[med-svn] r13840 - in trunk/packages/babraham/fastqc/trunk/debian: . patches

[olivier sallou]

Author: osallou-guest
Date: 2013-06-05 15:12:46 +0000 (Wed, 05 Jun 2013)
New Revision: 13840

Added:
   trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading
Modified:
   trunk/packages/babraham/fastqc/trunk/debian/changelog
   trunk/packages/babraham/fastqc/trunk/debian/patches/series
Log:
Close bug 697604, give debian path to load resources

Modified: trunk/packages/babraham/fastqc/trunk/debian/changelog
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/changelog	2013-06-05 14:43:13 UTC (rev 13839)
+++ trunk/packages/babraham/fastqc/trunk/debian/changelog	2013-06-05 15:12:46 UTC (rev 13840)
@@ -1,3 +1,10 @@
+fastqc (0.10.1+dfsg-2) unstable; urgency=low
+
+  * Add patch to fix Templates and Contaminants loading
+    in non interactive mode (Closes: #697604) 
+
+ -- Olivier Sallou <osallou at debian.org>  Wed, 05 Jun 2013 17:08:44 +0200
+
 fastqc (0.10.1+dfsg-1) unstable; urgency=low
 
   * Initial release (Closes: #670353)

Added: trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading	                        (rev 0)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/fix_icon_loading	2013-06-05 15:12:46 UTC (rev 13840)
@@ -0,0 +1,44 @@
+Subject: issue when loading resources
+Description: in Debian, templates and other resources are not embedded in Jar file.
+ This is a problem when app tries to access the resources.
+ This patch provides the path in Debian hierarcy to find resources.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-06-05
+Forwarded: no
+--- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
++++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java
+@@ -167,12 +167,12 @@
+ 		data.append("\n");
+ 		
+ 		// Add in the icon files for pass/fail/warn
+-		File templatesDir = new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons").getFile(),"UTF-8"));
++		File templatesDir = new File("/usr/share/fastqc/Templates/Icons");
+ 		String [] names = templatesDir.list();
+ 		for (int n=0;n<names.length;n++) {
+ 			if (names[n].toLowerCase().endsWith(".png") || names[n].toLowerCase().endsWith(".jpg") || names[n].toLowerCase().endsWith(".jpeg")) {
+ 				zip.putNextEntry(new ZipEntry(folderName()+"/Icons/"+names[n]));
+-				FileInputStream fileIn = new FileInputStream(new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/Icons/"+names[n]).getFile(),"UTF-8")));
++				FileInputStream fileIn = new FileInputStream(new File("/usr/share/fastqc/Templates/Icons/"+names[n]));
+ 				int len;
+ 				while ((len = fileIn.read(buffer)) > 0) { 
+ 					zip.write(buffer, 0, len); 
+@@ -235,7 +235,7 @@
+ 	
+ 	private void addTemplate (String filename, String date) throws IOException {
+ 		
+-		BufferedReader br = new BufferedReader(new FileReader(new File(URLDecoder.decode(ClassLoader.getSystemResource("Templates/header_template.html").getFile(),"UTF-8"))));
++		BufferedReader br = new BufferedReader(new FileReader(new File("/usr/share/fastqc/Templates/header_template.html")));
+ 		String line;
+ 		while ((line = br.readLine())!=null) {
+ 			
+--- a/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
++++ b/uk/ac/babraham/FastQC/Sequence/Contaminant/ContaminentFinder.java
+@@ -60,7 +60,7 @@
+ 		
+ 		try {
+ 			
+-			File contaminantFile = new File (URLDecoder.decode(ClassLoader.getSystemResource("Contaminants/contaminant_list.txt").getFile(),"UTF-8"));
++			File contaminantFile = new File ("/usr/share/fastqc/Contaminants/contaminant_list.txt");
+ 			
+ 			if (System.getProperty("fastqc.contaminant_file") != null && System.getProperty("fastqc.contaminant_file").length()>0) {
+ 				contaminantFile = new File(System.getProperty("fastqc.contaminant_file"));

Modified: trunk/packages/babraham/fastqc/trunk/debian/patches/series
===================================================================
--- trunk/packages/babraham/fastqc/trunk/debian/patches/series	2013-06-05 14:43:13 UTC (rev 13839)
+++ trunk/packages/babraham/fastqc/trunk/debian/patches/series	2013-06-05 15:12:46 UTC (rev 13840)
@@ -1,3 +1,4 @@
 Makefile.patch
 fastqc.patch
 fix-help-call.patch
+fix_icon_loading