adding faceted browsing setup file

bin/prepare-nested-structure.pl

@@ -19,23 +19,13 @@
 my @seqTracks;
 my %definedTracks;
 my @rootChildren = ('Favourites');
+my %seq;
 
 my $trackRel = "tracks";
 my $trackDir = "$outdir/$trackRel";
 mkdir($outdir) unless (-d $outdir);
 mkdir($trackDir) unless (-d $trackDir);
 
-my $config = JsonGenerator::readJSON($confFile);
-
-eval "require $config->{db_adaptor}; 1" or die $@;
-
-
-my $db = eval {$config->{db_adaptor}->new(%{$config->{db_args}})} or warn $@;
-die "Could not open database: $@" unless $db;
-
-$db->strict_bounds_checking(1) if $db->can('strict_bounds_checking');
-$db->absolute(1)               if $db->can('absolute');
-
 my @refSeqs = @{JsonGenerator::readJSON("$outdir/refSeqs.js", [], 1)};
 die "run prepare-refseqs.pl first to supply information about your reference sequences" if $#refSeqs < 0;
 my @trackInfo = @{JsonGenerator::readJSON("$outdir/trackInfo.js", [], 1)};
@@ -50,6 +40,7 @@
             $categories{'SequenceTrack'} = [$track->{"key"}];
         }
         $definedTracks{$track->{"key"}} = 2;
+        $seq{$track->{"key"}} = 1;
     }
     else {
         $definedTracks{$track->{"key"}} = 1;
@@ -60,9 +51,20 @@
 $definedTracks{'General'} = 3;
 $definedTracks{'Favourites'} = 3;
 
+if($confFile) {
 
-my @tracks = @{$config->{tracks}};
+my $config = JsonGenerator::readJSON($confFile);
 
+eval "require $config->{db_adaptor}; 1" or die $@;
+
+
+my $db = eval {$config->{db_adaptor}->new(%{$config->{db_args}})} or warn $@;
+die "Could not open database: $@" unless $db;
+
+$db->strict_bounds_checking(1) if $db->can('strict_bounds_checking');
+$db->absolute(1)               if $db->can('absolute');
+
+my @tracks = @{$config->{tracks}};
 foreach my $track (@tracks) {
     my $group;
     if(! $track->{"category"}) {
@@ -85,7 +87,22 @@
         $categories{$group} = [$track->{"track"}];
     }
     $definedTracks{$track->{"track"}} = 2;
-} 
+}
+}
+else {
+foreach my $track (@trackInfo) {
+    my $group = "General";
+if(!$seq{$track->{"key"}}) {
+    if($categories{$group}) {
+        push @{$categories{$group}}, $track->{"key"};
+    }
+    else {
+        $categories{$group} = [$track->{"key"}];
+    }
+}
+    $definedTracks{$track->{"key"}} = 2;
+}
+}
 
 foreach my $category (keys %categories) {
     my @children_ref = ();

bin/setup-faceted-browsing.pl

@@ -0,0 +1,112 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin qw($Bin);
+use lib "$Bin/../lib";
+
+use Getopt::Long;
+use JsonGenerator;
+use Data::Dumper;
+use HTML::Template;
+
+my $confFile;
+my $outdir = "data";
+GetOptions("conf=s" => \$confFile,
+           "out=s" => $outdir);
+
+my %possible_track_info = ();
+my %possible_track_info_options = ();
+my @tracks;
+my @facetes;
+my @track_fields;
+
+mkdir($outdir) unless (-d $outdir);
+
+if($confFile) {
+
+    my $config = JsonGenerator::readJSON($confFile);
+
+    eval "require $config->{db_adaptor}; 1" or die $@;
+
+    @tracks = @{$config->{tracks}};
+
+    if($config->{facets}) {
+        @facetes = @{$config->{facets}};
+    }
+    if($config->{extra_track_info}) {
+        @track_fields = @{$config->{extra_track_info}};
+    }
+}
+else {
+    my @trackInfo = @{JsonGenerator::readJSON("$outdir/trackInfo.js", [], 1)};
+    die "run biodb-to-json.pl first to supply information about your track sequences" if $#trackInfo < 0;
+
+    @tracks = @trackInfo;
+}
+
+my @browsing_tracks;
+foreach my $track (@tracks) {
+    foreach my $key (keys %$track) {
+        if($possible_track_info{$key}) {
+            $possible_track_info{$key} += 1;
+        }
+        else {
+            $possible_track_info{$key} = 1;
+            $possible_track_info_options{$key}{$track->{$key}} = 0;
+        }
+        $possible_track_info_options{$key}{$track->{$key}} += 1;
+    }
+
+    if($confFile) {
+        $track->{'label'} = $track->{'key'};
+        delete $track->{'key'};
+    }
+
+    if($confFile || ($track->{'type'} ne 'TrackGroup' && $track->{'type'} ne 'ROOT')) {
+        push @browsing_tracks, $track;
+    }
+}
+@tracks = @browsing_tracks;
+
+JsonGenerator::writeJSON("$outdir/faceted_browsing.json",
+                               {
+                                   'items' => \@tracks,
+                               });
+
+# create faceted_browser.html file for iframe to work
+
+if(!@facetes || !@track_fields) {
+    my $num_tracks = @tracks;
+    my $populate_facetes = !@facetes;
+    my $populate_track_fields = !@track_fields;
+    foreach my $field (keys %possible_track_info) {
+        my $num_field_options = $possible_track_info_options{$field};
+        my $num_field_populated = $possible_track_info{$field};
+
+        my $max_times_used = 0;
+        foreach my $option (keys %{$possible_track_info_options{$field}}) {
+            my $times_used = $possible_track_info_options{$field}{$option};
+            if($times_used > $max_times_used) {
+                $max_times_used = $times_used;
+            }
+        }
+
+        if($populate_facetes && ($field ne 'type') && ($max_times_used >= 2) && ($num_field_options >= 2)) {
+            push @facetes, { field => $field , label => $field};
+        }
+        if($populate_track_fields && ($field ne 'track') && ($field ne 'type') && ($field ne 'key') && ($field ne 'label') && ($field ne 'url') && ($num_field_populated >= (int $num_tracks*0.5))) {
+            push @track_fields, { field_label => $field , field_name => $field};
+        }
+    }
+}
+
+my $template = HTML::Template->new(filename => 'faceted_browsing.tmpl');
+
+$template->param( BROWSING_FACETES => \@facetes);
+$template->param( TRACK_INFO_FIELDS => \@track_fields);
+
+open(my $out_file, ">faceted_browsing.html");
+print $out_file $template->output;
+