#! /bin/sh
#
#	This script should be run by cron, once a week
#
#	This script will use anonymous ftp to genbak.bio.net to
#	retrieve the latest updates to the embl library
#
#	Updates appear to be made every Monday mid afternoon PST
#	We should transfer them at 6am Tuesday
#	The crontab file should look like:
#
#	    # SunOS
#	    0 6 * * 2 /nfs/al/pubseq/pubseq/seqlibs/getEMBLupdates
#
#	    # Alliant Concentrix
#	    0 6 * * 2 pubseq /nfs/al/pubseq/pubseq/seqlibs/getEMBLupdates
#
#

#
# Set defaults
#
PROGS=/nfs/al/pubseq/pubseq/inhouse/staden/src/indexseqlibs
NEWDIR=embl-updates-new
OLDDIR=embl-updates-old
CURDIR=embl-updates
FILE=emseq.all.Z
SEQLIBS=/nfs/al/pubseq/pubseq/seqlibs
RECIPIENT=pubseq
# test
#CURDIR=embl-updates-test
#FILE=em1230.seq.Z

#
# report
# for interactive mode use: REPORT=/dev/stty
#
REPORT=${SEQLIBS}/EMBLupdate.$$

echo "getEMBLupdates Version 1.0" >> ${REPORT}
echo Started: `date` >> ${REPORT}

cd $SEQLIBS

#
# Remove old directory
#
if test -d $OLDDIR; then
	echo Removing old directory $OLDDIR >> ${REPORT}
	/bin/rm -r $OLDDIR
fi

#
# Build new directory with all the stuff we need
#
if test -d $NEWDIR; then
	echo Removing existing new directory $NEWDIR >> ${REPORT}
	/bin/rm -r $NEWDIR
fi
mkdir $NEWDIR
cd $NEWDIR

#
# Get files via ftp
#
echo FTP-ing latest updates >> ${REPORT}
ftp -v 134.172.1.160 << EOF >> ${REPORT}
cd pub/db/embl-newdata
type binary
get README
get $FILE emseq.all.Z
EOF

#
# Report errors during ftp
#
if test $? -eq 1; then
	echo Error: Transferring files >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# Check files transferred
#
if test ! -f emseq.all.Z ; then
	echo Error: File not transferred >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# Uncompress
#
echo Uncompressing update file >> ${REPORT}
uncompress emseq.all.Z
if test $? -eq 1; then
	echo Error: Cannot uncompressing file >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# Create indices
#

#
# entry name index
#
echo Building entryname index >> ${REPORT}
emblentryname.script >> ${REPORT}
if test $? -ne 0; then
	echo Error: Failed to make entry name index >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# accession number index
#
echo Building accession number index >> ${REPORT}
emblaccession.script >> ${REPORT}
if test $? -ne 0; then
	echo Error: Failed to make accession number index >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# free text index
#
echo Building free text index >> ${REPORT}
emblfreetext.script >> ${REPORT}
if test $? -ne 0; then
	echo Error: Failed to make free text index >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# Author name index
#
echo Building author index >> ${REPORT}
emblauthor.script >> ${REPORT}
if test $? -ne 0; then
	echo Error: Failed to make author index >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi

#
# brief title index
#
echo Building brief title index >> ${REPORT}
embltitle.script >> ${REPORT}
if test $? -ne 0; then
	echo Error: Failed to brief title index >> ${REPORT}
	mail ${RECIPIENT} < ${REPORT}
	exit 1
fi


#
# switch databases
#
echo Switching databases >> ${REPORT}
cd $SEQLIBS
if test -d $CURDIR; then
	mv $CURDIR $OLDDIR
fi
mv $NEWDIR $CURDIR

#
# finish up
#
echo "" >> ${REPORT}
echo "===========================README==========================" >> ${REPORT}
cat $CURDIR/README >> ${REPORT}
echo "" >> ${REPORT}
echo "---------------------------README--------------------------" >> ${REPORT}
echo Update successful >> ${REPORT}
echo Finished: `date` >> ${REPORT}

mail ${RECIPIENT} < ${REPORT}
exit 0
#