debian/changelog

@@ -15,7 +15,8 @@ berkeley-express (1.5.2+dfsg-1) UNRELEASED; urgency=medium
     package name as per cme and general considerations)
   * debhelper 11
   * express-doc.pdf is not in upstream source any more
-  * Exclude binaries and other unneeded files
+  * Exclude binaries and other unneeded files like download archives
+    of previous versions
   * provide html documentation
   * avoid privace breach JS in html doc
 

debian/copyright

@@ -3,7 +3,9 @@ Upstream-Name: eXpress
 Source: http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz
 Files-Excluded: */linux_build
                 */osx_build
+                */*win_build
                 */express.xcodeproj
+                */downloads
 
 Files: *
 Copyright: © 2011-2013 Adam Roberts, Lior Pachter, UC Berkeley

debian/patches/privacy-breach.patch

@@ -14,14 +14,14 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    })();
  
  </script>
-@@ -90,15 +87,9 @@
+@@ -90,15 +87,7 @@
  
          <!-- Search form -->    
  <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
 -<script src="http://www.google.com/jsapi" type="text/javascript"></script>
  <script type="text/javascript"> 
-   google.load('search', '1', {language : 'en'});
-   google.setOnLoadCallback(function() {
+-  google.load('search', '1', {language : 'en'});
+-  google.setOnLoadCallback(function() {
 -    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
 -    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
 -    var options = new google.search.DrawOptions();
@@ -42,14 +42,14 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    })();
  
  </script>
-@@ -95,15 +92,9 @@
+@@ -95,15 +92,7 @@
  
          <!-- Search form -->    
  <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
 -<script src="http://www.google.com/jsapi" type="text/javascript"></script>
  <script type="text/javascript"> 
-   google.load('search', '1', {language : 'en'});
-   google.setOnLoadCallback(function() {
+-  google.load('search', '1', {language : 'en'});
+-  google.setOnLoadCallback(function() {
 -    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
 -    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
 -    var options = new google.search.DrawOptions();
@@ -70,14 +70,22 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    })();
  
  </script>
-@@ -89,7 +86,6 @@
+@@ -89,15 +86,7 @@
  
          <!-- Search form -->    
  <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
 -<script src="http://www.google.com/jsapi" type="text/javascript"></script>
  <script type="text/javascript"> 
-   google.load('search', '1', {language : 'en'});
-   google.setOnLoadCallback(function() {
+-  google.load('search', '1', {language : 'en'});
+-  google.setOnLoadCallback(function() {
+-    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
+-    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
+-    var options = new google.search.DrawOptions();
+-    options.enableSearchboxOnly("http://www.google.com/cse?cx=017113487431020499685:jdftct1emrw", null, true);
+-    customSearchControl.draw('cse-search-form', options);
+   }, true);
+ </script>
+ <link rel="stylesheet" href="css/googlesearch.css" type="text/css" />
 --- a/html/overview.html
 +++ b/html/overview.html
 @@ -17,9 +17,6 @@
@@ -90,14 +98,14 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    })();
  
  </script>
-@@ -91,15 +88,9 @@
+@@ -91,15 +88,7 @@
  
          <!-- Search form -->    
  <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
 -<script src="http://www.google.com/jsapi" type="text/javascript"></script>
  <script type="text/javascript"> 
-   google.load('search', '1', {language : 'en'});
-   google.setOnLoadCallback(function() {
+-  google.load('search', '1', {language : 'en'});
+-  google.setOnLoadCallback(function() {
 -    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
 -    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
 -    var options = new google.search.DrawOptions();
@@ -118,14 +126,14 @@ Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
    })();
  
  </script>
-@@ -89,15 +86,9 @@
+@@ -89,15 +86,7 @@
  
          <!-- Search form -->    
  <div class="searchform" id="cse-search-form" style="padding-top:4px; width:30%;">Loading</div>
 -<script src="http://www.google.com/jsapi" type="text/javascript"></script>
  <script type="text/javascript"> 
-   google.load('search', '1', {language : 'en'});
-   google.setOnLoadCallback(function() {
+-  google.load('search', '1', {language : 'en'});
+-  google.setOnLoadCallback(function() {
 -    var customSearchControl = new google.search.CustomSearchControl('017113487431020499685:jdftct1emrw');
 -    customSearchControl.setResultSetSize(google.search.Search.FILTERED_CSE_RESULTSET);
 -    var options = new google.search.DrawOptions();