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 <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
