[med-svn] [Git][med-team/milib][master] 7 commits: Catching IOException newly raised by fasterxml classes
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Sun Jun 28 06:32:55 BST 2026
Pierre Gruet pushed to branch master at Debian Med / milib
Commits:
df3d3e4e by Pierre Gruet at 2026-06-28T06:58:08+02:00
Catching IOException newly raised by fasterxml classes
- - - - -
c2b009cd by Pierre Gruet at 2026-06-28T06:58:46+02:00
Rewriting d/watch with Version 5
- - - - -
f59c23bc by Pierre Gruet at 2026-06-28T06:59:26+02:00
Removing Priority: optional, which is now defaults
- - - - -
9ddb56f6 by Pierre Gruet at 2026-06-28T06:59:38+02:00
Removing R-R-R: no, which is now defaults
- - - - -
8e074649 by Pierre Gruet at 2026-06-28T07:00:04+02:00
Raising Standards version to 4.7.4
- - - - -
f4b6fe9d by Pierre Gruet at 2026-06-28T07:01:00+02:00
Updating changelog
- - - - -
2041b7da by Pierre Gruet at 2026-06-28T07:01:10+02:00
Upload to unstable
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/uncaught_IOException.patch
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+milib (2.2.0+dfsg-2) unstable; urgency=medium
+
+ * Catching IOException newly raised by fasterxml classes
+ (Closes: #1139472)
+ * Raising Standards version to 4.7.4:
+ - Removing Priority: optional, which is now defaults
+ - Removing R-R-R: no, which is now defaults
+ * Rewriting d/watch with Version 5
+
+ -- Pierre Gruet <pgt at debian.org> Sun, 28 Jun 2026 07:01:05 +0200
+
milib (2.2.0+dfsg-1) unstable; urgency=medium
* New upstream version 2.2.0+dfsg
=====================================
debian/control
=====================================
@@ -3,7 +3,6 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Steffen Moeller <moeller at debian.org>,
Pierre Gruet <pgt at debian.org>
Section: java
-Priority: optional
Build-Depends: debhelper-compat (= 13),
default-jdk,
gradle-debian-helper,
@@ -22,11 +21,10 @@ Build-Depends-Indep: junit4 <!nocheck>,
libmockito-java <!nocheck>,
libredberry-pipe-java,
libtrove3-java
-Standards-Version: 4.6.2
+Standards-Version: 4.7.4
Vcs-Browser: https://salsa.debian.org/med-team/milib
Vcs-Git: https://salsa.debian.org/med-team/milib.git
Homepage: https://milaboratory.com/
-Rules-Requires-Root: no
Package: libmilib-java
Architecture: all
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ build_gradle.patch
guava_interface.patch
deactivate_test_reading_build_properties.patch
flaky_test.patch
+uncaught_IOException.patch
=====================================
debian/patches/uncaught_IOException.patch
=====================================
@@ -0,0 +1,84 @@
+Description: catching IOException newly thrown by
+ com.fasterxml.jackson.databind.ObjectMapper
+Author: Pierre Gruet <pgt at debian.org>
+Bug-Debian: https://bugs.debian.org/1139472
+Forwarded: no
+Last-Update: 2026-06-28
+
+--- a/src/main/java/com/milaboratory/util/ReportUtil.java
++++ b/src/main/java/com/milaboratory/util/ReportUtil.java
+@@ -89,6 +89,8 @@
+ return content.getBytes(StandardCharsets.UTF_8);
+ } catch (JsonProcessingException e) {
+ throw new RuntimeException(e);
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+
+--- a/src/main/java/com/milaboratory/util/GlobalObjectMappers.java
++++ b/src/main/java/com/milaboratory/util/GlobalObjectMappers.java
+@@ -42,7 +42,12 @@
+ private static ObjectMapper PRETTY = null;
+
+ public static String toOneLine(Object object) throws JsonProcessingException {
+- String str = GlobalObjectMappers.getOneLine().writeValueAsString(object);
++ String str;
++ try {
++ str = GlobalObjectMappers.getOneLine().writeValueAsString(object);
++ } catch (IOException e) {
++ throw new RuntimeException(e);
++ }
+
+ if (str.contains("\n"))
+ throw new RuntimeException("Internal error.");
+--- a/src/main/java/com/milaboratory/core/alignment/kaligner2/KAlignerParameters2.java
++++ b/src/main/java/com/milaboratory/core/alignment/kaligner2/KAlignerParameters2.java
+@@ -21,6 +21,8 @@
+ import com.milaboratory.core.sequence.NucleotideSequence;
+ import com.milaboratory.util.GlobalObjectMappers;
+
++import java.io.IOException;
++
+ /**
+ * @author Dmitry Bolotin
+ * @author Stanislav Poslavsky
+@@ -712,6 +714,8 @@
+ return "KAlignerParameters" + GlobalObjectMappers.getPretty().writeValueAsString(this);
+ } catch (JsonProcessingException e) {
+ return "Error...";
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+ }
+--- a/src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java
++++ b/src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java
+@@ -24,6 +24,7 @@
+ import com.milaboratory.core.sequence.Sequence;
+ import com.milaboratory.util.GlobalObjectMappers;
+
++import java.io.IOException;
+ import java.io.ObjectStreamException;
+
+ /**
+@@ -155,6 +156,8 @@
+ return GlobalObjectMappers.getPretty().writeValueAsString(this);
+ } catch (JsonProcessingException e) {
+ throw new RuntimeException(e);
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+
+--- a/src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java
++++ b/src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java
+@@ -630,6 +630,8 @@
+ return "KAlignerParameters" + GlobalObjectMappers.getPretty().writeValueAsString(this);
+ } catch (JsonProcessingException e) {
+ return "Error...";
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+ }
=====================================
debian/watch
=====================================
@@ -1,3 +1,9 @@
-version=4
-opts="repack, compression=xz, dversionmangle=auto, repacksuffix=+dfsg, filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/milaboratory/milib/tags .*/(?:.*?)([\d\.]+)\.tar\.gz
+Version: 5
+
+Source: https://github.com/milaboratory/milib/tags
+Matching-Pattern: .*/(?:.*?)([\d\.]+)\.tar\.gz
+Compression: xz
+Dversionmangle: auto
+Filenamemangle: s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%
+Repack: yes
+Repacksuffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/6cbd8fa8442adc06e673fad396df6f117ebeb754...2041b7da9d9fa8e4402f1f2d1af133fa8364a8e2
--
View it on GitLab: https://salsa.debian.org/med-team/milib/-/compare/6cbd8fa8442adc06e673fad396df6f117ebeb754...2041b7da9d9fa8e4402f1f2d1af133fa8364a8e2
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