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From: Egon W. <eg...@us...> - 2003-09-26 19:28:43
|
Update of /cvsroot/woc/woc2/source/publish In directory sc8-pr-cvs1:/tmp/cvs-serv22051/publish Added Files: .cvsignore Log Message: Added .cvsignore to ignore autogenerated autotools files --- NEW FILE: .cvsignore --- configure Makefile Makefile.in |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:28:43
|
Update of /cvsroot/woc/woc2/source/manuals In directory sc8-pr-cvs1:/tmp/cvs-serv22051/manuals Added Files: .cvsignore Log Message: Added .cvsignore to ignore autogenerated autotools files --- NEW FILE: .cvsignore --- configure Makefile Makefile.in |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:28:43
|
Update of /cvsroot/woc/woc2/source/manuals/maint In directory sc8-pr-cvs1:/tmp/cvs-serv22051/manuals/maint Added Files: .cvsignore Log Message: Added .cvsignore to ignore autogenerated autotools files --- NEW FILE: .cvsignore --- configure Makefile Makefile.in |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:28:43
|
Update of /cvsroot/woc/woc2/source In directory sc8-pr-cvs1:/tmp/cvs-serv22051 Modified Files: .cvsignore Added Files: VERSION Log Message: Added .cvsignore to ignore autogenerated autotools files --- NEW FILE: VERSION --- 20030926 Index: .cvsignore =================================================================== RCS file: /cvsroot/woc/woc2/source/.cvsignore,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -r1.1 -r1.2 *** .cvsignore 26 Sep 2003 19:19:29 -0000 1.1 --- .cvsignore 26 Sep 2003 19:28:28 -0000 1.2 *************** *** 1,4 **** --- 1,6 ---- aclocal.m4 autom4te.cache + config.log + config.status configure Makefile |
Update of /cvsroot/woc/woc2/source
In directory sc8-pr-cvs1:/tmp/cvs-serv19995
Added Files:
.cvsignore AUTHORS COPYING ChangeLog INSTALL NEWS README
bootstrap install-sh missing mkinstalldirs
Log Message:
Files to make a dist
--- NEW FILE: .cvsignore ---
aclocal.m4
autom4te.cache
configure
Makefile
Makefile.in
--- NEW FILE: AUTHORS ---
Egon Willighagen
Geert Josten
--- NEW FILE: COPYING ---
All software is licensed GPL.
--- NEW FILE: ChangeLog ---
--- NEW FILE: INSTALL ---
--- NEW FILE: NEWS ---
--- NEW FILE: README ---
--- NEW FILE: bootstrap ---
#! /bin/sh -e
# bootstrap this software
aclocal && automake --gnu && autoconf
--- NEW FILE: install-sh ---
#!/bin/sh
#
# install - install a program, script, or datafile
# This comes from X11R5 (mit/util/scripts/install.sh).
#
# Copyright 1991 by the Massachusetts Institute of Technology
#
# Permission to use, copy, modify, distribute, and sell this software and its
# documentation for any purpose is hereby granted without fee, provided that
# the above copyright notice appear in all copies and that both that
# copyright notice and this permission notice appear in supporting
# documentation, and that the name of M.I.T. not be used in advertising or
# publicity pertaining to distribution of the software without specific,
# written prior permission. M.I.T. makes no representations about the
# suitability of this software for any purpose. It is provided "as is"
# without express or implied warranty.
#
# Calling this script install-sh is preferred over install.sh, to prevent
# `make' implicit rules from creating a file called install from it
# when there is no Makefile.
#
# This script is compatible with the BSD install script, but was written
# from scratch. It can only install one file at a time, a restriction
# shared with many OS's install programs.
# set DOITPROG to echo to test this script
# Don't use :- since 4.3BSD and earlier shells don't like it.
doit="${DOITPROG-}"
# put in absolute paths if you don't have them in your path; or use env. vars.
mvprog="${MVPROG-mv}"
cpprog="${CPPROG-cp} -p"
chmodprog="${CHMODPROG-chmod}"
chownprog="${CHOWNPROG-chown}"
chgrpprog="${CHGRPPROG-chgrp}"
stripprog="${STRIPPROG-strip}"
rmprog="${RMPROG-rm}"
mkdirprog="${MKDIRPROG-mkdir}"
transformbasename=""
transform_arg=""
instcmd="$mvprog"
chmodcmd="$chmodprog 0755"
chowncmd=""
chgrpcmd=""
stripcmd=""
rmcmd="$rmprog -f"
mvcmd="$mvprog"
src=""
dst=""
dir_arg=""
while [ x"$1" != x ]; do
case $1 in
-c) instcmd="$cpprog"
shift
continue;;
-d) dir_arg=true
shift
continue;;
-m) chmodcmd="$chmodprog $2"
shift
shift
continue;;
-o) chowncmd="$chownprog $2"
shift
shift
continue;;
-g) chgrpcmd="$chgrpprog $2"
shift
shift
continue;;
-s) stripcmd="$stripprog"
shift
continue;;
-t=*) transformarg=`echo $1 | sed 's/-t=//'`
shift
continue;;
-b=*) transformbasename=`echo $1 | sed 's/-b=//'`
shift
continue;;
*) if [ x"$src" = x ]
then
src=$1
else
# this colon is to work around a 386BSD /bin/sh bug
:
dst=$1
fi
shift
continue;;
esac
done
if [ x"$src" = x ]
then
echo "install: no input file specified"
exit 1
else
true
fi
if [ x"$dir_arg" != x ]; then
dst=$src
src=""
if [ -d $dst ]; then
instcmd=:
chmodcmd=""
else
instcmd=mkdir
fi
else
# Waiting for this to be detected by the "$instcmd $src $dsttmp" command
# might cause directories to be created, which would be especially bad
# if $src (and thus $dsttmp) contains '*'.
if [ -f $src -o -d $src ]
then
true
else
echo "install: $src does not exist"
exit 1
fi
if [ x"$dst" = x ]
then
echo "install: no destination specified"
exit 1
else
true
fi
# If destination is a directory, append the input filename; if your system
# does not like double slashes in filenames, you may need to add some logic
if [ -d $dst ]
then
dst="$dst"/`basename $src`
else
true
fi
fi
## this sed command emulates the dirname command
dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'`
# Make sure that the destination directory exists.
# this part is taken from Noah Friedman's mkinstalldirs script
# Skip lots of stat calls in the usual case.
if [ ! -d "$dstdir" ]; then
defaultIFS='
'
IFS="${IFS-${defaultIFS}}"
oIFS="${IFS}"
# Some sh's can't handle IFS=/ for some reason.
IFS='%'
set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'`
IFS="${oIFS}"
pathcomp=''
while [ $# -ne 0 ] ; do
pathcomp="${pathcomp}${1}"
shift
if [ ! -d "${pathcomp}" ] ;
then
$mkdirprog "${pathcomp}"
else
true
fi
pathcomp="${pathcomp}/"
done
fi
if [ x"$dir_arg" != x ]
then
$doit $instcmd $dst &&
if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else true ; fi &&
if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else true ; fi &&
if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else true ; fi &&
if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else true ; fi
else
# If we're going to rename the final executable, determine the name now.
if [ x"$transformarg" = x ]
then
dstfile=`basename $dst`
else
dstfile=`basename $dst $transformbasename |
sed $transformarg`$transformbasename
fi
# don't allow the sed command to completely eliminate the filename
if [ x"$dstfile" = x ]
then
dstfile=`basename $dst`
else
true
fi
# Make a temp file name in the proper directory.
dsttmp=$dstdir/#inst.$$#
# Move or copy the file name to the temp name
$doit $instcmd $src $dsttmp &&
trap "rm -f ${dsttmp}" 0 &&
# and set any options; do chmod last to preserve setuid bits
# If any of these fail, we abort the whole thing. If we want to
# ignore errors from any of these, just make sure not to ignore
# errors from the above "$doit $instcmd $src $dsttmp" command.
if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else true;fi &&
if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else true;fi &&
if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else true;fi &&
if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else true;fi &&
# Now rename the file to the real destination.
$doit $rmcmd -f $dstdir/$dstfile &&
$doit $mvcmd $dsttmp $dstdir/$dstfile
fi &&
exit 0
--- NEW FILE: missing ---
#! /bin/sh
# Common stub for a few missing GNU programs while installing.
# Copyright (C) 1996, 1997, 1999 Free Software Foundation, Inc.
# Originally by Fran,cois Pinard <pi...@ir...>, 1996.
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2, or (at your option)
# any later version.
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
# 02111-1307, USA.
if test $# -eq 0; then
echo 1>&2 "Try \`$0 --help' for more information"
exit 1
fi
run=:
case "$1" in
--run)
# Try to run requested program, and just exit if it succeeds.
run=
shift
"$@" && exit 0
;;
esac
# If it does not exist, or fails to run (possibly an outdated version),
# try to emulate it.
case "$1" in
-h|--h|--he|--hel|--help)
echo "\
$0 [OPTION]... PROGRAM [ARGUMENT]...
Handle \`PROGRAM [ARGUMENT]...' for when PROGRAM is missing, or return an
error status if there is no known handling for PROGRAM.
Options:
-h, --help display this help and exit
-v, --version output version information and exit
--run try to run the given command, and emulate it if it fails
Supported PROGRAM values:
aclocal touch file \`aclocal.m4'
autoconf touch file \`configure'
autoheader touch file \`config.h.in'
automake touch all \`Makefile.in' files
bison create \`y.tab.[ch]', if possible, from existing .[ch]
flex create \`lex.yy.c', if possible, from existing .c
lex create \`lex.yy.c', if possible, from existing .c
makeinfo touch the output file
tar try tar, gnutar, gtar, then tar without non-portable flags
yacc create \`y.tab.[ch]', if possible, from existing .[ch]"
;;
-v|--v|--ve|--ver|--vers|--versi|--versio|--version)
echo "missing 0.2 - GNU automake"
;;
-*)
echo 1>&2 "$0: Unknown \`$1' option"
echo 1>&2 "Try \`$0 --help' for more information"
exit 1
;;
aclocal)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified \`acinclude.m4' or \`configure.in'. You might want
to install the \`Automake' and \`Perl' packages. Grab them from
any GNU archive site."
touch aclocal.m4
;;
autoconf)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified \`configure.in'. You might want to install the
\`Autoconf' and \`GNU m4' packages. Grab them from any GNU
archive site."
touch configure
;;
autoheader)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified \`acconfig.h' or \`configure.in'. You might want
to install the \`Autoconf' and \`GNU m4' packages. Grab them
from any GNU archive site."
files=`sed -n 's/^[ ]*A[CM]_CONFIG_HEADER(\([^)]*\)).*/\1/p' configure.in`
test -z "$files" && files="config.h"
touch_files=
for f in $files; do
case "$f" in
*:*) touch_files="$touch_files "`echo "$f" |
sed -e 's/^[^:]*://' -e 's/:.*//'`;;
*) touch_files="$touch_files $f.in";;
esac
done
touch $touch_files
;;
automake)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified \`Makefile.am', \`acinclude.m4' or \`configure.in'.
You might want to install the \`Automake' and \`Perl' packages.
Grab them from any GNU archive site."
find . -type f -name Makefile.am -print |
sed 's/\.am$/.in/' |
while read f; do touch "$f"; done
;;
bison|yacc)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified a \`.y' file. You may need the \`Bison' package
in order for those modifications to take effect. You can get
\`Bison' from any GNU archive site."
rm -f y.tab.c y.tab.h
if [ $# -ne 1 ]; then
eval LASTARG="\${$#}"
case "$LASTARG" in
*.y)
SRCFILE=`echo "$LASTARG" | sed 's/y$/c/'`
if [ -f "$SRCFILE" ]; then
cp "$SRCFILE" y.tab.c
fi
SRCFILE=`echo "$LASTARG" | sed 's/y$/h/'`
if [ -f "$SRCFILE" ]; then
cp "$SRCFILE" y.tab.h
fi
;;
esac
fi
if [ ! -f y.tab.h ]; then
echo >y.tab.h
fi
if [ ! -f y.tab.c ]; then
echo 'main() { return 0; }' >y.tab.c
fi
;;
lex|flex)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified a \`.l' file. You may need the \`Flex' package
in order for those modifications to take effect. You can get
\`Flex' from any GNU archive site."
rm -f lex.yy.c
if [ $# -ne 1 ]; then
eval LASTARG="\${$#}"
case "$LASTARG" in
*.l)
SRCFILE=`echo "$LASTARG" | sed 's/l$/c/'`
if [ -f "$SRCFILE" ]; then
cp "$SRCFILE" lex.yy.c
fi
;;
esac
fi
if [ ! -f lex.yy.c ]; then
echo 'main() { return 0; }' >lex.yy.c
fi
;;
makeinfo)
echo 1>&2 "\
WARNING: \`$1' is missing on your system. You should only need it if
you modified a \`.texi' or \`.texinfo' file, or any other file
indirectly affecting the aspect of the manual. The spurious
call might also be the consequence of using a buggy \`make' (AIX,
DU, IRIX). You might want to install the \`Texinfo' package or
the \`GNU make' package. Grab either from any GNU archive site."
file=`echo "$*" | sed -n 's/.*-o \([^ ]*\).*/\1/p'`
if test -z "$file"; then
file=`echo "$*" | sed 's/.* \([^ ]*\) *$/\1/'`
file=`sed -n '/^@setfilename/ { s/.* \([^ ]*\) *$/\1/; p; q; }' $file`
fi
touch $file
;;
tar)
shift
if test -n "$run"; then
echo 1>&2 "ERROR: \`tar' requires --run"
exit 1
fi
# we have already tried tar in the generic part
gnutar ${1+"$@"} && exit 0
gtar ${1+"$@"} && exit 0
firstarg="$1"
if shift; then
case "$firstarg" in
*o*)
firstarg=`echo "$firstarg" | sed s/o//`
tar "$firstarg" ${1+"$@"} && exit 0
;;
esac
case "$firstarg" in
*h*)
firstarg=`echo "$firstarg" | sed s/h//`
tar "$firstarg" ${1+"$@"} && exit 0
;;
esac
fi
echo 1>&2 "\
WARNING: I can't seem to be able to run \`tar' with the given arguments.
You may want to install GNU tar or Free paxutils, or check the
command line arguments."
exit 1
;;
*)
echo 1>&2 "\
WARNING: \`$1' is needed, and you do not seem to have it handy on your
system. You might have modified some files without having the
proper tools for further handling them. Check the \`README' file,
it often tells you about the needed prerequirements for installing
this package. You may also peek at any GNU archive site, in case
some other package would contain this missing \`$1' program."
exit 1
;;
esac
exit 0
--- NEW FILE: mkinstalldirs ---
#! /bin/sh
# mkinstalldirs --- make directory hierarchy
# Author: Noah Friedman <fri...@pr...>
# Created: 1993-05-16
# Public domain
# $Id: mkinstalldirs,v 1.1 2003/09/26 19:19:29 egonw Exp $
errstatus=0
for file
do
set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'`
shift
pathcomp=
for d
do
pathcomp="$pathcomp$d"
case "$pathcomp" in
-* ) pathcomp=./$pathcomp ;;
esac
if test ! -d "$pathcomp"; then
echo "mkdir $pathcomp"
mkdir "$pathcomp" || lasterr=$?
if test ! -d "$pathcomp"; then
errstatus=$lasterr
fi
fi
pathcomp="$pathcomp/"
done
done
exit $errstatus
# mkinstalldirs ends here
|
|
From: Egon W. <eg...@us...> - 2003-09-26 19:08:20
|
Update of /cvsroot/woc/woc2/source In directory sc8-pr-cvs1:/tmp/cvs-serv18176/source Added Files: configure.in Log Message: Some more corrections --- NEW FILE: configure.in --- dnl dnl $Id: configure.in,v 1.1 2003/09/26 19:08:05 egonw Exp $ dnl AC_INIT() AM_INIT_AUTOMAKE(wocbin, `cat VERSION`) AC_OUTPUT([ maint/Makefile publish/wocjava/Makefile publish/Makefile manuals/maint/Makefile manuals/publish/Makefile manuals/Makefile Makefile ]) |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:08:20
|
Update of /cvsroot/woc/woc2/layout In directory sc8-pr-cvs1:/tmp/cvs-serv18176/layout Added Files: configure.in Log Message: Some more corrections --- NEW FILE: configure.in --- dnl dnl $Id: configure.in,v 1.1 2003/09/26 19:08:05 egonw Exp $ dnl AC_INIT() AM_INIT_AUTOMAKE(woc, `cat VERSION`) AC_OUTPUT([ woc/webdocs/Makefile woc/cgi/Makefile iupac/webdocs/Makefile iupac/cgi/Makefile translations/webdocs/Makefile translations/cgi/Makefile generic/webdocs/Makefile generic/cgi/Makefile generic/Makefile Makefile ]) |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:08:19
|
Update of /cvsroot/woc/woc2/project In directory sc8-pr-cvs1:/tmp/cvs-serv18176/project Removed Files: Makefile.am Log Message: Some more corrections --- Makefile.am DELETED --- |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:08:18
|
Update of /cvsroot/woc/woc2/data In directory sc8-pr-cvs1:/tmp/cvs-serv18176/data Added Files: configure.in Log Message: Some more corrections --- NEW FILE: configure.in --- dnl dnl $Id: configure.in,v 1.1 2003/09/26 19:08:04 egonw Exp $ dnl AC_INIT() AM_INIT_AUTOMAKE(woc, `cat VERSION`) AC_OUTPUT([ iupac/wml/Makefile iupac/Makefile woc/wml/Makefile woc/dadml/Makefile woc/Makefile Makefile ]) |
|
From: Egon W. <eg...@us...> - 2003-09-26 19:01:21
|
Update of /cvsroot/woc/woc2 In directory sc8-pr-cvs1:/tmp/cvs-serv17055 Removed Files: Makefile.am VERSION bootstrap configure.in Log Message: Removed crap way to high up in the level --- Makefile.am DELETED --- --- VERSION DELETED --- --- bootstrap DELETED --- --- configure.in DELETED --- |
|
From: Egon W. <eg...@us...> - 2003-09-26 18:43:33
|
Update of /cvsroot/woc/woc2 In directory sc8-pr-cvs1:/tmp/cvs-serv13503 Log Message: Second dir struct design Status: Vendor Tag: vendor Release Tags: start N woc2/Makefile.am N woc2/bootstrap N woc2/configure.in N woc2/VERSION N woc2/data/Makefile.am N woc2/data/iupac/Makefile.am N woc2/data/iupac/wml/Makefile.am N woc2/data/woc/Makefile.am N woc2/data/woc/wml/Makefile.am N woc2/data/woc/dadml/Makefile.am N woc2/source/Makefile.am N woc2/source/maint/Makefile.am N woc2/source/publish/Makefile.am N woc2/source/publish/wocjava/Makefile.am N woc2/source/manuals/Makefile.am N woc2/source/manuals/maint/Makefile.am N woc2/source/manuals/publish/Makefile.am N woc2/layout/Makefile.am N woc2/layout/woc/webdocs/Makefile.am N woc2/layout/woc/cgi/Makefile.am N woc2/layout/iupac/webdocs/Makefile.am N woc2/layout/iupac/cgi/Makefile.am N woc2/layout/translations/webdocs/Makefile.am N woc2/layout/translations/cgi/Makefile.am N woc2/layout/generic/Makefile.am N woc2/layout/generic/webdocs/Makefile.am N woc2/layout/generic/cgi/Makefile.am N woc2/project/Makefile.am No conflicts created by this import ***** Bogus filespec: - ***** Bogus filespec: Imported ***** Bogus filespec: sources |
|
From: Egon W. <eg...@us...> - 2003-09-17 12:07:03
|
Update of /cvsroot/woc/woc/bin/news In directory sc8-pr-cvs1:/tmp/cvs-serv30719 Modified Files: news.xml Log Message: Added news item about new URL Index: news.xml =================================================================== RCS file: /cvsroot/woc/woc/bin/news/news.xml,v retrieving revision 1.3 retrieving revision 1.4 diff -C2 -r1.3 -r1.4 *** news.xml 26 Nov 2002 12:07:40 -0000 1.3 --- news.xml 17 Sep 2003 12:06:56 -0000 1.4 *************** *** 2,5 **** --- 2,11 ---- <!DOCTYPE ITEM SYSTEM "news.dtd"> <NEWS> + <ITEM ID="20030917"> + <DATUM>17 september 2003</DATUM> + <TEKST> + De nieuwe URL voor het WOC is: http://www.woc.sci.kun.nl/. + </TEKST> + </ITEM> <ITEM ID="20021126"> <DATUM>26 november 2002</DATUM> |
|
From: Egon W. <eg...@us...> - 2002-11-26 12:07:42
|
Update of /cvsroot/woc/woc/bin/news In directory sc8-pr-cvs1:/tmp/cvs-serv25670 Modified Files: news.xml Log Message: Added recent news. Index: news.xml =================================================================== RCS file: /cvsroot/woc/woc/bin/news/news.xml,v retrieving revision 1.2 retrieving revision 1.3 diff -C2 -r1.2 -r1.3 *** news.xml 11 Jun 2002 13:34:09 -0000 1.2 --- news.xml 26 Nov 2002 12:07:40 -0000 1.3 *************** *** 2,5 **** --- 2,31 ---- <!DOCTYPE ITEM SYSTEM "news.dtd"> <NEWS> + <ITEM ID="20021126"> + <DATUM>26 november 2002</DATUM> + <TEKST> + De verbinding met het internet van de KUN is gisteravond verbroken, en pas + vandaag om 13:00 uur hersteld. Gedurende deze tijd is het WOC onbereikbaar + geweest. + </TEKST> + </ITEM> + <ITEM ID="20021122"> + <DATUM>22 november 2002</DATUM> + <TEKST> + Er is en nieuwe versie van <a href="http://jmol.sf.net">Jmol</a> uit. + Het voor ons meest interessante aspect van deze nieuwe versie, is dat het + vertaald is naar het Nederlands. + </TEKST> + </ITEM> + <ITEM ID="20021021"> + <DATUM>21 oktober 2002</DATUM> + <TEKST> + Het Linux/KDE programma <a href="http://edu.kde.org/kalzium">Kalzium</a> + heeft sinds kort een door het WOC mede ontwikkelde Nederlandstalige + gebruikersinterface, die met versie 3.1 van KDE gedistribueerd zal worden. + In de ontwikkelingsversie kan vanuit Kalzium ook informatie uit het + WOC opgevraagd worden over elementen. + </TEKST> + </ITEM> <ITEM ID="20020606"> <DATUM>6 juni 2002</DATUM> |
|
From: Geert J. <gj...@us...> - 2002-09-03 19:40:57
|
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc/files In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc/files Added Files: DictFile.java FileReadAble.java FileWriteAble.java ItemFile.java ItemWriteFile.java LetterFile.java SLetterFile.java ShortLetterFile.java WMLHandler.java WMLReadFile.java WocListHandler.java WocListReadFile.java WocReportFile.java XItemFile.java Log Message: --- NEW FILE: DictFile.java --- package com.egonw.woc.files; import com.objectspace.jgl.*; import java.io.*; import java.lang.*; import java.util.*; import com.egonw.util.*; import com.egonw.woc.*; import com.egonw.woc.util.*; import com.egonw.woc.wml.*; import com.egonw.woc.predicate.*; public class DictFile extends HtmlWriteFile implements FileWriteAble { private OrderedSet words; private String loc; private String lang; private Path repository; public DictFile(Path repository, String fn, String landcode) throws IOException { super(fn); words = new OrderedSet(new LessFWord()); this.loc = "Vertalingen"; this.lang = landcode; this.repository = repository; } public String getName() { return ("DictFile"); } public void setLocation(String location) { this.loc = location; } public void close() throws IOException { super.close(); } public void start() { super.start(); writeLine("<head>"); writeLine(" <base href=\"" + repository.getHtmlRoot() + "\">"); writeLine(" <link rel=\"stylesheet\" href=\"" + repository.getHtmlRoot() + repository.getCSSSubDir() + "woc.css\" type=\"text/css\">"); writeLine(" <script src=\"" + repository.getJavascriptSubDir() + "browsertest.js\"></script>"); writeLine(" <script src=\"" + repository.getJavascriptSubDir() + "location.js\"></script>"); writeLine(" <script>"); writeLine(" <!--"); writeLine(" setLocation(\"" + this.loc + "\");"); writeLine(" // -->"); writeLine(" </script>"); writeLine("</head>"); writeLine("<body class=\"main\">"); writeLine("<hr>"); writeLine("<table border=0 celpadding=0 cellspacing=0 width=100%>"); } public void end() { // dump alle woorden Enumeration ewords = words.elements(); while (ewords.hasMoreElements()) { FWord fword = (FWord)ewords.nextElement(); writeLine("<tr><td class=\"main\">"); writeLine( fword.getFWord() ); writeLine("</td><td>"); writeLine("<a href=\"" + repository.getItemFileSubDir() + fword.getAnchor() + ".shtml\">" + fword.getDWord() + "</a>"); writeLine("</td>"); } // print normale eind writeLine("</table>"); writeLine("<hr></body>"); super.end(); } public void startItems(Item first) {}; public void endItems(Item last) {}; public void writeItem(Item item) { if (item.contains(XItem.XNAME)) { String dword = new String(); String eword = new String(); FWord fword = new FWord(this.lang); Vector names = (Vector)item.get(XItem.XNAME); Enumeration e = names.elements(); while (e.hasMoreElements()) { XNAME xname = (XNAME)e.nextElement(); int check = 0; Enumeration langs = xname.elements(); while (langs.hasMoreElements()) { XLANG xl = (XLANG)langs.nextElement(); if (xl.getID().equals("NL")) { dword = xl.getValue(); check++; } else if (xl.getID().equals(this.lang)) { eword = xl.getValue(); check++; } } if (check == 2) { fword.setFWord(eword); fword.setDWord(dword); fword.setAnchor((String)item.get(Item.ANCHOR)); words.add(fword); } } } } }; --- NEW FILE: FileReadAble.java --- package com.egonw.woc.files; import com.egonw.util.*; import com.egonw.woc.*; import com.egonw.woc.exception.*; public interface FileReadAble { Item readItem() throws WocException; String getName(); } --- NEW FILE: FileWriteAble.java --- package com.egonw.woc.files; import java.io.*; import com.egonw.util.*; import com.egonw.woc.*; import com.egonw.woc.exception.*; public interface FileWriteAble { void start(); void end(); void startItems(Item first); void endItems(Item last); void writeItem(Item i) throws IOException; String getName(); } --- NEW FILE: ItemFile.java --- package com.egonw.woc.files; import org.xml.sax.Parser; import org.xml.sax.DocumentHandler; import org.xml.sax.helpers.ParserFactory; import java.io.*; import java.text.*; import java.util.*; import java.net.*; import java.util.*; import com.egonw.util.*; import com.egonw.woc.*; import com.egonw.woc.wml.*; import com.egonw.woc.util.*; import com.egonw.woc.predicate.*; import org.openscience.dadml.*; import org.openscience.dadml.filereaders.*; import org.openscience.dadml.tools.*; /** * WriteFile with special HTML-format functions. * * @author Egon Willighagen * @version 1.1, 23/01/98 */ public class ItemFile extends HtmlWriteFile { private Path repository; private DBDEFLIST dbdeflist; protected String titel; protected String locatie; protected String style; protected String letter; protected String lang; protected int mode; protected int count; public static int SHORT = 1; public static int LONG = 2; public ItemFile(Path repository, String fn) throws IOException { super(fn); this.titel = "Woordenboek Organische Chemie"; this.locatie = ""; this.style = "woc"; this.lang = "nl"; this.mode = SHORT; this.letter = "no"; this.count = 0; this.repository = repository; } public ItemFile(Path repository, String fn, DBDEFLIST list) throws IOException { this(repository, fn); this.dbdeflist = list; } public void close() throws IOException { super.close(); } public void setTitle(String titel) { this.titel = titel; } public void setLocatie(String locatie) { this.locatie = locatie; } public void setStyle(String style) { this.style = style; } public void setLang(String lang) { this.lang = lang; } public void setMode(int mode) { this.mode = mode; } public void setLetter() { this.letter = "yes"; } public void start() { super.start(); } public void startItems(Item i) { writeLine("<head>"); writeLine(" <title>" + this.titel + "</title>"); writeLine(" <base href=\"" + repository.getHtmlRoot() + "\">"); writeLine(" <link rel=\"stylesheet\" href=\"" + repository.getHtmlRoot() + repository.getCSSSubDir() + this.style + ".css\" type=\"text/css\">"); Vector keys = ItemInfo.listKeywords(i); if (!keys.isEmpty() && this.letter.equals("no")) { write(" <META name=\"keywords\" content=\""); Enumeration vals = keys.elements(); while (vals.hasMoreElements()) { write((String)vals.nextElement()); if (vals.hasMoreElements()) { write (", "); } } writeLine("\">"); } writeLine(" <script src=\"" + repository.getJavascriptSubDir() + "isframe.js\"></script>"); writeLine(" <script src=\"" + repository.getJavascriptSubDir() + "browsertest.js\"></script>"); // check frame writeLine(" <script>"); writeLine(" <!--"); if (this.letter.equals("no")) { writeLine(" checkFrame(\"" + (String)i.get(XItem.XFILENAME) + "\");"); } writeLine(" // -->"); writeLine(" </script>"); writeLine("</head>"); writeLine("<body class=\"main\">"); writeLine("<hr>"); } /** * Ends the writing to a Html-format file. */ public void end() { writeLine("<hr>"); writeLine("</font>"); SimpleDateFormat longdate = new SimpleDateFormat ("dd MMM yyyy"); SimpleDateFormat year = new SimpleDateFormat ("yyyy"); Date current = new Date(); writeLine("<center><i>Last updated on " + longdate.format(current) + ". © Copyright " + year.format(current) + " Woordenboek Organische Chemie</i></center>"); writeLine("<center>U bent bezoeker "); writeLine("<!--WEBBOT bot=\"HTMLMarkup\" startspan ALT=\"Site Meter\" -->"); writeLine("<script>var site=\"woccounter\"</script>"); writeLine("<script language=\"JavaScript1.2\" src=\"http://www.sitemeter.com/js/counter.js?site=woccounter\">"); writeLine("</script>"); writeLine("<noscript>"); writeLine("<a href=\"http://www.sitemeter.com/stats.asp?site=woccounter\" target=_top>"); writeLine("<img src=\"http://www.sitemeter.com/meter.asp?site=woccounter\" alt=\"Site Meter\" nosave border=0></a>"); writeLine("</noscript>"); writeLine("<script>document.write(\"//\"+\"-\"+\"-\"+\">\");</script>"); writeLine("<!-- Copyright 1999 Site Meter -->"); writeLine("<!--WEBBOT bot=\"HTMLMarkup\" Endspan -->"); writeLine(".</center>"); writeLine("</body>"); super.end(); } public void endItems(Item last) {}; public void writeItem(Item i) throws IOException { //Titelregel writeLine("<TABLE border=\"0\" width=100%>"); if (i.contains(XItem.XSEEONLY)) { DefRegel(); KopZieRegel(i); } else { DefRegel(); KopRegel(i); ReactieRegel(i); InfoRegel(i); VoorbeeldRegel(i); ZieVergRegel(i); LinksRegel(i); BronnenRegel(i); // ModelsRegel(i); TopicMapRegel(i); DbsRegel(i); ToLongRegel(i); } writeLine("</TABLE>"); } private void DefRegel() { writeLine("<TR border=0 width=100%>"); writeLine("<TD width=5%></TD>"); writeLine("<TD width=5%></TD>"); writeLine("<TD width=50%></TD>"); writeLine("<TD width=40%></TD>"); writeLine("</TR>"); } private void KopZieRegel(Item i) { try { writeLine("<TR border=\"0\" width=\"100%\">"); writeLine("<TD valign=top colspan=\"4\">"); write("<a class=\"item\" name=\"" + i.get(Item.ANCHOR) + "\">"); write("<B>"); if (i.result(new IsChemical())) { write("<img alt=\"chemical: \" src=\"gui/pictures/static_azijnzuur.gif" + QUOT + " height=" + QUOT + "10" + QUOT + " width=" + QUOT + "10" + QUOT + ">"); }; if (i.contains(Item.EIGENNAME)) { write(toItalic((String)i.get(Item.NAME))); } else { write((String)i.get(Item.NAME)); } writeLine("</B></a> "); write("zie <i>"); Enumeration zies = ((Vector)i.get(Item.ZIE)).elements(); while (zies.hasMoreElements()) { String zie = (String)zies.nextElement(); writeLine("<a href=\"" + repository.getHtmlRoot() + repository.getItemFileSubDir() + i.get(XItem.XFILENAME) + ".shtml\">" + zie + "</a>"); if (zies.hasMoreElements()) writeLine(", "); } writeLine("</i>"); writeLine("</TD>"); } catch (NullPointerException e) { System.out.println("titel regel"); } } private void KopRegel(Item i) { try { writeLine("<TR border=\"0\" width=\"100%\">"); if (i.contains(Item.SUBITEM)) { writeLine("<TD></td>"); writeLine("<td colspan=2>"); } else { writeLine("<TD valign=top colspan=3>"); } write("<a class=\"item\" name=\"" + i.get(XItem.XFILENAME) + "\">"); write("<B>"); if (i.result(new IsChemical())) { write("<img alt=\"chemical: \" src=\"gui/pictures/static_azijnzuur.gif" + QUOT + " height=" + QUOT + "10" + QUOT + " width=" + QUOT + "10" + QUOT + ">"); }; if (i.contains(Item.EIGENNAME)) { write(toItalic((String)i.get(Item.NAME))); } else { write((String)i.get(Item.NAME)); } if (i.contains(Item.FUNCTIE)) { write(" " + toItalic((String)i.get(Item.FUNCTIE))); } writeLine("</B></a>"); if (mode == LONG) { if (i.contains(Item.LIDWOORD)) writeLine(", <i>" + i.get(Item.LIDWOORD) + "</i>"); if (i.contains(XItem.XMEERVOUD)) { // System.out.println(" ... meervoud gevonden..."); writeLine(", <i>mv. " + ((XNODE)i.get(XItem.XMEERVOUD)).getCDATA() + "</i>"); } } if (i.contains(Item.CASNR)) { writeLine(" (" + toItalic((String)i.get(Item.CASNR)) + ")"); } writeLine("</TD>"); writeLine("<TD width=40% align=right>"); writeButtonBar(i); writeLine("</td></tr>"); } catch (NullPointerException e) { System.out.println("titel regel"); } } private void ReactieRegel(Item i) { try { //reactie if (i.contains(XItem.XMEDIA)) { Enumeration e = ((Vector)i.get(XItem.XMEDIA)).elements(); while (e.hasMoreElements()) { XNODE x = (XNODE)e.nextElement(); if (x.containsATT("MIME")) { if (x.getATT("MIME").equals("image/gif") && x.containsATT("VIEW") && x.getATT("VIEW").equals("TOP") ) { writeLine("<TR border=0 width=100%>"); writeLine("<TD width=5%></td>"); writeLine("<TD colspan=3>"); write("<img src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir()); if (x.containsATT("PATH")) { write(x.getATT("PATH") + "/"); } else if (i.contains(Item.PICTUREDIR)) { write((String)i.get(Item.PICTUREDIR)+ "/"); } writeLine(x.getCDATA().trim() + "\">"); if (x.containsATT("TITLE")) { write("<br><i>" + x.getATT("TITLE") + "</i>"); } writeLine("</TD></tr>"); } } } } else if (i.contains(Item.REACTIE)) { writeLine("<TR border=0 width=100%>"); writeLine("<TD width=5%></td>"); writeLine("<TD colspan=3>"); write("<img src=" + QUOT + repository.getHtmlRoot() + repository.getPictureSubDir()); if (i.contains(Item.PICTUREDIR)) write((String)i.get(Item.PICTUREDIR)+ "/"); writeLine((String)i.get(Item.REACTIE)+ QUOT + ">"); writeLine("</TD></tr>"); } } catch (NullPointerException e) { System.out.println("Fout bij schrijven van info regel"); } } private void InfoRegel(Item i) { try { //inforegel writeLine("<TR border=\"0\" width=\"100%\">"); writeLine("<TD width=5%></td>"); writeLine("<TD colspan=\"2\" valign=\"top\">"); writeLine("<P>"); if (i.contains(Item.LEVEN)) writeLine("<i>" + i.get(Item.LEVEN) + "</i><br>"); if (i.contains(XItem.XFORMULA)) { Enumeration formulas = ((Vector)i.get(XItem.XFORMULA)).elements(); while (formulas.hasMoreElements()) { XNODE xn = (XNODE)formulas.nextElement(); if (xn.containsATT("CLASS")) { if (xn.getATT("CLASS").equals("STRUCTURAL")) { Bruto f = new Bruto(xn.getCDATA()); write("<br><b>structuurformule</b>: " + f.toHTMLString()); } else if (xn.getATT("CLASS").equals("GROUP-LEFT")) { Bruto f = new Bruto(xn.getCDATA()); write("<br><b>functionele groep</b>: "); if (xn.containsATT("ORDER")) { if (xn.getATT("ORDER").equals("2")) { writeLine(f.toHTMLString() + "="); } else if (xn.getATT("ORDER").equals("1")) { writeLine(f.toHTMLString() + "-"); } } else { writeLine(f.toHTMLString() + "-"); } } else if (xn.getATT("CLASS").equals("GROUP-RIGHT")) { Bruto f = new Bruto(xn.getCDATA()); write("<br><b>functionele groep</b>: "); if (xn.containsATT("ORDER")) { if (xn.getATT("ORDER").equals("2")) { writeLine( "=" + f.toHTMLString()); } else if (xn.getATT("ORDER").equals("1")) { writeLine( "-" + f.toHTMLString()); } } else { writeLine( "-" + f.toHTMLString()); } } else if (xn.getATT("CLASS").equals("STOICH")) { StoichFormule sf = new StoichFormule(xn.getCDATA()); writeLine("<br><b>formule</b>: " + sf.toHTMLString()); } else if (xn.getATT("CLASS").equals("CLASS")) { StoichFormule sf = new StoichFormule(xn.getCDATA()); writeLine("<br><b>klasse</b>: " + sf.toHTMLString()); } else if (xn.getATT("CLASS").equals("ION") && xn.containsATT("CHARGE")) { StoichFormule sf = new StoichFormule(xn.getCDATA()); writeLine("<br><b>ion</b>: " + sf.toHTMLString() + "<sup>" + xn.getATT("CHARGE") + "</sup>"); } } writeLine("<br>"); } } if (i.contains(Item.FORMULA)) { writeLine("<b>formule</b>: " + ((Raw)i.get(Item.FORMULA)).toHTMLString() + "<br>"); } else if (i.contains(Item.BRUTO)) { writeLine("<b>brutoformule</b>: " + ((Bruto)i.get(Item.BRUTO)).toHTMLString()); writeLine("<br>"); } if (i.contains(Item.TRIVIALNAME)) { writeLine("<b>synoniemen</b>: "); Enumeration values = ((Vector)i.get(Item.TRIVIALNAME)).elements(); while (values.hasMoreElements()) { String triv = (String)values.nextElement(); write("<i>" + triv + "</i>"); if (values.hasMoreElements()) write(", "); } writeLine("<br>"); } if (i.contains(Item.IUPACNAME)) { write("<b>IUPAC naam</b>: "); write("<i>" + (String)i.get(Item.IUPACNAME) + "</i><br>"); } if (i.contains(XItem.XAFKORT)) { write("<b>afkorting</b>: "); Enumeration afkortingen = ((Vector)i.get(XItem.XAFKORT)).elements(); while (afkortingen.hasMoreElements()) { write("<i>" + ((XNODE)afkortingen.nextElement()).getCDATA() + "</i>"); if (afkortingen.hasMoreElements()) { writeLine(", "); } else { writeLine("<br>"); } } } else if (i.contains(Item.AFKORT)) { write("<b>afkorting</b>: "); writeLine("<i>" + i.get(Item.AFKORT) + "</i><br>"); } if (mode == LONG) { //print Engelse & Duitse woorden if (i.contains(Item.ENGLISH) || i.contains(XItem.XGERMAN) || i.contains(XItem.XLATIN) || i.contains(XItem.XFRENCH) || i.contains(XItem.XSPANISH) || i.contains(XItem.XITALIAN)) writeLine("<P>"); if (i.contains(Item.ENGLISH)) { writeLine("<b>engelse vertaling</b>: " + (String)i.get(Item.ENGLISH) + "<br>"); } if (i.contains(XItem.XGERMAN)) { writeLine("<b>duitse vertaling</b>: " + (String)i.get(XItem.XGERMAN) + "<br>"); } if (i.contains(XItem.XFRENCH)) { writeLine("<b>franse vertaling</b>: " + (String)i.get(XItem.XFRENCH) + "<br>"); } if (i.contains(XItem.XSPANISH)) { writeLine("<b>spaanse vertaling</b>: " + (String)i.get(XItem.XSPANISH) + "<br>"); } if (i.contains(XItem.XITALIAN)) { writeLine("<b>italiaanse vertaling</b>: " + (String)i.get(XItem.XITALIAN) + "<br>"); } if (i.contains(XItem.XLATIN)) { writeLine("<b>latijnse vertaling</b>: " + (String)i.get(XItem.XLATIN) + "<br>"); } if (i.contains(XItem.XFRYSIAN)) { writeLine("<b>friese vertaling</b>: " + (String)i.get(XItem.XFRYSIAN) + "<br>"); } } if (i.contains(Item.GROUP)) { writeLine("<b>Groepen</b>: "); Enumeration groepen = ((Vector)i.get(Item.GROUP)).elements(); while (groepen.hasMoreElements()) { String group = (String)groepen.nextElement(); String anchor = Convert.NAMELikeToANCHORLike(group); writeLine("<a href=\"" + repository.getHtmlRoot() + repository.getItemFileSubDir() + anchor + ".shtml\">" + group + "</a>"); if (groepen.hasMoreElements()) writeLine(", "); } writeLine("<br>"); } if (mode == LONG) { //print Indices if (i.contains(Item.CASNR) || i.contains(XItem.XENR) || i.contains(XItem.XUNNR)) writeLine("<p>"); if (i.contains(Item.CASNR)) { writeLine("<b>CAS Nummer</b>: " + (String)i.get(Item.CASNR) + "<br>"); } if (i.contains(XItem.XNSC)) { writeLine("<b>NSC Nummer</b>: " + (String)i.get(XItem.XNSC) + "<br>"); } if (i.contains(XItem.XENR)) { writeLine("<b>E-Nummer</b>: E" + (String)i.get(XItem.XENR) + "<br>"); } if (i.contains(XItem.XUNNR)) { writeLine("<b>UN Nummer</b>: " + (String)i.get(XItem.XUNNR) + "<br>"); } } if (i.contains(XItem.XDISCDATE) || i.contains(XItem.XDISCPLACE)) { writeLine("<P><b>Ontdekking</b>:"); writeLine("<br />datum: "); if (i.contains(XItem.XDISCDATE)) { writeLine((String)i.get(XItem.XDISCDATE)); } writeLine("<br />plaats: "); if (i.contains(XItem.XDISCPLACE)) { writeLine((String)i.get(XItem.XDISCPLACE)); } writeLine("</P>"); } if (ItemInfo.containsFysicalProps(i) || i.contains(XItem.XPKA) || i.contains(XItem.XPKB)) { if (mode == LONG) { writeLine("<P>"); // het volgende is voor niet Java'ers if (i.contains(Item.BOILINGPOINT)) writeLine("<i>Kookpunt : " + i.get(Item.BOILINGPOINT) + "<sup>o</sup>C</i><br>"); if (i.contains(Item.MELTINGPOINT)) writeLine("<i>Smeltpunt : " + i.get(Item.MELTINGPOINT) + " <sup>o</sup>C</i><br>"); if (i.contains(XItem.XFLASH)) writeLine("<i>Vlampunt : " + i.get(XItem.XFLASH) + " <sup>o</sup>C</i><br>"); if (i.contains(Item.MASS)) writeLine("<i>Massa : " + i.get(Item.MASS) + " g/mol</i><br>"); if (i.contains(Item.RHO)) writeLine("<i>Dichtheid : " + i.get(Item.RHO) + " g/ml</i><br>"); if (i.contains(Item.DIPOOL)) writeLine("<i>Dipool : " + i.get(Item.DIPOOL) + " D</i><br>"); if (i.contains(XItem.XPKA)) writeLine("<i>pK<sub>a</sub> : " + i.get(XItem.XPKA) + "</i><br>"); if (i.contains(XItem.XPKB)) writeLine("<i>pK<sub>b</sub> : " + i.get(XItem.XPKB) + "</i><br>"); } writeLine("<br>"); } if (i.contains(Item.COMMENT)) { write("<p>"); Enumeration comments = ((Vector)i.get(Item.COMMENT)).elements(); if (!ItemInfo.hasMoreThanOneComment(i)) { writeLine((Memo)comments.nextElement()); } else { writeLine("<table width=\"100%\">"); int j=0; while (comments.hasMoreElements()) { Memo m = (Memo)comments.nextElement(); j++; writeLine("<tr>\n<td valign=\"top\" width=\"10\"><b>" + Integer.toString(j) + ".</b></td>"); writeLine("<td valign=\"top\">"); writeLine(m); writeLine("</td>\n</tr>"); } writeLine("</table>"); } } writeLine(" "); writeLine("</TD>"); writeLine("<TD width=40% valign=top align=center>"); writeRightPicture(i); writeLine("</td>"); writeLine("</tr>"); } catch (NullPointerException e) { System.out.println("Fout bij schrijven van info regel"); } } private void VoorbeeldRegel(Item i) { try { writeLine("<TR>"); writeLine("<TD colspan=2></td>"); writeLine("<TD width=55% bgcolor=\"silver\">"); if (i.contains(Item.VOORBEELD)) { Enumeration comments = ((Vector)i.get(Item.VOORBEELD)).elements(); if (!ItemInfo.hasMoreThanOneVoorbeeld(i)) { writeLine("<b><i>Voorbeeld</i></b> "); writeLine((Memo)comments.nextElement()); } else { int j=0; while (comments.hasMoreElements()) { Memo m = (Memo)comments.nextElement(); j++; writeLine("<b>Voorbeeld " + Integer.toString(j) + ".</b> "); writeLine(m); } } } writeLine("</TD>"); writeLine("</TR>"); } catch (NullPointerException e) { System.out.println("Fout bij schrijven van info regel"); } } private void ZieVergRegel(Item i) { try { //Zie-Vergelijkregel if (i.contains(Item.ZIE)) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); write("Zie <i>"); Enumeration zies = ((Vector)i.get(Item.ZIE)).elements(); while (zies.hasMoreElements()) { String zie = (String)zies.nextElement(); String anchor = Convert.NAMELikeToANCHORLike(zie); writeLine("<a href=\"" + repository.getHtmlRoot() + repository.getItemFileSubDir() + anchor + ".shtml\">" + zie + "</a>"); if (zies.hasMoreElements()) writeLine(", "); } writeLine("</i></td></tr>"); } if (i.contains(Item.VERGELIJK)) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); write("Vergelijk <i>"); Enumeration verg = ((Vector)i.get(Item.VERGELIJK)).elements(); while (verg.hasMoreElements()) { String vergelijk = (String)verg.nextElement(); String anchor = Convert.NAMELikeToANCHORLike(vergelijk); writeLine("<a href=\"" + repository.getHtmlRoot() + repository.getItemFileSubDir() + anchor + ".shtml\">" + vergelijk + "</a>"); if (verg.hasMoreElements()) writeLine(", "); } writeLine("</i></td></tr>"); } } catch (NullPointerException e) { System.out.println("zie/vgl regel"); } } private void ModelsRegel(Item i) { try { //Bronnen's if (ItemInfo.containsModels(i) && mode == LONG) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); writeLine("<P>Modellen: "); if (i.contains(Item.PICTUREFILE)) { writeLine("<a href=" + QUOT + repository.getHtmlRoot() + repository.getPictureSubDir() + ((Picture)i.get(Item.PICTUREFILE)).path() + QUOT + ">GIF</a>"); if (i.contains(Item.PDB) || i.contains(Item.MOL) || i.contains(Item.XYZFILE)) writeLine(", "); } if (i.contains(Item.MOL)) { writeLine("<a href=" + QUOT + repository.getHtmlRoot() + repository.getModelsSubDir() + repository.getMolSubDir() + ((String)i.get(Item.MOL)) + QUOT + ">MOL (2D)</a>"); if (i.contains(Item.PDB) || i.contains(Item.XYZFILE)) writeLine(", "); } if (i.contains(Item.PDB)) { writeLine("<a href=" + QUOT + repository.getHtmlRoot() + repository.getModelsSubDir() + repository.getPdbSubDir() + ((String)i.get(Item.PDB)) + QUOT + ">PDB</a>"); if (i.contains(Item.XYZFILE)) writeLine(", "); } if (i.contains(Item.XYZFILE)) { writeLine("<a href=" + QUOT + repository.getHtmlRoot() + repository.getModelsSubDir() + repository.getXyzSubDir() + ((String)i.get(Item.XYZFILE)) + QUOT + ">XYZ</a>"); } } writeLine("</P></td></tr>"); } catch (NullPointerException e) { System.out.println("bronnen regel"); }; } private void DbsRegel(Item i) { try { //Andere Databases if (mode == LONG && i.contains(Item.CASNR)) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); writeLine("<P><img src=" + QUOT + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/dbs.gif" + QUOT + "><br>"); writeLine("<ul><div class=\"small\"><b>NB:</b> Hieronder staan links naar andere databases. Een link betekent NIET dat de "+ "andere database ook echt informatie heeft."); Hashtable indexlist = new Hashtable(); indexlist.put("CAS-NUMBER", i.get(Item.CASNR)); if (i.contains(XItem.XENR)) { indexlist.put("E-NUMBER", i.get(XItem.XENR)); } if (dbdeflist != null) { writeLine("<p>"); Enumeration list = this.dbdeflist.elements(); while (list.hasMoreElements()) { Enumeration indices = indexlist.keys(); DBDEF dbdef = (DBDEF)(list.nextElement()); // System.err.println("Trying: " + dbdef.getTITLE()); while (indices.hasMoreElements()) { String index = (String)(indices.nextElement()); // System.err.println("Index: " + index); if (DBDEFInfo.hasINDEX(dbdef, index)) { writeLine("<b>" +dbdef.getTITLE() + "</b><br />"); Enumeration fields = dbdef.fields(); while (fields.hasMoreElements()) { FIELD f = (FIELD)fields.nextElement(); Enumeration findices = f.getINDEX(); while (findices.hasMoreElements()) { INDEX ind = (INDEX)findices.nextElement(); if (ind.getTYPE().equals(index)) { String url = dbdef.getURL() + ind.getACCESS_PREFIX() + indexlist.get(index) + ind.getACCESS_SUFFIX(); // System.err.println("Downloading: " + url); try { URL u = new URL(url); URLConnection conn = u.openConnection(); if (conn instanceof HttpURLConnection) { if (((HttpURLConnection)conn).getResponseCode() == HttpURLConnection.HTTP_OK) { writeLine("<dd><a href=\"" + url + "\">" + f.getNAME() + "</a></dd><br />"); } } else { writeLine("<dd><a href=\"" + url + "\">" + f.getNAME() + "</a></dd><br />"); } } catch (MalformedURLException mue) { System.err.println("OpenDADMLFrame: Malformed URL" + mue); } catch (Exception fnfe) { // System.err.println("OpenDADMLFrame: File Not Found." + fnfe); } } } } } } } } else { // Oud mechanism, gebruik makend van SSI write("<p><!--#include virtual=\"/cgi-bin-woc/ssi/dadml.pl?"); write("CAS-NUMBER+" + (String)i.get(Item.CASNR)); if (i.contains(XItem.XENR)) { write("+E-NUMBER+" + (String)i.get(XItem.XENR)); } writeLine("\"-->"); } writeLine("</div></ul>"); writeLine("</P></td></tr>"); } } catch (NullPointerException e) { System.out.println("databases"); }; } private void TopicMapRegel(Item i) { if (mode == LONG && i.contains(XItem.XTOPICMAP)) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); writeLine("<b>Samenhang</b>:<br><ul>"); write("<!--#include virtual=\"/cgi-bin-woc/ssi/topicmap.pl?"); write((String)i.get(XItem.ANCHOR)); writeLine(".xml\"-->"); writeLine("</ul></td></tr>"); } } private void LinksRegel(Item i) { try { //URL's if (i.contains(Item.URL)) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); writeLine("<img src=" + QUOT + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/urls.gif" + QUOT + "><br>"); writeLine("<dd>"); Enumeration urls = ((Vector)i.get(Item.URL)).elements(); while (urls.hasMoreElements()) { String url = (String)urls.nextElement(); writeLine("<dt><a href=" + QUOT + url + QUOT + " target=" + QUOT + "_MoreInfo" + QUOT + ">" + url + "</a>"); if (urls.hasMoreElements()) writeLine(", "); } writeLine("</dd>"); writeLine("</td></tr>"); } } catch (NullPointerException e) { System.out.println("url regel"); }; } private void BronnenRegel(Item i) { try { //Bronnen's if (i.contains(Item.BRON) && (this.mode == LONG)) { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); writeLine("<p>Bronnen: "); writeLine("<ul>"); Enumeration bronnen = ((Vector)i.get(Item.BRON)).elements(); while (bronnen.hasMoreElements()) { String bron = (String)bronnen.nextElement(); writeLine("[<a href=" + QUOT + repository.getHtmlRoot() + repository.getBronnenFile() + "#" + bron + QUOT + " target=" + QUOT + "_BronInfo" + QUOT + ">" + bron + "</a>]<br>"); if (bronnen.hasMoreElements()) writeLine(", "); } writeLine("</ul>"); writeLine("</td></tr>"); } } catch (NullPointerException e) { System.out.println("bronnen regel"); }; } private void ToLongRegel(Item i) { if (ItemInfo.containsLongInfo(i) && mode == SHORT) { try { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); if (i.contains(XItem.XGROUP)) { String anchor = Convert.NAMELikeToANCHORLike((String)i.get(Item.NAME)); writeLine("<a href=\"" + repository.getHtmlRoot() + repository.getGroupFileSubDir() + anchor + ".html\">Alle items</a><br>"); } else { String anchor = Convert.NAMELikeToANCHORLike((String)i.get(Item.NAME)); writeLine("<a href=" + QUOT + repository.getHtmlRoot() + repository.getItemFileSubDir() + anchor + ".shtml\">Meer informatie</a><br>"); } writeLine("</td></tr>"); } catch (NullPointerException e) { System.out.println("ToLongRegel"); }; } else if (ItemInfo.containsLongInfo(i)) { try { writeLine("<tr width=100%>"); writeLine("<td width=5%></td>"); writeLine("<td colspan=3 align=left valign=top>"); if (i.contains(XItem.XGROUP)) { String anchor = Convert.NAMELikeToANCHORLike((String)i.get(Item.NAME)); writeLine("<a href=\"" + repository.getHtmlRoot() + repository.getGroupFileSubDir() + anchor + ".html\">Alle items</a><br>"); } writeLine("</td></tr>"); } catch (NullPointerException e) { System.out.println("ToLongRegel"); }; } } private void writeButtonBar(Item i) { if (i.contains(Item.XYZFILE) || i.contains(Item.PDB)) { if (i.contains(Item.PICTUREFILE)) { write("<a href=\"" + repository.getCgiBinRoot() + "viewer/viewer.pl?"); write((String)i.get(Item.NAME) + "+" + (String)i.get(Item.CASNR)); write("\">"); } writeLine("<img src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/xyzfile.gif\" heigth=16 width=16 border=0></a>"); } if (i.contains(Item.CASNR)) { write("<a href=\"" + repository.getCgiBinRoot() + "msds/link.pl?"); write((String)i.get(Item.CASNR)+ "\">"); writeLine("<img src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/msds.gif\"" + " heigth=16 width=16 border=0></a>"); } if (i.contains(Item.CASNR)) { write("<a href=\"" + repository.getCgiBinRoot() + "spectra.pl?"); // bug XXXXX write((String)i.get(Item.NAME) + "+"); write((String)i.get(Item.CASNR)+ "\">"); writeLine("<img src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/ir.gif\" heigth=16 width=16 border=0></a>"); } if (i.contains(XItem.XGROUP)) { write("<a href=\"" + repository.getCgiBinRoot() + "tree/tree.pl?repos=" + repository.getName() + "&query="); if (i.contains(XItem.WOCNR)) { write((String)i.get(XItem.WOCNR)); } else { write((String)i.get(Item.NAME)); } writeLine("\"><img src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/map.gif\" heigth=\"16\" width=\"16\" border=\"0\"></a>"); } if (i.contains(Item.ENGLISH)) { write("<a href=\"" + repository.getCgiBinRoot() + "search/netsearch.pl?lang=EN&query="); write((String)i.get(XItem.WOCNR) + "\">"); writeLine("<img alt=\"Laat het WOC meer informatie zoeken op het internet...\" " + "src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir() + "system/searchmachine.gif\" heigth=\"16\" width=\"16\" border=\"0\"></a>"); } } private void writeRightPicture(Item i) { if (i.contains(XItem.XMEDIA)) { Enumeration e = ((Vector)i.get(XItem.XMEDIA)).elements(); while (e.hasMoreElements()) { XNODE x = (XNODE)e.nextElement(); if (x.containsATT("MIME")) { if (x.getATT("MIME").equals("image/gif") && (!x.containsATT("VIEW") || !x.getATT("VIEW").equals("TOP")) ) { writeLine(" <center>"); if (i.contains(Item.MOL)) write("<a href=\"" + repository.getHtmlRoot() + repository.getModelsSubDir() + repository.getMolSubDir() + i.get(Item.MOL) + "\">"); write("<img border=\"0\" src=\"" + repository.getHtmlRoot() + repository.getPictureSubDir()); if (x.containsATT("PATH")) { write(x.getATT("PATH") + "/"); } else if (i.contains(Item.PICTUREDIR)) { write((String)i.get(Item.PICTUREDIR)+ "/"); } writeLine(x.getCDATA().trim() + "\">"); if (i.contains(Item.MOL)) writeLine("</a>"); if (x.containsATT("TITLE")) { write("<br><i>" + x.getATT("TITLE") + "</i>"); } writeLine("</TD></tr>"); } } } } else if (i.contains(Item.PICTUREFILE)) { writeLine(" <center>"); if (i.contains(Item.MOL)) write("<a href=" + QUOT + repository.getHtmlRoot() + repository.getModelsSubDir() + repository.getMolSubDir() + i.get(Item.MOL) + QUOT + ">"); if (i.contains(Item.PICTUREDIR)) { writeLine(" <img src=" + QUOT + repository.getHtmlRoot() + repository.getPictureSubDir() + (String)i.get(Item.PICTUREDIR) + "/" + ((Picture)i.get(Item.PICTUREFILE)).path() + QUOT + " border=0><br>"); if (i.contains(Item.MOL)) writeLine("</a>"); writeLine("<i>" + ((Picture)i.get(Item.PICTUREFILE)).subtitle() + "</i>"); } else { writeLine(" <img src=" + QUOT + repository.getHtmlRoot() + repository.getPictureSubDir() + ((Picture)i.get(Item.PICTUREFILE)).path() + QUOT + "><br>"); if (i.contains(Item.MOL)) writeLine("</a>"); writeLine("<i>" + ((Picture)i.get(Item.PICTUREFILE)).subtitle() + "</i>"); } writeLine(" </center>"); } else if (i.contains(Item.SMILE)) { } } }; --- NEW FILE: ItemWriteFile.java --- package com.egonw.woc.files; import org.xml.sax.Parser; import org.xml.sax.DocumentHandler; import org.xml.sax.helpers.ParserFactory; import java.io.*; import java.text.*; import java.util.*; import java.net.*; import com.egonw.util.*; import com.egonw.woc.*; import com.egonw.woc.util.*; import org.openscience.dadml.*; import org.openscience.dadml.filereaders.*; import org.openscience.dadml.tools.*; /** * WriteFile with special HTML-format functions. * * @author Egon Willighagen * @version 1.1, 23/01/98 */ public class ItemWriteFile extends ItemFile implements FileWriteAble { public ItemWriteFile(Path repository, String fn) throws IOException { super(repository, fn); } public ItemWriteFile(Path repository, String fn, int mode) throws IOException { super(repository, fn); super.setMode(mode); } public ItemWriteFile(Path repository, String fn, int mode, DBDEFLIST list) throws IOException { super(repository, fn, list); super.setMode(mode); } public String getName() { return "ItemWriteFile"; } public void start() { super.start(); } public void end() { super.end(); } public void startItems(Item first) { super.startItems(first); }; public void endItems(Item last) { super.endItems(last); }; public void writeItem(Item i) throws IOException { super.writeItem(i); } }; --- NEW FILE: LetterFile.java --- package com.egonw.woc.files; import java.io.*; import java.text.*; import java.util.Enumeration; import com.egonw.woc.*; import com.egonw.woc.util.*; import com.egonw.woc.exception.*; /** * WriteFile with special HTML-format functions. * * @author Egon Willighagen * @version 1.0, 24/11/97 */ public class LetterFile extends ItemFile implements FileWriteAble { private Path repository; public LetterFile(Path repository, String fn) throws IOException { super(repository, fn); this.repository = repository; } public LetterFile(Path repository, char c) throws IOException { super(repository, repository.getPhysicalRoot() + repository.getLetterFileSubDir() + c + ".html"); this.repository = repository; super.setLocatie("Letter " + c); } public String getName() { return ("LetterFile"); } public void close() throws IOException { super.close(); } public void start() { super.start(); } public void end() { super.end(); } public void startItems(Item first) { super.startItems(first); }; public void endItems(Item last) { super.endItems(last); }; public void writeItem(Item i) throws IOException { super.writeItem(i); } }; --- NEW FILE: SLetterFile.java --- package com.egonw.woc.files; import java.io.*; import java.text.*; import java.util.*; import com.egonw.woc.*; import com.egonw.woc.util.*; import com.egonw.woc.exception.*; /** * WriteFile with special HTML-format functions. * * @author Egon Willighagen * @version 1.0, 24/11/97 */ public class SLetterFile extends ItemFile implements FileWriteAble { private Path repository; private char letter; private int up; private int count; private int down; private int total; private Vector items; private Item first; private Item last; public SLetterFile(Path repository, char letter, int count) throws IOException { super(repository, repository.getPhysicalRoot() + repository.getLetterFileSubDir() + letter + count + ".html"); super.setLocatie("Letter " + letter); super.setLetter(); this.letter = letter; this.count = count; this.up = 0; this.down = 0; this.items = new Vector(); this.first = new Item(); this.last = new Item(); this.repository = repository; } public void setUp(int i) { this.up = i; } public void setDown(int i) { this.down = i; } public void setTotal(int i) { this.total = i; } public String getName() { return ("SLetterFile"); } public void close() throws IOException { super.close(); } public void start() { super.start(); } public void end() { if ( up > 0 ) writeLine(" <a href=\"" + repository.getLetterFileSubDir() + letter + up + ".html\"><img src=\"gui/pictures/up.gif\" border=\"0\"> Blader terug</a>"); writeLine(" " + first.get(Item.NAME) + " <i>t/m</i> " + last.get(Item.NAME)); if ( down > 0 ) writeLine(" <a href=\"" + repository.getLetterFileSubDir() + letter + down + ".html\"><img src=\"gui/pictures/down.gif\" border=\"0\"> Blader verder</a>"); if (this.total > 1) { write(" [ "); for ( int i = 1; i <= this.total; i++) { if (this.count == i) { writeLine(" <b>" + i + "</b> "); } else { write(" <a href=\"" + repository.getLetterFileSubDir() + letter + i + ".html\">" + i + "</a> "); } } writeLine("]"); } writeLine(" <hr>"); Item item = new Item(); Enumeration eitems = items.elements(); while (eitems.hasMoreElements()) { item = (Item)eitems.nextElement(); try { super.writeItem(item); } catch (IOException e) {} } if ( down > 0 ) { writeLine(" <hr>"); writeLine(" <a href=\"" + repository.getLetterFileSubDir() + letter + down + ".html\"><img src=\"gui/pictures/down.gif\" border=\"0\"> Blader verder</a>"); } super.end(); } public void startItems(Item first) { super.startItems(first); this.first = first; }; public void endItems(Item last) { super.endItems(last); this.last = last; }; public void writeItem(Item i) throws IOException { items.addElement(i); } }; --- NEW FILE: ShortLetterFile.java --- package com.egonw.woc.files; import java.io.*; import java.text.*; import java.util.*; import com.egonw.woc.*; import com.egonw.woc.util.*; import com.egonw.woc.exception.*; public class ShortLetterFile implements FileWriteAble { private char letter; private int aantal; private int count; private String locatie; private SLetterFile activeFile; private Vector files; private Vector items; private Path repository; public ShortLetterFile(Path repository, char letter, int aantal) throws IOException { this.locatie = ""; this.aantal = aantal; this.count = 0; this.files = new Vector(); this.letter = letter; this.repository = repository; } public String getName() { return ("ShortLetterFile"); } public void close() throws IOException { } public void start() { items = new Vector(); } public void end() { // Zit er nog iets in items? (Ja, minstens 1 item) // Zo ja, dan nog een file erbij if (!items.isEmpty()) { files.addElement(items); } // Dump Items naar files count = 0; Enumeration efiles = files.elements(); int total = files.size(); while (efiles.hasMoreElements()) { count++; try { activeFile = new SLetterFile(repository, letter, count); activeFile.setTotal( total ); if (count > 1) activeFile.setUp(count - 1); Vector efile = (Vector)efiles.nextElement(); if (efiles.hasMoreElements()) activeFile.setDown(count + 1); activeFile.setLocatie(locatie); activeFile.start(); Enumeration eitems = efile.elements(); // een file heeft altijd meer dan 1 item (risky) Item i = (Item)eitems.nextElement(); activeFile.startItems(i); activeFile.writeItem(i); while (eitems.hasMoreElements()) { i = (Item)eitems.nextElement(); activeFile.writeItem(i); } activeFile.endItems(i); activeFile.end(); activeFile.close(); } catch (IOException e) { System.out.println("Hier gaat iets niet goed!"); System.out.println(e.toString()); e.printStackTrace(); System.exit(1); } } } public void startItems(Item first) {}; public void endItems(Item last) {}; public void writeItem(Item i) throws IOException { count++; if (count > aantal) { count = 1; files.addElement(items); items = new Vector(); } items.addElement(i); } }; --- NEW FILE: WMLHandler.java --- package com.egonw.woc.files; import java.util.*; import java.io.*; import org.openscience.dadml.*; import com.egonw.woc.*; import com.egonw.woc.exception.*; import com.egonw.woc.wml.*; import com.egonw.woc.util.*; import org.xml.sax.*; import org.xml.sax.helpers.*; import javax.xml.transform.*; public class WMLHandler extends DefaultHandler { private final int UNKNOWN = -1; private final int DICT = -2; private final int LANG = -3; private final int INDEX = -4; private final int ANY = -6; private final int WOC = -7; private final int REFERENCE = -8; private final int XSL = -9; private final int IMPORT = -10; private final int TMASSOC = -11; private final int TMASSOCRL = -12; private final int EXCLUDE = 13; private final int CI_MSDS = 1; private final int CI_CAS = 2; private final int CI_SMILES = 3; private final int CI_WOC = 4; private final int CI_UNNR = 5; private final int CI_ENR = 6; private final int CI_NSC = 7; private XItem item; private int CurrentElement; private int CI; private String NameClass; private Memo memo; private StringBuffer xslString; private String importFile; private XNODE media; private XNODE formula; private XNODE insert; private XNODE abbrev; private XNODE meervoud; private boolean any_on; private boolean xsl_on; private boolean lang_on; private XNAME xname; private XLANG xlang; private TopicMap tm; private Vector names; private Vector formulas; private Vector medias; private Vector v; private Vector groups; private Vector zies; private Vector vergs; private TMAssoc rls; private String DiscDate; private String DiscPlace; private String DiscPersons; private Path repository; private javax.xml.transform.TransformerFactory tFactory; public WMLHandler (Path repository) { item = new XItem(); xname = new XNAME(); this.repository = repository; tFactory = TransformerFactory.newInstance(); }; public XItem returnItem () { return (XItem)item; } public void startDocument () { item = new XItem(); any_on = false; xsl_on = false; } public void endDocument () {} public void startElement (String URI, String name, String qname, Attributes atts) { setCurrentElement(name); switch (CurrentElement) { case ANY : StringBuffer sb = new StringBuffer(); sb.append("<" + name); for (int i = 0; i < atts.getLength(); i++) { sb.append(" " + atts.getQName(i) + "=\"" + atts.getValue(i) + "\""); } sb.append(">"); memo.add(sb.toString()); break; case XSL : xslString.append("<" + name); for (int i = 0; i < atts.getLength(); i++) { xslString.append(" " + atts.getQName(i) + "=\"" + atts.getValue(i) + "\""); } xslString.append(">"); break; case XItem.XTOPICMAP: tm = new TopicMap(); break; case TMASSOC: rls = new TMAssoc(); for (int i = 0; i < atts.getLength(); i++) { if (atts.getQName(i).equals("id")) { rls.setName(atts.getValue(i)); } } break; case TMASSOCRL: for (int i = 0; i < atts.getLength(); i++) { if (atts.getQName(i).equals("xlink:href")) { rls.addRL(atts.getValue(i)); } }; break; case XItem.XDISCDATE: DiscDate = new String(); break; case XItem.XDISCPLACE: DiscPlace = new String(); break; case WOC : medias = new Vector(); break; case XItem.XAFKORT : abbrev = new XNODE(); break; case XItem.XMEERVOUD : meervoud = new XNODE(); break; case Item.ITEM : for (int i = 0; i < atts.getLength(); i++) { if (atts.getQName(i).equals("CODE") || atts.getQName(i).equals("FILE")) { item.add(XItem.XFILENAME, atts.getValue(i)); } else if (atts.getQName(i).equals("ID")) { item.add(XItem.WOCNR, atts.getValue(i)); } else if (atts.getQName(i).equals("CLASS")) { XTYPE xt = new XTYPE(); if (item.contains(XItem.XTYPE)) { xt = (XTYPE)item.get(XItem.XTYPE); } if ( atts.getValue(i).equals("CHEMICAL")) { item.add(Item.CHEMICAL, new String()); xt.setType(XTYPE.CHEMICAL); } else if (atts.getValue(i).equals("ABBREV")) { xt.setType(XTYPE.ABBREV); } else if (atts.getValue(i).equals("POLYMER")) { xt.setType(XTYPE.POLYMER); } else if (atts.getValue(i).equals("MIXTURE")) { xt.setType(XTYPE.MIXTURE); } else if (atts.getValue(i).equals("GROUP")) { xt.setType(XTYPE.GROUP); } else if (atts.getValue(i).equals("NOMENCLATURE")) { xt.setType(XTYPE.IUPAC_RULE); } else if (atts.getValue(i).equals("REACTION")) { xt.setType(XTYPE.REACTION); } item.add(XItem.XTYPE, xt); } } item.add(Item.PICTUREDIR, "other"); groups = new Vector(); zies = new Vector(); vergs = new Vector(); break; case Item.NAME : xname = new XNAME(); for (int i = 0; i < atts.getLength(); i++) { if (atts.getQName(i).equals("CLASS")) { xname.setCLASS(atts.getValue(i)); } } break; case DICT : names = new Vector(); formulas = new Vector(); v = new Vector(); break; case REFERENCE : v = new Vector(); break; case INDEX : // System.out.println("Index found"); for (int i = 0; i < atts.getLength(); i++) { // System.out.println(" Att: " + atts.getQName(i)); // System.out.println(" " + atts.getValue(i)); if (atts.getQName(i).equals("CLASS")) { if (atts.getValue(i).equals("MSDS-CODE")) { CI = CI_MSDS; } else if (atts.getValue(i).equals("SMILES")) { CI = CI_SMILES; } else if (atts.getValue(i).equals("CAS-NUMBER")) { CI = CI_CAS; } else if (atts.getValue(i).equals("WOC-NUMBER")) { CI = CI_WOC; } else if (atts.getValue(i).equals("UN-NUMBER")) { CI = CI_UNNR; } else if (atts.getValue(i).equals("NSC-NUMBER")) { CI = CI_NSC; } else if (atts.getValue(i).equals("E-NUMBER")) { CI = CI_ENR; } else { CI = UNKNOWN; } } } break; case XItem.XMEDIA : media = new XNODE(); for (int i = 0; i < atts.getLength(); i++) media.setATT(atts.getQName(i), atts.getValue(i)); break; case XItem.XINSERTS : insert = new XNODE(); for (int i = 0; i < atts.getLength(); i++) insert.setATT(atts.getQName(i), atts.getValue(i)); break; case XItem.XFORMULA : formula = new XNODE(); for (int i = 0; i < atts.getLength(); i++) formula.setATT(atts.getQName(i), atts.getValue(i)); break; case LANG : xlang = new XLANG(); for (int i = 0; i < atts.getLength(); i++) { if (atts.getQName(i).equals("ID")) { xlang.setID(atts.getValue(i)); } else if (atts.getQName(i).equals("LIDWOORD")) { xlang.setLIDWOORD(atts.getValue(i)); } } break; case Item.COMMENT : memo = new Memo(); break; case IMPORT : String importItem = ""; String importMacro = ""; importFile = ""; for (int i = 0; i < atts.getLength(); i++) { if (atts.getQName(i).equals("select")) { importItem = atts.getValue(i); } else if (atts.getQName(i).equals("macro")) { importMacro = atts.getValue(i); } else if (atts.getQName(i).equals("ITEM")) { importFile = atts.getValue(i); } } xslString = new StringBuffer(); xslString.append("<xsl:stylesheet xmlns:xsl=\"http://www.w3.org/XSL/Transform/1.0\">\n"); // expand macro's String repos = importItem.substring(importItem.indexOf("@")+1); String item = importItem.substring(0,importItem.indexOf("@")); Path irepos = new Path(repos); if (importMacro.equals("picture")) { xslString.append(" <xsl:import href=\"file://" + irepos.getPhysicalRoot() + irepos.getWMLSubDir() + "/picture.xsl\"/>"); } // deduce importFile if not given if (importItem.length() > 0) { // oke import:* was used if (importItem.indexOf("@") == -1) { System.out.println("Error: import:* select does not specify repository!"); } else { importFile = irepos.getPhysicalRoot() + irepos.getWMLSubDir() + "/" + item + ".xml"; } } else { importFile = repository.getPhysicalRoot() + repository.getDataSubDir() + importFile; } //System.out.println("XSLT: importing " + importFile); break; case Item.VOORBEELD : memo = new Memo(); break; } } public void endElement (String URI, String name, String qname) { setCurrentElement(name); switch (CurrentElement) { case ANY : StringBuffer sb = new StringBuffer(); sb.append("</" + name + ">"); memo.add(sb.toString()); break; case XSL : xslString.append("</" + name + ">"); break; case Item.ITEM : if (!groups.isEmpty()) { groups.trimToSize(); item.add(Item.GROUP, groups); } if (!zies.isEmpty()) { zies.trimToSize(); item.add(Item.ZIE, zies); } if (!vergs.isEmpty()) { vergs.trimToSize(); item.add(Item.VERGELIJK, vergs); } break; case XItem.XDISCDATE : item.add(XItem.XDISCDATE, DiscDate); break; case XItem.XDISCPLACE : item.add(XItem.XDISCPLACE, DiscPlace); break; case XItem.XTOPICMAP : item.add(XItem.XTOPICMAP, tm); break; case TMASSOC: tm.addAssocRL(rls); break; case TMASSOCRL: break; case Item.NAME : names.addElement(xname); break; case LANG : xname.addLANG(xlang); break; case DICT : if (!names.isEmpty()) { names.trimToSize(); item.add(XItem.XNAME, names); } if (!item.contains(Item.NAME)) { // get name from DICT Enumeration xnames = names.elements(); while (xnames.hasMoreElements() && !item.contains(Item.NAME)) { XNAME xname = (XNAME)(xnames.nextElement()); if (xname.getName("NL").length() > 0) { // System.out.println("Deducing name from DICT..."); item.add(Item.NAME, xname.getName("NL")); } } } if (!formulas.isEmpty()) { formulas.trimToSize(); item.add(XItem.XFORMULA, formulas); } if (!v.isEmpty()) { v.trimToSize(); item.add(XItem.XAFKORT, v); } if (!item.contains(Item.NAME)) { // get name from DICT Enumeration xnames = v.elements(); while (xnames.hasMoreElements() && !item.contains(Item.NAME)) { XNODE xname = (XNODE)(xnames.nextElement()); if (xname.getCDATA().length() > 0) { // System.out.println("Deducing name from DICT..."); item.add(Item.NAME, xname.getCDATA()); } } } if (!item.contains(Item.NAME)) { System.out.println("No suitable name detected (" + item.get(XItem.XCODE) + ")!"); // System.out.println(names.toString()); } break; case REFERENCE : if (!v.isEmpty()) { v.trimToSize(); item.add(Item.URL, v); } break; case Item.COMMENT : Vector commentlist; if (item.contains(Item.COMMENT)) { commentlist = (Vector)item.get(Item.COMMENT); } else { commentlist = new Vector(); } /** return platte tekst */ commentlist.addElement( memo ); /** vervang oude Vector met nieuwe */ item.add(Item.COMMENT,commentlist); break; case IMPORT : xslString.append("\n</xsl:stylesheet>"); // System.out.println(xslString.toString()); // and here should begin the hidious task of parsing the // xsl code String URL = "file://" + importFile; // System.out.println(URL); File in = new File(importFile); if (!in.exists()) { System.out.println("File (" + importFile + ") not found!"); System.exit(1); } OutputStream htmlStream = (OutputStream)new ByteArrayOutputStream(); try { Transformer transformer = tFactory.newTransformer( new javax.xml.transform.stream.StreamSource( new StringBufferInputStream(xslString.toString()) ) ); transformer.transform( new javax.xml.transform.stream.StreamSource("URL"), new javax.xml.transform.stream.StreamResult(htmlStream) ); memo.add(htmlStream.toString()); } catch (Exception e) { System.out.println("Error while parsing: " + e); } break; case Item.VOORBEELD : Vector vblist; if (item.contains(Item.VOORBEELD)) { vblist = (Vector)item.get(Item.VOORBEELD); } else { vblist = new Vector(); } /** return platte tekst */ vblist.addElement( memo ); /** vervang oude Vector met nieuwe */ ite... [truncated message content] |
|
From: Geert J. <gj...@us...> - 2002-09-03 19:40:57
|
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc/util
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc/util
Added Files:
Convert.java ConvertAble.java Enumerator.java Expander.java
GroupAdder.java ItemInfo.java IupacExtender.java Markup.java
Memo.java MergeItems.java Path.java RepositoryDefHandler.java
TopicExpander.java
Log Message:
--- NEW FILE: Convert.java ---
package com.egonw.woc.util;
public class Convert {
public static String charInString(String s, char one, char two) {
StringBuffer result = new StringBuffer();
for (int i = 0; i < s.length(); i++) {
if (s.charAt(i) == one) {
result.append(two);
} else {
result.append(one);
}
}
return result.toString();
}
public static String firstLetterUpperCase(String s) {
StringBuffer result = new StringBuffer();
if (s.length() > 0) {
if (Character.isLetter(s.charAt(0))) {
String firstLetter = new String((new Character(s.charAt(0))).toString());
result.append(firstLetter.toUpperCase());
} else
result.append(s.charAt(0));
for (int i = 1; i < s.length(); i++)
result.append(s.charAt(i));
}
return result.toString();
}
public static String firstUpperCase(String s) {
StringBuffer result = new StringBuffer();
s = new String(s.toLowerCase().trim());
result.append(getTillFirstLetter(s));
result.append(firstLetterUpperCase(stripTillFirstLetter(s)));
return result.toString();
}
public static String NAMELikeToANCHORLike(String s) {
StringBuffer result = new StringBuffer(); char c;
s = s.toLowerCase().trim();
for (int i=0; i < s.length(); i++) {
c = s.charAt(i);
if ( (int)c >= 97 && (int)c <= 122 ) {
result.append(c);
} else if ( (c == '1') || (c == '2') || (c == '3') ||
(c == '4') || (c == '5') || (c == '6') ||
(c == '7') || (c == '8') || (c == '9') ||
(c == '0') ) {
result.append(c);
} else if ( c == ' ' ) {
result.append('_');
} else if ( c == '-' ) {
result.append(c);
} else {};
}
return result.toString();
}
public static String GROUPLikeToANCHORLike(String s) {
return NAMELikeToANCHORLike(s);
}
public static String GROUPLikeToNAMELike(String s) {
//ofwel: maak van alle _ een spatie
StringBuffer result = new StringBuffer(); char c;
for (int i=0; i < s.length(); i++) {
c = s.charAt(i);
if ( c == '_' ) {
result.append(' ');
} else {
result.append(c);
};
}
return result.toString();
}
public static String getTillFirstLetter(String s) {
StringBuffer sb = new StringBuffer();
int i = 0;
while ((i<s.length()) && (!Character.isLetter(s.charAt(i)))) {
sb.append(s.charAt(i));
i++;
}
return sb.toString();
}
public static String stripTillFirstLetter(String s) {
StringBuffer sb = new StringBuffer();
int i = 0;
while ((i<s.length()) && (!Character.isLetter(s.charAt(i))))
i++;
while (i < s.length()) {
sb.append(s.charAt(i));
i++;
}
return sb.toString();
}
}
--- NEW FILE: ConvertAble.java ---
package com.egonw.woc.util;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.exception.*;
public interface ConvertAble {
void set(WoordTable wt);
void set(ReportFile rf);
WoordTable convert();
String getName();
}
--- NEW FILE: Enumerator.java ---
package com.egonw.woc.util;
import java.util.Vector;
import java.util.Enumeration;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.files.*;
import com.egonw.woc.exception.*;
import com.egonw.woc.wml.*;
public final class Enumerator implements ConvertAble {
private WoordTable wt;
private ReportFile rf;
public Enumerator() {};
public String getName() {
return "Enumerator";
}
public void set(WoordTable wt) {
this.wt = wt;
}
public void set(ReportFile rf) {
if (rf instanceof WocReportFile) this.rf = rf;
}
public WoordTable convert() {
WoordTable result = new WoordTable();
if (wt != null) {
Item i;
char letter = ' ';
int j = 1;
Enumeration values = wt.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
if (letter != ((String)i.get(Item.NAME)).toLowerCase().charAt(0)) {
letter = ((String)i.get(Item.NAME)).toLowerCase().charAt(0);
j = 1;
} else {
j++;
}
i.add(Item.NUMBER, i);
try {
result.add(i);
} catch (WocNotification wn) {
if (this.rf != null) {
((WocReportFile)rf).reportWocNotification(wn);
}
}
}
}
return result;
}
}
--- NEW FILE: Expander.java ---
package com.egonw.woc.util;
import java.util.Vector;
import java.util.Enumeration;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.files.*;
import com.egonw.woc.wml.*;
import com.egonw.woc.exception.*;
public final class Expander implements ConvertAble {
private WoordTable wt;
private ReportFile rf;
public Expander() {};
public String getName() {
return "Expander";
}
public void set(WoordTable wt) {
this.wt = wt;
}
public void set(ReportFile rf) {
if (rf instanceof WocReportFile) this.rf = rf;
}
public WoordTable convert() {
WoordTable result = new WoordTable();
if (wt != null) {
try { result.add(wt); } catch (WocNotification wn) {};
Item i;
XItem j;
Enumeration values = wt.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
/** expand IUPACNAME */
if (i.contains(Item.IUPACNAME)) {
j = new XItem();
j.add(XItem.XFILENAME, i.get(XItem.XFILENAME));
j.add(Item.NAME, (String)i.get(Item.IUPACNAME));
if (i.contains(Item.CHEMICAL)) {
j.add(Item.CHEMICAL, new String());
}
Vector zie = new Vector();
zie.addElement((String)i.get(Item.NAME));
j.add(Item.ZIE, zie);
j.add(XItem.XSEEONLY, Boolean.TRUE);
try {
result.add(j);
} catch (WocNotification wn) {
if (this.rf != null) {
((WocReportFile)rf).reportWocNotification(wn);
}
}
}
/** expand TRIVIALNAMEs */
if (i.contains(Item.TRIVIALNAME)) {
Vector trivnames = (Vector)i.get(Item.TRIVIALNAME);
Enumeration values_two = trivnames.elements();
while (values_two.hasMoreElements()) {
String trivialName = (String)values_two.nextElement();
j = new XItem();
j.add(XItem.XFILENAME, i.get(XItem.XFILENAME));
j.add(Item.NAME, trivialName);
/** nieuwe vector met over te nemen (otn) triviale namen **/
Enumeration otn_values = trivnames.elements();
Vector newTrivials = new Vector();
while (otn_values.hasMoreElements()) {
String waarde = (String)otn_values.nextElement();
if (!waarde.equals(trivialName) && (waarde.length() != 0))
newTrivials.addElement(waarde);
}
if (newTrivials.size() > 0 )
j.add(Item.TRIVIALNAME, newTrivials);
if (i.contains(Item.IUPACNAME))
j.add(Item.IUPACNAME, (String)i.get(Item.IUPACNAME));
Vector zie = new Vector();
zie.addElement((String)i.get(Item.NAME));
j.add(Item.ZIE, zie);
j.add(XItem.XSEEONLY, Boolean.TRUE);
try {
result.add(j);
} catch (WocNotification wn) {
if (this.rf != null) {
((WocReportFile)rf).reportWocNotification(wn);
}
}
}
}
/** expand ABBREVs */
if (i.contains(XItem.XAFKORT)) {
Vector trivnames = (Vector)i.get(XItem.XAFKORT);
Enumeration values_two = trivnames.elements();
while (values_two.hasMoreElements()) {
Object o = values_two.nextElement();
if (o instanceof String) {
System.out.println(i.get(Item.NAME) + " -> AFK: " +
o);
} else {
XNODE trivialName = (XNODE)o;
j = new XItem();
j.add(XItem.XFILENAME, i.get(XItem.XFILENAME));
j.add(Item.NAME, (String)trivialName.getCDATA());
XTYPE xt = new XTYPE();
xt.setType(XTYPE.ABBREV);
j.add(XItem.XTYPE, xt);
Memo m = new Memo();
Vector zie = new Vector();
zie.addElement((String)i.get(Item.NAME));
j.add(Item.ZIE, zie);
m.add("Afkorting van " + (String)i.get(Item.NAME) + ".");
Vector comments = new Vector();
comments.add(m);
j.add(Item.COMMENT, comments);
try {
result.add(j);
} catch (WocNotification wn) {
if (this.rf != null) {
((WocReportFile)rf).reportWocNotification(wn);
}
}
}
}
}
}
}
return result;
}
}
--- NEW FILE: GroupAdder.java ---
package com.egonw.woc.util;
import com.objectspace.jgl.*;
import com.objectspace.jgl.algorithms.*;
import com.objectspace.jgl.predicates.*;
import java.util.Vector;
import java.util.Enumeration;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.files.*;
import com.egonw.woc.predicate.*;
import com.egonw.woc.exception.*;
public final class GroupAdder implements ConvertAble {
private WoordTable wt;
private ReportFile rf;
public GroupAdder() {};
public String getName() {
return "Group Adder";
}
public void set(WoordTable wt) {
this.wt = wt;
}
public void set(ReportFile rf) {
if (rf instanceof WocReportFile) this.rf = rf;
}
public WoordTable convert() {
WoordTable result = wt;
if (this.wt != null) {
Enumeration groepen = extractGroups(wt);
while (groepen.hasMoreElements()) {
String groep = (String)groepen.nextElement();
try {
result.add(convertGroupItems(
returnGroupItems(wt, groep), groep)
);
} catch (WocNotification wn) {
if (this.rf != null) {
((WocReportFile)rf).reportWocNotification(wn);
}
}
}
}
return result;
}
public static Enumeration extractGroups(WoordTable wt) {
// bepaal alle groepen in de WOC
Enumeration values = wt.elements();
OrderedSet groepen = new OrderedSet( new LessString() );
while ( values.hasMoreElements() ) {
Item i = (Item)values.nextElement();
if (i.contains(Item.GROUP)) {
Enumeration groups = ((Vector)i.get(Item.GROUP)).elements();
while (groups.hasMoreElements()) {
String value = (String)groepen.add(groups.nextElement());
}
}
}
return groepen.elements();
}
public static WoordTable returnGroupItems(WoordTable wt, String group) {
// bepaal alle item die binnen een groep horen
WoordTable result = new WoordTable();
try {
UnaryPredicate predicate = new BindSecondPredicate(
new IsGroup(), new String(group) );
result.add((Container)Filtering.select(wt, predicate ));
} catch (WocNotification wn) {
System.out.println("Unreported WocNotification");
} finally { return result; }
}
public static Item convertGroupItems(WoordTable wt, String group) {
// maak een nieuwe groep van alle item
group = Convert.GROUPLikeToNAMELike(group);
XItem result = new XItem();
result.add(XItem.XFILENAME, group);
result.add(Item.NAME, group);
result.add(XItem.XGROUP, new String("yes"));
StringBuffer comment = new StringBuffer();
Enumeration values = wt.elements();
while ( values.hasMoreElements() ) {
Item i = (Item)values.nextElement();
comment.append(i.get(Item.NAME));
if (values.hasMoreElements()) comment.append(", ");
}
Vector commentlist = new Vector();
Memo m = new Memo();
m.add("<P>Voorbeelden van " + group + " zijn: ");
m.add(comment.toString());
m.add("</P>");
commentlist.addElement( m );
result.add(Item.COMMENT,commentlist);
return result;
}
}
--- NEW FILE: ItemInfo.java ---
package com.egonw.woc.util;
import java.util.*;
import com.egonw.woc.*;
import com.egonw.woc.wml.*;
public class ItemInfo {
public static Vector listKeywords(Item i) {
/* returns a Vector of Strings */
Vector v = new Vector();
if (i.contains(XItem.XNAME)) {
Enumeration names = ((Vector)i.get(XItem.XNAME)).elements();
while (names.hasMoreElements()) {
Enumeration langs = ((XNAME)names.nextElement()).elements();
while (langs.hasMoreElements()) {
v.addElement(((XLANG)langs.nextElement()).getValue());
}
}
}
return v;
}
public static boolean containsLongInfo(Item i) {
return (containsModels(i) || i.contains(Item.VERVOEGINGEN) ||
i.contains(Item.LIDWOORD) || i.contains(Item.CASNR) ||
i.contains(XItem.XGROUP) || i.contains(XItem.XGERMAN) ||
i.contains(Item.ENGLISH));
}
public static boolean containsModels(Item i) {
return (i.contains(Item.MOL) || i.contains(Item.PDB) ||
i.contains(Item.XYZFILE));
}
public static boolean containsFysicalProps(Item i) {
return (i.contains(Item.MASS) || i.contains(Item.RHO) ||
i.contains(Item.BOILINGPOINT) ||
i.contains(Item.MELTINGPOINT) ||
i.contains(Item.DIPOOL));
}
public static boolean hasMoreThanOneComment(Item i) {
boolean result = false;
if (i.contains(Item.COMMENT)) {
result = ( ((Vector)i.get(Item.COMMENT)).size() > 1 );
}
return result;
}
public static boolean hasMoreThanOneVoorbeeld(Item i) {
boolean result = false;
if (i.contains(Item.VOORBEELD)) {
result = ( ((Vector)i.get(Item.VOORBEELD)).size() > 1 );
}
return result;
}
}
--- NEW FILE: IupacExtender.java ---
package com.egonw.woc.util;
import com.objectspace.jgl.*;
import com.objectspace.jgl.predicates.*;
import com.objectspace.jgl.algorithms.*;
import java.util.*;
import java.io.Serializable;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.predicate.*;
import com.egonw.woc.exception.*;
import com.egonw.woc.files.*;
public final class IupacExtender implements ConvertAble {
private WoordTable wt;
private ReportFile rf;
public IupacExtender () {};
public String getName() {
return "IupacExtend";
}
public void set(WoordTable wt) {
this.wt = wt;
}
public void set(ReportFile rf) {
if (rf instanceof WocReportFile) this.rf = rf;
}
public WoordTable convert() {
WoordTable result = new WoordTable();
if (wt != null) {
Enumeration v = wt.elements();
while ( v.hasMoreElements() ) {
Item item = (Item)v.nextElement();
try {
result.add(extendIupacNamespace(item));
} catch (WocNotification wn) {
System.out.println("Error encountered in item : " + item.toString());
}
}
}
return result;
}
private Item extendIupacNamespace(Item i) {
if (i.contains(Item.COMMENT)) {
Vector result = new Vector();
Enumeration comments = ((Vector)i.get(Item.COMMENT)).elements();
while ( comments.hasMoreElements() ) {
result.addElement(this.comment((Memo)comments.nextElement(),
(String)i.get(Item.NAME)));
}
i.add(Item.COMMENT, result);
}
if (i.contains(Item.VOORBEELD)) {
Vector result = new Vector();
Enumeration comments = ((Vector)i.get(Item.VOORBEELD)).elements();
while ( comments.hasMoreElements() ) {
result.addElement(this.comment((Memo)comments.nextElement(),
(String)i.get(Item.NAME)));
}
i.add(Item.COMMENT, result);
}
return i;
}
private Memo comment(Memo m, String name) {
Memo r = new Memo();
Enumeration values = m.elements();
while ( values.hasMoreElements() ) {
String regel = (String)values.nextElement();
if (regel.indexOf("<iupac:def>") != -1) {
regel = replace(regel, "iupac:def", "i");
}
if (regel.indexOf("</iupac:def>") != -1) {
regel = replace(regel, "iupac:def", "i");
}
if (regel.indexOf("<iupac:regel>") != -1) {
regel = replace(regel, "iupac:regel", "a href=\"\"");
}
if (regel.indexOf("</iupac:regel>") != -1) {
regel = replace(regel, "iupac:regel", "a");
}
if (regel.indexOf("<iupac:term>") != -1) {
regel = replace(regel, "iupac:term", "i><b");
}
if (regel.indexOf("</iupac:term>") != -1) {
regel = replace(regel, "iupac:term", "b></i");
}
r.add(regel);
}
return r;
}
private String replace(String in, String old, String with) {
StringBuffer sb = new StringBuffer(in);
int index = in.indexOf(old);
if (index != -1) {
sb.replace(index, index + old.length(), with);
}
return sb.toString();
}
}
--- NEW FILE: Markup.java ---
package com.egonw.woc.util;
import com.objectspace.jgl.*;
import com.objectspace.jgl.predicates.*;
import com.objectspace.jgl.algorithms.*;
import java.util.*;
import java.io.Serializable;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.predicate.*;
import com.egonw.woc.exception.*;
import com.egonw.woc.files.*;
public final class Markup implements ConvertAble {
private WoordTable wt;
private ReportFile rf;
public Markup () {};
public String getName() {
return "MarkUp";
}
public void set(WoordTable wt) {
this.wt = wt;
}
public void set(ReportFile rf) {
if (rf instanceof WocReportFile) this.rf = rf;
}
public WoordTable convert() {
WoordTable result = new WoordTable();
if (wt != null) {
Enumeration v = wt.elements();
while ( v.hasMoreElements() ) {
try {
result.add(this.commentsInItem((Item)v.nextElement()));
} catch (WocNotification wn) {
if (this.rf != null) {
((WocReportFile)rf).reportWocNotification(wn);
}
}
}
}
return result;
}
public Item commentsInItem(Item i) {
if (i.contains(Item.COMMENT)) {
Vector result = new Vector();
Enumeration comments = ((Vector)i.get(Item.COMMENT)).elements();
while ( comments.hasMoreElements() ) {
result.addElement(this.comment((Memo)comments.nextElement(),
(String)i.get(Item.NAME)));
}
i.add(Item.COMMENT, result);
}
return i;
}
public Memo comment(Memo m, String name) {
Memo r = new Memo();
Enumeration values = m.elements();
while ( values.hasMoreElements() ) {
StringBuffer tot = new StringBuffer();
StringTokenizer st = new StringTokenizer(
(String)values.nextElement(),
"\n\t\r.,;:?!'` \"",true);
while (st.hasMoreTokens()) {
String token = st.nextToken();
UnaryPredicate up = new BindSecondPredicate( new IsSource(),
token );
System.out.println(token);
if (Finding.some((Container)this.wt, up)) {
String anchor = Convert.NAMELikeToANCHORLike(token);
tot.append("<a href=" + HtmlWriteFile.QUOT + "../letters/" +
anchor.substring(0,1) + ".html#" + anchor +
HtmlWriteFile.QUOT + ">" + token + "</a>");
} else {
tot.append(token);
}
}
r.add(tot.toString());
}
return r;
}
}
--- NEW FILE: Memo.java ---
package com.egonw.woc.util;
import java.util.Vector;
public class Memo extends Vector{
public Memo() {
super(5,3);
}
public void add(String s) {
super.addElement(s);
}
public void empty() {
super.removeAllElements();
}
public int count() {
return super.size();
}
public String getLine(int i) {
return (String)super.elementAt(i-1);
}
}
--- NEW FILE: MergeItems.java ---
package com.egonw.woc.util;
import java.util.Vector;
import java.util.Enumeration;
import com.egonw.woc.*;
import com.egonw.woc.files.*;
import com.egonw.woc.exception.*;
public final class MergeItems {
public static Item comment(Item i, Item j) {
Item result = i;
return result;
}
}
--- NEW FILE: Path.java ---
package com.egonw.woc.util;
import java.io.*;
import java.util.*;
import com.egonw.woc.exception.*;
import org.xml.sax.*;
import org.xml.sax.helpers.*;
/**
* Class that defines the path to certain files.
*
* @author Egon Willighagen
* @version 1.1, 04/09/2000
*/
public class Path {
private Hashtable defs;
private String name;
public Path(String repository) {
this(repository, "file:///vol/www/woc/bin/repository_def.xml");
}
public Path(String repository, String url) {
defs = new Hashtable();
name = repository;
// parse the repository document
try {
String parserName = "org.apache.xerces.parsers.SAXParser";
XMLReader parser = (XMLReader)Class.forName(parserName).newInstance();
ContentHandler handler = new RepositoryDefHandler(repository);
parser.setContentHandler(handler);
parser.setFeature("http://xml.org/sax/features/validation", false);
parser.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd",
false);
parser.parse(url);
if (((RepositoryDefHandler)handler).foundRepository()) {
defs = ((RepositoryDefHandler)handler).returnDefs();
} else {
throw new WocException("Repository (" + repository + ") not found!");
}
} catch (Exception e) {
System.err.println("Error: " + e);
System.exit(1);
}
}
public String getName() { return this.name; };
public String getPhysicalRoot() { return (String)defs.get("PhysicalRoot"); };
public String getDataSubDir() { return (String)defs.get("DataSubDir"); };
public String getWMLSubDir() { return (String)defs.get("WMLSubDir"); };
public String getHtmlRoot() { return (String)defs.get("HtmlRoot"); };
public String getCgiBinRoot() { return (String)defs.get("CgiBinRoot"); };
public String getLetterFileSubDir() { return (String)defs.get("LetterFileSubDir"); };
public String getItemFileSubDir() { return (String)defs.get("ItemFileSubDir"); };
public String getGroupFileSubDir() { return (String)defs.get("GroupFileSubDir"); };
public String getIndexFileSubDir() { return (String)defs.get("IndexFileSubDir"); };
public String getPictureSubDir() { return (String)defs.get("PictureSubDir"); };
public String getCSSSubDir() { return (String)defs.get("CSSSubDir"); };
public String getLocatieSubDir() { return (String)defs.get("LocatieSubDir"); };
public String getJavascriptSubDir() { return (String)defs.get("JavascriptSubDir"); };
public String getJavaSubDir() { return (String)defs.get("JavaSubDir"); };
public String getModelsSubDir() { return (String)defs.get("ModelsSubDir"); };
public String getDADMLSubDir() { return (String)defs.get("DADMLSubDir"); };
public String getMolSubDir() { return (String)defs.get("MolSubDir"); };
public String getPdbSubDir() { return (String)defs.get("PdbSubDir"); };
public String getXyzSubDir() { return (String)defs.get("XyzSubDir"); };
public String getCmlSubDir() { return (String)defs.get("CmlSubDir"); };
public String getPhysPropSubDir() { return (String)defs.get("PhysPropSubDir"); };
public String getGifSubDir() { return (String)defs.get("GifSubDir"); };
public String getBronnenFile() { return (String)defs.get("BronnenFile"); };
public String getDatabasesFile() { return (String)defs.get("DatabasesFile"); };
}
--- NEW FILE: RepositoryDefHandler.java ---
package com.egonw.woc.util;
import java.util.*;
import java.io.*;
import org.openscience.dadml.*;
import com.egonw.woc.*;
import com.egonw.woc.exception.*;
import com.egonw.woc.wml.*;
import com.egonw.woc.util.*;
import org.xml.sax.*;
import org.xml.sax.helpers.*;
public class RepositoryDefHandler extends DefaultHandler {
private final int UNKNOWN = -1;
private final int GENERAL = 1;
private final int SPECIFIC = 2;
private final int PATH = 3;
private int CurrentElement;
private boolean general;
private String current_repository;
private String wanted_repository;
private String current_path_name;
private String current_path;
private Hashtable defs;
private boolean found_repository;
public RepositoryDefHandler (String repository) {
this.wanted_repository = repository;
this.defs = new Hashtable();
};
public boolean foundRepository() {
return found_repository;
}
public Hashtable returnDefs() {
return defs;
}
public void startDocument () {
general = false;
CurrentElement = UNKNOWN;
current_repository = "";
found_repository = false;
}
public void endDocument () {
}
public void startElement (String URI, String name, String qname, Attributes atts) {
setCurrentElement(name);
switch (CurrentElement) {
case GENERAL :
general = true;
break;
case PATH :
for (int i = 0; i < atts.getLength(); i++) {
if (atts.getQName(i).equals("id")) {
current_path_name = atts.getValue(i);
}
}
break;
case SPECIFIC :
for (int i = 0; i < atts.getLength(); i++) {
if (atts.getQName(i).equals("repository")) {
current_repository = atts.getValue(i);
if (current_repository.equals(wanted_repository)) {
found_repository = true;
}
}
}
break;
}
}
public void endElement(String URI, String name, String qname) {
setCurrentElement(name);
switch (CurrentElement) {
case GENERAL :
general = false;
break;
case PATH :
if (current_repository.equals(wanted_repository) || general) {
defs.put(current_path_name, current_path);
// System.out.println("Added: " + current_path_name + " -> " +
// current_path);
} else {
//System.out.println("Not added: " + current_path_name + " -> " +
// current_path);
}
current_path_name = "";
current_path = "";
break;
case SPECIFIC :
current_repository = "";
break;
}
}
public void characters (char ch[], int start, int length) {
switch (CurrentElement) {
case PATH :
current_path = toString(ch, start, length).trim();
break;
}
}
private void setCurrentElement(String name) {
if (name.equals("general")) {
CurrentElement = GENERAL;
} else if (name.equals("specific")) {
CurrentElement = SPECIFIC;
} else if (name.equals("path")) {
CurrentElement = PATH;
} else {
CurrentElement = UNKNOWN;
};
}
private String toString(char ch[], int start, int length) {
StringBuffer x = new StringBuffer();
for (int i =0; i < length; i++)
x.append(ch[start+i]);
return x.toString();
}
}
--- NEW FILE: TopicExpander.java ---
package com.egonw.woc.util;
import java.util.Vector;
import java.util.Enumeration;
import com.egonw.util.*;
import com.egonw.woc.*;
import com.egonw.woc.files.*;
import com.egonw.woc.wml.*;
import com.egonw.woc.exception.*;
public final class TopicExpander implements ConvertAble {
private WoordTable wt;
private ReportFile rf;
public TopicExpander() {};
public String getName() {
return "Topic Map Expander";
}
public void set(WoordTable wt) {
this.wt = wt;
}
public void set(ReportFile rf) {
if (rf instanceof WocReportFile) this.rf = rf;
}
public WoordTable convert() {
WoordTable result = new WoordTable();
if (wt != null) {
try { result.add(wt); } catch (WocNotification wn) {};
Item i;
XItem j;
TopicMap tm;
Enumeration values = wt.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
if (i.contains(XItem.XTOPICMAP)) {
tm = (TopicMap)i.get(XItem.XTOPICMAP);
Enumeration assocs = tm.getAssocs();
while (assocs.hasMoreElements()) {
TMAssoc assoc = (TMAssoc)assocs.nextElement();
if (assoc.getName().equals("at-heeft-als-zuurrest")) {
try {
//System.out.println("Nieuwe zuurrest");
String zuurrest = (String)(assoc.getRLs()).nextElement();
//System.out.println(zuurrest);
j = new XItem();
j.add(XItem.XFILENAME, i.get(XItem.XFILENAME));
j.add(Item.NAME, zuurrest);
Vector commentlist = new Vector();
Memo m = new Memo();
m.add("Zuurrest van " + (String)i.get(Item.NAME) + ".");
commentlist.addElement(m);
j.add(Item.COMMENT, commentlist);
Vector zie = new Vector();
zie.addElement((String)i.get(Item.NAME));
j.add(Item.ZIE, zie);
try {
result.add(j);
} catch (WocException e) {
// item is al aanwezig
System.out.println("zuurrest van " +(String)i.get(Item.NAME));
}
} catch (Exception e) {
//System.out.println("oops... foutje");
};
}
}
}
}
}
return result;
}
}
|
|
From: Geert J. <gj...@us...> - 2002-09-03 19:40:57
|
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc/wml
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc/wml
Added Files:
CMLHandler.java TMAssoc.java TopicMap.java XLANG.java
XNAME.java XNODE.java
Log Message:
--- NEW FILE: CMLHandler.java ---
package com.egonw.woc.wml;
import java.util.*;
import org.openscience.dadml.*;
import com.egonw.woc.*;
import com.egonw.woc.exception.*;
import com.egonw.woc.wml.*;
import com.egonw.woc.util.*;
import org.xml.sax.*;
import org.xml.sax.helpers.*;
public class CMLHandler extends DefaultHandler {
private final int UNKNOWN = -1;
private final int ANY = -2;
private final int STRING = -3;
private final int FLOAT = -4;
private final int MOLECULE = -5;
private int CurrentElement;
private String TITLE = "";
private String value = "";
XItem item;
public CMLHandler () {
item = new XItem();
};
public XItem updateItem (XItem i) {
if (item.contains(Item.BRUTO))
i.add(Item.BRUTO, (Bruto)item.get(Item.BRUTO));
if (item.contains(Item.MASS))
i.add(Item.MASS, (String)item.get(Item.MASS));
if (item.contains(Item.BOILINGPOINT))
i.add(Item.BOILINGPOINT, (String)item.get(Item.BOILINGPOINT));
if (item.contains(Item.MELTINGPOINT))
i.add(Item.MELTINGPOINT, (String)item.get(Item.MELTINGPOINT));
if (item.contains(XItem.XFLASH))
i.add(XItem.XFLASH, (String)item.get(XItem.XFLASH));
if (item.contains(Item.RHO))
i.add(Item.RHO, (String)item.get(Item.RHO));
if (item.contains(Item.DIPOOL))
i.add(Item.DIPOOL, (String)item.get(Item.DIPOOL));
if (item.contains(XItem.XPKA))
i.add(XItem.XPKA, (String)item.get(XItem.XPKA));
if (item.contains(XItem.XPKB))
i.add(XItem.XPKB, (String)item.get(XItem.XPKB));
return i;
}
public void startDocument () {
item = new XItem();
}
public void endDocument () {}
public void startElement (String name, AttributeList atts) {
setCurrentElement(name);
switch (CurrentElement) {
case ANY :
break;
case FLOAT :
for (int i = 0; i < atts.getLength(); i++) {
if (atts.getName(i).equals("title"))
TITLE = atts.getValue(i);
}
break;
case STRING :
for (int i = 0; i < atts.getLength(); i++) {
if (atts.getName(i).equals("title"))
TITLE = atts.getValue(i);
}
break;
}
}
public void endElement (String name) {
setCurrentElement(name);
switch (CurrentElement) {
case ANY :
break;
case STRING :
if (TITLE.equals("Stoichiometry")) {
item.add(Item.BRUTO, new Bruto(value));
}
TITLE = "";
break;
case FLOAT :
if (TITLE.equals("Density")) {
item.add(Item.DIPOOL, value);
} else if (TITLE.equals("MeltingPoint")) {
item.add(Item.MELTINGPOINT, value);
} else if (TITLE.equals("BoilingPoint")) {
item.add(Item.BOILINGPOINT, value);
} else if (TITLE.equals("FlashPoint")) {
item.add(XItem.XFLASH, value);
} else if (TITLE.equals("Density")) {
item.add(Item.RHO, value);
} else if (TITLE.equals("pKa")) {
item.add(XItem.XPKA, value);
} else if (TITLE.equals("pKb")) {
item.add(XItem.XPKB, value);
}
TITLE = "";
break;
}
}
public void characters (char ch[], int start, int length) {
switch (CurrentElement) {
case ANY :
break;
case FLOAT :
if (TITLE.length() > 0)
value = toString(ch, start, length).trim();
break;
case STRING :
if (TITLE.length() > 0)
value = toString(ch, start, length).trim();
break;
}
}
private void setCurrentElement(String name) {
if (name.equals("molecule")) {
CurrentElement = MOLECULE;
} else if (name.equals("float")) {
CurrentElement = FLOAT;
} else if (name.equals("string")) {
CurrentElement = STRING;
} else {
CurrentElement = UNKNOWN;
};
}
private String toString(char ch[], int start, int length) {
StringBuffer x = new StringBuffer();
for (int i =0; i < length; i++)
x.append(ch[start+i]);
return x.toString();
}
}
--- NEW FILE: TMAssoc.java ---
package com.egonw.woc.wml;
import java.util.*;
public class TMAssoc {
private Vector rls;
private String name;
public TMAssoc () {
rls = new Vector(2,1);
}
public void setName(String name) {
this.name = name;
}
public String getName() {
return this.name;
}
public void addRL(String rl) {
rls.addElement(rl);
}
public Enumeration getRLs() {
return rls.elements();
}
}
--- NEW FILE: TopicMap.java ---
package com.egonw.woc.wml;
import java.util.*;
public class TopicMap {
private Vector assocs;
private String currentAssoc;
public TopicMap () {
assocs = new Vector(3,1);
}
public void addAssocRL(TMAssoc assoc) {
assocs.addElement(assoc);
}
public Enumeration getAssocs() {
return assocs.elements();
}
}
--- NEW FILE: XLANG.java ---
package com.egonw.woc.wml;
import java.util.*;
public class XLANG {
private String id;
private String lw;
private String value;
public XLANG() {
id = "";
value = "";
}
public String getID() {
return this.id;
}
public void setID(String c) {
this.id = c;
}
public String getLIDWOORD() {
return this.lw;
}
public void setLIDWOORD(String c) {
this.lw = c;
}
public String getValue() {
return this.value;
}
public void setValue(String s) {
this.value = s;
}
}
--- NEW FILE: XNAME.java ---
package com.egonw.woc.wml;
import java.util.*;
public class XNAME {
private String klasse;
private Vector langs;
public XNAME() {
klasse = "";
langs = new Vector();
}
public String getCLASS() {
return this.klasse;
}
public void setCLASS(String c) {
this.klasse = c;
}
public void addLANG(XLANG l) {
langs.addElement(l);
}
public Enumeration elements() {
return langs.elements();
}
public String getName(String lang) {
String r = "";
Enumeration names = elements();
while (names.hasMoreElements()) {
XLANG l = (XLANG)(names.nextElement());
if (l.getID().equals(lang)) {
r = l.getValue();
}
}
return r;
}
}
--- NEW FILE: XNODE.java ---
package com.egonw.woc.wml;
import java.util.*;
public class XNODE {
private String cdata;
private Hashtable atts;
public XNODE() {
cdata = "";
atts = new Hashtable();
}
public boolean containsATT(String s) {
return atts.containsKey(s);
}
public String getATT(String s) {
return (String)atts.get(s);
}
public void setATT(String s, String t) {
atts.put(s,t);
}
public void setCDATA(String s) {
cdata = s;
}
public String getCDATA() {
return cdata;
}
public String toString() {
return "XNODE(" + cdata + "): " + atts.toString();
}
}
|
|
From: Geert J. <gj...@us...> - 2002-09-03 19:40:57
|
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc/tools In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc/tools Added Files: GroupFiles.java MaakLosseItems.java SimpleAddItem.java Woord.java Log Message: --- NEW FILE: GroupFiles.java --- package com.egonw.woc.tools; import com.objectspace.jgl.*; import com.objectspace.jgl.algorithms.*; import com.objectspace.jgl.predicates.*; import java.io.*; import java.util.*; import com.egonw.woc.*; import com.egonw.woc.files.*; import com.egonw.woc.util.*; import com.egonw.woc.predicate.*; import com.egonw.woc.exception.*; class GroupFiles { private static String title = "WOC.GroupFiles"; private static String version = "1.3"; private static String date = "2002-01-27"; private static Path repository; public static void main(String[] args) { String reposdeffile = "file:///vol/www/woc/bin/repository_def.xml"; String repos = "woc"; System.out.println(title + " v." + version + " (" + date + ")"); int length = args.length; if (length > 0) { System.out.println("Parsing arguments..."); for (int i = 0; i < length; i++) { if (args[i].equals("-r") && ((i+1) < length)) { repos = args[i+1]; System.out.println(" repository: " + args[i+1]); i++; } else if (args[i].equals("-R") && ((i+1) < length)) { reposdeffile = args[i+1]; System.out.println(" reposdeffile: " + args[i+1]); i++; } else { System.out.println("Unknown option: " + args[i]); System.exit(1); } } } // setting default repository String url = "file:///" + reposdeffile; repository = new Path("woc", url); WocEngine we = new WocEngine(repository); we.setWoordTable(new WoordTable()); try { we.setWocReportFile(new WocReportFile("WMLreport.txt")); } catch (IOException e) { System.out.println(e); } String readfile = "woclist.xml"; System.out.println("Reading " + readfile + "..."); WocListReadFile rf = new WocListReadFile(repository, readfile); we.setReadFile((FileReadAble)rf); we.read(); System.out.println("Expanding items..."); we.setConvertAble(new Expander()); we.convert(); System.out.println("Adding group items..."); we.setConvertAble(new GroupAdder()); we.convert(); System.out.println("Marking up items..."); we.setConvertAble(new Markup()); //we.convert(); System.out.print("Writing data..."); Enumeration groepen = GroupAdder.extractGroups( we.getWT() ); while (groepen.hasMoreElements()) { String groep = (String)groepen.nextElement(); UnaryPredicate predicate = new BindSecondPredicate( new IsGroup(), new String(groep) ); we.setFilterPredicate(predicate); try { ItemWriteFile iwf = new ItemWriteFile(repository, repository.getPhysicalRoot() + repository.getGroupFileSubDir() + Convert.GROUPLikeToANCHORLike(groep) + ".html"); we.setWriteFile((FileWriteAble)iwf); we.write(); iwf.close(); } catch (IOException e) { System.out.println(e); } } } } --- NEW FILE: MaakLosseItems.java --- package com.egonw.woc.tools; import com.objectspace.jgl.*; import com.objectspace.jgl.algorithms.*; import com.objectspace.jgl.predicates.*; import java.io.*; import java.util.*; import com.egonw.woc.*; import com.egonw.woc.util.*; import com.egonw.woc.files.*; import com.egonw.woc.predicate.*; import com.egonw.woc.exception.*; import org.openscience.dadml.*; import org.openscience.dadml.filereaders.*; import org.openscience.dadml.tools.*; class MaakLosseItems { private static final String pClass = "org.apache.xerces.parsers.SAXParser"; private static String title = "WOC.MaakLosseItems"; private static String version = "1.5.0"; private static String date = "2002-01-27"; private static Path repository; public static void main(String[] args) { String reposdeffile = "file:///vol/www/woc/bin/repository_def.xml"; String repos = "woc"; System.out.println(title + " v." + version + " (" + date + ")"); int length = args.length; if (length > 0) { System.out.println("Parsing arguments..."); for (int i = 0; i < length; i++) { if ("-r".equals(args[i]) && ((i+1) < length)) { repos = args[i+1]; System.out.println(" repository: " + args[i+1]); i++; } else if ("-R".equals(args[i]) && ((i+1) < length)) { reposdeffile = args[i+1]; System.out.println(" reposdeffile: " + args[i+1]); i++; } else { System.out.println("Unknown option: " + args[i]); System.exit(1); } } } // setting default repository String url = "file://" + reposdeffile; repository = new Path(repos, url); WocEngine we = new WocEngine(repository); we.setWoordTable(new WoordTable()); try { we.setWocReportFile(new WocReportFile("WMLreport.txt")); } catch (IOException e) { System.out.println(e); } String readfile = "woclist.xml"; System.out.println("Reading " + readfile + "..."); WocListReadFile rf = new WocListReadFile(repository, readfile); we.setReadFile((FileReadAble)rf); we.read(); System.out.println("Downloading DADML database definitions..."); DBDEFLIST dbdeflist = new DBDEFLIST(); DBLIST dblist = new DBLIST(); String superXML = "http://www.sci.kun.nl/woc/super.xml"; try { // System.err.println("Downloading: " + superXML); dblist = DBLISTFileReader.read(superXML, pClass); } catch (Exception supererror) { System.err.println(supererror.toString()); return; } Enumeration dbases = dblist.databases(); while (dbases.hasMoreElements()) { DATABASE db = (DATABASE)dbases.nextElement(); String dburl = db.getURL()+db.getDefinition(); DBDEF dbdef = new DBDEF(); try { // System.err.println("Downloading: " + dburl); dbdef = DBDEFFileReader.read(dburl, pClass); dbdeflist.addDBDEF(dbdef); } catch (Exception deferror) { System.err.println(deferror.toString()); return; } } //System.out.println("Expanding items..."); //we.setConvertAble(new Expander()); //we.convert(); //we.setConvertAble(new TopicExpander()); //we.convert(); System.out.println("Adding group items..."); we.setConvertAble(new GroupAdder()); we.convert(); //System.out.println("Marking up items..."); //we.setConvertAble(new Markup()); //we.convert(); System.out.println("Writing data..."); Enumeration values = we.getWTElements(); while (values.hasMoreElements()) { Item i = (Item)values.nextElement(); we.setFilterPredicate( new BindSecondPredicate( new IsName(), (String)i.get(Item.NAME) ) ); try { System.out.println(" " + (String)i.get(Item.NAME) + " -> " + (String)i.get(XItem.XFILENAME)); ItemWriteFile iwf = new ItemWriteFile(repository, repository.getPhysicalRoot() + repository.getItemFileSubDir() + (String)i.get(XItem.XFILENAME) + ".shtml", ItemFile.LONG, dbdeflist); we.setWriteFile((FileWriteAble)iwf); we.write(); iwf.close(); } catch (IOException e) { System.out.println(e); }; }; } } --- NEW FILE: SimpleAddItem.java --- package com.egonw.woc.tools; import com.objectspace.jgl.*; import com.objectspace.jgl.algorithms.*; import com.objectspace.jgl.predicates.*; import java.io.*; import java.util.*; import com.egonw.woc.*; import com.egonw.woc.files.*; import com.egonw.woc.util.*; import com.egonw.woc.predicate.*; import com.egonw.woc.exception.*; import org.openscience.dadml.*; import org.openscience.dadml.filereaders.*; import org.openscience.dadml.tools.*; class SimpleAddItem { private static final String pClass = "org.apache.xerces.parsers.SAXParser"; private static String title = "WOC.SimpleAddItem"; private static String version = "1.4"; private static String date = "23-02-2001"; private static Path repository; private static String module = ""; public static void main(String[] args) { System.out.println(title + " v." + version + " (" + date + ")"); int length = args.length; String reposdeffile = "file:///vol/www/woc/bin/repository_def.xml"; String repos = "woc"; if (length > 0) { String f = ""; if (length > 1) { System.out.println("Parsing arguments..."); for (int i = 0; i < length; i++) { if (args[i].equals("-r") && ((i+1) < length)) { i++; System.out.println(" repository: " + args[i]); repos = args[i]; } else if (args[i].equals("-R") && ((i+1) < length)) { i++; reposdeffile = args[i]; System.out.println(" reposdeffile: " + reposdeffile); } else if (args[i].equals("-m") && ((i+1) < length)) { i++; module = args[i]; System.out.println(" module: " + args[i]); } } // file is considered the last argument f = args[length-1]; } else { f = args[0]; } // setting default repository String url = "file://" + reposdeffile; repository = new Path(repos, url); WocEngine we = new WocEngine(repository); we.setWoordTable(new WoordTable()); try { we.setWocReportFile(new WocReportFile("WMLreport.txt")); } catch (IOException e) { System.out.println(e); } System.out.println("Reading data..."); if (!(f.endsWith(".xml"))) { f = f + ".xml"; } WMLReadFile rf = new WMLReadFile(repository, f); we.setReadFile((FileReadAble)rf); we.read(); System.out.println("Downloading DADML database definitions..."); DBDEFLIST dbdeflist = new DBDEFLIST(); DBLIST dblist = new DBLIST(); String superXML = "http://www.sci.kun.nl/woc/super.xml"; try { System.err.println("Downloading: " + superXML); dblist = DBLISTFileReader.read(superXML, pClass); } catch (Exception supererror) { System.err.println(supererror.toString()); return; } Enumeration dbases = dblist.databases(); while (dbases.hasMoreElements()) { DATABASE db = (DATABASE)dbases.nextElement(); String dburl = db.getURL()+db.getDefinition(); DBDEF dbdef = new DBDEF(); try { System.err.println("Downloading: " + dburl); dbdef = DBDEFFileReader.read(dburl, pClass); dbdeflist.addDBDEF(dbdef); } catch (Exception deferror) { System.err.println(deferror.toString()); return; } } System.out.println("Expanding item..."); we.setConvertAble(new Expander()); we.convert(); // System.out.println("Marking up items..."); // if (module.length() > 0) { // try { // Class c = Woord.class.getClassLoader().loadClass("com.egonw.woc.util." + module); // we.setConvertAble((ConvertAble)c.newInstance()); // we.convert(); // } catch (ClassCastException e) { // System.out.println("Object " + module + " is not a module!"); // } catch (ClassNotFoundException e) { // System.out.println("Module " + module + " not found!"); // } catch (Exception e) { // System.out.println("Error: " + e); // } // } System.out.print("Writing data..."); Enumeration values = we.getWTElements(); while (values.hasMoreElements()) { Item i = (Item)values.nextElement(); System.out.println("Processing: " +(String)i.get(Item.NAME)); we.setFilterPredicate( new BindSecondPredicate( new IsName(), (String)i.get(Item.NAME) ) ); try { String filename = repository.getPhysicalRoot() + repository.getItemFileSubDir() + (String)i.get(Item.ANCHOR) + ".shtml"; System.out.println("Filename: " + filename); ItemWriteFile iwf = new ItemWriteFile(repository, filename, ItemFile.LONG, dbdeflist); we.setWriteFile((FileWriteAble)iwf); we.write(); iwf.close(); } catch (IOException e) { System.out.println(e); }; }; System.out.println(); } else { System.out.println("syntax: java SimpleAddItem [-r repository] <item.xml>"); } } } --- NEW FILE: Woord.java --- package com.egonw.woc.tools; import com.objectspace.jgl.*; import com.objectspace.jgl.algorithms.*; import com.objectspace.jgl.predicates.*; import java.io.*; import java.util.*; import com.egonw.woc.*; import com.egonw.woc.files.*; import com.egonw.woc.util.*; import com.egonw.woc.predicate.*; import com.egonw.woc.exception.*; class Woord { private static String title = "WOC.Woord"; private static String version = "1.5.0"; private static String date = "2002-01-27"; private static String path = "woc"; private static Path repository; private static String module = ""; public static void main(String[] args) { String reposdeffile = "file:///vol/www/woc/bin/repository_def.xml"; String repos = "woc"; System.out.println(title + " v." + version + " (" + date + ")"); int length = args.length; if (length > 0) { System.out.println("Parsing arguments..."); for (int i = 0; i < length; i++) { if (args[i].equals("-r") && ((i+1) < length)) { i++; path = args[i]; System.out.println(" repository: " + args[i]); } else if ("-R".equals(args[i]) && ((i+1) < length)) { reposdeffile = args[i+1]; System.out.println(" reposdeffile: " + args[i+1]); i++; } else { System.out.println("Unknown option: " + args[i]); System.exit(1); } } } // setting default repository String url = "file://" + reposdeffile; repository = new Path("woc", url); WocEngine we = new WocEngine(repository); we.setWoordTable(new WoordTable()); try { we.setWocReportFile(new WocReportFile("WMLreport.txt")); } catch (IOException e) { System.out.println(e); } String readfile = "woclist.xml"; System.out.println("Reading " + readfile + "..."); WocListReadFile rf = new WocListReadFile(repository, readfile); we.setReadFile((FileReadAble)rf); we.read(); System.out.println("Expanding items..."); we.setConvertAble(new Expander()); we.convert(); we.setConvertAble(new TopicExpander()); we.convert(); System.out.println("Adding group items..."); we.setConvertAble(new GroupAdder()); we.convert(); System.out.println("Marking up items..."); if (module.length() > 0) { try { Class c = Woord.class.getClassLoader().loadClass(module); we.setConvertAble((ConvertAble)c.newInstance()); we.convert(); } catch (ClassCastException e) { System.out.println("Object " + module + " is not a module!"); } catch (ClassNotFoundException e) { System.out.println("Module " + module + " not found!"); } catch (Exception e) { System.out.println("Error: " + e); } } System.out.print("Writing data..."); for (int i=97;i<=122;i++) { we.setFilterPredicate( new BindSecondPredicate( new SortsAsLetter(), new Character((char)i) ) ); try { we.setWriteFile((FileWriteAble)(new ShortLetterFile(repository, (char)i, 10))); } catch (IOException e) { System.out.println(e); }; we.write(); System.out.print("."); }; } } |
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc/predicate
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc/predicate
Added Files:
HasBrutoFormule.java HasEnglishWord.java HasField.java
HasGermanWord.java HasItem.java HasURL.java IsAfkorting.java
IsChemical.java IsCode.java IsGroup.java IsName.java
IsSource.java LessBrutoFormule.java LessCasNumber.java
LessEnglishWord.java LessFWord.java LessGermanWord.java
LessWocWord.java SortsAsLetter.java StartsWith.java
Log Message:
--- NEW FILE: HasBrutoFormule.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class HasBrutoFormule implements UnaryPredicate {
public boolean execute( Object object ) {
return ((Item)object).contains(Item.BRUTO);
}
}
--- NEW FILE: HasEnglishWord.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class HasEnglishWord implements UnaryPredicate {
public boolean execute( Object object ) {
return ((Item)object).contains(Item.ENGLISH);
}
}
--- NEW FILE: HasField.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class HasField implements BinaryPredicate
{
public boolean execute( Object first, Object second ) {
if (!(first instanceof Item) || !(second instanceof Integer)) {
return false;
} else {
return ((Item)first).contains( ((Integer)second).intValue() );
}
}
}
--- NEW FILE: HasGermanWord.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class HasGermanWord implements UnaryPredicate {
public boolean execute( Object object ) {
return ((Item)object).contains(XItem.XGERMAN);
}
}
--- NEW FILE: HasItem.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
/**
* HasItem is a binary predicate that
* returns true if the first operand (an Item) has
* the name of the second operand
*/
public final class HasItem implements BinaryPredicate
{
/**
* Return true if the first operand is greater than the second operand.
* @param first The first operand.
necessary.
* @param second The second operand.
necessary.
* @return first.get(Item.NAME).equals(second)
*/
public boolean execute( Object first, Object second )
{
boolean result = false;
if (first instanceof Item && second instanceof String)
result = ((String)((Item)first).get(Item.NAME)).equals(second);
return result;
}
}
--- NEW FILE: HasURL.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class HasURL implements UnaryPredicate {
public boolean execute( Object object ) {
return ((Item)object).contains(Item.URL);
}
}
--- NEW FILE: IsAfkorting.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class IsAfkorting implements UnaryPredicate {
public boolean execute( Object object ) {
boolean result = false;
if (((Item)object).contains(XItem.XTYPE)) {
XTYPE xt = (XTYPE)((Item)object).get(XItem.XTYPE);
result = xt.isType(XTYPE.ABBREV);
};
return result;
}
}
--- NEW FILE: IsChemical.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class IsChemical implements UnaryPredicate {
public boolean execute( Object object ) {
boolean result = false;
if (((Item)object).contains(XItem.XTYPE)) {
XTYPE xt = (XTYPE)((Item)object).get(XItem.XTYPE);
result = (((Item)object).contains(Item.CHEMICAL) ||
((Item)object).contains(Item.CASNR) ||
xt.isType(XTYPE.CHEMICAL) ||
xt.isType(XTYPE.POLYMER) ||
xt.isType(XTYPE.MIXTURE));
} else {
result = (((Item)object).contains(Item.CHEMICAL) ||
((Item)object).contains(Item.CASNR));
}
return result;
}
}
--- NEW FILE: IsCode.java ---
package com.egonw.woc.predicate;
import java.util.Vector;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class IsCode implements BinaryPredicate
{
public boolean execute( Object first, Object second )
{
return ((String)((Item)first).get(XItem.XCODE)).toLowerCase().equals(((String)second).toLowerCase());
}
}
--- NEW FILE: IsGroup.java ---
package com.egonw.woc.predicate;
import java.util.Vector;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
/**
* Checks wether this Item belongs to a group.
*/
public final class IsGroup implements BinaryPredicate
{
/**
* Return true if the Group field of
* the item first contains the value of the second operand.
* @param first The first operand. Must be off class Item.
* @param second The second operand. Must be a string.
* @return
*/
public boolean execute( Object first, Object second )
{
if (((Item)first).contains(Item.GROUP)) {
return ((Vector)((Item)first).get(Item.GROUP)).contains(second);
} else { return false; }
}
}
--- NEW FILE: IsName.java ---
package com.egonw.woc.predicate;
import java.util.Vector;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
/**
* Checks wether this Item belongs to a group.
*/
public final class IsName implements BinaryPredicate
{
/**
* Return true if the Name field of
* the item first contains the value of the second operand.
* @param first The item to be checked.
* @param second The name that the item should have.
* @return
*/
public boolean execute( Object first, Object second )
{
return ((String)((Item)first).get(Item.NAME)).toLowerCase().equals(((String)second).toLowerCase());
}
}
--- NEW FILE: IsSource.java ---
package com.egonw.woc.predicate;
import java.util.*;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
/**
* Checks wether this Item belongs to a group.
*/
public final class IsSource implements BinaryPredicate
{
/**
*/
public boolean execute( Object first, Object second ) {
boolean result = false;
result = ((String)((Item)first).get(Item.NAME)).toLowerCase().equals(second);
//if (((Item)first).contains(Item.VERVOEGINGEN)) {
// Enumeration vvn = ((Vector)((Item)first).get(Item.VERVOEGINGEN)).elements();
// while (vvn.hasMoreElements())
// result = (result || ((String)vvn.nextElement()).toLowerCase().equals(second));
//}
return result;
}
}
--- NEW FILE: LessBrutoFormule.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class LessBrutoFormule implements BinaryPredicate {
private String pakSymbool(String s) {
StringBuffer sb = new StringBuffer();
if (s.length() >= 2) {
char c = s.charAt(0);
if (Character.isLetter(c) && Character.isUpperCase(c)) {
sb.append(c);
c = s.charAt(1);
if (Character.isLetter(c) && Character.isLowerCase(c))
sb.append(c);
}
} else if (s.length() >= 1) {
char c= s.charAt(0);
if (Character.isLetter(c) && Character.isUpperCase(c)) {
sb.append(c);
}
}
return sb.toString();
}
private String pakAantal(String s) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < s.length(); i++) {
char c = s.charAt(i);
if (Character.isDigit(c)) {
sb.append(c);
} else {
i = s.length();
}
}
return sb.toString();
}
private String stripSymbool(String s) {
int start = 0;
if (s.length() >= 2) {
char c = s.charAt(0);
if (Character.isLetter(c) && Character.isUpperCase(c)) {
start = 1;
c = s.charAt(1);
if (Character.isLetter(c) && Character.isLowerCase(c))
start = 2;
}
} else if (s.length() >= 1) {
char c= s.charAt(0);
if (Character.isLetter(c) && Character.isUpperCase(c)) {
start = 1;
}
}
String result = "";
if (s.length() > start)
result = new String(s.substring(start));
return result;
}
private String stripAantal(String s) {
while ((s.length() > 0) && (Character.isDigit(s.charAt(0)))) {
if (s.length() > 1) { s = new String(s.substring(1)); }
else { s = new String(); };
}
return s;
}
public boolean execute( Object first, Object second ) {
boolean result = false;
if ( !((Item)first).contains(Item.BRUTO) ) {
result = true;
} else if ( !((Item)second).contains(Item.BRUTO) ) {
result = false;
} else {
String eerste = ((Bruto)((Item)first).get(Item.BRUTO)).toString();
String tweede = ((Bruto)((Item)second).get(Item.BRUTO)).toString();
String tekenE = new String();
String tekenT = new String();
String digitE = new String();
String digitT = new String();
boolean succes = false;
while (!succes) {
tekenE = new String(pakSymbool(eerste));
tekenT = new String(pakSymbool(tweede));
eerste = new String(stripSymbool(eerste));
tweede = new String(stripSymbool(tweede));
digitE = new String(pakAantal(eerste));
digitT = new String(pakAantal(tweede));
eerste = new String(stripAantal(eerste));
tweede = new String(stripAantal(tweede));
if (tekenE.equals(tekenT)) {
if (digitE.equals(digitT)) {
if (tekenE.length() == 0) succes = true;
} else {
if (digitE.length() == digitT.length()) {
result = (digitE.compareTo(digitT) < 0);
} else {
result = (digitE.length() < digitT.length());
}
succes = true;
}
} else {
succes = true;
result = (tekenE.compareTo(tekenT) < 0);
}
}
}
return result;
}
}
--- NEW FILE: LessCasNumber.java ---
package com.egonw.woc.predicate;
import java.util.*;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class LessCasNumber implements BinaryPredicate {
public boolean execute( Object first, Object second ) {
boolean result = false;
if (((Item)first).contains(Item.CASNR)) {
if (((Item)second).contains(Item.CASNR)) {
// assume altijd drie tokens
StringTokenizer st1 = new StringTokenizer((String)((Item)first).get(Item.CASNR), "-");
StringTokenizer st2 = new StringTokenizer((String)((Item)second).get(Item.CASNR), "-");
int i = Integer.parseInt(st1.nextToken());
int j = Integer.parseInt(st2.nextToken());
if ( i == j ) {
if ( Integer.parseInt(st1.nextToken()) <=
Integer.parseInt(st2.nextToken()) ) {
result = true;
} else {
result = false;
}
} else if ( i < j ) {
result = true;
} else {
result = false;
}
} else {
result = false;
}
} else {
result = true;
}
return result;
}
}
--- NEW FILE: LessEnglishWord.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class LessEnglishWord implements BinaryPredicate {
public boolean execute( Object first, Object second ) {
try {
return (
strip((String)((Item)first).get(Item.ENGLISH))).compareTo(
strip((String)((Item)second).get(Item.ENGLISH))) < 0;
} catch (NullPointerException e) {
if (((Item)first).contains(Item.ENGLISH)) {
return false;
} else {
return true;
}
}
}
private String strip(String s) {
StringBuffer sb = new StringBuffer();
int i = 0;
while ((i <= s.length() -1) && (!Character.isLetter(s.charAt(i))))
i++;
while (i <= s.length() -1) {
sb.append(s.charAt(i));
i++;
}
return sb.toString();
}
}
--- NEW FILE: LessFWord.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class LessFWord implements BinaryPredicate {
public boolean execute( Object first, Object second ) {
try {
return
strip(((FWord)first).getFWord()).compareTo(
strip(((FWord)second).getFWord())) < 0;
} catch (NullPointerException e) {
return false;
}
}
private String strip(String s) {
StringBuffer sb = new StringBuffer();
int i = 0;
while ((i <= s.length() -1) && (!Character.isLetter(s.charAt(i))))
i++;
while (i <= s.length() -1) {
sb.append(s.charAt(i));
i++;
}
return sb.toString();
}
}
--- NEW FILE: LessGermanWord.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
public final class LessGermanWord implements BinaryPredicate {
public boolean execute( Object first, Object second ) {
try {
return (
strip((String)((Item)first).get(XItem.XGERMAN))).compareTo(
strip((String)((Item)second).get(XItem.XGERMAN))) < 0;
} catch (NullPointerException e) {
if (((Item)first).contains(XItem.XGERMAN)) {
return false;
} else {
return true;
}
}
}
private String strip(String s) {
StringBuffer sb = new StringBuffer();
int i = 0;
while ((i <= s.length() -1) && (!Character.isLetter(s.charAt(i))))
i++;
while (i <= s.length() -1) {
sb.append(s.charAt(i));
i++;
}
return sb.toString();
}
}
--- NEW FILE: LessWocWord.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
/**
* Sorts items by strings.
*
* @author Egon Willighagen
* @version 1.1, 2/7/98
*
* 2/7/98: placed in com.egonw.woc
* 24/2/98: Now skips the first non-characters for sorting
*
*/
public final class LessWocWord implements BinaryPredicate {
public boolean execute( Object first, Object second ) {
return strip(first.toString().toLowerCase()).compareTo(
strip(second.toString().toLowerCase()) ) < 0;
}
private String strip(String s) {
StringBuffer sb = new StringBuffer();
int i = 0;
while ((i <= s.length() -1) && (!Character.isLetter(s.charAt(i))))
i++;
while (i <= s.length() -1) {
sb.append(s.charAt(i));
i++;
}
return sb.toString();
}
}
--- NEW FILE: SortsAsLetter.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
import com.egonw.woc.util.*;
/**
* StartsWith is a binary predicate that
* returns true if the first operand as a string
* starts with the second operand as a string.
*/
public final class SortsAsLetter implements BinaryPredicate
{
/**
* Return true if the first operand is greater than the second operand.
* @param first The first operand. necessary.
* @param second The second operand. necessary.
* @return first.toString().startsWith( second.toString()
*/
public boolean execute( Object first, Object second ) {
return Convert.stripTillFirstLetter(first.toString()).startsWith( second.toString() );
}
}
--- NEW FILE: StartsWith.java ---
package com.egonw.woc.predicate;
import com.objectspace.jgl.*;
import com.egonw.woc.*;
/**
* StartsWith is a binary predicate that
* returns true if the first operand as a string
* starts with the second operand as a string.
*/
public final class StartsWith implements BinaryPredicate
{
/**
* Return true if the first operand is greater than the second operand.
* @param first The first operand.
necessary.
* @param second The second operand.
necessary.
* @return first.toString().startsWith( second.toString()
*/
public boolean execute( Object first, Object second )
{
return first.toString().startsWith( second.toString() );
}
}
|
Update of /cvsroot/woc/woc/src/woc/wocjava
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava
Added Files:
Changelog Makefile.am Makefile.am.new repository_def.xml
repository_def.xml.in wocjava.jar woclist.pl woclist.sh
Log Message:
--- NEW FILE: Changelog ---
2002-02-12
----------
* spaanse, italiaanse, franse en friese vertalingen worden nu ook gegeven
--- NEW FILE: Makefile.am ---
##### CONFIGURE DEFINITIONS #####
PREFIX="@prefix@"
##### GLOBAL DEFINITIONS #####
JAVAC=${JAVA_HOME}/bin/javac
JAR=${JAVA_HOME}/bin/jar
JAVA=${JAVA_HOME}/java
javalibdir=${PREFIX}/shared/lib/java
##### AUTOMAKE SPECIALS #####
wocjavajardir=${javalibdir}/woc
wocjavajar_DATA= wocjava.jar
CLEANFILES= ${wocjavajar_DATA}
##### LOCAL DEFINITIONS #####
sourcedir=source
builddir=build
woctree=com/egonw/woc
_JARS:=`ls -1 ${javalibdir}/*.jar ${wocjavajardir}/*.jar | perl -ne "s/\n|\r/:/g; print;"`
_WOCFILES=`cd ${sourcedir}; find ${woctree} -name "*.java" | perl -ne "s/\n|\r/ /g; print;"`
## _WOCFILES wordt recursief omgezet naar WOCFILES
JAVAFILES=${WOCFILES:%=${sourcedir}/%}
CLASSFILES=${WOCFILES:.java=.class}
DEPCLASSFILES=${CLASSFILES:%=${builddir}/%}
##### RULES #####
${wocjavajar_DATA}: FORCE
@${MAKE} "JARS=${_JARS}" "WOCFILES=${_WOCFILES}" "${wocjavajar_DATA}-build"
FORCE:
#${wocjavajar_DATA}-build: echo-vars ${DEPCLASSFILES}
${wocjavajar_DATA}-build: ${DEPCLASSFILES}
@echo "..Packing Class files to '${wocjavajar_DATA}'.."
@cd build; "${JAR}" cf "../${wocjavajar_DATA}" ${CLASSFILES}
## debugging purpose, put echo-vars as first prerequisite in rule above
echo-vars:
echo ${WOCFILES} > /dev/null
cat
echo ${JAVAFILES} > /dev/null
cat
echo ${CLASSFILES} > /dev/null
cat
echo ${DEPCLASSFILES} > /dev/null
cat
${DEPCLASSFILES}: ${JAVAFILES}
@echo "..Compiling Java files to Class files.."
mkdir -p build
@if [ "$$OSTYPE" = "cygwin32" ] || [ "$$OSTYPE" = "cygwin" ] || ["$$OSTYPE" = "posix" ] ; then \
"${JAVAC}" -classpath `cygpath --path --windows "${JARS}"` -d build -O ${JAVAFILES} ; \
else \
"${JAVAC}" -classpath "${JARS}" -d build -O ${JAVAFILES} ; \
fi
clean:
rm -f "${CLEANFILES}"
cd ${builddir}; rm -fR *
--- NEW FILE: Makefile.am.new ---
##### GLOBAL DEFINITIONS #####
JAVAC=${JAVA_HOME}/bin/javac
JAR=${JAVA_HOME}/bin/jar
JAVA=${JAVA_HOME}/java
## prefix is set by configure
## libdir should be set by configure as well?
#javalibdir=${libdir}/java
javalibdir=${prefix}/shared/lib/java
##### AUTOMAKE SPECIALS #####
wocjavajardir=${javalibdir}/woc
reposdir=${prefix}/shared/etc
wocjavajar_DATA= wocjava.jar
# repos_DATA= repository_def.xml
CLEANFILES= wocjava.jar
# CLEANFILES= repository_def.xml wocjava.jar
##### LOCAL DEFINITIONS #####
sourcedir=source
builddir=build
woctree=com/egonw/woc
_JARS:=`ls -1 ${javalibdir}/*.jar ${wocjavajardir}/*.jar | perl -ne "s/\n|\r/:/g; print;"`
#_WOCFILES=`cd ${sourcedir}; find ${woctree} -name "*.java" | perl -ne "s/\n|\r/ /g; print;"`
_WOCFILES=`ls -1 ${sourcedir}/${woctree}/*.java | perl -ne "s/\n|\r/ /g; print;"`
## _WOCFILES wordt recursief omgezet naar WOCFILES
JAVAFILES:=${WOCFILES:%=${sourcedir}/%}
CLASSFILES:=${WOCFILES:.java=.class}
DEPCLASSFILES:=${CLASSFILES:%=${builddir}/%}
##### RULES #####
VPATH *.java ${sourcedir}/${woctree}
VPATH *.java ${sourcedir}/${woctree}/*
VPATH *.class ${builddir}/${woctree}
VPATH *.class ${builddir}/${woctree}/*
#${wocjavajar_DATA}: FORCE
# @${MAKE} "JARS=${_JARS}" "WOCFILES=${_WOCFILES}" "${wocjavajar_DATA}-build"
FORCE:
#${wocjavajar_DATA}-build: echo-vars ${DEPCLASSFILES}
#${wocjavajar_DATA}-build: ${DEPCLASSFILES}
#${wocjavajar_DATA}: ${builddir}/${woctree}/*.class ${builddir}/${woctree}/*/*.class
${wocjavajar_DATA}-build: ${CLASSFILES}
@echo "..Packing Class files to '${wocjavajar_DATA}'.."
@cd build; "${JAR}" cf "../${wocjavajar_DATA}" ${CLASSFILES}
## debugging purpose, put echo-vars as first prerequisite in rule above
echo-vars:
echo ${WOCFILES} > /dev/null
cat
echo ${JAVAFILES} > /dev/null
cat
echo ${CLASSFILES} > /dev/null
cat
echo ${DEPCLASSFILES} > /dev/null
cat
echo $(patsubst ${builddir}/%,${sourcedir}/%,$(@:.class=.java)) > /dev/null
cat
#${DEPCLASSFILES}: ${JAVAFILES}
# @echo "..Compiling Java files to Class files.."
# mkdir -p build
# @if [ "$$OSTYPE" = "cygwin32" ] || [ "$$OSTYPE" = "cygwin" ] || ["$$OSTYPE" = "posix" ] ; then \
# "${JAVAC}" -classpath `cygpath --path --windows "${JARS}"` -d build -O ${JAVAFILES} ; \
# else \
# "${JAVAC}" -classpath "${JARS}" -d build -O ${JAVAFILES} ; \
# fi
#%.class: $(patsubst ${builddir}/%,${sourcedir}/%,$(@:.class=.java))
#${builddir}%: $(patsubst ${builddir}%,${sourcedir}%,$@)
#%.class:
${builddir}/${woctree}/*.class ${builddir}/${woctree}/*/*.class: $@ FORCE
@echo "..Compiling Java files $< to Class files $@.."
mkdir -p build
@if [ "$$OSTYPE" = "cygwin32" ] || [ "$$OSTYPE" = "cygwin" ] || ["$$OSTYPE" = "posix" ] ; then \
"${JAVAC}" -classpath `cygpath --path --windows "${JARS}"` -d build -O $< ; \
else \
"${JAVAC}" -classpath "${JARS}" -d build -O $< ; \
fi
clean:
rm -f "${wocjavajar_DATA}"
cd ${builddir}; rm -fR *
--- NEW FILE: repository_def.xml ---
<repositories>
<!-- definitions of repositories consist mostly of directory
names -->
<general>
<path id="PhysicalRoot">/cygdrive/e/woc/wocnew/web-docs/</path>
<!-- definition of DADML dirs -->
<path id="DADMLSubDir">data/dadml/</path>
<path id="MolSubDir">mol/</path>
<path id="PdbSubDir">pdb/</path>
<path id="XyzSubDir">xyz/</path>
<path id="CmlSubDir">cml/</path>
<path id="PhysPropSubDir">fysisch/cml/</path>
<path id="GifSubDir">gifgalary/</path>
<!-- website -->
<path id="HtmlRoot">http://www-woc.sci.kun.nl/</path>
<path id="CgiBinRoot">http://www-woc.sci.kun.nl/cgi-bin/</path>
<path id="JavaSubDir">java/</path>
<!-- other -->
<path id="BronnenFile">woc_bron.html</path>
<path id="DatabasesFile">super.xml</path>
</general>
<specific repository="woc">
<!-- source -->
<path id="DataSubDir">data/</path>
<path id="WMLSubDir">data/wml</path>
<path id="PictureSubDir">data/pictures/</path>
<path id="ModelsSubDir">data/compounds/</path>
<!-- website -->
<path id="LetterFileSubDir">gui/letters/</path>
<path id="ItemFileSubDir">gui/items/</path>
<path id="GroupFileSubDir">gui/groups/</path>
<path id="IndexFileSubDir">gui/index/</path>
<path id="CSSSubDir">gui/styles/</path>
<path id="LocatieSubDir">gui/locatie/</path>
<path id="JavascriptSubDir">gui/javascript/</path>
</specific>
<specific repository="iupac">
<!-- source -->
<path id="DataSubDir">iupac/data/</path>
<path id="WMLSubDir">iupac/data/wml</path>
<path id="PictureSubDir">iupac/data/pictures/</path>
<path id="ModelsSubDir">iupac/data/compounds/</path>
<!-- website -->
<path id="LetterFileSubDir">iupac/gui/letters/</path>
<path id="ItemFileSubDir">iupac/gui/items/</path>
<path id="GroupFileSubDir">iupac/gui/groups/</path>
<path id="IndexFileSubDir">iupac/gui/index/</path>
<path id="CSSSubDir">iupac/gui/styles/</path>
<path id="LocatieSubDir">iupac/gui/locatie/</path>
<path id="JavascriptSubDir">iupac/gui/javascript/</path>
</specific>
</repositories>
--- NEW FILE: repository_def.xml.in ---
<repositories>
<!-- definitions of repositories consist mostly of directory
names -->
<general>
<path id="PhysicalRoot">@PHYSPATH@/web-docs/</path>
<!-- definition of DADML dirs -->
<path id="DADMLSubDir">data/dadml/</path>
<path id="MolSubDir">mol/</path>
<path id="PdbSubDir">pdb/</path>
<path id="XyzSubDir">xyz/</path>
<path id="CmlSubDir">cml/</path>
<path id="PhysPropSubDir">fysisch/cml/</path>
<path id="GifSubDir">gifgalary/</path>
<!-- website -->
<path id="HtmlRoot">http://@SERVER_HOSTNAME@/</path>
<path id="CgiBinRoot">http://@SERVER_HOSTNAME@/cgi-bin/</path>
<path id="JavaSubDir">java/</path>
<!-- other -->
<path id="BronnenFile">woc_bron.html</path>
<path id="DatabasesFile">super.xml</path>
</general>
<specific repository="woc">
<!-- source -->
<path id="DataSubDir">data/</path>
<path id="WMLSubDir">data/wml</path>
<path id="PictureSubDir">data/pictures/</path>
<path id="ModelsSubDir">data/compounds/</path>
<!-- website -->
<path id="LetterFileSubDir">gui/letters/</path>
<path id="ItemFileSubDir">gui/items/</path>
<path id="GroupFileSubDir">gui/groups/</path>
<path id="IndexFileSubDir">gui/index/</path>
<path id="CSSSubDir">gui/styles/</path>
<path id="LocatieSubDir">gui/locatie/</path>
<path id="JavascriptSubDir">gui/javascript/</path>
</specific>
<specific repository="iupac">
<!-- source -->
<path id="DataSubDir">iupac/data/</path>
<path id="WMLSubDir">iupac/data/wml</path>
<path id="PictureSubDir">iupac/data/pictures/</path>
<path id="ModelsSubDir">iupac/data/compounds/</path>
<!-- website -->
<path id="LetterFileSubDir">iupac/gui/letters/</path>
<path id="ItemFileSubDir">iupac/gui/items/</path>
<path id="GroupFileSubDir">iupac/gui/groups/</path>
<path id="IndexFileSubDir">iupac/gui/index/</path>
<path id="CSSSubDir">iupac/gui/styles/</path>
<path id="LocatieSubDir">iupac/gui/locatie/</path>
<path id="JavascriptSubDir">iupac/gui/javascript/</path>
</specific>
</repositories>
--- NEW FILE: wocjava.jar ---
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[truncated message content] |
|
From: Geert J. <gj...@us...> - 2002-09-03 19:40:56
|
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc
Added Files:
Bruto.java FWord.java Formule.java Item.java Picture.java
Raw.java Smile.java StoichFormule.java WocEngine.java
WoordTable.java XItem.java XTYPE.java
Log Message:
--- NEW FILE: Bruto.java ---
package com.egonw.woc;
import java.lang.Character;
public class Bruto extends Formule {
public Bruto(String s) {
super(s);
}
public String toString() {
return super.value();
}
public String toHTMLString() {
StringBuffer resultaat = new StringBuffer();
boolean PrevCharIsDigit = false;
//waarde moet geconverteerd worden
for (int i=0; i < super.value().length(); i++) {
Character c = new Character(super.value().charAt(i));
if (c.isLetter(c.charValue())) {
if (PrevCharIsDigit) { resultaat.append("</font></sub>"); };
resultaat.append(c.charValue());
PrevCharIsDigit = false;
};
if (c.isDigit(c.charValue())) {
if (!PrevCharIsDigit) { resultaat.append("<sub><font size=-1>"); };
resultaat.append(c.charValue());
PrevCharIsDigit = true;
};
if (c.charValue() == ')' || c.charValue() == '(') {
if (PrevCharIsDigit) { resultaat.append("</font></sub>"); };
resultaat.append(c.charValue());
if (PrevCharIsDigit) { resultaat.append("<sub><font size=-1>"); };
}
};
if (PrevCharIsDigit) { resultaat.append("</font></sub>"); };
return resultaat.toString();
}
}
--- NEW FILE: FWord.java ---
package com.egonw.woc;
import com.objectspace.jgl.*;
import com.egonw.woc.util.*;
public class FWord {
private String lang;
private String fword;
private String dword;
private String anchor;
public FWord(String lang) {
this.lang = lang;
this.fword = new String();
this.dword = new String();
this.anchor = new String();
}
public void setFWord(String s) { this.fword = s; }
public void setDWord(String s) { this.dword = s; }
public void setAnchor(String s) { this.anchor = s; }
public String getFWord() { return this.fword; }
public String getDWord() { return this.dword; }
public String getAnchor() { return this.anchor; }
public boolean equals(String s) {
return fword.equals(s);
}
public int hashCode() {
return (this.fword).hashCode();
}
public String toString() {
return this.fword;
}
}
--- NEW FILE: Formule.java ---
package com.egonw.woc;
public class Formule {
private String value;
protected Formule() {
value = new String();
}
protected Formule(String s) {
value = new String(s);
}
public final boolean isEmpty() {
return (value.length() == 0);
}
public final String value() {
return value;
}
}
--- NEW FILE: Item.java ---
package com.egonw.woc;
import com.objectspace.jgl.*;
import com.egonw.woc.util.*;
/**
* Class that defines a item and specifies the field information
* for the Woc-file format.
*
* @author Egon Willighagen
* @version 2.0, 1/7/98
*/
public class Item {
private Object data[];
private boolean isEmpty;
public final static int ITEM = 0;
public final static int ANCHOR = 1;
public final static int NAME = 2;
public final static int GROUP = 3;
public final static int TRIVIALNAME = 4;
public final static int EIGENNAME = 5;
public final static int SUBITEM = 6;
public final static int PICTUREFILE = 7;
public final static int XYZFILE = 8;
public final static int ENGLISH = 9;
public final static int COMMENT = 10;
public final static int FORMULA = 11;
public final static int MASS = 12;
public final static int BOILINGPOINT = 13;
public final static int MELTINGPOINT = 14;
public final static int ZIE = 15;
public final static int VERGELIJK = 16;
public final static int IUPACNAME = 17;
public final static int MSDS = 18;
public final static int SMILE = 19;
public final static int LEVEN = 20;
public final static int BRUTO = 21;
public final static int DIPOOL = 22;
public final static int CASNR = 23;
public final static int RHO = 24;
public final static int PDB = 25;
public final static int REACTIE = 26;
public final static int URL = 27;
public final static int BRON = 28;
public final static int MOL = 29;
public final static int LIDWOORD = 30;
public final static int VERVOEGINGEN = 31;
public final static int FUNCTIE = 32;
public final static int CHEMICAL = 33;
public final static int VOORBEELD = 34;
public final static int AFKORT = 35;
public final static int PICTUREDIR = 36;
public final static int NUMBER = 37;
public final static int NUMBER_OF_TYPES = 38;
public Item() {
data = new Object[NUMBER_OF_TYPES];
for (int i=0; i<NUMBER_OF_TYPES; i++) {
data[i] = null;
}
isEmpty = true;
}
public boolean isEmpty() {
boolean rv = true;
for (int i=0; i<NUMBER_OF_TYPES; i++) {
if (data[i] != null) {
rv = false;
}
}
return rv;
}
public void add(int code, Object o) {
isEmpty = false;
if (code == ANCHOR) {
} else if (code >= NUMBER_OF_TYPES) {
} else {
data[code] = o;
}
}
public void remove(int code) {
data[code] = null;
}
public Object get(int code) {
if (code == ANCHOR) {
return (Object)Convert.NAMELikeToANCHORLike((String)get(Item.NAME));
} else if (code >= NUMBER_OF_TYPES) {
return null;
} else {
return data[code];
}
}
public boolean contains(int code) {
if (code == ANCHOR) {
return true;
} else if (code >= NUMBER_OF_TYPES) {
return false;
} else {
return (data[code] != null);
}
}
public boolean equals(Item i) {
return (((String)get(ANCHOR)).equals(i.get(ANCHOR)));
}
public int hashCode() {
if (contains(NAME)) {
return (int)get(NAME).hashCode();
} else {
return 0;
}
}
public String toString() {
return Convert.NAMELikeToANCHORLike((String)get(NAME));
}
public boolean result(UnaryPredicate up) {
return up.execute(this);
}
}
--- NEW FILE: Picture.java ---
package com.egonw.woc;
import com.egonw.woc.util.*;
public class Picture {
private String onderschrift;
private String path;
public Picture() {
path = new String();
onderschrift = new String();
}
public Picture(String dir) {
path = dir;
onderschrift = "";
}
public Picture(String dir, String subtitle) {
path = dir;
onderschrift = subtitle;
}
public String path() {
return path;
}
public String subtitle() {
return onderschrift;
}
public boolean hasSubtitle() {
return (onderschrift.length() != 0);
}
public void finalize() throws Throwable {
super.finalize();
}
}
--- NEW FILE: Raw.java ---
package com.egonw.woc;
import java.lang.Character;
public class Raw extends Formule {
public Raw() {
super();
}
public Raw(String s) {
super(s);
}
public String toString() {
return super.value();
}
public String toHTMLString() {
StringBuffer resultaat = new StringBuffer();
if (bevatHTMLCode()) {
//is al in HTML-formaat of bevat (veel) fouten
return super.value();
} else {
//waarde moet geconverteerd worden
for (int i=0; i < super.value().length(); i++) {
Character c = new Character(super.value().charAt(i));
if (c.isLetter(c.charValue())) {
resultaat.append(c.charValue()); };
if (c.isDigit(c.charValue())) { resultaat.append("<sub>");
resultaat.append(c.charValue()); resultaat.append("</sub>"); };
if ((c.charValue() == '+') ||
(c.charValue() == '-')) {
resultaat.append("<sup>");
resultaat.append(c.charValue());
resultaat.append("</sup>");
}
if ((c.charValue() == '(') || (c.charValue() == ']') ) {
resultaat.append(c.charValue());
}
// else: er zit een fout teken in de Smile
// deze routine zou dan een fout moeten geven!
};
}
return resultaat.toString();
}
private boolean bevatHTMLCode() {
return (super.value().indexOf("<sub>") != -1);
}
}
--- NEW FILE: Smile.java ---
package com.egonw.woc;
import java.lang.*;
public class Smile extends Formule {
public Smile() {
super();
}
public Smile(String s) {
super(s);
}
private String toHexString() {
StringBuffer resultaat = new StringBuffer();
for (int i=0; i< super.value().length(); i++) {
resultaat.append(Integer.toHexString((int)super.value().charAt(i)));
}
return resultaat.toString();
}
public String toHTMLString() {
StringBuffer resultaat = new StringBuffer();
resultaat.append("<IMG HEIGHT=64 WIDTH=96 ALIGN=MIDDLE SRC='http://www.ch.ic.ac.uk/daycgi/smi2gif-small?" + toHexString() + "'>");
return resultaat.toString();
}
public String toString() {
return super.value();
}
}
--- NEW FILE: StoichFormule.java ---
package com.egonw.woc;
import java.lang.Character;
public class StoichFormule extends Formule {
public StoichFormule(String s) {
super(s);
}
public String toString() {
return super.value();
}
public String toHTMLString() {
StringBuffer resultaat = new StringBuffer();
boolean PrevCharIsDigit = false;
//waarde moet geconverteerd worden
for (int i=0; i < super.value().length(); i++) {
Character c = new Character(super.value().charAt(i));
if (c.isLetter(c.charValue())) {
if ((c.charValue() != 'n') && (c.charValue() != 'm')) {
if (PrevCharIsDigit) { resultaat.append("</font></sub>"); };
resultaat.append(c.charValue());
PrevCharIsDigit = false;
} else {
if (!PrevCharIsDigit) {
resultaat.append("<sub><font size=-1>");
PrevCharIsDigit = true;
};
resultaat.append(c.charValue());
}
} else if (c.isDigit(c.charValue())) {
if (!PrevCharIsDigit) { resultaat.append("<sub><font size=-1>"); };
resultaat.append(c.charValue());
PrevCharIsDigit = true;
} else if ((c.charValue() == '+') || (c.charValue() == '-')) {
resultaat.append(c.charValue());
PrevCharIsDigit = true;
}
};
if (PrevCharIsDigit) { resultaat.append("</font></sub>"); };
return resultaat.toString();
}
}
--- NEW FILE: WocEngine.java ---
package com.egonw.woc;
import com.objectspace.jgl.*;
import com.objectspace.jgl.algorithms.*;
import java.util.*;
import java.io.*;
import com.egonw.woc.*;
import com.egonw.woc.files.*;
import com.egonw.woc.util.*;
import com.egonw.woc.predicate.*;
import com.egonw.woc.exception.*;
public class WocEngine {
private WocReportFile wrf;
private WoordTable wt;
private FileReadAble wocrf;
private FileWriteAble wocwf;
private UnaryPredicate up;
private BinaryPredicate sorter;
private ConvertAble ca;
private Path repository;
public WocEngine(Path repository) {
this.repository = repository;
wrf = null;
wt = null;
wocrf = null;
up = null;
}
public Enumeration getWTElements() {
return wt.elements();
}
public WoordTable getWT() {
return wt;
}
public void setWocReportFile(WocReportFile wrf) {
this.wrf = wrf;
}
public void setReadFile(FileReadAble wocrf) {
this.wocrf = wocrf;
}
public void setWriteFile(FileWriteAble wocwf) {
this.wocwf = wocwf;
}
public void setWoordTable(WoordTable wt) {
this.wt = wt;
}
public void setFilterPredicate(UnaryPredicate up) {
this.up = up;
}
public void setConvertAble(ConvertAble ca) {
this.ca = ca;
}
public void setSortingPredicate(BinaryPredicate sorter) {
this.sorter = sorter;
}
public void sort() {
try {
if (wt == null) {
if (wrf != null) wrf.reportText("WocEngine: No WoordTable set.");
} else if (sorter == null) {
if (wrf != null) wrf.reportText("WocEngine: No SortingPredicate set.");
} else {
WoordTable sorted = new WoordTable( sorter );
if (wrf != null) wrf.addHeader("Sorting WoordTable: " + sorter);
sorted.add(wt);
wt = sorted;
}
} catch (WocException e) {
if (e instanceof WocFatalError) {
if (wrf != null) wrf.reportWocFatalError((WocFatalError)e);
} else if (e instanceof WocNotification) {
if (wrf != null) wrf.reportWocNotification((WocNotification)e);
};
} catch (Exception e) {
if (wrf != null) {
if (e instanceof NullPointerException) {
wrf.reportException(e);
wrf.reportText("Possibly predicate does not sort null!!");
} else {
wrf.reportException(e);
}
}
}
}
public void read() {
if (wt == null) {
if (wrf != null) wrf.reportText("WocEngine: No WoordTable set.");
} else if (wocrf == null) {
if (wrf != null) wrf.reportText("WocEngine: No WocReadFile set.");
} else {
if (wrf != null) wrf.addHeader("Reading Items");
try {
if (wocrf instanceof WocListReadFile) {
wt = ((WocListReadFile)wocrf).read();
} else {
Item item = wocrf.readItem();
while (!item.isEmpty()) {
if (up == null) {
wt.add(item);
} else {
if (up.execute(item)) wt.add(item);
}
item = wocrf.readItem();
};
};
} catch (WocException e) {
if (e instanceof WocFatalError) {
if (wrf != null) wrf.reportWocFatalError((WocFatalError)e);
} else if (e instanceof WocNotification) {
if (wrf != null) wrf.reportWocNotification((WocNotification)e);
} else {
System.out.println(e);
}
};
}
}
public void write() {
try {
if (wt == null) {
if (wrf != null) wrf.reportText("WocEngine: No WoordTable set.");
} else if (wocwf == null) {
if (wrf != null) wrf.reportText("WocEngine: No WocWriteFile set.");
} else {
if (wrf != null) {
wrf.addHeader("Writing Items");
if (up !=null) wrf.addHeader(((Object)up).toString());
}
wocwf.start();
Enumeration values = wt.elements();
boolean first = true;
Item last = null;
while (values.hasMoreElements()) {
Item i = (Item)values.nextElement();
if (up == null) {
if (first) {
wocwf.startItems(i);
first = false;
}
wocwf.writeItem(i);
last = i;
} else {
// mag hij door filter?
if (up.execute(i)) {
if (first) {
wocwf.startItems(i);
first = false;
}
wocwf.writeItem(i);
last = i;
}
}
}
if (last != null) wocwf.endItems(last);
wocwf.end();
}
} catch (IOException e) {
if (wrf != null) wrf.addHeader("Write Error");
}
}
public void convert() {
if (wt == null) {
if (wrf != null) wrf.reportText("WocEngine: No WoordTable set.");
} else if (ca == null) {
if (wrf != null) wrf.reportText("WocEngine: No ConvertAble set.");
} else {
if (wrf != null) {
wrf.addHeader("Converting Items : " + ca.getName());
wrf.reportText(wt.size() + " items");
ca.set(wrf);
}
ca.set(wt);
wt = ca.convert();
if (wrf != null) wrf.reportText(wt.size() + " items");
};
};
};
--- NEW FILE: WoordTable.java ---
package com.egonw.woc;
import com.objectspace.jgl.*;
import com.objectspace.jgl.predicates.*;
import com.objectspace.jgl.algorithms.*;
import java.util.*;
import java.io.Serializable;
import com.egonw.woc.files.*;
import com.egonw.woc.util.*;
import com.egonw.woc.exception.*;
import com.egonw.woc.predicate.*;
public class WoordTable extends OrderedSet {
public WoordTable() {
this( new LessWocWord() );
}
public WoordTable(Item i) {
super( new LessWocWord() );
super.add(i);
}
public WoordTable(BinaryPredicate bp) {
super( bp );
}
public SList toSList() {
SList s = new SList();
Item i;
Enumeration values = super.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
s.add(i);
}
return s;
}
public void add(WoordTable wt) throws WocNotification {
Item i;
Enumeration values = wt.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
add(i);
}
}
public void add(Container c) throws WocNotification {
Item i;
Enumeration values = c.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
add(i);
}
}
public WoordTable merge(WoordTable wt) throws WocNotification {
WoordTable tabel = new WoordTable();
Enumeration values = super.elements();
Item i;
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
tabel.add(i);
}
values = wt.elements();
while ( values.hasMoreElements() ) {
i = (Item)values.nextElement();
tabel.add(i);
}
return tabel;
}
public void add(Item i) throws WocNotification {
if (i == null) {
throw new EmptyItemNotification(i);
} else if (!i.contains(Item.NAME)) {
throw new IncompleteItemNotification(i);
} else {
UnaryPredicate predicate =
new BindSecondPredicate( new HasItem(),
(String)i.get(Item.NAME) );
Item value = (Item)Finding.detect(this, predicate);
if (value != null) {
// samenvoegen ?
// bv. als tweede een groep is
if (i.contains(XItem.XGROUP)) {
// als de laatste een groep is
value.add(XItem.XGROUP, new String());
} else if (i.contains(Item.COMMENT)) {
Vector commentlist = (Vector)i.get(Item.COMMENT);
if (value.contains(Item.COMMENT)) {
Vector commentlist2 = (Vector)value.get(Item.COMMENT);
Enumeration enum = commentlist.elements();
while (enum.hasMoreElements()) {
commentlist2.addElement( (Memo)enum.nextElement() );
}
value.add(Item.COMMENT, commentlist2);
} else {
value.add(Item.COMMENT, commentlist);
}
// zie lijst ook copieren... vanwege afkortingen...
try {
Vector zielist = (Vector)i.get(Item.ZIE);
if (value.contains(Item.ZIE)) {
Vector zielist2 = (Vector)value.get(Item.ZIE);
Enumeration enum = zielist.elements();
while (enum.hasMoreElements()) {
zielist2.addElement((String)enum.nextElement() );
}
value.add(Item.ZIE, zielist2);
} else {
value.add(Item.ZIE, zielist);
}
} catch (Exception e) {
System.err.println(e.toString());
e.printStackTrace();
}
} else {
// als er geen group bijzit
throw new DuplicateItemNotification(i);
}
} else {
super.add(i);
}
}
}
}
--- NEW FILE: XItem.java ---
package com.egonw.woc;
import java.util.*;
import com.objectspace.jgl.*;
import com.egonw.woc.util.*;
import com.egonw.woc.wml.*;
public class XItem extends Item {
private Object data[];
public final static int XNAME = 100;
public final static int XMEDIA = 101;
public final static int XINSERTS = 102;
public final static int XREACTIE = 103;
public final static int XFORMULA = 104;
public final static int XGERMAN = 105;
public final static int XAFKORT = 106;
public final static int XGROUP = 107;
public final static int XTYPE = 108;
public final static int WOCNR = 109;
public final static int XUNNR = 110;
public final static int XENR = 111;
public final static int XTOPICMAP = 112;
public final static int XLATIN = 113;
public final static int XNSC = 114;
public final static int XFLASH = 115;
public final static int XSEEONLY = 116;
public final static int XMEERVOUD = 117;
public final static int XPKA = 118;
public final static int XPKB = 119;
public final static int XFILENAME = 120;
public final static int XCODE = 120; // thus degenerate with XFILENAME
public final static int XDISCDATE = 121;
public final static int XDISCPLACE = 122;
public final static int XDISCPERSON = 123;
public final static int XFRENCH = 124;
public final static int XSPANISH = 125;
public final static int XITALIAN = 126;
public final static int XFRYSIAN = 127;
public final static int NUMBER_OF_TYPES = 28;
public XItem() {
super();
this.data = new Object[NUMBER_OF_TYPES];
for (int i=0; i < NUMBER_OF_TYPES; i++) {
this.data[i] = null;
}
}
public boolean isEmpty() {
boolean rv = true;
for (int i=0; i < NUMBER_OF_TYPES; i++) {
if (this.data[i] != null) {
rv = false;
}
}
return super.isEmpty() && rv;
}
public void add(int code, Object o) {
if (code >= 100) {
this.data[code-100] = o;
} else {
super.add(code, o);
}
}
public void remove(int code) {
if (code >= 100) {
this.data[code-100] = null;
} else {
super.remove(code);
}
}
public Object get(int code) {
Object o = null;
if (code >= 100) {
switch (code) {
case XItem.XITALIAN :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("IT"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
case XItem.XFRYSIAN :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("FY"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
case XItem.XFRENCH :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("FR"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
case XItem.XSPANISH :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("SP"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
case XItem.XGERMAN :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("DE"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
case XItem.XLATIN :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("LATIN"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
default:
o = this.data[code-100];
break;
}
} else {
switch (code) {
case Item.ENGLISH :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
StringBuffer sb = new StringBuffer();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("EN"))
sb.append(xl.getValue() + ", ");
}
}
o = sb.toString().substring(0, sb.length() - 2);
}
break;
case Item.IUPACNAME :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
if (xname.getCLASS().equals("IUPAC")) {
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("NL")) o = xl.getValue();
}
}
}
}
break;
case Item.AFKORT :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
if (xname.getCLASS().equals("ABBREV")) {
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("NL")) o = xl.getValue();
}
}
}
} else if (super.contains(Item.AFKORT)) {
o = super.get(Item.AFKORT);
}
break;
case Item.TRIVIALNAME :
Vector b = new Vector();
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
if (xname.getCLASS().equals("TRIVIAL")) {
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("NL") &&
!xl.getValue().equals(get(Item.NAME)))
b.addElement( xl.getValue() );
}
}
}
}
o = b;
break;
case Item.PDB :
String s = "";
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME")) {
if (x.getATT("MIME").equals("chemical/x-pdb"))
s = x.getCDATA();
}
}
o = s;
};
break;
case Item.MOL :
s = "";
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME")) {
if (x.getATT("MIME").equals("chemical/x-mdl-molfile"))
s = x.getCDATA();
}
}
o = s;
};
break;
case Item.PICTUREFILE :
Picture p = new Picture();
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME")) {
if (x.getATT("MIME").equals("image/gif") &&
(!x.containsATT("VIEW") || !x.getATT("VIEW").equals("TOP") ) ) {
String file = x.getCDATA().trim();
if (x.containsATT("TITLE")) {
p = new Picture(file, x.getATT("TITLE"));
} else {
p = new Picture(file);
}
}
}
}
o = p;
};
break;
case Item.REACTIE :
s = "";
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME") && x.containsATT("VIEW")) {
if (x.getATT("MIME").equals("image/gif") &&
x.getATT("VIEW").equals("TOP")) {
s = x.getCDATA().trim();
}
}
}
o = s;
};
break;
default :
o = super.get(code);
break;
}
}
return o;
}
public boolean contains(int code) {
boolean b = false;
if (code >= 100) {
switch (code) {
case XItem.XGERMAN :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("DE"))
b = true;
}
}
}
break;
case XItem.XLATIN :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("LATIN"))
b = true;
}
}
}
break;
default:
b = (this.data[code-100] != null);
break;
}
} else {
switch (code) {
case Item.ENGLISH :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("EN"))
b = true;
}
}
}
break;
case Item.TRIVIALNAME :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
if (xname.getCLASS().equals("TRIVIAL")) {
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("NL") &&
!xl.getValue().equals(get(Item.NAME)))
b = true;
}
}
}
}
break;
case Item.IUPACNAME :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
if (xname.getCLASS().equals("IUPAC")) {
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("NL")) b = true;
}
}
}
}
break;
case Item.AFKORT :
if (contains(XItem.XNAME)) {
Vector names = (Vector)get(XItem.XNAME);
Enumeration e = names.elements();
while (e.hasMoreElements()) {
XNAME xname = (XNAME)e.nextElement();
if (xname.getCLASS().equals("ABBREV")) {
Enumeration langs = xname.elements();
while (langs.hasMoreElements()) {
XLANG xl = (XLANG)langs.nextElement();
if (xl.getID().equals("NL")) b = true;
}
}
}
} else {
b = super.contains(Item.AFKORT);
}
break;
case Item.PDB :
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME")) {
if (x.getATT("MIME").equals("chemical/x-pdb"))
b = true;
}
}
}
break;
case Item.MOL :
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME")) {
if (x.getATT("MIME").equals("chemical/x-mdl-molfile"))
b = true;
}
}
}
break;
case Item.PICTUREFILE :
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME")) {
if (x.getATT("MIME").equals("image/gif") &&
(!x.containsATT("VIEW") ||
!x.getATT("VIEW").equals("TOP") ) )
b = true;
}
}
};
break;
case Item.REACTIE :
if (contains(XItem.XMEDIA)) {
Vector v = (Vector)get(XItem.XMEDIA);
Enumeration e = v.elements();
while (e.hasMoreElements()) {
XNODE x = (XNODE)e.nextElement();
if (x.containsATT("MIME") && x.containsATT("VIEW")) {
if (x.getATT("MIME").equals("image/gif") &&
x.getATT("VIEW").equals("TOP")) {
b = true;
}
}
}
};
break;
default :
b = super.contains(code);
break;
}
}
return b;
}
}
--- NEW FILE: XTYPE.java ---
package com.egonw.woc;
import java.util.*;
import com.objectspace.jgl.*;
import com.egonw.woc.util.*;
import com.egonw.woc.wml.*;
public class XTYPE {
public final static int CHEMICAL = 1;
public final static int ABBREV = 2;
public final static int VERW = 4;
public final static int REACTION = 8;
public final static int IUPAC_RULE = 16;
public final static int POLYMER = 32;
public final static int MIXTURE = 64;
public final static int GROUP = 128;
private final static int TOTAL_TYPES = 3;
private int value;
public XTYPE() {
value = 0;
}
public void setType(int type) {
if (!isType(type)) {
value += type;
}
}
public boolean isType(int type) {
boolean result = false;
int foo = value;
for (int i = TOTAL_TYPES ; i > 0; i--) {
if (((foo - power(2,i-1)) >= 0)) {
if ( power(2,i-1) == type ) result = true;
foo -= power(2,i-1);
}
}
return result;
}
private int power(int number, int power) {
int result = 1;
for (int i=1; i<=power; i++) {
result = result * number;
}
return result;
}
}
|
Update of /cvsroot/woc/woc/src/woc/src/index
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/src/index
Added Files:
Makefile.am genlangxslts.pl genlangxslts.pl.in
index.abbrev.xsl index.bruto.xsl index.cas2smiles.xsl
index.en.xsl index.enum.xsl index.nl.xsl index.smiles2cas.xsl
index.vnnum.xsl makechemtrans.sh templindex.XX-XX.xsl
update.sh update.sh.in woclist.pl woclist.pl.in woclist.sh
woclist.sh.in
Log Message:
--- NEW FILE: Makefile.am ---
bindir=${prefix}/bin/index
bin_SCRIPTS = \
woclist.sh \
woclist.pl \
genlangxslts.pl \
update.sh
CLEANFILES = $(bin_SCRIPTS)
--- NEW FILE: genlangxslts.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
my %langs = (
"NL" => {
"EN" => "Dutch",
"NL" => "Nederlands",
},
"EN" => {
"EN" => "English",
"NL" => "Engels",
},
"DE" => {
"EN" => "German",
"NL" => "Duits",
},
"IT" => {
"EN" => "Italian",
"NL" => "Italiaans",
},
"FR" => {
"EN" => "French",
"NL" => "Frans",
},
"ES" => {
"EN" => "Spanish",
"NL" => "Spaans",
},
"LA" => {
"EN" => "Latin",
"NL" => "Latijn",
},
"FY" => {
"EN" => "Frysian",
"NL" => "Fries",
},
);
foreach my $from (keys(%langs)) {
foreach my $to (keys(%langs)) {
print "$from -> $to$/";
open(INPUT, "<templindex.XX-XX.xsl");
open(OUTPUT, ">index.$from-$to.xsl");
while(<INPUT>) {
s/#FROM#/$from/;
s/#TO#/$to/;
print OUTPUT;
}
}
}
open(OUTPUT, ">makechemtrans.sh");
print OUTPUT "#! /usr/bin/sh\n";
print OUTPUT "# This script is autogenerated with genlangxslts.pl! Do not edit!\n\n";
print OUTPUT "all=\"";
foreach my $from (keys(%langs)) {
foreach my $to (keys(%langs)) {
if ($from ne $to) {
print OUTPUT "index.$from-$to \\\n";
}
}
}
print OUTPUT "\"\n\n";
print OUTPUT "update.sh \$all\n";
`chmod 755 makechemtrans.sh`
--- NEW FILE: genlangxslts.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
my %langs = (
"NL" => {
"EN" => "Dutch",
"NL" => "Nederlands",
},
"EN" => {
"EN" => "English",
"NL" => "Engels",
},
"DE" => {
"EN" => "German",
"NL" => "Duits",
},
"IT" => {
"EN" => "Italian",
"NL" => "Italiaans",
},
"FR" => {
"EN" => "French",
"NL" => "Frans",
},
"ES" => {
"EN" => "Spanish",
"NL" => "Spaans",
},
"LA" => {
"EN" => "Latin",
"NL" => "Latijn",
},
"FY" => {
"EN" => "Frysian",
"NL" => "Fries",
},
);
foreach my $from (keys(%langs)) {
foreach my $to (keys(%langs)) {
print "$from -> $to$/";
open(INPUT, "<templindex.XX-XX.xsl");
open(OUTPUT, ">index.$from-$to.xsl");
while(<INPUT>) {
s/#FROM#/$from/;
s/#TO#/$to/;
print OUTPUT;
}
}
}
open(OUTPUT, ">makechemtrans.sh");
print OUTPUT "#! @PATHTOSH@\n";
print OUTPUT "# This script is autogenerated with genlangxslts.pl! Do not edit!\n\n";
print OUTPUT "all=\"";
foreach my $from (keys(%langs)) {
foreach my $to (keys(%langs)) {
if ($from ne $to) {
print OUTPUT "index.$from-$to \\\n";
}
}
}
print OUTPUT "\"\n\n";
print OUTPUT "update.sh \$all\n";
`chmod 755 makechemtrans.sh`
--- NEW FILE: index.abbrev.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xsl:version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Afkortingen");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM/DICT/ABBREV">
<xsl:sort />
<tr>
<td class="main"><xsl:value-of select="."/></td>
<xsl:choose>
<xsl:when test="../NAME/LANG[@ID='NL']">
<td class="main">
<a href="http://www.sci.kun.nl/woc/gui/items/{../../@FILE}.shtml">
<xsl:value-of select="../NAME/LANG[@ID='NL']"/></a>
</td>
</xsl:when>
<xsl:otherwise>
<td class="main">
<a href="http://www.sci.kun.nl/woc/gui/items/{../../@FILE}.shtml">
<xsl:value-of select="../../@NAME"/></a>
</td>
</xsl:otherwise>
</xsl:choose>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<!-- Poging A, B, C, etc.. voor de delen te zetten
xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'A'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'B'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'C'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'D'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'E'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'F'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'G'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'H'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'I'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'J'"/>
</xsl:call-template>
<xsl:call-template name="letter-deel">
<xsl:with-param name="letter" select="'K'"/>
</xsl:call-template>
</table>
</xsl:template>
<xsl:template name="letter-deel">
<xsl:param name="letter" select="."/>
<H3><xsl:value-of select="$letter"/></H3>
<xsl:for-each select="ITEM/DICT/ABBREV[starts-with(string(),$letter)]">
<xsl:sort />
<tr>
<td class="main"><a href="http://www.sci.kun.nl/woc/gui/items/{../../@FILE}.shtml"><xsl:value-of select="."/></a></td>
<td class="main"><a href="http://www.sci.kun.nl/woc/gui/items/{../../@FILE}.shtml"><xsl:value-of select="../NAME/LANG[@ID='NL']"/></a></td>
</tr>
</xsl:for-each>
</xsl:template-->
</xsl:stylesheet>
--- NEW FILE: index.bruto.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet version="1.0"
xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<!-- xsl:output mode="html"/ -->
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Bruto Formule lijst");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist"/>
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM/molecule/string[@title='StoichiometryID']">
<xsl:sort select="."/>
<tr>
<td class="main"><xsl:apply-templates select="../string[@title='Stoichiometry']"/></td>
<td class="main">
<a href="http://www.sci.kun.nl/woc/gui/items/{../../@FILE}.shtml">
<xsl:value-of select="../../@NAME" /></a></td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
<xsl:template match="sub">
<sub><xsl:apply-templates /></sub>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: index.cas2smiles.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Nederlands-Engels");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="NAME">
<xsl:apply-templates/>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM">
<xsl:sort select="INDEX[@CLASS='CAS-NUMBER']"/>
<xsl:for-each select="INDEX[@CLASS='CAS-NUMBER']">
<xsl:if test=".">
<tr>
<td class="main"><a href="http://www.sci.kun.nl/woc/gui/items/{../@FILE}.shtml"><xsl:value-of select="."/></a></td>
<td class="main"><xsl:value-of select="../INDEX[@CLASS='SMILES']"/></td>
</tr>
</xsl:if>
</xsl:for-each>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: index.en.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Afkortingen");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="//LANG[@ID='EN']">
<xsl:sort select="."/>
<tr>
<td class="main">
<a href="http://www.sci.kun.nl/woc/gui/items/{../../../@FILE}.shtml"><xsl:value-of select="."/></a>
</td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: index.enum.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" xsl:version="1.0">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Nederlands-Engels");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="NAME">
<xsl:apply-templates/>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM">
<xsl:sort select="INDEX[@CLASS='E-NUMBER']"/>
<xsl:for-each select="INDEX[@CLASS='E-NUMBER']">
<xsl:if test=".">
<tr>
<td class="main"><xsl:text>E</xsl:text><xsl:value-of select="."/></td>
<td class="main"><a href="http://www.sci.kun.nl/woc/gui/items/{../@FILE}.shtml"><xsl:value-of select="../@NAME"/></a></td>
</tr>
</xsl:if>
</xsl:for-each>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: index.nl.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xsl:version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Afkortingen");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="//LANG[@ID='NL']">
<xsl:sort select="."/>
<tr>
<td class="main">
<a href="http://www.sci.kun.nl/woc/gui/items/{../../../@FILE}.shtml"><xsl:value-of select="."/></a>
</td>
</tr>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: index.smiles2cas.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Nederlands-Engels");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="NAME">
<xsl:apply-templates/>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM">
<xsl:sort select="INDEX[@CLASS='SMILES']"/>
<xsl:for-each select="INDEX[@CLASS='SMILES']">
<xsl:if test=".">
<tr>
<td class="main"><a href="http://www.sci.kun.nl/woc/gui/items/{../@FILE}.shtml"><xsl:value-of select="."/></a></td>
<td class="main"><xsl:value-of select="../INDEX[@CLASS='CAS-NUMBER']"/></td>
</tr>
</xsl:if>
</xsl:for-each>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: index.vnnum.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output mode="html"/>
<xsl:template match="/">
<html>
<head>
<base href="http://www.sci.kun.nl/woc/"/>
<link rel="stylesheet" href="http://www.sci.kun.nl/woc/gui/styles/woc.css" type="text/css"/>
<script src="gui/javascript/isframe.js"></script>
<script src="gui/javascript/browsertest.js"></script>
<script src="gui/javascript/location.js"></script>
<script><xsl:comment>
setLocation("Nederlands-Engels");
// </xsl:comment>
</script>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="NAME">
<xsl:apply-templates/>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM">
<xsl:sort select="INDEX[@CLASS='UN-NUMBER']"/>
<xsl:for-each select="INDEX[@CLASS='UN-NUMBER']">
<xsl:if test=".">
<tr>
<td class="main">UN <xsl:value-of select="."/></td>
<td class="main"><a href="http://www.sci.kun.nl/woc/gui/items/{../@FILE}.shtml"><xsl:value-of select="../@NAME"/></a></td>
</tr>
</xsl:if>
</xsl:for-each>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: makechemtrans.sh ---
#! /usr/bin/sh
# This script is autogenerated with genlangxslts.pl! Do not edit!
all="index.EN-FR \
index.EN-ES \
index.EN-DE \
index.EN-NL \
index.EN-IT \
index.EN-LA \
index.EN-FY \
index.FR-EN \
index.FR-ES \
index.FR-DE \
index.FR-NL \
index.FR-IT \
index.FR-LA \
index.FR-FY \
index.ES-EN \
index.ES-FR \
index.ES-DE \
index.ES-NL \
index.ES-IT \
index.ES-LA \
index.ES-FY \
index.DE-EN \
index.DE-FR \
index.DE-ES \
index.DE-NL \
index.DE-IT \
index.DE-LA \
index.DE-FY \
index.NL-EN \
index.NL-FR \
index.NL-ES \
index.NL-DE \
index.NL-IT \
index.NL-LA \
index.NL-FY \
index.IT-EN \
index.IT-FR \
index.IT-ES \
index.IT-DE \
index.IT-NL \
index.IT-LA \
index.IT-FY \
index.LA-EN \
index.LA-FR \
index.LA-ES \
index.LA-DE \
index.LA-NL \
index.LA-IT \
index.LA-FY \
index.FY-EN \
index.FY-FR \
index.FY-ES \
index.FY-DE \
index.FY-NL \
index.FY-IT \
index.FY-LA \
"
update.sh $all
--- NEW FILE: templindex.XX-XX.xsl ---
<?xml version="1.0"?>
<xsl:stylesheet xsl:version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
<!-- This stylesheet is autogenerated with genlangxslts.pl! Do not edit! -->
<xsl:template match="/">
<html>
<head>
<base href="http://www-woc.sci.kun.nl/"/>
<link rel="stylesheet" href="http://www-woc.sci.kun.nl/gui/styles/woc.css" type="text/css"/>
</head>
<body class="main">
<hr/>
<xsl:apply-templates select="woclist" />
<hr/>
</body>
</html>
</xsl:template>
<xsl:template match="NAME">
<xsl:apply-templates/>
</xsl:template>
<xsl:template match="woclist">
<table border="0" celpadding="0" cellspacing="0" width="100%">
<xsl:for-each select="ITEM/DICT/NAME">
<xsl:sort select="LANG[@ID='#FROM#']"/>
<xsl:for-each select="LANG[@ID='#FROM#']">
<xsl:if test="../LANG[@ID='#TO#']">
<tr>
<td class="main"><xsl:value-of select="."/></td>
<td class="main"><a href="http://www-woc.sci.kun.nl/gui/items/{../../../@FILE}.shtml"><xsl:value-of select="../LANG[@ID='#TO#']"/></a></td>
</tr>
</xsl:if>
</xsl:for-each>
</xsl:for-each>
</table>
</xsl:template>
</xsl:stylesheet>
--- NEW FILE: update.sh ---
#! /usr/bin/sh -f
name="woclist"
baseuri="http://www-woc.sci.kun.nl/gui/index"
htmldir="../../web-docs/gui/index"
datadir="."
# The default makes all indices except for the pages
# translating words XX-XX. Those are done with the
# script makechemtrans.pl.
all="index.abbrev index.bruto index.nl index.enum index.vnnum \
index.smiles2cas index.cas2smiles"
if test "x$1" = "x"
then
echo "Usage: update.pl xml"
echo "Usage: update.pl [web] all"
echo "Usage: update.pl [web] <index-name> ..."
else
if test "x$1" = "xxml"
then
echo "Creating new $datadir/$name.xml..."
$datadir/$name.sh
exit
fi
if test "x$1" = "xweb"
then
echo "Content-type: text/html"
echo ""
shift
fi
if test "x$1" = "xall";
then
shift
./update.sh $all
else
for index in $*
do
echo "Parsing $datadir/$name.xml against $datadir/$index.xsl..."
xsltproc $datadir/$index.xsl $datadir/$name.xml > $htmldir/$index.html
chmod 664 $htmldir/$index.html
# chgrp wwwwoc $htmldir/$index.html
done
echo "Done!"
fi
fi
--- NEW FILE: update.sh.in ---
#! @PATHTOSH@ -f
name="woclist"
baseuri="http://www-woc.sci.kun.nl/gui/index"
htmldir="../../web-docs/gui/index"
datadir="."
# The default makes all indices except for the pages
# translating words XX-XX. Those are done with the
# script makechemtrans.pl.
all="index.abbrev index.bruto index.nl index.enum index.vnnum \
index.smiles2cas index.cas2smiles"
if test "x$1" = "x"
then
echo "Usage: update.pl xml"
echo "Usage: update.pl [web] all"
echo "Usage: update.pl [web] <index-name> ..."
else
if test "x$1" = "xxml"
then
echo "Creating new $datadir/$name.xml..."
$datadir/$name.sh
exit
fi
if test "x$1" = "xweb"
then
echo "Content-type: text/html"
echo ""
shift
fi
if test "x$1" = "xall";
then
shift
./update.sh $all
else
for index in $*
do
echo "Parsing $datadir/$name.xml against $datadir/$index.xsl..."
xsltproc $datadir/$index.xsl $datadir/$name.xml > $htmldir/$index.html
chmod 664 $htmldir/$index.html
# chgrp wwwwoc $htmldir/$index.html
done
echo "Done!"
fi
fi
--- NEW FILE: woclist.pl ---
#! /usr/bin/perl
use strict;
use diagnostics;
# Author: Geert Josten
# hulp-script gebruikt door wocml.sh
my $cmldir="../../data/dadml/physicalprop/cml";
my $infile;
my $outfile;
if (@ARGV >= 2) {
$infile = shift;
$outfile = shift;
} else {
$infile = "woclist.tmp2.xml";
$outfile = "woclist.xml";
}
open (INFILE, "$infile");
open (OUTFILE, ">$outfile");
#print eerste regel alvast
$_ = <INFILE>; print OUTFILE;
while (<INFILE>) {
my $file;
if (/ITEM.*?CODE=/i) {
s/CODE/FILE/i;
print OUTFILE;
} elsif (/INSERT.*PhysicalProperties.*>(.*)</i) {
my @inserts = `awk '/<molecule/,/<\\/molecule/{print " ",\$0}' $cmldir/$1`;
foreach my $insert (@inserts) {
if ($insert =~ /^(.*Stoichiometry.*>)(.*)(<.*)$/i) {
my $pre = $1;
my $bruto = $2;
my $brutoID = $2;
my $post = $3;
$bruto =~ s/(\d+)/<sub>$1<\/sub>/ig;
print OUTFILE $pre,$bruto,$post,$/;
$pre =~ s/Stoichiometry/StoichiometryID/i;
$brutoID =~ s/(\d+)/{$1}/ig;
while ($brutoID =~ /\{(\d+?)\}/) {
my $number = sprintf "%04i", $1;
$brutoID =~ s/\{\d+?\}/$number/;
}
print OUTFILE $pre,$brutoID,$post,$/;
} else {
print OUTFILE $insert;
}
}
} elsif (/\<\?xml.*\?\>/i) {
s/\<\?xml.*\?\>//i;
print OUTFILE;
} else {
print OUTFILE;
}
}
# zoals in Convert.java
sub NAMELikeToANCHORLike {
# heeft 1 parameter
my $param = shift @_;
$param =~ s/^\s*(.*?)\s*$/$1/ig;
$param =~ s/\ /\_/g;
$param =~ s/[,|.|<|>]//g;
$param =~ tr/[A-Z]/[a-z]/;
return $param;
}
--- NEW FILE: woclist.pl.in ---
#! @PATHTOPERL@
use strict;
use diagnostics;
# Author: Geert Josten
# hulp-script gebruikt door wocml.sh
my $cmldir="../../data/dadml/physicalprop/cml";
my $infile;
my $outfile;
if (@ARGV >= 2) {
$infile = shift;
$outfile = shift;
} else {
$infile = "woclist.tmp2.xml";
$outfile = "woclist.xml";
}
open (INFILE, "$infile");
open (OUTFILE, ">$outfile");
#print eerste regel alvast
$_ = <INFILE>; print OUTFILE;
while (<INFILE>) {
my $file;
if (/ITEM.*?CODE=/i) {
s/CODE/FILE/i;
print OUTFILE;
} elsif (/INSERT.*PhysicalProperties.*>(.*)</i) {
my @inserts = `awk '/<molecule/,/<\\/molecule/{print " ",\$0}' $cmldir/$1`;
foreach my $insert (@inserts) {
if ($insert =~ /^(.*Stoichiometry.*>)(.*)(<.*)$/i) {
my $pre = $1;
my $bruto = $2;
my $brutoID = $2;
my $post = $3;
$bruto =~ s/(\d+)/<sub>$1<\/sub>/ig;
print OUTFILE $pre,$bruto,$post,$/;
$pre =~ s/Stoichiometry/StoichiometryID/i;
$brutoID =~ s/(\d+)/{$1}/ig;
while ($brutoID =~ /\{(\d+?)\}/) {
my $number = sprintf "%04i", $1;
$brutoID =~ s/\{\d+?\}/$number/;
}
print OUTFILE $pre,$brutoID,$post,$/;
} else {
print OUTFILE $insert;
}
}
} elsif (/\<\?xml.*\?\>/i) {
s/\<\?xml.*\?\>//i;
print OUTFILE;
} else {
print OUTFILE;
}
}
# zoals in Convert.java
sub NAMELikeToANCHORLike {
# heeft 1 parameter
my $param = shift @_;
$param =~ s/^\s*(.*?)\s*$/$1/ig;
$param =~ s/\ /\_/g;
$param =~ s/[,|.|<|>]//g;
$param =~ tr/[A-Z]/[a-z]/;
return $param;
}
--- NEW FILE: woclist.sh ---
#! /usr/bin/sh -e
# Author: Geert Josten
NAME="woclist"
EXT=".xml"
TEMP=".tmp"
TEMP2=".tmp2"
WMLDIR="../../data/wml"
# cmldir is in perl-stukje gedefinieerd
echo "" > $NAME$TEMP
cat `find $WMLDIR/123 -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/a -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/b -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/c -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/d -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/e -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/f -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/g -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/h -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/i -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/j -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/k -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/l -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/m -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/n -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/o -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/p -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/q -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/r -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/s -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/t -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/u -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/v -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/w -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/x -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/y -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/z -name "*.xml" | grep -v templates` >> $NAME$TEMP
echo '<?xml version="1.0" encoding="ISO-8859-1"?>' > $NAME$TEMP2
echo '<!DOCTYPE ITEM SYSTEM "../../lib/xml/dtd/'$NAME'.dtd">' >> $NAME$TEMP2
echo '<'$NAME' xmlns:xsl="http://www.w3.org/1999/XSL/Transform"' >> $NAME$TEMP2
echo ' xmlns:import="http://www.sci.kun.nl/woc/import"' >> $NAME$TEMP2
echo ' xmlns:xlink="http://www.sci.kun.nl/woc/topicmap">' >> $NAME$TEMP2
awk "/<ITEM/,/<\/ITEM/{print}" $NAME$TEMP >> $NAME$TEMP2
echo '</'$NAME'>' >> $NAME$TEMP2
/usr/bin/perl $NAME.pl $NAME$TEMP2 $NAME$EXT
rm $NAME$TEMP $NAME$TEMP2
# chgrp wwwwoc $NAME$EXT
chmod 664 $NAME$EXT
--- NEW FILE: woclist.sh.in ---
#! @PATHTOSH@ -e
# Author: Geert Josten
NAME="woclist"
EXT=".xml"
TEMP=".tmp"
TEMP2=".tmp2"
WMLDIR="../../data/wml"
# cmldir is in perl-stukje gedefinieerd
echo "" > $NAME$TEMP
cat `find $WMLDIR/123 -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/a -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/b -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/c -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/d -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/e -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/f -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/g -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/h -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/i -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/j -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/k -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/l -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/m -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/n -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/o -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/p -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/q -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/r -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/s -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/t -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/u -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/v -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/w -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/x -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/y -name "*.xml" | grep -v templates` >> $NAME$TEMP
cat `find $WMLDIR/z -name "*.xml" | grep -v templates` >> $NAME$TEMP
echo '<?xml version="1.0" encoding="ISO-8859-1"?>' > $NAME$TEMP2
echo '<!DOCTYPE ITEM SYSTEM "../../lib/xml/dtd/'$NAME'.dtd">' >> $NAME$TEMP2
echo '<'$NAME' xmlns:xsl="http://www.w3.org/1999/XSL/Transform"' >> $NAME$TEMP2
echo ' xmlns:import="http://www.sci.kun.nl/woc/import"' >> $NAME$TEMP2
echo ' xmlns:xlink="http://www.sci.kun.nl/woc/topicmap">' >> $NAME$TEMP2
awk "/<ITEM/,/<\/ITEM/{print}" $NAME$TEMP >> $NAME$TEMP2
echo '</'$NAME'>' >> $NAME$TEMP2
@PATHTOPERL@ $NAME.pl $NAME$TEMP2 $NAME$EXT
rm $NAME$TEMP $NAME$TEMP2
# chgrp wwwwoc $NAME$EXT
chmod 664 $NAME$EXT
|
|
From: Geert J. <gj...@us...> - 2002-09-03 19:40:56
|
Update of /cvsroot/woc/woc/src/woc/wocjava/source/com/egonw/woc/exception
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/wocjava/source/com/egonw/woc/exception
Added Files:
BadCommentNotification.java BadItemNotification.java
DuplicateItemNotification.java EmptyItemNotification.java
IncompleteItemNotification.java UnknownFieldNotification.java
WocException.java WocFatalError.java WocNotification.java
Log Message:
--- NEW FILE: BadCommentNotification.java ---
package com.egonw.woc.exception;
import com.egonw.woc.*;
/**
* Signals that an error occured during the reading of a Woc-format file.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class BadCommentNotification extends BadItemNotification {
public BadCommentNotification(Item i) {
super(i);
}
}
--- NEW FILE: BadItemNotification.java ---
package com.egonw.woc.exception;
import com.egonw.woc.*;
/**
* Signals that an error occured during the reading of a Woc-format file.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class BadItemNotification extends WocNotification {
public BadItemNotification(Item i) {
super(i);
}
}
--- NEW FILE: DuplicateItemNotification.java ---
package com.egonw.woc.exception;
import com.egonw.util.*;
import com.egonw.woc.*;
/**
* Signals an non-terminal error.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class DuplicateItemNotification extends WocNotification {
/**
* Constructs a <code>DuplicateItemException</code>.
*/
public DuplicateItemNotification(Item i) {
super(i);
}
}
--- NEW FILE: EmptyItemNotification.java ---
package com.egonw.woc.exception;
import com.egonw.woc.*;
/**
* Signals an non-terminal error.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class EmptyItemNotification extends WocNotification {
/**
* Constructs a <code>EmptyItemException</code>.
*/
public EmptyItemNotification(Item i) {
super(i);
}
}
--- NEW FILE: IncompleteItemNotification.java ---
package com.egonw.woc.exception;
import com.egonw.util.*;
import com.egonw.woc.*;
/**
* Signals an non-terminal error.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class IncompleteItemNotification extends WocNotification {
/**
* Constructs a <code>IncompleteItemException</code>.
*/
public IncompleteItemNotification(Item i) {
super(i);
}
}
--- NEW FILE: UnknownFieldNotification.java ---
package com.egonw.woc.exception;
import com.egonw.woc.*;
/**
* Signals that an error occured during the reading of a Woc-format file.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class UnknownFieldNotification extends BadItemNotification {
public UnknownFieldNotification(Item i) {
super(i);
}
}
--- NEW FILE: WocException.java ---
package com.egonw.woc.exception;
import java.lang.Exception;
/**
* Signals an non-terminal error.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class WocException extends Exception {
/**
* Constructs a <code>WocException</code> with no detail message.
*/
public WocException() {
super();
}
/**
* Constructs a <code>WocException</code> with a detail message.
*/
public WocException(String s) {
super(s);
}
}
--- NEW FILE: WocFatalError.java ---
package com.egonw.woc.exception;
import com.egonw.util.*;
/**
* Signals an non-terminal error.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class WocFatalError extends WocException {
/**
* Constructs a <code>WocFatalError</code> with no detail message.
*/
public WocFatalError() {
super();
}
/**
* Constructs a <code>WocFatalError</code> with a detail message.
*/
public WocFatalError(String s) {
super();
}
}
--- NEW FILE: WocNotification.java ---
package com.egonw.woc.exception;
import com.egonw.util.*;
import com.egonw.woc.*;
/**
* Signals an non-terminal error.
*
* @author Egon Willighagen
* @version 1.0, 1/7/98
*/
public class WocNotification extends WocException {
private Item i;
/**
* Constructs a <code>WocException</code> with no detail message.
*/
public WocNotification(Item i) {
super();
this.i = i;
}
/**
* Returns the item.
*/
public String toString() {
return (String)i.get(Item.NAME);
}
}
|
Update of /cvsroot/woc/woc/src/woc/src/wml2html
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/src/wml2html
Added Files:
Makefile.am insert-item insert-item.in make-groups
make-groups.in make-items make-items.in make-woord
make-woord.in
Log Message:
--- NEW FILE: Makefile.am ---
##### CONFIGURE DEFINITIONS #####
PREFIX="@prefix@"
##### GLOBAL DEFINITIONS #####
##### AUTOMAKE SPECIALS #####
wml2htmlbindir=${PREFIX}/content/bin/wml2html
wml2htmlbin_SCRIPTS= \
make-items \
make-groups \
make-woord \
insert-item
CLEANFILES= WMLreport.txt ${bin_SCRIPTS}
##### LOCAL DEFINITIONS #####
##### RULES #####
--- NEW FILE: insert-item ---
#! /bin/sh
prefix="/cygdrive/e/woc/wocnew"
JAVA=/cygdrive/d/aanplant/jdk1.2.2/bin/java
PERL=/usr/bin/perl
if (test $# = 1)
then
:
else
echo "syntax: insert-item <item.xml>"
exit 1
fi
if (test -d ${prefix}/web-docs/gui/items)
then
:
else
mkdir -p ${prefix}/web-docs/gui/items
fi
JARS=`ls -1 ../../lib/java/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
OPTIONS="-r woc -R ${prefix}/bin/wml2html/repository_def.xml"
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ]
|| [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
OPTIONS=`cygpath --path --windows "$OPTIONS"`
fi
${JAVA} -cp ${JARS} com.egonw.woc.tools.SimpleAddItem ${OPTIONS} $1
--- NEW FILE: insert-item.in ---
#! /bin/sh
prefix="@prefix@"
JAVA=@PATHTOJAVA@
PERL=@PATHTOPERL@
if (test $# = 1)
then
:
else
echo "syntax: insert-item <item.xml>"
exit 1
fi
if (test -d ${prefix}/web-docs/gui/items)
then
:
else
mkdir -p ${prefix}/web-docs/gui/items
fi
JARS=`ls -1 ../../lib/java/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
OPTIONS="-r woc -R ${prefix}/bin/wml2html/repository_def.xml"
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ]
|| [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
OPTIONS=`cygpath --path --windows "$OPTIONS"`
fi
${JAVA} -cp ${JARS} com.egonw.woc.tools.SimpleAddItem ${OPTIONS} $1
--- NEW FILE: make-groups ---
#! /bin/sh
prefix="/cygdrive/e/woc/wocnew"
JAVA=java
#/cygdrive/d/aanplant/jdk1.2.2/bin/java
PERL=/usr/bin/perl
JARS=`ls -1 ../../lib/java/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
REPOSDEFFILE=`pwd`/repository_def.xml
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ]
|| [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
REPOSDEFFILE=`cygpath --path --windows "$REPOSDEFFILE"`
fi
OPTIONS="-r woc -R $REPOSDEFFILE"
echo ${JAVA} -cp ${JARS} com.egonw.woc.tools.GroupFiles ${OPTIONS}
${JAVA} -cp ${JARS} com.egonw.woc.tools.GroupFiles ${OPTIONS}
--- NEW FILE: make-groups.in ---
#! /bin/sh
prefix="@prefix@"
JAVA=java
#@PATHTOJAVA@
PERL=@PATHTOPERL@
JARS=`ls -1 ../../lib/java/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
REPOSDEFFILE=`pwd`/repository_def.xml
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ]
|| [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
REPOSDEFFILE=`cygpath --path --windows "$REPOSDEFFILE"`
fi
OPTIONS="-r woc -R $REPOSDEFFILE"
echo ${JAVA} -cp ${JARS} com.egonw.woc.tools.GroupFiles ${OPTIONS}
${JAVA} -cp ${JARS} com.egonw.woc.tools.GroupFiles ${OPTIONS}
--- NEW FILE: make-items ---
#! /bin/sh
JAVA=/cygdrive/d/aanplant/jdk1.2.2/bin/java
PERL=/usr/bin/perl
JARS=`ls -1 ../../lib/java/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
OPTIONS="-r `pwd`/repository_def.xml"
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ]
|| [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
OPTIONS=`cygpath --path --windows "$OPTIONS"`
fi
${JAVA} -cp ${JARS} com.egonw.woc.tools.MaakLosseItems ${OPTIONS}
--- NEW FILE: make-items.in ---
#! /bin/sh
JAVA=@PATHTOJAVA@
PERL=@PATHTOPERL@
JARS=`ls -1 ../../lib/java/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
OPTIONS="-r `pwd`/repository_def.xml"
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ]
|| [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
OPTIONS=`cygpath --path --windows "$OPTIONS"`
fi
${JAVA} -cp ${JARS} com.egonw.woc.tools.MaakLosseItems ${OPTIONS}
--- NEW FILE: make-woord ---
#! /bin/sh
##### CONFIGURE DEFINITIONS #####
PREFIX="/cygdrive/e/woc/wocnew"
JAVA="/cygdrive/d/aanplant/jdk1.2.2/bin/java"
PERL="/usr/bin/perl"
javalibdir=${PREFIX}/shared/lib/java
##### GLOBAL DEFINITIONS #####
wocjavajardir=${javalibdir}/woc
reposdir=${PREFIX}/shared/etc
repos_DATA=repository_def.xml
##### LOCAL DEFINITIONS #####
JARS=`ls -1 ${javalibdir}/*.jar ${wocjavajardir}/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
REPOSDEFFILE="$reposdir/$repos_DATA"
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ] || [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
REPOSDEFFILE=/`cygpath --path --windows "$REPOSDEFFILE"`
fi
##### EXECUTION #####
echo ${JAVA} -cp ${JARS} com.egonw.woc.tools.Woord -r ${REPOSDEFFILE}
${JAVA} -cp ${JARS} com.egonw.woc.tools.Woord -r ${REPOSDEFFILE}
--- NEW FILE: make-woord.in ---
#! /bin/sh
##### CONFIGURE DEFINITIONS #####
PREFIX="@prefix@"
JAVA="@PATHTOJAVA@"
PERL="@PATHTOPERL@"
javalibdir=${PREFIX}/shared/lib/java
##### GLOBAL DEFINITIONS #####
wocjavajardir=${javalibdir}/woc
reposdir=${PREFIX}/shared/etc
repos_DATA=repository_def.xml
##### LOCAL DEFINITIONS #####
JARS=`ls -1 ${javalibdir}/*.jar ${wocjavajardir}/*.jar | ${PERL} -ne "s/\n|\r/:/g; print;"`
REPOSDEFFILE="$reposdir/$repos_DATA"
# convert the unix path to windows
if [ "$OSTYPE" = "cygwin32" ] || [ "$OSTYPE" = "cygwin" ] || [ "$OSTYPE" = "posix" ] ; then
JARS=`cygpath --path --windows "$JARS"`
REPOSDEFFILE=/`cygpath --path --windows "$REPOSDEFFILE"`
fi
##### EXECUTION #####
echo ${JAVA} -cp ${JARS} com.egonw.woc.tools.Woord -r ${REPOSDEFFILE}
${JAVA} -cp ${JARS} com.egonw.woc.tools.Woord -r ${REPOSDEFFILE}
|
Update of /cvsroot/woc/woc/src/woc/src/check
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/src/check
Added Files:
Makefile.am check_filenames.pl check_filenames.pl.in
list-cas.pl list-cas.pl.in test-wmls-op-wellformed.pl
test-wmls-op-wellformed.pl.in voeg-fysische-gegevens-toe.pl
voeg-fysische-gegevens-toe.pl.in voeg-gif-mime-toe.pl
voeg-gif-mime-toe.pl.in voeg-pdb-mime-toe.pl
voeg-pdb-mime-toe.pl.in voeg-woc-nummer-toe.pl
voeg-woc-nummer-toe.pl.in voeg_stylesheet_toe.pl
voeg_stylesheet_toe.pl.in zet-fysisch-props-op-extensie-xml.pl
zet-fysisch-props-op-extensie-xml.pl.in
zet-wmls-op-ISO-8859-1-encoding.pl
zet-wmls-op-ISO-8859-1-encoding.pl.in
zoek-cas-bij-pdbs-voor-dadml.pl
zoek-cas-bij-pdbs-voor-dadml.pl.in zoek-chems-zonder-cas.pl
zoek-chems-zonder-cas.pl.in
zoek-chems-zonder-fysische-props.pl
zoek-chems-zonder-fysische-props.pl.in zoek-pdbs-zonder-wml.pl
zoek-pdbs-zonder-wml.pl.in zoek-wmls-bij-groepen.pl
zoek-wmls-bij-groepen.pl.in zoek-wmls-zonder-giflink.pl
zoek-wmls-zonder-giflink.pl.in
zoek-xmls-met-cas-zonder-2dcml.pl
zoek-xmls-met-cas-zonder-2dcml.pl.in
Log Message:
--- NEW FILE: Makefile.am ---
bindir=${prefix}/bin/check
bin_SCRIPTS = \
check_filenames.pl \
list-cas.pl \
test-wmls-op-wellformed.pl \
voeg-fysische-gegevens-toe.pl \
voeg-gif-mime-toe.pl \
voeg-pdb-mime-toe.pl \
voeg-woc-nummer-toe.pl \
voeg_stylesheet_toe.pl \
zet-fysisch-props-op-extensie-xml.pl \
zet-wmls-op-ISO-8859-1-encoding.pl \
zoek-cas-bij-pdbs-voor-dadml.pl \
zoek-chems-zonder-cas.pl \
zoek-chems-zonder-fysische-props.pl \
zoek-pdbs-zonder-wml.pl \
zoek-wmls-bij-groepen.pl \
zoek-wmls-zonder-giflink.pl \
zoek-xmls-met-cas-zonder-2dcml.pl
CLEANFILES = $(bin_SCRIPTS)
--- NEW FILE: check_filenames.pl ---
#! /usr/bin/perl -w
use strict;
if (scalar(@ARGV) == 0) {
print "syntax: check_filenames.pl <*.wml>$/";
exit 0;
}
my @wmlfiles = @ARGV;
my %accepted_codes = ();
my $filecount = 0;
my $filesparsed = 0;
my $codesadded = 0;
my $hasid = 0;
my $wrongid = 0;
foreach my $file (@wmlfiles) {
$filecount++;
my @content = ();
my $changed = 0;
my $correctcode = $file;
$correctcode =~ s/.*\/(.*).xml/$1/;
if (open (OPENFILE, "<$file")) {
print "Checking $file ($correctcode)...$/";
@content = <OPENFILE>;
for (my $i=0; $i < scalar(@content); $i++) {
my $line = $content[$i];
if ($line =~ /<ITEM(.*?)>/i) {
$filesparsed++;
my $args = $1;
if ($args =~ /CODE=\"(.*?)\"/) {
$hasid++;
my $code = $1;
$code =~ s/\n//g;
print " Code: $code$/";
$accepted_codes{"$code"} = "yes";
if ($code ne $correctcode) {
$wrongid++;
print " -> it should be: $correctcode$/";
print " Old: $line";
my $newline = "<ITEM$args CODE=\"$correctcode\">$/";
print " New: $newline";
$content[$i] = $newline;
$changed = 1;
}
} else {
# should correct this file
print " Old: $line";
my $newline = "<ITEM$args CODE=\"$correctcode\">$/";
print " New: $newline";
$accepted_codes{"$correctcode"} = "yes";
$content[$i] = $newline;
$changed = 1;
}
}
}
close(OPENFILE);
}
if ($changed) {
if (open(OPENFILE, ">$file")) {
$codesadded++;
print OPENFILE @content;
} else {
print "ERROR: file $file could not be saved!";
}
}
}
# now come the process of checking references
my $wrong_group = "";
foreach my $file (@wmlfiles) {
my @content = ();
my $correctcode = $file;
$correctcode =~ s/.*\/(.*).xml/$1/;
if (open (OPENFILE, "<$file")) {
print "Checking references in $file ($correctcode)...$/";
@content = <OPENFILE>;
foreach my $line (@content) {
if ($line =~ /<GROUP>(.*)<\/GROUP>/i) {
my $group = $1;
print " checking GROUP $group...$/";
if (!($accepted_codes{"$group"})) {
print " ERROR: unknown GROUP $group$/";
}
}
}
}
}
print "----------------------------------------$/";
print " files : $filecount$/";
print " checked : $filesparsed$/";
print " code : $hasid$/";
print " corrected: $wrongid$/";
print " added : $codesadded$/";
print "----------------------------------------$/";
--- NEW FILE: check_filenames.pl.in ---
#! @PATHTOPERL@ -w
use strict;
if (scalar(@ARGV) == 0) {
print "syntax: check_filenames.pl <*.wml>$/";
exit 0;
}
my @wmlfiles = @ARGV;
my %accepted_codes = ();
my $filecount = 0;
my $filesparsed = 0;
my $codesadded = 0;
my $hasid = 0;
my $wrongid = 0;
foreach my $file (@wmlfiles) {
$filecount++;
my @content = ();
my $changed = 0;
my $correctcode = $file;
$correctcode =~ s/.*\/(.*).xml/$1/;
if (open (OPENFILE, "<$file")) {
print "Checking $file ($correctcode)...$/";
@content = <OPENFILE>;
for (my $i=0; $i < scalar(@content); $i++) {
my $line = $content[$i];
if ($line =~ /<ITEM(.*?)>/i) {
$filesparsed++;
my $args = $1;
if ($args =~ /CODE=\"(.*?)\"/) {
$hasid++;
my $code = $1;
$code =~ s/\n//g;
print " Code: $code$/";
$accepted_codes{"$code"} = "yes";
if ($code ne $correctcode) {
$wrongid++;
print " -> it should be: $correctcode$/";
print " Old: $line";
my $newline = "<ITEM$args CODE=\"$correctcode\">$/";
print " New: $newline";
$content[$i] = $newline;
$changed = 1;
}
} else {
# should correct this file
print " Old: $line";
my $newline = "<ITEM$args CODE=\"$correctcode\">$/";
print " New: $newline";
$accepted_codes{"$correctcode"} = "yes";
$content[$i] = $newline;
$changed = 1;
}
}
}
close(OPENFILE);
}
if ($changed) {
if (open(OPENFILE, ">$file")) {
$codesadded++;
print OPENFILE @content;
} else {
print "ERROR: file $file could not be saved!";
}
}
}
# now come the process of checking references
my $wrong_group = "";
foreach my $file (@wmlfiles) {
my @content = ();
my $correctcode = $file;
$correctcode =~ s/.*\/(.*).xml/$1/;
if (open (OPENFILE, "<$file")) {
print "Checking references in $file ($correctcode)...$/";
@content = <OPENFILE>;
foreach my $line (@content) {
if ($line =~ /<GROUP>(.*)<\/GROUP>/i) {
my $group = $1;
print " checking GROUP $group...$/";
if (!($accepted_codes{"$group"})) {
print " ERROR: unknown GROUP $group$/";
}
}
}
}
}
print "----------------------------------------$/";
print " files : $filecount$/";
print " checked : $filesparsed$/";
print " code : $hasid$/";
print " corrected: $wrongid$/";
print " added : $codesadded$/";
print "----------------------------------------$/";
--- NEW FILE: list-cas.pl ---
#! /usr/bin/perl -w
#
# Make a list of all cas-nummers of which compounds are given
#
use strict;
use diagnostics;
my $debug = "";
my $wmldir = "../../data/wml";
opendir (DIR, $wmldir) || die "$wmldir: $!$/";
my @files = grep {/\.xml/i} readdir(DIR);
closedir (DIR) || die "$wmldir: $!$/";
foreach my $file (@files) {
my $cas = `grep -i CAS-NUMBER $wmldir/$file`;
if ($cas) {
chomp ($cas);
$cas =~ s/\s*<INDEX.*?>\s*//ig;
$cas =~ s/\s*<\/INDEX.*?>\s*//ig;
print "$cas$/";
}
}
--- NEW FILE: list-cas.pl.in ---
#! @PATHTOPERL@ -w
#
# Make a list of all cas-nummers of which compounds are given
#
use strict;
use diagnostics;
my $debug = "";
my $wmldir = "../../data/wml";
opendir (DIR, $wmldir) || die "$wmldir: $!$/";
my @files = grep {/\.xml/i} readdir(DIR);
closedir (DIR) || die "$wmldir: $!$/";
foreach my $file (@files) {
my $cas = `grep -i CAS-NUMBER $wmldir/$file`;
if ($cas) {
chomp ($cas);
$cas =~ s/\s*<INDEX.*?>\s*//ig;
$cas =~ s/\s*<\/INDEX.*?>\s*//ig;
print "$cas$/";
}
}
--- NEW FILE: test-wmls-op-wellformed.pl ---
#! /usr/bin/perl -w
use strict;
if (! @ARGV) {
die "Usage: $0 <xml-files>$/";
}
use XML::Parser;
my $parser = new XML::Parser(ErrorContext => 2);
my $nr_files = @ARGV;
my $nr_notexist = 0;
my $nr_processed = 0;
my $nr_warnings = 0;
my $nr_ignored = 0;
my $nr_okay = 0;
foreach my $file (@ARGV) {
if (! (-e $file)) {
warn "$file: does not exist!!!$/";
$nr_notexist++;
} else {
print "Processing $file... ";
eval {
$parser->parsefile("$file");
};
if ($@) {
if ($@ =~ /<sub>/i) {
print "Probably found a <SUB> tag inside an attribute, ignoring...$/";
$nr_ignored++;
} elsif ($@ =~ /<i>/i) {
print "Probably found a <I> tag inside an attribute, ignoring...$/";
$nr_ignored++;
} else {
warn "$/$@$/";
$nr_warnings++;
}
} else {
print "Okay!$/";
$nr_okay++;
}
$nr_processed++;
}
}
if ($nr_files) {
print " -------------------------$/";
print "Files processed : $nr_files$/";
if ($nr_warnings || $nr_ignored) {
print " checked okay : $nr_okay$/";
print " warnings : $nr_warnings$/" if $nr_warnings;
print " ignored warnings : $nr_ignored$/" if $nr_ignored;
} else {
print " all files checked okay!$/";
}
print "Non-existing files : $nr_notexist$/" if ($nr_notexist);
} else {
print "No files to process!$/";
}
--- NEW FILE: test-wmls-op-wellformed.pl.in ---
#! @PATHTOPERL@ -w
use strict;
if (! @ARGV) {
die "Usage: $0 <xml-files>$/";
}
use XML::Parser;
my $parser = new XML::Parser(ErrorContext => 2);
my $nr_files = @ARGV;
my $nr_notexist = 0;
my $nr_processed = 0;
my $nr_warnings = 0;
my $nr_ignored = 0;
my $nr_okay = 0;
foreach my $file (@ARGV) {
if (! (-e $file)) {
warn "$file: does not exist!!!$/";
$nr_notexist++;
} else {
print "Processing $file... ";
eval {
$parser->parsefile("$file");
};
if ($@) {
if ($@ =~ /<sub>/i) {
print "Probably found a <SUB> tag inside an attribute, ignoring...$/";
$nr_ignored++;
} elsif ($@ =~ /<i>/i) {
print "Probably found a <I> tag inside an attribute, ignoring...$/";
$nr_ignored++;
} else {
warn "$/$@$/";
$nr_warnings++;
}
} else {
print "Okay!$/";
$nr_okay++;
}
$nr_processed++;
}
}
if ($nr_files) {
print " -------------------------$/";
print "Files processed : $nr_files$/";
if ($nr_warnings || $nr_ignored) {
print " checked okay : $nr_okay$/";
print " warnings : $nr_warnings$/" if $nr_warnings;
print " ignored warnings : $nr_ignored$/" if $nr_ignored;
} else {
print " all files checked okay!$/";
}
print "Non-existing files : $nr_notexist$/" if ($nr_notexist);
} else {
print "No files to process!$/";
}
--- NEW FILE: voeg-fysische-gegevens-toe.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "yes";
my $wmldir = "../../data/wml";
my $physpropdir = "../../data/dadml/physicalprop/cml";
my $existsfile = "tmp-physprop-exists-";
# tellers
my $nr_foundCAS = 0;
my $nr_already_linked = 0;
my $nr_gelinkt = 0;
my $nr_mislukte_links = 0;
opendir (physpropDIR, $physpropdir) || die "$physpropdir: $!$/";
my @physpropfiles = grep {/\.xml/i} readdir(physpropDIR);
closedir (physpropDIR) || die "$physpropdir: $!$/";
&create_existskeyfile ("NUMBER");
&create_existskeyfile ("PhysicalProp");
# Loop over all files
foreach my $physpropfile (@physpropfiles) {
my $cas = $physpropfile;
$cas =~ s/\.xml//ig;
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
$nr_foundCAS++;
print "NUMBER found:\t$nummatch$/" if ($debug);
my $linkmatch = &exists (("PhysicalProp" => $cas));
if ($linkmatch) {
$nr_already_linked++;
print "physprop-link found:\t$linkmatch$/" if ($debug);
} else {
print "$cas.xml can be linked!!:\t$nummatch$/";
#print "\tMEDIA-tag toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
my ($wmlfile) = split (":", $nummatch);
print "Going to chage $wmldir/$wmlfile and add $cas...$/" if $debug;
if (&voeg_link_toe("$wmldir/$wmlfile", $cas)) {
$nr_gelinkt++;
} else {
$nr_mislukte_links++;
}
#}
}
} else {
print "Dangling physprop-file $cas.xml$/";
}
}
&remove_existskeyfile ("NUMBER");
&remove_existskeyfile ("PhysicalProp");
# Print statistics
print " ----------------------------$/";
print "Files checked : ",scalar @physpropfiles, $/;
if ($nr_foundCAS) {
print " CAS or WOC number found : $nr_foundCAS$/";
my $nr_linkable = $nr_foundCAS - $nr_already_linked;
if ($nr_linkable) {
print " Linkable matches : ", $nr_foundCAS - $nr_already_linked,$/;
print " Added links : $nr_gelinkt$/" if $nr_gelinkt;
print " Links failed to add : $nr_mislukte_links$/" if $nr_mislukte_links;
my $nr_skipped_links = $nr_linkable - $nr_gelinkt - $nr_mislukte_links;
print " Skipped links : ", $nr_skipped_links,$/ if $nr_skipped_links;
print " Already linked matches : $nr_already_linked$/";
} else {
print " Already linked matches : $nr_already_linked$/";
print " No linkable matches...$/";
}
} else {
print "Not one file name matched an item name...$/";
}
my $nr_danglingphysprops = @physpropfiles - $nr_foundCAS;
print " Dangling files found : $nr_danglingphysprops$/";
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
sub voeg_link_toe {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
if (open (FILE, $file)) {
while (<FILE>) {
if (/<\/ITEM/i) {
push (@XML_data, " <INSERT MIME=\"chemical/cml\" CLASS=\"PhysicalProperties\">$cas.xml</INSERT>$/");
push (@XML_data, $_);
$changed = "True";
} else {
push (@XML_data, $_);
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
print " about to store changed file...$/" if $debug;
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "INSERT-tag added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
--- NEW FILE: voeg-fysische-gegevens-toe.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "yes";
my $wmldir = "../../data/wml";
my $physpropdir = "../../data/dadml/physicalprop/cml";
my $existsfile = "tmp-physprop-exists-";
# tellers
my $nr_foundCAS = 0;
my $nr_already_linked = 0;
my $nr_gelinkt = 0;
my $nr_mislukte_links = 0;
opendir (physpropDIR, $physpropdir) || die "$physpropdir: $!$/";
my @physpropfiles = grep {/\.xml/i} readdir(physpropDIR);
closedir (physpropDIR) || die "$physpropdir: $!$/";
&create_existskeyfile ("NUMBER");
&create_existskeyfile ("PhysicalProp");
# Loop over all files
foreach my $physpropfile (@physpropfiles) {
my $cas = $physpropfile;
$cas =~ s/\.xml//ig;
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
$nr_foundCAS++;
print "NUMBER found:\t$nummatch$/" if ($debug);
my $linkmatch = &exists (("PhysicalProp" => $cas));
if ($linkmatch) {
$nr_already_linked++;
print "physprop-link found:\t$linkmatch$/" if ($debug);
} else {
print "$cas.xml can be linked!!:\t$nummatch$/";
#print "\tMEDIA-tag toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
my ($wmlfile) = split (":", $nummatch);
print "Going to chage $wmldir/$wmlfile and add $cas...$/" if $debug;
if (&voeg_link_toe("$wmldir/$wmlfile", $cas)) {
$nr_gelinkt++;
} else {
$nr_mislukte_links++;
}
#}
}
} else {
print "Dangling physprop-file $cas.xml$/";
}
}
&remove_existskeyfile ("NUMBER");
&remove_existskeyfile ("PhysicalProp");
# Print statistics
print " ----------------------------$/";
print "Files checked : ",scalar @physpropfiles, $/;
if ($nr_foundCAS) {
print " CAS or WOC number found : $nr_foundCAS$/";
my $nr_linkable = $nr_foundCAS - $nr_already_linked;
if ($nr_linkable) {
print " Linkable matches : ", $nr_foundCAS - $nr_already_linked,$/;
print " Added links : $nr_gelinkt$/" if $nr_gelinkt;
print " Links failed to add : $nr_mislukte_links$/" if $nr_mislukte_links;
my $nr_skipped_links = $nr_linkable - $nr_gelinkt - $nr_mislukte_links;
print " Skipped links : ", $nr_skipped_links,$/ if $nr_skipped_links;
print " Already linked matches : $nr_already_linked$/";
} else {
print " Already linked matches : $nr_already_linked$/";
print " No linkable matches...$/";
}
} else {
print "Not one file name matched an item name...$/";
}
my $nr_danglingphysprops = @physpropfiles - $nr_foundCAS;
print " Dangling files found : $nr_danglingphysprops$/";
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
sub voeg_link_toe {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
if (open (FILE, $file)) {
while (<FILE>) {
if (/<\/ITEM/i) {
push (@XML_data, " <INSERT MIME=\"chemical/cml\" CLASS=\"PhysicalProperties\">$cas.xml</INSERT>$/");
push (@XML_data, $_);
$changed = "True";
} else {
push (@XML_data, $_);
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
print " about to store changed file...$/" if $debug;
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "INSERT-tag added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
--- NEW FILE: voeg-gif-mime-toe.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $gifdir = "../../data/dadml/2d/gif";
my $existsfile = "tmp-gifmime-exists";
# tellers
my $nr_foundCAS = 0;
my $nr_already_linked = 0;
my $nr_gelinkt = 0;
my $nr_mislukte_links = 0;
my $nr_dadmlpath_added = 0;
opendir (GIFDIR, $gifdir) || die "$gifdir: $!$/";
my @giffiles = grep {/\.gif/i} readdir(GIFDIR);
closedir (GIFDIR) || die "$gifdir: $!$/";
&create_existskeyfile ("NUMBER");
&create_existskeyfile ("gif");
# Loop over all files
foreach my $giffile (@giffiles) {
my $cas = $giffile;
$cas =~ s/\.gif//ig;
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
my ($wmlfile) = split (":", $nummatch);
$nr_foundCAS++;
print "NUMBER found:\t$nummatch$/" if ($debug);
my $linkmatch = &exists (("gif" => $cas));
if ($linkmatch) {
#print "$cas.gif already linked!!:\t$nummatch$/";
$nr_already_linked++;
print "GIF-link found:\t$linkmatch$/" if ($debug);
if ($linkmatch !~ /PATH/i) {
#print "\tPATH-attribuut toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
&add_dadml_path ("$wmldir/$wmlfile", $cas);
$nr_dadmlpath_added++;
#}
}
} else {
print "$cas.gif can be linked!!:\t$nummatch$/";
#print "\tMEDIA-tag toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
if (&voeg_link_toe("$wmldir/$wmlfile", $cas)) {
$nr_gelinkt++;
} else {
$nr_mislukte_links++;
}
#}
}
} else {
print "Dangling GIF-file $cas.gif$/";
}
}
&remove_existskeyfile ("NUMBER");
&remove_existskeyfile ("gif");
# Print statistics
print " ----------------------------$/";
print "Files checked : ",scalar @giffiles, $/;
if ($nr_foundCAS) {
print " CAS or WOC number found : $nr_foundCAS$/";
my $nr_linkable = $nr_foundCAS - $nr_already_linked;
if ($nr_linkable) {
print " Linkable matches : ", $nr_foundCAS - $nr_already_linked,$/;
print " Added links : $nr_gelinkt$/" if $nr_gelinkt;
print " Links failed to add : $nr_mislukte_links$/" if $nr_mislukte_links;
my $nr_skipped_links = $nr_linkable - $nr_gelinkt - $nr_mislukte_links;
print " Skipped links : $nr_skipped_links$/" if $nr_skipped_links;
print " Already linked matches : $nr_already_linked$/";
print " PATH-attibutes added : $nr_dadmlpath_added$/" if $nr_dadmlpath_added;
} else {
print " Already linked matches : $nr_already_linked$/";
print " PATH-attibutes added : $nr_dadmlpath_added$/" if $nr_dadmlpath_added;
print " No linkable matches...$/";
}
} else {
print "Not one file name matched an item name...$/";
}
my $nr_danglingGIFs = @giffiles - $nr_foundCAS;
print " Dangling files found : $nr_danglingGIFs$/";
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
sub voeg_link_toe {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
my $has_WOC = `grep -i "<WOC>" $file`;
my $has_DICT = `grep -i "<DICT>" $file` if (! $has_WOC);
my $has_INDEX = `grep -i "<INDEX" $file` if (! $has_WOC);
my $last_was_INDEX = "";
my $indent = "";
if (open (FILE, $file)) {
if ($has_WOC) {
while (<FILE>) {
if (/^(\s*)<WOC>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_INDEX) {
while (<FILE>) {
if (/^(\s*)<INDEX/i) {
$indent = $1;
push (@XML_data, $_);
$last_was_INDEX = "True";
} elsif ($last_was_INDEX && ! /<INDEX/i) {
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
push (@XML_data, $_);
$changed = "True";
$last_was_INDEX = "";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_DICT) {
while (<FILE>) {
if (/^(\s*)<\/DICT>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} else {
while (<FILE>) {
if (/^(\s*)<ITEM/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "MEDIA-tag added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
sub add_dadml_path {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
if (open (FILE, $file)) {
while (<FILE>) {
if (/MEDIA.*image\/gif.*$cas/i) {
s/MIME=\"image\/gif\">/MIME=\"image\/gif\" PATH=\"dadml\">/ig;
push (@XML_data, $_);
$changed = "True";
} else {
push (@XML_data, $_);
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "PATH-attribute added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
--- NEW FILE: voeg-gif-mime-toe.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $gifdir = "../../data/dadml/2d/gif";
my $existsfile = "tmp-gifmime-exists";
# tellers
my $nr_foundCAS = 0;
my $nr_already_linked = 0;
my $nr_gelinkt = 0;
my $nr_mislukte_links = 0;
my $nr_dadmlpath_added = 0;
opendir (GIFDIR, $gifdir) || die "$gifdir: $!$/";
my @giffiles = grep {/\.gif/i} readdir(GIFDIR);
closedir (GIFDIR) || die "$gifdir: $!$/";
&create_existskeyfile ("NUMBER");
&create_existskeyfile ("gif");
# Loop over all files
foreach my $giffile (@giffiles) {
my $cas = $giffile;
$cas =~ s/\.gif//ig;
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
my ($wmlfile) = split (":", $nummatch);
$nr_foundCAS++;
print "NUMBER found:\t$nummatch$/" if ($debug);
my $linkmatch = &exists (("gif" => $cas));
if ($linkmatch) {
#print "$cas.gif already linked!!:\t$nummatch$/";
$nr_already_linked++;
print "GIF-link found:\t$linkmatch$/" if ($debug);
if ($linkmatch !~ /PATH/i) {
#print "\tPATH-attribuut toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
&add_dadml_path ("$wmldir/$wmlfile", $cas);
$nr_dadmlpath_added++;
#}
}
} else {
print "$cas.gif can be linked!!:\t$nummatch$/";
#print "\tMEDIA-tag toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
if (&voeg_link_toe("$wmldir/$wmlfile", $cas)) {
$nr_gelinkt++;
} else {
$nr_mislukte_links++;
}
#}
}
} else {
print "Dangling GIF-file $cas.gif$/";
}
}
&remove_existskeyfile ("NUMBER");
&remove_existskeyfile ("gif");
# Print statistics
print " ----------------------------$/";
print "Files checked : ",scalar @giffiles, $/;
if ($nr_foundCAS) {
print " CAS or WOC number found : $nr_foundCAS$/";
my $nr_linkable = $nr_foundCAS - $nr_already_linked;
if ($nr_linkable) {
print " Linkable matches : ", $nr_foundCAS - $nr_already_linked,$/;
print " Added links : $nr_gelinkt$/" if $nr_gelinkt;
print " Links failed to add : $nr_mislukte_links$/" if $nr_mislukte_links;
my $nr_skipped_links = $nr_linkable - $nr_gelinkt - $nr_mislukte_links;
print " Skipped links : $nr_skipped_links$/" if $nr_skipped_links;
print " Already linked matches : $nr_already_linked$/";
print " PATH-attibutes added : $nr_dadmlpath_added$/" if $nr_dadmlpath_added;
} else {
print " Already linked matches : $nr_already_linked$/";
print " PATH-attibutes added : $nr_dadmlpath_added$/" if $nr_dadmlpath_added;
print " No linkable matches...$/";
}
} else {
print "Not one file name matched an item name...$/";
}
my $nr_danglingGIFs = @giffiles - $nr_foundCAS;
print " Dangling files found : $nr_danglingGIFs$/";
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
sub voeg_link_toe {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
my $has_WOC = `grep -i "<WOC>" $file`;
my $has_DICT = `grep -i "<DICT>" $file` if (! $has_WOC);
my $has_INDEX = `grep -i "<INDEX" $file` if (! $has_WOC);
my $last_was_INDEX = "";
my $indent = "";
if (open (FILE, $file)) {
if ($has_WOC) {
while (<FILE>) {
if (/^(\s*)<WOC>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_INDEX) {
while (<FILE>) {
if (/^(\s*)<INDEX/i) {
$indent = $1;
push (@XML_data, $_);
$last_was_INDEX = "True";
} elsif ($last_was_INDEX && ! /<INDEX/i) {
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
push (@XML_data, $_);
$changed = "True";
$last_was_INDEX = "";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_DICT) {
while (<FILE>) {
if (/^(\s*)<\/DICT>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} else {
while (<FILE>) {
if (/^(\s*)<ITEM/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"image/gif\" PATH=\"dadml\">$cas.gif</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "MEDIA-tag added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
sub add_dadml_path {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
if (open (FILE, $file)) {
while (<FILE>) {
if (/MEDIA.*image\/gif.*$cas/i) {
s/MIME=\"image\/gif\">/MIME=\"image\/gif\" PATH=\"dadml\">/ig;
push (@XML_data, $_);
$changed = "True";
} else {
push (@XML_data, $_);
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "PATH-attribute added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
--- NEW FILE: voeg-pdb-mime-toe.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $pdbdir = "../../data/dadml/3d/pdb";
my $existsfile = "tmp-pdbmime-exists";
# tellers
my $nr_foundCAS = 0;
my $nr_already_linked = 0;
my $nr_gelinkt = 0;
my $nr_mislukte_links = 0;
opendir (PDBDIR, $pdbdir) || die "$pdbdir: $!$/";
my @pdbfiles = grep {/\.pdb/i} readdir(PDBDIR);
closedir (PDBDIR) || die "$pdbdir: $!$/";
&create_existskeyfile ("NUMBER");
&create_existskeyfile ("x-pdb");
# Loop over all files
foreach my $pdbfile (@pdbfiles) {
my $cas = $pdbfile;
$cas =~ s/\.pdb//ig;
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
$nr_foundCAS++;
print "NUMBER found:\t$nummatch$/" if ($debug);
my $linkmatch = &exists (("x-pdb" => $cas));
if ($linkmatch) {
$nr_already_linked++;
print "PDB-link found:\t$linkmatch$/" if ($debug);
} else {
print "$cas.pdb can be linked!!:\t$nummatch$/";
#print "\tMEDIA-tag toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
my ($wmlfile) = split (":", $nummatch);
if (&voeg_link_toe("$wmldir/$wmlfile", $cas)) {
$nr_gelinkt++;
} else {
$nr_mislukte_links++;
}
#}
}
} else {
print "Dangling PDB-file $cas.pdb$/";
}
}
&remove_existskeyfile ("NUMBER");
&remove_existskeyfile ("x-pdb");
# Print statistics
print " ----------------------------$/";
print "Files checked : ",scalar @pdbfiles, $/;
if ($nr_foundCAS) {
print " CAS or WOC number found : $nr_foundCAS$/";
my $nr_linkable = $nr_foundCAS - $nr_already_linked;
if ($nr_linkable) {
print " Linkable matches : ", $nr_foundCAS - $nr_already_linked,$/;
print " Added links : $nr_gelinkt$/" if $nr_gelinkt;
print " Links failed to add : $nr_mislukte_links$/" if $nr_mislukte_links;
my $nr_skipped_links = $nr_linkable - $nr_gelinkt - $nr_mislukte_links;
print " Skipped links : ", $nr_skipped_links,$/ if $nr_skipped_links;
print " Already linked matches : $nr_already_linked$/";
} else {
print " Already linked matches : $nr_already_linked$/";
print " No linkable matches...$/";
}
} else {
print "Not one file name matched an item name...$/";
}
my $nr_danglingPDBs = @pdbfiles - $nr_foundCAS;
print " Dangling files found : $nr_danglingPDBs$/";
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
sub voeg_link_toe {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
my $has_WOC = `grep -i "<WOC>" $file`;
my $has_DICT = `grep -i "<DICT>" $file` if (! $has_WOC);
my $has_INDEX = `grep -i "<INDEX" $file` if (! $has_WOC);
my $last_was_INDEX = "";
my $indent = "";
if (open (FILE, $file)) {
if ($has_WOC) {
while (<FILE>) {
if (/^(\s*)<WOC>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_INDEX) {
while (<FILE>) {
if (/^(\s*)<INDEX/i) {
$indent = $1;
push (@XML_data, $_);
$last_was_INDEX = "True";
} elsif ($last_was_INDEX && ! /<INDEX/i) {
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
push (@XML_data, $_);
$changed = "True";
$last_was_INDEX = "";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_DICT) {
while (<FILE>) {
if (/^(\s*)<\/DICT>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} else {
while (<FILE>) {
if (/^(\s*)<ITEM/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "MEDIA-tag added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
--- NEW FILE: voeg-pdb-mime-toe.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $pdbdir = "../../data/dadml/3d/pdb";
my $existsfile = "tmp-pdbmime-exists";
# tellers
my $nr_foundCAS = 0;
my $nr_already_linked = 0;
my $nr_gelinkt = 0;
my $nr_mislukte_links = 0;
opendir (PDBDIR, $pdbdir) || die "$pdbdir: $!$/";
my @pdbfiles = grep {/\.pdb/i} readdir(PDBDIR);
closedir (PDBDIR) || die "$pdbdir: $!$/";
&create_existskeyfile ("NUMBER");
&create_existskeyfile ("x-pdb");
# Loop over all files
foreach my $pdbfile (@pdbfiles) {
my $cas = $pdbfile;
$cas =~ s/\.pdb//ig;
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
$nr_foundCAS++;
print "NUMBER found:\t$nummatch$/" if ($debug);
my $linkmatch = &exists (("x-pdb" => $cas));
if ($linkmatch) {
$nr_already_linked++;
print "PDB-link found:\t$linkmatch$/" if ($debug);
} else {
print "$cas.pdb can be linked!!:\t$nummatch$/";
#print "\tMEDIA-tag toevoegen aan wml? ";
#$_ = <STDIN>;
#if (/^(j|y)/i) {
my ($wmlfile) = split (":", $nummatch);
if (&voeg_link_toe("$wmldir/$wmlfile", $cas)) {
$nr_gelinkt++;
} else {
$nr_mislukte_links++;
}
#}
}
} else {
print "Dangling PDB-file $cas.pdb$/";
}
}
&remove_existskeyfile ("NUMBER");
&remove_existskeyfile ("x-pdb");
# Print statistics
print " ----------------------------$/";
print "Files checked : ",scalar @pdbfiles, $/;
if ($nr_foundCAS) {
print " CAS or WOC number found : $nr_foundCAS$/";
my $nr_linkable = $nr_foundCAS - $nr_already_linked;
if ($nr_linkable) {
print " Linkable matches : ", $nr_foundCAS - $nr_already_linked,$/;
print " Added links : $nr_gelinkt$/" if $nr_gelinkt;
print " Links failed to add : $nr_mislukte_links$/" if $nr_mislukte_links;
my $nr_skipped_links = $nr_linkable - $nr_gelinkt - $nr_mislukte_links;
print " Skipped links : ", $nr_skipped_links,$/ if $nr_skipped_links;
print " Already linked matches : $nr_already_linked$/";
} else {
print " Already linked matches : $nr_already_linked$/";
print " No linkable matches...$/";
}
} else {
print "Not one file name matched an item name...$/";
}
my $nr_danglingPDBs = @pdbfiles - $nr_foundCAS;
print " Dangling files found : $nr_danglingPDBs$/";
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
sub voeg_link_toe {
my $file = shift;
my $cas = shift;
my $succes = "True";
my @XML_data;
my $changed = "";
print "Processing $file ";
my $has_WOC = `grep -i "<WOC>" $file`;
my $has_DICT = `grep -i "<DICT>" $file` if (! $has_WOC);
my $has_INDEX = `grep -i "<INDEX" $file` if (! $has_WOC);
my $last_was_INDEX = "";
my $indent = "";
if (open (FILE, $file)) {
if ($has_WOC) {
while (<FILE>) {
if (/^(\s*)<WOC>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_INDEX) {
while (<FILE>) {
if (/^(\s*)<INDEX/i) {
$indent = $1;
push (@XML_data, $_);
$last_was_INDEX = "True";
} elsif ($last_was_INDEX && ! /<INDEX/i) {
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
push (@XML_data, $_);
$changed = "True";
$last_was_INDEX = "";
} else {
push (@XML_data, $_);
}
}
} elsif ($has_DICT) {
while (<FILE>) {
if (/^(\s*)<\/DICT>/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
} else {
while (<FILE>) {
if (/^(\s*)<ITEM/i) {
$indent = $1;
push (@XML_data, $_);
push (@XML_data, "$indent<WOC>$/");
push (@XML_data, "$indent <MEDIA MIME=\"chemical/x-pdb\">$cas.pdb</MEDIA>$/");
push (@XML_data, "$indent</WOC>$/");
$changed = "True";
} else {
push (@XML_data, $_);
}
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
$succes = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "MEDIA-tag added...$/";
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$succes = "";
}
} else {
print "No changes...$/";
}
return ($succes);
}
--- NEW FILE: voeg-woc-nummer-toe.pl ---
#! /usr/bin/perl -w
use strict;
my $wmldir = "../../data/wml";
my @item_start_elements = `grep -i "ITEM" $wmldir/*.xml | grep -i "ID="`;
# make a list of current ID's
my @idlist;
foreach my $elem (@item_start_elements) {
$elem =~ /ID=\"WOC(.*?)\".*/i;
#print $1 . "$/";
push (@idlist, $1);
}
# sort thislist
@idlist = sort @idlist;
# what is the highest ID?
my $highestid = $idlist[-1];
#print "Highest in use: WOC" . $highestid ."$/";
my $nextfree = sprintf "%08i", $highestid + 1;
print "First free: WOC" . $nextfree ."$/";
# next step is to browse trough all files and add numbers
my @wmlfiles = <$wmldir/*.xml>;
foreach my $file (@wmlfiles) {
my $mustbeupdated = 0;
if (open (OPENFILE, $file)) {
while ( <OPENFILE> ) {
if (/<ITEM(.*?)>/) {
# oke start element ITEM found
if ($1 =~ /ID=\"WOC(.*?)\".*/) {
# oke, has ID at this moment... print it
print "ID found in $file: $1$/";
} else {
# oke, no ID at this moment... add it...
$mustbeupdated = 1;
}
}
}
}
if ($mustbeupdated) {
print "Updating $file...$/";
my @inputfile = ();
if (open (OPENFILE, $file)) {
while (<OPENFILE> ) {
if (/(<ITEM\ )(.*>)/) {
$_ = "$1ID=\"WOC$nextfree\" $2$/";
# raise next free ID
$nextfree = sprintf "%08i", $nextfree + 1;
}
push (@inputfile, $_);
}
if (open (OPENFILE, ">$file")) {
print OPENFILE @inputfile;
}
}
}
}
--- NEW FILE: voeg-woc-nummer-toe.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $wmldir = "../../data/wml";
my @item_start_elements = `grep -i "ITEM" $wmldir/*.xml | grep -i "ID="`;
# make a list of current ID's
my @idlist;
foreach my $elem (@item_start_elements) {
$elem =~ /ID=\"WOC(.*?)\".*/i;
#print $1 . "$/";
push (@idlist, $1);
}
# sort thislist
@idlist = sort @idlist;
# what is the highest ID?
my $highestid = $idlist[-1];
#print "Highest in use: WOC" . $highestid ."$/";
my $nextfree = sprintf "%08i", $highestid + 1;
print "First free: WOC" . $nextfree ."$/";
# next step is to browse trough all files and add numbers
my @wmlfiles = <$wmldir/*.xml>;
foreach my $file (@wmlfiles) {
my $mustbeupdated = 0;
if (open (OPENFILE, $file)) {
while ( <OPENFILE> ) {
if (/<ITEM(.*?)>/) {
# oke start element ITEM found
if ($1 =~ /ID=\"WOC(.*?)\".*/) {
# oke, has ID at this moment... print it
print "ID found in $file: $1$/";
} else {
# oke, no ID at this moment... add it...
$mustbeupdated = 1;
}
}
}
}
if ($mustbeupdated) {
print "Updating $file...$/";
my @inputfile = ();
if (open (OPENFILE, $file)) {
while (<OPENFILE> ) {
if (/(<ITEM\ )(.*>)/) {
$_ = "$1ID=\"WOC$nextfree\" $2$/";
# raise next free ID
$nextfree = sprintf "%08i", $nextfree + 1;
}
push (@inputfile, $_);
}
if (open (OPENFILE, ">$file")) {
print OPENFILE @inputfile;
}
}
}
}
--- NEW FILE: voeg_stylesheet_toe.pl ---
#! /usr/bin/perl -w
use strict;
my $dir = "../../data/dadml/fysisch/cml";
# next step is to browse trough all files and add numbers
my @files = <$dir/*.xml>;
my $insert = "<\?xml-stylesheet type=\"text\/xsl\" href=\"http:\/\/www.sci.kun.nl\/woc\/data\/dadml\/fysisch\/cml\/cml.xsl\" \?>\n";
foreach my $file (@files) {
my $mustbeupdated = 1;
if (open (OPENFILE, $file)) {
while ( <OPENFILE> ) {
if (/<\?xml-stylesheet/) {
$mustbeupdated = 0;
}
}
}
if ($mustbeupdated) {
print "Updating $file...$/";
my @inputfile = ();
if (open (OPENFILE, $file)) {
while (<OPENFILE> ) {
if (/<molecule/i) {
push (@inputfile, $insert);
}
push (@inputfile, $_);
}
if (open (OPENFILE, ">$file")) {
print OPENFILE @inputfile;
}
}
}
}
--- NEW FILE: voeg_stylesheet_toe.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $dir = "../../data/dadml/fysisch/cml";
# next step is to browse trough all files and add numbers
my @files = <$dir/*.xml>;
my $insert = "<\?xml-stylesheet type=\"text\/xsl\" href=\"http:\/\/www.sci.kun.nl\/woc\/data\/dadml\/fysisch\/cml\/cml.xsl\" \?>\n";
foreach my $file (@files) {
my $mustbeupdated = 1;
if (open (OPENFILE, $file)) {
while ( <OPENFILE> ) {
if (/<\?xml-stylesheet/) {
$mustbeupdated = 0;
}
}
}
if ($mustbeupdated) {
print "Updating $file...$/";
my @inputfile = ();
if (open (OPENFILE, $file)) {
while (<OPENFILE> ) {
if (/<molecule/i) {
push (@inputfile, $insert);
}
push (@inputfile, $_);
}
if (open (OPENFILE, ">$file")) {
print OPENFILE @inputfile;
}
}
}
}
--- NEW FILE: zet-fysisch-props-op-extensie-xml.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $nr_changed = 0;
### de lange versie van opendir ###
#opendir (WMLDIR, $wmldir) || die "WMLDIR: $!$/";
#my @wmlfiles = grep {/\.xml/i} readdir(WMLDIR);
#closedir (WMLDIR) || die "$wmldir: $!$/";
### de korte versie van opendir ###
#my @wmlfiles = <$wmldir/*.xml>;
### Loop over all files ###
# met een foreach over @ARGV kun je het script aanroepen met ../wml/*.xml
# dit wordt door de shell al uitgevouwen tot ../wml/azijnzuur.xml etc..
foreach my $wmlfile (@ARGV) {
my @file = ();
my $change_needed = "";
print "Reading $wmlfile... ";
open (FILE, "<$wmlfile") || die "$wmlfile: $!$/";
while (<FILE>) {
my $line = $_;
if ($line =~ m/<INSERT.*?>(.*?)\.cml<\/INSERT>/) {
my $casnummer = $1;
$change_needed = "yes";
print "new extension necessary ($casnummer, $line)...";
push (@file, " <INSERT MIME=\"chemical/cml\" CLASS=\"PhysicalProperties\">$casnummer.xml<\/INSERT>$/");
} else {
push (@file, $line);
}
}
close(FILE);
if ($change_needed eq "yes") {
open (OUT, ">$wmldir/$wmlfile") || die "File $wmlfile not writeable!$/";
foreach my $line (@file) {
print OUT $line;
}
close(OUT);
print "Changed!$/";
} else {
print "Nothing done!$/";
}
}
print "-----------------$/";
print "Files changed: $nr_changed$/";
--- NEW FILE: zet-fysisch-props-op-extensie-xml.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $nr_changed = 0;
### de lange versie van opendir ###
#opendir (WMLDIR, $wmldir) || die "WMLDIR: $!$/";
#my @wmlfiles = grep {/\.xml/i} readdir(WMLDIR);
#closedir (WMLDIR) || die "$wmldir: $!$/";
### de korte versie van opendir ###
#my @wmlfiles = <$wmldir/*.xml>;
### Loop over all files ###
# met een foreach over @ARGV kun je het script aanroepen met ../wml/*.xml
# dit wordt door de shell al uitgevouwen tot ../wml/azijnzuur.xml etc..
foreach my $wmlfile (@ARGV) {
my @file = ();
my $change_needed = "";
print "Reading $wmlfile... ";
open (FILE, "<$wmlfile") || die "$wmlfile: $!$/";
while (<FILE>) {
my $line = $_;
if ($line =~ m/<INSERT.*?>(.*?)\.cml<\/INSERT>/) {
my $casnummer = $1;
$change_needed = "yes";
print "new extension necessary ($casnummer, $line)...";
push (@file, " <INSERT MIME=\"chemical/cml\" CLASS=\"PhysicalProperties\">$casnummer.xml<\/INSERT>$/");
} else {
push (@file, $line);
}
}
close(FILE);
if ($change_needed eq "yes") {
open (OUT, ">$wmldir/$wmlfile") || die "File $wmlfile not writeable!$/";
foreach my $line (@file) {
print OUT $line;
}
close(OUT);
print "Changed!$/";
} else {
print "Nothing done!$/";
}
}
print "-----------------$/";
print "Files changed: $nr_changed$/";
--- NEW FILE: zet-wmls-op-ISO-8859-1-encoding.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $nr_changed = 0;
### de lange versie van opendir ###
#opendir (WMLDIR, $wmldir) || die "WMLDIR: $!$/";
#my @wmlfiles = grep {/\.xml/i} readdir(WMLDIR);
#closedir (WMLDIR) || die "$wmldir: $!$/";
### de korte versie van opendir ###
#my @wmlfiles = <$wmldir/*.xml>;
### Loop over all files ###
# met een foreach over @ARGV kun je het script aanroepen met ../wml/*.xml
# dit wordt door de shell al uitgevouwen tot ../wml/azijnzuur.xml etc..
foreach my $wmlfile (@ARGV) {
my @file = ();
my $change_needed = "";
print "Reading $wmlfile... ";
if (open (FILE, "<$wmlfile")) {
while (<FILE>) {
my $line = $_;
if (($line =~ m/<\?xml.*?\?>/) && ($line !~ m/ISO-8859-1/)) {
$change_needed = "yes";
print "new encoding necessary... ";
unshift (@file, "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>$/");
# geen push maar een unshift, om deze regel pertinent als eerste te krijgen #
} else {
push (@file, $line);
}
}
close(FILE);
} else {
warn "$wmlfile: $!$/";
}
if ($change_needed eq "yes") {
if (open (OUT, ">$wmldir/$wmlfile")) {
foreach my $line (@file) {
print OUT $line;
}
close(OUT);
print "Changed!$/";
$nr_changed++;
} else {
warn "File $wmlfile not writeable!$/";
}
} else {
print "Nothing done!$/";
}
}
print "-----------------$/";
print "Files changed: $nr_changed$/";
--- NEW FILE: zet-wmls-op-ISO-8859-1-encoding.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $nr_changed = 0;
### de lange versie van opendir ###
#opendir (WMLDIR, $wmldir) || die "WMLDIR: $!$/";
#my @wmlfiles = grep {/\.xml/i} readdir(WMLDIR);
#closedir (WMLDIR) || die "$wmldir: $!$/";
### de korte versie van opendir ###
#my @wmlfiles = <$wmldir/*.xml>;
### Loop over all files ###
# met een foreach over @ARGV kun je het script aanroepen met ../wml/*.xml
# dit wordt door de shell al uitgevouwen tot ../wml/azijnzuur.xml etc..
foreach my $wmlfile (@ARGV) {
my @file = ();
my $change_needed = "";
print "Reading $wmlfile... ";
if (open (FILE, "<$wmlfile")) {
while (<FILE>) {
my $line = $_;
if (($line =~ m/<\?xml.*?\?>/) && ($line !~ m/ISO-8859-1/)) {
$change_needed = "yes";
print "new encoding necessary... ";
unshift (@file, "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>$/");
# geen push maar een unshift, om deze regel pertinent als eerste te krijgen #
} else {
push (@file, $line);
}
}
close(FILE);
} else {
warn "$wmlfile: $!$/";
}
if ($change_needed eq "yes") {
if (open (OUT, ">$wmldir/$wmlfile")) {
foreach my $line (@file) {
print OUT $line;
}
close(OUT);
print "Changed!$/";
$nr_changed++;
} else {
warn "File $wmlfile not writeable!$/";
}
} else {
print "Nothing done!$/";
}
}
print "-----------------$/";
print "Files changed: $nr_changed$/";
--- NEW FILE: zoek-cas-bij-pdbs-voor-dadml.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $pdbdir = "../../data/compounds/pdb/new";
my $existsfile = "tmp-find-cas-exists";
opendir (PDBDIR, $pdbdir) || die "$pdbdir: $!$/";
my @pdbfiles = grep {/\.pdb/i} readdir(PDBDIR);
closedir (PDBDIR) || die "$pdbdir: $!$/";
&create_existskeyfile ("LANG");
foreach my $pdbfile (@pdbfiles) {
$pdbfile =~ s/\.pdb//ig;
$pdbfile =~ tr/A-Z/a-z/;
my $namematch = &exists (("LANG" => $pdbfile));
if ($namematch) {
print "NAME match for $pdbfile.pdb:\t$namematch$/" if $debug;
my ($wmlfile) = split (":", $namematch);
$wmlfile =~ s/^\s*//i;
print "WMLFILE:$wmlfile.$/" if $debug;
my $cas = `grep -i CAS-NUMBER $wmldir/$wmlfile`;
if ($cas) {
chomp ($cas);
$cas =~ s/\s*<INDEX.*?>\s*//ig;
$cas =~ s/\s*<\/INDEX.*?>\s*//ig;
print "CAS number $cas\tfound for $pdbfile.pdb\tin $wmlfile$/";
} else {
print "no CAS number found for $pdbfile.pdb in $wmlfile$/" if $debug;
}
} else {
print "Dangling PDB-file $pdbfile.pdb$/" if $debug;
}
}
&remove_existskeyfile ("LANG");
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
--- NEW FILE: zoek-cas-bij-pdbs-voor-dadml.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "";
my $wmldir = "../../data/wml";
my $pdbdir = "../../data/compounds/pdb/new";
my $existsfile = "tmp-find-cas-exists";
opendir (PDBDIR, $pdbdir) || die "$pdbdir: $!$/";
my @pdbfiles = grep {/\.pdb/i} readdir(PDBDIR);
closedir (PDBDIR) || die "$pdbdir: $!$/";
&create_existskeyfile ("LANG");
foreach my $pdbfile (@pdbfiles) {
$pdbfile =~ s/\.pdb//ig;
$pdbfile =~ tr/A-Z/a-z/;
my $namematch = &exists (("LANG" => $pdbfile));
if ($namematch) {
print "NAME match for $pdbfile.pdb:\t$namematch$/" if $debug;
my ($wmlfile) = split (":", $namematch);
$wmlfile =~ s/^\s*//i;
print "WMLFILE:$wmlfile.$/" if $debug;
my $cas = `grep -i CAS-NUMBER $wmldir/$wmlfile`;
if ($cas) {
chomp ($cas);
$cas =~ s/\s*<INDEX.*?>\s*//ig;
$cas =~ s/\s*<\/INDEX.*?>\s*//ig;
print "CAS number $cas\tfound for $pdbfile.pdb\tin $wmlfile$/";
} else {
print "no CAS number found for $pdbfile.pdb in $wmlfile$/" if $debug;
}
} else {
print "Dangling PDB-file $pdbfile.pdb$/" if $debug;
}
}
&remove_existskeyfile ("LANG");
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
--- NEW FILE: zoek-chems-zonder-cas.pl ---
#! /usr/bin/perl -w
use strict;
my $debug = "";
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $nr_checked = 0;
my $nr_chemicals = 0;
my $nr_groups = 0;
my $nr_noCAS = 0;
# Loop over all files
foreach my $arg (@ARGV) {
&look_for_CAS_in_file ($arg);
}
# Print statistics
print " ------------------------$/";
print "Files checked : $nr_checked$/";
if ($nr_chemicals) {
print "Chemicals found : $nr_chemicals$/";
print "Chemical groups found : $nr_groups$/" if ($nr_groups);
if ($nr_noCAS) {
print "Chemicals without CAS : $nr_noCAS$/";
} else {
print "All chemicals had CAS!$/";
}
} else {
print "No Chemicals found.$/";
}
sub look_for_CAS_in_file {
my $file = shift;
my $changed = "";
print "Processing $file\t";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
my $group = "";
while (<FILE>) {
if (/CHEMICAL/i) {
print "CHEMICAL! " if (!$chemical); # 1 hit is enough #
$chemical = "True";
$nr_chemicals++;
} elsif (/CLASS="GROUP"/i) {
print "GROUP! " if (!$group); # 1 hit is enough #
$group = "True";
$nr_groups++;
} elsif (/(CAS|WOC)-NUMBER/i && /\>(.+?)\</) {
my $type = $1;
print "$type number found...$/" if ($debug && ! $cas_found); # 1 hit is enough #
$cas_found = "True";
}
}
if ($chemical && !$group && !$cas_found) {
$nr_noCAS++;
print "No CAS number found...$/";
} else {
print "$/" unless $debug;
}
close (FILE) || warn "$file: $!$/";
$nr_checked++;
} else {
warn "$file: $!$/";
}
}
--- NEW FILE: zoek-chems-zonder-cas.pl.in ---
#! @PATHTOPERL@ -w
use strict;
my $debug = "";
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $nr_checked = 0;
my $nr_chemicals = 0;
my $nr_groups = 0;
my $nr_noCAS = 0;
# Loop over all files
foreach my $arg (@ARGV) {
&look_for_CAS_in_file ($arg);
}
# Print statistics
print " ------------------------$/";
print "Files checked : $nr_checked$/";
if ($nr_chemicals) {
print "Chemicals found : $nr_chemicals$/";
print "Chemical groups found : $nr_groups$/" if ($nr_groups);
if ($nr_noCAS) {
print "Chemicals without CAS : $nr_noCAS$/";
} else {
print "All chemicals had CAS!$/";
}
} else {
print "No Chemicals found.$/";
}
sub look_for_CA...
[truncated message content] |
Update of /cvsroot/woc/woc/src/woc/src/cas
In directory usw-pr-cvs1:/tmp/cvs-serv23171/woc/src/cas
Added Files:
CAS2NSC.txt CAS2SMILES.txt CAS2UN.txt Makefile.am
add_nsc_number.pl add_nsc_number.pl.in add_numbers.pl
add_numbers.pl.in add_smiles.pl add_smiles.pl.in
add_un_nummers.pl add_un_nummers.pl.in check_cas_nummers.pl
check_cas_nummers.pl.in check_doublenumbers.pl
check_doublenumbers.pl.in zoek-UNs-zonder-wml.pl
zoek-UNs-zonder-wml.pl.in
Log Message:
--- NEW FILE: CAS2NSC.txt ---
100-00-5 9792
100-01-6 9797
100-02-7 1317
100-06-1 5601
100-06-1 209523
100-07-2 86125
100-09-4 7926
100-09-4 32742
100-10-7 5517
100-11-8 4609
100-12-9 858
100-14-1 9803
100-15-2 5390
100-16-3 4079
100-17-4 5507
100-18-5 84198
100-19-6 41590
100-20-9 41885
100-21-0 36973
[...126750 lines suppressed...]
998-29-8 96837
998-30-1 124134
998-40-3 91700
998-41-4 111642
998-91-4 2321
998-91-4 224119
998-98-1 79255
999-21-3 4799
999-23-5 6406
999-29-1 58406
999-30-4 16588
999-33-7 223056
999-37-1 509380
999-47-3 34835
999-50-8 58807
999-55-3 20945
999-68-8 93208
999-79-1 525131
999-81-5 34858
999-97-3 93895
--- NEW FILE: CAS2SMILES.txt ---
100-00-5 [N+]([O-])(=O)C1=CC=C(Cl)C=C1
100-01-6 [N+]([O-])(=O)C1=CC=C(N)C=C1
100-02-7 [N+]([O-])(=O)C1=CC=C(O)C=C1
100-06-1 C(C)(=O)C1=CC=C(OC)C=C1
100-09-4 C(=O)(O)C1=CC=C(OC)C=C1
100-10-7 N(C)(C)C1=CC=C(C=O)C=C1
100-11-8 [N+]([O-])(=O)C1=CC=C(CBr)C=C1
100-12-9 [N+]([O-])(=O)C1=CC=C(CC)C=C1
100-14-1 [N+]([O-])(=O)C1=CC=C(CCl)C=C1
100-15-2 [N+]([O-])(=O)C1=CC=C(NC)C=C1
100-16-3 [N+]([O-])(=O)C1=CC=C(NN)C=C1
100-17-4 [N+]([O-])(=O)C1=CC=C(OC)C=C1
100-23-2 N(C)(C)C1=CC=C([N+](=O)[O-])C=C1
100-25-4 [N+]([O-])(=O)C1=CC=C([N+](=O)[O-])C=C1
100-26-5 C(=O)(O)C1=CC=C(C(=O)O)N=C1
100-28-7 [N+]([O-])(=O)C1=CC=C(N=C=O)C=C1
100-29-8 [N+]([O-])(=O)C1=CC=C(OCC)C=C1
100-32-3 [N+]([O-])(=O)C2=CC=C(SSC1=CC=C([N+](=O)[O-])C=C1)C=C2
100-33-4 C(=N)(N)C2=CC=C(OCCCCCOC1=CC=C(C(=N)N)C=C1)C=C2
[...9537 lines suppressed...]
99-87-6 C(C)(C)C1=CC=C(C)C=C1
99-88-7 C(C)(C)C1=CC=C(N)C=C1
99-89-8 C(C)(C)C1=CC=C(O)C=C1
99-91-2 C(C)(=O)C1=CC=C(Cl)C=C1
99-92-3 C(C)(=O)C1=CC=C(N)C=C1
99-93-4 C(C)(=O)C1=CC=C(O)C=C1
99-94-5 C(=O)(O)C1=CC=C(C)C=C1
99-96-7 C(=O)(O)C1=CC=C(O)C=C1
99-97-8 N(C)(C)C1=CC=C(C)C=C1
99-98-9 N(C)(C)C1=CC=C(N)C=C1
99-99-0 [N+]([O-])(=O)C1=CC=C(C)C=C1
992-59-6 S(=O)(=O)(O)C1=C6C(=C(N)C(=C1)N=NC5=C(C)C=C(C4=CC(=C(N=NC3=C(N)C2=C(C=CC=C2)C(=C3)S(=O)(=O)O)C=C4)C)C=C5)C=CC=C6
994-31-0 [Sn](CC)(CC)(CC)Cl
996-19-0 S(=O)(=O)(O)O.C(NN)(=N)N
996-97-4 N(C(CCCCCCC)=O)(CC)CC
996-98-5 C(C(NN)=O)(NN)=O
997-95-5 N(CC(C)C)(CC(C)C)N=O
998-91-4 C(=CC(OCC)=O)(OCC)C
999-21-3 C(C=CC(OCC=C)=O)(OCC=C)=O
999-23-5 N(CCN(CCC#N)C)(CCC#N)C
--- NEW FILE: CAS2UN.txt ---
#CAS-nummer <=> UN-nummer
100-00-5 1578
100-01-6 1661
100-02-7 1663
100-25-4 1597
100-37-8 2686
100-39-0 1737
100-40-3 1993
100-41-4 1175
100-42-5 2055
100-44-7 1738
100-47-0 2224
100-51-6 2810
100-52-7 1990
100-61-8 2294
100-63-0 2572
100-80-1 2618
100-97-0 1328
10024-97-2 1070
10025-67-9 1828
10025-69-1 2923
10025-78-2 1295
10025-87-3 1810
10025-91-9 1733
10026-04-7 1818
10026-13-8 1806
10031-13-7 1618
10035-10-6 1048
10045-94-0 1625
10048-95-0 1685
101-02-0 2811
101-68-8 2489
101-72-4 2811
101-77-9 2651
101-84-8 3077
10102-18-8 2630
10102-44-0 1067
10103-50-1 1622
10103-61-4 1557
10108-64-2 2570
10112-91-1 2025
10124-50-2 1678
10192-30-0 2693
102-82-9 2542
10265-92-6 2783
10290-12-7 1586
10294-33-4 2692
10294-34-5 1741
10326-27-9 1564
10361-37-2 1564
104-15-4 2585
104-94-9 02431
105-46-4 1123
105-58-8 2366
105-74-8 2124,
106-35-4 1224
106-42-3 1307
106-44-5 2076
106-46-7 2811
106-47-8 2018
106-48-9 2020
106-49-0 1708
106-50-3 1673
106-51-4 2587
106-87-6 2810
106-88-7 3022
106-89-8 2023
106-92-3 2219
106-93-4 1605
106-97-8 1011
106-98-9 1012
106-99-0 1010
107-01-7 1012
107-02-8 1092
107-05-1 1100
107-06-2 1184
107-07-3 1135
107-10-8 1277
107-11-9 2334
107-12-0 2404
107-13-1 1093
107-14-2 2668
107-15-3 1604
107-18-6 1098
107-19-7 2929
107-20-0 2232
107-30-2 1239
107-31-3 1243
107-39-1 2050
107-40-4 2050
107-49-3 3018
107-83-5 1208
107-87-9 1249
107-98-2 3092
108-01-0 2051
108-03-2 2608
108-05-4 1301
108-10-1 1245
108-11-2 2053
108-18-9 1158
108-20-3 1159
108-21-4 1220
108-23-6 2407
108-24-7 1715
108-31-6 2215
108-38-3 1307
108-39-4 2076
108-42-9 2019
108-43-0 2020
108-44-1 1708
108-46-3 2876
108-65-6 1993
108-67-8 2325
108-70-3 2321
108-77-0 2670
108-83-8 1157
108-87-2 2296
108-88-3 1294
108-89-4 2313
108-90-7 1134
108-91-8 2357
108-94-1 1915
108-95-2 1671
108-98-5 2337
108-99-6 2313
109-06-8 2313
109-55-7 2734
109-60-4 1276
109-66-0 1265
109-69-3 1127
109-73-9 1125
109-79-5 2347
109-86-4 1188
109-87-5 1234
109-89-7 1154
109-92-2 1302
109-94-4 1190
109-99-9 2056
110-00-9 2389
110-01-0 2412
110-02-1 2414
110-12-3 2302
110-16-7 1759
110-19-0 1213
110-43-0 1110
110-49-6 1189
110-54-3 1208
110-63-4 2810
110-80-5 1171
110-82-7 1145
110-83-8 2256
110-86-1 1282
110-89-4 2401
110-91-8 2054
11097-69-1 2315
111-14-8 3265
111-15-9 1172
111-30-8 2810
111-40-0 2079
111-65-9 1262
111-66-0 1993
111-69-3 2205
111-76-2 2369
111-84-2 1920
1113-38-8 2811
112-24-3 2259
112-55-0 1228
114-26-1 2757
115-11-7 1055
115-29-7 2761
115-32-2 2761
116-06-3 2757
116-29-0 2761
118-74-1 2729
118-75-2 2588
118-96-7 0209
119-93-7 2811
120-36-5 2765
120-51-4 2810
120-71-8 2431
120-80-9 2811
120-82-1 2321
120-83-2 2020
120-92-3 2245
12001-29-5 2590
12057-74-8 2011
12079-65-1 2811
121-14-2 2038
121-43-7 2416
121-44-8 1296
121-69-7 2253
121-75-5 3082
12108-13-3 2810
12122-67-7 2771
12125-01-8 2505
12136-45-7 2033
122-14-5 3018
122-34-9 2763
122-39-4 2811
122-52-1 2323
122-79-2 2810
123-05-7 1191
123-31-9 2662
123-38-6 1275
123-51-3 1105
123-54-6 2310
123-62-6 2496
123-72-8 1129
123-77-3 3242
123-86-4 1123
123-91-1 1165
123-92-2 1104
124-02-7 2359
124-09-4 2280
124-18-5 2247
124-38-9 1013
124-40-3 1032
124-41-4 1431
124-58-3 1557
124-63-0 3246
12427-38-2 2210
126-30-7 1325
126-75-0 3018
126-98-7 3079
126-99-8 1991
127-18-4 1897
1300-73-8 1711
1302-42-7 2812
1303-28-2 1559
1304-28-5 1884
1304-29-6 1449
1305-62-0 1759
1305-78-8 1910
1306-19-0 2570
1309-64-4 1549
131-17-9 2810
131-52-2 2567
1310-58-3 1813
1310-65-2 2680
1310-66-3 2680
1310-73-2 1823
1312-73-8 1382
1313-99-1 2811
1314-34-7 3285
1314-56-3 1807
1314-62-1 2862
1314-84-7 1714
1317-36-8 3288
13171-21-6 3018
1319-77-3 2076,
1321-65-9 2811
1327-53-3 1561
133-06-2 2773
1333-74-0 1049
1333-82-0 1463
1333-86-4 1361
1336-21-6 2672
1338-02-9 3009
13463-39-3 1259
13463-40-6 1994
13477-00-4 1445
13494-80-9 2811
137-26-8 2771
137-30-4 2771
137-32-6 1105
13768-86-0 2928
13952-84-6 1992
140-88-5 1917
141-32-2 2348
141-43-5 2491
141-66-2 3018
141-78-6 1173
141-79-7 1229
142-04-1 1548
142-28-9 1992
142-62-1 2829
142-82-5 1206
142-96-1 1149
143-10-2 1228
143-33-9 1689
144-49-0 2642
144-62-7 2923
14484-64-1 2771
14977-61-8 1758
151-50-8 1680
151-56-4 1185
151-67-7 1610
1563-66-2 2757
1569-69-3 3054
15950-66-0 2020
15972-60-8 2588
1600-27-7 1629
16219-75-3 1993
1634-04-4 2398
16752-77-5 2757
16871-90-2 2655
16872-11-0 1775
1689-83-4 2588
16893-85-9 2674
16961-83-4 1778
17702-41-9 1868
17804-35-2 2757
1836-75-5 2779
1897-45-6 2588
1910-42-5 2781
1912-24-9 2763
1912-26-1 2763
1918-00-9 2769
19287-45-7 1911
19624-22-7 1380
19750-95-9 2588
2032-59-9 2757
2050-92-2 2841
20816-12-0 2471
20859-73-8 1397
2104-64-5 2783
21908-53-2 1641
22224-92-6 2783
2243-62-1 None
2303-17-5 2757
2310-17-0 2783
2425-06-1 2773
25013-15-4 2618
25057-89-0 2588
25154-52-3 3082
25154-54-5 1597
2524-04-1 2751
25321-14-6 2038
25340-17-4 2049
2551-62-4 1080
26628-22-8 1687
2807-30-9 1993
2813-95-8 3014
28434-00-6 2902
2855-13-2 2289
287-92-3 1146
2893-78-9 2465
2921-88-2 2783
298-00-0 2783
299-86-5 2783
300-76-5 3018
301-04-2 1616
302-01-2 2029
302-17-0 2811
30525-89-4 2213
309-00-2 2761
3173-53-3 2488
3209-22-1 1578
3268-49-3 2785
333-41-5 3018
3333-67-3 2811
3383-96-8 2783
3452-97-9 n.o.s
353-50-4 2417
353-59-3 1974
35400-43-2 3018
3689-24-5 1704
3710-30-3 2309
3724-65-0 2823
3811-04-9 1485
39300-45-3 3013
3982-91-0 1837
4098-71-9 2290
4109-96-0 2189
4170-30-3 1143
420-04-2 3276
431-03-8 2346
479-45-8 0208
485-31-4 2779
50-00-0 1198
50-29-3 2761
50-78-2 2811
504-29-0 2671
506-68-3 1889
506-77-4 1589
506-78-5 1588
506-93-4 1467
506-96-7 1716
507-09-5 2436
51-28-5 1320
513-36-0 1127
51630-58-1 2902
52-51-7 3241
52-68-6 2783
52315-07-8 2902
52645-53-1 2902
528-29-0 1597
52918-63-5 2588
532-27-4 1697
5329-14-6 2967
533-74-4 2588
54-11-5 1654
540-59-0 1150
540-84-1 1262
541-41-3 1182
542-88-1 2249
542-92-7 1993
55-38-9 3018
55-63-0 0143
55-68-5 1895
554-00-7 1590
554-13-2 2811
556-52-5 2810
558-13-4 2516
56-23-5 1846
56-35-9 3020
56-38-2 3018
56-72-4 3027
563-12-2 3018
563-80-4 2397
57-06-7 1545
57-14-7 1163
57-24-9 1692
57-57-8 2810
57-74-9 2996
58-08-2 1544
58-89-9 2761
583-59-5 2617
583-78-8 2020
584-02-1 1105
584-79-2 2902
584-84-9 2078
59-50-7 2669
590-01-2 1914
590-18-1 1012
591-35-5 2020
591-78-6 1224
592-01-8 1575
592-27-8 1262
592-41-6 2370
592-57-4 1993
592-84-7 1128
594-42-3 1670
60-24-2 2966
60-29-7 1155
60-34-4 1244
60-35-5 2811
60-41-3 1692
60-51-5 2783
60-57-1 2761
602-01-7 2038
606-20-2 2038
608-27-5 1590
608-31-1 1590
608-73-1 2761
61-82-5 2588
610-39-9 2038
610-40-2 1577
611-06-3 1578
611-15-4 2618
6164-98-3 2588
61789-51-3 2001
61790-14-5 2810
62-38-4 1674
62-53-3 1547
62-55-5 2811
62-56-6 2810
62-73-7 3018
62-74-8 2629
62-75-9 2810
622-45-7 2243
622-97-9 2618
624-64-6 1012
624-83-9 2480
626-38-0 1104
626-93-7 2282
628-63-7 1104
63-25-2 2757
630-08-0 1016
63989-69-5 1607
64-17-5 1170
64-18-6 1779
64-19-7 2789
64-67-5 1594
640-15-3 3018
6484-52-2 1942
65-30-5 1658
65-31-6 1659
66-81-9 2588
67-56-1 1230
67-63-0 1219
67-64-1 1090
67-66-3 1888
674-82-8 2521
68-12-2 2265
68085-85-8 2902
681-84-5 2606
6834-92-0 1759
68694-11-1 2588
6923-22-4 2783
70-30-4 2875
71-23-8 1274
71-36-3 1120
71-41-0 1105
71-43-2 1114
71-55-6 2831
732-11-6 2783
74-82-8 1971
74-83-9 1062
74-84-0 1035
74-85-1 1962
74-86-2 1001
74-87-3 1063
74-89-5 1061
74-90-8 1051
74-93-1 1064
74-95-3 2664
74-97-5 1887
74-98-6 1978
74-99-7 1954
7439-90-9 1970
7439-92-1 3288
7439-93-2 1415
7439-95-4 1418
7439-95-4 1869
7439-97-6 2809
7440-01-9 1065
7440-16-6 3089
7440-28-0 1707
7440-29-1 2975
7440-36-0 2871
7440-37-1 1951
7440-38-2 1558
7440-39-3 1400
7440-41-7 1567
7440-43-9 2570
7440-44-0 1361
7440-48-4 3178
7440-58-6 2545
7440-59-7 1963
7440-63-3 2036
7440-66-6 1436
7440-70-2 1401
7446-08-4 2811
7446-09-5 1079
7446-18-6 1707
7487-94-7 1624
75-00-3 1037
75-01-4 1086
75-02-5 1860
75-04-7 1036
75-05-8 1648
75-07-0 1089
75-08-1 2363
75-09-2 1593
75-15-0 1131
75-18-3 1164
75-20-7 1402
75-21-8 1040
75-25-2 2515
75-31-0 1221
75-34-3 2362
75-35-4 1303
75-36-5 1717
75-38-7 1959
75-43-4 1029
75-44-5 1076
75-45-6 1018
75-46-7 1984
75-50-3 1083
75-52-5 1261
75-54-7 1242
75-55-8 1921
75-56-9 1280
75-63-8 1009
75-65-0 1120
75-69-4 1017
75-71-8 1028
75-72-9 1022
75-73-0 1982
75-74-1 1649
75-77-4 1298
75-79-6 1250
75-86-5 1541
75-91-2 3109
75-98-9 1759
7550-45-0 1838
7580-67-8 1414
759-94-4 2992
76-15-3 1020
76-44-8 2761
7601-89-0 1502
7616-94-6 3083
7631-99-4 1498
7632-00-0 1500
7637-07-2 1008
7646-78-8 1827
7647-01-0 1050
7664-38-2 1805
7664-39-3 1052
7664-41-7 1005
7664-93-9 1830
768-52-5 2810
7681-52-9 1791
7697-37-2 2031
77-58-7 2788
77-78-1 1595
7704-34-9 1350
7719-12-2 1809
7722-84-1 2015
7723-14-0 1381
7726-95-6 1744
7727-37-9 1066
7727-37-9 1977
7727-43-7 1564
7757-79-1 1486
7758-01-2 1484
7758-09-0 1488
7761-88-8 1493
7772-99-8 2923
7775-09-9 1495
7778-43-0 1685
7778-44-1 1573
7778-74-7 1489
7779-88-6 1514
7782-41-4 1045
7782-44-7 1072
7782-44-7 1073
7782-49-2 2658
7782-50-5 1017
7782-65-2 2192
7783-00-8 2811
7783-06-4 1053
7783-07-5 2202
7783-35-9 1645
7783-41-7 2190
7783-47-3 3288
7783-54-2 2451
7783-61-1 1859
7783-70-2 1732
7783-79-1 2194
7783-81-5 2978
7784-34-1 1560
7784-40-9 1617
7784-41-0 1677
7784-42-1 2188
7784-44-3 1546
7786-34-7 3018
7789-06-2 2811
7789-30-2 1745
7789-38-0 1494
7790-91-2 1749
7791-23-3 2879
7791-25-5 1834
78-00-2 1649
78-10-4 1292
78-30-8 2574
78-34-2 3018
78-78-4 1265
78-79-5 1218
78-81-9 1214
78-83-1 1212
78-84-2 2045
78-85-3 2396
78-87-5 1279
78-90-0 2258
78-92-2 1120
78-93-3 1193
78-95-5 1695
78-96-6 2735
78-99-9 1992
7803-51-2 2199
7803-52-3 2676
7803-62-5 2203
786-19-6 3018
79-00-5 3082
79-01-6 1710
79-04-9 1752
79-06-1 2074
79-07-2 2811
79-09-4 1848
79-10-7 2218
79-11-8 1751
79-20-9 1231
79-22-1 1238
79-24-3 2842
79-27-6 2504
79-34-5 1702
79-36-7 1765
79-41-4 2531
79-43-6 1764
79-46-9 2608
80-15-9 3109
80-62-6 1247
8001-35-2 2761
8008-20-6 1223
8018-01-7 2771
8052-41-3 1268
81-81-2 3027
811-97-2 3159
818-08-6 3146
822-06-0 2281
83-79-4 2588
836-30-6 1325
84-74-2 3082
85-44-9 2214
86-50-0 2783
86-88-4 1651
867-27-6 3018
87-61-6 2811
87-66-1 2811
87-68-3 2279
87-86-5 3155
873-66-5 2618
88-06-2 2020
88-72-2 1664
88-73-3 1578
88-74-4 1661
88-85-7 2779
88-89-1 0154
89-98-5 1760
90-04-0 2431
90-30-2 2811
90035-08-8 3027
91-22-5 2656
91-64-5 2811
91465-08-6 2588
919-86-8 3018
92-67-1 2811
92-87-5 1885
93-58-3 2938
93-65-2 2765
93-76-5 2765
933-75-5 2020
933-78-8 2020
935-95-5 2020
94-36-0 3102
94-74-6 2765
94-75-7 2765
944-22-9 3018
95-47-6 1307
95-48-7 2076
95-50-1 1591
95-51-2 2019
95-53-4 1708
95-55-6 2512
95-57-8 2021
95-76-1 1590
95-80-7 1709
95-82-9 1590
95-95-4 2020
95266-40-3 2588
957-51-7 2588
96-12-8 2872
96-14-0 1208
96-18-4 2810
96-22-0 1156
96-33-3 1919
97-00-7 1577
97-02-9 1596
97-63-2 2277
98-00-0 2874
98-01-1 1199
98-05-5 1557
98-07-7 2226
98-82-8 1918
98-83-9 2303
98-87-3 1886
98-88-4 1736
98-95-3 1662
99-09-2 1661
99-54-7 1578
99-65-0 1597
99-87-6 2046
99-97-8 2810
99-99-0 1664
999-61-1 1760
--- NEW FILE: Makefile.am ---
bindir=${prefix}/bin/cas
bin_SCRIPTS = \
add_nsc_number.pl \
add_numbers.pl \
add_smiles.pl \
add_un_nummers.pl \
check_cas_nummers.pl \
check_doublenumbers.pl \
zoek-UNs-zonder-wml.pl
CLEANFILES = $(bin_SCRIPTS)
--- NEW FILE: add_nsc_number.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $CAS_NSC_table_file = "CAS2NSC.txt";
my @CAS_NSC_table;
my $nr_NSC_numbers = 0;
my $nr_added_NSC_numbers = 0;
my $nr_unable = 0;
# Read CAS<=>NSC table
if (open (FILE, $CAS_NSC_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_NSC_table, $_);
}
close (FILE) || die "$CAS_NSC_table_file: $!$/";
} else {
die "$CAS_NSC_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_NSC_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_NSC_numbers) {
print "NSC numbers found : $nr_NSC_numbers$/";
} else {
print "No NSC numbers found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_added_NSC_numbers) {
print "NSC numbers added : $nr_added_NSC_numbers$/";
print "NSC numbers total : ",$nr_NSC_numbers+$nr_added_NSC_numbers,$/;
} else {
print "No NSC numbers added.$/";
}
sub add_NSC_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
my $CAS_line = $_;
my $NSC_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /NSC-NUMBER/) {
push (@XML_data, $next_line);
$nr_NSC_numbers++;
} else {
my $NSC_number;
if ($NSC_number = &get_NSC_number($CAS_number)) {
$NSC_line =~ s/CAS-NUMBER/NSC-NUMBER/;
$NSC_line =~ s/\>.*?\</\>$NSC_number\</;
push (@XML_data, $NSC_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "NSC number added...$/";
$nr_added_NSC_numbers++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_NSC_number {
my $CAS_number = shift;
my $NSC_number = "";
foreach my $line (@CAS_NSC_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$NSC_number = $1;
}
}
return $NSC_number;
}
--- NEW FILE: add_nsc_number.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $CAS_NSC_table_file = "CAS2NSC.txt";
my @CAS_NSC_table;
my $nr_NSC_numbers = 0;
my $nr_added_NSC_numbers = 0;
my $nr_unable = 0;
# Read CAS<=>NSC table
if (open (FILE, $CAS_NSC_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_NSC_table, $_);
}
close (FILE) || die "$CAS_NSC_table_file: $!$/";
} else {
die "$CAS_NSC_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_NSC_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_NSC_numbers) {
print "NSC numbers found : $nr_NSC_numbers$/";
} else {
print "No NSC numbers found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_added_NSC_numbers) {
print "NSC numbers added : $nr_added_NSC_numbers$/";
print "NSC numbers total : ",$nr_NSC_numbers+$nr_added_NSC_numbers,$/;
} else {
print "No NSC numbers added.$/";
}
sub add_NSC_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
my $CAS_line = $_;
my $NSC_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /NSC-NUMBER/) {
push (@XML_data, $next_line);
$nr_NSC_numbers++;
} else {
my $NSC_number;
if ($NSC_number = &get_NSC_number($CAS_number)) {
$NSC_line =~ s/CAS-NUMBER/NSC-NUMBER/;
$NSC_line =~ s/\>.*?\</\>$NSC_number\</;
push (@XML_data, $NSC_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "NSC number added...$/";
$nr_added_NSC_numbers++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_NSC_number {
my $CAS_number = shift;
my $NSC_number = "";
foreach my $line (@CAS_NSC_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$NSC_number = $1;
}
}
return $NSC_number;
}
--- NEW FILE: add_numbers.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
my $number_type = "SMILES";
# Check command line options
if (@ARGV < 1) {
print "Usage: $0 [-type <TYPE>] <xml-files>$/";
print "\t<TYPE> = (SMILES | UN[-NUMBER] | NSC[-NUMBER])$/";
exit;
} elsif ((@ARGV >= 3) && ($ARGV[0] =~ /^-t/i)) {
shift @ARGV;
$number_type = shift @ARGV;
}
# Global variables
my $CAS_Lookup_table_file = "CAS2SMILES.txt";
my @CAS_Lookup_table;
my $nr_numbers = 0;
my $nr_added_numbers = 0;
my $nr_unable = 0;
my $nr_double = 0;
if ($number_type =~ /^SMILES/i) {
$number_type = "SMILES";
$CAS_Lookup_table_file = "CAS2SMILES.txt";
} elsif ($number_type =~ /^NSC/i) {
$number_type = "NSC-NUMBER";
$CAS_Lookup_table_file = "CAS2NSC.txt";
} elsif ($number_type =~ /^UN/i) {
$number_type = "UN-NUMBER";
$CAS_Lookup_table_file = "CAS2UN.txt";
} else {
print "Error: unrecognized type $number_type!$/";
print "Usage: $0 [-type <TYPE>] <xml-files>$/";
print "\t<TYPE> = (SMILES | UN[-NUMBER] | NSC[-NUMBER])$/";
exit;
}
# Read CAS<=><TYPE> table
if (open (FILE, $CAS_Lookup_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_Lookup_table, $_);
}
close (FILE) || die "$CAS_Lookup_table_file: $!$/";
} else {
die "$CAS_Lookup_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_numbers) {
print "$number_type strings found : $nr_numbers$/";
} else {
print "No $number_type strings found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_double) {
print "Double $number_type strings: $nr_double$/" if ($nr_double);
}
if ($nr_added_numbers) {
print "$number_type strings added : $nr_added_numbers$/";
print "$number_type strings total : ",$nr_numbers+$nr_added_numbers,$/;
} else {
print "No $number_type strings added.$/";
}
sub add_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
my $number_found = "";
my $double_number = "";
my @numbers = ();
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
if (!$number_found) {
my $CAS_line = $_;
my $number_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /$number_type/) {
push (@XML_data, $next_line);
$number_found = "True";
} else {
my $number;
if ($number = &get_number($CAS_number)) {
$number_line =~ s/CAS-NUMBER/$number_type/;
$number_line =~ s/\>.*?\</\>$number\</;
push (@numbers, $number);
push (@XML_data, $number_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
}
} elsif (/$number_type/ && /\>(.+?)\</) {
push (@numbers, $1);
if (!$number_found) {
push (@XML_data, $_);
$number_found = "True";
} else {
$double_number = "True";
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($double_number) {
print "Double $number_type string found!";
$nr_numbers++;
$nr_double++;
$changed = "True";
} elsif ($number_found) {
print "No changes needed...$/";
$nr_numbers++;
$changed = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
if ($double_number) {
print " Attempting to remove...$/";
} else {
print "$number_type number added...$/";
$nr_added_numbers++;
}
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_number {
my $CAS_number = shift;
my $number = "";
foreach my $line (@CAS_Lookup_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$number = $1;
}
}
return $number;
}
--- NEW FILE: add_numbers.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
my $number_type = "SMILES";
# Check command line options
if (@ARGV < 1) {
print "Usage: $0 [-type <TYPE>] <xml-files>$/";
print "\t<TYPE> = (SMILES | UN[-NUMBER] | NSC[-NUMBER])$/";
exit;
} elsif ((@ARGV >= 3) && ($ARGV[0] =~ /^-t/i)) {
shift @ARGV;
$number_type = shift @ARGV;
}
# Global variables
my $CAS_Lookup_table_file = "CAS2SMILES.txt";
my @CAS_Lookup_table;
my $nr_numbers = 0;
my $nr_added_numbers = 0;
my $nr_unable = 0;
my $nr_double = 0;
if ($number_type =~ /^SMILES/i) {
$number_type = "SMILES";
$CAS_Lookup_table_file = "CAS2SMILES.txt";
} elsif ($number_type =~ /^NSC/i) {
$number_type = "NSC-NUMBER";
$CAS_Lookup_table_file = "CAS2NSC.txt";
} elsif ($number_type =~ /^UN/i) {
$number_type = "UN-NUMBER";
$CAS_Lookup_table_file = "CAS2UN.txt";
} else {
print "Error: unrecognized type $number_type!$/";
print "Usage: $0 [-type <TYPE>] <xml-files>$/";
print "\t<TYPE> = (SMILES | UN[-NUMBER] | NSC[-NUMBER])$/";
exit;
}
# Read CAS<=><TYPE> table
if (open (FILE, $CAS_Lookup_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_Lookup_table, $_);
}
close (FILE) || die "$CAS_Lookup_table_file: $!$/";
} else {
die "$CAS_Lookup_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_numbers) {
print "$number_type strings found : $nr_numbers$/";
} else {
print "No $number_type strings found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_double) {
print "Double $number_type strings: $nr_double$/" if ($nr_double);
}
if ($nr_added_numbers) {
print "$number_type strings added : $nr_added_numbers$/";
print "$number_type strings total : ",$nr_numbers+$nr_added_numbers,$/;
} else {
print "No $number_type strings added.$/";
}
sub add_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
my $number_found = "";
my $double_number = "";
my @numbers = ();
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
if (!$number_found) {
my $CAS_line = $_;
my $number_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /$number_type/) {
push (@XML_data, $next_line);
$number_found = "True";
} else {
my $number;
if ($number = &get_number($CAS_number)) {
$number_line =~ s/CAS-NUMBER/$number_type/;
$number_line =~ s/\>.*?\</\>$number\</;
push (@numbers, $number);
push (@XML_data, $number_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
}
} elsif (/$number_type/ && /\>(.+?)\</) {
push (@numbers, $1);
if (!$number_found) {
push (@XML_data, $_);
$number_found = "True";
} else {
$double_number = "True";
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($double_number) {
print "Double $number_type string found!";
$nr_numbers++;
$nr_double++;
$changed = "True";
} elsif ($number_found) {
print "No changes needed...$/";
$nr_numbers++;
$changed = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
if ($double_number) {
print " Attempting to remove...$/";
} else {
print "$number_type number added...$/";
$nr_added_numbers++;
}
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_number {
my $CAS_number = shift;
my $number = "";
foreach my $line (@CAS_Lookup_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$number = $1;
}
}
return $number;
}
--- NEW FILE: add_smiles.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $CAS_SMILES_table_file = "CAS2SMILES.txt";
my @CAS_SMILES_table;
my $nr_SMILES_numbers = 0;
my $nr_added_SMILES_numbers = 0;
my $nr_unable = 0;
my $nr_double = 0;
# Read CAS<=>SMILES table
if (open (FILE, $CAS_SMILES_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_SMILES_table, $_);
}
close (FILE) || die "$CAS_SMILES_table_file: $!$/";
} else {
die "$CAS_SMILES_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_SMILES_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_SMILES_numbers) {
print "SMILES strings found : $nr_SMILES_numbers$/";
} else {
print "No SMILES strings found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_double) {
print "Double SMILES strings: $nr_double$/" if ($nr_double);
}
if ($nr_added_SMILES_numbers) {
print "SMILES strings added : $nr_added_SMILES_numbers$/";
print "SMILES strings total : ",$nr_SMILES_numbers+$nr_added_SMILES_numbers,$/;
} else {
print "No SMILES strings added.$/";
}
sub add_SMILES_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
my $smiles_found = "";
my $double_smiles = "";
my @smiles = ();
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
if (!$smiles_found) {
my $CAS_line = $_;
my $SMILES_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /SMILES/) {
push (@XML_data, $next_line);
$smiles_found = "True";
} else {
my $SMILES_number;
if ($SMILES_number = &get_SMILES_number($CAS_number)) {
$SMILES_line =~ s/CAS-NUMBER/SMILES/;
$SMILES_line =~ s/\>.*?\</\>$SMILES_number\</;
push (@XML_data, $SMILES_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
}
} elsif (/SMILES/ && /\>(.+?)\</) {
if (!$smiles_found) {
push (@XML_data, $_);
$smiles_found = "True";
} else {
$double_smiles = "True";
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($double_smiles) {
print "Double SMILES string found!";
$nr_SMILES_numbers++;
$nr_double++;
$changed = "True";
} elsif ($smiles_found) {
print "No changes needed...$/";
$nr_SMILES_numbers++;
$changed = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
if ($double_smiles) {
print " Attempting to remove...$/";
} else {
print "SMILES number added...$/";
$nr_added_SMILES_numbers++;
}
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_SMILES_number {
my $CAS_number = shift;
my $SMILES_number = "";
foreach my $line (@CAS_SMILES_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$SMILES_number = $1;
}
}
return $SMILES_number;
}
--- NEW FILE: add_smiles.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $CAS_SMILES_table_file = "CAS2SMILES.txt";
my @CAS_SMILES_table;
my $nr_SMILES_numbers = 0;
my $nr_added_SMILES_numbers = 0;
my $nr_unable = 0;
my $nr_double = 0;
# Read CAS<=>SMILES table
if (open (FILE, $CAS_SMILES_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_SMILES_table, $_);
}
close (FILE) || die "$CAS_SMILES_table_file: $!$/";
} else {
die "$CAS_SMILES_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_SMILES_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_SMILES_numbers) {
print "SMILES strings found : $nr_SMILES_numbers$/";
} else {
print "No SMILES strings found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_double) {
print "Double SMILES strings: $nr_double$/" if ($nr_double);
}
if ($nr_added_SMILES_numbers) {
print "SMILES strings added : $nr_added_SMILES_numbers$/";
print "SMILES strings total : ",$nr_SMILES_numbers+$nr_added_SMILES_numbers,$/;
} else {
print "No SMILES strings added.$/";
}
sub add_SMILES_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
my $smiles_found = "";
my $double_smiles = "";
my @smiles = ();
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
if (!$smiles_found) {
my $CAS_line = $_;
my $SMILES_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /SMILES/) {
push (@XML_data, $next_line);
$smiles_found = "True";
} else {
my $SMILES_number;
if ($SMILES_number = &get_SMILES_number($CAS_number)) {
$SMILES_line =~ s/CAS-NUMBER/SMILES/;
$SMILES_line =~ s/\>.*?\</\>$SMILES_number\</;
push (@XML_data, $SMILES_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
}
} elsif (/SMILES/ && /\>(.+?)\</) {
if (!$smiles_found) {
push (@XML_data, $_);
$smiles_found = "True";
} else {
$double_smiles = "True";
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($double_smiles) {
print "Double SMILES string found!";
$nr_SMILES_numbers++;
$nr_double++;
$changed = "True";
} elsif ($smiles_found) {
print "No changes needed...$/";
$nr_SMILES_numbers++;
$changed = "";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
if ($double_smiles) {
print " Attempting to remove...$/";
} else {
print "SMILES number added...$/";
$nr_added_SMILES_numbers++;
}
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_SMILES_number {
my $CAS_number = shift;
my $SMILES_number = "";
foreach my $line (@CAS_SMILES_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$SMILES_number = $1;
}
}
return $SMILES_number;
}
--- NEW FILE: add_un_nummers.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $CAS_UN_table_file = "CAS2UN.txt";
my @CAS_UN_table;
my $nr_UN_numbers = 0;
my $nr_added_UN_numbers = 0;
my $nr_unable = 0;
# Read CAS<=>UN table
if (open (FILE, $CAS_UN_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_UN_table, $_);
}
close (FILE) || die "$CAS_UN_table_file: $!$/";
} else {
die "$CAS_UN_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_UN_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_UN_numbers) {
print "UN numbers found : $nr_UN_numbers$/";
} else {
print "No UN numbers found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_added_UN_numbers) {
print "UN numbers added : $nr_added_UN_numbers$/";
print "UN numbers total : ",$nr_UN_numbers+$nr_added_UN_numbers,$/;
} else {
print "No UN numbers added.$/";
}
sub add_UN_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
my $CAS_line = $_;
my $UN_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /UN-NUMBER/) {
push (@XML_data, $next_line);
$nr_UN_numbers++;
} else {
my $UN_number;
if ($UN_number = &get_UN_number($CAS_number)) {
$UN_line =~ s/CAS-NUMBER/UN-NUMBER/;
$UN_line =~ s/\>.*?\</\>$UN_number\</;
push (@XML_data, $UN_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "UN number added...$/";
$nr_added_UN_numbers++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_UN_number {
my $CAS_number = shift;
my $UN_number = "";
foreach my $line (@CAS_UN_table) {
if ($line =~ /^$CAS_number\s*\<\=\>\s*(.*)/) {
$UN_number = $1;
}
}
return $UN_number;
}
--- NEW FILE: add_un_nummers.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my $CAS_UN_table_file = "CAS2UN.txt";
my @CAS_UN_table;
my $nr_UN_numbers = 0;
my $nr_added_UN_numbers = 0;
my $nr_unable = 0;
# Read CAS<=>UN table
if (open (FILE, $CAS_UN_table_file)) {
while (<FILE>) {
chomp;
push (@CAS_UN_table, $_);
}
close (FILE) || die "$CAS_UN_table_file: $!$/";
} else {
die "$CAS_UN_table_file: $!$/";
}
# Loop over all files
foreach my $arg (@ARGV) {
&add_UN_number_to_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_UN_numbers) {
print "UN numbers found : $nr_UN_numbers$/";
} else {
print "No UN numbers found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_added_UN_numbers) {
print "UN numbers added : $nr_added_UN_numbers$/";
print "UN numbers total : ",$nr_UN_numbers+$nr_added_UN_numbers,$/;
} else {
print "No UN numbers added.$/";
}
sub add_UN_number_to_file {
my $file = shift;
my @XML_data;
my $changed = "";
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/CAS-NUMBER/i && /\>(.+?)\</) {
$cas_found = "True";
my $CAS_line = $_;
my $UN_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /UN-NUMBER/) {
push (@XML_data, $next_line);
$nr_UN_numbers++;
} else {
my $UN_number;
if ($UN_number = &get_UN_number($CAS_number)) {
$UN_line =~ s/CAS-NUMBER/UN-NUMBER/;
$UN_line =~ s/\>.*?\</\>$UN_number\</;
push (@XML_data, $UN_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "UN number added...$/";
$nr_added_UN_numbers++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_UN_number {
my $CAS_number = shift;
my $UN_number = "";
foreach my $line (@CAS_UN_table) {
if ($line =~ /^$CAS_number\s*\<\=\>\s*(.*)/) {
$UN_number = $1;
}
}
return $UN_number;
}
--- NEW FILE: check_cas_nummers.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
# Check argument line
if (@ARGV == 0) {
print "Usage: $0 <XML-files>$/";
exit;
}
# Global variables
my $nr_ignored = 0;
my $nr_inserted = 0;
my $nr_unable = 0;
# Loop over all files
foreach my $arg (@ARGV) {
&check_CAS_and_WOC_numbers_in_file ($arg);
}
# Print statistics
print " ------------------------$/";
if ($nr_ignored + $nr_inserted == 0) {
print "All files passed check.$/";
} else {
print "Errors ignored : $nr_ignored$/" if ($nr_ignored);
print "Unable to changes : $nr_unable$/" if ($nr_unable);
print "Check digits inserted: $nr_inserted$/" if ($nr_inserted);
}
sub check_CAS_and_WOC_numbers_in_file {
my $file = shift;
my @XML_data;
my $changed = "";
print "Processing $file, ";
if (open (FILE, $file)) {
while (<FILE>) {
if (/(CAS|WOC)-NUMBER.*?\>(.+?)\</) {
my $type = $1;
my $line = $_;
my $number = $2;
my $check = &check_digit ($number);
if (!$check) {
print "$/ Wrong check digit or typing error in $type number in $file! Ignoring error...$/ ";
$nr_ignored++;
#chop ($number);
#chop ($number);
#$number = &check_digit ($number);
#$line =~ s/\>.*?\</\>$number\</;
#print "Corrected...$/";
#$nr_corrected++;
#$changed = "True";
} elsif ($check =~ /Error/i) {
print "$/ $check in $file! Ignoring error...$/ ";
$nr_ignored++;
} elsif ($check !~ /Correct/i) {
print "$/ Missing check digit of $type number in $file!$/ ";
$number = &check_digit ($number);
$line =~ s/\>.*?\</\>$number\</;
$changed = "True";
}
push (@XML_data, $line);
} else {
push (@XML_data, $_);
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die "$file: $!$/";
print "Check digit inserted...$/";
$nr_inserted++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
--- NEW FILE: check_cas_nummers.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
# Check argument line
if (@ARGV == 0) {
print "Usage: $0 <XML-files>$/";
exit;
}
# Global variables
my $nr_ignored = 0;
my $nr_inserted = 0;
my $nr_unable = 0;
# Loop over all files
foreach my $arg (@ARGV) {
&check_CAS_and_WOC_numbers_in_file ($arg);
}
# Print statistics
print " ------------------------$/";
if ($nr_ignored + $nr_inserted == 0) {
print "All files passed check.$/";
} else {
print "Errors ignored : $nr_ignored$/" if ($nr_ignored);
print "Unable to changes : $nr_unable$/" if ($nr_unable);
print "Check digits inserted: $nr_inserted$/" if ($nr_inserted);
}
sub check_CAS_and_WOC_numbers_in_file {
my $file = shift;
my @XML_data;
my $changed = "";
print "Processing $file, ";
if (open (FILE, $file)) {
while (<FILE>) {
if (/(CAS|WOC)-NUMBER.*?\>(.+?)\</) {
my $type = $1;
my $line = $_;
my $number = $2;
my $check = &check_digit ($number);
if (!$check) {
print "$/ Wrong check digit or typing error in $type number in $file! Ignoring error...$/ ";
$nr_ignored++;
#chop ($number);
#chop ($number);
#$number = &check_digit ($number);
#$line =~ s/\>.*?\</\>$number\</;
#print "Corrected...$/";
#$nr_corrected++;
#$changed = "True";
} elsif ($check =~ /Error/i) {
print "$/ $check in $file! Ignoring error...$/ ";
$nr_ignored++;
} elsif ($check !~ /Correct/i) {
print "$/ Missing check digit of $type number in $file!$/ ";
$number = &check_digit ($number);
$line =~ s/\>.*?\</\>$number\</;
$changed = "True";
}
push (@XML_data, $line);
} else {
push (@XML_data, $_);
}
}
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die "$file: $!$/";
print "Check digit inserted...$/";
$nr_inserted++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
--- NEW FILE: check_doublenumbers.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my @NUMBER_count = ();
my @NUMBER_doublecount = ();
# Loop over all files
foreach my $arg (@ARGV) {
&check_numbers_in_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_SMILES_numbers) {
print "SMILES strings found : $nr_SMILES_numbers$/";
} else {
print "No SMILES strings found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_double) {
print "Double SMILES strings: $nr_double$/" if ($nr_double);
}
if ($nr_added_SMILES_numbers) {
print "SMILES strings added : $nr_added_SMILES_numbers$/";
print "SMILES strings total : ",$nr_SMILES_numbers+$nr_added_SMILES_numbers,$/;
} else {
print "No SMILES strings added.$/";
}
sub check_numbers_in_file {
my $file = shift;
my @XML_data;
my $changed = "";
my $doubles_found = "";
my $mismatching_doubles_found = "";
my @NUMBERS = ();
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/INDEX CLASS/i && /\>(.+?)\</) {
$number_found = "True";
my $CAS_line = $_;
my $SMILES_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /SMILES/) {
push (@XML_data, $next_line);
$smiles_found = "True";
} else {
my $SMILES_number;
if ($SMILES_number = &get_SMILES_number($CAS_number)) {
$SMILES_line =~ s/CAS-NUMBER/SMILES/;
$SMILES_line =~ s/\>.*?\</\>$SMILES_number\</;
push (@XML_data, $SMILES_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
}
} elsif (/SMILES/ && /\>(.+?)\</) {
if (!$smiles_found) {
push (@XML_data, $_);
$smiles_found = "True";
} else {
$double_smiles = "True";
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($double_smiles) {
print "Double SMILES string found...$/";
$nr_SMILES_numbers++;
$nr_double++;
} elsif ($changed && $smiles_found) {
print "No changes needed...$/";
$nr_SMILES_numbers++;
} elsif ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "SMILES number added...$/";
$nr_added_SMILES_numbers++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_SMILES_number {
my $CAS_number = shift;
my $SMILES_number = "";
foreach my $line (@CAS_SMILES_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$SMILES_number = $1;
}
}
return $SMILES_number;
}
--- NEW FILE: check_doublenumbers.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
# Check command line options
if (@ARGV == 0) {
print "Usage: $0 <xml-files>$/";
exit;
}
# Global variables
my @NUMBER_count = ();
my @NUMBER_doublecount = ();
# Loop over all files
foreach my $arg (@ARGV) {
&check_numbers_in_file ($arg);
}
# Print statistics
print " ------------------$/";
if ($nr_SMILES_numbers) {
print "SMILES strings found : $nr_SMILES_numbers$/";
} else {
print "No SMILES strings found.$/";
}
if ($nr_unable) {
print "Unable to changes: $nr_unable$/" if ($nr_unable);
}
if ($nr_double) {
print "Double SMILES strings: $nr_double$/" if ($nr_double);
}
if ($nr_added_SMILES_numbers) {
print "SMILES strings added : $nr_added_SMILES_numbers$/";
print "SMILES strings total : ",$nr_SMILES_numbers+$nr_added_SMILES_numbers,$/;
} else {
print "No SMILES strings added.$/";
}
sub check_numbers_in_file {
my $file = shift;
my @XML_data;
my $changed = "";
my $doubles_found = "";
my $mismatching_doubles_found = "";
my @NUMBERS = ();
print "Processing $file. ";
if (open (FILE, $file)) {
my $cas_found = "";
my $chemical = "";
while (<FILE>) {
if (/CHEMICAL/i) {
push (@XML_data, $_);
$chemical = "True";
} elsif (/INDEX CLASS/i && /\>(.+?)\</) {
$number_found = "True";
my $CAS_line = $_;
my $SMILES_line = $CAS_line;
my $CAS_number = $1;
push (@XML_data, $CAS_line);
my $next_line = <FILE> if (!eof(FILE));
if ($next_line =~ /SMILES/) {
push (@XML_data, $next_line);
$smiles_found = "True";
} else {
my $SMILES_number;
if ($SMILES_number = &get_SMILES_number($CAS_number)) {
$SMILES_line =~ s/CAS-NUMBER/SMILES/;
$SMILES_line =~ s/\>.*?\</\>$SMILES_number\</;
push (@XML_data, $SMILES_line);
$changed = "True";
}
push (@XML_data, $next_line);
}
}
} elsif (/SMILES/ && /\>(.+?)\</) {
if (!$smiles_found) {
push (@XML_data, $_);
$smiles_found = "True";
} else {
$double_smiles = "True";
}
} elsif (/WOC-NUMBER/ && /\>(.+?)\</) {
push (@XML_data, $_);
$cas_found = "True";
} else {
push (@XML_data, $_);
}
}
print "No CAS number found!! " if ($chemical && !$cas_found);
close (FILE) || warn "$file: $!$/";
} else {
warn "$file: $!$/";
}
if ($double_smiles) {
print "Double SMILES string found...$/";
$nr_SMILES_numbers++;
$nr_double++;
} elsif ($changed && $smiles_found) {
print "No changes needed...$/";
$nr_SMILES_numbers++;
} elsif ($changed) {
if (open (FILE, ">$file")) {
foreach my $line (@XML_data) {
print FILE $line;
}
close (FILE) || die $!;
print "SMILES number added...$/";
$nr_added_SMILES_numbers++;
} else {
warn "$file: $!$/";
print "Unable to change...$/";
$nr_unable++;
}
} else {
print "No changes...$/";
}
}
sub get_SMILES_number {
my $CAS_number = shift;
my $SMILES_number = "";
foreach my $line (@CAS_SMILES_table) {
if ($line =~ /^$CAS_number\s*(.*)/) {
$SMILES_number = $1;
}
}
return $SMILES_number;
}
--- NEW FILE: zoek-UNs-zonder-wml.pl ---
#! /usr/bin/perl -w
use strict;
use diagnostics;
my $debug = "";
my $wmldir = "../../web-docs/data/wml";
my $existsfile = "tmp-nowml-exists";
# Check command line options
#if (@ARGV == 0) {
# print "Usage: $0 <xml-files>$/";
# exit;
#}
# Global variables
my $CAS_UN_table_file = "CAS-UN.table";
my @CAS_UN_table;
my $nr_UN_numbers = 0;
my $nr_added_UN_numbers = 0;
my $nr_unable = 0;
# Read CAS<=>UN table
if (open (FILE, $CAS_UN_table_file)) {
<FILE>; # skip first line (comment) #
while (<FILE>) {
chomp;
push (@CAS_UN_table, $_);
}
close (FILE) || die "$CAS_UN_table_file: $!$/";
} else {
die "$CAS_UN_table_file: $!$/";
}
&create_existskeyfile ("NUMBER");
foreach my $line (@CAS_UN_table) {
my ($cas) = split (/\s*<=>\s*/, $line);
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
print "NUMBER found:\t$nummatch$/" if ($debug);
} else {
print "Dangling CAS/UN pair: $line$/";
}
}
&remove_existskeyfile ("NUMBER");
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
--- NEW FILE: zoek-UNs-zonder-wml.pl.in ---
#! @PATHTOPERL@ -w
use strict;
use diagnostics;
my $debug = "";
my $wmldir = "../../web-docs/data/wml";
my $existsfile = "tmp-nowml-exists";
# Check command line options
#if (@ARGV == 0) {
# print "Usage: $0 <xml-files>$/";
# exit;
#}
# Global variables
my $CAS_UN_table_file = "CAS-UN.table";
my @CAS_UN_table;
my $nr_UN_numbers = 0;
my $nr_added_UN_numbers = 0;
my $nr_unable = 0;
# Read CAS<=>UN table
if (open (FILE, $CAS_UN_table_file)) {
<FILE>; # skip first line (comment) #
while (<FILE>) {
chomp;
push (@CAS_UN_table, $_);
}
close (FILE) || die "$CAS_UN_table_file: $!$/";
} else {
die "$CAS_UN_table_file: $!$/";
}
&create_existskeyfile ("NUMBER");
foreach my $line (@CAS_UN_table) {
my ($cas) = split (/\s*<=>\s*/, $line);
my $nummatch = &exists (("NUMBER" => $cas));
if ($nummatch) {
print "NUMBER found:\t$nummatch$/" if ($debug);
} else {
print "Dangling CAS/UN pair: $line$/";
}
}
&remove_existskeyfile ("NUMBER");
sub create_existskeyfile {
my $key = shift;
`grep -i $key $wmldir/*.xml > $existsfile$key`;
}
sub remove_existskeyfile {
my $key = shift;
`rm $existsfile$key`;
}
sub exists {
my %filters = @_;
foreach my $key (keys %filters) {
my $out = `grep -i $filters{$key} $existsfile$key`;
if ($out) {
chomp ($out);
$out =~ s/$wmldir\///ig;
$out =~ s/:\s*/:\t/ig;
return "$out";
}
}
return "";
}
|
