put the generated faceted_browsing.html in the output data directory …

…next to faceted_browsing.json, rather than in the jbrowse root
GMOD · Jan 11, 2012 · 8c7ce12 · 8c7ce12
1 parent 33b3799
commit 8c7ce12
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Showing 4 changed files with 22 additions and 22 deletions.
diff --git a/bin/setup-faceted-browsing.pl b/bin/setup-faceted-browsing.pl
@@ -1,10 +1,11 @@
 #!/usr/bin/env perl
-
 use strict;
 use warnings;
 
+use Cwd 'realpath';
 use FindBin qw($Bin);
 use lib "$Bin/../lib";
+use File::Spec;
 
 use Getopt::Long;
 use JsonGenerator;
@@ -99,10 +100,11 @@
     }
 }
 
-my $template = HTML::Template->new(filename => 'faceted_browsing.tmpl');
+my $template = HTML::Template->new(filename => "$Bin/../faceted_browsing.tmpl");
 
-$template->param( BROWSING_FACETES => \@facetes, JSON_PATH => "$outdir/faceted_browsing.json" );
+my $rel_basedir = File::Spec->abs2rel( realpath("$Bin/.."), $outdir );
+$template->param( BROWSING_FACETES => \@facetes, REL_BASEDIR => "$rel_basedir/" );
 
-open(my $out_file, ">faceted_browsing.html");
+open(my $out_file, ">", "$outdir/faceted_browsing.html");
 print $out_file $template->output;
 
diff --git a/faceted_browsing.tmpl b/faceted_browsing.tmpl
@@ -6,16 +6,16 @@
 
   <head>
     <title>JBrowse</title>
-    <link rel="stylesheet" type="text/css" href="genome.css"></link>
-    <link rel="stylesheet" type="text/css" href="faceted.css"></link>
+    <link rel="stylesheet" type="text/css" href="<TMPL_VAR NAME=REL_BASEDIR>genome.css"></link>
+    <link rel="stylesheet" type="text/css" href="<TMPL_VAR NAME=REL_BASEDIR>faceted.css"></link>
     <style type="text/css">
       html, body { height: 100%; width: 100%; padding: 0; border: 0; }
     </style>
-    <link href="<TMPL_VAR NAME=JSON_PATH>" type="application/json" rel="exhibit/data"/>
-    <link rel='stylesheet' href='http://www.simile-widgets.org/styles/common.css' type='text/css' />
+    <link href="faceted_browsing.json" type="application/json" rel="exhibit/data"/>
+    <link rel="stylesheet" href="http://www.simile-widgets.org/styles/common.css" type="text/css" />
     <script src="http://api.simile-widgets.org/exhibit/2.2.0/exhibit-api.js" type="text/javascript"></script>
-    <script src="prototype.js" type="text/javascript"></script>
-    <script src="js/Faceted.js" type="text/javascript"></script>
+    <script src="<TMPL_VAR NAME=REL_BASEDIR>prototype.js" type="text/javascript"></script>
+    <script src="<TMPL_VAR NAME=REL_BASEDIR>js/Faceted.js" type="text/javascript"></script>
   </head>
 
   <body> 

diff --git a/js/Browser.js b/js/Browser.js
@@ -54,12 +54,10 @@ var Browser = function(params) {
     var refSeqs = params.refSeqs;
     var trackData = params.trackData;
     this.deferredFunctions = [];
-    this.dataRoot = params.dataRoot;
-    var dataRoot;
-    if ("dataRoot" in params)
-        dataRoot = params.dataRoot;
-    else
-        dataRoot = "";
+    var dataRoot = params.dataRoot || "";
+    //no trailing slashes on dataRoot
+    dataRoot.replace(/\/+$/,"");
+    this.dataRoot = dataRoot;
 
     this.names = new LazyTrie(dataRoot + "/names/lazy-",
 			      dataRoot + "/names/root.json");
@@ -856,7 +854,7 @@ Browser.prototype.createTrackList = function(parent, params) {
 
         // faceted browisng page runs from an iframe
         facetedIframe = document.createElement("iframe");
-        facetedIframe.src = "faceted_browsing.html"; 
+        facetedIframe.src = dataRoot + "/faceted_browsing.html"; 
         facetedIframe.setAttribute("name","browsing_window");
         facetedIframe.setAttribute("frameborder","0");
         facetedIframe.height = "100%";
@@ -1197,7 +1195,7 @@ Browser.prototype.createTrackList = function(parent, params) {
                                      {
                                          changeCallback: changeCallback,
                                          trackPadding: brwsr.view.trackPadding,
-                                         baseUrl: brwsr.dataRoot,
+                                         baseUrl: brwsr.dataRoot + "/",
                                          charWidth: brwsr.view.charWidth,
                                          seqHeight: brwsr.view.seqHeight
                                      });

diff --git a/test_harness.html b/test_harness.html
@@ -57,12 +57,12 @@
 
            // load the proper refSeqs and trackInfo based on the data path passed as a query arg
            var dataRoot = queryParams.data || 'data';
-           if( ! dataRoot.match(/\/$/) ) dataRoot = dataRoot + '/';
+           dataRoot.replace(/\/+$/,""); //trim off any trailing slashes
 
            var conf_url = queryParams.conf || 'conf.js';
-           dojo.forEach( [ dataRoot + 'refSeqs.js',
-                           dataRoot + 'trackInfo.js',
-                           dataRoot + 'overviewTrackInfo.js',
+           dojo.forEach( [ dataRoot + '/refSeqs.js',
+                           dataRoot + '/trackInfo.js',
+                           dataRoot + '/overviewTrackInfo.js',
                            conf_url
                          ],
                          function(file) {