From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1QnFjt-00066q-5w for garchives@archives.gentoo.org; Sat, 30 Jul 2011 20:02:25 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 0AFC521C06B for ; Sat, 30 Jul 2011 20:02:23 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id C9BF221C06D for ; Sat, 30 Jul 2011 19:22:45 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher ADH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C5F111B401D for ; Sat, 30 Jul 2011 19:22:44 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 3A1D98003D for ; Sat, 30 Jul 2011 19:22:44 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <85b7bd86f5737125ae7d6eeee78080bd8169dc0c.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/gbrowse/ChangeLog sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch sci-biology/gbrowse/files/symlink.patch sci-biology/gbrowse/gbrowse-2.39.ebuild X-VCS-Directories: sci-biology/gbrowse/files/ sci-biology/gbrowse/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 85b7bd86f5737125ae7d6eeee78080bd8169dc0c Date: Sat, 30 Jul 2011 19:22:44 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: X-Archives-Hash: bd146ce6ec904c4e0b89edffa92217ee commit: 85b7bd86f5737125ae7d6eeee78080bd8169dc0c Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sat Jul 30 19:22:30 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Jul 30 19:22:30 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D85b7bd86 Make sure portage does not run gbrowse_metadb_config.pl otherwise sandbox= violation occurs when modifying /var/www/gbrowse2/databases/users.sqlite= * file, maybe we could copy these during src_install to the {}, fix there= and copy back to live filesystem? Improve error handling in gbrowse_meta= db_config.pl. Fix symlink creation during install procedure. (Portage version: 2.1.10.7/git/Linux i686, unsigned Manifest commit) --- sci-biology/gbrowse/ChangeLog | 14 +++++ .../files/disable-gbrowse_metadb_config.pl.patch | 19 +++++++ .../gbrowse/files/gbrowse_metadb_config.pl.patch | 55 ++++++++++++++= ++++++ sci-biology/gbrowse/files/symlink.patch | 11 ++++ sci-biology/gbrowse/gbrowse-2.39.ebuild | 9 ++- 5 files changed, 105 insertions(+), 3 deletions(-) diff --git a/sci-biology/gbrowse/ChangeLog b/sci-biology/gbrowse/ChangeLo= g index a55fdce..b64e880 100644 --- a/sci-biology/gbrowse/ChangeLog +++ b/sci-biology/gbrowse/ChangeLog @@ -3,6 +3,20 @@ # $Header: /var/cvsroot/gentoo-x86/sci-biology/generic-genome-browser/Ch= angeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $ =20 30 Jul 2011; Martin Mokrejs + gbrowse-2.39.ebuild, +files/disable-gbrowse_metadb_config.pl.patch, + +files/gbrowse_metadb_config.pl.patch, +files/symlink.patch: + Make sure portage does not run gbrowse_metadb_config.pl otherwise sand= box + violation occurs when modifying /var/www/gbrowse2/databases/users.sqli= te* + file, maybe we could copy these during src_install to the {}, fix ther= e and + copy back to live filesystem? Improve error handling in + gbrowse_metadb_config.pl. Fix symlink creation during install procedur= e. + gbrowse-2.39.ebuild files/GBrowseInstall.pm-2.39.patch files/destdir.p= atch + files/disable-gbrowse_metadb_config.pl.patch files/fix-PNG-export.patc= h + files/gbrowse-slave.default files/gbrowse-slave.init.d + files/gbrowse.conf.vhosts.d files/gbrowse_metadb_config.pl.patch + files/symlink.patch + + 30 Jul 2011; Martin Mokrejs gbrowse-2.39.ebuild, +files/fix-PNG-export.patch: sci-biology/gbrowse: add missing brackets cause a perl error while exp= orting a PNG image gbrowse-2.39.ebuild files/fix-PNG-export.patch diff --git a/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.p= atch b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch new file mode 100644 index 0000000..1e96bb8 --- /dev/null +++ b/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch @@ -0,0 +1,19 @@ +--- install_util/GBrowseInstall.pm.ori 2011-07-30 20:42:02.000000000 +02= 00 ++++ install_util/GBrowseInstall.pm 2011-07-30 20:42:19.000000000 +0200 +@@ -486,11 +486,11 @@ + my $base =3D basename($self->install_path->{htdocs}); +=20 + # Configure the databases, if needed. +- print STDERR "Updating user account database...\n"; +- my $metadb_script =3D File::Spec->catfile("bin", "gbrowse_metadb_co= nfig.pl"); +- my $perl =3D $self->perl; +- my @inc =3D map{"-I$_"} split ':',$self->added_to_INC; +- system $perl,@inc,$metadb_script; ++# print STDERR "Updating user account database...\n"; ++# my $metadb_script =3D File::Spec->catfile("bin", "gbrowse_metadb_c= onfig.pl"); ++# my $perl =3D $self->perl; ++# my @inc =3D map{"-I$_"} split ':',$self->added_to_INC; ++# system $perl,@inc,$metadb_script; + system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.= $userdata; +=20 + # if (Module::Build->y_n( diff --git a/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch b/s= ci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch new file mode 100644 index 0000000..0f7d5d3 --- /dev/null +++ b/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch @@ -0,0 +1,55 @@ +--- bin/gbrowse_metadb_config.pl.ori 2011-07-30 19:57:33.000000000 +0200 ++++ bin/gbrowse_metadb_config.pl 2011-07-30 20:04:51.000000000 +0200 +@@ -703,9 +703,9 @@ + local $database->{AutoCommit} =3D 0; + local $database->{RaiseError} =3D 1; + eval { +- $database->do("delete from $table"); +- $database->do("insert into $table (schema_version) values ($version)")= ; +- $database->commit(); ++ $database->do("delete from $table") or warn "delete from $table failed= with: $database->errstr"; ++ $database->do("insert into $table (schema_version) values ($version)")= or warn "insert into $table (schema_version) values ($version) failed wi= th: $database->errstr"; ++ $database->commit() or warn "commitfailed with: $database->errstr"; + }; + if ($@) { + warn "update failed due to $@. Rolling back"; +@@ -768,11 +768,11 @@ + $insert_user->finish; + # rename the current users table + $database->do('drop table users') +- or die "Couldn't drop old users table"; ++ or die "Couldn't drop old users table: $database->errstr"; + $database->do('alter table users_new rename to users') +- or die "Couldn't rename new users table"; ++ or die "Couldn't rename new users table: $database->errstr"; + $database->do('create index index_session on session(username)') +- or die "Couldn't index sessions table"; ++ or die "Couldn't index sessions table: $database->errstr"; +=20 + # now do the uploads table + # this upgrades to latest version 0 +@@ -808,9 +808,9 @@ + $insert->finish(); +=20 + $database->do('drop table uploads') +- or die "Couldn't drop old uploads table"; ++ or die "Couldn't drop old uploads table: $database->errstr"; + $database->do('alter table uploads_new rename to uploads') +- or die "Couldn't rename new uploads table"; ++ or die "Couldn't rename new uploads table: $database->errstr"; +=20 + # now do the openid_users table + # this creates the new one +@@ -916,10 +916,10 @@ + $select->finish; + $insert->finish; + $database->do('drop table users') +- or die "Couldn't drop old users table"; ++ or die "Couldn't drop old users table: $database->errstr"; +=20 + $database->do('alter table users_new rename to users') +- or die "Couldn't rename new users table"; ++ or die "Couldn't rename new users table: $database->errstr"; + $database->commit(); + }; + =20 diff --git a/sci-biology/gbrowse/files/symlink.patch b/sci-biology/gbrows= e/files/symlink.patch new file mode 100644 index 0000000..e6df771 --- /dev/null +++ b/sci-biology/gbrowse/files/symlink.patch @@ -0,0 +1,11 @@ +--- install_util/GBrowseInstall.pm.ori 2011-07-30 19:41:55.000000000 +02= 00 ++++ install_util/GBrowseInstall.pm 2011-07-30 19:42:31.000000000 +0200 +@@ -465,7 +465,7 @@ + chown $uid,-1,$destdir.$htdocs; + { + local $> =3D $uid; +- symlink($images,$htdocs_i); # so symlinkifowner match works! ++ symlink($images,$destdir.$htdocs_i) or warn "symlink($images,$d= estdir.$htdocs_i) failed: $!\n"; # so symlinkifowner match works! + } + chown $>,-1,$destdir.$self->install_path->{htdocs}; +=20 diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrows= e/gbrowse-2.39.ebuild index c0bcf25..d4cee63 100644 --- a/sci-biology/gbrowse/gbrowse-2.39.ebuild +++ b/sci-biology/gbrowse/gbrowse-2.39.ebuild @@ -28,7 +28,7 @@ SRC_URI=3D" LICENSE=3D"Artistic" # webapp ebuilds do not set SLOT KEYWORDS=3D"~x86 ~amd64" -IUSE=3D"cgi fastcgi minimal mysql postgres svg test" # lwp moby scf +IUSE=3D"cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf =20 S=3D"${WORKDIR}/${MY_P}" =20 @@ -48,6 +48,7 @@ DEPEND=3D" >=3Ddev-perl/JSON-2.510.0 dev-perl/libwww-perl svg? ( dev-perl/GD-SVG ) + pdf? ( media-gfx/inkscape ) mysql? ( dev-perl/DBD-mysql ) postgres? ( dev-perl/DBD-Pg ) sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, = aka Jim Kent's src @@ -92,6 +93,9 @@ src_prepare() { epatch "${FILESDIR}"/GBrowseInstall.pm-"${PV}".patch || die "Failed to = apply GBrowseInstall.pm-"${PV}".patch" epatch "${FILESDIR}"/destdir.patch || die "Failed to apply destdir.patc= h" epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-P= NG-export.patch" + epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patc= h" + epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to a= pply gbrowse_metadb_config.pl.patch" + epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Fai= led to apply disable-gbrowse_metadb_config.pl.patch" } =20 src_configure() { @@ -145,8 +149,7 @@ src_install() { pkg_postinst() { webapp_pkg_postinst || die "webapp_pkg_postinst failed" =20 - einfo "Please run gbrowse_metadb_config.pl to update SQlite flatfiles o= r the live database" - einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbr= owse_metadb_config.pl.pm.patch" + einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles o= f the live database." } =20 src_test() {