[med-svn] r8380 - trunk/packages/gmod/chado/trunk/debian

[olivier sallou]

Author: osallou-guest
Date: 2011-11-02 11:18:02 +0000 (Wed, 02 Nov 2011)
New Revision: 8380

Modified:
   trunk/packages/gmod/chado/trunk/debian/postinst
   trunk/packages/gmod/chado/trunk/debian/testdb.pl
Log:
trap specific codes to manage db actions

Modified: trunk/packages/gmod/chado/trunk/debian/postinst
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/postinst	2011-11-02 10:02:09 UTC (rev 8379)
+++ trunk/packages/gmod/chado/trunk/debian/postinst	2011-11-02 11:18:02 UTC (rev 8380)
@@ -1,40 +1,50 @@
 #!/bin/bash
 
-set -e
+set -E
+trap onexit ERR
 
+function onexit() {
+	EXITCODE=$?
+        if [ $EXITCODE -eq 102 ]; 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 100 ]; then
+          make load_schema
+          make prepdb
+          make clean &> /dev/null
+          rm -f /usr/share/gmod/chado/pgpass
+	  exit 0
+        fi
+        if [ $EXITCODE -eq 101 ]; then
+          make update
+          make clean &> /dev/null
+          rm -f /usr/share/gmod/chado/pgpass
+          exit 0 
+        fi
+    exit $EXITCODE
+}
+
+
 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 [ $EXITCODE -eq 1 ]; then
-	  make update
-	fi
-	make clean
-
+	  export GMOD_ROOT=/usr/share/gmod/chado
+          . /etc/gmod/gmod-chado.conf
+	  cd /usr/share/gmod/chado
+	  export CHADO_DB_NAME=gmod-chado
+	  perl Makefile.PL update GMOD_ROOT=/usr/share/gmod/chado DBNAME=$CHADO_DB_NAME  DBUSER=$DBUSER DBPASS=$DBPASS DBHOST=$DBHOST DBPORT=$DBPORT DBDRIVER=PostgreSQL  SIMPLE=Y RECONFIGURE=1 LOCAL_TMP=/tmp/chado &> /dev/null
+	  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
         else
            echo "Application is not yet configured."
 	   echo "To install or upgrade the database:"

Modified: trunk/packages/gmod/chado/trunk/debian/testdb.pl
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/testdb.pl	2011-11-02 10:02:09 UTC (rev 8379)
+++ trunk/packages/gmod/chado/trunk/debian/testdb.pl	2011-11-02 11:18:02 UTC (rev 8380)
@@ -15,22 +15,20 @@
 
 my $db_conf = Bio::GMOD::DB::Config->new($gmod_conf,'gmod-chado');
 
-my $dbh = $db_conf->dbh or exit 2;
+my $dbh = $db_conf->dbh or exit 102;
 
 my $nbtables = $dbh->prepare("select count(*) as nbtables from pg_tables");
-$nbtables->execute() or exit 2;
+$nbtables->execute() or exit 102;
 my $arrayref = $nbtables->fetchrow_arrayref();
 $nbtables   = $$arrayref[0];
+$dbh->disconnect;
 
 if($nbtables>0) {
    print "Database already exists, update it\n";
-  exit 0;
+  exit 101;
 }
 else {
-  print "Empty database\n";
-  exit 1;
+  print "Empty database, create it\n";
+  exit 100;
 }
 
-$dbh->disconnect;
-
-print STDOUT "nb: ".$nbtables;