arbitrary string consisting of letters (at least one) and optional digits. If you do not specify a citation key, &appname; will create one automatically. In the case of references, the publication year is appended to the last name of the first author. If this string is not unique, a sequential suffix starting at "a" through "z", then "aa" and so forth, is tested until a unique string is found. The same algorithm is used for extended note keys, but instead of an author name the user name serves as the base.</para>
+	</listitem>
+	<listitem>
+	  <para>If no reprint status is specified, &appname; inserts "NOT IN FILE" as the default value.</para>
+	</listitem>
+	<listitem>
+	  <para>If your extended notes do not specify a date, &appname; will use the current date and insert that instead.</para>
+	</listitem>
+      </itemizedlist>
+    </sect2>
+    <sect2>
+      <title>Information that &appname; mangles</title>
+      <para>Citation keys are supposed to work as ID values in SGML and XML documents. To avoid any character encoding hassles, only the first 127 characters of the US-ASCII character set are permitted. These characters work in most character encodings. Any characters outside of the permitted range will simply be deleted from a citation key, regardless of whether it is specified by the dataset or generated from the author name.</para>
+      <para>Periodical names and author/editor names receive some special treatment in order to make them usable for &appname;. Both periodical names and person names should be provided in a particular format. However, if you retrieve your data from an electronic source instead of writing them from scratch, the names may not conform to the rules. In order to make best use of these data, &appname; attempts to normalize the incoming periodical and person names until they conform to the rules.</para>
+      <para>There is a good reason for this normalization. Consider a periodical name like "The Journal of Biological Chemistry" . Different electronic sources may abbreviate this as one of:</para>
+      <itemizedlist>
+	<listitem>
+	  <para>J.Biol.Chem.</para>
+	</listitem>
+	<listitem>
+	  <para>J. Biol. Chem.</para>
+	</listitem>
+	<listitem>
+	  <para>J Biol Chem</para>
+	</listitem>
+      </itemizedlist>
+      <para>Although a human reader does not have a hard time to guess that we're looking at the same journal in all three cases, a database is too stupid to understand this. If you add the periodical abbreviations as they are, you'll end up having three different journal entries. As a consequence, a query like <command moreinfo="none">getref :JO:='J.Biol.Chem.'</command> will miss two out of three papers published in that journal. This is not a good thing.</para>
+      <sect3>
+	<title>Periodical names</title>
+	<para>&appname; normalizes abbreviated periodical names like this: First, the name is tokenized. Separators are periods and spaces. If a token has a trailing period, it is assumed to be an abbreviated word and used as such. If a token has no trailing period, the token is compared to an internal list of unabbreviated words (see the <link linkend="app-a-command-listword">listword</link> and <link linkend="app-a-command-addword">addword</link> commands for further information about this list). If a match is found, no period is added. If no match is found, the token is assumed to be an abbreviation of something else and a period is added. Spaces after periods will be removed as one separator is sufficient. If we consider the three versions of the journal name above, all versions would be normalized to the first one.</para>
+      </sect3>
+      <sect3>
+	<title>Person names</title>
+	<para>The names of authors and editors are normalized like this: Everything to the left of the first comma is assumed to be the last name and remains untouched. The next item (separated by either a space, a period, or both) is assumed to be the firstname. If it consists of one capital letter, a period is added and any trailing spaces are removed. If the firstname is spelled out, it is used as such. All following name parts to the left of the second comma, if any, are assumed to be middle names. Each part receives the same treatment as a firstname. Finally, everything to the right of the second comma, if any, is assumed to be a honorific or lineage part and used as such. All spaces following either a period or a comma are removed. A few examples should make this procedure clear:</para>
+	<itemizedlist>
+	  <listitem>
+	    <para>"Miller, John S" -> "Miller,John S."</para>
+	  </listitem>
+	  <listitem>
+	    <para>"Chun, H-K" -> "Chun,H.-K."</para>
+	  </listitem>
+	  <listitem>
+	    <para>"Delorie, DJ" -> "Delorie,DJ"</para>
+	  </listitem>
+	  <listitem>
+	    <para>"Doe, J S" -> "Doe,J.S."</para>
+	  </listitem>
+	  <listitem>
+	    <para>"Random,Jane,Jr." -> "Random,Jane,Jr."</para>
+	  </listitem>
+	</itemizedlist>
+	<para>The last example shows that your data will not be modified as long as they stick to the input format.</para>
+      </sect3>
+    </sect2>
+  </sect1>
 </chapter>
 

Index: refdb-manual-chapter13.sgml
===================================================================
RCS file: /cvsroot/refdb/refdb/doc/refdb-manual-chapter13.sgml,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -U2 -r1.15 -r1.16
--- refdb-manual-chapter13.sgml	8 Feb 2004 00:32:45 -0000	1.15
+++ refdb-manual-chapter13.sgml	17 Feb 2004 22:14:40 -0000	1.16
@@ -169,5 +169,5 @@
 	  </row>
 	  <row>
-	    <entry>encoding</entry>
+	    <entry>toencoding</entry>
 	    <entry>(the database encoding)</entry>
 	    <entry>The character encoding for the bibliography output. If this is not specified, the data will use the same encoding as the database.</entry>

Index: refdb-manual-chapter7.sgml
===================================================================
RCS file: /cvsroot/refdb/refdb/doc/refdb-manual-chapter7.sgml,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -U2 -r1.15 -r1.16
--- refdb-manual-chapter7.sgml	8 Feb 2004 00:32:45 -0000	1.15
+++ refdb-manual-chapter7.sgml	17 Feb 2004 22:14:40 -0000	1.16
@@ -227,7 +227,6 @@
       </simplesect>
     </sect2>
-    <sect2>
+    <sect2 id="app-a-command-addword">
       <title>addword</title>
-      <anchor id="app-admin-command-addword">
       <simplesect>
 	<title>Synopsis</title>
@@ -564,5 +563,5 @@
 	</note>
 	<note>
-	  <para>For a brief description of the purpose of reserved words, see the <link linkend="app-admin-Command-addword"><command>addword</command></link> command.</para>
+	  <para>For a brief description of the purpose of reserved words, see the <link linkend="app-a-Command-addword"><command>addword</command></link> command.</para>
 	</note>
       </simplesect>

[Refdb-cvs] CVS: refdb/examples xnoteset.xml,1.2,1.3 testrefs.xml,1.3,1.4

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/examples
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2526/examples

Modified Files:
	xnoteset.xml testrefs.xml 
Log Message:
updated to new DTD versions

Index: xnoteset.xml
===================================================================
RCS file: /cvsroot/refdb/refdb/examples/xnoteset.xml,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -U2 -r1.2 -r1.3
--- xnoteset.xml	30 Dec 2003 23:57:05 -0000	1.2
+++ xnoteset.xml	17 Feb 2004 22:13:07 -0000	1.3
@@ -7,26 +7,26 @@
 <xnoteset>
 
-<xnote id="1" date="2003-10-12">
-  <title>myfirstnote</title>
+  <xnote id="1" date="2003-10-12">
+    <title>myfirstnote</title>
 
-  <content>the note proper</content>
-  <keyword>biochemistry</keyword>
-  <keyword>enzymes</keyword>
-  <link type="reference" target="WANG2002"/>
-  <link type="reference" target="Phadke1994"/>
-  <link type="author" target="Walsh,N."/>
-  <link type="journalabbrev" target="Biochem.Pharmacol."/>
-</xnote>
+    <content>the note proper</content>
+    <keyword>biochemistry</keyword>
+    <keyword>enzymes</keyword>
+    <link type="reference" target="WANG2002"/>
+    <link type="reference" target="Phadke1994"/>
+    <link type="author" target="Walsh,N."/>
+    <link type="journalabbrev" target="Biochem.Pharmacol."/>
+  </xnote>
 
-<xnote id="2" key="secondnote">
-  <title>mysecondnote</title>
+  <xnote id="2" key="secondnote">
+    <title>mysecondnote</title>
 
-  <content type="application/xhtml+xml" xml:lang="en-us"><para id='2' style='bold'>the note proper</para></content>
-  <keyword>biochemistry</keyword>
-  <keyword>enzymes</keyword>
-  <link type="reference" target="Phadke1994"/>
-  <link type="author" target="Walsh,N."/>
-  <link type="journalabbrev" target="Biochem.Pharmacol."/>
-</xnote>
+    <content type="application/xhtml+xml" xml:lang="en-us"><para id='2' style='bold'>the note proper</para></content>
+    <keyword>biochemistry</keyword>
+    <keyword>enzymes</keyword>
+    <link type="reference" target="Phadke1994"/>
+    <link type="author" target="Walsh,N."/>
+    <link type="journalabbrev" target="Biochem.Pharmacol."/>
+  </xnote>
 
 </xnoteset>

Index: testrefs.xml
===================================================================
RCS file: /cvsroot/refdb/refdb/examples/testrefs.xml,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -U2 -r1.3 -r1.4
--- testrefs.xml	25 Jan 2004 13:15:11 -0000	1.3
+++ testrefs.xml	17 Feb 2004 22:13:07 -0000	1.4
@@ -1,230 +1,258 @@
-<?xml version="1.0"? encoding="UTF-8">
+<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.2//EN" "http://refdb.sourceforge.net/dtd/risx/risx-1.02/risx.dtd">
 <ris>
-<entry type="BOOK" id="31" citekey="MILLER1999">
-<publication>
-<title>My first book about dinosaurs</title>
-<author>
-<lastname>Miller</lastname>
-<firstname>A</firstname>
-</author>
-<author>
-<lastname>Myers</lastname>
-<firstname>B</firstname>
-<middlename>B</middlename>
-<suffix>Jr.</suffix>
-</author>
-<pubinfo>
-<pubdate type="primary">
-<date>
-<year>1999</year>
-</date>
-</pubdate>
-<city>Sebastopol</city>
-<publisher>O'Reilly</publisher>
-<serial>1-56592-580-7</serial>
-<address>mi...@di...</address>
-<url>http://www.dinosaurs.upenn.edu/</url>
-</pubinfo>
-</publication>
-<set>
-<title>My first book series</title>
-<author>
-<lastname>Smith</lastname>
-<firstname>K</firstname>
-</author>
-</set>
-<libinfo user="markus">
-<notes>Not bad, after all</notes>
-<reprint status="ONREQUEST">
-<date>
-<year>2002</year>
-<month>2</month>
-<day>24</day>
-</date>
-</reprint>
-<availability type="useroot">palaeontology/dinosaurs/millera2002.pdf</availability>
-</libinfo>
-<contents>
-<abstract>Dinosaurs were big animals that ate a lot</abstract>
-<keyword>dinosaurs</keyword>
-<keyword>evolution</keyword>
-<keyword>animals</keyword>
-</contents>
-</entry>
-<entry type="CHAP" id="32" citekey="WALSH1999">
-<part>
-<title>XML: Principles, Tools, and Techniques</title>
-<author>
-<lastname>Walsh</lastname>
-<firstname>N</firstname>
-</author>
-</part>
-<publication>
-<title>Guide to XML</title>
-<author>
-<lastname>Connolly</lastname>
-<firstname>D</firstname>
-</author>
-<pubinfo>
-<pubdate type="primary">
-<date>
-<year>1999</year>
-</date>
-</pubdate>
-<city>Sebastopol</city>
-<publisher>O'Reilly</publisher>
-</pubinfo>
-</publication>
-<libinfo user="markus"><notes>Not bad</notes>
-<reprint status="NOTINFILE"/></libinfo>
-<contents><abstract>An introduction how to deal with XML</abstract>
-<keyword>XML</keyword>
-<keyword>computer</keyword>
-<keyword>markup languages</keyword>
-</contents>
-</entry>
-<entry type="CONF" id="33" citekey="PHADKE1994"><part><title>Application of global positioning systems to electrical systems synchronized phasor measurements techniques and uses</title>
-<author><lastname>Phadke</lastname>
-<firstname>Arun</firstname>
-<middlename>G</middlename>
-</author>
-</part>
-<publication><title>Colloquium on Developments in the Use of Global Positioning Systems (GPS) in Power Systems,Feb 8 1994</title>
-<pubinfo><pubdate type="primary"><date><year>1994</year>
-<month>02</month>
-<day>08</day>
-</date>
-</pubdate>
-<issue>032</issue>
-<startpage>4/1</startpage>
-<endpage>4/2</endpage>
-<city>London,USA</city>
-<publisher>IEE,Stevenage,Engl</publisher>
-<serial>0963-3308</serial>
-<address>Virginia Tech, Blacksburg, VA, USA</address>
-</pubinfo>
-</publication>
-<set><title>IEE Colloquium (Digest)</title>
-</set>
-<libinfo user="markus"><reprint status="NOTINFILE"/></libinfo>
-<contents><abstract>GPS navigational satellites provide an ideal method for distributing a common timing pulse at any point in the power network. Receivers of GPS transmission can reproduce the 1 pulse-per-second at any location on earth with better than 1 &amp;mu;sec accuracy.  Thus, if GPS receivers are built into each measuring system, phasors measured by these systems could be used as simultaneous measurements from all points of the power system, offering far more accuracy than needed for performing engineering analysis functions.</abstract>
-<keyword>Global positioning system</keyword>
-<keyword>Electric power systems</keyword>
-<keyword>Digital computers</keyword>
-<keyword>Electric current measurement</keyword>
-<keyword>Voltage measurement</keyword>
-<keyword>Communication satellites</keyword>
-<keyword>Satellite relay systems</keyword>
-<keyword>Iterative methods</keyword>
-<keyword>Algorithms</keyword>
-<keyword>Units of measurement</keyword>
-</contents>
-</entry>
-<entry type="STAT" id="34" citekey="ANONYMOUS0"><publication><title>The Anti-Riot Act</title>
-<pubinfo><pubdate type="primary"><date><year>1968</year>
-</date>
-</pubdate>
-<pubdate type="secondary"><date></date>
-</pubdate>
-<volume>Code Number: 18 U.S.C.</volume>
-<issue>Public Law Number: P.L. 90-284</issue>
-<startpage>Sections 2101, 2102</startpage>
-</pubinfo>
-</publication>
-<libinfo user="markus"><reprint status="NOTINFILE"/></libinfo>
-<contents></contents>
-</entry>
-<entry type="JOUR" id="35" citekey="WANG2002"><part><title>Inhibition of superoxide anion generation by YC-1 in rat neutrophils through cyclic GMP-dependent and -independent mechanisms</title>
-<author><lastname>Wang</lastname>
-<firstname>J</firstname>
-<middlename>P</middlename>
-</author>
-<author><lastname>Chang</lastname>
-<firstname>L</firstname>
-<middlename>C</middlename>
-</author>
-<author><lastname>Raung</lastname>
-<firstname>S</firstname>
-<middlename>L</middlename>
-</author>
-<author><lastname>Hsu</lastname>
-<firstname>M</firstname>
-<middlename>F</middlename>
-</author>
-<author><lastname>Huang</lastname>
-<firstname>L</firstname>
-<middlename>J</middlename>
-</author>
-<author><lastname>Kuo</lastname>
-<firstname>S</firstname>
-<middlename>C</middlename>
-</author>
-</part>
-<publication><title type="abbrev">Biochem.Pharmacol.</title>
-<pubinfo>
-<pubdate type="primary">
-<date>
-<year>2002</year>
-</date>
-<otherinfo>Feb 15</otherinfo>
-</pubdate>
-<volume>63</volume>
-<issue>4</issue>
-<startpage>577</startpage>
-<endpage>85</endpage>
-<address>Department of Education and Research, Taichung Veterans General Hospital, 160 Chung Kang Road, Sec. 3, 407, ROC, Taichung, Taiwan. w1...@vg...</address>
-</pubinfo>
-</publication>
-<libinfo user="markus"><reprint status="NOTINFILE"/></libinfo>
-<contents><abstract>3-(5'-Hydroxymethyl-2'-furyl)-1-benzyl indazole (YC-1), a soluble guanylyl cyclase (sGC) activator, inhibited formyl-methionyl-leucyl-phenylalanine (fMLP)-induced superoxide anion (O(2)*(-)) generation and O(2) consumption in rat neutrophils (IC(50) values of 12.7+/-3.1 and 17.7+/-6.9 microM, respectively). Inhibition of O(2)*(-) generation by YC-1 was partially reversed by the cyclic GMP-lowering agent 6-anilinoquinoline-5,8-quinone (LY83583) and by the Rp isomer of 8-(4-chlorophenylthio)guanosine-3',5'-monophosphorothioate (Rp-8-pCPT-cGMPS), a cyclic GMP-dependent protein kinase inhibitor. In cell-free systems, YC-1 failed to alter O(2)*(-) generation during dihydroxyfumaric acid autoxidation, phorbol 12-myristate 13-acetate (PMA)-activated neutrophil particulate NADPH oxidase preparation, and arachidonic acid-induced NADPH oxidase activation. YC-1 increased cellular cyclic GMP levels through the activation of sGC and the inhibition of cyclic GMP-hydrolyzing phosphodiesterase activity. The plateau phase, but not the initial spike, of fMLP-induced [Ca(2+)](i) changes was inhibited by YC-1 (IC(50) about 15 microM). fMLP- but not PMA-induced phospholipase D activation was inhibited by YC-1 (IC(50) about 28 microM). Membrane-associated ADP-ribosylation factor and Rho A in cell activation was also reduced by YC-1 at a similar concentration range. Neither cytosolic protein kinase C (PKC) activity nor PKC membrane translocation was altered by YC-1. YC-1 did not affect either fMLP-induced phosphatidylinositol 3-kinase activation or p38 mitogen-activated protein kinase phosphorylation, but slightly attenuated the phosphorylation of extracellular signal-regulated kinase. Collectively, these results indicate that the inhibition of the fMLP-induced respiratory burst by YC-1 is mediated by cyclic GMP-dependent and -independent signaling mechanisms.</abstract>
-<keyword>translocation</keyword>
-</contents>
-</entry>
-<entry type="CONF" id="36" citekey="JACKQUET1995B"><part><title>Radiation induced translocations</title>
-<author><lastname>Jackquet</lastname>
-</author>
-<author><lastname>De Saint Georges</lastname>
-<firstname>J</firstname>
-<middlename>M</middlename>
-</author>
-<author><lastname>Couwberghs</lastname>
-<firstname>T</firstname>
-</author>
-<author><lastname>Melis</lastname>
-<firstname>H</firstname>
-</author>
-<author><lastname>Joris</lastname>
-<firstname>J</firstname>
-</author>
-<author><lastname>Machiels</lastname>
-<firstname>W</firstname>
-</author>
-<author><lastname>Bens</lastname>
-<firstname>M</firstname>
-</author>
-</part>
-<publication><pubinfo><pubdate type="primary"><date><year>2003</year>
-</date>
-</pubdate>
-<pubdate type="secondary"><date><year>1995</year>
-</date>
-<otherinfo>August 27 - September 1</otherinfo>
-</pubdate>
-<volume>2</volume>
-<startpage>2275</startpage>
-<endpage>81</endpage>
-<city>New York</city>
-<publisher>Uitgeverij de standaard</publisher>
-</pubinfo>
-</publication>
-<set><title>10th Intern Congress of Radiation Research</title>
-</set>
-<libinfo user="markus"><reprint status="INFILE"/></libinfo>
-<contents><abstract>blablablalablalbl balalblaalb baalhalbllaalalbalalbalbal</abstract>
-<keyword>conf</keyword>
-<keyword>radiation</keyword>
-<keyword>translocation</keyword>
-</contents>
-</entry>
+  <entry type="BOOK" id="31" citekey="MILLER1999">
+    <publication>
+      <title>My first book about dinosaurs</title>
+      <author>
+	<lastname>Miller</lastname>
+	<firstname>A</firstname>
+      </author>
+      <author>
+	<lastname>Myers</lastname>
+	<firstname>B</firstname>
+	<middlename>B</middlename>
+	<suffix>Jr.</suffix>
+      </author>
+      <pubinfo>
+	<pubdate type="primary">
+	  <date>
+	    <year>1999</year>
+	  </date>
+	</pubdate>
+	<city>Sebastopol</city>
+	<publisher>O'Reilly</publisher>
+	<serial>1-56592-580-7</serial>
+	<address>mi...@di...</address>
+	<url>http://www.dinosaurs.upenn.edu/</url>
+      </pubinfo>
+    </publication>
+    <set>
+      <title>My first book series</title>
+      <author>
+	<lastname>Smith</lastname>
+	<firstname>K</firstname>
+      </author>
+    </set>
+    <libinfo user="markus">
+      <notes>Not bad, after all</notes>
+      <reprint status="ONREQUEST">
+	<date>
+	  <year>2002</year>
+	  <month>2</month>
+	  <day>24</day>
+	</date>
+      </reprint>
+      <availability type="useroot">palaeontology/dinosaurs/millera2002.pdf</availability>
+    </libinfo>
+    <contents>
+      <abstract>Dinosaurs were big animals that ate a lot</abstract>
+      <keyword>dinosaurs</keyword>
+      <keyword>evolution</keyword>
+      <keyword>animals</keyword>
+    </contents>
+  </entry>
+  <entry type="CHAP" id="32" citekey="WALSH1999">
+    <part>
+      <title>XML: Principles, Tools, and Techniques</title>
+      <author>
+	<lastname>Walsh</lastname>
+	<firstname>N</firstname>
+      </author>
+    </part>
+    <publication>
+      <title>Guide to XML</title>
+      <author>
+	<lastname>Connolly</lastname>
+	<firstname>D</firstname>
+      </author>
+      <pubinfo>
+	<pubdate type="primary">
+	  <date>
+	    <year>1999</year>
+	  </date>
+	</pubdate>
+	<city>Sebastopol</city>
+	<publisher>O'Reilly</publisher>
+      </pubinfo>
+    </publication>
+    <libinfo user="markus"><notes>Not bad</notes>
+      <reprint status="NOTINFILE"/></libinfo>
+    <contents><abstract>An introduction how to deal with XML</abstract>
+      <keyword>XML</keyword>
+      <keyword>computer</keyword>
+      <keyword>markup languages</keyword>
+    </contents>
+  </entry>
+  <entry type="CONF" id="33" citekey="PHADKE1994"><part><title>Application of global positioning systems to electrical systems synchronized phasor measurements techniques and uses</title>
+      <author><lastname>Phadke</lastname>
+	<firstname>Arun</firstname>
+	<middlename>G</middlename>
+      </author>
+    </part>
+    <publication><title>Colloquium on Developments in the Use of Global Positioning Systems (GPS) in Power Systems,Feb 8 1994</title>
+      <pubinfo><pubdate type="primary"><date><year>1994</year>
+	    <month>02</month>
+	    <day>08</day>
+	  </date>
+	</pubdate>
+	<issue>032</issue>
+	<startpage>4/1</startpage>
+	<endpage>4/2</endpage>
+	<city>London,USA</city>
+	<publisher>IEE,Stevenage,Engl</publisher>
+	<serial>0963-3308</serial>
+	<address>Virginia Tech, Blacksburg, VA, USA</address>
+      </pubinfo>
+    </publication>
+    <set><title>IEE Colloquium (Digest)</title>
+    </set>
+    <libinfo user="markus"><reprint status="NOTINFILE"/></libinfo>
+    <contents><abstract>GPS navigational satellites provide an ideal method for distributing a common timing pulse at any point in the power network. Receivers of GPS transmission can reproduce the 1 pulse-per-second at any location on earth with better than 1 &amp;mu;sec accuracy.  Thus, if GPS receivers are built into each measuring system, phasors measured by these systems could be used as simultaneous measurements from all points of the power system, offering far more accuracy than needed for performing engineering analysis functions.</abstract>
+      <keyword>Global positioning system</keyword>
+      <keyword>Electric power systems</keyword>
+      <keyword>Digital computers</keyword>
+      <keyword>Electric current measurement</keyword>
+      <keyword>Voltage measurement</keyword>
+      <keyword>Communication satellites</keyword>
+      <keyword>Satellite relay systems</keyword>
+      <keyword>Iterative methods</keyword>
+      <keyword>Algorithms</keyword>
+      <keyword>Units of measurement</keyword>
+    </contents>
+  </entry>
+  <entry type="STAT" id="34" citekey="ANONYMOUS0"><publication><title>The Anti-Riot Act</title>
+      <pubinfo><pubdate type="primary"><date><year>1968</year>
+	  </date>
+	</pubdate>
+	<pubdate type="secondary"><date></date>
+	</pubdate>
+	<volume>Code Number: 18 U.S.C.</volume>
+	<issue>Public Law Number: P.L. 90-284</issue>
+	<startpage>Sections 2101, 2102</startpage>
+      </pubinfo>
+    </publication>
+    <libinfo user="markus"><reprint status="NOTINFILE"/></libinfo>
+    <contents></contents>
+  </entry>
+  <entry type="JOUR" id="35" citekey="WANG2002"><part><title>Inhibition of superoxide anion generation by YC-1 in rat neutrophils through cyclic GMP-dependent and -independent mechanisms</title>
+      <author><lastname>Wang</lastname>
+	<firstname>J</firstname>
+	<middlename>P</middlename>
+      </author>
+      <author><lastname>Chang</lastname>
+	<firstname>L</firstname>
+	<middlename>C</middlename>
+      </author>
+      <author><lastname>Raung</lastname>
+	<firstname>S</firstname>
+	<middlename>L</middlename>
+      </author>
+      <author><lastname>Hsu</lastname>
+	<firstname>M</firstname>
+	<middlename>F</middlename>
+      </author>
+      <author><lastname>Huang</lastname>
+	<firstname>L</firstname>
+	<middlename>J</middlename>
+      </author>
+      <author><lastname>Kuo</lastname>
+	<firstname>S</firstname>
+	<middlename>C</middlename>
+      </author>
+    </part>
+    <publication><title type="abbrev">Biochem.Pharmacol.</title>
+      <pubinfo>
+	<pubdate type="primary">
+	  <date>
+	    <year>2002</year>
+	  </date>
+	  <otherinfo>Feb 15</otherinfo>
+	</pubdate>
+	<volume>63</volume>
+	<issue>4</issue>
+	<startpage>577</startpage>
+	<endpage>85</endpage>
+	<address>Department of Education and Research, Taichung Veterans General Hospital, 160 Chung Kang Road, Sec. 3, 407, ROC, Taichung, Taiwan. w1...@vg...</address>
+      </pubinfo>
+    </publication>
+    <libinfo user="markus"><reprint status="NOTINFILE"/></libinfo>
+    <contents><abstract>3-(5'-Hydroxymethyl-2'-furyl)-1-benzyl indazole (YC-1), a soluble guanylyl cyclase (sGC) activator, inhibited formyl-methionyl-leucyl-phenylalanine (fMLP)-induced superoxide anion (O(2)*(-)) generation and O(2) consumption in rat neutrophils (IC(50) values of 12.7+/-3.1 and 17.7+/-6.9 microM, respectively). Inhibition of O(2)*(-) generation by YC-1 was partially reversed by the cyclic GMP-lowering agent 6-anilinoquinoline-5,8-quinone (LY83583) and by the Rp isomer of 8-(4-chlorophenylthio)guanosine-3',5'-monophosphorothioate (Rp-8-pCPT-cGMPS), a cyclic GMP-dependent protein kinase inhibitor. In cell-free systems, YC-1 failed to alter O(2)*(-) generation during dihydroxyfumaric acid autoxidation, phorbol 12-myristate 13-acetate (PMA)-activated neutrophil particulate NADPH oxidase preparation, and arachidonic acid-induced NADPH oxidase activation. YC-1 increased cellular cyclic GMP levels through the activation of sGC and the inhibition of cyclic GMP-hydrolyzing phosphodiesterase activity. The plateau phase, but not the initial spike, of fMLP-induced [Ca(2+)](i) changes was inhibited by YC-1 (IC(50) about 15 microM). fMLP- but not PMA-induced phospholipase D activation was inhibited by YC-1 (IC(50) about 28 microM). Membrane-associated ADP-ribosylation factor and Rho A in cell activation was also reduced by YC-1 at a similar concentration range. Neither cytosolic protein kinase C (PKC) activity nor PKC membrane translocation was altered by YC-1. YC-1 did not affect either fMLP-induced phosphatidylinositol 3-kinase activation or p38 mitogen-activated protein kinase phosphorylation, but slightly attenuated the phosphorylation of extracellular signal-regulated kinase. Collectively, these results indicate that the inhibition of the fMLP-induced respiratory burst by YC-1 is mediated by cyclic GMP-dependent and -independent signaling mechanisms.</abstract>
+      <keyword>translocation</keyword>
+    </contents>
+  </entry>
+  <entry type="CONF" id="36" citekey="JACKQUET1995B"><part><title>Radiation induced translocations</title>
+      <author><lastname>Jackquet</lastname>
+      </author>
+      <author><lastname>De Saint Georges</lastname>
+	<firstname>J</firstname>
+	<middlename>M</middlename>
+      </author>
+      <author><lastname>Couwberghs</lastname>
+	<firstname>T</firstname>
+      </author>
+      <author><lastname>Melis</lastname>
+	<firstname>H</firstname>
+      </author>
+      <author><lastname>Joris</lastname>
+	<firstname>J</firstname>
+      </author>
+      <author><lastname>Machiels</lastname>
+	<firstname>W</firstname>
+      </author>
+      <author><lastname>Bens</lastname>
+	<firstname>M</firstname>
+      </author>
+    </part>
+    <publication><pubinfo><pubdate type="primary"><date><year>2003</year>
+	  </date>
+	</pubdate>
+	<pubdate type="secondary"><date><year>1995</year>
+	  </date>
+	  <otherinfo>August 27 - September 1</otherinfo>
+	</pubdate>
+	<volume>2</volume>
+	<startpage>2275</startpage>
+	<endpage>81</endpage>
+	<city>New York</city>
+	<publisher>Uitgeverij de standaard</publisher>
+      </pubinfo>
+    </publication>
+    <set><title>10th Intern Congress of Radiation Research</title>
+    </set>
+    <libinfo user="markus"><reprint status="INFILE"/></libinfo>
+    <contents><abstract>blablablalablalbl balalblaalb baalhalbllaalalbalalbalbal</abstract>
+      <keyword>conf</keyword>
+      <keyword>radiation</keyword>
+      <keyword>translocation</keyword>
+    </contents>
+  </entry>
+  <entry type="BOOK" id="37" citekey="smith1975metalloporphyrins">
+    <publication>
+      <title>Porphyrins and metalloporphyrins</title>
+      <author>
+	<lastname>Smith</lastname>
+	<firstname>K</firstname>
+	<middlename>M</middlename>
+      </author>
+      <pubinfo>
+	<pubdate>
+	  <date>
+	    <year>1975</year>
+	  </date>
+	</pubdate>
+	<city>Amsterdam</city>
+	<publisher>Elsevier Scientific Publishing Company</publisher>
+      </pubinfo>
+    </publication>
+    <libinfo user="markus">
+      <reprint status="NOTINFILE" />
+    </libinfo>
+    <contents>
+      <keyword>Porphyrins</keyword>
+      <keyword>Metalloporphyrins</keyword>
+      <keyword>Spectrophotometry [methods]</keyword>
+      <keyword>spectroscopy</keyword>
+    </contents>
+  </entry>
 </ris>

[Refdb-cvs] CVS: refdb/src refdbc.c,1.69,1.70

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2084/src

Modified Files:
	refdbc.c 
Log Message:
addnote(): outtype not required

Index: refdbc.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/refdbc.c,v
retrieving revision 1.69
retrieving revision 1.70
diff -u -U2 -r1.69 -r1.70
--- refdbc.c	11 Feb 2004 23:47:23 -0000	1.69
+++ refdbc.c	17 Feb 2004 22:11:54 -0000	1.70
@@ -3823,8 +3823,8 @@
   }
 
-  if (*outtype) {
-    strcat(outbuffer, " -t ");
-    strcat(outbuffer, outtype);
-  }
+/*   if (*outtype) { */
+/*     strcat(outbuffer, " -t "); */
+/*     strcat(outbuffer, outtype); */
+/*   } */
 /*    free(newarg); */
 /*    newarg = NULL; */

[Refdb-cvs] CVS: refdb/src noteshandler.c,1.17,1.18 risdb.c,1.42,1.43 risxhandler.c,1.27,1.28

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9425

Modified Files:
	noteshandler.c risdb.c risxhandler.c 
Log Message:
use hostname instead of server_ip for temporary citation key

Index: noteshandler.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/noteshandler.c,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -U2 -r1.17 -r1.18
--- noteshandler.c	15 Feb 2004 23:40:05 -0000	1.17
+++ noteshandler.c	16 Feb 2004 21:38:05 -0000	1.18
@@ -370,5 +370,5 @@
 	if (!*(ptr_andata->real_key)) {
 	  /* use pid to avoid problems with concurrent inserts */
-	  sprintf(ptr_andata->real_key, "dummy%s%d", ptr_andata->ptr_clrequest->server_ip, getpid());
+	  snprintf(ptr_andata->real_key, 256, "dummy%s%d", ptr_andata->ptr_clrequest->my_hostname, getpid());
 	}
 

Index: risdb.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risdb.c,v
retrieving revision 1.42
retrieving revision 1.43
diff -u -U2 -r1.42 -r1.43
--- risdb.c	15 Feb 2004 23:40:05 -0000	1.42
+++ risdb.c	16 Feb 2004 21:38:05 -0000	1.43
@@ -523,5 +523,7 @@
   /* start inserting the new data */
   if (create_new) {
-    sprintf(sql_command, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY%s%d\')", ptr_clrequest->server_ip, getpid());
+    /* if my_hostname is too long, the db will chop off the string
+       which is ok */
+    sprintf(sql_command, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY%s%d\')", ptr_clrequest->my_hostname, getpid());
     /* insert a new empty dataset into the main table to start with */
     LOG_PRINT(LOG_DEBUG, sql_command);
@@ -1330,5 +1332,7 @@
     if (strcmp(my_dbi_conn_get_cap(conn, "transaction"), "t")) {
       /* we have to delete the junk reference manually */
-      delete_ref_by_id(n_refdb_id, conn, ptr_clrequest, &delresult);
+      if (n_refdb_id) { /* if no id, no dataset was added anyway */
+	delete_ref_by_id(n_refdb_id, conn, ptr_clrequest, &delresult);
+      }
     }
     else {

Index: risxhandler.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risxhandler.c,v
retrieving revision 1.27
retrieving revision 1.28
diff -u -U2 -r1.27 -r1.28
--- risxhandler.c	15 Feb 2004 23:40:05 -0000	1.27
+++ risxhandler.c	16 Feb 2004 21:38:06 -0000	1.28
@@ -380,5 +380,5 @@
 	/* generate temporary citekey if necessary */
 	if (!*(ptr_ardata->real_citekey)) {
-	  sprintf(ptr_ardata->real_citekey, "DUMMY%s%d", ptr_ardata->ptr_clrequest->server_ip, getpid());
+	  snprintf(ptr_ardata->real_citekey, 256, "DUMMY%s%d", ptr_ardata->ptr_clrequest->my_hostname, getpid());
 	}
 
@@ -627,4 +627,5 @@
       (ptr_ardata->n_skip)--;
       (ptr_ardata->skipped_count)++;
+      (ptr_ardata->set_count)++;
 
       /* close transaction of skipped dataset, if any */

[Refdb-cvs] CVS: refdb/src refdbd.c,1.73,1.74

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv9196

Modified Files:
	refdbd.c 
Log Message:
set my_hostname in client request structure

Index: refdbd.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/refdbd.c,v
retrieving revision 1.73
retrieving revision 1.74
diff -u -U2 -r1.73 -r1.74
--- refdbd.c	7 Feb 2004 14:47:29 -0000	1.73
+++ refdbd.c	16 Feb 2004 21:36:11 -0000	1.74
@@ -760,4 +760,5 @@
 	  FD_SET(client_sockfd, &readfds);
 
+	  gethostname(ptr_clrequest->my_hostname, 256);
 	  strcpy(ptr_clrequest->client_ip, inet_ntoa(client_address.sin_addr));
 	  sprintf(msg_buffer, "adding client %s on fd %d", ptr_clrequest->client_ip, client_sockfd);

[Refdb-cvs] CVS: refdb/src refdbd.h.in,1.6,1.7

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv7789

Modified Files:
	refdbd.h.in 
Log Message:
added my_hostname to struct CLIENT_REQUEST

Index: refdbd.h.in
===================================================================
RCS file: /cvsroot/refdb/refdb/src/refdbd.h.in,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -U2 -r1.6 -r1.7
--- refdbd.h.in	15 Feb 2004 22:56:30 -0000	1.6
+++ refdbd.h.in	16 Feb 2004 21:25:24 -0000	1.7
@@ -52,4 +52,5 @@
   char passwd[PREFS_BUF_LEN]; /* password for database authentication */
   char server_ip[PREFS_BUF_LEN]; /* hostname or IP address of database server */
+  char my_hostname[256]; /* hostname of box running refdbd */
   char dbs_port_address[PREFS_BUF_LEN]; /* port where database server listens */
   char dbserver[PREFS_BUF_LEN]; /* name of the libdbi driver */

[Refdb-cvs] CVS: refdb/src refdbdnote.c,1.24,1.25 refdbdref.c,1.64,1.65

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24897

Modified Files:
	refdbdnote.c refdbdref.c 
Log Message:
add ptr_clrequest to expat handler global data

Index: refdbdnote.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/refdbdnote.c,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -U2 -r1.24 -r1.25
--- refdbdnote.c	15 Feb 2004 23:02:42 -0000	1.24
+++ refdbdnote.c	15 Feb 2004 23:41:27 -0000	1.25
@@ -172,4 +172,5 @@
 				      specify user */
     andata.ptr_id_sentinel = ptr_sentinel;
+    andata.ptr_clrequest = ptr_clrequest;
     andata.ptr_first = NULL;
     andata.nmem_error = 0;

Index: refdbdref.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/refdbdref.c,v
retrieving revision 1.64
retrieving revision 1.65
diff -u -U2 -r1.64 -r1.65
--- refdbdref.c	15 Feb 2004 23:05:02 -0000	1.64
+++ refdbdref.c	15 Feb 2004 23:41:27 -0000	1.65
@@ -419,4 +419,5 @@
       *(ardata.real_citekey) = '\0';
       *(ardata.type) = '\0';
+      ardata.ptr_clrequest = ptr_clrequest;
       ardata.ptr_id_sentinel = ptr_sentinel;
       ardata.ptr_first = NULL;

[Refdb-cvs] CVS: refdb/src noteshandler.c,1.16,1.17 risxhandler.c,1.26,1.27 risdb.c,1.41,1.42

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24630

Modified Files:
	noteshandler.c risxhandler.c risdb.c 
Log Message:
added server ip to make temporary citation key really unique

Index: noteshandler.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/noteshandler.c,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -U2 -r1.16 -r1.17
--- noteshandler.c	15 Feb 2004 22:58:15 -0000	1.16
+++ noteshandler.c	15 Feb 2004 23:40:05 -0000	1.17
@@ -34,6 +34,7 @@
 
 #include "refdb.h"
-#include "strfncs.h"
 #include "linklist.h"
+#include "refdbd.h"
+#include "strfncs.h"
 #include "xmlhandler.h"
 #include "noteshandler.h"
@@ -369,5 +370,5 @@
 	if (!*(ptr_andata->real_key)) {
 	  /* use pid to avoid problems with concurrent inserts */
-	  sprintf(ptr_andata->real_key, "dummy%d", getpid());
+	  sprintf(ptr_andata->real_key, "dummy%s%d", ptr_andata->ptr_clrequest->server_ip, getpid());
 	}
 

Index: risxhandler.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risxhandler.c,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -U2 -r1.26 -r1.27
--- risxhandler.c	15 Feb 2004 23:09:25 -0000	1.26
+++ risxhandler.c	15 Feb 2004 23:40:05 -0000	1.27
@@ -380,5 +380,5 @@
 	/* generate temporary citekey if necessary */
 	if (!*(ptr_ardata->real_citekey)) {
-	  sprintf(ptr_ardata->real_citekey, "DUMMY%d", getpid());
+	  sprintf(ptr_ardata->real_citekey, "DUMMY%s%d", ptr_ardata->ptr_clrequest->server_ip, getpid());
 	}
 
@@ -1650,5 +1650,5 @@
 
       /* insert new citekey if required */
-      if (!strcmp(ptr_ardata->real_citekey, "0") && ptr_ardata->create_new) {
+      if (!strncmp(ptr_ardata->real_citekey, "DUMMY", 5) && ptr_ardata->create_new) {
 	citekey = get_unique_citekey(ptr_ardata->conn, ptr_ardata->first_author, atoi(ptr_ardata->ck_year), ptr_ardata->n_refdb_id, 0 /* ref */);
 	

Index: risdb.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risdb.c,v
retrieving revision 1.41
retrieving revision 1.42
diff -u -U2 -r1.41 -r1.42
--- risdb.c	15 Feb 2004 23:07:19 -0000	1.41
+++ risdb.c	15 Feb 2004 23:40:05 -0000	1.42
@@ -523,5 +523,5 @@
   /* start inserting the new data */
   if (create_new) {
-    sprintf(sql_command, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY%d\')", getpid());
+    sprintf(sql_command, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY%s%d\')", ptr_clrequest->server_ip, getpid());
     /* insert a new empty dataset into the main table to start with */
     LOG_PRINT(LOG_DEBUG, sql_command);

[Refdb-cvs] CVS: refdb/src risxhandler.h,1.9,1.10

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24440

Modified Files:
	risxhandler.h 
Log Message:
added ptr_clrequest to struct addrisx_data

Index: risxhandler.h
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risxhandler.h,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -U2 -r1.9 -r1.10
--- risxhandler.h	17 Jan 2004 22:50:20 -0000	1.9
+++ risxhandler.h	15 Feb 2004 23:38:30 -0000	1.10
@@ -55,4 +55,5 @@
   struct elstack* ptr_first; /* start of the element stack */
   struct PERIODICAL_INFO perinfo; /* periodical name synonyms */
+  struct CLIENT_REQUEST* ptr_clrequest; 
   Lilid* ptr_id_sentinel; /* linked list for added IDs */
   dbi_conn conn;

[Refdb-cvs] CVS: refdb/src noteshandler.h,1.5,1.6

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv24230

Modified Files:
	noteshandler.h 
Log Message:
added ptr_clrequest to struct addnotes_data

Index: noteshandler.h
===================================================================
RCS file: /cvsroot/refdb/refdb/src/noteshandler.h,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -U2 -r1.5 -r1.6
--- noteshandler.h	17 Jan 2004 22:50:20 -0000	1.5
+++ noteshandler.h	15 Feb 2004 23:37:57 -0000	1.6
@@ -47,4 +47,5 @@
   unsigned long long n_user_id; /* database id of current user */
   struct elstack* ptr_first; /* start of the element stack */
+  struct CLIENT_REQUEST* ptr_clrequest;
   Lilid* ptr_id_sentinel; /* linked list for added IDs */
   dbi_conn conn;

[Refdb-cvs] CVS: refdb/src risxhandler.c,1.25,1.26

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv17516

Modified Files:
	risxhandler.c 
Log Message:
use unique temporary citation key

Index: risxhandler.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risxhandler.c,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -U2 -r1.25 -r1.26
--- risxhandler.c	7 Feb 2004 14:52:47 -0000	1.25
+++ risxhandler.c	15 Feb 2004 23:09:25 -0000	1.26
@@ -380,5 +380,5 @@
 	/* generate temporary citekey if necessary */
 	if (!*(ptr_ardata->real_citekey)) {
-	  sprintf(ptr_ardata->real_citekey, ULLSPEC, (unsigned long long)0);
+	  sprintf(ptr_ardata->real_citekey, "DUMMY%d", getpid());
 	}
 
@@ -1698,5 +1698,5 @@
 	if (strcmp(my_dbi_conn_get_cap(ptr_ardata->conn, "transaction"), "t")) {
 	  /* we have to delete the junk reference manually */
-	  sprintf(sql_command, "DELETE FROM t_refdb WHERE refdb_citekey=\'DUMMY\'");
+	  sprintf(sql_command, "DELETE FROM t_refdb WHERE refdb_citekey=\'DUMMY%d\'", getpid());
 	  LOG_PRINT(LOG_DEBUG, sql_command);
 	  dbires = dbi_conn_query(ptr_ardata->conn, sql_command);

[Refdb-cvs] CVS: refdb/src risdb.c,1.40,1.41

[Markus H. <mho...@us...>]

Update of /cvsroot/refdb/refdb/src
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv16708

Modified Files:
	risdb.c 
Log Message:
use unique temporary citation key

Index: risdb.c
===================================================================
RCS file: /cvsroot/refdb/refdb/src/risdb.c,v
retrieving revision 1.40
retrieving revision 1.41
diff -u -U2 -r1.40 -r1.41
--- risdb.c	11 Feb 2004 20:40:36 -0000	1.40
+++ risdb.c	15 Feb 2004 23:07:19 -0000	1.41
@@ -273,4 +273,5 @@
   struct AUTHOR_INFO* ptr_ainfo;
   struct RISDATA* ptr_risdata;
+  struct DELRESULT delresult;
 
   sentinel.ptr_mem = NULL;
@@ -522,7 +523,8 @@
   /* start inserting the new data */
   if (create_new) {
+    sprintf(sql_command, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY%d\')", getpid());
     /* insert a new empty dataset into the main table to start with */
-    LOG_PRINT(LOG_DEBUG, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY\')");
-    dbires = dbi_conn_query(conn, "INSERT INTO t_refdb (refdb_type,refdb_citekey) VALUES (\'DUMMY\',\'DUMMY\')");
+    LOG_PRINT(LOG_DEBUG, sql_command);
+    dbires = dbi_conn_query(conn, sql_command);
     if (!dbires) {
       LOG_PRINT(LOG_WARNING, "insert into t_refdb failed");
@@ -1328,11 +1330,5 @@
     if (strcmp(my_dbi_conn_get_cap(conn, "transaction"), "t")) {
       /* we have to delete the junk reference manually */
-      sprintf(sql_command, "DELETE FROM t_refdb WHERE refdb_citekey=\'DUMMY\'");
-      LOG_PRINT(LOG_DEBUG, sql_command);
-      dbires = dbi_conn_query(conn, sql_command);
-      if (!dbires) {
-	LOG_PRINT(LOG_INFO, "removing junk reference failed");
-      }
-      dbi_result_free(dbires);
+      delete_ref_by_id(n_refdb_id, conn, ptr_clrequest, &delresult);
     }
     else {