[med-svn] r8072 - trunk/packages/gmod/chado/trunk/debian
olivier sallou
osallou-guest at alioth.debian.org
Tue Oct 4 15:22:47 UTC 2011
Author: osallou-guest
Date: 2011-10-04 15:22:46 +0000 (Tue, 04 Oct 2011)
New Revision: 8072
Added:
trunk/packages/gmod/chado/trunk/debian/README.source
trunk/packages/gmod/chado/trunk/debian/testdb.pl
Modified:
trunk/packages/gmod/chado/trunk/debian/control
trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs
trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs
trunk/packages/gmod/chado/trunk/debian/postinst
trunk/packages/gmod/chado/trunk/debian/rules
Log:
add test script for postinst
Added: trunk/packages/gmod/chado/trunk/debian/README.source
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/README.source (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/README.source 2011-10-04 15:22:46 UTC (rev 8072)
@@ -0,0 +1,2 @@
+Chado is patched to adapt to Debian file system hierarchy, using quilt.
+For more info on quilt, see /usr/share/doc/quilt/README.source.
Modified: trunk/packages/gmod/chado/trunk/debian/control
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/control 2011-10-04 14:57:04 UTC (rev 8071)
+++ trunk/packages/gmod/chado/trunk/debian/control 2011-10-04 15:22:46 UTC (rev 8072)
@@ -3,8 +3,13 @@
Priority: optional
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Scott Cain <scain at cpan.org>, Steffen Moeller <moeller at debian.org>, Olivier Sallou <olivier.sallou at irisa.fr>
-Build-Depends: debhelper (>= 8)
-Build-Depends-Indep: perl, libtemplate-perl, libclass-dbi-pg-perl, libclass-dbi-pager-perl, libxml-libxslt-perl, liblog-log4perl-perl
+Build-Depends: debhelper (>= 8), quilt
+Build-Depends-Indep: perl, libtemplate-perl, libclass-dbi-pg-perl, libclass-dbi-pager-perl, libxml-libxslt-perl, liblog-log4perl-perl,
+bioperl, libgo-perl, libdbd-pg-perl, libdbi-perl, libgd-gd2-perl,libdigest-md5-file-perl, libgraph-perl, libdata-stag-perl,
+libxml-perl, libmodule-build-perl, libclass-dbi-perl, libclass-dbi-pg-perl, libclass-dbi-pager-perl, libxml-simple-perl,
+libwww-perl, libtemplate-perl, libcgi-session-perl, liblog-log4perl-perl, libsql-translator-perl
+
+
Standards-Version: 3.9.2
Homepage: http://gmod.org/wiki/Chado
Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/chado/trunk/
@@ -12,7 +17,7 @@
Package: libchado-perl
Architecture: all
-Depends: ${misc:Depends}, ${perl:Depends}
+Depends: ${misc:Depends}, ${perl:Depends}, postgresql-client
Recommends: xsltproc
Description: database schema and tools for genomic data
Chado is a relational database schema that underlies many GMOD
Modified: trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs 2011-10-04 14:57:04 UTC (rev 8071)
+++ trunk/packages/gmod/chado/trunk/debian/libchado-perl.dirs 2011-10-04 15:22:46 UTC (rev 8072)
@@ -1,3 +1,4 @@
usr/share/gmod/chado/bin
etc/gmod
-tmp
+usr/share/perl5
+usr/share/gmod/chado/lib/Bio/Chado
Modified: trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs 2011-10-04 14:57:04 UTC (rev 8071)
+++ trunk/packages/gmod/chado/trunk/debian/libchado-perl.docs 2011-10-04 15:22:46 UTC (rev 8072)
@@ -1,5 +1,6 @@
README.Apollo
README
+INSTALL.Chado
modules/phylogeny/examples/README
modules/sequence/bdgp/README
modules/sequence/apollo-bridge/sample_db/README
Modified: trunk/packages/gmod/chado/trunk/debian/postinst
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/postinst 2011-10-04 14:57:04 UTC (rev 8071)
+++ trunk/packages/gmod/chado/trunk/debian/postinst 2011-10-04 15:22:46 UTC (rev 8072)
@@ -5,7 +5,11 @@
case "$1" in
configure)
if [ -e /etc/gmod/gmod-chado.conf ]; then
- perl /usr/share/gmod/chado/Makefile.PL update
+ . /etc/gmod/gmod-chado.conf
+ cd /usr/share/gmod/chado
+ export CHADO_DB_NAME=gmod-chado
+ perl Makefile.PL update GMOD_ROOT=/usr/share/gmod/chado DBNAME=$CHADO_DB_NAME DBUSER=$DBUSER DBPASS=$DBPASS DBHOST=$DBHOST DBPORT=$DBPORT DBDRIVER=PostgreSQL SIMPLE=Y RECONFIGURE=1 LOCAL_TMP=/tmp/chado
+
else
echo "Application is not yet configured."
echo "To install or upgrade the database:"
Modified: trunk/packages/gmod/chado/trunk/debian/rules
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/rules 2011-10-04 14:57:04 UTC (rev 8071)
+++ trunk/packages/gmod/chado/trunk/debian/rules 2011-10-04 15:22:46 UTC (rev 8072)
@@ -17,19 +17,24 @@
dh $@ --buildsystem=perl_makemaker
override_dh_auto_configure:
- perl Makefile.PL INSTALL_BASE=/usr DBNAME=$(CHADO_DB_NAME) DBUSER=chado DBPASSWORD=chado DBHOST=localhost DBPORT=5432 GMOD_ROOT=$(GMOD_ROOT) DBDRIVER=PostgreSQL RECONFIGURE=1 SIMPLE=Y LOCAL_TMP=/tmp
+ perl Makefile.PL INSTALL_BASE=/usr DBNAME=$(CHADO_DB_NAME) DBUSER=chado DBPASS=chado DBHOST=localhost DBPORT=5432 GMOD_ROOT=$(GMOD_ROOT) DBDRIVER=PostgreSQL RECONFIGURE=1 SIMPLE=Y LOCAL_TMP=$(CURDIR)/debian/libchado-perl/tmp
override_dh_install:
dh_install -O--buildsystem=perl_makemaker
- sed -i 's/SQLFILE=\/.*\/libchado-perl/SQLFILE=/' debian/libchado-perl/conf/gmod-chado.conf
- sed -i 's/TMP=\/.*\/tmp/CONF=\/tmp/' debian/libchado-perl/conf/gmod.conf
- sed -i 's/CONF=.*\/conf/CONF=\/etc\/gmod/' debian/libchado-perl/conf/gmod.conf
- #mv $(GMOD_ROOT)/conf/* debian/libchado-perl/etc/gmod/
+ sed -i 's/SQLFILE=\/.*\/libchado-perl/SQLFILE=/' debian/libchado-perl/usr/share/gmod/chado/conf/gmod-chado.conf
+ sed -i 's/TMP=\/.*\/tmp/CONF=\/tmp/' debian/libchado-perl/usr/share/gmod/chado/conf/gmod.conf
+ sed -i 's/CONF=.*\/conf/CONF=\/etc\/gmod/' debian/libchado-perl/usr/share/gmod/chado/conf/gmod.conf
+ mv $(GMOD_ROOT)/conf/* debian/libchado-perl/etc/gmod/
# Give exexution rights to perl scripts
find debian/libchado-perl/ -name *.pl | xargs chmod 755
+ find debian/libchado-perl/ -name *.tmpl | xargs chmod 644
+ find debian/libchado-perl/ -name *.pm | xargs chmod 644
+ find debian/libchado-perl/ -name *.pod | xargs rm -f
+ find debian/libchado-perl/ -name .packlist | xargs rm -f
mv debian/libchado-perl/usr/bin/* debian/libchado-perl/usr/share/gmod/chado/bin/
- mv debian/libchado-perl/usr/share/gmod/chado/bin/*.pl debian/libchado-perl/usr/bin/
- rename 's/\.pl//' debian/libchado-perl/usr/bin/*.pl
+ 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/
override_dh_auto_test:
echo "Not testing."
Added: trunk/packages/gmod/chado/trunk/debian/testdb.pl
===================================================================
--- trunk/packages/gmod/chado/trunk/debian/testdb.pl (rev 0)
+++ trunk/packages/gmod/chado/trunk/debian/testdb.pl 2011-10-04 15:22:46 UTC (rev 8072)
@@ -0,0 +1,16 @@
+#!/usr/bin/perl
+
+use Bio::GMOD::DB::Config;
+use DBI;
+
+my $conf = Bio::GMOD::Config->new();
+#my $tmpdir = $conf->tmp();
+#my $confdir = $conf->conf();
+
+
+
+my $dbconf = Bio::GMOD::DB::Config->new($conf, 'gmod-chado');
+
+
+my $dbh = DBI->connect( $dbconf->dsn(), $dbconf->user(), $dbconf->password() )
+ or die "couldn't create db connection:$!";
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