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authorMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2011-07-30 21:22:30 +0200
committerMartin Mokrejs <mmokrejs@fold.natur.cuni.cz>2011-07-30 21:22:30 +0200
commit85b7bd86f5737125ae7d6eeee78080bd8169dc0c (patch)
treebdce85bb9248c6039ce00061439bea5049708a41 /sci-biology/gbrowse/files
parentsci-biology/gbrowse: add missing brackets cause a perl error while exporting ... (diff)
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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)
Diffstat (limited to 'sci-biology/gbrowse/files')
-rw-r--r--sci-biology/gbrowse/files/disable-gbrowse_metadb_config.pl.patch19
-rw-r--r--sci-biology/gbrowse/files/gbrowse_metadb_config.pl.patch55
-rw-r--r--sci-biology/gbrowse/files/symlink.patch11
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};
+