#!/bin/bash
getmetainfo
a=`pwd`
b=`basename $a`

echo $b

mysql -N -r -u bsse --password=theycconnection -h yellowcouch.org -D BsseSampleTracking >send-tmp-cmd <<EOF
SELECT CONCAT(
'chmod -R ugo-rwx,u=rwX,',permission,' Data\n',
'chgrp -R ',\`group\`,' Data\n',
'rsync -xav --delete --delete-excluded --exclude "*-tmp-*" --exclude "Images" --exclude "*~" --exclude "s_',mask,'*" Data/ ',hostdirectory,E.institute,'-',E.pi,'-',sample_id,'-',flow_id,'-',lane_id
) as command
FROM FlowCells F
JOIN Id2External I ON (F.sample_id=I.id)
JOIN External E ON (E.external_id=I.external_id)
JOIN Cust2Target C
JOIN ExcludeMask USING (lane_id)
WHERE C.institute=E.institute and C.pi=E.pi and flow_id='$b' and lane_id='$1'

UNION

SELECT CONCAT(
'chmod -R ugo-rwx,u=rwX,',permission,' Data\n',
'chgrp -R ',\`group\`,' Data\n',
'rsync -xav --delete --delete-excluded --exclude "*-tmp-*" --exclude "Images" --exclude "*~" --exclude "s_',mask,'*" Data/ ',hostdirectory,E.institute,'-',E.pi,'-',sample_id,'-',flow_id,'-',lane_id
) as command
FROM FlowCells F
JOIN Id2Others O ON (F.sample_id=O.id)
JOIN Cust2Target C
JOIN ExcludeMask USING (lane_id)
JOIN Id2External I2 ON (F.sample_id=I2.id)
JOIN External E ON (E.external_id=I2.external_id)
WHERE C.institute=O.institute and C.pi=O.pi and flow_id='$b' and lane_id='$1'

EOF

chmod 700 send-tmp-cmd
cat send-tmp-cmd
./send-tmp-cmd
rm send-tmp-cmd