[gentoo-commits] proj/sci:master commit in: sci-biology/gbrowse/files/, sci-biology/gbrowse/

[Martin Mokrejs]

commit:     85b7bd86f5737125ae7d6eeee78080bd8169dc0c
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 30 19:22:30 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 30 19:22:30 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=85b7bd86

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_metadb_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/ChangeLog
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/ChangeLog,v 1.10 2007/07/29 17:07:38 phreak Exp $
 
   30 Jul 2011; Martin Mokrejs <mmokrejs@×××××××××××××××.cz>
+  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 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_metadb_config.pl. Fix symlink creation during install procedure.
+  gbrowse-2.39.ebuild files/GBrowseInstall.pm-2.39.patch files/destdir.patch
+  files/disable-gbrowse_metadb_config.pl.patch files/fix-PNG-export.patch
+  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 <mmokrejs@×××××××××××××××.cz>
   gbrowse-2.39.ebuild, +files/fix-PNG-export.patch:
   sci-biology/gbrowse: add missing brackets cause a perl error while exporting
   a PNG image gbrowse-2.39.ebuild files/fix-PNG-export.patch

diff --git a/sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch 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 +0200
++++ install_util/GBrowseInstall.pm	2011-07-30 20:42:19.000000000 +0200
+@@ -486,11 +486,11 @@
+     my $base = basename($self->install_path->{htdocs});
+ 
+     # Configure the databases, if needed.
+-    print STDERR "Updating user account database...\n";
+-    my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
+-    my $perl          = $self->perl;
+-    my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
+-    system $perl,@inc,$metadb_script;
++#    print STDERR "Updating user account database...\n";
++#    my $metadb_script = File::Spec->catfile("bin", "gbrowse_metadb_config.pl");
++#    my $perl          = $self->perl;
++#    my @inc           = map{"-I$_"} split ':',$self->added_to_INC;
++#    system $perl,@inc,$metadb_script;
+     system 'sudo','chown','-R',"$uid.$gid",$destdir.$sessions,$destdir.$userdata;
+ 
+ #    if (Module::Build->y_n(

diff --git a/sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch b/sci-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} = 0;
+     local $database->{RaiseError} = 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 with: $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";
+ 
+ 	# now do the uploads table
+ 	# this upgrades to latest version 0
+@@ -808,9 +808,9 @@
+ 	$insert->finish();
+ 
+ 	$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";
+ 
+ 	# 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";
+ 
+ 	$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();
+     };
+     

diff --git a/sci-biology/gbrowse/files/symlink.patch b/sci-biology/gbrowse/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 +0200
++++ install_util/GBrowseInstall.pm	2011-07-30 19:42:31.000000000 +0200
+@@ -465,7 +465,7 @@
+     chown $uid,-1,$destdir.$htdocs;
+     {
+ 	local $> = $uid;
+-	symlink($images,$htdocs_i);  # so symlinkifowner match works!
++        symlink($images,$destdir.$htdocs_i) or warn "symlink($images,$destdir.$htdocs_i) failed: $!\n";  # so symlinkifowner match works!
+     }
+     chown $>,-1,$destdir.$self->install_path->{htdocs};
+ 

diff --git a/sci-biology/gbrowse/gbrowse-2.39.ebuild b/sci-biology/gbrowse/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="
 LICENSE="Artistic"
 # webapp ebuilds do not set SLOT
 KEYWORDS="~x86 ~amd64"
-IUSE="cgi fastcgi minimal mysql postgres svg test" # lwp moby scf
+IUSE="cgi fastcgi minimal mysql pdf postgres svg test" # lwp moby scf
 
 S="${WORKDIR}/${MY_P}"
 
@@ -48,6 +48,7 @@ DEPEND="
 	>=dev-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.patch"
 	epatch "${FILESDIR}"/fix-PNG-export.patch || die "Failed to apply fix-PNG-export.patch"
+	epatch "${FILESDIR}"/symlink.patch || die "Failed to apply symlink.patch"
+	epatch "${FILESDIR}"/gbrowse_metadb_config.pl.patch || die "Failed to apply gbrowse_metadb_config.pl.patch"
+	epatch "${FILESDIR}"/disable-gbrowse_metadb_config.pl.patch || die "Failed to apply disable-gbrowse_metadb_config.pl.patch"
 }
 
 src_configure() {
@@ -145,8 +149,7 @@ src_install() {
 pkg_postinst() {
 	webapp_pkg_postinst || die "webapp_pkg_postinst failed"
 
-	einfo "Please run gbrowse_metadb_config.pl to update SQlite flatfiles or the live database"
-	einfo "This was disabled by "${FILESDIR}"/GBrowseInstall.pm-disable-gbrowse_metadb_config.pl.pm.patch"
+	einfo "Please run gbrowse_metadb_config.pl to update SQLite flatfiles of the live database."
 }
 
 src_test() {