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 <[email protected]> +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 +
