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)

3 files changed, 85 insertions, 0 deletions

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 000000000..1e96bb8c6
--- /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 000000000..0f7d5d373
--- /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 000000000..e6df771ee
--- /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};
+