[med-svn] [picard-tools] 02/04: Remove patches applied upstream

[Andreas Tille]

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tille pushed a commit to branch master
in repository picard-tools.

commit 335b0e9900f9efb8a0c720ac35f7d778db2574d8
Author: Andreas Tille <tille at debian.org>
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

-- 
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