#!/bin/bash -e

rsyncargs="-avz --partial"
onedb=0
special=0

args=`getopt pnqd: $*`
if [ $? != 0 ] ; then
    echo "USAGE: doDownloads.sh [-p] [-n] [-q] [-d <database>]"
    echo -e "\t-d: process only <database>.  If not specified, all dbs listed in the file 'databases' are processed.  The arguments 'gbdb', 'html', 'hgFixed', 'proteinDB', 'uniProt' are treated as special cases."
    echo -e "\t-p: show progress"
    echo -e "\t-n: dry run"
    echo -e "\t-q: quiet"
    exit 1
fi
set -- $args

for i
do
    case "$i"
    in
	-p)
	    rsyncargs="$rsyncargs --progress"
	    shift;;
	-n)
	    rsyncargs="$rsyncargs -n"
	    shift;;
	-q)
	    rsyncargs="$rsyncargs -q"
	    shift;;
	-d) 
	    if [[ $2 == "html" || $2 == "gbdb" || $2 == "hgFixed" || $2 == "proteinDB" || $2 == "uniProt" ]] ; then 
		special=$2
	    else 
		DBS=$2
	    fi
	    onedb=1
	    shift
	    shift;;
	--)
	    shift
	    break;;
    esac
done

if [ $onedb != 1 ] ; then
    DBS=`grep -v '^#' /usr/data/mirror-download/databases`
fi

if [ $special == 0 ] ; then
    for db in $DBS ; do 
	echo "Rsyncing database $db..."
	mkdir -p /usr/data/mirror-download/$db/database 

	if [ $db == "cb1" ] ; then    #special case
	    src=cbJul2002    
	else
	    src=$db
	fi

	rsync $rsyncargs --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/$src/database/ /usr/data/mirror-download/$db/database/
    done
fi


# gbdb
if [[ $onedb == 0 || $special == "gbdb" ]] ; then
    echo "Rsyncing gbdb..."
    rsync $rsyncargs --exclude-from=/usr/data/mirror-download/gbdb.exclude rsync://hgdownload.cse.ucsc.edu/gbdb/ /gbdb/
    # FIXME: somehow need to handle deletions, but can't delete local data
fi

# html
if [[ $onedb == 0 || $special == "html" ]] ; then
    echo "Rsyncing html..."
    rsync $rsyncargs rsync://hgdownload.cse.ucsc.edu/htdocs/ /var/www/html-browser/
fi

# hgFixed
if [[ $onedb == 0 || $special == "hgFixed" ]] ; then
    echo "Rsyncing hgFixed..."
    mkdir -p /usr/data/mirror-download/hgFixed
    rsync $rsyncargs --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/hgFixed/ /usr/data/mirror-download/hgFixed/
fi

# proteinDB
if [[ $onedb == 0 || $special == "proteinDB" ]] ; then
    echo "Rsyncing proteinDB..."
    mkdir -p /usr/data/mirror-download/proteinDB
    rsync $rsyncargs --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/proteinDB/ /usr/data/mirror-download/proteinDB/
fi

# uniProt
if [[ $onedb == 0 || $special == "uniProt" ]] ; then
    echo "Rsyncing uniProt..."
    mkdir -p /usr/data/mirror-download/uniProt
    rsync $rsyncargs --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/genome/goldenPath/uniProt/ /usr/data/mirror-download/uniProt/
fi

# FIXME: need better solution for this
#wget http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql

echo "Done."