[gentoo-commits] repo/gentoo:master commit in: sci-biology/bioperl-db/, sci-biology/bioperl-db/files/

[Kent Fredric]

commit:     c16e51d89ade3ee46c780185a2aad20555ab154b
Author:     Kent Fredric <kentnl <AT> gentoo <DOT> org>
AuthorDate: Mon Jul 17 23:55:34 2017 +0000
Commit:     Kent Fredric <kentnl <AT> gentoo <DOT> org>
CommitDate: Tue Jul 18 04:38:03 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c16e51d8

sci-biology/bioperl-db: EAPI6/-R1 Bump

- Test infa overhauled slightly
- EAPI6ified
- More test changes planned
- -r1 bump mostly for double-safety around EAPI6 changes

Package-Manager: Portage-2.3.6, Repoman-2.3.2

 sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild  | 61 ++++++++++++++++++++++
 .../bioperl-db/files/bioperl-db-1.6.9-db.patch     | 57 ++++++++++++++++++++
 2 files changed, 118 insertions(+)

diff --git a/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
new file mode 100644
index 00000000000..fd3a4280fa0
--- /dev/null
+++ b/sci-biology/bioperl-db/bioperl-db-1.6.9-r1.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+BIOPERL_RELEASE=1.6.9
+
+DIST_NAME=BioPerl-DB
+DIST_AUTHOR=CJFIELDS
+DIST_VERSION=1.006900
+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"
+
+DIST_TEST="do" # Parallelism probably bad
+
+RDEPEND="
+	>=sci-biology/bioperl-${PV}
+	dev-perl/DBD-mysql
+	dev-perl/DBI
+	sci-biology/biosql"
+DEPEND="${RDEPEND}
+	dev-perl/Module-Build
+	test? (
+		dev-perl/Data-Stag
+		dev-perl/Sub-Uplevel
+		dev-perl/Test-Warn
+		dev-perl/Test-Exception
+		virtual/perl-Test-Simple
+	)
+"
+
+src_prepare() {
+	if use test; then
+		eapply "${FILESDIR}/${PN}-1.6.9-db.patch"
+		einfo "Using the following configuration details for test database:"
+		einfo "  GENTOO_DB_TEST_HOST     : ${GENTOO_DB_TEST_HOST:=localhost}"
+		einfo "  GENTOO_DB_TEST_USER     : ${GENTOO_DB_TEST_USER:=portage}"
+		einfo "  GENTOO_DB_TEST_PORT     : ${GENTOO_DB_TEST_PORT:=3306}"
+		einfo "  GENTOO_DB_TEST_PASSWOWRD: ${GENTOO_DB_TEST_PASSWORD:=sekrit}"
+		einfo "  GENTOO_DB_TEST_DATABASE : ${GENTOO_DB_TEST_DB:=biosql_test}"
+		einfo "Please ensure the relevant mysql database is configured and/or tweak"
+		einfo "environment variables to suit"
+		export GENTOO_DB_TEST_HOST GENTOO_DB_TEST_USER GENTOO_DB_TEST_PORT GENTOO_DB_TEST_PASSWORD GENTOO_DB_TEST_DB
+	fi
+	perl-module_src_prepare
+}
+src_install() {
+	mydoc="AUTHORS BUGS FAQ"
+	perl-module_src_install
+}
+src_test() {
+	einfo "Removing bundled test libraries t/lib"
+	rm -r "${S}/t/lib" || die "Cannot remove t/lib"
+	perl-module_src_test
+}

diff --git a/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch
new file mode 100644
index 00000000000..9a2d5e7bb0b
--- /dev/null
+++ b/sci-biology/bioperl-db/files/bioperl-db-1.6.9-db.patch
@@ -0,0 +1,57 @@
+From a63725a70ab6d5cbf419d1896007b49609ac5cfa Mon Sep 17 00:00:00 2001
+From: Kent Fredric <kentfredric@×××××.com>
+Date: Tue, 18 Jul 2017 11:06:05 +1200
+Subject: [PATCH] Add env db test controls
+
+---
+ Build.PL           | 10 +++++-----
+ t/DBTestHarness.pm | 11 ++++++-----
+ 2 files changed, 11 insertions(+), 10 deletions(-)
+
+diff --git a/Build.PL b/Build.PL
+index ecc402e..4d55f3a 100755
+--- a/Build.PL
++++ b/Build.PL
+@@ -97,11 +97,11 @@ sub biosql_conf {
+         or die "Error: could not write to config file '$config_file'\n";
+     
+     my %config = (driver     => $drivers[0],
+-                  host       => '127.0.0.1',
+-                  user       => 'root',
+-                  port       => 3306,
+-                  password   => '',
+-                  dbname     => 'bioseqdb',
++                  host       => $ENV{GENTOO_DB_TEST_HOST},
++                  user       => $ENV{GENTOO_DB_TEST_USER},
++                  port       => $ENV{GENTOO_DB_TEST_PORT},
++                  password   => $ENV{GENTOO_DB_TEST_PASSWORD},
++                  dbname     => $ENV{GENTOO_DB_TEST_DB},
+                   database   => 'biosql',
+                   schema_sql => '../biosql-schema/sql/biosqldb-mysql.sql');
+     
+diff --git a/t/DBTestHarness.pm b/t/DBTestHarness.pm
+index b660429..bd0b3b7 100755
+--- a/t/DBTestHarness.pm
++++ b/t/DBTestHarness.pm
+@@ -47,12 +47,13 @@ my $counter=0;
+ # Default settings as a hash
+ my $dflt = {
+     'driver'        => 'mysql',
+-    'host'          => 'localhost',
+-    'user'          => 'root',
+-    'port'          => undef,
+-    'password'      => '',
++    'host'          => $ENV{GENTOO_DB_HOST},
++    'user'          => $ENV{GENTOO_DB_TEST_USER},
++    'port'          => ( defined $ENV{GENTOO_DB_TEST_PORT} and length $ENV{GENTOO_DB_TEST_PORT} ) ?
++                       $ENV{GENTOO_DB_TEST_PORT} : undef,
++    'password'      => $ENV{GENTOO_DB_TEST_PASSWORD},
+     'schema_sql'    => ['../biosql-schema/sql/biosqldb-mysql.sql'],
+-    'database'      => 'biosql',
++    'database'      => $ENV{GENTOO_DB_TEST_DB},
+     'module'        => 'Bio::DB::BioSQL::DBAdaptor'
+     };
+ 
+-- 
+2.13.1
+