[med-svn] r8375 - trunk/packages/gmod/chado/trunk/debian

[olivier sallou]

Author: osallou-guest
Date: 2011-11-02 08:50:09 +0000 (Wed, 02 Nov 2011)
New Revision: 8375

Modified:
   trunk/packages/gmod/chado/trunk/debian/postinst
   trunk/packages/gmod/chado/trunk/debian/rules
   trunk/packages/gmod/chado/trunk/debian/testdb.pl
Log:
set db test script to check if new install or update to launch correct target

Modified: trunk/packages/gmod/chado/trunk/debian/postinst
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/postinst	2011-11-01 19:06:35 UTC (rev 8374)
+++ trunk/packages/gmod/chado/trunk/debian/postinst	2011-11-02 08:50:09 UTC (rev 8375)
@@ -5,10 +5,35 @@
 case "$1" in
     configure)
         if [ -e /etc/gmod/gmod-chado.conf ]; then
+	export GMOD_ROOT=/usr/share/gmod/chado
         . /etc/gmod/gmod-chado.conf
 	cd /usr/share/gmod/chado
 	export CHADO_DB_NAME=gmod-chado
 	perl Makefile.PL update GMOD_ROOT=/usr/share/gmod/chado DBNAME=$CHADO_DB_NAME  DBUSER=$DBUSER DBPASS=$DBPASS DBHOST=$DBHOST DBPORT=$DBPORT DBDRIVER=PostgreSQL  SIMPLE=Y RECONFIGURE=1 LOCAL_TMP=/tmp/chado
+	export PATH=$PATH:/usr/share/gmod/chado/bin
+	#echo "*:*:*:$DBUSER:$DBPASS" > /usr/share/gmod/chado/pgpass
+	#chmod 0600 /usr/share/gmod/chado/pgpass
+	#export PGPASSFILE=/usr/share/gmod/chado/pgpass
+	# Need to detect with testdb if access to db is ok or need to be configured
+	perl /usr/share/gmod/chado/bin/testdb.pl
+	EXITCODE=$?
+	if [ $EXITCODE -eq 2 ]; then
+	  echo "Database access not correctly configured"
+	  echo "Check your configuration and run manually the database update:"
+	  echo "cd /usr/share/gmod/chado/"
+	  echo "make load_schema for a new install"
+	  echo "OR"
+	  echo "make update to upgrade the schema from a previous install"
+	  exit 0
+	fi
+	if [ $EXITCODE -eq 0 ]; then	
+	  make load_schema
+	  make prepdb
+	fi
+	if [ $EXITCODE -eq 1 ]; then
+	  make update
+	fi
+	make clean
 
         else
            echo "Application is not yet configured."

Modified: trunk/packages/gmod/chado/trunk/debian/rules
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/rules	2011-11-01 19:06:35 UTC (rev 8374)
+++ trunk/packages/gmod/chado/trunk/debian/rules	2011-11-02 08:50:09 UTC (rev 8375)
@@ -35,6 +35,7 @@
 	mv debian/libchado-perl/usr/lib/perl5/* debian/libchado-perl/usr/share/perl5/
 	rm -rf debian/libchado-perl/usr/lib/perl5
 	mv debian/libchado-perl/usr/man debian/libchado-perl/usr/share/
+	cp debian/testdb.pl debian/libchado-perl/usr/share/gmod/chado/bin/
 
 override_dh_auto_test:
 	echo "Not testing."

Modified: trunk/packages/gmod/chado/trunk/debian/testdb.pl
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/testdb.pl	2011-11-01 19:06:35 UTC (rev 8374)
+++ trunk/packages/gmod/chado/trunk/debian/testdb.pl	2011-11-02 08:50:09 UTC (rev 8375)
@@ -1,16 +1,36 @@
-#!/usr/bin/perl
+#!/usr/bin/perl -w
+use strict;
 
+use DBI;
+use Bio::GMOD::Config;
 use Bio::GMOD::DB::Config;
-use DBI;
+use Getopt::Long;
+use URI::Escape;
 
-my $conf    = Bio::GMOD::Config->new();
-#my $tmpdir  = $conf->tmp();
-#my $confdir = $conf->conf();
 
 
+my $gmod_conf = $ENV{'GMOD_ROOT'} ?
+                Bio::GMOD::Config->new($ENV{'GMOD_ROOT'}) :
+                Bio::GMOD::Config->new();
 
-my $dbconf  = Bio::GMOD::DB::Config->new($conf, 'gmod-chado');
+my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,'gmod-chado');
 
+my $dbh = $db_conf->dbh or exit 2;
 
-my $dbh = DBI->connect( $dbconf->dsn(), $dbconf->user(), $dbconf->password() )
-        or die "couldn't create db connection:$!";
+my $nbtables = $dbh->prepare("select count(*) as nbtables from pg_tables");
+$nbtables->execute() or exit 2;
+my $arrayref = $nbtables->fetchrow_arrayref();
+$nbtables   = $$arrayref[0];
+
+if($nbtables>0) {
+   print "Database already exists, update it\n";
+  exit 0;
+}
+else {
+  print "Empty database\n";
+  exit 1;
+}
+
+$dbh->disconnect;
+
+print STDOUT "nb: ".$nbtables;