#! /bin/sh
# file: make-pbi G. Moody 5 March 2008
# Last revised: 24 May 2013
#
# If the PhysioBank Index is out-of-date, this script rebuilds and reloads it
# into the PhysioBank Simple Query Server (pbsqs), starting pbsqs if needed.
# Otherwise, it checks to see if pbsqs is running, restarts it if needed, and
# does nothing else.
#
# Rebuilding the entire index from scratch may require several hours. The
# processing is input-bound since each .hea and each annotation file must be
# read, but they can be parsed very quickly. If multiple copies of the data
# on different physical devices are available, it's easy to parallelize the
# process by building two or more single-collection indices simultaneously,
# but this won't help if all of the inputs are located on the same device.
BINDIR=/usr/local/bin
PBDIR=/home/physionet/html/physiobank/database
PATH=$BINDIR:$PATH:/sbin
export PATH
UPDATE=0
cd $PBDIR
# Update the single-collection indices as needed.
for D in `wfdbcat DBS | cut -f 1`
do
I=`echo $D | sed s+/+_+g`
# If a collection's RECORDS list is newer than its index, update the index.
if [ $D/RECORDS -nt pbi/$I ]
then
(
# The order of records in the index is important! Don't change the
# next line, which determines the record order. (The search
# algorithm exploits the ordering for speed; the server checks the
# record order when loading the index and refuses to run if it
# finds sorting errors.)
for R in `wfdbcat $D/RECORDS | LC_ALL=C sort`
do
echo $D/$R
case $D in
mimic2db)
T=`echo $R | cut -c 1-6`T
echo $D/${R}${T} ;;
mimic2wdb/3*)
N=`basename $R`n
echo $D/$R$N ;;
esac
done
) | pbindex >/tmp/pbi-$I-$$ 2>/tmp/pbi-errors-$I-$$
mv -f /tmp/pbi-$I-$$ pbi/$I
if [ -s /tmp/pbi-errors-$I-$$ ]
then
mv -f /tmp/pbi-errors-$I-$$ /tmp/pbi-errors-$I
else
rm -f /tmp/pbi-errors-$I-$$
fi
UPDATE=1
fi
done
case $UPDATE in
0) # The index is up-to-date already -- just restart the PhysioBank Simple
# Query Server if it isn't running.
pidof pbsqsd >/dev/null || ( pbsqsd; echo pbsqsd restarted ) ;;
1) # An update is needed. First, save the most recent version of the index.
mv physiobank-index physiobank-index~
# Rebuild the index from the single-collection indices. Note that the
# indices are ordered using the same sort as for the records within each
# index.
for D in `wfdbcat DBS | cut -f 1 | LC_ALL=C sort | sed s+/+_+g`
do
cat pbi/$D >>physiobank-index
done
echo PhysioBank Index updated
# Force the server to reload the index, or start the server if needed.
killall -HUP pbsqsd 2>/dev/null || ( pbsqsd; echo pbsqsd restarted )
# Give the server a chance to start loading the index.
sleep 2
# Regenerate the list of all records known to the server by querying it.
# This list is needed by 'pbs-not'.
pbsqsc "record ?" >RECORDS-ALL
;;
esac