This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository picard-tools.
commit 335b0e9900f9efb8a0c720ac35f7d778db2574d8 Author: Andreas Tille <[email protected]> Date: Sun Mar 13 07:56:14 2016 +0100 Remove patches applied upstream --- debian/patches/00-for-upstream-fix-testsuite | 24 ------------- debian/patches/01-for-upstream-fix-classloader | 47 -------------------------- debian/patches/series | 2 -- 3 files changed, 73 deletions(-) diff --git a/debian/patches/00-for-upstream-fix-testsuite b/debian/patches/00-for-upstream-fix-testsuite deleted file mode 100644 index 3a6c393..0000000 --- a/debian/patches/00-for-upstream-fix-testsuite +++ /dev/null @@ -1,24 +0,0 @@ -Description: Fix a bug in the testsuite - This patch fixes the number of arguments of the - testIlluminaDataProviderMissingDatas function. -Origin: vendor -Forwarded: yes ---- a/src/tests/java/picard/illumina/parser/IlluminaDataProviderTest.java -+++ b/src/tests/java/picard/illumina/parser/IlluminaDataProviderTest.java -@@ -259,10 +259,12 @@ public class IlluminaDataProviderTest { - } - - @Test(dataProvider = "badData", expectedExceptions = {PicardException.class, IllegalArgumentException.class}) -- public void testIlluminaDataProviderMissingDatas(final int lane, -- final IlluminaDataType[] actualDts, -- final String illuminaConfigStr, -- final File basecallsDirectory) -+ public void testIlluminaDataProviderMissingDatas( -+ final String testName, final int lane, final int size, -+ final List<Integer> tiles, -+ final IlluminaDataType[] actualDts, -+ final String illuminaConfigStr, -+ final File basecallsDirectory) - throws Exception { - final IlluminaDataProviderFactory factory = new IlluminaDataProviderFactory(basecallsDirectory, lane, new ReadStructure(illuminaConfigStr), bclQualityEvaluationStrategy, actualDts); - factory.makeDataProvider(); diff --git a/debian/patches/01-for-upstream-fix-classloader b/debian/patches/01-for-upstream-fix-classloader deleted file mode 100644 index 1d9974b..0000000 --- a/debian/patches/01-for-upstream-fix-classloader +++ /dev/null @@ -1,47 +0,0 @@ -Description: Fix a bug in path handling - This patch fixes the convertion from URL to path so that paths - containing the '+' character are not converted to ' '. As the - Debian package has +dfsg suffix in its version string, sbuilder - create a directory with this string and the test suite suffer - from this bug. -Origin: vendor -Forwarded: yes ---- a/src/java/picard/cmdline/ClassFinder.java -+++ b/src/java/picard/cmdline/ClassFinder.java -@@ -30,7 +30,8 @@ import java.io.File; - import java.io.IOException; - import java.net.URL; - import java.net.URLClassLoader; --import java.net.URLDecoder; -+import java.net.URI; -+import java.net.URISyntaxException; - import java.util.*; - import java.util.zip.ZipEntry; - import java.util.zip.ZipFile; -@@ -63,7 +64,7 @@ public class ClassFinder { - // but the jarPath is remembered so that the iteration over the classpath skips anything other than - // the jarPath. - jarPath = jarFile.getCanonicalPath(); -- final URL[] urls = {new URL("file", "", jarPath)}; -+ final URL[] urls = {new File(jarPath).toURI().toURL()}; - loader = new URLClassLoader(urls, Thread.currentThread().getContextClassLoader()); - } - -@@ -95,9 +96,14 @@ public class ClassFinder { - while (urls.hasMoreElements()) { - try { - String urlPath = urls.nextElement().getFile(); -- urlPath = URLDecoder.decode(urlPath, "UTF-8"); -- if ( urlPath.startsWith("file:") ) { -- urlPath = urlPath.substring(5); -+ // convert URL to URI -+ // http://bugs.java.com/bugdatabase/view_bug.do?bug_id=4466485 -+ // using URLDecode does not work if urlPath has a '+' character -+ try { -+ URI uri = new URI(urlPath); -+ urlPath = uri.getPath(); -+ } catch (URISyntaxException e) { -+ log.warn("Cannot convert to URI the " + urlPath + " URL"); - } - if (urlPath.indexOf('!') > 0) { - urlPath = urlPath.substring(0, urlPath.indexOf('!')); diff --git a/debian/patches/series b/debian/patches/series index f213547..a81bb03 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1 @@ -00-for-upstream-fix-testsuite -01-for-upstream-fix-classloader 10-build.xml -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
