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# Copyright 1999-2022 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
BIOPERL_RELEASE=1.6.9
DIST_NAME=BioPerl-DB
DIST_AUTHOR=CJFIELDS
DIST_VERSION=1.006900
DIST_TEST="do" # Parallelism probably bad
inherit perl-module
DESCRIPTION="Perl tools for bioinformatics - Perl API that accesses the BioSQL schema"
HOMEPAGE="http://www.bioperl.org/"
SLOT="0"
KEYWORDS="amd64 x86"
IUSE="test"
RESTRICT="test"
RDEPEND="
>=sci-biology/bioperl-${PV}
dev-perl/DBD-mysql
dev-perl/DBI
sci-biology/biosql"
DEPEND="
${RDEPEND}
test? (
dev-perl/Data-Stag
dev-perl/Sub-Uplevel
dev-perl/Test-Warn
dev-perl/Test-Exception
virtual/perl-Test-Simple
)"
BDEPEND="dev-perl/Module-Build"
PATCHES=( "${FILESDIR}"/${PN}-1.6.9-db.patch )
src_prepare() {
export GENTOO_DB_HOSTNAME=localhost
perl-module_src_prepare
}
src_test() {
einfo "Removing bundled test libraries t/lib"
rm -r "${S}/t/lib" || die "Cannot remove t/lib"
ebegin "Setting up test database"
local mysql_install_db="${EPREFIX}/usr/share/mariadb/scripts/mysql_install_db"
[[ ! -x "${mysql_install_db}" ]] && mysql_install_db="${EPREFIX}/usr/bin/mysql_install_db"
[[ ! -x "${mysql_install_db}" ]] && die "mysql_install_db command not found!"
local mysqld="${EPREFIX}/usr/sbin/mysqld"
local socket="${T}/mysql.sock"
local pidfile="${T}/mysql.pid"
local datadir="${T}/mysql-data-dir"
local mysql="${EPREFIX}/usr/bin/mysql"
mkdir -p "${datadir}" || die "Can't make mysql database dir";
chmod 755 "${datadir}" || die "Can't fix mysql database dir perms";
"${mysql_install_db}" \
--basedir="${EPREFIX}/usr" \
--datadir="${datadir}" \
--user=$(whoami) \
|| die "Failed to initalize test database"
"${mysqld}" \
--no-defaults \
--user=$(whoami) \
--skip-networking \
--skip-grant \
--socket="${socket}" \
--pid-file="${pidfile}" \
--datadir="${datadir}" &
local maxtry=20
while ! [[ -S "${socket}" || "${maxtry}" -lt 1 ]] ; do
maxtry=$((${maxtry}-1))
echo -n "."
sleep 1
done
local rc=1
[[ -S "${socket}" ]] && rc=0
eend ${rc}
[[ ${rc} -ne 0 ]] && die "Failed to start mysqld test instance"
export MYSQL_UNIX_PORT="${socket}"
perl-module_src_test
ebegin "Shutting down mysql test database"
pkill -F "${pidfile}"
eend $?
}
src_install() {
mydoc="AUTHORS BUGS FAQ"
perl-module_src_install
}
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