all regression tests work again

Build.PL

@@ -18,6 +18,7 @@ my $build = GBrowseInstall->new(
     requires     => {
 	'perl'                => '5.008',
 	'Bio::Root::Version'  => '1.005002',
+	'Bio::Graphics'       => 0,
 	'GD'                  => '2.07',
 	'IO::String'          => 0,
 	'CGI::Session'        => '4.02',
@@ -27,11 +28,15 @@ my $build = GBrowseInstall->new(
 	'JSON'                => 0,
 	'LWP'                 => 0,
     },
-    recommends  => { 'BerkeleyDB' => 0.32 },
+    recommends  => { 
+	'DB_File::Lock'       => 0,
+	'DBI'                 => 0,
+	'DBD::mysql'          => 0,
+	'DBD::Pg'             => 0,
+    },
     script_files => [
 	'bin/gbrowse_slave',
 	'bin/make_das_conf.pl',
-	'bin/gbrowse_slave',
 # not sure if these still work
 #	'bin/register_moby_services.pl',
 #	'bin/process_wormbase.pl',

MANIFEST

@@ -68,6 +68,7 @@ conf/plugins/Submitter.pm
 conf/plugins/test.pm
 conf/plugins/TestFinder.pm
 conf/slave_preload.conf
+conf/yeast_simple.conf
 conf/yeast_chr1+2.conf
 conf/yeast_renderfarm.conf
 contrib/ace2gff.pl

conf/GBrowse.conf

@@ -70,7 +70,7 @@ head =
 header =
 
 # At the footer
-footer = <hr /><pre>$Id: GBrowse.conf,v 1.34 2008-11-26 21:16:12 lstein Exp $</pre>
+footer = <hr /><pre>$Id: GBrowse.conf,v 1.35 2008-12-19 03:11:00 lstein Exp $</pre>
 
 # Various places where you can insert your own HTML -- see configuration docs
 html1 = 
@@ -112,7 +112,11 @@ annotation edit cols   = 100
 default source = yeast
 
 [yeast]
-description   = S. cerevisiae chromosomes I & II
+description   = Yeast chromosomes 1+2 (basic)
+path          = yeast_simple.conf
+
+[yeast_advanced]
+description   = Yeast chromosomes 1+2 (advanced)
 path          = yeast_chr1+2.conf
 
 [renderfarm]

conf/yeast_chr1+2.conf

@@ -1,5 +1,5 @@
 [GENERAL]
-description   = S. cerevisiae chromosomes I and II
+description   = Yeast chromosomes 1+2 (advanced)
 database      = scaffolds
 
 initial landmark = chrI:143000..180000

conf/yeast_simple.conf

@@ -0,0 +1,187 @@
+[GENERAL]
+description   = Yeast chromosomes 1+2 (basic)
+database      = scaffolds
+
+initial landmark = chrI:143000..180000
+
+# color of the selection rectangle
+hilite fill    = beige
+hilite outline = red
+
+default features = Genes
+		   ORFs
+		   tRNAs
+		   CDS
+		   Transp
+		   Centro:overview
+		   Landmarks:region
+
+# examples to show in the introduction
+examples = chrI
+	   chrII
+	   chrI:80,000..120,000
+	   "membrane trafficking"
+	   NUT21
+	   YAL063C
+
+# "automatic" classes to try when an unqualified identifier is given
+automatic classes = Symbol Gene Clone
+
+#################################
+# database definitions
+#################################
+
+[scaffolds:database]
+db_adaptor    = Bio::DB::SeqFeature::Store
+db_args       = -adaptor memory
+                -dir    $DATABASES/yeast_scaffolds
+
+[annotations:database]
+db_adaptor    = Bio::DB::SeqFeature::Store
+db_args       = -adaptor memory
+                -dir    $DATABASES/yeast_chr1+2
+
+
+# Default glyph settings
+[TRACK DEFAULTS]
+glyph       = generic
+database    = annotations
+height      = 8
+bgcolor     = cyan
+fgcolor     = cyan
+label density = 25
+bump density  = 100
+
+### TRACK CONFIGURATION ####
+# the remainder of the sections configure individual tracks
+
+[Centro:overview]
+feature       = centromere
+bgcolor       = blue
+glyph         = dot
+fgcolor       = black
+height        = 8
+point         = 1
+key           = Centromeres
+
+[tRNA:overview]
+feature       = tRNA
+glyph         = generic
+bgcolor       = lightgray
+fgcolor       = black
+height        = 4
+stranded      = 1
+description   = 1
+key           = tRNAs
+
+[RegionLandmarks:region]
+glyph        = dna
+global feature = 1
+database     = scaffolds
+height       = 40
+gc_window    = auto
+do_gc        = 1
+strand       = both
+fgcolor      = red
+axis_color   = blue
+key          = GC Content
+
+[Genes]
+feature      = gene
+glyph        = so_transcript
+bgcolor      = yellow
+forwardcolor = yellow
+reversecolor = turquoise
+label        = sub { my $f = shift;
+                     my $name = $f->display_name;
+                     my @aliases = $f->attributes('Alias');
+                     $name .= " (@aliases)" if @aliases;
+		     $name;
+  } 
+height       = 6
+description  = 0
+key          = Named gene
+
+[CDS]
+feature      = CDS
+glyph        = cds
+description  = 0
+height       = 26
+sixframe     = 1
+label        = sub {shift->name . " reading frame"}
+key          = CDS
+citation     = This track shows CDS reading frames.
+
+[tRNAs]
+feature       = tRNA
+glyph         = generic
+bgcolor       = lightgray
+fgcolor       = black
+height        = 4
+stranded      = 1
+description   = 1
+key           = tRNAs
+
+[Transp]
+feature       = LTR_retrotransposon
+glyph         = segments
+bgcolor       = yellow
+fgcolor       = black
+height        = 5
+stranded      = 1
+key           = Transposons
+
+[LTRs]
+feature       = long_terminal_repeat
+fgcolor       = black
+glyph         = anchored_arrow
+height        = 6
+key           = Long Terminal Repeats
+
+[Translation]
+glyph        = translation
+global feature = 1
+database     = scaffolds
+height       = 40
+fgcolor      = purple
+strand       = +1
+translation  = 6frame
+key          = 6-frame translation
+
+[TranslationF]
+glyph        = translation
+global feature = 1
+database     = scaffolds
+height       = 20
+fgcolor      = purple
+strand       = +1
+translation  = 3frame
+key          = 3-frame translation (forward)
+
+[DNA/GC Content]
+glyph        = dna
+global feature = 1
+database     = scaffolds
+height       = 40
+do_gc        = 1
+gc_window    = auto
+strand       = both
+fgcolor      = red
+axis_color   = blue
+
+[TranslationR]
+glyph        = translation
+global feature = 1
+database     = scaffolds
+height       = 20
+fgcolor      = blue
+strand       = -1
+translation  = 3frame
+key          = 3-frame translation (reverse)
+
+[ncRNA]
+feature       = RNAd rRNA:sgd snRNA:sgd snoRNA:sgd
+fgcolor       = orange
+glyph         = generic
+description   = 1
+key           = Noncoding RNAs

install_util/GBrowseInstall.pm

@@ -69,7 +69,10 @@ sub ACTION_demo {
     open STDOUT,"<&",$saveout;
 
     # fix GBrowse.conf to point to correct directories
-    for my $f ('GBrowse.conf','yeast_chr1+2.conf','yeast_renderfarm.conf') {
+    for my $f ('GBrowse.conf',
+	       'yeast_simple.conf',
+	       'yeast_chr1+2.conf',
+	       'yeast_renderfarm.conf') {
 	my $in  = IO::File->new("$dir/conf/$f")         or die $!;
 	my $out = IO::File->new("$dir/conf/$f.new",'>') or die $!;
 	while (<$in>) {

lib/Bio/Graphics/Browser/Render/Slave.pm

@@ -233,25 +233,26 @@ sub render_tracks {
     my $panel_args      = thaw param('panel_args');
 
     $self->Debug("render_tracks(): Opening database...");
-    my $db = $datasource->open_database($tracks->[0] || 'general');
+    my $db = $datasource->open_database();
     $self->Debug("render_tracks(): Got database handle $db");
     $self->Debug("rendering tracks @$tracks");
 
     # extract segments
     my ($segment) = $db->segment(-name	=> $settings->{'ref'},
 				 -start	=> $settings->{'start'},
 				 -stop	=> $settings->{'stop'});
-    $self->Fatal("Can't get segment for $settings->{ref}:$settings->{start}..$settings->{stop}")
+    $self->Fatal("Can't get segment for $settings->{ref}:$settings->{start}..$settings->{stop} (1)")
 	unless $segment;
 
     # BUG: duplicated code from Render.pm -- move into a common place
+    $panel_args->{section} ||= '';  # prevent uninit variable warnings
     if ($panel_args->{section} eq 'overview') {
 	$segment = Bio::Graphics::Browser::Region->whole_segment($segment,$settings);
     } elsif ($panel_args->{section} eq 'region') {
 	$segment  = Bio::Graphics::Browser::Region->region_segment($segment,$settings);
     }
 
-    $self->Fatal("Can't get segment for $settings->{ref}:$settings->{start}..$settings->{stop}")
+    $self->Fatal("Can't get segment for $settings->{ref}:$settings->{start}..$settings->{stop} (2)")
 	unless $segment;
 
     # generate the panels

lib/Bio/Graphics/Browser/Render/Slave/Status.pm

@@ -1,5 +1,5 @@
 package Bio::Graphics::Browser::Render::Slave::Status;
-# $Id: Status.pm,v 1.2 2008-12-18 18:42:00 lstein Exp $
+# $Id: Status.pm,v 1.3 2008-12-19 03:11:01 lstein Exp $
 
 # This module keeps track of when slaves were last contacted and their
 # current status. If a slave is down and there are alternatives defined,
@@ -8,9 +8,8 @@ package Bio::Graphics::Browser::Render::Slave::Status;
 
 use strict;
 use warnings;
-use DB_File::Lock;
 use Fcntl qw(:flock O_RDWR O_CREAT);
-
+use DB_File;
 use constant INITIAL_DELAY => 30;   # initially recheck a down server after 30 sec
 use constant MAX_DELAY     => 600;  # periodically recheck at 10 min intervals max
 use constant DECAY         => 1.5;  # at each subsequent failure, increase recheck interval by this amount
@@ -19,13 +18,23 @@ use constant DEBUG         => 0;
 sub new {
     my $class      = shift;
     my $path       = shift;
-    return bless { path=>$path },ref $class || $class;
+    my $has_dbfilelock = eval "require DB_File::Lock; 1";
+
+    return bless { 
+	path       => $path,
+	canlock    => $has_dbfilelock,
+    },ref $class || $class;
 }
 
+sub can_lock { shift->{dbfilelock} }
+
 sub db {
     my $self  = shift;
     my $write = shift;
 
+    return $self->{hash} ||= {} 
+           unless $self->can_lock;
+
     my $locking    = $write ? 'write' : 'read';
     my $mode       = $write ? O_CREAT|O_RDWR : O_RDONLY;
     my $perms      = 0666;

lib/Bio/Graphics/Browser/RenderPanels.pm

@@ -579,8 +579,8 @@ sub run_remote_requests {
 	    $response_line =~ s/^\d+//;  # get rid of status code
 	    $requests->{$_}->flag_error($response_line) foreach keys %{$renderers{$uri}};
 	}
-	CORE::exit(0);  # from CHILD
       }
+      CORE::exit(0);  # from CHILD
   }
 }
 

lib/Bio/Graphics/Karyotype.pm

@@ -1,6 +1,6 @@
 package Bio::Graphics::Karyotype;
 
-# $Id: Karyotype.pm,v 1.8 2008-11-14 18:55:00 lstein Exp $
+# $Id: Karyotype.pm,v 1.9 2008-12-19 03:11:01 lstein Exp $
 # Utility class to create a display of a karyotype and a series of "hits" on the individual chromosomes
 # Used for searching
 
@@ -186,6 +186,7 @@ sub feature2link {
  	           : $class    ? "$class:$name" 
  		   : $name;
     my $dbid  = $_->gbrowse_dbid if $_ && $_->can('gbrowse_dbid');
+    $dbid   ||= '';
     return "$url$fid;dbid=$dbid";
 }