[med-svn] [Git][med-team/berkeley-express][master] 2 commits: avoid privace breach JS in html doc
Andreas Tille
gitlab at salsa.debian.org
Sun Apr 8 16:59:13 BST 2018
Andreas Tille pushed to branch master at Debian Med / berkeley-express
Commits:
8d4868df by Andreas Tille at 2018-04-08T17:14:11+02:00
avoid privace breach JS in html doc
- - - - -
51690b0e by Andreas Tille at 2018-04-08T17:14:41+02:00
Fix installation of html doc
- - - - -
6 changed files:
- + debian/berkeley-express-doc.doc-base
- + debian/berkeley-express-doc.install
- debian/berkeley-express.install
- debian/changelog
- + debian/patches/privacy-breach.patch
- debian/patches/series
Changes:
=====================================
debian/berkeley-express-doc.doc-base
=====================================
--- /dev/null
+++ b/debian/berkeley-express-doc.doc-base
@@ -0,0 +1,24 @@
+Document: express
+Title: doxygen documentation for eXpress
+Author: Adam Roberts, Lior Pachter
+Abstract: Streaming quantification for high-throughput sequencing
+ eXpress is a streaming tool for quantifying the abundances of a set of
+ target sequences from sampled subsequences. Example applications include
+ transcript-level RNA-Seq quantification, allele-specific/haplotype
+ expression analysis (from RNA-Seq), transcription factor binding
+ quantification in ChIP-Seq, and analysis of metagenomic data. It is
+ based on an online-EM algorithm that results in space (memory)
+ requirements proportional to the total size of the target sequences and
+ time requirements that are proportional to the number of sampled
+ fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
+ quantify much larger samples than other currently available tools
+ greatly reducing computing infrastructure requirements. eXpress can be
+ used to build lightweight high-throughput sequencing processing
+ pipelines when coupled with a streaming aligner (such as Bowtie), as
+ output can be piped directly into eXpress, effectively eliminating the
+ need to store read alignments in memory or on disk.
+Section: Science/Biology
+
+Format: html
+Files: /usr/share/doc/berkeley-express/html/*
+Index: /usr/share/doc/berkeley-express/html/index.html
=====================================
debian/berkeley-express-doc.install
=====================================
--- /dev/null
+++ b/debian/berkeley-express-doc.install
@@ -0,0 +1 @@
+html usr/share/doc/berkeley-express
=====================================
debian/berkeley-express.install
=====================================
--- a/debian/berkeley-express.install
+++ b/debian/berkeley-express.install
@@ -1,2 +1 @@
usr/bin/express usr/lib/debian-med/bin/
-html usr/share/doc/berkeley-express
\ No newline at end of file
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -17,6 +17,7 @@ berkeley-express (1.5.2+dfsg-1) UNRELEASED; urgency=medium
* express-doc.pdf is not in upstream source any more
* Exclude binaries and other unneeded files
* provide html documentation
+ * avoid privace breach JS in html doc
-- Steffen Moeller <moeller at debian.org> Fri, 17 Nov 2017 23:39:43 +0100
=====================================
debian/patches/privacy-breach.patch
=====================================
--- /dev/null
+++ b/debian/patches/privacy-breach.patch
@@ -0,0 +1,136 @@
+Description: avoid privace breach JS in html doc
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 07 Apr 2018 21:47:43 +0200
+
+--- a/html/faq.html
++++ b/html/faq.html
+@@ -17,9 +17,6 @@
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+@@ -90,15 +87,9 @@
+
+ <!-- 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() {
+- 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/index.html
++++ b/html/index.html
+@@ -17,9 +17,6 @@
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+@@ -95,15 +92,9 @@
+
+ <!-- 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() {
+- 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/manual.html
++++ b/html/manual.html
+@@ -17,9 +17,6 @@
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+@@ -89,7 +86,6 @@
+
+ <!-- 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() {
+--- a/html/overview.html
++++ b/html/overview.html
+@@ -17,9 +17,6 @@
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+@@ -91,15 +88,9 @@
+
+ <!-- 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() {
+- 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/tutorial.html
++++ b/html/tutorial.html
+@@ -17,9 +17,6 @@
+ _gaq.push(['_trackPageview']);
+
+ (function() {
+- var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
+- ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
+- var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
+ })();
+
+ </script>
+@@ -89,15 +86,9 @@
+
+ <!-- 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() {
+- 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" />
=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ fix-bamtools-path
drop-zlib
gcc-6.patch
correct-debug-flags.patch
+privacy-breach.patch
View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/compare/fb534e2646f6c6d1b0c42ba2f637bf0d84767595...51690b0eec44b4dec5ea21bef5810b9ecaa9ec7d
---
View it on GitLab: https://salsa.debian.org/med-team/berkeley-express/compare/fb534e2646f6c6d1b0c42ba2f637bf0d84767595...51690b0eec44b4dec5ea21bef5810b9ecaa9ec7d
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