Update dependencies to fix vulnerabilities (#1544)

igvteam · Aug 15, 2024 · b611dbc · b611dbc
1 parent d372765
commit b611dbc
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Showing 2 changed files with 15 additions and 12 deletions.
diff --git a/build.gradle b/build.gradle
@@ -101,35 +101,38 @@ configurations {
     }
 }
 
+def amazonVersion = '2.27.4'
+def xmlGraphicsVersion = '1.17'
+
 dependencies {
     implementation(
             fileTree(dir: 'lib', include: '*.jar'), // first search on disk (old behavior), then maven repos
             [group: 'com.google.code.gson', name: 'gson', version: '2.8.9'],
             [group: 'org.apache.commons', name: 'commons-math3', version: '3.6.1'],
             [group: 'commons-io', name: 'commons-io', version: '2.7'],
-            [group: 'org.apache.commons', name: 'commons-compress', version: '1.21'],
-            [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.7.3'],
+            [group: 'org.apache.commons', name: 'commons-compress', version: '1.26.0'],
+            [group: 'org.xerial.snappy', name: 'snappy-java', version: '1.1.10.4'],
             [group: 'org.apache.commons', name: 'commons-jexl', version: '2.1.1'],
             [group: 'org.apache.commons', name: 'commons-lang3', version: '3.9'],
-            [group: 'com.github.samtools', name: 'htsjdk', version: '4.0.2'],
+            [group: 'com.github.samtools', name: 'htsjdk', version: '4.1.1'],
             [group: 'org.swinglabs', name: 'swing-layout', version: '1.0.3'],
             [group: 'com.formdev', name: 'jide-oss', version: '3.7.12'],
             [group: 'com.google.guava', name: 'guava', version: '32.1.3-jre'],
-            [group: 'org.apache.xmlgraphics', name: 'batik-dom', version: '1.11'],
-            [group: 'org.apache.xmlgraphics', name: 'batik-svggen', version: '1.11'],
-            [group: 'org.apache.xmlgraphics', name: 'batik-codec', version: '1.11'],
+            [group: 'org.apache.xmlgraphics', name: 'batik-dom', version: xmlGraphicsVersion],
+            [group: 'org.apache.xmlgraphics', name: 'batik-svggen', version: xmlGraphicsVersion],
+            [group: 'org.apache.xmlgraphics', name: 'batik-codec', version: xmlGraphicsVersion],
             [group: 'org.netbeans.external', name: 'AbsoluteLayout', version: 'RELEASE110'],
 
             // Amazon deps
-            [group: 'software.amazon.awssdk', name: 'cognitoidentity', version: '2.16.7'],
-            [group: 'software.amazon.awssdk', name: 'sts', version: '2.16.7'],
-            [group: 'software.amazon.awssdk', name: 's3', version: '2.16.7'],
-            [group: 'software.amazon.awssdk', name: 'sso', version: '2.16.7']
+            [group: 'software.amazon.awssdk', name: 'cognitoidentity', version: amazonVersion],
+            [group: 'software.amazon.awssdk', name: 'sts', version: amazonVersion],
+            [group: 'software.amazon.awssdk', name: 's3', version: amazonVersion],
+            [group: 'software.amazon.awssdk', name: 'sso', version: amazonVersion]
     )
 
     testImplementation(
             [group: 'junit', name: 'junit', version: '4.13.1'],
-            [group: 'com.sparkjava', name: 'spark-core', version: '2.7.2'],
+            [group: 'com.sparkjava', name: 'spark-core', version: '2.9.4'],
             [group: 'org.glassfish.jersey.core', name: 'jersey-common', version: '2.34']
     )
     testRuntimeOnly(

diff --git a/src/main/java/module-info.java b/src/main/java/module-info.java
@@ -42,6 +42,6 @@
     requires software.amazon.awssdk.services.sts;
     requires software.amazon.awssdk.http;
     requires software.amazon.awssdk.utils;
-    requires com.fasterxml.jackson.core;
+
     requires jide.oss;
 }