added fixes for FastCGI stability

GMOD · Jun 8, 2009 · 020f4dd · 020f4dd
1 parent c9d8507
commit 020f4dd
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Showing 5 changed files with 29 additions and 9 deletions.
diff --git a/cgi-bin/gb2/gbrowse b/cgi-bin/gb2/gbrowse
@@ -7,11 +7,17 @@ use Bio::Graphics::Browser::Render::HTML;
 
 umask 022;
 
-my $fcgi = Bio::Graphics::Browser::Render->fcgi_request;
+my $fcgi   = Bio::Graphics::Browser::Render->fcgi_request;
 
 if ($fcgi) {
 
-    while ($fcgi->Accept >= 0) {
+    my $FCGI_DONE = 0;
+    $SIG{TERM} = sub {
+	print STDERR "[$$] FastCGI termination signalled. Will exit.\n";
+	$FCGI_DONE = 1;
+    };
+
+    while (!$FCGI_DONE && ($fcgi->Accept >= 0)) {
 	my $globals = Bio::Graphics::Browser->open_globals;
 	CGI->initialize_globals();
 	Bio::Graphics::Browser::Render::HTML->new($globals)->run();

diff --git a/cgi-bin/gb2/gbrowse_details b/cgi-bin/gb2/gbrowse_details
@@ -6,7 +6,7 @@ use Bio::Graphics::Browser::RegionSearch;
 use Bio::Graphics::Browser::Markup;
 use Bio::Graphics::Glyph::generic;
 
-our $VERSION = '$Id: gbrowse_details,v 1.13 2009-05-14 21:46:09 lstein Exp $';
+our $VERSION = '$Id: gbrowse_details,v 1.14 2009-06-08 19:24:04 lstein Exp $';
 our ($INDEX,%COLORS,%URLS,%formatterCache);
 
 
@@ -24,7 +24,13 @@ my $fcgi = Bio::Graphics::Browser::Render->fcgi_request;
 
 if ($fcgi) {
 
-    while ($fcgi->Accept >= 0) {
+    my $FCGI_DONE = 0;
+    $SIG{TERM} = sub {
+	print STDERR "[$$] FastCGI termination signalled. Will exit.\n";
+	$FCGI_DONE = 1;
+    };
+
+    while (!$FCGI_DONE && ($fcgi->Accept >= 0)) {
 	CGI->initialize_globals();
 	DetailRenderer->new($conf)->run();
 	$fcgi->Finish();

diff --git a/cgi-bin/gb2/gbrowse_img b/cgi-bin/gb2/gbrowse_img
@@ -1,6 +1,6 @@
 #!/usr/bin/perl -w
 
-# $Id: gbrowse_img,v 1.10 2009-05-22 14:33:38 lstein Exp $
+# $Id: gbrowse_img,v 1.11 2009-06-08 19:24:04 lstein Exp $
 
 use strict;
 
@@ -28,7 +28,13 @@ umask 022;
 my $fcgi = Bio::Graphics::Browser::Render->fcgi_request;
 if ($fcgi) {
 
-    while ($fcgi->Accept >= 0) {
+    my $FCGI_DONE = 0;
+    $SIG{TERM} = sub {
+	print STDERR "[$$] FastCGI termination signalled. Will exit.\n";
+	$FCGI_DONE = 1;
+    };
+
+    while (!$FCGI_DONE && ($fcgi->Accept >= 0)) {
 	my $globals = Bio::Graphics::Browser->open_globals;
 	CGI->initialize_globals();
 	GBrowse_img->new($globals)->run();

diff --git a/lib/Bio/Graphics/Browser/RegionSearch.pm b/lib/Bio/Graphics/Browser/RegionSearch.pm
@@ -116,7 +116,9 @@ sub init_databases {
 	next if $state->{dbid} && $state->{dbid} ne $dbid;
 	my $search_options = $source->setting($dbid => 'search options') || '';
 
-	next if $search_options eq 'none';  # ignore this in the search
+	# this can't be right - we need to do id searches
+	# next if $search_options eq 'none';  
+
 	$dbs{$dbid}{options} ||= $search_options;
 	$dbs{$dbid}{remotes}{$remote}++ if $remote;
     }

diff --git a/lib/Bio/Graphics/Browser/RenderPanels.pm b/lib/Bio/Graphics/Browser/RenderPanels.pm
@@ -1926,8 +1926,8 @@ sub make_link {
     my $end   = CGI::escape($feature->end);
     my $src   = CGI::escape(eval{$feature->source} || '');
     my $url   = CGI->request_uri || '../..';
-    my $id    = eval {$feature->primary_id};
-    my $dbid  = eval {$feature->gbrowse_dbid};
+    my $dbid  = eval {CGI::escape($feature->gbrowse_dbid)};
+    my $id    = eval {CGI::escape($feature->primary_id)};
     $url      =~ s!/gbrowse.*!!;
     $url      .= "/gbrowse_details/$ds_name?ref=$ref;start=$start;end=$end";
     $url      .= ";name=$name"     if defined $name;