sci-biology/gbrowse-2.26: fixed sanbox violation but webap-config bug pops up afterwards (happens later during install)

(Portage version: 2.1.9.43/git/Linux i686, unsigned Manifest commit)

1 files changed, 25 insertions, 5 deletions

diff --git a/sci-biology/gbrowse/gbrowse-2.26.ebuild b/sci-biology/gbrowse/gbrowse-2.26.ebuild
index b525bcca3..89000cfd4 100644
--- a/sci-biology/gbrowse/gbrowse-2.26.ebuild
+++ b/sci-biology/gbrowse/gbrowse-2.26.ebuild
@@ -50,7 +50,6 @@ DEPEND=">=dev-lang/perl-5.8.8
 #    *  Bio::DB::Sam is not installed
 #    *  DBD::Pg is not installed
 
-
 RDEPEND="${DEPEND}
 	>=www-servers/apache-2.0.47
 	www-apache/mod_fastcgi
@@ -81,12 +80,17 @@ RDEPEND="${DEPEND}
 src_prepare() {
 	sed -i 's/return unless -t STDIN/return/' install_util/GBrowseInstall.pm || die
 	sed -i 's/process_/bp_process_/g' INSTALL || die
-	epatch "${FILESDIR}"/GBrowseInstall.pm.patch || die "Failed to patch"
+	epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to patch"
+	epatch "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl"${PV}".pm.patch || die "Failed to patch"
 }
 
 src_configure() {
 	# GBROWSE_ROOT is the root path in SRC_URI to be prepended
 	# /usr/share/webapps/gbrowse/2.03/htdocs/etc/gbrowse/GBrowse.conf
+
+	# if we use CONF="${D}${MY_HTDOCSDIR}"/etc/gbrowse the the install process
+	# will not find currently installed config files and therefore place *.conf
+	# files into "{$S}"/blib/conf/*.conf instead of creating "{$S}"/blib/conf/*.conf.new
 	webapp_src_preinst
 	perl Makefile.PL \
 		HTDOCS="${MY_HTDOCSDIR}" \
@@ -104,6 +108,12 @@ src_configure() {
 		DO_XS=1 \
 		NONROOT=1 \
 		|| die
+
+	#sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/install_util/GBrowseInstall.pm || die
+	#sed -i 's#DBI:SQLite:#DBI:SQLite:'${D}'#' "${S}"/conf/GBrowse.conf || die
+	#sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/build_params
+	#sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/config_data
+	#sed -i 's#/var/www/gbrowse2/databases/#'${D}'/var/www/gbrowse2/databases/#' "${S}"/_build/runtime_params
 }
 
 src_install() {
@@ -111,25 +121,35 @@ src_install() {
 	perl-module_src_install
 
 	# TODO: write our own readme
-	webapp_postinst_txt en "${S}"/INSTALL
-	webapp_src_install || die "Failed running webapp_src_install"
+	webapp_src_preinst
+	webapp_postinst_txt en "${S}"/INSTALL || die
+	webapp_src_install
 
 	# should create a /etc/init.d/ startup script based on this
 	# /var/tmp/portage/sci-biology/gbrowse-2.03/work/GBrowse-2.03/etc/init.d/gbrowse-slave
 
+	# pre-create the directory so we can force its owner later on
+	mkdir -p "${D}"/var/www/gbrowse2/databases || die
 	chown -R apache.apache "${D}"/var/www/gbrowse2/databases || die
-
 	mkdir -p "${D}"/var/www/localhost/htdocs/gbrowse || die
+
 	ln -s "${D}"/var/tmp/gbrowse2/images "${D}"/var/www/localhost/htdocs/gbrowse/i || die
 
 	einfo "Probably you want to install a cron job to remove the generated temporary images:"
 	einfo "find /var/tmp/gbrowse2/images -type f -atime +20 -print -exec rm {}"
 
 	einfo "Make sure you compiled apache with +cgi and copy ${FILESDIR}/gbrowse.conf.vhosts.d to /etc/apache2/vhosts.d/"
+
+	sed -i "s#"${D}"##g" "${S}"/install_util/GBrowseInstall.pm || die
+	sed -i "s#"${D}"##" "${S}"/blib/conf/GBrowse.conf*
+	sed -i 's#DBI:SQLite:'${D}'/var/www/gbrowse2/databases/#DBI:SQLite:/var/www/gbrowse2/databases/#' "${S}"/install_util/GBrowseInstall.pm || die
 }
 
 pkg_postinst() {
 	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+
+	einfo "Please run gbrowse_metadb_config.pl to upate SQlite flatfiles or the live database"
+	einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch"
 }
 
 src_test() {